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diff --git a/doc/Eqs/pair_comb1.jpg b/doc/Eqs/pair_comb1.jpg
index d92f37be1..e0711ca97 100644
Binary files a/doc/Eqs/pair_comb1.jpg and b/doc/Eqs/pair_comb1.jpg differ
diff --git a/doc/Eqs/pair_comb2.jpg b/doc/Eqs/pair_comb2.jpg
index c73a174ac..8b0e5ba51 100644
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diff --git a/doc/Eqs/pair_comb2.tex b/doc/Eqs/pair_comb2.tex
index faa664ef0..cd022cc7f 100644
--- a/doc/Eqs/pair_comb2.tex
+++ b/doc/Eqs/pair_comb2.tex
@@ -1,22 +1,23 @@
-\documentclass[12pt]{article}
+\documentclass[10pt]{article}
\begin{document}
\begin{table}[h]
-\begin{tabular}{|c|c|c|c|c|c|c|c|}
+\begin{tabular}{|c|c|c|c|c|c|c|c|c|}
\hline
- & $O$ & $Cu$ & $N$ & $C$ & $H$ & $Ti$ & $Zn$ \\ \hline
-$O$ & F & F & F & F & F & F & F \\ \hline
-$Cu$ & F & F & P & F & F & P & F \\ \hline
-$N$ & F & P & F & M & F & P & P \\ \hline
-$C$ & F & F & M & F & F & M & M \\ \hline
-$H$ & F & F & F & F & F & M & M \\ \hline
-$Ti$ & F & P & P & M & M & F & P \\ \hline
-$Zn$ & F & F & P & M & M & P & F \\ \hline
-\multicolumn{8}{l}{F: Fully optimized} \\
-\multicolumn{8}{l}{M: Only optimized for dimer molecule} \\
-\multicolumn{8}{l}{P: in Progress but have it from mixing rule} \\
+ & $O$ & $Cu$ & $N$ & $C$ & $H$ & $Ti$ & $Zn$ & $Zr$ \\ \hline
+$O$ & F & F & F & F & F & F & F & F\\ \hline
+$Cu$ & F & F & P & F & F & P & F & P \\ \hline
+$N$ & F & P & F & M & F & P & P & P \\ \hline
+$C$ & F & F & M & F & F & M & M & M \\ \hline
+$H$ & F & F & F & F & F & M & M & F \\ \hline
+$Ti$ & F & P & P & M & M & F & P & P \\ \hline
+$Zn$ & F & F & P & M & M & P & F & P \\ \hline
+$Zr$ & F & P & P & M & F & P & P & F \\ \hline
+\multicolumn{9}{l}{F: Fully optimized} \\
+\multicolumn{9}{l}{M: Only optimized for dimer molecule} \\
+\multicolumn{9}{l}{P: in Progress but have it from mixing rule} \\
\end{tabular}
\end{table}
\end{document}
diff --git a/doc/Manual.html b/doc/Manual.html
index 0a1af6de4..c48b5219d 100644
--- a/doc/Manual.html
+++ b/doc/Manual.html
@@ -1,435 +1,435 @@
<HTML>
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="1 Feb 2014 version">
+<META NAME="docnumber" CONTENT="6 Feb 2014 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H1></H1>
<CENTER><H3>LAMMPS-ICMS Documentation
</H3></CENTER>
-<CENTER><H4>1 Feb 2014 version
+<CENTER><H4>6 Feb 2014 version
</H4></CENTER>
<H4>Version info:
</H4>
<P>The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on <A HREF = "http://lammps.sandia.gov/bug.html">this page of
the WWW site</A>. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
</P>
<P>LAMMPS-ICMS is an experimental variant of LAMMPS with additional
features made available for testing before they will be submitted
for inclusion into the official LAMMPS tree. The source code is
based on the official LAMMPS svn repository mirror at the Institute
for Computational Molecular Science at Temple University and generally
kept up-to-date as much as possible. Sometimes, e.g. when additional
development work is needed to adapt the upstream changes into
LAMMPS-ICMS it can take longer until synchronization; and occasionally,
e.g. in case of the rewrite of the multi-threading support, the
development will be halted except for important bugfixes until
all features of LAMMPS-ICMS fully compatible with the upstream
version or replaced by alternate implementations.
</P>
<UL><LI>If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of upstream LAMMPS, but may be
missing some new features in LAMMPS-ICMS.
<LI>If you browse the HTML doc pages included in your tarball, they
describe the version you have, however, not all new features in
LAMMPS-ICMS are documented immediately.
<LI>The <A HREF = "Manual.pdf">PDF file</A> on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch.
<LI>There is also a <A HREF = "Developer.pdf">Developer.pdf</A> file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS.
</UL>
<P>LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
</P>
<P>LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
</P>
<P>The primary developers of LAMMPS are <A HREF = "http://www.sandia.gov/~sjplimp">Steve Plimpton</A>, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> at
http://lammps.sandia.gov has more information about the code and its
uses.
</P>
<HR>
<P>The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
</P>
<P>Once you are familiar with LAMMPS, you may want to bookmark <A HREF = "Section_commands.html#comm">this
page</A> at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
</P>
<P><A HREF = "Manual.pdf">PDF file</A> of the entire manual, generated by
<A HREF = "http://www.easysw.com/htmldoc">htmldoc</A>
</P>
<OL><LI><A HREF = "Section_intro.html">Introduction</A>
<UL> 1.1 <A HREF = "Section_intro.html#intro_1">What is LAMMPS</A>
<BR>
1.2 <A HREF = "Section_intro.html#intro_2">LAMMPS features</A>
<BR>
1.3 <A HREF = "Section_intro.html#intro_3">LAMMPS non-features</A>
<BR>
1.4 <A HREF = "Section_intro.html#intro_4">Open source distribution</A>
<BR>
1.5 <A HREF = "Section_intro.html#intro_5">Acknowledgments and citations</A>
<BR></UL>
<LI><A HREF = "Section_start.html">Getting started</A>
<UL> 2.1 <A HREF = "Section_start.html#start_1">What's in the LAMMPS distribution</A>
<BR>
2.2 <A HREF = "Section_start.html#start_2">Making LAMMPS</A>
<BR>
2.3 <A HREF = "Section_start.html#start_3">Making LAMMPS with optional packages</A>
<BR>
2.4 <A HREF = "Section_start.html#start_4">Building LAMMPS via the Make.py script</A>
<BR>
2.5 <A HREF = "Section_start.html#start_5">Building LAMMPS as a library</A>
<BR>
2.6 <A HREF = "Section_start.html#start_6">Running LAMMPS</A>
<BR>
2.7 <A HREF = "Section_start.html#start_7">Command-line options</A>
<BR>
2.8 <A HREF = "Section_start.html#start_8">Screen output</A>
<BR>
2.9 <A HREF = "Section_start.html#start_9">Tips for users of previous versions</A>
<BR></UL>
<LI><A HREF = "Section_commands.html">Commands</A>
<UL> 3.1 <A HREF = "Section_commands.html#cmd_1">LAMMPS input script</A>
<BR>
3.2 <A HREF = "Section_commands.html#cmd_2">Parsing rules</A>
<BR>
3.3 <A HREF = "Section_commands.html#cmd_3">Input script structure</A>
<BR>
3.4 <A HREF = "Section_commands.html#cmd_4">Commands listed by category</A>
<BR>
3.5 <A HREF = "Section_commands.html#cmd_5">Commands listed alphabetically</A>
<BR></UL>
<LI><A HREF = "Section_packages.html">Packages</A>
<UL> 4.1 <A HREF = "Section_packages.html#pkg_1">Standard packages</A>
<BR>
4.2 <A HREF = "Section_packages.html#pkg_2">User packages</A>
<BR></UL>
<LI><A HREF = "Section_accelerate.html">Accelerating LAMMPS performance</A>
<UL> 5.1 <A HREF = "Section_accelerate.html#acc_1">Measuring performance</A>
<BR>
5.2 <A HREF = "Section_accelerate.html#acc_2">General strategies</A>
<BR>
5.3 <A HREF = "Section_accelerate.html#acc_3">Packages with optimized styles</A>
<BR>
5.4 <A HREF = "Section_accelerate.html#acc_4">OPT package</A>
<BR>
5.5 <A HREF = "Section_accelerate.html#acc_5">USER-OMP package</A>
<BR>
5.6 <A HREF = "Section_accelerate.html#acc_6">GPU package</A>
<BR>
5.7 <A HREF = "Section_accelerate.html#acc_7">USER-CUDA package</A>
<BR>
5.8 <A HREF = "Section_accelerate.html#acc_8">Comparison of GPU and USER-CUDA packages</A>
<BR></UL>
<LI><A HREF = "Section_howto.html">How-to discussions</A>
<UL> 6.1 <A HREF = "Section_howto.html#howto_1">Restarting a simulation</A>
<BR>
6.2 <A HREF = "Section_howto.html#howto_2">2d simulations</A>
<BR>
6.3 <A HREF = "Section_howto.html#howto_3">CHARMM and AMBER force fields</A>
<BR>
6.4 <A HREF = "Section_howto.html#howto_4">Running multiple simulations from one input script</A>
<BR>
6.5 <A HREF = "Section_howto.html#howto_5">Multi-replica simulations</A>
<BR>
6.6 <A HREF = "Section_howto.html#howto_6">Granular models</A>
<BR>
6.7 <A HREF = "Section_howto.html#howto_7">TIP3P water model</A>
<BR>
6.8 <A HREF = "Section_howto.html#howto_8">TIP4P water model</A>
<BR>
6.9 <A HREF = "Section_howto.html#howto_9">SPC water model</A>
<BR>
6.10 <A HREF = "Section_howto.html#howto_10">Coupling LAMMPS to other codes</A>
<BR>
6.11 <A HREF = "Section_howto.html#howto_11">Visualizing LAMMPS snapshots</A>
<BR>
6.12 <A HREF = "Section_howto.html#howto_12">Triclinic (non-orthogonal) simulation boxes</A>
<BR>
6.13 <A HREF = "Section_howto.html#howto_13">NEMD simulations</A>
<BR>
6.14 <A HREF = "Section_howto.html#howto_14">Finite-size spherical and aspherical particles</A>
<BR>
6.15 <A HREF = "Section_howto.html#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A>
<BR>
6.16 <A HREF = "Section_howto.html#howto_16">Thermostatting, barostatting, and compute temperature</A>
<BR>
6.17 <A HREF = "Section_howto.html#howto_17">Walls</A>
<BR>
6.18 <A HREF = "Section_howto.html#howto_18">Elastic constants</A>
<BR>
6.19 <A HREF = "Section_howto.html#howto_19">Library interface to LAMMPS</A>
<BR>
6.20 <A HREF = "Section_howto.html#howto_20">Calculating thermal conductivity</A>
<BR>
6.21 <A HREF = "Section_howto.html#howto_21">Calculating viscosity</A>
<BR></UL>
<LI><A HREF = "Section_example.html">Example problems</A>
<LI><A HREF = "Section_perf.html">Performance & scalability</A>
<LI><A HREF = "Section_tools.html">Additional tools</A>
<LI><A HREF = "Section_modify.html">Modifying & extending LAMMPS</A>
<UL> 10.1 <A HREF = "Section_modify.html#mod_1">Atom styles</A>
<BR>
10.2 <A HREF = "Section_modify.html#mod_2">Bond, angle, dihedral, improper potentials</A>
<BR>
10.3 <A HREF = "Section_modify.html#mod_3">Compute styles</A>
<BR>
10.4 <A HREF = "Section_modify.html#mod_4">Dump styles</A>
<BR>
10.5 <A HREF = "Section_modify.html#mod_5">Dump custom output options</A>
<BR>
10.6 <A HREF = "Section_modify.html#mod_6">Fix styles</A>
<BR>
10.7 <A HREF = "Section_modify.html#mod_7">Input script commands</A>
<BR>
10.8 <A HREF = "Section_modify.html#mod_8">Kspace computations</A>
<BR>
10.9 <A HREF = "Section_modify.html#mod_9">Minimization styles</A>
<BR>
10.10 <A HREF = "Section_modify.html#mod_10">Pairwise potentials</A>
<BR>
10.11 <A HREF = "Section_modify.html#mod_11">Region styles</A>
<BR>
10.12 <A HREF = "Section_modify.html#mod_12">Body styles</A>
<BR>
10.13 <A HREF = "Section_modify.html#mod_13">Thermodynamic output options</A>
<BR>
10.14 <A HREF = "Section_modify.html#mod_14">Variable options</A>
<BR>
10.15 <A HREF = "Section_modify.html#mod_15">Submitting new features for inclusion in LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_python.html">Python interface</A>
<UL> 11.1 <A HREF = "Section_python.html#py_1">Building LAMMPS as a shared library</A>
<BR>
11.2 <A HREF = "Section_python.html#py_2">Installing the Python wrapper into Python</A>
<BR>
11.3 <A HREF = "Section_python.html#py_3">Extending Python with MPI to run in parallel</A>
<BR>
11.4 <A HREF = "Section_python.html#py_4">Testing the Python-LAMMPS interface</A>
<BR>
11.5 <A HREF = "Section_python.html#py_5">Using LAMMPS from Python</A>
<BR>
11.6 <A HREF = "Section_python.html#py_6">Example Python scripts that use LAMMPS</A>
<BR></UL>
<LI><A HREF = "Section_errors.html">Errors</A>
<UL> 12.1 <A HREF = "Section_errors.html#err_1">Common problems</A>
<BR>
12.2 <A HREF = "Section_errors.html#err_2">Reporting bugs</A>
<BR>
12.3 <A HREF = "Section_errors.html#err_3">Error & warning messages</A>
<BR></UL>
<LI><A HREF = "Section_history.html">Future and history</A>
<UL> 13.1 <A HREF = "Section_history.html#hist_1">Coming attractions</A>
<BR>
13.2 <A HREF = "Section_history.html#hist_2">Past versions</A>
<BR></UL>
</OL>
</BODY>
</HTML>
diff --git a/doc/Manual.txt b/doc/Manual.txt
index d15ad2c85..dd8d134d5 100644
--- a/doc/Manual.txt
+++ b/doc/Manual.txt
@@ -1,273 +1,273 @@
<HEAD>
<TITLE>LAMMPS-ICMS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="1 Feb 2014 version">
+<META NAME="docnumber" CONTENT="6 Feb 2014 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
<BODY>
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
<H1></H1>
LAMMPS-ICMS Documentation :c,h3
-1 Feb 2014 version :c,h4
+6 Feb 2014 version :c,h4
Version info: :h4
The LAMMPS "version" is the date when it was released, such as 1 May
2010. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it immediately, and post a notice on "this page of
the WWW site"_bug. Each dated copy of LAMMPS contains all the
features and bug-fixes up to and including that version date. The
version date is printed to the screen and logfile every time you run
LAMMPS. It is also in the file src/version.h and in the LAMMPS
directory name created when you unpack a tarball, and at the top of
the first page of the manual (this page).
LAMMPS-ICMS is an experimental variant of LAMMPS with additional
features made available for testing before they will be submitted
for inclusion into the official LAMMPS tree. The source code is
based on the official LAMMPS svn repository mirror at the Institute
for Computational Molecular Science at Temple University and generally
kept up-to-date as much as possible. Sometimes, e.g. when additional
development work is needed to adapt the upstream changes into
LAMMPS-ICMS it can take longer until synchronization; and occasionally,
e.g. in case of the rewrite of the multi-threading support, the
development will be halted except for important bugfixes until
all features of LAMMPS-ICMS fully compatible with the upstream
version or replaced by alternate implementations.
If you browse the HTML doc pages on the LAMMPS WWW site, they always
describe the most current version of upstream LAMMPS, but may be
missing some new features in LAMMPS-ICMS. :ulb,l
If you browse the HTML doc pages included in your tarball, they
describe the version you have, however, not all new features in
LAMMPS-ICMS are documented immediately. :l
The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of every patch. :l
There is also a "Developer.pdf"_Developer.pdf file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS. :ule,l
LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
Simulator.
LAMMPS is a classical molecular dynamics simulation code designed to
run efficiently on parallel computers. It was developed at Sandia
National Laboratories, a US Department of Energy facility, with
funding from the DOE. It is an open-source code, distributed freely
under the terms of the GNU Public License (GPL).
The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan
Thompson, and Paul Crozier who can be contacted at
sjplimp,athomps,pscrozi at sandia.gov. The "LAMMPS WWW Site"_lws at
http://lammps.sandia.gov has more information about the code and its
uses.
:link(bug,http://lammps.sandia.gov/bug.html)
:link(sjp,http://www.sandia.gov/~sjplimp)
:line
The LAMMPS documentation is organized into the following sections. If
you find errors or omissions in this manual or have suggestions for
useful information to add, please send an email to the developers so
we can improve the LAMMPS documentation.
Once you are familiar with LAMMPS, you may want to bookmark "this
page"_Section_commands.html#comm at Section_commands.html#comm since
it gives quick access to documentation for all LAMMPS commands.
"PDF file"_Manual.pdf of the entire manual, generated by
"htmldoc"_http://www.easysw.com/htmldoc
"Introduction"_Section_intro.html :olb,l
1.1 "What is LAMMPS"_intro_1 :ulb,b
1.2 "LAMMPS features"_intro_2 :b
1.3 "LAMMPS non-features"_intro_3 :b
1.4 "Open source distribution"_intro_4 :b
1.5 "Acknowledgments and citations"_intro_5 :ule,b
"Getting started"_Section_start.html :l
2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b
2.2 "Making LAMMPS"_start_2 :b
2.3 "Making LAMMPS with optional packages"_start_3 :b
2.4 "Building LAMMPS via the Make.py script"_start_4 :b
2.5 "Building LAMMPS as a library"_start_5 :b
2.6 "Running LAMMPS"_start_6 :b
2.7 "Command-line options"_start_7 :b
2.8 "Screen output"_start_8 :b
2.9 "Tips for users of previous versions"_start_9 :ule,b
"Commands"_Section_commands.html :l
3.1 "LAMMPS input script"_cmd_1 :ulb,b
3.2 "Parsing rules"_cmd_2 :b
3.3 "Input script structure"_cmd_3 :b
3.4 "Commands listed by category"_cmd_4 :b
3.5 "Commands listed alphabetically"_cmd_5 :ule,b
"Packages"_Section_packages.html :l
4.1 "Standard packages"_pkg_1 :ulb,b
4.2 "User packages"_pkg_2 :ule,b
"Accelerating LAMMPS performance"_Section_accelerate.html :l
5.1 "Measuring performance"_acc_1 :ulb,b
5.2 "General strategies"_acc_2 :b
5.3 "Packages with optimized styles"_acc_3 :b
5.4 "OPT package"_acc_4 :b
5.5 "USER-OMP package"_acc_5 :b
5.6 "GPU package"_acc_6 :b
5.7 "USER-CUDA package"_acc_7 :b
5.8 "Comparison of GPU and USER-CUDA packages"_acc_8 :ule,b
"How-to discussions"_Section_howto.html :l
6.1 "Restarting a simulation"_howto_1 :ulb,b
6.2 "2d simulations"_howto_2 :b
6.3 "CHARMM and AMBER force fields"_howto_3 :b
6.4 "Running multiple simulations from one input script"_howto_4 :b
6.5 "Multi-replica simulations"_howto_5 :b
6.6 "Granular models"_howto_6 :b
6.7 "TIP3P water model"_howto_7 :b
6.8 "TIP4P water model"_howto_8 :b
6.9 "SPC water model"_howto_9 :b
6.10 "Coupling LAMMPS to other codes"_howto_10 :b
6.11 "Visualizing LAMMPS snapshots"_howto_11 :b
6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b
6.13 "NEMD simulations"_howto_13 :b
6.14 "Finite-size spherical and aspherical particles"_howto_14 :b
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b
6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b
6.17 "Walls"_howto_17 :b
6.18 "Elastic constants"_howto_18 :b
6.19 "Library interface to LAMMPS"_howto_19 :b
6.20 "Calculating thermal conductivity"_howto_20 :b
6.21 "Calculating viscosity"_howto_21 :ule,b
"Example problems"_Section_example.html :l
"Performance & scalability"_Section_perf.html :l
"Additional tools"_Section_tools.html :l
"Modifying & extending LAMMPS"_Section_modify.html :l
10.1 "Atom styles"_mod_1 :ulb,b
10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b
10.3 "Compute styles"_mod_3 :b
10.4 "Dump styles"_mod_4 :b
10.5 "Dump custom output options"_mod_5 :b
10.6 "Fix styles"_mod_6 :b
10.7 "Input script commands"_mod_7 :b
10.8 "Kspace computations"_mod_8 :b
10.9 "Minimization styles"_mod_9 :b
10.10 "Pairwise potentials"_mod_10 :b
10.11 "Region styles"_mod_11 :b
10.12 "Body styles"_mod_12 :b
10.13 "Thermodynamic output options"_mod_13 :b
10.14 "Variable options"_mod_14 :b
10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b
"Python interface"_Section_python.html :l
11.1 "Building LAMMPS as a shared library"_py_1 :ulb,b
11.2 "Installing the Python wrapper into Python"_py_2 :b
11.3 "Extending Python with MPI to run in parallel"_py_3 :b
11.4 "Testing the Python-LAMMPS interface"_py_4 :b
11.5 "Using LAMMPS from Python"_py_5 :b
11.6 "Example Python scripts that use LAMMPS"_py_6 :ule,b
"Errors"_Section_errors.html :l
12.1 "Common problems"_err_1 :ulb,b
12.2 "Reporting bugs"_err_2 :b
12.3 "Error & warning messages"_err_3 :ule,b
"Future and history"_Section_history.html :l
13.1 "Coming attractions"_hist_1 :ulb,b
13.2 "Past versions"_hist_2 :ule,b
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diff --git a/doc/Section_commands.html b/doc/Section_commands.html
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--- a/doc/Section_commands.html
+++ b/doc/Section_commands.html
@@ -1,717 +1,718 @@
<HTML>
<CENTER><A HREF = "Section_start.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Section_packages.html">Next Section</A>
</CENTER>
<HR>
<H3>3. Commands
</H3>
<P>This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.
</P>
3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>
<HR>
<HR>
<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script
</H4>
<P>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.
</P>
<P>In many cases, the ordering of commands in an input script is not
important. However the following rules apply:
</P>
<P>(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
</P>
<PRE>timestep 0.5
run 100
run 100
</PRE>
<P>does something different than this sequence:
</P>
<PRE>run 100
timestep 0.5
run 100
</PRE>
<P>In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.
</P>
<P>(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.
</P>
<P>(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
<A HREF = "read_data.html">read_data</A> command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the <A HREF = "processors.html">processors</A> and
<A HREF = "boundary.html">boundary</A> commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
</P>
<P>Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. <A HREF = "Section_errors.html">This section</A> gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
</P>
<HR>
<A NAME = "cmd_2"></A><H4>3.2 Parsing rules
</H4>
<P>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
</P>
<P>Here is how each line in the input script is parsed by LAMMPS:
</P>
<P>(1) If the last printable character on the line is a "&" character
(with no surrounding quotes), the command is assumed to continue on
the next line. The next line is concatenated to the previous line by
removing the "&" character and newline. This allows long commands to
be continued across two or more lines.
</P>
<P>(2) All characters from the first "#" character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
</P>
<P>(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).
</P>
<P>If the $ is followed by curly brackets, then the variable name is the
text inside the curly brackets. If no curly brackets follow the $,
then the variable name is the single character immediately following
the $. Thus ${myTemp} and $x refer to variable names "myTemp" and
"x".
</P>
<P>How the variable is converted to a text string depends on what style
of variable it is; see the <A HREF = "variable">variable</A> doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple "words" (space
separated) which will then be interpreted as multiple arguments in the
input command. The variable can also store a numeric formula which
will be evaluated and its numeric result returned as a string.
</P>
<P>As a special case, if the $ is followed by parenthesis, then the text
inside the parenthesis is treated as an "immediate" variable and
evaluated as an <A HREF = "variable.html">equal-style variable</A>. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:
</P>
<PRE>variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
</PRE>
<P>can be replaced by
</P>
<PRE>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
</PRE>
<P>so that you do not have to define (or discard) a temporary variable X.
</P>
<P>Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
</P>
<PRE>variable a equal 2
variable b2 equal 4
print "B2 = ${b$a}"
</PRE>
<P>Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
<A HREF = "variable.html">equal-style variable</A>.
</P>
<P>See the <A HREF = "variable.html">variable</A> command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
</P>
<P>(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
</P>
<P>(5) The first word is the command name. All successive words in the
line are arguments.
</P>
<P>(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either double or single quotes. A long single
argument enclosed in quotes can even span multiple lines if the "&"
character is used, as described above. E.g.
</P>
<PRE>print "Volume = $v"
print 'Volume = $v'
variable a string "red green blue &
purple orange cyan"
if "$<I>steps</I> > 1000" then quit
</PRE>
<P>The quotes are removed when the single argument is stored internally.
</P>
<P>See the <A HREF = "dump_modify.html">dump modify format</A> or <A HREF = "print.html">print</A> or
<A HREF = "if.html">if</A> commands for examples. A "#" or "$" character that is
between quotes will not be treated as a comment indicator in (2) or
substituted for as a variable in (3).
</P>
<P>IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a <A HREF = "print.html">print</A> command as part of an
<A HREF = "if.html">if</A> or <A HREF = "run.html">run every</A> command), then the double and
single quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
</P>
<HR>
<H4><A NAME = "cmd_3"></A>3.3 Input script structure
</H4>
<P>This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
<A HREF = "Section_example.html">Section_example</A>, and animated on the <A HREF = "http://lammps.sandia.gov">LAMMPS
WWW Site</A>.
</P>
<P>A LAMMPS input script typically has 4 parts:
</P>
<OL><LI>Initialization
<LI>Atom definition
<LI>Settings
<LI>Run a simulation
</OL>
<P>The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.
</P>
<P>(1) Initialization
</P>
<P>Set parameters that need to be defined before atoms are created or
read-in from a file.
</P>
<P>The relevant commands are <A HREF = "units.html">units</A>,
<A HREF = "dimension.html">dimension</A>, <A HREF = "newton.html">newton</A>,
<A HREF = "processors.html">processors</A>, <A HREF = "boundary.html">boundary</A>,
<A HREF = "atom_style.html">atom_style</A>, <A HREF = "atom_modify.html">atom_modify</A>.
</P>
<P>If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "bond_style.html">bond_style</A>,
<A HREF = "angle_style.html">angle_style</A>, <A HREF = "dihedral_style.html">dihedral_style</A>,
<A HREF = "improper_style.html">improper_style</A>.
</P>
<P>(2) Atom definition
</P>
<P>There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the <A HREF = "read_data.html">read_data</A> or
<A HREF = "read_restart.html">read_restart</A> commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: <A HREF = "lattice.html">lattice</A>,
<A HREF = "region.html">region</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "create_atoms.html">create_atoms</A>. The entire set of atoms can be
duplicated to make a larger simulation using the
<A HREF = "replicate.html">replicate</A> command.
</P>
<P>(3) Settings
</P>
<P>Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
</P>
<P>Force field coefficients are set by these commands (they can also be
set in the read-in files): <A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "angle_coeff.html">angle_coeff</A>,
<A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
<A HREF = "improper_coeff.html">improper_coeff</A>,
<A HREF = "kspace_style.html">kspace_style</A>, <A HREF = "dielectric.html">dielectric</A>,
<A HREF = "special_bonds.html">special_bonds</A>.
</P>
<P>Various simulation parameters are set by these commands:
<A HREF = "neighbor.html">neighbor</A>, <A HREF = "neigh_modify.html">neigh_modify</A>,
<A HREF = "group.html">group</A>, <A HREF = "timestep.html">timestep</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "min_style.html">min_style</A>, <A HREF = "min_modify.html">min_modify</A>.
</P>
<P>Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The <A HREF = "fix.html">fix</A> command comes in many flavors.
</P>
<P>Various computations can be specified for execution during a
simulation using the <A HREF = "compute.html">compute</A>,
<A HREF = "compute_modify.html">compute_modify</A>, and <A HREF = "variable.html">variable</A>
commands.
</P>
<P>Output options are set by the <A HREF = "thermo.html">thermo</A>, <A HREF = "dump.html">dump</A>,
and <A HREF = "restart.html">restart</A> commands.
</P>
<P>(4) Run a simulation
</P>
<P>A molecular dynamics simulation is run using the <A HREF = "run.html">run</A>
command. Energy minimization (molecular statics) is performed using
the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
(replica-exchange) simulation can be run using the
<A HREF = "temper.html">temper</A> command.
</P>
<HR>
<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category
</H4>
<P>This section lists all LAMMPS commands, grouped by category. The
<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<P>Initialization:
</P>
<P><A HREF = "atom_modify.html">atom_modify</A>, <A HREF = "atom_style.html">atom_style</A>,
<A HREF = "boundary.html">boundary</A>, <A HREF = "dimension.html">dimension</A>,
<A HREF = "newton.html">newton</A>, <A HREF = "processors.html">processors</A>, <A HREF = "units.html">units</A>
</P>
<P>Atom definition:
</P>
<P><A HREF = "create_atoms.html">create_atoms</A>, <A HREF = "create_box.html">create_box</A>,
<A HREF = "lattice.html">lattice</A>, <A HREF = "read_data.html">read_data</A>,
<A HREF = "read_dump.html">read_dump</A>, <A HREF = "read_restart.html">read_restart</A>,
<A HREF = "region.html">region</A>, <A HREF = "replicate.html">replicate</A>
</P>
<P>Force fields:
</P>
<P><A HREF = "angle_coeff.html">angle_coeff</A>, <A HREF = "angle_style.html">angle_style</A>,
<A HREF = "bond_coeff.html">bond_coeff</A>, <A HREF = "bond_style.html">bond_style</A>,
<A HREF = "dielectric.html">dielectric</A>, <A HREF = "dihedral_coeff.html">dihedral_coeff</A>,
<A HREF = "dihedral_style.html">dihedral_style</A>,
<A HREF = "improper_coeff.html">improper_coeff</A>,
<A HREF = "improper_style.html">improper_style</A>,
<A HREF = "kspace_modify.html">kspace_modify</A>, <A HREF = "kspace_style.html">kspace_style</A>,
<A HREF = "pair_coeff.html">pair_coeff</A>, <A HREF = "pair_modify.html">pair_modify</A>,
<A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_write.html">pair_write</A>,
<A HREF = "special_bonds.html">special_bonds</A>
</P>
<P>Settings:
</P>
<P><A HREF = "communicate.html">communicate</A>, <A HREF = "group.html">group</A>, <A HREF = "mass.html">mass</A>,
<A HREF = "min_modify.html">min_modify</A>, <A HREF = "min_style.html">min_style</A>,
<A HREF = "neigh_modify.html">neigh_modify</A>, <A HREF = "neighbor.html">neighbor</A>,
<A HREF = "reset_timestep.html">reset_timestep</A>, <A HREF = "run_style.html">run_style</A>,
<A HREF = "set.html">set</A>, <A HREF = "timestep.html">timestep</A>, <A HREF = "velocity.html">velocity</A>
</P>
<P>Fixes:
</P>
<P><A HREF = "fix.html">fix</A>, <A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "unfix.html">unfix</A>
</P>
<P>Computes:
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "compute_modify.html">compute_modify</A>,
<A HREF = "uncompute.html">uncompute</A>
</P>
<P>Output:
</P>
<P><A HREF = "dump.html">dump</A>, <A HREF = "dump_image.html">dump image</A>,
<A HREF = "dump_modify.html">dump_modify</A>, <A HREF = "dump_image.html">dump movie</A>,
<A HREF = "restart.html">restart</A>, <A HREF = "thermo.html">thermo</A>,
<A HREF = "thermo_modify.html">thermo_modify</A>, <A HREF = "thermo_style.html">thermo_style</A>,
<A HREF = "undump.html">undump</A>, <A HREF = "write_data.html">write_data</A>,
<A HREF = "write_dump.html">write_dump</A>, <A HREF = "write_restart.html">write_restart</A>
</P>
<P>Actions:
</P>
<P><A HREF = "delete_atoms.html">delete_atoms</A>, <A HREF = "delete_bonds.html">delete_bonds</A>,
<A HREF = "displace_atoms.html">displace_atoms</A>, <A HREF = "change_box.html">change_box</A>,
<A HREF = "minimize.html">minimize</A>, <A HREF = "neb.html">neb</A> <A HREF = "prd.html">prd</A>,
<A HREF = "rerun.html">rerun</A>, <A HREF = "run.html">run</A>, <A HREF = "temper.html">temper</A>
</P>
<P>Miscellaneous:
</P>
<P><A HREF = "clear.html">clear</A>, <A HREF = "echo.html">echo</A>, <A HREF = "if.html">if</A>,
<A HREF = "include.html">include</A>, <A HREF = "jump.html">jump</A>, <A HREF = "label.html">label</A>,
<A HREF = "log.html">log</A>, <A HREF = "next.html">next</A>, <A HREF = "print.html">print</A>,
<A HREF = "shell.html">shell</A>, <A HREF = "variable.html">variable</A>
</P>
<HR>
<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands
</H4>
<P>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <A HREF = "#cmd_4">previous
section</A> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_coeff.html">angle_coeff</A></TD><TD ><A HREF = "angle_style.html">angle_style</A></TD><TD ><A HREF = "atom_modify.html">atom_modify</A></TD><TD ><A HREF = "atom_style.html">atom_style</A></TD><TD ><A HREF = "balance.html">balance</A></TD><TD ><A HREF = "bond_coeff.html">bond_coeff</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "bond_style.html">bond_style</A></TD><TD ><A HREF = "boundary.html">boundary</A></TD><TD ><A HREF = "box.html">box</A></TD><TD ><A HREF = "change_box.html">change_box</A></TD><TD ><A HREF = "clear.html">clear</A></TD><TD ><A HREF = "communicate.html">communicate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute.html">compute</A></TD><TD ><A HREF = "compute_modify.html">compute_modify</A></TD><TD ><A HREF = "create_atoms.html">create_atoms</A></TD><TD ><A HREF = "create_box.html">create_box</A></TD><TD ><A HREF = "delete_atoms.html">delete_atoms</A></TD><TD ><A HREF = "delete_bonds.html">delete_bonds</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dielectric.html">dielectric</A></TD><TD ><A HREF = "dihedral_coeff.html">dihedral_coeff</A></TD><TD ><A HREF = "dihedral_style.html">dihedral_style</A></TD><TD ><A HREF = "dimension.html">dimension</A></TD><TD ><A HREF = "displace_atoms.html">displace_atoms</A></TD><TD ><A HREF = "dump.html">dump</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dump_image.html">dump image</A></TD><TD ><A HREF = "dump_modify.html">dump_modify</A></TD><TD ><A HREF = "dump_image.html">dump movie</A></TD><TD ><A HREF = "echo.html">echo</A></TD><TD ><A HREF = "fix.html">fix</A></TD><TD ><A HREF = "fix_modify.html">fix_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "group.html">group</A></TD><TD ><A HREF = "if.html">if</A></TD><TD ><A HREF = "improper_coeff.html">improper_coeff</A></TD><TD ><A HREF = "improper_style.html">improper_style</A></TD><TD ><A HREF = "include.html">include</A></TD><TD ><A HREF = "jump.html">jump</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "kspace_modify.html">kspace_modify</A></TD><TD ><A HREF = "kspace_style.html">kspace_style</A></TD><TD ><A HREF = "label.html">label</A></TD><TD ><A HREF = "lattice.html">lattice</A></TD><TD ><A HREF = "log.html">log</A></TD><TD ><A HREF = "mass.html">mass</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "minimize.html">minimize</A></TD><TD ><A HREF = "min_modify.html">min_modify</A></TD><TD ><A HREF = "min_style.html">min_style</A></TD><TD ><A HREF = "molecule.html">molecule</A></TD><TD ><A HREF = "neb.html">neb</A></TD><TD ><A HREF = "neigh_modify.html">neigh_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "neighbor.html">neighbor</A></TD><TD ><A HREF = "newton.html">newton</A></TD><TD ><A HREF = "next.html">next</A></TD><TD ><A HREF = "package.html">package</A></TD><TD ><A HREF = "pair_coeff.html">pair_coeff</A></TD><TD ><A HREF = "pair_modify.html">pair_modify</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_style.html">pair_style</A></TD><TD ><A HREF = "pair_write.html">pair_write</A></TD><TD ><A HREF = "partition.html">partition</A></TD><TD ><A HREF = "prd.html">prd</A></TD><TD ><A HREF = "print.html">print</A></TD><TD ><A HREF = "processors.html">processors</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "quit.html">quit</A></TD><TD ><A HREF = "read_data.html">read_data</A></TD><TD ><A HREF = "read_dump.html">read_dump</A></TD><TD ><A HREF = "read_restart.html">read_restart</A></TD><TD ><A HREF = "region.html">region</A></TD><TD ><A HREF = "replicate.html">replicate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "rerun.html">rerun</A></TD><TD ><A HREF = "reset_timestep.html">reset_timestep</A></TD><TD ><A HREF = "restart.html">restart</A></TD><TD ><A HREF = "run.html">run</A></TD><TD ><A HREF = "run_style.html">run_style</A></TD><TD ><A HREF = "set.html">set</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "shell.html">shell</A></TD><TD ><A HREF = "special_bonds.html">special_bonds</A></TD><TD ><A HREF = "suffix.html">suffix</A></TD><TD ><A HREF = "tad.html">tad</A></TD><TD ><A HREF = "temper.html">temper</A></TD><TD ><A HREF = "thermo.html">thermo</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "thermo_modify.html">thermo_modify</A></TD><TD ><A HREF = "thermo_style.html">thermo_style</A></TD><TD ><A HREF = "timestep.html">timestep</A></TD><TD ><A HREF = "uncompute.html">uncompute</A></TD><TD ><A HREF = "undump.html">undump</A></TD><TD ><A HREF = "unfix.html">unfix</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "units.html">units</A></TD><TD ><A HREF = "variable.html">variable</A></TD><TD ><A HREF = "velocity.html">velocity</A></TD><TD ><A HREF = "write_data.html">write_data</A></TD><TD ><A HREF = "write_dump.html">write_dump</A></TD><TD ><A HREF = "write_restart.html">write_restart</A>
</TD></TR></TABLE></DIV>
<P>These are commands contributed by users, which can be used if <A HREF = "Section_start.html#start_3">LAMMPS
is built with the appropriate package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "group2ndx.html">group2ndx</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Fix styles
</H4>
<P>See the <A HREF = "fix.html">fix</A> command for one-line descriptions
of each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_adapt.html">adapt</A></TD><TD ><A HREF = "fix_addforce.html">addforce</A></TD><TD ><A HREF = "fix_append_atoms.html">append/atoms</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce</A></TD><TD ><A HREF = "fix_ave_atom.html">ave/atom</A></TD><TD ><A HREF = "fix_ave_correlate.html">ave/correlate</A></TD><TD ><A HREF = "fix_ave_histo.html">ave/histo</A></TD><TD ><A HREF = "fix_ave_spatial.html">ave/spatial</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_ave_time.html">ave/time</A></TD><TD ><A HREF = "fix_balance.html">balance</A></TD><TD ><A HREF = "fix_bond_break.html">bond/break</A></TD><TD ><A HREF = "fix_bond_create.html">bond/create</A></TD><TD ><A HREF = "fix_bond_swap.html">bond/swap</A></TD><TD ><A HREF = "fix_box_relax.html">box/relax</A></TD><TD ><A HREF = "fix_deform.html">deform</A></TD><TD ><A HREF = "fix_deposit.html">deposit</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_drag.html">drag</A></TD><TD ><A HREF = "fix_dt_reset.html">dt/reset</A></TD><TD ><A HREF = "fix_efield.html">efield</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d</A></TD><TD ><A HREF = "fix_evaporate.html">evaporate</A></TD><TD ><A HREF = "fix_external.html">external</A></TD><TD ><A HREF = "fix_freeze.html">freeze</A></TD><TD ><A HREF = "fix_gcmc.html">gcmc</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_gld.html">gld</A></TD><TD ><A HREF = "fix_gravity.html">gravity</A></TD><TD ><A HREF = "fix_heat.html">heat</A></TD><TD ><A HREF = "fix_indent.html">indent</A></TD><TD ><A HREF = "fix_langevin.html">langevin</A></TD><TD ><A HREF = "fix_lineforce.html">lineforce</A></TD><TD ><A HREF = "fix_momentum.html">momentum</A></TD><TD ><A HREF = "fix_move.html">move</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_msst.html">msst</A></TD><TD ><A HREF = "fix_neb.html">neb</A></TD><TD ><A HREF = "fix_nh.html">nph</A></TD><TD ><A HREF = "fix_nphug.html">nphug</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere</A></TD><TD ><A HREF = "fix_nh.html">npt</A></TD><TD ><A HREF = "fix_npt_asphere.html">npt/asphere</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_sphere.html">npt/sphere</A></TD><TD ><A HREF = "fix_nve.html">nve</A></TD><TD ><A HREF = "fix_nve_asphere.html">nve/asphere</A></TD><TD ><A HREF = "fix_nve_asphere_noforce.html">nve/asphere/noforce</A></TD><TD ><A HREF = "fix_nve_body.html">nve/body</A></TD><TD ><A HREF = "fix_nve_limit.html">nve/limit</A></TD><TD ><A HREF = "fix_nve_line.html">nve/line</A></TD><TD ><A HREF = "fix_nve_noforce.html">nve/noforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nve_sphere.html">nve/sphere</A></TD><TD ><A HREF = "fix_nve_tri.html">nve/tri</A></TD><TD ><A HREF = "fix_nh.html">nvt</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere</A></TD><TD ><A HREF = "fix_orient_fcc.html">orient/fcc</A></TD><TD ><A HREF = "fix_planeforce.html">planeforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_poems.html">poems</A></TD><TD ><A HREF = "fix_pour.html">pour</A></TD><TD ><A HREF = "fix_press_berendsen.html">press/berendsen</A></TD><TD ><A HREF = "fix_print.html">print</A></TD><TD ><A HREF = "fix_property_atom.html">property/atom</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/bonds</A></TD><TD ><A HREF = "fix_recenter.html">recenter</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_restrain.html">restrain</A></TD><TD ><A HREF = "fix_rigid.html">rigid</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nph</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small</A></TD><TD ><A HREF = "fix_setforce.html">setforce</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake</A></TD><TD ><A HREF = "fix_spring.html">spring</A></TD><TD ><A HREF = "fix_spring_rg.html">spring/rg</A></TD><TD ><A HREF = "fix_spring_self.html">spring/self</A></TD><TD ><A HREF = "fix_srd.html">srd</A></TD><TD ><A HREF = "fix_store_force.html">store/force</A></TD><TD ><A HREF = "fix_store_state.html">store/state</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
+<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale.html">temp/rescale</A></TD><TD ><A HREF = "fix_thermal_conductivity.html">thermal/conductivity</A></TD><TD ><A HREF = "fix_tmd.html">tmd</A></TD><TD ><A HREF = "fix_ttm.html">ttm</A></TD><TD ><A HREF = "fix_tune_kspace.html">tune/kspace</A></TD><TD ><A HREF = "fix_vector.html">vector</A></TD><TD ><A HREF = "fix_viscosity.html">viscosity</A></TD><TD ><A HREF = "fix_viscous.html">viscous</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_wall.html">wall/colloid</A></TD><TD ><A HREF = "fix_wall_gran.html">wall/gran</A></TD><TD ><A HREF = "fix_wall.html">wall/harmonic</A></TD><TD ><A HREF = "fix_wall.html">wall/lj1043</A></TD><TD ><A HREF = "fix_wall.html">wall/lj126</A></TD><TD ><A HREF = "fix_wall.html">wall/lj93</A></TD><TD ><A HREF = "fix_wall_piston.html">wall/piston</A></TD><TD ><A HREF = "fix_wall_reflect.html">wall/reflect</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "fix_wall_region.html">wall/region</A></TD><TD ><A HREF = "fix_wall_srd.html">wall/srd</A>
</TD></TR></TABLE></DIV>
<P>These are fix styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_ti_spring.html">ti/spring</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated fix styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "fix_freeze.html">freeze/cuda</A></TD><TD ><A HREF = "fix_addforce.html">addforce/cuda</A></TD><TD ><A HREF = "fix_aveforce.html">aveforce/cuda</A></TD><TD ><A HREF = "fix_enforce2d.html">enforce2d/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/cuda</A></TD><TD ><A HREF = "fix_gravity.html">gravity/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh.html">nph/omp</A></TD><TD ><A HREF = "fix_nphug.html">nphug/omp</A></TD><TD ><A HREF = "fix_nph_asphere.html">nph/asphere/omp</A></TD><TD ><A HREF = "fix_nph_sphere.html">nph/sphere/omp</A></TD><TD ><A HREF = "fix_nh.html">npt/cuda</A></TD><TD ><A HREF = "fix_nh.html">npt/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_npt_asphere.html">npt/asphere/omp</A></TD><TD ><A HREF = "fix_npt_sphere.html">npt/sphere/omp</A></TD><TD ><A HREF = "fix_nh.html">nve/cuda</A></TD><TD ><A HREF = "fix_nve.html">nve/omp</A></TD><TD ><A HREF = "fix_nve_sphere.html">nve/sphere/omp</A></TD><TD ><A HREF = "fix_nh.html">nvt/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_nh.html">nvt/omp</A></TD><TD ><A HREF = "fix_nvt_asphere.html">nvt/asphere/omp</A></TD><TD ><A HREF = "fix_nvt_sllod.html">nvt/sllod/omp</A></TD><TD ><A HREF = "fix_nvt_sphere.html">nvt/sphere/omp</A></TD><TD ><A HREF = "fix_qeq_comb.html">qeq/comb/omp</A></TD><TD ><A HREF = "fix_rigid.html">rigid/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_rigid.html">rigid/nph/omp</A></TD><TD ><A HREF = "fix_rigid.html">rigid/npt/omp</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nve/omp</A></TD><TD ><A HREF = "fix_rigid.html">rigid/nvt/omp</A></TD><TD ><A HREF = "fix_rigid.html">rigid/small/omp</A></TD><TD ><A HREF = "fix_setforce.html">setforce/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "fix_shake.html">shake/cuda</A></TD><TD ><A HREF = "fix_temp_berendsen.html">temp/berendsen/cuda</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/cuda</A></TD><TD ><A HREF = "fix_temp_rescale.html">temp/rescale/limit/cuda</A></TD><TD ><A HREF = "fix_viscous.html">viscous/cuda</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Compute styles
</H4>
<P>See the <A HREF = "compute.html">compute</A> command for one-line descriptions of
each style or click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_angle_local.html">angle/local</A></TD><TD ><A HREF = "compute_atom_molecule.html">atom/molecule</A></TD><TD ><A HREF = "compute_body_local.html">body/local</A></TD><TD ><A HREF = "compute_bond_local.html">bond/local</A></TD><TD ><A HREF = "compute_centro_atom.html">centro/atom</A></TD><TD ><A HREF = "compute_cluster_atom.html">cluster/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_cna_atom.html">cna/atom</A></TD><TD ><A HREF = "compute_com.html">com</A></TD><TD ><A HREF = "compute_com_molecule.html">com/molecule</A></TD><TD ><A HREF = "compute_contact_atom.html">contact/atom</A></TD><TD ><A HREF = "compute_coord_atom.html">coord/atom</A></TD><TD ><A HREF = "compute_damage_atom.html">damage/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_inertia_molecule.html">inertia/molecule</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
+<TR ALIGN="center"><TD ><A HREF = "compute_dihedral_local.html">dihedral/local</A></TD><TD ><A HREF = "compute_dilatation_atom.html">dilatation/atom</A></TD><TD ><A HREF = "compute_displace_atom.html">displace/atom</A></TD><TD ><A HREF = "compute_erotate_asphere.html">erotate/asphere</A></TD><TD ><A HREF = "compute_erotate_rigid.html">erotate/rigid</A></TD><TD ><A HREF = "compute_erotate_sphere.html">erotate/sphere</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_erotate_sphere_atom.html">erotate/sphere/atom</A></TD><TD ><A HREF = "compute_event_displace.html">event/displace</A></TD><TD ><A HREF = "compute_group_group.html">group/group</A></TD><TD ><A HREF = "compute_gyration.html">gyration</A></TD><TD ><A HREF = "compute_gyration_molecule.html">gyration/molecule</A></TD><TD ><A HREF = "compute_heat_flux.html">heat/flux</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_improper_local.html">improper/local</A></TD><TD ><A HREF = "compute_inertia_molecule.html">inertia/molecule</A></TD><TD ><A HREF = "compute_ke.html">ke</A></TD><TD ><A HREF = "compute_ke_atom.html">ke/atom</A></TD><TD ><A HREF = "compute_ke_rigid.html">ke/rigid</A></TD><TD ><A HREF = "compute_msd.html">msd</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_msd_molecule.html">msd/molecule</A></TD><TD ><A HREF = "compute_msd_nongauss.html">msd/nongauss</A></TD><TD ><A HREF = "compute_pair.html">pair</A></TD><TD ><A HREF = "compute_pair_local.html">pair/local</A></TD><TD ><A HREF = "compute_pe.html">pe</A></TD><TD ><A HREF = "compute_pe_atom.html">pe/atom</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_plasticity_atom.html">plasticity/atom</A></TD><TD ><A HREF = "compute_pressure.html">pressure</A></TD><TD ><A HREF = "compute_property_atom.html">property/atom</A></TD><TD ><A HREF = "compute_property_local.html">property/local</A></TD><TD ><A HREF = "compute_property_molecule.html">property/molecule</A></TD><TD ><A HREF = "compute_rdf.html">rdf</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_reduce.html">reduce</A></TD><TD ><A HREF = "compute_reduce.html">reduce/region</A></TD><TD ><A HREF = "compute_slice.html">slice</A></TD><TD ><A HREF = "compute_stress_atom.html">stress/atom</A></TD><TD ><A HREF = "compute_temp.html">temp</A></TD><TD ><A HREF = "compute_temp_asphere.html">temp/asphere</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_com.html">temp/com</A></TD><TD ><A HREF = "compute_temp_deform.html">temp/deform</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial</A></TD><TD ><A HREF = "compute_temp_profile.html">temp/profile</A></TD><TD ><A HREF = "compute_temp_ramp.html">temp/ramp</A></TD><TD ><A HREF = "compute_temp_region.html">temp/region</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "compute_temp_sphere.html">temp/sphere</A></TD><TD ><A HREF = "compute_ti.html">ti</A></TD><TD ><A HREF = "compute_vacf.html">vacf</A></TD><TD ><A HREF = "compute_voronoi_atom.html">voronoi/atom</A>
</TD></TR></TABLE></DIV>
<P>These are compute styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_ackland_atom.html">ackland/atom</A></TD><TD ><A HREF = "compute_basal_atom.html">basal/atom</A></TD><TD ><A HREF = "compute_ke_eff.html">ke/eff</A></TD><TD ><A HREF = "compute_ke_atom_eff.html">ke/atom/eff</A></TD><TD ><A HREF = "compute_meso_e_atom.html">meso_e/atom</A></TD><TD ><A HREF = "compute_meso_rho_atom.html">meso_rho/atom</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "compute_meso_t_atom.html">meso_t/atom</A></TD><TD ><A HREF = "compute_temp_eff.html">temp/eff</A></TD><TD ><A HREF = "compute_temp_deform_eff.html">temp/deform/eff</A></TD><TD ><A HREF = "compute_temp_region_eff.html">temp/region/eff</A></TD><TD ><A HREF = "compute_temp_rotate.html">temp/rotate</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated compute styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "compute_pe.html">pe/cuda</A></TD><TD ><A HREF = "compute_pressure.html">pressure/cuda</A></TD><TD ><A HREF = "compute_temp.html">temp/cuda</A></TD><TD ><A HREF = "compute_temp_partial.html">temp/partial/cuda</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Pair_style potentials
</H4>
<P>See the <A HREF = "pair_style.html">pair_style</A> command for an overview of pair
potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_none.html">none</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid</A></TD><TD ><A HREF = "pair_hybrid.html">hybrid/overlay</A></TD><TD ><A HREF = "pair_adp.html">adp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_airebo.html">airebo</A></TD><TD ><A HREF = "pair_beck.html">beck</A></TD><TD ><A HREF = "pair_body.html">body</A></TD><TD ><A HREF = "pair_bop.html">bop</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born</A></TD><TD ><A HREF = "pair_born.html">born/coul/long</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm</A></TD><TD ><A HREF = "pair_born.html">born/coul/wolf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_brownian.html">brownian</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly</A></TD><TD ><A HREF = "pair_buck.html">buck</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/long</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/msm</A></TD><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long</A></TD><TD ><A HREF = "pair_colloid.html">colloid</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_comb.html">comb</A></TD><TD ><A HREF = "pair_comb.html">comb3</A></TD><TD ><A HREF = "pair_coul.html">coul/cut</A></TD><TD ><A HREF = "pair_coul.html">coul/debye</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/dsf</A></TD><TD ><A HREF = "pair_coul.html">coul/long</A></TD><TD ><A HREF = "pair_coul.html">coul/msm</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat</A></TD><TD ><A HREF = "pair_dsmc.html">dsmc</A></TD><TD ><A HREF = "pair_eam.html">eam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy</A></TD><TD ><A HREF = "pair_eam.html">eam/fs</A></TD><TD ><A HREF = "pair_eim.html">eim</A></TD><TD ><A HREF = "pair_gauss.html">gauss</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse</A></TD><TD ><A HREF = "pair_kim.html">kim</A></TD><TD ><A HREF = "pair_lcbop.html">lcbop</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_line_lj.html">line/lj</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/msm</A></TD><TD ><A HREF = "pair_class2.html">lj/class2</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long</A></TD><TD ><A HREF = "pair_dipole.html">lj/long/dipole/long</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/tip4p/long</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lubricate.html">lubricate/poly</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU</A></TD><TD ><A HREF = "pair_lubricateU.html">lubricateU/poly</A></TD><TD ><A HREF = "pair_meam.html">meam</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_mie.html">mie/cut</A></TD><TD ><A HREF = "pair_morse.html">morse</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic</A></TD><TD ><A HREF = "pair_nm.html">nm/cut</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD><TD ><A HREF = "pair_resquared.html">resquared</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long</A></TD></TR>
-<TR ALIGN="center"><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A></TD><TD ><A HREF = "pair_zbl.html">zbl</A>
+<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/long</A></TD><TD ><A HREF = "pair_peri.html">peri/eps</A></TD><TD ><A HREF = "pair_peri.html">peri/lps</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_peri.html">peri/pmb</A></TD><TD ><A HREF = "pair_peri.html">peri/ves</A></TD><TD ><A HREF = "pair_reax.html">reax</A></TD><TD ><A HREF = "pair_airebo.html">rebo</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared</A></TD><TD ><A HREF = "pair_soft.html">soft</A></TD><TD ><A HREF = "pair_sw.html">sw</A></TD><TD ><A HREF = "pair_table.html">table</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">tip4p/long</A></TD><TD ><A HREF = "pair_tri_lj.html">tri/lj</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid</A></TD></TR>
+<TR ALIGN="center"><TD ><A HREF = "pair_zbl.html">zbl</A>
</TD></TR></TABLE></DIV>
<P>These are pair styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_awpmd.html">awpmd/cut</A></TD><TD ><A HREF = "pair_coul_diel.html">coul/diel</A></TD><TD ><A HREF = "pair_eam.html">eam/cd</A></TD><TD ><A HREF = "pair_edip.html">edip</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eff.html">eff/cut</A></TD><TD ><A HREF = "pair_gauss.html">gauss/cut</A></TD><TD ><A HREF = "pair_list.html">list</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_meam_spline.html">meam/spline</A></TD><TD ><A HREF = "pair_meam_sw_spline.html">meam/sw/spline</A></TD><TD ><A HREF = "pair_reax_c.html">reax/c</A></TD><TD ><A HREF = "pair_sph_heatconduction.html">sph/heatconduction</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sph_idealgas.html">sph/idealgas</A></TD><TD ><A HREF = "pair_sph_lj.html">sph/lj</A></TD><TD ><A HREF = "pair_sph_rhosum.html">sph/rhosum</A></TD><TD ><A HREF = "pair_sph_taitwater.html">sph/taitwater</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sph_taitwater_morris.html">sph/taitwater/morris</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/table</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated pair styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "pair_adp.html">adp/omp</A></TD><TD ><A HREF = "pair_airebo.html">airebo/omp</A></TD><TD ><A HREF = "pair_beck.html">beck/gpu</A></TD><TD ><A HREF = "pair_beck.html">beck/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/long/cuda</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/gpu</A></TD><TD ><A HREF = "pair_born.html">born/coul/long/omp</A></TD><TD ><A HREF = "pair_born.html">born/coul/msm/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_born.html">born/coul/wolf/gpu</A></TD><TD ><A HREF = "pair_born.html">born/coul/wolf/omp</A></TD><TD ><A HREF = "pair_born.html">born/gpu</A></TD><TD ><A HREF = "pair_born.html">born/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_brownian.html">brownian/omp</A></TD><TD ><A HREF = "pair_brownian.html">brownian/poly/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/cut/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/cuda</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/gpu</A></TD><TD ><A HREF = "pair_buck.html">buck/coul/long/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/coul/msm/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/cuda</A></TD><TD ><A HREF = "pair_buck_long.html">buck/long/coul/long/omp</A></TD><TD ><A HREF = "pair_buck.html">buck/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_buck.html">buck/omp</A></TD><TD ><A HREF = "pair_colloid.html">colloid/gpu</A></TD><TD ><A HREF = "pair_colloid.html">colloid/omp</A></TD><TD ><A HREF = "pair_comb.html">comb/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/cut/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/debye/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/dsf/gpu</A></TD><TD ><A HREF = "pair_coul.html">coul/dsf/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_coul.html">coul/long/gpu</A></TD><TD ><A HREF = "pair_coul.html">coul/long/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/msm/omp</A></TD><TD ><A HREF = "pair_coul.html">coul/wolf</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dpd.html">dpd/omp</A></TD><TD ><A HREF = "pair_dpd.html">dpd/tstat/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/alloy/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/alloy/opt</A></TD><TD ><A HREF = "pair_eam.html">eam/cd/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/fs/cuda</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/fs/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eam.html">eam/gpu</A></TD><TD ><A HREF = "pair_eam.html">eam/omp</A></TD><TD ><A HREF = "pair_eam.html">eam/opt</A></TD><TD ><A HREF = "pair_edip.html">edip/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_eim.html">eim/omp</A></TD><TD ><A HREF = "pair_gauss.html">gauss/gpu</A></TD><TD ><A HREF = "pair_gauss.html">gauss/omp</A></TD><TD ><A HREF = "pair_gayberne.html">gayberne/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gayberne.html">gayberne/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hertz/history/omp</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/cuda</A></TD><TD ><A HREF = "pair_gran.html">gran/hooke/history/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gran.html">gran/hooke/omp</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/lj/omp</A></TD><TD ><A HREF = "pair_hbond_dreiding.html">hbond/dreiding/morse/omp</A></TD><TD ><A HREF = "pair_line_lj.html">line/lj/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/charmm/implicit/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/cuda</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/gpu</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/omp</A></TD><TD ><A HREF = "pair_charmm.html">lj/charmm/coul/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/cut/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/coul/long/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/coul/msm/omp</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/cuda</A></TD><TD ><A HREF = "pair_class2.html">lj/class2/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_class2.html">lj/class2/omp</A></TD><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/debye/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/dsf/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/long/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/coul/msm/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/cuda</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut/gpu</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/cut/omp</A></TD><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_dipole.html">lj/cut/dipole/sf/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/experimental/cuda</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/gpu</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj.html">lj/cut/opt</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/cut/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/omp</A></TD><TD ><A HREF = "pair_lj.html">lj/cut/tip4p/long/opt</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_expand.html">lj/expand/cuda</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/gpu</A></TD><TD ><A HREF = "pair_lj_expand.html">lj/expand/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_gromacs.html">lj/gromacs/coul/gromacs/omp</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/cuda</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/gpu</A></TD><TD ><A HREF = "pair_gromacs.html">lj/gromacs/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_long.html">lj/long/coul/long/opt</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/gpu</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/long/omp</A></TD><TD ><A HREF = "pair_sdk.html">lj/sdk/coul/msm/omp</A></TD><TD ><A HREF = "pair_lj_sf.html">lj/sf/omp</A></TD><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj_smooth.html">lj/smooth/omp</A></TD><TD ><A HREF = "pair_lj_smooth_linear.html">lj/smooth/linear/omp</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/cuda</A></TD><TD ><A HREF = "pair_lj96.html">lj96/cut/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_lj96.html">lj96/cut/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/omp</A></TD><TD ><A HREF = "pair_lubricate.html">lubricate/poly/omp</A></TD><TD ><A HREF = "pair_meam_spline.html">meam/spline/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_mie.html">mie/cut/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/cuda</A></TD><TD ><A HREF = "pair_morse.html">morse/gpu</A></TD><TD ><A HREF = "pair_morse.html">morse/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_morse.html">morse/opt</A></TD><TD ><A HREF = "pair_nb3b_harmonic.html">nb3b/harmonic/omp</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/omp</A></TD><TD ><A HREF = "pair_nm.html">nm/cut/coul/cut/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_nm.html">nm/cut/coul/long/omp</A></TD><TD ><A HREF = "pair_peri.html">peri/lps/omp</A></TD><TD ><A HREF = "pair_peri.html">peri/pmb/omp</A></TD><TD ><A HREF = "pair_airebo.html">rebo/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_resquared.html">resquared/gpu</A></TD><TD ><A HREF = "pair_resquared.html">resquared/omp</A></TD><TD ><A HREF = "pair_soft.html">soft/gpu</A></TD><TD ><A HREF = "pair_soft.html">soft/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_sw.html">sw/cuda</A></TD><TD ><A HREF = "pair_sw.html">sw/gpu</A></TD><TD ><A HREF = "pair_sw.html">sw/omp</A></TD><TD ><A HREF = "pair_table.html">table/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_table.html">table/omp</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/cuda</A></TD><TD ><A HREF = "pair_tersoff.html">tersoff/omp</A></TD><TD ><A HREF = "pair_tersoff_mod.html">tersoff/mod/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tersoff.html">tersoff/table/omp</A></TD><TD ><A HREF = "pair_tersoff_zbl.html">tersoff/zbl/omp</A></TD><TD ><A HREF = "pair_coul.html">tip4p/cut/omp</A></TD><TD ><A HREF = "pair_coul.html">tip4p/long/omp</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_tri_lj.html">tri/lj/omp</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/gpu</A></TD><TD ><A HREF = "pair_yukawa.html">yukawa/omp</A></TD><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/gpu</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "pair_yukawa_colloid.html">yukawa/colloid/omp</A></TD><TD ><A HREF = "pair_zbl.html">zbl/omp</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Bond_style potentials
</H4>
<P>See the <A HREF = "bond_style.html">bond_style</A> command for an overview of bond
potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_none.html">none</A></TD><TD WIDTH="100"><A HREF = "bond_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "bond_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "bond_fene.html">fene</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_fene_expand.html">fene/expand</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "bond_morse.html">morse</A></TD><TD WIDTH="100"><A HREF = "bond_nonlinear.html">nonlinear</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_quartic.html">quartic</A></TD><TD WIDTH="100"><A HREF = "bond_table.html">table</A>
</TD></TR></TABLE></DIV>
<P>These are bond styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "bond_harmonic_shift.html">harmonic/shift</A></TD><TD ><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated bond styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "bond_fene.html">fene/omp</A></TD><TD WIDTH="100"><A HREF = "bond_fene_expand.html">fene/expand/omp</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic.html">harmonic/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_harmonic_shift.html">harmonic/shift/omp</A></TD><TD WIDTH="100"><A HREF = "bond_harmonic_shift_cut.html">harmonic/shift/cut/omp</A></TD><TD WIDTH="100"><A HREF = "bond_morse.html">morse/omp</A></TD><TD WIDTH="100"><A HREF = "bond_nonlinear.html">nonlinear/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "bond_quartic.html">quartic/omp</A></TD><TD WIDTH="100"><A HREF = "bond_table.html">table/omp</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Angle_style potentials
</H4>
<P>See the <A HREF = "angle_style.html">angle_style</A> command for an overview of
angle potentials. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_none.html">none</A></TD><TD WIDTH="100"><A HREF = "angle_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_periodic.html">cosine/periodic</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "angle_table.html">table</A>
</TD></TR></TABLE></DIV>
<P>These are angle styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "angle_sdk.html">sdk</A></TD><TD ><A HREF = "angle_cosine_shift.html">cosine/shift</A></TD><TD ><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp</A></TD><TD ><A HREF = "angle_dipole.html">dipole</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "angle_fourier.html">fourier</A></TD><TD ><A HREF = "angle_fourier_simple.html">fourier/simple</A></TD><TD ><A HREF = "angle_quartic.html">quartic</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated angle styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_charmm.html">charmm/omp</A></TD><TD WIDTH="100"><A HREF = "angle_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine.html">cosine/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_delta.html">cosine/delta/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_cosine_periodic.html">cosine/periodic/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_shift.html">cosine/shift/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_shift_exp.html">cosine/shift/exp/omp</A></TD><TD WIDTH="100"><A HREF = "angle_cosine_squared.html">cosine/squared/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "angle_dipole.html">dipole/omp</A><A HREF = "angle_fourier.html">fourier/omp</A></TD><TD WIDTH="100"><A HREF = "angle_fourier_simple.html">fourier/simple/omp</A></TD><TD WIDTH="100"><A HREF = "angle_harmonic.html">harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "angle_quartic.html">quartic/omp</A><A HREF = "angle_table.html">table/omp</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Dihedral_style potentials
</H4>
<P>See the <A HREF = "dihedral_style.html">dihedral_style</A> command for an overview
of dihedral potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_none.html">none</A></TD><TD WIDTH="100"><A HREF = "dihedral_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "dihedral_charmm.html">charmm</A></TD><TD WIDTH="100"><A HREF = "dihedral_class2.html">class2</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_helix.html">helix</A></TD><TD WIDTH="100"><A HREF = "dihedral_multi_harmonic.html">multi/harmonic</A></TD><TD WIDTH="100"><A HREF = "dihedral_opls.html">opls</A>
</TD></TR></TABLE></DIV>
<P>These are dihedral styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp</A></TD><TD ><A HREF = "dihedral_fourier.html">fourier</A></TD><TD ><A HREF = "dihedral_nharmonic.html">nharmonic</A></TD><TD ><A HREF = "dihedral_quadratic.html">quadratic</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "dihedral_table.html">table</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated dihedral styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_charmm.html">charmm/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_cosine_shift_exp.html">cosine/shift/exp/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_fourier.html">fourier/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_harmonic.html">harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_helix.html">helix/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_multi_harmonic.html">multi/harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_nharmonic.html">nharmonic/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "dihedral_opls.html">opls/omp</A><A HREF = "dihedral_quadratic.html">quadratic/omp</A></TD><TD WIDTH="100"><A HREF = "dihedral_table.html">table/omp</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Improper_style potentials
</H4>
<P>See the <A HREF = "improper_style.html">improper_style</A> command for an overview
of improper potentials. Click on the style itself for a full
description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_none.html">none</A></TD><TD WIDTH="100"><A HREF = "improper_hybrid.html">hybrid</A></TD><TD WIDTH="100"><A HREF = "improper_class2.html">class2</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella</A>
</TD></TR></TABLE></DIV>
<P>These are improper styles contributed by users, which can be used if
<A HREF = "Section_start.html#start_3">LAMMPS is built with the appropriate
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "improper_cossq.html">cossq</A></TD><TD ><A HREF = "improper_fourier.html">fourier</A></TD><TD ><A HREF = "improper_ring.html">ring</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated improper styles, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_class2.html">class2/omp</A></TD><TD WIDTH="100"><A HREF = "improper_cossq.html">cossq/omp</A></TD><TD WIDTH="100"><A HREF = "improper_cvff.html">cvff/omp</A></TD><TD WIDTH="100"><A HREF = "improper_fourier.html">fourier/omp</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "improper_harmonic.html">harmonic/omp</A></TD><TD WIDTH="100"><A HREF = "improper_ring.html">ring/omp</A></TD><TD WIDTH="100"><A HREF = "improper_umbrella.html">umbrella/omp</A>
</TD></TR></TABLE></DIV>
<HR>
<H4>Kspace solvers
</H4>
<P>See the <A HREF = "kspace_style.html">kspace_style</A> command for an overview of
Kspace solvers. Click on the style itself for a full description:
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">ewald</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">ewald/disp</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">msm</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">msm/cg</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">pppm</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/cg</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/disp</A></TD><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/disp/tip4p</A></TD></TR>
<TR ALIGN="center"><TD WIDTH="100"><A HREF = "kspace_style.html">pppm/tip4p</A>
</TD></TR></TABLE></DIV>
<P>These are accelerated Kspace solvers, which can be used if LAMMPS is
built with the <A HREF = "Section_accelerate.html">appropriate accelerated
package</A>.
</P>
<DIV ALIGN=center><TABLE BORDER=1 >
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">ewald/omp</A></TD><TD ><A HREF = "kspace_style.html">msm/omp</A></TD><TD ><A HREF = "kspace_style.html">msm/cg/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/cuda</A></TD></TR>
<TR ALIGN="center"><TD ><A HREF = "kspace_style.html">pppm/gpu</A></TD><TD ><A HREF = "kspace_style.html">pppm/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/cg/omp</A></TD><TD ><A HREF = "kspace_style.html">pppm/tip4p/omp</A>
</TD></TR></TABLE></DIV>
</HTML>
diff --git a/doc/Section_commands.txt b/doc/Section_commands.txt
index 50ce40680..758d73f17 100644
--- a/doc/Section_commands.txt
+++ b/doc/Section_commands.txt
@@ -1,1221 +1,1225 @@
"Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
3. Commands :h3
This section describes how a LAMMPS input script is formatted and the
input script commands used to define a LAMMPS simulation.
3.1 "LAMMPS input script"_#cmd_1
3.2 "Parsing rules"_#cmd_2
3.3 "Input script structure"_#cmd_3
3.4 "Commands listed by category"_#cmd_4
3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
:line
:line
3.1 LAMMPS input script :link(cmd_1),h4
LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
command causes LAMMPS to take some action. It may set an internal
variable, read in a file, or run a simulation. Most commands have
default settings, which means you only need to use the command if you
wish to change the default.
In many cases, the ordering of commands in an input script is not
important. However the following rules apply:
(1) LAMMPS does not read your entire input script and then perform a
simulation with all the settings. Rather, the input script is read
one line at a time and each command takes effect when it is read.
Thus this sequence of commands:
timestep 0.5
run 100
run 100 :pre
does something different than this sequence:
run 100
timestep 0.5
run 100 :pre
In the first case, the specified timestep (0.5 fmsec) is used for two
simulations of 100 timesteps each. In the 2nd case, the default
timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5
fmsec timestep is used for the 2nd one.
(2) Some commands are only valid when they follow other commands. For
example you cannot set the temperature of a group of atoms until atoms
have been defined and a group command is used to define which atoms
belong to the group.
(3) Sometimes command B will use values that can be set by command A.
This means command A must precede command B in the input script if it
is to have the desired effect. For example, the
"read_data"_read_data.html command initializes the system by setting
up the simulation box and assigning atoms to processors. If default
values are not desired, the "processors"_processors.html and
"boundary"_boundary.html commands need to be used before read_data to
tell LAMMPS how to map processors to the simulation box.
Many input script errors are detected by LAMMPS and an ERROR or
WARNING message is printed. "This section"_Section_errors.html gives
more information on what errors mean. The documentation for each
command lists restrictions on how the command can be used.
:line
3.2 Parsing rules :link(cmd_2),h4
Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
are specified command arguments. Upper case letters may be used in
file names or user-chosen ID strings.
Here is how each line in the input script is parsed by LAMMPS:
(1) If the last printable character on the line is a "&" character
(with no surrounding quotes), the command is assumed to continue on
the next line. The next line is concatenated to the previous line by
removing the "&" character and newline. This allows long commands to
be continued across two or more lines.
(2) All characters from the first "#" character onward are treated as
comment and discarded. See an exception in (6). Note that a
comment after a trailing "&" character will prevent the command from
continuing on the next line. Also note that for multi-line commands a
single leading "#" will comment out the entire command.
(3) The line is searched repeatedly for $ characters, which indicate
variables that are replaced with a text string. See an exception in
(6).
If the $ is followed by curly brackets, then the variable name is the
text inside the curly brackets. If no curly brackets follow the $,
then the variable name is the single character immediately following
the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and
"x".
How the variable is converted to a text string depends on what style
of variable it is; see the "variable"_variable doc page for details.
It can be a variable that stores multiple text strings, and return one
of them. The returned text string can be multiple "words" (space
separated) which will then be interpreted as multiple arguments in the
input command. The variable can also store a numeric formula which
will be evaluated and its numeric result returned as a string.
As a special case, if the $ is followed by parenthesis, then the text
inside the parenthesis is treated as an "immediate" variable and
evaluated as an "equal-style variable"_variable.html. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:
variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete :pre
can be replaced by
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
so that you do not have to define (or discard) a temporary variable X.
Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.
Thus you cannot do this:
variable a equal 2
variable b2 equal 4
print "B2 = $\{b$a\}" :pre
Nor can you specify this $($x-1.0) for an immediate variable, but
you could use $(v_x-1.0), since the latter is valid syntax for an
"equal-style variable"_variable.html.
See the "variable"_variable.html command for more details of how
strings are assigned to variables and evaluated, and how they can be
used in input script commands.
(4) The line is broken into "words" separated by whitespace (tabs,
spaces). Note that words can thus contain letters, digits,
underscores, or punctuation characters.
(5) The first word is the command name. All successive words in the
line are arguments.
(6) If you want text with spaces to be treated as a single argument,
it can be enclosed in either double or single quotes. A long single
argument enclosed in quotes can even span multiple lines if the "&"
character is used, as described above. E.g.
print "Volume = $v"
print 'Volume = $v'
variable a string "red green blue &
purple orange cyan"
if "${steps} > 1000" then quit :pre
The quotes are removed when the single argument is stored internally.
See the "dump modify format"_dump_modify.html or "print"_print.html or
"if"_if.html commands for examples. A "#" or "$" character that is
between quotes will not be treated as a comment indicator in (2) or
substituted for as a variable in (3).
IMPORTANT NOTE: If the argument is itself a command that requires a
quoted argument (e.g. using a "print"_print.html command as part of an
"if"_if.html or "run every"_run.html command), then the double and
single quotes can be nested in the usual manner. See the doc pages
for those commands for examples. Only one of level of nesting is
allowed, but that should be sufficient for most use cases.
:line
3.3 Input script structure :h4,link(cmd_3)
This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
sample input scripts; the corresponding problems are discussed in
"Section_example"_Section_example.html, and animated on the "LAMMPS
WWW Site"_lws.
A LAMMPS input script typically has 4 parts:
Initialization
Atom definition
Settings
Run a simulation :ol
The last 2 parts can be repeated as many times as desired. I.e. run a
simulation, change some settings, run some more, etc. Each of the 4
parts is now described in more detail. Remember that almost all the
commands need only be used if a non-default value is desired.
(1) Initialization
Set parameters that need to be defined before atoms are created or
read-in from a file.
The relevant commands are "units"_units.html,
"dimension"_dimension.html, "newton"_newton.html,
"processors"_processors.html, "boundary"_boundary.html,
"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
If force-field parameters appear in the files that will be read, these
commands tell LAMMPS what kinds of force fields are being used:
"pair_style"_pair_style.html, "bond_style"_bond_style.html,
"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
"improper_style"_improper_style.html.
(2) Atom definition
There are 3 ways to define atoms in LAMMPS. Read them in from a data
or restart file via the "read_data"_read_data.html or
"read_restart"_read_restart.html commands. These files can contain
molecular topology information. Or create atoms on a lattice (with no
molecular topology), using these commands: "lattice"_lattice.html,
"region"_region.html, "create_box"_create_box.html,
"create_atoms"_create_atoms.html. The entire set of atoms can be
duplicated to make a larger simulation using the
"replicate"_replicate.html command.
(3) Settings
Once atoms and molecular topology are defined, a variety of settings
can be specified: force field coefficients, simulation parameters,
output options, etc.
Force field coefficients are set by these commands (they can also be
set in the read-in files): "pair_coeff"_pair_coeff.html,
"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
"dihedral_coeff"_dihedral_coeff.html,
"improper_coeff"_improper_coeff.html,
"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
"special_bonds"_special_bonds.html.
Various simulation parameters are set by these commands:
"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
"group"_group.html, "timestep"_timestep.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"min_style"_min_style.html, "min_modify"_min_modify.html.
Fixes impose a variety of boundary conditions, time integration, and
diagnostic options. The "fix"_fix.html command comes in many flavors.
Various computations can be specified for execution during a
simulation using the "compute"_compute.html,
"compute_modify"_compute_modify.html, and "variable"_variable.html
commands.
Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
and "restart"_restart.html commands.
(4) Run a simulation
A molecular dynamics simulation is run using the "run"_run.html
command. Energy minimization (molecular statics) is performed using
the "minimize"_minimize.html command. A parallel tempering
(replica-exchange) simulation can be run using the
"temper"_temper.html command.
:line
3.4 Commands listed by category :link(cmd_4),h4
This section lists all LAMMPS commands, grouped by category. The
"next section"_#cmd_5 lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
Initialization:
"atom_modify"_atom_modify.html, "atom_style"_atom_style.html,
"boundary"_boundary.html, "dimension"_dimension.html,
"newton"_newton.html, "processors"_processors.html, "units"_units.html
Atom definition:
"create_atoms"_create_atoms.html, "create_box"_create_box.html,
"lattice"_lattice.html, "read_data"_read_data.html,
"read_dump"_read_dump.html, "read_restart"_read_restart.html,
"region"_region.html, "replicate"_replicate.html
Force fields:
"angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html,
"bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html,
"dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html,
"pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html,
"pair_style"_pair_style.html, "pair_write"_pair_write.html,
"special_bonds"_special_bonds.html
Settings:
"communicate"_communicate.html, "group"_group.html, "mass"_mass.html,
"min_modify"_min_modify.html, "min_style"_min_style.html,
"neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html,
"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
"set"_set.html, "timestep"_timestep.html, "velocity"_velocity.html
Fixes:
"fix"_fix.html, "fix_modify"_fix_modify.html, "unfix"_unfix.html
Computes:
"compute"_compute.html, "compute_modify"_compute_modify.html,
"uncompute"_uncompute.html
Output:
"dump"_dump.html, "dump image"_dump_image.html,
"dump_modify"_dump_modify.html, "dump movie"_dump_image.html,
"restart"_restart.html, "thermo"_thermo.html,
"thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html,
"undump"_undump.html, "write_data"_write_data.html,
"write_dump"_write_dump.html, "write_restart"_write_restart.html
Actions:
"delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html,
"displace_atoms"_displace_atoms.html, "change_box"_change_box.html,
"minimize"_minimize.html, "neb"_neb.html "prd"_prd.html,
"rerun"_rerun.html, "run"_run.html, "temper"_temper.html
Miscellaneous:
"clear"_clear.html, "echo"_echo.html, "if"_if.html,
"include"_include.html, "jump"_jump.html, "label"_label.html,
"log"_log.html, "next"_next.html, "print"_print.html,
"shell"_shell.html, "variable"_variable.html
:line
3.5 Individual commands :h4,link(cmd_5),link(comm)
This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The "previous
section"_#cmd_4 lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
in the command's documentation.
"angle_coeff"_angle_coeff.html,
"angle_style"_angle_style.html,
"atom_modify"_atom_modify.html,
"atom_style"_atom_style.html,
"balance"_balance.html,
"bond_coeff"_bond_coeff.html,
"bond_style"_bond_style.html,
"boundary"_boundary.html,
"box"_box.html,
"change_box"_change_box.html,
"clear"_clear.html,
"communicate"_communicate.html,
"compute"_compute.html,
"compute_modify"_compute_modify.html,
"create_atoms"_create_atoms.html,
"create_box"_create_box.html,
"delete_atoms"_delete_atoms.html,
"delete_bonds"_delete_bonds.html,
"dielectric"_dielectric.html,
"dihedral_coeff"_dihedral_coeff.html,
"dihedral_style"_dihedral_style.html,
"dimension"_dimension.html,
"displace_atoms"_displace_atoms.html,
"dump"_dump.html,
"dump image"_dump_image.html,
"dump_modify"_dump_modify.html,
"dump movie"_dump_image.html,
"echo"_echo.html,
"fix"_fix.html,
"fix_modify"_fix_modify.html,
"group"_group.html,
"if"_if.html,
"improper_coeff"_improper_coeff.html,
"improper_style"_improper_style.html,
"include"_include.html,
"jump"_jump.html,
"kspace_modify"_kspace_modify.html,
"kspace_style"_kspace_style.html,
"label"_label.html,
"lattice"_lattice.html,
"log"_log.html,
"mass"_mass.html,
"minimize"_minimize.html,
"min_modify"_min_modify.html,
"min_style"_min_style.html,
"molecule"_molecule.html,
"neb"_neb.html,
"neigh_modify"_neigh_modify.html,
"neighbor"_neighbor.html,
"newton"_newton.html,
"next"_next.html,
"package"_package.html,
"pair_coeff"_pair_coeff.html,
"pair_modify"_pair_modify.html,
"pair_style"_pair_style.html,
"pair_write"_pair_write.html,
"partition"_partition.html,
"prd"_prd.html,
"print"_print.html,
"processors"_processors.html,
"quit"_quit.html,
"read_data"_read_data.html,
"read_dump"_read_dump.html,
"read_restart"_read_restart.html,
"region"_region.html,
"replicate"_replicate.html,
"rerun"_rerun.html,
"reset_timestep"_reset_timestep.html,
"restart"_restart.html,
"run"_run.html,
"run_style"_run_style.html,
"set"_set.html,
"shell"_shell.html,
"special_bonds"_special_bonds.html,
"suffix"_suffix.html,
"tad"_tad.html,
"temper"_temper.html,
"thermo"_thermo.html,
"thermo_modify"_thermo_modify.html,
"thermo_style"_thermo_style.html,
"timestep"_timestep.html,
"uncompute"_uncompute.html,
"undump"_undump.html,
"unfix"_unfix.html,
"units"_units.html,
"variable"_variable.html,
"velocity"_velocity.html,
"write_data"_write_data.html,
"write_dump"_write_dump.html,
"write_restart"_write_restart.html :tb(c=6,ea=c)
These are commands contributed by users, which can be used if "LAMMPS
is built with the appropriate package"_Section_start.html#start_3.
"group2ndx"_group2ndx.html :tb(c=1,ea=c)
:line
Fix styles :h4
See the "fix"_fix.html command for one-line descriptions
of each style or click on the style itself for a full description:
"adapt"_fix_adapt.html,
"addforce"_fix_addforce.html,
"append/atoms"_fix_append_atoms.html,
"aveforce"_fix_aveforce.html,
"ave/atom"_fix_ave_atom.html,
"ave/correlate"_fix_ave_correlate.html,
"ave/histo"_fix_ave_histo.html,
"ave/spatial"_fix_ave_spatial.html,
"ave/time"_fix_ave_time.html,
"balance"_fix_balance.html,
"bond/break"_fix_bond_break.html,
"bond/create"_fix_bond_create.html,
"bond/swap"_fix_bond_swap.html,
"box/relax"_fix_box_relax.html,
"deform"_fix_deform.html,
"deposit"_fix_deposit.html,
"drag"_fix_drag.html,
"dt/reset"_fix_dt_reset.html,
"efield"_fix_efield.html,
"enforce2d"_fix_enforce2d.html,
"evaporate"_fix_evaporate.html,
"external"_fix_external.html,
"freeze"_fix_freeze.html,
"gcmc"_fix_gcmc.html,
"gld"_fix_gld.html,
"gravity"_fix_gravity.html,
"heat"_fix_heat.html,
"indent"_fix_indent.html,
"langevin"_fix_langevin.html,
"lineforce"_fix_lineforce.html,
"momentum"_fix_momentum.html,
"move"_fix_move.html,
"msst"_fix_msst.html,
"neb"_fix_neb.html,
"nph"_fix_nh.html,
"nphug"_fix_nphug.html,
"nph/asphere"_fix_nph_asphere.html,
"nph/sphere"_fix_nph_sphere.html,
"npt"_fix_nh.html,
"npt/asphere"_fix_npt_asphere.html,
"npt/sphere"_fix_npt_sphere.html,
"nve"_fix_nve.html,
"nve/asphere"_fix_nve_asphere.html,
"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
"nve/body"_fix_nve_body.html,
"nve/limit"_fix_nve_limit.html,
"nve/line"_fix_nve_line.html,
"nve/noforce"_fix_nve_noforce.html,
"nve/sphere"_fix_nve_sphere.html,
"nve/tri"_fix_nve_tri.html,
"nvt"_fix_nh.html,
"nvt/asphere"_fix_nvt_asphere.html,
"nvt/sllod"_fix_nvt_sllod.html,
"nvt/sphere"_fix_nvt_sphere.html,
"orient/fcc"_fix_orient_fcc.html,
"planeforce"_fix_planeforce.html,
"poems"_fix_poems.html,
"pour"_fix_pour.html,
"press/berendsen"_fix_press_berendsen.html,
"print"_fix_print.html,
"property/atom"_fix_property_atom.html,
"qeq/comb"_fix_qeq_comb.html,
"reax/bonds"_fix_reax_bonds.html,
"recenter"_fix_recenter.html,
"restrain"_fix_restrain.html,
"rigid"_fix_rigid.html,
"rigid/nph"_fix_rigid.html,
"rigid/npt"_fix_rigid.html,
"rigid/nve"_fix_rigid.html,
"rigid/nvt"_fix_rigid.html,
"rigid/small"_fix_rigid.html,
"setforce"_fix_setforce.html,
"shake"_fix_shake.html,
"spring"_fix_spring.html,
"spring/rg"_fix_spring_rg.html,
"spring/self"_fix_spring_self.html,
"srd"_fix_srd.html,
"store/force"_fix_store_force.html,
"store/state"_fix_store_state.html,
"temp/berendsen"_fix_temp_berendsen.html,
"temp/rescale"_fix_temp_rescale.html,
"thermal/conductivity"_fix_thermal_conductivity.html,
"tmd"_fix_tmd.html,
"ttm"_fix_ttm.html,
"tune/kspace"_fix_tune_kspace.html,
+"vector"_fix_vector.html,
"viscosity"_fix_viscosity.html,
"viscous"_fix_viscous.html,
"wall/colloid"_fix_wall.html,
"wall/gran"_fix_wall_gran.html,
"wall/harmonic"_fix_wall.html,
"wall/lj1043"_fix_wall.html,
"wall/lj126"_fix_wall.html,
"wall/lj93"_fix_wall.html,
"wall/piston"_fix_wall_piston.html,
"wall/reflect"_fix_wall_reflect.html,
"wall/region"_fix_wall_region.html,
"wall/srd"_fix_wall_srd.html :tb(c=8,ea=c)
These are fix styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"addtorque"_fix_addtorque.html,
"atc"_fix_atc.html,
"colvars"_fix_colvars.html,
"imd"_fix_imd.html,
"langevin/eff"_fix_langevin_eff.html,
"lb/fluid"_fix_lb_fluid.html,
"lb/momentum"_fix_lb_momentum.html,
"lb/pc"_fix_lb_pc.html,
"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
"lb/viscous"_fix_lb_viscous.html,
"meso"_fix_meso.html,
"meso/stationary"_fix_meso_stationary.html,
"nph/eff"_fix_nh_eff.html,
"npt/eff"_fix_nh_eff.html,
"nve/eff"_fix_nve_eff.html,
"nvt/eff"_fix_nh_eff.html,
"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
"phonon"_fix_phonon.html,
"qeq/reax"_fix_qeq_reax.html,
"qmmm"_fix_qmmm.html,
"reax/c/bonds"_fix_reax_bonds.html,
"reax/c/species"_fix_reaxc_species.html,
"smd"_fix_smd.html,
"temp/rescale/eff"_fix_temp_rescale_eff.html,
"ti/rs"_fix_ti_rs.html,
"ti/spring"_fix_ti_spring.html :tb(c=6,ea=c)
These are accelerated fix styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"freeze/cuda"_fix_freeze.html,
"addforce/cuda"_fix_addforce.html,
"aveforce/cuda"_fix_aveforce.html,
"enforce2d/cuda"_fix_enforce2d.html,
"gravity/cuda"_fix_gravity.html,
"gravity/omp"_fix_gravity.html,
"nph/omp"_fix_nh.html,
"nphug/omp"_fix_nphug.html,
"nph/asphere/omp"_fix_nph_asphere.html,
"nph/sphere/omp"_fix_nph_sphere.html,
"npt/cuda"_fix_nh.html,
"npt/omp"_fix_nh.html,
"npt/asphere/omp"_fix_npt_asphere.html,
"npt/sphere/omp"_fix_npt_sphere.html,
"nve/cuda"_fix_nh.html,
"nve/omp"_fix_nve.html,
"nve/sphere/omp"_fix_nve_sphere.html,
"nvt/cuda"_fix_nh.html,
"nvt/omp"_fix_nh.html,
"nvt/asphere/omp"_fix_nvt_asphere.html,
"nvt/sllod/omp"_fix_nvt_sllod.html,
"nvt/sphere/omp"_fix_nvt_sphere.html,
"qeq/comb/omp"_fix_qeq_comb.html,
"rigid/omp"_fix_rigid.html,
"rigid/nph/omp"_fix_rigid.html,
"rigid/npt/omp"_fix_rigid.html,
"rigid/nve/omp"_fix_rigid.html,
"rigid/nvt/omp"_fix_rigid.html,
"rigid/small/omp"_fix_rigid.html,
"setforce/cuda"_fix_setforce.html,
"shake/cuda"_fix_shake.html,
"temp/berendsen/cuda"_fix_temp_berendsen.html,
"temp/rescale/cuda"_fix_temp_rescale.html,
"temp/rescale/limit/cuda"_fix_temp_rescale.html,
"viscous/cuda"_fix_viscous.html :tb(c=6,ea=c)
:line
Compute styles :h4
See the "compute"_compute.html command for one-line descriptions of
each style or click on the style itself for a full description:
"angle/local"_compute_angle_local.html,
"atom/molecule"_compute_atom_molecule.html,
"body/local"_compute_body_local.html,
"bond/local"_compute_bond_local.html,
"centro/atom"_compute_centro_atom.html,
"cluster/atom"_compute_cluster_atom.html,
"cna/atom"_compute_cna_atom.html,
"com"_compute_com.html,
"com/molecule"_compute_com_molecule.html,
"contact/atom"_compute_contact_atom.html,
"coord/atom"_compute_coord_atom.html,
"damage/atom"_compute_damage_atom.html,
"dihedral/local"_compute_dihedral_local.html,
+"dilatation/atom"_compute_dilatation_atom.html,
"displace/atom"_compute_displace_atom.html,
"erotate/asphere"_compute_erotate_asphere.html,
"erotate/rigid"_compute_erotate_rigid.html,
"erotate/sphere"_compute_erotate_sphere.html,
"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
"event/displace"_compute_event_displace.html,
"group/group"_compute_group_group.html,
"gyration"_compute_gyration.html,
"gyration/molecule"_compute_gyration_molecule.html,
"heat/flux"_compute_heat_flux.html,
"improper/local"_compute_improper_local.html,
"inertia/molecule"_compute_inertia_molecule.html,
"ke"_compute_ke.html,
"ke/atom"_compute_ke_atom.html,
"ke/rigid"_compute_ke_rigid.html,
"msd"_compute_msd.html,
"msd/molecule"_compute_msd_molecule.html,
"msd/nongauss"_compute_msd_nongauss.html,
"pair"_compute_pair.html,
"pair/local"_compute_pair_local.html,
"pe"_compute_pe.html,
"pe/atom"_compute_pe_atom.html,
+"plasticity/atom"_compute_plasticity_atom.html,
"pressure"_compute_pressure.html,
"property/atom"_compute_property_atom.html,
"property/local"_compute_property_local.html,
"property/molecule"_compute_property_molecule.html,
"rdf"_compute_rdf.html,
"reduce"_compute_reduce.html,
"reduce/region"_compute_reduce.html,
"slice"_compute_slice.html,
"stress/atom"_compute_stress_atom.html,
"temp"_compute_temp.html,
"temp/asphere"_compute_temp_asphere.html,
"temp/com"_compute_temp_com.html,
"temp/deform"_compute_temp_deform.html,
"temp/partial"_compute_temp_partial.html,
"temp/profile"_compute_temp_profile.html,
"temp/ramp"_compute_temp_ramp.html,
"temp/region"_compute_temp_region.html,
"temp/sphere"_compute_temp_sphere.html,
"ti"_compute_ti.html,
"vacf"_compute_vacf.html,
"voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c)
These are compute styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"ackland/atom"_compute_ackland_atom.html,
"basal/atom"_compute_basal_atom.html,
"ke/eff"_compute_ke_eff.html,
"ke/atom/eff"_compute_ke_atom_eff.html,
"meso_e/atom"_compute_meso_e_atom.html,
"meso_rho/atom"_compute_meso_rho_atom.html,
"meso_t/atom"_compute_meso_t_atom.html,
"temp/eff"_compute_temp_eff.html,
"temp/deform/eff"_compute_temp_deform_eff.html,
"temp/region/eff"_compute_temp_region_eff.html,
"temp/rotate"_compute_temp_rotate.html :tb(c=6,ea=c)
These are accelerated compute styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"pe/cuda"_compute_pe.html,
"pressure/cuda"_compute_pressure.html,
"temp/cuda"_compute_temp.html,
"temp/partial/cuda"_compute_temp_partial.html :tb(c=6,ea=c)
:line
Pair_style potentials :h4
See the "pair_style"_pair_style.html command for an overview of pair
potentials. Click on the style itself for a full description:
"none"_pair_none.html,
"hybrid"_pair_hybrid.html,
"hybrid/overlay"_pair_hybrid.html,
"adp"_pair_adp.html,
"airebo"_pair_airebo.html,
"beck"_pair_beck.html,
"body"_pair_body.html,
"bop"_pair_bop.html,
"born"_pair_born.html,
"born/coul/long"_pair_born.html,
"born/coul/msm"_pair_born.html,
"born/coul/wolf"_pair_born.html,
"brownian"_pair_brownian.html,
"brownian/poly"_pair_brownian.html,
"buck"_pair_buck.html,
"buck/coul/cut"_pair_buck.html,
"buck/coul/long"_pair_buck.html,
"buck/coul/msm"_pair_buck.html,
"buck/long/coul/long"_pair_buck_long.html,
"colloid"_pair_colloid.html,
"comb"_pair_comb.html,
"comb3"_pair_comb.html,
"coul/cut"_pair_coul.html,
"coul/debye"_pair_coul.html,
"coul/dsf"_pair_coul.html,
"coul/long"_pair_coul.html,
"coul/msm"_pair_coul.html,
"coul/wolf"_pair_coul.html,
"dpd"_pair_dpd.html,
"dpd/tstat"_pair_dpd.html,
"dsmc"_pair_dsmc.html,
"eam"_pair_eam.html,
"eam/alloy"_pair_eam.html,
"eam/fs"_pair_eam.html,
"eim"_pair_eim.html,
"gauss"_pair_gauss.html,
"gayberne"_pair_gayberne.html,
"gran/hertz/history"_pair_gran.html,
"gran/hooke"_pair_gran.html,
"gran/hooke/history"_pair_gran.html,
"hbond/dreiding/lj"_pair_hbond_dreiding.html,
"hbond/dreiding/morse"_pair_hbond_dreiding.html,
"kim"_pair_kim.html,
"lcbop"_pair_lcbop.html,
"line/lj"_pair_line_lj.html,
"lj/charmm/coul/charmm"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit"_pair_charmm.html,
"lj/charmm/coul/long"_pair_charmm.html,
"lj/charmm/coul/msm"_pair_charmm.html,
"lj/class2"_pair_class2.html,
"lj/class2/coul/cut"_pair_class2.html,
"lj/class2/coul/long"_pair_class2.html,
"lj/cut"_pair_lj.html,
"lj/cut/coul/cut"_pair_lj.html,
"lj/cut/coul/debye"_pair_lj.html,
"lj/cut/coul/dsf"_pair_lj.html,
"lj/cut/coul/long"_pair_lj.html,
"lj/cut/coul/msm"_pair_lj.html,
"lj/cut/dipole/cut"_pair_dipole.html,
"lj/cut/dipole/long"_pair_dipole.html,
"lj/cut/tip4p/cut"_pair_lj.html,
"lj/cut/tip4p/long"_pair_lj.html,
"lj/expand"_pair_lj_expand.html,
"lj/gromacs"_pair_gromacs.html,
"lj/gromacs/coul/gromacs"_pair_gromacs.html,
"lj/long/coul/long"_pair_lj_long.html,
"lj/long/dipole/long"_pair_dipole.html,
"lj/long/tip4p/long"_pair_lj_long.html,
"lj/smooth"_pair_lj_smooth.html,
"lj/smooth/linear"_pair_lj_smooth_linear.html,
"lj96/cut"_pair_lj96.html,
"lubricate"_pair_lubricate.html,
"lubricate/poly"_pair_lubricate.html,
"lubricateU"_pair_lubricateU.html,
"lubricateU/poly"_pair_lubricateU.html,
"meam"_pair_meam.html,
"mie/cut"_pair_mie.html,
"morse"_pair_morse.html,
"nb3b/harmonic"_pair_nb3b_harmonic.html,
"nm/cut"_pair_nm.html,
"nm/cut/coul/cut"_pair_nm.html,
"nm/cut/coul/long"_pair_nm.html,
+"peri/eps"_pair_peri.html,
"peri/lps"_pair_peri.html,
"peri/pmb"_pair_peri.html,
"peri/ves"_pair_peri.html,
"reax"_pair_reax.html,
"rebo"_pair_airebo.html,
"resquared"_pair_resquared.html,
"soft"_pair_soft.html,
"sw"_pair_sw.html,
"table"_pair_table.html,
"tersoff"_pair_tersoff.html,
"tersoff/mod"_pair_tersoff_mod.html,
"tersoff/zbl"_pair_tersoff_zbl.html,
"tip4p/cut"_pair_coul.html,
"tip4p/long"_pair_coul.html,
"tri/lj"_pair_tri_lj.html,
"yukawa"_pair_yukawa.html,
"yukawa/colloid"_pair_yukawa_colloid.html,
"zbl"_pair_zbl.html :tb(c=4,ea=c)
These are pair styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"awpmd/cut"_pair_awpmd.html,
"coul/diel"_pair_coul_diel.html,
"eam/cd"_pair_eam.html,
"edip"_pair_edip.html,
"eff/cut"_pair_eff.html,
"gauss/cut"_pair_gauss.html,
"list"_pair_list.html,
"lj/cut/dipole/sf"_pair_dipole.html,
"lj/sdk"_pair_sdk.html,
"lj/sdk/coul/long"_pair_sdk.html,
"lj/sdk/coul/msm"_pair_sdk.html,
"lj/sf"_pair_lj_sf.html,
"meam/spline"_pair_meam_spline.html,
"meam/sw/spline"_pair_meam_sw_spline.html,
"reax/c"_pair_reax_c.html,
"sph/heatconduction"_pair_sph_heatconduction.html,
"sph/idealgas"_pair_sph_idealgas.html,
"sph/lj"_pair_sph_lj.html,
"sph/rhosum"_pair_sph_rhosum.html,
"sph/taitwater"_pair_sph_taitwater.html,
"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
"tersoff/table"_pair_tersoff.html :tb(c=4,ea=c)
These are accelerated pair styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"adp/omp"_pair_adp.html,
"airebo/omp"_pair_airebo.html,
"beck/gpu"_pair_beck.html,
"beck/omp"_pair_beck.html,
"born/coul/long/cuda"_pair_born.html,
"born/coul/long/gpu"_pair_born.html,
"born/coul/long/omp"_pair_born.html,
"born/coul/msm/omp"_pair_born.html,
"born/coul/wolf/gpu"_pair_born.html,
"born/coul/wolf/omp"_pair_born.html,
"born/gpu"_pair_born.html,
"born/omp"_pair_born.html,
"brownian/omp"_pair_brownian.html,
"brownian/poly/omp"_pair_brownian.html,
"buck/coul/cut/cuda"_pair_buck.html,
"buck/coul/cut/gpu"_pair_buck.html,
"buck/coul/cut/omp"_pair_buck.html,
"buck/coul/long/cuda"_pair_buck.html,
"buck/coul/long/gpu"_pair_buck.html,
"buck/coul/long/omp"_pair_buck.html,
"buck/coul/msm/omp"_pair_buck.html,
"buck/cuda"_pair_buck.html,
"buck/long/coul/long/omp"_pair_buck_long.html,
"buck/gpu"_pair_buck.html,
"buck/omp"_pair_buck.html,
"colloid/gpu"_pair_colloid.html,
"colloid/omp"_pair_colloid.html,
"comb/omp"_pair_comb.html,
"coul/cut/omp"_pair_coul.html,
"coul/debye/omp"_pair_coul.html,
"coul/dsf/gpu"_pair_coul.html,
"coul/dsf/omp"_pair_coul.html,
"coul/long/gpu"_pair_coul.html,
"coul/long/omp"_pair_coul.html,
"coul/msm/omp"_pair_coul.html,
"coul/wolf"_pair_coul.html,
"dpd/omp"_pair_dpd.html,
"dpd/tstat/omp"_pair_dpd.html,
"eam/alloy/cuda"_pair_eam.html,
"eam/alloy/gpu"_pair_eam.html,
"eam/alloy/omp"_pair_eam.html,
"eam/alloy/opt"_pair_eam.html,
"eam/cd/omp"_pair_eam.html,
"eam/cuda"_pair_eam.html,
"eam/fs/cuda"_pair_eam.html,
"eam/fs/gpu"_pair_eam.html,
"eam/fs/omp"_pair_eam.html,
"eam/fs/opt"_pair_eam.html,
"eam/gpu"_pair_eam.html,
"eam/omp"_pair_eam.html,
"eam/opt"_pair_eam.html,
"edip/omp"_pair_edip.html,
"eim/omp"_pair_eim.html,
"gauss/gpu"_pair_gauss.html,
"gauss/omp"_pair_gauss.html,
"gayberne/gpu"_pair_gayberne.html,
"gayberne/omp"_pair_gayberne.html,
"gran/hertz/history/omp"_pair_gran.html,
"gran/hooke/cuda"_pair_gran.html,
"gran/hooke/history/omp"_pair_gran.html,
"gran/hooke/omp"_pair_gran.html,
"hbond/dreiding/lj/omp"_pair_hbond_dreiding.html,
"hbond/dreiding/morse/omp"_pair_hbond_dreiding.html,
"line/lj/omp"_pair_line_lj.html,
"lj/charmm/coul/charmm/cuda"_pair_charmm.html,
"lj/charmm/coul/charmm/omp"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit/cuda"_pair_charmm.html,
"lj/charmm/coul/charmm/implicit/omp"_pair_charmm.html,
"lj/charmm/coul/long/cuda"_pair_charmm.html,
"lj/charmm/coul/long/gpu"_pair_charmm.html,
"lj/charmm/coul/long/omp"_pair_charmm.html,
"lj/charmm/coul/long/opt"_pair_charmm.html,
"lj/class2/coul/cut/cuda"_pair_class2.html,
"lj/class2/coul/cut/omp"_pair_class2.html,
"lj/class2/coul/long/cuda"_pair_class2.html,
"lj/class2/coul/long/gpu"_pair_class2.html,
"lj/class2/coul/long/omp"_pair_class2.html,
"lj/class2/coul/msm/omp"_pair_class2.html,
"lj/class2/cuda"_pair_class2.html,
"lj/class2/gpu"_pair_class2.html,
"lj/class2/omp"_pair_class2.html,
"lj/long/coul/long/omp"_pair_lj_long.html,
"lj/cut/coul/cut/cuda"_pair_lj.html,
"lj/cut/coul/cut/gpu"_pair_lj.html,
"lj/cut/coul/cut/omp"_pair_lj.html,
"lj/cut/coul/debye/cuda"_pair_lj.html,
"lj/cut/coul/debye/gpu"_pair_lj.html,
"lj/cut/coul/debye/omp"_pair_lj.html,
"lj/cut/coul/dsf/gpu"_pair_lj.html,
"lj/cut/coul/dsf/omp"_pair_lj.html,
"lj/cut/coul/long/cuda"_pair_lj.html,
"lj/cut/coul/long/gpu"_pair_lj.html,
"lj/cut/coul/long/omp"_pair_lj.html,
"lj/cut/coul/long/opt"_pair_lj.html,
"lj/cut/coul/msm/gpu"_pair_lj.html,
"lj/cut/coul/msm/opt"_pair_lj.html,
"lj/cut/cuda"_pair_lj.html,
"lj/cut/dipole/cut/gpu"_pair_dipole.html,
"lj/cut/dipole/cut/omp"_pair_dipole.html,
"lj/cut/dipole/sf/gpu"_pair_dipole.html,
"lj/cut/dipole/sf/omp"_pair_dipole.html,
"lj/cut/experimental/cuda"_pair_lj.html,
"lj/cut/gpu"_pair_lj.html,
"lj/cut/omp"_pair_lj.html,
"lj/cut/opt"_pair_lj.html,
"lj/cut/tip4p/cut/omp"_pair_lj.html,
"lj/cut/tip4p/long/omp"_pair_lj.html,
"lj/cut/tip4p/long/opt"_pair_lj.html,
"lj/expand/cuda"_pair_lj_expand.html,
"lj/expand/gpu"_pair_lj_expand.html,
"lj/expand/omp"_pair_lj_expand.html,
"lj/gromacs/coul/gromacs/cuda"_pair_gromacs.html,
"lj/gromacs/coul/gromacs/omp"_pair_gromacs.html,
"lj/gromacs/cuda"_pair_gromacs.html,
"lj/gromacs/gpu"_pair_gromacs.html,
"lj/gromacs/omp"_pair_gromacs.html,
"lj/long/coul/long/opt"_pair_lj_long.html,
"lj/sdk/gpu"_pair_sdk.html,
"lj/sdk/omp"_pair_sdk.html,
"lj/sdk/coul/long/gpu"_pair_sdk.html,
"lj/sdk/coul/long/omp"_pair_sdk.html,
"lj/sdk/coul/msm/omp"_pair_sdk.html,
"lj/sf/omp"_pair_lj_sf.html,
"lj/smooth/cuda"_pair_lj_smooth.html,
"lj/smooth/omp"_pair_lj_smooth.html,
"lj/smooth/linear/omp"_pair_lj_smooth_linear.html,
"lj96/cut/cuda"_pair_lj96.html,
"lj96/cut/gpu"_pair_lj96.html,
"lj96/cut/omp"_pair_lj96.html,
"lubricate/omp"_pair_lubricate.html,
"lubricate/poly/omp"_pair_lubricate.html,
"meam/spline/omp"_pair_meam_spline.html,
"mie/cut/gpu"_pair_mie.html,
"morse/cuda"_pair_morse.html,
"morse/gpu"_pair_morse.html,
"morse/omp"_pair_morse.html,
"morse/opt"_pair_morse.html,
"nb3b/harmonic/omp"_pair_nb3b_harmonic.html,
"nm/cut/omp"_pair_nm.html,
"nm/cut/coul/cut/omp"_pair_nm.html,
"nm/cut/coul/long/omp"_pair_nm.html,
"peri/lps/omp"_pair_peri.html,
"peri/pmb/omp"_pair_peri.html,
"rebo/omp"_pair_airebo.html,
"resquared/gpu"_pair_resquared.html,
"resquared/omp"_pair_resquared.html,
"soft/gpu"_pair_soft.html,
"soft/omp"_pair_soft.html,
"sw/cuda"_pair_sw.html,
"sw/gpu"_pair_sw.html,
"sw/omp"_pair_sw.html,
"table/gpu"_pair_table.html,
"table/omp"_pair_table.html,
"tersoff/cuda"_pair_tersoff.html,
"tersoff/omp"_pair_tersoff.html,
"tersoff/mod/omp"_pair_tersoff_mod.html,
"tersoff/table/omp"_pair_tersoff.html,
"tersoff/zbl/omp"_pair_tersoff_zbl.html,
"tip4p/cut/omp"_pair_coul.html,
"tip4p/long/omp"_pair_coul.html,
"tri/lj/omp"_pair_tri_lj.html,
"yukawa/gpu"_pair_yukawa.html,
"yukawa/omp"_pair_yukawa.html,
"yukawa/colloid/gpu"_pair_yukawa_colloid.html,
"yukawa/colloid/omp"_pair_yukawa_colloid.html,
"zbl/omp"_pair_zbl.html :tb(c=4,ea=c)
:line
Bond_style potentials :h4
See the "bond_style"_bond_style.html command for an overview of bond
potentials. Click on the style itself for a full description:
"none"_bond_none.html,
"hybrid"_bond_hybrid.html,
"class2"_bond_class2.html,
"fene"_bond_fene.html,
"fene/expand"_bond_fene_expand.html,
"harmonic"_bond_harmonic.html,
"morse"_bond_morse.html,
"nonlinear"_bond_nonlinear.html,
"quartic"_bond_quartic.html,
"table"_bond_table.html :tb(c=4,ea=c,w=100)
These are bond styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"harmonic/shift"_bond_harmonic_shift.html,
"harmonic/shift/cut"_bond_harmonic_shift_cut.html :tb(c=4,ea=c)
These are accelerated bond styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"class2/omp"_bond_class2.html,
"fene/omp"_bond_fene.html,
"fene/expand/omp"_bond_fene_expand.html,
"harmonic/omp"_bond_harmonic.html,
"harmonic/shift/omp"_bond_harmonic_shift.html,
"harmonic/shift/cut/omp"_bond_harmonic_shift_cut.html,
"morse/omp"_bond_morse.html,
"nonlinear/omp"_bond_nonlinear.html,
"quartic/omp"_bond_quartic.html,
"table/omp"_bond_table.html :tb(c=4,ea=c,w=100)
:line
Angle_style potentials :h4
See the "angle_style"_angle_style.html command for an overview of
angle potentials. Click on the style itself for a full description:
"none"_angle_none.html,
"hybrid"_angle_hybrid.html,
"charmm"_angle_charmm.html,
"class2"_angle_class2.html,
"cosine"_angle_cosine.html,
"cosine/delta"_angle_cosine_delta.html,
"cosine/periodic"_angle_cosine_periodic.html,
"cosine/squared"_angle_cosine_squared.html,
"harmonic"_angle_harmonic.html,
"table"_angle_table.html :tb(c=4,ea=c,w=100)
These are angle styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"sdk"_angle_sdk.html,
"cosine/shift"_angle_cosine_shift.html,
"cosine/shift/exp"_angle_cosine_shift_exp.html,
"dipole"_angle_dipole.html,
"fourier"_angle_fourier.html,
"fourier/simple"_angle_fourier_simple.html,
"quartic"_angle_quartic.html :tb(c=4,ea=c)
These are accelerated angle styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"charmm/omp"_angle_charmm.html,
"class2/omp"_angle_class2.html,
"cosine/omp"_angle_cosine.html,
"cosine/delta/omp"_angle_cosine_delta.html,
"cosine/periodic/omp"_angle_cosine_periodic.html,
"cosine/shift/omp"_angle_cosine_shift.html,
"cosine/shift/exp/omp"_angle_cosine_shift_exp.html,
"cosine/squared/omp"_angle_cosine_squared.html,
"dipole/omp"_angle_dipole.html
"fourier/omp"_angle_fourier.html,
"fourier/simple/omp"_angle_fourier_simple.html,
"harmonic/omp"_angle_harmonic.html,
"quartic/omp"_angle_quartic.html
"table/omp"_angle_table.html :tb(c=4,ea=c,w=100)
:line
Dihedral_style potentials :h4
See the "dihedral_style"_dihedral_style.html command for an overview
of dihedral potentials. Click on the style itself for a full
description:
"none"_dihedral_none.html,
"hybrid"_dihedral_hybrid.html,
"charmm"_dihedral_charmm.html,
"class2"_dihedral_class2.html,
"harmonic"_dihedral_harmonic.html,
"helix"_dihedral_helix.html,
"multi/harmonic"_dihedral_multi_harmonic.html,
"opls"_dihedral_opls.html :tb(c=4,ea=c,w=100)
These are dihedral styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cosine/shift/exp"_dihedral_cosine_shift_exp.html,
"fourier"_dihedral_fourier.html,
"nharmonic"_dihedral_nharmonic.html,
"quadratic"_dihedral_quadratic.html,
"table"_dihedral_table.html :tb(c=4,ea=c)
These are accelerated dihedral styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"charmm/omp"_dihedral_charmm.html,
"class2/omp"_dihedral_class2.html,
"cosine/shift/exp/omp"_dihedral_cosine_shift_exp.html,
"fourier/omp"_dihedral_fourier.html,
"harmonic/omp"_dihedral_harmonic.html,
"helix/omp"_dihedral_helix.html,
"multi/harmonic/omp"_dihedral_multi_harmonic.html,
"nharmonic/omp"_dihedral_nharmonic.html,
"opls/omp"_dihedral_opls.html
"quadratic/omp"_dihedral_quadratic.html,
"table/omp"_dihedral_table.html :tb(c=4,ea=c,w=100)
:line
Improper_style potentials :h4
See the "improper_style"_improper_style.html command for an overview
of improper potentials. Click on the style itself for a full
description:
"none"_improper_none.html,
"hybrid"_improper_hybrid.html,
"class2"_improper_class2.html,
"cvff"_improper_cvff.html,
"harmonic"_improper_harmonic.html,
"umbrella"_improper_umbrella.html :tb(c=4,ea=c,w=100)
These are improper styles contributed by users, which can be used if
"LAMMPS is built with the appropriate
package"_Section_start.html#start_3.
"cossq"_improper_cossq.html,
"fourier"_improper_fourier.html,
"ring"_improper_ring.html :tb(c=4,ea=c)
These are accelerated improper styles, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"class2/omp"_improper_class2.html,
"cossq/omp"_improper_cossq.html,
"cvff/omp"_improper_cvff.html,
"fourier/omp"_improper_fourier.html,
"harmonic/omp"_improper_harmonic.html,
"ring/omp"_improper_ring.html,
"umbrella/omp"_improper_umbrella.html :tb(c=4,ea=c,w=100)
:line
Kspace solvers :h4
See the "kspace_style"_kspace_style.html command for an overview of
Kspace solvers. Click on the style itself for a full description:
"ewald"_kspace_style.html,
"ewald/disp"_kspace_style.html,
"msm"_kspace_style.html,
"msm/cg"_kspace_style.html,
"pppm"_kspace_style.html,
"pppm/cg"_kspace_style.html,
"pppm/disp"_kspace_style.html,
"pppm/disp/tip4p"_kspace_style.html,
"pppm/tip4p"_kspace_style.html :tb(c=4,ea=c,w=100)
These are accelerated Kspace solvers, which can be used if LAMMPS is
built with the "appropriate accelerated
package"_Section_accelerate.html.
"ewald/omp"_kspace_style.html,
"msm/omp"_kspace_style.html,
"msm/cg/omp"_kspace_style.html,
"pppm/cuda"_kspace_style.html,
"pppm/gpu"_kspace_style.html,
"pppm/omp"_kspace_style.html,
"pppm/cg/omp"_kspace_style.html,
"pppm/tip4p/omp"_kspace_style.html :tb(c=4,ea=c)
diff --git a/doc/compute_damage_atom.html b/doc/compute_damage_atom.html
index 0d0e378f5..198351c56 100644
--- a/doc/compute_damage_atom.html
+++ b/doc/compute_damage_atom.html
@@ -1,58 +1,67 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute damage/atom command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID damage/atom
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>damage/atom = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all damage/atom
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the per-atom damage for each atom
-in a group. Please see the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
+in a group. This is a quantity relevant for <A HREF = "pair_peri.html">Peridynamics
+models</A>.
+</P>
+<P>The "damage" of a Peridymaics particles is based on the bond breakage
+between the particle and its neighbors. If all the bonds are broken
+the particle is considered to be fully damaged.
+</P>
+<P>See the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
guide</A> for a formal
definition of "damage" and more details about Peridynamics as it is
implemented in LAMMPS.
</P>
-<P>The value of the damage will be 0.0 for atoms not in the specified
-compute group.
+<P>This command can be used with all the Peridynamic pair styles.
+</P>
+<P>The damage value will be 0.0 for atoms not in the specified compute
+group.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#howto_15">Section_howto 15</A> for an overview of
LAMMPS output options.
</P>
-<P>The per-atom vector values will be a number >= 0.0, as explained
-above.
+<P>The per-atom vector values are unitlesss numbers (damage) >= 0.0.
</P>
<P><B>Restrictions:</B>
</P>
<P>This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
-<P><A HREF = "dump.html">dump custom</A>
+<P><A HREF = "compute_dilatation.html">compute dilatation</A>, <A HREF = "compute_plasticity.html">compute
+plasticity</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_damage_atom.txt b/doc/compute_damage_atom.txt
index 3c640d61e..5b6b2a51f 100644
--- a/doc/compute_damage_atom.txt
+++ b/doc/compute_damage_atom.txt
@@ -1,53 +1,62 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute damage/atom command :h3
[Syntax:]
compute ID group-ID damage/atom :pre
ID, group-ID are documented in "compute"_compute.html command
damage/atom = style name of this compute command :ul
[Examples:]
compute 1 all damage/atom :pre
[Description:]
Define a computation that calculates the per-atom damage for each atom
-in a group. Please see the "PDLAMMPS user
+in a group. This is a quantity relevant for "Peridynamics
+models"_pair_peri.html.
+
+The "damage" of a Peridymaics particles is based on the bond breakage
+between the particle and its neighbors. If all the bonds are broken
+the particle is considered to be fully damaged.
+
+See the "PDLAMMPS user
guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for a formal
definition of "damage" and more details about Peridynamics as it is
implemented in LAMMPS.
-The value of the damage will be 0.0 for atoms not in the specified
-compute group.
+This command can be used with all the Peridynamic pair styles.
+
+The damage value will be 0.0 for atoms not in the specified compute
+group.
[Output info:]
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"Section_howto 15"_Section_howto.html#howto_15 for an overview of
LAMMPS output options.
-The per-atom vector values will be a number >= 0.0, as explained
-above.
+The per-atom vector values are unitlesss numbers (damage) >= 0.0.
[Restrictions:]
This compute is part of the PERI package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
-"dump custom"_dump.html
+"compute dilatation"_compute_dilatation.html, "compute
+plasticity"_compute_plasticity.html
[Default:] none
diff --git a/doc/compute_dilatation.html b/doc/compute_dilatation.html
new file mode 100644
index 000000000..1e984cd31
--- /dev/null
+++ b/doc/compute_dilatation.html
@@ -0,0 +1,70 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute dilatation/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID dilatation/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in compute command
+<LI>dilation/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all dilatation/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom dilatation for each
+atom in a group. This is a quantity relevant for <A HREF = "pair_peri.html">Peridynamics
+models</A>.
+</P>
+<P>For small deformation, dilatation of is the measure of the volumetric
+strain.
+</P>
+<P>The dilatation "theta" for each peridynamic particle I is calculated
+as a sum over its neighbors with unbroken bonds, where the
+contribution of the IJ pair is a function of the change in bond length
+(versus the initial length in the reference state), the volume
+fraction of the particles and an influence function. See the
+<A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS user
+guide</A> for a formal
+definition of dilatation.
+</P>
+<P>This command can only be used with a subset of the Peridynamic <A HREF = "pair_peri.html">pair
+styles</A>: peri/lps, peri/ves and peri/eps.
+</P>
+<P>The dilatation value will be 0.0 for atoms not in the specified
+compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+Section_howto 15 for an overview of LAMMPS output options.
+</P>
+<P>The per-atom vector values are unitlesss numbers (theta) >= 0.0.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the PERI package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_damage.html">compute damage</A>, <A HREF = "compute_plasticity.html">compute
+plasticity</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/compute_dilatation.txt b/doc/compute_dilatation.txt
new file mode 100644
index 000000000..f3b3328b5
--- /dev/null
+++ b/doc/compute_dilatation.txt
@@ -0,0 +1,65 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute dilatation/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID dilatation/atom :pre
+
+ID, group-ID are documented in compute command
+dilation/atom = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all dilatation/atom :pre
+
+[Description:]
+
+Define a computation that calculates the per-atom dilatation for each
+atom in a group. This is a quantity relevant for "Peridynamics
+models"_pair_peri.html.
+
+For small deformation, dilatation of is the measure of the volumetric
+strain.
+
+The dilatation "theta" for each peridynamic particle I is calculated
+as a sum over its neighbors with unbroken bonds, where the
+contribution of the IJ pair is a function of the change in bond length
+(versus the initial length in the reference state), the volume
+fraction of the particles and an influence function. See the
+"PDLAMMPS user
+guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for a formal
+definition of dilatation.
+
+This command can only be used with a subset of the Peridynamic "pair
+styles"_pair_peri.html: peri/lps, peri/ves and peri/eps.
+
+The dilatation value will be 0.0 for atoms not in the specified
+compute group.
+
+[Output info:]
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+Section_howto 15 for an overview of LAMMPS output options.
+
+The per-atom vector values are unitlesss numbers (theta) >= 0.0.
+
+[Restrictions:]
+
+This compute is part of the PERI package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"compute damage"_compute_damage.html, "compute
+plasticity"_compute_plasticity.html
+
+[Default:] none
diff --git a/doc/compute_plasticity.html b/doc/compute_plasticity.html
new file mode 100644
index 000000000..0c3dfeb16
--- /dev/null
+++ b/doc/compute_plasticity.html
@@ -0,0 +1,72 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>compute plasticity/atom command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>compute ID group-ID plasticity/atom
+</PRE>
+<UL><LI>ID, group-ID are documented in compute command
+<LI>plasticity/atom = style name of this compute command
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>compute 1 all plasticity/atom
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Define a computation that calculates the per-atom plasticity for each
+atom in a group. This is a quantity relevant for <A HREF = "pair_peri.html">Peridynamics
+models</A>.
+</P>
+<P>The plasticity for a Peridynamic particle is the so-called consistency
+parameter (lambda). For elastic deformation lambda = 0, otherwise
+lambda > 0 for plastic deformation. For details, see
+<A HREF = "#Mitchell">(Mitchell)</A> and the PDF doc included in the LAMMPS
+distro in <A HREF = "PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</A>.
+</P>
+<P>This command can be invoked for one of the Peridynamic <A HREF = "pair_peri.html">pair
+styles</A>: peri/eps.
+</P>
+<P>The plasticity value will be 0.0 for atoms not in the specified
+compute group.
+</P>
+<P><B>Output info:</B>
+</P>
+<P>This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+Section_howto 15 for an overview of LAMMPS output options.
+</P>
+<P>The per-atom vector values are unitlesss numbers (lambda) >= 0.0.
+</P>
+<P><B>Restrictions:</B>
+</P>
+<P>This compute is part of the PERI package. It is only enabled if
+LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute_damage.html">compute damage</A>, <A HREF = "compute_dilatation.html">compute
+dilatation</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Mitchell"></A>
+
+<P><B>(Mitchell)</B> Mitchell, "A non-local, ordinary-state-based
+viscoelasticity model for peridynamics", Sandia National Lab Report,
+8064:1-28 (2011).
+</P>
+</HTML>
diff --git a/doc/compute_plasticity.txt b/doc/compute_plasticity.txt
new file mode 100644
index 000000000..29882213a
--- /dev/null
+++ b/doc/compute_plasticity.txt
@@ -0,0 +1,66 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+compute plasticity/atom command :h3
+
+[Syntax:]
+
+compute ID group-ID plasticity/atom :pre
+
+ID, group-ID are documented in compute command
+plasticity/atom = style name of this compute command :ul
+
+[Examples:]
+
+compute 1 all plasticity/atom :pre
+
+[Description:]
+
+Define a computation that calculates the per-atom plasticity for each
+atom in a group. This is a quantity relevant for "Peridynamics
+models"_pair_peri.html.
+
+The plasticity for a Peridynamic particle is the so-called consistency
+parameter (lambda). For elastic deformation lambda = 0, otherwise
+lambda > 0 for plastic deformation. For details, see
+"(Mitchell)"_#Mitchell and the PDF doc included in the LAMMPS
+distro in "doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf.
+
+This command can be invoked for one of the Peridynamic "pair
+styles"_pair_peri.html: peri/eps.
+
+The plasticity value will be 0.0 for atoms not in the specified
+compute group.
+
+[Output info:]
+
+This compute calculates a per-atom vector, which can be accessed by
+any command that uses per-atom values from a compute as input. See
+Section_howto 15 for an overview of LAMMPS output options.
+
+The per-atom vector values are unitlesss numbers (lambda) >= 0.0.
+
+[Restrictions:]
+
+This compute is part of the PERI package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
+[Related commands:]
+
+"compute damage"_compute_damage.html, "compute
+dilatation"_compute_dilatation.html
+
+[Default:] none
+
+:line
+
+:link(Mitchell)
+[(Mitchell)] Mitchell, "A non-local, ordinary-state-based
+viscoelasticity model for peridynamics", Sandia National Lab Report,
+8064:1-28 (2011).
diff --git a/doc/compute_vacf.html b/doc/compute_vacf.html
index 0ddd75831..a46344aa7 100644
--- a/doc/compute_vacf.html
+++ b/doc/compute_vacf.html
@@ -1,70 +1,76 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>compute vacf command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>compute ID group-ID vacf
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "compute.html">compute</A> command
<LI>vacf = style name of this compute command
</UL>
<P><B>Examples:</B>
</P>
<PRE>compute 1 all vacf
compute 1 upper vacf
</PRE>
<P><B>Description:</B>
</P>
<P>Define a computation that calculates the velocity auto-correlation
function (VACF), averaged over a group of atoms. Each atom's
contribution to the VACF is its current velocity vector dotted into
its initial velocity vector at the time the compute was specified.
</P>
<P>A vector of four quantites is calculated by this compute. The first 3
elements of the vector are vx * vx0 (and similarly for the y and z
components), summed and averaged over atoms in the group. Vx is the
current x-component of velocity for the atom, vx0 is the initial
x-component of velocity for the atom. The 4th element of the vector
is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and
averaged over atoms in the group.
</P>
<P>The integral of the VACF versus time is proportional to the diffusion
-coefficient of the diffusing atoms.
+coefficient of the diffusing atoms. This can be computed in the
+following manner, using the <A HREF = "variable.html">variable trap()</A> function:
</P>
+<PRE>compute 2 all vacf
+fix 5 all vector 1 c_2<B>4</B>
+variable diff equal dt*trap(f_5)
+thermo_style custom step v_diff
+</PRE>
<P>IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a <A HREF = "read_restart.html">restart file</A>,
then you should use the same ID for this compute, as in the original
run. This is so that the created fix will also have the same ID, and
thus be initialized correctly with atom velocities from the restart
file.
</P>
<P><B>Output info:</B>
</P>
<P>This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The vector values are "intensive". The vector values will be in
velocity^2 <A HREF = "units.html">units</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute_msd.html">compute msd</A>
</P>
<P><B>Default:</B> none
</P>
</HTML>
diff --git a/doc/compute_vacf.txt b/doc/compute_vacf.txt
index b397d9945..bb1e157a2 100644
--- a/doc/compute_vacf.txt
+++ b/doc/compute_vacf.txt
@@ -1,65 +1,71 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
compute vacf command :h3
[Syntax:]
compute ID group-ID vacf :pre
ID, group-ID are documented in "compute"_compute.html command
vacf = style name of this compute command :ul
[Examples:]
compute 1 all vacf
compute 1 upper vacf :pre
[Description:]
Define a computation that calculates the velocity auto-correlation
function (VACF), averaged over a group of atoms. Each atom's
contribution to the VACF is its current velocity vector dotted into
its initial velocity vector at the time the compute was specified.
A vector of four quantites is calculated by this compute. The first 3
elements of the vector are vx * vx0 (and similarly for the y and z
components), summed and averaged over atoms in the group. Vx is the
current x-component of velocity for the atom, vx0 is the initial
x-component of velocity for the atom. The 4th element of the vector
is the total VACF, i.e. (vx*vx0 + vy*vy0 + vz*vz0), summed and
averaged over atoms in the group.
The integral of the VACF versus time is proportional to the diffusion
-coefficient of the diffusing atoms.
+coefficient of the diffusing atoms. This can be computed in the
+following manner, using the "variable trap()"_variable.html function:
+
+compute 2 all vacf
+fix 5 all vector 1 c_2[4]
+variable diff equal dt*trap(f_5)
+thermo_style custom step v_diff :pre
IMPORTANT NOTE: If you want the quantities calculated by this compute
to be continuous when running from a "restart file"_read_restart.html,
then you should use the same ID for this compute, as in the original
run. This is so that the created fix will also have the same ID, and
thus be initialized correctly with atom velocities from the restart
file.
[Output info:]
This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The vector values are "intensive". The vector values will be in
velocity^2 "units"_units.html.
[Restrictions:] none
[Related commands:]
"compute msd"_compute_msd.html
[Default:] none
diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html
index 1e987bf02..77c0fd34d 100644
--- a/doc/fix_ave_time.html
+++ b/doc/fix_ave_time.html
@@ -1,333 +1,334 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>fix ave/time command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ...
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>ave/time = style name of this fix command
<LI>Nevery = use input values every this many timesteps
<LI>Nrepeat = # of times to use input values for calculating averages
<LI>Nfreq = calculate averages every this many timesteps
<LI>one or more input values can be listed
<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
<PRE> c_ID = global scalar, vector, or array calculated by a compute with ID
c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID
f_ID = global scalar, vector, or array calculated by a fix with ID
f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name
</PRE>
<LI>zero or more keyword/arg pairs may be appended
<LI>keyword = <I>mode</I> or <I>file</I> or <I>ave</I> or <I>start</I> or <I>off</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
<PRE> <I>mode</I> arg = <I>scalar</I> or <I>vector</I>
scalar = all input values are global scalars
vector = all input values are global vectors or global arrays
<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
one = output a new average value every Nfreq steps
running = output cummulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
<I>start</I> args = Nstart
Nstart = start averaging on this timestep
<I>off</I> arg = M = do not average this value
M = value # from 1 to Nvalues
<I>file</I> arg = filename
filename = name of file to output time averages to
<I>overwrite</I> arg = none = overwrite output file with only latest output
<I>title1</I> arg = string
string = text to print as 1st line of output file
<I>title2</I> arg = string
string = text to print as 2nd line of output file
<I>title3</I> arg = string
string = text to print as 3rd line of output file, only for vector mode
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &
title1 "My output values"
fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
</PRE>
<P><B>Description:</B>
</P>
<P>Use one or more global values as inputs every few timesteps, and
average them over longer timescales. The resulting averages can be
used by other <A HREF = "Section_howto.html#howto_15">output commands</A> such as
<A HREF = "thermo_style.html">thermo_style custom</A>, and can also be written to a
file. Note that if no time averaging is done, this command can be
used as a convenient way to simply output one or more global values to
a file.
</P>
<P>The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
</P>
<P>Each listed value can be the result of a <A HREF = "compute.html">compute</A> or
<A HREF = "fix.html">fix</A> or the evaluation of an equal-style
<A HREF = "variable.html">variable</A>. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
you wish to spatial- or time-average or histogram per-atom quantities
from a compute, fix, or variable, then see the <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>,
or <A HREF = "fix_ave_histo.html">fix ave/histo</A> commands. If you wish to sum a
per-atom quantity into a single global quantity, see the <A HREF = "compute_reduce.html">compute
reduce</A> command.
</P>
<P><A HREF = "compute.html">Computes</A> that produce global quantities are those which
do not have the word <I>atom</I> in their style name. Only a few
<A HREF = "fix.html">fixes</A> produce global quantities. See the doc pages for
individual fixes for info on which ones produce such values.
<A HREF = "variable.html">Variables</A> of style <I>equal</I> are the only ones that can
be used with this fix. Variables of style <I>atom</I> cannot be used,
since they produce per-atom values.
</P>
<P>The input values must either be all scalars or all vectors (or
arrays), depending on the setting of the <I>mode</I> keyword. In both
cases, the averaging is performed independently on each input value.
I.e. each input scalar is averaged independently and each element of
each input vector (or array) is averaged independently.
</P>
<P>If <I>mode</I> = vector, then the input values may either be vectors or
arrays and all must be the same "length", which is the length of the
vector or number of rows in the array. If a global array is listed,
then it is the same as if the individual columns of the array had been
listed one by one. E.g. these 2 fix ave/time commands are equivalent,
since the <A HREF = "compute_rdf.html">compute rdf</A> command creates, in this
case, a global array with 3 columns, each of length 50:
</P>
<PRE>compute myRDF all rdf 50 1 2
fix 1 all ave/time 100 1 100 c_myRDF file tmp1.rdf mode vector
fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
</PRE>
<HR>
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
timesteps the input values will be used in order to contribute to the
average. The final averaged quantities are generated on timesteps
that are a mlutiple of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
quantities, computed in the preceding portion of the simulation every
<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
</P>
<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps
100,200,etc.
</P>
<HR>
<P>If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If <I>mode</I> = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
the global vector calculated by the compute is used. If <I>mode</I> =
vector, then if no bracketed term is appended, the global vector
calculated by the compute is used. Or if the compute calculates an
array, all of the columns of the global array are used as if they had
been specified as individual vectors (see description above). If a
bracketed term is appended, the Ith column of the global array
calculated by the compute is used.
</P>
<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/time. Or it can be a compute defined
not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
output</A> or other fixes such as <A HREF = "fix_nh.html">fix
nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add them
to LAMMPS</A>.
</P>
<P>If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If <I>mode</I> = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
global vector calculated by the fix is used. If <I>mode</I> = vector, then
if no bracketed term is appended, the global vector calculated by the
fix is used. Or if the fix calculates an array, all of the columns of
the global array are used as if they had been specified as individual
vectors (see description above). If a bracketed term is appended, the
Ith column of the global array calculated by the fix is used.
</P>
<P>Note that some fixes only produce their values on certain timesteps,
which must be compatible with <I>Nevery</I>, else an error will result.
Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
LAMMPS</A>.
</P>
<P>If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Variables can only be
used as input for <I>mode</I> = scalar. Only equal-style variables can be
referenced. See the <A HREF = "variable.html">variable</A> command for details.
Note that variables of style <I>equal</I> define a formula which can
reference individual atom properties or thermodynamic keywords, or
they can invoke other computes, fixes, or variables when they are
evaluated, so this is a very general means of specifying quantities to
time average.
</P>
<HR>
<P>Additional optional keywords also affect the operation of this fix.
</P>
<P>If the <I>mode</I> keyword is set to <I>scalar</I>, then all input values must
be global scalars, or elements of global vectors. If the <I>mode</I>
keyword is set to <I>vector</I>, then all input values must be global
vectors, or columns of global arrays. They can also be global arrays,
which are converted into a series of global vectors (one per column),
as explained above.
</P>
<P>The <I>ave</I> keyword determines how the values produced every <I>Nfreq</I>
steps are averaged with values produced on previous steps that were
multiples of <I>Nfreq</I>, before they are accessed by another output
command or written to a file.
</P>
<P>If the <I>ave</I> setting is <I>one</I>, then the values produced on timesteps
that are multiples of <I>Nfreq</I> are independent of each other; they are
output as-is without further averaging.
</P>
<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
cummulative sense before being output. Each output value is thus the
average of the value produced on that timestep with all preceding
values. This running average begins when the fix is defined; it can
only be restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A>
command, or by re-defining the fix by re-specifying it.
</P>
<P>If the <I>ave</I> setting is <I>window</I>, then the values produced on
timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
a moving "window" of time, so that the last M values are used to
produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
on step 10000 will be the average of the individual values on steps
8000,9000,10000. Outputs on early steps will average over less than M
values if they are not available.
</P>
<P>The <I>start</I> keyword specifies what timestep averaging will begin on.
The default is step 0. Often input values can be 0.0 at time 0, so
setting <I>start</I> to a larger value can avoid including a 0.0 in a
running or windowed average.
</P>
<P>The <I>off</I> keyword can be used to flag any of the input values. If a
value is flagged, it will not be time averaged. Instead the most
recent input value will always be stored and output. This is useful
if one of more of the inputs produced by a compute or fix or variable
are effectively constant or are simply current values. E.g. they are
being written to a file with other time-averaged values for purposes
of creating well-formatted output.
</P>
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
steps, one quantity or vector of quantities is written to the file for
each input value specified in the fix ave/time command. For <I>mode</I> =
scalar, this means a single line is written each time output is
performed. Thus the file ends up to be a series of lines, i.e. one
column of numbers for each input value. For <I>mode</I> = vector, an array
of numbers is written each time output is performed. The number of
rows is the length of the input vectors, and the number of columns is
the number of values. Thus the file ends up to be a series of these
array sections.
</P>
<P>The <I>overwrite</I> keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the <I>ave running</I> setting.
</P>
<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
the strings that will be printed as the first 2 or 3 lines of the
output file, assuming the <I>file</I> keyword was used. LAMMPS uses
default values for each of these, so they do not need to be specified.
</P>
<P>By default, these header lines are as follows for <I>mode</I> = scalar:
</P>
<PRE># Time-averaged data for fix ID
# TimeStep value1 value2 ...
</PRE>
<P>In the first line, ID is replaced with the fix-ID. In the second line
the values are replaced with the appropriate fields from the fix
ave/time command. There is no third line in the header of the file,
so the <I>title3</I> setting is ignored when <I>mode</I> = scalar.
</P>
<P>By default, these header lines are as follows for <I>mode</I> = vector:
</P>
<PRE># Time-averaged data for fix ID
# TimeStep Number-of-rows
# Row value1 value2 ...
</PRE>
<P>In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section
of output. In the third line the values are replaced with the
appropriate fields from the fix ave/time command.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
are relevant to this fix.
</P>
<P>This fix produces a global scalar or global vector or global array
which can be accessed by various <A HREF = "Section_howto.html#howto_15">output
commands</A>. The values can only be
accessed on timesteps that are multiples of <I>Nfreq</I> since that is when
averaging is performed.
</P>
<P>A scalar is produced if only a single input value is averaged and
<I>mode</I> = scalar. A vector is produced if multiple input values are
averaged for <I>mode</I> = scalar, or a single input value for <I>mode</I> =
vector. In the first case, the length of the vector is the number of
inputs. In the second case, the length of the vector is the same as
the length of the input vector. An array is produced if multiple
input values are averaged and <I>mode</I> = vector. The global array has #
of rows = length of the input vectors and # of columns = number of
inputs.
</P>
<P>If the fix prouduces a scalar or vector, then the scalar and each
-element of the vector can be either "intensive" or "extensive". If
-the fix produces an array, then all elements in the array must be the
-same, either "intensive" or "extensive". If a compute or fix provides
-the value being time averaged, then the compute or fix determines
-whether the value is intensive or extensive; see the doc page for that
-compute or fix for further info. Values produced by a variable are
-treated as intensive.
+element of the vector can be either "intensive" or "extensive",
+depending on whether the values contributing to the scalar or vector
+element are "intensive" or "extensive". If the fix produces an array,
+then all elements in the array must be the same, either "intensive" or
+"extensive". If a compute or fix provides the value being time
+averaged, then the compute or fix determines whether the value is
+intensive or extensive; see the doc page for that compute or fix for
+further info. Values produced by a variable are treated as intensive.
</P>
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
minimization</A>.
</P>
<P><B>Restrictions:</B> none
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_spatial.html">fix
ave/spatial</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
</P>
-<P><B>Default:</B> none
+<P><B>Default:</B>
</P>
<P>The option defaults are mode = scalar, ave = one, start = 0, no file
output, title 1,2,3 = strings as described above, and no off settings
for any input values.
</P>
</HTML>
diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt
index 79c46324f..26fc0bc0b 100644
--- a/doc/fix_ave_time.txt
+++ b/doc/fix_ave_time.txt
@@ -1,318 +1,319 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix ave/time command :h3
[Syntax:]
fix ID group-ID ave/time Nevery Nrepeat Nfreq value1 value2 ... keyword args ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
ave/time = style name of this fix command :l
Nevery = use input values every this many timesteps :l
Nrepeat = # of times to use input values for calculating averages :l
Nfreq = calculate averages every this many timesteps :l
one or more input values can be listed :l
value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
c_ID = global scalar, vector, or array calculated by a compute with ID
c_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a compute with ID
f_ID = global scalar, vector, or array calculated by a fix with ID
f_ID\[I\] = Ith component of global vector or Ith column of global array calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name :pre
zero or more keyword/arg pairs may be appended :l
keyword = {mode} or {file} or {ave} or {start} or {off} or {overwrite} or {title1} or {title2} or {title3} :l
{mode} arg = {scalar} or {vector}
scalar = all input values are global scalars
vector = all input values are global vectors or global arrays
{ave} args = {one} or {running} or {window M}
one = output a new average value every Nfreq steps
running = output cummulative average of all previous Nfreq steps
window M = output average of M most recent Nfreq steps
{start} args = Nstart
Nstart = start averaging on this timestep
{off} arg = M = do not average this value
M = value # from 1 to Nvalues
{file} arg = filename
filename = name of file to output time averages to
{overwrite} arg = none = overwrite output file with only latest output
{title1} arg = string
string = text to print as 1st line of output file
{title2} arg = string
string = text to print as 2nd line of output file
{title3} arg = string
string = text to print as 3rd line of output file, only for vector mode :pre
:ule
[Examples:]
fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
fix 1 all ave/time 100 5 1000 c_thermo_press\[2\] ave window 20 &
title1 "My output values"
fix 1 all ave/time 1 100 1000 f_indent f_indent\[1\] file temp.indent off 1 :pre
[Description:]
Use one or more global values as inputs every few timesteps, and
average them over longer timescales. The resulting averages can be
used by other "output commands"_Section_howto.html#howto_15 such as
"thermo_style custom"_thermo_style.html, and can also be written to a
file. Note that if no time averaging is done, this command can be
used as a convenient way to simply output one or more global values to
a file.
The group specified with this command is ignored. However, note that
specified values may represent calculations performed by computes and
fixes which store their own "group" definitions.
Each listed value can be the result of a "compute"_compute.html or
"fix"_fix.html or the evaluation of an equal-style
"variable"_variable.html. In each case, the compute, fix, or variable
must produce a global quantity, not a per-atom or local quantity. If
you wish to spatial- or time-average or histogram per-atom quantities
from a compute, fix, or variable, then see the "fix
ave/spatial"_fix_ave_spatial.html, "fix ave/atom"_fix_ave_atom.html,
or "fix ave/histo"_fix_ave_histo.html commands. If you wish to sum a
per-atom quantity into a single global quantity, see the "compute
reduce"_compute_reduce.html command.
"Computes"_compute.html that produce global quantities are those which
do not have the word {atom} in their style name. Only a few
"fixes"_fix.html produce global quantities. See the doc pages for
individual fixes for info on which ones produce such values.
"Variables"_variable.html of style {equal} are the only ones that can
be used with this fix. Variables of style {atom} cannot be used,
since they produce per-atom values.
The input values must either be all scalars or all vectors (or
arrays), depending on the setting of the {mode} keyword. In both
cases, the averaging is performed independently on each input value.
I.e. each input scalar is averaged independently and each element of
each input vector (or array) is averaged independently.
If {mode} = vector, then the input values may either be vectors or
arrays and all must be the same "length", which is the length of the
vector or number of rows in the array. If a global array is listed,
then it is the same as if the individual columns of the array had been
listed one by one. E.g. these 2 fix ave/time commands are equivalent,
since the "compute rdf"_compute_rdf.html command creates, in this
case, a global array with 3 columns, each of length 50:
compute myRDF all rdf 50 1 2
fix 1 all ave/time 100 1 100 c_myRDF file tmp1.rdf mode vector
fix 2 all ave/time 100 1 100 c_myRDF\[1\] c_myRDF\[2\] c_myRDF\[3\] file tmp2.rdf mode vector :pre
:line
The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
timesteps the input values will be used in order to contribute to the
average. The final averaged quantities are generated on timesteps
that are a mlutiple of {Nfreq}. The average is over {Nrepeat}
quantities, computed in the preceding portion of the simulation every
{Nevery} timesteps. {Nfreq} must be a multiple of {Nevery} and
{Nevery} must be non-zero even if {Nrepeat} is 1. Also, the timesteps
contributing to the average value cannot overlap, i.e. Nfreq >
(Nrepeat-1)*Nevery is required.
For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
timesteps 90,92,94,96,98,100 will be used to compute the final average
on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps
100,200,etc.
:line
If a value begins with "c_", a compute ID must follow which has been
previously defined in the input script. If {mode} = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
the global vector calculated by the compute is used. If {mode} =
vector, then if no bracketed term is appended, the global vector
calculated by the compute is used. Or if the compute calculates an
array, all of the columns of the global array are used as if they had
been specified as individual vectors (see description above). If a
bracketed term is appended, the Ith column of the global array
calculated by the compute is used.
Note that there is a "compute reduce"_compute_reduce.html command
which can sum per-atom quantities into a global scalar or vector which
can thus be accessed by fix ave/time. Or it can be a compute defined
not in your input script, but by "thermodynamic
output"_thermo_style.html or other fixes such as "fix
nvt"_fix_nh.html or "fix temp/rescale"_fix_temp_rescale.html. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and "add them
to LAMMPS"_Section_modify.html.
If a value begins with "f_", a fix ID must follow which has been
previously defined in the input script. If {mode} = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
global vector calculated by the fix is used. If {mode} = vector, then
if no bracketed term is appended, the global vector calculated by the
fix is used. Or if the fix calculates an array, all of the columns of
the global array are used as if they had been specified as individual
vectors (see description above). If a bracketed term is appended, the
Ith column of the global array calculated by the fix is used.
Note that some fixes only produce their values on certain timesteps,
which must be compatible with {Nevery}, else an error will result.
Users can also write code for their own fix styles and "add them to
LAMMPS"_Section_modify.html.
If a value begins with "v_", a variable name must follow which has
been previously defined in the input script. Variables can only be
used as input for {mode} = scalar. Only equal-style variables can be
referenced. See the "variable"_variable.html command for details.
Note that variables of style {equal} define a formula which can
reference individual atom properties or thermodynamic keywords, or
they can invoke other computes, fixes, or variables when they are
evaluated, so this is a very general means of specifying quantities to
time average.
:line
Additional optional keywords also affect the operation of this fix.
If the {mode} keyword is set to {scalar}, then all input values must
be global scalars, or elements of global vectors. If the {mode}
keyword is set to {vector}, then all input values must be global
vectors, or columns of global arrays. They can also be global arrays,
which are converted into a series of global vectors (one per column),
as explained above.
The {ave} keyword determines how the values produced every {Nfreq}
steps are averaged with values produced on previous steps that were
multiples of {Nfreq}, before they are accessed by another output
command or written to a file.
If the {ave} setting is {one}, then the values produced on timesteps
that are multiples of {Nfreq} are independent of each other; they are
output as-is without further averaging.
If the {ave} setting is {running}, then the values produced on
timesteps that are multiples of {Nfreq} are summed and averaged in a
cummulative sense before being output. Each output value is thus the
average of the value produced on that timestep with all preceding
values. This running average begins when the fix is defined; it can
only be restarted by deleting the fix via the "unfix"_unfix.html
command, or by re-defining the fix by re-specifying it.
If the {ave} setting is {window}, then the values produced on
timesteps that are multiples of {Nfreq} are summed and averaged within
a moving "window" of time, so that the last M values are used to
produce the output. E.g. if M = 3 and Nfreq = 1000, then the output
on step 10000 will be the average of the individual values on steps
8000,9000,10000. Outputs on early steps will average over less than M
values if they are not available.
The {start} keyword specifies what timestep averaging will begin on.
The default is step 0. Often input values can be 0.0 at time 0, so
setting {start} to a larger value can avoid including a 0.0 in a
running or windowed average.
The {off} keyword can be used to flag any of the input values. If a
value is flagged, it will not be time averaged. Instead the most
recent input value will always be stored and output. This is useful
if one of more of the inputs produced by a compute or fix or variable
are effectively constant or are simply current values. E.g. they are
being written to a file with other time-averaged values for purposes
of creating well-formatted output.
The {file} keyword allows a filename to be specified. Every {Nfreq}
steps, one quantity or vector of quantities is written to the file for
each input value specified in the fix ave/time command. For {mode} =
scalar, this means a single line is written each time output is
performed. Thus the file ends up to be a series of lines, i.e. one
column of numbers for each input value. For {mode} = vector, an array
of numbers is written each time output is performed. The number of
rows is the length of the input vectors, and the number of columns is
the number of values. Thus the file ends up to be a series of these
array sections.
The {overwrite} keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the {ave running} setting.
The {title1} and {title2} and {title3} keywords allow specification of
the strings that will be printed as the first 2 or 3 lines of the
output file, assuming the {file} keyword was used. LAMMPS uses
default values for each of these, so they do not need to be specified.
By default, these header lines are as follows for {mode} = scalar:
# Time-averaged data for fix ID
# TimeStep value1 value2 ... :pre
In the first line, ID is replaced with the fix-ID. In the second line
the values are replaced with the appropriate fields from the fix
ave/time command. There is no third line in the header of the file,
so the {title3} setting is ignored when {mode} = scalar.
By default, these header lines are as follows for {mode} = vector:
# Time-averaged data for fix ID
# TimeStep Number-of-rows
# Row value1 value2 ... :pre
In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section
of output. In the third line the values are replaced with the
appropriate fields from the fix ave/time command.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
No information about this fix is written to "binary restart
files"_restart.html. None of the "fix_modify"_fix_modify.html options
are relevant to this fix.
This fix produces a global scalar or global vector or global array
which can be accessed by various "output
commands"_Section_howto.html#howto_15. The values can only be
accessed on timesteps that are multiples of {Nfreq} since that is when
averaging is performed.
A scalar is produced if only a single input value is averaged and
{mode} = scalar. A vector is produced if multiple input values are
averaged for {mode} = scalar, or a single input value for {mode} =
vector. In the first case, the length of the vector is the number of
inputs. In the second case, the length of the vector is the same as
the length of the input vector. An array is produced if multiple
input values are averaged and {mode} = vector. The global array has #
of rows = length of the input vectors and # of columns = number of
inputs.
If the fix prouduces a scalar or vector, then the scalar and each
-element of the vector can be either "intensive" or "extensive". If
-the fix produces an array, then all elements in the array must be the
-same, either "intensive" or "extensive". If a compute or fix provides
-the value being time averaged, then the compute or fix determines
-whether the value is intensive or extensive; see the doc page for that
-compute or fix for further info. Values produced by a variable are
-treated as intensive.
+element of the vector can be either "intensive" or "extensive",
+depending on whether the values contributing to the scalar or vector
+element are "intensive" or "extensive". If the fix produces an array,
+then all elements in the array must be the same, either "intensive" or
+"extensive". If a compute or fix provides the value being time
+averaged, then the compute or fix determines whether the value is
+intensive or extensive; see the doc page for that compute or fix for
+further info. Values produced by a variable are treated as intensive.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
ave/spatial"_fix_ave_spatial.html, "fix ave/histo"_fix_ave_histo.html,
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
-[Default:] none
+[Default:]
The option defaults are mode = scalar, ave = one, start = 0, no file
output, title 1,2,3 = strings as described above, and no off settings
for any input values.
diff --git a/doc/fix_vector.html b/doc/fix_vector.html
new file mode 100644
index 000000000..9acb53eab
--- /dev/null
+++ b/doc/fix_vector.html
@@ -0,0 +1,159 @@
+<HTML>
+<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix vector command
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID vector Nevery value1 value2 ...
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+
+<LI>ave/time = style name of this fix command
+
+<LI>Nevery = use input values every this many timesteps
+
+<LI>one or more input values can be listed
+
+<LI>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name
+
+<PRE> c_ID = global scalar calculated by a compute with ID
+ c_ID[I] = Ith component of global vector calculated by a compute with ID
+ f_ID = global scalar calculated by a fix with ID
+ f_ID[I] = Ith component of global vector calculated by a fix with ID
+ v_name = global value calculated by an equal-style variable with name
+</PRE>
+
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all vector 100 c_myTemp
+fix 1 all vector 5 c_myTemp v_integral
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Use one or more global values as inputs every few timesteps, and
+simply store them. For a single specified value, the values are
+stored as a global vector of growing length For multiple specified
+values, they are stored as rows in a global array, whose number of
+rows is growing. The resulting vector or array can be used by other
+<A HREF = "Section_howto.html#howto_15">output commands</A>.
+</P>
+<P>One way to to use this command is to accumulate a vector that is
+time-integrated using the <A HREF = "variable.html">variable trap()</A> function.
+For example the velocity auto-correlation function (VACF) can be
+time-integrated, to yield a diffusion coefficient, as follows:
+</P>
+<PRE>compute 2 all vacf
+fix 5 all vector 1 c_2<B>4</B>
+variable diff equal dt*trap(f_5)
+thermo_style custom step v_diff
+</PRE>
+<P>The group specified with this command is ignored. However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+</P>
+<P>Each listed value can be the result of a <A HREF = "compute.html">compute</A> or
+<A HREF = "fix.html">fix</A> or the evaluation of an equal-style
+<A HREF = "variable.html">variable</A>. In each case, the compute, fix, or variable
+must produce a global quantity, not a per-atom or local quantity.
+And the global quantity must be a scalar, not a vector or array.
+</P>
+<P><A HREF = "compute.html">Computes</A> that produce global quantities are those which
+do not have the word <I>atom</I> in their style name. Only a few
+<A HREF = "fix.html">fixes</A> produce global quantities. See the doc pages for
+individual fixes for info on which ones produce such values.
+<A HREF = "variable.html">Variables</A> of style <I>equal</I> are the only ones that can
+be used with this fix. Variables of style <I>atom</I> cannot be used,
+since they produce per-atom values.
+</P>
+<P>The <I>Nevery</I> argument specifies on what timesteps the input values
+will be used in order to be stored. Only timesteps that a multiple
+of <I>Nevery</I>, including timestep 0, will contribute values.
+</P>
+<HR>
+
+<P>If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the global scalar calculated by the compute is used. If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the compute is used.
+</P>
+<P>Note that there is a <A HREF = "compute_reduce.html">compute reduce</A> command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix vector. Or it can be a compute defined
+not in your input script, but by <A HREF = "thermo_style.html">thermodynamic
+output</A> or other fixes such as <A HREF = "fix_nh.html">fix nvt</A>
+or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>. See the doc pages for
+these commands which give the IDs of these computes. Users can also
+write code for their own compute styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the global scalar calculated by the fix is used. If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the fix is used.
+</P>
+<P>Note that some fixes only produce their values on certain timesteps,
+which must be compatible with <I>Nevery</I>, else an error will result.
+Users can also write code for their own fix styles and <A HREF = "Section_modify.html">add them to
+LAMMPS</A>.
+</P>
+<P>If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. Only equal-style
+variables can be referenced. See the <A HREF = "variable.html">variable</A> command
+for details. Note that variables of style <I>equal</I> define a formula
+which can reference individual atom properties or thermodynamic
+keywords, or they can invoke other computes, fixes, or variables when
+they are evaluated, so this is a very general means of specifying
+quantities to be stored by fix vector.
+</P>
+<HR>
+
+<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
+</P>
+<P>No information about this fix is written to <A HREF = "restart.html">binary restart
+files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
+are relevant to this fix.
+</P>
+<P>This fix produces a global vector or global array which can be
+accessed by various <A HREF = "Section_howto.html#howto_15">output commands</A>.
+The values can only be accessed on timesteps that are multiples of
+<I>Nevery</I>.
+</P>
+<P>A vector is produced if only a single input value is specified.
+An array is produced if multiple input values are specified.
+The length of the vector or the number of rows in the array grows
+by 1 every <I>Nevery</I> timesteps.
+</P>
+<P>If the fix prouduces a vector, then the entire vector will be either
+"intensive" or "extensive", depending on whether the values stored in
+the vector are "intensive" or "extensive". If the fix produces an
+array, then all elements in the array must be the same, either
+"intensive" or "extensive". If a compute or fix provides the value
+stored, then the compute or fix determines whether the value is
+intensive or extensive; see the doc page for that compute or fix for
+further info. Values produced by a variable are treated as intensive.
+</P>
+<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
+the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
+minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "compute.html">compute</A>, <A HREF = "variable.html">variable</A>
+</P>
+<P><B>Default:</B> none
+</P>
+</HTML>
diff --git a/doc/fix_vector.txt b/doc/fix_vector.txt
new file mode 100644
index 000000000..5dd73c4fb
--- /dev/null
+++ b/doc/fix_vector.txt
@@ -0,0 +1,148 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix vector command :h3
+
+[Syntax:]
+
+fix ID group-ID vector Nevery value1 value2 ... :pre
+
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+ave/time = style name of this fix command :l
+Nevery = use input values every this many timesteps :l
+one or more input values can be listed :l
+value = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l
+ c_ID = global scalar calculated by a compute with ID
+ c_ID\[I\] = Ith component of global vector calculated by a compute with ID
+ f_ID = global scalar calculated by a fix with ID
+ f_ID\[I\] = Ith component of global vector calculated by a fix with ID
+ v_name = global value calculated by an equal-style variable with name :pre
+:ule
+
+[Examples:]
+
+fix 1 all vector 100 c_myTemp
+fix 1 all vector 5 c_myTemp v_integral :pre
+
+[Description:]
+
+Use one or more global values as inputs every few timesteps, and
+simply store them. For a single specified value, the values are
+stored as a global vector of growing length For multiple specified
+values, they are stored as rows in a global array, whose number of
+rows is growing. The resulting vector or array can be used by other
+"output commands"_Section_howto.html#howto_15.
+
+One way to to use this command is to accumulate a vector that is
+time-integrated using the "variable trap()"_variable.html function.
+For example the velocity auto-correlation function (VACF) can be
+time-integrated, to yield a diffusion coefficient, as follows:
+
+compute 2 all vacf
+fix 5 all vector 1 c_2[4]
+variable diff equal dt*trap(f_5)
+thermo_style custom step v_diff :pre
+
+The group specified with this command is ignored. However, note that
+specified values may represent calculations performed by computes and
+fixes which store their own "group" definitions.
+
+Each listed value can be the result of a "compute"_compute.html or
+"fix"_fix.html or the evaluation of an equal-style
+"variable"_variable.html. In each case, the compute, fix, or variable
+must produce a global quantity, not a per-atom or local quantity.
+And the global quantity must be a scalar, not a vector or array.
+
+"Computes"_compute.html that produce global quantities are those which
+do not have the word {atom} in their style name. Only a few
+"fixes"_fix.html produce global quantities. See the doc pages for
+individual fixes for info on which ones produce such values.
+"Variables"_variable.html of style {equal} are the only ones that can
+be used with this fix. Variables of style {atom} cannot be used,
+since they produce per-atom values.
+
+The {Nevery} argument specifies on what timesteps the input values
+will be used in order to be stored. Only timesteps that a multiple
+of {Nevery}, including timestep 0, will contribute values.
+
+:line
+
+If a value begins with "c_", a compute ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the global scalar calculated by the compute is used. If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the compute is used.
+
+Note that there is a "compute reduce"_compute_reduce.html command
+which can sum per-atom quantities into a global scalar or vector which
+can thus be accessed by fix vector. Or it can be a compute defined
+not in your input script, but by "thermodynamic
+output"_thermo_style.html or other fixes such as "fix nvt"_fix_nh.html
+or "fix temp/rescale"_fix_temp_rescale.html. See the doc pages for
+these commands which give the IDs of these computes. Users can also
+write code for their own compute styles and "add them to
+LAMMPS"_Section_modify.html.
+
+If a value begins with "f_", a fix ID must follow which has been
+previously defined in the input script. If no bracketed term is
+appended, the global scalar calculated by the fix is used. If a
+bracketed term is appended, the Ith element of the global vector
+calculated by the fix is used.
+
+Note that some fixes only produce their values on certain timesteps,
+which must be compatible with {Nevery}, else an error will result.
+Users can also write code for their own fix styles and "add them to
+LAMMPS"_Section_modify.html.
+
+If a value begins with "v_", a variable name must follow which has
+been previously defined in the input script. Only equal-style
+variables can be referenced. See the "variable"_variable.html command
+for details. Note that variables of style {equal} define a formula
+which can reference individual atom properties or thermodynamic
+keywords, or they can invoke other computes, fixes, or variables when
+they are evaluated, so this is a very general means of specifying
+quantities to be stored by fix vector.
+
+:line
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html. None of the "fix_modify"_fix_modify.html options
+are relevant to this fix.
+
+This fix produces a global vector or global array which can be
+accessed by various "output commands"_Section_howto.html#howto_15.
+The values can only be accessed on timesteps that are multiples of
+{Nevery}.
+
+A vector is produced if only a single input value is specified.
+An array is produced if multiple input values are specified.
+The length of the vector or the number of rows in the array grows
+by 1 every {Nevery} timesteps.
+
+If the fix prouduces a vector, then the entire vector will be either
+"intensive" or "extensive", depending on whether the values stored in
+the vector are "intensive" or "extensive". If the fix produces an
+array, then all elements in the array must be the same, either
+"intensive" or "extensive". If a compute or fix provides the value
+stored, then the compute or fix determines whether the value is
+intensive or extensive; see the doc page for that compute or fix for
+further info. Values produced by a variable are treated as intensive.
+
+No parameter of this fix can be used with the {start/stop} keywords of
+the "run"_run.html command. This fix is not invoked during "energy
+minimization"_minimize.html.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"compute"_compute.html, "variable"_variable.html
+
+[Default:] none
diff --git a/doc/pair_comb.html b/doc/pair_comb.html
index a09ca8732..38e59ffd2 100644
--- a/doc/pair_comb.html
+++ b/doc/pair_comb.html
@@ -1,198 +1,199 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style comb command
</H3>
<H3>pair_style comb/omp command
</H3>
<H3>pair_style comb3 command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style comb
pair_style comb3 keyword
</PRE>
<PRE>keyword = <I>polar</I>
<I>polar</I> value = <I>polar_on</I> or <I>polar_off</I> = whether or not to include atomic polarization
</PRE>
</UL>
<P><B>Examples:</B>
</P>
<PRE>pair_style comb
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O
</PRE>
<PRE>pair_style comb3 polar_off
pair_coeff * * ../potentials/ffield.comb3 O Cu N C O
</PRE>
<P><B>Description:</B>
</P>
<P>Style <I>comb</I> computes the second-generation variable charge COMB
(Charge-Optimized Many-Body) potential. Style <I>comb3</I> computes the
third-generation COMB potential. These COMB potentials are described
in <A HREF = "#COMB">(COMB)</A> and <A HREF = "#COMB3">(COMB3)</A>. Briefly, the total energy
<I>E<sub>T</sub></I> of a system of atoms is given by
</P>
<CENTER><IMG SRC = "Eqs/pair_comb1.jpg">
</CENTER>
<P>where <I>E<sub>i</sub><sup>self</sup></I> is the self-energy of atom <I>i</I>
(including atomic ionization energies and electron affinities),
<I>E<sub>ij</sub><sup>short</sup></I> is the bond-order potential between
atoms <I>i</I> and <I>j</I>,
<I>E<sub>ij</sub><sup>Coul</sup></I> is the Coulomb interactions,
<I>E<sup>polar</sup></I> is the polarization term for organic systems
(style <I>comb3</I> only),
<I>E<sup>vdW</sup></I> is the van der Waals energy (style <I>comb3</I> only),
<I>E<sup>barr</sup></I> is a charge barrier function, and
<I>E<sup>corr</sup></I> are angular correction terms.
</P>
<P>The COMB potentials (styles <I>comb</I> and <I>comb3</I>) are variable charge
potentials. The equilibrium charge on each atom is calculated by the
electronegativity equalization (QEq) method. See <A HREF = "#Rick">Rick</A> for
further details. This is implemented by the <A HREF = "fix_qeq_comb.html">fix
qeq/comb</A> command, which should normally be
specified in the input script when running a model with the COMB
potential. The <A HREF = "fix_qeq_comb.html">fix qeq/comb</A> command has options
that determine how often charge equilibration is performed, its
convergence criterion, and which atoms are included in the
calculation.
</P>
<P>Only a single pair_coeff command is used with the <I>comb</I> and <I>comb3</I>
styles which specifies the COMB potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the potential file in the pair_coeff
command, where N is the number of LAMMPS atom types.
</P>
<P>For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
use the following pair_coeff command:
</P>
<PRE>pair_coeff * * ../potentials/ffield.comb Si Hf O Si
</PRE>
<P>The first two arguments must be * * so as to span all LAMMPS atom
types. The first and last Si arguments map LAMMPS atom types 1 and 4
to the Si element in the <I>ffield.comb</I> file. The second Hf argument
maps LAMMPS atom type 2 to the Hf element, and the third O argument
maps LAMMPS atom type 3 to the O element in the potential file. If a
mapping value is specified as NULL, the mapping is not performed.
This can be used when a <I>comb</I> potential is used as part of the
<I>hybrid</I> pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
</P>
<P>For style <I>comb</I>, the provided potential file <I>ffield.comb</I> contains
all currently-available 2nd generation COMB parameterizations: for Si,
Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
<I>comb3</I>, the potential file <I>ffield.comb3</I> contains all
currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
-H, Ti and Zn. The status of the optimization of the compounds, for
+H, Ti, Zn and Zr. The status of the optimization of the compounds, for
example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
following table:
</P>
<CENTER><IMG SRC = "Eqs/pair_comb2.jpg">
</CENTER>
<P>For style <I>comb3</I>, in addition to ffield.comb3, a special parameter
file, <I>lib.comb3</I>, that is exclusively used for C/O/H systems, will be
automatically loaded if carbon atom is detected in LAMMPS input
structure. Keyword <I>polar</I> indicates whether the force field includes
the atomic polarization. Since the equilibration of the polarization
has not yet been implemented, it can only set polar_off at present.
</P>
<P>IMPORTANT NOTE: You can not use potential file <I>ffield.comb</I> with
style <I>comb3</I>, nor file <I>ffield.comb3</I> with style <I>comb</I>.
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
the same as the corresponding style without the suffix. They have
been optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
</P>
<P>These pair styles does not support the <A HREF = "pair_modify.html">pair_modify</A>
shift, table, and tail options.
</P>
<P>These pair styles do not write its information to <A HREF = "restart.html">binary restart
files</A>, since it is stored in potential files. Thus, you
need to re-specify the pair_style, pair_coeff, and <A HREF = "fix_qeq_comb.html">fix
qeq/comb</A> commands in an input script that reads a
restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. It does not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
<P>These pair styles are part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more info.
</P>
<P>These pair styles requires the <A HREF = "newton.html">newton</A> setting to be "on"
for pair interactions.
</P>
<P>The COMB potentials in the <I>ffield.comb</I> and <I>ffield.comb3</I> files provided
with LAMMPS (see the potentials directory) are parameterized for metal
<A HREF = "units.html">units</A>. You can use the COMB potential with any LAMMPS
units, but you would need to create your own COMB potential file with
coefficients listed in the appropriate units if your simulation
doesn't use "metal" units.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_style.html">pair_style</A>, <A HREF = "pair_coeff.html">pair_coeff</A>,
<A HREF = "fix_qeq_comb.html">fix_qeq/comb</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "COMB"></A>
-<P><B>(COMB)</B> S. R. Phillpot and S. B. Sinnott, Science 325, 1634-1635 (2009)
+<P><B>(COMB)</B> T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
+S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
</P>
<A NAME = "COMB3"></A>
<P><B>(COMB3)</B> T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
-Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R,
-in press (DOI: 10.1016/j.mser.2013.07.001)
+Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
+255-279 (2013).
</P>
<A NAME = "Rick"></A>
<P><B>(Rick)</B> S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
(1994).
</P>
</HTML>
diff --git a/doc/pair_comb.txt b/doc/pair_comb.txt
index bc92b12db..9b87404d5 100644
--- a/doc/pair_comb.txt
+++ b/doc/pair_comb.txt
@@ -1,186 +1,187 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style comb command :h3
pair_style comb/omp command :h3
pair_style comb3 command :h3
[Syntax:]
pair_style comb
pair_style comb3 keyword :pre
keyword = {polar}
{polar} value = {polar_on} or {polar_off} = whether or not to include atomic polarization :pre
:ule
[Examples:]
pair_style comb
pair_coeff * * ../potentials/ffield.comb Si
pair_coeff * * ../potentials/ffield.comb Hf Si O :pre
pair_style comb3 polar_off
pair_coeff * * ../potentials/ffield.comb3 O Cu N C O :pre
[Description:]
Style {comb} computes the second-generation variable charge COMB
(Charge-Optimized Many-Body) potential. Style {comb3} computes the
third-generation COMB potential. These COMB potentials are described
in "(COMB)"_#COMB and "(COMB3)"_#COMB3. Briefly, the total energy
{E<sub>T</sub>} of a system of atoms is given by
:c,image(Eqs/pair_comb1.jpg)
where {E<sub>i</sub><sup>self</sup>} is the self-energy of atom {i}
(including atomic ionization energies and electron affinities),
{E<sub>ij</sub><sup>short</sup>} is the bond-order potential between
atoms {i} and {j},
{E<sub>ij</sub><sup>Coul</sup>} is the Coulomb interactions,
{E<sup>polar</sup>} is the polarization term for organic systems
(style {comb3} only),
{E<sup>vdW</sup>} is the van der Waals energy (style {comb3} only),
{E<sup>barr</sup>} is a charge barrier function, and
{E<sup>corr</sup>} are angular correction terms.
The COMB potentials (styles {comb} and {comb3}) are variable charge
potentials. The equilibrium charge on each atom is calculated by the
electronegativity equalization (QEq) method. See "Rick"_#Rick for
further details. This is implemented by the "fix
qeq/comb"_fix_qeq_comb.html command, which should normally be
specified in the input script when running a model with the COMB
potential. The "fix qeq/comb"_fix_qeq_comb.html command has options
that determine how often charge equilibration is performed, its
convergence criterion, and which atoms are included in the
calculation.
Only a single pair_coeff command is used with the {comb} and {comb3}
styles which specifies the COMB potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the potential file in the pair_coeff
command, where N is the number of LAMMPS atom types.
For example, if your LAMMPS simulation of a Si/SiO<sub>2</sub>/
HfO<sub>2</sub> interface has 4 atom types, and you want the 1st and
last to be Si, the 2nd to be Hf, and the 3rd to be O, and you would
use the following pair_coeff command:
pair_coeff * * ../potentials/ffield.comb Si Hf O Si :pre
The first two arguments must be * * so as to span all LAMMPS atom
types. The first and last Si arguments map LAMMPS atom types 1 and 4
to the Si element in the {ffield.comb} file. The second Hf argument
maps LAMMPS atom type 2 to the Hf element, and the third O argument
maps LAMMPS atom type 3 to the O element in the potential file. If a
mapping value is specified as NULL, the mapping is not performed.
This can be used when a {comb} potential is used as part of the
{hybrid} pair style. The NULL values are placeholders for atom types
that will be used with other potentials.
For style {comb}, the provided potential file {ffield.comb} contains
all currently-available 2nd generation COMB parameterizations: for Si,
Cu, Hf, Ti, O, their oxides and Zr, Zn and U metals. For style
{comb3}, the potential file {ffield.comb3} contains all
currently-available 3rd generation COMB paramterizations: O, Cu, N, C,
-H, Ti and Zn. The status of the optimization of the compounds, for
+H, Ti, Zn and Zr. The status of the optimization of the compounds, for
example Cu<sub>2</sub>O, TiN and hydrocarbons, are given in the
following table:
:c,image(Eqs/pair_comb2.jpg)
For style {comb3}, in addition to ffield.comb3, a special parameter
file, {lib.comb3}, that is exclusively used for C/O/H systems, will be
automatically loaded if carbon atom is detected in LAMMPS input
structure. Keyword {polar} indicates whether the force field includes
the atomic polarization. Since the equilibration of the polarization
has not yet been implemented, it can only set polar_off at present.
IMPORTANT NOTE: You can not use potential file {ffield.comb} with
style {comb3}, nor file {ffield.comb3} with style {comb}.
:line
Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
the same as the corresponding style without the suffix. They have
been optimized to run faster, depending on your available hardware, as
discussed in "Section_accelerate"_Section_accelerate.html of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, where types I and J correspond to
two different element types, mixing is performed by LAMMPS as
described above from values in the potential file.
These pair styles does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
These pair styles do not write its information to "binary restart
files"_restart.html, since it is stored in potential files. Thus, you
need to re-specify the pair_style, pair_coeff, and "fix
qeq/comb"_fix_qeq_comb.html commands in an input script that reads a
restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
These pair styles are part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package (which it is by default). See
the "Making LAMMPS"_Section_start.html#start_3 section for more info.
These pair styles requires the "newton"_newton.html setting to be "on"
for pair interactions.
The COMB potentials in the {ffield.comb} and {ffield.comb3} files provided
with LAMMPS (see the potentials directory) are parameterized for metal
"units"_units.html. You can use the COMB potential with any LAMMPS
units, but you would need to create your own COMB potential file with
coefficients listed in the appropriate units if your simulation
doesn't use "metal" units.
[Related commands:]
"pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html,
"fix_qeq/comb"_fix_qeq_comb.html
[Default:] none
:line
:link(COMB)
-[(COMB)] S. R. Phillpot and S. B. Sinnott, Science 325, 1634-1635 (2009)
+[(COMB)] T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and
+S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
:link(COMB3)
[(COMB3)] T. Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek,
-Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R,
-in press (DOI: 10.1016/j.mser.2013.07.001)
+Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74,
+255-279 (2013).
:link(Rick)
[(Rick)] S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
(1994).
diff --git a/doc/pair_peri.html b/doc/pair_peri.html
index 76c3fb872..7ddd9b4ee 100644
--- a/doc/pair_peri.html
+++ b/doc/pair_peri.html
@@ -1,198 +1,228 @@
<HTML>
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
</CENTER>
<HR>
<H3>pair_style peri/pmb command
</H3>
<H3>pair_style peri/pmb/omp command
</H3>
<H3>pair_style peri/lps command
</H3>
<H3>pair_style peri/lps/omp command
</H3>
<H3>pair_style peri/ves command
</H3>
+<H3>pair_style peri/eps command
+</H3>
<P><B>Syntax:</B>
</P>
<PRE>pair_style style
</PRE>
-<UL><LI>style = <I>peri/pmb</I> or <I>peri/lps</I> or <I>peri/ves</I>
-</UL>
+<P>style = <I>peri/pmb</I> or <I>peri/lps</I> or <I>peri/ves</I> or <I>peri/eps</I>:ul
+</P>
<P><B>Examples:</B>
</P>
<PRE>pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
</PRE>
<PRE>pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
</PRE>
<PRE>pair_style peri/ves
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
</PRE>
+<PRE>pair_style peri/eps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
+</PRE>
<P><B>Description:</B>
</P>
<P>The peridynamic pair styles implement material models that can be used
at the mescscopic and macroscopic scales.
</P>
<P>Style <I>peri/pmb</I> implements the Peridynamic bond-based prototype
microelastic brittle (PMB) model.
</P>
<P>Style <I>peri/lps</I> implements the Peridynamic state-based linear
peridynamic solid (LPS) model.
</P>
<P>Style <I>peri/ves</I> implements the Peridynamic state-based linear
peridynamic viscoelastic solid (VES) model.
</P>
+<P>Style <I>peri/eps</I> implements the Peridynamic state-based elastic-plastic
+solid (EPS) model.
+</P>
<P>The canonical papers on Peridynamics are <A HREF = "#Silling2000">(Silling 2000)</A>
and <A HREF = "#Silling2007">(Silling 2007)</A>. The implementation of Peridynamics
in LAMMPS is described in <A HREF = "#Parks">(Parks)</A>. Also see the <A HREF = "http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf">PDLAMMPS
user guide</A> for
-more details about the implementation of peridynamics in LAMMPS.
-</P>
-<P>The peridynamic VES model in PDLAMMPS is implemented by R. Rahman and
-J.T Foster at University of Texas at San Antonio. The VES formulation
-is described in <A HREF = "#Mitchell">(Mitchell)</A>. An additional PDF doc with
-details is in <A HREF = "PDF/PDLammps_VES.pdf">doc/PDF/PDLammps_VES.pdf</A>. For
-questions regarding VES implementation in LAMMPS please contact Rezwan
-Rahman: rezwanur.rahman at utsa.edu.
+more details about its implementation.
+</P>
+<P>The peridynamic VES and EPS models in PDLAMMPS were implemented by
+R. Rahman and J. T. Foster at University of Texas at San Antonio. The
+original VES formulation is described in "(Mitchell2011)" and the
+original EPS formulation is in "(Mitchell2011a)". Additional PDF docs
+that describe the VES and EPS implementations are include in the
+LAMMPS distro in <A HREF = "PDF/PDLammps_VES.pdf">doc/PDF/PDLammps_VES.pdf</A> and
+<A HREF = "PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</A>. For questions
+regarding the VES and EPS models in LAMMPS you can contact R. Rahman
+(rezwanur.rahman at utsa.edu).
</P>
<P>The following coefficients must be defined for each pair of atom types
via the <A HREF = "pair_coeff.html">pair_coeff</A> command as in the examples above,
or in the data file or restart files read by the
<A HREF = "read_data.html">read_data</A> or <A HREF = "read_restart.html">read_restart</A>
commands, or by mixing as described below.
</P>
<P>For the <I>peri/pmb</I> style:
</P>
<UL><LI>c (energy/distance/volume^2 units)
<LI>horizon (distance units)
<LI>s00 (unitless)
<LI>alpha (unitless)
</UL>
<P>C is the effectively a spring constant for Peridynamic bonds, the
horizon is a cutoff distance for truncating interactions, and s00 and
alpha are used as a bond breaking criteria. The units of c are such
that c/distance = stiffness/volume^2, where stiffness is
energy/distance^2 and volume is distance^3. See the users guide for
more details.
</P>
<P>For the <I>peri/lps</I> style:
</P>
<UL><LI>K (force/area units)
<LI>G (force/area units)
<LI>horizon (distance units)
<LI>s00 (unitless)
<LI>alpha (unitless)
</UL>
<P>K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and alpha are
used as a bond breaking criteria. See the users guide for more
details.
</P>
<P>For the <I>peri/ves</I> style:
</P>
<UL><LI>K (force/area units)
<LI>G (force/area units)
<LI>horizon (distance units)
<LI>s00 (unitless)
<LI>alpha (unitless)
<LI>m_lambdai (unitless)
<LI>m_taubi (unitless)
</UL>
-<P>The same as for <I>peri/lps</I>, K is the bulk modulus and G is the shear
-modulus. The horizon is a cutoff distance for truncating interactions,
-and s00 and alpha are used as a bond breaking criteria. m_lambdai and
-m_taubi are the viscoelastic relaxation parameter and time constant,
+<P>K is the bulk modulus and G is the shear modulus. The horizon is a
+cutoff distance for truncating interactions, and s00 and alpha are
+used as a bond breaking criteria. m_lambdai and m_taubi are the
+viscoelastic relaxation parameter and time constant,
respectively. m_lambdai varies within zero to one. For very small
values of m_lambdai the viscoelsatic model responds very similar to a
-linear elastic model. For details see the description in
-<A HREF = "#Mitchell">(Mitchell)</A>.
+linear elastic model. For details please see the description in
+"(Mtchell2011)".
+</P>
+<P>For the <I>peri/eps</I> style:
+</P>
+<P>K (force/area units)
+G (force/area units)
+horizon (distance units)
+s00 (unitless)
+alpha (unitless)
+m_yield_stress (force/area units)
+</P>
+<P>K is the bulk modulus and G is the shear modulus. The horizon is a
+cutoff distance and s00 and alpha are used as a bond breaking
+criteria. m_yield_stress is the yield stress of the material. For
+details please see the description in "(Mtchell2011a)".
</P>
<HR>
<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>omp</I>, or <I>opt</I> suffix are functionally
the same as the corresponding style without the suffix. They have
been optimized to run faster, depending on your available hardware, as
discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A> of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
</P>
<P>These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A>
section for more info.
</P>
<P>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
switch</A> when you invoke LAMMPS, or you can
use the <A HREF = "suffix.html">suffix</A> command in your input script.
</P>
<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
more instructions on how to use the accelerated styles effectively.
</P>
<HR>
<P><B>Mixing, shift, table, tail correction, restart, rRESPA info</B>:
</P>
<P>These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
</P>
<P>These pair styles do not support the <A HREF = "pair_modify.html">pair_modify</A>
shift option.
</P>
<P>The <A HREF = "pair_modify.html">pair_modify</A> table and tail options are not
relevant for these pair styles.
</P>
<P>These pair styles write their information to <A HREF = "restart.html">binary restart
files</A>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
</P>
<P>These pair styles can only be used via the <I>pair</I> keyword of the
<A HREF = "run_style.html">run_style respa</A> command. They do not support the
<I>inner</I>, <I>middle</I>, <I>outer</I> keywords.
</P>
<HR>
<P><B>Restrictions:</B>
</P>
-<P>The <I>peri/pmb</I>, <I>peri/lps</I> and <I>peri/ves</I> styles are part of the PERI
-package. They are only enabled if LAMMPS was built with that package.
-See the <A HREF = "Section_start.html#start_3">Making LAMMPS</A> section for more
-info.
+<P>All of these styles are part of the PERI package. They are only
+enabled if LAMMPS was built with that package. See the <A HREF = "Section_start.html#start_3">Making
+LAMMPS</A> section for more info.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "pair_coeff.html">pair_coeff</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Parks"></A>
<P><B>(Parks)</B> Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11),
777-783 (2008).
</P>
<A NAME = "Silling2000"></A>
<P><B>(Silling 2000)</B> Silling, J Mech Phys Solids, 48, 175-209 (2000).
</P>
<A NAME = "Silling2007"></A>
<P><B>(Silling 2007)</B> Silling, Epton, Weckner, Xu, Askari, J Elasticity,
88, 151-184 (2007).
</P>
-<A NAME = "Mitchell"></A>
+<A NAME = "Mitchell2011"></A>
-<P><B>(Mitchell)</B> Mitchell, "A non-local, ordinary-state-based
-viscoelasticity model for peridynamics", Sandia National Lab Report,
+<P><B>(Mitchell2011)</B> Mitchell. A non-local, ordinary-state-based
+viscoelasticity model for peridynamics. Sandia National Lab Report,
8064:1-28 (2011).
</P>
+<A NAME = "Mitchell2011a"></A>
+
+<P><B>(Mitchell2011a)</B> Mitchell. A Nonlocal, Ordinary, State-Based
+Plasticity Model for Peridynamics. Sandia National Lab Report,
+3166:1-34 (2011).
+</P>
</HTML>
diff --git a/doc/pair_peri.txt b/doc/pair_peri.txt
index bcb4e3e63..376c8a808 100644
--- a/doc/pair_peri.txt
+++ b/doc/pair_peri.txt
@@ -1,185 +1,213 @@
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
pair_style peri/pmb command :h3
pair_style peri/pmb/omp command :h3
pair_style peri/lps command :h3
pair_style peri/lps/omp command :h3
pair_style peri/ves command :h3
+pair_style peri/eps command :h3
[Syntax:]
pair_style style :pre
-style = {peri/pmb} or {peri/lps} or {peri/ves} :ul
+style = {peri/pmb} or {peri/lps} or {peri/ves} or {peri/eps}:ul
[Examples:]
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25 :pre
pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 :pre
pair_style peri/ves
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001 :pre
+pair_style peri/eps
+pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43 :pre
+
[Description:]
The peridynamic pair styles implement material models that can be used
at the mescscopic and macroscopic scales.
Style {peri/pmb} implements the Peridynamic bond-based prototype
microelastic brittle (PMB) model.
Style {peri/lps} implements the Peridynamic state-based linear
peridynamic solid (LPS) model.
Style {peri/ves} implements the Peridynamic state-based linear
peridynamic viscoelastic solid (VES) model.
+Style {peri/eps} implements the Peridynamic state-based elastic-plastic
+solid (EPS) model.
+
The canonical papers on Peridynamics are "(Silling 2000)"_#Silling2000
and "(Silling 2007)"_#Silling2007. The implementation of Peridynamics
in LAMMPS is described in "(Parks)"_#Parks. Also see the "PDLAMMPS
user guide"_http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf for
-more details about the implementation of peridynamics in LAMMPS.
-
-The peridynamic VES model in PDLAMMPS is implemented by R. Rahman and
-J.T Foster at University of Texas at San Antonio. The VES formulation
-is described in "(Mitchell)"_#Mitchell. An additional PDF doc with
-details is in "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf. For
-questions regarding VES implementation in LAMMPS please contact Rezwan
-Rahman: rezwanur.rahman at utsa.edu.
+more details about its implementation.
+
+The peridynamic VES and EPS models in PDLAMMPS were implemented by
+R. Rahman and J. T. Foster at University of Texas at San Antonio. The
+original VES formulation is described in "(Mitchell2011)" and the
+original EPS formulation is in "(Mitchell2011a)". Additional PDF docs
+that describe the VES and EPS implementations are include in the
+LAMMPS distro in "doc/PDF/PDLammps_VES.pdf"_PDF/PDLammps_VES.pdf and
+"doc/PDF/PDLammps_EPS.pdf"_PDF/PDLammps_EPS.pdf. For questions
+regarding the VES and EPS models in LAMMPS you can contact R. Rahman
+(rezwanur.rahman at utsa.edu).
The following coefficients must be defined for each pair of atom types
via the "pair_coeff"_pair_coeff.html command as in the examples above,
or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands, or by mixing as described below.
For the {peri/pmb} style:
c (energy/distance/volume^2 units)
horizon (distance units)
s00 (unitless)
alpha (unitless) :ul
C is the effectively a spring constant for Peridynamic bonds, the
horizon is a cutoff distance for truncating interactions, and s00 and
alpha are used as a bond breaking criteria. The units of c are such
that c/distance = stiffness/volume^2, where stiffness is
energy/distance^2 and volume is distance^3. See the users guide for
more details.
For the {peri/lps} style:
K (force/area units)
G (force/area units)
horizon (distance units)
s00 (unitless)
alpha (unitless) :ul
K is the bulk modulus and G is the shear modulus. The horizon is a
cutoff distance for truncating interactions, and s00 and alpha are
used as a bond breaking criteria. See the users guide for more
details.
For the {peri/ves} style:
K (force/area units)
G (force/area units)
horizon (distance units)
s00 (unitless)
alpha (unitless)
m_lambdai (unitless)
m_taubi (unitless) :ul
-The same as for {peri/lps}, K is the bulk modulus and G is the shear
-modulus. The horizon is a cutoff distance for truncating interactions,
-and s00 and alpha are used as a bond breaking criteria. m_lambdai and
-m_taubi are the viscoelastic relaxation parameter and time constant,
+K is the bulk modulus and G is the shear modulus. The horizon is a
+cutoff distance for truncating interactions, and s00 and alpha are
+used as a bond breaking criteria. m_lambdai and m_taubi are the
+viscoelastic relaxation parameter and time constant,
respectively. m_lambdai varies within zero to one. For very small
values of m_lambdai the viscoelsatic model responds very similar to a
-linear elastic model. For details see the description in
-"(Mitchell)"_#Mitchell.
+linear elastic model. For details please see the description in
+"(Mtchell2011)".
+
+For the {peri/eps} style:
+
+K (force/area units)
+G (force/area units)
+horizon (distance units)
+s00 (unitless)
+alpha (unitless)
+m_yield_stress (force/area units)
+
+K is the bulk modulus and G is the shear modulus. The horizon is a
+cutoff distance and s00 and alpha are used as a bond breaking
+criteria. m_yield_stress is the yield stress of the material. For
+details please see the description in "(Mtchell2011a)".
:line
Styles with a {cuda}, {gpu}, {omp}, or {opt} suffix are functionally
the same as the corresponding style without the suffix. They have
been optimized to run faster, depending on your available hardware, as
discussed in "Section_accelerate"_Section_accelerate.html of the
manual. The accelerated styles take the same arguments and should
produce the same results, except for round-off and precision issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-OMP and OPT
packages, respectively. They are only enabled if LAMMPS was built with
those packages. See the "Making LAMMPS"_Section_start.html#start_3
section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
These pair styles do not support mixing. Thus, coefficients for all
I,J pairs must be specified explicitly.
These pair styles do not support the "pair_modify"_pair_modify.html
shift option.
The "pair_modify"_pair_modify.html table and tail options are not
relevant for these pair styles.
These pair styles write their information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
These pair styles can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. They do not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
-The {peri/pmb}, {peri/lps} and {peri/ves} styles are part of the PERI
-package. They are only enabled if LAMMPS was built with that package.
-See the "Making LAMMPS"_Section_start.html#start_3 section for more
-info.
+All of these styles are part of the PERI package. They are only
+enabled if LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Parks)
[(Parks)] Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11),
777-783 (2008).
:link(Silling2000)
[(Silling 2000)] Silling, J Mech Phys Solids, 48, 175-209 (2000).
:link(Silling2007)
[(Silling 2007)] Silling, Epton, Weckner, Xu, Askari, J Elasticity,
88, 151-184 (2007).
-:link(Mitchell)
-[(Mitchell)] Mitchell, "A non-local, ordinary-state-based
-viscoelasticity model for peridynamics", Sandia National Lab Report,
+:link(Mitchell2011)
+[(Mitchell2011)] Mitchell. A non-local, ordinary-state-based
+viscoelasticity model for peridynamics. Sandia National Lab Report,
8064:1-28 (2011).
+
+:link(Mitchell2011a)
+[(Mitchell2011a)] Mitchell. A Nonlocal, Ordinary, State-Based
+Plasticity Model for Peridynamics. Sandia National Lab Report,
+3166:1-34 (2011).
diff --git a/examples/KAPPA/in.heat b/examples/KAPPA/in.heat
index a49ee97d8..b9eb6d66a 100644
--- a/examples/KAPPA/in.heat
+++ b/examples/KAPPA/in.heat
@@ -1,76 +1,76 @@
# sample LAMMPS input script for thermal conductivity of liquid LJ
# use fix heat to add/subtract energy from 2 regions
# settings
variable x equal 10
variable y equal 10
variable z equal 20
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create $t 87287
pair_style lj/cut ${rc}
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# heat layers
region hot block INF INF INF INF 0 1
region cold block INF INF INF INF 10 11
compute Thot all temp/region hot
compute Tcold all temp/region cold
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
thermo 100
run 1000
velocity all scale $t
unfix 1
# 2nd equilibration run
fix 1 all nve
fix hot all heat 1 100.0 region hot
fix cold all heat 1 -100.0 region cold
thermo_style custom step temp c_Thot c_Tcold
thermo 1000
run 10000
# thermal conductivity calculation
compute ke all ke/atom
variable temp atom c_ke/1.5
fix 2 all ave/spatial 10 100 1000 z lower 0.05 v_temp &
- file heat.temp.profile units reduced
+ file profile.heat units reduced
variable tdiff equal f_2[11][3]-f_2[1][3]
fix ave all ave/time 1 1 1000 v_tdiff ave running start 13000
thermo_style custom step temp c_Thot c_Tcold v_tdiff f_ave
run 20000
diff --git a/examples/KAPPA/in.heatflux b/examples/KAPPA/in.heatflux
index c56b20971..04be77e90 100644
--- a/examples/KAPPA/in.heatflux
+++ b/examples/KAPPA/in.heatflux
@@ -1,79 +1,79 @@
# sample LAMMPS input script for thermal conductivity of liquid LJ
# Green-Kubo method via compute heat/flux and fix ave/correlate
# settings
variable x equal 10
variable y equal 10
variable z equal 10
variable rho equal 0.6
variable t equal 1.35
variable rc equal 2.5
#variable rho equal 0.85
#variable t equal 0.7
#variable rc equal 3.0
variable p equal 200 # correlation length
variable s equal 10 # sample interval
variable d equal $p*$s # dump interval
# setup problem
units lj
atom_style atomic
lattice fcc ${rho}
region box block 0 $x 0 $y 0 $z
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create $t 87287
pair_style lj/cut ${rc}
pair_coeff 1 1 1.0 1.0
neighbor 0.3 bin
neigh_modify delay 0 every 1
# 1st equilibration run
fix 1 all nvt temp $t $t 0.5
thermo 100
run 1000
velocity all scale $t
unfix 1
# thermal conductivity calculation
reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom virial
compute flux all heat/flux myKE myPE myStress
variable Jx equal c_flux[1]/vol
variable Jy equal c_flux[2]/vol
variable Jz equal c_flux[3]/vol
fix 1 all nve
fix JJ all ave/correlate $s $p $d &
c_flux[1] c_flux[2] c_flux[3] type auto &
- file heatflux.flux.profile ave running
+ file profile.heatflux ave running
variable scale equal $s*dt/$t/$t/vol
variable k11 equal trap(f_JJ[3])*${scale}
variable k22 equal trap(f_JJ[4])*${scale}
variable k33 equal trap(f_JJ[5])*${scale}
thermo $d
thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 100000
variable kappa equal (v_k11+v_k22+v_k33)/3.0
print "running average conductivity: ${kappa}"
diff --git a/examples/comb/data.comb3-OHCCu b/examples/comb/data.comb3-OHCCu
index a68523ab8..0625504eb 100644
--- a/examples/comb/data.comb3-OHCCu
+++ b/examples/comb/data.comb3-OHCCu
@@ -1,695 +1,695 @@
data.test Cu2O(110)-graphene-OH
- 682 atoms
+ 682 atoms
+
+ 5 atom types
- 5 atom types
+ 0.0000 21.3000 xlo xhi
+ 0.0000 24.6000 ylo yhi
+ 0.0000 33.8162 zlo zhi
+ 0.000 0.000 0.000 xy xz yz
- 0.00000 21.30000 xlo xhi
- 0.00000 24.60000 ylo yhi
- 0.00000 23.81620 zlo zhi
- 0.0 0.0 0.0 xy xz yz
-
-Atoms
+ Atoms
# ATOMS id type q x y z
-1 1 -0.769123 8.45621 6.03653 0.0976449
-2 2 0.611017 16.0099 4.52565 0.00102433
-3 2 0.619339 20.2793 7.55712 -0.00150832
-4 1 -0.750617 14.9921 21.071 0.102896
-5 1 -0.767855 6.49163 15.1069 0.0996268
-6 2 0.425598 3.21239 22.7278 0.0216791
-7 1 -0.74251 8.44553 24.5439 0.120487
-8 1 -0.769079 12.7191 6.04409 0.102374
-9 2 0.602011 20.2689 1.48815 23.8126
-10 2 0.610438 16.0154 13.5861 23.8052
-11 2 0.609789 11.7393 1.47972 23.8122
-12 1 -0.773858 19.3269 9.0626 0.115159
-13 1 -0.767911 10.7743 3.01107 0.100231
-14 2 0.60782 7.46709 16.6067 0.00191274
-15 2 0.599991 16.0148 16.5982 -0.000617927
-16 1 -0.741057 4.16603 24.5399 0.120671
-17 1 -0.749485 10.7367 21.0821 0.108909
-18 2 0.630171 7.46807 19.6336 23.8108
-19 2 0.604265 3.19691 7.5427 23.8123
-20 2 0.614008 20.2686 13.5905 23.8051
-21 1 -0.773574 21.2208 18.1228 0.0933083
-22 1 -0.746241 21.2191 24.5281 0.135302
-23 1 -0.770824 2.22607 3.02101 0.110896
-24 1 -0.742779 12.7048 24.5411 0.121782
-25 2 0.606562 11.746 13.586 23.8111
-26 1 -0.772917 2.23551 9.06357 0.0991271
-27 2 0.60514 16.003 7.5488 -0.000709082
-28 1 -0.770797 15.04 9.06486 0.0970965
-29 2 0.608332 7.47542 1.48076 23.8151
-30 1 -0.750366 6.45593 21.0891 0.10325
-31 2 0.597975 3.20052 1.48752 23.8091
-32 1 -0.769956 16.9812 6.04631 0.106327
-33 2 0.599247 11.7399 4.52913 23.813
-34 1 -0.769026 8.44345 12.068 0.110137
-35 1 -0.77142 6.51071 9.05369 0.111236
-36 2 0.611023 16.0078 10.5628 23.8094
-37 1 -0.769833 19.3252 3.02386 0.100801
-38 1 -0.752573 2.19769 21.0893 0.104233
-39 2 0.596674 16.0145 1.48403 0.00279292
-40 2 0.431298 20.2859 22.7179 0.027154
-41 1 -0.768336 4.17198 12.0737 0.09626
-42 1 -0.768624 6.51542 3.01655 0.111473
-43 1 -0.771194 2.22841 15.1051 0.107803
-44 1 -0.768992 4.18582 6.04703 0.0981162
-45 1 -0.755961 19.275 21.0852 0.115119
-46 1 -0.768902 15.0536 3.02401 0.116547
-47 1 -0.770016 10.7707 15.0886 0.109583
-48 2 0.602412 11.7399 7.54914 23.8106
-49 1 -0.771575 12.7113 18.1098 0.102352
-50 1 -0.772837 4.17761 18.1206 0.105278
-51 1 -0.771647 12.7202 12.0767 0.107035
-52 1 -0.774079 21.227 12.0792 0.0961184
-53 2 0.616026 20.2771 10.5646 23.8083
-54 2 0.635783 16.0106 19.6226 23.8113
-55 2 0.591918 7.4699 13.5804 23.8101
-56 1 -0.768332 15.0491 15.0869 0.0992011
-57 1 -0.769472 10.7698 9.06316 0.111058
-58 2 0.630818 11.741 19.622 23.8098
-59 1 -0.772744 16.9824 12.071 0.099304
-60 2 0.422461 11.7518 22.7194 0.0336345
-61 1 -0.774292 21.221 6.04671 0.111422
-62 2 0.610942 7.46914 10.5662 0.00213254
-63 1 -0.772443 19.3161 15.0946 0.112636
-64 2 0.595019 3.19973 4.52509 23.8105
-65 2 0.417347 7.47984 22.7208 0.0261967
-66 2 0.628852 3.19706 19.6296 23.8118
-67 2 0.605685 11.7369 10.5613 23.8138
-68 2 0.605657 7.47749 7.53982 23.8142
-69 1 -0.771922 16.9855 18.1212 0.0934479
-70 2 0.605268 3.20555 16.6066 -0.000489731
-71 2 0.612882 3.20113 10.5717 23.8044
-72 2 0.605992 11.7441 16.5965 -0.000134756
-73 2 0.640047 20.2664 19.6262 23.8037
-74 2 0.61649 20.2792 4.52506 23.8065
-75 2 0.59832 3.19447 13.5853 23.8098
-76 2 0.608836 20.2744 16.6038 23.8116
-77 1 -0.742759 16.9865 24.5358 0.141347
-78 1 -0.771642 8.43934 18.1231 0.0993605
-79 2 0.408897 16.0222 22.7169 0.0228131
-80 2 0.607338 7.47533 4.53008 0.0010266
-81 2 0.445033 9.60489 15.0882 1.5004
-82 2 0.450494 5.32974 6.03044 1.49367
-83 2 0.446689 9.59994 12.0762 1.49226
-84 2 0.451533 5.33644 9.05044 1.4892
-85 2 0.538987 18.1497 21.1497 1.49399
-86 2 0.445799 1.06161 6.03183 1.50122
-87 2 0.441169 9.60198 6.03019 1.49685
-88 2 0.446451 9.61665 3.01821 1.49676
-89 2 0.448388 1.06215 12.0711 1.49301
-90 2 0.524331 5.3363 24.5194 1.49282
-91 2 0.454038 1.07682 15.0902 1.49207
-92 2 0.53754 1.07857 24.5377 1.49764
-93 2 0.426862 18.1444 18.1067 1.49225
-94 2 0.433886 13.87 18.1101 1.49688
-95 2 0.433411 13.8745 15.0882 1.4917
-96 2 0.533502 9.59475 24.5206 1.49348
-97 2 0.442192 5.32973 18.1199 1.49886
-98 2 0.450504 13.8766 12.0728 1.4968
-99 2 0.446306 18.1454 9.06093 1.496
-100 2 0.452786 13.8781 3.01581 1.49351
-101 2 0.446197 1.0738 9.05905 1.4943
-102 2 0.442572 18.1364 12.0681 1.49593
-103 2 0.440415 18.1373 6.04176 1.49628
-104 2 0.530672 13.8759 21.159 1.49374
-105 2 0.448135 5.34441 15.0965 1.49675
-106 2 0.531078 5.3391 21.1557 1.49074
-107 2 0.426494 1.05977 18.1113 1.49715
-108 2 0.433992 5.33387 12.0705 1.48926
-109 2 0.528513 13.8743 24.5199 1.49419
-110 2 0.449555 9.61669 9.0527 1.50039
-111 2 0.546167 18.1417 24.5212 1.50108
-112 2 0.440717 18.15 3.00771 1.49794
-113 2 0.450668 13.8678 6.04047 1.49008
-114 2 0.4416 5.34251 3.01186 1.49826
-115 2 0.529086 1.07696 21.1485 1.49596
-116 2 0.446775 18.1476 15.0918 1.49548
-117 2 0.520477 9.61297 21.1485 1.50117
-118 2 0.427761 9.59974 18.1088 1.50119
-119 2 0.447199 13.878 9.05435 1.49002
-120 2 0.462953 1.07333 3.01797 1.49406
-121 2 0.393455 11.7445 16.5993 3.01494
-122 1 -0.76307 8.54662 15.0859 3.02014
-123 2 0.410757 11.7413 13.5863 3.01152
-124 2 0.395665 3.20619 10.5609 3.01493
-125 2 0.184843 15.9961 22.7517 3.01615
-126 1 -0.756123 12.8573 21.0654 3.0043
-127 1 -0.752336 17.1447 21.0829 3.00274
-128 1 -0.763198 10.6714 6.04963 3.01864
-129 2 0.409249 11.7447 7.5474 3.01475
-130 1 -0.764709 14.9516 18.1092 3.01638
-131 1 -0.763517 10.6734 12.0901 3.0146
-132 1 -0.762859 14.9416 6.04483 3.00595
-133 2 0.408252 7.46333 10.5597 3.0101
-134 2 0.388122 11.7347 10.5703 3.01396
-135 1 -0.76412 19.2078 12.072 3.01077
-136 1 -0.765408 0.0291499 3.0274 3.00097
-137 1 -0.745864 10.6631 24.525 3.01854
-138 2 0.403102 3.19564 16.5986 3.01103
-139 1 -0.762589 4.27923 9.05691 3.00408
-140 2 0.190345 20.2433 22.7445 3.01101
-141 2 0.382794 7.46608 1.48789 3.00669
-142 2 0.396065 20.2803 7.54655 3.01894
-143 2 0.414195 7.47615 4.53308 3.01252
-144 2 0.393869 20.2696 13.5854 3.01666
-145 2 0.405708 20.2722 10.569 3.01776
-146 1 -0.763729 8.54007 9.06175 3.00958
-147 2 0.378315 11.7395 1.49104 3.01423
-148 1 -0.763254 17.0851 15.0961 3.01252
-149 2 0.386604 11.744 4.53136 3.01737
-150 1 -0.762945 12.8181 9.05354 3.00523
-151 1 -0.76081 17.0932 3.01865 3.01422
-152 2 0.375949 20.2801 1.47724 3.01367
-153 2 0.419965 20.2725 4.53619 3.01004
-154 2 0.410429 16.0147 16.6022 3.01722
-155 1 -0.746876 19.2121 24.5284 3.00927
-156 2 0.432469 20.2677 19.6175 3.01844
-157 2 0.410301 16.01 19.6306 3.00949
-158 1 -0.745363 2.13416 24.5266 3.01663
-159 1 -0.764752 6.39701 18.1176 3.01917
-160 1 -0.75434 4.33625 21.0733 3.01383
-161 2 0.428127 7.46574 19.6221 3.01567
-162 2 0.393171 16.0039 13.5842 3.0162
-163 1 -0.764305 0.0249641 15.1047 3.00892
-164 2 0.411061 3.1974 4.53156 3.01506
-165 1 -0.765743 2.14046 18.1158 3.01947
-166 1 -0.755391 0.068377 21.0715 3.00517
-167 2 0.182853 7.45015 22.7498 3.01874
-168 1 -0.764846 14.934 12.0733 3.01598
-169 2 0.419096 3.20312 19.6338 3.00953
-170 2 0.400623 16.0091 7.54702 3.01602
-171 1 -0.767041 19.214 18.1181 3.02033
-172 1 -0.762737 12.8123 15.0922 3.01778
-173 2 0.180434 3.18671 22.751 3.01136
-174 1 -0.744373 14.9418 24.5329 3.01449
-175 1 -0.763558 19.2237 6.0329 3.01309
-176 1 -0.763029 4.28013 15.1007 3.01903
-177 1 -0.762171 17.0827 9.0675 3.00477
-178 2 0.402208 7.4699 13.5805 3.01706
-179 1 -0.764605 2.12552 12.0758 3.01109
-180 2 0.38784 7.46578 16.5973 3.02007
-181 1 -0.760318 12.8184 3.01127 3.0104
-182 2 0.380718 16.0074 1.49067 3.01161
-183 2 0.394514 16.0076 4.5271 3.01998
-184 1 -0.743339 6.41246 24.5298 3.01425
-185 1 -0.761972 4.27285 3.02774 3.01865
-186 1 -0.764102 2.13402 6.03355 3.01244
-187 1 -0.764191 6.40471 12.0714 3.01895
-188 1 -0.7645 0.0367277 9.06542 3.01241
-189 1 -0.766583 10.6805 18.1257 3.02106
-190 1 -0.754367 8.59106 21.0627 3.02096
-191 2 0.436434 11.739 19.6281 3.01145
-192 2 0.18079 11.7238 22.7616 3.01895
-193 2 0.372167 3.19506 1.4852 3.01265
-194 1 -0.764592 6.4082 6.0365 3.00106
-195 2 0.409464 20.2786 16.608 3.01548
-196 2 0.406537 16.0096 10.5686 3.01361
-197 2 0.3943 3.20748 7.54208 3.00935
-198 2 0.399561 7.46896 7.55134 3.00759
-199 1 -0.762413 8.53658 3.02899 3.00525
-200 2 0.390999 3.20744 13.5842 3.00843
-201 2 0.407709 5.33142 9.06105 4.52771
-202 2 0.413819 9.61122 15.0893 4.52601
-203 2 0.392561 5.33443 6.03816 4.522
-204 2 0.416517 1.06403 9.05559 4.52415
-205 2 0.401678 9.61054 12.0796 4.5323
-206 2 0.393569 18.1383 18.1121 4.53374
-207 2 0.398342 9.6083 9.06107 4.52107
-208 2 0.400612 18.1499 15.0878 4.53165
-209 2 0.410872 9.60625 6.04097 4.5258
-210 2 0.403092 1.06395 15.0975 4.53027
-211 2 0.405357 18.1502 12.0759 4.52986
-212 2 0.383437 18.1518 9.06208 4.53137
-213 2 0.409418 5.34231 3.00808 4.52185
-214 2 0.394883 1.06676 3.01487 4.52945
-215 2 0.476769 18.1403 21.1576 4.53289
-216 2 0.395639 13.8767 18.1169 4.52712
-217 2 0.409904 1.06699 12.0742 4.52843
-218 2 0.39109 9.60224 3.01919 4.53098
-219 2 0.479703 5.33171 24.5118 4.52475
-220 2 0.40855 18.1485 3.0102 4.53168
-221 2 0.495644 9.5982 24.5121 4.52184
-222 2 0.48207 18.1478 24.5211 4.52759
-223 2 0.48905 13.8695 21.1491 4.52159
-224 2 0.495005 5.34236 21.1609 4.53347
-225 2 0.410066 13.8755 15.0921 4.52534
-226 2 0.396366 5.33434 18.1127 4.53248
-227 2 0.414849 13.87 12.0809 4.52912
-228 2 0.395921 18.1386 6.03934 4.52273
-229 2 0.398581 13.8733 6.03048 4.52864
-230 2 0.484778 1.06851 21.1515 4.52792
-231 2 0.399341 1.0699 6.04057 4.52229
-232 2 0.413648 5.33112 15.0931 4.52888
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+ 681 1 -0.241615000E+00 0.103127000E+02 0.105349000E+02 0.192692400E+02
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diff --git a/examples/comb/in.comb3 b/examples/comb/in.comb3
index 601fe9263..a75b7d983 100644
--- a/examples/comb/in.comb3
+++ b/examples/comb/in.comb3
@@ -1,34 +1,34 @@
# Graphene-OH on Cu2O (110) surface
units metal
atom_style charge
dimension 3
boundary p p p
read_data data.comb3-OHCCu
mass 1 16.0
mass 2 63.5
mass 3 1.00
mass 4 12.0
mass 5 12.0
pair_style comb3 polar_off
pair_coeff * * ffield.comb3 O Cu H C C
neighbor 2.0 bin
neigh_modify every 1 delay 0 check yes
#dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
#dump_modify 1 element O Cu H C C
fix 1 all nve
-fix 2 all qeq/comb 10 1e-3 file fq.out
+fix 2 all qeq/comb 10 31e-3 file fq.out
timestep 0.00020
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
thermo_modify norm yes
velocity all create 300.0 2398378
thermo 10
run 100
diff --git a/potentials/ffield.comb3 b/potentials/ffield.comb3
index cb0d83e6f..4a98f78c6 100644
--- a/potentials/ffield.comb3
+++ b/potentials/ffield.comb3
@@ -1,349 +1,522 @@
- # ffield.comb3 file for LAMMPS/COMB3, converted from COMB3 code parameters O Cu N C H Ti Zn
- # Converted on: 20131005 000249
+ # ffield.comb3 file for LAMMPS/COMB3, converted from COMB3 code parameters O Cu N C H Ti Zn Zr
+ # Converted on: 2014-01-30
#
# Please cite the following publication for the use of LAMMPS-COMB3.
- # Tao Liang, Tzu-Ray Shan, Yu-Ting Cheng, Bryce D. Devine, Mark Noordhoek, Yangzhong Li, Zhize Lu, Simon R. Phillpot,and Susan B. Sinnott, "Classical atomistic simulations of surfaces and heterogeneous interfaces with the charge-optimized many body (COMB) potentials", Materials Science and Engineering: Reports, in press.
+ # Tao Liang, Tzu-Ray Shan, Yu-Ting Cheng, Bryce D. Devine, Mark Noordhoek, Yangzhong Li, Zhize Lu, Simon R. Phillpot,and Susan B. Sinnott, "Classical atomistic simulations of surfaces and heterogeneous interfaces with the charge-optimized many body (COMB) potentials", Materials Science and Engineering: Reports, 74 (2013) 255-279.
+ # List of Changes since 2013-Sep:
+ # 1) CH4 has been changed.
+ # 2) Include ZrO2 force fields
+ # 3) Change correction terms from Legendre polynomials and bond bending to 6th order polynomials.
#
-O O O 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O O Cu 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O O N 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O O C 3 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O O H 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O O Ti 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O O Zn 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1966411E+01 0.2521788E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3258854E+01 0.6881635E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5295119E+01 0.4956339E+04 0.3258854E+01 0.2600000E+01 0.2000000E+00 0.1417783E+02 0.1600164E+02 0.1257097E+01 -0.5652039E+01 -0.2046884E+00 0.1826597E+01 0.8565567E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Cu O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Cu Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Cu N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Cu C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Cu H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Cu Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Cu Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2435700E+00 0.8576372E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2253174E+01 0.2450000E+01 0.1500000E+00 0.2251128E-02 0.1783032E-02 0.1816425E-01 0.3013329E-02 0.2789347E-02 0.4218284E-02 0.7035424E-03 0.3486652E-01 -0.1232266E-01 0.1965112E-01 -0.2119645E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O N O 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1608740E-02 0.1000000E-02 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.2889513E+01 0.2250000E+01 0.1500000E+00 0.9974699E+01 0.2683124E+02 0.5129581E+01 -0.1687901E+02 0.1929454E+01 0.2064311E+00 0.2644439E+00 -0.2525391E-03 -0.3838929E-03 -0.8530755E-04 -0.2072918E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O N Cu 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1608740E-02 0.1000000E-02 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.2889513E+01 0.2250000E+01 0.1500000E+00 0.9974699E+01 0.2683124E+02 0.5129581E+01 -0.1687901E+02 0.1929454E+01 0.2064311E+00 0.2644439E+00 -0.2525391E-03 -0.3838929E-03 -0.8530755E-04 -0.2072918E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O N N 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1608740E-02 0.1000000E-02 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.2889513E+01 0.2250000E+01 0.1500000E+00 0.9974699E+01 0.2683124E+02 0.5129581E+01 -0.1687901E+02 0.1929454E+01 0.2064311E+00 0.2644439E+00 -0.2525391E-03 -0.3838929E-03 -0.8530755E-04 -0.2072918E-03 -0.2838913E-03 -0.3149859E-03 -0.2142877E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6194749E-03 0.5350017E-04 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O N C 3 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1608740E-02 0.1000000E-02 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.2889513E+01 0.2250000E+01 0.1500000E+00 0.9974699E+01 0.2683124E+02 0.5129581E+01 -0.1687901E+02 0.1929454E+01 0.2064311E+00 0.2644439E+00 -0.2525391E-03 -0.3838929E-03 -0.8530755E-04 -0.2072918E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O N H 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1608740E-02 0.1000000E-02 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.2889513E+01 0.2250000E+01 0.1500000E+00 0.9974699E+01 0.2683124E+02 0.5129581E+01 -0.1687901E+02 0.1929454E+01 0.2064311E+00 0.2644439E+00 -0.2525391E-03 -0.3838929E-03 -0.8530755E-04 -0.2072918E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O N Ti 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.1608740E-02 0.1000000E-02 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.2889513E+01 0.2250000E+01 0.1500000E+00 0.9974699E+01 0.2683124E+02 0.5129581E+01 -0.1687901E+02 0.1929454E+01 0.2064311E+00 0.2644439E+00 -0.2525391E-03 -0.3838929E-03 -0.8530755E-04 -0.2072918E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
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-O C O 3 1 3 0 1 1 0 0 1 0.0000000E+00 0.3950000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.8969574E-01 0.1694354E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.4729859E-02 0.1750000E+01 0.1500000E+00 -0.9737722E-02 -0.1148593E-03 -0.2680837E-01 -0.1483529E+01 -0.9605482E-03 -0.7917773E+00 0.2353023E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O C Cu 3 1 2 0 1 1 0 0 1 0.0000000E+00 0.3950000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.8969574E-01 0.1694354E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.4729859E-02 0.1750000E+01 0.1500000E+00 -0.9737722E-02 -0.1148593E-03 -0.2680837E-01 -0.1483529E+01 -0.9605482E-03 -0.7917773E+00 0.2353023E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
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-O C Ti 3 1 2 0 1 1 0 0 1 0.0000000E+00 0.3950000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.8969574E-01 0.1694354E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.4729859E-02 0.1750000E+01 0.1500000E+00 -0.9737722E-02 -0.1148593E-03 -0.2680837E-01 -0.1483529E+01 -0.9605482E-03 -0.7917773E+00 0.2353023E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O C Zn 3 1 2 0 1 1 0 0 1 0.0000000E+00 0.3950000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.8969574E-01 0.1694354E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.4729859E-02 0.1750000E+01 0.1500000E+00 -0.9737722E-02 -0.1148593E-03 -0.2680837E-01 -0.1483529E+01 -0.9605482E-03 -0.7917773E+00 0.2353023E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O H O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2198296E+01 0.4749058E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 0.1491702E+01 0.4463727E+01 0.5355258E+01 0.2997975E+01 0.1203065E+01 0.2486002E+00 0.2085342E-01 -0.4874351E-01 0.6218981E-01 0.2217044E-01 0.6755488E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O H Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2198296E+01 0.4749058E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 0.1491702E+01 0.4463727E+01 0.5355258E+01 0.2997975E+01 0.1203065E+01 0.2486002E+00 0.2085342E-01 -0.4874351E-01 0.6218981E-01 0.2217044E-01 0.6755488E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O H N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2198296E+01 0.4749058E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 0.1491702E+01 0.4463727E+01 0.5355258E+01 0.2997975E+01 0.1203065E+01 0.2486002E+00 0.2085342E-01 -0.4874351E-01 0.6218981E-01 0.2217044E-01 0.6755488E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
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-O H Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2198296E+01 0.4749058E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 0.1491702E+01 0.4463727E+01 0.5355258E+01 0.2997975E+01 0.1203065E+01 0.2486002E+00 0.2085342E-01 -0.4874351E-01 0.6218981E-01 0.2217044E-01 0.6755488E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O H Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2198296E+01 0.4749058E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 0.1491702E+01 0.4463727E+01 0.5355258E+01 0.2997975E+01 0.1203065E+01 0.2486002E+00 0.2085342E-01 -0.4874351E-01 0.6218981E-01 0.2217044E-01 0.6755488E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Ti O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.3664105E+00 0.7617877E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2349167E+01 0.2316396E+03 0.1850898E+01 0.2234412E+03 0.1898804E+01 0.1584172E+03 0.2912146E+01 0.1665803E+04 0.2560299E+01 0.3000000E+01 0.2000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 -0.2605400E-02 0.4360350E-01 -0.5658400E-01 0.1121330E+00 -0.1678830E-01 -0.3942600E-02 0.7482930E-01 -0.1501655E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Ti Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.3664105E+00 0.7617877E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2349167E+01 0.2316396E+03 0.1850898E+01 0.2234412E+03 0.1898804E+01 0.1584172E+03 0.2912146E+01 0.1665803E+04 0.2560299E+01 0.3000000E+01 0.2000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 -0.2605400E-02 0.4360350E-01 -0.5658400E-01 0.1121330E+00 -0.1678830E-01 -0.3942600E-02 0.7482930E-01 -0.1501655E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Ti N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.3664105E+00 0.7617877E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2349167E+01 0.2316396E+03 0.1850898E+01 0.2234412E+03 0.1898804E+01 0.1584172E+03 0.2912146E+01 0.1665803E+04 0.2560299E+01 0.3000000E+01 0.2000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 -0.2605400E-02 0.4360350E-01 -0.5658400E-01 0.1121330E+00 -0.1678830E-01 -0.3942600E-02 0.7482930E-01 -0.1501655E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Ti C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.3664105E+00 0.7617877E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2349167E+01 0.2316396E+03 0.1850898E+01 0.2234412E+03 0.1898804E+01 0.1584172E+03 0.2912146E+01 0.1665803E+04 0.2560299E+01 0.3000000E+01 0.2000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 -0.2605400E-02 0.4360350E-01 -0.5658400E-01 0.1121330E+00 -0.1678830E-01 -0.3942600E-02 0.7482930E-01 -0.1501655E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Ti H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.3664105E+00 0.7617877E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2349167E+01 0.2316396E+03 0.1850898E+01 0.2234412E+03 0.1898804E+01 0.1584172E+03 0.2912146E+01 0.1665803E+04 0.2560299E+01 0.3000000E+01 0.2000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 -0.2605400E-02 0.4360350E-01 -0.5658400E-01 0.1121330E+00 -0.1678830E-01 -0.3942600E-02 0.7482930E-01 -0.1501655E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Ti Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.3664105E+00 0.7617877E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2349167E+01 0.2316396E+03 0.1850898E+01 0.2234412E+03 0.1898804E+01 0.1584172E+03 0.2912146E+01 0.1665803E+04 0.2560299E+01 0.3000000E+01 0.2000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 -0.2605400E-02 0.4360350E-01 -0.5658400E-01 0.1121330E+00 -0.1678830E-01 -0.3942600E-02 0.7482930E-01 -0.1501655E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Ti Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.3664105E+00 0.7617877E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2349167E+01 0.2316396E+03 0.1850898E+01 0.2234412E+03 0.1898804E+01 0.1584172E+03 0.2912146E+01 0.1665803E+04 0.2560299E+01 0.3000000E+01 0.2000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 -0.2605400E-02 0.4360350E-01 -0.5658400E-01 0.1121330E+00 -0.1678830E-01 -0.3942600E-02 0.7482930E-01 -0.1501655E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Zn O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2381800E+00 0.3970778E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1072713E+01 0.2800000E+01 0.2000001E+00 -0.3040657E-01 0.2652378E+00 -0.1582586E+00 -0.4621471E+00 0.9702852E+00 0.8742132E+00 0.5556172E+00 0.1379238E-01 0.1333006E+00 0.1067606E+00 0.1178399E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Zn Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2381800E+00 0.3970778E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1072713E+01 0.2800000E+01 0.2000001E+00 -0.3040657E-01 0.2652378E+00 -0.1582586E+00 -0.4621471E+00 0.9702852E+00 0.8742132E+00 0.5556172E+00 0.1379238E-01 0.1333006E+00 0.1067606E+00 0.1178399E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Zn N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2381800E+00 0.3970778E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1072713E+01 0.2800000E+01 0.2000001E+00 -0.3040657E-01 0.2652378E+00 -0.1582586E+00 -0.4621471E+00 0.9702852E+00 0.8742132E+00 0.5556172E+00 0.1379238E-01 0.1333006E+00 0.1067606E+00 0.1178399E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Zn C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2381800E+00 0.3970778E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1072713E+01 0.2800000E+01 0.2000001E+00 -0.3040657E-01 0.2652378E+00 -0.1582586E+00 -0.4621471E+00 0.9702852E+00 0.8742132E+00 0.5556172E+00 0.1379238E-01 0.1333006E+00 0.1067606E+00 0.1178399E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Zn H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2381800E+00 0.3970778E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1072713E+01 0.2800000E+01 0.2000001E+00 -0.3040657E-01 0.2652378E+00 -0.1582586E+00 -0.4621471E+00 0.9702852E+00 0.8742132E+00 0.5556172E+00 0.1379238E-01 0.1333006E+00 0.1067606E+00 0.1178399E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Zn Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2381800E+00 0.3970778E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1072713E+01 0.2800000E+01 0.2000001E+00 -0.3040657E-01 0.2652378E+00 -0.1582586E+00 -0.4621471E+00 0.9702852E+00 0.8742132E+00 0.5556172E+00 0.1379238E-01 0.1333006E+00 0.1067606E+00 0.1178399E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-O Zn Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.4956339E+04 0.6881635E+03 0.5295119E+01 0.3258854E+01 0.1000000E+01 -0.2000000E+01 0.6000000E+01 0.7664409E-02 -0.1213951E+01 -0.2000000E+01 0.6000000E+01 0.6599630E+01 0.5955097E+01 0.7604334E+00 0.9388015E-02 0.1371794E+01 0.2381800E+00 0.3970778E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3056900E+00 -0.1539170E+01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1072713E+01 0.2800000E+01 0.2000001E+00 -0.3040657E-01 0.2652378E+00 -0.1582586E+00 -0.4621471E+00 0.9702852E+00 0.8742132E+00 0.5556172E+00 0.1379238E-01 0.1333006E+00 0.1067606E+00 0.1178399E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu O O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu O Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu O N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu O C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 -0.8176172E+00 -0.6894538E+00 0.4146729E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu O H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu O Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu O Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 -0.2288704E+00 0.5307763E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2092751E+01 0.9347170E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2353223E+01 0.1336466E+04 0.2229919E+01 0.2450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 -0.1082528E-01 0.9698014E-02 -0.4508018E-01 0.2173814E-01 0.1557732E+00 -0.9365586E-02 0.1494216E+00 -0.9015916E-02 -0.9550571E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Cu O 2 2 3 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Cu Cu 2 2 2 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.7307800E-01 0.0000000E+00 0.1967800E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Cu N 2 2 3 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Cu C 2 2 1 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Cu H 2 2 2 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Cu Ti 2 2 2 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Cu Zn 2 2 2 0 0 0 0 4 1 0.1000000E-01 0.3450000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1467089E+01 0.1028261E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2712035E+01 0.7123527E+03 0.1467089E+01 0.3350000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu N O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu N Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu N N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu N C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu N H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu N Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu N Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu C O 2 1 3 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 -0.7593005E-02 -0.6757765E+00 -0.1392280E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu C Cu 2 1 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu C N 2 1 3 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu C C 2 1 1 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu C H 2 1 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu C Ti 2 1 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu C Zn 2 1 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3345035E-02 0.1000000E-01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.3178819E+00 0.2650000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.9062441E+00 -0.9880102E-03 0.5560993E-02 -0.8710045E-01 -0.7891008E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu H O 2 2 3 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8272982E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu H Cu 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8272982E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu H N 2 2 3 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8272982E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu H C 2 2 1 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8272982E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu H H 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8272982E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu H Ti 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8272982E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu H Zn 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3034638E+00 0.1016911E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.8272982E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Ti O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Ti Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Ti N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Ti C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Ti H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Ti Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Ti Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1322960E+01 0.1097041E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2424023E+01 0.6066238E+03 0.1322960E+01 0.3660422E+01 0.1277175E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2310550E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Zn O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Zn Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Zn N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Zn C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Zn H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Zn Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Cu Zn Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7123527E+03 0.1028261E+03 0.2712035E+01 0.1467089E+01 0.1000000E+01 -0.2000000E+01 0.2000000E+01 0.3490214E+00 -0.1339472E+00 -0.2000000E+01 0.2000000E+01 0.3652316E+01 0.3213926E+01 0.7478102E+00 0.1172919E+00 0.1397263E+01 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3051574E+00 0.4677531E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2474687E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N O O 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N O Cu 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N O N 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N O C 3 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N O H 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N O Ti 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N O Zn 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.2068698E+00 0.2696627E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4703396E+01 0.3251258E+03 0.4798425E+01 0.3778823E+03 0.2951760E+01 0.3111556E+03 0.6118996E+01 0.7859391E+04 0.4700678E+00 0.2250000E+01 0.1500000E+00 0.4957188E-03 -0.2765761E-03 0.1006819E+01 0.9564232E+00 0.2767543E+00 0.3123805E+00 0.2343152E+00 0.4471950E-04 0.6936042E-03 -0.1032065E-03 0.4032635E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Cu O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Cu Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Cu N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Cu C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Cu H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Cu Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Cu Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2602819E+01 0.4649418E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3965036E+01 0.2335175E+04 0.2602819E+01 0.2683537E+01 0.1537150E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N N O 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N N Cu 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N N N 3 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N N C 3 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N N H 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N N Ti 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N N Zn 3 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3738549E+01 0.2102296E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.5218037E+01 0.7654973E+04 0.3738549E+01 0.2150000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N C O 3 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N C Cu 3 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N C N 3 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N C C 3 1 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N C H 3 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N C Ti 3 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N C Zn 3 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.2942366E+01 0.1994335E+01 0.1504261E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N H O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N H Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N H N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N H C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N H H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N H Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N H Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1242126E+01 0.9436434E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5143069E+00 0.1950000E+01 0.1500000E+00 0.1508833E+00 -0.3508835E+00 0.1879419E+01 -0.6135678E-01 0.1018086E-01 0.1773759E+00 0.3381936E-01 -0.8757369E-03 0.4295447E-03 -0.4655969E-03 -0.6389393E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Ti O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.3364171E+01 0.2723439E+01 0.2094778E+00 0.0000000E+00 0.2300000E-04 0.2138790E-01 0.2660987E+00 0.5399989E+00 -0.1031722E+00 0.6130910E-01 -0.5288010E-01 -0.3431400E-01 0.2029010E-01 0.2078790E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Ti Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.3364171E+01 0.2723439E+01 0.2094778E+00 0.0000000E+00 0.2300000E-04 0.2138790E-01 0.2660987E+00 0.5399989E+00 -0.1031722E+00 0.6130910E-01 -0.5288010E-01 -0.3431400E-01 0.2029010E-01 0.2078790E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Ti N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.3364171E+01 0.2723439E+01 0.2094778E+00 0.0000000E+00 0.2300000E-04 0.2138790E-01 0.2660987E+00 0.5399989E+00 -0.1031722E+00 0.6130910E-01 -0.5288010E-01 -0.3431400E-01 0.2029010E-01 0.2078790E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Ti C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.3364171E+01 0.2723439E+01 0.2094778E+00 0.0000000E+00 0.2300000E-04 0.2138790E-01 0.2660987E+00 0.5399989E+00 -0.1031722E+00 0.6130910E-01 -0.5288010E-01 -0.3431400E-01 0.2029010E-01 0.2078790E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Ti H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.3364171E+01 0.2723439E+01 0.2094778E+00 0.0000000E+00 0.2300000E-04 0.2138790E-01 0.2660987E+00 0.5399989E+00 -0.1031722E+00 0.6130910E-01 -0.5288010E-01 -0.3431400E-01 0.2029010E-01 0.2078790E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Ti Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.3364171E+01 0.2723439E+01 0.2094778E+00 0.0000000E+00 0.2300000E-04 0.2138790E-01 0.2660987E+00 0.5399989E+00 -0.1031722E+00 0.6130910E-01 -0.5288010E-01 -0.3431400E-01 0.2029010E-01 0.2078790E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Ti Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.3364171E+01 0.2723439E+01 0.2094778E+00 0.0000000E+00 0.2300000E-04 0.2138790E-01 0.2660987E+00 0.5399989E+00 -0.1031722E+00 0.6130910E-01 -0.5288010E-01 -0.3431400E-01 0.2029010E-01 0.2078790E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Zn O 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Zn Cu 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Zn N 3 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Zn C 3 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Zn H 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Zn Ti 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-N Zn Zn 3 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.7654973E+04 0.2102296E+04 0.5218037E+01 0.3738549E+01 0.1000000E+01 -0.3000000E+01 0.5000000E+01 0.1969380E+00 -0.6887839E+00 -0.3000000E+01 0.5000000E+01 0.6209731E+01 0.9292255E+01 -0.1254466E+01 0.2863502E+00 0.1438711E+01 0.1048322E+01 0.3911805E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.5167863E+00 -0.5521364E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.8126646E+00 0.1724015E+01 0.6985961E+00 0.2838323E+00 0.1691325E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C O O 1 3 3 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2207326E+01 0.6855216E-02 0.4689982E-01 -0.2120127E-02 0.7648779E+01 0.5539746E+01 0.2267948E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C O Cu 1 3 2 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2207326E+01 0.6855216E-02 0.4689982E-01 -0.2120127E-02 0.7648779E+01 0.5539746E+01 0.2267948E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1222566E+00 -0.1057511E+01 0.4042368E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.4778176E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C O N 1 3 3 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2207326E+01 0.6855216E-02 0.4689982E-01 -0.2120127E-02 0.7648779E+01 0.5539746E+01 0.2267948E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C O C 1 3 1 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2207326E+01 0.6855216E-02 0.4689982E-01 -0.2120127E-02 0.7648779E+01 0.5539746E+01 0.2267948E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C O H 1 3 2 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2207326E+01 0.6855216E-02 0.4689982E-01 -0.2120127E-02 0.7648779E+01 0.5539746E+01 0.2267948E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C O Ti 1 3 2 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2207326E+01 0.6855216E-02 0.4689982E-01 -0.2120127E-02 0.7648779E+01 0.5539746E+01 0.2267948E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C O Zn 1 3 2 0 2 2 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.2210059E+00 0.1105030E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.5384622E+00 0.1027172E+02 0.6728805E+00 0.5247337E+01 0.7520943E+00 0.8011457E+01 0.7713576E+01 0.4546971E+04 0.0000000E+00 0.1750000E+01 0.1500000E+00 -0.2207326E+01 0.6855216E-02 0.4689982E-01 -0.2120127E-02 0.7648779E+01 0.5539746E+01 0.2267948E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Cu O 1 2 3 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 -0.6015934E-01 -0.1081446E+01 0.3005737E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 -0.1000000E+01 0.2609641E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Cu Cu 1 2 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Cu N 1 2 3 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Cu C 1 2 1 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Cu H 1 2 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Cu Ti 1 2 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Cu Zn 1 2 2 0 0 0 0 2 1 0.1128090E-01 0.3425000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 -0.1166463E+00 0.5832316E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3178819E+00 0.6046844E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.4030754E+01 0.7480554E+03 0.0000000E+00 0.2650000E+01 0.1500000E+00 -0.2404352E+00 -0.2745729E+00 0.3905948E+00 0.5023326E+00 0.1194375E+00 0.1717656E+00 0.1214693E+00 -0.1153438E-02 -0.1318113E-02 -0.1081672E-02 0.7362141E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C N O 1 3 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.0000000E+00 0.1994335E+01 0.1504261E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C N Cu 1 3 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.0000000E+00 0.1994335E+01 0.1504261E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C N N 1 3 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.0000000E+00 0.1994335E+01 0.1504261E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C N C 1 3 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.0000000E+00 0.1994335E+01 0.1504261E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C N H 1 3 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.0000000E+00 0.1994335E+01 0.1504261E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C N Ti 1 3 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.0000000E+00 0.1994335E+01 0.1504261E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C N Zn 1 3 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2942366E+01 0.1068239E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3956221E+01 0.2620968E+04 0.0000000E+00 0.1994335E+01 0.1504261E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C C O 1 1 3 1 3 3 1 1 1 0.1272586E-01 0.3400000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4794940E+01 0.1321954E+05 0.1496616E+01 0.3181490E+02 0.1508583E+01 0.2818426E+02 0.4965431E+01 0.1705446E+05 0.0000000E+00 0.1850000E+01 0.1500000E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C C Cu 1 1 2 1 3 3 1 1 1 0.1272586E-01 0.3400000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4794940E+01 0.1321954E+05 0.1496616E+01 0.3181490E+02 0.1508583E+01 0.2818426E+02 0.4965431E+01 0.1705446E+05 0.0000000E+00 0.1850000E+01 0.1500000E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C C N 1 1 3 1 3 3 1 1 1 0.1272586E-01 0.3400000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4794940E+01 0.1321954E+05 0.1496616E+01 0.3181490E+02 0.1508583E+01 0.2818426E+02 0.4965431E+01 0.1705446E+05 0.0000000E+00 0.1850000E+01 0.1500000E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C C C 1 1 1 1 3 3 1 1 1 0.1272586E-01 0.3400000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4794940E+01 0.1321954E+05 0.1496616E+01 0.3181490E+02 0.1508583E+01 0.2818426E+02 0.4965431E+01 0.1705446E+05 0.0000000E+00 0.1850000E+01 0.1500000E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C C H 1 1 2 1 3 3 1 1 1 0.1272586E-01 0.3400000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4794940E+01 0.1321954E+05 0.1496616E+01 0.3181490E+02 0.1508583E+01 0.2818426E+02 0.4965431E+01 0.1705446E+05 0.0000000E+00 0.1850000E+01 0.1500000E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C C Ti 1 1 2 1 3 3 1 1 1 0.1272586E-01 0.3400000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4794940E+01 0.1321954E+05 0.1496616E+01 0.3181490E+02 0.1508583E+01 0.2818426E+02 0.4965431E+01 0.1705446E+05 0.0000000E+00 0.1850000E+01 0.1500000E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C C Zn 1 1 2 1 3 3 1 1 1 0.1272586E-01 0.3400000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4794940E+01 0.1321954E+05 0.1496616E+01 0.3181490E+02 0.1508583E+01 0.2818426E+02 0.4965431E+01 0.1705446E+05 0.0000000E+00 0.1850000E+01 0.1500000E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C H O 1 2 3 2 4 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.1232245E+01 0.9390230E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.0000000E+00 0.1750000E+01 0.1500000E+00 0.2137845E-01 0.2584961E+00 0.9693971E+00 -0.2841071E-02 -0.6152264E+00 0.2276591E+00 -0.4745915E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C H Cu 1 2 2 2 4 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.1232245E+01 0.9390230E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.0000000E+00 0.1750000E+01 0.1500000E+00 0.2137845E-01 0.2584961E+00 0.9693971E+00 -0.2841071E-02 -0.6152264E+00 0.2276591E+00 -0.4745915E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C H N 1 2 3 2 4 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.1232245E+01 0.9390230E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.0000000E+00 0.1750000E+01 0.1500000E+00 0.2137845E-01 0.2584961E+00 0.9693971E+00 -0.2841071E-02 -0.6152264E+00 0.2276591E+00 -0.4745915E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C H C 1 2 1 2 4 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.1232245E+01 0.9390230E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.0000000E+00 0.1750000E+01 0.1500000E+00 0.2137845E-01 0.2584961E+00 0.9693971E+00 -0.2841071E-02 -0.6152264E+00 0.2276591E+00 -0.4745915E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C H H 1 2 2 2 4 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.1232245E+01 0.9390230E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.0000000E+00 0.1750000E+01 0.1500000E+00 0.2137845E-01 0.2584961E+00 0.9693971E+00 -0.2841071E-02 -0.6152264E+00 0.2276591E+00 -0.4745915E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C H Ti 1 2 2 2 4 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.1232245E+01 0.9390230E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.0000000E+00 0.1750000E+01 0.1500000E+00 0.2137845E-01 0.2584961E+00 0.9693971E+00 -0.2841071E-02 -0.6152264E+00 0.2276591E+00 -0.4745915E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C H Zn 1 2 2 2 4 0 0 1 1 0.8112054E-02 0.3105000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.1232245E+01 0.9390230E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.4187692E+00 0.5977828E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.6260171E+01 0.2731344E+03 0.0000000E+00 0.1750000E+01 0.1500000E+00 0.2137845E-01 0.2584961E+00 0.9693971E+00 -0.2841071E-02 -0.6152264E+00 0.2276591E+00 -0.4745915E-03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Ti O 1 2 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.0000000E+00 0.2719221E+01 0.1443428E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Ti Cu 1 2 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.0000000E+00 0.2719221E+01 0.1443428E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Ti N 1 2 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.0000000E+00 0.2719221E+01 0.1443428E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Ti C 1 2 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.0000000E+00 0.2719221E+01 0.1443428E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Ti H 1 2 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.0000000E+00 0.2719221E+01 0.1443428E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Ti Ti 1 2 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.0000000E+00 0.2719221E+01 0.1443428E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Ti Zn 1 2 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.0000000E+00 0.2719221E+01 0.1443428E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Zn O 1 2 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.0000000E+00 0.2543722E+01 0.1395593E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Zn Cu 1 2 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.0000000E+00 0.2543722E+01 0.1395593E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Zn N 1 2 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.0000000E+00 0.2543722E+01 0.1395593E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Zn C 1 2 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.0000000E+00 0.2543722E+01 0.1395593E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Zn H 1 2 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.0000000E+00 0.2543722E+01 0.1395593E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Zn Ti 1 2 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.0000000E+00 0.2543722E+01 0.1395593E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-C Zn Zn 1 2 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.8973872E+03 0.5428043E+03 0.2694404E+01 0.2146183E+01 0.1000000E+01 -0.4000000E+01 0.4000000E+01 0.3059601E+00 -0.1186725E+00 -0.4000000E+01 0.4000000E+01 0.5372531E+01 0.5914404E+01 0.3946687E+00 0.3059477E-01 0.1112389E+01 0.8166928E+00 0.2681866E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.8065243E+00 0.2346083E-01 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.0000000E+00 0.2543722E+01 0.1395593E+00 0.4672280E+00 0.8021770E+00 -0.1693873E+00 -0.7132275E+00 -0.8606539E-01 0.3610864E+00 0.2482604E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H O O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H O Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H O N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H O C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H O H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H O Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.2043225E+01 0.9434805E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3043947E+01 0.1634356E+03 0.2043225E+01 0.1650000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
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-H Cu N 2 2 3 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H Cu C 2 2 1 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H Cu H 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H Cu Ti 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H Cu Zn 2 2 2 0 0 0 0 2 1 0.7190967E-02 0.3130000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.9027938E+00 0.1628007E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3444484E+01 0.2208881E+03 0.9027938E+00 0.2150000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
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-H N Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
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-H N H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1077726E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1134424E+01 0.3847649E+01 0.1026156E+01 0.4294827E+01 0.9793743E+00 0.3877552E+01 0.7588333E+01 0.1407592E+04 0.5436308E+00 0.1950000E+01 0.1500000E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
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-H Ti Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H Ti N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-H Ti C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.8906987E+02 0.3572707E+02 0.4216932E+01 0.1948353E+01 0.1000000E+01 -0.5366516E+00 0.1000000E+01 0.5000000E-02 -0.5000000E-02 -0.5000000E+00 0.5000000E+00 0.5359305E+01 0.8240603E+01 0.0000000E+00 0.0000000E+00 0.2000000E+01 -0.1000000E-02 0.1000000E-02 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01 0.1000000E+01 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 -0.6979045E+00 -0.2515194E+00 0.1477481E+01 0.2298515E+00 -0.9541016E+00 0.3823360E+00 0.6759455E+01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
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-Ti N N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.1093141E+01 0.2723439E+01 0.2094778E+00 0.2600000E-05 0.2240000E-04 -0.1133732E+00 0.5849360E-01 0.1868480E+00 0.2194018E+00 0.2801788E+00 -0.3010560E-01 -0.6455300E-01 -0.1688100E-02 -0.6711610E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti N C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.1093141E+01 0.2723439E+01 0.2094778E+00 0.2600000E-05 0.2240000E-04 -0.1133732E+00 0.5849360E-01 0.1868480E+00 0.2194018E+00 0.2801788E+00 -0.3010560E-01 -0.6455300E-01 -0.1688100E-02 -0.6711610E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti N H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.1093141E+01 0.2723439E+01 0.2094778E+00 0.2600000E-05 0.2240000E-04 -0.1133732E+00 0.5849360E-01 0.1868480E+00 0.2194018E+00 0.2801788E+00 -0.3010560E-01 -0.6455300E-01 -0.1688100E-02 -0.6711610E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti N Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.1093141E+01 0.2723439E+01 0.2094778E+00 0.2600000E-05 0.2240000E-04 -0.1133732E+00 0.5849360E-01 0.1868480E+00 0.2194018E+00 0.2801788E+00 -0.3010560E-01 -0.6455300E-01 -0.1688100E-02 -0.6711610E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti N Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1866843E+01 0.1949579E+03 0.2104133E+01 0.1729030E+03 0.2569293E+01 0.1981206E+03 0.3084136E+01 0.1876811E+04 0.1093141E+01 0.2723439E+01 0.2094778E+00 0.2600000E-05 0.2240000E-04 -0.1133732E+00 0.5849360E-01 0.1868480E+00 0.2194018E+00 0.2801788E+00 -0.3010560E-01 -0.6455300E-01 -0.1688100E-02 -0.6711610E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti C O 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti C Cu 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti C N 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti C C 2 1 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti C H 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti C Ti 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti C Zn 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1662507E+01 0.2520535E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2415207E+01 0.6808662E+03 0.1662507E+01 0.2719221E+01 0.1443428E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti H O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti H Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti H N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti H C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti H H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti H Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti H Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1563592E+01 0.6466508E+02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3176471E+01 0.2145049E+03 0.1563592E+01 0.2275575E+01 0.2043439E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Ti O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Ti Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Ti N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Ti C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Ti H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Ti Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.7307800E-01 0.0000000E+00 0.1967800E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Ti Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1178831E+01 0.1170421E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2136010E+01 0.5165873E+03 0.1178831E+01 0.4000000E+01 0.1000000E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Zn O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Zn Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Zn N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Zn C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Zn H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Zn Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Ti Zn Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5165873E+03 0.1170421E+03 0.2136010E+01 0.1178831E+01 0.5660482E+00 -0.4000000E+01 0.4000000E+01 0.5000000E-02 -0.5000020E-01 -0.4000000E+01 0.4000000E+01 0.3095768E+01 0.4230280E+01 -0.1039759E+01 0.3574280E+00 0.7243519E+00 0.3656345E+00 0.7648498E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.3350000E+00 0.7229326E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.5504001E-01 -0.6554936E-01 -0.1304334E+00 0.9305440E-01 0.2266737E+00 0.1466059E+00 0.7718281E-01 -0.1231823E-01 0.1750793E+00 0.6608536E-01 -0.7610935E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn O O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn O Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn O N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn O C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn O H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn O Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn O Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.2592011E+01 0.1898343E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1986354E+01 0.4237569E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2842371E+01 0.1369285E+04 0.1549384E+01 0.2800000E+01 0.2000001E+00 0.2288437E-01 -0.9920014E-02 0.1147701E-01 -0.1995657E-01 0.3955190E-01 -0.1381147E-01 0.4348548E-01 -0.1052353E-01 0.1368662E-01 0.1795660E-01 0.1337706E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Cu O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Cu Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Cu N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Cu C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Cu H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Cu Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Cu Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3975000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3090363E+00 0.9266199E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1900813E+01 0.4166952E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774643E+01 0.1318299E+04 0.1900813E+01 0.3450000E+01 0.1500000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2275729E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn N O 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn N Cu 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn N N 2 3 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn N C 2 3 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn N H 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn N Ti 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn N Zn 2 3 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.3051554E+01 0.1839526E+04 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3928305E+01 0.4525937E+04 0.3051554E+01 0.2742590E+01 0.1349090E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn C O 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn C Cu 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn C N 2 1 3 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn C C 2 1 1 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn C H 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn C Ti 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn C Zn 2 1 2 0 0 0 0 0 1 0.0000000E+00 0.3950000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2370800E+01 0.6135085E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3034762E+01 0.1858657E+04 0.2370800E+01 0.2543722E+01 0.1395593E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn H O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn H Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn H N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn H C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn H H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn H Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn H Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.3655000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.2500000E+00 0.2500000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2728951E+01 0.1190255E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.3725902E+01 0.5775554E+03 0.2728951E+01 0.2450000E+01 0.1500001E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Ti O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Ti Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Ti N 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Ti C 2 2 1 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Ti H 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Ti Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Ti Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1771695E+01 0.4340405E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2387291E+01 0.1175732E+04 0.1771695E+01 0.3741651E+01 0.1002231E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774033E-02 0.2783002E-02 0.1013396E-02 -0.2212792E-02 0.1191381E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Zn O 2 2 3 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
-Zn Zn Cu 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.2675921E+04 0.1609601E+04 0.2638572E+01 0.2364559E+01 0.6267391E+00 -0.4000000E+01 0.4000000E+01 0.5296103E+00 -0.5004044E+00 -0.4000000E+01 0.4000000E+01 0.3389925E+01 0.8162758E+01 -0.3381140E+01 0.9216813E+00 0.6734390E+00 0.3398138E+00 0.6702070E+00 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2221666E+00 0.6200000E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.2352653E+01 0.4948113E+03 0.2330411E+01 0.5107761E+03 0.2288269E+01 0.5300215E+03 0.2626286E+01 0.2842165E+04 0.2364559E+01 0.3500000E+01 0.9999990E-01 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.2774000E-02 0.2783000E-02 0.1013400E-02 -0.2212800E-02 0.1191400E-02 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01
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+Zr Zr Ti 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01
+Zr Zr Zn 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01
+Zr Zr Zr 2 2 2 0 0 0 0 0 1 0.0000000E+00 0.4500000E+01 0.5046808E+03 0.1136065E+03 0.1821408E+01 0.1062282E+01 0.1000000E+01 -0.2000000E+01 0.4000000E+01 0.1999880E+01 -0.1040199E+00 -0.2000000E+01 0.4000000E+01 0.3302770E+01 0.2957410E+01 0.1331500E+00 0.3161000E-01 0.1831535E+01 -0.1791861E+01 0.1228965E+01 0.5000000E+00 0.5000000E+00 0.1100000E+02 0.2000000E+00 0.3871027E+00 0.0000000E+00 0.1000000E+01 0.5000000E+00 0.1062282E+01 0.1136065E+03 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1821408E+01 0.5046808E+03 0.2071488E+01 0.3820000E+01 0.1000000E+00 0.5764650E+00 0.6403220E+00 0.4243000E-02 0.5968300E-01 0.4370760E+00 0.5652700E-01 0.7202000E-02 -0.5879890E-02 0.1010734E+01 -0.6194480E-02 -0.9101515E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.0000000E+00 0.1000000E+01 0.0000000E+00 0.1000000E+01
diff --git a/potentials/lib.comb3 b/potentials/lib.comb3
index 7ba67ff18..f47427842 100644
--- a/potentials/lib.comb3
+++ b/potentials/lib.comb3
@@ -1,24303 +1,24302 @@
- 0.3200000E+01 0.3700000E+01 0.2000000E+01 0.3000000E+01 0.4050000E+01 0.4350000E+01 #cccuts,radcuts,chcuts
- 0.5880000E-01 0.1013000E+00 0.1040000E+00 -0.1740000E-01 -0.6030000E-01 0.1076000E+00 0.9460000E-01 #CH angle function when
+ 0.3200000E+01 0.3700000E+01 0.2000000E+01 0.3000000E+01 0.3200000E+01 0.3700000E+01 #cccuts,radcuts,chcuts
+-0.4005944E-02 0.4719551E+00 0.1621693E+00 -0.2101856E-01 0.2410780E+00 -0.1209284E-01 -0.1471218E+00 #CH angle function when
4 3 1 # # of bonds for PCN,rad,tor spl
4 4 4 # max # of PCN spline func
4 4 11 # max # rad & tor spline func
1 9 0.2000000E+00 0.1000000E+00 # pcn spline function at limit
2 9 0.7000000E+01 0.2000000E+00 # pcn spline function at limit
3 9 0.2000000E+01 0.1000000E+00 # pcn spline function at limit
4 9 0.3000000E+01 0.2500000E+00 # pcn spline function at limit
20000
1 0.1050002E-01 0.9464586E-01 0.4980258E-01
2 0.1050949E-01 0.9465088E-01 0.5072564E-01
3 0.1051895E-01 0.9465600E-01 0.5164770E-01
4 0.1052842E-01 0.9466121E-01 0.5256876E-01
5 0.1053789E-01 0.9466652E-01 0.5348882E-01
6 0.1054735E-01 0.9467191E-01 0.5440789E-01
7 0.1055682E-01 0.9467740E-01 0.5532596E-01
8 0.1056629E-01 0.9468298E-01 0.5624304E-01
9 0.1057576E-01 0.9468865E-01 0.5715912E-01
10 0.1058523E-01 0.9469441E-01 0.5807421E-01
11 0.1059470E-01 0.9470026E-01 0.5898830E-01
12 0.1060417E-01 0.9470621E-01 0.5990140E-01
13 0.1061364E-01 0.9471224E-01 0.6081351E-01
14 0.1062311E-01 0.9471837E-01 0.6172463E-01
15 0.1063258E-01 0.9472459E-01 0.6263475E-01
16 0.1064205E-01 0.9473090E-01 0.6354388E-01
17 0.1065153E-01 0.9473730E-01 0.6445202E-01
18 0.1066100E-01 0.9474379E-01 0.6535917E-01
19 0.1067048E-01 0.9475037E-01 0.6626533E-01
20 0.1067995E-01 0.9475704E-01 0.6717050E-01
21 0.1068943E-01 0.9476380E-01 0.6807469E-01
22 0.1069890E-01 0.9477065E-01 0.6897788E-01
23 0.1070838E-01 0.9477760E-01 0.6988009E-01
24 0.1071786E-01 0.9478463E-01 0.7078131E-01
25 0.1072734E-01 0.9479175E-01 0.7168154E-01
26 0.1073682E-01 0.9479897E-01 0.7258079E-01
27 0.1074630E-01 0.9480627E-01 0.7347905E-01
28 0.1075578E-01 0.9481366E-01 0.7437632E-01
29 0.1076526E-01 0.9482114E-01 0.7527262E-01
30 0.1077474E-01 0.9482872E-01 0.7616792E-01
31 0.1078423E-01 0.9483638E-01 0.7706225E-01
32 0.1079371E-01 0.9484413E-01 0.7795559E-01
33 0.1080320E-01 0.9485197E-01 0.7884794E-01
34 0.1081268E-01 0.9485990E-01 0.7973932E-01
35 0.1082217E-01 0.9486792E-01 0.8062972E-01
36 0.1083166E-01 0.9487602E-01 0.8151913E-01
37 0.1084114E-01 0.9488422E-01 0.8240756E-01
38 0.1085063E-01 0.9489251E-01 0.8329502E-01
39 0.1086012E-01 0.9490088E-01 0.8418149E-01
40 0.1086961E-01 0.9490934E-01 0.8506698E-01
41 0.1087910E-01 0.9491789E-01 0.8595150E-01
42 0.1088860E-01 0.9492653E-01 0.8683504E-01
43 0.1089809E-01 0.9493526E-01 0.8771760E-01
44 0.1090758E-01 0.9494408E-01 0.8859918E-01
45 0.1091708E-01 0.9495298E-01 0.8947979E-01
46 0.1092657E-01 0.9496197E-01 0.9035942E-01
47 0.1093607E-01 0.9497105E-01 0.9123808E-01
48 0.1094557E-01 0.9498022E-01 0.9211576E-01
49 0.1095507E-01 0.9498947E-01 0.9299247E-01
50 0.1096457E-01 0.9499882E-01 0.9386820E-01
51 0.1097407E-01 0.9500825E-01 0.9474296E-01
52 0.1098357E-01 0.9501777E-01 0.9561675E-01
53 0.1099307E-01 0.9502737E-01 0.9648957E-01
54 0.1100257E-01 0.9503706E-01 0.9736141E-01
55 0.1101208E-01 0.9504684E-01 0.9823228E-01
56 0.1102158E-01 0.9505671E-01 0.9910218E-01
57 0.1103109E-01 0.9506666E-01 0.9997112E-01
58 0.1104060E-01 0.9507670E-01 0.1008391E+00
59 0.1105010E-01 0.9508683E-01 0.1017061E+00
60 0.1105961E-01 0.9509705E-01 0.1025721E+00
61 0.1106912E-01 0.9510735E-01 0.1034372E+00
62 0.1107863E-01 0.9511773E-01 0.1043012E+00
63 0.1108815E-01 0.9512821E-01 0.1051644E+00
64 0.1109766E-01 0.9513877E-01 0.1060265E+00
65 0.1110717E-01 0.9514941E-01 0.1068877E+00
66 0.1111669E-01 0.9516014E-01 0.1077479E+00
67 0.1112621E-01 0.9517096E-01 0.1086072E+00
68 0.1113572E-01 0.9518186E-01 0.1094655E+00
69 0.1114524E-01 0.9519285E-01 0.1103228E+00
70 0.1115476E-01 0.9520393E-01 0.1111792E+00
71 0.1116428E-01 0.9521509E-01 0.1120346E+00
72 0.1117381E-01 0.9522634E-01 0.1128890E+00
73 0.1118333E-01 0.9523767E-01 0.1137425E+00
74 0.1119285E-01 0.9524908E-01 0.1145950E+00
75 0.1120238E-01 0.9526059E-01 0.1154466E+00
76 0.1121191E-01 0.9527217E-01 0.1162972E+00
77 0.1122143E-01 0.9528385E-01 0.1171468E+00
78 0.1123096E-01 0.9529560E-01 0.1179955E+00
79 0.1124049E-01 0.9530745E-01 0.1188432E+00
80 0.1125002E-01 0.9531937E-01 0.1196900E+00
81 0.1125956E-01 0.9533138E-01 0.1205358E+00
82 0.1126909E-01 0.9534348E-01 0.1213806E+00
83 0.1127863E-01 0.9535566E-01 0.1222245E+00
84 0.1128816E-01 0.9536792E-01 0.1230674E+00
85 0.1129770E-01 0.9538027E-01 0.1239094E+00
86 0.1130724E-01 0.9539271E-01 0.1247504E+00
87 0.1131678E-01 0.9540522E-01 0.1255905E+00
88 0.1132632E-01 0.9541782E-01 0.1264296E+00
89 0.1133586E-01 0.9543051E-01 0.1272677E+00
90 0.1134540E-01 0.9544328E-01 0.1281049E+00
91 0.1135495E-01 0.9545613E-01 0.1289412E+00
92 0.1136450E-01 0.9546907E-01 0.1297765E+00
93 0.1137404E-01 0.9548208E-01 0.1306108E+00
94 0.1138359E-01 0.9549519E-01 0.1314442E+00
95 0.1139314E-01 0.9550837E-01 0.1322767E+00
96 0.1140269E-01 0.9552164E-01 0.1331082E+00
97 0.1141225E-01 0.9553500E-01 0.1339387E+00
98 0.1142180E-01 0.9554843E-01 0.1347683E+00
99 0.1143136E-01 0.9556195E-01 0.1355970E+00
100 0.1144091E-01 0.9557555E-01 0.1364247E+00
101 0.1145047E-01 0.9558923E-01 0.1372514E+00
102 0.1146003E-01 0.9560300E-01 0.1380772E+00
103 0.1146959E-01 0.9561685E-01 0.1389021E+00
104 0.1147915E-01 0.9563078E-01 0.1397260E+00
105 0.1148872E-01 0.9564479E-01 0.1405490E+00
106 0.1149828E-01 0.9565889E-01 0.1413710E+00
107 0.1150785E-01 0.9567307E-01 0.1421921E+00
108 0.1151742E-01 0.9568733E-01 0.1430122E+00
109 0.1152699E-01 0.9570167E-01 0.1438314E+00
110 0.1153656E-01 0.9571610E-01 0.1446496E+00
111 0.1154613E-01 0.9573060E-01 0.1454669E+00
112 0.1155570E-01 0.9574519E-01 0.1462833E+00
113 0.1156528E-01 0.9575986E-01 0.1470987E+00
114 0.1157486E-01 0.9577461E-01 0.1479132E+00
115 0.1158443E-01 0.9578944E-01 0.1487267E+00
116 0.1159401E-01 0.9580435E-01 0.1495393E+00
117 0.1160360E-01 0.9581935E-01 0.1503510E+00
118 0.1161318E-01 0.9583442E-01 0.1511617E+00
119 0.1162276E-01 0.9584958E-01 0.1519715E+00
120 0.1163235E-01 0.9586482E-01 0.1527803E+00
121 0.1164194E-01 0.9588014E-01 0.1535882E+00
122 0.1165152E-01 0.9589554E-01 0.1543952E+00
123 0.1166111E-01 0.9591102E-01 0.1552012E+00
124 0.1167071E-01 0.9592658E-01 0.1560063E+00
125 0.1168030E-01 0.9594222E-01 0.1568105E+00
126 0.1168989E-01 0.9595794E-01 0.1576137E+00
127 0.1169949E-01 0.9597374E-01 0.1584160E+00
128 0.1170909E-01 0.9598962E-01 0.1592173E+00
129 0.1171869E-01 0.9600558E-01 0.1600178E+00
130 0.1172829E-01 0.9602162E-01 0.1608173E+00
131 0.1173789E-01 0.9603775E-01 0.1616158E+00
132 0.1174750E-01 0.9605395E-01 0.1624134E+00
133 0.1175710E-01 0.9607023E-01 0.1632101E+00
134 0.1176671E-01 0.9608659E-01 0.1640059E+00
135 0.1177632E-01 0.9610303E-01 0.1648007E+00
136 0.1178593E-01 0.9611955E-01 0.1655946E+00
137 0.1179555E-01 0.9613615E-01 0.1663876E+00
138 0.1180516E-01 0.9615283E-01 0.1671797E+00
139 0.1181478E-01 0.9616958E-01 0.1679708E+00
140 0.1182439E-01 0.9618642E-01 0.1687610E+00
141 0.1183401E-01 0.9620334E-01 0.1695502E+00
142 0.1184363E-01 0.9622033E-01 0.1703386E+00
143 0.1185326E-01 0.9623740E-01 0.1711260E+00
144 0.1186288E-01 0.9625456E-01 0.1719124E+00
145 0.1187251E-01 0.9627179E-01 0.1726980E+00
146 0.1188214E-01 0.9628910E-01 0.1734826E+00
147 0.1189177E-01 0.9630648E-01 0.1742663E+00
148 0.1190140E-01 0.9632395E-01 0.1750491E+00
149 0.1191103E-01 0.9634149E-01 0.1758310E+00
150 0.1192067E-01 0.9635912E-01 0.1766119E+00
151 0.1193030E-01 0.9637682E-01 0.1773919E+00
152 0.1193994E-01 0.9639459E-01 0.1781710E+00
153 0.1194958E-01 0.9641245E-01 0.1789492E+00
154 0.1195922E-01 0.9643038E-01 0.1797265E+00
155 0.1196887E-01 0.9644840E-01 0.1805028E+00
156 0.1197851E-01 0.9646648E-01 0.1812782E+00
157 0.1198816E-01 0.9648465E-01 0.1820527E+00
158 0.1199781E-01 0.9650289E-01 0.1828263E+00
159 0.1200746E-01 0.9652122E-01 0.1835989E+00
160 0.1201711E-01 0.9653961E-01 0.1843707E+00
161 0.1202677E-01 0.9655809E-01 0.1851415E+00
162 0.1203643E-01 0.9657664E-01 0.1859114E+00
163 0.1204608E-01 0.9659527E-01 0.1866804E+00
164 0.1205575E-01 0.9661398E-01 0.1874484E+00
165 0.1206541E-01 0.9663276E-01 0.1882156E+00
166 0.1207507E-01 0.9665162E-01 0.1889818E+00
167 0.1208474E-01 0.9667056E-01 0.1897472E+00
168 0.1209441E-01 0.9668957E-01 0.1905116E+00
169 0.1210408E-01 0.9670866E-01 0.1912751E+00
170 0.1211375E-01 0.9672783E-01 0.1920377E+00
171 0.1212342E-01 0.9674707E-01 0.1927993E+00
172 0.1213310E-01 0.9676639E-01 0.1935601E+00
173 0.1214277E-01 0.9678578E-01 0.1943199E+00
174 0.1215245E-01 0.9680525E-01 0.1950789E+00
175 0.1216214E-01 0.9682480E-01 0.1958369E+00
176 0.1217182E-01 0.9684442E-01 0.1965940E+00
177 0.1218150E-01 0.9686411E-01 0.1973503E+00
178 0.1219119E-01 0.9688389E-01 0.1981056E+00
179 0.1220088E-01 0.9690374E-01 0.1988599E+00
180 0.1221057E-01 0.9692366E-01 0.1996134E+00
181 0.1222027E-01 0.9694366E-01 0.2003660E+00
182 0.1222996E-01 0.9696373E-01 0.2011177E+00
183 0.1223966E-01 0.9698388E-01 0.2018685E+00
184 0.1224936E-01 0.9700411E-01 0.2026183E+00
185 0.1225906E-01 0.9702441E-01 0.2033673E+00
186 0.1226876E-01 0.9704478E-01 0.2041153E+00
187 0.1227847E-01 0.9706523E-01 0.2048625E+00
188 0.1228818E-01 0.9708575E-01 0.2056087E+00
189 0.1229789E-01 0.9710635E-01 0.2063541E+00
190 0.1230760E-01 0.9712702E-01 0.2070985E+00
191 0.1231731E-01 0.9714777E-01 0.2078420E+00
192 0.1232703E-01 0.9716859E-01 0.2085847E+00
193 0.1233675E-01 0.9718949E-01 0.2093264E+00
194 0.1234647E-01 0.9721046E-01 0.2100672E+00
195 0.1235619E-01 0.9723150E-01 0.2108071E+00
196 0.1236591E-01 0.9725262E-01 0.2115462E+00
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1929 0.3603473E-01 0.1842179E+00 0.5349037E+00
1930 0.3605315E-01 0.1842714E+00 0.5347426E+00
1931 0.3607158E-01 0.1843249E+00 0.5345814E+00
1932 0.3609002E-01 0.1843783E+00 0.5344199E+00
1933 0.3610846E-01 0.1844318E+00 0.5342583E+00
1934 0.3612690E-01 0.1844852E+00 0.5340965E+00
1935 0.3614535E-01 0.1845386E+00 0.5339345E+00
1936 0.3616381E-01 0.1845920E+00 0.5337723E+00
1937 0.3618227E-01 0.1846453E+00 0.5336099E+00
1938 0.3620074E-01 0.1846987E+00 0.5334473E+00
1939 0.3621921E-01 0.1847520E+00 0.5332845E+00
1940 0.3623769E-01 0.1848054E+00 0.5331216E+00
1941 0.3625617E-01 0.1848587E+00 0.5329584E+00
1942 0.3627466E-01 0.1849119E+00 0.5327951E+00
1943 0.3629316E-01 0.1849652E+00 0.5326316E+00
1944 0.3631165E-01 0.1850185E+00 0.5324679E+00
1945 0.3633016E-01 0.1850717E+00 0.5323040E+00
1946 0.3634867E-01 0.1851249E+00 0.5321399E+00
1947 0.3636718E-01 0.1851781E+00 0.5319756E+00
1948 0.3638570E-01 0.1852313E+00 0.5318112E+00
1949 0.3640423E-01 0.1852845E+00 0.5316466E+00
1950 0.3642276E-01 0.1853377E+00 0.5314817E+00
1951 0.3644130E-01 0.1853908E+00 0.5313167E+00
1952 0.3645984E-01 0.1854439E+00 0.5311515E+00
1953 0.3647839E-01 0.1854970E+00 0.5309862E+00
1954 0.3649694E-01 0.1855501E+00 0.5308206E+00
1955 0.3651550E-01 0.1856032E+00 0.5306549E+00
1956 0.3653406E-01 0.1856562E+00 0.5304890E+00
1957 0.3655263E-01 0.1857093E+00 0.5303228E+00
1958 0.3657120E-01 0.1857623E+00 0.5301566E+00
1959 0.3658978E-01 0.1858153E+00 0.5299901E+00
1960 0.3660836E-01 0.1858683E+00 0.5298234E+00
1961 0.3662695E-01 0.1859213E+00 0.5296566E+00
1962 0.3664555E-01 0.1859742E+00 0.5294896E+00
1963 0.3666415E-01 0.1860272E+00 0.5293224E+00
1964 0.3668275E-01 0.1860801E+00 0.5291550E+00
1965 0.3670137E-01 0.1861330E+00 0.5289875E+00
1966 0.3671998E-01 0.1861859E+00 0.5288197E+00
1967 0.3673860E-01 0.1862388E+00 0.5286518E+00
1968 0.3675723E-01 0.1862916E+00 0.5284837E+00
1969 0.3677586E-01 0.1863445E+00 0.5283154E+00
1970 0.3679450E-01 0.1863973E+00 0.5281470E+00
1971 0.3681314E-01 0.1864501E+00 0.5279783E+00
1972 0.3683179E-01 0.1865029E+00 0.5278095E+00
1973 0.3685044E-01 0.1865557E+00 0.5276405E+00
1974 0.3686910E-01 0.1866084E+00 0.5274714E+00
1975 0.3688776E-01 0.1866612E+00 0.5273020E+00
1976 0.3690643E-01 0.1867139E+00 0.5271325E+00
1977 0.3692511E-01 0.1867666E+00 0.5269628E+00
1978 0.3694378E-01 0.1868193E+00 0.5267929E+00
1979 0.3696247E-01 0.1868719E+00 0.5266229E+00
1980 0.3698116E-01 0.1869246E+00 0.5264526E+00
1981 0.3699985E-01 0.1869772E+00 0.5262822E+00
1982 0.3701855E-01 0.1870299E+00 0.5261117E+00
1983 0.3703726E-01 0.1870825E+00 0.5259409E+00
1984 0.3705597E-01 0.1871350E+00 0.5257700E+00
1985 0.3707469E-01 0.1871876E+00 0.5255989E+00
1986 0.3709341E-01 0.1872402E+00 0.5254276E+00
1987 0.3711213E-01 0.1872927E+00 0.5252562E+00
1988 0.3713087E-01 0.1873452E+00 0.5250845E+00
1989 0.3714960E-01 0.1873977E+00 0.5249128E+00
1990 0.3716835E-01 0.1874502E+00 0.5247408E+00
1991 0.3718709E-01 0.1875027E+00 0.5245687E+00
1992 0.3720585E-01 0.1875551E+00 0.5243963E+00
1993 0.3722460E-01 0.1876075E+00 0.5242239E+00
1994 0.3724337E-01 0.1876600E+00 0.5240512E+00
1995 0.3726214E-01 0.1877124E+00 0.5238784E+00
1996 0.3728091E-01 0.1877647E+00 0.5237054E+00
1997 0.3729969E-01 0.1878171E+00 0.5235322E+00
1998 0.3731847E-01 0.1878694E+00 0.5233589E+00
1999 0.3733726E-01 0.1879218E+00 0.5231854E+00
2000 0.3735606E-01 0.1879741E+00 0.5230117E+00
2001 0.3737486E-01 0.1880264E+00 0.5228379E+00
2002 0.3739366E-01 0.1880786E+00 0.5226639E+00
2003 0.3741247E-01 0.1881309E+00 0.5224897E+00
2004 0.3743129E-01 0.1881831E+00 0.5223153E+00
2005 0.3745011E-01 0.1882354E+00 0.5221408E+00
2006 0.3746894E-01 0.1882876E+00 0.5219661E+00
2007 0.3748777E-01 0.1883398E+00 0.5217913E+00
2008 0.3750661E-01 0.1883919E+00 0.5216163E+00
2009 0.3752545E-01 0.1884441E+00 0.5214411E+00
2010 0.3754429E-01 0.1884962E+00 0.5212657E+00
2011 0.3756315E-01 0.1885483E+00 0.5210902E+00
2012 0.3758200E-01 0.1886004E+00 0.5209145E+00
2013 0.3760087E-01 0.1886525E+00 0.5207387E+00
2014 0.3761973E-01 0.1887046E+00 0.5205626E+00
2015 0.3763861E-01 0.1887566E+00 0.5203865E+00
2016 0.3765749E-01 0.1888087E+00 0.5202101E+00
2017 0.3767637E-01 0.1888607E+00 0.5200336E+00
2018 0.3769526E-01 0.1889127E+00 0.5198569E+00
2019 0.3771415E-01 0.1889646E+00 0.5196801E+00
2020 0.3773305E-01 0.1890166E+00 0.5195031E+00
2021 0.3775195E-01 0.1890685E+00 0.5193260E+00
2022 0.3777086E-01 0.1891205E+00 0.5191486E+00
2023 0.3778978E-01 0.1891724E+00 0.5189711E+00
2024 0.3780870E-01 0.1892243E+00 0.5187935E+00
2025 0.3782762E-01 0.1892761E+00 0.5186157E+00
2026 0.3784655E-01 0.1893280E+00 0.5184377E+00
2027 0.3786549E-01 0.1893798E+00 0.5182596E+00
2028 0.3788443E-01 0.1894316E+00 0.5180813E+00
2029 0.3790338E-01 0.1894834E+00 0.5179028E+00
2030 0.3792233E-01 0.1895352E+00 0.5177242E+00
2031 0.3794128E-01 0.1895870E+00 0.5175454E+00
2032 0.3796024E-01 0.1896387E+00 0.5173665E+00
2033 0.3797921E-01 0.1896905E+00 0.5171874E+00
2034 0.3799818E-01 0.1897422E+00 0.5170082E+00
2035 0.3801716E-01 0.1897939E+00 0.5168288E+00
2036 0.3803614E-01 0.1898455E+00 0.5166492E+00
2037 0.3805513E-01 0.1898972E+00 0.5164695E+00
2038 0.3807412E-01 0.1899488E+00 0.5162896E+00
2039 0.3809312E-01 0.1900004E+00 0.5161095E+00
2040 0.3811212E-01 0.1900520E+00 0.5159293E+00
2041 0.3813113E-01 0.1901036E+00 0.5157490E+00
2042 0.3815014E-01 0.1901552E+00 0.5155685E+00
2043 0.3816916E-01 0.1902067E+00 0.5153878E+00
2044 0.3818818E-01 0.1902583E+00 0.5152070E+00
2045 0.3820721E-01 0.1903098E+00 0.5150260E+00
2046 0.3822624E-01 0.1903613E+00 0.5148449E+00
2047 0.3824528E-01 0.1904128E+00 0.5146636E+00
2048 0.3826433E-01 0.1904642E+00 0.5144821E+00
2049 0.3828338E-01 0.1905156E+00 0.5143005E+00
2050 0.3830243E-01 0.1905671E+00 0.5141188E+00
2051 0.3832149E-01 0.1906185E+00 0.5139369E+00
2052 0.3834055E-01 0.1906699E+00 0.5137548E+00
2053 0.3835962E-01 0.1907212E+00 0.5135726E+00
2054 0.3837870E-01 0.1907726E+00 0.5133902E+00
2055 0.3839778E-01 0.1908239E+00 0.5132077E+00
2056 0.3841686E-01 0.1908752E+00 0.5130250E+00
2057 0.3843595E-01 0.1909265E+00 0.5128422E+00
2058 0.3845505E-01 0.1909778E+00 0.5126592E+00
2059 0.3847415E-01 0.1910290E+00 0.5124761E+00
2060 0.3849325E-01 0.1910803E+00 0.5122928E+00
2061 0.3851236E-01 0.1911315E+00 0.5121094E+00
2062 0.3853148E-01 0.1911827E+00 0.5119258E+00
2063 0.3855060E-01 0.1912339E+00 0.5117421E+00
2064 0.3856973E-01 0.1912850E+00 0.5115582E+00
2065 0.3858886E-01 0.1913362E+00 0.5113742E+00
2066 0.3860799E-01 0.1913873E+00 0.5111900E+00
2067 0.3862714E-01 0.1914384E+00 0.5110057E+00
2068 0.3864628E-01 0.1914895E+00 0.5108212E+00
2069 0.3866543E-01 0.1915406E+00 0.5106366E+00
2070 0.3868459E-01 0.1915917E+00 0.5104518E+00
2071 0.3870375E-01 0.1916427E+00 0.5102669E+00
2072 0.3872292E-01 0.1916937E+00 0.5100818E+00
2073 0.3874209E-01 0.1917447E+00 0.5098966E+00
2074 0.3876127E-01 0.1917957E+00 0.5097113E+00
2075 0.3878045E-01 0.1918466E+00 0.5095257E+00
2076 0.3879964E-01 0.1918976E+00 0.5093401E+00
2077 0.3881883E-01 0.1919485E+00 0.5091543E+00
2078 0.3883803E-01 0.1919994E+00 0.5089684E+00
2079 0.3885723E-01 0.1920503E+00 0.5087823E+00
2080 0.3887644E-01 0.1921012E+00 0.5085960E+00
2081 0.3889565E-01 0.1921520E+00 0.5084097E+00
2082 0.3891487E-01 0.1922029E+00 0.5082231E+00
2083 0.3893409E-01 0.1922537E+00 0.5080365E+00
2084 0.3895332E-01 0.1923045E+00 0.5078496E+00
2085 0.3897255E-01 0.1923552E+00 0.5076627E+00
2086 0.3899179E-01 0.1924060E+00 0.5074756E+00
2087 0.3901103E-01 0.1924567E+00 0.5072884E+00
2088 0.3903028E-01 0.1925075E+00 0.5071010E+00
2089 0.3904953E-01 0.1925582E+00 0.5069134E+00
2090 0.3906879E-01 0.1926088E+00 0.5067258E+00
2091 0.3908806E-01 0.1926595E+00 0.5065380E+00
2092 0.3910732E-01 0.1927101E+00 0.5063500E+00
2093 0.3912660E-01 0.1927608E+00 0.5061619E+00
2094 0.3914588E-01 0.1928114E+00 0.5059737E+00
2095 0.3916516E-01 0.1928620E+00 0.5057853E+00
2096 0.3918445E-01 0.1929125E+00 0.5055968E+00
2097 0.3920374E-01 0.1929631E+00 0.5054082E+00
2098 0.3922304E-01 0.1930136E+00 0.5052194E+00
2099 0.3924234E-01 0.1930641E+00 0.5050304E+00
2100 0.3926165E-01 0.1931146E+00 0.5048414E+00
2101 0.3928097E-01 0.1931651E+00 0.5046522E+00
2102 0.3930029E-01 0.1932156E+00 0.5044628E+00
2103 0.3931961E-01 0.1932660E+00 0.5042733E+00
2104 0.3933894E-01 0.1933164E+00 0.5040837E+00
2105 0.3935827E-01 0.1933668E+00 0.5038939E+00
2106 0.3937761E-01 0.1934172E+00 0.5037040E+00
2107 0.3939696E-01 0.1934675E+00 0.5035140E+00
2108 0.3941631E-01 0.1935179E+00 0.5033238E+00
2109 0.3943566E-01 0.1935682E+00 0.5031335E+00
2110 0.3945502E-01 0.1936185E+00 0.5029431E+00
2111 0.3947438E-01 0.1936688E+00 0.5027525E+00
2112 0.3949375E-01 0.1937191E+00 0.5025618E+00
2113 0.3951313E-01 0.1937693E+00 0.5023709E+00
2114 0.3953251E-01 0.1938195E+00 0.5021800E+00
2115 0.3955189E-01 0.1938697E+00 0.5019888E+00
2116 0.3957128E-01 0.1939199E+00 0.5017976E+00
2117 0.3959068E-01 0.1939701E+00 0.5016062E+00
2118 0.3961008E-01 0.1940203E+00 0.5014147E+00
2119 0.3962948E-01 0.1940704E+00 0.5012230E+00
2120 0.3964889E-01 0.1941205E+00 0.5010312E+00
2121 0.3966830E-01 0.1941706E+00 0.5008393E+00
2122 0.3968772E-01 0.1942207E+00 0.5006473E+00
2123 0.3970715E-01 0.1942707E+00 0.5004551E+00
2124 0.3972658E-01 0.1943208E+00 0.5002628E+00
2125 0.3974601E-01 0.1943708E+00 0.5000703E+00
2126 0.3976545E-01 0.1944208E+00 0.4998777E+00
2127 0.3978490E-01 0.1944708E+00 0.4996850E+00
2128 0.3980435E-01 0.1945207E+00 0.4994922E+00
2129 0.3982380E-01 0.1945707E+00 0.4992992E+00
2130 0.3984326E-01 0.1946206E+00 0.4991061E+00
2131 0.3986273E-01 0.1946705E+00 0.4989129E+00
2132 0.3988219E-01 0.1947204E+00 0.4987195E+00
2133 0.3990167E-01 0.1947702E+00 0.4985260E+00
2134 0.3992115E-01 0.1948201E+00 0.4983324E+00
2135 0.3994063E-01 0.1948699E+00 0.4981387E+00
2136 0.3996012E-01 0.1949197E+00 0.4979448E+00
2137 0.3997962E-01 0.1949695E+00 0.4977508E+00
2138 0.3999912E-01 0.1950192E+00 0.4975567E+00
2139 0.4001862E-01 0.1950690E+00 0.4973624E+00
2140 0.4003813E-01 0.1951187E+00 0.4971680E+00
2141 0.4005764E-01 0.1951684E+00 0.4969735E+00
2142 0.4007716E-01 0.1952181E+00 0.4967789E+00
2143 0.4009669E-01 0.1952678E+00 0.4965841E+00
2144 0.4011622E-01 0.1953174E+00 0.4963892E+00
2145 0.4013575E-01 0.1953671E+00 0.4961942E+00
2146 0.4015529E-01 0.1954167E+00 0.4959991E+00
2147 0.4017484E-01 0.1954663E+00 0.4958038E+00
2148 0.4019438E-01 0.1955158E+00 0.4956084E+00
2149 0.4021394E-01 0.1955654E+00 0.4954129E+00
2150 0.4023350E-01 0.1956149E+00 0.4952173E+00
2151 0.4025306E-01 0.1956644E+00 0.4950215E+00
2152 0.4027263E-01 0.1957139E+00 0.4948256E+00
2153 0.4029220E-01 0.1957634E+00 0.4946296E+00
2154 0.4031178E-01 0.1958128E+00 0.4944335E+00
2155 0.4033137E-01 0.1958623E+00 0.4942372E+00
2156 0.4035096E-01 0.1959117E+00 0.4940408E+00
2157 0.4037055E-01 0.1959611E+00 0.4938443E+00
2158 0.4039015E-01 0.1960105E+00 0.4936477E+00
2159 0.4040975E-01 0.1960598E+00 0.4934510E+00
2160 0.4042936E-01 0.1961091E+00 0.4932541E+00
2161 0.4044897E-01 0.1961585E+00 0.4930571E+00
2162 0.4046859E-01 0.1962078E+00 0.4928600E+00
2163 0.4048821E-01 0.1962570E+00 0.4926628E+00
2164 0.4050784E-01 0.1963063E+00 0.4924655E+00
2165 0.4052748E-01 0.1963555E+00 0.4922680E+00
2166 0.4054711E-01 0.1964047E+00 0.4920704E+00
2167 0.4056676E-01 0.1964539E+00 0.4918727E+00
2168 0.4058640E-01 0.1965031E+00 0.4916749E+00
2169 0.4060606E-01 0.1965523E+00 0.4914769E+00
2170 0.4062572E-01 0.1966014E+00 0.4912789E+00
2171 0.4064538E-01 0.1966505E+00 0.4910807E+00
2172 0.4066505E-01 0.1966996E+00 0.4908824E+00
2173 0.4068472E-01 0.1967487E+00 0.4906840E+00
2174 0.4070439E-01 0.1967978E+00 0.4904855E+00
2175 0.4072408E-01 0.1968468E+00 0.4902868E+00
2176 0.4074376E-01 0.1968958E+00 0.4900881E+00
2177 0.4076346E-01 0.1969448E+00 0.4898892E+00
2178 0.4078315E-01 0.1969938E+00 0.4896902E+00
2179 0.4080286E-01 0.1970428E+00 0.4894911E+00
2180 0.4082256E-01 0.1970917E+00 0.4892918E+00
2181 0.4084227E-01 0.1971406E+00 0.4890925E+00
2182 0.4086199E-01 0.1971895E+00 0.4888931E+00
2183 0.4088171E-01 0.1972384E+00 0.4886935E+00
2184 0.4090144E-01 0.1972873E+00 0.4884938E+00
2185 0.4092117E-01 0.1973361E+00 0.4882940E+00
2186 0.4094090E-01 0.1973849E+00 0.4880941E+00
2187 0.4096065E-01 0.1974337E+00 0.4878941E+00
2188 0.4098039E-01 0.1974825E+00 0.4876939E+00
2189 0.4100014E-01 0.1975313E+00 0.4874937E+00
2190 0.4101990E-01 0.1975800E+00 0.4872933E+00
2191 0.4103966E-01 0.1976287E+00 0.4870928E+00
2192 0.4105942E-01 0.1976774E+00 0.4868923E+00
2193 0.4107919E-01 0.1977261E+00 0.4866916E+00
2194 0.4109897E-01 0.1977747E+00 0.4864907E+00
2195 0.4111875E-01 0.1978234E+00 0.4862898E+00
2196 0.4113853E-01 0.1978720E+00 0.4860888E+00
2197 0.4115832E-01 0.1979206E+00 0.4858877E+00
2198 0.4117812E-01 0.1979692E+00 0.4856864E+00
2199 0.4119792E-01 0.1980177E+00 0.4854850E+00
2200 0.4121772E-01 0.1980663E+00 0.4852836E+00
2201 0.4123753E-01 0.1981148E+00 0.4850820E+00
2202 0.4125734E-01 0.1981633E+00 0.4848803E+00
2203 0.4127716E-01 0.1982118E+00 0.4846785E+00
2204 0.4129699E-01 0.1982602E+00 0.4844766E+00
2205 0.4131681E-01 0.1983087E+00 0.4842746E+00
2206 0.4133665E-01 0.1983571E+00 0.4840725E+00
2207 0.4135649E-01 0.1984055E+00 0.4838702E+00
2208 0.4137633E-01 0.1984539E+00 0.4836679E+00
2209 0.4139618E-01 0.1985022E+00 0.4834655E+00
2210 0.4141603E-01 0.1985506E+00 0.4832629E+00
2211 0.4143589E-01 0.1985989E+00 0.4830603E+00
2212 0.4145575E-01 0.1986472E+00 0.4828575E+00
2213 0.4147562E-01 0.1986954E+00 0.4826546E+00
2214 0.4149549E-01 0.1987437E+00 0.4824516E+00
2215 0.4151537E-01 0.1987919E+00 0.4822486E+00
2216 0.4153525E-01 0.1988401E+00 0.4820454E+00
2217 0.4155513E-01 0.1988883E+00 0.4818421E+00
2218 0.4157502E-01 0.1989365E+00 0.4816387E+00
2219 0.4159492E-01 0.1989847E+00 0.4814352E+00
2220 0.4161482E-01 0.1990328E+00 0.4812316E+00
2221 0.4163473E-01 0.1990809E+00 0.4810279E+00
2222 0.4165464E-01 0.1991290E+00 0.4808241E+00
2223 0.4167455E-01 0.1991771E+00 0.4806202E+00
2224 0.4169447E-01 0.1992251E+00 0.4804162E+00
2225 0.4171440E-01 0.1992732E+00 0.4802121E+00
2226 0.4173433E-01 0.1993212E+00 0.4800078E+00
2227 0.4175426E-01 0.1993692E+00 0.4798035E+00
2228 0.4177420E-01 0.1994171E+00 0.4795991E+00
2229 0.4179415E-01 0.1994651E+00 0.4793946E+00
2230 0.4181409E-01 0.1995130E+00 0.4791900E+00
2231 0.4183405E-01 0.1995609E+00 0.4789852E+00
2232 0.4185401E-01 0.1996088E+00 0.4787804E+00
2233 0.4187397E-01 0.1996567E+00 0.4785755E+00
2234 0.4189394E-01 0.1997045E+00 0.4783705E+00
2235 0.4191391E-01 0.1997524E+00 0.4781653E+00
2236 0.4193389E-01 0.1998002E+00 0.4779601E+00
2237 0.4195387E-01 0.1998479E+00 0.4777548E+00
2238 0.4197386E-01 0.1998957E+00 0.4775494E+00
2239 0.4199385E-01 0.1999435E+00 0.4773439E+00
2240 0.4201385E-01 0.1999912E+00 0.4771383E+00
2241 0.4203385E-01 0.2000389E+00 0.4769325E+00
2242 0.4205385E-01 0.2000866E+00 0.4767267E+00
2243 0.4207387E-01 0.2001342E+00 0.4765208E+00
2244 0.4209388E-01 0.2001819E+00 0.4763148E+00
2245 0.4211390E-01 0.2002295E+00 0.4761087E+00
2246 0.4213393E-01 0.2002771E+00 0.4759025E+00
2247 0.4215396E-01 0.2003247E+00 0.4756962E+00
2248 0.4217399E-01 0.2003722E+00 0.4754898E+00
2249 0.4219403E-01 0.2004198E+00 0.4752834E+00
2250 0.4221408E-01 0.2004673E+00 0.4750768E+00
2251 0.4223413E-01 0.2005148E+00 0.4748701E+00
2252 0.4225418E-01 0.2005623E+00 0.4746633E+00
2253 0.4227424E-01 0.2006097E+00 0.4744565E+00
2254 0.4229430E-01 0.2006572E+00 0.4742495E+00
2255 0.4231437E-01 0.2007046E+00 0.4740425E+00
2256 0.4233444E-01 0.2007520E+00 0.4738353E+00
2257 0.4235452E-01 0.2007993E+00 0.4736281E+00
2258 0.4237460E-01 0.2008467E+00 0.4734207E+00
2259 0.4239469E-01 0.2008940E+00 0.4732133E+00
2260 0.4241478E-01 0.2009413E+00 0.4730058E+00
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1 3 2 9
-0.24061710471567E+04 0.77196186889708E+03 -0.82030454223510E+02 0.28895977805369E+01 0.32082280628756E+04 -0.10292824918628E+04 0.10937393896468E+03 -0.38527970407158E+01 -0.13176650972525E+04 0.42274102344364E+03 -0.44921439217636E+02 0.15823987845797E+01 0.17186936051119E+03 -0.55140133492649E+02 0.58593181588221E+01 -0.20639984146692E+00 0.20051425392972E+04 -0.64330155741423E+03 0.68358711852925E+02 -0.24079981504474E+01 -0.26735233857296E+04 0.85773540988564E+03 -0.91144949137233E+02 0.32106642005965E+01 0.10980542477104E+04 -0.35228418620303E+03 0.37434532681364E+02 -0.13186656538164E+01 -0.14322446709266E+03 0.45950111243874E+02 -0.48827651323518E+01 0.17199986788910E+00
-0.55141419830674E+03 0.17690792828891E+03 -0.18798645759554E+02 0.66219949137303E+00 0.73521893107565E+03 -0.23587723771855E+03 0.25064861012739E+02 -0.88293265516404E+00 -0.30196491812036E+03 0.96878151205834E+02 -0.10294496487375E+02 0.36263305479952E+00 0.39386728450481E+02 -0.12636280592065E+02 0.13427604113967E+01 -0.47299963669502E-01 0.50128563482431E+02 -0.16082538935356E+02 0.17089677963231E+01 -0.60199953761185E-01 -0.66838084643241E+02 0.21443385247141E+02 -0.22786237284308E+01 0.80266605014913E-01 0.27451356192760E+02 -0.88071046550758E+01 0.93586331703409E+00 -0.32966641345411E-01 -0.35806116773165E+01 0.11487527810968E+01 -0.12206912830879E+00 0.42999966972275E-02
1 3 2 10
0.21391365085915E+04 -0.60284756151214E+03 0.56572205185890E+02 -0.17678814120591E+01 -0.28521820114553E+04 0.80379674868286E+03 -0.75429606914520E+02 0.23571752160788E+01 0.11714318975620E+04 -0.33013080749474E+03 0.30980017125607E+02 -0.96812553517520E+00 -0.15279546489939E+03 0.43060540108010E+02 -0.40408717989922E+01 0.12627724371850E+00 -0.17826137571596E+04 0.50237296792679E+03 -0.47143504321575E+02 0.14732345100492E+01 0.23768183428794E+04 -0.66983062390238E+03 0.62858005762100E+02 -0.19643126800656E+01 -0.97619324796833E+03 0.27510900624562E+03 -0.25816680938005E+02 0.80677127931267E+00 0.12732955408283E+03 -0.35883783423342E+02 0.33673931658268E+01 -0.10523103643209E+00
0.49021878321888E+03 -0.13815256617987E+03 0.12964463688433E+02 -0.40513949026354E+00 -0.65362504429184E+03 0.18420342157315E+03 -0.17285951584578E+02 0.54018598701805E+00 0.26845314319129E+03 -0.75654976717546E+02 0.70995872579515E+01 -0.22186210181098E+00 -0.35015627372777E+02 0.98680404414190E+01 -0.92603312060237E+00 0.28938535018824E-01 -0.44565343928989E+02 0.12559324198170E+02 -0.11785876080394E+01 0.36830862751231E-01 0.59420458571985E+02 -0.16745765597560E+02 0.15714501440525E+01 -0.49107817001641E-01 -0.24404831199208E+02 0.68777251561405E+01 -0.64541702345014E+00 0.20169281982817E-01 0.31832388520706E+01 -0.89709458558355E+00 0.84184829145670E-01 -0.26307759108022E-02
1 3 3 1
-0.11425615154207E+02 -0.10338640697300E+02 0.73847433552146E+01 -0.14769486710429E+01 0.95213459618390E+01 0.86155339144170E+01 -0.61539527960122E+01 0.12307905592024E+01 -0.26183701395057E+01 -0.23692718264647E+01 0.16923370189033E+01 -0.33846740378067E+00 0.23803364904597E+00 0.21538834786043E+00 -0.15384881990030E+00 0.30769763980061E-01 0.95213459618390E+01 0.86155339144170E+01 -0.61539527960122E+01 0.12307905592024E+01 -0.79344549681991E+01 -0.71796115953475E+01 0.51282939966768E+01 -0.10256587993354E+01 0.21819751162548E+01 0.19743931887206E+01 -0.14102808490861E+01 0.28205616981722E+00 -0.19836137420498E+00 -0.17949028988369E+00 0.12820734991692E+00 -0.25641469983384E-01
-0.26183701395057E+01 -0.23692718264647E+01 0.16923370189033E+01 -0.33846740378067E+00 0.21819751162548E+01 0.19743931887206E+01 -0.14102808490861E+01 0.28205616981722E+00 -0.60004315697006E+00 -0.54295812689816E+00 0.38782723349868E+00 -0.77565446699737E-01 0.54549377906369E-01 0.49359829718014E-01 -0.35257021227153E-01 0.70514042454306E-02 0.23803364904597E+00 0.21538834786043E+00 -0.15384881990030E+00 0.30769763980061E-01 -0.19836137420498E+00 -0.17949028988369E+00 0.12820734991692E+00 -0.25641469983384E-01 0.54549377906369E-01 0.49359829718014E-01 -0.35257021227153E-01 0.70514042454306E-02 -0.49590343551245E-02 -0.44872572470922E-02 0.32051837479230E-02 -0.64103674958460E-03
1 3 3 2
-0.17333409838378E+02 0.14769486710429E+01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.12037090165541E+02 0.10256587993354E+01 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00
-0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.91030494376901E+00 0.77565446699737E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 -0.75231813534629E-02 0.64103674958460E-03 0.00000000000000E+00 0.00000000000000E+00
1 3 3 3
-0.17333409838378E+02 0.14769486710429E+01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.12037090165541E+02 0.10256587993354E+01 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00
-0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.91030494376901E+00 0.77565446699737E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 -0.75231813534629E-02 0.64103674958460E-03 0.00000000000000E+00 0.00000000000000E+00
1 3 3 4
-0.17333409838378E+02 0.14769486710429E+01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.12037090165541E+02 0.10256587993354E+01 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00
-0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.91030494376901E+00 0.77565446699737E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 -0.75231813534629E-02 0.64103674958460E-03 0.00000000000000E+00 0.00000000000000E+00
1 3 3 5
-0.17333409838378E+02 0.14769486710429E+01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.12037090165541E+02 0.10256587993354E+01 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00
-0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.91030494376901E+00 0.77565446699737E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 -0.75231813534629E-02 0.64103674958460E-03 0.00000000000000E+00 0.00000000000000E+00
1 3 3 6
-0.17333409838378E+02 0.14769486710429E+01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.12037090165541E+02 0.10256587993354E+01 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00
-0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.91030494376901E+00 0.77565446699737E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 -0.75231813534629E-02 0.64103674958460E-03 0.00000000000000E+00 0.00000000000000E+00
1 3 3 7
-0.17333409838378E+02 0.14769486710429E+01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 0.14444508198649E+02 -0.12307905592024E+01 0.00000000000000E+00 0.00000000000000E+00 -0.12037090165541E+02 0.10256587993354E+01 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00
-0.39722397546284E+01 0.33846740378067E+00 0.00000000000000E+00 0.00000000000000E+00 0.33101997955237E+01 -0.28205616981722E+00 0.00000000000000E+00 0.00000000000000E+00 -0.91030494376901E+00 0.77565446699737E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 0.36111270496622E+00 -0.30769763980061E-01 0.00000000000000E+00 0.00000000000000E+00 -0.30092725413851E+00 0.25641469983384E-01 0.00000000000000E+00 0.00000000000000E+00 0.82754994888091E-01 -0.70514042454306E-02 0.00000000000000E+00 0.00000000000000E+00 -0.75231813534629E-02 0.64103674958460E-03 0.00000000000000E+00 0.00000000000000E+00
1 3 3 8
-0.75574327068776E+03 0.26812495397776E+03 -0.32049039099365E+02 0.12819615639746E+01 0.62978605890647E+03 -0.22343746164814E+03 0.26707532582805E+02 -0.10683013033122E+01 -0.17319116619928E+03 0.61445301953238E+02 -0.73445714602713E+01 0.29378285841085E+00 0.15744651472662E+02 -0.55859365412034E+01 0.66768831457011E+00 -0.26707532582805E-01 0.62978605890647E+03 -0.22343746164814E+03 0.26707532582805E+02 -0.10683013033122E+01 -0.52482171575539E+03 0.18619788470678E+03 -0.22256277152337E+02 0.89025108609349E+00 0.14432597183273E+03 -0.51204418294365E+02 0.61204762168927E+01 -0.24481904867571E+00 -0.13120542893885E+02 0.46549471176695E+01 -0.55640692880843E+00 0.22256277152337E-01
-0.17319116619928E+03 0.61445301953238E+02 -0.73445714602713E+01 0.29378285841085E+00 0.14432597183273E+03 -0.51204418294365E+02 0.61204762168927E+01 -0.24481904867571E+00 -0.39689642254001E+02 0.14081215030950E+02 -0.16831309596455E+01 0.67325238385820E-01 0.36081492958183E+01 -0.12801104573591E+01 0.15301190542232E+00 -0.61204762168927E-02 0.15744651472662E+02 -0.55859365412034E+01 0.66768831457011E+00 -0.26707532582805E-01 -0.13120542893885E+02 0.46549471176695E+01 -0.55640692880843E+00 0.22256277152337E-01 0.36081492958183E+01 -0.12801104573591E+01 0.15301190542232E+00 -0.61204762168927E-02 -0.32801357234712E+00 0.11637367794174E+00 -0.13910173220211E-01 0.55640692880843E-03
1 3 3 9
0.27499097681791E+04 -0.88224213588238E+03 0.93749090541154E+02 -0.33023974634707E+01 -0.22915914734825E+04 0.73520177990198E+03 -0.78124242117628E+02 0.27519978862256E+01 0.63018765520770E+03 -0.20218048947304E+03 0.21484166582348E+02 -0.75679941871203E+00 -0.57289786837064E+02 0.18380044497550E+02 -0.19531060529407E+01 0.68799947155640E-01 -0.22915914734825E+04 0.73520177990198E+03 -0.78124242117628E+02 0.27519978862256E+01 0.19096595612355E+04 -0.61266814991832E+03 0.65103535098024E+02 -0.22933315718547E+01 -0.52515637933975E+03 0.16848374122754E+03 -0.17903472151957E+02 0.63066618226003E+00 0.47741489030886E+02 -0.15316703747958E+02 0.16275883774506E+01 -0.57333289296366E-01
0.63018765520770E+03 -0.20218048947304E+03 0.21484166582348E+02 -0.75679941871203E+00 -0.52515637933975E+03 0.16848374122754E+03 -0.17903472151957E+02 0.63066618226003E+00 0.14441800431843E+03 -0.46333028837573E+02 0.49234548417880E+01 -0.17343320012151E+00 -0.13128909483494E+02 0.42120935306884E+01 -0.44758680379891E+00 0.15766654556501E-01 -0.57289786837064E+02 0.18380044497550E+02 -0.19531060529407E+01 0.68799947155640E-01 0.47741489030886E+02 -0.15316703747958E+02 0.16275883774506E+01 -0.57333289296366E-01 -0.13128909483494E+02 0.42120935306884E+01 -0.44758680379891E+00 0.15766654556501E-01 0.11935372257722E+01 -0.38291759369895E+00 0.40689709436265E-01 -0.14333322324092E-02
1 3 3 10
-0.24447274383903E+04 0.68896864172816E+03 -0.64653948783875E+02 0.20204358994961E+01 0.20372728653252E+04 -0.57414053477347E+03 0.53878290653229E+02 -0.16836965829134E+01 -0.56025003796443E+03 0.15788864706270E+03 -0.14816529929638E+02 0.46301656030118E+00 0.50931821633130E+02 -0.14353513369337E+02 0.13469572663307E+01 -0.42092414572835E-01 0.20372728653252E+04 -0.57414053477347E+03 0.53878290653229E+02 -0.16836965829134E+01 -0.16977273877710E+04 0.47845044564456E+03 -0.44898575544357E+02 0.14030804857612E+01 0.46687503163703E+03 -0.13157387255225E+03 0.12347108274698E+02 -0.38584713358432E+00 -0.42443184694275E+02 0.11961261141114E+02 -0.11224643886089E+01 0.35077012144029E-01
-0.56025003796443E+03 0.15788864706270E+03 -0.14816529929638E+02 0.46301656030118E+00 0.46687503163703E+03 -0.13157387255225E+03 0.12347108274698E+02 -0.38584713358432E+00 -0.12839063370018E+03 0.36182814951870E+02 -0.33954547755420E+01 0.10610796173569E+00 0.11671875790926E+02 -0.32893468138063E+01 0.30867770686746E+00 -0.96461783396080E-02 0.50931821633130E+02 -0.14353513369337E+02 0.13469572663307E+01 -0.42092414572835E-01 -0.42443184694275E+02 0.11961261141114E+02 -0.11224643886089E+01 0.35077012144029E-01 0.11671875790926E+02 -0.32893468138063E+01 0.30867770686746E+00 -0.96461783396080E-02 -0.10610796173569E+01 0.29903152852785E+00 -0.28061609715223E-01 0.87692530360073E-03
- # LAMMPS/COMB3 carbon spline values, converted from HELL code parameters.
- # Converter written by Ray Shan @ MSE, UF (Apr 2011)
- # Converter modified by TAO LIANG @ MSE, UF (June 2012)
- # Converted on: 20131005 000249
+ # LAMMPS/COMB3 carbon spline values, converted from COMB code parameters.
+ # Converter generated by TAO LIANG @ MSE, UF (June 2012)
+ # Converted on: 2014-01-27
diff --git a/src/MANYBODY/pair_comb3.cpp b/src/MANYBODY/pair_comb3.cpp
index 37f87788b..574b89baf 100644
--- a/src/MANYBODY/pair_comb3.cpp
+++ b/src/MANYBODY/pair_comb3.cpp
@@ -1,4058 +1,4007 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ray Shan (Sandia, tnshan@sandia.gov)
Updates and debug: Tao Liang (U Florida, liang75@ufl.edu)
Dundar Yilmaz (dundar.yilmaz@zirve.edu.tr)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_comb3.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "group.h"
#include "update.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXLINE 1024
#define DELTA 4
#define PGDELTA 1
#define MAXNEIGH 24
/* ---------------------------------------------------------------------- */
PairComb3::PairComb3(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
restartinfo = 0;
one_coeff = 1;
ghostneigh = 1;
nmax = 0;
NCo = NULL;
bbij = NULL;
nelements = 0;
elements = NULL;
nparams = 0;
maxparam = 0;
params = NULL;
elem2param = NULL;
intype = NULL;
afb = NULL;
dafb = NULL;
fafb = NULL;
dfafb = NULL;
ddfafb = NULL;
phin = NULL;
dphin = NULL;
erpaw = NULL;
vvdw = NULL;
vdvdw = NULL;
dpl = NULL;
xcctmp = NULL;
xchtmp = NULL;
xcotmp = NULL;
sht_num = NULL;
sht_first = NULL;
ipage = NULL;
pgsize = oneatom = 0;
cflag = 0;
// set comm size needed by this Pair
comm_forward = 1;
comm_reverse = 1;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairComb3::~PairComb3()
{
memory->destroy(NCo);
if (elements)
for (int i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
memory->sfree(params);
memory->destroy(elem2param);
memory->destroy(afb);
memory->destroy(dpl);
memory->destroy(dafb);
memory->destroy(fafb);
memory->destroy(phin);
memory->destroy(bbij);
memory->destroy(vvdw);
memory->destroy(vdvdw);
memory->destroy(dphin);
memory->destroy(erpaw);
memory->destroy(dfafb);
memory->destroy(ddfafb);
memory->destroy(xcctmp);
memory->destroy(xchtmp);
memory->destroy(xcotmp);
memory->destroy(intype);
memory->destroy(sht_num);
memory->sfree(sht_first);
delete [] ipage;
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cutghost);
delete [] map;
delete [] esm;
}
}
/* ---------------------------------------------------------------------- */
void PairComb3::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cutghost,n+1,n+1,"pair:cutghost");
map = new int[n+1];
esm = new double[n];
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairComb3::settings(int narg, char **arg)
{
if (strcmp(arg[0],"polar_on") == 0) {
pol_flag = 1;
if (comm->me == 0) fprintf(screen,
" PairComb3: polarization is on \n");
} else if (strcmp(arg[0],"polar_off") == 0) {
pol_flag = 0;
if (comm->me == 0) fprintf(screen,
" PairComb3: polarization is off \n");
} else {
error->all(FLERR,"Illegal pair_style command");
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairComb3::coeff(int narg, char **arg)
{
int i,j,n;
double r;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
// nelements = # of unique elements
// elements = list of element names
if (elements) {
for (i = 0; i < nelements; i++) delete [] elements[i];
delete [] elements;
}
elements = new char*[atom->ntypes];
for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
nelements = 0;
for (i = 3; i < narg; i++) {
if ((strcmp(arg[i],"C") == 0) && (cflag == 0)) {
if( comm->me == 0) fprintf(screen,
" PairComb3: Found C: reading additional library file \n");
read_lib();
cflag = 1;
}
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < nelements; j++)
if (strcmp(arg[i],elements[j]) == 0) break;
map[i-2] = j;
if (j == nelements) {
n = strlen(arg[i]) + 1;
elements[j] = new char[n];
strcpy(elements[j],arg[i]);
nelements++;
}
}
// read potential file and initialize potential parameters
read_file(arg[2]);
setup();
n = atom->ntypes;
// generate Wolf 1/r energy and van der Waals look-up tables
tables();
// clear setflag since coeff() called once with I,J = * *
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
int count = 0;
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairComb3::init_style()
{
if (atom->tag_enable == 0)
error->all(FLERR,"Pair style COMB3 requires atom IDs");
if (force->newton_pair == 0)
error->all(FLERR,"Pair style COMB3 requires newton pair on");
if (!atom->q_flag)
error->all(FLERR,"Pair style COMB3 requires atom attribute q");
// need a full neighbor list
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->ghost = 1;
// local Comb neighbor list
// create pages if first time or if neighbor pgsize/oneatom has changed
int create = 0;
if (ipage == NULL) create = 1;
if (pgsize != neighbor->pgsize) create = 1;
if (oneatom != neighbor->oneatom) create = 1;
if (create) {
delete [] ipage;
pgsize = neighbor->pgsize;
oneatom = neighbor->oneatom;
int nmypage = comm->nthreads;
ipage = new MyPage<int>[nmypage];
for (int i = 0; i < nmypage; i++)
ipage[i].init(oneatom,pgsize);
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairComb3::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
cutghost[j][i] = cutghost[i][j] = cutmax;
return cutmax;
}
/* ---------------------------------------------------------------------- */
void PairComb3::read_lib()
{
unsigned int maxlib = 1024;
int i,j,k,l,n,nwords,m;
int ii,jj,kk,ll,mm,iii;
double tmp;
char s[maxlib];
char **words1 = new char*[80];
char **words2 = new char*[70];
MPI_Comm_rank(world,&comm->me);
// open libraray file on proc 0
if(comm->me == 0) {
FILE *fp = fopen("lib.comb3","r");
if (fp == NULL) {
char str[128];
- sprintf(str,"Cannot open COMB3 C library file");
+ sprintf(str,"Cannot open COMB3 C library file \n");
error->one(FLERR,str);
}
// read and store at the same time
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
ccutoff[0] = atof(words1[0]);
ccutoff[1] = atof(words1[1]);
ccutoff[2] = atof(words1[2]);
ccutoff[3] = atof(words1[3]);
ccutoff[4] = atof(words1[4]);
ccutoff[5] = atof(words1[5]);
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
ch_a[0] = atof(words1[0]);
ch_a[1] = atof(words1[1]);
ch_a[2] = atof(words1[2]);
ch_a[3] = atof(words1[3]);
ch_a[4] = atof(words1[4]);
ch_a[5] = atof(words1[5]);
ch_a[6] = atof(words1[6]);
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
nsplpcn = atoi(words1[0]);
nsplrad = atoi(words1[1]);
nspltor = atoi(words1[2]);
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
maxx = atoi(words1[0]);
maxy = atoi(words1[1]);
maxz = atoi(words1[2]);
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
maxxc = atoi(words1[0]);
maxyc = atoi(words1[1]);
maxconj = atoi(words1[2]);
for (l=0; l<nsplpcn; l++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
maxxcn[l] = atoi(words1[1]);
vmaxxcn[l] = atof(words1[2]);
dvmaxxcn[l] = atof(words1[3]);
}
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
ntab = atoi(words1[0]);
for (i=0; i<ntab+1; i++){
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
pang[i] = atof(words1[1]);
dpang[i] = atof(words1[2]);
ddpang[i] = atof(words1[3]);
}
for (l=0; l<nsplpcn; l++)
for (i=0; i<maxx+1; i++)
for (j=0; j<maxy+1; j++)
for (k=0; k<maxz+1; k++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
ll = atoi(words1[0])-1;
ii = atoi(words1[1]);
jj = atoi(words1[2]);
kk = atoi(words1[3]);
pcn_grid[ll][ii][jj][kk] = atof(words1[4]);
pcn_gridx[ll][ii][jj][kk] = atof(words1[5]);
pcn_gridy[ll][ii][jj][kk] = atof(words1[6]);
pcn_gridz[ll][ii][jj][kk] = atof(words1[7]);
}
for (l=0; l<nsplpcn; l++)
for (i=0; i<maxx; i++)
for (j=0; j<maxy; j++)
for (k=0; k<maxz; k++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
ll = atoi(words1[0])-1;
ii = atoi(words1[1]);
jj = atoi(words1[2]);
kk = atoi(words1[3]);
for(iii=0; iii<2; iii++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
for(m=0; m<32 ; m++) {
mm=iii*32+m;
pcn_cubs[ll][ii][jj][kk][mm] = atof(words1[m]);
}
}
}
for (l=0; l<nsplrad; l++)
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
ll = atoi(words1[0])-1;
ii = atoi(words1[1]);
jj = atoi(words1[2]);
kk = atoi(words1[3])-1;
rad_grid[ll][ii][jj][kk] = atof(words1[4]);
rad_gridx[ll][ii][jj][kk] = atof(words1[5]);
rad_gridy[ll][ii][jj][kk] = atof(words1[6]);
rad_gridz[ll][ii][jj][kk] = atof(words1[7]);
}
for (l=0; l<nsplrad; l++)
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
ll = atoi(words1[0])-1;
ii = atoi(words1[1]);
jj = atoi(words1[2]);
kk = atoi(words1[3])-1;
for (iii=0; iii<2; iii++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
for(m=0; m<32 ; m++){
mm=iii*32+m;
rad_spl[ll][ii][jj][kk][mm] = atof(words1[m]);
}
}
}
for (l=0; l<nspltor; l++)
for (i=0; i<maxxc+1; i++)
for (j=0; j<maxyc+1; j++)
for (k=0; k<maxconj; k++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
ll = atoi(words1[0])-1;
ii = atoi(words1[1]);
jj = atoi(words1[2]);
kk = atoi(words1[3])-1;
tor_grid[ll][ii][jj][kk] = atof(words1[4]);
tor_gridx[ll][ii][jj][kk] = atof(words1[5]);
tor_gridy[ll][ii][jj][kk] = atof(words1[6]);
tor_gridz[ll][ii][jj][kk] = atof(words1[7]);
}
for (l=0; l<nspltor; l++)
for (i=0; i<maxxc; i++)
for (j=0; j<maxyc; j++)
for (k=0; k<maxconj-1; k++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
ll = atoi(words1[0])-1;
ii = atoi(words1[1]);
jj = atoi(words1[2]);
kk = atoi(words1[3])-1;
for(iii=0; iii<2; iii++) {
fgets(s,maxlib,fp);
nwords = 0;
words1[nwords++] = strtok(s," \t\n\r\f");
while (words1[nwords++] = strtok(NULL," \t\n\r\f"))continue;
for (m=0; m<32 ; m++){
mm=iii*32+m;
tor_spl[ll][ii][jj][kk][mm] = atof(words1[m]);
}
}
}
fclose(fp);
}
k = 0;
for (i=0; i<4; i++)
for (j=0; j<4; j++) {
iin2[k][0] = i;
iin2[k][1] = j;
k ++;
}
l = 0;
for (i=0; i<4; i++)
for (j=0; j<4; j++)
for (k=0; k<4; k++) {
iin3[l][0] = i;
iin3[l][1] = j;
iin3[l][2] = k;
l ++;
}
MPI_Bcast(&ccutoff[0],6,MPI_DOUBLE,0,world);
MPI_Bcast(&ch_a[0],7,MPI_DOUBLE,0,world);
MPI_Bcast(&nsplpcn,1,MPI_INT,0,world);
MPI_Bcast(&nsplrad,1,MPI_INT,0,world);
MPI_Bcast(&nspltor,1,MPI_INT,0,world);
MPI_Bcast(&maxx,1,MPI_INT,0,world);
MPI_Bcast(&maxy,1,MPI_INT,0,world);
MPI_Bcast(&maxz,1,MPI_INT,0,world);
MPI_Bcast(&maxxc,1,MPI_INT,0,world);
MPI_Bcast(&maxyc,1,MPI_INT,0,world);
MPI_Bcast(&maxconj,1,MPI_INT,0,world);
MPI_Bcast(&maxxcn,4,MPI_INT,0,world);
MPI_Bcast(&vmaxxcn,4,MPI_DOUBLE,0,world);
MPI_Bcast(&dvmaxxcn,4,MPI_DOUBLE,0,world);
MPI_Bcast(&ntab,1,MPI_INT,0,world);
MPI_Bcast(&pang[0],20001,MPI_DOUBLE,0,world);
MPI_Bcast(&dpang[0],20001,MPI_DOUBLE,0,world);
MPI_Bcast(&ddpang[0],20001,MPI_DOUBLE,0,world);
MPI_Bcast(&pcn_grid[0][0][0][0],500,MPI_DOUBLE,0,world);
MPI_Bcast(&pcn_gridx[0][0][0][0],500,MPI_DOUBLE,0,world);
MPI_Bcast(&pcn_gridy[0][0][0][0],500,MPI_DOUBLE,0,world);
MPI_Bcast(&pcn_gridz[0][0][0][0],500,MPI_DOUBLE,0,world);
MPI_Bcast(&pcn_cubs[0][0][0][0][0],16384,MPI_DOUBLE,0,world);
MPI_Bcast(&rad_grid[0][0][0][0],825,MPI_DOUBLE,0,world);
MPI_Bcast(&rad_gridx[0][0][0][0],825,MPI_DOUBLE,0,world);
MPI_Bcast(&rad_gridy[0][0][0][0],825,MPI_DOUBLE,0,world);
MPI_Bcast(&rad_gridz[0][0][0][0],825,MPI_DOUBLE,0,world);
MPI_Bcast(&rad_spl[0][0][0][0][0],30720,MPI_DOUBLE,0,world);
MPI_Bcast(&tor_grid[0][0][0][0],275,MPI_DOUBLE,0,world);
MPI_Bcast(&tor_gridx[0][0][0][0],275,MPI_DOUBLE,0,world);
MPI_Bcast(&tor_gridy[0][0][0][0],275,MPI_DOUBLE,0,world);
MPI_Bcast(&tor_gridz[0][0][0][0],275,MPI_DOUBLE,0,world);
MPI_Bcast(&tor_spl[0][0][0][0][0],10240,MPI_DOUBLE,0,world);
MPI_Bcast(&iin2[0][0],32,MPI_INT,0,world);
MPI_Bcast(&iin3[0][0],192,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
void PairComb3::read_file(char *file)
{
int params_per_line = 74;
char **words = new char*[params_per_line+1];
if (params) delete [] params;
params = NULL;
nparams = 0;
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = fopen(file,"r");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open COMB3 potential file %s",file);
error->one(FLERR,str);
}
}
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
int n,nwords,ielement,jelement,kelement;
char line[MAXLINE],*ptr;
int eof = 0;
nwords=0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
// strip comment, skip line if blank
if (ptr = strchr(line,'#')) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
// concatenate additional lines until have params_per_line words
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if (ptr = strchr(line,'#')) *ptr = '\0';
nwords = atom->count_words(line);
}
if (nwords != params_per_line){
error->all(FLERR,"Incorrect format in COMB3 potential file");
}
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while (words[nwords++] = strtok(NULL," \t\n\r\f")) continue;
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next line
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (strcmp(words[2],elements[kelement]) == 0) break;
if (kelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].ielementgp = atoi(words[3]);
params[nparams].jelementgp = atoi(words[4]);
params[nparams].kelementgp = atoi(words[5]);
params[nparams].ang_flag = atoi(words[6]);
params[nparams].pcn_flag = atoi(words[7]);
params[nparams].rad_flag = atoi(words[8]);
params[nparams].tor_flag = atoi(words[9]);
params[nparams].vdwflag = atof(words[10]);
params[nparams].powerm = atof(words[11]);
params[nparams].veps = atof(words[12]);
params[nparams].vsig = atof(words[13]);
params[nparams].paaa = atof(words[14]);
params[nparams].pbbb = atof(words[15]);
params[nparams].lami = atof(words[16]);
params[nparams].alfi = atof(words[17]);
params[nparams].powern = atof(words[18]);
params[nparams].QL = atof(words[19]);
params[nparams].QU = atof(words[20]);
params[nparams].DL = atof(words[21]);
params[nparams].DU = atof(words[22]);
params[nparams].qmin = atof(words[23]);
params[nparams].qmax = atof(words[24]);
params[nparams].chi = atof(words[25]);
params[nparams].dj = atof(words[26]);
params[nparams].dk = atof(words[27]);
params[nparams].dl = atof(words[28]);
params[nparams].esm = atof(words[29]);
params[nparams].cmn1 = atof(words[30]);
params[nparams].cmn2 = atof(words[31]);
params[nparams].pcmn1 = atof(words[32]);
params[nparams].pcmn2 = atof(words[33]);
params[nparams].coulcut = atof(words[34]);
params[nparams].polz = atof(words[35]);
params[nparams].curl = atof(words[36]);
params[nparams].curlcut1 = atof(words[37]);
params[nparams].curlcut2 = atof(words[38]);
params[nparams].curl0 = atof(words[39]);
params[nparams].alpha1 = atof(words[40]);
params[nparams].bigB1 = atof(words[41]);
params[nparams].alpha2 = atof(words[42]);
params[nparams].bigB2 = atof(words[43]);
params[nparams].alpha3 = atof(words[44]);
params[nparams].bigB3 = atof(words[45]);
params[nparams].lambda = atof(words[46]);
params[nparams].bigA = atof(words[47]);
params[nparams].beta = atof(words[48]);
params[nparams].bigr = atof(words[49]);
params[nparams].bigd = atof(words[50]);
params[nparams].pcos6 = atof(words[51]);
params[nparams].pcos5 = atof(words[52]);
params[nparams].pcos4 = atof(words[53]);
params[nparams].pcos3 = atof(words[54]);
params[nparams].pcos2 = atof(words[55]);
params[nparams].pcos1 = atof(words[56]);
params[nparams].pcos0 = atof(words[57]);
params[nparams].pcna = atof(words[58]);
params[nparams].pcnb = atof(words[59]);
params[nparams].pcnc = atof(words[60]);
params[nparams].pcnd = atof(words[61]);
- params[nparams].plp1 = atof(words[62]);
- params[nparams].plp2 = atof(words[63]);
- params[nparams].plp3 = atof(words[64]);
- params[nparams].plp4 = atof(words[65]);
- params[nparams].plp5 = atof(words[66]);
- params[nparams].plp6 = atof(words[67]);
- params[nparams].addrep = atof(words[68]);
- params[nparams].pbb1=atof(words[69]);
- params[nparams].pbb2=atof(words[70]);
- params[nparams].ptork1=atof(words[71]);
- params[nparams].ptork2=atof(words[72]);
+ params[nparams].p6p0 = atof(words[62]);
+ params[nparams].p6p1 = atof(words[63]);
+ params[nparams].p6p2 = atof(words[64]);
+ params[nparams].p6p3 = atof(words[65]);
+ params[nparams].p6p4 = atof(words[66]);
+ params[nparams].p6p5 = atof(words[67]);
+ params[nparams].p6p6 = atof(words[68]);
+ params[nparams].ptork1=atof(words[69]);
+ params[nparams].ptork2=atof(words[70]);
+ params[nparams].addrepr=atof(words[71]);
+ params[nparams].addrep=atof(words[72]);
params[nparams].pcross = atof(words[73]);
params[nparams].powermint = int(params[nparams].powerm);
// parameter sanity checks
if (params[nparams].lambda < 0.0 || params[nparams].powern < 0.0 ||
params[nparams].beta < 0.0 || params[nparams].alpha1 < 0.0 ||
params[nparams].bigB1< 0.0 || params[nparams].bigA< 0.0 ||
params[nparams].bigB2< 0.0 || params[nparams].alpha2 <0.0 ||
params[nparams].bigB3< 0.0 || params[nparams].alpha3 <0.0 ||
params[nparams].bigr < 0.0 || params[nparams].bigd < 0.0 ||
params[nparams].bigd > params[nparams].bigr ||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
- params[nparams].addrep < 0.0 || params[nparams].powermint < 1.0 ||
+ params[nparams].addrepr < 0.0 || params[nparams].powermint < 1.0 ||
params[nparams].QL > 0.0 || params[nparams].QU < 0.0 ||
params[nparams].DL < 0.0 || params[nparams].DU > 0.0 ||
params[nparams].pcross < 0.0 ||
params[nparams].esm < 0.0 || params[nparams].veps < 0.0 ||
params[nparams].vsig < 0.0 || params[nparams].vdwflag < 0.0
)
error->all(FLERR,"Illegal COMB3 parameter");
nparams++;
}
delete [] words;
}
/* ---------------------------------------------------------------------- */
void PairComb3::setup()
{
int i,j,k,m,n;
// set elem2param for all element triplet combinations
// must be a single exact match to lines read from file
// do not allow for ACB in place of ABC
memory->destroy(elem2param);
memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
for (i = 0; i < nelements; i++)
for (j = 0; j < nelements; j++)
for (k = 0; k < nelements; k++) {
n = -1;
for (m = 0; m < nparams; m++) {
if (i == params[m].ielement && j == params[m].jelement &&
k == params[m].kelement) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = m;
}
}
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
elem2param[i][j][k] = n;
}
// compute parameter values derived from inputs
for (m = 0; m < nparams; m++) {
params[m].cut = params[m].bigr + params[m].bigd;
params[m].cutsq = params[m].cut*params[m].cut;
params[m].c1 = pow(2.0*params[m].powern*1.0e-16,-1.0/params[m].powern);
params[m].c2 = pow(2.0*params[m].powern*1.00e-8,-1.0/params[m].powern);
params[m].c3 = 1.0/params[m].c2;
params[m].c4 = 1.0/params[m].c1;
params[m].Qo = (params[m].QU+params[m].QL)/2.0; // (A22)
params[m].dQ = (params[m].QU-params[m].QL)/2.0; // (A21)
params[m].aB = 1.0 /
(1.0-pow(fabs(params[m].Qo/params[m].dQ),10)); // (A20)
params[m].bB = pow(fabs(params[m].aB),0.1)/params[m].dQ; // (A19)
params[m].nD = log(params[m].DU/(params[m].DU-params[m].DL))/
log(params[m].QU/(params[m].QU-params[m].QL));
params[m].bD = (pow((params[m].DL-params[m].DU),(1.0/params[m].nD)))/
(params[m].QU-params[m].QL);
params[m].lcut = params[m].coulcut;
params[m].lcutsq = params[m].lcut*params[m].lcut;
}
// set cutmax to max of all params
cutmin = cutmax = 0.0;
polar = 0;
for (m = 0; m < nparams; m++) {
if (params[m].cutsq > cutmin) cutmin = params[m].cutsq + 2.0;
if (params[m].lcut > cutmax) cutmax = params[m].lcut;
}
chicut1 = 7.0;
chicut2 = cutmax;
}
/* ---------------------------------------------------------------------- */
void PairComb3::Short_neigh()
{
int n,nj,*neighptrj,icontrol;
int iparam_ij,iparam_ji,iparam_jk,*ilist,*jlist,*numneigh,**firstneigh;
int inum,jnum,i,j,k,l,ii,jj,kk,ll,itype,jtype,ktype,ltype;
- tagint itag,jtag;
+ tagint itag, jtag;
double rr1,rr2,rsq1,rsq2,delrj[3],delrk[3];
int sht_knum,*sht_klist;
double **x = atom->x;
+ tagint *tag = atom->tag;
int *type = atom->type;
int ntype = atom->ntypes;
int nlocal = atom->nlocal;
int *klist,knum;
if (atom->nmax > nmax) {
memory->sfree(sht_first);
nmax = atom->nmax;
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
"pair:sht_first");
memory->grow(dpl,nmax,3,"pair:dpl");
memory->grow(xcctmp,nmax,"pair:xcctmp");
memory->grow(xchtmp,nmax,"pair:xchtmp");
memory->grow(xcotmp,nmax,"pair:xcotmp");
memory->grow(NCo,nmax,"pair:NCo");
memory->grow(sht_num,nmax,"pair:sht_num");
memory->grow(bbij,nmax,MAXNEIGH,"pair:bbij");
}
inum = list->inum + list->gnum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// create COMB neighbor list
ipage->reset();
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
+ itag = tag[i];
dpl[i][0] = dpl[i][1] = dpl[i][2] = 0.0;
nj = 0;
neighptrj = ipage->vget();
itype = map[type[i]];
jlist = firstneigh[i];
jnum = numneigh[i];
NCo[i] = 0.0;
xcctmp[i] = 0.0;
xchtmp[i] = 0.0;
xcotmp[i] = 0.0;
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
+ jtag = tag[j];
delrj[0] = x[i][0] - x[j][0];
delrj[1] = x[i][1] - x[j][1];
delrj[2] = x[i][2] - x[j][2];
rsq1 = vec3_dot(delrj,delrj);
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
iparam_ji = elem2param[jtype][itype][itype];
if (rsq1 > cutmin) continue;
neighptrj[nj++] = j;
rr1 = sqrt(rsq1);
NCo[i] += comb_fc(rr1,&params[iparam_ij]) * params[iparam_ij].pcross;
icontrol = params[iparam_ij].jelementgp;
if( icontrol == 1)
xcctmp[i] += comb_fc(rr1,&params[iparam_ij]) * params[iparam_ij].pcross;
if (icontrol == 2)
xchtmp[i] += comb_fc(rr1,&params[iparam_ij]) * params[iparam_ij].pcross;
if (icontrol == 3)
xcotmp[i] += comb_fc(rr1,&params[iparam_ij]) * params[iparam_ij].pcross;
}
sht_first[i] = neighptrj;
sht_num[i] = nj;
ipage->vgot(nj);
if (ipage->status())
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
}
// communicating coordination number to all nodes
pack_flag = 2;
comm->forward_comm_pair(this);
}
/* ---------------------------------------------------------------------- */
void PairComb3::compute(int eflag, int vflag)
{
int i,ii,k,kk,j,jj,im,inum,jnum,itype,jtype,ktype;
int iparam_i,iparam_ij,iparam_ji;
int iparam_ijk,iparam_jik,iparam_ikj,iparam_jli,iparam_jki,iparam_ikl;
int sht_jnum,*sht_jlist,sht_lnum,*sht_llist;
int sht_mnum,*sht_mlist,sht_pnum,*sht_plist;
int *ilist,*jlist,*numneigh,**firstneigh,mr1,mr2,mr3,inty,nj;
- tagint itag,jtag;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
double rr,rsq,rsq1,rsq2,rsq3,iq,jq,yaself;
double fqi,fqij,eng_tmp,vionij,fvionij,sr1,sr2,sr3;
double zeta_ij,prefac_ij1,prefac_ij2,prefac_ij3,prefac_ij4,prefac_ij5;
double zeta_ji,prefac_ji1,prefac_ji2,prefac_ji3,prefac_ji4,prefac_ji5;
double delrj[3],delrk[3],delri[3],fi[3],fj[3],fk[3],fl[3];
- double elp_ij,elp_ji,filp[3],fjlp[3],fklp[3],fllp[3];
+ double ep6p_ij,ep6p_ji,fip6p[3],fjp6p[3],fkp6p[3],flp6p[3];
double potal,fac11,fac11e;
+ tagint itag, jtag;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
int ntype = atom->ntypes;
tagint *tag = atom->tag;
int *type = atom->type;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
// coordination terms
int n;
double xcn, ycn, xcccnij, xchcnij, xcocnij;
double kcn, lcn;
int torindx;
// torsion and radical variables
int l, ll, ltype, m, mm, mtype, p, pp, ptype;
int iparam_jil, iparam_ijl, iparam_ki, iparam_lj,iparam_jk;
int iparam_jl, iparam_ik, iparam_km, iparam_lp;
double kconjug, lconjug, kradtot, lradtot;
double delrl[3], delrm[3], delrp[3], ddprx[3], srmu;
double zet_addi,zet_addj;
double rikinv,rjlinv,rik_hat[3],rjl_hat[3];
evdwl = ecoul = eng_tmp = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = vflag_atom = 0;
// Build short range neighbor list
Short_neigh();
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
yaself = vionij = fvionij = fpair = 0.0;
// self energy correction term: potal
potal_calc(potal,fac11,fac11e);
// generate initial dipole tensor
if (pol_flag )
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itag = tag[i];
itype = map[type[i]];
iq = q[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
jq = q[j];
delrj[0] = x[j][0] - x[i][0];
delrj[1] = x[j][1] - x[i][1];
delrj[2] = x[j][2] - x[i][2];
rsq = vec3_dot(delrj,delrj);
iparam_ij = elem2param[itype][jtype][jtype];
iparam_ji = elem2param[jtype][itype][itype];
if (rsq > params[iparam_ij].lcutsq) continue;
tri_point(rsq, mr1, mr2, mr3, sr1, sr2, sr3);
dipole_init(&params[iparam_ij],&params[iparam_ji],fac11,delrj
,rsq,mr1,mr2,mr3,sr1,sr2,sr3,iq,jq,i,j);
}
}
// loop over full neighbor list of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
itag = tag[i];
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
iq = q[i];
nj = 0;
iparam_i = elem2param[itype][itype][itype];
// self energy, only on i atom
yaself = self(&params[iparam_i],iq);
// dipole self energy
if (pol_flag)
yaself += dipole_self(&params[iparam_i],i);
if (evflag) ev_tally(i,i,nlocal,0,0.0,yaself,0.0,0.0,0.0,0.0);
// two-body interactions (long:R + A, short: only R)
jlist = firstneigh[i];
jnum = numneigh[i];
sht_jlist = sht_first[i];
sht_jnum = sht_num[i];
// long range interactions
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
jtag = tag[j];
if (itag > jtag) {
if ((itag+jtag) % 2 == 0) continue;
} else if (itag < jtag) {
if ((itag+jtag) % 2 == 1) continue;
} else {
if (x[j][2] < x[i][2]) continue;
if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
}
jtype = map[type[j]];
jq = q[j];
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
iparam_ij = elem2param[itype][jtype][jtype];
iparam_ji = elem2param[jtype][itype][itype];
if (rsq > params[iparam_ij].lcutsq) continue;
inty = intype[itype][jtype];
// three-point interpolation
tri_point(rsq, mr1, mr2, mr3, sr1, sr2, sr3);
// Q-indenpendent: van der Waals
vdwaals(inty,mr1,mr2,mr3,rsq,sr1,sr2,sr3,eng_tmp,fpair);
evdwl = eng_tmp;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
if (evflag)
ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
// Q-dependent: Coulombic, field, polarization
// 1/r energy and forces
direct(&params[iparam_ij], &params[iparam_ji],
mr1, mr2, mr3, rsq, sr1, sr2, sr3, iq, jq,
fac11, fac11e, eng_tmp, fvionij, i, j);
vionij = eng_tmp;
// field correction to self energy
field(&params[iparam_ij], &params[iparam_ji],rsq,iq,jq,
eng_tmp,fvionij);
vionij += eng_tmp;
// sums up long range Q-dependent forces (excluding dipole)
f[i][0] += delx*fvionij;
f[i][1] += dely*fvionij;
f[i][2] += delz*fvionij;
f[j][0] -= delx*fvionij;
f[j][1] -= dely*fvionij;
f[j][2] -= delz*fvionij;
// sums up long range Q-dependent energies (excluding dipole)
if (evflag)
ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
// polarization field
if (pol_flag) {
dipole_calc(&params[iparam_ij], &params[iparam_ji],fac11,
delx,dely,delz,rsq,mr1,mr2,mr3,
sr1,sr2,sr3,iq,jq,i,j,eng_tmp,fvionij,ddprx);
vionij = eng_tmp;
// sums up dipole energies
if (evflag)
ev_tally(i,j,nlocal,newton_pair,0.0,vionij,fvionij,delx,dely,delz);
// sums up dipole forces
f[i][0] += (ddprx[0] + delx*fvionij);
f[i][1] += (ddprx[1] + dely*fvionij);
f[i][2] += (ddprx[2] + delz*fvionij);
f[j][0] -= (ddprx[0] + delx*fvionij);
f[j][1] -= (ddprx[1] + dely*fvionij);
f[j][2] -= (ddprx[2] + delz*fvionij);
}
if (rsq > params[iparam_ij].cutsq) continue;
repulsive(&params[iparam_ij], &params[iparam_ji], rsq,
fpair, eflag, eng_tmp, iq, jq);
evdwl = eng_tmp;
// repulsion is pure two-body, sums up pair repulsive forces
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
if (evflag)
ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
}
// many-body interactions: start of short-range
xcn = NCo[i];
for (jj = 0; jj < sht_jnum; jj++) {
j = sht_jlist[jj];
sht_llist = sht_first[j];
sht_lnum = sht_num[j];
jtag = tag[j];
if ( jtag <= itag ) continue ;
ycn = NCo[j];
jtype = map[type[j]];
iparam_ij = elem2param[itype][jtype][jtype];
iparam_ji = elem2param[jtype][itype][itype];
delrj[0] = x[j][0] - xtmp;
delrj[1] = x[j][1] - ytmp;
delrj[2] = x[j][2] - ztmp;
rsq1 = vec3_dot(delrj,delrj);
if (rsq1 > params[iparam_ij].cutsq) continue;
nj ++;
// this Qj for q-dependent BSi
jq = q[j];
// accumulate bondorder zeta for each i-j interaction via k and l loops
zeta_ij = 0.0;
bbtor = 0.0;
kconjug = 0.0;
for (kk = 0; kk < sht_jnum; kk++) { // kk is neighbor of ii
k = sht_jlist[kk];
if (j == k) continue;
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];
iparam_ikj = elem2param[itype][ktype][jtype];
iparam_jik = elem2param[jtype][itype][ktype];
iparam_ik = elem2param[itype][ktype][ktype];
delrk[0] = x[k][0] - xtmp;
delrk[1] = x[k][1] - ytmp;
delrk[2] = x[k][2] - ztmp;
rsq2 = vec3_dot(delrk,delrk);
if (rsq2 > params[iparam_ik].cutsq) continue;
// 3-body zeta in bond order
zeta_ij += zeta(&params[iparam_ijk], &params[iparam_ik],
rsq1, rsq2, delrj, delrk, i, xcn);
// radical initialization: apply only to CC,CO,OC bonds
if (params[iparam_ij].rad_flag > 0 &&
params[iparam_ik].ielementgp == 1 &&
params[iparam_ik].jelementgp == 1) {
iparam_ki = elem2param[ktype][itype][itype];
kcn=NCo[k];
kconjug += rad_init(rsq2,&params[iparam_ki],i,kradtot,kcn);
}
// torsion: i-j-k-l: apply to all C-C bonds
if( params[iparam_ij].tor_flag != 0 ) {
srmu = vec3_dot(delrj,delrk)/(sqrt(rsq1*rsq2));
srmu = sqrt(1.0-srmu*srmu);
if(srmu > 0.1) {
for (ll = 0; ll < sht_lnum; ll++) { // ll is neighbor of jj
l = sht_llist[ll];
if(l==i || l==j || l==k) continue;
ltype = map[type[l]];
delrl[0] = x[l][0] - x[j][0];
delrl[1] = x[l][1] - x[j][1];
delrl[2] = x[l][2] - x[j][2];
rsq3 = vec3_dot(delrl,delrl);
iparam_jl = elem2param[jtype][ltype][ltype];
if (rsq3 > params[iparam_jl].cutsq) continue;
iparam_ikl = elem2param[itype][ktype][ltype];
torindx = params[iparam_ij].tor_flag;
bbtor += bbtor1(torindx, &params[iparam_ikl],&params[iparam_jl],
rsq1,rsq2,rsq3,delrj,delrk,delrl,srmu);
}
}
}
}
zeta_ji = 0.0;
lconjug = 0.0;
for (ll = 0; ll < sht_lnum; ll++) {
l = sht_llist[ll];
if (l == i) continue;
ltype = map[type[l]];
iparam_jil = elem2param[jtype][itype][ltype];
iparam_ijl = elem2param[itype][jtype][ltype];
iparam_jl = elem2param[jtype][ltype][ltype];
iparam_lj = elem2param[ltype][jtype][jtype];
delrk[0] = x[l][0] - x[j][0];
delrk[1] = x[l][1] - x[j][1];
delrk[2] = x[l][2] - x[j][2];
rsq2 = vec3_dot(delrk,delrk);
delrl[0] = x[l][0] - x[j][0];
delrl[1] = x[l][1] - x[j][1];
delrl[2] = x[l][2] - x[j][2];
rsq2 = vec3_dot(delrl,delrl);
if (rsq2 > params[iparam_jl].cutsq) continue;
vec3_scale(-1,delrj,delrl); // ji_hat is -(ij_hat)
zeta_ji += zeta(&params[iparam_jil], &params[iparam_jl]
, rsq1, rsq2, delrl, delrk, j, ycn);
// radical initialization: apply only to CC,CO,OC bonds
if(params[iparam_ji].rad_flag > 0
&& params[iparam_jl].ielementgp == 1
&& params[iparam_jl].jelementgp == 1) {
iparam_lj = elem2param[ltype][jtype][jtype];
lcn=NCo[l];
lconjug += rad_init(rsq2,&params[iparam_lj],j,lradtot,lcn);
}
}
force_zeta(&params[iparam_ij], &params[iparam_ji],
rsq1, xcn, ycn, zeta_ij, zeta_ji, fpair,
prefac_ij1, prefac_ij2, prefac_ij3, prefac_ij4, prefac_ij5,
prefac_ji1, prefac_ji2, prefac_ji3, prefac_ji4, prefac_ji5,
eflag, eng_tmp, iq, jq, i, j, nj, bbtor, kconjug, lconjug);
evdwl = eng_tmp;
- selflp(&params[iparam_ij],&params[iparam_ji],rsq1,eng_tmp,fpair);
+ selfp6p(&params[iparam_ij],&params[iparam_ji],rsq1,eng_tmp,fpair);
evdwl += eng_tmp;
f[i][0] += delrj[0]*fpair;
f[i][1] += delrj[1]*fpair;
f[i][2] += delrj[2]*fpair;
f[j][0] -= delrj[0]*fpair;
f[j][1] -= delrj[1]*fpair;
f[j][2] -= delrj[2]*fpair;
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,-fpair,-delrj[0],-delrj[1],-delrj[2]);
// attractive term via loop over k (3-body forces: i-j-k)
zet_addi=0;
zet_addj=0;
for (kk = 0; kk < sht_jnum; kk++) {
k = sht_jlist[kk];
if (j == k) continue;
sht_mlist = sht_first[k];
sht_mnum = sht_num[k];
ktype = map[type[k]];
iparam_ijk = elem2param[itype][jtype][ktype];
iparam_ikj = elem2param[itype][ktype][jtype];
iparam_jki = elem2param[jtype][ktype][itype];
iparam_jik = elem2param[jtype][itype][ktype];
iparam_ik = elem2param[itype][ktype][ktype];
delrk[0] = x[k][0] - xtmp;
delrk[1] = x[k][1] - ytmp;
delrk[2] = x[k][2] - ztmp;
rsq2 = vec3_dot(delrk,delrk);
if (rsq2 > params[iparam_ik].cutsq) continue;
// BO-dependent 3-body E & F
attractive(&params[iparam_ijk], &params[iparam_jik],&params[iparam_ikj],
prefac_ij1, prefac_ij2, prefac_ij3, prefac_ij4, prefac_ij5,
rsq1,rsq2,delrj,delrk,fi,fj,fk,i,xcn);
- elp_ij = elp(&params[iparam_ijk],&params[iparam_ikj],rsq1,rsq2,delrj,delrk,zet_addi);
- flp(&params[iparam_ijk],&params[iparam_ikj],rsq1,rsq2,delrj,delrk,filp,fjlp,fklp);
+ ep6p_ij = ep6p(&params[iparam_ijk],&params[iparam_ikj],rsq1,rsq2,delrj,delrk,zet_addi);
+ fp6p(&params[iparam_ijk],&params[iparam_ikj],rsq1,rsq2,delrj,delrk,fip6p,fjp6p,fkp6p);
// Sums up i-j-k forces: LP contribution
for (im = 0; im < 3; im++) {
- fi[im] += filp[im];
- fj[im] += fjlp[im];
- fk[im] += fklp[im];
+ fi[im] += fip6p[im];
+ fj[im] += fjp6p[im];
+ fk[im] += fkp6p[im];
}
// Sums up i-j-k forces: Tallies into global force vector
for (im = 0; im < 3; im++) {
f[i][im] += fi[im];
f[j][im] += fj[im];
f[k][im] += fk[im];
}
// torsion and radical: apply to all C-C bonds
if( params[iparam_ijk].tor_flag != 0 && fabs(ptorr)>1.0e-8) {
srmu = vec3_dot(delrj,delrk)/(sqrt(rsq1*rsq2));
srmu = sqrt(1.0-srmu*srmu);
if(srmu > 0.1) {
for (ll = 0; ll < sht_lnum; ll++) { // ll is neighbor of jj
l = sht_llist[ll];
if (l==i||l==j||l==k) continue;
ltype = map[type[l]];
delrl[0] = x[l][0] - x[j][0];
delrl[1] = x[l][1] - x[j][1];
delrl[2] = x[l][2] - x[j][2];
rsq3 = vec3_dot(delrl,delrl);
iparam_jl = elem2param[jtype][ltype][ltype];
if (rsq3 > params[iparam_jl].cutsq) continue;
iparam_ikl = elem2param[itype][ktype][ltype];
torindx = params[iparam_ij].tor_flag;
tor_force(torindx, &params[iparam_ikl], &params[iparam_jl],srmu,
rsq1,rsq2,rsq3,delrj,delrk,delrl);
for (im = 0; im < 3; im++) {
f[i][im] += fi_tor[im];
f[j][im] += fj_tor[im];
f[k][im] += fk_tor[im];
f[l][im] += fl_tor[im];
}
}
}
}
if( params[iparam_ijk].rad_flag>=1 &&
params[iparam_ijk].ielementgp==1 &&
params[iparam_ijk].kelementgp==1) {
iparam_ki = elem2param[ktype][itype][itype];
kcn=NCo[k];
double rik=sqrt(rsq2);
kradtot = -comb_fc(rik,&params[iparam_ki])*params[iparam_ki].pcross+kcn;
rad_forceik(&params[iparam_ki],rsq2,delrk,kconjug,kradtot);
for (im = 0; im < 3; im++) {
f[i][im] += fi_rad[im];
f[k][im] += fk_rad[im];
}
if (fabs(radtmp) > 1.0e-12) {
for (mm = 0; mm < sht_mnum; mm++) { // mm is neighbor of kk
m = sht_mlist[mm];
if (m == k) continue;
mtype = map[type[m]];
delrm[0] = x[m][0] - x[k][0];
delrm[1] = x[m][1] - x[k][1];
delrm[2] = x[m][2] - x[k][2];
rsq3 = vec3_dot(delrm,delrm);
iparam_km = elem2param[ktype][mtype][mtype];
iparam_ki = elem2param[ktype][itype][itype];
if (rsq3 > params[iparam_km].cutsq) continue;
rad_force(&params[iparam_km],rsq3,delrm,radtmp);
for (im = 0; im < 3; im++) {
f[k][im] += fj_rad[im];
f[m][im] += fk_rad[im];
}
}
}
}
if (evflag)
- ev_tally(i,j,nlocal,newton_pair,elp_ij,0.0,0.0,0.0,0.0,0.0);
+ ev_tally(i,j,nlocal,newton_pair,ep6p_ij,0.0,0.0,0.0,0.0,0.0);
if (vflag_atom)
v_tally3(i,j,k,fj,fk,delrj,delrk);
} // k-loop
// attractive term via loop over l (3-body forces: j-i-l)
for (ll = 0; ll < sht_lnum; ll++) {
l = sht_llist[ll];
if (l == i) continue;
sht_plist = sht_first[l];
sht_pnum = sht_num[l];
ltype = map[type[l]];
iparam_jil = elem2param[jtype][itype][ltype];
iparam_jli = elem2param[jtype][ltype][itype];
iparam_ijl = elem2param[itype][jtype][ltype];
iparam_jl = elem2param[jtype][ltype][ltype];
delrk[0] = x[l][0] - x[j][0];
delrk[1] = x[l][1] - x[j][1];
delrk[2] = x[l][2] - x[j][2];
delri[0] = x[i][0] - x[j][0];
delri[1] = x[i][1] - x[j][1];
delri[2] = x[i][2] - x[j][2];
rsq2 = vec3_dot(delrk,delrk);
if (rsq2 > params[iparam_jl].cutsq) continue;
vec3_scale(-1,delrj,delrl);
attractive(&params[iparam_jil],&params[iparam_ijl],&params[iparam_jli],
prefac_ji1,prefac_ji2,prefac_ji3,prefac_ji4,prefac_ji5,
rsq1,rsq2,delrl,delrk,fj,fi,fl,j,ycn);
// BO-independent 3-body j-i-l LP and BB correction and forces
- elp_ji = elp(&params[iparam_jil],&params[iparam_jli],rsq1,rsq2,delrl,delrk,zet_addj);
- flp(&params[iparam_jil],&params[iparam_jli],rsq1,rsq2,delrl,delrk,fjlp,filp,fllp);
+ ep6p_ji = ep6p(&params[iparam_jil],&params[iparam_jli],rsq1,rsq2,delrl,delrk,zet_addj);
+ fp6p(&params[iparam_jil],&params[iparam_jli],rsq1,rsq2,delrl,delrk,fjp6p,fip6p,flp6p);
if (evflag)
- ev_tally(j,i,nlocal,newton_pair,elp_ji,0.0,0.0,0.0,0.0,0.0);
+ ev_tally(j,i,nlocal,newton_pair,ep6p_ji,0.0,0.0,0.0,0.0,0.0);
// BO-dependent 3-body E & F
for (im = 0; im < 3; im++) {
- fj[im] += fjlp[im];
- fi[im] += filp[im];
- fl[im] += fllp[im];
+ fj[im] += fjp6p[im];
+ fi[im] += fip6p[im];
+ fl[im] += flp6p[im];
}
// Sums up j-i-l forces: Tallies into global force vector
for (im = 0; im < 3; im++) {
f[j][im] += fj[im];
f[i][im] += fi[im];
f[l][im] += fl[im];
}
// radical i-j-l-p: apply to all CC,CO,OC bonds
if( params[iparam_jil].rad_flag >= 1 &&
params[iparam_jil].ielementgp == 1 &&
params[iparam_jil].kelementgp == 1 ) {
iparam_lj = elem2param[ltype][jtype][jtype];
lcn=NCo[l];
double rjl=sqrt(rsq2);
lradtot=-comb_fc(rjl,&params[iparam_lj])*params[iparam_lj].pcross +lcn;
rad_forceik(&params[iparam_lj],rsq2,delrk,lconjug,lradtot);
for (im = 0; im < 3; im++) {
f[j][im] += fi_rad[im];
f[l][im] += fk_rad[im];
}
if (fabs(radtmp)>1.0e-12) {
for (pp = 0; pp < sht_pnum; pp++) { // pp is neighbor of ll
p = sht_plist[pp];
if (p == l) continue;
ptype = map[type[p]];
delrp[0] = x[p][0] - x[l][0];
delrp[1] = x[p][1] - x[l][1];
delrp[2] = x[p][2] - x[l][2];
rsq3 = vec3_dot(delrp,delrp);
iparam_lp = elem2param[ltype][ptype][ptype];
if (rsq3 > params[iparam_lp].cutsq) continue;
vec3_scale(-1,delrj,delrj);
rad_force(&params[iparam_lp],rsq3,delrp,radtmp);
vec3_scale(-1,delrj,delrj);
for (im = 0; im < 3; im++) {
f[l][im] += fj_rad[im];
f[p][im] += fk_rad[im];
}
}
}
}
if (vflag_atom)
v_tally3(j,i,l,fi,fl,delrl,delrk);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ---------------------------------------------------------------------- */
void PairComb3::repulsive(Param *parami, Param *paramj, double rsq,
double &fforce,int eflag, double &eng, double iq, double jq)
{
double r,tmp_fc,tmp_fc_d,tmp_exp,Di,Dj;
double caj,vrcs,fvrcs,fforce_tmp;
double LamDiLamDj,fcdA,rlm1,bigA;
double romi = parami->addrep;
double rrcs = parami->bigr + parami->bigd;
+ double addr = parami->addrepr;
r = sqrt(rsq);
if (r > rrcs) return ;
tmp_fc = comb_fc(r,parami);
tmp_fc_d = comb_fc_d(r,parami);
Di = parami->DU + pow(fabs(parami->bD*(parami->QU-iq)),parami->nD);
Dj = paramj->DU + pow(fabs(paramj->bD*(paramj->QU-jq)),paramj->nD);
bigA = parami->bigA;
rlm1 = parami->lambda;
fcdA = tmp_fc_d - tmp_fc * rlm1;
LamDiLamDj = exp(0.5*(parami->lami*Di+paramj->lami*Dj)-rlm1*r);
caj = bigA * LamDiLamDj;
fforce = -caj * fcdA;
// additional repulsion
vrcs = 1.0; fvrcs = 0.0;
- if (romi > 0.0) {
- vrcs += romi * pow((1.0-r/rrcs),2.0);
- fvrcs = romi * 2.0 * (r/rrcs-1.0)/rrcs;
+ if (romi != 0.0 && r < addr) {
+ vrcs += romi * pow((1.0-r/addr),2.0);
+ fvrcs = romi * 2.0 * (r/addr-1.0)/addr;
fforce = fforce*vrcs - caj * tmp_fc * vrcs * fvrcs;
}
fforce /= r;
// eng = repulsive energy
eng = caj * tmp_fc * vrcs;
}
/* ---------------------------------------------------------------------- */
double PairComb3::zeta(Param *parami, Param *paramj, double rsqij,
double rsqik, double *delrij, double *delrik, int i, double xcn)
{
double rij,rik,costheta,arg,ex_delr,rlm3;
rij = sqrt(rsqij);
if (rij > parami->bigr+parami->bigd) return 0.0;
rik = sqrt(rsqik);
costheta = vec3_dot(delrij,delrik) / (rij*rik);
rlm3 = parami->beta;
arg = pow(rlm3*(rij-rik),int(parami->powermint));
if (arg > 69.0776) ex_delr = 1.e30;
else if (arg < -69.0776) ex_delr = 0.0;
else ex_delr = exp(arg);
return comb_fc(rik,paramj) * comb_gijk(costheta,parami,xcn) * ex_delr;
}
/* ---------------------------------------------------------------------- */
-void PairComb3::selflp(Param *parami, Param *paramj, double rsq,
+void PairComb3::selfp6p(Param *parami, Param *paramj, double rsq,
double &eng, double &force)
{
double r,comtti,comttj,fcj,fcj_d;
double lp1,lp2,lp3,lp4,lp5,lp6;
r=sqrt(rsq);
fcj=comb_fc(r,parami);
fcj_d=comb_fc_d(r,parami);
comtti = comttj = 0.0;
- if (fabs(parami->plp1) > 1.0e-6 || fabs(parami->plp2) > 1.0e-6
- || fabs(parami->plp3) > 1.0e-6 || fabs(parami->plp4) > 1.0e-6
- || fabs(parami->plp5) > 1.0e-6 || fabs(parami->plp6) > 1.0e-6 ) {
- double pilp1 = parami->plp1, pilp2 = parami->plp2, pilp3 = parami->plp3;
- double pilp4 = parami->plp4, pilp5 = parami->plp5, pilp6 = parami->plp6;
- comtti = pilp1 + pilp2 + pilp3 + pilp4 + pilp5 + pilp6;
- }
+ double pilp0 = parami->p6p0;
+ double pilp1 = parami->p6p1, pilp2 = parami->p6p2, pilp3 = parami->p6p3;
+ double pilp4 = parami->p6p4, pilp5 = parami->p6p5, pilp6 = parami->p6p6;
+ comtti = pilp0 + pilp1 + pilp2 + pilp3 + pilp4 + pilp5 + pilp6;
- if (fabs(paramj->plp1) > 1.0e-6 || fabs(paramj->plp2) > 1.0e-6
- || fabs(paramj->plp3) > 1.0e-6 || fabs(paramj->plp4) > 1.0e-6
- || fabs(paramj->plp5) > 1.0e-6 || fabs(paramj->plp6) > 1.0e-6) {
- double pjlp1 = paramj->plp1, pjlp2 = paramj->plp2, pjlp3 = paramj->plp3;
- double pjlp4 = paramj->plp4, pjlp5 = paramj->plp5, pjlp6 = paramj->plp6;
- comttj = pjlp1 + pjlp2 + pjlp3 + pjlp4 + pjlp5 + pjlp6;
- }
+ double pjlp0 = paramj->p6p0;
+ double pjlp1 = paramj->p6p1, pjlp2 = paramj->p6p2, pjlp3 = paramj->p6p3;
+ double pjlp4 = paramj->p6p4, pjlp5 = paramj->p6p5, pjlp6 = paramj->p6p6;
+ comttj = pjlp0 + pjlp1 + pjlp2 + pjlp3 + pjlp4 + pjlp5 + pjlp6;
eng = 0.5 * fcj * (comtti + comttj);
force += 0.5 * fcj_d * (comtti + comttj)/r;
}
/* ---------------------------------------------------------------------- */
-double PairComb3::elp(Param *paramj, Param *paramk, double rsqij, double rsqik,
+double PairComb3::ep6p(Param *paramj, Param *paramk, double rsqij, double rsqik,
double *delrij, double *delrik , double &zet_add)
{
- int con_flag, plp_flag;
- con_flag = plp_flag = 0;
- if (fabs(paramj->pbb2) > 1.0e-6) con_flag = 1;
- if (fabs(paramj->plp1) > 1.0e-6 || fabs(paramj->plp2) > 1.0e-6
- || fabs(paramj->plp3) > 1.0e-6 || fabs(paramj->plp4) > 1.0e-6
- || fabs(paramj->plp5) > 1.0e-6 || fabs(paramj->plp6) > 1.0e-6 )
- plp_flag = 1;
-
- if(con_flag || plp_flag) {
- double rij,rik,costheta,lp1,lp2,lp3,lp4,lp5,lp6;
- double rmu,rmu2,rmu3,rmu4,rmu5,rmu6,comtt,fcj,fck,fcj_d;
- double pplp1 = paramj->plp1, pplp2 = paramj->plp2, pplp3 = paramj->plp3;
- double pplp4 = paramj->plp4, pplp5 = paramj->plp5, pplp6 = paramj->plp6;
-
+ double comtt;
+ double pplp0 = paramj->p6p0;
+ double pplp1 = paramj->p6p1, pplp2 = paramj->p6p2, pplp3 = paramj->p6p3;
+ double pplp4 = paramj->p6p4, pplp5 = paramj->p6p5, pplp6 = paramj->p6p6;
+ double rij,rik,costheta,lp0,lp1,lp2,lp3,lp4,lp5,lp6;
+ double rmu,rmu2,rmu3,rmu4,rmu5,rmu6,fcj,fck,fcj_d;
+ comtt=0.0;
rij = sqrt(rsqij);
rik = sqrt(rsqik);
costheta = vec3_dot(delrij,delrik) / (rij*rik);
fcj = comb_fc(rij,paramj);
fcj_d = comb_fc_d(rij,paramj);
fck = comb_fc(rik,paramk);
- rmu = costheta;
-
- // Legendre Polynomial functions
- if (plp_flag) {
- rmu2 = rmu *rmu; rmu3 = rmu2*rmu; rmu4 = rmu3*rmu;
- rmu5 = rmu4*rmu; rmu6 = rmu5*rmu;
- lp1 = pplp1*rmu;
- lp2 = pplp2*0.5*(3.0*rmu2-1.0);
- lp3 = pplp3*0.5*(5.0*rmu3-3.0*rmu);
- lp4 = pplp4*(35.0*rmu4-30.0*rmu2+3.0)/8.0;
- lp5 = pplp5*(63.0*rmu5-70.0*rmu3+15.0*rmu)/8.0;
- lp6 = pplp6*(231.0*rmu6-315.0*rmu4+105.0*rmu2-5.0)/16.0;
- comtt = lp1 + lp2 + lp3 + lp4 + lp5 + lp6;
- }
- else {comtt = 0.0;}
-
- // bond-bending terms
-
- if (con_flag) {
- double c123 = paramj->pbb1;
- comtt += paramj->pbb2 *(rmu-c123)*(rmu-c123);
- }
+ rmu = costheta;
+ rmu2 = rmu *rmu; rmu3 = rmu2*rmu; rmu4 = rmu3*rmu;
+ rmu5 = rmu4*rmu; rmu6 = rmu5*rmu;
+ lp0 = pplp0;
+ lp1 = pplp1*rmu;
+ lp2 = pplp2*rmu2;
+ lp3 = pplp3*rmu3;
+ lp4 = pplp4*rmu4;
+ lp5 = pplp5*rmu5;
+ lp6 = pplp6*rmu6;
+ comtt = lp0 + lp1 + lp2 + lp3 + lp4 + lp5 + lp6;
return 0.5 * fck * comtt *fcj;
}
- return 0.0;
-}
/*---------------------------------------------------------------------- */
-void PairComb3::flp(Param *paramij,Param *paramik, double rsqij, double rsqik,
+void PairComb3::fp6p(Param *paramij,Param *paramik, double rsqij, double rsqik,
double *delrij, double *delrik, double *drilp,
double *drjlp, double *drklp)
{
- int con_flag, plp_flag;
- double ffj1,ffj2,ffk1,ffk2,com5k;
-
- con_flag = plp_flag = 0;
- ffj1 = 0.0; ffj2 = 0.0; ffk1 = 0.0; ffk2 = 0.0;
- if (fabs(paramij->pbb2) > 1.0e-6) con_flag = 1;
- if (fabs(paramij->plp1) > 1.0e-6 || fabs(paramij->plp2) > 1.0e-6
- || fabs(paramij->plp3) > 1.0e-6 || fabs(paramij->plp4) > 1.0e-6
- || fabs(paramij->plp5) > 1.0e-6 || fabs(paramij->plp6) > 1.0e-6 )
-
- plp_flag=1;
-
- if(con_flag || plp_flag) {
- double rij,rik,costheta;
- double rmu,comtt,comtt_d,com4k,com5,fcj,fcj_d,fck,fck_d;
+ double pplp0 = paramij->p6p0;
+ double pplp1 = paramij->p6p1, pplp2 = paramij->p6p2, pplp3 = paramij->p6p3;
+ double pplp4 = paramij->p6p4, pplp5 = paramij->p6p5, pplp6 = paramij->p6p6;
+ double ffj1,ffj2,ffk1,ffk2;
+ double rij,rik,costheta;
+ double rmu,comtt,comtt_d,com4k,com5,com5k,fcj,fcj_d,fck,fck_d;
+ double lp0,lp1,lp2,lp3,lp4,lp5,lp6;
+ double lp1_d,lp2_d,lp3_d,lp4_d,lp5_d,lp6_d;
+ double rmu2, rmu3, rmu4, rmu5, rmu6;
+ ffj1 = 0.0, ffj2 = 0.0;
+ ffk1 = 0.0, ffk2 = 0.0;
+
rij = sqrt(rsqij); rik = sqrt(rsqik);
costheta = vec3_dot(delrij,delrik) / (rij*rik);
fcj = comb_fc(rij,paramij);
fck = comb_fc(rik,paramik);
fcj_d = comb_fc_d(rij,paramij);
fck_d = comb_fc_d(rik,paramik);
rmu = costheta;
-
- // Legendre Polynomial functions and derivatives
-
- if (plp_flag) {
- double lp1,lp2,lp3,lp4,lp5,lp6;
- double lp1_d,lp2_d,lp3_d,lp4_d,lp5_d,lp6_d;
- double rmu2, rmu3, rmu4, rmu5, rmu6;
- double pplp1 = paramij->plp1, pplp2 = paramij->plp2, pplp3 = paramij->plp3;
- double pplp4 = paramij->plp4, pplp5 = paramij->plp5, pplp6 = paramij->plp6;
+
rmu2 = rmu *rmu; rmu3 = rmu2*rmu;
rmu4 = rmu3*rmu; rmu5 = rmu4*rmu; rmu6 = rmu5*rmu;
+ lp0 = pplp0;
lp1 = pplp1*rmu;
- lp2 = pplp2*0.5*(3.0*rmu2-1.0);
- lp3 = pplp3*0.5*(5.0*rmu3-3.0*rmu);
- lp4 = pplp4*(35.0*rmu4-30.0*rmu2+3.0)/8.0;
- lp5 = pplp5*(63.0*rmu5-70.0*rmu3+15.0*rmu)/8.0;
- lp6 = pplp6*(231.0*rmu6-315.0*rmu4+105.0*rmu2-5.0)/16.0;
+ lp2 = pplp2*rmu2;
+ lp3 = pplp3*rmu3;
+ lp4 = pplp4*rmu4;
+ lp5 = pplp5*rmu5;
+ lp6 = pplp6*rmu6;
lp1_d = pplp1;
- lp2_d = pplp2*3.0*rmu;
- lp3_d = pplp3*(7.5*rmu2-1.5);
- lp4_d = pplp4*(140.0*rmu3-60.0*rmu)/8.0;
- lp5_d = pplp5*(315.0*rmu4-210.0*rmu2+15.0)/8.0;
- lp6_d = pplp6*(1386.0*rmu5-1260.0*rmu3+210.0)/16.0;
- comtt = lp1 + lp2 + lp3 + lp4 + lp5 + lp6;
+ lp2_d = pplp2*2.0*rmu;
+ lp3_d = pplp3*3.0*rmu2;
+ lp4_d = pplp4*4.0*rmu3;
+ lp5_d = pplp5*5.0*rmu4;
+ lp6_d = pplp6*6.0*rmu5;
+ comtt = lp0 + lp1 + lp2 + lp3 + lp4 + lp5 + lp6;
comtt_d = lp1_d + lp2_d + lp3_d + lp4_d + lp5_d + lp6_d;
- } else {
- comtt = 0.0;
- comtt_d = 0.0;
- }
-
- // bond-bending terms derivatives
- if (con_flag) {
- double c123 = paramij->pbb1;
- comtt += paramij->pbb2 *(rmu-c123)*(rmu-c123);
- comtt_d += 2.0*paramij->pbb2*(rmu-c123);
- }
-
- com4k = fcj * fck_d * comtt;
- com5 = fcj * fck * comtt_d;
-
- com5k = fck * comtt * fcj_d;
- ffj1 = 0.5*(-com5/(rij*rik));
- ffj2 = 0.5*(com5*rmu/rsqij-com5k/rij);
- ffk1 = ffj1;
- ffk2 = 0.5*(-com4k/rik+com5*rmu/rsqik);
- } else {
- ffj1 = 0.0; ffj2 = 0.0;
- ffk1 = 0.0; ffk2 = 0.0;
- }
-
+ com4k = fcj * fck_d * comtt;
+ com5 = fcj * fck * comtt_d;
+ com5k = fck * comtt * fcj_d;
+
+ ffj1 = 0.5*(-com5/(rij*rik));
+ ffj2 = 0.5*(com5*rmu/rsqij-com5k/rij);
+ ffk1 = ffj1;
+ ffk2 = 0.5*(-com4k/rik+com5*rmu/rsqik);
+
// j-atom
vec3_scale(ffj1,delrik,drjlp);
vec3_scaleadd(ffj2,delrij,drjlp,drjlp);
// k-atom
vec3_scale(ffk1,delrij,drklp);
vec3_scaleadd(ffk2,delrik,drklp,drklp);
// i-atom
vec3_add(drjlp,drklp,drilp);
vec3_scale(-1.0,drilp,drilp);
}
/* ---------------------------------------------------------------------- */
void PairComb3::force_zeta(Param *parami, Param *paramj, double rsq,
double xcn, double ycn, double &zeta_ij, double &zeta_ji, double &fforce,
double &prefac_ij1, double &prefac_ij2, double &prefac_ij3,
double &prefac_ij4, double &prefac_ij5,
double &prefac_ji1, double &prefac_ji2, double &prefac_ji3,
double &prefac_ji4, double &prefac_ji5,
int eflag, double &eng, double iq, double jq,
int i, int j, int nj, double bbtor, double kconjug, double lconjug)
{
double r,att_eng,att_force,bij; // att_eng is -cbj
double boij, dbij1, dbij2, dbij3, dbij4, dbij5;
double boji, dbji1, dbji2, dbji3, dbji4, dbji5;
double pradx, prady;
-
int inti=parami->ielement;
int intj=paramj->ielement;
- tagint *tag=atom->tag;
- tagint itag=tag[i];
- tagint jtag=tag[j];
r = sqrt(rsq);
if (r > parami->bigr + parami->bigd) return;
comb_fa(r, parami, paramj, iq, jq, att_eng, att_force);
comb_bij_d(zeta_ij,parami,r,i,boij,dbij1,dbij2,dbij3,dbij4,dbij5,xcn);
comb_bij_d(zeta_ji,paramj,r,j,boji,dbji1,dbji2,dbji3,dbji4,dbji5,ycn);
bij = 0.5*(boij + boji);
// radical energy
if ( parami->rad_flag>0 ) {
rad_calc( r, parami, paramj, kconjug, lconjug, i, j, xcn, ycn);
bij += brad[0];
pradx = brad[1]*att_eng;
prady = brad[2]*att_eng;
brad[3] = 1.0 * brad[3]*att_eng;
}
// torsion energy
if ( parami->tor_flag!=0) {
tor_calc( r, parami, paramj, kconjug, lconjug, i, j, xcn, ycn);
bij += btor[0] * bbtor;
ptorr = att_eng * btor[0];
pradx += 1.0 * btor[1] * bbtor * att_eng;
prady += 1.0 * btor[2] * bbtor * att_eng;
brad[3]+= 1.0 * btor[3] * bbtor * att_eng;
}
fforce = 1.0*bij*att_force/r; // divide by r will done compute
bbij[i][nj] = bij;
prefac_ij1 = -0.5*att_eng*dbij1; // prefac_ij1 = -pfij
prefac_ij2 = -0.5*att_eng*dbij2; // prefac_ij2 = -pfij1
prefac_ij3 = -0.5*att_eng*dbij3; // prefac_ij3 = -pfij2
prefac_ij4 = -0.5*att_eng*dbij4; // prefac_ij4 = -pfij3
prefac_ij5 = -0.5*att_eng*dbij5; // prefac_ij5 = -pfij4
prefac_ji1 = -0.5*att_eng*dbji1; // prefac_ji1 = -pfji
prefac_ji2 = -0.5*att_eng*dbji2; // prefac_ji2 = -pfji1
prefac_ji3 = -0.5*att_eng*dbji3; // prefac_ji3 = -pfji2
prefac_ji4 = -0.5*att_eng*dbji4; // prefac_ji4 = -pfji3
prefac_ji5 = -0.5*att_eng*dbji5; // prefac_ji5 = -pfji4
// combines com6 & com7 below
if ( parami->rad_flag>0 || parami->tor_flag!=0 ) {
prefac_ij2-=pradx;
prefac_ji2-=prady;
}
// eng = attraction energy
if (eflag) eng = 1.0*bij*att_eng;
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fc(double r, Param *param)
{
double r_inn = param->bigr - param->bigd;
double r_out = param->bigr + param->bigd;
if (r <= r_inn) return 1.0;
if (r >= r_out) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(r-r_inn)/(r_out-r_inn)));
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fc_d(double r, Param *param)
{
double r_inn = param->bigr - param->bigd;
double r_out = param->bigr + param->bigd;
if (r <= r_inn) return 0.0;
if (r >= r_out) return 0.0;
return -MY_PI2/(r_out-r_inn)*sin(MY_PI*(r-r_inn)/(r_out-r_inn));
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fccc(double xcn)
{
double cut1 = ccutoff[0];
double cut2 = ccutoff[1];
if (xcn <= cut1) return 1.0;
if (xcn >= cut2) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(xcn-cut1)/(cut2-cut1)));
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fccc_d(double xcn)
{
double cut1 = ccutoff[0];
double cut2 = ccutoff[1];
if (xcn <= cut1) return 0.0;
if (xcn >= cut2) return 0.0;
return -MY_PI2/(cut2-cut1)*sin(MY_PI*(xcn-cut1)/(cut2-cut1));
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fcch(double xcn)
{
double cut1 = ccutoff[2];
double cut2 = ccutoff[3];
if (xcn <= cut1) return 1.0;
if (xcn >= cut2) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(xcn-cut1)/(cut2-cut1)));
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fcch_d(double xcn)
{
double cut1 = ccutoff[2];
double cut2 = ccutoff[3];
if (xcn <= cut1) return 0.0;
if (xcn >= cut2) return 0.0;
return -MY_PI2/(cut2-cut1)*sin(MY_PI*(xcn-cut1)/(cut2-cut1));
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fccch(double xcn)
{
double cut1 = ccutoff[4];
double cut2 = ccutoff[5];
if (xcn <= cut1) return 1.0;
if (xcn >= cut2) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(xcn-cut1)/(cut2-cut1)));
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fccch_d(double xcn)
{
double cut1 = ccutoff[4];
double cut2 = ccutoff[5];
if (xcn <= cut1) return 0.0;
if (xcn >= cut2) return 0.0;
return -MY_PI2/(cut2-cut1)*sin(MY_PI*(xcn-cut1)/(cut2-cut1));
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fcsw(double rsq)
{
double r = sqrt(rsq);
if (r <= chicut1) return 1.0;
if (r >= chicut2) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(r-chicut1)/(chicut2-chicut1)));
}
/* ---------------------------------------------------------------------- */
double PairComb3::self(Param *param, double qi)
{
double self_tmp, cmin, cmax, qmin, qmax;
double s1=param->chi, s2=param->dj, s3=param->dk, s4=param->dl;
self_tmp = 0.0;
qmin = param->qmin;
qmax = param->qmax;
cmin = cmax = 100.0;
self_tmp = qi*(s1+qi*(s2+qi*(s3+qi*s4)));
if (qi < qmin) self_tmp += cmin * pow((qi-qmin),4);
if (qi > qmax) self_tmp += cmax * pow((qi-qmax),4);
return self_tmp;
}
/* ---------------------------------------------------------------------- */
void PairComb3::comb_fa(double r, Param *parami, Param *paramj, double iq,
double jq, double &att_eng, double &att_force)
{
double bigB,Bsi,FBsi;
double qi,qj,Di,Dj;
double AlfDiAlfDj, YYBn, YYBj;
double rlm2 = parami->alpha1;
double alfij1= parami->alpha1;
double alfij2= parami->alpha2;
double alfij3= parami->alpha3;
double pbij1= parami->bigB1;
double pbij2= parami->bigB2;
double pbij3= parami->bigB3;
if (r > parami->bigr + parami->bigd) Bsi = 0.0;
qi = iq; qj = jq;
Di = Dj = Bsi = FBsi = bigB = 0.0;
Di = parami->DU + pow(fabs(parami->bD*(parami->QU-qi)),parami->nD);
Dj = paramj->DU + pow(fabs(paramj->bD*(paramj->QU-qj)),paramj->nD);
YYBn = (parami->aB-fabs(pow(parami->bB*(qi-parami->Qo),10)));
YYBj = (paramj->aB-fabs(pow(paramj->bB*(qj-paramj->Qo),10)));
if (YYBn*YYBj > 0.0 ) {
AlfDiAlfDj = exp(0.5*(parami->alfi*Di+paramj->alfi*Dj));
Bsi = (pbij1*exp(-alfij1*r)+pbij2*exp(-alfij2*r)+pbij3*exp(-alfij3*r))*
sqrt(YYBn*YYBj)*AlfDiAlfDj; // Bsi is cbj
att_eng = -Bsi * comb_fc(r,parami);
att_force = -(Bsi*comb_fc_d(r,parami)-comb_fc(r,parami)*sqrt(YYBn*YYBj)*
AlfDiAlfDj*(alfij1*pbij1*exp(-alfij1*r)+
alfij2*pbij2*exp(-alfij2*r)+alfij3*pbij3*exp(-alfij3*r)));
} else {
att_eng = 0.0;
att_force = 0.0;
}
}
/* ---------------------------------------------------------------------- */
void PairComb3::comb_bij_d(double zet, Param *param, double r, int i,
double &tbij, double &tbij1, double &tbij2,
double &tbij3, double &tbij4, double &tbij5, double xcn)
{
double pcorn,dpcorn,dxccij,dxchij,dxcoij;
double zeta = zet;
double zetang,tmp_tbij, pow_n;
pcorn = dpcorn = dxccij = dxchij = dxcoij = 0.0;
coord(param,r,i,pcorn,dpcorn,dxccij,dxchij,dxcoij,xcn); // coordination term
zetang=zeta;
pow_n=param->powern;
zeta = pow(zetang,pow_n)+pcorn;
tmp_tbij=pow_n*pow(zetang,(pow_n-1.0));
if ((1.0 + zeta) < 0.1 ){
zeta=0.1-1.0;
tbij = pow(1.0 + zeta, -0.5/pow_n);
tbij1=0.0;
}
else if (zeta > param->c1) {
tbij = pow(zeta,-0.5/pow_n);
tbij1 = -0.5/pow_n*pow(zeta,(-0.5/pow_n-1.0));
} else if (zeta > param->c2) {
tbij = pow(zeta,-0.5/pow_n)-0.5/pow_n*pow(zeta,(-0.5/pow_n-1.0));
tbij1 = -0.5/pow_n/zeta;
} else if (fabs(zeta) < param->c4) {
tbij = 1.0;
tbij1 = 0.0;
} else if (fabs(zeta) < param->c3) {
tbij = 1.0 - zeta/(2.0*pow_n);
tbij1 = -1/(2.0*pow_n);
} else {
tbij = pow(1.0 + zeta, -0.5/pow_n);
tbij1 = -0.5/pow_n * pow(1.0 + zeta,(-1.0-0.5/pow_n));
}
tbij2 = tbij1 * dpcorn;
tbij3 = tbij1 * dxccij;
tbij4 = tbij1 * dxchij;
tbij5 = tbij1 * dxcoij;
tbij1 = tbij1 * tmp_tbij;
}
/* ---------------------------------------------------------------------- */
void PairComb3::coord(Param *param, double r, int i,
double &pcorn, double &dpcorn, double &dxccij,
double &dxchij, double &dxcoij, double xcn)
{
int n,nn,ixmin,iymin,izmin;
double xcntot,xcccn,xchcn,xcocn;
int tri_flag= param-> pcn_flag;
int iele_gp= param->ielementgp;
int jele_gp= param->jelementgp;
int kele_gp= param->kelementgp;
double pan = param->pcna;
double pbn = param->pcnb;
double pcn = param->pcnc;
double pdn = param->pcnd;
xcccn = xchcn = xcocn = 0.0;
xcccn = xcctmp[i];
xchcn = xchtmp[i];
xcocn = xcotmp[i];
xcntot = -comb_fc(r,param)*param->pcross + xcn;
pcorn = dpcorn = dxccij = dxchij = dxcoij = 0.0;
pcorn = 0.0; dpcorn = 0.0;
if(xcntot < 0.0) xcntot = 0.0;
if (tri_flag>0) {
if(jele_gp==1) xcccn = xcccn-comb_fc(r,param)*param->pcross;
if(jele_gp==2) xchcn = xchcn-comb_fc(r,param)*param->pcross;
if(jele_gp==3) xcocn = xcocn-comb_fc(r,param)*param->pcross;
if(xcccn < 0.0) xcccn = 0.0;
if(xchcn < 0.0) xchcn = 0.0;
if(xcocn < 0.0) xcocn = 0.0;
if(xcccn > maxx) xcccn = maxx;
if(xchcn > maxy) xchcn = maxy;
if(xcocn > maxz) xcocn = maxz;
double xcntritot=xcccn+xchcn+xcocn;
if(xcntritot > maxxcn[tri_flag-1]) {
pcorn = vmaxxcn[tri_flag-1]+(xcntot-maxxcn[tri_flag-1])*dvmaxxcn[tri_flag-1];
dxccij = dxchij = dxcoij = dvmaxxcn[tri_flag-1];
}
else {
ixmin=int(xcccn+1.0e-12);
iymin=int(xchcn+1.0e-12);
izmin=int(xcocn+1.0e-12);
if (fabs(float(ixmin)-xcccn)>1.0e-8 ||
fabs(float(iymin)-xchcn)>1.0e-8 ||
fabs(float(izmin)-xcocn)>1.0e-8) {
cntri_int(tri_flag,xcccn,xchcn,xcocn,ixmin,iymin,izmin,
pcorn,dxccij,dxchij,dxcoij,param);
}
else {
pcorn = pcn_grid[tri_flag-1][ixmin][iymin][izmin];
dxccij = pcn_gridx[tri_flag-1][ixmin][iymin][izmin];
dxchij = pcn_gridy[tri_flag-1][ixmin][iymin][izmin];
dxcoij = pcn_gridz[tri_flag-1][ixmin][iymin][izmin];
}
}
} else {
pcorn = pan*xcntot+pbn*exp(pcn*xcntot)+pdn;
dpcorn = pan+pbn*pcn*exp(pcn*xcntot);
}
}
/* ---------------------------------------------------------------------- */
void PairComb3::cntri_int(int tri_flag, double xval, double yval,
double zval, int ixmin, int iymin, int izmin, double &vval,
double &dvalx, double &dvaly, double &dvalz, Param *param)
{
int i, j, k;
double x;
vval = 0.0; dvalx = 0.0; dvaly = 0.0; dvalz = 0.0;
if(ixmin >= maxx-1) { ixmin=maxx-1; }
if(iymin >= maxy-1) { iymin=maxy-1; }
if(izmin >= maxz-1) { izmin=maxz-1; }
for (j=0; j<64; j++) {
x = pcn_cubs[tri_flag-1][ixmin][iymin][izmin][j]
*pow(xval,iin3[j][0])*pow(yval,iin3[j][1])
*pow(zval,iin3[j][2]);
vval += x;
if(xval>1.0e-8) {dvalx += x*iin3[j][0]/xval;}
if(yval>1.0e-8) {dvaly += x*iin3[j][1]/yval;}
if(zval>1.0e-8) {dvalz += x*iin3[j][2]/zval;}
}
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_gijk(double costheta, Param *param, double nco_tmp)
{
double rmu1 = costheta;
double rmu2 = rmu1*rmu1;
double rmu3 = rmu2*rmu1;
double rmu4 = rmu3*rmu1;
double rmu5 = rmu4*rmu1;
double rmu6 = rmu5*rmu1;
double co6 = param->pcos6*rmu6;
double co5 = param->pcos5*rmu5;
double co4 = param->pcos4*rmu4;
double co3 = param->pcos3*rmu3;
double co2 = param->pcos2*rmu2;
double co1 = param->pcos1*rmu1;
double co0 = param->pcos0;
double pcross = param->pcross;
double gmu;
if (param->ang_flag==1) {
double qtheta, gmu1, gmu2, rrmu, astep;
int k;
qtheta = comb_fccc(nco_tmp);
astep = 2.0/ntab;
rrmu = (rmu1+1.0)/astep;
k = int(rrmu);
gmu1 = co6+co5+co4+co3+co2+co1+co0;
gmu2 = pang[k]+(pang[k+1]-pang[k])*(rrmu-k);
gmu = gmu2+qtheta*(gmu1-gmu2);
return gmu*pcross;
} else if (param->ang_flag==2){
double qtheta, gmu1, gmu2;
double ch6 = ch_a[6]*rmu6;
double ch5 = ch_a[5]*rmu5;
double ch4 = ch_a[4]*rmu4;
double ch3 = ch_a[3]*rmu3;
double ch2 = ch_a[2]*rmu2;
double ch1 = ch_a[1]*rmu1;
double ch0 = ch_a[0];
qtheta = comb_fccch(nco_tmp);
gmu1 = co6+co5+co4+co3+co2+co1+co0;
gmu2 = ch6+ch5+ch4+ch3+ch2+ch1+ch0;
gmu = gmu2+qtheta*(gmu1-gmu2);
return gmu*pcross;
} else {
gmu = co6+co5+co4+co3+co2+co1+co0;
return gmu*pcross;
}
}
/* ---------------------------------------------------------------------- */
void PairComb3::comb_gijk_d(double costheta, Param *param, double nco_tmp,
double &gijk_d, double &com3jk)
{
double rmu1 = costheta;
double rmu2 = rmu1*rmu1;
double rmu3 = rmu2*rmu1;
double rmu4 = rmu3*rmu1;
double rmu5 = rmu4*rmu1;
double rmu6 = rmu5*rmu1;
double co6 = param->pcos6; //*rmu5*6.0;
double co5 = param->pcos5; //*rmu4*5.0;
double co4 = param->pcos4; //*rmu3*4.0;
double co3 = param->pcos3; //*rmu2*3.0;
double co2 = param->pcos2; //*rmu1*2.0;
double co1 = param->pcos1;
double co0 = param->pcos0;
double pcross = param->pcross;
gijk_d = com3jk = 0.0;
if (param->ang_flag==1) {
double qtheta, dqtheta, gmu1, gmu2, dgmu1,dgmu2, rrmu, astep;
int k;
qtheta = comb_fccc(nco_tmp);
dqtheta = comb_fccc_d(nco_tmp);
astep = 2.0/ntab;
rrmu = (rmu1+1.0)/astep;
k = int(rrmu);
gmu1 =rmu6*co6+rmu5*co5+rmu4*co4
+rmu3*co3+rmu2*co2+rmu1*co1+co0;
dgmu1 =6.0*rmu5*co6+5.0*rmu4*co5+4.0*rmu3*co4
+3.0*rmu2*co3+2.0*rmu1*co2+co1;
gmu2 = pang[k]+(pang[k+1]-pang[k])*(rrmu-k);
dgmu2 = dpang[k]+(dpang[k+1]-dpang[k])*(rrmu-k);
gijk_d = pcross*(dgmu2+qtheta*(dgmu1-dgmu2));
com3jk = dqtheta * (gmu1-gmu2);
} else if(param->ang_flag==2) {
double qtheta, dqtheta, gmu1, gmu2, dgmu1,dgmu2;
double ch6 = ch_a[6];
double ch5 = ch_a[5];
double ch4 = ch_a[4];
double ch3 = ch_a[3];
double ch2 = ch_a[2];
double ch1 = ch_a[1];
double ch0 = ch_a[0];
qtheta = comb_fccch(nco_tmp);
dqtheta = comb_fccch_d(nco_tmp);
gmu1 =rmu6*co6+rmu5*co5+rmu4*co4
+rmu3*co3+rmu2*co2+rmu1*co1+co0;
dgmu1 =6.0*rmu5*co6+5.0*rmu4*co5+4.0*rmu3*co4
+3.0*rmu2*co3+2.0*rmu1*co2+co1;
gmu2 =rmu6*ch6+rmu5*ch5+rmu4*ch4
+rmu3*ch3+rmu2*ch2+rmu1*ch1+ch0;
dgmu2 =6.0*rmu5*ch6+5.0*rmu4*ch5+4.0*rmu3*ch4
+3.0*rmu2*ch3+2.0*rmu1*ch2+ch1;
gijk_d = pcross*(dgmu2+qtheta*(dgmu1-dgmu2));
com3jk = dqtheta * (gmu1-gmu2);
} else {
gijk_d = pcross*(6.0*rmu5*co6+5.0*rmu4*co5+4.0*rmu3*co4
+3.0*rmu2*co3+2.0*rmu1*co2+co1);
com3jk = 0.0;
}
}
/*------------------------------------------------------------------------- */
void PairComb3::attractive(Param *parami, Param *paramj , Param *paramk, double prefac_ij1,
double prefac_ij2, double prefac_ij3, double prefac_ij4,
double prefac_ij5, double rsqij, double rsqik, double *delrij,
double *delrik, double *fi, double *fj,double *fk, int i, double xcn)
{
double rij_hat[3],rik_hat[3];
double rij,rijinv,rik,rikinv;
rij = sqrt(rsqij);
rijinv = 1.0/rij;
vec3_scale(rijinv,delrij,rij_hat);
rik = sqrt(rsqik);
rikinv = 1.0/rik;
vec3_scale(rikinv,delrik,rik_hat);
comb_zetaterm_d(prefac_ij1, prefac_ij2, prefac_ij3, prefac_ij4, prefac_ij5,
rij_hat, rij,rik_hat, rik, fi, fj, fk, parami, paramj, paramk,xcn);
}
/* ---------------------------------------------------------------------- */
void PairComb3::comb_zetaterm_d(double prefac_ij1, double prefac_ij2,
double prefac_ij3, double prefac_ij4, double prefac_ij5,
double *rij_hat, double rij, double *rik_hat, double rik, double *dri,
double *drj, double *drk, Param *parami, Param *paramj, Param *paramk, double xcn)
{
double gijk,gijk_d,ex_delr,ex_delr_d,fc_i,fc_k,dfc_j,dfc,cos_theta,tmp,rlm3;
double dcosdri[3],dcosdrj[3],dcosdrk[3],dfc_i,dfc_k;
double dbij1, dbij2, dbij3, dbij4, com6, com7, com3j, com3k, com3jk;
int mint = int(parami->powermint);
double pcrossi = parami->pcross;
double pcrossj = paramj->pcross;
double pcrossk = paramk->pcross;
int icontrol = parami->pcn_flag;
fc_i = comb_fc(rij,parami);
dfc_i = comb_fc_d(rij,parami);
fc_k = comb_fc(rik,paramk);
dfc_k = comb_fc_d(rik,paramk);
dfc_j = comb_fc_d(rij,paramj);
rlm3 = parami->beta;
tmp = pow(rlm3*(rij-rik),mint);
if (tmp > 69.0776) ex_delr = 1.e30;
else if (tmp < -69.0776) ex_delr = 0.0;
else ex_delr = exp(tmp);
ex_delr *= pcrossi;
cos_theta = vec3_dot(rij_hat,rik_hat);
gijk = comb_gijk(cos_theta,parami,xcn);
comb_gijk_d(cos_theta,parami,xcn,gijk_d,com3jk);
costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
// com6 & com7
if(icontrol > 0){
if(parami->kelementgp==1) {com6 = prefac_ij3*pcrossk*dfc_k;}
if(parami->kelementgp==2) {com6 = prefac_ij4*pcrossk*dfc_k;}
if(parami->kelementgp==3) {com6 = prefac_ij5*pcrossk*dfc_k;}
if(parami->rad_flag>=1 || parami->tor_flag!=0)
{com6+=prefac_ij2*pcrossk*dfc_k;}
} else {
com6 = prefac_ij2*pcrossi*dfc_k;
}
if (parami->ang_flag==1 || parami->ang_flag==2) {
com3j = com3jk*ex_delr*pcrossk*pcrossj*fc_k*dfc_i;
com3k = com3jk*ex_delr*pcrossk*pcrossk*fc_k*dfc_k;
} else {
com3j = 0.0;
com3k = 0.0;
}
ex_delr_d = mint*pow(rlm3,mint)*pow((rij-rik),(mint-1))*ex_delr; // com3
vec3_scale(-dfc_k*gijk*ex_delr,rik_hat,dri); // com1
vec3_scaleadd(fc_k*gijk_d*ex_delr,dcosdri,dri,dri); // com2
vec3_scaleadd(fc_k*gijk*ex_delr_d,rik_hat,dri,dri); // com3 cont'd
vec3_scaleadd(-fc_k*gijk*ex_delr_d,rij_hat,dri,dri); // com3 sums j
vec3_scaleadd(-com3k,rik_hat,dri,dri); // com3k
vec3_scaleadd(-com3j,rij_hat,dri,dri); // com3j
vec3_scale(prefac_ij1,dri,dri);
vec3_scaleadd(-com6,rik_hat,dri,dri); // com6
vec3_scale(fc_k*gijk_d*ex_delr,dcosdrj,drj); // com2
vec3_scaleadd(fc_k*gijk*ex_delr_d,rij_hat,drj,drj); // com3 cont'd
vec3_scaleadd(com3j,rij_hat,drj,drj); // com3j
vec3_scale(prefac_ij1,drj,drj);
vec3_scale(dfc_k*gijk*ex_delr,rik_hat,drk); // com1
vec3_scaleadd(fc_k*gijk_d*ex_delr,dcosdrk,drk,drk); // com2
vec3_scaleadd(-fc_k*gijk*ex_delr_d,rik_hat,drk,drk); // com3 cont'd
vec3_scaleadd(com3k,rik_hat,drk,drk); // com3k
vec3_scale(prefac_ij1,drk,drk);
vec3_scaleadd(com6,rik_hat,drk,drk); // com6
}
/* ---------------------------------------------------------------------- */
void PairComb3::costheta_d(double *rij_hat, double rij, double *rik_hat,
double rik, double *dri, double *drj, double *drk)
{
double cos_theta = vec3_dot(rij_hat,rik_hat);
vec3_scaleadd(-cos_theta,rij_hat,rik_hat,drj);
vec3_scale(1.0/rij,drj,drj);
vec3_scaleadd(-cos_theta,rik_hat,rij_hat,drk);
vec3_scale(1.0/rik,drk,drk);
vec3_add(drj,drk,dri);
vec3_scale(-1.0,dri,dri);
}
/* ---------------------------------------------------------------------- */
void PairComb3::tables()
{
int i,j,k,m, nntypes, ncoul,nnbuf, ncoul_lim, inty, itype, jtype;
int iparam_i, iparam_ij, iparam_ji, it, jt;
double r,dra,drin,drbuf,rc,z,zr,zrc,ea,eb,ea3,eb3,alf;
double exp2er,exp2ersh,fafash,dfafash,F1,dF1,ddF1,E1,E2,E3,E4;
double exp2ear,exp2ebr,exp2earsh,exp2ebrsh,fafbsh,dfafbsh;
double afbshift, dafbshift, exp2ershift;
int n = nelements;
int *type = atom->type;
int nlocal = atom->nlocal;
dra = 0.001;
drin = 0.100;
drbuf = 0.100;
nnbuf = int(drbuf/dra) +1;
rc = cutmax;
alf = 0.20;
nmax = atom->nmax;
nntypes = int((n+1)*n/2.0)+1;
ncoul = int((rc-drin)/dra)+ nnbuf;
ncoul_lim = int(ncoul * 1.20);
// allocate arrays
memory->create(intype,n,n,"pair:intype");
memory->create(erpaw,ncoul_lim,3,"pair:erpaw");
memory->create(fafb,ncoul_lim,nntypes,"pair:fafb");
memory->create(dfafb,ncoul_lim,nntypes,"pair:dfafb");
memory->create(ddfafb,ncoul_lim,nntypes,"pair:ddfafb");
memory->create(phin,ncoul_lim,nntypes,"pair:phin");
memory->create(dphin,ncoul_lim,nntypes,"pair:dphin");
memory->create(afb,ncoul_lim,nntypes,"pair:afb");
memory->create(dafb,ncoul_lim,nntypes,"pair:dafb");
memory->create(vvdw,ncoul,nntypes,"pair:vvdw");
memory->create(vdvdw,ncoul,nntypes,"pair:vdvdw");
memory->create(dpl,nmax,3,"pair:dpl");
memory->create(bbij,nmax,MAXNEIGH,"pair:bbij");
memory->create(xcctmp,nmax,"pair:xcctmp");
memory->create(xchtmp,nmax,"pair:xchtmp");
memory->create(xcotmp,nmax,"pair:xcotmp");
memory->create(NCo,nmax,"pair:NCo");
memory->create(sht_num,nmax,"pair:sht_num");
sht_first = (int **) memory->smalloc(nmax*sizeof(int *),
"pair:sht_first");
// set interaction number: 0-0=0, 1-1=1, 0-1=1-0=2
m = 0; k = n;
for (i = 0; i < n; i++) {
for (j = 0; j < n; j++) {
if (j == i) {
intype[i][j] = m;
m += 1;
} else if (j != i && j > i) {
intype[i][j] = k;
k += 1;
} else if (j != i && j < i) {
intype[i][j] = intype[j][i];
}
}
}
// default arrays to zero
for (i = 0; i < ncoul; i ++) {
for (j = 0; j < nntypes; j ++) {
fafb[i][j] = 0.0;
dfafb[i][j] = 0.0;
ddfafb[i][j] = 0.0;
phin[i][j] = 0.0;
dphin[i][j] = 0.0;
afb[i][j] = 0.0;
dafb[i][j] = 0.0;
}
}
// direct 1/r energy with Slater 1S orbital overlap
for (i = 0; i < n; i++) {
r = drin - dra;
itype = i;
iparam_i = elem2param[itype][itype][itype];
z = params[iparam_i].esm;
exp2ershift = exp(-2.0*z*rc);
afbshift = -exp2ershift*(z+1.0/rc);
dafbshift = exp2ershift*(2.0*z*z+2.0*z/rc+1.0/(rc*rc));
for (j = 0; j < ncoul; j++) {
exp2er = exp(-2.0 * z * r);
phin[j][i] = 1.0 - exp2er * (1.0 + 2.0 * z * r * (1.0 + z * r));
dphin[j][i] = (4.0 * exp2er * z * z * z * r * r);
afb[j][i] = -exp2er*(z+1.0/r)-afbshift-(r-rc)*dafbshift;
dafb[j][i] = -(exp2er*(2.0*z*z+2.0*z/r+1.0/(r*r))-dafbshift);
r += dra;
}
}
for (i = 0; i < n; i ++) {
for (j = 0; j < n; j ++) {
r = drin - dra;
if (j == i) {
itype = i;
inty = intype[itype][itype];
iparam_i = elem2param[itype][itype][itype];
z = params[iparam_i].esm;
zrc = z * rc;
exp2ersh = exp(-2.0 * zrc);
fafash = -exp2ersh * (1.0 / rc +
z * (11.0/8.0 + 3.0/4.0*zrc + zrc*zrc/6.0));
dfafash = exp2ersh * (1.0/(rc*rc) + 2.0*z/rc +
z*z*(2.0 + 7.0/6.0*zrc + zrc*zrc/3.0));
for (k = 0; k < ncoul; k ++) {
zr = z * r;
exp2er = exp(-2.0*zr);
F1 = -exp2er * (1.0 / r +
z * (11.0/8.0 + 3.0/4.0*zr + zr*zr/6.0));
dF1 = exp2er * (1.0/(r*r) + 2.0*z/r +
z*z*(2.0 + 7.0/6.0*zr + zr*zr/3.0));
ddF1 = -exp2er * (2.0/(r*r*r) + 4.0*z/(r*r) + 4.0*z*z/r +
z*z*z/3.0*(17.0/2.0 + 5.0*zr + 2.0*zr*zr));
fafb[k][inty] = F1-fafash-(r-rc)*dfafash;
dfafb[k][inty] = -(dF1 - dfafash);
ddfafb[k][inty] = ddF1;
r += dra;
}
} else if (j != i) {
itype = i;
jtype = j;
inty = intype[itype][jtype];
iparam_ij = elem2param[itype][jtype][jtype];
ea = params[iparam_ij].esm;
ea3 = ea*ea*ea;
iparam_ji = elem2param[jtype][itype][itype];
eb = params[iparam_ji].esm;
eb3 = eb*eb*eb;
E1 = ea*eb3*eb/((ea+eb)*(ea+eb)*(ea-eb)*(ea-eb));
E2 = eb*ea3*ea/((ea+eb)*(ea+eb)*(eb-ea)*(eb-ea));
E3 = (3.0*ea*ea*eb3*eb-eb3*eb3) /
((ea+eb)*(ea+eb)*(ea+eb)*(ea-eb)*(ea-eb)*(ea-eb));
E4 = (3.0*eb*eb*ea3*ea-ea3*ea3) /
((ea+eb)*(ea+eb)*(ea+eb)*(eb-ea)*(eb-ea)*(eb-ea));
exp2earsh = exp(-2.0*ea*rc);
exp2ebrsh = exp(-2.0*eb*rc);
fafbsh = -exp2earsh*(E1 + E3/rc)-exp2ebrsh*(E2 + E4/rc);
dfafbsh =
exp2earsh*(2.0*ea*(E1+E3/rc)+E3/(rc*rc)) +
exp2ebrsh*(2.0*eb*(E2+E4/rc)+E4/(rc*rc));
for (k = 0; k < ncoul; k ++) {
exp2ear = exp(-2.0*ea*r);
exp2ebr = exp(-2.0*eb*r);
fafb[k][inty] =
- exp2ear*(E1+E3/r) - exp2ebr*(E2+E4/r)
- fafbsh - (r-rc) * dfafbsh;
dfafb[k][inty] = -(exp2ear*(2.0*ea*(E1+E3/r) + E3/(r*r))
+ exp2ebr*(2.0*eb*(E2+E4/r) + E4/(r*r))- dfafbsh);
ddfafb[k][inty] = -exp2ear*(4.0*ea*ea*(E1+E3/r)+4.0*ea*E3/(r*r)
+2.0*E3/(r*r*r))
-exp2ebr*(4.0*eb*eb*(E2+E4/r)+4.0*eb*E4/(r*r)
+2.0*E4/(r*r*r));
r += dra;
}
}
}
}
for (i = 0; i < ncoul_lim; i ++) {
r = dra * (i-1) + drin;
erpaw[i][0] = erfc(r*alf);
erpaw[i][1] = exp(-r*r*alf*alf);
}
// end wolf summation
// van der Waals
int ii,jj;
double **rvdw, *cc2, *cc3, *vrc, *rrc;
double r6, r7, r12, r13, rf6, rf12, drf7, drf13;
double drcc, temp6, temp7, temp12, temp13;
double vsigt, vepst, vdwt, dvdwt;
vrc = new double[13];
rrc = new double[13];
cc2 = new double[nntypes];
cc3 = new double[nntypes];
memory->create(rvdw,2,nntypes,"pair:rvdw");
vrc[0] = rc;
for (i=1; i<13; i++) {
vrc[i] = vrc[i-1] * vrc[0];
}
// generate spline coefficients for CC, CH, HH vdw
for (ii = 0; ii < n; ii ++) {
for (jj = ii; jj < n; jj ++) {
itype = ii;
jtype = jj;
inty = intype[itype][jtype];
iparam_ij = elem2param[itype][jtype][jtype];
// parameter check: eps > 0
if(params[iparam_ij].vdwflag > 0) {
if(params[iparam_ij].vdwflag==1){
rvdw[0][inty] = params[iparam_ij].bigr + params[iparam_ij].bigd;
}
else {
rvdw[0][inty] = params[iparam_ij].bigr - params[iparam_ij].bigd;
}
rvdw[1][inty] = params[iparam_ij].vsig * 0.950;
- // radius check: outer radius vs. sigma
+ // radius check: outter radius vs. sigma
if( rvdw[0][inty] > rvdw[1][inty] )
- error->all(FLERR,"Error in vdw spline: inner radius > outer radius");
+ error->all(FLERR,"Error in vdw spline: inner radius > outter radius");
rrc[0] = rvdw[1][inty];
for (i=1; i<13; i++)
rrc[i] = rrc[i-1] * rrc[0];
drcc = rrc[0] - rvdw[0][inty];
temp6 = 1.0/rrc[5]-1.0/vrc[5]+6.0*(rrc[0]-vrc[0])/vrc[6];
temp7 = 6.0*(1.0/vrc[6]-1.0/rrc[6]);
temp12 = 1.0/rrc[11]-1.0/vrc[11]+(rrc[0]-vrc[0])*12.0/vrc[12];
temp13 = 12.0*(1.0/vrc[12]-1.0/rrc[12]);
vsigt = params[iparam_ij].vsig;
vepst = params[iparam_ij].veps;
vsigt = vsigt*vsigt*vsigt*vsigt*vsigt*vsigt;
vdwt = vepst*(vsigt*vsigt*temp12-vsigt*temp6);
dvdwt = vepst*(vsigt*vsigt*temp13-vsigt*temp7);
cc2[inty] = (3.0/drcc*vdwt-dvdwt)/drcc;
cc3[inty] = (vdwt/(drcc*drcc)-cc2[inty] )/drcc;
}
}
}
// generate vdw look-up table
for (ii = 0; ii < n; ii ++) {
for (jj = ii; jj < n; jj ++) {
itype = ii;
jtype = jj;
inty = intype[itype][jtype];
iparam_ij = elem2param[itype][jtype][jtype];
r = drin;
for (k = 0; k < ncoul; k ++) {
r6 = r*r*r*r*r*r;
r7 = r6 * r;
rf6 = 1.0/r6-1.0/vrc[5]+(r-vrc[0])*6.0/vrc[6];
drf7 = 6.0*(1.0/vrc[6]-1.0/r7);
vsigt = params[iparam_ij].vsig;
vepst = params[iparam_ij].veps;
vsigt = vsigt*vsigt*vsigt*vsigt*vsigt*vsigt;
if(params[iparam_ij].vdwflag>0) {
if(r <= rvdw[0][inty]) {
vvdw[k][inty] = 0.0;
vdvdw[k][inty] = 0.0;
}
else if ( r > rvdw[0][inty] && r <= rvdw[1][inty]) {
drcc = r-rvdw[0][inty];
vvdw[k][inty] = drcc*drcc*(drcc*cc3[inty]+cc2[inty]);
vdvdw[k][inty] = drcc*(3.0*drcc*cc3[inty]+2.0*cc2[inty]);
} else {
r12 = r6*r6;
r13 = r6*r7;
rf12 = 1.0/r12-1.0/vrc[11]+(r-vrc[0])*12.0/vrc[12];
drf13= 12.0*(1.0/vrc[12]-1.0/r13);
vvdw[k][inty] = vepst*(vsigt*vsigt*rf12-vsigt*rf6);
vdvdw[k][inty] = vepst*(vsigt*vsigt*drf13-vsigt*drf7);
}
} else {
vvdw[k][inty]=0.0;
vdvdw[k][inty]=0.0;
}
r += dra;
}
}
}
delete [] vrc;
delete [] rrc;
delete [] cc2;
delete [] cc3;
memory->destroy(rvdw);
}
/* ---------------------------------------------------------------------- */
void PairComb3::potal_calc(double &calc1, double &calc2, double &calc3)
{
double alf,rcoul,esucon;
int m;
rcoul = 0.0;
for (m = 0; m < nparams; m++)
if (params[m].lcut > rcoul) rcoul = params[m].lcut;
alf = 0.20;
esucon = force->qqr2e;
calc2 = (erfc(rcoul*alf)/rcoul/rcoul+2.0*alf/MY_PIS*
exp(-alf*alf*rcoul*rcoul)/rcoul)*esucon/rcoul;
calc3 = (erfc(rcoul*alf)/rcoul)*esucon;
calc1 = -(alf/MY_PIS*esucon+calc3*0.5);
}
/* ---------------------------------------------------------------------- */
void PairComb3::tri_point(double rsq, int &mr1, int &mr2,
int &mr3, double &sr1, double &sr2, double &sr3)
{
double r, rin, dr, dd, rr1, rridr, rridr2;
rin = 0.1000; dr = 0.0010;
r = sqrt(rsq);
if (r < rin + 2.0*dr) r = rin + 2.0*dr;
if (r > cutmax - 2.0*dr) r = cutmax - 2.0*dr;
rridr = (r-rin)/dr;
mr1 = int(rridr) ;
dd = rridr - float(mr1);
if (dd > 0.5) mr1 += 1;
rr1 = float(mr1)*dr;
rridr = (r - rin - rr1)/dr;
rridr2 = rridr * rridr;
sr1 = (rridr2 - rridr) * 0.50;
sr2 = 1.0 - rridr2;
sr3 = (rridr2 + rridr) * 0.50;
mr2 = mr1 + 1;
mr3 = mr1 + 2;
}
/* ---------------------------------------------------------------------- */
void PairComb3::vdwaals(int inty, int mr1, int mr2, int mr3, double rsq,
double sr1, double sr2, double sr3,
double &eng, double &fforce)
{
double r = sqrt(rsq);
eng = 1.0*(sr1*vvdw[mr1-1][inty]+sr2*vvdw[mr2-1][inty]+sr3*vvdw[mr3-1][inty]);
fforce = -1.0/r*(sr1*vdvdw[mr1-1][inty]+sr2*vdvdw[mr2-1][inty]+sr3*vdvdw[mr3-1][inty]);
}
/* ---------------------------------------------------------------------- */
void PairComb3::direct(Param *parami, Param *paramj, int mr1,
int mr2, int mr3, double rsq, double sr1, double sr2, double sr3,
double iq, double jq, double fac11, double fac11e,
double &pot_tmp, double &for_tmp, int i, int j)
{
double r,erfcc,fafbnl,potij,chrij,esucon;
double r3,erfcd,dfafbnl,smf2,dvdrr,ddvdrr,alf,alfdpi;
double afbn,afbj,sme1n,sme1j,sme1,sme2,dafbn, dafbj,smf1n,smf1j;
double curli = parami->curl;
double curlj = paramj->curl;
int inti = parami->ielement;
int intj = paramj->ielement;
int inty = intype[inti][intj];
double curlcutij1 = parami->curlcut1;
double curlcutij2 = parami->curlcut2;
double curlcutji1 = paramj->curlcut1;
double curlcutji2 = paramj->curlcut2;
double curlij0 = parami->curl0;
double curlji0 = paramj->curl0;
double curlij1,curlji1,dcurlij,dcurlji;
double fcp1j,xcoij,xcoji;
int icurl, jcurl;
int ielegp = parami->ielementgp;
int jelegp = paramj->ielementgp;
r = sqrt(rsq);
r3 = r * rsq;
alf = 0.20;
alfdpi = 2.0*alf/MY_PIS;
esucon = force->qqr2e;
pot_tmp = for_tmp = 0.0;
icurl=jcurl=0;
if(ielegp==2 && curli>curlij0) {
icurl=1;
curlij1=curli;
}
if(jelegp==2 && curlj>curlji0) {
jcurl=1;
curlji1=curlj;
}
if(icurl==1 || jcurl ==1) {
xcoij = xcotmp[i];
xcoji = xcotmp[j];
fcp1j = comb_fc_d(r,parami);
if(icurl==1) {
curli=curlij1+(curlij0-curlij1)*comb_fc_curl(xcoij,parami);
dcurlij=fcp1j*(curlij0-curlij1)*comb_fc_curl_d(xcoij,parami);
}
if(jcurl==1) {
curlj=curlji1+(curlji0-curlji1)*comb_fc_curl(xcoji,paramj);
dcurlji=fcp1j*(curlji0-curlji1)*comb_fc_curl_d(xcoji,paramj);
}
}
erfcc = sr1*erpaw[mr1][0] + sr2*erpaw[mr2][0] + sr3*erpaw[mr3][0];
afbn = sr1*afb[mr1][inti] + sr2*afb[mr2][inti] + sr3*afb[mr3][inti];
afbj = sr1*afb[mr1][intj] + sr2*afb[mr2][intj] + sr3*afb[mr3][intj];
fafbnl= sr1*fafb[mr1][inty] + sr2*fafb[mr2][inty] + sr3*fafb[mr3][inty];
potij = (erfcc/r * esucon - fac11e);
sme1n = iq*curlj*(afbn-fafbnl)*esucon;
sme1j = jq*curli*(afbj-fafbnl)*esucon;
sme1 = sme1n + sme1j;
sme2 = (potij + fafbnl * esucon) * iq * jq;
pot_tmp = 1.0 * (sme1+sme2);
// 1/r force (wrt r)
erfcd = sr1*erpaw[mr1][1] + sr2*erpaw[mr2][1] + sr3*erpaw[mr3][1];
dafbn = sr1*dafb[mr1][inti] + sr2*dafb[mr2][inti] + sr3*dafb[mr3][inti];
dafbj = sr1*dafb[mr1][intj] + sr2*dafb[mr2][intj] + sr3*dafb[mr3][intj];
dfafbnl= sr1*dfafb[mr1][inty] + sr2*dfafb[mr2][inty] + sr3*dfafb[mr3][inty];
dvdrr = (erfcc/r3+alfdpi*erfcd/rsq)*esucon-fac11;
ddvdrr = (2.0*erfcc/r3 + 2.0*alfdpi*erfcd*(1.0/rsq+alf*alf))*esucon;
smf1n = iq * curlj * (dafbn-dfafbnl)*esucon/r;
smf1j = jq * curli * (dafbj-dfafbnl)*esucon/r;
if(jcurl==1 && ielegp == 3 && dcurlji != 0.0){
smf1n += dcurlji*iq*(afbn-fafbnl)*esucon/r;
}
if(icurl==1 && jelegp == 3 && dcurlij != 0.0){
smf1j += dcurlij*jq*(afbj-fafbnl)*esucon/r;
}
smf2 = dvdrr + dfafbnl * esucon/r;
for_tmp = 1.0 * iq * jq * smf2 + smf1n + smf1j;
}
/* ---------------------------------------------------------------------- */
void PairComb3::field(Param *parami, Param *paramj, double rsq, double iq,
double jq, double &eng_tmp,double &for_tmp)
{
double r,r3,r4,r5,r6,rc,rc2,rc3,rc4,rc5,rc6;
double cmi1,cmi2,cmj1,cmj2,pcmi1,pcmi2,pcmj1,pcmj2;
double rf3i,rcf3i,rf5i,rcf5i;
double drf3i,drcf3i,drf5i,drcf5i;
double rf3,rf5,drf4,drf6;
double smpn,smpl,rfx1,rfx2;
r = sqrt(rsq);
r3 = r * r * r;
r4 = r3 * r;
r5 = r4 * r;
r6 = r5 * r;
rc = parami->lcut;
rc2 = rc * rc;
rc3 = rc*rc*rc;
rc4 = rc3 * rc;
rc5 = rc4 * rc;
rc6 = rc5 * rc;
cmi1 = parami->cmn1;
cmi2 = parami->cmn2;
cmj1 = paramj->cmn1;
cmj2 = paramj->cmn2;
pcmi1 = parami->pcmn1;
pcmi2 = parami->pcmn2;
pcmj1 = paramj->pcmn1;
pcmj2 = paramj->pcmn2;
rf3i = r3/(pow(r3,2)+pow(pcmi1,3));
rcf3i = rc3/(pow(rc3,2)+pow(pcmi1,3));
rf5i = r5/(pow(r5,2)+pow(pcmi2,5));
rcf5i = rc5/(pow(rc5,2)+pow(pcmi2,5));
drf3i = 3/r*rf3i-6*rsq*rf3i*rf3i;
drcf3i = 3/rc*rcf3i-6*rc2*rcf3i*rcf3i;
drf5i = 5/r*rf5i-10*r4*rf5i*rf5i;
drcf5i = 5/rc*rcf5i-10*rc4*rcf5i*rcf5i;
rf3 = rf3i-rcf3i-(r-rc)*drcf3i;
rf5 = rf5i-rcf5i-(r-rc)*drcf5i;
drf4 = drf3i - drcf3i;
drf6 = drf5i - drcf5i;
// field correction energy
smpn = jq*(cmi1*rf3+jq*cmi2*rf5);
smpl = iq*(cmj1*rf3+iq*cmj2*rf5);
eng_tmp = 1.0 * (smpn + smpl);
// field correction force
rfx1 = jq*(cmi1*drf4+jq*cmi2*drf6)/r;
rfx2 = iq*(cmj1*drf4+iq*cmj2*drf6)/r;
for_tmp -= 1.0 * (rfx1 + rfx2);
}
/* ---------------------------------------------------------------------- */
double PairComb3::rad_init(double rsq2,Param *param,int i,
double &radtot, double cnconj)
{
int n;
double r, fc1k, radcut,radcut1,radcut2;
r = sqrt(rsq2);
fc1k = comb_fc(r,param);
radtot = -fc1k * param->pcross + cnconj;
radcut = comb_fcch(radtot);
return fc1k * param->pcross * radcut;
}
/* ---------------------------------------------------------------------- */
void PairComb3::rad_calc(double r, Param *parami, Param *paramj,
double kconjug, double lconjug, int i, int j, double xcn, double ycn)
{
int ixmin, iymin, izmin, n;
int radindx;
double xrad, yrad, zcon, vrad, pradx, prady, pradz;
vrad = pradx = prady = pradz = 0.0;
xrad = -comb_fc(r,parami)*parami->pcross + xcn;
yrad = -comb_fc(r,paramj)*paramj->pcross + ycn;
zcon = 1.0 + pow(kconjug,2) + pow(lconjug,2);
if(xrad < 0.0) xrad = 0.0;
if(yrad < 0.0) yrad = 0.0;
if(zcon < 1.0) zcon = 1.0;
if(xrad > maxxc) xrad = maxxc;
if(yrad > maxyc) yrad = maxyc;
if(zcon > maxconj) zcon = maxconj;
ixmin = int(xrad+1.0e-12);
iymin = int(yrad+1.0e-12);
izmin = int(zcon+1.0e-12);
radindx=parami->rad_flag-1;
if (fabs(float(ixmin)-xrad)>1.0e-8 ||
fabs(float(iymin)-yrad)>1.0e-8 ||
fabs(float(izmin)-zcon)>1.0e-8) {
rad_int(radindx,xrad,yrad,zcon,ixmin,iymin,izmin,
vrad,pradx,prady,pradz);
} else {
vrad = rad_grid[radindx][ixmin][iymin][izmin-1];
pradx = rad_gridx[radindx][ixmin][iymin][izmin-1];
prady = rad_gridy[radindx][ixmin][iymin][izmin-1];
pradz = rad_gridz[radindx][ixmin][iymin][izmin-1];
}
brad[0] = vrad;
brad[1] = pradx;
brad[2] = prady;
brad[3] = pradz;
}
/* ---------------------------------------------------------------------- */
void PairComb3::rad_int(int radindx,double xrad, double yrad, double zcon, int l,
int m, int n, double &vrad, double &pradx, double &prady,
double &pradz)
{
int j;
double x;
vrad = pradx = prady = pradz = 0.0;
if(l >= maxxc-1) { l=maxxc-1;}
if(m >= maxyc-1) { m=maxyc-1; }
if(n >= maxconj-1) { n=maxconj-1;}
for (j=0; j<64; j++) {
x = rad_spl[radindx][l][m][n-1][j] * pow(xrad,iin3[j][0])
* pow(yrad,iin3[j][1]) * pow(zcon,iin3[j][2]);
vrad += x;
if(xrad > 1.0e-8) pradx += x*iin3[j][0]/xrad;
if(yrad > 1.0e-8) prady += x*iin3[j][1]/yrad;
if(zcon > 1.0e-8) pradz += x*iin3[j][2]/zcon;
}
}
/* ---------------------------------------------------------------------- */
void PairComb3::rad_forceik(Param *paramk, double rsq2, double *delrk,
double conjug, double radtot)
{
int nm;
double rik, fc1k, fcp1k;
double pradk, ffkk2, fktmp[3];
double radcut = comb_fcch(radtot);
double dradcut = comb_fcch_d(radtot);
for (nm=0; nm<3; nm++) {
fi_rad[nm] = fk_rad[nm] = 0.0;
}
radtmp =0.0;
rik = sqrt(rsq2);
fc1k = comb_fc(rik, paramk);
fcp1k = comb_fc_d(rik,paramk);
pradk = brad[3]*fcp1k*radcut*paramk->pcross*2.0*conjug;
radtmp= brad[3]*fc1k*dradcut*paramk->pcross*2.0*conjug;
ffkk2 = -pradk/rik;
for (nm=0; nm<3; nm++) {
fktmp[nm] = - ffkk2 * delrk[nm];
}
for (nm=0; nm<3; nm++) {
fi_rad[nm] = fktmp[nm];
fk_rad[nm] = -fktmp[nm];
}
}
/* ---------------------------------------------------------------------- */
void PairComb3::rad_force(Param *paramm, double rsq3,
double *delrm, double dpradk)
{
int nm;
double rkm, fc1m, fcp1m;
double comkm, ffmm2, fkm[3];
for (nm=0; nm<3; nm++) {
fj_rad[nm] = fk_rad[nm] = 0.0;
fkm[nm]=0.0;
}
rkm = sqrt(rsq3);
fc1m = comb_fc(rkm, paramm);
fcp1m = comb_fc_d(rkm, paramm);
comkm = dpradk * fcp1m * paramm->pcross;
ffmm2 = -comkm/rkm;
for (nm=0; nm<3; nm++) {
fkm[nm] = -ffmm2 * delrm[nm];
}
for (nm=0; nm<3; nm++) {
fj_rad[nm] = fkm[nm];
fk_rad[nm] = -fkm[nm];
}
}
/* ---------------------------------------------------------------------- */
double PairComb3::bbtor1(int torindx, Param *paramk, Param *paraml,
double rsq1, double rsq2, double rsq3, double *delrj,
double *delrk, double *delrl, double srmu)
{
double rmul, rij, rik, rjl;
rij = sqrt(rsq1);
rik = sqrt(rsq2);
rjl = sqrt(rsq3);
vec3_scale(-1.0,delrl,delrl);
rmul = vec3_dot(delrj,delrl)/(rij*rjl);
vec3_scale(-1.0,delrl,delrl);
rmul = sqrt(1.0-rmul*rmul);
if(rmul > 0.1 ) {
double fc1k, fc1l, TT1, TT2, rmut, btt, tork[3], torl[3];
fc1k = comb_fc(rik,paramk);
fc1l = comb_fc(rjl,paraml);
TT1 = rik*rjl*rij*rij*srmu*rmul;
tork[0] = delrk[1]*delrj[2] - delrk[2]*delrj[1];
torl[0] = delrj[1]*delrl[2] - delrj[2]*delrl[1];
tork[1] = delrk[2]*delrj[0] - delrk[0]*delrj[2];
torl[1] = delrj[2]*delrl[0] - delrj[0]*delrl[2];
tork[2] = delrk[0]*delrj[1] - delrk[1]*delrj[0];
torl[2] = delrj[0]*delrl[1] - delrj[1]*delrl[0];
TT2 = vec3_dot(tork,torl);
rmut = pow((TT2/TT1),2);
if(torindx>=1) {
btt = 1.0 - rmut;
return btt * fc1k * fc1l;
}
else {
btt=paramk->ptork1-TT2/TT1;
btt=paramk->ptork2*pow(btt,2);
return btt * fc1k * fc1l;
}
} else {
return 0.0;
}
}
/* ---------------------------------------------------------------------- */
void PairComb3::tor_calc(double r, Param *parami, Param *paramj,
double kconjug, double lconjug, int i, int j, double xcn, double ycn)
{
int ixmin, iymin, izmin, n;
double vtor, dtorx, dtory, dtorz;
double xtor, ytor, zcon;
int torindx;
vtor = dtorx = dtory = dtorz = 0.0;
torindx=parami->tor_flag;
if(torindx<0){
vtor=1.0;
dtorx=0.0;
dtory=0.0;
dtorz=0.0;
} else {
xtor = -comb_fc(r, parami) * parami->pcross + xcn;
ytor = -comb_fc(r, paramj) * paramj->pcross + ycn;
zcon = 1.0 + pow(kconjug,2) + pow(lconjug,2);
if (xtor < 0.0) xtor = 0.0;
if (ytor < 0.0) ytor = 0.0;
if (zcon < 1.0) zcon = 1.0;
if (xtor > maxxc) xtor = maxxc;
if (ytor > maxyc) ytor = maxyc;
if (zcon > maxconj) zcon = maxconj;
ixmin = int(xtor+1.0e-12);
iymin = int(ytor+1.0e-12);
izmin = int(zcon+1.0e-12);
torindx=torindx-1;
if (fabs(float(ixmin)-xtor)>1.0e-8 ||
fabs(float(iymin)-ytor)>1.0e-8 ||
fabs(float(izmin)-zcon)>1.0e-8) {
tor_int(torindx,xtor,ytor,zcon,ixmin,iymin,izmin,
vtor,dtorx,dtory,dtorz);
} else {
vtor = tor_grid[torindx][ixmin][iymin][izmin-1];
dtorx = tor_gridx[torindx][ixmin][iymin][izmin-1];
dtory = tor_gridy[torindx][ixmin][iymin][izmin-1];
dtorz = tor_gridz[torindx][ixmin][iymin][izmin-1];
}
}
btor[0] = vtor;
btor[1] = dtorx;
btor[2] = dtory;
btor[3] = dtorz;
}
/* ---------------------------------------------------------------------- */
void PairComb3::tor_int(int torindx,double xtor, double ytor, double zcon, int l,
int m, int n, double &vtor, double &dtorx, double &dtory, double &dtorz)
{
int j;
double x;
vtor = dtorx = dtory = dtorz = 0.0;
if(l >= maxxc-1) { l=maxxc-1; } //boundary condition changed
if(m >= maxyc-1) { m=maxyc-1; }
if(n >= maxconj-1) { n=maxconj-1; }
for (j=0; j<64; j++) {
x = tor_spl[torindx][l][m][n-1][j] * pow(xtor,iin3[j][0])
* pow(ytor,iin3[j][1]) * pow(zcon,iin3[j][2]);
vtor += x;
if(xtor > 1.0e-8 ) dtorx += x*iin3[j][0]/xtor;
if(ytor > 1.0e-8 ) dtory += x*iin3[j][1]/ytor;
if(zcon > 1.0e-8 ) dtorz += x*iin3[j][2]/zcon;
}
}
/* ---------------------------------------------------------------------- */
void PairComb3::tor_force(int torindx, Param *paramk, Param *paraml,
double srmu, double rsq1,double rsq2, double rsq3,
double *delrj, double *delrk, double *delrl)
{
int nm;
double rmu, rmul, srmul, rij, rik, rjl;
for (nm=0; nm<3; nm++) {
fi_tor[nm] = fj_tor[nm] = fk_tor[nm] = fl_tor[nm] = 0.0;
}
rij = sqrt(rsq1);
rik = sqrt(rsq2);
rjl = sqrt(rsq3);
rmu = vec3_dot(delrj,delrk)/(rij*rik);
vec3_scale(-1.0,delrl,delrl);
rmul = vec3_dot(delrj,delrl)/(rij*rjl);
vec3_scale(-1.0,delrl,delrl);
srmul = sqrt(1.0-rmul*rmul);
if(acos(rmul) > MY_PI) srmul = -srmul;
if(srmul > 0.1 ) {
double fc1k, fcp1k, fc1l, fcp1l, srmul2, dt1dik, dt1djl;
double TT1, TT2, rmut, btt, tork[3], torl[3];
double dt2dik[3], dt2djl[3], dt2dij[3], AA, AA2;
double tfij[4], tfik[2], tfjl[2], tjx[3], tjy[3], tjz[3];
double tkx[2], tky[2], tkz[2], tlx[2], tly[2], tlz[2];
fc1k = comb_fc(rik,paramk);
fcp1k = comb_fc_d(rik,paramk);
fc1l = comb_fc(rjl,paraml);
fcp1l = comb_fc_d(rjl,paraml);
srmul2 = pow(srmul,2);
TT1 = rik*rjl*rij*rij*srmu*srmul;
dt1dik = -rmu/pow(srmu,2);
dt1djl = -rmul/srmul2;
tork[0] = delrk[1]*delrj[2] - delrk[2]*delrj[1];
torl[0] = delrj[1]*delrl[2] - delrj[2]*delrl[1];
tork[1] = delrk[2]*delrj[0] - delrk[0]*delrj[2];
torl[1] = delrj[2]*delrl[0] - delrj[0]*delrl[2];
tork[2] = delrk[0]*delrj[1] - delrk[1]*delrj[0];
torl[2] = delrj[0]*delrl[1] - delrj[1]*delrl[0];
TT2 = vec3_dot(tork,torl);
dt2dik[0] = -delrj[1]*torl[2] + delrj[2]*torl[1];
dt2dik[1] = -delrj[2]*torl[0] + delrj[0]*torl[2];
dt2dik[2] = -delrj[0]*torl[1] + delrj[1]*torl[0];
dt2djl[0] = delrj[1]*tork[2] - delrj[2]*tork[1];
dt2djl[1] = delrj[2]*tork[0] - delrj[0]*tork[2];
dt2djl[2] = delrj[0]*tork[1] - delrj[1]*tork[0];
dt2dij[0] = -delrk[2]*torl[1] + delrl[2]*tork[1]
+ delrk[1]*torl[2] - delrl[1]*tork[2];
dt2dij[1] = -delrk[0]*torl[2] + delrl[0]*tork[2]
+ delrk[2]*torl[0] - delrl[2]*tork[0];
dt2dij[2] = -delrk[1]*torl[0] + delrl[1]*tork[0]
+ delrk[0]*torl[1] - delrl[0]*tork[1];
rmut = TT2/TT1;
if(torindx>=1) {
btt = 1.0 - pow(rmut,2);
AA = -2.0 * ptorr * rmut * fc1k * fc1l / TT1;
}
else {
btt=paramk->ptork1-rmut;
btt=paramk->ptork2*pow(btt,2);
AA = -2.0 * ptorr * paramk->ptork2 *
(paramk->ptork1-rmut) * fc1k * fc1l /TT1;
}
AA2 = AA * TT2;
tfij[0] = -(dt1dik*AA2)/rij/rik;
tfij[1] = AA2/rij/rij - dt1dik*AA2*rmu/rij/rij;
tfij[2] = -dt1djl*AA2/rij/rjl;
tfij[3] = AA2/rij/rij - dt1djl*AA2*rmul/rij/rij;
tfik[0] = tfij[0];
tfik[1] = (AA2/rik - btt*ptorr*fc1l*fcp1k)/rik -
dt1dik*AA2*rmu/rik/rik;
tfjl[0] = tfij[2];
tfjl[1] = (AA2/rjl - btt*ptorr*fc1k*fcp1l)/rjl -
dt1djl*AA2*rmul/rjl/rjl;
tjx[0] = tfij[0]*delrk[0] - tfij[1]*delrj[0];
tjy[0] = tfij[0]*delrk[1] - tfij[1]*delrj[1];
tjz[0] = tfij[0]*delrk[2] - tfij[1]*delrj[2];
tjx[1] = -tfij[2]*delrl[0] - tfij[3]*delrj[0];
tjy[1] = -tfij[2]*delrl[1] - tfij[3]*delrj[1];
tjz[1] = -tfij[2]*delrl[2] - tfij[3]*delrj[2];
tjx[2] = -dt2dij[0] * AA;
tjy[2] = -dt2dij[1] * AA;
tjz[2] = -dt2dij[2] * AA;
tkx[0] = tfik[0]*delrj[0] - tfik[1]*delrk[0];
tky[0] = tfik[0]*delrj[1] - tfik[1]*delrk[1];
tkz[0] = tfik[0]*delrj[2] - tfik[1]*delrk[2];
tkx[1] = -dt2dik[0] * AA;
tky[1] = -dt2dik[1] * AA;
tkz[1] = -dt2dik[2] * AA;
tlx[0] = -tfjl[0]*delrj[0] - tfjl[1]*delrl[0];
tly[0] = -tfjl[0]*delrj[1] - tfjl[1]*delrl[1];
tlz[0] = -tfjl[0]*delrj[2] - tfjl[1]*delrl[2];
tlx[1] = -dt2djl[0] * AA;
tly[1] = -dt2djl[1] * AA;
tlz[1] = -dt2djl[2] * AA;
fi_tor[0] = tjx[0]+tjx[1]+tjx[2]+tkx[0]+tkx[1];
fi_tor[1] = tjy[0]+tjy[1]+tjy[2]+tky[0]+tky[1];
fi_tor[2] = tjz[0]+tjz[1]+tjz[2]+tkz[0]+tkz[1];
fj_tor[0] = -tjx[0]-tjx[1]-tjx[2]+tlx[0]+tlx[1];
fj_tor[1] = -tjy[0]-tjy[1]-tjy[2]+tly[0]+tly[1];
fj_tor[2] = -tjz[0]-tjz[1]-tjz[2]+tlz[0]+tlz[1];
fk_tor[0] = -tkx[0]-tkx[1];
fk_tor[1] = -tky[0]-tky[1];
fk_tor[2] = -tkz[0]-tkz[1];
fl_tor[0] = -tlx[0]-tlx[1];
fl_tor[1] = -tly[0]-tly[1];
fl_tor[2] = -tlz[0]-tlz[1];
}
}
/* ---------------------------------------------------------------------- */
double PairComb3::combqeq(double *qf_fix, int &igroup)
{
- int i,j,ii,jj,itype,jtype,jnum;
+ int i,j,ii, jj,itype,jtype,jnum;
int iparam_i,iparam_ji,iparam_ij;
int *ilist,*jlist,*numneigh,**firstneigh;
int mr1,mr2,mr3,inty,nj;
- tagint itag,jtag;
double xtmp,ytmp,ztmp,rr,rsq,rsq1,rsq2,delrj[3],zeta_ij;
double iq,jq,fqi,fqj,fqij,fqji,yaself,yaself_d,sr1,sr2,sr3;
double rr_sw,ij_sw,ji_sw,fq_swi,fq_swj;
double potal,fac11,fac11e;
int sht_jnum,*sht_jlist;
+ tagint itag, jtag;
double **x = atom->x;
double *q = atom->q;
tagint *tag = atom->tag;
int *type = atom->type;
int inum = list->inum;
int *mask = atom->mask;
int groupbit = group->bitmask[igroup];
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// Derivative debugging
int nlocal = atom->nlocal;
double fqself, fqdirect, fqfield, fqshort, fqdipole, fqtot;
fqself = fqdirect = fqfield = fqshort = fqdipole = fqtot = 0.0;
qf = qf_fix;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit)
qf[i] = 0.0;
dpl[i][0] = dpl[i][1] = dpl[i][2] = 0.0;
}
// communicating charge force to all nodes, first forward then reverse
pack_flag = 1;
comm->forward_comm_pair(this);
// self energy correction term: potal
potal_calc(potal,fac11,fac11e);
// loop over full neighbor list of my atoms
fqi = fqj = fqij = fqji = 0.0;
for (ii = 0; ii < inum; ii ++) {
i = ilist[ii];
itag = tag[i];
nj = 0;
if (mask[i] & groupbit) {
itype = map[type[i]];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
iq = q[i];
iparam_i = elem2param[itype][itype][itype];
// charge force from self energy
fqi =0.0;
fqi = qfo_self(&params[iparam_i],iq);
fq_swi = fqi;
jlist = firstneigh[i];
jnum = numneigh[i];
sht_jlist = sht_first[i];
sht_jnum = sht_num[i];
// two-body interactions
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
jtag = tag[j];
if (itag >= jtag) continue;
jtype = map[type[j]];
inty = intype[itype][jtype];
jq = q[j];
delrj[0] = xtmp - x[j][0];
delrj[1] = ytmp - x[j][1];
delrj[2] = ztmp - x[j][2];
rsq1 = vec3_dot(delrj,delrj);
iparam_ij = elem2param[itype][jtype][jtype];
iparam_ji = elem2param[jtype][itype][itype];
// long range q-dependent
if (rsq1 > params[iparam_ij].lcutsq) continue;
// polynomial three-point interpolation
tri_point(rsq1,mr1,mr2,mr3,sr1,sr2,sr3);
// 1/r charge forces
qfo_direct(&params[iparam_ij],&params[iparam_ji],
mr1,mr2,mr3,rsq1,sr1,sr2,sr3,fac11e,fqij,fqji,
iq,jq,i,j);
fqi += fqij; qf[j] += fqji;
// field correction to self energy and charge force
qfo_field(&params[iparam_ij],&params[iparam_ji],rsq1,
iq,jq,fqij,fqji);
fqi += fqij; qf[j] += fqji;
// polarization field charge force
if (pol_flag) {
qfo_dipole(fac11,mr1,mr2,mr3,inty,rsq1,delrj,sr1,sr2,sr3,
fqij,fqji,i,j);
fqi += fqij; qf[j] += fqji;
}
}
for (jj = 0; jj < sht_jnum; jj++) {
j = sht_jlist[jj];
jtag = tag[j];
if (itag >= jtag) continue;
jtype = map[type[j]];
inty = intype[itype][jtype];
jq = q[j];
delrj[0] = xtmp - x[j][0];
delrj[1] = ytmp - x[j][1];
delrj[2] = ztmp - x[j][2];
rsq1 = vec3_dot(delrj,delrj);
iparam_ij = elem2param[itype][jtype][jtype];
iparam_ji = elem2param[jtype][itype][itype];
if (rsq1 >= params[iparam_ij].cutsq) continue;
nj ++;
// charge force in Aij and Bij
qfo_short(&params[iparam_ij],&params[iparam_ji],
rsq1,iq,jq,fqij,fqji,i,j,nj);
fqi += fqij; qf[j] += fqji;
}
qf[i] += fqi;
}
}
comm->reverse_comm_pair(this);
// sum charge force on each node and return it
double eneg = 0.0;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
if (mask[i] & groupbit){
eneg += qf[i];
- itag=tag[i];
+ itag=tag[i];
}
}
double enegtot;
MPI_Allreduce(&eneg,&enegtot,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Bcast(&enegtot,1,MPI_DOUBLE,0,world);
return enegtot;
}
/* ---------------------------------------------------------------------- */
double PairComb3::qfo_self(Param *param, double qi)
{
double self_d,cmin,cmax,qmin,qmax;
double s1 = param->chi;
double s2 = param->dj;
double s3 = param->dk;
double s4 = param->dl;
self_d = 0.0;
qmin = param->qmin;
qmax = param->qmax;
cmin = cmax = 100.0;
self_d = s1+qi*(2.0*s2+qi*(3.0*s3+qi*4.0*s4));
if (qi < qmin) self_d += 4.0 * cmin * pow((qi-qmin),3);
if (qi > qmax) self_d += 4.0 * cmax * pow((qi-qmax),3);
return self_d;
}
/* ---------------------------------------------------------------------- */
void PairComb3::qfo_direct(Param *parami, Param *paramj, int mr1,
int mr2, int mr3, double rsq, double sr1, double sr2,
double sr3, double fac11e, double &fqij, double &fqji,
double iq, double jq, int i, int j)
{
double r, erfcc, erfcd, fafbnl, vm, vmfafb, esucon;
double afbn, afbj, sme1n, sme1j;
double curli = parami->curl;
double curlj = paramj->curl;
int inti = parami->ielement;
int intj = paramj->ielement;
int inty = intype[inti][intj];
double curlcutij1 = parami->curlcut1;
double curlcutij2 = parami->curlcut2;
double curlcutji1 = paramj->curlcut1;
double curlcutji2 = paramj->curlcut2;
double curlij0 = parami->curl0;
double curlji0 = paramj->curl0;
double curlij1,curlji1;
int icurl, jcurl;
int ielegp = parami->ielementgp;
int jelegp = paramj->ielementgp;
r = sqrt(rsq);
esucon=force->qqr2e;
icurl = jcurl = 0;
if(ielegp==2 && curli>curlij0) {
icurl=1;
curlij1=curli;
}
if(jelegp==2 && curlj>curlji0) {
jcurl=1;
curlji1=curlj;
}
if(icurl==1 || jcurl ==1) {
double xcoij= xcotmp[i];
double xcoji= xcotmp[j];
if(icurl==1) {
curli=curlij1+(curlij0-curlij1)*comb_fc_curl(xcoij,parami);
}
if(jcurl==1) {
curlj=curlji1+(curlji0-curlji1)*comb_fc_curl(xcoji,paramj);
}
}
// 1/r force (wrt q)
erfcc = sr1*erpaw[mr1][0] + sr2*erpaw[mr2][0] + sr3*erpaw[mr3][0];
erfcd = sr1*erpaw[mr1][1] + sr2*erpaw[mr2][1] + sr3*erpaw[mr3][1];
fafbnl= sr1*fafb[mr1][inty] + sr2*fafb[mr2][inty] + sr3*fafb[mr3][inty];
afbn = sr1*afb[mr1][inti] + sr2*afb[mr2][inti] + sr3*afb[mr3][inti];
afbj = sr1*afb[mr1][intj] + sr2*afb[mr2][intj] + sr3*afb[mr3][intj];
vm = (erfcc/r * esucon - fac11e);
vmfafb = vm + esucon * fafbnl;
sme1n = curlj * (afbn - fafbnl) * esucon;
sme1j = curli * (afbj - fafbnl) * esucon;
fqij = 1.0 * (jq * vmfafb + sme1n);
fqji = 1.0 * (iq * vmfafb + sme1j);
}
/* ---------------------------------------------------------------------- */
void PairComb3::qfo_field(Param *parami, Param *paramj, double rsq,
double iq,double jq, double &fqij, double &fqji)
{
double r,r3,r4,r5,r6,rc,rc2,rc3,rc4,rc5,rc6;
double cmi1,cmi2,cmj1,cmj2,pcmi1,pcmi2,pcmj1,pcmj2;
double rf3i,rcf3i,rf5i,rcf5i;
double drf3i,drcf3i,drf5i,drcf5i,rf3,rf5;
r = sqrt(rsq);
r3 = r * rsq;
r4 = r * r3;
r5 = r3 * rsq;
r6 = r * r5;
rc = parami->lcut;
rc2= rc*rc;
rc3 = rc*rc*rc;
rc4 = rc3 * rc;
rc5 = rc4 * rc;
rc6 = rc5 * rc;
cmi1 = parami->cmn1;
cmi2 = parami->cmn2;
cmj1 = paramj->cmn1;
cmj2 = paramj->cmn2;
pcmi1 = parami->pcmn1;
pcmi2 = parami->pcmn2;
pcmj1 = paramj->pcmn1;
pcmj2 = paramj->pcmn2;
rf3i = r3/(pow(r3,2)+pow(pcmi1,3));
rcf3i = rc3/(pow(rc3,2)+pow(pcmi1,3));
rf5i = r5/(pow(r5,2)+pow(pcmi2,5));
rcf5i = rc5/(pow(rc5,2)+pow(pcmi2,5));
drf3i = 3/r*rf3i-6*rsq*rf3i*rf3i;
drcf3i = 3/rc*rcf3i-6*rc2*rcf3i*rcf3i;
drf5i = 5/r*rf5i-10*r4*rf5i*rf5i;
drcf5i = 5/rc*rcf5i-10*rc4*rcf5i*rcf5i;
rf3 = rf3i-rcf3i-(r-rc)*drcf3i;
rf5 = rf5i-rcf5i-(r-rc)*drcf5i;
// field correction charge force
fqij = 1.0 * cmj1*rf3+2.0*iq*cmj2*rf5;
fqji = 1.0 * cmi1*rf3+2.0*jq*cmi2*rf5;
}
/* ---------------------------------------------------------------------- */
void PairComb3::qfo_dipole(double fac11, int mr1, int mr2, int mr3,
int inty, double rsq, double *delrj, double sr1, double sr2,
double sr3, double &fqij, double &fqji, int i, int j)
{
double erfcc, erfcd, dvdrr, dfafbnl, smf2;
double r, r3, alfdpi, esucon;
r = sqrt(rsq);
r3 = r * rsq;
alfdpi = 0.4/MY_PIS;
esucon = force->qqr2e;
erfcc = sr1*erpaw[mr1][0] + sr2*erpaw[mr2][0] + sr3*erpaw[mr3][0];
erfcd = sr1*erpaw[mr1][1] + sr2*erpaw[mr2][1] + sr3*erpaw[mr3][1];
dvdrr = (erfcc/r3+alfdpi*erfcd/rsq)*esucon-fac11;
dfafbnl= sr1*dfafb[mr1][inty] + sr2*dfafb[mr2][inty] + sr3*dfafb[mr3][inty];
smf2 = (dvdrr + dfafbnl*esucon)/r;
fqij = dpl[i][0]*delrj[0] + dpl[i][1]*delrj[1] +dpl[i][2]*delrj[2];
fqji = dpl[j][0]*delrj[0] + dpl[j][1]*delrj[1] +dpl[j][2]*delrj[2];
fqij *= smf2;
fqji *= smf2;
}
/* ---------------------------------------------------------------------- */
void PairComb3::qfo_short(Param *parami, Param *paramj, double rsq,
double iq, double jq, double &fqij, double &fqji,
int i, int j, int nj)
{
double r, tmp_fc, Asi, Asj, vrcs;
double Di, Dj, dDi, dDj, Bsi, Bsj, dBsi, dBsj;
double QUchi, QOchi, QUchj, QOchj;
double bij, caj, cbj, caqpn, caqpj, cbqpn, cbqpj;
double LamDiLamDj, AlfDiAlfDj;
+ double addr = parami->addrepr;
double romi = parami->addrep;
double rrcs = parami->bigr + parami->bigd;
double rlm1 = parami->lambda;
double alfij1= parami->alpha1;
double alfij2= parami->alpha2;
double alfij3= parami->alpha3;
double pbij1= parami->bigB1;
double pbij2= parami->bigB2;
double pbij3= parami->bigB3;
caj = cbj = caqpn = caqpj = cbqpn = cbqpj = 0.0;
r = sqrt(rsq);
tmp_fc = comb_fc(r,parami);
bij = bbij[i][nj];
// additional repulsion
- if (romi > 0.0) vrcs = romi * pow((1.0-r/rrcs),2.0);
+ if (romi != 0.0 && r < addr) vrcs = romi * pow((1.0-r/addr),2.0);
QUchi = (parami->QU - iq) * parami->bD;
QUchj = (paramj->QU - jq) * paramj->bD;
QOchi = (iq - parami->Qo) * parami->bB;
QOchj = (jq - paramj->Qo) * paramj->bB;
if (iq < parami->QL-0.2) {
iq = parami->QL-0.2;
Di = parami->DL;
dDi = Bsi = dBsi = 0.0;
} else if (iq > parami->QU+0.2) {
iq = parami->QU+0.2;
Di = parami->DU;
dDi = Bsi = dBsi = 0.0;
} else {
Di = parami->DU + pow(QUchi,parami->nD); // YYDin
dDi = -parami->nD * parami->bD * pow(QUchi,(parami->nD-1.0)); // YYDiqp
Bsi = parami->aB - pow(QOchi,10); // YYBsin
dBsi = -parami->bB * 10.0 * pow(QOchi,9.0); // YYBsiqp
}
if (jq < paramj->QL-0.2) {
jq = paramj->QL-0.2;
Dj = paramj->DL;
dDj = Bsj = dBsj = 0.0;
} else if (jq > paramj->QU+0.2) {
jq = paramj->QU+0.2;
Dj = paramj->DU;
dDj = Bsj = dBsj = 0.0;
} else {
Dj = paramj->DU + pow(QUchj,paramj->nD); // YYDij
dDj = -paramj->nD * paramj->bD * pow(QUchj,(paramj->nD-1.0)); // YYDiqpj
Bsj = paramj->aB - pow(QOchj,10); // YYBsij
dBsj = -paramj->bB * 10.0 * pow(QOchj,9.0); // YYBsiqpj
}
LamDiLamDj = exp(0.5*(parami->lami*Di+paramj->lami*Dj)-rlm1*r);
caj = 0.5 * tmp_fc * parami->bigA * LamDiLamDj;
if (Bsi*Bsj > 0.0) {
AlfDiAlfDj = exp(0.5*(parami->alfi*Di+paramj->alfi*Dj));
cbj=-0.5*tmp_fc*bij*sqrt(Bsi*Bsj)*AlfDiAlfDj*
(pbij1*exp(-alfij1*r)+pbij2*exp(-alfij2*r)+pbij3*exp(-alfij3*r));
cbqpn = cbj * (parami->alfi * dDi + dBsi/Bsi);
cbqpj = cbj * (paramj->alfi * dDj + dBsj/Bsj);
} else {
cbj = cbqpn = cbqpj = 0.0;
}
caqpn = caj * parami->lami * dDi;
caqpj = caj * paramj->lami * dDj;
fqij = 1.0 * (caqpn + cbqpn);
fqji = 1.0 * (caqpj + cbqpj);
}
/* ---------------------------------------------------------------------- */
void PairComb3::dipole_init(Param *parami, Param *paramj, double fac11,
double *delrj, double rsq, int mr1, int mr2, int mr3, double sr1,
double sr2, double sr3, double iq, double jq, int i, int j)
{
double erfcc, erfcd, dvdrr, dfafbnl, smf2, phinn, phinj, efn, efj;
double r, r3, alfdpi, esucon;
double rcd, rct, tmurn, tmurj, poln[3], polj[3], Qext[3];
int nm;
int inti = parami->ielement;
int intj = paramj->ielement;
int inty = intype[inti][intj];
for(nm=0; nm<3; nm++) Qext[nm] = 0.0;
r = sqrt(rsq);
r3 = r * rsq;
rcd = 1.0/(r3);
rct = 3.0*rcd/rsq;
alfdpi = 0.4/MY_PIS;
esucon = force->qqr2e;
erfcc = sr1*erpaw[mr1][0] + sr2*erpaw[mr2][0] + sr3*erpaw[mr3][0];
erfcd = sr1*erpaw[mr1][1] + sr2*erpaw[mr2][1] + sr3*erpaw[mr3][1];
dvdrr = (erfcc/r3+alfdpi*erfcd/rsq)*esucon-fac11;
dfafbnl= sr1*dfafb[mr1][inty] + sr2*dfafb[mr2][inty] + sr3*dfafb[mr3][inty];
smf2 = dvdrr/esucon + dfafbnl/r;
phinn = sr1*phin[mr1][inti] + sr2*phin[mr2][inti] + sr3*phin[mr3][inti];
phinj = sr1*phin[mr1][intj] + sr2*phin[mr2][intj] + sr3*phin[mr3][intj];
efn = jq * smf2;
efj = iq * smf2;
tmurn = dpl[i][0]*delrj[0] + dpl[i][1]*delrj[1] + dpl[i][2]*delrj[2];
tmurj = dpl[j][0]*delrj[0] + dpl[j][1]*delrj[1] + dpl[j][2]*delrj[2];
for (nm=0; nm<3; nm++) {
poln[nm] = (tmurj*delrj[nm]*rct - dpl[j][nm]*rcd)*phinj;
polj[nm] = (tmurn*delrj[nm]*rct - dpl[i][nm]*rcd)*phinn;
}
for (nm=0; nm<3; nm++) {
dpl[i][nm] += (Qext[nm]/esucon + delrj[nm]*efn + poln[nm])*parami->polz*0.50;
dpl[j][nm] += (Qext[nm]/esucon - delrj[nm]*efj + polj[nm])*paramj->polz*0.50;
}
}
/* ---------------------------------------------------------------------- */
double PairComb3::dipole_self(Param *parami, int i)
{
double esucon = force->qqr2e;
double apn = parami->polz;
double selfdpV = 0.0;
if (apn != 0.0) {
selfdpV= (dpl[i][0]*dpl[i][0]+dpl[i][1]*dpl[i][1]+dpl[i][2]*dpl[i][2])
*esucon/(2.0*apn); }
return selfdpV;
}
/* ---------------------------------------------------------------------- */
void PairComb3::dipole_calc(Param *parami, Param *paramj, double fac11,
double delx, double dely, double delz, double rsq,
int mr1, int mr2, int mr3, double sr1, double sr2, double sr3,
double iq, double jq, int i, int j, double &vionij,
double &fvionij, double *ddprx)
{
double erfcc, erfcd, dvdrr, dfafbnl, ef, phinn, phinj, efn, efj;
double r, r3, alf, alfdpi, esucon, dphinn, dphinj, ddfafbnl;
double def, defn, defj, tmun, tmuj, emuTmu, edqn, edqj, ddvdrr;
double rcd, rct, tmurn, tmurj, tmumu, poln[3], polj[3], delr1[3];
double demuTmu, ddpr, dcoef;
int nm;
int inti = parami->ielement;
int intj = paramj->ielement;
int inty = intype[inti][intj];
r = sqrt(rsq);
r3 = r * rsq;
esucon = force->qqr2e;
rcd = esucon/r3;
rct = 3.0*rcd/rsq;
alf = 0.2;
alfdpi = 2.0*alf/MY_PIS;
delr1[0] = delx;
delr1[1] = dely;
delr1[2] = delz;
// generate energy & force information from tables
erfcc = sr1*erpaw[mr1][0] + sr2*erpaw[mr2][0] + sr3*erpaw[mr3][0];
erfcd = sr1*erpaw[mr1][1] + sr2*erpaw[mr2][1] + sr3*erpaw[mr3][1];
dvdrr = (erfcc/r3+alfdpi*erfcd/rsq)*esucon-fac11;
ddvdrr = (2.0*erfcc/r3 + 2.0*alfdpi*erfcd*(1.0/rsq+alf*alf))*esucon;
dfafbnl= sr1*dfafb[mr1][inty] + sr2*dfafb[mr2][inty] + sr3*dfafb[mr3][inty];
phinn = sr1*phin[mr1][inti] + sr2*phin[mr2][inti] + sr3*phin[mr3][inti];
phinj = sr1*phin[mr1][intj] + sr2*phin[mr2][intj] + sr3*phin[mr3][intj];
dphinn = sr1*dphin[mr1][inti] + sr2*dphin[mr2][inti] + sr3*dphin[mr3][inti];
dphinj = sr1*dphin[mr1][intj] + sr2*dphin[mr2][intj] + sr3*dphin[mr3][intj];
ddfafbnl= sr1*ddfafb[mr1][inty] + sr2*ddfafb[mr2][inty] + sr3*ddfafb[mr3][inty];
ef = (dvdrr + dfafbnl * esucon)/r;
efn = jq * ef;
efj = -iq * ef;
def = (ddvdrr + ddfafbnl * esucon)/r;
defn = jq * def;
defj = -iq * def;
// dipole - dipole field tensor (Tij)
tmurn = dpl[i][0]*delr1[0] + dpl[i][1]*delr1[1] + dpl[i][2]*delr1[2];
tmurj = dpl[j][0]*delr1[0] + dpl[j][1]*delr1[1] + dpl[j][2]*delr1[2];
tmumu = dpl[i][0]*dpl[j][0] + dpl[i][1]*dpl[j][1] + dpl[i][2]*dpl[j][2];
for (nm=0; nm<3; nm++) {
poln[nm] = (tmurj*delr1[nm]*rct - dpl[j][nm]*rcd);
polj[nm] = (tmurn*delr1[nm]*rct - dpl[i][nm]*rcd);
}
tmun = dpl[j][0]*polj[0] + dpl[j][1]*polj[1] + dpl[j][2]*polj[2];
tmuj = dpl[i][0]*poln[0] + dpl[i][1]*poln[1] + dpl[i][2]*poln[2];
// dipole - dipole energy
emuTmu = -0.5*(tmun*phinn+tmuj*phinj);
// dipole - charge energy
edqn = -0.5 * (tmurn * efn);
edqj = -0.5 * (tmurj * efj);
// overall dipole energy
vionij = emuTmu + edqn + edqj;
// dipole - dipole force
demuTmu = (tmun*dphinn + tmuj*dphinj)/r;
ddpr = 5.0*tmurn*tmurj/rsq - tmumu;
dcoef = rct * (phinn+phinj);
for (nm = 0; nm < 3; nm ++) {
ddprx[nm] = dcoef * (ddpr*delr1[nm] - tmurn*dpl[j][nm] - tmurj*dpl[i][nm])
+ demuTmu * delr1[nm];
}
// dipole - charge force
fvionij = -tmurn*defn - tmurj*defj;
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fc_curl(double rocn, Param *param)
{
double r_inn = param->curlcut1;
double r_out = param->curlcut2;
if (rocn <= r_inn) return 1.0;
if (rocn >= r_out) return 0.0;
return 0.5*(1.0 + cos(MY_PI*(rocn-r_inn)/(r_out-r_inn)));
}
/* ---------------------------------------------------------------------- */
double PairComb3::comb_fc_curl_d(double rocn, Param *param)
{
double r_inn = param->curlcut1;
double r_out = param->curlcut2;
if (rocn <= r_inn) return 0.0;
if (rocn >= r_out) return 0.0;
return -MY_PI2/(r_out-r_inn)*sin(MY_PI*(rocn-r_inn)/(r_out-r_inn));
}
/* ---------------------------------------------------------------------- */
int PairComb3::heaviside(double rr)
{
if (rr <= 0.0) return 0;
else return 1;
}
/* ---------------------------------------------------------------------- */
double PairComb3::switching(double rr)
{
if (rr <= 0.0) return 1.0;
else if (rr >= 1.0) return 0.0;
else return heaviside(-rr)+heaviside(rr)*heaviside(1.0-rr)
* (1.0-(3.0-2.0*rr)*rr*rr);
}
/* ---------------------------------------------------------------------- */
double PairComb3::switching_d(double rr)
{
if (rr <= 0.0) return 0.0;
else if (rr >= 1.0) return 0.0;
else return heaviside(rr)*heaviside(1.0-rr)
* 6.0*rr*(rr-1.0);
}
/* ---------------------------------------------------------------------- */
int PairComb3::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
if (pack_flag == 1) {
for (i = 0; i < n; i ++) {
j = list[i];
buf[m++] = qf[j];
}
} else if (pack_flag == 2) {
for (i = 0; i < n; i ++) {
j = list[i];
buf[m++] = NCo[j];
}
}
return 1;
}
/* ---------------------------------------------------------------------- */
void PairComb3::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n ;
if (pack_flag == 1) {
for (i = first; i < last; i++)
qf[i] = buf[m++];
} else if (pack_flag == 2) {
for (i = first; i < last; i++)
NCo[i] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int PairComb3::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
if (pack_flag == 1) {
for (i = first; i < last; i++)
buf[m++] = qf[i];
} else if (pack_flag == 2) {
for (i = first; i < last; i++)
buf[m++] = NCo[i];
}
return 1;
}
/* ---------------------------------------------------------------------- */
void PairComb3::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
if (pack_flag == 1) {
for (i = 0; i < n; i++) {
j = list[i];
qf[j] += buf[m++];
}
} else if (pack_flag == 2) {
for (i = 0; i < n; i++) {
j = list[i];
NCo[j] += buf[m++];
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairComb3::memory_usage()
{
double bytes = maxeatom * sizeof(double);
bytes += maxvatom*6 * sizeof(double);
bytes += nmax * sizeof(int);
bytes += nmax * 8.0 * sizeof(double);
bytes += 25000*2*sizeof(double);
for (int i = 0; i < comm->nthreads; i++)
bytes += ipage[i].size();
return bytes;
}
diff --git a/src/MANYBODY/pair_comb3.h b/src/MANYBODY/pair_comb3.h
index 689d19aa6..6dac64e56 100644
--- a/src/MANYBODY/pair_comb3.h
+++ b/src/MANYBODY/pair_comb3.h
@@ -1,340 +1,333 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(comb3,PairComb3)
#else
#ifndef LMP_PAIR_COMB3_H
#define LMP_PAIR_COMB3_H
#include "pair.h"
#include "my_page.h"
namespace LAMMPS_NS {
class PairComb3 : public Pair {
public:
PairComb3(class LAMMPS *);
virtual ~PairComb3();
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
double init_one(int, int);
double memory_usage();
virtual double combqeq(double *, int &);
// general potential parameters
protected:
struct Param {
int ielement,jelement,kelement,powermint;
int ielementgp,jelementgp,kelementgp; //element group
int ang_flag,pcn_flag,rad_flag,tor_flag; //angle, coordination,radical, torsion flag
double lami,lambda,alfi,alpha1,alpha2,alpha3,beta;
double pcos6,pcos5,pcos4,pcos3,pcos2,pcos1,pcos0;
double gamma,powerm,powern,bigA,bigB1,bigB2,bigB3;
double bigd,bigr,cut,cutsq,c1,c2,c3,c4;
- double plp1,plp2,plp3,plp4,plp5,plp6;
- double pbb1,pbb2,ptork1,ptork2;
- double addrep, vdwflag;
+ double p6p0,p6p1,p6p2,p6p3,p6p4,p6p5,p6p6;
+ double ptork1,ptork2;
+ double addrepr,addrep, vdwflag;
double QU,QL,DU,DL,Qo,dQ,aB,bB,nD,bD,qmin,qmax;
double chi,dj,dk,dl,dm,esm,cmn1,cmn2,pcmn1,pcmn2;
double coulcut, lcut, lcutsq;
double veps, vsig, pcna, pcnb, pcnc, pcnd, polz, curl, pcross;
double paaa, pbbb;
double curlcut1, curlcut2, curl0;
};
// general setups
int nelements; // # of unique elements
int ***elem2param; // mapping from element triplets to parameters
int *map; // mapping from atom types to elements
int nparams; // # of stored parameter sets
int maxparam; // max # of parameter sets
double PI,PI2,PI4,PIsq; // PIs
double cutmin; // min cutoff for all elements
double cutmax; // max cutoff for all elements
double precision; // tolerance for QEq convergence
char **elements; // names of unique elements
Param *params; // parameter set for an I-J-K interaction
int debug_eng1, debug_eng2, debug_fq; // logic controlling debugging outputs
int pack_flag;
// Short range neighbor list
void Short_neigh();
int pgsize, oneatom;
int *sht_num, **sht_first;
MyPage<int> *ipage;
// loop up tables and flags
int nmax, **intype;
int pol_flag, polar;
double *qf, **bbij, *charge, *NCo;
double *esm, **fafb, **dfafb, **ddfafb, **phin, **dphin, **erpaw;
double **vvdw, **vdvdw;
double **afb, **dafb;
double **dpl, bytes;
double *xcctmp, *xchtmp, *xcotmp;
// additional carbon parameters
int cflag;
int nsplpcn,nsplrad,nspltor;
int maxx,maxy,maxz,maxxc,maxyc,maxconj;
int maxxcn[4];
double vmaxxcn[4],dvmaxxcn[4];
int ntab;
double iin2[16][2],iin3[64][3];
double brad[4], btor[4], bbtor, ptorr;
double fi_tor[3], fj_tor[3], fk_tor[3], fl_tor[3];
double radtmp, fi_rad[3], fj_rad[3], fk_rad[3];
double ccutoff[6],ch_a[7];
//COMB3-v18 arrays for CHO
// We wanna dynamic arrays
// C angle arrays, size = ntab+1
double pang[20001];
double dpang[20001];
double ddpang[20001];
//coordination spline arrays
double pcn_grid[4][5][5][5];
double pcn_gridx[4][5][5][5];
double pcn_gridy[4][5][5][5];
double pcn_gridz[4][5][5][5];
double pcn_cubs[4][4][4][4][64];
//coordination spline arrays
double rad_grid[3][5][5][11];
double rad_gridx[3][5][5][11];
double rad_gridy[3][5][5][11];
double rad_gridz[3][5][5][11];
double rad_spl[3][4][4][10][64];
//torsion spline arrays
double tor_grid[1][5][5][11];
double tor_gridx[1][5][5][11];
double tor_gridy[1][5][5][11];
double tor_gridz[1][5][5][11];
double tor_spl[1][4][4][10][64];
// initialization functions
void allocate();
void read_lib();
void setup();
virtual void read_file(char *);
// cutoff functions
double comb_fc(double, Param *);
double comb_fc_d(double, Param *);
double comb_fc_curl(double, Param *);
double comb_fc_curl_d(double, Param *);
double comb_fccc(double);
double comb_fccc_d(double);
double comb_fcch(double);
double comb_fcch_d(double);
double comb_fccch(double);
double comb_fccch_d(double);
double comb_fcsw(double);
// short range terms
void attractive(Param *, Param *, Param *, double, double, double, double,
double, double, double, double *, double *, double *,
double *, double *, int, double);
virtual void comb_fa(double, Param *, Param *, double, double,
double &, double &);
virtual void repulsive(Param *, Param *,double, double &, int,
double &, double, double);
// bond order terms
double comb_bij(double, Param *, double, int, double);
double comb_gijk(double, Param *, double);
void comb_gijk_d(double, Param *, double, double &, double &);
double zeta(Param *, Param *, double, double, double *, double *, int, double);
void comb_bij_d(double, Param *, double, int, double &,
double &, double &, double &, double &, double &, double);
void coord(Param *, double, int, double &, double &,
double &, double &, double &, double);
void comb_zetaterm_d(double, double, double, double, double,
double *, double, double *, double, double *, double *,
double *, Param *, Param *, Param *, double);
void costheta_d(double *, double, double *, double,
double *, double *, double *);
void force_zeta(Param *, Param *, double, double, double, double &,
double &, double &, double &, double &, double &, double &,
double &, double &, double &, double &, double &, double &,
int, double &, double,double, int, int, int,
double , double , double);
void cntri_int(int, double, double, double, int, int, int,
double &, double &, double &, double &, Param *);
// Legendre polynomials
- void selflp(Param *, Param *, double, double &, double &);
- double elp(Param *, Param *, double, double, double *, double * ,double &);
- void flp(Param *, Param *, double, double, double *, double *, double *,
+ void selfp6p(Param *, Param *, double, double &, double &);
+ double ep6p(Param *, Param *, double, double, double *, double * ,double &);
+ void fp6p(Param *, Param *, double, double, double *, double *, double *,
double *, double *);
// long range q-dependent terms
double self(Param *, double);
void tables();
void potal_calc(double &, double &, double &);
void tri_point(double, int &, int &, int &, double &, double &,
double &);
void vdwaals(int,int,int,int,double,double,double,double,
double &, double &);
void direct(Param *, Param *, int,int,int,double,double,
double,double,double,double, double,double,double &,double &,
int, int);
void field(Param *, Param *,double,double,double,double &,double &);
int heaviside(double);
double switching(double);
double switching_d(double);
double chicut1, chicut2;
// radical terms
double rad_init(double, Param *, int, double &, double);
void rad_calc(double, Param *, Param *, double, double, int,
int, double, double);
void rad_int(int , double, double, double, int, int, int,
double &, double &, double &, double &);
void rad_forceik(Param *, double, double *, double, double);
void rad_force(Param *, double, double *, double);
// torsion terms
double bbtor1(int, Param *, Param *, double, double, double,
double *, double *, double *, double); //modified by TAO
void tor_calc(double, Param *, Param *, double, double, int,
int, double, double);
void tor_int(int , double, double, double, int, int, int,
double &, double &, double &, double &);
void tor_force(int, Param *, Param *, double, double, double,
double, double *, double *, double *); //modified by TAO
// charge force terms
double qfo_self(Param *, double);
void qfo_short(Param *, Param *, double, double, double,
double &, double &, int, int, int);
void qfo_direct(Param *, Param *, int, int, int, double,
double, double, double, double, double &, double &,
double, double, int, int);
void qfo_field(Param *, Param *,double,double ,double ,double &, double &);
void qfo_dipole(double, int, int, int, int, double, double *, double,
double, double, double &, double &, int, int);
void qsolve(double *);
// dipole - polarization terms
double dipole_self(Param *, int);
void dipole_init(Param *, Param *, double, double *, double,
int, int, int, double, double, double, double, double, int , int);
void dipole_calc(Param *, Param *, double, double, double, double, double,
int, int, int, double, double, double, double, double, int , int,
double &, double &, double *);
// communication functions
int pack_reverse_comm(int, int, double *);
void unpack_reverse_comm(int, int *, double *);
int pack_comm(int , int *, double *, int, int *);
void unpack_comm(int , int , double *);
// vector functions, inline for efficiency
inline double vec3_dot(double *x, double *y) {
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
}
inline void vec3_add(double *x, double *y, double *z) {
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
}
inline void vec3_scale(double k, double *x, double *y) {
y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
}
inline void vec3_scaleadd(double k, double *x, double *y, double *z) {
z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
}
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
-E: Pair style COMB3 requires atom IDs
+E: Pair style COMB requires atom IDs
-This is a requirement to use this potential.
+This is a requirement to use the AIREBO potential.
-E: Pair style COMB3 requires newton pair on
+E: Pair style COMB requires newton pair on
-See the newton command. This is a restriction to use the COMB3
+See the newton command. This is a restriction to use the COMB
potential.
-E: Pair style COMB3 requires atom attribute q
+E: Pair style COMB requires atom attribute q
-The atom style defined does not have this attribute.
+Self-explanatory.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
-E: Cannot open COMB3 C library file
-
-The extra lib.comb3 file for carbon cannot be opened. Check that it
-exists.
-
-E: Cannot open COMB3 potential file %s
+E: Cannot open COMB potential file %s
The specified COMB potential file cannot be opened. Check that the
path and name are correct.
-E: Incorrect format in COMB3 potential file
+E: Incorrect format in COMB potential file
Incorrect number of words per line in the potential file.
-E: Illegal COMB3 parameter
+E: Illegal COMB parameter
One or more of the coefficients defined in the potential file is
invalid.
E: Potential file has duplicate entry
The potential file for a SW or Tersoff potential has more than
one entry for the same 3 ordered elements.
E: Potential file is missing an entry
The potential file for a SW or Tersoff potential does not have a
needed entry.
-E: Neighbor list overflow, boost neigh_modify one
+W: Pair COMB charge %.10f with force %.10f hit min barrier
-There are too many neighbors of a single atom. Use the neigh_modify
-command to increase the max number of neighbors allowed for one atom.
-You may also want to boost the page size.
+Something is possibly wrong with your model.
-E: Error in vdw spline: inner radius > outer radius
+W: Pair COMB charge %.10f with force %.10f hit max barrier
-Self-explanatory.
+Something is possibly wrong with your model.
*/
diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_damage_atom.cpp
index 9b51cd34b..7a8cbfd3d 100644
--- a/src/PERI/compute_damage_atom.cpp
+++ b/src/PERI/compute_damage_atom.cpp
@@ -1,131 +1,130 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
#include "string.h"
#include "compute_damage_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "comm.h"
#include "force.h"
#include "pair_peri_pmb.h"
#include "fix_peri_neigh.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeDamageAtom::ComputeDamageAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute damage/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
nmax = 0;
damage = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeDamageAtom::~ComputeDamageAtom()
{
memory->destroy(damage);
}
/* ---------------------------------------------------------------------- */
void ComputeDamageAtom::init()
{
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
if (strcmp(modify->compute[i]->style,"damage/peri") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning(FLERR,"More than one compute damage/atom");
// find associated PERI_NEIGH fix that must exist
ifix_peri = -1;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
if (ifix_peri == -1)
error->all(FLERR,"Compute damage/atom requires peridynamic potential");
}
/* ---------------------------------------------------------------------- */
void ComputeDamageAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow damage array if necessary
if (atom->nlocal > nmax) {
memory->destroy(damage);
nmax = atom->nmax;
memory->create(damage,nmax,"damage/atom:damage");
vector_atom = damage;
}
// compute damage for each atom in group
int nlocal = atom->nlocal;
int *mask = atom->mask;
double *vfrac = atom->vfrac;
double *vinter = ((FixPeriNeigh *) modify->fix[ifix_peri])->vinter;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
int i,j,jj,jnum;
double damage_temp;
for (i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
jnum = npartner[i];
damage_temp = 0.0;
-
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
-
+
// look up local index of this partner particle
// skip if particle is "lost"
-
+
j = atom->map(partner[i][jj]);
if (j < 0) continue;
-
+
damage_temp += vfrac[j];
}
- }
- else damage_temp = vinter[i];
- if (vinter[i] != 0.0) damage[i] = 1.0 - damage_temp/vinter[i];
- else damage[i] = 0.0;
+ if (vinter[i] != 0.0) damage[i] = 1.0 - damage_temp/vinter[i];
+ else damage[i] = 0.0;
+
+ } else damage[i] = 0.0;
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeDamageAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}
diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_dilatation_atom.cpp
similarity index 55%
copy from src/PERI/compute_damage_atom.cpp
copy to src/PERI/compute_dilatation_atom.cpp
index 9b51cd34b..366c5bcda 100644
--- a/src/PERI/compute_damage_atom.cpp
+++ b/src/PERI/compute_dilatation_atom.cpp
@@ -1,131 +1,127 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing author: Mike Parks (SNL)
+ Contributing author: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
#include "string.h"
-#include "compute_damage_atom.h"
+#include "compute_dilatation_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "comm.h"
#include "force.h"
+#include "pair.h"
+#include "pair_peri_lps.h"
#include "pair_peri_pmb.h"
+#include "pair_peri_ves.h"
+#include "pair_peri_eps.h"
#include "fix_peri_neigh.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeDamageAtom::ComputeDamageAtom(LAMMPS *lmp, int narg, char **arg) :
+ComputeDilatationAtom::
+ComputeDilatationAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
- if (narg != 3) error->all(FLERR,"Illegal compute damage/atom command");
+ if (narg != 3) error->all(FLERR,"Illegal compute Dilatation/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
nmax = 0;
- damage = NULL;
+ dilatation = NULL;
}
/* ---------------------------------------------------------------------- */
-ComputeDamageAtom::~ComputeDamageAtom()
+ComputeDilatationAtom::~ComputeDilatationAtom()
{
- memory->destroy(damage);
+ memory->destroy(dilatation);
}
/* ---------------------------------------------------------------------- */
-void ComputeDamageAtom::init()
+void ComputeDilatationAtom::init()
{
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style,"damage/peri") == 0) count++;
+ if (strcmp(modify->compute[i]->style,"dilatation/peri") == 0) count++;
if (count > 1 && comm->me == 0)
- error->warning(FLERR,"More than one compute damage/atom");
+ error->warning(FLERR,"More than one compute dilatation/atom");
+
+ // check PD pair style
+
+ isPMB = isLPS = isVES = isEPS = 0;
+ if (force->pair_match("peri/pmb",1)) isPMB = 1;
+ if (force->pair_match("peri/lps",1)) isLPS = 1;
+ if (force->pair_match("peri/ves",1)) isVES = 1;
+ if (force->pair_match("peri/eps",1)) isEPS = 1;
+
+ if (isPMB)
+ error->all(FLERR,"Compute dilatation/atom cannot be used "
+ "with this pair style");
// find associated PERI_NEIGH fix that must exist
- ifix_peri = -1;
+ int ifix_peri = -1;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
if (ifix_peri == -1)
- error->all(FLERR,"Compute damage/atom requires peridynamic potential");
+ error->all(FLERR,"Compute dilatation/atom requires Peridynamic pair style");
}
/* ---------------------------------------------------------------------- */
-void ComputeDamageAtom::compute_peratom()
+void ComputeDilatationAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
- // grow damage array if necessary
+ // grow dilatation array if necessary
if (atom->nlocal > nmax) {
- memory->destroy(damage);
+ memory->destroy(dilatation);
nmax = atom->nmax;
- memory->create(damage,nmax,"damage/atom:damage");
- vector_atom = damage;
+ memory->create(dilatation,nmax,"dilatation/atom:dilatation");
+ vector_atom = dilatation;
}
- // compute damage for each atom in group
-
- int nlocal = atom->nlocal;
- int *mask = atom->mask;
- double *vfrac = atom->vfrac;
- double *vinter = ((FixPeriNeigh *) modify->fix[ifix_peri])->vinter;
- tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
- int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
- int i,j,jj,jnum;
-
- double damage_temp;
+ // extract dilatation for each atom in group
- for (i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- jnum = npartner[i];
- damage_temp = 0.0;
+ double *theta;
+ Pair *anypair = force->pair_match("peri",0);
+ if (isLPS) theta = ((PairPeriLPS *) anypair)->theta;
+ if (isVES) theta = ((PairPeriVES *) anypair)->theta;
+ if (isEPS) theta = ((PairPeriEPS *) anypair)->theta;
- for (jj = 0; jj < jnum; jj++) {
- if (partner[i][jj] == 0) continue;
-
- // look up local index of this partner particle
- // skip if particle is "lost"
-
- j = atom->map(partner[i][jj]);
- if (j < 0) continue;
-
- damage_temp += vfrac[j];
- }
- }
- else damage_temp = vinter[i];
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
- if (vinter[i] != 0.0) damage[i] = 1.0 - damage_temp/vinter[i];
- else damage[i] = 0.0;
- }
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) dilatation[i] = theta[i];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
-double ComputeDamageAtom::memory_usage()
+double ComputeDilatationAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}
diff --git a/src/PERI/compute_dilatation_atom.h b/src/PERI/compute_dilatation_atom.h
new file mode 100644
index 000000000..5e839cc3d
--- /dev/null
+++ b/src/PERI/compute_dilatation_atom.h
@@ -0,0 +1,48 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(dilatation/atom,ComputeDilatationAtom)
+
+#else
+
+#ifndef LMP_COMPUTE_DILATATION_ATOM_H
+#define LMP_COMPUTE_DILATATION_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeDilatationAtom : public Compute {
+ friend class PairPeriPMB;
+ friend class PairPeriLPS;
+ friend class PairPeriVES;
+ friend class PairPeriEPS;
+ public:
+ ComputeDilatationAtom(class LAMMPS *, int, char **);
+ ~ComputeDilatationAtom();
+ void init();
+ void compute_peratom();
+ double memory_usage();
+
+ private:
+ int nmax;
+ double *dilatation;
+ int isPMB,isLPS,isVES,isEPS;
+};
+
+}
+
+#endif
+#endif
diff --git a/src/PERI/compute_damage_atom.cpp b/src/PERI/compute_plasticity_atom.cpp
similarity index 57%
copy from src/PERI/compute_damage_atom.cpp
copy to src/PERI/compute_plasticity_atom.cpp
index 9b51cd34b..ac089fe7a 100644
--- a/src/PERI/compute_damage_atom.cpp
+++ b/src/PERI/compute_plasticity_atom.cpp
@@ -1,131 +1,111 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing author: Mike Parks (SNL)
+ Contributing author: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
#include "string.h"
-#include "compute_damage_atom.h"
+#include "compute_plasticity_atom.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "comm.h"
#include "force.h"
#include "pair_peri_pmb.h"
#include "fix_peri_neigh.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-ComputeDamageAtom::ComputeDamageAtom(LAMMPS *lmp, int narg, char **arg) :
+ComputePlasticityAtom::
+ComputePlasticityAtom(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
- if (narg != 3) error->all(FLERR,"Illegal compute damage/atom command");
+ if (narg != 3) error->all(FLERR,"Illegal compute plasticity/atom command");
+
+ if (!force->pair_match("peri/eps",1))
+ error->all(FLERR,"Compute plasticity/atom cannot be used "
+ "with this pair style");
peratom_flag = 1;
size_peratom_cols = 0;
nmax = 0;
- damage = NULL;
+ plasticity = NULL;
}
/* ---------------------------------------------------------------------- */
-ComputeDamageAtom::~ComputeDamageAtom()
+ComputePlasticityAtom::~ComputePlasticityAtom()
{
- memory->destroy(damage);
+ memory->destroy(plasticity);
}
/* ---------------------------------------------------------------------- */
-void ComputeDamageAtom::init()
+void ComputePlasticityAtom::init()
{
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
- if (strcmp(modify->compute[i]->style,"damage/peri") == 0) count++;
+ if (strcmp(modify->compute[i]->style,"plasticity/peri") == 0) count++;
if (count > 1 && comm->me == 0)
- error->warning(FLERR,"More than one compute damage/atom");
+ error->warning(FLERR,"More than one compute plasticity/atom");
// find associated PERI_NEIGH fix that must exist
ifix_peri = -1;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
if (ifix_peri == -1)
- error->all(FLERR,"Compute damage/atom requires peridynamic potential");
+ error->all(FLERR,"Compute plasticity/atom requires Peridynamic pair style");
}
/* ---------------------------------------------------------------------- */
-void ComputeDamageAtom::compute_peratom()
+void ComputePlasticityAtom::compute_peratom()
{
invoked_peratom = update->ntimestep;
// grow damage array if necessary
if (atom->nlocal > nmax) {
- memory->destroy(damage);
+ memory->destroy(plasticity);
nmax = atom->nmax;
- memory->create(damage,nmax,"damage/atom:damage");
- vector_atom = damage;
+ memory->create(plasticity,nmax,"plasticity/atom:plasticity");
+ vector_atom = plasticity;
}
- // compute damage for each atom in group
+ // extract plasticity for each atom in group
- int nlocal = atom->nlocal;
- int *mask = atom->mask;
- double *vfrac = atom->vfrac;
- double *vinter = ((FixPeriNeigh *) modify->fix[ifix_peri])->vinter;
- tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
- int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
- int i,j,jj,jnum;
-
- double damage_temp;
-
- for (i = 0; i < nlocal; i++) {
- if (mask[i] & groupbit) {
- jnum = npartner[i];
- damage_temp = 0.0;
-
- for (jj = 0; jj < jnum; jj++) {
- if (partner[i][jj] == 0) continue;
+ double *lambdaValue = ((FixPeriNeigh *) modify->fix[ifix_peri])->lambdaValue;
- // look up local index of this partner particle
- // skip if particle is "lost"
-
- j = atom->map(partner[i][jj]);
- if (j < 0) continue;
-
- damage_temp += vfrac[j];
- }
- }
- else damage_temp = vinter[i];
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
- if (vinter[i] != 0.0) damage[i] = 1.0 - damage_temp/vinter[i];
- else damage[i] = 0.0;
- }
+ for (int i = 0; i < nlocal; i++)
+ if (mask[i] & groupbit) plasticity[i] = lambdaValue[i];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
-double ComputeDamageAtom::memory_usage()
+double ComputePlasticityAtom::memory_usage()
{
double bytes = nmax * sizeof(double);
return bytes;
}
diff --git a/src/PERI/compute_plasticity_atom.h b/src/PERI/compute_plasticity_atom.h
new file mode 100644
index 000000000..9800b1253
--- /dev/null
+++ b/src/PERI/compute_plasticity_atom.h
@@ -0,0 +1,44 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(plasticity/atom,ComputePlasticityAtom)
+
+#else
+
+#ifndef LMP_COMPUTE_PLASTICITY_ATOM_H
+#define LMP_COMPUTE_PLASTICITY_ATOM_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputePlasticityAtom : public Compute {
+ public:
+ ComputePlasticityAtom(class LAMMPS *, int, char **);
+ ~ComputePlasticityAtom();
+ void init();
+ void compute_peratom();
+ double memory_usage();
+
+ private:
+ int nmax;
+ double *plasticity;
+ int ifix_peri;
+};
+
+}
+
+#endif
+#endif
diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index 23e0a392a..190bc0460 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -1,608 +1,646 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Mike Parks (SNL), Ezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
#include "math.h"
#include "fix_peri_neigh.h"
#include "pair_peri_pmb.h"
#include "pair_peri_lps.h"
#include "pair_peri_ves.h"
+#include "pair_peri_eps.h"
#include "atom.h"
#include "domain.h"
#include "force.h"
#include "comm.h"
#include "update.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "pair.h"
#include "lattice.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixPeriNeigh::FixPeriNeigh(LAMMPS *lmp,int narg, char **arg) :
Fix(lmp, narg, arg)
{
- isPMB = isLPS = isVES = 0;
+ isPMB = isLPS = isVES = isEPS = 0;
if (force->pair_match("peri/pmb",1)) isPMB = 1;
if (force->pair_match("peri/lps",1)) isLPS = 1;
if (force->pair_match("peri/ves",1)) isVES = 1;
+ if (force->pair_match("peri/eps",1)) isEPS = 1;
restart_global = 1;
restart_peratom = 1;
first = 1;
// perform initial allocation of atom-based arrays
// register with atom class
// set maxpartner = 1 as placeholder
maxpartner = 1;
npartner = NULL;
partner = NULL;
deviatorextention = NULL;
deviatorBackextention = NULL;
+ deviatorPlasticextension = NULL;
+ lambdaValue = NULL;
r0 = NULL;
vinter = NULL;
wvolume = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
// initialize npartner to 0 so atom migration is OK the 1st time
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) npartner[i] = 0;
// set comm sizes needed by this fix
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
FixPeriNeigh::~FixPeriNeigh()
{
// unregister this fix so atom class doesn't invoke it any more
atom->delete_callback(id,0);
atom->delete_callback(id,1);
// delete locally stored arrays
memory->destroy(npartner);
memory->destroy(partner);
memory->destroy(deviatorextention);
memory->destroy(deviatorBackextention);
+ memory->destroy(deviatorPlasticextension);
+ memory->destroy(lambdaValue);
memory->destroy(r0);
memory->destroy(vinter);
memory->destroy(wvolume);
}
/* ---------------------------------------------------------------------- */
int FixPeriNeigh::setmask()
{
int mask = 0;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPeriNeigh::init()
{
if (!first) return;
// need a full neighbor list once
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
neighbor->requests[irequest]->occasional = 1;
// compute PD scale factor, stored in Atom class, used by DumpCFG
int nlocal = atom->nlocal;
double vone = 0.0;
for (int i = 0; i < nlocal; i++) vone += atom->vfrac[i];
double vave;
MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
if (atom->natoms) vave /= atom->natoms;
if (vave > 0.0) atom->pdscale = 1.44 / pow(vave,1.0/3.0);
else atom->pdscale = 1.0;
}
/* ---------------------------------------------------------------------- */
void FixPeriNeigh::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ----------------------------------------------------------------------
For minimization: setup as with dynamics
------------------------------------------------------------------------- */
void FixPeriNeigh::min_setup(int vflag)
{
setup(vflag);
}
/* ----------------------------------------------------------------------
create initial list of neighbor partners via call to neighbor->build()
must be done in setup (not init) since fix init comes before neigh init
------------------------------------------------------------------------- */
void FixPeriNeigh::setup(int vflag)
{
int i,j,ii,jj,itype,jtype,inum,jnum;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
int *ilist,*jlist,*numneigh;
int **firstneigh;
double **x = atom->x;
double *vfrac = atom->vfrac;
int *type = atom->type;
tagint *tag = atom->tag;
int nlocal = atom->nlocal;
// only build list of bonds on very first run
if (!first) return;
first = 0;
// invoke full neighbor list (will copy or build if necessary)
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// scan neighbor list to set maxpartner
Pair *anypair = force->pair_match("peri",0);
double **cutsq = anypair->cutsq;
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq <= cutsq[itype][jtype]) npartner[i]++;
}
}
maxpartner = 0;
for (i = 0; i < nlocal; i++) maxpartner = MAX(maxpartner,npartner[i]);
int maxall;
MPI_Allreduce(&maxpartner,&maxall,1,MPI_INT,MPI_MAX,world);
maxpartner = maxall;
// realloc arrays with correct value for maxpartner
memory->destroy(partner);
memory->destroy(deviatorextention);
memory->destroy(deviatorBackextention);
+ memory->destroy(deviatorPlasticextension);
+ memory->destroy(lambdaValue);
memory->destroy(r0);
memory->destroy(npartner);
npartner = NULL;
partner = NULL;
deviatorextention = NULL;
deviatorBackextention = NULL;
+ deviatorPlasticextension = NULL;
+ lambdaValue = NULL;
r0 = NULL;
grow_arrays(atom->nmax);
// create partner list and r0 values from neighbor list
// compute vinter for each atom
for (i = 0; i < nlocal; i++) {
npartner[i] = 0;
vinter[i] = 0.0;
wvolume[i] = 0.0;
+ if (isEPS) lambdaValue[i] = 0.0;
}
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq <= cutsq[itype][jtype]) {
partner[i][npartner[i]] = tag[j];
if (isVES)
deviatorextention[i][npartner[i]] =
deviatorBackextention[i][npartner[i]] = 0.0;
+ if (isEPS)
+ deviatorPlasticextension[i][npartner[i]] = 0.0;
r0[i][npartner[i]] = sqrt(rsq);
npartner[i]++;
vinter[i] += vfrac[j];
}
}
}
// sanity check: does any atom appear twice in any neigborlist?
// should only be possible if using pbc and domain < 2*delta
if (domain->xperiodic || domain->yperiodic || domain->zperiodic) {
for (i = 0; i < nlocal; i++) {
jnum = npartner[i];
for (jj = 0; jj < jnum; jj++) {
for (int kk = jj+1; kk < jnum; kk++) {
if (partner[i][jj] == partner[i][kk])
error->one(FLERR,"Duplicate particle in PeriDynamic bond - "
"simulation box is too small");
}
}
}
}
// compute wvolume for each atom
double **x0 = atom->x0;
double half_lc = 0.5*(domain->lattice->xlattice);
double vfrac_scale;
PairPeriLPS *pairlps = static_cast<PairPeriLPS*>(anypair);
PairPeriPMB *pairpmb = static_cast<PairPeriPMB*>(anypair);
PairPeriVES *pairves = static_cast<PairPeriVES*>(anypair);
+ PairPeriEPS *paireps = static_cast<PairPeriEPS*>(anypair);
for (i = 0; i < nlocal; i++) {
double xtmp0 = x0[i][0];
double ytmp0 = x0[i][1];
double ztmp0 = x0[i][2];
jnum = npartner[i];
itype = type[i];
// loop over partners of particle i
for (jj = 0; jj < jnum; jj++) {
// if bond already broken, skip this partner
if (partner[i][jj] == 0) continue;
// lookup local index of partner particle
j = atom->map(partner[i][jj]);
// skip if particle is "lost"
if (j < 0) continue;
double delx0 = xtmp0 - x0[j][0];
double dely0 = ytmp0 - x0[j][1];
double delz0 = ztmp0 - x0[j][2];
+
double rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
double delta = sqrt(cutsq[itype][jtype]);
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
// for PMB, influence = 1.0, otherwise invoke influence function
-
if (isPMB)
wvolume[i] += 1.0 * rsq0 * vfrac[j] * vfrac_scale;
else if (isLPS)
wvolume[i] += pairlps->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
else if (isVES)
wvolume[i] += pairves->influence_function(delx0,dely0,delz0) *
rsq0 * vfrac[j] * vfrac_scale;
+ else if (isEPS)
+ wvolume[i] += paireps->influence_function(delx0,dely0,delz0) *
+ rsq0 * vfrac[j] * vfrac_scale;
}
}
// communicate wvolume to ghosts
comm->forward_comm_fix(this);
// bond statistics
int n = 0;
for (i = 0; i < nlocal; i++) n += npartner[i];
int nall;
MPI_Allreduce(&n,&nall,1,MPI_INT,MPI_SUM,world);
if (comm->me == 0) {
if (screen) {
fprintf(screen,"Peridynamic bonds:\n");
fprintf(screen," total # of bonds = %d\n",nall);
fprintf(screen," bonds/atom = %g\n",(double)nall/atom->natoms);
}
if (logfile) {
fprintf(logfile,"Peridynamic bonds:\n");
fprintf(logfile," total # of bonds = %d\n",nall);
fprintf(logfile," bonds/atom = %g\n",(double)nall/atom->natoms);
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double FixPeriNeigh::memory_usage()
{
int nmax = atom->nmax;
int bytes = nmax * sizeof(int);
- bytes += nmax*maxpartner * sizeof(int);
+ bytes += nmax*maxpartner * sizeof(tagint);
bytes += nmax*maxpartner * sizeof(double);
if (isVES) {
bytes += nmax*maxpartner * sizeof(double);
bytes += nmax*maxpartner * sizeof(double);
}
+ if (isEPS) {
+ bytes += nmax*maxpartner * sizeof(double);
+ bytes += nmax * sizeof(double);
+ }
bytes += nmax * sizeof(double);
bytes += nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
allocate local atom-based arrays
------------------------------------------------------------------------- */
void FixPeriNeigh::grow_arrays(int nmax)
{
memory->grow(npartner,nmax,"peri_neigh:npartner");
memory->grow(partner,nmax,maxpartner,"peri_neigh:partner");
if (isVES) {
memory->grow(deviatorextention,nmax,maxpartner,
"peri_neigh:deviatorextention");
memory->grow(deviatorBackextention,nmax,maxpartner,
"peri_neigh:deviatorBackextention");
}
+ if (isEPS) memory->grow(deviatorPlasticextension,nmax,maxpartner,
+ "peri_neigh:deviatorPlasticextension");
memory->grow(r0,nmax,maxpartner,"peri_neigh:r0");
+ if (isEPS) memory->grow(lambdaValue,nmax,"peri_neigh:lambdaValue");
memory->grow(vinter,nmax,"peri_neigh:vinter");
memory->grow(wvolume,nmax,"peri_neigh:wvolume");
}
/* ----------------------------------------------------------------------
copy values within local atom-based arrays
------------------------------------------------------------------------- */
void FixPeriNeigh::copy_arrays(int i, int j, int delflag)
{
npartner[j] = npartner[i];
for (int m = 0; m < npartner[j]; m++) {
partner[j][m] = partner[i][m];
if (isVES) {
deviatorextention[j][m] = deviatorextention[i][m];
deviatorBackextention[j][m] = deviatorBackextention[i][m];
}
+ if (isEPS)
+ deviatorPlasticextension[j][m] = deviatorPlasticextension[i][m];
r0[j][m] = r0[i][m];
}
+ if (isEPS) lambdaValue[j] = lambdaValue[i];
vinter[j] = vinter[i];
wvolume[j] = wvolume[i];
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for exchange with another proc
------------------------------------------------------------------------- */
int FixPeriNeigh::pack_exchange(int i, double *buf)
{
// compact list by eliminating partner = 0 entries
// set buf[0] after compaction
int m = 1;
for (int n = 0; n < npartner[i]; n++) {
if (partner[i][n] == 0) continue;
buf[m++] = partner[i][n];
if (isVES) {
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
}
+ if (isEPS) buf[m++] = deviatorPlasticextension[i][n];
buf[m++] = r0[i][n];
}
if (isVES) buf[0] = m/4;
- else buf[0] = m/2;
+ else if (isEPS) buf[0] = m/3;
+ else buf[0] = m/2;
+ if (isEPS) buf[m++] = lambdaValue[i];
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based arrays from exchange with another proc
------------------------------------------------------------------------- */
int FixPeriNeigh::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
npartner[nlocal] = static_cast<int> (buf[m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<tagint> (buf[m++]);
if (isVES) {
deviatorextention[nlocal][n] = buf[m++];
deviatorBackextention[nlocal][n] = buf[m++];
}
+ if (isEPS) deviatorPlasticextension[nlocal][n] = buf[m++];
r0[nlocal][n] = buf[m++];
}
+ if (isEPS) lambdaValue[nlocal] = buf[m++];
vinter[nlocal] = buf[m++];
wvolume[nlocal] = buf[m++];
return m;
}
/* ---------------------------------------------------------------------- */
int FixPeriNeigh::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = wvolume[j];
}
return 1;
}
/* ---------------------------------------------------------------------- */
void FixPeriNeigh::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++)
wvolume[i] = buf[m++];
}
/* ----------------------------------------------------------------------
pack entire state of Fix into one write
------------------------------------------------------------------------- */
void FixPeriNeigh::write_restart(FILE *fp)
{
int n = 0;
double list[2];
list[n++] = first;
list[n++] = maxpartner;
if (comm->me == 0) {
int size = n * sizeof(double);
fwrite(&size,sizeof(int),1,fp);
fwrite(list,sizeof(double),n,fp);
}
}
/* ----------------------------------------------------------------------
use state info from restart file to restart the Fix
------------------------------------------------------------------------- */
void FixPeriNeigh::restart(char *buf)
{
int n = 0;
double *list = (double *) buf;
first = static_cast<int> (list[n++]);
maxpartner = static_cast<int> (list[n++]);
// grow 2D arrays now, cannot change size of 2nd array index later
grow_arrays(atom->nmax);
}
/* ----------------------------------------------------------------------
pack values in local atom-based arrays for restart file
------------------------------------------------------------------------- */
int FixPeriNeigh::pack_restart(int i, double *buf)
{
int m = 0;
if (isVES) buf[m++] = 4*npartner[i] + 4;
+ else if (isEPS) buf[m++] = 3*npartner[i] + 5;
else buf[m++] = 2*npartner[i] + 4;
-
buf[m++] = npartner[i];
for (int n = 0; n < npartner[i]; n++) {
buf[m++] = partner[i][n];
if (isVES) {
buf[m++] = deviatorextention[i][n];
buf[m++] = deviatorBackextention[i][n];
}
+ if (isEPS) buf[m++] = deviatorPlasticextension[i][n];
buf[m++] = r0[i][n];
}
+ if (isEPS) buf[m++] = lambdaValue[i];
buf[m++] = vinter[i];
buf[m++] = wvolume[i];
return m;
}
/* ----------------------------------------------------------------------
unpack values from atom->extra array to restart the fix
------------------------------------------------------------------------- */
void FixPeriNeigh::unpack_restart(int nlocal, int nth)
{
double **extra = atom->extra;
// skip to Nth set of extra values
int m = 0;
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
m++;
npartner[nlocal] = static_cast<int> (extra[nlocal][m++]);
for (int n = 0; n < npartner[nlocal]; n++) {
partner[nlocal][n] = static_cast<tagint> (extra[nlocal][m++]);
if (isVES) {
deviatorextention[nlocal][n] = extra[nlocal][m++];
deviatorBackextention[nlocal][n] = extra[nlocal][m++];
}
+ if (isEPS) deviatorPlasticextension[nlocal][n] = extra[nlocal][m++];
r0[nlocal][n] = extra[nlocal][m++];
}
+ if (isEPS) lambdaValue[nlocal] = extra[nlocal][m++];
vinter[nlocal] = extra[nlocal][m++];
wvolume[nlocal] = extra[nlocal][m++];
}
/* ----------------------------------------------------------------------
maxsize of any atom's restart data
------------------------------------------------------------------------- */
int FixPeriNeigh::maxsize_restart()
{
if (isVES) return 4*maxpartner + 4;
+ if (isEPS) return 3*maxpartner + 5;
return 2*maxpartner + 4;
}
/* ----------------------------------------------------------------------
size of atom nlocal's restart data
------------------------------------------------------------------------- */
int FixPeriNeigh::size_restart(int nlocal)
{
if (isVES) return 4*npartner[nlocal] + 4;
+ if (isEPS) return 3*npartner[nlocal] + 5;
return 2*npartner[nlocal] + 4;
}
diff --git a/src/PERI/fix_peri_neigh.h b/src/PERI/fix_peri_neigh.h
index cdde88c37..1797f7ce7 100644
--- a/src/PERI/fix_peri_neigh.h
+++ b/src/PERI/fix_peri_neigh.h
@@ -1,90 +1,92 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(PERI_NEIGH,FixPeriNeigh)
#else
#ifndef LMP_FIX_PERI_NEIGH_H
#define LMP_FIX_PERI_NEIGH_H
#include "fix.h"
namespace LAMMPS_NS {
class FixPeriNeigh : public Fix {
friend class PairPeriPMB;
friend class PairPeriPMBOMP;
friend class PairPeriLPS;
- friend class PairPeriVES; //NEW
+ friend class PairPeriVES;
+ friend class PairPeriEPS;
friend class PairPeriLPSOMP;
friend class ComputeDamageAtom;
+ friend class ComputePlasticityAtom;
public:
FixPeriNeigh(class LAMMPS *,int, char **);
virtual ~FixPeriNeigh();
int setmask();
void init();
void init_list(int, class NeighList *);
void setup(int);
void min_setup(int);
double memory_usage();
void grow_arrays(int);
void copy_arrays(int, int, int);
int pack_exchange(int, double *);
int unpack_exchange(int, double *);
void write_restart(FILE *);
void restart(char *);
int pack_restart(int, double *);
void unpack_restart(int, int);
int size_restart(int);
int maxsize_restart();
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
protected:
int first; // flag for first time initialization
int maxpartner; // max # of peridynamic neighs for any atom
int *npartner; // # of neighbors for each atom
tagint **partner; // neighs for each atom, stored as global IDs
double **deviatorextention; // Deviatoric extention
double **deviatorBackextention; // Deviatoric back extention
+ double **deviatorPlasticextension; // Deviatoric plastic extension
+ double *lambdaValue;
double **r0; // initial distance to partners
- double **r1; // Instanteneous distance to partners *** NEW ***
- double *thetaOld; // Dilatation Old one
+ double **r1; // instanteneous distance to partners
+ double *thetaValue; // dilatation
double *vinter; // sum of vfrac for bonded neighbors
double *wvolume; // weighted volume of particle
- int isPMB;
- int isLPS;
- int isVES;
+ int isPMB,isLPS,isVES,isEPS; // which flavor of PD
class NeighList *list;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Duplicate particle in PeriDynamic bond - simulation box is too small
This is likely because your box length is shorter than 2 times
the bond length.
*/
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_eps.cpp
similarity index 70%
copy from src/PERI/pair_peri_ves.cpp
copy to src/PERI/pair_peri_eps.cpp
index ec7852feb..fe03ac53a 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_eps.cpp
@@ -1,724 +1,843 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
- Contributing authors: Ezwanur Rahman, J.T. Foster (UTSA)
+ Contributing author: Rezwanur Rahman, John Foster (UTSA)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
-#include "pair_peri_ves.h"
+#include "pair_peri_eps.h"
#include "atom.h"
#include "domain.h"
#include "lattice.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_peri_neigh.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
-PairPeriVES::PairPeriVES(LAMMPS *lmp) : Pair(lmp)
+PairPeriEPS::PairPeriEPS(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
no_virial_fdotr_compute = 1;
single_enable = 0;
ifix_peri = -1;
nmax = 0;
s0_new = NULL;
theta = NULL;
bulkmodulus = NULL;
shearmodulus = NULL;
s00 = alpha = NULL;
cut = NULL;
- m_lambdai = NULL;
- m_taubi = NULL;
+ m_yieldstress = NULL;
// set comm size needed by this Pair
// comm_reverse not needed
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
-PairPeriVES::~PairPeriVES()
+PairPeriEPS::~PairPeriEPS()
{
if (ifix_peri >= 0) modify->delete_fix("PERI_NEIGH");
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(bulkmodulus);
memory->destroy(shearmodulus);
memory->destroy(s00);
memory->destroy(alpha);
memory->destroy(cut);
- memory->destroy(m_lambdai);
- memory->destroy(m_taubi);
+ memory->destroy(m_yieldstress);
memory->destroy(theta);
memory->destroy(s0_new);
}
}
/* ---------------------------------------------------------------------- */
-void PairPeriVES::compute(int eflag, int vflag)
+void PairPeriEPS::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0,rsq0;
- double rsq,r,dr,dr1,rk,evdwl,fpair,fbond;
- double deltaed,fbondViscoElastic,fbondFinal;
- double decay,betai,lambdai,edbNp1,rkNew;
+ double rsq,r,dr,dr1,rk,rkNew,evdwl,fpair,fbond;
+ double ed,fbondElastoPlastic,fbondFinal;
+ double deltalambda,edpNp1;
int *ilist,*jlist,*numneigh,**firstneigh;
double d_ij,delta,stretch;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
double timestepsize = update->dt;
double *vfrac = atom->vfrac;
double *s0 = atom->s0;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
- double **deviatorextention =
- ((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorextention;
- double **deviatorBackextention =
- ((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorBackextention;
+ double **deviatorPlasticextension =
+ ((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorPlasticextension;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
+ double *lambdaValue = ((FixPeriNeigh *) modify->fix[ifix_peri])->lambdaValue;
// lc = lattice constant
// init_style guarantees it's the same in x, y, and z
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double vfrac_scale = 1.0;
// short-range forces
int newton_pair = force->newton_pair;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// need minimg() for x0 difference since not ghosted
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
-
+
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
r = sqrt(rsq);
// short-range interaction distance based on initial particle position
// 0.9 and 1.35 are constants
d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
// short-range contact forces
// 15 is constant taken from the EMU Theory Manual
// Silling, 12 May 2005, p 18
if (r < d_ij) {
dr = r - d_ij;
// kshort based upon short-range force constant
// of the bond-based theory used in PMB model
double kshort = (15.0 * 18.0 * bulkmodulus[itype][itype]) /
(3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype]);
rk = (kshort * vfrac[j]) * (dr / cut[itype][jtype]);
if (r > 0.0) fpair = -(rk/r);
else fpair = 0.0;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) evdwl = 0.5*rk*dr;
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,
fpair*vfrac[i],delx,dely,delz);
}
}
}
// grow bond forces array if necessary
+
+ int maxpartner = 0;
+ for (i = 0; i < nlocal; i++) maxpartner = MAX(maxpartner,npartner[i]);
+
if (atom->nmax > nmax) {
memory->destroy(s0_new);
memory->destroy(theta);
nmax = atom->nmax;
memory->create(s0_new,nmax,"pair:s0_new");
memory->create(theta,nmax,"pair:theta");
+
}
+
+ // ******** temp array to store Plastic extension *********** ///
+ double deviatorPlasticExtTemp[nlocal][maxpartner];
+ for (int ii = 0; ii < nlocal; ii++) {
+ for (int kk = 0; kk < maxpartner; kk++) {
+ deviatorPlasticExtTemp[ii][kk] = 0.0;
+ }
+ }
+ // ******** temp array to store Plastic extension *********** ///
+
+
// compute the dilatation on each particle
compute_dilatation();
// communicate dilatation (theta) of each particle
-
comm->forward_comm_pair(this);
// communicate weighted volume (wvolume) upon every reneighbor
if (neighbor->ago == 0)
comm->forward_comm_fix(modify->fix[ifix_peri]);
// volume-dependent part of the energy
if (eflag) {
for (i = 0; i < nlocal; i++) {
itype = type[i];
if (eflag_global)
eng_vdwl += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
if (eflag_atom)
eatom[i] += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
}
}
// loop over my particles and their partners
// partner list contains all bond partners, so I-J appears twice
// if bond already broken, skip this partner
// first = true if this is first neighbor of particle i
bool first;
- double omega_minus, omega_plus;
+ double omega_minus, omega_plus, omega;
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
itype = type[i];
jnum = npartner[i];
first = true;
+
+
+ double yieldStress = m_yieldstress[itype][itype];
+ double horizon = cut[itype][itype];
+ double tdnorm = compute_DeviatoricForceStateNorm(i);
+ double pointwiseYieldvalue = 25.0 * yieldStress *
+ yieldStress / 8 / M_PI / pow(horizon,5);
+
+
+ double fsurf = (tdnorm * tdnorm)/2 - pointwiseYieldvalue;
+ bool elastic = true;
+
+ double alphavalue = (15 * shearmodulus[itype][itype]) /wvolume[i];
+
+
+ if (fsurf>0) {
+ elastic = false;
+ deltalambda = ((tdnorm /sqrt(2.0 * pointwiseYieldvalue)) - 1.0) / alphavalue;
+ double templambda = lambdaValue[i];
+ lambdaValue[i] = templambda + deltalambda;
+ }
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
j = atom->map(partner[i][jj]);
-
- // check if lost a partner without first breaking bond
+ // check if lost a partner without first breaking bond
if (j < 0) {
partner[i][jj] = 0;
continue;
}
// compute force density, add to PD equation of motion
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
jtype = type[j];
delta = cut[itype][jtype];
r = sqrt(rsq);
dr = r - r0[i][jj];
// avoid roundoff errors
- if (fabs(dr) < 2.2204e-016) dr = 0.0;
+ if (fabs(dr) < 2.2204e-016) {
+ dr = 0.0;
+ }
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
-
+
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
+
+ //Elastic Part
+ rk = ((3.0 * bulkmodulus[itype][itype]) * ( (omega_plus * theta[i] / wvolume[i]) +
+ ( omega_minus * theta[j] / wvolume[j] ) ) ) * r0[i][jj];
- rk = ( (3.0 * bulkmodulus[itype][itype]) * vfrac[j] * vfrac_scale *
- ( (omega_plus * theta[i] / wvolume[i]) +
- ( omega_minus * theta[j] / wvolume[j] ) ) ) * r0[i][jj];
-
- if (r > 0.0) fbond = -(rk/r);
+ if (r > 0.0) fbond = -((rk/r) * vfrac[j] * vfrac_scale);
else fbond = 0.0;
-
- // for viscoelasticity
-
- lambdai=m_lambdai[itype][itype];
- double taui = m_taubi[itype][itype];
- double c1 = taui/timestepsize;
- decay=exp(-1.0/c1);
- betai=1.-c1*(1.-decay);
-
- double deviatoric_extension =
- dr - (theta[i]* r0[i][jj] / 3.0);
- deltaed = deviatoric_extension-deviatorextention[i][jj];
-
- // back extention at current step
-
- edbNp1 = deviatorextention[i][jj]*(1-decay) +
- deviatorBackextention[i][jj]*decay+betai*deltaed;
-
- rkNew = ((1-lambdai)*15.0) *
- ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
+
+ //Plastic part
+
+ double deviatoric_extension = dr - (theta[i]* r0[i][jj] / 3.0);
+ edpNp1 = deviatorPlasticextension[i][jj];
+
+
+ double tdtrialValue = ( 15 * shearmodulus[itype][itype]) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
- deviatoric_extension;
- rkNew += (lambdai*15.0) *
- ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
- ( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
- (deviatoric_extension-edbNp1);
-
- if (r > 0.0) fbondViscoElastic = -(rkNew/r);
- else fbondViscoElastic = 0.0;
-
- // total Force: elastic + viscoelastic
-
- fbondFinal=fbond+fbondViscoElastic;
- fbond=fbondFinal;
+ (deviatoric_extension - edpNp1);
+ if(elastic) {
+ rkNew = tdtrialValue;
+ }
+ else {
+ rkNew = (sqrt(2.0*pointwiseYieldvalue) * tdtrialValue) / tdnorm;
+ deviatorPlasticExtTemp[i][jj] = edpNp1 + rkNew * deltalambda;
+ }
+
+
+ if (r > 0.0) fbondElastoPlastic = -((rkNew/r) * vfrac[j] * vfrac_scale);
+ else fbondElastoPlastic = 0.0;
+
+
+ // total Force state: elastic + plastic
+ fbondFinal=fbond+fbondElastoPlastic;
+ fbond=fbondFinal;
+
+
f[i][0] += delx*fbond;
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
+
// since I-J is double counted, set newton off & use 1/2 factor and I,I
if (eflag) evdwl = (0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
- omega_plus * deviatoric_extension *
- deviatoric_extension) +
+ omega_plus * deviatoric_extension * deviatoric_extension) +
(0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
- omega_plus * (deviatoric_extension-edbNp1) *
- (deviatoric_extension-edbNp1)) * vfrac[j] * vfrac_scale;
+ omega_plus * (deviatoric_extension - edpNp1) *
+ (deviatoric_extension-edpNp1)) * vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,
0.5*fbond*vfrac[i],delx,dely,delz);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
- // store current deviatoric extention
-
- deviatorextention[i][jj]=deviatoric_extension;
- deviatorBackextention[i][jj]=edbNp1;
stretch = dr / r0[i][jj];
if (stretch > MIN(s0[i],s0[j])) partner[i][jj] = 0;
// update s0 for next timestep
if (first)
s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
else
s0_new[i] = MAX(s0_new[i],s00[itype][jtype] -
(alpha[itype][jtype] * stretch));
first = false;
}
}
// store new s0
for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
+
+ for (i = 0; i < nlocal; i++) {
+ jnum = npartner[i];
+ for (jj = 0; jj < jnum; jj++) {
+ double temp_data = deviatorPlasticExtTemp[i][jj];
+ deviatorPlasticextension[i][jj] = temp_data;
+ }
+ }
+
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
-void PairPeriVES::allocate()
+void PairPeriEPS::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(bulkmodulus,n+1,n+1,"pair:bulkmodulus");
memory->create(shearmodulus,n+1,n+1,"pair:shearmodulus");
memory->create(s00,n+1,n+1,"pair:s00");
memory->create(alpha,n+1,n+1,"pair:alpha");
memory->create(cut,n+1,n+1,"pair:cut");
- memory->create(m_lambdai,n+1,n+1,"pair:m_lambdai");
- memory->create(m_taubi,n+1,n+1,"pair:m_taubi");
+ memory->create(m_yieldstress,n+1,n+1,"pair:m_yieldstress");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
-void PairPeriVES::settings(int narg, char **arg)
+void PairPeriEPS::settings(int narg, char **arg)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
-void PairPeriVES::coeff(int narg, char **arg)
+void PairPeriEPS::coeff(int narg, char **arg)
{
- if (narg != 9) error->all(FLERR,"Incorrect args for pair coefficients");
+ if (narg != 8) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double bulkmodulus_one = atof(arg[2]);
double shearmodulus_one = atof(arg[3]);
double cut_one = atof(arg[4]);
double s00_one = atof(arg[5]);
double alpha_one = atof(arg[6]);
- double mlambdai_one = atof(arg[7]);
- double mtaui_one = atof(arg[8]);
+ double myieldstress_one = atof(arg[7]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
bulkmodulus[i][j] = bulkmodulus_one;
shearmodulus[i][j] = shearmodulus_one;
cut[i][j] = cut_one;
s00[i][j] = s00_one;
alpha[i][j] = alpha_one;
- m_lambdai[i][j] = mlambdai_one;
- m_taubi[i][j] = mtaui_one;
+ m_yieldstress[i][j] = myieldstress_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
-double PairPeriVES::init_one(int i, int j)
+double PairPeriEPS::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
bulkmodulus[j][i] = bulkmodulus[i][j];
shearmodulus[j][i] = shearmodulus[i][j];
s00[j][i] = s00[i][j];
alpha[j][i] = alpha[i][j];
cut[j][i] = cut[i][j];
- m_lambdai[j][i] = m_lambdai[i][j];
- m_taubi[j][i] = m_taubi[i][j];
-
+ m_yieldstress[j][i] = m_yieldstress[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
-void PairPeriVES::init_style()
+void PairPeriEPS::init_style()
{
// error checks
if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
if (domain->lattice == NULL)
error->all(FLERR,"Pair peri requires a lattice be defined");
if (domain->lattice->xlattice != domain->lattice->ylattice ||
domain->lattice->xlattice != domain->lattice->zlattice ||
domain->lattice->ylattice != domain->lattice->zlattice)
error->all(FLERR,"Pair peri lattice is not identical in x, y, and z");
// if first init, create Fix needed for storing fixed neighbors
if (ifix_peri == -1) {
char **fixarg = new char*[3];
fixarg[0] = (char *) "PERI_NEIGH";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "PERI_NEIGH";
modify->add_fix(3,fixarg);
delete [] fixarg;
}
// find associated PERI_NEIGH fix that must exist
// could have changed locations in fix list since created
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist");
neighbor->request(this);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
-void PairPeriVES::write_restart(FILE *fp)
+void PairPeriEPS::write_restart(FILE *fp)
{
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&bulkmodulus[i][j],sizeof(double),1,fp);
fwrite(&shearmodulus[i][j],sizeof(double),1,fp);
fwrite(&s00[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
- fwrite(&m_lambdai[i][j],sizeof(double),1,fp);
- fwrite(&m_taubi[i][j],sizeof(double),1,fp);
+ fwrite(&m_yieldstress[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
-void PairPeriVES::read_restart(FILE *fp)
+void PairPeriEPS::read_restart(FILE *fp)
{
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&bulkmodulus[i][j],sizeof(double),1,fp);
fread(&shearmodulus[i][j],sizeof(double),1,fp);
fread(&s00[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
- fread(&m_lambdai[i][j],sizeof(double),1,fp);
- fread(&m_taubi[i][j],sizeof(double),1,fp);
+ fread(&m_yieldstress[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&m_lambdai[i][j],1,MPI_DOUBLE,0,world);
- MPI_Bcast(&m_taubi[i][j],1,MPI_DOUBLE,0,world);
+ MPI_Bcast(&m_yieldstress[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
-double PairPeriVES::memory_usage()
+double PairPeriEPS::memory_usage()
{
double bytes = 2 * nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
influence function definition
------------------------------------------------------------------------- */
-double PairPeriVES::influence_function(double xi_x, double xi_y, double xi_z)
+double PairPeriEPS::influence_function(double xi_x, double xi_y, double xi_z)
{
double r = sqrt(xi_x*xi_x + xi_y*xi_y + xi_z*xi_z);
double omega;
-
+
if (fabs(r) < 2.2204e-016)
- error->one(FLERR,"Divide by 0 in influence function of pair peri/lps");
+ error->one(FLERR,"Divide by 0 in influence function");
omega = 1.0/r;
return omega;
}
/* ---------------------------------------------------------------------- */
-void PairPeriVES::compute_dilatation()
+void PairPeriEPS::compute_dilatation()
{
int i,j,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0;
double rsq,r,dr;
double delta;
double **x = atom->x;
int *type = atom->type;
double **x0 = atom->x0;
int nlocal = atom->nlocal;
double *vfrac = atom->vfrac;
double vfrac_scale = 1.0;
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
// compute the dilatation theta
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
jnum = npartner[i];
theta[i] = 0.0;
itype = type[i];
for (jj = 0; jj < jnum; jj++) {
// if bond already broken, skip this partner
-
if (partner[i][jj] == 0) continue;
// look up local index of this partner particle
-
j = atom->map(partner[i][jj]);
// skip if particle is "lost"
-
if (j < 0) continue;
// compute force density and add to PD equation of motion
-
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
r = sqrt(rsq);
dr = r - r0[i][jj];
if (fabs(dr) < 2.2204e-016) dr = 0.0;
jtype = type[j];
delta = cut[itype][jtype];
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
theta[i] += influence_function(delx0, dely0, delz0) * r0[i][jj] * dr *
vfrac[j] * vfrac_scale;
}
// if wvolume[i] is zero, then particle i has no bonds
// therefore, the dilatation is set to
if (wvolume[i] != 0.0) theta[i] = (3.0/wvolume[i]) * theta[i];
else theta[i] = 0;
}
}
+/* ---------------------------------------------------------------------- */
+
+double PairPeriEPS::compute_DeviatoricForceStateNorm(int i)
+{
+ int j,jj,jnum,itype,jtype;
+ double xtmp,ytmp,ztmp,delx,dely,delz;
+ double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0;
+ double rsq,r,dr;
+ double delta;
+ double tdtrial;
+ double norm = 0.0;
+
+ double **x = atom->x;
+ int *type = atom->type;
+ double **x0 = atom->x0;
+ double *s0 = atom->s0;
+ int nlocal = atom->nlocal;
+ double *vfrac = atom->vfrac;
+ double vfrac_scale = 1.0;
+
+ double lc = domain->lattice->xlattice;
+ double half_lc = 0.5*lc;
+
+ double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
+ tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
+ int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
+ double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
+ double **deviatorPlasticextension =
+ ((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorPlasticextension;
+
+ int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
+
+ // compute the dilatation theta
+
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ xtmp0 = x0[i][0];
+ ytmp0 = x0[i][1];
+ ztmp0 = x0[i][2];
+ jnum = npartner[i];
+ itype = type[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ if (partner[i][jj] == 0) continue;
+ j = atom->map(partner[i][jj]);
+ // check if lost a partner without first breaking bond
+ if (j < 0) {
+ partner[i][jj] = 0;
+ continue;
+ }
+ delx = xtmp - x[j][0];
+ dely = ytmp - x[j][1];
+ delz = ztmp - x[j][2];
+ if (periodic) domain->minimum_image(delx,dely,delz);
+ rsq = delx*delx + dely*dely + delz*delz;
+ delx0 = xtmp0 - x0[j][0];
+ dely0 = ytmp0 - x0[j][1];
+ delz0 = ztmp0 - x0[j][2];
+ if (periodic) domain->minimum_image(delx0,dely0,delz0);
+ r = sqrt(rsq);
+ dr = r - r0[i][jj];
+ if (fabs(dr) < 2.2204e-016) dr = 0.0;
+
+ // scale vfrac[j] if particle j near the horizon
+ double vfrac_scale;
+
+ jtype = type[j];
+ double delta = cut[itype][jtype];
+
+ // scale vfrac[j] if particle j near the horizon
+
+ if ((fabs(r0[i][jj] - delta)) <= half_lc)
+ vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
+ (1.0 + ((delta - half_lc)/(2*half_lc) ) );
+ else vfrac_scale = 1.0;
+
+ double ed = dr - (theta[i] * r0[i][jj])/3;
+ double edPNP1 = deviatorPlasticextension[i][jj];
+
+ jtype = type[j];
+ delta = cut[itype][jtype];
+
+ double omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
+ double omega_minus = influence_function(delx0,dely0,delz0);
+
+ double stretch = dr / r0[i][jj];
+
+ tdtrial = ( 15 * shearmodulus[itype][itype]) *
+ ((omega_plus * theta[i] / wvolume[i]) +
+ ( omega_minus * theta[j] / wvolume[j] ) ) * (ed - edPNP1);
+
+ norm += tdtrial * tdtrial * vfrac[j] * vfrac_scale;
+ }
+ return sqrt(norm);
+}
+
+
/* ----------------------------------------------------------------------
communication routines
---------------------------------------------------------------------- */
-int PairPeriVES::pack_comm(int n, int *list, double *buf,
+int PairPeriEPS::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = theta[j];
}
return 1;
}
/* ---------------------------------------------------------------------- */
-void PairPeriVES::unpack_comm(int n, int first, double *buf)
+void PairPeriEPS::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
theta[i] = buf[m++];
}
}
diff --git a/src/PERI/pair_peri_ves.h b/src/PERI/pair_peri_eps.h
similarity index 89%
copy from src/PERI/pair_peri_ves.h
copy to src/PERI/pair_peri_eps.h
index c21e60c9b..c6eacce1c 100644
--- a/src/PERI/pair_peri_ves.h
+++ b/src/PERI/pair_peri_eps.h
@@ -1,109 +1,111 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
-PairStyle(peri/ves,PairPeriVES)
+PairStyle(peri/eps,PairPeriEPS)
#else
-#ifndef LMP_PAIR_PERI_VES_H
-#define LMP_PAIR_PERI_VES_H
+#ifndef LMP_PAIR_PERI_EPS_H
+#define LMP_PAIR_PERI_EPS_H
#include "pair.h"
namespace LAMMPS_NS {
-class PairPeriVES : public Pair {
+class PairPeriEPS : public Pair {
public:
- PairPeriVES(class LAMMPS *);
- virtual ~PairPeriVES();
+ double *theta;
+
+ PairPeriEPS(class LAMMPS *);
+ virtual ~PairPeriEPS();
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *) {}
void read_restart_settings(FILE *) {}
double memory_usage();
double influence_function(double, double, double);
void compute_dilatation();
+ double compute_DeviatoricForceStateNorm(int);
protected:
int ifix_peri;
double **bulkmodulus;
double **shearmodulus;
double **s00, **alpha;
- double **cut, **m_lambdai, **m_taubi; //NEW: **m_lambdai,**m_taubi
+ double **cut, **m_yieldstress; //NEW: **m_yieldstress
double *s0_new;
- double *theta;
int nmax;
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Pair style peri requires atom style peri
Self-explanatory.
E: Pair peri requires an atom map, see atom_modify
Even for atomic systems, an atom map is required to find Peridynamic
bonds. Use the atom_modify command to define one.
E: Pair peri requires a lattice be defined
Use the lattice command for this purpose.
E: Pair peri lattice is not identical in x, y, and z
The lattice defined by the lattice command must be cubic.
E: Fix peri neigh does not exist
Somehow a fix that the pair style defines has been deleted.
E: Divide by 0 in influence function of pair peri/lps
This should not normally occur. It is likely a problem with your
model.
*/
diff --git a/src/PERI/pair_peri_lps.cpp b/src/PERI/pair_peri_lps.cpp
index 639ac6fb4..c8ee9548a 100644
--- a/src/PERI/pair_peri_lps.cpp
+++ b/src/PERI/pair_peri_lps.cpp
@@ -1,650 +1,649 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Parks (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "pair_peri_lps.h"
#include "atom.h"
#include "domain.h"
#include "lattice.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_peri_neigh.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairPeriLPS::PairPeriLPS(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
no_virial_fdotr_compute = 1;
single_enable = 0;
ifix_peri = -1;
nmax = 0;
s0_new = NULL;
theta = NULL;
bulkmodulus = NULL;
shearmodulus = NULL;
s00 = alpha = NULL;
cut = NULL;
// set comm size needed by this Pair
// comm_reverse not needed
comm_forward = 1; // for passing dilatation (theta)
}
/* ---------------------------------------------------------------------- */
PairPeriLPS::~PairPeriLPS()
{
if (ifix_peri >= 0) modify->delete_fix("PERI_NEIGH");
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(bulkmodulus);
memory->destroy(shearmodulus);
memory->destroy(s00);
memory->destroy(alpha);
memory->destroy(cut);
memory->destroy(theta);
memory->destroy(s0_new);
}
}
/* ---------------------------------------------------------------------- */
void PairPeriLPS::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0,rsq0;
double rsq,r,dr,rk,evdwl,fpair,fbond;
int *ilist,*jlist,*numneigh,**firstneigh;
double d_ij,delta,stretch;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
double *vfrac = atom->vfrac;
double *s0 = atom->s0;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
// lc = lattice constant
// init_style guarantees it's the same in x, y, and z
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double vfrac_scale = 1.0;
// short-range forces
int newton_pair = force->newton_pair;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// need minimg() for x0 difference since not ghosted
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
r = sqrt(rsq);
// short-range interaction distance based on initial particle position
// 0.9 and 1.35 are constants
d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
// short-range contact forces
// 15 is constant taken from the EMU Theory Manual
// Silling, 12 May 2005, p 18
if (r < d_ij) {
dr = r - d_ij;
// kshort based upon short-range force constant
// of the bond-based theory used in PMB model
double kshort = (15.0 * 18.0 * bulkmodulus[itype][itype]) /
(3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype]);
rk = (kshort * vfrac[j]) * (dr / cut[itype][jtype]);
if (r > 0.0) fpair = -(rk/r);
else fpair = 0.0;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) evdwl = 0.5*rk*dr;
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,
fpair*vfrac[i],delx,dely,delz);
}
}
}
// grow bond forces array if necessary
if (atom->nmax > nmax) {
memory->destroy(s0_new);
memory->destroy(theta);
nmax = atom->nmax;
memory->create(s0_new,nmax,"pair:s0_new");
memory->create(theta,nmax,"pair:theta");
}
// Compute the dilatation on each particle
compute_dilatation();
// communicate dilatation (theta) of each particle
comm->forward_comm_pair(this);
// communicate wighted volume (wvolume) upon every reneighbor
if (neighbor->ago == 0)
comm->forward_comm_fix(modify->fix[ifix_peri]);
// Volume-dependent part of the energy
if (eflag) {
for (i = 0; i < nlocal; i++) {
itype = type[i];
if (eflag_global)
eng_vdwl += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
if (eflag_atom)
eatom[i] += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
}
}
// loop over my particles and their partners
// partner list contains all bond partners, so I-J appears twice
// if bond already broken, skip this partner
// first = true if this is first neighbor of particle i
bool first;
double omega_minus, omega_plus;
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
itype = type[i];
jnum = npartner[i];
first = true;
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
j = atom->map(partner[i][jj]);
// check if lost a partner without first breaking bond
if (j < 0) {
partner[i][jj] = 0;
continue;
}
// compute force density, add to PD equation of motion
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
jtype = type[j];
delta = cut[itype][jtype];
r = sqrt(rsq);
dr = r - r0[i][jj];
// avoid roundoff errors
if (fabs(dr) < 2.2204e-016) dr = 0.0;
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
rk = ( (3.0 * bulkmodulus[itype][itype]) -
(5.0 * shearmodulus[itype][itype]) ) * vfrac[j] * vfrac_scale *
( (omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) * r0[i][jj];
rk += 15.0 * ( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) * dr;
if (r > 0.0) fbond = -(rk/r);
else fbond = 0.0;
f[i][0] += delx*fbond;
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
// since I-J is double counted, set newton off & use 1/2 factor and I,I
double deviatoric_extension = dr - (theta[i]* r0[i][jj] / 3.0);
if (eflag) evdwl = 0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus*(deviatoric_extension * deviatoric_extension) *
vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,
0.5*fbond*vfrac[i],delx,dely,delz);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
stretch = dr / r0[i][jj];
if (stretch > MIN(s0[i],s0[j])) partner[i][jj] = 0;
// update s0 for next timestep
if (first)
s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
else
s0_new[i] = MAX(s0_new[i],s00[itype][jtype] -
(alpha[itype][jtype] * stretch));
first = false;
}
}
// store new s0
for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairPeriLPS::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(bulkmodulus,n+1,n+1,"pair:bulkmodulus");
memory->create(shearmodulus,n+1,n+1,"pair:shearmodulus");
memory->create(s00,n+1,n+1,"pair:s00");
memory->create(alpha,n+1,n+1,"pair:alpha");
memory->create(cut,n+1,n+1,"pair:cut");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPeriLPS::settings(int narg, char **arg)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairPeriLPS::coeff(int narg, char **arg)
{
if (narg != 7) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double bulkmodulus_one = force->numeric(FLERR,arg[2]);
double shearmodulus_one = force->numeric(FLERR,arg[3]);
double cut_one = force->numeric(FLERR,arg[4]);
double s00_one = force->numeric(FLERR,arg[5]);
double alpha_one = force->numeric(FLERR,arg[6]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
bulkmodulus[i][j] = bulkmodulus_one;
shearmodulus[i][j] = shearmodulus_one;
cut[i][j] = cut_one;
s00[i][j] = s00_one;
alpha[i][j] = alpha_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairPeriLPS::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
bulkmodulus[j][i] = bulkmodulus[i][j];
shearmodulus[j][i] = shearmodulus[i][j];
s00[j][i] = s00[i][j];
alpha[j][i] = alpha[i][j];
cut[j][i] = cut[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairPeriLPS::init_style()
{
// error checks
if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
if (domain->lattice->xlattice != domain->lattice->ylattice ||
domain->lattice->xlattice != domain->lattice->zlattice ||
domain->lattice->ylattice != domain->lattice->zlattice)
error->all(FLERR,"Pair peri lattice is not identical in x, y, and z");
// if first init, create Fix needed for storing fixed neighbors
if (ifix_peri == -1) {
char **fixarg = new char*[3];
fixarg[0] = (char *) "PERI_NEIGH";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "PERI_NEIGH";
modify->add_fix(3,fixarg);
delete [] fixarg;
}
// find associated PERI_NEIGH fix that must exist
// could have changed locations in fix list since created
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist");
neighbor->request(this);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairPeriLPS::write_restart(FILE *fp)
{
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&bulkmodulus[i][j],sizeof(double),1,fp);
fwrite(&shearmodulus[i][j],sizeof(double),1,fp);
fwrite(&s00[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairPeriLPS::read_restart(FILE *fp)
{
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&bulkmodulus[i][j],sizeof(double),1,fp);
fread(&shearmodulus[i][j],sizeof(double),1,fp);
fread(&s00[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairPeriLPS::memory_usage()
{
double bytes = 2 * nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
influence function definition
------------------------------------------------------------------------- */
double PairPeriLPS::influence_function(double xi_x, double xi_y, double xi_z)
{
double r = sqrt(xi_x*xi_x + xi_y*xi_y + xi_z*xi_z);
double omega;
if (fabs(r) < 2.2204e-016)
error->one(FLERR,"Divide by 0 in influence function of pair peri/lps");
omega = 1.0/r;
return omega;
}
/* ---------------------------------------------------------------------- */
void PairPeriLPS::compute_dilatation()
{
int i,j,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0;
double rsq,r,dr;
double delta;
double **x = atom->x;
int *type = atom->type;
double **x0 = atom->x0;
int nlocal = atom->nlocal;
double *vfrac = atom->vfrac;
double vfrac_scale = 1.0;
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
// compute the dilatation theta
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
jnum = npartner[i];
theta[i] = 0.0;
itype = type[i];
for (jj = 0; jj < jnum; jj++) {
// if bond already broken, skip this partner
if (partner[i][jj] == 0) continue;
// Look up local index of this partner particle
j = atom->map(partner[i][jj]);
// Skip if particle is "lost"
if (j < 0) continue;
// Compute force density and add to PD equation of motion
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
r = sqrt(rsq);
dr = r - r0[i][jj];
if (fabs(dr) < 2.2204e-016) dr = 0.0;
jtype = type[j];
delta = cut[itype][jtype];
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
theta[i] += influence_function(delx0, dely0, delz0) * r0[i][jj] * dr *
vfrac[j] * vfrac_scale;
}
// if wvolume[i] is zero, then particle i has no bonds
// therefore, the dilatation is set to
if (wvolume[i] != 0.0) theta[i] = (3.0/wvolume[i]) * theta[i];
else theta[i] = 0;
}
}
/* ----------------------------------------------------------------------
communication routines
- ---------------------------------------------------------------------- */
+ ---------------------------------------------------------------------- */
int PairPeriLPS::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
-
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = theta[j];
}
return 1;
}
/* ---------------------------------------------------------------------- */
void PairPeriLPS::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
theta[i] = buf[m++];
}
}
diff --git a/src/PERI/pair_peri_lps.h b/src/PERI/pair_peri_lps.h
index 5d4afc907..b098746ba 100644
--- a/src/PERI/pair_peri_lps.h
+++ b/src/PERI/pair_peri_lps.h
@@ -1,105 +1,106 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(peri/lps,PairPeriLPS)
#else
#ifndef LMP_PAIR_PERI_LPS_H
#define LMP_PAIR_PERI_LPS_H
#include "pair.h"
namespace LAMMPS_NS {
class PairPeriLPS : public Pair {
public:
+ double *theta;
+
PairPeriLPS(class LAMMPS *);
virtual ~PairPeriLPS();
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *) {}
void read_restart_settings(FILE *) {}
double memory_usage();
double influence_function(double, double, double);
void compute_dilatation();
protected:
int ifix_peri;
double **bulkmodulus;
double **shearmodulus;
- double **s00, **alpha;
+ double **s00,**alpha;
double **cut;
double *s0_new;
- double *theta;
int nmax;
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Pair style peri requires atom style peri
Self-explanatory.
E: Pair peri requires an atom map, see atom_modify
Even for atomic systems, an atom map is required to find Peridynamic
bonds. Use the atom_modify command to define one.
E: Pair peri lattice is not identical in x, y, and z
The lattice defined by the lattice command must be cubic.
E: Fix peri neigh does not exist
Somehow a fix that the pair style defines has been deleted.
E: Divide by 0 in influence function of pair peri/lps
This should not normally occur. It is likely a problem with your
model.
*/
diff --git a/src/PERI/pair_peri_ves.cpp b/src/PERI/pair_peri_ves.cpp
index ec7852feb..baa826ea8 100644
--- a/src/PERI/pair_peri_ves.cpp
+++ b/src/PERI/pair_peri_ves.cpp
@@ -1,724 +1,724 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Ezwanur Rahman, J.T. Foster (UTSA)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "pair_peri_ves.h"
#include "atom.h"
#include "domain.h"
#include "lattice.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "fix_peri_neigh.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "update.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairPeriVES::PairPeriVES(LAMMPS *lmp) : Pair(lmp)
{
for (int i = 0; i < 6; i++) virial[i] = 0.0;
no_virial_fdotr_compute = 1;
single_enable = 0;
ifix_peri = -1;
nmax = 0;
s0_new = NULL;
theta = NULL;
bulkmodulus = NULL;
shearmodulus = NULL;
s00 = alpha = NULL;
cut = NULL;
m_lambdai = NULL;
m_taubi = NULL;
// set comm size needed by this Pair
// comm_reverse not needed
comm_forward = 1;
}
/* ---------------------------------------------------------------------- */
PairPeriVES::~PairPeriVES()
{
if (ifix_peri >= 0) modify->delete_fix("PERI_NEIGH");
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(bulkmodulus);
memory->destroy(shearmodulus);
memory->destroy(s00);
memory->destroy(alpha);
memory->destroy(cut);
memory->destroy(m_lambdai);
memory->destroy(m_taubi);
memory->destroy(theta);
memory->destroy(s0_new);
}
}
/* ---------------------------------------------------------------------- */
void PairPeriVES::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0,rsq0;
double rsq,r,dr,dr1,rk,evdwl,fpair,fbond;
double deltaed,fbondViscoElastic,fbondFinal;
double decay,betai,lambdai,edbNp1,rkNew;
int *ilist,*jlist,*numneigh,**firstneigh;
double d_ij,delta,stretch;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
double **f = atom->f;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
double timestepsize = update->dt;
double *vfrac = atom->vfrac;
double *s0 = atom->s0;
double **x0 = atom->x0;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
double **deviatorextention =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorextention;
double **deviatorBackextention =
((FixPeriNeigh *) modify->fix[ifix_peri])->deviatorBackextention;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
// lc = lattice constant
// init_style guarantees it's the same in x, y, and z
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double vfrac_scale = 1.0;
// short-range forces
int newton_pair = force->newton_pair;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
// need minimg() for x0 difference since not ghosted
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
rsq0 = delx0*delx0 + dely0*dely0 + delz0*delz0;
jtype = type[j];
r = sqrt(rsq);
// short-range interaction distance based on initial particle position
// 0.9 and 1.35 are constants
d_ij = MIN(0.9*sqrt(rsq0),1.35*lc);
// short-range contact forces
// 15 is constant taken from the EMU Theory Manual
// Silling, 12 May 2005, p 18
if (r < d_ij) {
dr = r - d_ij;
// kshort based upon short-range force constant
// of the bond-based theory used in PMB model
double kshort = (15.0 * 18.0 * bulkmodulus[itype][itype]) /
(3.141592653589793 * cutsq[itype][jtype] * cutsq[itype][jtype]);
rk = (kshort * vfrac[j]) * (dr / cut[itype][jtype]);
if (r > 0.0) fpair = -(rk/r);
else fpair = 0.0;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) evdwl = 0.5*rk*dr;
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,
fpair*vfrac[i],delx,dely,delz);
}
}
}
// grow bond forces array if necessary
if (atom->nmax > nmax) {
memory->destroy(s0_new);
memory->destroy(theta);
nmax = atom->nmax;
memory->create(s0_new,nmax,"pair:s0_new");
memory->create(theta,nmax,"pair:theta");
}
// compute the dilatation on each particle
compute_dilatation();
// communicate dilatation (theta) of each particle
comm->forward_comm_pair(this);
// communicate weighted volume (wvolume) upon every reneighbor
if (neighbor->ago == 0)
comm->forward_comm_fix(modify->fix[ifix_peri]);
// volume-dependent part of the energy
if (eflag) {
for (i = 0; i < nlocal; i++) {
itype = type[i];
if (eflag_global)
eng_vdwl += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
if (eflag_atom)
eatom[i] += 0.5 * bulkmodulus[itype][itype] * (theta[i] * theta[i]);
}
}
// loop over my particles and their partners
// partner list contains all bond partners, so I-J appears twice
// if bond already broken, skip this partner
// first = true if this is first neighbor of particle i
bool first;
double omega_minus, omega_plus;
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
itype = type[i];
jnum = npartner[i];
first = true;
-
+
for (jj = 0; jj < jnum; jj++) {
if (partner[i][jj] == 0) continue;
j = atom->map(partner[i][jj]);
// check if lost a partner without first breaking bond
if (j < 0) {
partner[i][jj] = 0;
continue;
}
// compute force density, add to PD equation of motion
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
jtype = type[j];
delta = cut[itype][jtype];
r = sqrt(rsq);
dr = r - r0[i][jj];
// avoid roundoff errors
if (fabs(dr) < 2.2204e-016) dr = 0.0;
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
omega_plus = influence_function(-1.0*delx0,-1.0*dely0,-1.0*delz0);
omega_minus = influence_function(delx0,dely0,delz0);
rk = ( (3.0 * bulkmodulus[itype][itype]) * vfrac[j] * vfrac_scale *
( (omega_plus * theta[i] / wvolume[i]) +
( omega_minus * theta[j] / wvolume[j] ) ) ) * r0[i][jj];
if (r > 0.0) fbond = -(rk/r);
else fbond = 0.0;
// for viscoelasticity
lambdai=m_lambdai[itype][itype];
double taui = m_taubi[itype][itype];
double c1 = taui/timestepsize;
decay=exp(-1.0/c1);
betai=1.-c1*(1.-decay);
double deviatoric_extension =
dr - (theta[i]* r0[i][jj] / 3.0);
deltaed = deviatoric_extension-deviatorextention[i][jj];
// back extention at current step
edbNp1 = deviatorextention[i][jj]*(1-decay) +
deviatorBackextention[i][jj]*decay+betai*deltaed;
rkNew = ((1-lambdai)*15.0) *
( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
deviatoric_extension;
rkNew += (lambdai*15.0) *
( shearmodulus[itype][itype] * vfrac[j] * vfrac_scale ) *
( (omega_plus / wvolume[i]) + (omega_minus / wvolume[j]) ) *
(deviatoric_extension-edbNp1);
if (r > 0.0) fbondViscoElastic = -(rkNew/r);
else fbondViscoElastic = 0.0;
// total Force: elastic + viscoelastic
fbondFinal=fbond+fbondViscoElastic;
fbond=fbondFinal;
f[i][0] += delx*fbond;
f[i][1] += dely*fbond;
f[i][2] += delz*fbond;
// since I-J is double counted, set newton off & use 1/2 factor and I,I
if (eflag) evdwl = (0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus * deviatoric_extension *
deviatoric_extension) +
(0.5 * 15 * (shearmodulus[itype][itype]/wvolume[i]) *
omega_plus * (deviatoric_extension-edbNp1) *
(deviatoric_extension-edbNp1)) * vfrac[j] * vfrac_scale;
if (evflag) ev_tally(i,i,nlocal,0,0.5*evdwl,0.0,
0.5*fbond*vfrac[i],delx,dely,delz);
// find stretch in bond I-J and break if necessary
// use s0 from previous timestep
// store current deviatoric extention
deviatorextention[i][jj]=deviatoric_extension;
deviatorBackextention[i][jj]=edbNp1;
stretch = dr / r0[i][jj];
if (stretch > MIN(s0[i],s0[j])) partner[i][jj] = 0;
// update s0 for next timestep
if (first)
s0_new[i] = s00[itype][jtype] - (alpha[itype][jtype] * stretch);
else
s0_new[i] = MAX(s0_new[i],s00[itype][jtype] -
(alpha[itype][jtype] * stretch));
first = false;
}
}
// store new s0
for (i = 0; i < nlocal; i++) s0[i] = s0_new[i];
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairPeriVES::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(bulkmodulus,n+1,n+1,"pair:bulkmodulus");
memory->create(shearmodulus,n+1,n+1,"pair:shearmodulus");
memory->create(s00,n+1,n+1,"pair:s00");
memory->create(alpha,n+1,n+1,"pair:alpha");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(m_lambdai,n+1,n+1,"pair:m_lambdai");
memory->create(m_taubi,n+1,n+1,"pair:m_taubi");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairPeriVES::settings(int narg, char **arg)
{
if (narg) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairPeriVES::coeff(int narg, char **arg)
{
if (narg != 9) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double bulkmodulus_one = atof(arg[2]);
double shearmodulus_one = atof(arg[3]);
double cut_one = atof(arg[4]);
double s00_one = atof(arg[5]);
double alpha_one = atof(arg[6]);
double mlambdai_one = atof(arg[7]);
double mtaui_one = atof(arg[8]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
bulkmodulus[i][j] = bulkmodulus_one;
shearmodulus[i][j] = shearmodulus_one;
cut[i][j] = cut_one;
s00[i][j] = s00_one;
alpha[i][j] = alpha_one;
m_lambdai[i][j] = mlambdai_one;
m_taubi[i][j] = mtaui_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairPeriVES::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
bulkmodulus[j][i] = bulkmodulus[i][j];
shearmodulus[j][i] = shearmodulus[i][j];
s00[j][i] = s00[i][j];
alpha[j][i] = alpha[i][j];
cut[j][i] = cut[i][j];
m_lambdai[j][i] = m_lambdai[i][j];
m_taubi[j][i] = m_taubi[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairPeriVES::init_style()
{
// error checks
if (!atom->peri_flag)
error->all(FLERR,"Pair style peri requires atom style peri");
if (atom->map_style == 0)
error->all(FLERR,"Pair peri requires an atom map, see atom_modify");
if (domain->lattice == NULL)
error->all(FLERR,"Pair peri requires a lattice be defined");
if (domain->lattice->xlattice != domain->lattice->ylattice ||
domain->lattice->xlattice != domain->lattice->zlattice ||
domain->lattice->ylattice != domain->lattice->zlattice)
error->all(FLERR,"Pair peri lattice is not identical in x, y, and z");
// if first init, create Fix needed for storing fixed neighbors
if (ifix_peri == -1) {
char **fixarg = new char*[3];
fixarg[0] = (char *) "PERI_NEIGH";
fixarg[1] = (char *) "all";
fixarg[2] = (char *) "PERI_NEIGH";
modify->add_fix(3,fixarg);
delete [] fixarg;
}
// find associated PERI_NEIGH fix that must exist
// could have changed locations in fix list since created
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"PERI_NEIGH") == 0) ifix_peri = i;
if (ifix_peri == -1) error->all(FLERR,"Fix peri neigh does not exist");
neighbor->request(this);
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairPeriVES::write_restart(FILE *fp)
{
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&bulkmodulus[i][j],sizeof(double),1,fp);
fwrite(&shearmodulus[i][j],sizeof(double),1,fp);
fwrite(&s00[i][j],sizeof(double),1,fp);
fwrite(&alpha[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
fwrite(&m_lambdai[i][j],sizeof(double),1,fp);
fwrite(&m_taubi[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairPeriVES::read_restart(FILE *fp)
{
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&bulkmodulus[i][j],sizeof(double),1,fp);
fread(&shearmodulus[i][j],sizeof(double),1,fp);
fread(&s00[i][j],sizeof(double),1,fp);
fread(&alpha[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
fread(&m_lambdai[i][j],sizeof(double),1,fp);
fread(&m_taubi[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&bulkmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&shearmodulus[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&s00[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&m_lambdai[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&m_taubi[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairPeriVES::memory_usage()
{
double bytes = 2 * nmax * sizeof(double);
return bytes;
}
/* ----------------------------------------------------------------------
influence function definition
------------------------------------------------------------------------- */
double PairPeriVES::influence_function(double xi_x, double xi_y, double xi_z)
{
double r = sqrt(xi_x*xi_x + xi_y*xi_y + xi_z*xi_z);
double omega;
if (fabs(r) < 2.2204e-016)
error->one(FLERR,"Divide by 0 in influence function of pair peri/lps");
omega = 1.0/r;
return omega;
}
/* ---------------------------------------------------------------------- */
void PairPeriVES::compute_dilatation()
{
int i,j,jj,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double xtmp0,ytmp0,ztmp0,delx0,dely0,delz0;
double rsq,r,dr;
double delta;
double **x = atom->x;
int *type = atom->type;
double **x0 = atom->x0;
int nlocal = atom->nlocal;
double *vfrac = atom->vfrac;
double vfrac_scale = 1.0;
double lc = domain->lattice->xlattice;
double half_lc = 0.5*lc;
double **r0 = ((FixPeriNeigh *) modify->fix[ifix_peri])->r0;
tagint **partner = ((FixPeriNeigh *) modify->fix[ifix_peri])->partner;
int *npartner = ((FixPeriNeigh *) modify->fix[ifix_peri])->npartner;
double *wvolume = ((FixPeriNeigh *) modify->fix[ifix_peri])->wvolume;
int periodic = domain->xperiodic || domain->yperiodic || domain->zperiodic;
// compute the dilatation theta
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
xtmp0 = x0[i][0];
ytmp0 = x0[i][1];
ztmp0 = x0[i][2];
jnum = npartner[i];
theta[i] = 0.0;
itype = type[i];
for (jj = 0; jj < jnum; jj++) {
// if bond already broken, skip this partner
if (partner[i][jj] == 0) continue;
// look up local index of this partner particle
j = atom->map(partner[i][jj]);
// skip if particle is "lost"
if (j < 0) continue;
// compute force density and add to PD equation of motion
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
if (periodic) domain->minimum_image(delx,dely,delz);
rsq = delx*delx + dely*dely + delz*delz;
delx0 = xtmp0 - x0[j][0];
dely0 = ytmp0 - x0[j][1];
delz0 = ztmp0 - x0[j][2];
if (periodic) domain->minimum_image(delx0,dely0,delz0);
r = sqrt(rsq);
dr = r - r0[i][jj];
if (fabs(dr) < 2.2204e-016) dr = 0.0;
jtype = type[j];
delta = cut[itype][jtype];
// scale vfrac[j] if particle j near the horizon
if ((fabs(r0[i][jj] - delta)) <= half_lc)
vfrac_scale = (-1.0/(2*half_lc))*(r0[i][jj]) +
(1.0 + ((delta - half_lc)/(2*half_lc) ) );
else vfrac_scale = 1.0;
theta[i] += influence_function(delx0, dely0, delz0) * r0[i][jj] * dr *
vfrac[j] * vfrac_scale;
}
// if wvolume[i] is zero, then particle i has no bonds
// therefore, the dilatation is set to
if (wvolume[i] != 0.0) theta[i] = (3.0/wvolume[i]) * theta[i];
else theta[i] = 0;
}
}
/* ----------------------------------------------------------------------
communication routines
---------------------------------------------------------------------- */
int PairPeriVES::pack_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = theta[j];
}
return 1;
}
/* ---------------------------------------------------------------------- */
void PairPeriVES::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
theta[i] = buf[m++];
}
}
diff --git a/src/PERI/pair_peri_ves.h b/src/PERI/pair_peri_ves.h
index c21e60c9b..fbf6ab8bd 100644
--- a/src/PERI/pair_peri_ves.h
+++ b/src/PERI/pair_peri_ves.h
@@ -1,109 +1,112 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(peri/ves,PairPeriVES)
#else
#ifndef LMP_PAIR_PERI_VES_H
#define LMP_PAIR_PERI_VES_H
#include "pair.h"
namespace LAMMPS_NS {
class PairPeriVES : public Pair {
public:
+ double *theta;
+
PairPeriVES(class LAMMPS *);
virtual ~PairPeriVES();
int pack_comm(int, int *, double *, int, int *);
void unpack_comm(int, int, double *);
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void init_style();
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *) {}
void read_restart_settings(FILE *) {}
double memory_usage();
double influence_function(double, double, double);
void compute_dilatation();
protected:
int ifix_peri;
double **bulkmodulus;
double **shearmodulus;
double **s00, **alpha;
- double **cut, **m_lambdai, **m_taubi; //NEW: **m_lambdai,**m_taubi
+ double **cut;
+ double **m_lambdai;
+ double **m_taubi;
double *s0_new;
- double *theta;
int nmax;
void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: All pair coeffs are not set
All pair coefficients must be set in the data file or by the
pair_coeff command before running a simulation.
E: Pair style peri requires atom style peri
Self-explanatory.
E: Pair peri requires an atom map, see atom_modify
Even for atomic systems, an atom map is required to find Peridynamic
bonds. Use the atom_modify command to define one.
E: Pair peri requires a lattice be defined
Use the lattice command for this purpose.
E: Pair peri lattice is not identical in x, y, and z
The lattice defined by the lattice command must be cubic.
E: Fix peri neigh does not exist
Somehow a fix that the pair style defines has been deleted.
E: Divide by 0 in influence function of pair peri/lps
This should not normally occur. It is likely a problem with your
model.
*/
diff --git a/src/fix_ave_time.cpp b/src/fix_ave_time.cpp
index eb6cb9e14..e0cf6cec3 100644
--- a/src/fix_ave_time.cpp
+++ b/src/fix_ave_time.cpp
@@ -1,949 +1,949 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "unistd.h"
#include "fix_ave_time.h"
#include "update.h"
+#include "force.h"
#include "modify.h"
#include "compute.h"
#include "group.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
-#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{COMPUTE,FIX,VARIABLE};
enum{ONE,RUNNING,WINDOW};
enum{SCALAR,VECTOR};
#define INVOKED_SCALAR 1
#define INVOKED_VECTOR 2
#define INVOKED_ARRAY 4
/* ---------------------------------------------------------------------- */
FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all(FLERR,"Illegal fix ave/time command");
MPI_Comm_rank(world,&me);
nevery = force->inumeric(FLERR,arg[3]);
nrepeat = force->inumeric(FLERR,arg[4]);
nfreq = force->inumeric(FLERR,arg[5]);
global_freq = nfreq;
// scan values to count them
// then read options so know mode = SCALAR/VECTOR before re-reading values
nvalues = 0;
int iarg = 6;
while (iarg < narg) {
if ((strncmp(arg[iarg],"c_",2) == 0) ||
(strncmp(arg[iarg],"f_",2) == 0) ||
(strncmp(arg[iarg],"v_",2) == 0)) {
nvalues++;
iarg++;
} else break;
}
options(narg,arg);
// parse values until one isn't recognized
// if mode = VECTOR and value is a global array:
// expand it as if columns listed one by one
// adjust nvalues accordingly via maxvalues
which = argindex = value2index = offcol = NULL;
ids = NULL;
int maxvalues = nvalues;
allocate_values(maxvalues);
nvalues = 0;
iarg = 6;
while (iarg < narg) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal fix ave/time command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
delete [] suffix;
if (mode == VECTOR && which[nvalues] == COMPUTE &&
argindex[nvalues] == 0) {
int icompute = modify->find_compute(ids[nvalues]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/time does not exist");
if (modify->compute[icompute]->array_flag) {
int ncols = modify->compute[icompute]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols-1;
}
} else if (mode == VECTOR && which[nvalues] == FIX &&
argindex[nvalues] == 0) {
int ifix = modify->find_fix(ids[nvalues]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/time does not exist");
if (modify->fix[ifix]->array_flag) {
int ncols = modify->fix[ifix]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols-1;
}
}
nvalues++;
iarg++;
} else break;
}
// set off columns now that nvalues is finalized
for (int i = 0; i < nvalues; i++) offcol[i] = 0;
for (int i = 0; i < noff; i++) {
if (offlist[i] < 1 || offlist[i] > nvalues)
error->all(FLERR,"Invalid fix ave/time off column");
offcol[offlist[i]-1] = 1;
}
// setup and error check
// for fix inputs, check that fix frequency is acceptable
if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0)
error->all(FLERR,"Illegal fix ave/time command");
if (nfreq % nevery || (nrepeat-1)*nevery >= nfreq)
error->all(FLERR,"Illegal fix ave/time command");
if (ave != RUNNING && overwrite)
error->all(FLERR,"Illegal fix ave/time command");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE && mode == SCALAR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
error->all(FLERR,"Fix ave/time compute does not calculate a scalar");
if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
error->all(FLERR,"Fix ave/time compute does not calculate a vector");
if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
error->all(FLERR,
"Fix ave/time compute vector is accessed out-of-range");
} else if (which[i] == COMPUTE && mode == VECTOR) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0)
error->all(FLERR,"Fix ave/time compute does not calculate a vector");
if (argindex[i] && modify->compute[icompute]->array_flag == 0)
error->all(FLERR,"Fix ave/time compute does not calculate an array");
if (argindex[i] &&
argindex[i] > modify->compute[icompute]->size_array_cols)
error->all(FLERR,"Fix ave/time compute array is accessed out-of-range");
} else if (which[i] == FIX && mode == SCALAR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
error->all(FLERR,"Fix ave/time fix does not calculate a scalar");
if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
error->all(FLERR,"Fix ave/time fix does not calculate a vector");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
error->all(FLERR,"Fix ave/time fix vector is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all(FLERR,
"Fix for fix ave/time not computed at compatible time");
} else if (which[i] == FIX && mode == VECTOR) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/time does not exist");
if (argindex[i] == 0 && modify->fix[ifix]->vector_flag == 0)
error->all(FLERR,"Fix ave/time fix does not calculate a vector");
if (argindex[i] && modify->fix[ifix]->array_flag == 0)
error->all(FLERR,"Fix ave/time fix does not calculate an array");
if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols)
error->all(FLERR,"Fix ave/time fix array is accessed out-of-range");
if (nevery % modify->fix[ifix]->global_freq)
error->all(FLERR,
"Fix for fix ave/time not computed at compatible time");
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/time does not exist");
if (input->variable->equalstyle(ivariable) == 0)
error->all(FLERR,"Fix ave/time variable is not equal-style variable");
if (mode == VECTOR)
error->all(FLERR,"Fix ave/time cannot use variable with vector mode");
}
}
// if VECTOR mode, check that all columns are same length
// nrows = # of rows in output array
if (mode == VECTOR) {
int length;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (argindex[i] == 0) length = modify->compute[icompute]->size_vector;
else length = modify->compute[icompute]->size_array_rows;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (argindex[i] == 0) length = modify->fix[ifix]->size_vector;
else length = modify->fix[ifix]->size_array_rows;
}
if (i == 0) nrows = length;
else if (length != nrows)
error->all(FLERR,"Fix ave/time columns are inconsistent lengths");
}
column = new double[nrows];
} else column = NULL;
// print file comment lines
// for mode = VECTOR, cannot use arg to print
// since array args may have been expanded to multiple vectors
if (fp && me == 0) {
if (title1) fprintf(fp,"%s\n",title1);
else fprintf(fp,"# Time-averaged data for fix %s\n",id);
if (title2) fprintf(fp,"%s\n",title2);
else if (mode == SCALAR) {
fprintf(fp,"# TimeStep");
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[6+i]);
fprintf(fp,"\n");
} else fprintf(fp,"# TimeStep Number-of-rows\n");
if (title3 && mode == VECTOR) fprintf(fp,"%s\n",title3);
else if (mode == VECTOR) {
fprintf(fp,"# Row");
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
if (argindex[i]) fprintf(fp,"[%d]",argindex[i]);
}
fprintf(fp,"\n");
}
filepos = ftell(fp);
}
delete [] title1;
delete [] title2;
delete [] title3;
// allocate memory for averaging
vector = vector_total = NULL;
vector_list = NULL;
array = array_total = NULL;
array_list = NULL;
if (mode == SCALAR) {
vector = new double[nvalues];
vector_total = new double[nvalues];
if (ave == WINDOW)
memory->create(vector_list,nwindow,nvalues,"ave/time:vector_list");
} else {
memory->create(array,nrows,nvalues,"ave/time:array");
memory->create(array_total,nrows,nvalues,"ave/time:array_total");
if (ave == WINDOW)
memory->create(array_list,nwindow,nrows,nvalues,"ave/time:array_list");
}
// this fix produces either a global scalar or vector or array
// SCALAR mode produces either a scalar or vector
// VECTOR mode produces either a vector or array
// intensive/extensive flags set by compute,fix,variable that produces value
extlist = NULL;
if (mode == SCALAR) {
if (nvalues == 1) {
scalar_flag = 1;
if (which[0] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[0])];
if (argindex[0] == 0) extscalar = compute->extscalar;
else if (compute->extvector >= 0) extscalar = compute->extvector;
else extscalar = compute->extlist[argindex[0]-1];
} else if (which[0] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[0])];
if (argindex[0] == 0) extscalar = fix->extscalar;
else if (fix->extvector >= 0) extscalar = fix->extvector;
else extscalar = fix->extlist[argindex[0]-1];
} else if (which[0] == VARIABLE)
extscalar = 0;
} else {
vector_flag = 1;
size_vector = nvalues;
extvector = -1;
extlist = new int[nvalues];
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[i])];
if (argindex[i] == 0) extlist[i] = compute->extscalar;
else if (compute->extvector >= 0) extlist[i] = compute->extvector;
else extlist[i] = compute->extlist[argindex[i]-1];
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[i])];
if (argindex[i] == 0) extlist[i] = fix->extscalar;
else if (fix->extvector >= 0) extlist[i] = fix->extvector;
else extlist[i] = fix->extlist[argindex[i]-1];
} else if (which[i] == VARIABLE)
extlist[i] = 0;
}
}
} else {
if (nvalues == 1) {
vector_flag = 1;
size_vector = nrows;
if (which[0] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[0])];
if (argindex[0] == 0) {
extvector = compute->extvector;
if (extvector == -1) {
extlist = new int[nrows];
for (int i = 0; i < nrows; i++) extlist[i] = compute->extlist[i];
}
} else extvector = compute->extarray;
} else if (which[0] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[0])];
if (argindex[0] == 0) {
extvector = fix->extvector;
if (extvector == -1) {
extlist = new int[nrows];
for (int i = 0; i < nrows; i++) extlist[i] = fix->extlist[i];
}
} else extvector = fix->extarray;
}
} else {
array_flag = 1;
size_array_rows = nrows;
size_array_cols = nvalues;
int value;
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[modify->find_compute(ids[i])];
if (argindex[i] == 0) value = compute->extvector;
else value = compute->extarray;
} else if (which[i] == FIX) {
Fix *fix = modify->fix[modify->find_fix(ids[i])];
if (argindex[i] == 0) value = fix->extvector;
else value = fix->extarray;
}
if (value == -1)
error->all(FLERR,"Fix ave/time cannot set output array "
"intensive/extensive from these inputs");
if (i == 0) extarray = value;
else if (value != extarray)
error->all(FLERR,"Fix ave/time cannot set output array "
"intensive/extensive from these inputs");
}
}
}
// initializations
// set vector_total/array_total to zero since it accumulates
irepeat = 0;
iwindow = window_limit = 0;
norm = 0;
if (mode == SCALAR)
for (int i = 0; i < nvalues; i++) vector_total[i] = 0.0;
else
for (int i = 0; i < nrows; i++)
for (int j = 0; j < nvalues; j++) array_total[i][j] = 0.0;
// nvalid = next step on which end_of_step does something
// add nvalid to all computes that store invocation times
// since don't know a priori which are invoked by this fix
// once in end_of_step() can set timestep for ones actually invoked
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
/* ---------------------------------------------------------------------- */
FixAveTime::~FixAveTime()
{
memory->destroy(which);
memory->destroy(argindex);
memory->destroy(value2index);
memory->destroy(offcol);
for (int i = 0; i < nvalues; i++) delete [] ids[i];
memory->sfree(ids);
delete [] extlist;
if (fp && me == 0) fclose(fp);
delete [] vector;
delete [] vector_total;
delete [] column;
memory->destroy(array);
memory->destroy(array_total);
memory->destroy(array_list);
}
/* ---------------------------------------------------------------------- */
int FixAveTime::setmask()
{
int mask = 0;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixAveTime::init()
{
// set current indices for all computes,fixes,variables
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) {
int icompute = modify->find_compute(ids[i]);
if (icompute < 0)
error->all(FLERR,"Compute ID for fix ave/time does not exist");
value2index[i] = icompute;
} else if (which[i] == FIX) {
int ifix = modify->find_fix(ids[i]);
if (ifix < 0)
error->all(FLERR,"Fix ID for fix ave/time does not exist");
value2index[i] = ifix;
} else if (which[i] == VARIABLE) {
int ivariable = input->variable->find(ids[i]);
if (ivariable < 0)
error->all(FLERR,"Variable name for fix ave/time does not exist");
value2index[i] = ivariable;
}
}
// need to reset nvalid if nvalid < ntimestep b/c minimize was performed
if (nvalid < update->ntimestep) {
irepeat = 0;
nvalid = nextvalid();
modify->addstep_compute_all(nvalid);
}
}
/* ----------------------------------------------------------------------
only does something if nvalid = current timestep
------------------------------------------------------------------------- */
void FixAveTime::setup(int vflag)
{
end_of_step();
}
/* ---------------------------------------------------------------------- */
void FixAveTime::end_of_step()
{
// skip if not step which requires doing something
bigint ntimestep = update->ntimestep;
if (ntimestep != nvalid) return;
if (mode == SCALAR) invoke_scalar(ntimestep);
else invoke_vector(ntimestep);
}
/* ---------------------------------------------------------------------- */
void FixAveTime::invoke_scalar(bigint ntimestep)
{
int i,m;
double scalar;
// zero if first step
if (irepeat == 0)
for (i = 0; i < nvalues; i++) vector[i] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (i = 0; i < nvalues; i++) {
m = value2index[i];
// invoke compute if not previously invoked
if (which[i] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[i] == 0) {
if (!(compute->invoked_flag & INVOKED_SCALAR)) {
compute->compute_scalar();
compute->invoked_flag |= INVOKED_SCALAR;
}
scalar = compute->scalar;
} else {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
scalar = compute->vector[argindex[i]-1];
}
// access fix fields, guaranteed to be ready
} else if (which[i] == FIX) {
if (argindex[i] == 0)
scalar = modify->fix[m]->compute_scalar();
else
scalar = modify->fix[m]->compute_vector(argindex[i]-1);
// evaluate equal-style variable
} else if (which[i] == VARIABLE)
scalar = input->variable->compute_equal(m);
// add value to vector or just set directly if offcol is set
if (offcol[i]) vector[i] = scalar;
else vector[i] += scalar;
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep + nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nvalues; i++)
if (offcol[i] == 0) vector[i] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (i = 0; i < nvalues; i++) vector_total[i] = vector[i];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nvalues; i++) vector_total[i] += vector[i];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nvalues; i++) {
vector_total[i] += vector[i];
if (window_limit) vector_total[i] -= vector_list[iwindow][i];
vector_list[iwindow][i] = vector[i];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nvalues; i++)
if (offcol[i]) vector_total[i] = norm*vector[i];
// output result to file
if (fp && me == 0) {
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT,ntimestep);
for (i = 0; i < nvalues; i++) fprintf(fp," %g",vector_total[i]/norm);
fprintf(fp,"\n");
fflush(fp);
if (overwrite) {
long fileend = ftell(fp);
ftruncate(fileno(fp),fileend);
}
}
}
/* ---------------------------------------------------------------------- */
void FixAveTime::invoke_vector(bigint ntimestep)
{
int i,j,m;
// zero if first step
if (irepeat == 0)
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array[i][j] = 0.0;
// accumulate results of computes,fixes,variables to local copy
// compute/fix/variable may invoke computes so wrap with clear/add
modify->clearstep_compute();
for (j = 0; j < nvalues; j++) {
m = value2index[j];
// invoke compute if not previously invoked
if (which[j] == COMPUTE) {
Compute *compute = modify->compute[m];
if (argindex[j] == 0) {
if (!(compute->invoked_flag & INVOKED_VECTOR)) {
compute->compute_vector();
compute->invoked_flag |= INVOKED_VECTOR;
}
double *cvector = compute->vector;
for (i = 0; i < nrows; i++)
column[i] = cvector[i];
} else {
if (!(compute->invoked_flag & INVOKED_ARRAY)) {
compute->compute_array();
compute->invoked_flag |= INVOKED_ARRAY;
}
double **carray = compute->array;
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = carray[i][icol];
}
// access fix fields, guaranteed to be ready
} else if (which[j] == FIX) {
Fix *fix = modify->fix[m];
if (argindex[j] == 0)
for (i = 0; i < nrows; i++)
column[i] = fix->compute_vector(i);
else {
int icol = argindex[j]-1;
for (i = 0; i < nrows; i++)
column[i] = fix->compute_array(i,icol);
}
}
// add columns of values to array or just set directly if offcol is set
if (offcol[j]) {
for (i = 0; i < nrows; i++)
array[i][j] = column[i];
} else {
for (i = 0; i < nrows; i++)
array[i][j] += column[i];
}
}
// done if irepeat < nrepeat
// else reset irepeat and nvalid
irepeat++;
if (irepeat < nrepeat) {
nvalid += nevery;
modify->addstep_compute(nvalid);
return;
}
irepeat = 0;
nvalid = ntimestep+nfreq - (nrepeat-1)*nevery;
modify->addstep_compute(nvalid);
// average the final result for the Nfreq timestep
double repeat = nrepeat;
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j] == 0) array[i][j] /= repeat;
// if ave = ONE, only single Nfreq timestep value is needed
// if ave = RUNNING, combine with all previous Nfreq timestep values
// if ave = WINDOW, combine with nwindow most recent Nfreq timestep values
if (ave == ONE) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] = array[i][j];
norm = 1;
} else if (ave == RUNNING) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) array_total[i][j] += array[i][j];
norm++;
} else if (ave == WINDOW) {
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++) {
array_total[i][j] += array[i][j];
if (window_limit) array_total[i][j] -= array_list[iwindow][i][j];
array_list[iwindow][i][j] = array[i][j];
}
iwindow++;
if (iwindow == nwindow) {
iwindow = 0;
window_limit = 1;
}
if (window_limit) norm = nwindow;
else norm = iwindow;
}
// insure any columns with offcol set are effectively set to last value
for (i = 0; i < nrows; i++)
for (j = 0; j < nvalues; j++)
if (offcol[j]) array_total[i][j] = norm*array[i][j];
// output result to file
if (fp && me == 0) {
if (overwrite) fseek(fp,filepos,SEEK_SET);
fprintf(fp,BIGINT_FORMAT " %d\n",ntimestep,nrows);
for (i = 0; i < nrows; i++) {
fprintf(fp,"%d",i+1);
for (j = 0; j < nvalues; j++) fprintf(fp," %g",array_total[i][j]/norm);
fprintf(fp,"\n");
}
fflush(fp);
}
}
/* ----------------------------------------------------------------------
return scalar value
------------------------------------------------------------------------- */
double FixAveTime::compute_scalar()
{
if (norm) return vector_total[0]/norm;
return 0.0;
}
/* ----------------------------------------------------------------------
return Ith vector value
------------------------------------------------------------------------- */
double FixAveTime::compute_vector(int i)
{
if (norm) {
if (mode == SCALAR) return vector_total[i]/norm;
if (mode == VECTOR) return array_total[i][0];
}
return 0.0;
}
/* ----------------------------------------------------------------------
return I,J array value
------------------------------------------------------------------------- */
double FixAveTime::compute_array(int i, int j)
{
if (norm) return array_total[i][j]/norm;
return 0.0;
}
/* ----------------------------------------------------------------------
parse optional args
------------------------------------------------------------------------- */
void FixAveTime::options(int narg, char **arg)
{
// option defaults
fp = NULL;
ave = ONE;
startstep = 0;
mode = SCALAR;
noff = 0;
offlist = NULL;
overwrite = 0;
title1 = NULL;
title2 = NULL;
title3 = NULL;
// optional args
int iarg = 6 + nvalues;
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (me == 0) {
fp = fopen(arg[iarg+1],"w");
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open fix ave/time file %s",arg[iarg+1]);
error->one(FLERR,str);
}
}
iarg += 2;
} else if (strcmp(arg[iarg],"ave") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (strcmp(arg[iarg+1],"one") == 0) ave = ONE;
else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING;
else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW;
else error->all(FLERR,"Illegal fix ave/time command");
if (ave == WINDOW) {
if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/time command");
nwindow = force->inumeric(FLERR,arg[iarg+2]);
if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/time command");
}
iarg += 2;
if (ave == WINDOW) iarg++;
} else if (strcmp(arg[iarg],"start") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
startstep = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"mode") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
if (strcmp(arg[iarg+1],"scalar") == 0) mode = SCALAR;
else if (strcmp(arg[iarg+1],"vector") == 0) mode = VECTOR;
else error->all(FLERR,"Illegal fix ave/time command");
iarg += 2;
} else if (strcmp(arg[iarg],"off") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");
memory->grow(offlist,noff+1,"ave/time:offlist");
offlist[noff++] = force->inumeric(FLERR,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"overwrite") == 0) {
overwrite = 1;
iarg += 1;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
delete [] title1;
int n = strlen(arg[iarg+1]) + 1;
title1 = new char[n];
strcpy(title1,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title2") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
delete [] title2;
int n = strlen(arg[iarg+1]) + 1;
title2 = new char[n];
strcpy(title2,arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title3") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/spatial command");
delete [] title3;
int n = strlen(arg[iarg+1]) + 1;
title3 = new char[n];
strcpy(title3,arg[iarg+1]);
iarg += 2;
} else error->all(FLERR,"Illegal fix ave/time command");
}
}
/* ----------------------------------------------------------------------
reallocate vectors for each input value, of length N
------------------------------------------------------------------------- */
void FixAveTime::allocate_values(int n)
{
memory->grow(which,n,"ave/time:which");
memory->grow(argindex,n,"ave/time:argindex");
memory->grow(value2index,n,"ave/time:value2index");
memory->grow(offcol,n,"ave/time:offcol");
ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/time:ids");
}
/* ----------------------------------------------------------------------
calculate nvalid = next step on which end_of_step does something
can be this timestep if multiple of nfreq and nrepeat = 1
else backup from next multiple of nfreq
startstep is lower bound on nfreq multiple
------------------------------------------------------------------------- */
bigint FixAveTime::nextvalid()
{
bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq;
while (nvalid < startstep) nvalid += nfreq;
if (nvalid-nfreq == update->ntimestep && nrepeat == 1)
nvalid = update->ntimestep;
else
nvalid -= (nrepeat-1)*nevery;
if (nvalid < update->ntimestep) nvalid += nfreq;
return nvalid;
}
/* ---------------------------------------------------------------------- */
void FixAveTime::reset_timestep(bigint ntimestep)
{
if (ntimestep > nvalid) error->all(FLERR,"Fix ave/time missed timestep");
}
diff --git a/src/fix_vector.cpp b/src/fix_vector.cpp
new file mode 100644
index 000000000..5e2ae4b56
--- /dev/null
+++ b/src/fix_vector.cpp
@@ -0,0 +1,319 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+ Contributing author: Pieter in 't Veld (SNL)
+------------------------------------------------------------------------- */
+
+#include "string.h"
+#include "fix_vector.h"
+#include "update.h"
+#include "force.h"
+#include "modify.h"
+#include "compute.h"
+#include "group.h"
+#include "input.h"
+#include "variable.h"
+#include "memory.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+enum{COMPUTE,FIX,VARIABLE};
+enum{ONE,RUNNING,WINDOW};
+enum{SCALAR,VECTOR};
+
+#define INVOKED_SCALAR 1
+#define INVOKED_VECTOR 2
+#define INVOKED_ARRAY 4
+
+/* ---------------------------------------------------------------------- */
+
+FixVector::FixVector(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg)
+{
+ if (narg < 5) error->all(FLERR,"Illegal fix vector command");
+
+ nevery = force->inumeric(FLERR,arg[3]);
+ if (nevery <= 0) error->all(FLERR,"Illegal fix vector command");
+
+ nvalues = narg-4;
+ which = new int[nvalues];
+ argindex = new int[nvalues];
+ value2index = new int[nvalues];
+ ids = new char*[nvalues];
+
+ nvalues = 0;
+ for (int iarg = 4; iarg < narg; iarg++) {
+ if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
+ else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
+ else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
+ else error->all(FLERR,"Illegal fix vector command");
+
+ int n = strlen(arg[iarg]);
+ char *suffix = new char[n];
+ strcpy(suffix,&arg[iarg][2]);
+
+ char *ptr = strchr(suffix,'[');
+ if (ptr) {
+ if (suffix[strlen(suffix)-1] != ']')
+ error->all(FLERR,"Illegal fix vector command");
+ argindex[nvalues] = atoi(ptr+1);
+ *ptr = '\0';
+ } else argindex[nvalues] = 0;
+
+ n = strlen(suffix) + 1;
+ ids[nvalues] = new char[n];
+ strcpy(ids[nvalues],suffix);
+ delete [] suffix;
+
+ nvalues++;
+ }
+
+ // setup and error check
+ // for fix inputs, check that fix frequency is acceptable
+
+ for (int i = 0; i < nvalues; i++) {
+ if (which[i] == COMPUTE) {
+ int icompute = modify->find_compute(ids[i]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for fix vector does not exist");
+ if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0)
+ error->all(FLERR,"Fix vector compute does not calculate a scalar");
+ if (argindex[i] && modify->compute[icompute]->vector_flag == 0)
+ error->all(FLERR,"Fix vector compute does not calculate a vector");
+ if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector)
+ error->all(FLERR,
+ "Fix vector compute vector is accessed out-of-range");
+
+ } else if (which[i] == FIX) {
+ int ifix = modify->find_fix(ids[i]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix vector does not exist");
+ if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0)
+ error->all(FLERR,"Fix vector fix does not calculate a scalar");
+ if (argindex[i] && modify->fix[ifix]->vector_flag == 0)
+ error->all(FLERR,"Fix vector fix does not calculate a vector");
+ if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector)
+ error->all(FLERR,"Fix vector fix vector is accessed out-of-range");
+ if (nevery % modify->fix[ifix]->global_freq)
+ error->all(FLERR,
+ "Fix for fix vector not computed at compatible time");
+
+ } else if (which[i] == VARIABLE) {
+ int ivariable = input->variable->find(ids[i]);
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix vector does not exist");
+ if (input->variable->equalstyle(ivariable) == 0)
+ error->all(FLERR,"Fix vector variable is not equal-style variable");
+ }
+ }
+
+ // this fix produces either a global vector or array
+ // intensive/extensive flags set by compute,fix,variable that produces value
+
+ int value,finalvalue;
+ for (int i = 0; i < nvalues; i++) {
+ if (which[i] == COMPUTE) {
+ Compute *compute = modify->compute[modify->find_compute(ids[i])];
+ if (argindex[0] == 0) value = compute->extscalar;
+ else if (compute->extvector >= 0) value = compute->extvector;
+ else value = compute->extlist[argindex[0]-1];
+ } else if (which[i] == FIX) {
+ Fix *fix = modify->fix[modify->find_fix(ids[i])];
+ if (argindex[i] == 0) value = fix->extvector;
+ else value = fix->extarray;
+ } else if (which[i] == VARIABLE) value = 0;
+ if (i == 0) finalvalue = value;
+ else if (value != finalvalue)
+ error->all(FLERR,"Fix vector cannot set output array "
+ "intensive/extensive from these inputs");
+ }
+
+ if (nvalues == 1) {
+ vector_flag = 1;
+ extvector = finalvalue;
+ } else {
+ array_flag = 1;
+ size_array_cols = nvalues;
+ extarray = finalvalue;
+ }
+
+ global_freq = nevery;
+
+ // ncount = current size of vector or array
+
+ vector = NULL;
+ array = NULL;
+ ncount = 0;
+ if (nvalues == 1) size_vector = 0;
+ else size_array_rows = 0;
+
+ // nextstep = next step on which end_of_step does something
+ // add nextstep to all computes that store invocation times
+ // since don't know a priori which are invoked by this fix
+ // once in end_of_step() can set timestep for ones actually invoked
+
+ bigint nextstep = (update->ntimestep/nevery)*nevery;
+ if (nextstep < update->ntimestep) nextstep += nevery;
+ modify->addstep_compute_all(nextstep);
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixVector::~FixVector()
+{
+ delete [] which;
+ delete [] argindex;
+ delete [] value2index;
+ for (int i = 0; i < nvalues; i++) delete [] ids[i];
+ delete [] ids;
+
+ memory->destroy(vector);
+ memory->destroy(array);
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixVector::setmask()
+{
+ int mask = 0;
+ mask |= END_OF_STEP;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixVector::init()
+{
+ // set current indices for all computes,fixes,variables
+
+ for (int i = 0; i < nvalues; i++) {
+ if (which[i] == COMPUTE) {
+ int icompute = modify->find_compute(ids[i]);
+ if (icompute < 0)
+ error->all(FLERR,"Compute ID for fix vector does not exist");
+ value2index[i] = icompute;
+
+ } else if (which[i] == FIX) {
+ int ifix = modify->find_fix(ids[i]);
+ if (ifix < 0)
+ error->all(FLERR,"Fix ID for fix vector does not exist");
+ value2index[i] = ifix;
+
+ } else if (which[i] == VARIABLE) {
+ int ivariable = input->variable->find(ids[i]);
+ if (ivariable < 0)
+ error->all(FLERR,"Variable name for fix vector does not exist");
+ value2index[i] = ivariable;
+ }
+ }
+
+ // reallocate vector or array for size at end of run
+
+ int nsize = (update->laststep-update->firststep+1) / nevery;
+ if (nvalues == 1) memory->grow(vector,ncount+nsize,"vector:vector");
+ else memory->grow(array,ncount+nsize,nvalues,"vector:array");
+}
+
+/* ----------------------------------------------------------------------
+ only does something if nvalid = current timestep
+------------------------------------------------------------------------- */
+
+void FixVector::setup(int vflag)
+{
+ end_of_step();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixVector::end_of_step()
+{
+ // skip if not step which requires doing something
+
+ if (update->ntimestep % nevery) return;
+
+ // accumulate results of computes,fixes,variables to local copy
+ // compute/fix/variable may invoke computes so wrap with clear/add
+
+ double *result;
+ if (nvalues == 1) result = &vector[ncount];
+ else result = array[ncount];
+
+ modify->clearstep_compute();
+
+ for (int i = 0; i < nvalues; i++) {
+ int m = value2index[i];
+
+ // invoke compute if not previously invoked
+
+ if (which[i] == COMPUTE) {
+ Compute *compute = modify->compute[m];
+
+ if (argindex[i] == 0) {
+ if (!(compute->invoked_flag & INVOKED_SCALAR)) {
+ compute->compute_scalar();
+ compute->invoked_flag |= INVOKED_SCALAR;
+ }
+ result[i] = compute->scalar;
+ } else {
+ if (!(compute->invoked_flag & INVOKED_VECTOR)) {
+ compute->compute_vector();
+ compute->invoked_flag |= INVOKED_VECTOR;
+ }
+ result[i] = compute->vector[argindex[i]-1];
+ }
+
+ // access fix fields, guaranteed to be ready
+
+ } else if (which[i] == FIX) {
+ if (argindex[i] == 0)
+ result[i] = modify->fix[m]->compute_scalar();
+ else
+ result[i] = modify->fix[m]->compute_vector(argindex[i]-1);
+
+ // evaluate equal-style variable
+
+ } else if (which[i] == VARIABLE)
+ result[i] = input->variable->compute_equal(m);
+ }
+
+ // trigger computes on next needed step
+
+ modify->addstep_compute(update->ntimestep + nevery);
+
+ // update size of vector or array
+
+ ncount++;
+ if (nvalues == 1) size_vector++;
+ else size_array_rows++;
+}
+
+/* ----------------------------------------------------------------------
+ return Ith vector value
+------------------------------------------------------------------------- */
+
+double FixVector::compute_vector(int i)
+{
+ return vector[i];
+}
+
+/* ----------------------------------------------------------------------
+ return I,J array value
+------------------------------------------------------------------------- */
+
+double FixVector::compute_array(int i, int j)
+{
+ return array[i][j];
+}
diff --git a/src/fix_vector.h b/src/fix_vector.h
new file mode 100644
index 000000000..4bfed79e0
--- /dev/null
+++ b/src/fix_vector.h
@@ -0,0 +1,151 @@
+/* ----------------------------------------------------------------------
+ LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+ http://lammps.sandia.gov, Sandia National Laboratories
+ Steve Plimpton, sjplimp@sandia.gov
+
+ Copyright (2003) Sandia Corporation. Under the terms of Contract
+ DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+ certain rights in this software. This software is distributed under
+ the GNU General Public License.
+
+ See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(vector,FixVector)
+
+#else
+
+#ifndef LMP_FIX_VECTOR_H
+#define LMP_FIX_VECTOR_H
+
+#include "stdio.h"
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixVector : public Fix {
+ public:
+ FixVector(class LAMMPS *, int, char **);
+ ~FixVector();
+ int setmask();
+ void init();
+ void setup(int);
+ void end_of_step();
+ double compute_vector(int);
+ double compute_array(int,int);
+
+ private:
+ int nvalues;
+ int *which,*argindex,*value2index,*offcol;
+ char **ids;
+
+ int ncount; // # of values currently in growing vector or array
+ double *vector;
+ double **array;
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Illegal ... command
+
+Self-explanatory. Check the input script syntax and compare to the
+documentation for the command. You can use -echo screen as a
+command-line option when running LAMMPS to see the offending line.
+
+E: Compute ID for fix ave/time does not exist
+
+Self-explanatory.
+
+E: Fix ID for fix ave/time does not exist
+
+Self-explanatory.
+
+E: Invalid fix ave/time off column
+
+Self-explantory.
+
+E: Fix ave/time compute does not calculate a scalar
+
+Self-explantory.
+
+E: Fix ave/time compute does not calculate a vector
+
+Self-explantory.
+
+E: Fix ave/time compute vector is accessed out-of-range
+
+The index for the vector is out of bounds.
+
+E: Fix ave/time compute does not calculate an array
+
+Self-explanatory.
+
+E: Fix ave/time compute array is accessed out-of-range
+
+An index for the array is out of bounds.
+
+E: Fix ave/time fix does not calculate a scalar
+
+Self-explanatory.
+
+E: Fix ave/time fix does not calculate a vector
+
+Self-explanatory.
+
+E: Fix ave/time fix vector is accessed out-of-range
+
+The index for the vector is out of bounds.
+
+E: Fix for fix ave/time not computed at compatible time
+
+Fixes generate their values on specific timesteps. Fix ave/time
+is requesting a value on a non-allowed timestep.
+
+E: Fix ave/time fix does not calculate an array
+
+Self-explanatory.
+
+E: Fix ave/time fix array is accessed out-of-range
+
+An index for the array is out of bounds.
+
+E: Variable name for fix ave/time does not exist
+
+Self-explanatory.
+
+E: Fix ave/time variable is not equal-style variable
+
+Self-explanatory.
+
+E: Fix ave/time cannot use variable with vector mode
+
+Variables produce scalar values.
+
+E: Fix ave/time columns are inconsistent lengths
+
+Self-explanatory.
+
+E: Fix ave/time cannot set output array intensive/extensive from these inputs
+
+One of more of the vector inputs has individual elements which are
+flagged as intensive or extensive. Such an input cannot be flagged as
+all intensive/extensive when turned into an array by fix ave/time.
+
+E: Cannot open fix ave/time file %s
+
+The specified file cannot be opened. Check that the path and name are
+correct.
+
+E: Fix ave/time missed timestep
+
+You cannot reset the timestep to a value beyond where the fix
+expects to next perform averaging.
+
+*/
diff --git a/src/version.h b/src/version.h
index 1cac5f59e..6d0926922 100644
--- a/src/version.h
+++ b/src/version.h
@@ -1 +1 @@
-#define LAMMPS_VERSION "1 Feb 2014"
+#define LAMMPS_VERSION "6 Feb 2014"
diff --git a/tools/moltemplate/common/amber/amberparm2lt.sh b/tools/moltemplate/common/amber/amberparm2lt.sh
index 314f21150..d27897a7b 100755
--- a/tools/moltemplate/common/amber/amberparm2lt.sh
+++ b/tools/moltemplate/common/amber/amberparm2lt.sh
@@ -1,193 +1,203 @@
#!/bin/sh
if ! which amberparm_mass_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_mass_to_lt.py\" not found. (Update your PATH?)\n" >&2
exit 2
fi
if ! which amberparm_pair_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_pair_to_lt.py\" not found. (Update your PATH?)\n" >&2
exit 2
fi
if ! which amberparm_bond_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_bond_to_lt.py\" not found. (Update your PATH?)\n" >&2
exit 2
fi
if ! which amberparm_angle_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_angle_to_lt.py\" not found. (Update your PATH?)\n" >&2
exit 2
fi
if ! which amberparm_dihedral_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_dihedral_to_lt.py\" not found. (Update your PATH?)\n" >&2
exit 2
fi
if ! which amberparm_improper_to_lt.py > /dev/null; then
echo "\nError: \"amberparm_improper_to_lt.py\" not found. (Update your PATH?)\n" >&2
exit 2
fi
SYNTAX_MSG=$(cat <<EOF
Typical Usage:
amberparm2lt.sh gaff.dat GAFF > gaff.lt
You can also try:
amberparm2lt.sh parm94.dat "AMBERFF94 inherits GAFF" > amberff94.lt
(However, this later usage may not work.
You may need to manually split the .dat file and run these scripts instead:
amberparm_pair_to_lt.py, amberparm_bond_to_lt.py, amberparm_angle_to_lt.py...)
Be sure that all of these .py files are in your PATH as well.)
EOF
)
if [ "$#" != "2" ]; then
echo "${SYNTAX_MSG}" >&2
echo "" >&2
echo "Error: This script requires two arguments," >&2
echo " 1) the name of the amber parm file to be converted (eg \"gaff.dat\")" >&2
echo " 2) the name of the moltemplate object to be created (eg \"GAFF\")" >&2
echo " (This may include the \"inherits\" keyword and parent classes.)" >&2
exit 1
fi
MOLTEMPLATE_USAGE_MSG=$(cat <<EOF
# Background information and usage explanation:
# This file contanis a list of atom types and rules for generating bonded
# interactions between these atoms (hopefully) according to AMBER conventions.
# By using the atom types shown below in your own molecules, bonds and angular
# interactions will be automatically generated.
# AMBER (GAFF) force-field parameters will also be assigned to each angle
# interaction (according to these atom types).
# One way to apply the GAFF force field to a particular type of molecule, is
# to use the "inherits" keyword when you define that molecule. For example:
# import("gaff.lt")
# MoleculeType inherits GAFF {
# write_once("Data Atoms") {
# \$atom:C1 \$mol:... @atom:cx 0.0 4.183 3.194 13.285
# \$atom:C2 \$mol:... @atom:cx 0.0 4.291 4.618 13.382
# : : :
# }
# }
#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.)
EOF
)
# (Note that the full name of the atom type in this example is "@atom:/GAFF/cx"
# You can always refer to atom types this way as well. Using "inherits GAFF"
# allows you to use more conventient "@atom:cx" shorthand notation instead.)
echo "####################################################################"
echo "# To use this, LAMMPS currently must be compiled with the USER-MISC package."
echo "# (Type \"make yes-user-misc\" into the shell before compiling LAMMPS.)"
echo "####################################################################"
echo "# This moltemplate (LT) file was generated automatically using"
echo "# amberparm2lt.sh $1 $2"
echo "####################################################################"
echo "$MOLTEMPLATE_USAGE_MSG"
echo "####################################################################"
echo "# Moltemplate can not assign atom charge. You must assign atomic"
echo "# charges yourself. (Moltemplate is only a simple text manipulation tool.)"
echo "####################################################################"
echo ""
echo ""
#PARM_FILE='gaff.dat'
PARM_FILE=$1
# sections are separated by blank lines
# some sections have comment lines at the beginning
# The 1st section is the mass (note: skip the first line)
tail -n +2 < "$PARM_FILE" | \
awk -v n=1 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
> "${PARM_FILE}.mass"
# The 2nd section has the list of 2-body bond force-field params
awk -v n=2 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
| tail -n +2 \
> "${PARM_FILE}.bond"
# The 3rd section has the list of 3-body angle force-field params
awk -v n=3 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
> "${PARM_FILE}.angle"
# The 4th section has the list of 4-body dihedral force-field params
awk -v n=4 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
> "${PARM_FILE}.dihedral"
# The 5th section has the list of 4-body improper force-field params
awk -v n=5 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
> "${PARM_FILE}.improper"
# The 6th section has the hbond-parameters (no-longer used. ignore)
awk -v n=6 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
> "${PARM_FILE}.hbond"
# The 7th "section" is just a blank line. (skip that)
# The 8th section has the list of non-bonded ("pair") force-field parameters
awk -v n=8 '{if (NF==0) nblanks++; else {if (nblanks+1==n) print $0}}' \
< "$PARM_FILE" \
| tail -n +2 \
> "${PARM_FILE}.pair"
amberparm_mass_to_lt.py < "${PARM_FILE}.mass" > "${PARM_FILE}.mass.lt"
amberparm_pair_to_lt.py < "${PARM_FILE}.pair" > "${PARM_FILE}.pair.lt"
amberparm_bond_to_lt.py < "${PARM_FILE}.bond" > "${PARM_FILE}.bond.lt"
amberparm_angle_to_lt.py < "${PARM_FILE}.angle" > "${PARM_FILE}.angle.lt"
amberparm_dihedral_to_lt.py \
< "${PARM_FILE}.dihedral" > "${PARM_FILE}.dihedral.lt"
amberparm_improper_to_lt.py \
< "${PARM_FILE}.improper" > "${PARM_FILE}.improper.lt"
echo "$2 {"
echo ""
echo " # ----------------------------------------------------------------------"
#echo " # This file was automatically generated by \"common/amber/amberparm2lt.sh\""
echo " # The basic atom nomenclature and conventions are explained here:"
echo " # http://ambermd.org/antechamber/gaff.pdf"
echo " # For reference, the original gaff.dat file and format documenation are here:"
echo " # http://ambermd.org/AmberTools-get.html"
echo " # http://ambermd.org/formats.html#parm.dat"
echo " # ----------------------------------------------------------------------"
echo ""
cat "$PARM_FILE.mass.lt" \
"$PARM_FILE.pair.lt" \
"$PARM_FILE.bond.lt" \
"$PARM_FILE.angle.lt" \
"$PARM_FILE.dihedral.lt" \
"$PARM_FILE.improper.lt"
AMBER_STYLES_INIT=$(cat <<EOF
write_once("In Init") {
# Default styles and settings for AMBER based force-fields:
units real
atom_style full
bond_style hybrid harmonic
angle_style hybrid harmonic
dihedral_style hybrid fourier
improper_style hybrid cvff
- pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
- kspace_style pppm 0.0001
- # If long-range coulombic forces are not needed, replace the previous two
- # lines with "pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 10.0"
+ pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
+
+ # NOTE: Long-range coulombic forces were disabled intentionally. (See below)
+ # If you want to use long-range electrostatics, uncomment these lines:
+ #
+ #pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
+ #kspace_style pppm 0.0001
+ #
+ # Instead I use hybrid lj/charmm/coul/charmm by default, because
+ # LAMMPS complains if you attempt to use lj/charmm/coul/long on a
+ # system if it does not contain any charged particles.
+ # Currently, moltemplate does not assign atomic charge,
+ # so this problem occurs frequently.
+
pair_modify mix arithmetic
special_bonds amber
}
EOF
)
echo "$AMBER_STYLES_INIT"
echo ""
echo "}"
echo ""
echo ""
diff --git a/tools/moltemplate/common/amber/amberparm_pair_to_lt.py b/tools/moltemplate/common/amber/amberparm_pair_to_lt.py
index 4ed9defdb..3bb9ddea5 100755
--- a/tools/moltemplate/common/amber/amberparm_pair_to_lt.py
+++ b/tools/moltemplate/common/amber/amberparm_pair_to_lt.py
@@ -1,20 +1,31 @@
#!/usr/bin/env python
import sys
lines_gaff = sys.stdin.readlines()
-pair_style = 'lj/charmm/coul/long'
+
+#pair_style = 'lj/charmm/coul/long'
+
+ # NOTE: Long-range coulombic forces were disabled intentionally. (See below)
+ # If you want to use long-range electrostatics, uncomment these lines:
+ # Instead I use hybrid lj/charmm/coul/charmm by default, because
+ # LAMMPS complains if you attempt to use lj/charmm/coul/long on a
+ # system if it does not contain any charged particles.
+ # Currently, moltemplate does not assign atomic charge,
+ # so this problem occurs frequently.
+
+pair_style = 'lj/charmm/coul/charmm'
sys.stdout.write(' write_once(\"In Settings\") {\n')
for i in range(0, len(lines_gaff)):
line = lines_gaff[i]
tokens= line.split()
atype = tokens[0]
sig=tokens[1]
eps=tokens[2]
comments=' '.join(tokens[3:])
sys.stdout.write(' pair_coeff @atom:'+atype+' @atom:'+atype+' '+pair_style+' '+eps+' '+sig+' # '+comments+'\n')
sys.stdout.write(' } # (end of pair_coeffs)\n')
sys.stdout.write('\n')
diff --git a/tools/moltemplate/common/gaff.lt b/tools/moltemplate/common/gaff.lt
index 4361abf35..16d002081 100644
--- a/tools/moltemplate/common/gaff.lt
+++ b/tools/moltemplate/common/gaff.lt
@@ -1,11383 +1,11393 @@
-# This is the January 2013 version of gaff from AmberTools13.
+# This is the January 2013 version of GAFF (from AmberTools13).
####################################################################
# To use this, LAMMPS currently must be compiled with the USER-MISC package.
# (Type "make yes-user-misc" into the shell before compiling LAMMPS.)
####################################################################
# This moltemplate (LT) file was generated automatically using
# amberparm2lt.sh gaff.dat GAFF
####################################################################
# Background information and usage explanation:
# This file contanis a list of atom types and rules for generating bonded
# interactions between these atoms (hopefully) according to AMBER conventions.
# By using the atom types shown below in your own molecules, bonds and angular
# interactions will be automatically generated.
# AMBER (GAFF) force-field parameters will also be assigned to each angle
# interaction (according to these atom types).
# One way to apply the GAFF force field to a particular type of molecule, is
# to use the "inherits" keyword when you define that molecule. For example:
# import("gaff.lt")
# MoleculeType inherits GAFF {
# write_once("Data Atoms") {
# $atom:C1 $mol:... @atom:cx 0.0 4.183 3.194 13.285
# $atom:C2 $mol:... @atom:cx 0.0 4.291 4.618 13.382
# : : :
# }
# }
#(See "Inheritance" and "short names vs. full names" in the moltemplate manual.)
####################################################################
# Moltemplate can not assign atom charge. You must assign atomic
# charges yourself. (Moltemplate is only a simple text manipulation tool.)
####################################################################
GAFF {
# ----------------------------------------------------------------------
# The basic atom nomenclature and conventions are explained here:
# http://ambermd.org/antechamber/gaff.pdf
# For reference, the original gaff.dat file and format documenation are here:
# http://ambermd.org/AmberTools-get.html
# http://ambermd.org/formats.html#parm.dat
# ----------------------------------------------------------------------
write_once("Data Masses") {
@atom:c 12.01 # Sp2 C carbonyl group
@atom:c1 12.01 # Sp C
@atom:c2 12.01 # Sp2 C
@atom:c3 12.01 # Sp3 C
@atom:ca 12.01 # Sp2 C in pure aromatic systems
@atom:cp 12.01 # Head Sp2 C that connect two rings in biphenyl sys.
@atom:cq 12.01 # Head Sp2 C that connect two rings in biphenyl sys. identical to cp
@atom:cc 12.01 # Sp2 carbons in non-pure aromatic systems
@atom:cd 12.01 # Sp2 carbons in non-pure aromatic systems, identical to cc
@atom:ce 12.01 # Inner Sp2 carbons in conjugated systems
@atom:cf 12.01 # Inner Sp2 carbons in conjugated systems, identical to ce
@atom:cg 12.01 # Inner Sp carbons in conjugated systems
@atom:ch 12.01 # Inner Sp carbons in conjugated systems, identical to cg
@atom:cx 12.01 # Sp3 carbons in triangle systems
@atom:cy 12.01 # Sp3 carbons in square systems
@atom:cu 12.01 # Sp2 carbons in triangle systems
@atom:cv 12.01 # Sp2 carbons in square systems
@atom:cz 12.01 # Sp2 carbon in guanidine group
@atom:h1 1.008 # H bonded to aliphatic carbon with 1 electrwd. group
@atom:h2 1.008 # H bonded to aliphatic carbon with 2 electrwd. group
@atom:h3 1.008 # H bonded to aliphatic carbon with 3 electrwd. group
@atom:h4 1.008 # H bonded to non-sp3 carbon with 1 electrwd. group
@atom:h5 1.008 # H bonded to non-sp3 carbon with 2 electrwd. group
@atom:ha 1.008 # H bonded to aromatic carbon
@atom:hc 1.008 # H bonded to aliphatic carbon without electrwd. group
@atom:hn 1.008 # H bonded to nitrogen atoms
@atom:ho 1.008 # Hydroxyl group
@atom:hp 1.008 # H bonded to phosphate
@atom:hs 1.008 # Hydrogen bonded to sulphur
@atom:hw 1.008 # Hydrogen in water
@atom:hx 1.008 # H bonded to C next to positively charged group
@atom:f 19.00 # Fluorine
@atom:cl 35.45 # Chlorine
@atom:br 79.90 # Bromine
@atom:i 126.9 # Iodine
@atom:n 14.01 # Sp2 nitrogen in amide groups
@atom:n1 14.01 # Sp N
@atom:n2 14.01 # aliphatic Sp2 N with two connected atoms
@atom:n3 14.01 # Sp3 N with three connected atoms
@atom:n4 14.01 # Sp3 N with four connected atoms
@atom:na 14.01 # Sp2 N with three connected atoms
@atom:nb 14.01 # Sp2 N in pure aromatic systems
@atom:nc 14.01 # Sp2 N in non-pure aromatic systems
@atom:nd 14.01 # Sp2 N in non-pure aromatic systems, identical to nc
@atom:ne 14.01 # Inner Sp2 N in conjugated systems
@atom:nf 14.01 # Inner Sp2 N in conjugated systems, identical to ne
@atom:nh 14.01 # Amine N connected one or more aromatic rings
@atom:no 14.01 # Nitro N
@atom:o 16.00 # Oxygen with one connected atom
@atom:oh 16.00 # Oxygen in hydroxyl group
@atom:os 16.00 # Ether and ester oxygen
@atom:ow 16.00 # Oxygen in water
@atom:p2 30.97 # Phosphate with two connected atoms
@atom:p3 30.97 # Phosphate with three connected atoms, such as PH3
@atom:p4 30.97 # Phosphate with three connected atoms, such as O=P(CH3)2
@atom:p5 30.97 # Phosphate with four connected atoms, such as O=P(OH)3
@atom:pb 30.97 # Sp2 P in pure aromatic systems
@atom:pc 30.97 # Sp2 P in non-pure aromatic systems
@atom:pd 30.97 # Sp2 P in non-pure aromatic systems, identical to pc
@atom:pe 30.97 # Inner Sp2 P in conjugated systems
@atom:pf 30.97 # Inner Sp2 P in conjugated systems, identical to pe
@atom:px 30.97 # Special p4 in conjugated systems
@atom:py 30.97 # Special p5 in conjugated systems
@atom:s 32.06 # S with one connected atom
@atom:s2 32.06 # S with two connected atom, involved at least one double bond
@atom:s4 32.06 # S with three connected atoms
@atom:s6 32.06 # S with four connected atoms
@atom:sh 32.06 # Sp3 S connected with hydrogen
@atom:ss 32.06 # Sp3 S in thio-ester and thio-ether
@atom:sx 32.06 # Special s4 in conjugated systems
@atom:sy 32.06 # Special s6 in conjugated systems
} # (end of masses)
write_once("In Settings") {
- pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/long 0.0157 1.3870 # Veenstra et al JCC,8,(1992),963
- pair_coeff @atom:h2 @atom:h2 lj/charmm/coul/long 0.0157 1.2870 # Veenstra et al JCC,8,(1992),963
- pair_coeff @atom:h3 @atom:h3 lj/charmm/coul/long 0.0157 1.1870 # Veenstra et al JCC,8,(1992),963
- pair_coeff @atom:h4 @atom:h4 lj/charmm/coul/long 0.0150 1.4090 # Spellmeyer, one electrowithdr. neighbor
- pair_coeff @atom:h5 @atom:h5 lj/charmm/coul/long 0.0150 1.3590 # Spellmeyer, two electrowithdr. neighbor
- pair_coeff @atom:ha @atom:ha lj/charmm/coul/long 0.0150 1.4590 # Spellmeyer
- pair_coeff @atom:hc @atom:hc lj/charmm/coul/long 0.0157 1.4870 # OPLS
- pair_coeff @atom:hn @atom:hn lj/charmm/coul/long 0.0157 0.6000 # !Ferguson base pair geom.
- pair_coeff @atom:ho @atom:ho lj/charmm/coul/long 0.0000 0.0000 # OPLS Jorgensen, JACS,110,(1988),1657
- pair_coeff @atom:hp @atom:hp lj/charmm/coul/long 0.0157 0.6000 # same to hs (be careful !)
- pair_coeff @atom:hs @atom:hs lj/charmm/coul/long 0.0157 0.6000 # W. Cornell CH3SH --> CH3OH FEP
- pair_coeff @atom:hw @atom:hw lj/charmm/coul/long 0.0000 0.0000 # OPLS Jorgensen, JACS,110,(1988),1657
- pair_coeff @atom:hx @atom:hx lj/charmm/coul/long 0.0157 1.1000 # Veenstra et al JCC,8,(1992),963
- pair_coeff @atom:o @atom:o lj/charmm/coul/long 0.2100 1.6612 # OPLS
- pair_coeff @atom:oh @atom:oh lj/charmm/coul/long 0.2104 1.7210 # OPLS
- pair_coeff @atom:os @atom:os lj/charmm/coul/long 0.1700 1.6837 # OPLS ether
- pair_coeff @atom:ow @atom:ow lj/charmm/coul/long 0.1520 1.7683 # TIP3P water model
- pair_coeff @atom:c @atom:c lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:c1 @atom:c1 lj/charmm/coul/long 0.2100 1.9080 # cp C DLM 11/2007 well depth from OPLS replacing 0.0860
- pair_coeff @atom:c2 @atom:c2 lj/charmm/coul/long 0.0860 1.9080 # sp2 atom in the middle of C=CD-CD=C
- pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/long 0.1094 1.9080 # OPLS
- pair_coeff @atom:ca @atom:ca lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cc @atom:cc lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cd @atom:cd lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:ce @atom:ce lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cf @atom:cf lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cg @atom:cg lj/charmm/coul/long 0.2100 1.9080 # DLM 12/2007 as c1
- pair_coeff @atom:ch @atom:ch lj/charmm/coul/long 0.2100 1.9080 # DLM 12/2007 as c1
- pair_coeff @atom:cp @atom:cp lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cq @atom:cq lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cu @atom:cu lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cv @atom:cv lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cx @atom:cx lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cy @atom:cy lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:cz @atom:cz lj/charmm/coul/long 0.0860 1.9080 # OPLS
- pair_coeff @atom:n @atom:n lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:n1 @atom:n1 lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:n2 @atom:n2 lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:n3 @atom:n3 lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:n4 @atom:n4 lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:na @atom:na lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:nb @atom:nb lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:nc @atom:nc lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:nd @atom:nd lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:ne @atom:ne lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:nf @atom:nf lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:nh @atom:nh lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:no @atom:no lj/charmm/coul/long 0.1700 1.8240 # OPLS
- pair_coeff @atom:s @atom:s lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:s2 @atom:s2 lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:s4 @atom:s4 lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:s6 @atom:s6 lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:sx @atom:sx lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:sy @atom:sy lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:sh @atom:sh lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:ss @atom:ss lj/charmm/coul/long 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
- pair_coeff @atom:p2 @atom:p2 lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:p3 @atom:p3 lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:p4 @atom:p4 lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:p5 @atom:p5 lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:pb @atom:pb lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:pc @atom:pc lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:pd @atom:pd lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:pe @atom:pe lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:pf @atom:pf lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:px @atom:px lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:py @atom:py lj/charmm/coul/long 0.2000 2.1000 # JCC,7,(1986),230;
- pair_coeff @atom:f @atom:f lj/charmm/coul/long 0.061 1.75 # Gough et al. JCC 13,(1992),963.
- pair_coeff @atom:cl @atom:cl lj/charmm/coul/long 0.265 1.948 # Fox, JPCB,102,8070,(98),flex.mdl CHCl3
- pair_coeff @atom:br @atom:br lj/charmm/coul/long 0.420 2.02 # Junmei, 2010
- pair_coeff @atom:i @atom:i lj/charmm/coul/long 0.50 2.15 # Junmei, 2010
+ pair_coeff @atom:h1 @atom:h1 lj/charmm/coul/charmm 0.0157 1.3870 # Veenstra et al JCC,8,(1992),963
+ pair_coeff @atom:h2 @atom:h2 lj/charmm/coul/charmm 0.0157 1.2870 # Veenstra et al JCC,8,(1992),963
+ pair_coeff @atom:h3 @atom:h3 lj/charmm/coul/charmm 0.0157 1.1870 # Veenstra et al JCC,8,(1992),963
+ pair_coeff @atom:h4 @atom:h4 lj/charmm/coul/charmm 0.0150 1.4090 # Spellmeyer, one electrowithdr. neighbor
+ pair_coeff @atom:h5 @atom:h5 lj/charmm/coul/charmm 0.0150 1.3590 # Spellmeyer, two electrowithdr. neighbor
+ pair_coeff @atom:ha @atom:ha lj/charmm/coul/charmm 0.0150 1.4590 # Spellmeyer
+ pair_coeff @atom:hc @atom:hc lj/charmm/coul/charmm 0.0157 1.4870 # OPLS
+ pair_coeff @atom:hn @atom:hn lj/charmm/coul/charmm 0.0157 0.6000 # !Ferguson base pair geom.
+ pair_coeff @atom:ho @atom:ho lj/charmm/coul/charmm 0.0000 0.0000 # OPLS Jorgensen, JACS,110,(1988),1657
+ pair_coeff @atom:hp @atom:hp lj/charmm/coul/charmm 0.0157 0.6000 # same to hs (be careful !)
+ pair_coeff @atom:hs @atom:hs lj/charmm/coul/charmm 0.0157 0.6000 # W. Cornell CH3SH --> CH3OH FEP
+ pair_coeff @atom:hw @atom:hw lj/charmm/coul/charmm 0.0000 0.0000 # OPLS Jorgensen, JACS,110,(1988),1657
+ pair_coeff @atom:hx @atom:hx lj/charmm/coul/charmm 0.0157 1.1000 # Veenstra et al JCC,8,(1992),963
+ pair_coeff @atom:o @atom:o lj/charmm/coul/charmm 0.2100 1.6612 # OPLS
+ pair_coeff @atom:oh @atom:oh lj/charmm/coul/charmm 0.2104 1.7210 # OPLS
+ pair_coeff @atom:os @atom:os lj/charmm/coul/charmm 0.1700 1.6837 # OPLS ether
+ pair_coeff @atom:ow @atom:ow lj/charmm/coul/charmm 0.1520 1.7683 # TIP3P water model
+ pair_coeff @atom:c @atom:c lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:c1 @atom:c1 lj/charmm/coul/charmm 0.2100 1.9080 # cp C DLM 11/2007 well depth from OPLS replacing 0.0860
+ pair_coeff @atom:c2 @atom:c2 lj/charmm/coul/charmm 0.0860 1.9080 # sp2 atom in the middle of C=CD-CD=C
+ pair_coeff @atom:c3 @atom:c3 lj/charmm/coul/charmm 0.1094 1.9080 # OPLS
+ pair_coeff @atom:ca @atom:ca lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cc @atom:cc lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cd @atom:cd lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:ce @atom:ce lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cf @atom:cf lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cg @atom:cg lj/charmm/coul/charmm 0.2100 1.9080 # DLM 12/2007 as c1
+ pair_coeff @atom:ch @atom:ch lj/charmm/coul/charmm 0.2100 1.9080 # DLM 12/2007 as c1
+ pair_coeff @atom:cp @atom:cp lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cq @atom:cq lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cu @atom:cu lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cv @atom:cv lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cx @atom:cx lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cy @atom:cy lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:cz @atom:cz lj/charmm/coul/charmm 0.0860 1.9080 # OPLS
+ pair_coeff @atom:n @atom:n lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:n1 @atom:n1 lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:n2 @atom:n2 lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:n3 @atom:n3 lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:n4 @atom:n4 lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:na @atom:na lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:nb @atom:nb lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:nc @atom:nc lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:nd @atom:nd lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:ne @atom:ne lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:nf @atom:nf lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:nh @atom:nh lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:no @atom:no lj/charmm/coul/charmm 0.1700 1.8240 # OPLS
+ pair_coeff @atom:s @atom:s lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
+ pair_coeff @atom:s2 @atom:s2 lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
+ pair_coeff @atom:s4 @atom:s4 lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
+ pair_coeff @atom:s6 @atom:s6 lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
+ pair_coeff @atom:sx @atom:sx lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
+ pair_coeff @atom:sy @atom:sy lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
+ pair_coeff @atom:sh @atom:sh lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
+ pair_coeff @atom:ss @atom:ss lj/charmm/coul/charmm 0.2500 2.0000 # W. Cornell CH3SH and CH3SCH3 FEP's
+ pair_coeff @atom:p2 @atom:p2 lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:p3 @atom:p3 lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:p4 @atom:p4 lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:p5 @atom:p5 lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:pb @atom:pb lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:pc @atom:pc lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:pd @atom:pd lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:pe @atom:pe lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:pf @atom:pf lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:px @atom:px lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:py @atom:py lj/charmm/coul/charmm 0.2000 2.1000 # JCC,7,(1986),230;
+ pair_coeff @atom:f @atom:f lj/charmm/coul/charmm 0.061 1.75 # Gough et al. JCC 13,(1992),963.
+ pair_coeff @atom:cl @atom:cl lj/charmm/coul/charmm 0.265 1.948 # Fox, JPCB,102,8070,(98),flex.mdl CHCl3
+ pair_coeff @atom:br @atom:br lj/charmm/coul/charmm 0.420 2.02 # Junmei, 2010
+ pair_coeff @atom:i @atom:i lj/charmm/coul/charmm 0.50 2.15 # Junmei, 2010
} # (end of pair_coeffs)
write_once("In Settings") {
bond_coeff @bond:ow-hw harmonic 553.0 0.9572 # TIP3P_Water 1
bond_coeff @bond:br-br harmonic 123.2 2.5420 # SOURCE1 4 0.0000
bond_coeff @bond:br-c1 harmonic 352.7 1.7870 # SOURCE2 4 0.0024
bond_coeff @bond:br-c2 harmonic 278.7 1.8830 # SOURCE1 31 0.0000
bond_coeff @bond:br-c harmonic 240.3 1.9460 # SOURCE2 2 0.0285
bond_coeff @bond:br-c3 harmonic 229.5 1.9660 # SOURCE1 100 0.0000
bond_coeff @bond:br-ca harmonic 269.6 1.8970 # SOURCE1 127 0.0058
bond_coeff @bond:br-cc harmonic 277.6 1.8847 # SOURCE4 39 0.0068
bond_coeff @bond:br-cx harmonic 261.4 1.9100 # SOURCE1 8 0.0000
bond_coeff @bond:br-i harmonic 142.4 2.6710 # SOURCE1 2 0.0245
bond_coeff @bond:br-n1 harmonic 330.4 1.8600 # SOUECE3 1
bond_coeff @bond:br-n2 harmonic 219.0 2.0380 # SOURCE3 5 0.1082
bond_coeff @bond:br-n harmonic 320.2 1.8730 # SOURCE3 4 0.0046
bond_coeff @bond:br-n3 harmonic 265.9 1.9520 # SOURCE3 2 0.0000
bond_coeff @bond:br-n4 harmonic 282.4 1.9260 # SOURCE3 3 0.0013
bond_coeff @bond:br-na harmonic 237.3 2.0020 # SOURCE3 7 0.2156
bond_coeff @bond:br-nh harmonic 270.9 1.9440 # SOURCE3 1 0.0000
bond_coeff @bond:br-no harmonic 191.0 2.1010 # SOURCE3 1 0.0000
bond_coeff @bond:br-o harmonic 278.9 1.8000 # SOUECE3 1
bond_coeff @bond:br-oh harmonic 237.2 1.8660 # SOURCE3 1 0.0000
bond_coeff @bond:br-os harmonic 225.6 1.8870 # SOURCE3 2 0.0000
bond_coeff @bond:br-p2 harmonic 174.3 2.2100 # SOURCE3 9 0.0510
bond_coeff @bond:br-p3 harmonic 167.0 2.2310 # SOURCE3 3 0.0101
bond_coeff @bond:br-p4 harmonic 188.8 2.1710 # SOUECE3 1
bond_coeff @bond:br-p5 harmonic 179.3 2.1960 # SOURCE3 3 0.0099
bond_coeff @bond:br-s harmonic 170.6 2.2200 # SOUECE3 1
bond_coeff @bond:br-s4 harmonic 134.3 2.3410 # SOURCE3 1 0.0000
bond_coeff @bond:br-s6 harmonic 172.7 2.2140 # SOURCE3 3 0.0443
bond_coeff @bond:br-sh harmonic 174.4 2.2090 # SOURCE3 1 0.0000
bond_coeff @bond:br-ss harmonic 176.6 2.2030 # SOURCE3 3 0.0035
bond_coeff @bond:c1-c1 harmonic 986.2 1.1810 # SOURCE1 265 0.0031
bond_coeff @bond:c1-c2 harmonic 625.0 1.3070 # SOURCE1 18 0.0000
bond_coeff @bond:c1-c3 harmonic 368.3 1.4700 # SOURCE1 215 0.0017
bond_coeff @bond:c1-ca harmonic 404.1 1.4400 # SOUECE3 1
bond_coeff @bond:c1-ce harmonic 607.4 1.3153 # SOURCE4 6 0.0086
bond_coeff @bond:c1-cg harmonic 845.8 1.2220 # SOURCE3 22 0.0101
bond_coeff @bond:c1-ch harmonic 845.8 1.2220 # SOURCE3 22 same_as_c1-cg
bond_coeff @bond:c1-cl harmonic 419.7 1.6310 # SOURCE2 6 0.0050
bond_coeff @bond:c1-cx harmonic 399.1 1.4440 # SOURCE1 38 0.0000
bond_coeff @bond:c1-f harmonic 469.4 1.2700 # SOURCE2 2 0.0085
bond_coeff @bond:c1-ha harmonic 375.9 1.0660 # SOURCE3 63 0.0035
bond_coeff @bond:c1-hc harmonic 385.6 1.0600 # SOUECE3 1
bond_coeff @bond:c1-i harmonic 318.8 1.9890 # SOURCE2 4 0.0032
bond_coeff @bond:c1-n1 harmonic 1014.5 1.1380 # SOURCE1 170 0.0055
bond_coeff @bond:c1-n2 harmonic 769.8 1.2100 # SOURCE3 5 0.0115
bond_coeff @bond:c1-n3 harmonic 409.8 1.3920 # SOURCE2 1 0.0000
bond_coeff @bond:c1-n4 harmonic 378.2 1.4170 # SOURCE3 3 0.0032
bond_coeff @bond:c1-n harmonic 503.0 1.3300 # SOUECE3 1
bond_coeff @bond:c1-na harmonic 452.0 1.3620 # SOURCE3 8 0.0034
bond_coeff @bond:c1-ne harmonic 803.3 1.1986 # SOURCE4 10 0.0088
bond_coeff @bond:c1-nf harmonic 803.3 1.1986 # SOURCE4 10 same_as_c1-ne
bond_coeff @bond:c1-nh harmonic 485.0 1.3408 # SOURCE4 11 0.0037
bond_coeff @bond:c1-no harmonic 393.0 1.4050 # SOURCE3 3 0.0005
bond_coeff @bond:c1-o harmonic 777.0 1.1660 # SOURCE2 9 0.0052
bond_coeff @bond:c1-oh harmonic 435.6 1.3260 # SOURCE3 1 0.0000
bond_coeff @bond:c1-os harmonic 437.1 1.3250 # SOURCE3 3 0.0148
bond_coeff @bond:c1-p2 harmonic 289.3 1.7700 # SOUECE3 1
bond_coeff @bond:c1-p3 harmonic 275.1 1.7900 # SOUECE3 1
bond_coeff @bond:c1-p4 harmonic 275.1 1.7900 # SOUECE3 1
bond_coeff @bond:c1-p5 harmonic 302.2 1.7530 # SOURCE3 2 0.0000
bond_coeff @bond:c1-s2 harmonic 410.0 1.5950 # SOURCE3 1 0.0000
bond_coeff @bond:c1-s harmonic 371.8 1.6300 # SOURCE1 14 0.0000
bond_coeff @bond:c1-s4 harmonic 272.9 1.7460 # SOURCE3 2 0.0000
bond_coeff @bond:c1-s6 harmonic 290.4 1.7220 # SOURCE3 2 0.0000
bond_coeff @bond:c1-sh harmonic 324.5 1.6800 # SOUECE3 1
bond_coeff @bond:c1-ss harmonic 325.4 1.6790 # SOURCE1 10 0.0000
bond_coeff @bond:c2-c2 harmonic 589.7 1.3240 # SOURCE1 974 0.0096
bond_coeff @bond:c2-c3 harmonic 328.3 1.5080 # SOURCE1 2536 0.0021
bond_coeff @bond:c2-ca harmonic 357.2 1.4800 # SOUECE3 1
bond_coeff @bond:c2-cc harmonic 522.6 1.3600 # SOURCE1 771 0.0185
bond_coeff @bond:c2-cd harmonic 522.6 1.3600 # SOURCE1 771 0.0185
bond_coeff @bond:c2-ce harmonic 560.5 1.3390 # SOURCE3 62 0.0128
bond_coeff @bond:c2-cf harmonic 560.5 1.3390 # SOURCE3 62 same_as_c2-ce
bond_coeff @bond:c2-cl harmonic 328.8 1.7220 # SOURCE1 163 0.0098
bond_coeff @bond:c2-cu harmonic 573.9 1.3320 # SOURCE2 1 0.0000
bond_coeff @bond:c2-cx harmonic 353.3 1.4836 # SOURCE4 26 0.0064
bond_coeff @bond:c2-cy harmonic 331.7 1.5046 # SOURCE4 9 0.0053
bond_coeff @bond:c2-f harmonic 368.7 1.3400 # SOURCE1 34 0.0000
bond_coeff @bond:c2-h4 harmonic 348.6 1.0840 # SOURCE3 40 0.0058
bond_coeff @bond:c2-h5 harmonic 338.0 1.0915 # SOURCE4 42 0.0017
bond_coeff @bond:c2-ha harmonic 344.3 1.0870 # SOURCE3 797 0.0046
bond_coeff @bond:c2-hc harmonic 344.3 1.0870 # SOURCE3 789 0.0046
bond_coeff @bond:c2-hx harmonic 350.1 1.0830 # SOURCE3 3 0.0008
bond_coeff @bond:c2-i harmonic 223.2 2.1530 # SOURCE3 2 0.0000
bond_coeff @bond:c2-n1 harmonic 546.0 1.3060 # SOURCE3 4 0.0161
bond_coeff @bond:c2-n2 harmonic 581.1 1.2880 # SOURCE1 103 0.0100
bond_coeff @bond:c2-n3 harmonic 486.3 1.3400 # SOUECE3 1
bond_coeff @bond:c2-n harmonic 390.5 1.4070 # SOURCE3 9 0.0124
bond_coeff @bond:c2-n4 harmonic 309.1 1.4820 # SOURCE3 5 0.0064
bond_coeff @bond:c2-na harmonic 411.1 1.3910 # SOURCE3 31 0.0289
bond_coeff @bond:c2-nc harmonic 533.0 1.3130 # SOURCE1 99 0.0095
bond_coeff @bond:c2-nd harmonic 533.0 1.3130 # SOURCE1 99 same_as_c2-nc
bond_coeff @bond:c2-ne harmonic 597.7 1.2800 # SOURCE3 37 0.0110
bond_coeff @bond:c2-nf harmonic 597.7 1.2800 # SOURCE3 37 same_as_c2-ne
bond_coeff @bond:c2-nh harmonic 462.6 1.3550 # SOURCE3 38 0.0413
bond_coeff @bond:c2-no harmonic 345.6 1.4457 # SOURCE4 7 0.0087
bond_coeff @bond:c2-o harmonic 623.6 1.2244 # SOURCE4 15 0.0036
bond_coeff @bond:c2-oh harmonic 425.4 1.3330 # SOURCE1 53 0.0000
bond_coeff @bond:c2-os harmonic 392.6 1.3570 # SOURCE1 315 0.0097
bond_coeff @bond:c2-p2 harmonic 375.9 1.6700 # SOURCE3 62 0.0147
bond_coeff @bond:c2-p3 harmonic 246.6 1.8340 # SOURCE3 5 0.0042
bond_coeff @bond:c2-p4 harmonic 254.0 1.8220 # SOUECE3 1
bond_coeff @bond:c2-p5 harmonic 228.2 1.8658 # SOURCE4 5 0.0025
bond_coeff @bond:c2-pe harmonic 355.3 1.6910 # SOURCE3 52 0.0542
bond_coeff @bond:c2-pf harmonic 355.3 1.6910 # SOURCE3 52 same_as_c2-pe
bond_coeff @bond:c2-s2 harmonic 393.1 1.6100 # SOURCE2 1 0.0000
bond_coeff @bond:c2-s harmonic 281.5 1.7340 # SOURCE3 4 0.0034
bond_coeff @bond:c2-s4 harmonic 263.2 1.7600 # SOUECE3 1
bond_coeff @bond:c2-s6 harmonic 263.2 1.7600 # SOUECE3 1
bond_coeff @bond:c2-sh harmonic 252.0 1.7771 # SOURCE4 5 0.0037
bond_coeff @bond:c2-ss harmonic 280.0 1.7360 # SOURCE1 209 0.0155
bond_coeff @bond:c3-c3 harmonic 303.1 1.5350 # SOURCE1 14664 0.0048
bond_coeff @bond:c3-ca harmonic 323.5 1.5130 # SOURCE1 1813 0.0000
bond_coeff @bond:c3-cc harmonic 337.3 1.4990 # SOURCE3 50 0.0096
bond_coeff @bond:c3-cd harmonic 337.3 1.4990 # SOURCE3 50 0.0096
bond_coeff @bond:c3-ce harmonic 331.3 1.5050 # SOURCE3 9 0.0024
bond_coeff @bond:c3-cf harmonic 331.3 1.5050 # SOURCE3 9 same_as_c3-ce
bond_coeff @bond:c3-cl harmonic 279.0 1.7860 # SOURCE1 267 0.0194
bond_coeff @bond:c3-cu harmonic 359.4 1.4780 # SOURCE1 7 0.0000
bond_coeff @bond:c3-cv harmonic 347.6 1.4890 # SOURCE1 11 0.0000
bond_coeff @bond:c3-cx harmonic 322.5 1.5140 # SOURCE1 712 0.0045
bond_coeff @bond:c3-cy harmonic 308.5 1.5290 # SOURCE1 376 0.0000
bond_coeff @bond:c3-f harmonic 363.8 1.3440 # SOURCE1 617 0.0281
bond_coeff @bond:c3-h1 harmonic 335.9 1.0930 # SOURCE3 2175 0.0082
bond_coeff @bond:c3-h2 harmonic 326.4 1.1000 # SOURCE3 66 0.0280
bond_coeff @bond:c3-h3 harmonic 333.4 1.0948 # SOURCE4 25 0.0026
bond_coeff @bond:c3-hc harmonic 337.3 1.0920 # SOURCE3 2815 0.0059
bond_coeff @bond:c3-hx harmonic 338.7 1.0910 # SOURCE3 146 0.0066
bond_coeff @bond:c3-i harmonic 219.1 2.1620 # SOURCE1 15 0.0000
bond_coeff @bond:c3-n1 harmonic 325.1 1.4700 # SOURCE3 0
bond_coeff @bond:c3-n2 harmonic 313.8 1.4770 # SOURCE1 129 0.0138
bond_coeff @bond:c3-n harmonic 330.6 1.4600 # SOURCE1 187 0.0079
bond_coeff @bond:c3-n3 harmonic 320.6 1.4700 # SOURCE1 1678 0.0017
bond_coeff @bond:c3-n4 harmonic 293.6 1.4990 # SOURCE1 1370 0.0000
bond_coeff @bond:c3-na harmonic 334.7 1.4560 # SOURCE3 23 0.0119
bond_coeff @bond:c3-nc harmonic 334.7 1.4560 # SOURCE3 9 0.0109
bond_coeff @bond:c3-nd harmonic 334.7 1.4560 # SOURCE3 9 same_as_c3-nc
bond_coeff @bond:c3-nh harmonic 332.7 1.4580 # SOURCE3 27 0.0085
bond_coeff @bond:c3-no harmonic 265.4 1.5330 # SOURCE1 83 0.0212
bond_coeff @bond:c3-o harmonic 449.9 1.3165 # SOURCE4 8 0.0193
bond_coeff @bond:c3-oh harmonic 314.1 1.4260 # SOURCE1 914 0.0129
bond_coeff @bond:c3-os harmonic 301.5 1.4390 # SOURCE1 3123 0.0126
bond_coeff @bond:c3-p2 harmonic 234.3 1.8550 # SOURCE3 9 0.0125
bond_coeff @bond:c3-p3 harmonic 240.6 1.8440 # SOURCE3 109 0.0107
bond_coeff @bond:c3-p4 harmonic 247.2 1.8330 # SOURCE3 29 0.0138
bond_coeff @bond:c3-p5 harmonic 259.7 1.8130 # SOURCE1 84 0.0000
bond_coeff @bond:c3-px harmonic 252.7 1.8240 # SOURCE3 28 0.0098
bond_coeff @bond:c3-py harmonic 259.7 1.8130 # SOURCE3 13 0.0163
bond_coeff @bond:c3-s harmonic 212.9 1.8450 # SOURCE3 4 0.0185
bond_coeff @bond:c3-s4 harmonic 233.8 1.8070 # SOURCE1 139 0.0023
bond_coeff @bond:c3-s6 harmonic 254.0 1.7740 # SOURCE1 118 0.0103
bond_coeff @bond:c3-sh harmonic 225.3 1.8220 # SOURCE3 12 0.0051
bond_coeff @bond:c3-ss harmonic 225.8 1.8210 # SOURCE1 358 0.0075
bond_coeff @bond:c3-sx harmonic 232.6 1.8090 # SOURCE3 30 0.0067
bond_coeff @bond:c3-sy harmonic 248.9 1.7820 # SOURCE3 31 0.0039
bond_coeff @bond:ca-ca harmonic 478.4 1.3870 # SOURCE1 6228 0.0147
bond_coeff @bond:ca-cc harmonic 411.7 1.4340 # SOURCE1 80 0.0000
bond_coeff @bond:ca-cd harmonic 411.7 1.4340 # SOURCE1 80 0.0000
bond_coeff @bond:ca-ce harmonic 366.0 1.4720 # SOURCE1 71 0.0030
bond_coeff @bond:ca-cf harmonic 366.0 1.4720 # SOURCE1 71 0.0030
bond_coeff @bond:ca-cg harmonic 406.6 1.4380 # SOURCE1 71 0.0045
bond_coeff @bond:ca-ch harmonic 406.6 1.4380 # SOURCE1 71 0.0045
bond_coeff @bond:ca-cl harmonic 322.8 1.7290 # SOURCE1 704 0.0095
bond_coeff @bond:ca-cp harmonic 466.1 1.3950 # SOURCE3 14 0.0110
bond_coeff @bond:ca-cq harmonic 457.4 1.4009 # SOURCE4 14 0.0058
bond_coeff @bond:ca-cx harmonic 350.8 1.4860 # SOURCE1 98 0.0118
bond_coeff @bond:ca-cy harmonic 323.0 1.5135 # SOURCE4 8 0.0043
bond_coeff @bond:ca-f harmonic 363.8 1.3440 # SOURCE1 205 0.0089
bond_coeff @bond:ca-h4 harmonic 342.9 1.0880 # SOURCE3 57 0.0026
bond_coeff @bond:ca-h5 harmonic 347.2 1.0850 # SOURCE3 15 0.0048
bond_coeff @bond:ca-ha harmonic 344.3 1.0870 # SOURCE3 1496 0.0045
bond_coeff @bond:ca-i harmonic 252.4 2.0950 # SOURCE1 51 0.0000
bond_coeff @bond:ca-n1 harmonic 398.1 1.4000 # SOURCE3 0
bond_coeff @bond:ca-n2 harmonic 551.6 1.3030 # SOURCE4 7 0.0058
bond_coeff @bond:ca-n harmonic 372.3 1.4220 # SOURCE3 9 0.0098
bond_coeff @bond:ca-n4 harmonic 325.6 1.4650 # SOURCE1 23 0.0000
bond_coeff @bond:ca-na harmonic 470.3 1.3500 # SOURCE1 150 0.0103
bond_coeff @bond:ca-nb harmonic 483.1 1.3420 # SOURCE3 104 0.0076
bond_coeff @bond:ca-nc harmonic 492.9 1.3360 # SOURCE1 1826 0.0020
bond_coeff @bond:ca-nd harmonic 492.9 1.3360 # SOURCE1 1826 0.0020
bond_coeff @bond:ca-ne harmonic 361.8 1.4310 # SOURCE1 52 0.0000
bond_coeff @bond:ca-nf harmonic 361.8 1.4310 # SOURCE1 52 0.0000
bond_coeff @bond:ca-nh harmonic 449.0 1.3640 # SOURCE1 137 0.0085
bond_coeff @bond:ca-no harmonic 322.6 1.4680 # SOURCE1 556 0.0000
bond_coeff @bond:ca-o harmonic 610.0 1.2304 # SOURCE4 5 0.0026
bond_coeff @bond:ca-oh harmonic 386.1 1.3620 # SOURCE1 551 0.0000
bond_coeff @bond:ca-os harmonic 372.4 1.3730 # SOURCE1 1092 0.0071
bond_coeff @bond:ca-p2 harmonic 243.0 1.8400 # SOUECE3 1
bond_coeff @bond:ca-p3 harmonic 252.7 1.8240 # SOURCE1 145 0.0187
bond_coeff @bond:ca-p4 harmonic 264.3 1.8060 # SOUECE3 1
bond_coeff @bond:ca-p5 harmonic 271.6 1.7950 # SOURCE1 571 0.0028
bond_coeff @bond:ca-pe harmonic 249.6 1.8290 # SOURCE3 10 0.0042
bond_coeff @bond:ca-pf harmonic 249.6 1.8290 # SOURCE3 10 0.0042
bond_coeff @bond:ca-px harmonic 252.1 1.8250 # SOURCE3 5 0.0168
bond_coeff @bond:ca-py harmonic 268.3 1.7999 # SOURCE4 5 0.0072
bond_coeff @bond:ca-s harmonic 277.9 1.7390 # SOURCE3 2 0.0000
bond_coeff @bond:ca-s4 harmonic 245.2 1.7880 # SOURCE1 51 0.0048
bond_coeff @bond:ca-s6 harmonic 263.9 1.7590 # SOURCE1 229 0.0036
bond_coeff @bond:ca-sh harmonic 251.3 1.7783 # SOURCE4 12 0.0041
bond_coeff @bond:ca-ss harmonic 256.6 1.7700 # SOURCE1 297 0.0041
bond_coeff @bond:ca-sx harmonic 223.5 1.8252 # SOURCE4 24 0.0032
bond_coeff @bond:ca-sy harmonic 247.7 1.7840 # SOURCE3 13 0.0094
bond_coeff @bond:c-c1 harmonic 379.8 1.4600 # SOUECE3 1
bond_coeff @bond:c-c2 harmonic 449.9 1.4060 # SOURCE3 2 0.0370
bond_coeff @bond:c-c harmonic 290.1 1.5500 # SOURCE1 31 0.0100
bond_coeff @bond:c-c3 harmonic 328.3 1.5080 # SOURCE1 2949 0.0060
bond_coeff @bond:c-ca harmonic 349.7 1.4870 # SOURCE1 480 0.0055
bond_coeff @bond:c-cc harmonic 377.4 1.4620 # SOURCE3 132 0.0210
bond_coeff @bond:cc-cc harmonic 418.3 1.4290 # SOURCE1 740 0.0069
bond_coeff @bond:cc-cd harmonic 504.0 1.3710 # SOURCE3 523 0.0217
bond_coeff @bond:cc-ce harmonic 391.4 1.4502 # SOURCE4 157 0.0098
bond_coeff @bond:cc-cf harmonic 521.7 1.3605 # SOURCE4 27 0.0086
bond_coeff @bond:cc-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000
bond_coeff @bond:cc-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000
bond_coeff @bond:cc-cl harmonic 317.1 1.7359 # SOURCE4 55 0.0078
bond_coeff @bond:cc-cx harmonic 369.3 1.4691 # SOURCE4 18 0.0037
bond_coeff @bond:c-cd harmonic 377.4 1.4620 # SOURCE3 132 0.0210
bond_coeff @bond:c-ce harmonic 363.8 1.4740 # SOURCE1 601 0.0105
bond_coeff @bond:c-cf harmonic 363.8 1.4740 # SOURCE1 601 0.0105
bond_coeff @bond:cc-f harmonic 368.6 1.3401 # SOURCE4 24 0.0034
bond_coeff @bond:c-cg harmonic 389.3 1.4520 # SOURCE3 2 0.0000
bond_coeff @bond:c-ch harmonic 389.3 1.4520 # SOURCE3 2 same_as_c-cg
bond_coeff @bond:cc-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037
bond_coeff @bond:cc-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051
bond_coeff @bond:cc-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039
bond_coeff @bond:c-cl harmonic 293.5 1.7660 # SOURCE3 6 0.0250
bond_coeff @bond:cc-n2 harmonic 572.5 1.2923 # SOURCE4 61 0.0067
bond_coeff @bond:cc-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109
bond_coeff @bond:cc-n4 harmonic 299.0 1.4930 # SOURCE4 7 0.0148
bond_coeff @bond:cc-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144
bond_coeff @bond:cc-nc harmonic 431.6 1.3760 # SOURCE1 88 0.0000
bond_coeff @bond:cc-nd harmonic 494.6 1.3350 # SOURCE3 203 0.0239
bond_coeff @bond:cc-ne harmonic 427.4 1.3790 # SOURCE4 30 0.0126
bond_coeff @bond:cc-nf harmonic 580.1 1.2885 # SOURCE4 10 0.0112
bond_coeff @bond:cc-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040
bond_coeff @bond:cc-no harmonic 367.4 1.4262 # SOURCE4 133 0.0061
bond_coeff @bond:cc-oh harmonic 411.8 1.3427 # SOURCE4 64 0.0073
bond_coeff @bond:cc-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192
bond_coeff @bond:cc-pd harmonic 318.2 1.7330 # SOURCE3 84 0.0161
bond_coeff @bond:cc-sh harmonic 257.9 1.7681 # SOURCE4 8 0.0027
bond_coeff @bond:cc-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194
bond_coeff @bond:cc-sx harmonic 231.3 1.8113 # SOURCE4 16 0.0050
bond_coeff @bond:cc-sy harmonic 245.7 1.7872 # SOURCE4 33 0.0105
bond_coeff @bond:c-cu harmonic 441.4 1.4120 # SOURCE2 1 0.0000
bond_coeff @bond:c-cx harmonic 350.8 1.4860 # SOURCE1 105 0.0000
bond_coeff @bond:c-cy harmonic 308.5 1.5290 # SOURCE1 18 0.0000
bond_coeff @bond:cd-cd harmonic 418.3 1.4290 # SOURCE1 740 0.0069
bond_coeff @bond:cd-ce harmonic 504.8 1.3705 # SOURCE4 43 0.0138
bond_coeff @bond:cd-cf harmonic 381.8 1.4583 # SOURCE4 92 0.0079
bond_coeff @bond:cd-cg harmonic 420.9 1.4270 # SOURCE1 560 0.0000
bond_coeff @bond:cd-ch harmonic 420.9 1.4270 # SOURCE1 560 0.0000
bond_coeff @bond:cd-cl harmonic 317.3 1.7356 # SOURCE4 11 0.0080
bond_coeff @bond:cd-cx harmonic 358.6 1.4787 # SOURCE4 6 0.0029
bond_coeff @bond:cd-cy harmonic 330.9 1.5054 # SOURCE4 10 0.0008
bond_coeff @bond:cd-h4 harmonic 350.1 1.0830 # SOURCE3 599 0.0037
bond_coeff @bond:cd-h5 harmonic 356.0 1.0790 # SOURCE3 40 0.0051
bond_coeff @bond:cd-ha harmonic 347.2 1.0850 # SOURCE3 740 0.0039
bond_coeff @bond:cd-n2 harmonic 577.7 1.2897 # SOURCE4 20 0.0086
bond_coeff @bond:cd-n harmonic 426.0 1.3800 # SOURCE3 56 0.0109
bond_coeff @bond:cd-na harmonic 438.8 1.3710 # SOURCE3 440 0.0144
bond_coeff @bond:cd-nc harmonic 494.6 1.3350 # SOURCE3 203 0.0239
bond_coeff @bond:cd-nd harmonic 431.6 1.3760 # SOURCE1 88 0.0000
bond_coeff @bond:cd-ne harmonic 554.1 1.3017 # SOURCE4 13 0.0118
bond_coeff @bond:cd-nh harmonic 449.0 1.3640 # SOURCE3 6 0.0040
bond_coeff @bond:cd-oh harmonic 404.7 1.3479 # SOURCE4 57 0.0063
bond_coeff @bond:cd-os harmonic 376.1 1.3700 # SOURCE3 86 0.0192
bond_coeff @bond:cd-pc harmonic 318.2 1.7330 # SOURCE3 84 same_as_cc-pd
bond_coeff @bond:cd-ss harmonic 279.3 1.7370 # SOURCE3 52 0.0194
bond_coeff @bond:cd-sy harmonic 251.7 1.7777 # SOURCE4 22 0.0034
bond_coeff @bond:ce-ce harmonic 390.5 1.4510 # SOURCE1 66 0.0060
bond_coeff @bond:ce-cf harmonic 562.4 1.3380 # SOURCE1 543 0.0045
bond_coeff @bond:ce-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000
bond_coeff @bond:ce-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000
bond_coeff @bond:ce-cl harmonic 292.6 1.7671 # SOURCE4 24 0.0062
bond_coeff @bond:ce-cx harmonic 337.0 1.4993 # SOURCE4 5 0.0066
bond_coeff @bond:ce-cy harmonic 323.0 1.5135 # SOURCE4 17 0.0024
bond_coeff @bond:ce-h4 harmonic 337.8 1.0916 # SOURCE4 125 0.0033
bond_coeff @bond:ce-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056
bond_coeff @bond:ce-n1 harmonic 540.3 1.3090 # SOURCE4 10 0.0027
bond_coeff @bond:ce-n2 harmonic 599.8 1.2790 # SOURCE1 75 0.0000
bond_coeff @bond:ce-n harmonic 369.2 1.4246 # SOURCE4 130 0.0066
bond_coeff @bond:ce-na harmonic 373.8 1.4207 # SOURCE4 5 0.0051
bond_coeff @bond:ce-ne harmonic 381.8 1.4140 # SOURCE3 7 0.0103
bond_coeff @bond:ce-nf harmonic 571.9 1.2926 # SOURCE4 15 0.0042
bond_coeff @bond:ce-nh harmonic 410.8 1.3912 # SOURCE4 148 0.0104
bond_coeff @bond:ce-oh harmonic 395.9 1.3545 # SOURCE4 23 0.0100
bond_coeff @bond:ce-os harmonic 370.6 1.3745 # SOURCE4 39 0.0077
bond_coeff @bond:ce-p2 harmonic 259.1 1.8140 # SOUECE3 1
bond_coeff @bond:ce-pe harmonic 256.5 1.8180 # SOURCE3 8 0.0108
bond_coeff @bond:ce-px harmonic 254.6 1.8210 # SOURCE3 6 0.0046
bond_coeff @bond:ce-py harmonic 272.3 1.7940 # SOURCE3 5 0.0045
bond_coeff @bond:ce-s harmonic 324.5 1.6800 # SOUECE3 1
bond_coeff @bond:ce-ss harmonic 243.6 1.7906 # SOURCE4 10 0.0064
bond_coeff @bond:ce-sx harmonic 239.7 1.7970 # SOURCE3 5 0.0082
bond_coeff @bond:ce-sy harmonic 248.9 1.7820 # SOURCE3 5 0.0114
bond_coeff @bond:c-f harmonic 387.9 1.3250 # SOURCE2 6 0.0147
bond_coeff @bond:cf-cf harmonic 390.5 1.4510 # SOURCE1 66 0.0060
bond_coeff @bond:cf-cg harmonic 415.6 1.4310 # SOURCE1 22 0.0000
bond_coeff @bond:cf-ch harmonic 415.6 1.4310 # SOURCE1 22 0.0000
bond_coeff @bond:cf-h4 harmonic 334.5 1.0940 # SOURCE4 19 0.0019
bond_coeff @bond:cf-ha harmonic 341.5 1.0890 # SOURCE3 55 0.0056
bond_coeff @bond:cf-n1 harmonic 522.2 1.3190 # SOURCE3 3 0.0121
bond_coeff @bond:cf-n2 harmonic 599.8 1.2790 # SOURCE1 75 same_as_ce-n2
bond_coeff @bond:cf-n harmonic 362.6 1.4303 # SOURCE4 6 0.0082
bond_coeff @bond:cf-ne harmonic 575.1 1.2910 # SOURCE4 27 0.0083
bond_coeff @bond:cf-nf harmonic 381.8 1.4140 # SOURCE3 7 same_as_ce-ne
bond_coeff @bond:cf-nh harmonic 423.0 1.3822 # SOURCE4 20 0.0102
bond_coeff @bond:cf-oh harmonic 414.4 1.3408 # SOURCE4 14 0.0084
bond_coeff @bond:cf-os harmonic 387.2 1.3612 # SOURCE4 6 0.0111
bond_coeff @bond:cf-p2 harmonic 259.1 1.8140 # SOUECE3 1 same_as_ce-p2
bond_coeff @bond:cf-pf harmonic 256.5 1.8180 # SOURCE3 8 same_as_ce-pe
bond_coeff @bond:cf-px harmonic 254.6 1.8210 # SOURCE3 6 same_as_ce-px
bond_coeff @bond:cf-py harmonic 272.3 1.7940 # SOURCE3 5 same_as_ce-py
bond_coeff @bond:cf-s harmonic 324.5 1.6800 # SOUECE3 1 same_as_ce-s
bond_coeff @bond:cf-sx harmonic 239.7 1.7970 # SOURCE3 5 same_as_ce-sx
bond_coeff @bond:cf-sy harmonic 248.9 1.7820 # SOURCE3 5 same_as_ce-sy
bond_coeff @bond:cg-cg harmonic 494.2 1.3770 # SOURCE1 42 0.0000
bond_coeff @bond:cg-ch harmonic 949.5 1.1910 # SOURCE1 80 0.0015
bond_coeff @bond:cg-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018
bond_coeff @bond:cg-ne harmonic 509.5 1.3262 # SOURCE4 17 0.0009
bond_coeff @bond:cg-pe harmonic 429.8 1.6210 # SOURCE3 11 0.2008
bond_coeff @bond:c-h4 harmonic 310.5 1.1123 # SOURCE4 125 0.0023
bond_coeff @bond:c-h5 harmonic 319.4 1.1053 # SOURCE4 42 0.0028
bond_coeff @bond:c-ha harmonic 325.1 1.1010 # SOURCE3 53 0.0102
bond_coeff @bond:ch-ch harmonic 494.2 1.3770 # SOURCE1 42 0.0000
bond_coeff @bond:ch-n1 harmonic 994.7 1.1430 # SOURCE1 316 0.0018
bond_coeff @bond:ch-nf harmonic 509.5 1.3262 # SOURCE4 17 same_as_cg-ne
bond_coeff @bond:ch-pf harmonic 429.8 1.6210 # SOURCE3 11 same_as_cg-pe
bond_coeff @bond:c-i harmonic 198.9 2.2090 # SOURCE3 4 0.0365
bond_coeff @bond:cl-cl harmonic 143.3 2.2670 # SOURCE1 2 0.0395
bond_coeff @bond:cl-cx harmonic 301.8 1.7550 # SOURCE1 64 0.0000
bond_coeff @bond:cl-cy harmonic 292.0 1.7680 # SOURCE2 2 0.0070
bond_coeff @bond:cl-f harmonic 298.6 1.6480 # SOURCE2 2 0.0500
bond_coeff @bond:cl-i harmonic 163.5 2.5500 # SOURCE1 6 0.0893
bond_coeff @bond:cl-n1 harmonic 431.6 1.6300 # SOUECE3 1
bond_coeff @bond:cl-n2 harmonic 263.4 1.8190 # SOURCE3 6 0.1020
bond_coeff @bond:cl-n3 harmonic 290.4 1.7800 # SOURCE4 5 0.0021
bond_coeff @bond:cl-n harmonic 344.2 1.7140 # SOURCE4 5 0.0005
bond_coeff @bond:cl-n4 harmonic 311.1 1.7530 # SOURCE3 4 0.0098
bond_coeff @bond:cl-na harmonic 253.2 1.8350 # SOURCE3 7 0.2083
bond_coeff @bond:cl-nh harmonic 303.2 1.7630 # SOURCE3 1 0.0000
bond_coeff @bond:cl-no harmonic 250.1 1.8400 # SOURCE2 1 0.0000
bond_coeff @bond:cl-o harmonic 557.6 1.4830 # SOURCE3 4 0.0000
bond_coeff @bond:cl-oh harmonic 309.7 1.6900 # SOURCE2 1 0.0000
bond_coeff @bond:cl-os harmonic 278.8 1.7300 # SOURCE3 4 0.0000
bond_coeff @bond:cl-p2 harmonic 217.5 2.0700 # SOURCE3 6 0.0108
bond_coeff @bond:cl-p3 harmonic 249.4 2.0080 # SOURCE1 111 0.0000
bond_coeff @bond:cl-p4 harmonic 249.4 2.0080 # SOURCE1 111 0.0000
bond_coeff @bond:cl-p5 harmonic 249.4 2.0080 # SOURCE1 111 0.0000
bond_coeff @bond:cl-pb harmonic 255.6 1.9970 # SOURCE1 46 0.0000
bond_coeff @bond:cl-s harmonic 208.7 2.0720 # SOURCE1 6 0.0000
bond_coeff @bond:cl-s2 harmonic 172.7 2.1610 # SOURCE2 1 0.0000
bond_coeff @bond:cl-s4 harmonic 208.7 2.0720 # SOURCE1 6 0.0000
bond_coeff @bond:cl-s6 harmonic 208.7 2.0720 # SOURCE1 6 0.0000
bond_coeff @bond:cl-sh harmonic 208.7 2.0720 # SOURCE1 6 0.0000
bond_coeff @bond:cl-ss harmonic 208.7 2.0720 # SOURCE1 6 0.0000
bond_coeff @bond:cl-sx harmonic 208.7 2.0720 # SOURCE1 6 0.0000
bond_coeff @bond:cl-sy harmonic 208.7 2.0720 # SOURCE1 6 0.0000
bond_coeff @bond:c-n2 harmonic 374.6 1.4200 # SOUECE3 1
bond_coeff @bond:c-n4 harmonic 255.5 1.5460 # SOURCE3 4 0.0388
bond_coeff @bond:c-n harmonic 478.2 1.3450 # SOURCE1 1235 0.0215
bond_coeff @bond:c-nc harmonic 428.3 1.3784 # SOURCE4 70 0.0128
bond_coeff @bond:c-nd harmonic 391.2 1.4064 # SOURCE4 54 0.0130
bond_coeff @bond:c-ne harmonic 408.6 1.3929 # SOURCE4 47 0.0136
bond_coeff @bond:c-nf harmonic 404.8 1.3958 # SOURCE4 5 0.0122
bond_coeff @bond:c-no harmonic 260.1 1.5400 # SOUECE3 1
bond_coeff @bond:c-o harmonic 648.0 1.2140 # SOURCE1 3682 0.0165
bond_coeff @bond:c-oh harmonic 466.4 1.3060 # SOURCE1 271 0.0041
bond_coeff @bond:c-os harmonic 411.3 1.3430 # SOURCE1 1044 0.0171
bond_coeff @bond:c-p2 harmonic 210.3 1.9000 # SOUECE3 1
bond_coeff @bond:c-p3 harmonic 219.0 1.8830 # SOURCE3 6 0.0129
bond_coeff @bond:c-p4 harmonic 220.6 1.8800 # SOUECE3 1
bond_coeff @bond:c-p5 harmonic 219.8 1.8815 # SOURCE4 11 0.0078
bond_coeff @bond:cp-cp harmonic 346.5 1.4900 # SOURCE1 242 0.0010
bond_coeff @bond:cp-cq harmonic 419.3 1.4282 # SOURCE4 7 0.0034
bond_coeff @bond:c-pe harmonic 204.9 1.9110 # SOURCE3 3 0.0025
bond_coeff @bond:c-pf harmonic 204.9 1.9110 # SOURCE3 3 same_as_c-pe
bond_coeff @bond:cp-na harmonic 420.5 1.3840 # SOURCE4 7 0.0181
bond_coeff @bond:cp-nb harmonic 486.7 1.3398 # SOURCE4 70 0.0062
bond_coeff @bond:c-px harmonic 208.3 1.9040 # SOURCE3 1 0.0000
bond_coeff @bond:c-py harmonic 227.6 1.8670 # SOURCE3 6 0.0199
bond_coeff @bond:cq-cq harmonic 346.5 1.4900 # SOURCE1 242 0.0010
bond_coeff @bond:c-s harmonic 328.9 1.6750 # SOURCE1 401 0.0128
bond_coeff @bond:c-s4 harmonic 200.4 1.8700 # SOUECE3 1
bond_coeff @bond:c-s6 harmonic 200.4 1.8700 # SOUECE3 1
bond_coeff @bond:c-sh harmonic 249.6 1.7810 # SOURCE3 6 0.0171
bond_coeff @bond:c-ss harmonic 261.9 1.7620 # SOURCE1 20 0.0000
bond_coeff @bond:c-sx harmonic 193.3 1.8850 # SOURCE3 5 0.0088
bond_coeff @bond:c-sy harmonic 202.8 1.8650 # SOURCE3 5 0.0085
bond_coeff @bond:cu-cu harmonic 653.7 1.2940 # SOURCE1 10 0.0000
bond_coeff @bond:cu-cx harmonic 327.3 1.5090 # SOURCE1 20 0.0000
bond_coeff @bond:cu-ha harmonic 353.0 1.0810 # SOURCE2 3 0.0111
bond_coeff @bond:cv-cv harmonic 568.1 1.3350 # SOURCE1 25 0.0000
bond_coeff @bond:cv-cy harmonic 323.5 1.5130 # SOURCE1 50 0.0000
bond_coeff @bond:cv-ha harmonic 344.3 1.0870 # SOURCE3 2 0.0000
bond_coeff @bond:cx-cv harmonic 328.3 1.5080 # SOURCE1 2536 as
bond_coeff @bond:cx-cx harmonic 337.3 1.4990 # SOURCE1 1204 0.0183
bond_coeff @bond:cx-cy harmonic 321.5 1.5150 # SOURCE3 2 0.0000
bond_coeff @bond:cx-f harmonic 347.2 1.3580 # SOURCE2 3 0.0050
bond_coeff @bond:cx-h1 harmonic 344.3 1.0870 # SOURCE3 10 0.0017
bond_coeff @bond:cx-h2 harmonic 350.1 1.0830 # SOURCE3 2 0.0000
bond_coeff @bond:cx-hc harmonic 345.8 1.0860 # SOURCE3 44 0.0011
bond_coeff @bond:cx-hx harmonic 347.2 1.0850 # SOURCE4 5 0.0002
bond_coeff @bond:cx-n2 harmonic 309.1 1.4820 # SOURCE3 2 0.0000
bond_coeff @bond:cx-n3 harmonic 318.7 1.4720 # SOURCE1 134 0.0000
bond_coeff @bond:cx-n harmonic 350.6 1.4411 # SOURCE4 11 0.0092
bond_coeff @bond:cx-na harmonic 329.0 1.4616 # SOURCE4 11 0.0016
bond_coeff @bond:cx-nh harmonic 336.7 1.4541 # SOURCE4 83 0.0076
bond_coeff @bond:cx-oh harmonic 387.4 1.3610 # SOURCE3 3 0.0018
bond_coeff @bond:cx-os harmonic 320.1 1.4200 # SOURCE3 7 0.0222
bond_coeff @bond:cx-p3 harmonic 227.6 1.8670 # SOURCE2 1 0.0000
bond_coeff @bond:cx-s4 harmonic 225.3 1.8220 # SOURCE2 1 0.0000
bond_coeff @bond:cx-s6 harmonic 283.7 1.7310 # SOURCE2 1 0.0000
bond_coeff @bond:cx-ss harmonic 229.2 1.8150 # SOURCE2 1 0.0000
bond_coeff @bond:cy-cy harmonic 286.8 1.5540 # SOURCE1 742 0.0041
bond_coeff @bond:cy-f harmonic 355.5 1.3509 # SOURCE4 8 0.0047
bond_coeff @bond:cy-h1 harmonic 330.4 1.0970 # SOURCE3 17 0.0058
bond_coeff @bond:cy-h2 harmonic 335.8 1.0931 # SOURCE4 80 0.0019
bond_coeff @bond:cy-hc harmonic 334.5 1.0940 # SOURCE3 63 0.0014
bond_coeff @bond:cy-n harmonic 321.3 1.4693 # SOURCE4 250 0.0102
bond_coeff @bond:cy-n3 harmonic 307.2 1.4840 # SOURCE1 21 0.0000
bond_coeff @bond:cy-oh harmonic 325.2 1.4150 # SOURCE3 2 0.0000
bond_coeff @bond:cy-os harmonic 308.6 1.4316 # SOURCE4 23 0.0136
bond_coeff @bond:cy-s6 harmonic 209.6 1.8514 # SOURCE4 9 0.0166
bond_coeff @bond:cy-ss harmonic 211.3 1.8481 # SOURCE4 78 0.0080
bond_coeff @bond:cz-nh harmonic 487.8 1.3391 # SOURCE4 32 0.0045
bond_coeff @bond:f-n1 harmonic 375.7 1.4100 # SOUECE3 1
bond_coeff @bond:f-n2 harmonic 337.5 1.4440 # SOURCE3 5 0.0377
bond_coeff @bond:f-n3 harmonic 380.6 1.4060 # SOURCE1 9 0.0000
bond_coeff @bond:f-n harmonic 391.7 1.3970 # SOURCE3 3 0.0112
bond_coeff @bond:f-n4 harmonic 526.8 1.3080 # SOURCE3 2 0.0000
bond_coeff @bond:f-na harmonic 374.5 1.4110 # SOURCE3 7 0.0611
bond_coeff @bond:f-nh harmonic 357.1 1.4260 # SOURCE3 3 0.0085
bond_coeff @bond:f-no harmonic 314.4 1.4670 # SOURCE2 1 0.0000
bond_coeff @bond:f-o harmonic 442.2 1.3300 # SOUECE3 1
bond_coeff @bond:f-oh harmonic 305.4 1.4440 # SOURCE3 1 0.0000
bond_coeff @bond:f-os harmonic 326.2 1.4230 # SOURCE3 2 0.0000
bond_coeff @bond:f-p2 harmonic 287.3 1.5360 # SOURCE3 7 0.2054
bond_coeff @bond:f-p3 harmonic 254.5 1.5780 # SOURCE2 8 0.0103
bond_coeff @bond:f-p4 harmonic 246.0 1.5900 # SOUECE3 1
bond_coeff @bond:f-p5 harmonic 253.8 1.5790 # SOURCE1 72 0.0000
bond_coeff @bond:f-s2 harmonic 244.4 1.6430 # SOURCE2 1 0.0000
bond_coeff @bond:f-s harmonic 233.3 1.6600 # SOUECE3 1
bond_coeff @bond:f-s4 harmonic 282.4 1.5910 # SOURCE2 4 0.0065
bond_coeff @bond:f-s6 harmonic 312.1 1.5560 # SOURCE2 5 0.0220
bond_coeff @bond:f-sh harmonic 240.4 1.6490 # SOURCE3 1 0.0000
bond_coeff @bond:f-ss harmonic 250.5 1.6340 # SOURCE3 3 0.0156
bond_coeff @bond:hn-n1 harmonic 455.1 0.9860 # SOURCE2 1 0.0000
bond_coeff @bond:hn-n2 harmonic 375.5 1.0290 # SOURCE3 108 0.0096
bond_coeff @bond:hn-n3 harmonic 394.1 1.0180 # SOURCE3 157 0.0086
bond_coeff @bond:hn-n harmonic 410.2 1.0090 # SOURCE3 149 0.0098
bond_coeff @bond:hn-n4 harmonic 369.0 1.0330 # SOURCE3 264 0.0082
bond_coeff @bond:hn-na harmonic 406.6 1.0110 # SOURCE3 46 0.0107
bond_coeff @bond:hn-nh harmonic 401.2 1.0140 # SOURCE3 209 0.0091
bond_coeff @bond:hn-no harmonic 385.6 1.0230 # SOURCE3 1 0.0000
bond_coeff @bond:ho-o harmonic 357.9 0.9810 # SOURCE3 1 0.0000
bond_coeff @bond:ho-oh harmonic 369.6 0.9740 # SOURCE3 367 0.0105
bond_coeff @bond:hp-p2 harmonic 385.1 1.3360 # SOURCE3 87 0.1706
bond_coeff @bond:hp-p3 harmonic 303.1 1.4090 # SOURCE3 101 0.0617
bond_coeff @bond:hp-p4 harmonic 368.7 1.3490 # SOURCE3 17 0.1577
bond_coeff @bond:hp-p5 harmonic 305.0 1.4070 # SOURCE3 7 0.0062
bond_coeff @bond:hs-s harmonic 286.4 1.3530 # SOURCE3 1 0.0000
bond_coeff @bond:hs-s4 harmonic 266.4 1.3750 # SOURCE3 5 0.0004
bond_coeff @bond:hs-s6 harmonic 280.8 1.3590 # SOURCE3 5 0.0015
bond_coeff @bond:hs-sh harmonic 302.2 1.3370 # SOURCE3 98 0.0486
bond_coeff @bond:i-i harmonic 109.2 2.9170 # SOURCE1 1 0.0000
bond_coeff @bond:i-n1 harmonic 302.1 2.0600 # SOUECE3 1
bond_coeff @bond:i-n2 harmonic 182.6 2.3040 # SOURCE3 6 0.1186
bond_coeff @bond:i-n harmonic 278.3 2.0980 # SOURCE3 5 0.0156
bond_coeff @bond:i-n3 harmonic 231.8 2.1850 # SOURCE3 3 0.0437
bond_coeff @bond:i-n4 harmonic 246.6 2.1550 # SOURCE3 3 0.0168
bond_coeff @bond:i-na harmonic 260.5 2.1290 # SOURCE3 8 0.1276
bond_coeff @bond:i-nh harmonic 249.2 2.1500 # SOURCE3 1 0.0000
bond_coeff @bond:i-no harmonic 211.0 2.2310 # SOURCE3 1 0.0000
bond_coeff @bond:i-o harmonic 323.8 1.9800 # SOUECE3 1
bond_coeff @bond:i-oh harmonic 247.9 2.1010 # SOURCE3 2 0.0000
bond_coeff @bond:i-os harmonic 233.6 2.1290 # SOURCE3 3 0.0146
bond_coeff @bond:i-p2 harmonic 108.2 2.6430 # SOURCE3 6 0.0297
bond_coeff @bond:i-p3 harmonic 123.6 2.5660 # SOURCE3 3 0.0016
bond_coeff @bond:i-p4 harmonic 183.0 2.3520 # SOURCE3 4 0.2600
bond_coeff @bond:i-p5 harmonic 117.3 2.5960 # SOURCE3 3 0.0143
bond_coeff @bond:i-s harmonic 175.1 2.4300 # SOUECE3 1
bond_coeff @bond:i-s4 harmonic 82.8 2.8700 # SOUECE3 1
bond_coeff @bond:i-s6 harmonic 82.8 2.8700 # SOURCE3 1 0.0000
bond_coeff @bond:i-sh harmonic 138.5 2.5600 # SOUECE3 1
bond_coeff @bond:i-ss harmonic 135.9 2.5710 # SOURCE3 3 0.0065
bond_coeff @bond:n1-n1 harmonic 1221.7 1.1240 # SOURCE1 19 0.0000
bond_coeff @bond:n1-n2 harmonic 857.4 1.2160 # SOURCE1 19 0.0000
bond_coeff @bond:n1-n3 harmonic 535.7 1.3500 # SOUECE3 1
bond_coeff @bond:n1-n4 harmonic 518.2 1.3600 # SOUECE3 1
bond_coeff @bond:n1-na harmonic 535.7 1.3500 # SOUECE3 1
bond_coeff @bond:n1-nc harmonic 857.4 1.2160 # SOURCE1 38 0.0000
bond_coeff @bond:n1-nd harmonic 857.4 1.2160 # SOURCE1 38 0.0000
bond_coeff @bond:n1-ne harmonic 751.9 1.2520 # SOURCE2 1 0.0000
bond_coeff @bond:n1-nf harmonic 751.9 1.2520 # SOURCE2 1 same_as_n1-ne
bond_coeff @bond:n1-nh harmonic 553.9 1.3400 # SOUECE3 1
bond_coeff @bond:n1-no harmonic 454.8 1.4000 # SOUECE3 1
bond_coeff @bond:n1-o harmonic 617.5 1.2770 # SOURCE3 5 0.0438
bond_coeff @bond:n1-oh harmonic 569.8 1.3000 # SOUECE3 1
bond_coeff @bond:n1-os harmonic 550.5 1.3100 # SOUECE3 1
bond_coeff @bond:n1-p2 harmonic 358.8 1.6780 # SOURCE3 2 0.0282
bond_coeff @bond:n1-p3 harmonic 376.7 1.6600 # SOUECE3 1
bond_coeff @bond:n1-p4 harmonic 353.0 1.6800 # SOURCE3 0
bond_coeff @bond:n1-p5 harmonic 482.7 1.5710 # SOURCE1 132 0.0000
bond_coeff @bond:n1-s2 harmonic 604.3 1.4490 # SOURCE2 2 0.0010
bond_coeff @bond:n1-s harmonic 328.7 1.6590 # SOURCE3 6 0.0789
bond_coeff @bond:n1-s4 harmonic 336.8 1.6500 # SOUECE3 1
bond_coeff @bond:n1-s6 harmonic 670.3 1.4160 # SOURCE2 2 0.0000
bond_coeff @bond:n1-sh harmonic 376.1 1.6100 # SOUECE3 1
bond_coeff @bond:n1-ss harmonic 376.1 1.6100 # SOUECE3 1
bond_coeff @bond:n2-n2 harmonic 702.7 1.2710 # SOURCE3 27 0.0347
bond_coeff @bond:n2-n3 harmonic 574.8 1.3290 # SOURCE2 1 0.0000
bond_coeff @bond:n2-n4 harmonic 200.8 1.6790 # SOURCE3 7 0.3138
bond_coeff @bond:n2-na harmonic 503.9 1.3685 # SOURCE4 18 0.0066
bond_coeff @bond:n2-nc harmonic 743.9 1.2550 # SOURCE1 13 0.0000
bond_coeff @bond:n2-nd harmonic 743.9 1.2550 # SOURCE1 13 same_as_n2_nc
bond_coeff @bond:n2-ne harmonic 685.5 1.2780 # SOURCE3 30 0.0302
bond_coeff @bond:n2-nf harmonic 685.5 1.2780 # SOURCE3 30 same_as_n2-ne
bond_coeff @bond:n2-nh harmonic 525.1 1.3560 # SOURCE3 22 0.0300
bond_coeff @bond:n2-no harmonic 231.9 1.6260 # SOURCE3 4 0.1933
bond_coeff @bond:n2-o harmonic 789.9 1.2090 # SOURCE3 20 0.0344
bond_coeff @bond:n2-oh harmonic 416.2 1.3940 # SOURCE1 67 0.0000
bond_coeff @bond:n2-os harmonic 400.5 1.4060 # SOURCE3 10 0.0147
bond_coeff @bond:n2-p2 harmonic 438.3 1.6050 # SOURCE3 35 0.0737
bond_coeff @bond:n2-p3 harmonic 286.5 1.7640 # SOURCE3 7 0.0374
bond_coeff @bond:n2-p4 harmonic 317.7 1.7240 # SOUECE3 1
bond_coeff @bond:n2-p5 harmonic 445.8 1.5990 # SOURCE1 7 0.0000
bond_coeff @bond:n2-pe harmonic 527.9 1.5400 # SOURCE3 20 0.1392
bond_coeff @bond:n2-pf harmonic 527.9 1.5400 # SOURCE3 20 same_as_n2-pe
bond_coeff @bond:n2-s2 harmonic 499.0 1.5120 # SOURCE2 1 0.0000
bond_coeff @bond:n2-s4 harmonic 376.1 1.6100 # SOUECE3 1
bond_coeff @bond:n2-s harmonic 458.1 1.5410 # SOURCE1 37 0.0000
bond_coeff @bond:n2-s6 harmonic 444.6 1.5513 # SOURCE4 5 0.0011
bond_coeff @bond:n2-sh harmonic 266.6 1.7380 # SOURCE3 5 0.0511
bond_coeff @bond:n2-ss harmonic 331.4 1.6560 # SOURCE1 36 0.0000
bond_coeff @bond:n3-n3 harmonic 383.6 1.4540 # SOURCE1 44 0.0000
bond_coeff @bond:n3-n4 harmonic 434.9 1.4140 # SOURCE1 13 0.0000
bond_coeff @bond:n3-na harmonic 426.7 1.4200 # SOURCE1 68 0.0000
bond_coeff @bond:n3-nh harmonic 426.7 1.4200 # SOURCE1 68 0.0000
bond_coeff @bond:n3-no harmonic 394.5 1.4450 # SOURCE3 3 0.0208
bond_coeff @bond:n3-o harmonic 564.0 1.3030 # SOURCE3 4 0.1217
bond_coeff @bond:n3-oh harmonic 413.5 1.3960 # SOURCE1 28 0.0000
bond_coeff @bond:n3-os harmonic 359.6 1.4400 # SOURCE1 34 0.0315
bond_coeff @bond:n3-p2 harmonic 366.6 1.6700 # SOUECE3 1
bond_coeff @bond:n3-p3 harmonic 312.8 1.7300 # SOURCE1 40 0.0000
bond_coeff @bond:n3-p4 harmonic 341.1 1.6970 # SOURCE1 88 0.0000
bond_coeff @bond:n3-p5 harmonic 373.6 1.6630 # SOURCE1 501 0.0086
bond_coeff @bond:n3-py harmonic 338.1 1.7003 # SOURCE4 6 0.0044
bond_coeff @bond:n3-s harmonic 232.3 1.7920 # SOURCE3 3 0.0178
bond_coeff @bond:n3-s4 harmonic 251.3 1.7610 # SOURCE3 6 0.0766
bond_coeff @bond:n3-s6 harmonic 353.8 1.6320 # SOURCE1 99 0.0136
bond_coeff @bond:n3-sh harmonic 265.9 1.7390 # SOURCE3 3 0.0154
bond_coeff @bond:n3-ss harmonic 277.9 1.7220 # SOURCE3 5 0.0207
bond_coeff @bond:n3-sy harmonic 297.3 1.6964 # SOURCE4 226 0.0081
bond_coeff @bond:n4-n4 harmonic 349.9 1.4840 # SOURCE3 4 0.0089
bond_coeff @bond:n4-na harmonic 407.0 1.4350 # SOURCE3 9 0.0390
bond_coeff @bond:n4-nh harmonic 369.7 1.4660 # SOURCE3 5 0.0108
bond_coeff @bond:n4-no harmonic 354.2 1.4800 # SOUECE3 1
bond_coeff @bond:n4-o harmonic 463.6 1.3610 # SOURCE3 3 0.0041
bond_coeff @bond:n4-oh harmonic 408.2 1.4000 # SOURCE3 3 0.0115
bond_coeff @bond:n4-os harmonic 381.8 1.4210 # SOURCE3 5 0.0249
bond_coeff @bond:n4-p2 harmonic 185.9 1.9420 # SOURCE3 10 0.0643
bond_coeff @bond:n4-p3 harmonic 215.1 1.8800 # SOURCE3 5 0.0146
bond_coeff @bond:n4-p4 harmonic 187.6 1.9380 # SOURCE3 1 0.0000
bond_coeff @bond:n4-p5 harmonic 242.9 1.8300 # SOURCE3 5 0.0087
bond_coeff @bond:n4-py harmonic 204.2 1.9020 # SOURCE3 4 0.0000
bond_coeff @bond:n4-s harmonic 210.3 1.8320 # SOURCE3 3 0.0004
bond_coeff @bond:n4-s4 harmonic 151.0 1.9720 # SOURCE3 3 0.0198
bond_coeff @bond:n4-s6 harmonic 172.7 1.9140 # SOURCE3 5 0.0432
bond_coeff @bond:n4-sh harmonic 221.5 1.8110 # SOURCE3 3 0.0027
bond_coeff @bond:n4-ss harmonic 221.0 1.8120 # SOURCE3 5 0.0064
bond_coeff @bond:na-na harmonic 453.3 1.4010 # SOURCE1 40 0.0000
bond_coeff @bond:na-nb harmonic 546.5 1.3440 # SOURCE4 5 0.0070
bond_coeff @bond:na-nc harmonic 535.7 1.3500 # SOURCE3 152 0.0180
bond_coeff @bond:na-nd harmonic 535.7 1.3500 # SOURCE3 152 0.0180
bond_coeff @bond:na-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000
bond_coeff @bond:na-no harmonic 401.9 1.4390 # SOURCE3 9 0.0289
bond_coeff @bond:na-o harmonic 644.3 1.2650 # SOURCE1 25 0.0347
bond_coeff @bond:na-oh harmonic 412.2 1.3970 # SOURCE3 9 0.0217
bond_coeff @bond:na-os harmonic 355.2 1.4440 # SOURCE3 45 0.0423
bond_coeff @bond:na-p2 harmonic 297.8 1.7490 # SOURCE3 11 0.0192
bond_coeff @bond:na-p3 harmonic 288.0 1.7620 # SOURCE3 8 0.0113
bond_coeff @bond:na-p4 harmonic 492.4 1.5640 # SOURCE3 5 0.2161
bond_coeff @bond:na-p5 harmonic 325.3 1.7150 # SOURCE3 11 0.0238
bond_coeff @bond:na-pc harmonic 311.1 1.7320 # SOURCE3 81 0.0207
bond_coeff @bond:na-pd harmonic 311.1 1.7320 # SOURCE3 81 same_as_na-pc
bond_coeff @bond:na-py harmonic 327.8 1.7120 # SOURCE3 2 0.0000
bond_coeff @bond:na-s harmonic 248.7 1.7650 # SOURCE3 8 0.0095
bond_coeff @bond:na-s4 harmonic 231.7 1.7930 # SOURCE3 10 0.0421
bond_coeff @bond:na-s6 harmonic 274.3 1.7270 # SOURCE3 10 0.0201
bond_coeff @bond:na-sh harmonic 278.6 1.7210 # SOURCE3 9 0.0113
bond_coeff @bond:na-ss harmonic 270.1 1.7330 # SOURCE3 38 0.0412
bond_coeff @bond:na-sy harmonic 274.3 1.7270 # SOURCE3 1
bond_coeff @bond:nb-nb harmonic 550.2 1.3420 # SOURCE1 15 0.0314
bond_coeff @bond:nb-pb harmonic 461.1 1.5870 # SOURCE1 162 0.0091
bond_coeff @bond:nc-nc harmonic 486.8 1.3790 # SOURCE3 9 0.0164
bond_coeff @bond:nc-nd harmonic 602.9 1.3150 # SOURCE3 9 0.0221
bond_coeff @bond:nc-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188
bond_coeff @bond:nc-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000
bond_coeff @bond:nc-sy harmonic 439.8 1.5550 # SOURCE3 2
bond_coeff @bond:nd-nd harmonic 486.8 1.3790 # SOURCE3 9 0.0164
bond_coeff @bond:nd-os harmonic 414.9 1.3950 # SOURCE1 46 0.0188
bond_coeff @bond:nd-ss harmonic 433.5 1.5600 # SOURCE1 74 0.0000
bond_coeff @bond:nd-sy harmonic 439.8 1.5550 # SOURCE3 2
bond_coeff @bond:ne-ne harmonic 355.3 1.4790 # SOURCE3 19 0.1705
bond_coeff @bond:ne-nf harmonic 721.6 1.2635 # SOURCE4 25 0.0034
bond_coeff @bond:ne-o harmonic 736.4 1.2280 # SOURCE3 40 0.0255
bond_coeff @bond:ne-p2 harmonic 493.9 1.5630 # SOURCE3 14 0.1325
bond_coeff @bond:ne-pe harmonic 327.8 1.7120 # SOURCE3 28 0.1076
bond_coeff @bond:ne-px harmonic 336.6 1.7020 # SOURCE3 11 0.0883
bond_coeff @bond:ne-py harmonic 425.4 1.6157 # SOURCE4 10 0.0094
bond_coeff @bond:ne-s harmonic 463.5 1.5370 # SOURCE3 22 0.1708
bond_coeff @bond:ne-sx harmonic 207.3 1.8380 # SOURCE3 7 0.1060
bond_coeff @bond:ne-sy harmonic 257.1 1.7520 # SOURCE3 7 0.0814
bond_coeff @bond:nf-nf harmonic 355.3 1.4790 # SOURCE3 19 same_as_ne-ne
bond_coeff @bond:nf-o harmonic 736.4 1.2280 # SOURCE3 40 same_as_ne-o
bond_coeff @bond:nf-p2 harmonic 493.9 1.5630 # SOURCE3 14 same_as_ne-p2
bond_coeff @bond:nf-pf harmonic 327.8 1.7120 # SOURCE3 28 same_as_ne-pe
bond_coeff @bond:nf-px harmonic 336.6 1.7020 # SOURCE3 11 same_as_ne-px
bond_coeff @bond:nf-py harmonic 425.4 1.6157 # SOURCE4 10 same_as_ne-py
bond_coeff @bond:nf-s harmonic 463.5 1.5370 # SOURCE3 22 same_as_ne-s
bond_coeff @bond:nf-sx harmonic 207.3 1.8380 # SOURCE3 7 same_as_ne-sx
bond_coeff @bond:nf-sy harmonic 257.1 1.7520 # SOURCE3 7 same_as_ne-sy
bond_coeff @bond:nh-nh harmonic 453.3 1.4010 # SOURCE1 40 0.0000
bond_coeff @bond:nh-no harmonic 477.4 1.3850 # SOURCE4 7 0.0036
bond_coeff @bond:nh-o harmonic 596.2 1.2870 # SOURCE3 3 0.0450
bond_coeff @bond:nh-oh harmonic 389.9 1.4144 # SOURCE4 19 0.0064
bond_coeff @bond:nh-os harmonic 387.8 1.4161 # SOURCE4 6 0.0039
bond_coeff @bond:nh-p2 harmonic 357.8 1.6790 # SOURCE3 17 0.0872
bond_coeff @bond:nh-p3 harmonic 312.8 1.7300 # SOURCE3 3 0.0016
bond_coeff @bond:nh-p4 harmonic 333.1 1.7060 # SOURCE3 3 0.0008
bond_coeff @bond:nh-p5 harmonic 365.6 1.6710 # SOURCE3 3 0.0007
bond_coeff @bond:nh-s harmonic 237.0 1.7840 # SOURCE3 3 0.0076
bond_coeff @bond:nh-s4 harmonic 259.1 1.7490 # SOURCE3 3 0.0203
bond_coeff @bond:nh-s6 harmonic 297.2 1.6965 # SOURCE4 33 0.0062
bond_coeff @bond:nh-sh harmonic 288.3 1.7080 # SOURCE3 1 0.0000
bond_coeff @bond:nh-ss harmonic 288.3 1.7080 # SOURCE1 52 0.0015
bond_coeff @bond:nh-sy harmonic 283.5 1.7144 # SOURCE4 80 0.0066
bond_coeff @bond:n-n1 harmonic 553.9 1.3400 # SOUECE3 1
bond_coeff @bond:n-n2 harmonic 499.7 1.3710 # SOURCE3 9 0.0200
bond_coeff @bond:n-n3 harmonic 443.3 1.4080 # SOURCE3 5 0.0087
bond_coeff @bond:n-n4 harmonic 410.8 1.4320 # SOURCE3 5 0.0098
bond_coeff @bond:n-n harmonic 469.7 1.3900 # SOURCE3 5 0.0038
bond_coeff @bond:n-na harmonic 486.8 1.3790 # SOURCE3 11 0.0071
bond_coeff @bond:n-nc harmonic 524.9 1.3561 # SOURCE4 63 0.0104
bond_coeff @bond:n-nd harmonic 517.7 1.3603 # SOURCE4 13 0.0122
bond_coeff @bond:n-nh harmonic 451.2 1.4025 # SOURCE4 20 0.0074
bond_coeff @bond:n-no harmonic 381.2 1.4560 # SOURCE3 4 0.0327
bond_coeff @bond:n-o harmonic 646.6 1.2640 # SOURCE3 9 0.0381
bond_coeff @bond:n-oh harmonic 395.4 1.4100 # SOURCE3 6 0.0106
bond_coeff @bond:no-no harmonic 138.3 1.8240 # SOURCE3 1 0.0000
bond_coeff @bond:no-o harmonic 761.2 1.2190 # SOURCE1 1838 0.0049
bond_coeff @bond:no-oh harmonic 400.5 1.4060 # SOURCE2 1 0.0000
bond_coeff @bond:no-os harmonic 379.5 1.4229 # SOURCE4 53 0.0076
bond_coeff @bond:no-os harmonic 379.5 1.4229 # SOURCE4 53 0.0076
bond_coeff @bond:no-p2 harmonic 306.3 1.7380 # SOURCE3 10 0.2231
bond_coeff @bond:no-p3 harmonic 234.7 1.8440 # SOURCE3 3 0.0005
bond_coeff @bond:no-p4 harmonic 220.4 1.8700 # SOURCE3 3 0.0006
bond_coeff @bond:no-p5 harmonic 240.5 1.8340 # SOURCE3 4 0.0020
bond_coeff @bond:no-s harmonic 263.8 1.7420 # SOURCE3 2 0.0000
bond_coeff @bond:n-os harmonic 395.0 1.4103 # SOURCE4 30 0.0112
bond_coeff @bond:no-s4 harmonic 143.0 1.9960 # SOURCE3 3 0.0313
bond_coeff @bond:no-s6 harmonic 149.6 1.9760 # SOURCE3 3 0.0520
bond_coeff @bond:no-sh harmonic 225.4 1.8040 # SOURCE3 1 0.0000
bond_coeff @bond:no-ss harmonic 212.4 1.8280 # SOURCE3 3 0.0244
bond_coeff @bond:n-p2 harmonic 310.3 1.7330 # SOURCE3 8 0.0217
bond_coeff @bond:n-p3 harmonic 282.2 1.7700 # SOURCE3 9 0.0118
bond_coeff @bond:n-p4 harmonic 309.5 1.7340 # SOURCE3 1 0.0000
bond_coeff @bond:n-p5 harmonic 331.3 1.7080 # SOURCE4 6 0.0022
bond_coeff @bond:n-pc harmonic 304.8 1.7400 # SOURCE3 3 0.0010
bond_coeff @bond:n-pd harmonic 304.8 1.7400 # SOURCE3 3 same_as_n-pc
bond_coeff @bond:n-s harmonic 247.5 1.7670 # SOURCE3 3 0.0011
bond_coeff @bond:n-s4 harmonic 238.2 1.7820 # SOURCE3 4 0.0214
bond_coeff @bond:n-s6 harmonic 283.0 1.7151 # SOURCE4 13 0.0138
bond_coeff @bond:n-sh harmonic 273.6 1.7280 # SOURCE3 4 0.0128
bond_coeff @bond:n-ss harmonic 281.6 1.7170 # SOURCE3 7 0.0133
bond_coeff @bond:n-sy harmonic 282.9 1.7152 # SOURCE4 51 0.0079
bond_coeff @bond:oh-oh harmonic 340.5 1.4690 # SOURCE3 1 0.0000
bond_coeff @bond:oh-os harmonic 355.8 1.4547 # SOURCE4 19 0.0050
bond_coeff @bond:oh-p2 harmonic 316.8 1.6300 # SOURCE3 8 0.0916
bond_coeff @bond:oh-p3 harmonic 278.8 1.6770 # SOURCE3 3 0.0148
bond_coeff @bond:oh-p4 harmonic 307.4 1.6410 # SOURCE3 4 0.0092
bond_coeff @bond:oh-p5 harmonic 321.2 1.6250 # SOURCE3 92 0.0451
bond_coeff @bond:oh-py harmonic 332.1 1.6130 # SOURCE3 79 0.0138
bond_coeff @bond:oh-s harmonic 190.0 1.8120 # SOURCE3 2 0.0000
bond_coeff @bond:oh-s4 harmonic 256.3 1.6954 # SOURCE4 10 0.0091
bond_coeff @bond:oh-s6 harmonic 344.1 1.5880 # SOURCE3 13 0.0091
bond_coeff @bond:oh-sh harmonic 258.6 1.6920 # SOURCE3 2 0.0003
bond_coeff @bond:oh-ss harmonic 265.6 1.6820 # SOURCE3 4 0.0131
bond_coeff @bond:oh-sy harmonic 290.4 1.6490 # SOURCE4 33 0.0044
bond_coeff @bond:o-o harmonic 384.3 1.4300 # SOURCE3 2 0.0500
bond_coeff @bond:o-oh harmonic 294.6 1.5170 # SOURCE3 2 0.0000
bond_coeff @bond:o-os harmonic 306.3 1.5040 # SOURCE3 3 0.0117
bond_coeff @bond:o-p2 harmonic 449.7 1.5080 # SOURCE3 17 0.0306
bond_coeff @bond:o-p3 harmonic 440.4 1.5150 # SOURCE3 35 0.0297
bond_coeff @bond:o-p4 harmonic 456.4 1.5030 # SOURCE3 42 0.0749
bond_coeff @bond:o-p5 harmonic 487.7 1.4810 # SOURCE1 263 0.0205
bond_coeff @bond:o-pe harmonic 432.6 1.5210 # SOURCE3 20 0.0171
bond_coeff @bond:o-pf harmonic 432.6 1.5210 # SOURCE3 20 same_as_o-pe
bond_coeff @bond:o-px harmonic 459.2 1.5010 # SOURCE3 37 0.0160
bond_coeff @bond:o-py harmonic 477.5 1.4880 # SOURCE3 63 0.0091
bond_coeff @bond:o-s harmonic 194.8 1.8020 # SOURCE3 2 0.0000
bond_coeff @bond:o-s2 harmonic 333.6 1.5990 # SOURCE3 3 0.0707
bond_coeff @bond:o-s4 harmonic 448.7 1.4970 # SOURCE1 90 0.0000
bond_coeff @bond:o-s6 harmonic 541.1 1.4360 # SOURCE1 1038 0.0128
bond_coeff @bond:o-sh harmonic 328.0 1.6050 # SOURCE3 2 0.0000
bond_coeff @bond:os-os harmonic 343.6 1.4660 # SOURCE1 20 0.0067
bond_coeff @bond:os-p2 harmonic 371.9 1.5730 # SOURCE1 16 0.0000
bond_coeff @bond:os-p3 harmonic 272.2 1.6860 # SOURCE3 6 0.0201
bond_coeff @bond:os-p4 harmonic 311.6 1.6360 # SOURCE3 4 0.0057
bond_coeff @bond:os-p5 harmonic 342.5 1.6020 # SOURCE1 248 0.0400
bond_coeff @bond:os-py harmonic 328.5 1.6170 # SOURCE3 17 0.0139
bond_coeff @bond:os-s harmonic 195.8 1.8000 # SOURCE3 3 0.0052
bond_coeff @bond:o-ss harmonic 398.5 1.5370 # SOURCE3 3 0.0501
bond_coeff @bond:os-s4 harmonic 253.9 1.6990 # SOURCE3 8 0.0223
bond_coeff @bond:os-s6 harmonic 355.0 1.5770 # SOURCE1 75 0.0030
bond_coeff @bond:os-sh harmonic 273.6 1.6710 # SOURCE3 3 0.0106
bond_coeff @bond:os-ss harmonic 250.5 1.7040 # SOURCE3 9 0.0277
bond_coeff @bond:os-sy harmonic 253.9 1.6990 # SOURCE3 1 0.0000
bond_coeff @bond:o-sx harmonic 434.2 1.5080 # SOURCE3 40 0.0130
bond_coeff @bond:o-sy harmonic 493.0 1.4660 # SOURCE3 92 0.0114
bond_coeff @bond:p2-p2 harmonic 490.3 1.7860 # SOURCE3 25 0.3488
bond_coeff @bond:p2-p3 harmonic 211.9 2.1520 # SOURCE3 9 0.1777
bond_coeff @bond:p2-p4 harmonic 200.4 2.1790 # SOUECE3 1
bond_coeff @bond:p2-p5 harmonic 199.9 2.1800 # SOUECE3 1
bond_coeff @bond:p2-pe harmonic 401.6 1.8670 # SOURCE3 16 0.3571
bond_coeff @bond:p2-pf harmonic 401.6 1.8670 # SOURCE3 16 same_as_p2-pe
bond_coeff @bond:p2-s harmonic 361.6 1.7720 # SOURCE3 26 0.3014
bond_coeff @bond:p2-s4 harmonic 139.4 2.1900 # SOUECE3 1
bond_coeff @bond:p2-s6 harmonic 142.3 2.1800 # SOUECE3 1
bond_coeff @bond:p2-sh harmonic 224.0 1.9710 # SOURCE3 10 0.2829
bond_coeff @bond:p2-ss harmonic 226.6 1.9660 # SOURCE3 10 0.2739
bond_coeff @bond:p3-p3 harmonic 186.5 2.2140 # SOURCE1 41 0.0000
bond_coeff @bond:p3-p4 harmonic 185.7 2.2160 # SOURCE3 3 0.0011
bond_coeff @bond:p3-p5 harmonic 186.9 2.2130 # SOURCE3 9 0.0265
bond_coeff @bond:p3-s harmonic 179.7 2.0700 # SOUECE3 1
bond_coeff @bond:p3-s4 harmonic 173.2 2.0870 # SOURCE3 8 0.2235
bond_coeff @bond:p3-s6 harmonic 176.9 2.0770 # SOURCE3 11 0.1420
bond_coeff @bond:p3-sh harmonic 157.3 2.1320 # SOURCE3 3 0.0078
bond_coeff @bond:p3-ss harmonic 161.0 2.1210 # SOURCE3 3 0.0059
bond_coeff @bond:p4-p4 harmonic 273.1 2.0340 # SOURCE1 1 0.0000
bond_coeff @bond:p4-p5 harmonic 178.0 2.2370 # SOUECE3 1
bond_coeff @bond:p4-s harmonic 152.7 2.1460 # SOURCE3 5 0.0601
bond_coeff @bond:p4-s4 harmonic 123.2 2.2510 # SOUECE3 1
bond_coeff @bond:p4-s6 harmonic 118.9 2.2690 # SOUECE3 1
bond_coeff @bond:p4-sh harmonic 163.1 2.1150 # SOURCE3 4 0.0008
bond_coeff @bond:p4-ss harmonic 167.0 2.1040 # SOURCE3 4 0.0044
bond_coeff @bond:p5-p5 harmonic 261.4 2.0540 # SOURCE1 1 0.0000
bond_coeff @bond:p5-s harmonic 250.8 1.9220 # SOURCE1 89 0.0140
bond_coeff @bond:p5-s4 harmonic 191.9 2.0400 # SOUECE3 1
bond_coeff @bond:p5-s6 harmonic 191.9 2.0400 # SOUECE3 1
bond_coeff @bond:p5-sh harmonic 175.0 2.0820 # SOURCE3 3 0.0035
bond_coeff @bond:p5-ss harmonic 163.1 2.1149 # SOURCE4 24 0.0106
bond_coeff @bond:pe-pe harmonic 240.7 2.0920 # SOURCE3 7 0.1369
bond_coeff @bond:pe-pf harmonic 260.8 2.0550 # SOURCE3 1 0.0000
bond_coeff @bond:pe-px harmonic 291.4 2.0050 # SOURCE3 12 0.2609
bond_coeff @bond:pe-py harmonic 278.6 2.0250 # SOURCE3 12 0.2617
bond_coeff @bond:pe-s harmonic 374.7 1.7580 # SOURCE3 31 0.3197
bond_coeff @bond:pe-sx harmonic 145.9 2.1680 # SOURCE3 9 0.1743
bond_coeff @bond:pe-sy harmonic 133.0 2.2130 # SOURCE3 6 0.0127
bond_coeff @bond:pf-pf harmonic 240.7 2.0920 # SOURCE3 7 same_as_pe-pe
bond_coeff @bond:pf-px harmonic 291.4 2.0050 # SOURCE3 12 same_as_pe-px
bond_coeff @bond:pf-py harmonic 278.6 2.0250 # SOURCE3 12 same_as_pe-py
bond_coeff @bond:pf-s harmonic 374.7 1.7580 # SOURCE3 31 same_as_pe-s
bond_coeff @bond:pf-sx harmonic 145.9 2.1680 # SOURCE3 9 same_as_pe-sx
bond_coeff @bond:pf-sy harmonic 133.0 2.2130 # SOURCE3 6 same_as_pe-sy
bond_coeff @bond:px-py harmonic 192.3 2.1990 # SOURCE3 5 0.0238
bond_coeff @bond:px-sx harmonic 125.4 2.2420 # SOURCE3 3 0.0119
bond_coeff @bond:px-sy harmonic 123.7 2.2490 # SOURCE3 3 0.0272
bond_coeff @bond:py-py harmonic 197.5 2.1860 # SOURCE3 8 0.0132
bond_coeff @bond:py-sx harmonic 121.2 2.2590 # SOURCE3 7 0.0603
bond_coeff @bond:py-sy harmonic 141.7 2.1820 # SOURCE3 5 0.0047
bond_coeff @bond:s4-s4 harmonic 151.5 2.0800 # SOUECE3 1
bond_coeff @bond:s4-s6 harmonic 151.5 2.0800 # SOUECE3 1
bond_coeff @bond:s4-sh harmonic 125.7 2.1680 # SOURCE3 3 0.0227
bond_coeff @bond:s4-ss harmonic 126.2 2.1660 # SOURCE3 5 0.0247
bond_coeff @bond:s6-s6 harmonic 151.5 2.0800 # SOUECE3 1
bond_coeff @bond:s6-sh harmonic 142.6 2.1080 # SOURCE3 3 0.0144
bond_coeff @bond:s6-ss harmonic 139.6 2.1180 # SOURCE3 5 0.0209
bond_coeff @bond:sh-sh harmonic 158.9 2.0580 # SOURCE2 1 0.0000
bond_coeff @bond:sh-ss harmonic 155.8 2.0670 # SOURCE3 3 0.0029
bond_coeff @bond:s-s harmonic 169.0 2.0300 # SOURCE3 1 0.0000
bond_coeff @bond:s-s2 harmonic 229.2 1.8970 # SOURCE1 5 0.0000
bond_coeff @bond:s-s4 harmonic 152.8 2.0760 # SOURCE3 4 0.0345
bond_coeff @bond:s-s6 harmonic 166.0 2.0380 # SOURCE3 3 0.0311
bond_coeff @bond:s-sh harmonic 142.0 2.1100 # SOURCE3 2 0.0000
bond_coeff @bond:s-ss harmonic 148.5 2.0890 # SOURCE3 1 0.0000
bond_coeff @bond:ss-ss harmonic 161.7 2.0500 # SOURCE1 225 0.0015
bond_coeff @bond:sx-sx harmonic 80.9 2.3910 # SOURCE3 3 0.0185
bond_coeff @bond:sx-sy harmonic 105.3 2.2550 # SOURCE3 5 0.0737
bond_coeff @bond:sy-sy harmonic 106.4 2.2500 # SOURCE3 3 0.0289
} # (end of bond_coeffs)
write_once("Data Bonds By Type") {
@bond:ow-hw @atom:ow @atom:hw
@bond:br-br @atom:br @atom:br
@bond:br-c1 @atom:br @atom:c1
@bond:br-c2 @atom:br @atom:c2
@bond:br-c @atom:br @atom:c
@bond:br-c3 @atom:br @atom:c3
@bond:br-ca @atom:br @atom:ca
@bond:br-cc @atom:br @atom:cc
@bond:br-cx @atom:br @atom:cx
@bond:br-i @atom:br @atom:i
@bond:br-n1 @atom:br @atom:n1
@bond:br-n2 @atom:br @atom:n2
@bond:br-n @atom:br @atom:n
@bond:br-n3 @atom:br @atom:n3
@bond:br-n4 @atom:br @atom:n4
@bond:br-na @atom:br @atom:na
@bond:br-nh @atom:br @atom:nh
@bond:br-no @atom:br @atom:no
@bond:br-o @atom:br @atom:o
@bond:br-oh @atom:br @atom:oh
@bond:br-os @atom:br @atom:os
@bond:br-p2 @atom:br @atom:p2
@bond:br-p3 @atom:br @atom:p3
@bond:br-p4 @atom:br @atom:p4
@bond:br-p5 @atom:br @atom:p5
@bond:br-s @atom:br @atom:s
@bond:br-s4 @atom:br @atom:s4
@bond:br-s6 @atom:br @atom:s6
@bond:br-sh @atom:br @atom:sh
@bond:br-ss @atom:br @atom:ss
@bond:c1-c1 @atom:c1 @atom:c1
@bond:c1-c2 @atom:c1 @atom:c2
@bond:c1-c3 @atom:c1 @atom:c3
@bond:c1-ca @atom:c1 @atom:ca
@bond:c1-ce @atom:c1 @atom:ce
@bond:c1-cg @atom:c1 @atom:cg
@bond:c1-ch @atom:c1 @atom:ch
@bond:c1-cl @atom:c1 @atom:cl
@bond:c1-cx @atom:c1 @atom:cx
@bond:c1-f @atom:c1 @atom:f
@bond:c1-ha @atom:c1 @atom:ha
@bond:c1-hc @atom:c1 @atom:hc
@bond:c1-i @atom:c1 @atom:i
@bond:c1-n1 @atom:c1 @atom:n1
@bond:c1-n2 @atom:c1 @atom:n2
@bond:c1-n3 @atom:c1 @atom:n3
@bond:c1-n4 @atom:c1 @atom:n4
@bond:c1-n @atom:c1 @atom:n
@bond:c1-na @atom:c1 @atom:na
@bond:c1-ne @atom:c1 @atom:ne
@bond:c1-nf @atom:c1 @atom:nf
@bond:c1-nh @atom:c1 @atom:nh
@bond:c1-no @atom:c1 @atom:no
@bond:c1-o @atom:c1 @atom:o
@bond:c1-oh @atom:c1 @atom:oh
@bond:c1-os @atom:c1 @atom:os
@bond:c1-p2 @atom:c1 @atom:p2
@bond:c1-p3 @atom:c1 @atom:p3
@bond:c1-p4 @atom:c1 @atom:p4
@bond:c1-p5 @atom:c1 @atom:p5
@bond:c1-s2 @atom:c1 @atom:s2
@bond:c1-s @atom:c1 @atom:s
@bond:c1-s4 @atom:c1 @atom:s4
@bond:c1-s6 @atom:c1 @atom:s6
@bond:c1-sh @atom:c1 @atom:sh
@bond:c1-ss @atom:c1 @atom:ss
@bond:c2-c2 @atom:c2 @atom:c2
@bond:c2-c3 @atom:c2 @atom:c3
@bond:c2-ca @atom:c2 @atom:ca
@bond:c2-cc @atom:c2 @atom:cc
@bond:c2-cd @atom:c2 @atom:cd
@bond:c2-ce @atom:c2 @atom:ce
@bond:c2-cf @atom:c2 @atom:cf
@bond:c2-cl @atom:c2 @atom:cl
@bond:c2-cu @atom:c2 @atom:cu
@bond:c2-cx @atom:c2 @atom:cx
@bond:c2-cy @atom:c2 @atom:cy
@bond:c2-f @atom:c2 @atom:f
@bond:c2-h4 @atom:c2 @atom:h4
@bond:c2-h5 @atom:c2 @atom:h5
@bond:c2-ha @atom:c2 @atom:ha
@bond:c2-hc @atom:c2 @atom:hc
@bond:c2-hx @atom:c2 @atom:hx
@bond:c2-i @atom:c2 @atom:i
@bond:c2-n1 @atom:c2 @atom:n1
@bond:c2-n2 @atom:c2 @atom:n2
@bond:c2-n3 @atom:c2 @atom:n3
@bond:c2-n @atom:c2 @atom:n
@bond:c2-n4 @atom:c2 @atom:n4
@bond:c2-na @atom:c2 @atom:na
@bond:c2-nc @atom:c2 @atom:nc
@bond:c2-nd @atom:c2 @atom:nd
@bond:c2-ne @atom:c2 @atom:ne
@bond:c2-nf @atom:c2 @atom:nf
@bond:c2-nh @atom:c2 @atom:nh
@bond:c2-no @atom:c2 @atom:no
@bond:c2-o @atom:c2 @atom:o
@bond:c2-oh @atom:c2 @atom:oh
@bond:c2-os @atom:c2 @atom:os
@bond:c2-p2 @atom:c2 @atom:p2
@bond:c2-p3 @atom:c2 @atom:p3
@bond:c2-p4 @atom:c2 @atom:p4
@bond:c2-p5 @atom:c2 @atom:p5
@bond:c2-pe @atom:c2 @atom:pe
@bond:c2-pf @atom:c2 @atom:pf
@bond:c2-s2 @atom:c2 @atom:s2
@bond:c2-s @atom:c2 @atom:s
@bond:c2-s4 @atom:c2 @atom:s4
@bond:c2-s6 @atom:c2 @atom:s6
@bond:c2-sh @atom:c2 @atom:sh
@bond:c2-ss @atom:c2 @atom:ss
@bond:c3-c3 @atom:c3 @atom:c3
@bond:c3-ca @atom:c3 @atom:ca
@bond:c3-cc @atom:c3 @atom:cc
@bond:c3-cd @atom:c3 @atom:cd
@bond:c3-ce @atom:c3 @atom:ce
@bond:c3-cf @atom:c3 @atom:cf
@bond:c3-cl @atom:c3 @atom:cl
@bond:c3-cu @atom:c3 @atom:cu
@bond:c3-cv @atom:c3 @atom:cv
@bond:c3-cx @atom:c3 @atom:cx
@bond:c3-cy @atom:c3 @atom:cy
@bond:c3-f @atom:c3 @atom:f
@bond:c3-h1 @atom:c3 @atom:h1
@bond:c3-h2 @atom:c3 @atom:h2
@bond:c3-h3 @atom:c3 @atom:h3
@bond:c3-hc @atom:c3 @atom:hc
@bond:c3-hx @atom:c3 @atom:hx
@bond:c3-i @atom:c3 @atom:i
@bond:c3-n1 @atom:c3 @atom:n1
@bond:c3-n2 @atom:c3 @atom:n2
@bond:c3-n @atom:c3 @atom:n
@bond:c3-n3 @atom:c3 @atom:n3
@bond:c3-n4 @atom:c3 @atom:n4
@bond:c3-na @atom:c3 @atom:na
@bond:c3-nc @atom:c3 @atom:nc
@bond:c3-nd @atom:c3 @atom:nd
@bond:c3-nh @atom:c3 @atom:nh
@bond:c3-no @atom:c3 @atom:no
@bond:c3-o @atom:c3 @atom:o
@bond:c3-oh @atom:c3 @atom:oh
@bond:c3-os @atom:c3 @atom:os
@bond:c3-p2 @atom:c3 @atom:p2
@bond:c3-p3 @atom:c3 @atom:p3
@bond:c3-p4 @atom:c3 @atom:p4
@bond:c3-p5 @atom:c3 @atom:p5
@bond:c3-px @atom:c3 @atom:px
@bond:c3-py @atom:c3 @atom:py
@bond:c3-s @atom:c3 @atom:s
@bond:c3-s4 @atom:c3 @atom:s4
@bond:c3-s6 @atom:c3 @atom:s6
@bond:c3-sh @atom:c3 @atom:sh
@bond:c3-ss @atom:c3 @atom:ss
@bond:c3-sx @atom:c3 @atom:sx
@bond:c3-sy @atom:c3 @atom:sy
@bond:ca-ca @atom:ca @atom:ca
@bond:ca-cc @atom:ca @atom:cc
@bond:ca-cd @atom:ca @atom:cd
@bond:ca-ce @atom:ca @atom:ce
@bond:ca-cf @atom:ca @atom:cf
@bond:ca-cg @atom:ca @atom:cg
@bond:ca-ch @atom:ca @atom:ch
@bond:ca-cl @atom:ca @atom:cl
@bond:ca-cp @atom:ca @atom:cp
@bond:ca-cq @atom:ca @atom:cq
@bond:ca-cx @atom:ca @atom:cx
@bond:ca-cy @atom:ca @atom:cy
@bond:ca-f @atom:ca @atom:f
@bond:ca-h4 @atom:ca @atom:h4
@bond:ca-h5 @atom:ca @atom:h5
@bond:ca-ha @atom:ca @atom:ha
@bond:ca-i @atom:ca @atom:i
@bond:ca-n1 @atom:ca @atom:n1
@bond:ca-n2 @atom:ca @atom:n2
@bond:ca-n @atom:ca @atom:n
@bond:ca-n4 @atom:ca @atom:n4
@bond:ca-na @atom:ca @atom:na
@bond:ca-nb @atom:ca @atom:nb
@bond:ca-nc @atom:ca @atom:nc
@bond:ca-nd @atom:ca @atom:nd
@bond:ca-ne @atom:ca @atom:ne
@bond:ca-nf @atom:ca @atom:nf
@bond:ca-nh @atom:ca @atom:nh
@bond:ca-no @atom:ca @atom:no
@bond:ca-o @atom:ca @atom:o
@bond:ca-oh @atom:ca @atom:oh
@bond:ca-os @atom:ca @atom:os
@bond:ca-p2 @atom:ca @atom:p2
@bond:ca-p3 @atom:ca @atom:p3
@bond:ca-p4 @atom:ca @atom:p4
@bond:ca-p5 @atom:ca @atom:p5
@bond:ca-pe @atom:ca @atom:pe
@bond:ca-pf @atom:ca @atom:pf
@bond:ca-px @atom:ca @atom:px
@bond:ca-py @atom:ca @atom:py
@bond:ca-s @atom:ca @atom:s
@bond:ca-s4 @atom:ca @atom:s4
@bond:ca-s6 @atom:ca @atom:s6
@bond:ca-sh @atom:ca @atom:sh
@bond:ca-ss @atom:ca @atom:ss
@bond:ca-sx @atom:ca @atom:sx
@bond:ca-sy @atom:ca @atom:sy
@bond:c-c1 @atom:c @atom:c1
@bond:c-c2 @atom:c @atom:c2
@bond:c-c @atom:c @atom:c
@bond:c-c3 @atom:c @atom:c3
@bond:c-ca @atom:c @atom:ca
@bond:c-cc @atom:c @atom:cc
@bond:cc-cc @atom:cc @atom:cc
@bond:cc-cd @atom:cc @atom:cd
@bond:cc-ce @atom:cc @atom:ce
@bond:cc-cf @atom:cc @atom:cf
@bond:cc-cg @atom:cc @atom:cg
@bond:cc-ch @atom:cc @atom:ch
@bond:cc-cl @atom:cc @atom:cl
@bond:cc-cx @atom:cc @atom:cx
@bond:c-cd @atom:c @atom:cd
@bond:c-ce @atom:c @atom:ce
@bond:c-cf @atom:c @atom:cf
@bond:cc-f @atom:cc @atom:f
@bond:c-cg @atom:c @atom:cg
@bond:c-ch @atom:c @atom:ch
@bond:cc-h4 @atom:cc @atom:h4
@bond:cc-h5 @atom:cc @atom:h5
@bond:cc-ha @atom:cc @atom:ha
@bond:c-cl @atom:c @atom:cl
@bond:cc-n2 @atom:cc @atom:n2
@bond:cc-n @atom:cc @atom:n
@bond:cc-n4 @atom:cc @atom:n4
@bond:cc-na @atom:cc @atom:na
@bond:cc-nc @atom:cc @atom:nc
@bond:cc-nd @atom:cc @atom:nd
@bond:cc-ne @atom:cc @atom:ne
@bond:cc-nf @atom:cc @atom:nf
@bond:cc-nh @atom:cc @atom:nh
@bond:cc-no @atom:cc @atom:no
@bond:cc-oh @atom:cc @atom:oh
@bond:cc-os @atom:cc @atom:os
@bond:cc-pd @atom:cc @atom:pd
@bond:cc-sh @atom:cc @atom:sh
@bond:cc-ss @atom:cc @atom:ss
@bond:cc-sx @atom:cc @atom:sx
@bond:cc-sy @atom:cc @atom:sy
@bond:c-cu @atom:c @atom:cu
@bond:c-cx @atom:c @atom:cx
@bond:c-cy @atom:c @atom:cy
@bond:cd-cd @atom:cd @atom:cd
@bond:cd-ce @atom:cd @atom:ce
@bond:cd-cf @atom:cd @atom:cf
@bond:cd-cg @atom:cd @atom:cg
@bond:cd-ch @atom:cd @atom:ch
@bond:cd-cl @atom:cd @atom:cl
@bond:cd-cx @atom:cd @atom:cx
@bond:cd-cy @atom:cd @atom:cy
@bond:cd-h4 @atom:cd @atom:h4
@bond:cd-h5 @atom:cd @atom:h5
@bond:cd-ha @atom:cd @atom:ha
@bond:cd-n2 @atom:cd @atom:n2
@bond:cd-n @atom:cd @atom:n
@bond:cd-na @atom:cd @atom:na
@bond:cd-nc @atom:cd @atom:nc
@bond:cd-nd @atom:cd @atom:nd
@bond:cd-ne @atom:cd @atom:ne
@bond:cd-nh @atom:cd @atom:nh
@bond:cd-oh @atom:cd @atom:oh
@bond:cd-os @atom:cd @atom:os
@bond:cd-pc @atom:cd @atom:pc
@bond:cd-ss @atom:cd @atom:ss
@bond:cd-sy @atom:cd @atom:sy
@bond:ce-ce @atom:ce @atom:ce
@bond:ce-cf @atom:ce @atom:cf
@bond:ce-cg @atom:ce @atom:cg
@bond:ce-ch @atom:ce @atom:ch
@bond:ce-cl @atom:ce @atom:cl
@bond:ce-cx @atom:ce @atom:cx
@bond:ce-cy @atom:ce @atom:cy
@bond:ce-h4 @atom:ce @atom:h4
@bond:ce-ha @atom:ce @atom:ha
@bond:ce-n1 @atom:ce @atom:n1
@bond:ce-n2 @atom:ce @atom:n2
@bond:ce-n @atom:ce @atom:n
@bond:ce-na @atom:ce @atom:na
@bond:ce-ne @atom:ce @atom:ne
@bond:ce-nf @atom:ce @atom:nf
@bond:ce-nh @atom:ce @atom:nh
@bond:ce-oh @atom:ce @atom:oh
@bond:ce-os @atom:ce @atom:os
@bond:ce-p2 @atom:ce @atom:p2
@bond:ce-pe @atom:ce @atom:pe
@bond:ce-px @atom:ce @atom:px
@bond:ce-py @atom:ce @atom:py
@bond:ce-s @atom:ce @atom:s
@bond:ce-ss @atom:ce @atom:ss
@bond:ce-sx @atom:ce @atom:sx
@bond:ce-sy @atom:ce @atom:sy
@bond:c-f @atom:c @atom:f
@bond:cf-cf @atom:cf @atom:cf
@bond:cf-cg @atom:cf @atom:cg
@bond:cf-ch @atom:cf @atom:ch
@bond:cf-h4 @atom:cf @atom:h4
@bond:cf-ha @atom:cf @atom:ha
@bond:cf-n1 @atom:cf @atom:n1
@bond:cf-n2 @atom:cf @atom:n2
@bond:cf-n @atom:cf @atom:n
@bond:cf-ne @atom:cf @atom:ne
@bond:cf-nf @atom:cf @atom:nf
@bond:cf-nh @atom:cf @atom:nh
@bond:cf-oh @atom:cf @atom:oh
@bond:cf-os @atom:cf @atom:os
@bond:cf-p2 @atom:cf @atom:p2
@bond:cf-pf @atom:cf @atom:pf
@bond:cf-px @atom:cf @atom:px
@bond:cf-py @atom:cf @atom:py
@bond:cf-s @atom:cf @atom:s
@bond:cf-sx @atom:cf @atom:sx
@bond:cf-sy @atom:cf @atom:sy
@bond:cg-cg @atom:cg @atom:cg
@bond:cg-ch @atom:cg @atom:ch
@bond:cg-n1 @atom:cg @atom:n1
@bond:cg-ne @atom:cg @atom:ne
@bond:cg-pe @atom:cg @atom:pe
@bond:c-h4 @atom:c @atom:h4
@bond:c-h5 @atom:c @atom:h5
@bond:c-ha @atom:c @atom:ha
@bond:ch-ch @atom:ch @atom:ch
@bond:ch-n1 @atom:ch @atom:n1
@bond:ch-nf @atom:ch @atom:nf
@bond:ch-pf @atom:ch @atom:pf
@bond:c-i @atom:c @atom:i
@bond:cl-cl @atom:cl @atom:cl
@bond:cl-cx @atom:cl @atom:cx
@bond:cl-cy @atom:cl @atom:cy
@bond:cl-f @atom:cl @atom:f
@bond:cl-i @atom:cl @atom:i
@bond:cl-n1 @atom:cl @atom:n1
@bond:cl-n2 @atom:cl @atom:n2
@bond:cl-n3 @atom:cl @atom:n3
@bond:cl-n @atom:cl @atom:n
@bond:cl-n4 @atom:cl @atom:n4
@bond:cl-na @atom:cl @atom:na
@bond:cl-nh @atom:cl @atom:nh
@bond:cl-no @atom:cl @atom:no
@bond:cl-o @atom:cl @atom:o
@bond:cl-oh @atom:cl @atom:oh
@bond:cl-os @atom:cl @atom:os
@bond:cl-p2 @atom:cl @atom:p2
@bond:cl-p3 @atom:cl @atom:p3
@bond:cl-p4 @atom:cl @atom:p4
@bond:cl-p5 @atom:cl @atom:p5
@bond:cl-pb @atom:cl @atom:pb
@bond:cl-s @atom:cl @atom:s
@bond:cl-s2 @atom:cl @atom:s2
@bond:cl-s4 @atom:cl @atom:s4
@bond:cl-s6 @atom:cl @atom:s6
@bond:cl-sh @atom:cl @atom:sh
@bond:cl-ss @atom:cl @atom:ss
@bond:cl-sx @atom:cl @atom:sx
@bond:cl-sy @atom:cl @atom:sy
@bond:c-n2 @atom:c @atom:n2
@bond:c-n4 @atom:c @atom:n4
@bond:c-n @atom:c @atom:n
@bond:c-nc @atom:c @atom:nc
@bond:c-nd @atom:c @atom:nd
@bond:c-ne @atom:c @atom:ne
@bond:c-nf @atom:c @atom:nf
@bond:c-no @atom:c @atom:no
@bond:c-o @atom:c @atom:o
@bond:c-oh @atom:c @atom:oh
@bond:c-os @atom:c @atom:os
@bond:c-p2 @atom:c @atom:p2
@bond:c-p3 @atom:c @atom:p3
@bond:c-p4 @atom:c @atom:p4
@bond:c-p5 @atom:c @atom:p5
@bond:cp-cp @atom:cp @atom:cp
@bond:cp-cq @atom:cp @atom:cq
@bond:c-pe @atom:c @atom:pe
@bond:c-pf @atom:c @atom:pf
@bond:cp-na @atom:cp @atom:na
@bond:cp-nb @atom:cp @atom:nb
@bond:c-px @atom:c @atom:px
@bond:c-py @atom:c @atom:py
@bond:cq-cq @atom:cq @atom:cq
@bond:c-s @atom:c @atom:s
@bond:c-s4 @atom:c @atom:s4
@bond:c-s6 @atom:c @atom:s6
@bond:c-sh @atom:c @atom:sh
@bond:c-ss @atom:c @atom:ss
@bond:c-sx @atom:c @atom:sx
@bond:c-sy @atom:c @atom:sy
@bond:cu-cu @atom:cu @atom:cu
@bond:cu-cx @atom:cu @atom:cx
@bond:cu-ha @atom:cu @atom:ha
@bond:cv-cv @atom:cv @atom:cv
@bond:cv-cy @atom:cv @atom:cy
@bond:cv-ha @atom:cv @atom:ha
@bond:cx-cv @atom:cx @atom:cv
@bond:cx-cx @atom:cx @atom:cx
@bond:cx-cy @atom:cx @atom:cy
@bond:cx-f @atom:cx @atom:f
@bond:cx-h1 @atom:cx @atom:h1
@bond:cx-h2 @atom:cx @atom:h2
@bond:cx-hc @atom:cx @atom:hc
@bond:cx-hx @atom:cx @atom:hx
@bond:cx-n2 @atom:cx @atom:n2
@bond:cx-n3 @atom:cx @atom:n3
@bond:cx-n @atom:cx @atom:n
@bond:cx-na @atom:cx @atom:na
@bond:cx-nh @atom:cx @atom:nh
@bond:cx-oh @atom:cx @atom:oh
@bond:cx-os @atom:cx @atom:os
@bond:cx-p3 @atom:cx @atom:p3
@bond:cx-s4 @atom:cx @atom:s4
@bond:cx-s6 @atom:cx @atom:s6
@bond:cx-ss @atom:cx @atom:ss
@bond:cy-cy @atom:cy @atom:cy
@bond:cy-f @atom:cy @atom:f
@bond:cy-h1 @atom:cy @atom:h1
@bond:cy-h2 @atom:cy @atom:h2
@bond:cy-hc @atom:cy @atom:hc
@bond:cy-n @atom:cy @atom:n
@bond:cy-n3 @atom:cy @atom:n3
@bond:cy-oh @atom:cy @atom:oh
@bond:cy-os @atom:cy @atom:os
@bond:cy-s6 @atom:cy @atom:s6
@bond:cy-ss @atom:cy @atom:ss
@bond:cz-nh @atom:cz @atom:nh
@bond:f-n1 @atom:f @atom:n1
@bond:f-n2 @atom:f @atom:n2
@bond:f-n3 @atom:f @atom:n3
@bond:f-n @atom:f @atom:n
@bond:f-n4 @atom:f @atom:n4
@bond:f-na @atom:f @atom:na
@bond:f-nh @atom:f @atom:nh
@bond:f-no @atom:f @atom:no
@bond:f-o @atom:f @atom:o
@bond:f-oh @atom:f @atom:oh
@bond:f-os @atom:f @atom:os
@bond:f-p2 @atom:f @atom:p2
@bond:f-p3 @atom:f @atom:p3
@bond:f-p4 @atom:f @atom:p4
@bond:f-p5 @atom:f @atom:p5
@bond:f-s2 @atom:f @atom:s2
@bond:f-s @atom:f @atom:s
@bond:f-s4 @atom:f @atom:s4
@bond:f-s6 @atom:f @atom:s6
@bond:f-sh @atom:f @atom:sh
@bond:f-ss @atom:f @atom:ss
@bond:hn-n1 @atom:hn @atom:n1
@bond:hn-n2 @atom:hn @atom:n2
@bond:hn-n3 @atom:hn @atom:n3
@bond:hn-n @atom:hn @atom:n
@bond:hn-n4 @atom:hn @atom:n4
@bond:hn-na @atom:hn @atom:na
@bond:hn-nh @atom:hn @atom:nh
@bond:hn-no @atom:hn @atom:no
@bond:ho-o @atom:ho @atom:o
@bond:ho-oh @atom:ho @atom:oh
@bond:hp-p2 @atom:hp @atom:p2
@bond:hp-p3 @atom:hp @atom:p3
@bond:hp-p4 @atom:hp @atom:p4
@bond:hp-p5 @atom:hp @atom:p5
@bond:hs-s @atom:hs @atom:s
@bond:hs-s4 @atom:hs @atom:s4
@bond:hs-s6 @atom:hs @atom:s6
@bond:hs-sh @atom:hs @atom:sh
@bond:i-i @atom:i @atom:i
@bond:i-n1 @atom:i @atom:n1
@bond:i-n2 @atom:i @atom:n2
@bond:i-n @atom:i @atom:n
@bond:i-n3 @atom:i @atom:n3
@bond:i-n4 @atom:i @atom:n4
@bond:i-na @atom:i @atom:na
@bond:i-nh @atom:i @atom:nh
@bond:i-no @atom:i @atom:no
@bond:i-o @atom:i @atom:o
@bond:i-oh @atom:i @atom:oh
@bond:i-os @atom:i @atom:os
@bond:i-p2 @atom:i @atom:p2
@bond:i-p3 @atom:i @atom:p3
@bond:i-p4 @atom:i @atom:p4
@bond:i-p5 @atom:i @atom:p5
@bond:i-s @atom:i @atom:s
@bond:i-s4 @atom:i @atom:s4
@bond:i-s6 @atom:i @atom:s6
@bond:i-sh @atom:i @atom:sh
@bond:i-ss @atom:i @atom:ss
@bond:n1-n1 @atom:n1 @atom:n1
@bond:n1-n2 @atom:n1 @atom:n2
@bond:n1-n3 @atom:n1 @atom:n3
@bond:n1-n4 @atom:n1 @atom:n4
@bond:n1-na @atom:n1 @atom:na
@bond:n1-nc @atom:n1 @atom:nc
@bond:n1-nd @atom:n1 @atom:nd
@bond:n1-ne @atom:n1 @atom:ne
@bond:n1-nf @atom:n1 @atom:nf
@bond:n1-nh @atom:n1 @atom:nh
@bond:n1-no @atom:n1 @atom:no
@bond:n1-o @atom:n1 @atom:o
@bond:n1-oh @atom:n1 @atom:oh
@bond:n1-os @atom:n1 @atom:os
@bond:n1-p2 @atom:n1 @atom:p2
@bond:n1-p3 @atom:n1 @atom:p3
@bond:n1-p4 @atom:n1 @atom:p4
@bond:n1-p5 @atom:n1 @atom:p5
@bond:n1-s2 @atom:n1 @atom:s2
@bond:n1-s @atom:n1 @atom:s
@bond:n1-s4 @atom:n1 @atom:s4
@bond:n1-s6 @atom:n1 @atom:s6
@bond:n1-sh @atom:n1 @atom:sh
@bond:n1-ss @atom:n1 @atom:ss
@bond:n2-n2 @atom:n2 @atom:n2
@bond:n2-n3 @atom:n2 @atom:n3
@bond:n2-n4 @atom:n2 @atom:n4
@bond:n2-na @atom:n2 @atom:na
@bond:n2-nc @atom:n2 @atom:nc
@bond:n2-nd @atom:n2 @atom:nd
@bond:n2-ne @atom:n2 @atom:ne
@bond:n2-nf @atom:n2 @atom:nf
@bond:n2-nh @atom:n2 @atom:nh
@bond:n2-no @atom:n2 @atom:no
@bond:n2-o @atom:n2 @atom:o
@bond:n2-oh @atom:n2 @atom:oh
@bond:n2-os @atom:n2 @atom:os
@bond:n2-p2 @atom:n2 @atom:p2
@bond:n2-p3 @atom:n2 @atom:p3
@bond:n2-p4 @atom:n2 @atom:p4
@bond:n2-p5 @atom:n2 @atom:p5
@bond:n2-pe @atom:n2 @atom:pe
@bond:n2-pf @atom:n2 @atom:pf
@bond:n2-s2 @atom:n2 @atom:s2
@bond:n2-s4 @atom:n2 @atom:s4
@bond:n2-s @atom:n2 @atom:s
@bond:n2-s6 @atom:n2 @atom:s6
@bond:n2-sh @atom:n2 @atom:sh
@bond:n2-ss @atom:n2 @atom:ss
@bond:n3-n3 @atom:n3 @atom:n3
@bond:n3-n4 @atom:n3 @atom:n4
@bond:n3-na @atom:n3 @atom:na
@bond:n3-nh @atom:n3 @atom:nh
@bond:n3-no @atom:n3 @atom:no
@bond:n3-o @atom:n3 @atom:o
@bond:n3-oh @atom:n3 @atom:oh
@bond:n3-os @atom:n3 @atom:os
@bond:n3-p2 @atom:n3 @atom:p2
@bond:n3-p3 @atom:n3 @atom:p3
@bond:n3-p4 @atom:n3 @atom:p4
@bond:n3-p5 @atom:n3 @atom:p5
@bond:n3-py @atom:n3 @atom:py
@bond:n3-s @atom:n3 @atom:s
@bond:n3-s4 @atom:n3 @atom:s4
@bond:n3-s6 @atom:n3 @atom:s6
@bond:n3-sh @atom:n3 @atom:sh
@bond:n3-ss @atom:n3 @atom:ss
@bond:n3-sy @atom:n3 @atom:sy
@bond:n4-n4 @atom:n4 @atom:n4
@bond:n4-na @atom:n4 @atom:na
@bond:n4-nh @atom:n4 @atom:nh
@bond:n4-no @atom:n4 @atom:no
@bond:n4-o @atom:n4 @atom:o
@bond:n4-oh @atom:n4 @atom:oh
@bond:n4-os @atom:n4 @atom:os
@bond:n4-p2 @atom:n4 @atom:p2
@bond:n4-p3 @atom:n4 @atom:p3
@bond:n4-p4 @atom:n4 @atom:p4
@bond:n4-p5 @atom:n4 @atom:p5
@bond:n4-py @atom:n4 @atom:py
@bond:n4-s @atom:n4 @atom:s
@bond:n4-s4 @atom:n4 @atom:s4
@bond:n4-s6 @atom:n4 @atom:s6
@bond:n4-sh @atom:n4 @atom:sh
@bond:n4-ss @atom:n4 @atom:ss
@bond:na-na @atom:na @atom:na
@bond:na-nb @atom:na @atom:nb
@bond:na-nc @atom:na @atom:nc
@bond:na-nd @atom:na @atom:nd
@bond:na-nh @atom:na @atom:nh
@bond:na-no @atom:na @atom:no
@bond:na-o @atom:na @atom:o
@bond:na-oh @atom:na @atom:oh
@bond:na-os @atom:na @atom:os
@bond:na-p2 @atom:na @atom:p2
@bond:na-p3 @atom:na @atom:p3
@bond:na-p4 @atom:na @atom:p4
@bond:na-p5 @atom:na @atom:p5
@bond:na-pc @atom:na @atom:pc
@bond:na-pd @atom:na @atom:pd
@bond:na-py @atom:na @atom:py
@bond:na-s @atom:na @atom:s
@bond:na-s4 @atom:na @atom:s4
@bond:na-s6 @atom:na @atom:s6
@bond:na-sh @atom:na @atom:sh
@bond:na-ss @atom:na @atom:ss
@bond:na-sy @atom:na @atom:sy
@bond:nb-nb @atom:nb @atom:nb
@bond:nb-pb @atom:nb @atom:pb
@bond:nc-nc @atom:nc @atom:nc
@bond:nc-nd @atom:nc @atom:nd
@bond:nc-os @atom:nc @atom:os
@bond:nc-ss @atom:nc @atom:ss
@bond:nc-sy @atom:nc @atom:sy
@bond:nd-nd @atom:nd @atom:nd
@bond:nd-os @atom:nd @atom:os
@bond:nd-ss @atom:nd @atom:ss
@bond:nd-sy @atom:nd @atom:sy
@bond:ne-ne @atom:ne @atom:ne
@bond:ne-nf @atom:ne @atom:nf
@bond:ne-o @atom:ne @atom:o
@bond:ne-p2 @atom:ne @atom:p2
@bond:ne-pe @atom:ne @atom:pe
@bond:ne-px @atom:ne @atom:px
@bond:ne-py @atom:ne @atom:py
@bond:ne-s @atom:ne @atom:s
@bond:ne-sx @atom:ne @atom:sx
@bond:ne-sy @atom:ne @atom:sy
@bond:nf-nf @atom:nf @atom:nf
@bond:nf-o @atom:nf @atom:o
@bond:nf-p2 @atom:nf @atom:p2
@bond:nf-pf @atom:nf @atom:pf
@bond:nf-px @atom:nf @atom:px
@bond:nf-py @atom:nf @atom:py
@bond:nf-s @atom:nf @atom:s
@bond:nf-sx @atom:nf @atom:sx
@bond:nf-sy @atom:nf @atom:sy
@bond:nh-nh @atom:nh @atom:nh
@bond:nh-no @atom:nh @atom:no
@bond:nh-o @atom:nh @atom:o
@bond:nh-oh @atom:nh @atom:oh
@bond:nh-os @atom:nh @atom:os
@bond:nh-p2 @atom:nh @atom:p2
@bond:nh-p3 @atom:nh @atom:p3
@bond:nh-p4 @atom:nh @atom:p4
@bond:nh-p5 @atom:nh @atom:p5
@bond:nh-s @atom:nh @atom:s
@bond:nh-s4 @atom:nh @atom:s4
@bond:nh-s6 @atom:nh @atom:s6
@bond:nh-sh @atom:nh @atom:sh
@bond:nh-ss @atom:nh @atom:ss
@bond:nh-sy @atom:nh @atom:sy
@bond:n-n1 @atom:n @atom:n1
@bond:n-n2 @atom:n @atom:n2
@bond:n-n3 @atom:n @atom:n3
@bond:n-n4 @atom:n @atom:n4
@bond:n-n @atom:n @atom:n
@bond:n-na @atom:n @atom:na
@bond:n-nc @atom:n @atom:nc
@bond:n-nd @atom:n @atom:nd
@bond:n-nh @atom:n @atom:nh
@bond:n-no @atom:n @atom:no
@bond:n-o @atom:n @atom:o
@bond:n-oh @atom:n @atom:oh
@bond:no-no @atom:no @atom:no
@bond:no-o @atom:no @atom:o
@bond:no-oh @atom:no @atom:oh
@bond:no-os @atom:no @atom:os
@bond:no-os @atom:no @atom:os
@bond:no-p2 @atom:no @atom:p2
@bond:no-p3 @atom:no @atom:p3
@bond:no-p4 @atom:no @atom:p4
@bond:no-p5 @atom:no @atom:p5
@bond:no-s @atom:no @atom:s
@bond:n-os @atom:n @atom:os
@bond:no-s4 @atom:no @atom:s4
@bond:no-s6 @atom:no @atom:s6
@bond:no-sh @atom:no @atom:sh
@bond:no-ss @atom:no @atom:ss
@bond:n-p2 @atom:n @atom:p2
@bond:n-p3 @atom:n @atom:p3
@bond:n-p4 @atom:n @atom:p4
@bond:n-p5 @atom:n @atom:p5
@bond:n-pc @atom:n @atom:pc
@bond:n-pd @atom:n @atom:pd
@bond:n-s @atom:n @atom:s
@bond:n-s4 @atom:n @atom:s4
@bond:n-s6 @atom:n @atom:s6
@bond:n-sh @atom:n @atom:sh
@bond:n-ss @atom:n @atom:ss
@bond:n-sy @atom:n @atom:sy
@bond:oh-oh @atom:oh @atom:oh
@bond:oh-os @atom:oh @atom:os
@bond:oh-p2 @atom:oh @atom:p2
@bond:oh-p3 @atom:oh @atom:p3
@bond:oh-p4 @atom:oh @atom:p4
@bond:oh-p5 @atom:oh @atom:p5
@bond:oh-py @atom:oh @atom:py
@bond:oh-s @atom:oh @atom:s
@bond:oh-s4 @atom:oh @atom:s4
@bond:oh-s6 @atom:oh @atom:s6
@bond:oh-sh @atom:oh @atom:sh
@bond:oh-ss @atom:oh @atom:ss
@bond:oh-sy @atom:oh @atom:sy
@bond:o-o @atom:o @atom:o
@bond:o-oh @atom:o @atom:oh
@bond:o-os @atom:o @atom:os
@bond:o-p2 @atom:o @atom:p2
@bond:o-p3 @atom:o @atom:p3
@bond:o-p4 @atom:o @atom:p4
@bond:o-p5 @atom:o @atom:p5
@bond:o-pe @atom:o @atom:pe
@bond:o-pf @atom:o @atom:pf
@bond:o-px @atom:o @atom:px
@bond:o-py @atom:o @atom:py
@bond:o-s @atom:o @atom:s
@bond:o-s2 @atom:o @atom:s2
@bond:o-s4 @atom:o @atom:s4
@bond:o-s6 @atom:o @atom:s6
@bond:o-sh @atom:o @atom:sh
@bond:os-os @atom:os @atom:os
@bond:os-p2 @atom:os @atom:p2
@bond:os-p3 @atom:os @atom:p3
@bond:os-p4 @atom:os @atom:p4
@bond:os-p5 @atom:os @atom:p5
@bond:os-py @atom:os @atom:py
@bond:os-s @atom:os @atom:s
@bond:o-ss @atom:o @atom:ss
@bond:os-s4 @atom:os @atom:s4
@bond:os-s6 @atom:os @atom:s6
@bond:os-sh @atom:os @atom:sh
@bond:os-ss @atom:os @atom:ss
@bond:os-sy @atom:os @atom:sy
@bond:o-sx @atom:o @atom:sx
@bond:o-sy @atom:o @atom:sy
@bond:p2-p2 @atom:p2 @atom:p2
@bond:p2-p3 @atom:p2 @atom:p3
@bond:p2-p4 @atom:p2 @atom:p4
@bond:p2-p5 @atom:p2 @atom:p5
@bond:p2-pe @atom:p2 @atom:pe
@bond:p2-pf @atom:p2 @atom:pf
@bond:p2-s @atom:p2 @atom:s
@bond:p2-s4 @atom:p2 @atom:s4
@bond:p2-s6 @atom:p2 @atom:s6
@bond:p2-sh @atom:p2 @atom:sh
@bond:p2-ss @atom:p2 @atom:ss
@bond:p3-p3 @atom:p3 @atom:p3
@bond:p3-p4 @atom:p3 @atom:p4
@bond:p3-p5 @atom:p3 @atom:p5
@bond:p3-s @atom:p3 @atom:s
@bond:p3-s4 @atom:p3 @atom:s4
@bond:p3-s6 @atom:p3 @atom:s6
@bond:p3-sh @atom:p3 @atom:sh
@bond:p3-ss @atom:p3 @atom:ss
@bond:p4-p4 @atom:p4 @atom:p4
@bond:p4-p5 @atom:p4 @atom:p5
@bond:p4-s @atom:p4 @atom:s
@bond:p4-s4 @atom:p4 @atom:s4
@bond:p4-s6 @atom:p4 @atom:s6
@bond:p4-sh @atom:p4 @atom:sh
@bond:p4-ss @atom:p4 @atom:ss
@bond:p5-p5 @atom:p5 @atom:p5
@bond:p5-s @atom:p5 @atom:s
@bond:p5-s4 @atom:p5 @atom:s4
@bond:p5-s6 @atom:p5 @atom:s6
@bond:p5-sh @atom:p5 @atom:sh
@bond:p5-ss @atom:p5 @atom:ss
@bond:pe-pe @atom:pe @atom:pe
@bond:pe-pf @atom:pe @atom:pf
@bond:pe-px @atom:pe @atom:px
@bond:pe-py @atom:pe @atom:py
@bond:pe-s @atom:pe @atom:s
@bond:pe-sx @atom:pe @atom:sx
@bond:pe-sy @atom:pe @atom:sy
@bond:pf-pf @atom:pf @atom:pf
@bond:pf-px @atom:pf @atom:px
@bond:pf-py @atom:pf @atom:py
@bond:pf-s @atom:pf @atom:s
@bond:pf-sx @atom:pf @atom:sx
@bond:pf-sy @atom:pf @atom:sy
@bond:px-py @atom:px @atom:py
@bond:px-sx @atom:px @atom:sx
@bond:px-sy @atom:px @atom:sy
@bond:py-py @atom:py @atom:py
@bond:py-sx @atom:py @atom:sx
@bond:py-sy @atom:py @atom:sy
@bond:s4-s4 @atom:s4 @atom:s4
@bond:s4-s6 @atom:s4 @atom:s6
@bond:s4-sh @atom:s4 @atom:sh
@bond:s4-ss @atom:s4 @atom:ss
@bond:s6-s6 @atom:s6 @atom:s6
@bond:s6-sh @atom:s6 @atom:sh
@bond:s6-ss @atom:s6 @atom:ss
@bond:sh-sh @atom:sh @atom:sh
@bond:sh-ss @atom:sh @atom:ss
@bond:s-s @atom:s @atom:s
@bond:s-s2 @atom:s @atom:s2
@bond:s-s4 @atom:s @atom:s4
@bond:s-s6 @atom:s @atom:s6
@bond:s-sh @atom:s @atom:sh
@bond:s-ss @atom:s @atom:ss
@bond:ss-ss @atom:ss @atom:ss
@bond:sx-sx @atom:sx @atom:sx
@bond:sx-sy @atom:sx @atom:sy
@bond:sy-sy @atom:sy @atom:sy
} # (end of Bonds By Type)
write_once("In Settings") {
angle_coeff @angle:hw-ow-hw harmonic 42.730 104.520 # AMBER 1 TIP3P_water
angle_coeff @angle:hw-hw-ow harmonic 0.000 127.740 # AMBER 1 (found_in_crystallographic_water_with_3_bonds)
angle_coeff @angle:br-c1-br harmonic 57.760 180.000 # Guess 0
angle_coeff @angle:br-c1-c1 harmonic 54.930 180.000 # SOURCE3 1 0.0000
angle_coeff @angle:c1-c1-c1 harmonic 64.410 180.000 # SOURCE3 1 0.0000
angle_coeff @angle:c1-c1-c2 harmonic 60.840 180.000 # SOURCE3 2 0.0000
angle_coeff @angle:c1-c1-c3 harmonic 56.280 178.460 # SOURCE4 188 0.6631
angle_coeff @angle:c1-c1-ca harmonic 56.920 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-cl harmonic 55.270 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-f harmonic 61.020 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-ha harmonic 44.840 178.380 # SOURCE3 41 2.0683
angle_coeff @angle:c1-c1-hc harmonic 44.730 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-i harmonic 49.800 180.000 # SOURCE3 1 0.0000
angle_coeff @angle:c1-c1-n1 harmonic 67.170 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-n2 harmonic 65.170 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-n3 harmonic 59.770 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-n4 harmonic 59.090 179.560 # SOURCE3 3 0.3096
angle_coeff @angle:c1-c1-n harmonic 62.130 177.180 # SOURCE3 1 0.0000
angle_coeff @angle:c1-c1-na harmonic 61.230 176.750 # SOURCE3 8 2.9328
angle_coeff @angle:c1-c1-nh harmonic 61.440 179.270 # SOURCE3 3 0.2357
angle_coeff @angle:c1-c1-no harmonic 59.380 180.000 # SOURCE3 3 0.0000
angle_coeff @angle:c1-c1-o harmonic 66.790 180.000 # SOURCE3 1 0.0000
angle_coeff @angle:c1-c1-oh harmonic 62.700 176.650 # SOURCE3 1 0.0000
angle_coeff @angle:c1-c1-os harmonic 62.770 176.420 # SOURCE3 2 0.0000
angle_coeff @angle:c1-c1-p2 harmonic 51.510 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-p3 harmonic 52.470 169.630 # SOURCE3 2 0.0000
angle_coeff @angle:c1-c1-p4 harmonic 50.940 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-p5 harmonic 52.560 176.170 # SOURCE3 2 0.0000
angle_coeff @angle:c1-c1-s4 harmonic 68.490 167.470 # SOURCE3 2 0.0000
angle_coeff @angle:c1-c1-s6 harmonic 68.020 174.380 # SOURCE3 2 0.0000
angle_coeff @angle:c1-c1-s harmonic 70.430 179.970 # SOURCE3 1 0.0000
angle_coeff @angle:c1-c1-sh harmonic 68.520 180.000 # SOURCE3 1
angle_coeff @angle:c1-c1-ss harmonic 69.890 173.220 # SOURCE3 2 0.0000
angle_coeff @angle:c2-c1-c2 harmonic 58.200 180.000 # SOURCE3 1 0.0000
angle_coeff @angle:c2-c1-ce harmonic 58.180 179.010 # SOURCE4 6 0.4656
angle_coeff @angle:c2-c1-n1 harmonic 63.140 180.000 # HF/6-31G* 1
angle_coeff @angle:c2-c1-o harmonic 63.070 179.500 # SOURCE2 1 0.0000
angle_coeff @angle:c2-c1-s2 harmonic 71.800 172.980 # SOURCE3 1 0.0000
angle_coeff @angle:c3-c1-c3 harmonic 51.750 180.000 # Guess 0
angle_coeff @angle:c3-c1-cg harmonic 55.790 178.520 # SOURCE4 39 0.5063
angle_coeff @angle:c3-c1-n1 harmonic 58.100 178.500 # SOURCE4 77 0.5443
angle_coeff @angle:ca-c1-ca harmonic 52.830 180.000 # Guess 0
angle_coeff @angle:c-c1-c1 harmonic 56.330 180.000 # SOURCE3 1
angle_coeff @angle:cg-c1-ha harmonic 43.980 177.410 # SOURCE3 22 2.4947
angle_coeff @angle:ch-c1-ha harmonic 43.980 177.410 # SOURCE3 22 same_as_cg-c1-ha
angle_coeff @angle:cl-c1-cl harmonic 53.920 180.000 # Guess 0
angle_coeff @angle:f-c1-f harmonic 58.190 180.000 # Guess 0
angle_coeff @angle:i-c1-i harmonic 53.410 180.000 # Guess 0
angle_coeff @angle:n1-c1-n1 harmonic 93.200 102.010 # SOURCE3 1
angle_coeff @angle:n1-c1-n3 harmonic 63.710 169.700 # SOURCE2 1 0.0000
angle_coeff @angle:n1-c1-nh harmonic 64.020 177.430 # SOURCE4 7 0.7877
angle_coeff @angle:n1-c1-os harmonic 64.720 178.590 # SOURCE3 1 0.0000
angle_coeff @angle:n1-c1-p3 harmonic 53.480 171.200 # SOURCE2 1 0.0000
angle_coeff @angle:n1-c1-ss harmonic 70.640 178.680 # SOURCE3 1 0.0000
angle_coeff @angle:n2-c1-n2 harmonic 65.990 180.000 # Guess 0
angle_coeff @angle:n2-c1-o harmonic 69.150 171.790 # SOURCE3 2 0.3594
angle_coeff @angle:n2-c1-s harmonic 72.750 176.010 # SOURCE4 9 0.1123
angle_coeff @angle:n3-c1-n3 harmonic 57.360 180.000 # Guess 0
angle_coeff @angle:n4-c1-n4 harmonic 56.350 180.000 # Guess 0
angle_coeff @angle:na-c1-na harmonic 58.620 180.000 # Guess 0
angle_coeff @angle:ne-c1-o harmonic 69.390 172.330 # SOURCE3 1 0.0000
angle_coeff @angle:ne-c1-s harmonic 72.880 175.810 # SOURCE4 8 0.2356
angle_coeff @angle:nf-c1-o harmonic 69.390 172.330 # SOURCE3 1 same_as_ne-c1-o
angle_coeff @angle:nh-c1-nh harmonic 59.550 180.000 # Guess 0
angle_coeff @angle:n-c1-n harmonic 60.030 180.000 # Guess 0
angle_coeff @angle:no-c1-no harmonic 56.830 180.000 # Guess 0
angle_coeff @angle:oh-c1-oh harmonic 60.910 180.000 # Guess 0
angle_coeff @angle:o-c1-o harmonic 69.270 180.000 # Guess 0
angle_coeff @angle:os-c1-os harmonic 60.960 180.000 # Guess 0
angle_coeff @angle:p2-c1-p2 harmonic 50.310 180.000 # Guess 0
angle_coeff @angle:p3-c1-p3 harmonic 49.750 180.000 # Guess 0
angle_coeff @angle:p4-c1-p4 harmonic 49.750 180.000 # Guess 0
angle_coeff @angle:p5-c1-p5 harmonic 50.800 180.000 # Guess 0
angle_coeff @angle:s2-c1-s2 harmonic 89.430 180.000 # Guess 0
angle_coeff @angle:s4-c1-s4 harmonic 81.700 180.000 # Guess 0
angle_coeff @angle:s6-c1-s6 harmonic 82.840 180.000 # Guess 0
angle_coeff @angle:sh-c1-sh harmonic 84.910 180.000 # Guess 0
angle_coeff @angle:s-c1-s harmonic 87.510 180.000 # Guess 0
angle_coeff @angle:ss-c1-ss harmonic 84.960 180.000 # Guess 0
angle_coeff @angle:br-c2-br harmonic 68.560 115.060 # SOURCE3 1 0.0000
angle_coeff @angle:br-c2-c2 harmonic 63.970 118.960 # SOURCE4 6 0.4902
angle_coeff @angle:br-c2-c3 harmonic 63.710 115.330 # SOURCE4 6 0.5872
angle_coeff @angle:br-c2-ce harmonic 63.210 121.590 # SOURCE4 7 0.7078
angle_coeff @angle:br-c2-h4 harmonic 43.040 113.940 # SOURCE4 6 0.4017
angle_coeff @angle:br-c2-ha harmonic 43.180 113.280 # SOURCE3 1 0.0000
angle_coeff @angle:c1-c2-c1 harmonic 72.260 116.770 # SOURCE3 1
angle_coeff @angle:c1-c2-c2 harmonic 70.340 121.620 # SOURCE3 1
angle_coeff @angle:c1-c2-c3 harmonic 64.220 124.920 # SOURCE4 17 0.7576
angle_coeff @angle:c1-c2-f harmonic 67.990 124.900 # SOURCE2 1 0.0000
angle_coeff @angle:c1-c2-ha harmonic 50.430 121.370 # SOURCE3 8 0.0055
angle_coeff @angle:c2-c2-c2 harmonic 69.840 121.810 # SOURCE3 10 0.3843
angle_coeff @angle:c2-c2-c3 harmonic 64.330 123.420 # SOURCE3 41 2.6057
angle_coeff @angle:c2-c2-ca harmonic 66.880 117.000 # SOURCE3 1
angle_coeff @angle:c2-c2-cc harmonic 70.220 117.210 # SOURCE3 2 0.3418
angle_coeff @angle:c2-c2-cd harmonic 70.220 117.210 # SOURCE3 2 same_as_c2-c2-cc
angle_coeff @angle:c2-c2-cl harmonic 62.820 122.850 # SOURCE4 23 0.6711
angle_coeff @angle:c2-c2-cx harmonic 64.500 125.400 # SOURCE4 12 1.8494
angle_coeff @angle:c2-c2-cy harmonic 70.420 103.300 # SOURCE2 1 0.0000
angle_coeff @angle:c2-c2-f harmonic 68.110 122.920 # SOURCE4 12 0.5301
angle_coeff @angle:c2-c2-h4 harmonic 49.750 122.540 # SOURCE4 69 1.1900
angle_coeff @angle:c2-c2-ha harmonic 50.040 120.940 # SOURCE3 254 1.3150
angle_coeff @angle:c2-c2-hc harmonic 50.300 119.700 # SOURCE3 1
angle_coeff @angle:c2-c2-hx harmonic 48.980 126.450 # SOURCE3 3 0.0219
angle_coeff @angle:c2-c2-i harmonic 56.280 121.030 # SOURCE3 2 0.0000
angle_coeff @angle:c2-c2-n1 harmonic 71.690 122.980 # HF/6-31G* 1
angle_coeff @angle:c2-c2-n2 harmonic 71.290 126.010 # SOURCE3 1 0.0000
angle_coeff @angle:c2-c2-n3 harmonic 70.330 124.550 # SOURCE3 1
angle_coeff @angle:c2-c2-n4 harmonic 67.180 121.520 # SOURCE3 5 1.2656
angle_coeff @angle:c2-c2-n harmonic 68.860 123.200 # SOURCE4 15 1.8657
angle_coeff @angle:c2-c2-na harmonic 69.830 121.380 # SOURCE3 26 6.9463
angle_coeff @angle:c2-c2-nh harmonic 69.800 124.990 # SOURCE3 7 0.9929
angle_coeff @angle:c2-c2-no harmonic 67.520 124.090 # SOURCE4 6 1.2772
angle_coeff @angle:c2-c2-o harmonic 71.920 130.890 # SOURCE3 2 0.0201
angle_coeff @angle:c2-c2-oh harmonic 71.640 122.070 # SOURCE4 6 1.0883
angle_coeff @angle:c2-c2-os harmonic 71.040 121.890 # SOURCE4 33 1.3457
angle_coeff @angle:c2-c2-p2 harmonic 66.940 115.100 # SOURCE3 1
angle_coeff @angle:c2-c2-p3 harmonic 59.410 124.830 # SOURCE3 5 2.1222
angle_coeff @angle:c2-c2-p4 harmonic 61.010 119.760 # SOURCE3 1
angle_coeff @angle:c2-c2-p5 harmonic 58.230 125.970 # SOURCE3 1
angle_coeff @angle:c2-c2-s4 harmonic 79.550 119.840 # SOURCE3 1
angle_coeff @angle:c2-c2-s6 harmonic 79.490 120.010 # SOURCE3 1
angle_coeff @angle:c2-c2-s harmonic 77.520 129.370 # SOURCE3 2 0.0000
angle_coeff @angle:c2-c2-sh harmonic 77.030 125.700 # SOURCE3 3 1.3390
angle_coeff @angle:c2-c2-ss harmonic 79.470 122.860 # SOURCE4 13 1.7467
angle_coeff @angle:c3-c2-c3 harmonic 62.700 116.520 # SOURCE3 15 3.1001
angle_coeff @angle:c3-c2-cc harmonic 63.220 125.380 # SOURCE4 26 1.8978
angle_coeff @angle:c3-c2-cd harmonic 63.160 125.640 # SOURCE3 1 same_as_c3-c2-cc
angle_coeff @angle:c3-c2-ce harmonic 64.190 123.020 # SOURCE4 1189 1.9006
angle_coeff @angle:c3-c2-cf harmonic 63.960 123.870 # SOURCE4 99 1.2875
angle_coeff @angle:c3-c2-h4 harmonic 45.300 119.250 # SOURCE4 22 2.1707
angle_coeff @angle:c3-c2-ha harmonic 45.660 117.300 # SOURCE3 33 1.7453
angle_coeff @angle:c3-c2-hc harmonic 45.150 120.000 # SOURCE3 1
angle_coeff @angle:c3-c2-n2 harmonic 66.470 123.520 # SOURCE4 141 2.2935
angle_coeff @angle:c3-c2-n harmonic 66.790 114.800 # SOURCE4 12 1.8112
angle_coeff @angle:c3-c2-na harmonic 64.950 122.540 # SOURCE3 1 0.0000
angle_coeff @angle:c3-c2-ne harmonic 66.960 122.150 # SOURCE3 4 0.2197
angle_coeff @angle:c3-c2-nf harmonic 66.960 122.150 # SOURCE3 4 same_as_c3-c2-ne
angle_coeff @angle:c3-c2-nh harmonic 66.690 118.590 # SOURCE3 6 2.2622
angle_coeff @angle:c3-c2-o harmonic 67.880 123.180 # SOURCE4 5 0.9226
angle_coeff @angle:c3-c2-oh harmonic 68.500 115.040 # SOURCE4 36 2.0110
angle_coeff @angle:c3-c2-os harmonic 68.770 112.690 # SOURCE4 50 2.4254
angle_coeff @angle:c3-c2-p2 harmonic 62.400 122.740 # SOURCE3 2 0.0000
angle_coeff @angle:c3-c2-s harmonic 79.470 115.440 # SOURCE3 2 0.0115
angle_coeff @angle:c3-c2-ss harmonic 77.990 119.660 # SOURCE4 45 1.9732
angle_coeff @angle:ca-c2-ca harmonic 63.510 117.880 # SOURCE3 1
angle_coeff @angle:ca-c2-hc harmonic 45.280 123.300 # SOURCE3 1
angle_coeff @angle:c-c2-c2 harmonic 67.930 120.700 # SOURCE3 1
angle_coeff @angle:c-c2-c3 harmonic 63.870 119.700 # SOURCE3 1
angle_coeff @angle:c-c2-c harmonic 66.570 118.880 # SOURCE3 1
angle_coeff @angle:cc-c2-h4 harmonic 49.190 120.330 # SOURCE4 7 0.0865
angle_coeff @angle:cc-c2-ha harmonic 49.070 120.760 # SOURCE3 11 1.4155
angle_coeff @angle:cc-c2-nh harmonic 69.460 122.960 # SOURCE4 10 0.7347
angle_coeff @angle:cc-c2-o harmonic 72.800 123.590 # SOURCE4 6 0.0560
angle_coeff @angle:cd-c2-ha harmonic 49.070 120.760 # SOURCE3 11 1.4155
angle_coeff @angle:ce-c2-cl harmonic 62.430 123.900 # SOURCE4 11 0.3570
angle_coeff @angle:ce-c2-h4 harmonic 49.380 122.290 # SOURCE4 75 1.4008
angle_coeff @angle:ce-c2-ha harmonic 49.570 121.190 # SOURCE3 122 0.5318
angle_coeff @angle:ce-c2-na harmonic 68.820 123.710 # SOURCE4 6 2.0109
angle_coeff @angle:ce-c2-nh harmonic 70.640 120.720 # SOURCE4 93 2.2537
angle_coeff @angle:ce-c2-no harmonic 68.450 119.650 # SOURCE4 5 0.9817
angle_coeff @angle:ce-c2-o harmonic 73.660 123.080 # SOURCE4 5 0.2391
angle_coeff @angle:ce-c2-oh harmonic 70.900 123.270 # SOURCE4 42 1.8111
angle_coeff @angle:ce-c2-os harmonic 70.470 122.520 # SOURCE4 51 2.4680
angle_coeff @angle:cf-c2-ha harmonic 49.570 121.190 # SOURCE3 122 same_as_ce-c2-ha
angle_coeff @angle:c-c2-ha harmonic 47.670 121.330 # SOURCE3 4 0.2462
angle_coeff @angle:c-c2-hc harmonic 48.000 119.700 # SOURCE3 1
angle_coeff @angle:cl-c2-cl harmonic 64.100 114.270 # SOURCE4 10 0.5850
angle_coeff @angle:cl-c2-h4 harmonic 43.820 113.770 # SOURCE4 9 0.6228
angle_coeff @angle:cl-c2-ha harmonic 43.940 113.200 # SOURCE3 1 0.0000
angle_coeff @angle:cx-c2-ha harmonic 46.610 115.890 # SOURCE4 15 0.3682
angle_coeff @angle:f-c2-f harmonic 70.670 109.600 # SOURCE2 2 0.6000
angle_coeff @angle:f-c2-ha harmonic 51.250 110.000 # SOURCE2 1 0.0000
angle_coeff @angle:h4-c2-n2 harmonic 52.400 120.690 # SOURCE4 13 1.3105
angle_coeff @angle:h4-c2-n harmonic 50.480 113.570 # SOURCE4 26 1.0283
angle_coeff @angle:h4-c2-na harmonic 51.030 113.220 # SOURCE4 9 0.6345
angle_coeff @angle:h4-c2-ne harmonic 52.870 119.630 # SOURCE4 10 1.6786
angle_coeff @angle:h4-c2-nh harmonic 51.550 115.640 # SOURCE4 31 1.0081
angle_coeff @angle:h4-c2-no harmonic 49.390 113.380 # SOURCE4 6 0.1240
angle_coeff @angle:h4-c2-os harmonic 52.230 113.700 # SOURCE3 13 2.0464
angle_coeff @angle:h4-c2-ss harmonic 54.230 118.470 # SOURCE3 9 2.5335
angle_coeff @angle:h5-c2-n2 harmonic 52.410 120.160 # SOURCE4 27 1.8999
angle_coeff @angle:h5-c2-na harmonic 48.230 126.390 # SOURCE3 4 0.3299
angle_coeff @angle:h5-c2-ne harmonic 52.760 119.620 # SOURCE4 17 1.3235
angle_coeff @angle:h5-c2-nh harmonic 51.850 113.930 # SOURCE4 50 0.8394
angle_coeff @angle:ha-c2-ha harmonic 38.020 117.650 # SOURCE3 349 1.3426
angle_coeff @angle:ha-c2-n1 harmonic 51.830 120.760 # SOURCE3 8 0.6632
angle_coeff @angle:ha-c2-n2 harmonic 52.390 120.540 # SOURCE3 92 1.4571
angle_coeff @angle:ha-c2-n3 harmonic 52.440 113.540 # SOURCE3 1
angle_coeff @angle:ha-c2-n harmonic 50.490 113.400 # SOURCE3 4 1.2182
angle_coeff @angle:ha-c2-na harmonic 51.180 112.420 # SOURCE3 8 0.6507
angle_coeff @angle:ha-c2-ne harmonic 52.480 121.180 # SOURCE3 68 0.6824
angle_coeff @angle:ha-c2-nf harmonic 52.480 121.180 # SOURCE3 68 same_as_ha-c2-ne
angle_coeff @angle:ha-c2-nh harmonic 51.290 116.680 # SOURCE3 13 2.5734
angle_coeff @angle:ha-c2-no harmonic 49.640 112.140 # SOURCE3 2 0.0264
angle_coeff @angle:ha-c2-o harmonic 55.300 117.230 # SOURCE3 2 0.0201
angle_coeff @angle:ha-c2-oh harmonic 52.340 116.180 # SOURCE3 2 0.0000
angle_coeff @angle:ha-c2-os harmonic 52.430 112.690 # SOURCE3 13 2.5851
angle_coeff @angle:ha-c2-p2 harmonic 44.050 121.480 # SOURCE3 122 0.4329
angle_coeff @angle:ha-c2-p3 harmonic 41.120 114.310 # SOURCE3 3 0.0000
angle_coeff @angle:ha-c2-p4 harmonic 40.790 117.860 # SOURCE3 1
angle_coeff @angle:ha-c2-p5 harmonic 39.360 120.100 # SOURCE3 2 0.0000
angle_coeff @angle:ha-c2-pe harmonic 43.490 121.460 # SOURCE3 104 0.7821
angle_coeff @angle:ha-c2-pf harmonic 43.490 121.460 # SOURCE3 104 same_as_ha-c2-pe
angle_coeff @angle:ha-c2-s2 harmonic 58.460 118.740 # SOURCE3 2 0.0000
angle_coeff @angle:ha-c2-s4 harmonic 54.190 115.300 # SOURCE3 2 0.0000
angle_coeff @angle:ha-c2-s harmonic 54.950 115.700 # SOURCE3 2 0.0000
angle_coeff @angle:ha-c2-s6 harmonic 53.880 116.600 # SOURCE3 2 0.0000
angle_coeff @angle:ha-c2-sh harmonic 54.480 111.740 # SOURCE3 1 0.0000
angle_coeff @angle:ha-c2-ss harmonic 54.640 116.720 # SOURCE3 7 2.7543
angle_coeff @angle:hc-c2-hc harmonic 37.810 118.920 # SOURCE3 1
angle_coeff @angle:hc-c2-n2 harmonic 52.420 120.400 # SOURCE3 1
angle_coeff @angle:hc-c2-n harmonic 50.350 114.040 # SOURCE3 1
angle_coeff @angle:hc-c2-na harmonic 49.730 119.100 # SOURCE3 1
angle_coeff @angle:hc-c2-nh harmonic 52.030 113.360 # SOURCE3 1
angle_coeff @angle:hc-c2-no harmonic 49.640 112.120 # SOURCE3 1
angle_coeff @angle:hc-c2-oh harmonic 52.330 116.220 # SOURCE3 1
angle_coeff @angle:hc-c2-os harmonic 51.650 116.110 # SOURCE3 1
angle_coeff @angle:hc-c2-p3 harmonic 40.610 117.190 # SOURCE3 1
angle_coeff @angle:hc-c2-p5 harmonic 39.440 119.580 # SOURCE3 1
angle_coeff @angle:hc-c2-s4 harmonic 54.000 116.120 # SOURCE3 1
angle_coeff @angle:hc-c2-s6 harmonic 54.150 115.450 # SOURCE3 1
angle_coeff @angle:hc-c2-sh harmonic 53.550 115.630 # SOURCE3 1
angle_coeff @angle:hc-c2-ss harmonic 54.900 115.620 # SOURCE3 1
angle_coeff @angle:hx-c2-n4 harmonic 48.420 113.030 # SOURCE3 3 0.3873
angle_coeff @angle:i-c2-i harmonic 60.960 117.940 # SOURCE3 1 0.0000
angle_coeff @angle:n1-c2-n1 harmonic 73.610 124.150 # HF/6-31G* 1
angle_coeff @angle:n2-c2-n2 harmonic 77.960 113.820 # SOURCE3 1 0.0000
angle_coeff @angle:n2-c2-n4 harmonic 72.030 113.050 # SOURCE4 6 0.3318
angle_coeff @angle:n2-c2-na harmonic 71.710 123.620 # SOURCE3 1 0.0000
angle_coeff @angle:n2-c2-nh harmonic 72.620 124.270 # SOURCE3 12 2.4114
angle_coeff @angle:n2-c2-oh harmonic 74.360 122.080 # SOURCE3 1 0.0000
angle_coeff @angle:n2-c2-os harmonic 74.320 119.820 # SOURCE4 20 1.2664
angle_coeff @angle:n2-c2-ss harmonic 79.560 129.770 # SOURCE3 1 0.0000
angle_coeff @angle:n3-c2-n3 harmonic 73.450 118.470 # SOURCE3 1
angle_coeff @angle:n4-c2-n4 harmonic 67.720 113.930 # SOURCE3 1 0.0000
angle_coeff @angle:n4-c2-ss harmonic 81.510 116.260 # SOURCE4 7 2.4226
angle_coeff @angle:na-c2-na harmonic 73.650 109.330 # SOURCE3 3 3.0187
angle_coeff @angle:ne-c2-nh harmonic 73.020 123.570 # SOURCE4 126 2.4468
angle_coeff @angle:ne-c2-os harmonic 74.860 118.760 # SOURCE4 5 0.3382
angle_coeff @angle:ne-c2-ss harmonic 82.780 120.060 # SOURCE4 9 1.3423
angle_coeff @angle:nf-c2-nh harmonic 73.280 122.720 # SOURCE3 2 same_as_ne-c2-nh
angle_coeff @angle:nh-c2-nh harmonic 74.460 112.720 # SOURCE4 257 1.8176
angle_coeff @angle:nh-c2-oh harmonic 74.050 117.160 # SOURCE4 7 0.8698
angle_coeff @angle:nh-c2-os harmonic 74.320 114.290 # SOURCE4 18 1.0900
angle_coeff @angle:nh-c2-ss harmonic 85.090 111.550 # SOURCE4 37 1.1778
angle_coeff @angle:n-c2-n2 harmonic 70.560 125.950 # SOURCE3 2 5.0202
angle_coeff @angle:n-c2-n harmonic 71.550 113.230 # SOURCE3 1 0.0000
angle_coeff @angle:n-c2-na harmonic 74.570 105.420 # SOURCE3 1 0.0000
angle_coeff @angle:n-c2-ne harmonic 70.890 125.380 # SOURCE4 10 1.6819
angle_coeff @angle:n-c2-nh harmonic 74.200 109.140 # SOURCE4 22 1.5634
angle_coeff @angle:no-c2-no harmonic 69.430 113.900 # SOURCE3 1 0.0000
angle_coeff @angle:n-c2-ss harmonic 84.580 111.060 # SOURCE4 9 0.5522
angle_coeff @angle:oh-c2-oh harmonic 76.030 114.330 # SOURCE3 1 0.0000
angle_coeff @angle:o-c2-o harmonic 80.230 121.690 # SOURCE3 1
angle_coeff @angle:o-c2-oh harmonic 76.690 121.230 # SOURCE4 6 0.0958
angle_coeff @angle:o-c2-s harmonic 81.200 127.680 # SOURCE3 2 0.0547
angle_coeff @angle:os-c2-os harmonic 74.210 115.800 # SOURCE3 1 0.0000
angle_coeff @angle:p2-c2-p2 harmonic 62.800 129.800 # SOURCE3 1
angle_coeff @angle:p3-c2-p3 harmonic 60.610 115.540 # SOURCE3 1 0.0000
angle_coeff @angle:p5-c2-p5 harmonic 58.010 121.850 # SOURCE3 1
angle_coeff @angle:s4-c2-s4 harmonic 99.130 120.320 # SOURCE3 1
angle_coeff @angle:s4-c2-s6 harmonic 99.290 119.950 # SOURCE3 1
angle_coeff @angle:s6-c2-s6 harmonic 99.280 119.970 # SOURCE3 1
angle_coeff @angle:sh-c2-sh harmonic 102.460 110.480 # SOURCE3 1 0.0000
angle_coeff @angle:sh-c2-ss harmonic 100.350 117.820 # SOURCE3 1
angle_coeff @angle:s-c2-s harmonic 100.060 121.670 # SOURCE3 1
angle_coeff @angle:ss-c2-ss harmonic 100.540 120.240 # SOURCE3 1 0.0000
angle_coeff @angle:br-c3-br harmonic 67.460 109.030 # SOURCE4 6 0.5435
angle_coeff @angle:br-c3-c1 harmonic 62.770 111.800 # SOURCE2 3 0.2160
angle_coeff @angle:br-c3-c3 harmonic 63.030 109.250 # SOURCE3 10 0.5685
angle_coeff @angle:br-c3-c harmonic 62.920 110.370 # SOURCE4 13 2.4747
angle_coeff @angle:br-c3-h1 harmonic 43.120 103.040 # SOURCE3 5 0.3092
angle_coeff @angle:br-c3-h2 harmonic 42.340 107.100 # SOURCE4 7 0.2378
angle_coeff @angle:br-c3-hc harmonic 42.400 106.500 # SOURCE3 1
angle_coeff @angle:c1-c3-c1 harmonic 66.500 109.000 # SOURCE2 1 0.0000
angle_coeff @angle:c1-c3-c2 harmonic 65.000 111.110 # SOURCE4 12 0.7366
angle_coeff @angle:c1-c3-c3 harmonic 64.290 111.420 # SOURCE4 197 1.2106
angle_coeff @angle:c1-c3-ca harmonic 64.930 110.950 # SOURCE4 28 1.1203
angle_coeff @angle:c1-c3-cc harmonic 64.290 114.290 # SOURCE4 8 0.1535
angle_coeff @angle:c1-c3-cd harmonic 64.360 114.060 # SOURCE4 5 0.0462
angle_coeff @angle:c1-c3-cl harmonic 62.890 110.630 # SOURCE2 3 1.2257
angle_coeff @angle:c1-c3-h1 harmonic 48.350 109.290 # SOURCE4 133 0.5701
angle_coeff @angle:c1-c3-hc harmonic 48.250 109.750 # SOURCE3 12 0.8436
angle_coeff @angle:c1-c3-hx harmonic 47.760 112.050 # SOURCE4 17 0.2587
angle_coeff @angle:c1-c3-n3 harmonic 67.030 112.590 # SOURCE4 28 0.9555
angle_coeff @angle:c1-c3-n4 harmonic 66.530 112.040 # SOURCE4 11 0.5701
angle_coeff @angle:c1-c3-n harmonic 67.410 112.080 # SOURCE4 18 0.9568
angle_coeff @angle:c1-c3-nh harmonic 67.250 112.790 # SOURCE4 8 0.9453
angle_coeff @angle:c1-c3-oh harmonic 69.490 109.140 # SOURCE4 39 0.6500
angle_coeff @angle:c1-c3-os harmonic 69.270 108.880 # SOURCE4 31 0.9597
angle_coeff @angle:c2-c3-c2 harmonic 63.930 112.080 # SOURCE4 153 0.7742
angle_coeff @angle:c2-c3-c3 harmonic 63.530 111.440 # SOURCE4 2891 1.7167
angle_coeff @angle:c2-c3-ca harmonic 63.710 112.450 # SOURCE4 141 1.6755
angle_coeff @angle:c2-c3-cc harmonic 64.000 112.490 # SOURCE4 15 1.7250
angle_coeff @angle:c2-c3-cd harmonic 64.460 110.890 # SOURCE4 17 2.1339
angle_coeff @angle:c2-c3-ce harmonic 64.080 111.750 # SOURCE4 28 1.5646
angle_coeff @angle:c2-c3-cf harmonic 63.960 112.190 # SOURCE4 10 2.4554
angle_coeff @angle:c2-c3-cl harmonic 62.050 112.070 # SOURCE4 6 0.9936
angle_coeff @angle:c2-c3-cx harmonic 63.650 112.620 # SOURCE4 17 1.3287
angle_coeff @angle:c2-c3-cy harmonic 66.760 101.330 # SOURCE4 58 0.9262
angle_coeff @angle:c2-c3-f harmonic 66.520 110.960 # SOURCE4 25 0.2829
angle_coeff @angle:c2-c3-h1 harmonic 47.030 110.460 # SOURCE3 17 1.1525
angle_coeff @angle:c2-c3-h2 harmonic 46.840 111.190 # SOURCE4 17 0.8311
angle_coeff @angle:c2-c3-hc harmonic 47.030 110.490 # SOURCE3 159 0.7479
angle_coeff @angle:c2-c3-hx harmonic 46.830 111.450 # SOURCE4 20 0.9004
angle_coeff @angle:c2-c3-n2 harmonic 67.090 108.990 # SOURCE4 10 1.2025
angle_coeff @angle:c2-c3-n3 harmonic 66.470 111.520 # SOURCE4 158 1.4012
angle_coeff @angle:c2-c3-n harmonic 66.730 111.380 # SOURCE4 67 1.7559
angle_coeff @angle:c2-c3-na harmonic 66.240 113.300 # SOURCE4 27 1.2945
angle_coeff @angle:c2-c3-nh harmonic 67.100 110.270 # SOURCE4 56 1.8018
angle_coeff @angle:c2-c3-oh harmonic 68.180 110.210 # SOURCE4 220 1.4197
angle_coeff @angle:c2-c3-os harmonic 68.450 108.480 # SOURCE4 204 1.6082
angle_coeff @angle:c2-c3-s4 harmonic 79.190 109.730 # SOURCE4 6 0.1722
angle_coeff @angle:c2-c3-ss harmonic 80.520 104.970 # SOURCE3 2 2.2248
angle_coeff @angle:c3-c3-c3 harmonic 63.210 110.630 # SOURCE3 507 2.7845
angle_coeff @angle:c3-c3-ca harmonic 63.250 112.090 # SOURCE4 3859 1.5523
angle_coeff @angle:c3-c3-cc harmonic 63.570 111.920 # SOURCE4 695 1.6368
angle_coeff @angle:c3-c3-cd harmonic 64.690 108.100 # SOURCE3 5 same_as_c3-c3-cc
angle_coeff @angle:c3-c3-ce harmonic 63.650 111.220 # SOURCE4 395 1.7751
angle_coeff @angle:c3-c3-cf harmonic 63.900 110.370 # SOURCE4 95 1.5467
angle_coeff @angle:c3-c3-cl harmonic 62.200 110.330 # SOURCE3 20 1.1495
angle_coeff @angle:c3-c3-cx harmonic 63.300 111.820 # SOURCE4 179 2.4814
angle_coeff @angle:c3-c3-cy harmonic 63.630 109.620 # SOURCE3 5 2.0747
angle_coeff @angle:c3-c3-f harmonic 66.220 109.410 # SOURCE3 18 1.1878
angle_coeff @angle:c3-c3-h1 harmonic 46.360 110.070 # SOURCE3 457 1.1542
angle_coeff @angle:c3-c3-h2 harmonic 46.020 111.590 # SOURCE3 8 1.1217
angle_coeff @angle:c3-c3-hc harmonic 46.370 110.050 # SOURCE3 2092 0.6991
angle_coeff @angle:c3-c3-hx harmonic 46.020 111.740 # SOURCE3 15 1.2365
angle_coeff @angle:c3-c3-i harmonic 58.480 110.960 # SOURCE3 2 0.0000
angle_coeff @angle:c3-c3-n1 harmonic 66.640 108.860 # SOURCE4 9 0.8093
angle_coeff @angle:c3-c3-n2 harmonic 66.400 109.160 # SOURCE3 8 1.4079
angle_coeff @angle:c3-c3-n3 harmonic 66.180 110.380 # SOURCE3 69 2.9054
angle_coeff @angle:c3-c3-n4 harmonic 64.450 114.320 # SOURCE4 567 2.4412
angle_coeff @angle:c3-c3-n harmonic 65.850 112.130 # SOURCE3 31 2.0700
angle_coeff @angle:c3-c3-na harmonic 65.730 112.810 # SOURCE4 595 1.5050
angle_coeff @angle:c3-c3-nh harmonic 66.390 110.450 # SOURCE4 1514 1.3881
angle_coeff @angle:c3-c3-no harmonic 65.210 109.270 # SOURCE4 25 1.1817
angle_coeff @angle:c3-c3-o harmonic 68.590 112.970 # SOURCE4 14 1.0277
angle_coeff @angle:c3-c3-oh harmonic 67.720 109.430 # SOURCE3 48 1.5023
angle_coeff @angle:c3-c3-os harmonic 67.780 108.420 # SOURCE3 122 1.6759
angle_coeff @angle:c3-c3-p3 harmonic 60.410 113.190 # SOURCE4 15 0.2974
angle_coeff @angle:c3-c3-p5 harmonic 61.390 112.320 # SOURCE4 106 1.1753
angle_coeff @angle:c3-c3-s4 harmonic 78.670 110.070 # SOURCE4 38 0.8510
angle_coeff @angle:c3-c3-s6 harmonic 79.700 110.000 # SOURCE4 152 1.4278
angle_coeff @angle:c3-c3-sh harmonic 77.180 113.020 # SOURCE4 80 1.3442
angle_coeff @angle:c3-c3-ss harmonic 77.330 112.690 # SOURCE3 24 2.1842
angle_coeff @angle:c3-c3-sy harmonic 79.490 109.910 # SOURCE4 22 0.9248
angle_coeff @angle:ca-c3-ca harmonic 63.660 112.260 # SOURCE4 385 1.7047
angle_coeff @angle:ca-c3-cc harmonic 63.760 112.940 # SOURCE4 61 1.2579
angle_coeff @angle:ca-c3-cd harmonic 65.180 108.080 # SOURCE3 8 same_as_ca-c3-cc
angle_coeff @angle:ca-c3-ce harmonic 63.810 112.330 # SOURCE4 51 1.1929
angle_coeff @angle:ca-c3-cl harmonic 62.200 111.310 # SOURCE4 16 0.8077
angle_coeff @angle:ca-c3-cx harmonic 63.690 112.100 # SOURCE4 5 2.1117
angle_coeff @angle:ca-c3-f harmonic 66.140 111.760 # SOURCE4 449 0.3492
angle_coeff @angle:ca-c3-h1 harmonic 46.780 110.950 # SOURCE3 12 1.1170
angle_coeff @angle:ca-c3-h2 harmonic 47.030 109.660 # SOURCE4 29 1.2184
angle_coeff @angle:ca-c3-hc harmonic 46.960 110.150 # SOURCE3 47 1.2602
angle_coeff @angle:ca-c3-hx harmonic 46.690 111.440 # SOURCE4 33 0.4691
angle_coeff @angle:ca-c3-n2 harmonic 65.920 112.490 # SOURCE4 22 1.1043
angle_coeff @angle:ca-c3-n3 harmonic 66.180 112.130 # SOURCE4 387 1.2309
angle_coeff @angle:ca-c3-n4 harmonic 64.870 114.540 # SOURCE4 22 2.3986
angle_coeff @angle:ca-c3-n harmonic 66.290 112.430 # SOURCE4 201 1.5133
angle_coeff @angle:ca-c3-na harmonic 66.270 112.810 # SOURCE4 104 1.5807
angle_coeff @angle:ca-c3-nc harmonic 68.200 106.510 # SOURCE3 1 0.0000
angle_coeff @angle:ca-c3-nd harmonic 68.200 106.510 # SOURCE3 1 same_as_ca-c3-nc
angle_coeff @angle:ca-c3-nh harmonic 66.640 111.410 # SOURCE4 147 1.0074
angle_coeff @angle:ca-c3-oh harmonic 67.940 110.550 # SOURCE4 348 1.2310
angle_coeff @angle:ca-c3-os harmonic 68.190 108.890 # SOURCE4 411 1.0102
angle_coeff @angle:ca-c3-p5 harmonic 61.350 113.410 # SOURCE4 19 1.4444
angle_coeff @angle:ca-c3-s6 harmonic 79.570 111.360 # SOURCE4 15 1.4775
angle_coeff @angle:ca-c3-ss harmonic 78.350 110.660 # SOURCE4 78 1.4797
angle_coeff @angle:ca-c3-sx harmonic 78.680 110.800 # SOURCE4 16 0.5396
angle_coeff @angle:c-c3-c1 harmonic 64.560 112.640 # SOURCE4 11 1.0678
angle_coeff @angle:c-c3-c2 harmonic 64.140 111.320 # SOURCE4 92 1.8522
angle_coeff @angle:c-c3-c3 harmonic 63.790 110.530 # SOURCE3 62 1.9636
angle_coeff @angle:c-c3-c harmonic 64.060 111.610 # SOURCE4 151 2.1872
angle_coeff @angle:c-c3-ca harmonic 64.130 110.990 # SOURCE4 481 1.7257
angle_coeff @angle:c-c3-cc harmonic 63.940 112.690 # SOURCE4 61 1.4162
angle_coeff @angle:cc-c3-cc harmonic 63.640 114.440 # SOURCE4 9 0.7894
angle_coeff @angle:cc-c3-cd harmonic 67.300 102.350 # SOURCE3 1 0.0000
angle_coeff @angle:cc-c3-cx harmonic 63.850 112.550 # SOURCE4 5 1.4317
angle_coeff @angle:c-c3-cd harmonic 63.810 113.170 # SOURCE4 43 1.3583
angle_coeff @angle:c-c3-ce harmonic 64.020 111.980 # SOURCE4 16 2.1388
angle_coeff @angle:cc-c3-f harmonic 66.730 111.130 # SOURCE4 60 0.4791
angle_coeff @angle:cc-c3-h1 harmonic 47.030 111.620 # SOURCE3 20 1.0215
angle_coeff @angle:cc-c3-hc harmonic 47.200 110.860 # SOURCE3 85 1.0276
angle_coeff @angle:cc-c3-hx harmonic 47.170 111.020 # SOURCE4 9 0.7503
angle_coeff @angle:c-c3-cl harmonic 62.300 111.160 # SOURCE4 41 1.2257
angle_coeff @angle:cc-c3-n2 harmonic 66.850 110.470 # SOURCE4 11 0.5153
angle_coeff @angle:cc-c3-n3 harmonic 66.670 111.570 # SOURCE4 66 1.2287
angle_coeff @angle:cc-c3-n4 harmonic 64.880 115.580 # SOURCE4 6 1.1723
angle_coeff @angle:cc-c3-n harmonic 66.740 112.050 # SOURCE4 23 1.5593
angle_coeff @angle:cc-c3-na harmonic 66.430 113.390 # SOURCE4 8 0.8010
angle_coeff @angle:cc-c3-nc harmonic 68.370 107.040 # SOURCE3 2 0.0000
angle_coeff @angle:cc-c3-nh harmonic 66.500 113.020 # SOURCE4 14 1.6083
angle_coeff @angle:cc-c3-oh harmonic 68.010 111.510 # SOURCE4 61 1.4663
angle_coeff @angle:cc-c3-os harmonic 68.570 108.820 # SOURCE4 84 1.2451
angle_coeff @angle:cc-c3-p5 harmonic 60.750 116.230 # SOURCE4 6 0.7766
angle_coeff @angle:cc-c3-sh harmonic 77.340 114.020 # SOURCE3 1 same_as_cd-c3-sh
angle_coeff @angle:cc-c3-ss harmonic 78.390 111.090 # SOURCE4 35 0.8623
angle_coeff @angle:c-c3-cx harmonic 64.080 111.090 # SOURCE4 9 1.2357
angle_coeff @angle:cd-c3-cd harmonic 65.520 107.990 # SOURCE3 10 5.1937
angle_coeff @angle:cd-c3-f harmonic 66.530 111.800 # SOURCE4 9 0.4528
angle_coeff @angle:cd-c3-h1 harmonic 47.030 111.620 # SOURCE3 20 1.0215
angle_coeff @angle:cd-c3-hc harmonic 47.200 110.860 # SOURCE3 85 1.0276
angle_coeff @angle:cd-c3-n3 harmonic 66.960 110.590 # SOURCE4 45 1.4707
angle_coeff @angle:cd-c3-n harmonic 67.110 110.830 # SOURCE4 9 1.3462
angle_coeff @angle:cd-c3-nd harmonic 68.370 107.040 # SOURCE3 2 same_as_cc-c3-nc
angle_coeff @angle:cd-c3-nh harmonic 67.060 111.110 # SOURCE4 7 2.0959
angle_coeff @angle:cd-c3-oh harmonic 68.280 110.640 # SOURCE4 55 1.5008
angle_coeff @angle:cd-c3-os harmonic 67.810 111.280 # SOURCE3 7 same_as_cc-c3-os
angle_coeff @angle:cd-c3-sh harmonic 77.340 114.020 # SOURCE3 1 0.0000
angle_coeff @angle:cd-c3-ss harmonic 78.450 110.910 # SOURCE4 8 0.8705
angle_coeff @angle:ce-c3-ce harmonic 64.240 111.440 # SOURCE4 18 0.3695
angle_coeff @angle:ce-c3-cy harmonic 66.340 102.820 # SOURCE4 6 0.1191
angle_coeff @angle:ce-c3-h1 harmonic 47.280 109.650 # SOURCE4 98 0.9337
angle_coeff @angle:ce-c3-hc harmonic 47.000 110.980 # SOURCE3 27 0.1559
angle_coeff @angle:ce-c3-n3 harmonic 66.430 111.900 # SOURCE4 20 0.5035
angle_coeff @angle:ce-c3-n harmonic 67.090 110.410 # SOURCE4 6 1.1405
angle_coeff @angle:ce-c3-oh harmonic 68.000 111.050 # SOURCE4 17 1.5159
angle_coeff @angle:ce-c3-os harmonic 68.640 108.100 # SOURCE4 16 1.9583
angle_coeff @angle:ce-c3-ss harmonic 78.300 111.100 # SOURCE4 7 2.0156
angle_coeff @angle:c-c3-f harmonic 66.820 109.980 # SOURCE4 38 0.9895
angle_coeff @angle:cf-c3-cy harmonic 66.330 102.850 # SOURCE4 49 0.2818
angle_coeff @angle:cf-c3-h1 harmonic 47.350 109.340 # SOURCE4 21 0.7788
angle_coeff @angle:cf-c3-hc harmonic 47.000 110.980 # SOURCE3 27 same_as_ce-c3-hc
angle_coeff @angle:cf-c3-n3 harmonic 66.510 111.640 # SOURCE4 8 1.1575
angle_coeff @angle:c-c3-h1 harmonic 47.630 107.660 # SOURCE3 66 1.4015
angle_coeff @angle:c-c3-h2 harmonic 47.160 109.690 # SOURCE4 38 1.0614
angle_coeff @angle:c-c3-hc harmonic 47.200 109.680 # SOURCE3 614 0.6426
angle_coeff @angle:c-c3-hx harmonic 47.230 109.540 # SOURCE4 47 0.6627
angle_coeff @angle:cl-c3-cl harmonic 62.700 111.030 # SOURCE2 6 1.1324
angle_coeff @angle:cl-c3-f harmonic 63.600 109.020 # SOURCE4 15 0.3609
angle_coeff @angle:cl-c3-h1 harmonic 43.710 105.930 # SOURCE3 19 1.1883
angle_coeff @angle:cl-c3-h2 harmonic 43.490 107.140 # SOURCE4 50 0.5973
angle_coeff @angle:cl-c3-hc harmonic 43.360 107.650 # SOURCE2 2 2.2500
angle_coeff @angle:cl-c3-os harmonic 64.920 111.400 # SOURCE4 8 0.8275
angle_coeff @angle:cl-c3-ss harmonic 78.390 112.940 # SOURCE4 10 1.4625
angle_coeff @angle:c-c3-n2 harmonic 66.920 109.550 # SOURCE4 55 1.4579
angle_coeff @angle:c-c3-n3 harmonic 66.590 111.140 # SOURCE4 629 1.6673
angle_coeff @angle:c-c3-n4 harmonic 65.070 114.210 # SOURCE4 27 1.5388
angle_coeff @angle:c-c3-n harmonic 66.670 111.560 # SOURCE3 28 1.7981
angle_coeff @angle:c-c3-na harmonic 66.810 111.370 # SOURCE4 31 1.6229
angle_coeff @angle:c-c3-nh harmonic 67.360 109.430 # SOURCE4 42 1.7022
angle_coeff @angle:c-c3-oh harmonic 68.650 108.700 # SOURCE4 299 1.3415
angle_coeff @angle:c-c3-os harmonic 68.030 109.820 # SOURCE3 10 2.0612
angle_coeff @angle:c-c3-p5 harmonic 62.230 110.410 # SOURCE4 15 2.2683
angle_coeff @angle:c-c3-s6 harmonic 80.060 110.220 # SOURCE4 5 2.0076
angle_coeff @angle:c-c3-sh harmonic 79.050 108.820 # SOURCE4 12 0.8354
angle_coeff @angle:c-c3-ss harmonic 78.090 111.580 # SOURCE3 5 1.9506
angle_coeff @angle:cx-c3-cx harmonic 63.530 112.580 # SOURCE4 7 1.2211
angle_coeff @angle:cx-c3-h1 harmonic 47.040 109.640 # SOURCE4 175 0.8822
angle_coeff @angle:cx-c3-hc harmonic 46.920 110.200 # SOURCE4 356 0.8798
angle_coeff @angle:cx-c3-hx harmonic 46.380 112.810 # SOURCE4 12 0.0977
angle_coeff @angle:cx-c3-n3 harmonic 65.830 113.220 # SOURCE4 33 1.3978
angle_coeff @angle:cx-c3-n4 harmonic 68.880 101.510 # SOURCE4 12 0.0760
angle_coeff @angle:cx-c3-n harmonic 66.220 112.590 # SOURCE4 22 0.8034
angle_coeff @angle:cx-c3-oh harmonic 68.100 109.970 # SOURCE4 25 1.3176
angle_coeff @angle:cx-c3-os harmonic 68.400 108.160 # SOURCE4 26 1.0162
angle_coeff @angle:cy-c3-h1 harmonic 47.000 107.880 # SOURCE4 162 0.9624
angle_coeff @angle:cy-c3-hc harmonic 46.510 110.170 # SOURCE3 16 0.5693
angle_coeff @angle:cy-c3-n3 harmonic 65.630 112.720 # SOURCE4 7 1.0639
angle_coeff @angle:cy-c3-oh harmonic 67.220 111.560 # SOURCE4 138 0.5051
angle_coeff @angle:cy-c3-os harmonic 68.450 106.790 # SOURCE4 5 1.0955
angle_coeff @angle:f-c3-f harmonic 71.260 107.160 # SOURCE2 10 1.1324
angle_coeff @angle:f-c3-h1 harmonic 51.570 107.850 # SOURCE3 14 0.9537
angle_coeff @angle:f-c3-h2 harmonic 51.360 108.410 # SOURCE3 6 0.5081
angle_coeff @angle:f-c3-h3 harmonic 51.050 110.010 # SOURCE4 19 0.6811
angle_coeff @angle:f-c3-hc harmonic 51.330 108.920 # SOURCE2 5 3.0534
angle_coeff @angle:f-c3-n2 harmonic 69.230 110.400 # SOURCE2 3 2.6470
angle_coeff @angle:f-c3-os harmonic 70.660 110.610 # SOURCE4 45 1.1755
angle_coeff @angle:f-c3-p5 harmonic 63.700 107.250 # SOURCE4 11 1.1735
angle_coeff @angle:f-c3-s6 harmonic 81.220 109.670 # SOURCE4 24 0.4116
angle_coeff @angle:f-c3-ss harmonic 78.640 111.890 # SOURCE4 11 0.9479
angle_coeff @angle:h1-c3-h1 harmonic 39.180 109.550 # SOURCE3 1888 1.1205
angle_coeff @angle:h1-c3-n1 harmonic 49.990 107.310 # HF/6-31G* 1
angle_coeff @angle:h1-c3-n2 harmonic 49.260 109.610 # SOURCE3 63 1.0452
angle_coeff @angle:h1-c3-n3 harmonic 49.390 109.920 # SOURCE3 313 1.1810
angle_coeff @angle:h1-c3-n harmonic 49.820 109.320 # SOURCE3 91 1.0325
angle_coeff @angle:h1-c3-na harmonic 49.900 109.450 # SOURCE3 53 0.9555
angle_coeff @angle:h1-c3-nc harmonic 50.110 108.570 # SOURCE3 6 0.0764
angle_coeff @angle:h1-c3-nd harmonic 50.110 108.570 # SOURCE3 6 same_as_h1-c3-nc
angle_coeff @angle:h1-c3-nh harmonic 49.730 109.960 # SOURCE3 70 0.7000
angle_coeff @angle:h1-c3-no harmonic 48.660 105.150 # SOURCE4 16 0.4950
angle_coeff @angle:h1-c3-o harmonic 52.530 117.190 # SOURCE3 6 0.0003
angle_coeff @angle:h1-c3-oh harmonic 50.970 109.880 # SOURCE3 63 1.3172
angle_coeff @angle:h1-c3-os harmonic 50.840 108.820 # SOURCE3 541 0.8042
angle_coeff @angle:h1-c3-p5 harmonic 42.870 107.990 # SOURCE4 72 1.1862
angle_coeff @angle:h1-c3-s4 harmonic 54.280 108.660 # SOURCE3 201 0.3834
angle_coeff @angle:h1-c3-s harmonic 52.120 112.600 # SOURCE3 6 0.0026
angle_coeff @angle:h1-c3-s6 harmonic 55.510 108.110 # SOURCE3 160 0.5518
angle_coeff @angle:h1-c3-sh harmonic 53.660 109.210 # SOURCE3 22 1.2028
angle_coeff @angle:h1-c3-ss harmonic 53.660 109.340 # SOURCE3 356 0.6573
angle_coeff @angle:h1-c3-sx harmonic 54.210 108.690 # SOURCE3 90 0.2749
angle_coeff @angle:h1-c3-sy harmonic 55.250 108.090 # SOURCE3 93 0.2556
angle_coeff @angle:h2-c3-h2 harmonic 39.000 109.190 # SOURCE3 29 3.1352
angle_coeff @angle:h2-c3-i harmonic 38.690 104.990 # SOURCE3 2 0.0000
angle_coeff @angle:h2-c3-n2 harmonic 49.080 110.220 # SOURCE3 6 0.2133
angle_coeff @angle:h2-c3-n3 harmonic 49.370 109.800 # SOURCE4 189 1.2893
angle_coeff @angle:h2-c3-n harmonic 50.220 107.380 # SOURCE4 258 1.3140
angle_coeff @angle:h2-c3-na harmonic 50.270 107.660 # SOURCE3 6 1.4096
angle_coeff @angle:h2-c3-nc harmonic 49.850 109.470 # SOURCE3 10 0.3133
angle_coeff @angle:h2-c3-nd harmonic 49.850 109.470 # SOURCE3 10 same_as_h2-c3-nc
angle_coeff @angle:h2-c3-nh harmonic 49.600 110.330 # SOURCE4 102 1.0596
angle_coeff @angle:h2-c3-no harmonic 47.830 108.690 # SOURCE3 4 0.0000
angle_coeff @angle:h2-c3-o harmonic 54.380 108.970 # SOURCE3 4 0.0000
angle_coeff @angle:h2-c3-oh harmonic 51.290 108.300 # SOURCE3 6 0.5715
angle_coeff @angle:h2-c3-os harmonic 50.840 108.580 # SOURCE3 44 1.2773
angle_coeff @angle:h2-c3-s4 harmonic 54.330 108.580 # SOURCE3 8 0.2408
angle_coeff @angle:h2-c3-s harmonic 53.560 106.750 # SOURCE3 4 0.0000
angle_coeff @angle:h2-c3-s6 harmonic 55.940 106.540 # SOURCE4 27 0.9934
angle_coeff @angle:h2-c3-sh harmonic 54.020 107.870 # SOURCE3 6 0.4376
angle_coeff @angle:h2-c3-ss harmonic 53.590 109.750 # SOURCE3 10 0.3442
angle_coeff @angle:h3-c3-n3 harmonic 49.730 108.390 # SOURCE4 12 1.7932
angle_coeff @angle:h3-c3-nc harmonic 49.910 109.370 # SOURCE3 1 0.0000
angle_coeff @angle:h3-c3-nd harmonic 49.910 109.370 # SOURCE3 1 same_as_h3-c3-nc
angle_coeff @angle:h3-c3-nh harmonic 49.530 110.780 # SOURCE4 5 1.5993
angle_coeff @angle:h3-c3-os harmonic 50.090 112.030 # SOURCE4 17 1.0957
angle_coeff @angle:h3-c3-ss harmonic 53.680 109.270 # SOURCE4 8 0.8367
angle_coeff @angle:hc-c3-hc harmonic 39.430 108.350 # SOURCE3 2380 0.9006
angle_coeff @angle:hc-c3-i harmonic 38.620 104.990 # SOURCE3 1
angle_coeff @angle:hc-c3-n2 harmonic 49.290 109.500 # SOURCE3 1
angle_coeff @angle:hc-c3-n3 harmonic 49.420 109.800 # SOURCE2 5 2.0070
angle_coeff @angle:hc-c3-n4 harmonic 49.010 107.900 # SOURCE3 1
angle_coeff @angle:hc-c3-n harmonic 49.780 109.500 # SOURCE3 1
angle_coeff @angle:hc-c3-na harmonic 49.900 109.500 # SOURCE3 1
angle_coeff @angle:hc-c3-nh harmonic 49.380 111.540 # SOURCE3 1
angle_coeff @angle:hc-c3-no harmonic 48.190 107.200 # SOURCE2 1 0.0000
angle_coeff @angle:hc-c3-oh harmonic 51.070 109.500 # SOURCE3 1
angle_coeff @angle:hc-c3-os harmonic 50.870 108.700 # SOURCE2 13 2.3739
angle_coeff @angle:hc-c3-p2 harmonic 41.380 110.180 # SOURCE3 25 0.4057
angle_coeff @angle:hc-c3-p3 harmonic 41.660 110.140 # SOURCE3 325 0.5126
angle_coeff @angle:hc-c3-p4 harmonic 42.040 109.590 # SOURCE3 87 0.3196
angle_coeff @angle:hc-c3-p5 harmonic 42.540 109.640 # SOURCE3 69 0.8112
angle_coeff @angle:hc-c3-px harmonic 42.240 109.740 # SOURCE3 84 0.3474
angle_coeff @angle:hc-c3-py harmonic 42.560 109.540 # SOURCE3 39 0.1999
angle_coeff @angle:hc-c3-s4 harmonic 54.570 107.500 # SOURCE2 1 0.0000
angle_coeff @angle:hc-c3-s6 harmonic 55.480 108.200 # SOURCE3 1
angle_coeff @angle:hc-c3-sh harmonic 53.990 107.870 # SOURCE2 3 2.0981
angle_coeff @angle:hc-c3-ss harmonic 53.800 108.760 # SOURCE2 3 1.6891
angle_coeff @angle:hx-c3-hx harmonic 39.040 110.740 # SOURCE3 137 0.5531
angle_coeff @angle:hx-c3-n4 harmonic 49.020 107.910 # SOURCE3 148 0.5899
angle_coeff @angle:i-c3-i harmonic 61.980 113.120 # SOURCE3 1 0.0000
angle_coeff @angle:n1-c3-n1 harmonic 71.090 105.070 # HF/6-31G* 1
angle_coeff @angle:n2-c3-n2 harmonic 69.890 107.700 # SOURCE3 1 0.0000
angle_coeff @angle:n2-c3-nh harmonic 69.260 111.060 # SOURCE4 5 0.7868
angle_coeff @angle:n2-c3-oh harmonic 70.150 111.820 # SOURCE4 10 0.3451
angle_coeff @angle:n2-c3-os harmonic 70.040 111.230 # SOURCE4 6 1.0463
angle_coeff @angle:n3-c3-n3 harmonic 69.610 109.590 # SOURCE4 27 1.8125
angle_coeff @angle:n3-c3-nc harmonic 68.790 113.290 # SOURCE3 1 0.0000
angle_coeff @angle:n3-c3-nd harmonic 68.790 113.290 # SOURCE3 1 same_as_n3-c3-nc
angle_coeff @angle:n3-c3-nh harmonic 69.740 110.080 # SOURCE4 21 1.0686
angle_coeff @angle:n3-c3-oh harmonic 70.710 110.630 # SOURCE4 20 1.0177
angle_coeff @angle:n3-c3-os harmonic 71.150 108.330 # SOURCE4 17 1.9545
angle_coeff @angle:n3-c3-p5 harmonic 64.440 109.510 # SOURCE4 10 1.5002
angle_coeff @angle:n3-c3-ss harmonic 81.950 107.730 # SOURCE4 18 1.7621
angle_coeff @angle:n4-c3-n4 harmonic 67.130 113.320 # SOURCE3 1 0.0000
angle_coeff @angle:na-c3-na harmonic 69.060 113.490 # SOURCE3 1 0.0000
angle_coeff @angle:na-c3-os harmonic 71.270 109.060 # SOURCE4 170 0.5450
angle_coeff @angle:nc-c3-nc harmonic 69.960 110.610 # SOURCE3 1 0.0000
angle_coeff @angle:nc-c3-nh harmonic 69.340 112.430 # SOURCE3 1 0.0000
angle_coeff @angle:nc-c3-os harmonic 69.280 115.410 # SOURCE3 3 1.0288
angle_coeff @angle:nd-c3-nd harmonic 69.960 110.610 # SOURCE3 1 same_as_nc-c3-nc
angle_coeff @angle:nd-c3-nh harmonic 69.340 112.430 # SOURCE3 1 same_as_nc-c3-nh
angle_coeff @angle:nd-c3-os harmonic 69.280 115.410 # SOURCE3 3 same_as_nc-c3-os
angle_coeff @angle:nh-c3-nh harmonic 71.410 105.870 # SOURCE3 1 0.0000
angle_coeff @angle:nh-c3-oh harmonic 70.470 112.360 # SOURCE4 12 0.7775
angle_coeff @angle:nh-c3-os harmonic 71.260 108.930 # SOURCE4 17 1.3775
angle_coeff @angle:nh-c3-p5 harmonic 63.700 112.500 # SOURCE4 5 1.7371
angle_coeff @angle:nh-c3-ss harmonic 81.670 108.880 # SOURCE4 8 2.1521
angle_coeff @angle:n-c3-n2 harmonic 68.820 112.340 # SOURCE4 5 1.1443
angle_coeff @angle:n-c3-n3 harmonic 69.390 111.030 # SOURCE4 15 1.8216
angle_coeff @angle:n-c3-n harmonic 68.780 113.810 # SOURCE3 1 0.0000
angle_coeff @angle:n-c3-nh harmonic 70.540 108.340 # SOURCE4 11 2.1727
angle_coeff @angle:n-c3-oh harmonic 70.360 112.540 # SOURCE4 31 1.1295
angle_coeff @angle:no-c3-no harmonic 68.370 104.470 # SOURCE4 5 0.9726
angle_coeff @angle:n-c3-os harmonic 71.140 109.160 # SOURCE4 153 0.8778
angle_coeff @angle:n-c3-p5 harmonic 64.380 110.050 # SOURCE4 5 1.2965
angle_coeff @angle:oh-c3-oh harmonic 72.710 109.230 # SOURCE4 8 1.4978
angle_coeff @angle:oh-c3-os harmonic 72.380 109.210 # SOURCE4 85 1.1964
angle_coeff @angle:oh-c3-p5 harmonic 65.440 108.860 # SOURCE4 33 1.2025
angle_coeff @angle:oh-c3-sh harmonic 80.110 115.460 # SOURCE3 1 0.0000
angle_coeff @angle:o-c3-o harmonic 74.430 122.300 # SOURCE3 1 0.0000
angle_coeff @angle:os-c3-os harmonic 71.720 110.240 # SOURCE3 17 2.1340
angle_coeff @angle:os-c3-p5 harmonic 65.470 108.360 # SOURCE4 22 2.1937
angle_coeff @angle:os-c3-ss harmonic 82.720 107.980 # SOURCE4 20 1.7464
angle_coeff @angle:p2-c3-p2 harmonic 61.280 110.480 # SOURCE3 1 0.0000
angle_coeff @angle:p3-c3-p3 harmonic 61.730 110.160 # SOURCE3 1 0.0000
angle_coeff @angle:p5-c3-p5 harmonic 62.800 110.130 # SOURCE4 33 2.4116
angle_coeff @angle:p5-c3-ss harmonic 78.880 111.300 # SOURCE4 5 2.0560
angle_coeff @angle:s4-c3-s4 harmonic 99.950 112.290 # SOURCE3 2 1.2724
angle_coeff @angle:s4-c3-s6 harmonic 100.300 113.520 # SOURCE3 1
angle_coeff @angle:s6-c3-s6 harmonic 102.050 111.750 # SOURCE3 1 0.0000
angle_coeff @angle:sh-c3-sh harmonic 97.420 116.260 # SOURCE3 1 0.0000
angle_coeff @angle:sh-c3-ss harmonic 99.850 110.730 # SOURCE3 1
angle_coeff @angle:s-c3-s harmonic 93.400 123.350 # SOURCE3 1 0.0000
angle_coeff @angle:ss-c3-ss harmonic 99.950 110.570 # SOURCE4 15 1.4311
angle_coeff @angle:br-ca-br harmonic 67.310 117.600 # SOURCE3 1
angle_coeff @angle:br-ca-ca harmonic 63.480 118.130 # SOURCE3 8 0.6041
angle_coeff @angle:c1-ca-c1 harmonic 64.700 120.000 # SOURCE3 1
angle_coeff @angle:c1-ca-ca harmonic 65.860 120.000 # SOURCE3 1
angle_coeff @angle:c2-ca-c2 harmonic 62.950 120.000 # SOURCE3 1
angle_coeff @angle:c2-ca-ca harmonic 64.690 120.600 # SOURCE3 1
angle_coeff @angle:c3-ca-c2 harmonic 62.240 120.000 # SOURCE3 1
angle_coeff @angle:c3-ca-c3 harmonic 62.410 116.800 # SOURCE3 1
angle_coeff @angle:c3-ca-ca harmonic 63.840 120.630 # SOURCE3 60 0.7175
angle_coeff @angle:c3-ca-cp harmonic 63.700 120.630 # SOURCE3 60 0.7175
angle_coeff @angle:c3-ca-cq harmonic 63.590 120.630 # SOURCE3 60 0.7175
angle_coeff @angle:c3-ca-na harmonic 66.590 118.780 # SOURCE4 59 1.1184
angle_coeff @angle:c3-ca-nb harmonic 67.330 116.660 # SOURCE4 408 0.9380
angle_coeff @angle:ca-ca-ca harmonic 67.180 119.970 # SOURCE3 1969 0.3480
angle_coeff @angle:ca-ca-cc harmonic 65.990 120.100 # SOURCE3 103 0.3451
angle_coeff @angle:ca-ca-cd harmonic 65.990 120.100 # SOURCE3 103 0.3451
angle_coeff @angle:ca-ca-ce harmonic 64.880 120.660 # SOURCE3 14 0.1564
angle_coeff @angle:ca-ca-cf harmonic 64.880 120.660 # SOURCE3 14 same_as_ca-ca-ce
angle_coeff @angle:ca-ca-cg harmonic 65.900 120.050 # SOURCE3 6 0.2397
angle_coeff @angle:ca-ca-ch harmonic 65.900 120.050 # SOURCE3 6 same_as_ca-ca-cg
angle_coeff @angle:ca-ca-cl harmonic 62.920 119.400 # SOURCE4 2459 0.5283
angle_coeff @angle:ca-ca-cp harmonic 67.240 119.070 # SOURCE3 14 2.3077
angle_coeff @angle:ca-ca-cq harmonic 67.090 119.070 # SOURCE3 14 2.3077
angle_coeff @angle:ca-ca-cx harmonic 64.480 120.830 # SOURCE4 71 1.3062
angle_coeff @angle:ca-ca-cy harmonic 63.770 120.860 # SOURCE4 17 2.0287
angle_coeff @angle:ca-ca-f harmonic 67.510 118.950 # SOURCE4 967 0.3369
angle_coeff @angle:ca-ca-h4 harmonic 48.240 121.090 # SOURCE3 57 1.4696
angle_coeff @angle:ca-ca-ha harmonic 48.460 120.010 # SOURCE3 2980 0.2511
angle_coeff @angle:ca-ca-i harmonic 58.590 118.470 # SOURCE3 10 0.6181
angle_coeff @angle:ca-ca-n1 harmonic 68.920 118.500 # HF/6-31G* 1
angle_coeff @angle:ca-ca-n2 harmonic 70.950 119.570 # SOURCE3 1
angle_coeff @angle:ca-ca-n4 harmonic 67.280 118.410 # SOURCE3 6 0.1691
angle_coeff @angle:ca-ca-n harmonic 67.970 119.890 # SOURCE3 18 0.2095
angle_coeff @angle:ca-ca-na harmonic 70.210 118.340 # SOURCE3 54 3.6168
angle_coeff @angle:ca-ca-nb harmonic 69.160 122.630 # SOURCE3 83 1.1249
angle_coeff @angle:ca-ca-nc harmonic 70.140 119.720 # SOURCE3 22 3.3994
angle_coeff @angle:ca-ca-nd harmonic 70.140 119.720 # SOURCE3 22 3.3994
angle_coeff @angle:ca-ca-ne harmonic 67.740 119.880 # SOURCE3 24 0.3637
angle_coeff @angle:ca-ca-nf harmonic 67.740 119.880 # SOURCE3 24 0.3637
angle_coeff @angle:ca-ca-nh harmonic 69.340 120.130 # SOURCE3 193 0.6341
angle_coeff @angle:ca-ca-no harmonic 66.880 119.540 # SOURCE3 10 1.3187
angle_coeff @angle:ca-ca-o harmonic 71.850 123.290 # SOURCE4 11 1.2526
angle_coeff @angle:ca-ca-oh harmonic 69.850 119.940 # SOURCE3 14 0.1627
angle_coeff @angle:ca-ca-os harmonic 69.790 119.200 # SOURCE3 52 0.5240
angle_coeff @angle:ca-ca-p2 harmonic 61.520 114.360 # SOURCE3 1
angle_coeff @angle:ca-ca-p3 harmonic 60.320 120.730 # SOURCE3 6 0.1273
angle_coeff @angle:ca-ca-p4 harmonic 60.930 120.300 # SOURCE3 1
angle_coeff @angle:ca-ca-p5 harmonic 61.240 120.280 # SOURCE4 5 0.0177
angle_coeff @angle:ca-ca-pe harmonic 60.250 120.450 # SOURCE3 20 0.2719
angle_coeff @angle:ca-ca-pf harmonic 60.250 120.450 # SOURCE3 20 0.2719
angle_coeff @angle:ca-ca-px harmonic 60.340 120.530 # SOURCE3 10 0.4509
angle_coeff @angle:ca-ca-py harmonic 61.180 119.980 # SOURCE3 6 0.0670
angle_coeff @angle:ca-ca-s4 harmonic 78.120 119.150 # SOURCE3 1
angle_coeff @angle:ca-ca-s6 harmonic 78.690 120.540 # SOURCE4 36 1.2154
angle_coeff @angle:ca-ca-s harmonic 78.750 122.550 # SOURCE3 4 0.0000
angle_coeff @angle:ca-ca-sh harmonic 77.610 121.780 # SOURCE4 17 1.2849
angle_coeff @angle:ca-ca-ss harmonic 78.500 119.930 # SOURCE3 16 0.3901
angle_coeff @angle:ca-ca-sx harmonic 76.800 119.180 # SOURCE3 6 0.0434
angle_coeff @angle:ca-ca-sy harmonic 78.020 119.890 # SOURCE3 24 1.8813
angle_coeff @angle:c-ca-c3 harmonic 62.610 118.060 # SOURCE3 1
angle_coeff @angle:c-ca-c harmonic 62.650 120.000 # SOURCE3 1
angle_coeff @angle:c-ca-ca harmonic 64.640 120.140 # SOURCE3 40 0.4788
angle_coeff @angle:cc-ca-cp harmonic 64.690 124.300 # SOURCE4 10 0.6423
angle_coeff @angle:cc-ca-nb harmonic 69.060 118.450 # SOURCE4 35 1.6594
angle_coeff @angle:cd-ca-nb harmonic 69.340 117.500 # SOURCE4 29 1.8623
angle_coeff @angle:ce-ca-na harmonic 67.440 119.850 # SOURCE4 9 0.7001
angle_coeff @angle:ce-ca-nb harmonic 68.300 117.380 # SOURCE4 32 0.6890
angle_coeff @angle:cf-ca-nb harmonic 68.080 118.140 # SOURCE4 12 1.1775
angle_coeff @angle:cg-ca-cp harmonic 65.330 121.530 # SOURCE4 12 0.1831
angle_coeff @angle:c-ca-ha harmonic 46.510 115.900 # SOURCE3 1
angle_coeff @angle:cl-ca-cl harmonic 62.630 118.720 # SOURCE3 1
angle_coeff @angle:cl-ca-cp harmonic 62.600 120.310 # SOURCE4 18 0.5607
angle_coeff @angle:cl-ca-nb harmonic 65.810 116.150 # SOURCE4 50 0.6047
angle_coeff @angle:c-ca-nb harmonic 67.710 117.940 # SOURCE4 91 1.0536
angle_coeff @angle:c-ca-nc harmonic 64.400 130.800 # SOURCE3 1
angle_coeff @angle:c-ca-nd harmonic 64.400 130.800 # SOURCE3 1 same_as_c-ca-nc
angle_coeff @angle:cp-ca-f harmonic 67.180 119.390 # SOURCE4 16 0.1724
angle_coeff @angle:cp-ca-h4 harmonic 48.230 120.030 # SOURCE4 27 0.4431
angle_coeff @angle:cp-ca-ha harmonic 48.030 121.080 # SOURCE3 12 1.7484
angle_coeff @angle:cp-ca-na harmonic 73.000 108.790 # SOURCE4 165 0.5166
angle_coeff @angle:cp-ca-nb harmonic 68.640 123.720 # SOURCE4 50 0.8176
angle_coeff @angle:cp-ca-nh harmonic 68.740 121.520 # SOURCE4 11 0.5438
angle_coeff @angle:cp-ca-oh harmonic 69.340 120.960 # SOURCE4 12 1.1400
angle_coeff @angle:cp-ca-ss harmonic 80.870 112.750 # SOURCE4 8 0.6216
angle_coeff @angle:cp-ca-sy harmonic 80.930 111.180 # SOURCE3 2 0.0000
angle_coeff @angle:cq-ca-ha harmonic 47.860 121.080 # SOURCE3 12 1.7484
angle_coeff @angle:cq-ca-sy harmonic 80.860 111.180 # SOURCE3 2 0.0000
angle_coeff @angle:f-ca-f harmonic 68.050 117.500 # SOURCE3 1
angle_coeff @angle:f-ca-nb harmonic 71.690 114.580 # SOURCE4 19 0.2987
angle_coeff @angle:h4-ca-n harmonic 49.480 116.020 # SOURCE3 1
angle_coeff @angle:h4-ca-na harmonic 51.880 114.650 # SOURCE3 5 1.5484
angle_coeff @angle:h4-ca-nb harmonic 51.820 115.940 # SOURCE3 52 0.7370
angle_coeff @angle:h4-ca-nc harmonic 51.460 118.360 # SOURCE3 1
angle_coeff @angle:h4-ca-nd harmonic 51.460 118.360 # SOURCE3 1 same_as_h4-ca-nc
angle_coeff @angle:h4-ca-os harmonic 52.300 111.150 # SOURCE3 1
angle_coeff @angle:h4-ca-ss harmonic 53.660 116.190 # SOURCE3 1
angle_coeff @angle:h5-ca-nb harmonic 51.760 116.350 # SOURCE3 30 0.5545
angle_coeff @angle:h5-ca-nc harmonic 50.700 122.110 # SOURCE3 1
angle_coeff @angle:h5-ca-nd harmonic 50.700 122.110 # SOURCE3 1 same_as_h5-ca-nc
angle_coeff @angle:ha-ca-n2 harmonic 52.970 116.000 # SOURCE2 1 0.0000
angle_coeff @angle:ha-ca-p2 harmonic 39.570 122.560 # SOURCE3 1
angle_coeff @angle:i-ca-i harmonic 62.290 119.280 # SOURCE3 1
angle_coeff @angle:n1-ca-n1 harmonic 70.730 117.030 # HF/6-31G* 1
angle_coeff @angle:n2-ca-n2 harmonic 75.050 120.000 # SOURCE3 1
angle_coeff @angle:n2-ca-na harmonic 73.800 119.600 # SOURCE3 1
angle_coeff @angle:n4-ca-n4 harmonic 67.650 116.820 # SOURCE3 1
angle_coeff @angle:na-ca-na harmonic 76.480 107.650 # SOURCE4 5 0.8751
angle_coeff @angle:na-ca-nb harmonic 70.600 127.070 # SOURCE4 237 1.9392
angle_coeff @angle:na-ca-nh harmonic 72.480 118.620 # SOURCE4 29 0.9759
angle_coeff @angle:nb-ca-nb harmonic 70.780 127.190 # SOURCE4 585 1.1793
angle_coeff @angle:nb-ca-nc harmonic 70.900 127.320 # SOURCE4 8 0.8052
angle_coeff @angle:nb-ca-nd harmonic 71.250 126.080 # SOURCE4 14 0.9814
angle_coeff @angle:nb-ca-nh harmonic 73.200 116.950 # SOURCE4 765 0.8040
angle_coeff @angle:nb-ca-oh harmonic 73.570 117.300 # SOURCE4 64 0.9290
angle_coeff @angle:nb-ca-os harmonic 72.540 119.660 # SOURCE4 76 0.6493
angle_coeff @angle:nb-ca-sh harmonic 81.390 117.590 # SOURCE4 15 1.4616
angle_coeff @angle:nb-ca-ss harmonic 81.120 119.300 # SOURCE4 41 1.3420
angle_coeff @angle:nc-ca-nc harmonic 70.670 128.740 # SOURCE3 1
angle_coeff @angle:nc-ca-nh harmonic 72.770 118.860 # SOURCE3 1
angle_coeff @angle:nd-ca-nd harmonic 70.670 128.740 # SOURCE3 1 same_as_nc-ca-nc
angle_coeff @angle:nd-ca-nh harmonic 72.770 118.860 # SOURCE3 1 same_as_nc-ca-nh
angle_coeff @angle:nh-ca-nh harmonic 71.400 120.980 # SOURCE3 1
angle_coeff @angle:n-ca-nc harmonic 69.660 123.860 # SOURCE3 1
angle_coeff @angle:n-ca-nd harmonic 69.660 123.860 # SOURCE3 1 same_as_n-ca-nc
angle_coeff @angle:n-ca-nh harmonic 71.290 116.160 # SOURCE3 1
angle_coeff @angle:no-ca-no harmonic 67.420 117.140 # SOURCE3 1
angle_coeff @angle:oh-ca-oh harmonic 72.630 120.000 # SOURCE3 1
angle_coeff @angle:o-ca-o harmonic 78.210 126.820 # SOURCE3 1
angle_coeff @angle:os-ca-os harmonic 74.010 113.730 # SOURCE3 1
angle_coeff @angle:p2-ca-p2 harmonic 58.980 121.200 # SOURCE3 1
angle_coeff @angle:p3-ca-p3 harmonic 59.440 121.460 # SOURCE3 1
angle_coeff @angle:p5-ca-p5 harmonic 60.760 120.000 # SOURCE3 1
angle_coeff @angle:s4-ca-s4 harmonic 104.060 105.810 # SOURCE3 1
angle_coeff @angle:s6-ca-s6 harmonic 105.770 105.810 # SOURCE3 1
angle_coeff @angle:sh-ca-sh harmonic 98.150 120.240 # SOURCE3 1
angle_coeff @angle:s-ca-s harmonic 98.380 125.140 # SOURCE3 1
angle_coeff @angle:ss-ca-ss harmonic 100.760 115.150 # SOURCE3 1
angle_coeff @angle:br-c-br harmonic 66.910 113.100 # SOURCE3 1
angle_coeff @angle:br-c-c3 harmonic 63.340 110.740 # SOURCE3 1 0.0000
angle_coeff @angle:br-c-o harmonic 63.190 121.460 # SOURCE3 5 1.6264
angle_coeff @angle:c1-c-c1 harmonic 65.090 115.320 # SOURCE3 1
angle_coeff @angle:c1-c-o harmonic 69.920 122.340 # SOURCE3 1
angle_coeff @angle:c2-c-c2 harmonic 67.170 116.780 # SOURCE3 1
angle_coeff @angle:c2-c-ha harmonic 48.650 115.950 # SOURCE3 1
angle_coeff @angle:c2-c-o harmonic 72.770 119.120 # SOURCE3 2 0.0000
angle_coeff @angle:c2-c-s harmonic 81.850 119.160 # SOURCE3 2 0.0000
angle_coeff @angle:c3-c-c3 harmonic 62.820 116.050 # SOURCE3 11 1.0986
angle_coeff @angle:c3-c-ca harmonic 62.590 118.540 # SOURCE4 240 1.3614
angle_coeff @angle:c3-c-cc harmonic 63.240 118.000 # SOURCE4 21 0.9834
angle_coeff @angle:c3-c-cd harmonic 63.500 117.020 # SOURCE4 25 1.4755
angle_coeff @angle:c3-c-ce harmonic 63.470 116.250 # SOURCE4 188 1.1613
angle_coeff @angle:c3-c-cf harmonic 63.300 116.860 # SOURCE4 45 1.5859
angle_coeff @angle:c3-c-cg harmonic 64.260 115.000 # SOURCE2 1 0.0000
angle_coeff @angle:c3-c-ch harmonic 64.260 115.000 # SOURCE2 1 same_as_c3-c-cg
angle_coeff @angle:c3-c-cl harmonic 62.560 111.990 # SOURCE3 2 0.0125
angle_coeff @angle:c3-c-f harmonic 66.930 110.700 # SOURCE2 1 0.0000
angle_coeff @angle:c3-c-h4 harmonic 46.110 114.400 # SOURCE4 57 0.4032
angle_coeff @angle:c3-c-ha harmonic 46.010 115.220 # SOURCE3 15 0.3181
angle_coeff @angle:c3-c-i harmonic 56.870 112.940 # SOURCE3 1 0.0000
angle_coeff @angle:c3-c-n2 harmonic 66.620 114.530 # SOURCE3 1
angle_coeff @angle:c3-c-n4 harmonic 64.610 112.260 # SOURCE3 2 0.0000
angle_coeff @angle:c3-c-n harmonic 67.860 115.150 # SOURCE3 153 2.7443
angle_coeff @angle:c3-c-ne harmonic 68.090 111.390 # SOURCE4 11 2.1430
angle_coeff @angle:c3-c-nf harmonic 67.430 113.380 # SOURCE3 1 same_as_c3-c-ne
angle_coeff @angle:c3-c-o harmonic 68.030 123.110 # SOURCE3 267 3.0977
angle_coeff @angle:c3-c-oh harmonic 69.840 112.200 # SOURCE3 14 1.8324
angle_coeff @angle:c3-c-os harmonic 69.260 111.960 # SOURCE3 15 2.3072
angle_coeff @angle:c3-c-p3 harmonic 58.900 116.420 # SOURCE3 3 0.1291
angle_coeff @angle:c3-c-p5 harmonic 58.320 118.900 # SOURCE3 1
angle_coeff @angle:c3-c-pe harmonic 58.620 114.850 # SOURCE3 1 0.0000
angle_coeff @angle:c3-c-pf harmonic 58.620 114.850 # SOURCE3 1 same_as_c3-c-pe
angle_coeff @angle:c3-c-px harmonic 58.600 115.600 # SOURCE3 1 0.0000
angle_coeff @angle:c3-c-py harmonic 58.850 118.160 # SOURCE3 3 1.0735
angle_coeff @angle:c3-c-s4 harmonic 75.480 114.790 # SOURCE3 1
angle_coeff @angle:c3-c-s6 harmonic 75.500 114.720 # SOURCE3 1
angle_coeff @angle:c3-c-s harmonic 78.510 123.730 # SOURCE3 9 1.4528
angle_coeff @angle:c3-c-sh harmonic 78.430 114.210 # SOURCE3 3 2.3916
angle_coeff @angle:c3-c-ss harmonic 78.990 114.320 # SOURCE3 5 2.7478
angle_coeff @angle:c3-c-sx harmonic 75.280 113.970 # SOURCE3 3 0.0610
angle_coeff @angle:c3-c-sy harmonic 75.800 114.280 # SOURCE3 3 0.7341
angle_coeff @angle:ca-c-ca harmonic 63.030 118.580 # SOURCE4 144 2.1146
angle_coeff @angle:ca-c-cc harmonic 64.370 115.570 # SOURCE4 175 1.7981
angle_coeff @angle:ca-c-cd harmonic 63.940 117.130 # SOURCE4 82 1.7238
angle_coeff @angle:ca-c-ce harmonic 63.290 118.610 # SOURCE4 30 1.3375
angle_coeff @angle:ca-c-cf harmonic 62.800 120.470 # SOURCE4 6 1.3008
angle_coeff @angle:ca-c-h4 harmonic 46.520 115.140 # SOURCE4 30 0.7320
angle_coeff @angle:ca-c-ha harmonic 46.800 114.120 # SOURCE3 1 0.0000
angle_coeff @angle:ca-c-n harmonic 68.470 115.140 # SOURCE4 571 1.4648
angle_coeff @angle:ca-c-ne harmonic 67.750 114.390 # SOURCE4 5 0.2958
angle_coeff @angle:ca-c-o harmonic 68.670 123.440 # SOURCE3 18 2.5574
angle_coeff @angle:ca-c-oh harmonic 70.110 113.440 # SOURCE4 222 0.8421
angle_coeff @angle:ca-c-os harmonic 68.780 115.540 # SOURCE3 5 2.6708
angle_coeff @angle:ca-c-s harmonic 79.130 123.040 # SOURCE4 12 0.7935
angle_coeff @angle:ca-c-sh harmonic 77.270 118.630 # SOURCE3 1 0.0000
angle_coeff @angle:ca-c-ss harmonic 79.040 115.130 # SOURCE4 12 1.0069
angle_coeff @angle:br-cc-c harmonic 63.980 115.680 # SOURCE4 8 0.4970
angle_coeff @angle:br-cc-cc harmonic 61.820 124.890 # SOURCE4 8 1.9479
angle_coeff @angle:br-cc-cd harmonic 62.260 124.560 # SOURCE4 32 2.4696
angle_coeff @angle:br-cc-na harmonic 64.600 121.420 # SOURCE4 6 0.5507
angle_coeff @angle:c2-cc-c3 harmonic 63.270 126.110 # SOURCE3 2 0.0000
angle_coeff @angle:c2-cc-ca harmonic 65.400 124.420 # SOURCE4 15 1.7107
angle_coeff @angle:c2-cc-cc harmonic 66.340 121.390 # SOURCE4 29 2.2566
angle_coeff @angle:c2-cc-cd harmonic 69.090 117.020 # SOURCE3 2 0.0703
angle_coeff @angle:c2-cc-ha harmonic 48.690 122.720 # SOURCE3 2 0.0092
angle_coeff @angle:c2-cc-n harmonic 67.740 126.900 # SOURCE3 1 0.0000
angle_coeff @angle:c2-cc-os harmonic 70.020 121.060 # SOURCE4 11 0.8179
angle_coeff @angle:c-c-c3 harmonic 61.720 116.860 # SOURCE3 5 0.1653
angle_coeff @angle:c3-cc-ca harmonic 61.830 126.430 # SOURCE4 119 1.7751
angle_coeff @angle:c3-cc-cc harmonic 64.660 115.970 # SOURCE3 4 3.0507
angle_coeff @angle:c3-cc-cd harmonic 64.810 119.450 # SOURCE3 35 8.2040
angle_coeff @angle:c3-cc-cf harmonic 65.450 117.840 # SOURCE3 1 0.0000
angle_coeff @angle:c3-cc-ha harmonic 45.110 121.520 # SOURCE3 32 3.2091
angle_coeff @angle:c3-cc-n2 harmonic 65.940 126.280 # SOURCE4 8 2.1234
angle_coeff @angle:c3-cc-n harmonic 66.540 118.360 # SOURCE4 53 2.1705
angle_coeff @angle:c3-cc-na harmonic 65.440 122.990 # SOURCE4 477 1.5214
angle_coeff @angle:c3-cc-nc harmonic 65.880 121.000 # SOURCE4 66 0.8247
angle_coeff @angle:c3-cc-nd harmonic 65.890 123.750 # SOURCE4 275 1.8941
angle_coeff @angle:c3-cc-os harmonic 67.480 117.090 # SOURCE4 127 0.9464
angle_coeff @angle:c3-cc-ss harmonic 77.460 121.680 # SOURCE4 145 0.8647
angle_coeff @angle:c-c-c harmonic 62.300 111.680 # SOURCE3 2 6.1226
angle_coeff @angle:c-c-ca harmonic 61.730 118.340 # SOURCE4 26 1.0692
angle_coeff @angle:ca-cc-cc harmonic 67.660 111.040 # SOURCE3 9 7.9455
angle_coeff @angle:ca-cc-cd harmonic 68.230 113.510 # SOURCE3 26 7.4229
angle_coeff @angle:ca-cc-ce harmonic 62.580 127.870 # SOURCE4 11 1.7579
angle_coeff @angle:ca-cc-h4 harmonic 45.570 128.660 # SOURCE3 10 3.1167
angle_coeff @angle:ca-cc-ha harmonic 46.400 124.040 # SOURCE3 34 3.6691
angle_coeff @angle:ca-cc-n harmonic 68.240 118.420 # SOURCE4 17 2.2100
angle_coeff @angle:ca-cc-nc harmonic 67.790 120.310 # SOURCE4 46 0.6711
angle_coeff @angle:ca-cc-nd harmonic 67.840 123.280 # SOURCE4 182 2.3863
angle_coeff @angle:ca-cc-nh harmonic 67.460 122.450 # SOURCE4 9 1.4092
angle_coeff @angle:ca-cc-oh harmonic 70.020 116.510 # SOURCE4 12 1.7855
angle_coeff @angle:ca-cc-os harmonic 69.540 116.090 # SOURCE4 58 2.0472
angle_coeff @angle:ca-cc-ss harmonic 78.690 120.980 # SOURCE4 28 1.8865
angle_coeff @angle:c-cc-c2 harmonic 65.620 120.880 # SOURCE4 21 1.5157
angle_coeff @angle:c-cc-c3 harmonic 64.900 112.750 # SOURCE3 4 0.2063
angle_coeff @angle:c-cc-c harmonic 63.420 121.160 # SOURCE4 48 0.7193
angle_coeff @angle:c-c-cc harmonic 64.020 111.670 # SOURCE3 4 5.5146
angle_coeff @angle:c-cc-ca harmonic 63.550 122.950 # SOURCE3 1 0.0000
angle_coeff @angle:c-cc-cc harmonic 63.720 122.690 # SOURCE3 2 0.0000
angle_coeff @angle:cc-c-cc harmonic 64.820 115.970 # SOURCE4 37 1.4486
angle_coeff @angle:cc-cc-cc harmonic 67.880 110.700 # SOURCE3 54 3.4091
angle_coeff @angle:cc-cc-cd harmonic 68.160 114.190 # SOURCE3 517 6.5960
angle_coeff @angle:cc-cc-ce harmonic 63.140 126.050 # SOURCE4 10 2.3332
angle_coeff @angle:cc-cc-cf harmonic 65.650 123.920 # SOURCE3 1 0.0000
angle_coeff @angle:cc-cc-cg harmonic 64.740 121.850 # SOURCE4 6 0.8146
angle_coeff @angle:c-cc-cd harmonic 65.230 121.510 # SOURCE4 919 2.2603
angle_coeff @angle:cc-c-cd harmonic 65.730 112.790 # SOURCE3 1 0.0000
angle_coeff @angle:c-cc-ce harmonic 63.360 122.370 # SOURCE4 5 0.0254
angle_coeff @angle:cc-c-ce harmonic 64.640 115.680 # SOURCE4 6 1.2033
angle_coeff @angle:cc-cc-f harmonic 66.350 119.410 # SOURCE4 7 0.4917
angle_coeff @angle:c-cc-cg harmonic 64.980 118.140 # SOURCE4 7 0.7745
angle_coeff @angle:cc-cc-h4 harmonic 45.560 129.470 # SOURCE3 171 2.2734
angle_coeff @angle:cc-cc-ha harmonic 47.460 119.260 # SOURCE4 506 1.6808
angle_coeff @angle:c-cc-cl harmonic 62.790 116.010 # SOURCE4 19 0.9295
angle_coeff @angle:cc-cc-n2 harmonic 69.460 121.150 # SOURCE3 6 0.4642
angle_coeff @angle:cc-cc-n harmonic 67.950 119.890 # SOURCE3 36 0.2095
angle_coeff @angle:cc-cc-na harmonic 72.210 106.800 # SOURCE3 33 0.6297
angle_coeff @angle:cc-cc-nc harmonic 69.950 113.420 # SOURCE3 4 1.3957
angle_coeff @angle:cc-cc-nd harmonic 71.150 112.560 # SOURCE3 141 4.2871
angle_coeff @angle:cc-cc-nh harmonic 68.510 119.190 # SOURCE4 142 2.2114
angle_coeff @angle:cc-cc-oh harmonic 69.230 119.670 # SOURCE4 10 2.3619
angle_coeff @angle:cc-cc-os harmonic 69.380 117.090 # SOURCE4 99 2.4776
angle_coeff @angle:cc-cc-pd harmonic 63.840 115.360 # SOURCE3 84 same_as_cd-cd-pc
angle_coeff @angle:cc-cc-ss harmonic 80.780 115.020 # SOURCE3 2 0.0000
angle_coeff @angle:cc-cc-sy harmonic 74.830 128.360 # SOURCE4 8 0.9813
angle_coeff @angle:c-c-cd harmonic 64.020 111.670 # SOURCE3 4 5.5146
angle_coeff @angle:cd-cc-cd harmonic 67.630 121.160 # SOURCE4 42 2.0764
angle_coeff @angle:cd-cc-ce harmonic 63.480 129.500 # SOURCE4 139 2.1675
angle_coeff @angle:cd-cc-cl harmonic 61.780 123.720 # SOURCE4 48 1.9010
angle_coeff @angle:cd-cc-f harmonic 67.420 121.080 # SOURCE4 28 0.8788
angle_coeff @angle:cd-cc-h4 harmonic 47.190 129.110 # SOURCE3 418 3.1355
angle_coeff @angle:cd-cc-ha harmonic 48.350 122.890 # SOURCE3 584 2.9334
angle_coeff @angle:cd-cc-n harmonic 70.720 115.520 # SOURCE3 52 1.3322
angle_coeff @angle:cd-cc-na harmonic 72.910 109.420 # SOURCE3 265 2.6051
angle_coeff @angle:cd-cc-nc harmonic 70.990 114.980 # SOURCE3 23 5.3935
angle_coeff @angle:cd-cc-nh harmonic 68.380 125.040 # SOURCE3 1 0.0000
angle_coeff @angle:cd-cc-no harmonic 65.780 128.950 # SOURCE4 117 1.4740
angle_coeff @angle:cd-cc-oh harmonic 69.580 124.030 # SOURCE4 59 1.2544
angle_coeff @angle:cd-cc-os harmonic 69.960 120.300 # SOURCE3 64 5.4354
angle_coeff @angle:cd-cc-ss harmonic 82.940 111.220 # SOURCE4 692 1.2683
angle_coeff @angle:cd-cc-sy harmonic 76.410 125.160 # SOURCE4 19 1.1014
angle_coeff @angle:ce-cc-na harmonic 66.420 124.140 # SOURCE4 40 1.5665
angle_coeff @angle:ce-cc-nc harmonic 66.980 121.700 # SOURCE4 8 1.6500
angle_coeff @angle:ce-cc-nd harmonic 67.220 123.910 # SOURCE4 11 1.1451
angle_coeff @angle:ce-cc-os harmonic 68.210 119.170 # SOURCE4 59 0.7385
angle_coeff @angle:ce-cc-ss harmonic 78.460 120.940 # SOURCE4 31 1.2422
angle_coeff @angle:c-cc-f harmonic 66.160 116.870 # SOURCE4 16 0.5322
angle_coeff @angle:cg-cc-na harmonic 67.510 122.350 # SOURCE4 5 0.8112
angle_coeff @angle:cg-cc-ss harmonic 78.880 120.700 # SOURCE4 12 0.9090
angle_coeff @angle:cc-c-h4 harmonic 47.130 115.450 # SOURCE4 5 0.8021
angle_coeff @angle:c-cc-ha harmonic 46.990 117.020 # SOURCE3 56 1.9713
angle_coeff @angle:cl-cc-na harmonic 63.840 121.610 # SOURCE4 12 0.3436
angle_coeff @angle:cl-cc-nd harmonic 63.930 122.510 # SOURCE4 5 1.6568
angle_coeff @angle:cl-cc-ss harmonic 79.050 119.850 # SOURCE4 11 1.0626
angle_coeff @angle:c-cc-n2 harmonic 68.530 120.890 # SOURCE3 1 0.0000
angle_coeff @angle:c-cc-n harmonic 68.110 116.330 # SOURCE4 20 1.9278
angle_coeff @angle:cc-c-n harmonic 70.190 111.860 # SOURCE3 36 2.3407
angle_coeff @angle:c-cc-nc harmonic 66.280 123.150 # SOURCE4 23 2.1612
angle_coeff @angle:cc-c-nd harmonic 67.520 116.400 # SOURCE4 23 1.1407
angle_coeff @angle:c-cc-nd harmonic 70.070 112.910 # SOURCE3 1 0.0000
angle_coeff @angle:c-cc-ne harmonic 67.110 119.880 # SOURCE4 6 0.3139
angle_coeff @angle:cc-c-o harmonic 68.910 125.710 # SOURCE3 66 2.4784
angle_coeff @angle:c-cc-oh harmonic 70.150 113.450 # SOURCE4 35 1.3440
angle_coeff @angle:cc-c-oh harmonic 71.160 112.580 # SOURCE4 50 0.7342
angle_coeff @angle:c-cc-os harmonic 67.710 119.810 # SOURCE4 52 1.7157
angle_coeff @angle:cc-c-os harmonic 70.500 112.300 # SOURCE3 6 2.7842
angle_coeff @angle:cc-c-s harmonic 78.050 127.940 # SOURCE4 12 0.9342
angle_coeff @angle:cc-c-ss harmonic 80.330 112.520 # SOURCE4 10 0.6933
angle_coeff @angle:cx-cc-nd harmonic 65.680 127.750 # SOURCE4 12 1.7156
angle_coeff @angle:cx-cc-os harmonic 68.010 118.080 # SOURCE4 10 0.0955
angle_coeff @angle:cd-c-cd harmonic 64.770 116.170 # SOURCE4 19 1.1663
angle_coeff @angle:cd-c-cx harmonic 63.880 117.460 # SOURCE4 13 0.1625
angle_coeff @angle:cd-c-n harmonic 70.190 111.860 # SOURCE3 36 2.3407
angle_coeff @angle:cd-c-nc harmonic 68.310 115.760 # SOURCE4 10 0.7131
angle_coeff @angle:cd-c-nd harmonic 68.300 113.750 # SOURCE4 14 0.0860
angle_coeff @angle:cd-c-o harmonic 68.910 125.710 # SOURCE3 66 2.4784
angle_coeff @angle:cd-c-oh harmonic 70.770 113.840 # SOURCE4 35 1.1033
angle_coeff @angle:cd-c-os harmonic 70.500 112.300 # SOURCE3 6 2.7842
angle_coeff @angle:ce-c-ce harmonic 64.340 115.790 # SOURCE4 73 0.4467
angle_coeff @angle:ce-c-cf harmonic 64.040 116.890 # SOURCE4 11 1.6021
angle_coeff @angle:ce-c-cx harmonic 63.950 116.250 # SOURCE4 6 0.6351
angle_coeff @angle:ce-c-h4 harmonic 46.930 114.880 # SOURCE4 19 0.3355
angle_coeff @angle:ce-c-ha harmonic 46.930 115.220 # SOURCE3 7 2.4188
angle_coeff @angle:ce-c-n harmonic 68.880 115.010 # SOURCE3 2 0.5478
angle_coeff @angle:ce-c-o harmonic 69.270 122.920 # SOURCE3 17 3.5085
angle_coeff @angle:ce-c-oh harmonic 70.250 114.300 # SOURCE4 94 1.5074
angle_coeff @angle:ce-c-os harmonic 70.050 112.620 # SOURCE4 125 2.0061
angle_coeff @angle:ce-c-s harmonic 81.120 117.800 # SOURCE3 1 0.0000
angle_coeff @angle:ce-c-ss harmonic 80.920 110.390 # SOURCE4 5 0.6050
angle_coeff @angle:cf-c-cf harmonic 64.070 116.780 # SOURCE3 1 same_as_ce-c-ce
angle_coeff @angle:cf-c-ha harmonic 46.930 115.220 # SOURCE3 7 same_as_ce-c-ha
angle_coeff @angle:cf-c-n harmonic 68.800 115.290 # SOURCE4 30 1.1758
angle_coeff @angle:cf-c-o harmonic 69.270 122.920 # SOURCE3 17 3.5085
angle_coeff @angle:cf-c-oh harmonic 70.490 113.530 # SOURCE4 34 2.1382
angle_coeff @angle:cf-c-os harmonic 70.720 110.510 # SOURCE4 24 0.9128
angle_coeff @angle:cf-c-s harmonic 81.120 117.800 # SOURCE3 1 same_as_ce-c-s
angle_coeff @angle:cg-c-cg harmonic 65.440 115.380 # SOURCE3 1 0.0000
angle_coeff @angle:cg-c-ha harmonic 47.800 113.900 # SOURCE2 1 0.0000
angle_coeff @angle:cg-c-o harmonic 70.210 122.310 # SOURCE3 2 0.0000
angle_coeff @angle:c-c-h4 harmonic 44.620 116.360 # SOURCE4 5 0.5586
angle_coeff @angle:h4-cc-n harmonic 50.390 117.620 # SOURCE3 53 0.9721
angle_coeff @angle:h4-cc-na harmonic 50.220 119.660 # SOURCE3 294 2.4702
angle_coeff @angle:h4-cc-nc harmonic 50.000 120.030 # SOURCE3 16 2.3863
angle_coeff @angle:h4-cc-nd harmonic 51.390 119.110 # SOURCE3 135 1.6946
angle_coeff @angle:h4-cc-os harmonic 52.270 111.890 # SOURCE3 61 2.3500
angle_coeff @angle:h4-cc-ss harmonic 54.360 117.750 # SOURCE3 40 3.1156
angle_coeff @angle:h5-cc-n harmonic 50.870 115.610 # SOURCE4 10 0.8505
angle_coeff @angle:h5-cc-na harmonic 49.760 122.100 # SOURCE3 16 1.4626
angle_coeff @angle:h5-cc-nc harmonic 49.290 123.700 # SOURCE3 6 0.3547
angle_coeff @angle:h5-cc-nd harmonic 50.130 125.380 # SOURCE3 40 2.2157
angle_coeff @angle:h5-cc-os harmonic 51.300 116.330 # SOURCE3 12 3.2919
angle_coeff @angle:h5-cc-ss harmonic 53.390 122.000 # SOURCE3 6 0.7237
angle_coeff @angle:c-c-ha harmonic 44.850 115.430 # SOURCE2 3 0.6549
angle_coeff @angle:ha-cc-na harmonic 49.820 121.500 # SOURCE2 1 0.0000
angle_coeff @angle:ha-cc-nc harmonic 50.730 116.540 # SOURCE3 5 1.4482
angle_coeff @angle:ha-cc-nd harmonic 51.410 118.880 # SOURCE3 20 2.8923
angle_coeff @angle:ha-cc-os harmonic 52.490 110.860 # SOURCE3 7 1.3846
angle_coeff @angle:ha-cc-pd harmonic 42.350 121.760 # SOURCE3 84 same_as_ha-cd-pc
angle_coeff @angle:ha-cc-ss harmonic 53.490 121.640 # SOURCE2 5 1.3276
angle_coeff @angle:ch-c-ch harmonic 65.440 115.380 # SOURCE3 1 same_as_cg-c-cg
angle_coeff @angle:ch-c-ha harmonic 47.800 113.900 # SOURCE2 1 same_as_cg-c-ha
angle_coeff @angle:ch-c-o harmonic 70.210 122.310 # SOURCE3 2 same_as_cg-c-o
angle_coeff @angle:cl-c-cl harmonic 63.330 111.300 # SOURCE2 1 0.0000
angle_coeff @angle:cl-c-f harmonic 63.490 112.000 # SOURCE2 1 0.0000
angle_coeff @angle:cl-c-ha harmonic 43.460 109.900 # SOURCE2 1 0.0000
angle_coeff @angle:cl-c-o harmonic 64.280 121.510 # SOURCE3 6 1.6987
angle_coeff @angle:cl-c-s harmonic 77.210 127.600 # SOURCE2 1 0.0000
angle_coeff @angle:c-c-n harmonic 67.530 112.140 # SOURCE4 53 2.1247
angle_coeff @angle:na-cc-nc harmonic 70.660 121.830 # SOURCE4 169 1.0340
angle_coeff @angle:na-cc-nd harmonic 74.780 112.020 # SOURCE3 17 2.2434
angle_coeff @angle:na-cc-no harmonic 68.480 124.900 # SOURCE4 48 0.7933
angle_coeff @angle:na-cc-oh harmonic 73.310 117.260 # SOURCE4 16 0.9090
angle_coeff @angle:na-cc-sx harmonic 80.050 117.040 # SOURCE4 13 0.4187
angle_coeff @angle:na-cc-sy harmonic 79.760 120.550 # SOURCE4 7 1.7547
angle_coeff @angle:n-cc-c harmonic 68.190 116.060 # SOURCE3 1 0.0000
angle_coeff @angle:nc-cc-nd harmonic 72.510 118.690 # SOURCE3 9 6.6642
angle_coeff @angle:nc-cc-nh harmonic 72.700 115.660 # SOURCE4 12 1.0083
angle_coeff @angle:nc-cc-no harmonic 69.310 121.540 # SOURCE4 7 0.9221
angle_coeff @angle:nc-cc-ss harmonic 81.790 119.860 # SOURCE3 2 0.0000
angle_coeff @angle:nd-cc-nd harmonic 70.880 128.170 # SOURCE4 7 0.0269
angle_coeff @angle:nd-cc-ne harmonic 69.290 129.660 # SOURCE4 7 0.4306
angle_coeff @angle:nd-cc-nh harmonic 72.410 120.110 # SOURCE3 5 0.9313
angle_coeff @angle:nd-cc-no harmonic 69.900 122.680 # SOURCE4 16 0.3393
angle_coeff @angle:nd-cc-oh harmonic 72.800 122.190 # SOURCE4 11 0.7091
angle_coeff @angle:nd-cc-os harmonic 74.240 115.060 # SOURCE4 109 2.3512
angle_coeff @angle:nd-cc-sh harmonic 79.410 124.920 # SOURCE4 5 0.9563
angle_coeff @angle:nd-cc-ss harmonic 84.180 114.510 # SOURCE3 8 0.3449
angle_coeff @angle:nd-cc-sx harmonic 76.960 127.600 # SOURCE4 14 1.1650
angle_coeff @angle:nd-cc-sy harmonic 79.280 123.080 # SOURCE4 13 1.0531
angle_coeff @angle:ne-cc-ss harmonic 82.750 116.990 # SOURCE4 7 0.1657
angle_coeff @angle:nh-cc-nh harmonic 72.930 115.960 # SOURCE3 1 0.0000
angle_coeff @angle:nh-cc-os harmonic 72.780 117.270 # SOURCE4 13 0.7995
angle_coeff @angle:nh-cc-ss harmonic 81.210 122.040 # SOURCE4 80 1.2781
angle_coeff @angle:n-cc-n2 harmonic 74.770 114.480 # SOURCE4 15 2.3208
angle_coeff @angle:n-cc-na harmonic 70.450 122.180 # SOURCE4 46 2.2856
angle_coeff @angle:n-cc-nc harmonic 70.960 120.010 # SOURCE4 10 1.5583
angle_coeff @angle:n-cc-nd harmonic 71.200 122.710 # SOURCE4 141 1.6659
angle_coeff @angle:n-cc-nh harmonic 72.220 116.850 # SOURCE4 32 0.7619
angle_coeff @angle:no-cc-os harmonic 71.010 117.590 # SOURCE4 62 0.2199
angle_coeff @angle:no-cc-ss harmonic 80.690 121.100 # SOURCE4 10 0.0957
angle_coeff @angle:n-cc-ss harmonic 80.680 123.050 # SOURCE4 38 1.0101
angle_coeff @angle:c-c-o harmonic 67.160 120.990 # SOURCE4 233 2.0333
angle_coeff @angle:c-c-oh harmonic 68.200 113.230 # SOURCE3 5 0.5615
angle_coeff @angle:c-c-os harmonic 68.180 111.390 # SOURCE4 14 0.4038
angle_coeff @angle:os-cc-ss harmonic 78.460 132.010 # SOURCE3 1 0.0000
angle_coeff @angle:ss-cc-ss harmonic 100.050 121.280 # SOURCE4 20 2.4461
angle_coeff @angle:ss-cc-sy harmonic 98.380 121.770 # SOURCE4 20 0.4970
angle_coeff @angle:cx-c-cx harmonic 85.450 64.600 # SOURCE2 1 0.0000
angle_coeff @angle:cx-c-n harmonic 68.690 114.490 # SOURCE4 23 1.4914
angle_coeff @angle:cx-c-o harmonic 68.880 122.820 # SOURCE4 97 2.2075
angle_coeff @angle:cx-c-oh harmonic 70.490 112.320 # SOURCE4 10 0.6413
angle_coeff @angle:cx-c-os harmonic 70.060 111.480 # SOURCE4 16 1.3998
angle_coeff @angle:cy-c-cy harmonic 70.140 90.550 # SOURCE2 2 2.4500
angle_coeff @angle:cy-c-n harmonic 75.430 91.540 # SOURCE4 249 0.5104
angle_coeff @angle:cy-c-o harmonic 64.270 135.040 # SOURCE4 253 1.3450
angle_coeff @angle:cy-c-oh harmonic 69.090 112.480 # SOURCE4 5 1.0793
angle_coeff @angle:cy-c-os harmonic 74.550 94.890 # SOURCE4 8 0.6016
angle_coeff @angle:c2-cd-c3 harmonic 63.270 126.110 # SOURCE3 2 0.0000
angle_coeff @angle:c2-cd-ca harmonic 64.430 128.220 # SOURCE3 1 same_as_c2-cc-ca
angle_coeff @angle:c2-cd-cc harmonic 69.090 117.020 # SOURCE3 2 same_as_c2-cc-cd
angle_coeff @angle:c2-cd-cd harmonic 65.270 125.410 # SOURCE3 3 2.0867
angle_coeff @angle:c2-cd-ha harmonic 48.690 122.720 # SOURCE3 2 same_as_c2-cc-ha
angle_coeff @angle:c2-cd-n harmonic 67.740 126.900 # SOURCE3 1 same_as_c2-cc-n
angle_coeff @angle:c2-cd-os harmonic 70.530 119.310 # SOURCE3 2 same_as_c2-cc-os
angle_coeff @angle:c3-cd-ca harmonic 64.050 117.810 # SOURCE3 8 same_as_c3-cc-ca
angle_coeff @angle:c3-cd-cc harmonic 64.810 119.450 # SOURCE3 35 8.2040
angle_coeff @angle:c3-cd-cd harmonic 64.660 115.970 # SOURCE3 4 3.0507
angle_coeff @angle:c3-cd-ce harmonic 65.260 117.840 # SOURCE3 1 same_as_c3-cc-cf
angle_coeff @angle:c3-cd-ha harmonic 45.110 121.520 # SOURCE3 32 3.2091
angle_coeff @angle:c3-cd-n2 harmonic 64.650 131.550 # SOURCE3 1 same_as_c3-cc-n2
angle_coeff @angle:c3-cd-n harmonic 65.600 121.760 # SOURCE4 15 1.7884
angle_coeff @angle:c3-cd-na harmonic 65.670 122.140 # SOURCE4 155 1.5600
angle_coeff @angle:c3-cd-nc harmonic 66.940 119.910 # SOURCE4 200 1.6430
angle_coeff @angle:c3-cd-nd harmonic 65.900 120.920 # SOURCE4 243 0.8832
angle_coeff @angle:c3-cd-os harmonic 67.630 116.540 # SOURCE4 76 0.6353
angle_coeff @angle:c3-cd-ss harmonic 77.510 121.530 # SOURCE4 26 1.4478
angle_coeff @angle:ca-cd-cc harmonic 68.230 113.510 # SOURCE3 26 7.4229
angle_coeff @angle:ca-cd-cd harmonic 67.660 111.040 # SOURCE3 9 7.9455
angle_coeff @angle:ca-cd-ce harmonic 65.000 125.100 # SOURCE4 9 1.9265
angle_coeff @angle:ca-cd-h4 harmonic 45.570 128.660 # SOURCE3 10 3.1167
angle_coeff @angle:ca-cd-ha harmonic 46.400 124.040 # SOURCE3 34 3.6691
angle_coeff @angle:ca-cd-n harmonic 72.510 104.870 # SOURCE3 1 same_as_ca-cc-n
angle_coeff @angle:ca-cd-na harmonic 67.030 123.450 # SOURCE4 39 1.9138
angle_coeff @angle:ca-cd-nc harmonic 70.230 115.050 # SOURCE3 6 4.3938
angle_coeff @angle:ca-cd-nd harmonic 67.650 120.810 # SOURCE4 116 1.2165
angle_coeff @angle:ca-cd-oh harmonic 69.080 119.320 # SOURCE4 9 1.2731
angle_coeff @angle:ca-cd-os harmonic 70.040 114.450 # SOURCE4 76 2.2248
angle_coeff @angle:ca-cd-ss harmonic 79.130 119.640 # SOURCE4 15 1.8842
angle_coeff @angle:c-cd-c2 harmonic 65.380 121.760 # SOURCE3 1 same_as_c-cc-c2
angle_coeff @angle:c-cd-c3 harmonic 63.560 117.570 # SOURCE4 122 1.4868
angle_coeff @angle:c-cd-c harmonic 63.410 121.180 # SOURCE4 16 1.9017
angle_coeff @angle:c-cd-ca harmonic 63.550 122.950 # SOURCE3 1 same_as_c-cc-ca
angle_coeff @angle:c-cd-cc harmonic 65.280 121.320 # SOURCE4 789 2.4126
angle_coeff @angle:cc-cd-cc harmonic 68.010 119.800 # SOURCE4 91 1.1370
angle_coeff @angle:cc-cd-cd harmonic 68.160 114.190 # SOURCE3 517 6.5960
angle_coeff @angle:cc-cd-cf harmonic 64.080 126.280 # SOURCE4 71 2.2936
angle_coeff @angle:cc-cd-ch harmonic 64.920 126.050 # SOURCE4 30 1.4695
angle_coeff @angle:cc-cd-cl harmonic 61.810 123.620 # SOURCE4 14 1.9282
angle_coeff @angle:cc-cd-cy harmonic 63.930 122.130 # SOURCE4 10 0.8509
angle_coeff @angle:c-cd-cd harmonic 63.720 122.690 # SOURCE3 2 0.0000
angle_coeff @angle:c-cd-cf harmonic 63.000 123.100 # SOURCE4 5 2.3108
angle_coeff @angle:cc-cd-h4 harmonic 47.190 129.110 # SOURCE3 418 3.1355
angle_coeff @angle:cc-cd-ha harmonic 48.350 122.890 # SOURCE3 584 2.9334
angle_coeff @angle:c-cd-cl harmonic 62.750 116.190 # SOURCE4 5 1.0839
angle_coeff @angle:cc-cd-n harmonic 70.720 115.520 # SOURCE3 52 1.3322
angle_coeff @angle:cc-cd-na harmonic 72.910 109.420 # SOURCE3 265 2.6051
angle_coeff @angle:cc-cd-nc harmonic 69.420 123.820 # SOURCE4 14 0.3678
angle_coeff @angle:cc-cd-nd harmonic 72.030 111.680 # SOURCE4 1078 1.9168
angle_coeff @angle:cc-cd-nh harmonic 68.700 123.880 # SOURCE4 105 2.2114
angle_coeff @angle:cc-cd-oh harmonic 69.540 123.710 # SOURCE4 47 1.3029
angle_coeff @angle:cc-cd-os harmonic 69.960 120.300 # SOURCE3 64 5.4354
angle_coeff @angle:cc-cd-ss harmonic 82.380 112.740 # SOURCE4 192 2.2341
angle_coeff @angle:cc-cd-sy harmonic 76.890 124.690 # SOURCE4 22 0.6891
angle_coeff @angle:cd-cd-cd harmonic 67.880 110.700 # SOURCE3 54 3.4091
angle_coeff @angle:cd-cd-ce harmonic 65.800 122.560 # SOURCE4 38 1.7758
angle_coeff @angle:cd-cd-cf harmonic 62.580 127.560 # SOURCE4 32 2.4879
angle_coeff @angle:cd-cd-ch harmonic 63.320 127.380 # SOURCE4 21 0.9462
angle_coeff @angle:cd-cd-cy harmonic 63.170 120.930 # SOURCE4 6 1.2205
angle_coeff @angle:cd-cd-h4 harmonic 45.560 129.470 # SOURCE3 171 2.2734
angle_coeff @angle:cd-cd-ha harmonic 47.020 121.510 # SOURCE4 1245 2.1421
angle_coeff @angle:cd-cd-n2 harmonic 69.520 121.150 # SOURCE3 6 0.4642
angle_coeff @angle:cd-cd-n harmonic 67.950 119.890 # SOURCE3 36 0.2095
angle_coeff @angle:cd-cd-na harmonic 72.210 106.800 # SOURCE3 33 same_as_cc-cc-na
angle_coeff @angle:cd-cd-nc harmonic 71.150 112.560 # SOURCE3 141 4.2871
angle_coeff @angle:cd-cd-nd harmonic 67.440 122.020 # SOURCE4 101 2.1232
angle_coeff @angle:cd-cd-nh harmonic 68.260 120.050 # SOURCE4 86 1.2878
angle_coeff @angle:cd-cd-oh harmonic 68.090 123.300 # SOURCE4 17 2.3237
angle_coeff @angle:cd-cd-os harmonic 69.300 117.360 # SOURCE4 112 1.9292
angle_coeff @angle:cd-cd-pc harmonic 63.840 115.360 # SOURCE3 84 3.2889
angle_coeff @angle:cd-cd-ss harmonic 78.930 120.470 # SOURCE4 29 1.6911
angle_coeff @angle:ce-cd-nd harmonic 68.130 124.900 # SOURCE4 5 2.3975
angle_coeff @angle:cf-cd-na harmonic 66.090 124.600 # SOURCE4 8 1.6033
angle_coeff @angle:cf-cd-nc harmonic 67.940 120.490 # SOURCE4 26 1.3524
angle_coeff @angle:cf-cd-nd harmonic 66.910 121.180 # SOURCE4 29 1.3143
angle_coeff @angle:cf-cd-os harmonic 68.380 117.800 # SOURCE4 7 1.1308
angle_coeff @angle:cf-cd-ss harmonic 77.470 123.670 # SOURCE4 7 1.5823
angle_coeff @angle:c-cd-h4 harmonic 46.770 118.190 # SOURCE4 8 0.2226
angle_coeff @angle:c-cd-ha harmonic 46.990 117.020 # SOURCE3 56 1.9713
angle_coeff @angle:cl-cd-nc harmonic 63.230 125.300 # SOURCE3 1 same_as_cl-cc-nd
angle_coeff @angle:c-cd-n2 harmonic 68.580 120.890 # SOURCE3 1 same_as_c-cc-n2
angle_coeff @angle:c-cd-n harmonic 68.190 116.060 # SOURCE3 1 same_as_n-cc-c
angle_coeff @angle:c-cd-nc harmonic 67.450 121.860 # SOURCE4 46 2.4699
angle_coeff @angle:c-cd-nd harmonic 64.310 130.800 # SOURCE3 1 0.0000
angle_coeff @angle:c-cd-oh harmonic 69.870 114.020 # SOURCE4 18 0.9546
angle_coeff @angle:c-cd-os harmonic 68.070 118.550 # SOURCE4 26 2.1350
angle_coeff @angle:h4-cd-n harmonic 50.390 117.620 # SOURCE3 53 0.9721
angle_coeff @angle:h4-cd-na harmonic 50.220 119.660 # SOURCE3 294 2.4702
angle_coeff @angle:h4-cd-nc harmonic 51.390 119.110 # SOURCE3 135 1.6946
angle_coeff @angle:h4-cd-nd harmonic 50.000 120.030 # SOURCE3 16 2.3863
angle_coeff @angle:h4-cd-os harmonic 52.270 111.890 # SOURCE3 61 2.3500
angle_coeff @angle:h4-cd-ss harmonic 54.360 117.750 # SOURCE3 40 3.1156
angle_coeff @angle:h5-cd-n harmonic 50.820 115.830 # SOURCE4 10 0.2888
angle_coeff @angle:h5-cd-na harmonic 49.760 122.100 # SOURCE3 16 1.4626
angle_coeff @angle:h5-cd-nc harmonic 50.130 125.380 # SOURCE3 40 2.2157
angle_coeff @angle:h5-cd-nd harmonic 49.290 123.700 # SOURCE3 6 0.3547
angle_coeff @angle:h5-cd-os harmonic 51.300 116.330 # SOURCE3 12 3.2919
angle_coeff @angle:h5-cd-ss harmonic 53.390 122.000 # SOURCE3 6 0.7237
angle_coeff @angle:ha-cd-na harmonic 49.820 121.500 # SOURCE2 1 same_as_ha-cc-na
angle_coeff @angle:ha-cd-nc harmonic 51.410 118.880 # SOURCE3 20 2.8923
angle_coeff @angle:ha-cd-nd harmonic 50.730 116.540 # SOURCE3 5 1.4482
angle_coeff @angle:ha-cd-os harmonic 52.490 110.860 # SOURCE3 7 1.3846
angle_coeff @angle:ha-cd-pc harmonic 42.350 121.760 # SOURCE3 84 2.2216
angle_coeff @angle:ha-cd-ss harmonic 53.490 121.640 # SOURCE2 5 same_as_ha-cc-ss
angle_coeff @angle:na-cd-nc harmonic 74.780 112.020 # SOURCE3 17 2.2434
angle_coeff @angle:na-cd-nd harmonic 70.890 121.040 # SOURCE4 62 1.4580
angle_coeff @angle:na-cd-nh harmonic 72.430 116.980 # SOURCE4 46 1.4937
angle_coeff @angle:na-cd-ss harmonic 84.890 111.460 # SOURCE4 20 0.8600
angle_coeff @angle:nc-cd-nd harmonic 73.390 115.840 # SOURCE4 213 1.4060
angle_coeff @angle:nc-cd-nh harmonic 72.410 120.110 # SOURCE3 5 0.9313
angle_coeff @angle:nc-cd-oh harmonic 73.040 120.890 # SOURCE4 11 1.5340
angle_coeff @angle:nc-cd-os harmonic 73.420 117.640 # SOURCE4 100 1.8409
angle_coeff @angle:nc-cd-ss harmonic 84.180 114.510 # SOURCE3 8 0.3449
angle_coeff @angle:nd-cd-nd harmonic 69.470 125.580 # SOURCE4 13 0.4672
angle_coeff @angle:nd-cd-nh harmonic 72.140 117.470 # SOURCE4 23 1.5450
angle_coeff @angle:nd-cd-ss harmonic 81.790 119.860 # SOURCE3 2 same_as_nc-cc-ss
angle_coeff @angle:nh-cd-nh harmonic 72.930 115.960 # SOURCE3 1 same_as_nh-cc-nh
angle_coeff @angle:nh-cd-os harmonic 73.160 116.070 # SOURCE4 12 0.5342
angle_coeff @angle:nh-cd-ss harmonic 81.480 121.220 # SOURCE4 11 1.1514
angle_coeff @angle:n-cd-na harmonic 70.500 122.010 # SOURCE4 13 1.2061
angle_coeff @angle:n-cd-nc harmonic 70.990 123.410 # SOURCE4 88 0.9565
angle_coeff @angle:n-cd-nd harmonic 69.060 126.700 # SOURCE4 54 0.3231
angle_coeff @angle:n-cd-nh harmonic 72.210 116.880 # SOURCE4 47 0.3458
angle_coeff @angle:n-cd-ss harmonic 80.730 122.890 # SOURCE4 7 1.1978
angle_coeff @angle:oh-cd-os harmonic 75.470 111.610 # SOURCE4 6 1.1909
angle_coeff @angle:os-cd-ss harmonic 78.460 132.010 # SOURCE3 1 same_as_os-cc-ss
angle_coeff @angle:ss-cd-ss harmonic 99.630 122.300 # SOURCE3 2 same_as_ss-cc-ss
angle_coeff @angle:ss-cd-sy harmonic 98.720 121.620 # SOURCE4 19 0.4931
angle_coeff @angle:c2-ce-c3 harmonic 64.300 122.890 # SOURCE3 7 1.0449
angle_coeff @angle:c2-ce-ca harmonic 65.160 123.080 # SOURCE3 6 2.1589
angle_coeff @angle:c2-ce-cc harmonic 65.550 123.840 # SOURCE4 49 2.1264
angle_coeff @angle:c2-ce-ce harmonic 65.730 123.080 # SOURCE3 12 0.6518
angle_coeff @angle:c2-ce-cg harmonic 66.680 121.580 # SOURCE4 18 1.3663
angle_coeff @angle:c2-ce-cl harmonic 62.220 119.510 # SOURCE4 24 1.4963
angle_coeff @angle:c2-ce-h4 harmonic 48.640 125.580 # SOURCE4 11 0.9381
angle_coeff @angle:c2-ce-ha harmonic 49.560 121.100 # SOURCE3 46 2.4054
angle_coeff @angle:c2-ce-n1 harmonic 72.730 117.850 # SOURCE4 7 0.3180
angle_coeff @angle:c2-ce-n2 harmonic 70.340 128.700 # SOURCE3 1 0.0000
angle_coeff @angle:c2-ce-na harmonic 69.290 119.190 # SOURCE4 5 0.8452
angle_coeff @angle:c2-ce-ne harmonic 69.730 118.320 # SOURCE3 7 1.0468
angle_coeff @angle:c2-ce-oh harmonic 70.180 123.780 # SOURCE4 10 1.8182
angle_coeff @angle:c2-ce-p2 harmonic 61.560 118.240 # SOURCE3 1
angle_coeff @angle:c2-ce-pe harmonic 61.300 118.760 # SOURCE3 8 2.3984
angle_coeff @angle:c2-ce-px harmonic 60.970 119.720 # SOURCE3 6 0.5213
angle_coeff @angle:c2-ce-py harmonic 61.150 122.130 # SOURCE3 5 3.1367
angle_coeff @angle:c2-ce-sx harmonic 78.010 119.870 # SOURCE3 5 0.8557
angle_coeff @angle:c2-ce-sy harmonic 78.410 120.350 # SOURCE3 5 0.5401
angle_coeff @angle:c3-ce-ca harmonic 62.810 119.110 # SOURCE4 127 1.8824
angle_coeff @angle:c3-ce-cc harmonic 63.490 118.180 # SOURCE4 22 1.7743
angle_coeff @angle:c3-ce-ce harmonic 63.910 116.590 # SOURCE4 175 1.6539
angle_coeff @angle:c3-ce-cf harmonic 64.510 122.180 # SOURCE4 119 2.0632
angle_coeff @angle:c3-ce-cg harmonic 63.790 118.480 # SOURCE4 8 1.4756
angle_coeff @angle:c3-ce-n2 harmonic 66.940 122.640 # SOURCE4 76 2.0781
angle_coeff @angle:c3-ce-nf harmonic 67.240 120.750 # SOURCE4 6 2.1938
angle_coeff @angle:c3-ce-nh harmonic 65.740 119.900 # SOURCE4 5 0.9634
angle_coeff @angle:ca-ce-ca harmonic 63.870 117.820 # SOURCE4 100 0.9790
angle_coeff @angle:ca-ce-cc harmonic 64.120 118.640 # SOURCE4 12 0.8455
angle_coeff @angle:ca-ce-ce harmonic 63.840 119.620 # SOURCE4 14 1.9171
angle_coeff @angle:ca-ce-cf harmonic 64.090 127.310 # SOURCE4 132 1.9691
angle_coeff @angle:ca-ce-cl harmonic 62.350 114.220 # SOURCE4 6 1.3164
angle_coeff @angle:ca-ce-h4 harmonic 46.710 116.860 # SOURCE4 74 0.9179
angle_coeff @angle:ca-ce-ha harmonic 47.080 115.120 # SOURCE4 210 1.0763
angle_coeff @angle:ca-ce-n2 harmonic 68.510 120.720 # SOURCE3 1 0.0000
angle_coeff @angle:ca-ce-nf harmonic 67.770 122.500 # SOURCE4 11 2.3863
angle_coeff @angle:ca-ce-nh harmonic 67.850 115.510 # SOURCE4 93 0.9284
angle_coeff @angle:ca-ce-oh harmonic 68.500 117.180 # SOURCE4 5 0.5951
angle_coeff @angle:ca-ce-os harmonic 68.570 115.580 # SOURCE4 8 1.0735
angle_coeff @angle:ca-ce-ss harmonic 77.470 117.730 # SOURCE4 5 1.1596
angle_coeff @angle:c-ce-c2 harmonic 65.820 120.420 # SOURCE3 13 1.8877
angle_coeff @angle:c-ce-c3 harmonic 63.430 116.630 # SOURCE4 169 2.4309
angle_coeff @angle:c-ce-c harmonic 62.550 122.540 # SOURCE4 22 1.3987
angle_coeff @angle:c-ce-ca harmonic 63.790 117.980 # SOURCE4 8 1.5129
angle_coeff @angle:cc-ce-cd harmonic 63.280 130.360 # SOURCE4 5 2.3402
angle_coeff @angle:cc-ce-cf harmonic 65.060 125.790 # SOURCE4 39 1.5227
angle_coeff @angle:c-ce-cd harmonic 63.740 126.070 # SOURCE3 1 same_as_c-cf-cc
angle_coeff @angle:c-ce-ce harmonic 63.460 120.890 # SOURCE4 16 1.8719
angle_coeff @angle:c-ce-cf harmonic 64.260 126.410 # SOURCE3 2 5.7847
angle_coeff @angle:c-ce-cg harmonic 64.570 118.320 # SOURCE4 15 1.0595
angle_coeff @angle:cc-ce-h4 harmonic 47.610 115.400 # SOURCE4 29 0.8744
angle_coeff @angle:cc-ce-ha harmonic 47.630 115.360 # SOURCE4 66 0.9385
angle_coeff @angle:c-ce-cl harmonic 62.010 115.400 # SOURCE4 6 1.0958
angle_coeff @angle:cc-ce-n2 harmonic 68.910 121.690 # SOURCE4 52 2.2459
angle_coeff @angle:cc-ce-nh harmonic 67.360 119.170 # SOURCE4 8 2.1378
angle_coeff @angle:c-ce-cy harmonic 72.720 88.220 # SOURCE4 19 0.3234
angle_coeff @angle:cd-ce-ce harmonic 65.140 122.940 # SOURCE4 6 0.3490
angle_coeff @angle:cd-ce-ha harmonic 49.760 115.940 # SOURCE4 23 1.6379
angle_coeff @angle:ce-ce-ce harmonic 64.550 118.740 # SOURCE3 1 0.0000
angle_coeff @angle:ce-ce-cf harmonic 65.490 124.050 # SOURCE4 166 1.7004
angle_coeff @angle:ce-ce-cl harmonic 61.600 117.930 # SOURCE4 12 0.2639
angle_coeff @angle:ce-ce-h4 harmonic 47.060 118.000 # SOURCE4 10 0.8551
angle_coeff @angle:ce-ce-ha harmonic 47.500 115.900 # SOURCE3 12 0.4670
angle_coeff @angle:ce-ce-n1 harmonic 66.840 127.150 # SOURCE3 2 same_as_cf-cf-n1
angle_coeff @angle:ce-ce-n2 harmonic 68.520 123.000 # SOURCE3 2 0.0000
angle_coeff @angle:ce-ce-oh harmonic 69.180 116.890 # SOURCE4 11 2.0380
angle_coeff @angle:cf-ce-cg harmonic 66.060 123.940 # SOURCE4 21 1.4852
angle_coeff @angle:cf-ce-cy harmonic 60.530 137.740 # SOURCE4 13 0.3952
angle_coeff @angle:cf-ce-h4 harmonic 49.030 123.760 # SOURCE4 5 1.0909
angle_coeff @angle:cf-ce-ha harmonic 50.180 118.290 # SOURCE4 299 1.3038
angle_coeff @angle:cf-ce-n1 harmonic 72.090 120.030 # SOURCE4 6 1.9451
angle_coeff @angle:cf-ce-n harmonic 72.630 108.180 # SOURCE4 54 0.5772
angle_coeff @angle:cf-ce-nh harmonic 69.450 121.520 # SOURCE4 12 2.0106
angle_coeff @angle:cf-ce-oh harmonic 70.830 121.620 # SOURCE4 12 0.5995
angle_coeff @angle:cg-ce-cg harmonic 65.510 118.510 # SOURCE4 6 0.9614
angle_coeff @angle:cg-ce-ha harmonic 47.910 116.610 # SOURCE4 12 0.3943
angle_coeff @angle:cg-ce-n1 harmonic 69.540 119.500 # SOURCE2 1 0.0000
angle_coeff @angle:cg-ce-n2 harmonic 69.590 121.430 # SOURCE4 6 0.8382
angle_coeff @angle:c-ce-ha harmonic 46.590 117.260 # SOURCE3 11 2.7158
angle_coeff @angle:c-ce-n harmonic 66.170 118.730 # SOURCE4 129 1.5548
angle_coeff @angle:c-ce-nh harmonic 67.880 115.220 # SOURCE4 18 2.4886
angle_coeff @angle:c-ce-oh harmonic 68.230 117.920 # SOURCE4 5 1.4580
angle_coeff @angle:c-ce-os harmonic 69.050 113.780 # SOURCE4 21 1.8258
angle_coeff @angle:h4-ce-n1 harmonic 52.650 116.360 # SOURCE4 7 0.2182
angle_coeff @angle:h4-ce-n2 harmonic 52.370 121.520 # SOURCE4 105 1.2900
angle_coeff @angle:h4-ce-ne harmonic 49.720 115.810 # SOURCE4 7 1.9836
angle_coeff @angle:ha-ce-n1 harmonic 52.770 115.960 # SOURCE3 2 same_as_ha-cf-n1
angle_coeff @angle:ha-ce-n2 harmonic 52.850 119.510 # SOURCE3 2 0.4623
angle_coeff @angle:ha-ce-ne harmonic 49.160 118.590 # SOURCE3 5 1.1113
angle_coeff @angle:ha-ce-nh harmonic 50.580 114.990 # SOURCE3 1 0.0000
angle_coeff @angle:ha-ce-p2 harmonic 40.610 120.110 # SOURCE3 1
angle_coeff @angle:ha-ce-pe harmonic 40.640 119.330 # SOURCE3 6 0.8966
angle_coeff @angle:ha-ce-px harmonic 40.810 117.900 # SOURCE3 6 0.1809
angle_coeff @angle:ha-ce-py harmonic 41.340 118.720 # SOURCE3 3 0.3064
angle_coeff @angle:ha-ce-sx harmonic 52.960 115.450 # SOURCE3 3 0.6640
angle_coeff @angle:ha-ce-sy harmonic 53.580 114.860 # SOURCE3 3 0.4717
angle_coeff @angle:n2-ce-nh harmonic 71.550 124.860 # SOURCE4 83 2.0415
angle_coeff @angle:n2-ce-os harmonic 74.520 118.130 # SOURCE4 6 0.1367
angle_coeff @angle:n2-ce-ss harmonic 81.510 117.230 # SOURCE4 6 2.0518
angle_coeff @angle:ne-ce-ne harmonic 68.070 123.870 # SOURCE3 1 0.0000
angle_coeff @angle:ne-ce-nh harmonic 71.870 112.910 # SOURCE4 12 1.1263
angle_coeff @angle:nf-ce-nh harmonic 73.250 118.130 # SOURCE4 6 0.5842
angle_coeff @angle:pe-ce-pe harmonic 57.690 129.790 # SOURCE3 1 0.0000
angle_coeff @angle:py-ce-py harmonic 64.070 108.060 # SOURCE3 1 0.0000
angle_coeff @angle:sx-ce-sx harmonic 97.090 120.320 # SOURCE3 1 0.0000
angle_coeff @angle:sy-ce-sy harmonic 98.050 119.970 # SOURCE3 1 0.0000
angle_coeff @angle:c2-cf-c3 harmonic 64.300 122.890 # SOURCE3 7 same_as_c2-ce-c3
angle_coeff @angle:c2-cf-ca harmonic 65.160 123.080 # SOURCE3 6 same_as_c2-ce-ca
angle_coeff @angle:c2-cf-cd harmonic 65.810 122.050 # SOURCE4 23 1.7894
angle_coeff @angle:c2-cf-cf harmonic 65.730 123.080 # SOURCE3 12 same_as_c2-ce-ce
angle_coeff @angle:c2-cf-ch harmonic 66.510 122.220 # SOURCE3 3 same_as_c2-ce-cg
angle_coeff @angle:c2-cf-ha harmonic 49.560 121.100 # SOURCE3 46 same_as_c2-ce-ha
angle_coeff @angle:c2-cf-n2 harmonic 70.340 128.700 # SOURCE3 1 same_as_c2-ce-n2
angle_coeff @angle:c2-cf-nf harmonic 69.730 118.320 # SOURCE3 7 same_as_c2-ce-ne
angle_coeff @angle:c2-cf-p2 harmonic 61.560 118.240 # SOURCE3 1 same_as_c2-ce-p2
angle_coeff @angle:c2-cf-pf harmonic 61.300 118.760 # SOURCE3 8 same_as_c2-ce-pe
angle_coeff @angle:c2-cf-px harmonic 60.970 119.720 # SOURCE3 6 same_as_c2-ce-px
angle_coeff @angle:c2-cf-py harmonic 61.150 122.130 # SOURCE3 5 same_as_c2-ce-py
angle_coeff @angle:c2-cf-sx harmonic 78.010 119.870 # SOURCE3 5 same_as_c2-ce-sx
angle_coeff @angle:c2-cf-sy harmonic 78.410 120.350 # SOURCE3 5 same_as_c2-ce-sy
angle_coeff @angle:c3-cf-ca harmonic 62.650 119.700 # SOURCE4 51 1.2029
angle_coeff @angle:c3-cf-cd harmonic 63.300 118.280 # SOURCE4 17 0.8680
angle_coeff @angle:c3-cf-ce harmonic 64.550 122.030 # SOURCE4 102 1.9728
angle_coeff @angle:c3-cf-cf harmonic 63.520 118.010 # SOURCE4 69 0.9443
angle_coeff @angle:c3-cf-n2 harmonic 66.670 123.650 # SOURCE4 5 1.9155
angle_coeff @angle:ca-cf-ca harmonic 64.500 115.530 # SOURCE4 12 0.5692
angle_coeff @angle:ca-cf-cc harmonic 62.810 130.800 # SOURCE4 12 1.2696
angle_coeff @angle:ca-cf-cd harmonic 64.490 116.650 # SOURCE4 5 0.8685
angle_coeff @angle:ca-cf-ce harmonic 64.050 127.440 # SOURCE4 186 1.8735
angle_coeff @angle:ca-cf-ha harmonic 47.060 115.210 # SOURCE4 135 0.9402
angle_coeff @angle:ca-cf-n2 harmonic 68.510 120.720 # SOURCE3 1 same_as_ca-ce-n2
angle_coeff @angle:ca-cf-ne harmonic 67.710 122.810 # SOURCE4 11 2.3913
angle_coeff @angle:ca-cf-oh harmonic 69.220 115.690 # SOURCE4 6 0.8381
angle_coeff @angle:c-cf-c2 harmonic 65.820 120.420 # SOURCE3 13 same_as_c-ce-c2
angle_coeff @angle:c-cf-c3 harmonic 62.670 119.470 # SOURCE4 19 1.2665
angle_coeff @angle:c-cf-c harmonic 63.510 118.850 # SOURCE3 1 same_as_c-ce-c
angle_coeff @angle:c-cf-cc harmonic 63.930 126.070 # SOURCE3 1 0.0000
angle_coeff @angle:cc-cf-cf harmonic 64.530 126.040 # SOURCE4 6 1.0648
angle_coeff @angle:c-cf-cd harmonic 64.140 117.760 # SOURCE4 10 1.2451
angle_coeff @angle:c-cf-ce harmonic 64.260 126.410 # SOURCE3 2 same_as_c-ce-cf
angle_coeff @angle:cc-cf-ha harmonic 50.290 114.810 # SOURCE4 16 0.9788
angle_coeff @angle:cd-cf-ce harmonic 64.650 126.530 # SOURCE4 49 2.0998
angle_coeff @angle:cd-cf-ha harmonic 47.360 115.570 # SOURCE4 47 0.8973
angle_coeff @angle:cd-cf-n2 harmonic 69.140 120.020 # SOURCE4 17 2.4566
angle_coeff @angle:ce-cf-cf harmonic 65.420 124.330 # SOURCE4 175 1.6942
angle_coeff @angle:ce-cf-ch harmonic 66.150 123.630 # SOURCE4 20 1.3910
angle_coeff @angle:ce-cf-ha harmonic 50.240 117.980 # SOURCE4 356 1.4772
angle_coeff @angle:ce-cf-n harmonic 72.320 108.630 # SOURCE4 10 1.2271
angle_coeff @angle:ce-cf-oh harmonic 71.100 121.930 # SOURCE4 12 1.6250
angle_coeff @angle:cf-cf-cf harmonic 64.550 118.740 # SOURCE3 1 same_as_ce-ce-ce
angle_coeff @angle:cf-cf-h4 harmonic 47.050 117.940 # SOURCE4 9 0.8559
angle_coeff @angle:cf-cf-ha harmonic 47.500 115.900 # SOURCE3 12 0.4670
angle_coeff @angle:cf-cf-n1 harmonic 66.650 127.150 # SOURCE3 2 2.1936
angle_coeff @angle:cf-cf-n2 harmonic 69.760 118.660 # SOURCE4 11 1.2238
angle_coeff @angle:c-cf-ha harmonic 46.590 117.260 # SOURCE3 11 2.7158
angle_coeff @angle:ch-cf-ch harmonic 66.000 116.750 # SOURCE3 1 same_as_cg-ce-cg
angle_coeff @angle:ch-cf-ha harmonic 47.950 116.400 # SOURCE4 6 0.3381
angle_coeff @angle:ch-cf-n1 harmonic 69.330 119.500 # SOURCE2 1 same_as_cg-ce-n1
angle_coeff @angle:c-cf-n2 harmonic 70.160 114.880 # SOURCE4 5 1.3647
angle_coeff @angle:c-cf-n harmonic 66.600 116.790 # SOURCE4 8 0.8255
angle_coeff @angle:c-cf-nh harmonic 65.940 122.760 # SOURCE3 1 same_as_c-ce-nh
angle_coeff @angle:f-c-f harmonic 72.220 107.350 # SOURCE2 2 0.2500
angle_coeff @angle:h4-cf-n2 harmonic 52.210 122.140 # SOURCE4 11 0.9297
angle_coeff @angle:h4-cf-ne harmonic 52.280 120.210 # SOURCE4 6 0.8104
angle_coeff @angle:ha-cf-n1 harmonic 52.480 115.960 # SOURCE3 2 3.5425
angle_coeff @angle:ha-cf-n2 harmonic 52.850 119.510 # SOURCE3 2 same_as_ha-ce-n2
angle_coeff @angle:ha-cf-nf harmonic 49.160 118.590 # SOURCE3 5 same_as_ha-ce-ne
angle_coeff @angle:ha-cf-nh harmonic 50.850 114.990 # SOURCE3 1 same_as_ha-ce-nh
angle_coeff @angle:ha-cf-p2 harmonic 40.610 120.110 # SOURCE3 1 same_as_ha-ce-p2
angle_coeff @angle:ha-cf-pf harmonic 40.640 119.330 # SOURCE3 6 same_as_ha-ce-pe
angle_coeff @angle:ha-cf-px harmonic 40.810 117.900 # SOURCE3 6 same_as_ha-ce-px
angle_coeff @angle:ha-cf-py harmonic 41.340 118.720 # SOURCE3 3 same_as_ha-ce-py
angle_coeff @angle:ha-cf-sx harmonic 52.960 115.450 # SOURCE3 3 same_as_ha-ce-sx
angle_coeff @angle:ha-cf-sy harmonic 53.580 114.860 # SOURCE3 3 same_as_ha-ce-sy
angle_coeff @angle:n2-cf-nh harmonic 71.540 125.890 # SOURCE4 9 1.5587
angle_coeff @angle:nf-cf-nf harmonic 68.070 123.870 # SOURCE3 1 same_as_ne-ce-ne
angle_coeff @angle:f-c-o harmonic 73.210 123.440 # SOURCE3 1
angle_coeff @angle:pf-cf-pf harmonic 57.690 129.790 # SOURCE3 1 same_as_pe-ce-pe
angle_coeff @angle:py-cf-py harmonic 64.070 108.060 # SOURCE3 1 same_as_py-ce-py
angle_coeff @angle:f-c-s harmonic 80.250 124.000 # SOURCE2 1 0.0000
angle_coeff @angle:sx-cf-sx harmonic 97.090 120.320 # SOURCE3 1 same_as_sx-ce-sx
angle_coeff @angle:sy-cf-sy harmonic 98.050 119.970 # SOURCE3 1 same_as_sy-ce-sy
angle_coeff @angle:c1-cg-ca harmonic 56.530 179.460 # SOURCE4 17 0.3461
angle_coeff @angle:c1-cg-cc harmonic 56.970 178.600 # SOURCE4 6 0.3822
angle_coeff @angle:c1-cg-ce harmonic 56.960 178.000 # SOURCE4 6 0.4324
angle_coeff @angle:c1-cg-cg harmonic 58.180 179.660 # SOURCE4 16 0.1241
angle_coeff @angle:c1-cg-ne harmonic 62.730 170.020 # SOURCE3 4 1.1724
angle_coeff @angle:c1-cg-pe harmonic 56.730 173.290 # SOURCE3 11 4.9305
angle_coeff @angle:ca-cg-ch harmonic 56.940 179.490 # SOURCE4 5 0.3022
angle_coeff @angle:ca-cg-n1 harmonic 58.930 179.420 # SOURCE4 102 0.6923
angle_coeff @angle:c-cg-c1 harmonic 56.190 179.140 # SOURCE3 2 0.0000
angle_coeff @angle:cc-cg-n1 harmonic 59.440 178.460 # SOURCE4 24 0.7137
angle_coeff @angle:ce-cg-ch harmonic 57.380 177.980 # SOURCE4 9 0.4223
angle_coeff @angle:ce-cg-n1 harmonic 59.410 177.890 # SOURCE4 45 1.1337
angle_coeff @angle:n1-cg-ne harmonic 65.040 174.070 # SOURCE4 14 1.2208
angle_coeff @angle:h4-c-o harmonic 54.280 120.930 # SOURCE4 129 0.5769
angle_coeff @angle:h5-c-n harmonic 52.390 112.190 # SOURCE4 33 0.4220
angle_coeff @angle:h5-c-o harmonic 53.890 123.260 # SOURCE4 38 0.4806
angle_coeff @angle:ha-c-ha harmonic 37.860 115.610 # SOURCE3 4 0.0458
angle_coeff @angle:ha-c-i harmonic 36.710 110.580 # SOURCE3 1 0.0000
angle_coeff @angle:ha-c-n harmonic 52.400 112.370 # SOURCE3 4 0.6424
angle_coeff @angle:ha-c-o harmonic 54.270 121.940 # SOURCE3 51 2.3235
angle_coeff @angle:ha-c-oh harmonic 53.970 111.820 # SOURCE3 4 1.9375
angle_coeff @angle:ha-c-os harmonic 53.240 110.340 # SOURCE3 8 1.9344
angle_coeff @angle:ha-c-s harmonic 56.030 119.560 # SOURCE3 3 0.7586
angle_coeff @angle:c1-ch-ca harmonic 56.450 180.000 # SOURCE3 2 same_as_c1-cg-ca
angle_coeff @angle:c1-ch-cf harmonic 56.900 178.320 # SOURCE3 1 same_as_c1-cg-ce
angle_coeff @angle:c1-ch-ch harmonic 58.120 180.000 # SOURCE3 2 same_as_c1-cg-cg
angle_coeff @angle:c1-ch-nf harmonic 62.730 170.020 # SOURCE3 4 same_as_c1-cg-ne
angle_coeff @angle:c1-ch-pf harmonic 56.730 173.290 # SOURCE3 11 same_as_c1-cg-pe
angle_coeff @angle:ca-ch-cg harmonic 56.900 179.740 # SOURCE4 8 0.2890
angle_coeff @angle:ca-ch-n1 harmonic 58.830 180.000 # SOURCE3 1 same_as_ca-cg-n1
angle_coeff @angle:c-ch-c1 harmonic 56.190 179.140 # SOURCE3 2 same_as_c-cg-c1
angle_coeff @angle:cd-ch-n1 harmonic 59.410 178.620 # SOURCE4 26 0.2919
angle_coeff @angle:cf-ch-cg harmonic 57.400 177.900 # SOURCE4 8 0.4883
angle_coeff @angle:cf-ch-n1 harmonic 59.370 178.120 # SOURCE4 22 1.5200
angle_coeff @angle:cg-ch-ch harmonic 58.680 179.670 # SOURCE4 7 0.1439
angle_coeff @angle:n1-ch-nf harmonic 64.660 176.170 # SOURCE2 3 same_as_n1-cg-ne
angle_coeff @angle:i-c-i harmonic 59.790 116.450 # SOURCE3 1 0.0000
angle_coeff @angle:i-c-o harmonic 55.510 122.020 # SOURCE3 4 1.2961
angle_coeff @angle:f-cl-f harmonic 50.000 87.500 # SOURCE2 1 estimated_force_constant
angle_coeff @angle:n2-c-n2 harmonic 71.830 110.310 # SOURCE3 1
angle_coeff @angle:n2-c-o harmonic 73.020 122.500 # SOURCE3 1
angle_coeff @angle:n4-c-n4 harmonic 64.710 114.640 # SOURCE3 1 0.0000
angle_coeff @angle:n4-c-o harmonic 69.580 118.830 # SOURCE3 4 3.8516
angle_coeff @angle:nc-c-o harmonic 74.050 123.980 # SOURCE4 66 0.9502
angle_coeff @angle:nd-c-o harmonic 73.720 121.760 # SOURCE4 55 1.1138
angle_coeff @angle:ne-c-ne harmonic 73.220 110.310 # SOURCE3 1 0.0000
angle_coeff @angle:ne-c-o harmonic 72.940 126.030 # SOURCE4 39 0.9885
angle_coeff @angle:nf-c-nf harmonic 73.070 110.310 # SOURCE3 1 same_as_ne-c-ne
angle_coeff @angle:nf-c-o harmonic 73.320 124.390 # SOURCE3 3 same_as_ne-c-o
angle_coeff @angle:n-c-n harmonic 74.800 113.380 # SOURCE4 635 1.4358
angle_coeff @angle:n-c-nc harmonic 72.690 117.050 # SOURCE4 54 0.7020
angle_coeff @angle:n-c-nd harmonic 71.900 117.060 # SOURCE4 23 0.9856
angle_coeff @angle:n-c-ne harmonic 74.440 110.370 # SOURCE4 10 1.7492
angle_coeff @angle:n-c-o harmonic 75.830 122.030 # SOURCE3 221 2.3565
angle_coeff @angle:n-c-oh harmonic 76.220 113.630 # SOURCE4 5 1.1209
angle_coeff @angle:no-c-no harmonic 66.540 109.280 # SOURCE3 1
angle_coeff @angle:no-c-o harmonic 67.950 125.360 # SOURCE3 1
angle_coeff @angle:n-c-os harmonic 76.680 109.280 # SOURCE4 318 0.8749
angle_coeff @angle:n-c-s harmonic 83.180 123.880 # SOURCE3 5 1.2935
angle_coeff @angle:n-c-sh harmonic 83.030 112.610 # SOURCE4 8 1.2601
angle_coeff @angle:n-c-ss harmonic 84.610 110.420 # SOURCE4 59 1.5507
angle_coeff @angle:oh-c-oh harmonic 78.910 110.560 # SOURCE3 2 0.5498
angle_coeff @angle:oh-c-s harmonic 84.340 123.440 # SOURCE3 1 0.0000
angle_coeff @angle:o-c-o harmonic 78.170 130.380 # SOURCE4 429 1.0315
angle_coeff @angle:o-c-oh harmonic 77.380 122.880 # SOURCE3 33 2.1896
angle_coeff @angle:o-c-os harmonic 75.930 123.330 # SOURCE4 1708 1.0632
angle_coeff @angle:o-c-p2 harmonic 59.770 123.100 # SOURCE3 1
angle_coeff @angle:o-c-p3 harmonic 60.900 120.790 # SOURCE3 1
angle_coeff @angle:o-c-p5 harmonic 60.850 121.200 # SOURCE4 8 1.2117
angle_coeff @angle:o-c-pe harmonic 59.440 123.020 # SOURCE3 3 0.1404
angle_coeff @angle:o-c-pf harmonic 59.440 123.020 # SOURCE3 3 same_as_o-c-pe
angle_coeff @angle:o-c-px harmonic 60.640 119.100 # SOURCE3 1 0.0000
angle_coeff @angle:o-c-py harmonic 61.200 121.710 # SOURCE4 5 0.3133
angle_coeff @angle:o-c-s4 harmonic 77.510 121.150 # SOURCE3 1
angle_coeff @angle:o-c-s6 harmonic 78.060 119.450 # SOURCE3 1
angle_coeff @angle:o-c-s harmonic 86.330 120.440 # SOURCE3 2 0.0000
angle_coeff @angle:o-c-sh harmonic 81.240 121.410 # SOURCE3 4 1.4052
angle_coeff @angle:os-c-os harmonic 76.450 111.380 # SOURCE4 12 0.8309
angle_coeff @angle:o-c-ss harmonic 81.780 122.290 # SOURCE3 7 1.9240
angle_coeff @angle:os-c-s harmonic 83.310 125.030 # SOURCE4 18 0.9978
angle_coeff @angle:os-c-ss harmonic 83.910 113.630 # SOURCE4 5 0.7367
angle_coeff @angle:o-c-sx harmonic 76.880 121.150 # SOURCE3 5 3.6452
angle_coeff @angle:o-c-sy harmonic 78.310 119.320 # SOURCE3 5 2.4495
angle_coeff @angle:p2-c-p2 harmonic 58.960 113.750 # SOURCE3 1
angle_coeff @angle:p3-c-p3 harmonic 58.400 118.040 # SOURCE3 1 0.0000
angle_coeff @angle:p3-c-py harmonic 67.140 90.080 # SOURCE3 1 0.0000
angle_coeff @angle:p5-c-p5 harmonic 57.080 123.760 # SOURCE3 1
angle_coeff @angle:ca-cp-ca harmonic 67.250 118.330 # SOURCE4 521 0.6228
angle_coeff @angle:ca-cp-cp harmonic 64.140 121.140 # SOURCE4 979 1.4462
angle_coeff @angle:ca-cp-na harmonic 68.850 119.430 # SOURCE4 21 0.6591
angle_coeff @angle:ca-cp-nb harmonic 69.270 121.650 # SOURCE4 63 0.6564
angle_coeff @angle:cp-cp-cp harmonic 72.200 90.000 # SOURCE3 4 0.0000
angle_coeff @angle:cp-cp-cq harmonic 62.640 124.480 # SOURCE4 5 1.9038
angle_coeff @angle:cp-cp-nb harmonic 68.050 116.600 # SOURCE4 88 1.1887
angle_coeff @angle:pe-c-pe harmonic 58.620 113.770 # SOURCE3 1 0.0000
angle_coeff @angle:pf-c-pf harmonic 58.620 113.770 # SOURCE3 1 same_as_pe-c-pe
angle_coeff @angle:nb-cp-nb harmonic 71.310 125.720 # SOURCE4 5 0.6674
angle_coeff @angle:py-c-py harmonic 57.520 123.800 # SOURCE3 1 0.0000
angle_coeff @angle:ca-cq-ca harmonic 67.000 118.240 # SOURCE4 5 0.2181
angle_coeff @angle:ca-cq-cq harmonic 64.220 120.410 # SOURCE4 12 1.4029
angle_coeff @angle:ca-cq-nb harmonic 69.270 121.650 # SOURCE4 63 same as ca-cp-nb
angle_coeff @angle:cp-cq-cq harmonic 62.640 124.470 # SOURCE4 5 1.0864
angle_coeff @angle:cq-cq-cq harmonic 72.200 90.000 # SOURCE3 4 0.0000
angle_coeff @angle:cq-cq-nb harmonic 68.050 116.600 # SOURCE4 88 same as cp-cp-nb
angle_coeff @angle:s4-c-s4 harmonic 98.110 108.810 # SOURCE3 1
angle_coeff @angle:s6-c-s6 harmonic 95.130 115.750 # SOURCE3 1
angle_coeff @angle:sh-c-sh harmonic 100.060 115.330 # SOURCE3 1 0.0000
angle_coeff @angle:s-c-s harmonic 104.130 120.400 # SOURCE3 2 1.2766
angle_coeff @angle:s-c-sh harmonic 99.770 122.760 # SOURCE4 11 1.5734
angle_coeff @angle:s-c-ss harmonic 99.130 125.900 # SOURCE3 1 0.0000
angle_coeff @angle:ss-c-ss harmonic 102.180 113.000 # SOURCE3 1 0.0000
angle_coeff @angle:sx-c-sx harmonic 97.340 108.800 # SOURCE3 1 0.0000
angle_coeff @angle:sy-c-sy harmonic 95.370 115.780 # SOURCE3 1 0.0000
angle_coeff @angle:c2-cu-cx harmonic 58.560 148.210 # SOURCE4 6 1.8305
angle_coeff @angle:c-cu-cu harmonic 94.970 62.600 # SOURCE2 1 0.0000
angle_coeff @angle:cu-cu-cx harmonic 100.970 50.800 # SOURCE2 1 0.0000
angle_coeff @angle:cu-cu-ha harmonic 46.110 147.730 # SOURCE2 3 2.0950
angle_coeff @angle:cv-cv-cy harmonic 73.280 94.170 # SOURCE3 2 0.0000
angle_coeff @angle:cv-cv-ha harmonic 47.300 133.700 # SOURCE3 2 0.0000
angle_coeff @angle:cx-cv-cx harmonic 84.660 63.900 # SOURCE2 1 0.0000
angle_coeff @angle:cy-cv-ha harmonic 42.890 132.140 # SOURCE3 2 0.0000
angle_coeff @angle:c1-cx-cx harmonic 63.100 120.660 # SOURCE4 9 0.9067
angle_coeff @angle:c2-cx-cx harmonic 62.330 120.540 # SOURCE4 51 2.2377
angle_coeff @angle:c2-cx-h1 harmonic 46.630 115.780 # SOURCE4 8 0.2332
angle_coeff @angle:c2-cx-hc harmonic 46.770 115.100 # SOURCE4 12 0.7463
angle_coeff @angle:c2-cx-os harmonic 67.140 116.170 # SOURCE4 14 1.2782
angle_coeff @angle:c3-cx-c3 harmonic 63.000 114.480 # SOURCE4 46 1.9627
angle_coeff @angle:c3-cx-cx harmonic 61.820 120.060 # SOURCE4 448 2.1467
angle_coeff @angle:c3-cx-h1 harmonic 45.870 115.420 # SOURCE4 89 1.1096
angle_coeff @angle:c3-cx-hc harmonic 46.120 114.160 # SOURCE4 85 1.1118
angle_coeff @angle:c3-cx-n3 harmonic 64.310 118.500 # SOURCE4 17 2.4897
angle_coeff @angle:c3-cx-os harmonic 66.570 115.500 # SOURCE4 161 1.3016
angle_coeff @angle:ca-cx-cx harmonic 61.860 122.180 # SOURCE4 65 1.6898
angle_coeff @angle:ca-cx-h1 harmonic 46.810 114.570 # SOURCE4 7 0.6498
angle_coeff @angle:ca-cx-hc harmonic 47.050 113.410 # SOURCE4 18 0.7843
angle_coeff @angle:ca-cx-oh harmonic 69.250 112.930 # SOURCE3 1 0.0000
angle_coeff @angle:ca-cx-os harmonic 66.420 118.500 # SOURCE4 6 0.7514
angle_coeff @angle:c-cx-c3 harmonic 62.910 116.930 # SOURCE4 18 1.8253
angle_coeff @angle:cc-cx-cx harmonic 63.040 118.970 # SOURCE4 30 0.7725
angle_coeff @angle:cc-cx-hc harmonic 47.440 113.840 # SOURCE4 15 0.6682
angle_coeff @angle:c-cx-cx harmonic 62.960 117.960 # SOURCE4 147 1.8483
angle_coeff @angle:cd-cx-cx harmonic 62.450 120.460 # SOURCE4 9 0.8796
angle_coeff @angle:c-cx-h1 harmonic 46.270 117.250 # SOURCE4 24 0.7935
angle_coeff @angle:c-cx-hc harmonic 46.420 116.530 # SOURCE4 36 1.2830
angle_coeff @angle:cl-cx-cl harmonic 62.910 114.200 # SOURCE2 1 0.0000
angle_coeff @angle:cl-cx-cx harmonic 60.790 120.100 # SOURCE4 15 0.5917
angle_coeff @angle:cl-cx-h1 harmonic 43.410 111.430 # SOURCE3 1 0.0000
angle_coeff @angle:cl-cx-hc harmonic 42.580 115.800 # SOURCE2 1 0.0000
angle_coeff @angle:c-cx-os harmonic 67.250 115.590 # SOURCE4 36 0.8227
angle_coeff @angle:cu-cx-cu harmonic 91.530 54.600 # SOURCE2 1 0.0000
angle_coeff @angle:cu-cx-cx harmonic 88.720 58.500 # SOURCE4 7 0.1333
angle_coeff @angle:cu-cx-hc harmonic 45.490 118.090 # SOURCE4 7 1.0126
angle_coeff @angle:cx-cx-cx harmonic 87.900 60.000 # SOURCE4 681 0.6259
angle_coeff @angle:cx-cx-cy harmonic 67.540 100.530 # SOURCE3 4 0.0000
angle_coeff @angle:cx-cx-f harmonic 64.530 117.930 # SOURCE4 7 1.1613
angle_coeff @angle:cx-cx-h1 harmonic 45.450 119.660 # SOURCE3 12 0.4529
angle_coeff @angle:cx-cx-hc harmonic 45.790 117.920 # SOURCE3 92 1.1927
angle_coeff @angle:cx-cx-hx harmonic 45.470 119.620 # SOURCE4 9 0.1118
angle_coeff @angle:cx-cx-n3 harmonic 91.170 59.590 # SOURCE4 154 0.3104
angle_coeff @angle:cx-cx-na harmonic 62.940 125.850 # SOURCE4 16 2.0385
angle_coeff @angle:cx-cx-nh harmonic 92.030 59.150 # SOURCE4 116 0.6758
angle_coeff @angle:cx-cx-os harmonic 93.610 59.070 # SOURCE4 306 0.5253
angle_coeff @angle:cy-cx-hc harmonic 43.980 125.430 # SOURCE3 2 0.0000
angle_coeff @angle:f-cx-f harmonic 70.610 106.900 # SOURCE2 2 1.4000
angle_coeff @angle:f-cx-h1 harmonic 50.350 111.680 # SOURCE3 1 0.0000
angle_coeff @angle:f-cx-hc harmonic 50.220 112.300 # SOURCE2 1 0.0000
angle_coeff @angle:h1-cx-h1 harmonic 38.380 115.450 # SOURCE4 230 0.3302
angle_coeff @angle:h1-cx-n3 harmonic 47.970 116.430 # SOURCE4 173 1.4531
angle_coeff @angle:h1-cx-n harmonic 49.060 115.420 # SOURCE4 12 1.0443
angle_coeff @angle:h1-cx-na harmonic 49.960 108.670 # SOURCE4 8 1.6134
angle_coeff @angle:h1-cx-nh harmonic 48.500 116.320 # SOURCE4 151 1.0310
angle_coeff @angle:h1-cx-os harmonic 50.010 115.170 # SOURCE3 8 0.0226
angle_coeff @angle:h2-cx-h2 harmonic 37.870 119.430 # SOURCE3 1 0.0000
angle_coeff @angle:h2-cx-n2 harmonic 47.550 117.180 # SOURCE3 4 0.0000
angle_coeff @angle:hc-cx-hc harmonic 38.580 114.470 # SOURCE3 19 0.3295
angle_coeff @angle:hc-cx-os harmonic 50.250 114.100 # SOURCE2 1 0.0000
angle_coeff @angle:hx-cx-n4 harmonic 47.620 114.470 # SOURCE4 8 0.1059
angle_coeff @angle:n2-cx-n2 harmonic 102.060 50.160 # SOURCE3 1 0.0000
angle_coeff @angle:n-cx-oh harmonic 70.160 119.750 # SOURCE3 2 0.0000
angle_coeff @angle:n-cx-os harmonic 92.710 65.980 # SOURCE3 1 0.0000
angle_coeff @angle:oh-cx-oh harmonic 76.670 107.850 # SOURCE3 1 0.0000
angle_coeff @angle:oh-cx-os harmonic 71.640 118.120 # SOURCE3 4 1.3581
angle_coeff @angle:os-cx-os harmonic 70.900 115.840 # SOURCE4 7 2.0760
angle_coeff @angle:c2-cy-cy harmonic 66.570 100.400 # SOURCE2 1 0.0000
angle_coeff @angle:c3-cy-c3 harmonic 63.190 111.580 # SOURCE4 15 1.0060
angle_coeff @angle:c3-cy-cy harmonic 60.760 118.700 # SOURCE4 293 1.8510
angle_coeff @angle:c3-cy-h1 harmonic 46.160 111.770 # SOURCE4 119 0.4412
angle_coeff @angle:c3-cy-hc harmonic 46.210 111.550 # SOURCE3 5 0.6276
angle_coeff @angle:c3-cy-n3 harmonic 65.280 112.920 # SOURCE3 2 0.0000
angle_coeff @angle:c3-cy-n harmonic 68.320 104.050 # SOURCE4 122 0.5745
angle_coeff @angle:c3-cy-os harmonic 66.990 111.960 # SOURCE4 11 1.0668
angle_coeff @angle:c-cy-c3 harmonic 61.780 116.720 # SOURCE4 129 0.5236
angle_coeff @angle:cc-cy-cy harmonic 60.440 121.790 # SOURCE4 6 0.2155
angle_coeff @angle:c-cy-cy harmonic 71.810 84.990 # SOURCE4 263 0.6952
angle_coeff @angle:cd-cy-cy harmonic 60.650 120.880 # SOURCE4 13 0.5333
angle_coeff @angle:ce-cy-h2 harmonic 45.500 117.250 # SOURCE4 17 0.5351
angle_coeff @angle:ce-cy-n harmonic 74.690 88.020 # SOURCE4 14 0.1416
angle_coeff @angle:ce-cy-ss harmonic 74.010 121.330 # SOURCE4 13 0.1599
angle_coeff @angle:c-cy-h1 harmonic 45.890 113.100 # SOURCE4 71 0.7655
angle_coeff @angle:c-cy-hc harmonic 45.750 113.850 # SOURCE3 8 0.2067
angle_coeff @angle:cl-cy-cy harmonic 61.910 112.000 # SOURCE3 2 0.0000
angle_coeff @angle:cl-cy-h1 harmonic 44.060 106.590 # SOURCE3 1 0.0000
angle_coeff @angle:cl-cy-hc harmonic 42.600 114.000 # SOURCE2 1 0.0000
angle_coeff @angle:c-cy-n harmonic 64.320 117.390 # SOURCE4 70 1.0742
angle_coeff @angle:c-cy-os harmonic 66.270 114.420 # SOURCE4 6 1.2052
angle_coeff @angle:cv-cy-cy harmonic 71.460 86.670 # SOURCE4 6 1.1600
angle_coeff @angle:cv-cy-hc harmonic 46.060 114.470 # SOURCE4 7 0.4307
angle_coeff @angle:cx-cy-cy harmonic 66.080 101.230 # SOURCE3 4 0.0000
angle_coeff @angle:cx-cy-hc harmonic 45.250 118.300 # SOURCE2 3 5.7799
angle_coeff @angle:cy-cy-cy harmonic 70.160 87.610 # SOURCE3 32 1.5407
angle_coeff @angle:cy-cy-f harmonic 64.550 112.870 # SOURCE4 13 1.6772
angle_coeff @angle:cy-cy-h1 harmonic 44.870 114.840 # SOURCE3 20 2.5651
angle_coeff @angle:cy-cy-h2 harmonic 44.510 116.770 # SOURCE4 83 0.8683
angle_coeff @angle:cy-cy-hc harmonic 44.820 115.140 # SOURCE3 114 0.8364
angle_coeff @angle:cy-cy-n3 harmonic 73.470 87.580 # SOURCE3 4 0.6135
angle_coeff @angle:cy-cy-n harmonic 65.220 112.130 # SOURCE3 31 2.0700
angle_coeff @angle:cy-cy-na harmonic 63.370 119.700 # SOURCE4 9 0.3333
angle_coeff @angle:cy-cy-oh harmonic 66.000 114.190 # SOURCE3 4 0.0000
angle_coeff @angle:cy-cy-os harmonic 66.410 111.770 # SOURCE4 18 2.1334
angle_coeff @angle:cy-cy-s6 harmonic 74.590 117.460 # SOURCE4 7 1.2423
angle_coeff @angle:cy-cy-ss harmonic 74.450 118.180 # SOURCE4 55 0.9860
angle_coeff @angle:h1-cy-h1 harmonic 39.010 109.720 # SOURCE3 6 0.8087
angle_coeff @angle:h1-cy-n3 harmonic 48.210 113.360 # SOURCE3 6 1.4509
angle_coeff @angle:h1-cy-n harmonic 49.100 111.180 # SOURCE4 141 0.5848
angle_coeff @angle:h1-cy-oh harmonic 50.890 111.490 # SOURCE3 2 0.0000
angle_coeff @angle:h1-cy-os harmonic 50.530 110.940 # SOURCE3 8 0.6522
angle_coeff @angle:h1-cy-s6 harmonic 51.950 112.570 # SOURCE4 5 1.2943
angle_coeff @angle:h2-cy-n harmonic 48.420 114.440 # SOURCE4 88 0.7114
angle_coeff @angle:h2-cy-os harmonic 50.970 109.190 # SOURCE4 6 0.4162
angle_coeff @angle:h2-cy-s6 harmonic 53.300 106.850 # SOURCE4 6 0.3975
angle_coeff @angle:h2-cy-ss harmonic 52.700 109.730 # SOURCE4 92 0.7424
angle_coeff @angle:hc-cy-hc harmonic 39.240 109.040 # SOURCE3 28 0.5962
angle_coeff @angle:n-cy-os harmonic 71.620 107.500 # SOURCE4 9 2.3773
angle_coeff @angle:n-cy-s6 harmonic 82.570 103.450 # SOURCE4 6 0.7197
angle_coeff @angle:n-cy-ss harmonic 82.030 105.120 # SOURCE4 69 0.3987
angle_coeff @angle:nh-cz-nh harmonic 72.970 120.170 # SOURCE4 26 0.3964
angle_coeff @angle:br-n1-c1 harmonic 51.100 180.000 # HF/6-31G* 1
angle_coeff @angle:c1-n1-c1 harmonic 64.910 179.920 # HF/6-31G* 1
angle_coeff @angle:c1-n1-c2 harmonic 60.250 177.730 # HF/6-31G* 1
angle_coeff @angle:c1-n1-c3 harmonic 54.830 180.000 # HF/6-31G* 1
angle_coeff @angle:c1-n1-ca harmonic 56.970 179.990 # HF/6-31G* 1
angle_coeff @angle:c1-n1-cl harmonic 53.870 179.950 # HF/6-31G* 1
angle_coeff @angle:c1-n1-f harmonic 55.860 179.960 # HF/6-31G* 1
angle_coeff @angle:c1-n1-hn harmonic 45.620 179.980 # HF/6-31G* 1
angle_coeff @angle:c1-n1-i harmonic 46.230 179.950 # HF/6-31G* 1
angle_coeff @angle:c1-n1-n1 harmonic 66.890 180.000 # HF/6-31G* 1
angle_coeff @angle:c1-n1-n2 harmonic 65.700 171.560 # HF/6-31G* 1
angle_coeff @angle:c1-n1-n3 harmonic 60.690 175.590 # HF/6-31G* 1
angle_coeff @angle:c1-n1-n4 harmonic 59.680 179.690 # HF/6-31G* 1
angle_coeff @angle:c1-n1-na harmonic 59.950 180.000 # HF/6-31G* 1
angle_coeff @angle:c1-n1-nh harmonic 60.880 176.350 # HF/6-31G* 1
angle_coeff @angle:c1-n1-o harmonic 62.620 179.950 # HF/6-31G* 1
angle_coeff @angle:c1-n1-oh harmonic 62.880 174.310 # HF/6-31G* 1
angle_coeff @angle:c1-n1-os harmonic 62.150 176.610 # HF/6-31G* 1
angle_coeff @angle:c1-n1-p2 harmonic 53.810 172.830 # HF/6-31G* 1
angle_coeff @angle:c1-n1-p3 harmonic 54.260 173.510 # HF/6-31G* 1
angle_coeff @angle:c1-n1-p4 harmonic 53.620 173.640 # HF/6-31G* 1
angle_coeff @angle:c1-n1-p5 harmonic 56.480 177.280 # HF/6-31G* 1
angle_coeff @angle:c1-n1-s2 harmonic 76.360 178.110 # HF/6-31G* 1
angle_coeff @angle:c1-n1-s4 harmonic 69.870 169.600 # HF/6-31G* 1
angle_coeff @angle:c1-n1-s harmonic 67.470 179.990 # HF/6-31G* 1
angle_coeff @angle:c1-n1-s6 harmonic 78.230 175.920 # HF/6-31G* 1
angle_coeff @angle:c1-n1-sh harmonic 70.520 174.250 # HF/6-31G* 1
angle_coeff @angle:c1-n1-ss harmonic 70.160 176.060 # HF/6-31G* 1
angle_coeff @angle:c2-n1-n1 harmonic 61.580 180.000 # HF/6-31G* 1
angle_coeff @angle:c2-n1-o harmonic 73.090 116.940 # SOURCE3 2 0.0060
angle_coeff @angle:c2-n1-s harmonic 81.900 118.000 # SOURCE3 2 0.0121
angle_coeff @angle:c3-n1-n1 harmonic 56.300 180.000 # HF/6-31G* 1
angle_coeff @angle:ca-n1-n1 harmonic 58.540 180.000 # HF/6-31G* 1
angle_coeff @angle:ce-n1-o harmonic 71.350 122.400 # SOURCE3 1 same_as_cf-n1-o
angle_coeff @angle:ce-n1-s harmonic 82.090 117.340 # SOURCE3 1 same_as_cf-n1-s
angle_coeff @angle:cf-n1-o harmonic 71.060 122.400 # SOURCE3 1 0.0000
angle_coeff @angle:cf-n1-s harmonic 81.960 117.340 # SOURCE3 1 0.0000
angle_coeff @angle:cl-n1-n1 harmonic 55.230 179.940 # HF/6-31G* 1
angle_coeff @angle:f-n1-n1 harmonic 57.390 179.930 # HF/6-31G* 1
angle_coeff @angle:hn-n1-n1 harmonic 47.140 179.910 # HF/6-31G* 1
angle_coeff @angle:i-n1-n1 harmonic 47.260 179.940 # HF/6-31G* 1
angle_coeff @angle:n1-n1-n1 harmonic 68.970 179.970 # HF/6-31G* 1
angle_coeff @angle:n1-n1-n2 harmonic 67.650 171.570 # HF/6-31G* 1
angle_coeff @angle:n1-n1-n3 harmonic 62.490 175.090 # HF/6-31G* 1
angle_coeff @angle:n1-n1-n4 harmonic 61.310 179.910 # HF/6-31G* 1
angle_coeff @angle:n1-n1-na harmonic 61.630 179.970 # HF/6-31G* 1
angle_coeff @angle:n1-n1-nh harmonic 62.660 176.000 # HF/6-31G* 1
angle_coeff @angle:n1-n1-o harmonic 64.430 179.940 # HF/6-31G* 1
angle_coeff @angle:n1-n1-oh harmonic 64.780 173.770 # HF/6-31G* 1
angle_coeff @angle:n1-n1-os harmonic 64.010 176.120 # HF/6-31G* 1
angle_coeff @angle:n1-n1-p2 harmonic 54.850 174.710 # HF/6-31G* 1
angle_coeff @angle:n1-n1-p3 harmonic 55.500 174.270 # HF/6-31G* 1
angle_coeff @angle:n1-n1-s harmonic 69.160 180.000 # SOURCE3 1 0.0000
angle_coeff @angle:n1-n1-sh harmonic 72.150 175.070 # HF/6-31G* 1
angle_coeff @angle:n1-n1-ss harmonic 72.040 175.610 # HF/6-31G* 1
angle_coeff @angle:o-n1-p2 harmonic 66.900 116.050 # SOURCE3 1 0.0000
angle_coeff @angle:p2-n1-s harmonic 80.340 119.930 # SOURCE3 1 0.0000
angle_coeff @angle:br-n2-br harmonic 63.890 106.600 # SOURCE3 1
angle_coeff @angle:br-n2-c2 harmonic 59.130 112.400 # SOURCE3 1 0.0000
angle_coeff @angle:br-n2-n2 harmonic 61.080 110.420 # SOURCE3 1 0.0000
angle_coeff @angle:br-n2-o harmonic 60.100 114.470 # SOURCE3 1 0.0000
angle_coeff @angle:br-n2-p2 harmonic 63.250 111.030 # SOURCE3 1 0.0000
angle_coeff @angle:br-n2-s harmonic 78.980 115.780 # SOURCE3 1 0.0000
angle_coeff @angle:c1-n2-c1 harmonic 74.410 121.100 # SOURCE3 1
angle_coeff @angle:c1-n2-c3 harmonic 58.670 151.880 # SOURCE3 4 15.8282
angle_coeff @angle:c1-n2-cl harmonic 59.530 118.800 # SOURCE2 1 0.0000
angle_coeff @angle:c1-n2-hn harmonic 51.470 126.500 # SOURCE2 3 7.6267
angle_coeff @angle:c1-n2-n2 harmonic 76.750 113.400 # SOURCE3 1
angle_coeff @angle:c1-n2-o harmonic 79.200 113.590 # SOURCE3 1
angle_coeff @angle:c1-n2-p2 harmonic 66.970 119.570 # SOURCE3 1
angle_coeff @angle:c1-n2-s harmonic 88.340 117.670 # SOURCE3 1
angle_coeff @angle:c2-n2-c2 harmonic 70.760 118.180 # SOURCE3 1
angle_coeff @angle:c2-n2-c3 harmonic 66.130 115.300 # SOURCE3 8 4.2940
angle_coeff @angle:c2-n2-ca harmonic 69.830 119.940 # SOURCE3 1
angle_coeff @angle:c2-n2-cl harmonic 60.950 112.640 # SOURCE3 1 0.0000
angle_coeff @angle:c2-n2-f harmonic 68.300 108.140 # SOURCE3 1 0.0000
angle_coeff @angle:c2-n2-hn harmonic 52.630 110.330 # SOURCE3 9 0.6498
angle_coeff @angle:c2-n2-i harmonic 51.860 114.740 # SOURCE3 2 0.0139
angle_coeff @angle:c2-n2-n1 harmonic 75.450 115.090 # HF/6-31G* 1
angle_coeff @angle:c2-n2-n2 harmonic 77.940 103.590 # SOURCE3 2 0.0000
angle_coeff @angle:c2-n2-n3 harmonic 71.340 118.140 # SOURCE3 1
angle_coeff @angle:c2-n2-n4 harmonic 62.390 112.220 # SOURCE3 3 0.0406
angle_coeff @angle:c2-n2-n harmonic 70.160 117.980 # SOURCE4 11 0.9019
angle_coeff @angle:c2-n2-na harmonic 70.350 117.580 # SOURCE3 8 1.6671
angle_coeff @angle:c2-n2-nh harmonic 70.710 117.610 # SOURCE3 6 3.2642
angle_coeff @angle:c2-n2-no harmonic 64.220 111.540 # SOURCE3 1 0.0000
angle_coeff @angle:c2-n2-o harmonic 75.470 116.940 # SOURCE3 1
angle_coeff @angle:c2-n2-oh harmonic 72.080 110.890 # SOURCE4 22 1.2709
angle_coeff @angle:c2-n2-os harmonic 71.830 110.510 # SOURCE4 13 0.7888
angle_coeff @angle:c2-n2-p2 harmonic 67.180 116.000 # SOURCE3 1
angle_coeff @angle:c2-n2-p3 harmonic 61.270 119.300 # SOURCE3 3 2.8489
angle_coeff @angle:c2-n2-p4 harmonic 62.640 118.770 # SOURCE3 1
angle_coeff @angle:c2-n2-s4 harmonic 86.210 112.290 # SOURCE3 1
angle_coeff @angle:c2-n2-s6 harmonic 87.140 116.240 # SOURCE3 1
angle_coeff @angle:c2-n2-s harmonic 86.900 118.000 # SOURCE3 1
angle_coeff @angle:c2-n2-sh harmonic 79.840 115.480 # SOURCE3 1 0.0000
angle_coeff @angle:c2-n2-ss harmonic 82.230 118.040 # SOURCE3 4 2.2804
angle_coeff @angle:c3-n2-c3 harmonic 63.760 110.700 # SOURCE3 1
angle_coeff @angle:c3-n2-ca harmonic 65.970 114.950 # SOURCE4 5 0.9744
angle_coeff @angle:c3-n2-ce harmonic 65.370 118.520 # SOURCE4 113 1.6475
angle_coeff @angle:c3-n2-cf harmonic 65.320 118.690 # SOURCE4 10 1.2155
angle_coeff @angle:c3-n2-hn harmonic 45.180 118.400 # SOURCE3 1
angle_coeff @angle:c3-n2-n1 harmonic 68.640 116.200 # SOURCE4 12 0.5407
angle_coeff @angle:c3-n2-n2 harmonic 69.290 111.180 # SOURCE3 7 0.4349
angle_coeff @angle:c3-n2-nh harmonic 68.080 109.990 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n2-o harmonic 70.290 112.400 # SOURCE2 1 0.0000
angle_coeff @angle:c3-n2-p2 harmonic 64.870 114.210 # SOURCE3 2 2.2772
angle_coeff @angle:c3-n2-s6 harmonic 83.890 113.840 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n2-s harmonic 83.150 116.720 # SOURCE3 1 0.0000
angle_coeff @angle:ca-n2-ca harmonic 71.790 112.200 # SOURCE3 1
angle_coeff @angle:ca-n2-hn harmonic 50.010 120.000 # SOURCE3 1
angle_coeff @angle:ca-n2-n2 harmonic 74.000 113.530 # SOURCE3 1
angle_coeff @angle:ca-n2-o harmonic 75.260 116.000 # SOURCE2 1 0.0000
angle_coeff @angle:ca-n2-p2 harmonic 66.400 118.110 # SOURCE3 1
angle_coeff @angle:ca-n2-s harmonic 85.850 120.110 # SOURCE3 1
angle_coeff @angle:c-n2-c2 harmonic 66.220 120.970 # SOURCE3 1
angle_coeff @angle:c-n2-c harmonic 62.710 123.800 # SOURCE3 1
angle_coeff @angle:c-n2-ca harmonic 66.050 120.500 # SOURCE3 1
angle_coeff @angle:cc-n2-cl harmonic 60.100 115.790 # SOURCE3 1 same_as_cd-n2-cl
angle_coeff @angle:cc-n2-hn harmonic 52.300 111.140 # SOURCE4 12 0.8109
angle_coeff @angle:cc-n2-na harmonic 72.990 108.920 # SOURCE4 9 1.6245
angle_coeff @angle:cc-n2-nh harmonic 70.350 118.470 # SOURCE4 6 1.7995
angle_coeff @angle:cd-n2-cl harmonic 60.110 115.790 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n2-hn harmonic 52.630 110.090 # SOURCE4 8 0.6980
angle_coeff @angle:ce-n2-hn harmonic 52.730 111.120 # SOURCE4 68 0.2440
angle_coeff @angle:ce-n2-n harmonic 70.330 118.090 # SOURCE4 92 1.1048
angle_coeff @angle:ce-n2-nh harmonic 70.640 118.550 # SOURCE4 52 1.1425
angle_coeff @angle:ce-n2-o harmonic 77.370 112.160 # SOURCE3 1
angle_coeff @angle:ce-n2-oh harmonic 71.450 113.480 # SOURCE4 36 1.7049
angle_coeff @angle:ce-n2-os harmonic 71.290 112.780 # SOURCE4 33 0.8683
angle_coeff @angle:ce-n2-s harmonic 87.710 116.280 # SOURCE3 1
angle_coeff @angle:cf-n2-hn harmonic 53.860 106.500 # SOURCE3 1 same_as_ce-n2-hn
angle_coeff @angle:cf-n2-n harmonic 70.490 117.550 # SOURCE4 9 0.7822
angle_coeff @angle:cf-n2-nh harmonic 70.490 119.080 # SOURCE3 2 same_as_ce-n2-nh
angle_coeff @angle:cf-n2-o harmonic 77.370 112.160 # SOURCE3 1 same_as_ce-n2-o
angle_coeff @angle:cf-n2-oh harmonic 72.610 109.870 # SOURCE3 1 same_as_ce-n2-oh
angle_coeff @angle:cf-n2-os harmonic 70.950 113.870 # SOURCE4 7 0.6449
angle_coeff @angle:cf-n2-s harmonic 87.710 116.280 # SOURCE3 1 same_as_ce-n2-s
angle_coeff @angle:cl-n2-n1 harmonic 63.750 108.700 # SOURCE2 1 0.0000
angle_coeff @angle:cl-n2-n2 harmonic 63.120 110.470 # SOURCE3 1 0.0000
angle_coeff @angle:cl-n2-o harmonic 62.610 114.030 # SOURCE3 1
angle_coeff @angle:cl-n2-p2 harmonic 62.850 112.980 # SOURCE3 1 0.0000
angle_coeff @angle:cl-n2-s harmonic 79.610 115.770 # SOURCE3 1 0.0000
angle_coeff @angle:cx-n2-n2 harmonic 90.460 64.920 # SOURCE3 2 0.0000
angle_coeff @angle:f-n2-n2 harmonic 68.290 114.600 # SOURCE2 1 0.0000
angle_coeff @angle:f-n2-o harmonic 71.170 110.100 # SOURCE2 1 0.0000
angle_coeff @angle:f-n2-p2 harmonic 66.600 107.100 # SOURCE3 1 0.0000
angle_coeff @angle:f-n2-s harmonic 84.970 110.730 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n2-hn harmonic 38.610 120.000 # SOURCE3 1
angle_coeff @angle:hn-n2-n1 harmonic 55.330 114.100 # SOURCE2 1 0.0000
angle_coeff @angle:hn-n2-n2 harmonic 55.840 105.010 # SOURCE3 19 1.5183
angle_coeff @angle:hn-n2-ne harmonic 54.690 108.560 # SOURCE3 29 5.5708
angle_coeff @angle:hn-n2-nf harmonic 54.690 108.560 # SOURCE3 29 same_as_hn-n2-ne
angle_coeff @angle:hn-n2-o harmonic 57.610 107.370 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n2-p2 harmonic 46.310 112.090 # SOURCE3 18 4.0663
angle_coeff @angle:hn-n2-p4 harmonic 43.060 111.330 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n2-p5 harmonic 44.500 122.340 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n2-pe harmonic 48.420 111.410 # SOURCE3 20 4.9895
angle_coeff @angle:hn-n2-pf harmonic 48.420 111.410 # SOURCE3 20 same_as_hn-n2-pe
angle_coeff @angle:hn-n2-s2 harmonic 61.190 115.800 # SOURCE2 1 0.0000
angle_coeff @angle:hn-n2-s4 harmonic 58.650 111.210 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n2-s harmonic 62.150 108.170 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n2-s6 harmonic 60.520 112.590 # SOURCE3 2 0.0000
angle_coeff @angle:i-n2-n2 harmonic 53.710 111.790 # SOURCE3 1 0.0000
angle_coeff @angle:i-n2-o harmonic 52.330 116.820 # SOURCE3 1 0.0000
angle_coeff @angle:i-n2-p2 harmonic 57.140 113.260 # SOURCE3 1 0.0000
angle_coeff @angle:i-n2-s harmonic 71.310 116.850 # SOURCE3 1 0.0000
angle_coeff @angle:n1-n2-n1 harmonic 80.820 112.000 # HF/6-31G* 1
angle_coeff @angle:n2-n2-n1 harmonic 62.280 180.000 # dac_for_azides 0
angle_coeff @angle:n2-n2-n2 harmonic 78.200 109.490 # SOURCE3 2 0.0000
angle_coeff @angle:n2-n2-n3 harmonic 76.590 108.880 # SOURCE3 1
angle_coeff @angle:n2-n2-n4 harmonic 65.780 106.450 # SOURCE3 1 0.0000
angle_coeff @angle:n2-n2-na harmonic 74.180 112.230 # SOURCE3 1
angle_coeff @angle:n2-n2-nh harmonic 74.760 111.700 # SOURCE3 5 0.3475
angle_coeff @angle:n2-n2-no harmonic 67.680 105.970 # SOURCE3 1 0.0000
angle_coeff @angle:n2-n2-o harmonic 80.170 110.430 # SOURCE3 1
angle_coeff @angle:n2-n2-oh harmonic 74.020 111.510 # SOURCE3 1 0.0000
angle_coeff @angle:n2-n2-os harmonic 74.690 108.380 # SOURCE3 1 0.0000
angle_coeff @angle:n2-n2-p2 harmonic 71.160 109.150 # SOURCE3 1
angle_coeff @angle:n2-n2-p3 harmonic 64.580 113.050 # SOURCE3 1 0.0000
angle_coeff @angle:n2-n2-p4 harmonic 64.290 118.770 # SOURCE3 1
angle_coeff @angle:n2-n2-p5 harmonic 70.950 110.460 # SOURCE3 1
angle_coeff @angle:n2-n2-s4 harmonic 90.620 107.300 # SOURCE3 1
angle_coeff @angle:n2-n2-s6 harmonic 91.570 111.250 # SOURCE3 1
angle_coeff @angle:n2-n2-s harmonic 90.160 115.910 # SOURCE3 1
angle_coeff @angle:n2-n2-sh harmonic 83.540 111.100 # SOURCE3 1 0.0000
angle_coeff @angle:n2-n2-ss harmonic 86.650 112.140 # SOURCE3 1 0.0000
angle_coeff @angle:n3-n2-n3 harmonic 72.950 115.070 # SOURCE3 1
angle_coeff @angle:n3-n2-o harmonic 76.860 114.000 # SOURCE2 1 0.0000
angle_coeff @angle:n3-n2-p2 harmonic 68.490 115.340 # SOURCE3 1
angle_coeff @angle:n3-n2-s harmonic 88.540 117.130 # SOURCE3 1
angle_coeff @angle:n4-n2-n4 harmonic 59.970 106.700 # SOURCE3 1
angle_coeff @angle:n4-n2-o harmonic 64.860 112.200 # SOURCE3 1 0.0000
angle_coeff @angle:n4-n2-p2 harmonic 62.840 113.070 # SOURCE3 1 0.0000
angle_coeff @angle:n4-n2-s harmonic 79.030 118.500 # SOURCE3 1 0.0000
angle_coeff @angle:na-n2-na harmonic 73.470 107.000 # SOURCE3 1
angle_coeff @angle:na-n2-o harmonic 75.740 113.090 # SOURCE3 1 0.0000
angle_coeff @angle:na-n2-p2 harmonic 66.830 119.160 # SOURCE3 1 0.0000
angle_coeff @angle:na-n2-s harmonic 87.260 118.260 # SOURCE3 1 0.0000
angle_coeff @angle:ne-n2-nh harmonic 74.080 113.250 # SOURCE4 11 0.7711
angle_coeff @angle:ne-n2-o harmonic 79.970 110.310 # SOURCE3 1
angle_coeff @angle:ne-n2-s harmonic 89.910 116.220 # SOURCE3 1
angle_coeff @angle:nf-n2-nh harmonic 74.690 111.380 # SOURCE3 1 same_as_ne-n2-nh
angle_coeff @angle:nf-n2-o harmonic 79.970 110.310 # SOURCE3 1 same_as_ne-n2-o
angle_coeff @angle:nf-n2-s harmonic 89.910 116.220 # SOURCE3 1 same_as_ne-n2-s
angle_coeff @angle:nh-n2-nh harmonic 69.670 121.200 # SOURCE3 1
angle_coeff @angle:nh-n2-o harmonic 76.020 113.600 # SOURCE4 13 1.0945
angle_coeff @angle:nh-n2-p2 harmonic 67.100 118.830 # SOURCE3 2 0.1024
angle_coeff @angle:nh-n2-s harmonic 88.040 116.900 # SOURCE3 2 0.2276
angle_coeff @angle:n-n2-n2 harmonic 75.480 108.180 # SOURCE4 8 0.3496
angle_coeff @angle:n-n2-o harmonic 74.990 115.100 # SOURCE4 31 0.2796
angle_coeff @angle:no-n2-no harmonic 62.810 103.700 # SOURCE3 1
angle_coeff @angle:no-n2-o harmonic 70.400 100.760 # SOURCE3 1 0.0000
angle_coeff @angle:no-n2-p2 harmonic 64.250 111.950 # SOURCE3 1 0.0000
angle_coeff @angle:n-n2-p2 harmonic 67.320 117.300 # SOURCE3 1 0.0000
angle_coeff @angle:n-n2-s harmonic 88.140 115.740 # SOURCE3 1 0.0000
angle_coeff @angle:oh-n2-oh harmonic 74.840 101.700 # SOURCE3 1
angle_coeff @angle:oh-n2-p2 harmonic 67.990 115.110 # SOURCE3 1 0.0000
angle_coeff @angle:oh-n2-s harmonic 87.990 116.080 # SOURCE3 1 0.0000
angle_coeff @angle:o-n2-o harmonic 81.020 115.370 # SOURCE3 1
angle_coeff @angle:o-n2-oh harmonic 75.560 112.150 # SOURCE2 2 1.4500
angle_coeff @angle:o-n2-os harmonic 75.730 110.350 # SOURCE3 2 0.0042
angle_coeff @angle:o-n2-p2 harmonic 70.040 116.080 # SOURCE3 1
angle_coeff @angle:o-n2-p3 harmonic 65.080 113.430 # SOURCE3 1 0.0000
angle_coeff @angle:o-n2-p4 harmonic 67.340 110.610 # SOURCE3 1
angle_coeff @angle:o-n2-p5 harmonic 72.480 109.110 # SOURCE3 1
angle_coeff @angle:o-n2-pe harmonic 67.310 134.560 # SOURCE3 1
angle_coeff @angle:o-n2-pf harmonic 67.310 134.560 # SOURCE3 1 same_as_o-n2-pe
angle_coeff @angle:o-n2-s4 harmonic 91.280 108.910 # SOURCE3 1
angle_coeff @angle:o-n2-s6 harmonic 93.100 111.340 # SOURCE3 1
angle_coeff @angle:o-n2-s harmonic 91.240 117.180 # SOURCE3 1
angle_coeff @angle:o-n2-sh harmonic 82.970 114.980 # SOURCE3 1 0.0000
angle_coeff @angle:os-n2-os harmonic 71.250 110.290 # SOURCE3 1
angle_coeff @angle:os-n2-p2 harmonic 69.290 110.200 # SOURCE3 1 0.0000
angle_coeff @angle:o-n2-ss harmonic 86.560 115.340 # SOURCE3 1 0.0000
angle_coeff @angle:os-n2-s harmonic 89.190 112.230 # SOURCE3 1 0.0000
angle_coeff @angle:p2-n2-p2 harmonic 66.870 116.800 # SOURCE3 1
angle_coeff @angle:p2-n2-p3 harmonic 61.450 124.480 # SOURCE3 1 0.0000
angle_coeff @angle:p2-n2-p4 harmonic 61.350 128.370 # SOURCE3 1
angle_coeff @angle:p2-n2-p5 harmonic 65.160 123.470 # SOURCE3 1
angle_coeff @angle:p2-n2-s4 harmonic 86.260 112.100 # SOURCE3 1
angle_coeff @angle:p2-n2-s6 harmonic 86.440 115.700 # SOURCE3 1
angle_coeff @angle:p2-n2-s harmonic 85.910 117.840 # SOURCE3 1
angle_coeff @angle:p2-n2-sh harmonic 80.450 118.450 # SOURCE3 1 0.0000
angle_coeff @angle:p2-n2-ss harmonic 82.010 120.430 # SOURCE3 1 0.0000
angle_coeff @angle:p3-n2-p3 harmonic 59.930 120.400 # SOURCE3 1
angle_coeff @angle:p3-n2-s harmonic 80.080 120.860 # SOURCE3 1 0.0000
angle_coeff @angle:p4-n2-s harmonic 77.830 131.840 # SOURCE3 1
angle_coeff @angle:p5-n2-p5 harmonic 66.060 120.600 # SOURCE3 1
angle_coeff @angle:p5-n2-s harmonic 85.340 119.890 # SOURCE3 1
angle_coeff @angle:pe-n2-s harmonic 88.590 115.730 # SOURCE3 1
angle_coeff @angle:pf-n2-s harmonic 88.590 115.730 # SOURCE3 1 same_as_pe-n2-s
angle_coeff @angle:s4-n2-s4 harmonic 105.720 119.180 # SOURCE3 1
angle_coeff @angle:s4-n2-s6 harmonic 107.600 119.180 # SOURCE3 1
angle_coeff @angle:s6-n2-s6 harmonic 109.720 119.180 # SOURCE3 1
angle_coeff @angle:sh-n2-sh harmonic 96.030 123.930 # SOURCE3 1
angle_coeff @angle:sh-n2-ss harmonic 98.240 123.930 # SOURCE3 1
angle_coeff @angle:s-n2-s harmonic 109.670 120.880 # SOURCE3 1
angle_coeff @angle:s-n2-s4 harmonic 110.840 113.000 # SOURCE3 1
angle_coeff @angle:s-n2-s6 harmonic 109.880 119.610 # SOURCE3 1
angle_coeff @angle:s-n2-sh harmonic 101.850 122.050 # SOURCE3 1 0.0000
angle_coeff @angle:s-n2-ss harmonic 106.640 118.190 # SOURCE3 1 0.0000
angle_coeff @angle:ss-n2-ss harmonic 100.790 123.930 # SOURCE3 1
angle_coeff @angle:br-n3-br harmonic 66.540 107.150 # SOURCE3 1 0.0000
angle_coeff @angle:br-n3-c3 harmonic 62.700 106.930 # SOURCE3 2 0.0000
angle_coeff @angle:c1-n3-c1 harmonic 64.090 123.340 # SOURCE3 1
angle_coeff @angle:c1-n3-f harmonic 68.220 104.700 # SOURCE2 1 0.0000
angle_coeff @angle:c1-n3-hn harmonic 47.740 118.310 # SOURCE3 1
angle_coeff @angle:c1-n3-o harmonic 70.010 116.630 # SOURCE3 1
angle_coeff @angle:c2-n3-c2 harmonic 66.220 124.680 # SOURCE3 1
angle_coeff @angle:c2-n3-hn harmonic 49.110 119.380 # SOURCE3 1
angle_coeff @angle:c3-n3-c3 harmonic 64.010 110.900 # SOURCE3 40 2.3048
angle_coeff @angle:c3-n3-cl harmonic 62.170 107.230 # SOURCE3 3 0.3673
angle_coeff @angle:c3-n3-cx harmonic 62.450 116.320 # SOURCE4 24 0.5119
angle_coeff @angle:c3-n3-cy harmonic 61.690 118.260 # SOURCE4 14 0.8788
angle_coeff @angle:c3-n3-f harmonic 66.810 103.130 # SOURCE3 2 0.0000
angle_coeff @angle:c3-n3-hn harmonic 47.130 109.920 # SOURCE3 120 2.2590
angle_coeff @angle:c3-n3-i harmonic 56.980 108.480 # SOURCE3 2 0.0000
angle_coeff @angle:c3-n3-n2 harmonic 66.230 118.750 # SOURCE2 2 2.6500
angle_coeff @angle:c3-n3-n3 harmonic 66.760 108.150 # SOURCE3 15 1.3999
angle_coeff @angle:c3-n3-n4 harmonic 67.180 109.650 # SOURCE3 3 0.1146
angle_coeff @angle:c3-n3-n harmonic 66.670 111.750 # SOURCE4 50 1.6777
angle_coeff @angle:c3-n3-nh harmonic 66.370 111.890 # SOURCE4 21 1.3006
angle_coeff @angle:c3-n3-no harmonic 66.020 111.270 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n3-o harmonic 68.680 113.310 # SOURCE3 5 8.9081
angle_coeff @angle:c3-n3-oh harmonic 69.070 106.140 # SOURCE4 14 1.1040
angle_coeff @angle:c3-n3-os harmonic 68.480 104.950 # SOURCE4 9 0.9687
angle_coeff @angle:c3-n3-p3 harmonic 59.890 121.930 # SOURCE3 3 5.6009
angle_coeff @angle:c3-n3-p5 harmonic 62.050 119.810 # SOURCE4 58 1.8367
angle_coeff @angle:c3-n3-s4 harmonic 77.770 112.910 # SOURCE3 3 0.8983
angle_coeff @angle:c3-n3-s6 harmonic 80.590 116.570 # SOURCE4 73 1.8772
angle_coeff @angle:c3-n3-s harmonic 77.780 110.020 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n3-sh harmonic 78.550 112.700 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n3-ss harmonic 77.950 116.010 # SOURCE3 3 1.1944
angle_coeff @angle:c3-n3-sy harmonic 79.010 115.270 # SOURCE4 108 1.7647
angle_coeff @angle:cl-n3-cl harmonic 61.850 108.280 # SOURCE3 1 0.0000
angle_coeff @angle:cl-n3-hn harmonic 42.590 104.390 # SOURCE3 2 0.0000
angle_coeff @angle:cl-n3-n3 harmonic 63.750 107.650 # SOURCE3 1 0.0000
angle_coeff @angle:cx-n3-cx harmonic 86.390 60.710 # SOURCE4 57 0.2359
angle_coeff @angle:cx-n3-hn harmonic 47.150 109.570 # SOURCE4 26 0.7439
angle_coeff @angle:cx-n3-p5 harmonic 62.150 119.320 # SOURCE4 71 1.1948
angle_coeff @angle:cx-n3-py harmonic 60.630 121.750 # SOURCE4 10 1.0295
angle_coeff @angle:cy-n3-cy harmonic 70.040 90.870 # SOURCE4 10 0.5777
angle_coeff @angle:cy-n3-hn harmonic 46.250 112.120 # SOURCE4 9 1.9058
angle_coeff @angle:f-n3-f harmonic 67.710 102.220 # SOURCE2 4 0.7562
angle_coeff @angle:f-n3-hn harmonic 50.780 99.800 # SOURCE2 1 0.0000
angle_coeff @angle:hn-n3-hn harmonic 41.300 107.130 # SOURCE3 44 1.9687
angle_coeff @angle:hn-n3-i harmonic 35.430 109.980 # SOURCE3 2 0.0000
angle_coeff @angle:hn-n3-n1 harmonic 52.050 110.170 # HF/6-31G* 1
angle_coeff @angle:hn-n3-n2 harmonic 51.400 115.940 # SOURCE3 1
angle_coeff @angle:hn-n3-n3 harmonic 50.160 103.980 # SOURCE3 18 1.8593
angle_coeff @angle:hn-n3-n4 harmonic 50.870 106.400 # SOURCE3 5 0.5863
angle_coeff @angle:hn-n3-n harmonic 51.020 106.570 # SOURCE3 6 1.0767
angle_coeff @angle:hn-n3-na harmonic 50.320 107.890 # SOURCE3 1
angle_coeff @angle:hn-n3-nh harmonic 50.440 107.390 # SOURCE3 11 1.6294
angle_coeff @angle:hn-n3-no harmonic 50.250 104.780 # SOURCE3 3 1.1126
angle_coeff @angle:hn-n3-o harmonic 53.140 113.320 # SOURCE3 3 4.3945
angle_coeff @angle:hn-n3-oh harmonic 53.080 101.110 # SOURCE3 4 0.9921
angle_coeff @angle:hn-n3-os harmonic 51.670 100.920 # SOURCE3 6 0.7295
angle_coeff @angle:hn-n3-p2 harmonic 42.850 120.260 # SOURCE3 1
angle_coeff @angle:hn-n3-p3 harmonic 41.820 116.890 # SOURCE3 9 3.8816
angle_coeff @angle:hn-n3-p4 harmonic 43.440 113.050 # SOURCE3 2 0.0000
angle_coeff @angle:hn-n3-p5 harmonic 44.280 113.680 # SOURCE3 6 2.1781
angle_coeff @angle:hn-n3-s4 harmonic 53.750 108.930 # SOURCE3 7 1.7819
angle_coeff @angle:hn-n3-s harmonic 52.560 109.470 # SOURCE3 1
angle_coeff @angle:hn-n3-s6 harmonic 58.300 109.330 # SOURCE4 86 0.9610
angle_coeff @angle:hn-n3-sh harmonic 54.580 108.670 # SOURCE3 3 2.5025
angle_coeff @angle:hn-n3-ss harmonic 54.880 109.850 # SOURCE3 5 2.3215
angle_coeff @angle:hn-n3-sy harmonic 55.880 109.490 # SOURCE4 278 0.7897
angle_coeff @angle:i-n3-i harmonic 60.040 111.270 # SOURCE3 1 0.0000
angle_coeff @angle:n1-n3-n1 harmonic 72.400 113.210 # HF/6-31G* 1
angle_coeff @angle:n2-n3-n2 harmonic 71.820 118.730 # SOURCE3 1
angle_coeff @angle:n2-n3-o harmonic 74.130 114.910 # SOURCE3 1
angle_coeff @angle:n3-n3-n3 harmonic 69.570 105.710 # SOURCE3 3 0.3561
angle_coeff @angle:n4-n3-n4 harmonic 69.040 113.480 # SOURCE3 1 0.0000
angle_coeff @angle:n4-n3-nh harmonic 70.910 107.140 # SOURCE3 1
angle_coeff @angle:na-n3-na harmonic 69.210 112.000 # SOURCE3 1
angle_coeff @angle:nh-n3-nh harmonic 70.750 107.150 # SOURCE3 1 0.0000
angle_coeff @angle:n-n3-n harmonic 70.250 110.550 # SOURCE3 1 0.0000
angle_coeff @angle:no-n3-no harmonic 67.040 115.260 # SOURCE3 1 0.0000
angle_coeff @angle:oh-n3-oh harmonic 72.790 107.180 # SOURCE3 1 0.0000
angle_coeff @angle:o-n3-o harmonic 71.890 126.140 # SOURCE3 1
angle_coeff @angle:o-n3-p2 harmonic 66.640 117.020 # SOURCE3 1
angle_coeff @angle:o-n3-p4 harmonic 65.880 116.650 # SOURCE3 1
angle_coeff @angle:o-n3-s4 harmonic 81.710 114.090 # SOURCE3 1
angle_coeff @angle:o-n3-s6 harmonic 87.090 113.800 # SOURCE3 1
angle_coeff @angle:o-n3-s harmonic 78.520 119.810 # SOURCE3 1
angle_coeff @angle:os-n3-os harmonic 70.790 106.520 # SOURCE3 1 0.0000
angle_coeff @angle:p2-n3-p2 harmonic 60.890 130.130 # SOURCE3 1
angle_coeff @angle:p3-n3-p3 harmonic 61.530 118.740 # SOURCE3 3 3.3755
angle_coeff @angle:p4-n3-p4 harmonic 63.370 116.350 # SOURCE3 1
angle_coeff @angle:p5-n3-p5 harmonic 63.830 119.420 # SOURCE3 1 0.0000
angle_coeff @angle:s4-n3-s4 harmonic 96.310 120.020 # SOURCE3 1 0.0000
angle_coeff @angle:s4-n3-s6 harmonic 99.300 120.950 # SOURCE3 1
angle_coeff @angle:s6-n3-s6 harmonic 101.380 126.130 # SOURCE3 1 0.0000
angle_coeff @angle:sh-n3-sh harmonic 98.100 118.630 # SOURCE3 1 0.0000
angle_coeff @angle:sh-n3-ss harmonic 98.150 119.670 # SOURCE3 1
angle_coeff @angle:s-n3-s harmonic 90.470 131.360 # SOURCE3 1 0.0000
angle_coeff @angle:ss-n3-ss harmonic 98.680 119.570 # SOURCE3 1 0.0000
angle_coeff @angle:br-n4-br harmonic 65.140 114.820 # SOURCE3 1 0.0000
angle_coeff @angle:br-n4-hn harmonic 41.380 108.440 # SOURCE3 7 0.5630
angle_coeff @angle:c1-n4-c1 harmonic 65.530 113.870 # SOURCE3 1 0.0000
angle_coeff @angle:c1-n4-hn harmonic 48.620 110.190 # SOURCE3 7 1.0847
angle_coeff @angle:c2-n4-c2 harmonic 63.010 112.580 # SOURCE3 1 0.0000
angle_coeff @angle:c2-n4-c3 harmonic 63.100 110.960 # SOURCE4 13 2.4632
angle_coeff @angle:c2-n4-hn harmonic 46.430 111.360 # SOURCE3 13 1.2672
angle_coeff @angle:c3-n4-c3 harmonic 62.840 110.640 # SOURCE3 13 1.3060
angle_coeff @angle:c3-n4-ca harmonic 63.610 110.400 # SOURCE4 46 1.4643
angle_coeff @angle:c3-n4-cc harmonic 62.840 111.090 # SOURCE4 7 0.7065
angle_coeff @angle:c3-n4-cl harmonic 62.270 108.040 # SOURCE3 3 0.0000
angle_coeff @angle:c3-n4-hn harmonic 46.190 110.110 # SOURCE3 100 1.3136
angle_coeff @angle:c3-n4-n3 harmonic 66.730 108.720 # SOURCE3 2 0.0000
angle_coeff @angle:c3-n4-n4 harmonic 63.720 114.070 # SOURCE3 4 0.0000
angle_coeff @angle:c3-n4-n harmonic 66.200 109.260 # SOURCE4 7 1.9859
angle_coeff @angle:c3-n4-nh harmonic 64.760 111.730 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n4-no harmonic 65.250 109.080 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n4-o harmonic 67.250 111.660 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n4-oh harmonic 65.900 113.730 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n4-os harmonic 67.380 107.420 # SOURCE3 3 3.5920
angle_coeff @angle:c3-n4-p2 harmonic 56.830 112.520 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n4-p3 harmonic 58.790 110.730 # SOURCE3 3 2.1084
angle_coeff @angle:c3-n4-p5 harmonic 59.350 113.220 # SOURCE3 3 0.4021
angle_coeff @angle:c3-n4-s4 harmonic 72.410 108.230 # SOURCE3 3 0.4195
angle_coeff @angle:c3-n4-s6 harmonic 73.090 111.560 # SOURCE3 3 1.8851
angle_coeff @angle:c3-n4-s harmonic 74.940 113.550 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n4-sh harmonic 74.840 115.810 # SOURCE3 1 0.0000
angle_coeff @angle:c3-n4-ss harmonic 75.510 113.680 # SOURCE3 3 1.1405
angle_coeff @angle:ca-n4-ca harmonic 63.210 114.480 # SOURCE3 1 0.0000
angle_coeff @angle:ca-n4-hn harmonic 47.540 108.520 # SOURCE3 5 1.1693
angle_coeff @angle:c-n4-c harmonic 61.500 108.610 # SOURCE3 1 0.0000
angle_coeff @angle:c-n4-hn harmonic 44.680 110.860 # SOURCE3 10 1.0073
angle_coeff @angle:cl-n4-cl harmonic 60.960 114.910 # SOURCE3 1 0.0000
angle_coeff @angle:cl-n4-hn harmonic 42.500 108.870 # SOURCE3 7 0.7719
angle_coeff @angle:f-n4-f harmonic 70.470 109.050 # SOURCE3 1 0.0000
angle_coeff @angle:f-n4-hn harmonic 51.670 108.390 # SOURCE3 4 0.0000
angle_coeff @angle:hn-n4-hn harmonic 40.520 108.110 # SOURCE3 208 1.4126
angle_coeff @angle:hn-n4-i harmonic 36.440 108.720 # SOURCE3 7 1.2717
angle_coeff @angle:hn-n4-n1 harmonic 51.790 109.390 # HF/6-31G* 1
angle_coeff @angle:hn-n4-n2 harmonic 42.290 109.680 # SOURCE3 19 0.6266
angle_coeff @angle:hn-n4-n3 harmonic 49.850 110.400 # SOURCE3 11 0.7307
angle_coeff @angle:hn-n4-n4 harmonic 48.090 108.660 # SOURCE3 18 1.2967
angle_coeff @angle:hn-n4-n harmonic 49.590 109.080 # SOURCE3 13 1.6047
angle_coeff @angle:hn-n4-na harmonic 49.430 109.380 # SOURCE3 25 1.0758
angle_coeff @angle:hn-n4-nh harmonic 48.360 109.920 # SOURCE3 12 0.7304
angle_coeff @angle:hn-n4-no harmonic 49.190 104.380 # SOURCE3 2 0.0000
angle_coeff @angle:hn-n4-o harmonic 52.090 109.260 # SOURCE3 6 2.1203
angle_coeff @angle:hn-n4-oh harmonic 51.120 108.090 # SOURCE3 6 1.6728
angle_coeff @angle:hn-n4-os harmonic 50.150 109.390 # SOURCE3 10 1.4403
angle_coeff @angle:hn-n4-p2 harmonic 37.700 110.500 # SOURCE3 25 1.0664
angle_coeff @angle:hn-n4-p3 harmonic 39.300 109.890 # SOURCE3 10 2.3870
angle_coeff @angle:hn-n4-p4 harmonic 37.650 111.330 # SOURCE3 3 0.0000
angle_coeff @angle:hn-n4-p5 harmonic 40.530 110.000 # SOURCE3 10 1.0282
angle_coeff @angle:hn-n4-py harmonic 37.420 117.890 # SOURCE3 8 0.0000
angle_coeff @angle:hn-n4-s4 harmonic 46.920 110.100 # SOURCE3 6 0.8471
angle_coeff @angle:hn-n4-s harmonic 51.970 106.890 # SOURCE3 6 1.0775
angle_coeff @angle:hn-n4-s6 harmonic 48.900 108.940 # SOURCE3 10 0.5715
angle_coeff @angle:hn-n4-sh harmonic 52.260 108.560 # SOURCE3 6 0.8535
angle_coeff @angle:hn-n4-ss harmonic 52.080 109.170 # SOURCE3 10 0.8455
angle_coeff @angle:i-n4-i harmonic 58.990 118.490 # SOURCE3 1 0.0000
angle_coeff @angle:n1-n4-n1 harmonic 72.690 110.670 # HF/6-31G* 1
angle_coeff @angle:n2-n4-n2 harmonic 59.430 108.640 # SOURCE3 1 0.0000
angle_coeff @angle:n3-n4-n3 harmonic 69.790 111.070 # SOURCE3 1 0.0000
angle_coeff @angle:n4-n4-n4 harmonic 65.210 115.490 # SOURCE3 1 0.0000
angle_coeff @angle:na-n4-na harmonic 66.270 119.600 # SOURCE3 1 0.0000
angle_coeff @angle:nh-n4-nh harmonic 67.830 109.380 # SOURCE3 1 0.0000
angle_coeff @angle:n-n4-n harmonic 66.680 118.620 # SOURCE3 1 0.0000
angle_coeff @angle:oh-n4-oh harmonic 72.250 108.190 # SOURCE3 1 0.0000
angle_coeff @angle:o-n4-o harmonic 70.280 120.970 # SOURCE3 1 0.0000
angle_coeff @angle:os-n4-os harmonic 72.460 104.400 # SOURCE3 1 0.0000
angle_coeff @angle:p2-n4-p2 harmonic 55.970 113.910 # SOURCE3 2 0.0000
angle_coeff @angle:p3-n4-p3 harmonic 56.000 121.380 # SOURCE3 1 0.0000
angle_coeff @angle:p5-n4-p5 harmonic 61.270 107.020 # SOURCE3 1 0.0000
angle_coeff @angle:py-n4-py harmonic 73.000 69.790 # SOURCE3 2 0.0000
angle_coeff @angle:s4-n4-s4 harmonic 87.700 115.430 # SOURCE3 1
angle_coeff @angle:s6-n4-s6 harmonic 92.770 109.510 # SOURCE3 1 0.0000
angle_coeff @angle:sh-n4-sh harmonic 96.690 112.590 # SOURCE3 1 0.0000
angle_coeff @angle:s-n4-s harmonic 90.880 124.550 # SOURCE3 1 0.0000
angle_coeff @angle:ss-n4-ss harmonic 98.130 109.200 # SOURCE3 1 0.0000
angle_coeff @angle:br-na-br harmonic 60.550 123.000 # SOURCE3 1
angle_coeff @angle:br-na-c2 harmonic 63.610 100.480 # SOURCE3 2 1.0536
angle_coeff @angle:br-na-ca harmonic 57.150 124.810 # SOURCE3 1
angle_coeff @angle:br-na-cc harmonic 57.160 124.620 # SOURCE3 3 0.5348
angle_coeff @angle:br-na-cd harmonic 57.160 124.620 # SOURCE3 3 same_as_br-na-cc
angle_coeff @angle:br-na-nc harmonic 59.860 119.420 # SOURCE3 4 1.6703
angle_coeff @angle:br-na-nd harmonic 59.860 119.420 # SOURCE3 4 same_as_br-na-nc
angle_coeff @angle:br-na-os harmonic 63.920 104.990 # SOURCE3 1 0.0000
angle_coeff @angle:br-na-p2 harmonic 59.980 121.010 # SOURCE3 1
angle_coeff @angle:br-na-pc harmonic 60.360 120.260 # SOURCE3 3 2.1456
angle_coeff @angle:br-na-pd harmonic 60.360 120.260 # SOURCE3 3 same_as_br-na-pc
angle_coeff @angle:br-na-ss harmonic 79.050 112.280 # SOURCE3 1 0.0000
angle_coeff @angle:c1-na-c1 harmonic 67.200 117.200 # SOURCE3 1
angle_coeff @angle:c1-na-c2 harmonic 64.320 125.200 # SOURCE3 1
angle_coeff @angle:c1-na-ca harmonic 66.540 120.570 # SOURCE3 1
angle_coeff @angle:c1-na-cc harmonic 65.820 121.350 # SOURCE3 6 0.6517
angle_coeff @angle:c1-na-cd harmonic 65.820 121.350 # SOURCE3 6 0.6517
angle_coeff @angle:c1-na-nc harmonic 68.270 120.240 # SOURCE3 4 1.6849
angle_coeff @angle:c1-na-nd harmonic 68.270 120.240 # SOURCE3 4 same_as_c1-na-nc
angle_coeff @angle:c1-na-os harmonic 70.240 106.960 # SOURCE3 2 0.0000
angle_coeff @angle:c1-na-p2 harmonic 60.440 122.250 # SOURCE3 1
angle_coeff @angle:c1-na-pc harmonic 61.100 121.480 # SOURCE3 3 2.1681
angle_coeff @angle:c1-na-pd harmonic 61.100 121.480 # SOURCE3 3 same_as_c1-na-pc
angle_coeff @angle:c1-na-ss harmonic 78.330 118.300 # SOURCE3 1 0.0000
angle_coeff @angle:c2-na-c2 harmonic 67.800 110.370 # SOURCE3 6 0.5121
angle_coeff @angle:c2-na-c3 harmonic 64.230 117.200 # SOURCE3 2 0.0000
angle_coeff @angle:c2-na-ca harmonic 64.550 125.330 # SOURCE4 7 0.5648
angle_coeff @angle:c2-na-cc harmonic 63.980 125.750 # SOURCE3 10 1.5856
angle_coeff @angle:c2-na-cd harmonic 63.980 125.750 # SOURCE3 10 1.5856
angle_coeff @angle:c2-na-cl harmonic 63.280 101.010 # SOURCE3 2 1.5799
angle_coeff @angle:c2-na-f harmonic 68.640 103.110 # SOURCE3 1 0.0000
angle_coeff @angle:c2-na-hn harmonic 47.620 119.280 # SOURCE3 14 6.6027
angle_coeff @angle:c2-na-i harmonic 58.980 106.740 # SOURCE3 1 0.0000
angle_coeff @angle:c2-na-n1 harmonic 66.270 124.810 # HF/6-31G* 1
angle_coeff @angle:c2-na-n2 harmonic 65.800 125.000 # SOURCE3 1
angle_coeff @angle:c2-na-n3 harmonic 64.640 124.800 # SOURCE3 1
angle_coeff @angle:c2-na-n4 harmonic 65.190 121.320 # SOURCE3 1
angle_coeff @angle:c2-na-n harmonic 65.630 124.700 # SOURCE3 1
angle_coeff @angle:c2-na-na harmonic 65.140 124.600 # SOURCE3 1
angle_coeff @angle:c2-na-nc harmonic 67.270 121.140 # SOURCE4 5 1.0225
angle_coeff @angle:c2-na-nd harmonic 67.600 119.950 # SOURCE3 4 same_as_c2-na-nc
angle_coeff @angle:c2-na-nh harmonic 65.040 124.980 # SOURCE3 1
angle_coeff @angle:c2-na-no harmonic 64.340 124.200 # SOURCE3 1
angle_coeff @angle:c2-na-o harmonic 68.210 125.900 # SOURCE3 1
angle_coeff @angle:c2-na-oh harmonic 65.800 123.900 # SOURCE3 1
angle_coeff @angle:c2-na-os harmonic 68.530 110.330 # SOURCE3 4 3.2172
angle_coeff @angle:c2-na-p2 harmonic 60.200 122.140 # SOURCE3 1
angle_coeff @angle:c2-na-p3 harmonic 58.910 126.100 # SOURCE3 1
angle_coeff @angle:c2-na-p4 harmonic 64.460 125.000 # SOURCE3 1
angle_coeff @angle:c2-na-p5 harmonic 60.390 125.100 # SOURCE3 1
angle_coeff @angle:c2-na-pc harmonic 60.800 121.560 # SOURCE3 3 1.6252
angle_coeff @angle:c2-na-pd harmonic 60.800 121.560 # SOURCE3 3 same_as_c2-na-pc
angle_coeff @angle:c2-na-s4 harmonic 73.870 124.900 # SOURCE3 1
angle_coeff @angle:c2-na-s6 harmonic 76.240 124.400 # SOURCE3 1
angle_coeff @angle:c2-na-s harmonic 74.540 125.800 # SOURCE3 1
angle_coeff @angle:c2-na-sh harmonic 76.230 125.100 # SOURCE3 1
angle_coeff @angle:c2-na-ss harmonic 78.900 115.530 # SOURCE3 5 1.4036
angle_coeff @angle:c3-na-c3 harmonic 60.720 125.590 # SOURCE3 1 0.0000
angle_coeff @angle:c3-na-ca harmonic 63.150 124.360 # SOURCE3 5 4.2557
angle_coeff @angle:c3-na-cc harmonic 62.560 125.090 # SOURCE3 18 1.2138
angle_coeff @angle:c3-na-cd harmonic 62.560 125.090 # SOURCE3 18 1.2138
angle_coeff @angle:c3-na-cp harmonic 63.760 119.460 # SOURCE4 7 0.4108
angle_coeff @angle:c3-na-n2 harmonic 65.480 120.050 # SOURCE4 5 0.8795
angle_coeff @angle:c3-na-n harmonic 67.370 112.680 # SOURCE4 12 0.5122
angle_coeff @angle:c3-na-nc harmonic 65.740 120.460 # SOURCE3 8 2.1625
angle_coeff @angle:c3-na-nd harmonic 65.740 120.460 # SOURCE3 8 2.1625
angle_coeff @angle:c3-na-os harmonic 68.910 104.390 # SOURCE3 3 1.2017
angle_coeff @angle:c3-na-p2 harmonic 59.290 123.120 # SOURCE3 1
angle_coeff @angle:c3-na-pc harmonic 59.960 122.110 # SOURCE3 3 2.8504
angle_coeff @angle:c3-na-pd harmonic 59.960 122.110 # SOURCE3 3 same_as_c3-na-pc
angle_coeff @angle:c3-na-sh harmonic 80.220 110.280 # SOURCE3 1
angle_coeff @angle:c3-na-ss harmonic 79.610 110.870 # SOURCE3 3 0.8260
angle_coeff @angle:ca-na-ca harmonic 66.980 120.090 # SOURCE4 321 1.7366
angle_coeff @angle:ca-na-cc harmonic 68.460 113.150 # SOURCE3 18 9.8644
angle_coeff @angle:ca-na-cd harmonic 68.460 113.150 # SOURCE3 18 9.8644
angle_coeff @angle:ca-na-cl harmonic 57.170 124.790 # SOURCE3 1
angle_coeff @angle:ca-na-cp harmonic 65.880 120.960 # SOURCE4 20 1.2820
angle_coeff @angle:ca-na-cx harmonic 63.070 124.090 # SOURCE4 12 1.8167
angle_coeff @angle:ca-na-f harmonic 65.510 116.400 # SOURCE3 1
angle_coeff @angle:ca-na-hn harmonic 47.630 125.590 # SOURCE4 437 1.1893
angle_coeff @angle:ca-na-i harmonic 55.210 121.620 # SOURCE3 1
angle_coeff @angle:ca-na-n2 harmonic 68.210 119.850 # SOURCE4 6 1.2043
angle_coeff @angle:ca-na-n4 harmonic 66.370 120.190 # SOURCE3 1
angle_coeff @angle:ca-na-n harmonic 67.340 122.000 # SOURCE3 1
angle_coeff @angle:ca-na-na harmonic 66.290 123.760 # SOURCE3 1
angle_coeff @angle:ca-na-nb harmonic 68.180 122.160 # SOURCE4 7 0.8543
angle_coeff @angle:ca-na-nc harmonic 69.270 117.850 # SOURCE3 6 3.6536
angle_coeff @angle:ca-na-nd harmonic 69.270 117.850 # SOURCE3 6 same_as_ca-na-nc
angle_coeff @angle:ca-na-nh harmonic 66.140 124.330 # SOURCE4 7 1.3855
angle_coeff @angle:ca-na-o harmonic 71.140 119.990 # SOURCE4 51 1.2671
angle_coeff @angle:ca-na-oh harmonic 66.690 124.080 # SOURCE3 1
angle_coeff @angle:ca-na-os harmonic 69.700 109.460 # SOURCE3 1 0.0000
angle_coeff @angle:ca-na-p2 harmonic 59.660 125.850 # SOURCE3 1
angle_coeff @angle:ca-na-p3 harmonic 59.650 124.380 # SOURCE3 1
angle_coeff @angle:ca-na-p4 harmonic 65.120 124.970 # SOURCE3 1
angle_coeff @angle:ca-na-p5 harmonic 61.240 123.300 # SOURCE3 1
angle_coeff @angle:ca-na-pc harmonic 61.050 122.130 # SOURCE3 3 2.2393
angle_coeff @angle:ca-na-pd harmonic 61.050 122.130 # SOURCE3 3 same_as_ca-na-pc
angle_coeff @angle:ca-na-py harmonic 57.370 140.880 # SOURCE3 2 0.0000
angle_coeff @angle:ca-na-s4 harmonic 76.640 117.230 # SOURCE3 1
angle_coeff @angle:ca-na-s6 harmonic 77.900 120.690 # SOURCE3 1
angle_coeff @angle:ca-na-s harmonic 75.010 125.640 # SOURCE3 1
angle_coeff @angle:ca-na-sh harmonic 76.630 125.440 # SOURCE3 1
angle_coeff @angle:ca-na-ss harmonic 74.880 129.910 # SOURCE4 8 0.1449
angle_coeff @angle:cc-na-cc harmonic 68.940 109.900 # SOURCE3 109 1.5547
angle_coeff @angle:cc-na-cd harmonic 63.880 128.010 # SOURCE3 1 0.0000
angle_coeff @angle:cc-na-ce harmonic 63.050 126.610 # SOURCE4 8 0.5158
angle_coeff @angle:cc-na-cl harmonic 57.100 124.610 # SOURCE3 3 0.5208
angle_coeff @angle:cc-na-f harmonic 64.600 118.030 # SOURCE3 4 0.3081
angle_coeff @angle:cc-na-hn harmonic 46.990 125.660 # SOURCE4 549 1.5224
angle_coeff @angle:cc-na-i harmonic 54.340 125.700 # SOURCE3 6 0.7821
angle_coeff @angle:cc-na-n2 harmonic 66.830 122.960 # SOURCE3 15 0.9350
angle_coeff @angle:cc-na-n4 harmonic 65.900 120.310 # SOURCE3 10 3.4394
angle_coeff @angle:cc-na-n harmonic 66.520 123.190 # SOURCE3 13 0.3010
angle_coeff @angle:cc-na-na harmonic 65.910 123.430 # SOURCE3 23 0.2088
angle_coeff @angle:cc-na-nc harmonic 70.180 113.020 # SOURCE3 38 2.2867
angle_coeff @angle:cc-na-nd harmonic 66.370 126.350 # SOURCE4 94 1.1249
angle_coeff @angle:cc-na-nh harmonic 66.230 122.250 # SOURCE3 19 0.2010
angle_coeff @angle:cc-na-no harmonic 65.400 121.780 # SOURCE3 9 0.3521
angle_coeff @angle:cc-na-o harmonic 69.010 125.210 # SOURCE3 10 0.0124
angle_coeff @angle:cc-na-oh harmonic 66.670 122.380 # SOURCE3 10 0.1570
angle_coeff @angle:cc-na-os harmonic 67.340 115.740 # SOURCE3 41 5.4093
angle_coeff @angle:cc-na-p2 harmonic 59.490 125.860 # SOURCE3 14 2.2993
angle_coeff @angle:cc-na-p3 harmonic 59.280 125.250 # SOURCE3 8 0.1998
angle_coeff @angle:cc-na-p4 harmonic 64.080 127.730 # SOURCE3 7 3.6077
angle_coeff @angle:cc-na-p5 harmonic 60.690 124.700 # SOURCE3 13 1.4225
angle_coeff @angle:cc-na-s4 harmonic 75.240 121.030 # SOURCE3 10 0.5589
angle_coeff @angle:cc-na-s6 harmonic 77.180 122.190 # SOURCE3 10 0.9634
angle_coeff @angle:cc-na-s harmonic 74.800 125.660 # SOURCE3 8 0.1880
angle_coeff @angle:cc-na-sh harmonic 76.830 123.960 # SOURCE3 10 0.3424
angle_coeff @angle:cc-na-ss harmonic 76.340 124.220 # SOURCE4 8 0.1585
angle_coeff @angle:cd-na-cd harmonic 68.940 109.900 # SOURCE3 109 1.5547
angle_coeff @angle:cd-na-cl harmonic 57.100 124.610 # SOURCE3 3 same_as_cc-na-cl
angle_coeff @angle:cd-na-f harmonic 64.600 118.030 # SOURCE3 4 0.3081
angle_coeff @angle:cd-na-hn harmonic 47.070 125.220 # SOURCE4 312 1.1426
angle_coeff @angle:cd-na-i harmonic 54.340 125.700 # SOURCE3 6 0.7821
angle_coeff @angle:cd-na-n2 harmonic 66.830 122.960 # SOURCE3 15 0.9350
angle_coeff @angle:cd-na-n4 harmonic 65.900 120.310 # SOURCE3 10 3.4394
angle_coeff @angle:cd-na-n harmonic 66.520 123.190 # SOURCE3 13 0.3010
angle_coeff @angle:cd-na-na harmonic 65.910 123.430 # SOURCE3 23 0.2088
angle_coeff @angle:cd-na-nc harmonic 66.510 125.820 # SOURCE4 30 1.6776
angle_coeff @angle:cd-na-nd harmonic 70.180 113.020 # SOURCE3 38 2.2867
angle_coeff @angle:cd-na-nh harmonic 66.230 122.250 # SOURCE3 19 0.2010
angle_coeff @angle:cd-na-no harmonic 65.400 121.780 # SOURCE3 9 0.3521
angle_coeff @angle:cd-na-o harmonic 69.010 125.210 # SOURCE3 10 0.0124
angle_coeff @angle:cd-na-oh harmonic 66.670 122.380 # SOURCE3 10 0.1570
angle_coeff @angle:cd-na-os harmonic 65.210 123.420 # SOURCE4 7 2.3824
angle_coeff @angle:cd-na-p2 harmonic 59.490 125.860 # SOURCE3 14 2.2993
angle_coeff @angle:cd-na-p3 harmonic 59.280 125.250 # SOURCE3 8 0.1998
angle_coeff @angle:cd-na-p4 harmonic 64.080 127.730 # SOURCE3 7 same_as_cc-na-p4
angle_coeff @angle:cd-na-p5 harmonic 60.690 124.700 # SOURCE3 13 1.4225
angle_coeff @angle:cd-na-s4 harmonic 75.240 121.030 # SOURCE3 10 0.5589
angle_coeff @angle:cd-na-s6 harmonic 77.180 122.190 # SOURCE3 10 0.9634
angle_coeff @angle:cd-na-s harmonic 74.800 125.660 # SOURCE3 8 0.1880
angle_coeff @angle:cd-na-sh harmonic 76.830 123.960 # SOURCE3 10 0.3424
angle_coeff @angle:cd-na-ss harmonic 77.930 119.180 # SOURCE3 36 5.0538
angle_coeff @angle:cl-na-cl harmonic 56.330 122.800 # SOURCE3 1
angle_coeff @angle:cl-na-nc harmonic 59.890 119.360 # SOURCE3 4 1.7128
angle_coeff @angle:cl-na-nd harmonic 59.890 119.360 # SOURCE3 4 same_as_cl-na-nc
angle_coeff @angle:cl-na-os harmonic 63.040 106.580 # SOURCE3 1 0.0000
angle_coeff @angle:cl-na-p2 harmonic 58.340 121.290 # SOURCE3 1
angle_coeff @angle:cl-na-pc harmonic 58.780 120.510 # SOURCE3 3 2.1985
angle_coeff @angle:cl-na-pd harmonic 58.780 120.510 # SOURCE3 3 same_as_cl-na-pc
angle_coeff @angle:cl-na-ss harmonic 77.180 111.910 # SOURCE3 1 0.0000
angle_coeff @angle:f-na-f harmonic 62.220 120.200 # SOURCE3 1
angle_coeff @angle:f-na-nc harmonic 66.640 118.050 # SOURCE3 4 1.7931
angle_coeff @angle:f-na-nd harmonic 66.640 118.050 # SOURCE3 4 same_as_f-na-nc
angle_coeff @angle:f-na-os harmonic 69.150 103.860 # SOURCE3 1 0.0000
angle_coeff @angle:f-na-p2 harmonic 59.680 119.950 # SOURCE3 1
angle_coeff @angle:f-na-pc harmonic 60.340 119.100 # SOURCE3 3 2.3967
angle_coeff @angle:f-na-pd harmonic 60.340 119.100 # SOURCE3 3 same_as_f-na-pc
angle_coeff @angle:f-na-ss harmonic 80.160 108.010 # SOURCE3 1 0.0000
angle_coeff @angle:hn-na-hn harmonic 39.830 116.800 # SOURCE3 1
angle_coeff @angle:hn-na-n harmonic 50.900 111.260 # SOURCE4 5 1.1280
angle_coeff @angle:hn-na-nc harmonic 50.000 119.610 # SOURCE3 16 1.8079
angle_coeff @angle:hn-na-nd harmonic 50.000 119.610 # SOURCE3 16 1.8079
angle_coeff @angle:hn-na-os harmonic 51.440 101.410 # SOURCE3 7 3.0814
angle_coeff @angle:hn-na-p2 harmonic 40.320 122.520 # SOURCE3 1
angle_coeff @angle:hn-na-pc harmonic 40.940 121.480 # SOURCE3 3 2.9355
angle_coeff @angle:hn-na-pd harmonic 40.940 121.480 # SOURCE3 3 same_as_hn-na-pc
angle_coeff @angle:hn-na-ss harmonic 53.460 113.950 # SOURCE3 1 0.0000
angle_coeff @angle:i-na-i harmonic 58.320 124.200 # SOURCE3 1
angle_coeff @angle:i-na-nc harmonic 56.940 120.030 # SOURCE3 4 2.0032
angle_coeff @angle:i-na-nd harmonic 56.940 120.030 # SOURCE3 4 same_as_i-na-nc
angle_coeff @angle:i-na-os harmonic 59.850 109.910 # SOURCE3 1 0.0000
angle_coeff @angle:i-na-p2 harmonic 57.960 122.280 # SOURCE3 1
angle_coeff @angle:i-na-pc harmonic 58.320 121.400 # SOURCE3 3 2.4763
angle_coeff @angle:i-na-pd harmonic 58.320 121.400 # SOURCE3 3 same_as_i-na-pc
angle_coeff @angle:i-na-ss harmonic 74.730 118.400 # SOURCE3 1 0.0000
angle_coeff @angle:n2-na-n2 harmonic 70.350 116.710 # SOURCE3 1
angle_coeff @angle:n2-na-nc harmonic 69.850 119.960 # SOURCE3 4 4.5041
angle_coeff @angle:n2-na-nd harmonic 69.850 119.960 # SOURCE3 4 same_as_n2-na-nc
angle_coeff @angle:n2-na-os harmonic 70.330 111.530 # SOURCE3 1 0.0000
angle_coeff @angle:n2-na-p2 harmonic 61.200 124.880 # SOURCE3 1
angle_coeff @angle:n2-na-pc harmonic 62.110 123.180 # SOURCE3 3 4.7947
angle_coeff @angle:n2-na-pd harmonic 62.110 123.180 # SOURCE3 3 same_as_n2-na-pc
angle_coeff @angle:n2-na-ss harmonic 78.110 124.640 # SOURCE3 1 0.0000
angle_coeff @angle:n3-na-n3 harmonic 65.770 124.000 # SOURCE3 1
angle_coeff @angle:n4-na-n4 harmonic 68.570 111.700 # SOURCE3 1
angle_coeff @angle:n4-na-nc harmonic 69.090 116.440 # SOURCE3 4 3.6604
angle_coeff @angle:n4-na-nd harmonic 69.090 116.440 # SOURCE3 4 same_as_n4-na-nc
angle_coeff @angle:n4-na-os harmonic 71.610 102.970 # SOURCE3 1 0.0000
angle_coeff @angle:n4-na-p2 harmonic 60.870 123.560 # SOURCE3 1
angle_coeff @angle:n4-na-pc harmonic 61.710 121.980 # SOURCE3 3 4.4884
angle_coeff @angle:n4-na-pd harmonic 61.710 121.980 # SOURCE3 3 same_as_n4-na-pc
angle_coeff @angle:na-na-na harmonic 66.770 123.600 # SOURCE3 1
angle_coeff @angle:na-na-nc harmonic 69.080 119.640 # SOURCE3 4 1.6920
angle_coeff @angle:na-na-nd harmonic 69.080 119.640 # SOURCE3 4 same_as_na-na-nc
angle_coeff @angle:na-na-os harmonic 70.250 109.470 # SOURCE3 1 0.0000
angle_coeff @angle:na-na-p2 harmonic 61.690 121.720 # SOURCE3 1
angle_coeff @angle:na-na-pc harmonic 62.360 120.910 # SOURCE3 3 2.3033
angle_coeff @angle:na-na-pd harmonic 62.360 120.910 # SOURCE3 3 same_as_na-na-pc
angle_coeff @angle:na-na-ss harmonic 80.370 116.500 # SOURCE3 1 0.0000
angle_coeff @angle:nc-na-nc harmonic 71.200 117.080 # SOURCE3 31 1.8121
angle_coeff @angle:nc-na-nd harmonic 69.530 122.770 # SOURCE4 5 0.1352
angle_coeff @angle:nc-na-nh harmonic 68.820 120.550 # SOURCE3 8 1.1436
angle_coeff @angle:nc-na-no harmonic 68.190 119.150 # SOURCE3 4 1.6049
angle_coeff @angle:nc-na-o harmonic 72.040 122.790 # SOURCE3 6 1.3154
angle_coeff @angle:nc-na-oh harmonic 69.710 119.220 # SOURCE3 4 1.7201
angle_coeff @angle:nc-na-os harmonic 68.300 119.650 # SOURCE3 4 1.5019
angle_coeff @angle:nc-na-p2 harmonic 62.600 119.990 # SOURCE3 4 3.6009
angle_coeff @angle:nc-na-p3 harmonic 62.200 120.070 # SOURCE3 4 3.7188
angle_coeff @angle:nc-na-p4 harmonic 68.140 119.770 # SOURCE3 3 0.3747
angle_coeff @angle:nc-na-p5 harmonic 63.880 118.950 # SOURCE3 4 3.1194
angle_coeff @angle:nc-na-pc harmonic 63.450 118.660 # SOURCE3 27 1.5082
angle_coeff @angle:nc-na-s4 harmonic 77.870 119.200 # SOURCE3 4 2.3841
angle_coeff @angle:nc-na-s6 harmonic 80.300 119.240 # SOURCE3 4 2.2262
angle_coeff @angle:nc-na-s harmonic 77.910 122.260 # SOURCE3 4 0.9173
angle_coeff @angle:nc-na-sh harmonic 80.100 120.500 # SOURCE3 4 1.5016
angle_coeff @angle:nc-na-ss harmonic 79.650 120.500 # SOURCE3 4 1.5615
angle_coeff @angle:nd-na-nd harmonic 71.200 117.080 # SOURCE3 31 1.8121
angle_coeff @angle:nd-na-nh harmonic 68.820 120.550 # SOURCE3 8 same_as_nc-na-nh
angle_coeff @angle:nd-na-no harmonic 68.190 119.150 # SOURCE3 4 same_as_nc-na-no
angle_coeff @angle:nd-na-o harmonic 72.040 122.790 # SOURCE3 6 same_as_nc-na-o
angle_coeff @angle:nd-na-oh harmonic 69.710 119.220 # SOURCE3 4 same_as_nc-na-oh
angle_coeff @angle:nd-na-os harmonic 68.300 119.650 # SOURCE3 4 same_as_nc-na-os
angle_coeff @angle:nd-na-p2 harmonic 62.600 119.990 # SOURCE3 4 same_as_nc-na-p2
angle_coeff @angle:nd-na-p3 harmonic 62.200 120.070 # SOURCE3 4 same_as_nc-na-p3
angle_coeff @angle:nd-na-p4 harmonic 68.140 119.770 # SOURCE3 3 same_as_nc-na-p4
angle_coeff @angle:nd-na-p5 harmonic 63.880 118.950 # SOURCE3 4 same_as_nc-na-p5
angle_coeff @angle:nd-na-pd harmonic 63.450 118.660 # SOURCE3 27 same_as_nc-na-pc
angle_coeff @angle:nd-na-s4 harmonic 77.870 119.200 # SOURCE3 4 same_as_nc-na-s4
angle_coeff @angle:nd-na-s6 harmonic 80.300 119.240 # SOURCE3 4 same_as_nc-na-s6
angle_coeff @angle:nd-na-s harmonic 77.910 122.260 # SOURCE3 4 same_as_nc-na-s
angle_coeff @angle:nd-na-sh harmonic 80.100 120.500 # SOURCE3 4 same_as_nc-na-sh
angle_coeff @angle:nd-na-ss harmonic 79.650 120.500 # SOURCE3 4 same_as_nc-na-ss
angle_coeff @angle:nh-na-nh harmonic 66.770 123.600 # SOURCE3 1
angle_coeff @angle:nh-na-os harmonic 69.650 111.370 # SOURCE3 1 0.0000
angle_coeff @angle:nh-na-p2 harmonic 61.900 120.860 # SOURCE3 1
angle_coeff @angle:nh-na-pc harmonic 62.500 120.380 # SOURCE3 6 1.3513
angle_coeff @angle:nh-na-pd harmonic 62.500 120.380 # SOURCE3 6 same_as_nh-na-pc
angle_coeff @angle:nh-na-ss harmonic 81.840 112.350 # SOURCE3 2 5.2951
angle_coeff @angle:n-na-n harmonic 67.780 123.800 # SOURCE3 1
angle_coeff @angle:n-na-nc harmonic 69.610 119.850 # SOURCE3 4 1.6156
angle_coeff @angle:n-na-nd harmonic 69.610 119.850 # SOURCE3 4 same_as_n-na-nc
angle_coeff @angle:no-na-no harmonic 65.220 122.800 # SOURCE3 1
angle_coeff @angle:no-na-os harmonic 70.300 106.550 # SOURCE3 1 0.0000
angle_coeff @angle:no-na-pc harmonic 62.140 120.110 # SOURCE3 3 2.0821
angle_coeff @angle:no-na-pd harmonic 62.140 120.110 # SOURCE3 3 same_as_no-na-pc
angle_coeff @angle:n-na-os harmonic 72.340 104.710 # SOURCE3 1 0.0000
angle_coeff @angle:no-na-ss harmonic 80.360 114.950 # SOURCE3 1 0.0000
angle_coeff @angle:n-na-p2 harmonic 61.990 121.350 # SOURCE3 1
angle_coeff @angle:n-na-pc harmonic 62.650 120.640 # SOURCE3 3 2.0168
angle_coeff @angle:n-na-pd harmonic 62.650 120.640 # SOURCE3 3 same_as_n-na-pc
angle_coeff @angle:n-na-ss harmonic 80.800 116.100 # SOURCE3 1 0.0000
angle_coeff @angle:oh-na-oh harmonic 68.130 122.200 # SOURCE3 1
angle_coeff @angle:oh-na-p2 harmonic 62.330 120.760 # SOURCE3 1
angle_coeff @angle:oh-na-pc harmonic 63.000 119.990 # SOURCE3 3 2.1734
angle_coeff @angle:oh-na-pd harmonic 63.000 119.990 # SOURCE3 3 same_as_oh-na-pc
angle_coeff @angle:oh-na-ss harmonic 82.110 113.040 # SOURCE3 1 0.0000
angle_coeff @angle:o-na-o harmonic 74.030 126.200 # SOURCE3 1
angle_coeff @angle:o-na-os harmonic 70.760 118.390 # SOURCE3 1 0.0000
angle_coeff @angle:o-na-p2 harmonic 62.830 122.800 # SOURCE3 1
angle_coeff @angle:o-na-pc harmonic 63.490 122.340 # SOURCE3 3 1.2908
angle_coeff @angle:o-na-pd harmonic 63.490 122.340 # SOURCE3 3 same_as_o-na-pc
angle_coeff @angle:os-na-os harmonic 71.290 104.450 # SOURCE3 2 0.0983
angle_coeff @angle:os-na-p2 harmonic 62.590 117.860 # SOURCE3 1 0.0000
angle_coeff @angle:os-na-p3 harmonic 66.040 104.700 # SOURCE3 1 0.0000
angle_coeff @angle:os-na-p5 harmonic 65.290 111.410 # SOURCE3 1 0.0000
angle_coeff @angle:os-na-pc harmonic 62.490 119.910 # SOURCE3 3 1.9002
angle_coeff @angle:os-na-pd harmonic 62.490 119.910 # SOURCE3 3 same_as_os-na-pc
angle_coeff @angle:os-na-s4 harmonic 82.020 105.880 # SOURCE3 2 0.0000
angle_coeff @angle:os-na-s6 harmonic 82.010 112.000 # SOURCE3 2 0.0000
angle_coeff @angle:os-na-ss harmonic 82.680 109.640 # SOURCE3 3 4.1395
angle_coeff @angle:p2-na-p2 harmonic 60.320 120.910 # SOURCE3 1
angle_coeff @angle:p2-na-p3 harmonic 59.150 124.800 # SOURCE3 1
angle_coeff @angle:p2-na-p5 harmonic 60.140 123.990 # SOURCE3 1
angle_coeff @angle:p2-na-pc harmonic 60.660 120.720 # SOURCE3 3 0.2407
angle_coeff @angle:p2-na-pd harmonic 60.660 120.720 # SOURCE3 3 same_as_p2-na-pc
angle_coeff @angle:p2-na-s4 harmonic 74.880 122.470 # SOURCE3 1
angle_coeff @angle:p2-na-s6 harmonic 76.310 122.500 # SOURCE3 1
angle_coeff @angle:p2-na-s harmonic 75.690 121.850 # SOURCE3 1
angle_coeff @angle:p2-na-sh harmonic 76.680 121.750 # SOURCE3 1
angle_coeff @angle:p2-na-ss harmonic 76.380 121.880 # SOURCE3 1
angle_coeff @angle:p3-na-p3 harmonic 58.510 126.600 # SOURCE3 1
angle_coeff @angle:p3-na-pc harmonic 59.780 123.320 # SOURCE3 3 4.1781
angle_coeff @angle:p3-na-pd harmonic 59.780 123.320 # SOURCE3 3 same_as_p3-na-pc
angle_coeff @angle:p5-na-p5 harmonic 60.590 124.600 # SOURCE3 1
angle_coeff @angle:p5-na-pc harmonic 60.760 122.690 # SOURCE3 3 3.6738
angle_coeff @angle:p5-na-pd harmonic 60.760 122.690 # SOURCE3 3 same_as_p5-na-pc
angle_coeff @angle:p5-na-ss harmonic 78.220 118.520 # SOURCE3 1 0.0000
angle_coeff @angle:pc-na-pc harmonic 60.940 120.780 # SOURCE3 27 1.6457
angle_coeff @angle:pc-na-s4 harmonic 75.520 121.510 # SOURCE3 3 2.7242
angle_coeff @angle:pc-na-s6 harmonic 76.990 121.550 # SOURCE3 3 2.7065
angle_coeff @angle:pc-na-s harmonic 76.170 121.470 # SOURCE3 3 1.0668
angle_coeff @angle:pc-na-sh harmonic 77.280 121.080 # SOURCE3 3 1.8942
angle_coeff @angle:pc-na-ss harmonic 76.970 121.200 # SOURCE3 3 1.9295
angle_coeff @angle:pd-na-pd harmonic 60.940 120.780 # SOURCE3 27 same_as_pc-na-pc
angle_coeff @angle:pd-na-s4 harmonic 75.520 121.510 # SOURCE3 3 same_as_pc-na-s4
angle_coeff @angle:pd-na-s6 harmonic 76.990 121.550 # SOURCE3 3 same_as_pc-na-s6
angle_coeff @angle:pd-na-s harmonic 76.170 121.470 # SOURCE3 3 same_as_pc-na-s
angle_coeff @angle:pd-na-sh harmonic 77.280 121.080 # SOURCE3 3 same_as_pc-na-sh
angle_coeff @angle:pd-na-ss harmonic 76.970 121.200 # SOURCE3 3 same_as_pc-na-ss
angle_coeff @angle:py-na-py harmonic 76.600 78.250 # SOURCE3 1 0.0000
angle_coeff @angle:s4-na-s4 harmonic 92.990 124.200 # SOURCE3 1
angle_coeff @angle:s4-na-s6 harmonic 99.310 112.860 # SOURCE3 1
angle_coeff @angle:s4-na-ss harmonic 99.570 111.920 # SOURCE3 1 0.0000
angle_coeff @angle:s6-na-s6 harmonic 96.930 123.200 # SOURCE3 1
angle_coeff @angle:s6-na-ss harmonic 98.410 119.100 # SOURCE3 1 0.0000
angle_coeff @angle:sh-na-sh harmonic 96.720 124.600 # SOURCE3 1
angle_coeff @angle:sh-na-ss harmonic 98.710 118.790 # SOURCE3 1 0.0000
angle_coeff @angle:s-na-s harmonic 93.790 126.000 # SOURCE3 1
angle_coeff @angle:s-na-ss harmonic 100.150 112.490 # SOURCE3 1 0.0000
angle_coeff @angle:ss-na-ss harmonic 100.760 113.240 # SOURCE3 2 6.6084
angle_coeff @angle:sy-na-sy harmonic 96.930 123.200 # SOURCE3 1
angle_coeff @angle:ca-nb-ca harmonic 68.590 115.860 # SOURCE3 46 1.1645
angle_coeff @angle:ca-nb-cp harmonic 68.010 118.040 # SOURCE4 58 0.7819
angle_coeff @angle:ca-nb-cq harmonic 68.010 118.040 # SOURCE4 58 same as ca-nb-cp
angle_coeff @angle:ca-nb-nb harmonic 69.370 118.890 # SOURCE3 10 0.6031
angle_coeff @angle:cp-nb-nb harmonic 68.790 121.110 # SOURCE4 12 0.4315
angle_coeff @angle:nb-nb-nb harmonic 70.440 121.040 # SOURCE3 1 0.0000
angle_coeff @angle:br-n-br harmonic 66.590 116.200 # SOURCE3 1 0.0000
angle_coeff @angle:br-n-c harmonic 61.850 120.770 # SOURCE3 5 2.6390
angle_coeff @angle:br-n-ca harmonic 62.070 118.190 # SOURCE3 1
angle_coeff @angle:br-n-cc harmonic 62.340 118.190 # SOURCE3 1 same_as_br-n-cd
angle_coeff @angle:br-n-cd harmonic 62.340 118.190 # SOURCE3 1 0.0000
angle_coeff @angle:c1-n-c1 harmonic 73.520 102.690 # SOURCE3 1
angle_coeff @angle:c1-n-ca harmonic 65.900 118.880 # SOURCE3 1
angle_coeff @angle:c1-n-cc harmonic 67.020 118.880 # SOURCE3 1 same_as_c1-n-cd
angle_coeff @angle:c1-n-cd harmonic 67.020 118.880 # SOURCE3 1 0.0000
angle_coeff @angle:c2-n-c2 harmonic 65.180 116.750 # SOURCE3 1 0.0000
angle_coeff @angle:c2-n-c3 harmonic 63.060 119.980 # SOURCE4 23 2.3373
angle_coeff @angle:c2-n-ca harmonic 64.880 116.540 # SOURCE3 1
angle_coeff @angle:c2-n-cc harmonic 65.850 116.540 # SOURCE3 1 same_as_c2-n-cd
angle_coeff @angle:c2-n-cd harmonic 65.850 116.540 # SOURCE3 1 0.0000
angle_coeff @angle:c2-n-hn harmonic 47.330 118.360 # SOURCE4 40 1.8005
angle_coeff @angle:c3-n-c3 harmonic 63.130 115.560 # SOURCE4 392 2.0191
angle_coeff @angle:c3-n-ca harmonic 62.760 119.960 # SOURCE4 165 2.0808
angle_coeff @angle:c3-n-cc harmonic 63.380 120.810 # SOURCE4 172 1.6565
angle_coeff @angle:c3-n-cd harmonic 63.240 121.340 # SOURCE4 95 1.0297
angle_coeff @angle:c3-n-cy harmonic 62.510 117.110 # SOURCE4 49 1.0344
angle_coeff @angle:c3-n-hn harmonic 46.040 116.780 # SOURCE3 39 2.1985
angle_coeff @angle:c3-n-n2 harmonic 64.890 121.680 # SOURCE4 52 1.3175
angle_coeff @angle:c3-n-n harmonic 66.400 114.820 # SOURCE4 9 0.7008
angle_coeff @angle:c3-n-nc harmonic 66.990 115.190 # SOURCE4 41 0.8150
angle_coeff @angle:c3-n-nd harmonic 66.870 115.310 # SOURCE4 7 0.9993
angle_coeff @angle:c3-n-oh harmonic 66.880 113.050 # SOURCE4 31 0.8144
angle_coeff @angle:c3-n-os harmonic 66.990 112.650 # SOURCE4 16 1.5399
angle_coeff @angle:c3-n-sy harmonic 76.610 121.270 # SOURCE4 5 1.1298
angle_coeff @angle:ca-n-ca harmonic 64.310 117.390 # SOURCE4 39 1.6465
angle_coeff @angle:ca-n-cc harmonic 64.270 121.000 # SOURCE4 16 1.8986
angle_coeff @angle:ca-n-cd harmonic 68.060 107.900 # SOURCE4 18 0.3512
angle_coeff @angle:ca-n-cl harmonic 61.550 117.720 # SOURCE3 1
angle_coeff @angle:ca-n-f harmonic 64.620 114.920 # SOURCE3 1
angle_coeff @angle:ca-n-hn harmonic 47.360 115.940 # SOURCE4 537 1.8890
angle_coeff @angle:ca-n-i harmonic 56.580 119.300 # SOURCE3 1
angle_coeff @angle:ca-n-n2 harmonic 65.720 122.170 # SOURCE4 5 0.2545
angle_coeff @angle:ca-n-n4 harmonic 64.150 122.980 # SOURCE3 1
angle_coeff @angle:ca-n-n harmonic 66.300 118.540 # SOURCE4 21 0.3399
angle_coeff @angle:ca-n-na harmonic 66.330 119.310 # SOURCE4 16 0.3168
angle_coeff @angle:ca-n-nc harmonic 68.180 114.630 # SOURCE4 5 0.3030
angle_coeff @angle:ca-n-nd harmonic 68.570 113.030 # SOURCE3 1 same_as_ca-n-nc
angle_coeff @angle:ca-n-nh harmonic 66.600 116.450 # SOURCE3 1
angle_coeff @angle:ca-n-p2 harmonic 62.890 112.320 # SOURCE3 1
angle_coeff @angle:ca-n-p3 harmonic 58.640 125.110 # SOURCE3 1
angle_coeff @angle:ca-n-s4 harmonic 75.900 118.400 # SOURCE3 1
angle_coeff @angle:ca-n-s6 harmonic 78.480 117.320 # SOURCE3 1
angle_coeff @angle:ca-n-ss harmonic 78.660 116.600 # SOURCE3 1
angle_coeff @angle:c-n-c1 harmonic 68.470 117.040 # SOURCE3 1 0.0000
angle_coeff @angle:c-n-c2 harmonic 65.090 122.150 # SOURCE3 9 5.1016
angle_coeff @angle:c-n-c3 harmonic 63.920 121.350 # SOURCE3 54 2.3808
angle_coeff @angle:c3-nc-cd harmonic 67.600 109.510 # SOURCE3 9 5.4142
angle_coeff @angle:c-n-c harmonic 65.330 127.140 # SOURCE4 514 2.0111
angle_coeff @angle:c-n-ca harmonic 64.290 123.710 # SOURCE3 10 3.8159
angle_coeff @angle:ca-nc-ca harmonic 70.730 109.950 # SOURCE3 1
angle_coeff @angle:ca-nc-cd harmonic 72.670 104.240 # SOURCE4 187 1.2216
angle_coeff @angle:ca-nc-n harmonic 73.700 104.690 # SOURCE3 1
angle_coeff @angle:ca-nc-na harmonic 74.610 102.630 # SOURCE4 13 0.2570
angle_coeff @angle:ca-nc-os harmonic 73.070 104.500 # SOURCE4 9 0.1740
angle_coeff @angle:ca-nc-ss harmonic 85.860 116.290 # SOURCE3 1
angle_coeff @angle:c-n-cc harmonic 65.240 124.190 # SOURCE3 57 2.2262
angle_coeff @angle:c-nc-ca harmonic 66.430 120.660 # SOURCE3 1
angle_coeff @angle:cc-n-cc harmonic 68.800 108.920 # SOURCE3 11 0.3167
angle_coeff @angle:cc-nc-cc harmonic 68.600 110.190 # SOURCE3 1 0.0000
angle_coeff @angle:cc-nc-cd harmonic 70.480 107.470 # SOURCE3 26 5.4053
angle_coeff @angle:c-nc-cd harmonic 66.550 120.320 # SOURCE4 76 0.9196
angle_coeff @angle:cc-n-cl harmonic 62.010 117.720 # SOURCE3 1 same_as_cd-n-cl
angle_coeff @angle:cc-nc-na harmonic 73.380 102.970 # SOURCE3 1 0.0000
angle_coeff @angle:cc-nc-nd harmonic 72.540 107.940 # SOURCE3 6 1.4052
angle_coeff @angle:c-n-cd harmonic 65.240 124.190 # SOURCE3 57 2.2262
angle_coeff @angle:cd-nc-cd harmonic 68.020 119.060 # SOURCE4 7 0.1559
angle_coeff @angle:cd-nc-n harmonic 69.430 118.060 # SOURCE4 60 1.8266
angle_coeff @angle:cd-nc-na harmonic 74.240 103.730 # SOURCE3 122 2.3292
angle_coeff @angle:cd-nc-nc harmonic 72.470 106.430 # SOURCE4 9 0.7064
angle_coeff @angle:cd-nc-os harmonic 73.170 104.300 # SOURCE4 58 1.0231
angle_coeff @angle:cd-nc-ss harmonic 88.980 108.340 # SOURCE4 33 1.3882
angle_coeff @angle:c-n-ce harmonic 62.210 131.830 # SOURCE4 146 1.3048
angle_coeff @angle:cc-n-f harmonic 65.610 114.920 # SOURCE3 1 same_as_cd-n-f
angle_coeff @angle:cc-n-hn harmonic 48.080 118.710 # SOURCE4 170 2.2963
angle_coeff @angle:cc-n-i harmonic 56.610 119.300 # SOURCE3 1 same_as_cd-n-i
angle_coeff @angle:c-n-cl harmonic 62.720 116.350 # SOURCE4 11 0.6829
angle_coeff @angle:cc-n-n2 harmonic 70.090 110.870 # SOURCE3 1 same_as_cd-n-n2
angle_coeff @angle:cc-n-n harmonic 66.530 121.370 # SOURCE3 1 same_as_cd-n-n
angle_coeff @angle:cc-n-na harmonic 67.870 117.570 # SOURCE3 1 same_as_cd-n-na
angle_coeff @angle:cc-n-nc harmonic 70.120 111.950 # SOURCE4 13 0.6972
angle_coeff @angle:cc-n-nh harmonic 67.300 117.520 # SOURCE3 1 same_as_cd-n-nh
angle_coeff @angle:cc-n-no harmonic 66.400 115.920 # SOURCE3 1 same_as_cd-n-no
angle_coeff @angle:cc-n-o harmonic 70.070 120.540 # SOURCE3 1 same_as_cd-n-o
angle_coeff @angle:cc-n-oh harmonic 67.320 118.150 # SOURCE3 1 same_as_cd-n-oh
angle_coeff @angle:cc-n-os harmonic 68.060 115.560 # SOURCE3 1 same_as_cd-n-os
angle_coeff @angle:cc-n-p2 harmonic 63.340 112.320 # SOURCE3 1 same_as_cd-n-p2
angle_coeff @angle:cc-n-p3 harmonic 59.020 125.110 # SOURCE3 1 same_as_cd-n-p3
angle_coeff @angle:cc-n-p5 harmonic 61.710 121.000 # SOURCE3 1 same_as_cd-n-p5
angle_coeff @angle:cc-n-s4 harmonic 76.360 118.400 # SOURCE3 1 same_as_cd-n-s4
angle_coeff @angle:cc-n-s6 harmonic 79.070 117.320 # SOURCE3 1 same_as_cd-n-s6
angle_coeff @angle:cc-n-s harmonic 76.920 118.290 # SOURCE3 1 same_as_cd-n-s
angle_coeff @angle:cc-n-sh harmonic 78.020 119.130 # SOURCE3 1 same_as_cd-n-sh
angle_coeff @angle:cc-n-ss harmonic 79.250 116.600 # SOURCE3 2 same_as_cd-n-ss
angle_coeff @angle:c-n-cx harmonic 64.220 122.070 # SOURCE4 11 1.9478
angle_coeff @angle:c-n-cy harmonic 72.260 94.230 # SOURCE4 270 1.3777
angle_coeff @angle:cd-n-cd harmonic 68.800 108.920 # SOURCE3 11 same_as_cc-n-cc
angle_coeff @angle:cd-n-cl harmonic 62.010 117.720 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-f harmonic 65.610 114.920 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-hn harmonic 47.860 119.820 # SOURCE4 106 1.1020
angle_coeff @angle:cd-n-i harmonic 56.610 119.300 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-n2 harmonic 70.090 110.870 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-n harmonic 66.530 121.370 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-na harmonic 67.870 117.570 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-nd harmonic 69.680 113.030 # SOURCE3 1 same_as_cc-n-nc
angle_coeff @angle:cd-n-nh harmonic 67.300 117.520 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-no harmonic 66.400 115.920 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-o harmonic 70.070 120.540 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-oh harmonic 67.320 118.150 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-os harmonic 68.060 115.560 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-p2 harmonic 63.340 112.320 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-p3 harmonic 59.020 125.110 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-p5 harmonic 61.710 121.000 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-s4 harmonic 76.360 118.400 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-s6 harmonic 79.070 117.320 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-s harmonic 76.920 118.290 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-sh harmonic 78.020 119.130 # SOURCE3 1 0.0000
angle_coeff @angle:cd-n-ss harmonic 79.250 116.600 # SOURCE3 2 1.8318
angle_coeff @angle:ce-n-cy harmonic 64.680 111.970 # SOURCE4 142 2.1245
angle_coeff @angle:c-n-f harmonic 68.300 108.630 # SOURCE3 3 4.6785
angle_coeff @angle:cf-n-cy harmonic 64.910 110.790 # SOURCE4 10 1.1677
angle_coeff @angle:c-n-hn harmonic 49.210 118.460 # SOURCE3 157 2.4094
angle_coeff @angle:c-n-i harmonic 56.340 120.380 # SOURCE3 5 2.1600
angle_coeff @angle:cl-n-cl harmonic 63.240 111.690 # SOURCE3 1 0.0000
angle_coeff @angle:c-n-n2 harmonic 68.060 120.590 # SOURCE3 9 3.2410
angle_coeff @angle:c-n-n3 harmonic 67.130 120.430 # SOURCE3 5 0.9481
angle_coeff @angle:c-n-n4 harmonic 68.850 112.320 # SOURCE3 5 1.2622
angle_coeff @angle:c-n-n harmonic 68.180 118.420 # SOURCE3 10 2.8922
angle_coeff @angle:c-n-na harmonic 68.250 119.200 # SOURCE3 11 2.3032
angle_coeff @angle:na-nc-nd harmonic 75.970 105.470 # SOURCE3 6 0.6349
angle_coeff @angle:c-n-nc harmonic 67.170 125.230 # SOURCE4 72 2.1204
angle_coeff @angle:nc-nc-nd harmonic 73.150 111.150 # SOURCE3 3 same_as_nc-nd-nd
angle_coeff @angle:c-n-nd harmonic 67.140 124.930 # SOURCE4 12 2.2148
angle_coeff @angle:nd-nc-os harmonic 74.420 107.220 # SOURCE3 3 0.4707
angle_coeff @angle:c-n-nh harmonic 68.020 117.810 # SOURCE4 21 1.5935
angle_coeff @angle:c-n-no harmonic 66.470 118.160 # SOURCE3 4 5.4870
angle_coeff @angle:c-n-o harmonic 71.640 118.900 # SOURCE3 9 5.4085
angle_coeff @angle:c-n-oh harmonic 69.530 113.390 # SOURCE3 6 1.3345
angle_coeff @angle:c-n-os harmonic 69.600 113.140 # SOURCE3 7 3.0839
angle_coeff @angle:c-n-p2 harmonic 60.460 124.560 # SOURCE3 8 3.6907
angle_coeff @angle:c-n-p3 harmonic 59.910 122.540 # SOURCE3 9 4.4802
angle_coeff @angle:c-n-p4 harmonic 60.710 123.440 # SOURCE3 1 0.0000
angle_coeff @angle:c-n-p5 harmonic 60.230 128.500 # SOURCE4 6 0.5353
angle_coeff @angle:c-n-pc harmonic 60.840 122.230 # SOURCE3 3 2.8787
angle_coeff @angle:c-n-pd harmonic 60.840 122.230 # SOURCE3 3 same_as_c-n-pc
angle_coeff @angle:c-n-s4 harmonic 76.060 120.410 # SOURCE3 4 3.1760
angle_coeff @angle:c-n-s6 harmonic 77.030 125.010 # SOURCE4 13 1.6314
angle_coeff @angle:c-n-s harmonic 74.720 126.550 # SOURCE3 3 4.3365
angle_coeff @angle:c-n-sh harmonic 78.300 119.540 # SOURCE3 4 1.7681
angle_coeff @angle:c-n-ss harmonic 78.430 120.370 # SOURCE3 7 1.4450
angle_coeff @angle:c-n-sy harmonic 77.090 124.810 # SOURCE4 51 1.0517
angle_coeff @angle:cx-n-hn harmonic 46.260 118.580 # SOURCE4 5 0.3288
angle_coeff @angle:cx-n-os harmonic 97.400 54.040 # SOURCE3 1 0.0000
angle_coeff @angle:cy-n-hn harmonic 45.340 119.000 # SOURCE4 65 1.3840
angle_coeff @angle:c3-nd-cc harmonic 67.600 109.510 # SOURCE3 9 same_as_c3-nc-cd
angle_coeff @angle:ca-nd-ca harmonic 70.730 109.950 # SOURCE3 1 same_as_ca-nc-ca
angle_coeff @angle:ca-nd-cc harmonic 72.240 105.470 # SOURCE4 250 2.4919
angle_coeff @angle:ca-nd-n harmonic 73.580 104.690 # SOURCE3 1 same_as_ca-nc-n
angle_coeff @angle:ca-nd-na harmonic 74.060 104.160 # SOURCE3 1 same_as_ca-nc-na
angle_coeff @angle:ca-nd-nc harmonic 73.550 108.410 # SOURCE4 9 0.1575
angle_coeff @angle:ca-nd-os harmonic 73.130 104.340 # SOURCE3 1 same_as_ca-nc-os
angle_coeff @angle:ca-nd-ss harmonic 85.860 116.290 # SOURCE3 1 same_as_ca-nc-ss
angle_coeff @angle:c-nd-ca harmonic 65.700 120.660 # SOURCE3 1 same_as_c-nc-ca
angle_coeff @angle:c-nd-cc harmonic 65.710 120.680 # SOURCE4 62 1.4340
angle_coeff @angle:cc-nd-cc harmonic 68.900 116.040 # SOURCE4 10 0.2861
angle_coeff @angle:cc-nd-cd harmonic 71.090 105.630 # SOURCE4 1214 2.1301
angle_coeff @angle:cc-nd-n harmonic 73.800 104.150 # SOURCE3 4 same_as_cd-nc-n
angle_coeff @angle:cc-nd-na harmonic 74.240 103.730 # SOURCE3 122 2.3292
angle_coeff @angle:cc-nd-nd harmonic 71.970 107.920 # SOURCE4 346 1.6831
angle_coeff @angle:cc-nd-os harmonic 72.920 105.010 # SOURCE4 58 0.4186
angle_coeff @angle:cc-nd-ss harmonic 89.270 107.640 # SOURCE4 12 0.4724
angle_coeff @angle:cd-nd-cd harmonic 70.890 103.170 # SOURCE4 5 0.0317
angle_coeff @angle:cd-nd-na harmonic 73.380 102.970 # SOURCE3 1 same_as_cc-nc-na
angle_coeff @angle:cd-nd-nc harmonic 72.540 107.940 # SOURCE3 6 1.4052
angle_coeff @angle:na-nd-nc harmonic 75.970 105.470 # SOURCE3 6 0.6349
angle_coeff @angle:nc-nd-nd harmonic 73.100 111.300 # SOURCE4 58 0.2082
angle_coeff @angle:nc-nd-os harmonic 74.420 107.220 # SOURCE3 3 same_as_nd-nc-os
angle_coeff @angle:c1-ne-ca harmonic 60.080 152.480 # SOURCE4 8 1.5840
angle_coeff @angle:c1-ne-cg harmonic 66.000 140.000 # SOURCE2 1 0.0000
angle_coeff @angle:c2-ne-ca harmonic 66.060 120.920 # SOURCE4 53 1.9651
angle_coeff @angle:c2-ne-ce harmonic 67.330 118.170 # SOURCE3 3 1.2374
angle_coeff @angle:c2-ne-cg harmonic 68.360 123.580 # SOURCE4 12 0.8560
angle_coeff @angle:c2-ne-n2 harmonic 74.560 113.310 # SOURCE3 1
angle_coeff @angle:c2-ne-ne harmonic 69.170 110.860 # SOURCE3 7 4.5874
angle_coeff @angle:c2-ne-p2 harmonic 63.870 134.030 # SOURCE3 1
angle_coeff @angle:c2-ne-pe harmonic 62.610 120.520 # SOURCE3 8 8.1381
angle_coeff @angle:c2-ne-px harmonic 63.660 117.750 # SOURCE3 5 0.8581
angle_coeff @angle:c2-ne-py harmonic 66.630 117.040 # SOURCE3 3 1.4398
angle_coeff @angle:c2-ne-sx harmonic 77.140 111.980 # SOURCE3 3 0.4090
angle_coeff @angle:c2-ne-sy harmonic 77.530 120.970 # SOURCE4 6 0.2394
angle_coeff @angle:ca-ne-cf harmonic 65.630 121.760 # SOURCE4 9 1.9872
angle_coeff @angle:ca-ne-n2 harmonic 69.660 114.270 # SOURCE4 9 0.4600
angle_coeff @angle:ca-ne-nf harmonic 69.710 115.050 # SOURCE4 22 0.7409
angle_coeff @angle:ca-ne-o harmonic 71.100 113.960 # SOURCE3 3 1.1253
angle_coeff @angle:ca-ne-p2 harmonic 65.650 118.090 # SOURCE3 1 0.0000
angle_coeff @angle:ca-ne-s harmonic 83.220 120.110 # SOURCE3 1 0.0000
angle_coeff @angle:c-ne-c2 harmonic 67.860 118.530 # SOURCE3 3 3.2058
angle_coeff @angle:ce-ne-n2 harmonic 71.160 111.190 # SOURCE3 1 0.0000
angle_coeff @angle:ce-ne-o harmonic 72.260 112.160 # SOURCE3 1 0.0000
angle_coeff @angle:ce-ne-p2 harmonic 66.250 117.020 # SOURCE3 1 0.0000
angle_coeff @angle:ce-ne-s harmonic 84.980 116.280 # SOURCE3 1 0.0000
angle_coeff @angle:cg-ne-n1 harmonic 71.710 120.200 # SOURCE2 1 0.0000
angle_coeff @angle:cg-ne-n2 harmonic 73.160 113.390 # SOURCE3 1 0.0000
angle_coeff @angle:cg-ne-o harmonic 74.430 114.700 # SOURCE2 1 0.0000
angle_coeff @angle:cg-ne-p2 harmonic 66.960 119.570 # SOURCE3 1 0.0000
angle_coeff @angle:cg-ne-s harmonic 86.420 117.700 # SOURCE3 1 0.0000
angle_coeff @angle:c-ne-sy harmonic 78.040 116.050 # SOURCE4 6 1.2661
angle_coeff @angle:n2-ne-n2 harmonic 78.590 107.220 # SOURCE3 1
angle_coeff @angle:n2-ne-ne harmonic 70.940 110.720 # SOURCE3 9 6.1488
angle_coeff @angle:n2-ne-o harmonic 78.090 114.100 # SOURCE3 1 0.0000
angle_coeff @angle:n2-ne-p2 harmonic 72.370 109.660 # SOURCE3 1
angle_coeff @angle:n2-ne-pe harmonic 66.510 112.150 # SOURCE3 7 6.5273
angle_coeff @angle:n2-ne-px harmonic 65.740 115.970 # SOURCE3 3 1.9854
angle_coeff @angle:n2-ne-py harmonic 69.010 114.600 # SOURCE3 3 2.9261
angle_coeff @angle:n2-ne-s harmonic 90.200 115.900 # SOURCE3 1 0.0000
angle_coeff @angle:n2-ne-sx harmonic 80.750 107.290 # SOURCE3 1 0.0000
angle_coeff @angle:n2-ne-sy harmonic 82.850 111.210 # SOURCE3 1 0.0000
angle_coeff @angle:ne-ne-o harmonic 72.280 110.450 # SOURCE3 10 1.8535
angle_coeff @angle:ne-ne-p2 harmonic 67.420 114.390 # SOURCE3 6 4.0528
angle_coeff @angle:ne-ne-s harmonic 85.550 115.950 # SOURCE3 6 3.4604
angle_coeff @angle:o-ne-o harmonic 76.910 124.090 # SOURCE3 2 8.7534
angle_coeff @angle:o-ne-pe harmonic 61.880 132.320 # SOURCE3 11 23.9559
angle_coeff @angle:o-ne-px harmonic 68.040 110.620 # SOURCE3 1 0.0000
angle_coeff @angle:o-ne-py harmonic 71.120 110.790 # SOURCE3 4 1.6818
angle_coeff @angle:o-ne-s harmonic 91.120 117.190 # SOURCE3 2 0.0225
angle_coeff @angle:o-ne-sx harmonic 80.740 108.920 # SOURCE3 1 0.0000
angle_coeff @angle:o-ne-sy harmonic 83.600 111.340 # SOURCE3 1 0.0000
angle_coeff @angle:p2-ne-pe harmonic 65.270 116.810 # SOURCE3 1 0.0000
angle_coeff @angle:p2-ne-px harmonic 62.490 128.350 # SOURCE3 1 0.0000
angle_coeff @angle:p2-ne-py harmonic 65.650 123.470 # SOURCE3 1 0.0000
angle_coeff @angle:p2-ne-sx harmonic 80.480 112.120 # SOURCE3 1 0.0000
angle_coeff @angle:p2-ne-sy harmonic 81.800 115.730 # SOURCE3 1 0.0000
angle_coeff @angle:pe-ne-s harmonic 83.520 115.730 # SOURCE3 1 0.0000
angle_coeff @angle:px-ne-s harmonic 78.540 131.840 # SOURCE3 1 0.0000
angle_coeff @angle:py-ne-s harmonic 86.300 116.180 # SOURCE3 4 3.7135
angle_coeff @angle:s-ne-s harmonic 109.960 120.870 # SOURCE3 1 0.0000
angle_coeff @angle:s-ne-sx harmonic 101.960 112.960 # SOURCE3 1 0.0000
angle_coeff @angle:s-ne-sy harmonic 102.420 119.630 # SOURCE3 1 0.0000
angle_coeff @angle:c1-nf-ca harmonic 63.220 137.740 # SOURCE3 1 same_as_c1-ne-ca
angle_coeff @angle:c1-nf-ch harmonic 66.000 140.000 # SOURCE2 1 same_as_c1-ne-cg
angle_coeff @angle:c2-nf-ca harmonic 66.690 118.670 # SOURCE3 2 same_as_c2-ne-ca
angle_coeff @angle:c2-nf-cf harmonic 67.330 118.170 # SOURCE3 3 same_as_c2-ne-ce
angle_coeff @angle:c2-nf-n2 harmonic 74.560 113.310 # SOURCE3 1 same_as_c2-ne-n2
angle_coeff @angle:c2-nf-nf harmonic 69.170 110.860 # SOURCE3 7 same_as_c2-ne-ne
angle_coeff @angle:c2-nf-p2 harmonic 63.870 134.030 # SOURCE3 1 same_as_c2-ne-p2
angle_coeff @angle:c2-nf-pf harmonic 62.610 120.520 # SOURCE3 8 same_as_c2-ne-pe
angle_coeff @angle:c2-nf-px harmonic 63.660 117.750 # SOURCE3 5 same_as_c2-ne-px
angle_coeff @angle:c2-nf-py harmonic 66.630 117.040 # SOURCE3 3 same_as_c2-ne-py
angle_coeff @angle:c2-nf-sx harmonic 77.140 111.980 # SOURCE3 3 same_as_c2-ne-sx
angle_coeff @angle:c2-nf-sy harmonic 79.580 114.810 # SOURCE3 3 same_as_c2-ne-sy
angle_coeff @angle:ca-nf-ce harmonic 65.450 122.300 # SOURCE4 6 1.8938
angle_coeff @angle:ca-nf-n2 harmonic 70.020 113.110 # SOURCE3 2 same_as_ca-ne-n2
angle_coeff @angle:ca-nf-ne harmonic 69.660 115.190 # SOURCE4 22 0.6536
angle_coeff @angle:ca-nf-o harmonic 71.100 113.960 # SOURCE3 3 same_as_ca-ne-o
angle_coeff @angle:ca-nf-p2 harmonic 65.650 118.090 # SOURCE3 1 same_as_ca-ne-p2
angle_coeff @angle:ca-nf-s harmonic 83.220 120.110 # SOURCE3 1 same_as_ca-ne-s
angle_coeff @angle:c-nf-c2 harmonic 67.770 118.530 # SOURCE3 3 same_as_c-ne-c2
angle_coeff @angle:cf-nf-n2 harmonic 71.160 111.190 # SOURCE3 1 same_as_ce-ne-n2
angle_coeff @angle:cf-nf-o harmonic 72.260 112.160 # SOURCE3 1 same_as_ce-ne-o
angle_coeff @angle:cf-nf-p2 harmonic 66.250 117.020 # SOURCE3 1 same_as_ce-ne-p2
angle_coeff @angle:cf-nf-s harmonic 84.980 116.280 # SOURCE3 1 same_as_ce-ne-s
angle_coeff @angle:ch-nf-n1 harmonic 71.710 120.200 # SOURCE2 1 same_as_cg-ne-n1
angle_coeff @angle:ch-nf-n2 harmonic 73.160 113.390 # SOURCE3 1 same_as_cg-ne-n2
angle_coeff @angle:ch-nf-o harmonic 74.430 114.700 # SOURCE2 1 same_as_cg-ne-o
angle_coeff @angle:ch-nf-p2 harmonic 66.960 119.570 # SOURCE3 1 same_as_cg-ne-p2
angle_coeff @angle:ch-nf-s harmonic 86.420 117.700 # SOURCE3 1 same_as_cg-ne-s
angle_coeff @angle:f-n-f harmonic 67.900 102.980 # SOURCE3 1 0.0000
angle_coeff @angle:n2-nf-n2 harmonic 78.590 107.220 # SOURCE3 1 same_as_n2-ne-n2
angle_coeff @angle:n2-nf-nf harmonic 70.940 110.720 # SOURCE3 9 same_as_n2-ne-ne
angle_coeff @angle:n2-nf-o harmonic 78.090 114.100 # SOURCE3 1 same_as_n2-ne-o
angle_coeff @angle:n2-nf-p2 harmonic 72.370 109.660 # SOURCE3 1 same_as_n2-ne-p2
angle_coeff @angle:n2-nf-pf harmonic 66.510 112.150 # SOURCE3 7 same_as_n2-ne-pe
angle_coeff @angle:n2-nf-px harmonic 65.740 115.970 # SOURCE3 3 same_as_n2-ne-px
angle_coeff @angle:n2-nf-py harmonic 69.010 114.600 # SOURCE3 3 same_as_n2-ne-py
angle_coeff @angle:n2-nf-s harmonic 90.200 115.900 # SOURCE3 1 same_as_n2-ne-s
angle_coeff @angle:n2-nf-sx harmonic 80.750 107.290 # SOURCE3 1 same_as_n2-ne-sx
angle_coeff @angle:n2-nf-sy harmonic 82.850 111.210 # SOURCE3 1 same_as_n2-ne-sy
angle_coeff @angle:nf-nf-o harmonic 72.280 110.450 # SOURCE3 10 same_as_ne-ne-o
angle_coeff @angle:nf-nf-p2 harmonic 67.420 114.390 # SOURCE3 6 same_as_ne-ne-p2
angle_coeff @angle:nf-nf-s harmonic 85.550 115.950 # SOURCE3 6 same_as_ne-ne-s
angle_coeff @angle:o-nf-o harmonic 76.910 124.090 # SOURCE3 2 same_as_o-ne-o
angle_coeff @angle:o-nf-pf harmonic 61.880 132.320 # SOURCE3 11 same_as_o-ne-pe
angle_coeff @angle:o-nf-px harmonic 68.040 110.620 # SOURCE3 1 same_as_o-ne-px
angle_coeff @angle:o-nf-py harmonic 71.120 110.790 # SOURCE3 4 same_as_o-ne-py
angle_coeff @angle:o-nf-s harmonic 91.120 117.190 # SOURCE3 2 same_as_o-ne-s
angle_coeff @angle:o-nf-sx harmonic 80.740 108.920 # SOURCE3 1 same_as_o-ne-sx
angle_coeff @angle:o-nf-sy harmonic 83.600 111.340 # SOURCE3 1 same_as_o-ne-sy
angle_coeff @angle:p2-nf-pf harmonic 65.270 116.810 # SOURCE3 1 same_as_p2-ne-pe
angle_coeff @angle:p2-nf-px harmonic 62.490 128.350 # SOURCE3 1 same_as_p2-ne-px
angle_coeff @angle:p2-nf-py harmonic 65.650 123.470 # SOURCE3 1 same_as_p2-ne-py
angle_coeff @angle:p2-nf-sx harmonic 80.480 112.120 # SOURCE3 1 same_as_p2-ne-sx
angle_coeff @angle:p2-nf-sy harmonic 81.800 115.730 # SOURCE3 1 same_as_p2-ne-sy
angle_coeff @angle:pf-nf-s harmonic 83.520 115.730 # SOURCE3 1 same_as_pe-ne-s
angle_coeff @angle:px-nf-s harmonic 78.540 131.840 # SOURCE3 1 same_as_px-ne-s
angle_coeff @angle:py-nf-s harmonic 86.300 116.180 # SOURCE3 4 same_as_py-ne-s
angle_coeff @angle:s-nf-s harmonic 109.960 120.870 # SOURCE3 1 same_as_s-ne-s
angle_coeff @angle:s-nf-sx harmonic 101.960 112.960 # SOURCE3 1 same_as_s-ne-sx
angle_coeff @angle:s-nf-sy harmonic 102.420 119.630 # SOURCE3 1 same_as_s-ne-sy
angle_coeff @angle:br-nh-br harmonic 67.090 106.270 # SOURCE3 1
angle_coeff @angle:br-nh-ca harmonic 62.040 111.880 # SOURCE3 1 0.0000
angle_coeff @angle:br-nh-hn harmonic 42.110 101.560 # SOURCE3 1 0.0000
angle_coeff @angle:c1-nh-c1 harmonic 68.330 116.980 # SOURCE3 1 0.0000
angle_coeff @angle:c1-nh-c2 harmonic 66.360 122.710 # SOURCE4 5 1.0077
angle_coeff @angle:c1-nh-ca harmonic 66.220 122.360 # SOURCE3 3 1.2016
angle_coeff @angle:c1-nh-hn harmonic 49.550 117.300 # SOURCE4 8 0.7120
angle_coeff @angle:c2-nh-c2 harmonic 65.540 124.500 # SOURCE4 43 1.7515
angle_coeff @angle:c2-nh-c3 harmonic 63.170 123.710 # SOURCE3 8 3.5348
angle_coeff @angle:c2-nh-ca harmonic 64.590 127.340 # SOURCE4 97 2.4321
angle_coeff @angle:c2-nh-cc harmonic 64.990 125.770 # SOURCE4 6 1.4868
angle_coeff @angle:c2-nh-cd harmonic 64.840 126.330 # SOURCE4 5 0.9167
angle_coeff @angle:c2-nh-cx harmonic 63.080 124.440 # SOURCE4 10 1.6817
angle_coeff @angle:c2-nh-hn harmonic 49.620 114.890 # SOURCE4 1000 1.4571
angle_coeff @angle:c2-nh-n2 harmonic 68.360 120.000 # SOURCE4 33 1.1823
angle_coeff @angle:c2-nh-n3 harmonic 67.570 116.980 # SOURCE4 14 1.4183
angle_coeff @angle:c2-nh-no harmonic 66.090 125.630 # SOURCE4 7 0.7554
angle_coeff @angle:c2-nh-oh harmonic 69.450 112.510 # SOURCE4 12 1.1687
angle_coeff @angle:c2-nh-os harmonic 69.270 112.930 # SOURCE4 6 0.3945
angle_coeff @angle:c2-nh-sy harmonic 78.160 121.130 # SOURCE4 10 0.5133
angle_coeff @angle:c3-nh-c3 harmonic 63.530 114.440 # SOURCE4 523 2.1428
angle_coeff @angle:c3-nh-ca harmonic 64.560 117.770 # SOURCE3 8 1.7521
angle_coeff @angle:c3-nh-cc harmonic 63.650 121.180 # SOURCE3 1 0.0000
angle_coeff @angle:c3-nh-cd harmonic 64.170 119.220 # SOURCE4 162 2.4515
angle_coeff @angle:c3-nh-cf harmonic 63.620 119.920 # SOURCE4 20 1.8571
angle_coeff @angle:c3-nh-cz harmonic 63.010 125.510 # SOURCE4 12 0.5177
angle_coeff @angle:c3-nh-hn harmonic 46.460 114.950 # SOURCE3 19 2.4787
angle_coeff @angle:c3-nh-n2 harmonic 67.890 112.350 # SOURCE3 9 4.0058
angle_coeff @angle:c3-nh-n harmonic 67.100 111.710 # SOURCE4 6 2.4251
angle_coeff @angle:c3-nh-na harmonic 66.920 112.430 # SOURCE4 8 1.4219
angle_coeff @angle:c3-nh-p2 harmonic 60.930 123.350 # SOURCE3 1 0.0000
angle_coeff @angle:c3-nh-sy harmonic 78.350 116.120 # SOURCE4 13 1.2830
angle_coeff @angle:ca-nh-ca harmonic 64.340 127.460 # SOURCE3 2 0.0002
angle_coeff @angle:ca-nh-cc harmonic 63.730 129.910 # SOURCE4 29 1.3269
angle_coeff @angle:ca-nh-cd harmonic 63.880 129.310 # SOURCE4 9 1.5610
angle_coeff @angle:ca-nh-cl harmonic 62.010 113.150 # SOURCE3 1 0.0000
angle_coeff @angle:ca-nh-cx harmonic 63.110 123.630 # SOURCE4 36 0.5899
angle_coeff @angle:ca-nh-f harmonic 67.900 106.090 # SOURCE3 3 1.0660
angle_coeff @angle:ca-nh-hn harmonic 49.080 116.130 # SOURCE4 1780 1.2853
angle_coeff @angle:ca-nh-i harmonic 55.550 117.830 # SOURCE3 1 0.0000
angle_coeff @angle:ca-nh-n1 harmonic 69.370 117.130 # HF/6-31G* 1
angle_coeff @angle:ca-nh-n2 harmonic 67.820 121.110 # SOURCE4 19 0.9700
angle_coeff @angle:ca-nh-n3 harmonic 68.180 114.210 # SOURCE3 6 2.2412
angle_coeff @angle:ca-nh-n4 harmonic 68.560 108.940 # SOURCE3 5 0.6562
angle_coeff @angle:ca-nh-n harmonic 68.070 116.150 # SOURCE4 12 0.8135
angle_coeff @angle:ca-nh-na harmonic 68.580 114.540 # SOURCE3 8 0.7807
angle_coeff @angle:ca-nh-nh harmonic 68.490 114.870 # SOURCE3 6 2.1432
angle_coeff @angle:ca-nh-no harmonic 69.190 113.920 # SOURCE3 4 2.9561
angle_coeff @angle:ca-nh-o harmonic 69.640 121.920 # SOURCE3 2 3.9630
angle_coeff @angle:ca-nh-oh harmonic 69.150 112.800 # SOURCE3 1 0.0000
angle_coeff @angle:ca-nh-os harmonic 69.930 110.170 # SOURCE3 3 0.6448
angle_coeff @angle:ca-nh-p2 harmonic 61.620 125.270 # SOURCE3 8 5.1798
angle_coeff @angle:ca-nh-p3 harmonic 60.110 125.700 # SOURCE3 3 5.7796
angle_coeff @angle:ca-nh-p4 harmonic 61.180 124.010 # SOURCE3 3 2.5810
angle_coeff @angle:ca-nh-p5 harmonic 61.760 125.610 # SOURCE3 3 0.5287
angle_coeff @angle:ca-nh-s4 harmonic 78.630 115.620 # SOURCE3 3 0.3434
angle_coeff @angle:ca-nh-s6 harmonic 77.920 123.530 # SOURCE4 33 2.0385
angle_coeff @angle:ca-nh-s harmonic 75.150 122.540 # SOURCE3 3 2.7001
angle_coeff @angle:ca-nh-sh harmonic 78.190 121.410 # SOURCE3 1 0.0000
angle_coeff @angle:ca-nh-ss harmonic 78.160 121.500 # SOURCE3 3 2.6255
angle_coeff @angle:ca-nh-sy harmonic 76.750 125.260 # SOURCE4 41 1.7517
angle_coeff @angle:cc-nh-cx harmonic 63.320 122.820 # SOURCE4 42 1.1841
angle_coeff @angle:cc-nh-hn harmonic 48.860 117.160 # SOURCE3 11 2.6137
angle_coeff @angle:cc-nh-n2 harmonic 68.230 119.660 # SOURCE4 5 1.3903
angle_coeff @angle:cc-nh-sy harmonic 77.480 122.910 # SOURCE4 23 1.2029
angle_coeff @angle:cd-nh-cx harmonic 62.500 126.090 # SOURCE4 16 2.3269
angle_coeff @angle:cd-nh-hn harmonic 48.860 117.160 # SOURCE3 11 2.6137
angle_coeff @angle:ce-nh-hn harmonic 48.340 115.620 # SOURCE4 187 1.0421
angle_coeff @angle:ce-nh-o harmonic 66.820 129.430 # SOURCE3 1 0.0000
angle_coeff @angle:ce-nh-sy harmonic 80.450 112.970 # SOURCE4 7 1.0636
angle_coeff @angle:cf-nh-hn harmonic 48.620 115.620 # SOURCE4 16 1.3549
angle_coeff @angle:cf-nh-o harmonic 67.070 129.430 # SOURCE3 1 same_as_ce-nh-o
angle_coeff @angle:cl-nh-cl harmonic 62.930 106.600 # SOURCE3 1
angle_coeff @angle:cl-nh-hn harmonic 43.080 104.140 # SOURCE3 1 0.0000
angle_coeff @angle:cx-nh-cx harmonic 86.530 62.020 # SOURCE4 45 0.6189
angle_coeff @angle:cx-nh-hn harmonic 45.790 118.890 # SOURCE4 8 0.1391
angle_coeff @angle:cz-nh-hn harmonic 48.790 121.240 # SOURCE4 40 0.5682
angle_coeff @angle:f-nh-f harmonic 66.930 101.700 # SOURCE3 1 0.0000
angle_coeff @angle:f-nh-hn harmonic 49.800 101.230 # SOURCE3 1 0.0000
angle_coeff @angle:hn-nh-hn harmonic 40.050 114.850 # SOURCE4 1108 2.0811
angle_coeff @angle:hn-nh-i harmonic 36.550 107.570 # SOURCE3 1 0.0000
angle_coeff @angle:hn-nh-n1 harmonic 52.310 110.570 # HF/6-31G* 1
angle_coeff @angle:hn-nh-n2 harmonic 50.080 118.220 # SOURCE4 75 2.3319
angle_coeff @angle:hn-nh-n3 harmonic 50.050 109.120 # SOURCE3 5 2.3680
angle_coeff @angle:hn-nh-n4 harmonic 49.690 104.400 # SOURCE3 3 0.5056
angle_coeff @angle:hn-nh-n harmonic 50.890 107.960 # SOURCE4 16 1.2025
angle_coeff @angle:hn-nh-na harmonic 50.950 107.910 # SOURCE3 26 1.5528
angle_coeff @angle:hn-nh-nh harmonic 50.320 110.640 # SOURCE4 8 1.3390
angle_coeff @angle:hn-nh-no harmonic 50.990 109.930 # SOURCE4 7 0.2027
angle_coeff @angle:hn-nh-o harmonic 52.990 116.450 # SOURCE3 2 0.6063
angle_coeff @angle:hn-nh-oh harmonic 51.130 106.550 # SOURCE4 8 0.4590
angle_coeff @angle:hn-nh-os harmonic 51.510 104.760 # SOURCE3 3 0.4883
angle_coeff @angle:hn-nh-p2 harmonic 42.970 118.180 # SOURCE3 21 3.6927
angle_coeff @angle:hn-nh-p3 harmonic 41.930 116.190 # SOURCE3 3 3.0539
angle_coeff @angle:hn-nh-p4 harmonic 43.250 112.600 # SOURCE3 3 0.8237
angle_coeff @angle:hn-nh-p5 harmonic 43.730 115.260 # SOURCE3 3 0.9168
angle_coeff @angle:hn-nh-s4 harmonic 54.500 107.480 # SOURCE3 3 1.3960
angle_coeff @angle:hn-nh-s harmonic 51.650 114.370 # SOURCE3 1 0.0000
angle_coeff @angle:hn-nh-s6 harmonic 55.730 109.980 # SOURCE4 29 0.7478
angle_coeff @angle:hn-nh-sh harmonic 54.760 112.250 # SOURCE3 1 0.0000
angle_coeff @angle:hn-nh-ss harmonic 54.360 113.890 # SOURCE3 3 1.4030
angle_coeff @angle:hn-nh-sy harmonic 54.780 111.230 # SOURCE4 62 1.1413
angle_coeff @angle:i-nh-i harmonic 59.800 115.820 # SOURCE3 1
angle_coeff @angle:n1-nh-n1 harmonic 75.130 106.710 # HF/6-31G* 1
angle_coeff @angle:n2-nh-n2 harmonic 70.760 117.500 # SOURCE3 2 1.1907
angle_coeff @angle:n2-nh-n3 harmonic 69.630 115.540 # SOURCE3 1 0.0000
angle_coeff @angle:n2-nh-o harmonic 70.400 126.060 # SOURCE3 1 0.0000
angle_coeff @angle:n3-nh-n3 harmonic 69.520 110.980 # SOURCE3 1 0.0000
angle_coeff @angle:n4-nh-n4 harmonic 68.150 108.360 # SOURCE3 1 0.0000
angle_coeff @angle:na-nh-na harmonic 70.140 112.010 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n-hn harmonic 39.730 117.850 # SOURCE3 15 2.3694
angle_coeff @angle:nh-nh-nh harmonic 70.070 112.230 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n-i harmonic 36.080 117.240 # SOURCE3 2 0.4435
angle_coeff @angle:hn-n-n2 harmonic 49.620 118.330 # SOURCE3 5 2.2377
angle_coeff @angle:hn-n-n3 harmonic 48.690 117.220 # SOURCE4 37 1.3737
angle_coeff @angle:hn-n-n4 harmonic 48.900 112.680 # SOURCE3 3 1.9746
angle_coeff @angle:hn-n-n harmonic 50.140 113.120 # SOURCE3 7 3.2954
angle_coeff @angle:hn-n-na harmonic 50.400 113.550 # SOURCE3 8 1.9324
angle_coeff @angle:hn-n-nc harmonic 50.760 115.240 # SOURCE4 10 0.4966
angle_coeff @angle:hn-n-nh harmonic 49.740 113.130 # SOURCE4 12 1.2125
angle_coeff @angle:hn-n-no harmonic 48.710 110.110 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n-o harmonic 53.830 116.320 # SOURCE3 2 0.0175
angle_coeff @angle:n-nh-o harmonic 72.070 115.630 # SOURCE3 1
angle_coeff @angle:hn-n-oh harmonic 50.330 110.710 # SOURCE4 46 1.1278
angle_coeff @angle:no-nh-no harmonic 72.070 108.550 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n-os harmonic 50.520 109.820 # SOURCE4 12 0.6996
angle_coeff @angle:hn-n-p2 harmonic 41.490 118.050 # SOURCE3 7 3.0564
angle_coeff @angle:hn-n-p3 harmonic 40.240 119.630 # SOURCE3 2 0.0000
angle_coeff @angle:hn-n-p4 harmonic 41.880 115.710 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n-p5 harmonic 43.060 113.200 # SOURCE4 6 1.0341
angle_coeff @angle:hn-n-s4 harmonic 52.120 112.460 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n-s harmonic 52.060 114.920 # SOURCE3 2 0.0260
angle_coeff @angle:hn-n-s6 harmonic 54.500 112.180 # SOURCE4 6 0.6101
angle_coeff @angle:hn-n-sh harmonic 53.400 114.910 # SOURCE3 1 0.0000
angle_coeff @angle:hn-n-ss harmonic 53.620 115.600 # SOURCE3 3 0.6414
angle_coeff @angle:hn-n-sy harmonic 54.450 112.340 # SOURCE4 38 0.6039
angle_coeff @angle:oh-nh-oh harmonic 72.150 106.270 # SOURCE3 1
angle_coeff @angle:o-nh-o harmonic 72.240 128.060 # SOURCE3 1
angle_coeff @angle:os-nh-os harmonic 72.410 105.270 # SOURCE3 1
angle_coeff @angle:p2-nh-p2 harmonic 61.230 127.330 # SOURCE3 2 2.7857
angle_coeff @angle:p3-nh-p3 harmonic 59.950 125.080 # SOURCE3 1
angle_coeff @angle:p5-nh-p5 harmonic 65.370 112.760 # SOURCE3 1
angle_coeff @angle:s4-nh-s4 harmonic 100.210 112.390 # SOURCE3 1
angle_coeff @angle:s6-nh-s6 harmonic 99.870 120.270 # SOURCE3 1
angle_coeff @angle:sh-nh-sh harmonic 99.730 119.000 # SOURCE3 1
angle_coeff @angle:s-nh-s harmonic 95.590 118.730 # SOURCE3 1 0.0000
angle_coeff @angle:ss-nh-ss harmonic 99.620 119.250 # SOURCE3 1
angle_coeff @angle:i-n-i harmonic 60.660 118.200 # SOURCE3 1 0.0000
angle_coeff @angle:n2-n-n2 harmonic 70.160 116.890 # SOURCE3 1 0.0000
angle_coeff @angle:n3-n-n3 harmonic 68.020 117.940 # SOURCE3 1 0.0000
angle_coeff @angle:n4-n-n4 harmonic 68.420 112.690 # SOURCE3 1 0.0000
angle_coeff @angle:na-n-na harmonic 69.610 117.380 # SOURCE3 1 0.0000
angle_coeff @angle:nc-n-nc harmonic 71.080 116.410 # SOURCE3 1 0.0000
angle_coeff @angle:nc-n-p2 harmonic 63.760 117.210 # SOURCE3 1
angle_coeff @angle:nc-n-pc harmonic 63.550 117.210 # SOURCE3 1 0.0000
angle_coeff @angle:nd-n-nd harmonic 70.860 116.410 # SOURCE3 1 same_as_nc-n-nc
angle_coeff @angle:nd-n-p2 harmonic 63.720 117.210 # SOURCE3 1 same_as_nc-n-p2
angle_coeff @angle:nd-n-pd harmonic 63.510 117.210 # SOURCE3 1 same_as_nc-n-pc
angle_coeff @angle:nh-n-nh harmonic 69.100 115.180 # SOURCE3 1 0.0000
angle_coeff @angle:n-n-n harmonic 69.890 114.620 # SOURCE3 1 0.0000
angle_coeff @angle:no-n-no harmonic 68.520 108.660 # SOURCE3 1 0.0000
angle_coeff @angle:br-no-o harmonic 58.480 113.190 # SOURCE3 2 0.0000
angle_coeff @angle:c1-no-o harmonic 71.340 116.630 # SOURCE3 6 0.0000
angle_coeff @angle:c2-no-o harmonic 69.870 116.870 # SOURCE3 8 0.4200
angle_coeff @angle:c3-no-o harmonic 66.960 116.560 # SOURCE3 6 0.3959
angle_coeff @angle:ca-no-o harmonic 68.740 118.100 # SOURCE3 10 1.1524
angle_coeff @angle:cc-no-o harmonic 70.340 117.520 # SOURCE4 198 0.6255
angle_coeff @angle:cl-no-o harmonic 61.610 115.080 # SOURCE3 2 0.0000
angle_coeff @angle:c-no-o harmonic 67.100 115.260 # SOURCE3 1
angle_coeff @angle:hn-no-o harmonic 55.310 115.490 # SOURCE3 2 0.0000
angle_coeff @angle:oh-n-oh harmonic 72.050 107.260 # SOURCE3 1 0.0000
angle_coeff @angle:i-no-o harmonic 54.600 116.310 # SOURCE3 2 0.0000
angle_coeff @angle:n1-no-o harmonic 73.780 115.000 # HF/6-31G* 1
angle_coeff @angle:n2-no-o harmonic 65.790 115.100 # SOURCE2 2 2.4000
angle_coeff @angle:n3-no-o harmonic 72.010 115.560 # SOURCE3 6 0.6427
angle_coeff @angle:n4-no-o harmonic 72.870 109.000 # SOURCE3 2 0.0000
angle_coeff @angle:na-no-o harmonic 72.240 115.490 # SOURCE3 18 0.5640
angle_coeff @angle:nh-no-o harmonic 74.080 115.710 # SOURCE3 8 0.4811
angle_coeff @angle:n-no-o harmonic 71.670 115.410 # SOURCE3 8 0.3748
angle_coeff @angle:no-no-o harmonic 59.920 112.380 # SOURCE3 4 0.0000
angle_coeff @angle:o-n-o harmonic 73.390 128.610 # SOURCE3 3 1.0626
angle_coeff @angle:o-no-o harmonic 77.150 125.130 # SOURCE4 461 0.7605
angle_coeff @angle:o-no-oh harmonic 74.090 114.700 # SOURCE3 2 0.0000
angle_coeff @angle:o-no-os harmonic 73.710 114.010 # SOURCE3 8 0.9778
angle_coeff @angle:o-no-p2 harmonic 64.840 117.380 # SOURCE3 20 0.8083
angle_coeff @angle:o-no-p3 harmonic 61.420 116.780 # SOURCE3 6 0.4929
angle_coeff @angle:o-no-p4 harmonic 60.600 116.640 # SOURCE3 6 0.0089
angle_coeff @angle:o-no-p5 harmonic 61.770 116.690 # SOURCE3 8 0.4507
angle_coeff @angle:o-no-s4 harmonic 72.320 114.490 # SOURCE3 6 0.5674
angle_coeff @angle:o-no-s6 harmonic 73.140 114.390 # SOURCE3 6 0.8311
angle_coeff @angle:o-no-s harmonic 81.060 119.810 # SOURCE3 4 0.0042
angle_coeff @angle:o-no-sh harmonic 79.650 116.100 # SOURCE3 2 0.0000
angle_coeff @angle:o-no-ss harmonic 78.810 115.580 # SOURCE3 6 0.5860
angle_coeff @angle:os-n-os harmonic 72.280 106.530 # SOURCE3 1 0.0000
angle_coeff @angle:p2-n-p2 harmonic 61.200 119.620 # SOURCE3 1
angle_coeff @angle:p3-n-p3 harmonic 62.850 108.730 # SOURCE3 3 0.2591
angle_coeff @angle:p4-n-p4 harmonic 64.210 108.550 # SOURCE3 1
angle_coeff @angle:p5-n-p5 harmonic 67.920 99.990 # SOURCE3 1
angle_coeff @angle:pc-n-pc harmonic 60.950 119.620 # SOURCE3 1 0.0000
angle_coeff @angle:pd-n-pd harmonic 60.950 119.620 # SOURCE3 1 same_as_pc-n-pc
angle_coeff @angle:s4-n-s4 harmonic 97.760 113.750 # SOURCE3 1 0.0000
angle_coeff @angle:s6-n-s6 harmonic 99.030 119.680 # SOURCE3 1 0.0000
angle_coeff @angle:sh-n-sh harmonic 98.560 119.030 # SOURCE3 1 0.0000
angle_coeff @angle:s-n-s harmonic 93.680 126.000 # SOURCE3 1
angle_coeff @angle:ss-n-ss harmonic 99.420 118.490 # SOURCE3 1 0.0000
angle_coeff @angle:br-oh-ho harmonic 42.150 101.600 # SOURCE3 1 0.0000
angle_coeff @angle:c1-oh-ho harmonic 50.200 108.760 # SOURCE3 1 0.0000
angle_coeff @angle:c2-oh-ho harmonic 49.910 108.980 # SOURCE3 6 2.2379
angle_coeff @angle:c3-oh-ho harmonic 47.090 108.160 # SOURCE3 42 1.3034
angle_coeff @angle:ca-oh-ho harmonic 48.850 109.470 # SOURCE3 7 1.0405
angle_coeff @angle:cc-oh-ho harmonic 50.060 106.970 # SOURCE4 63 1.4230
angle_coeff @angle:cd-oh-ho harmonic 49.840 107.160 # SOURCE4 54 1.4035
angle_coeff @angle:ce-oh-ho harmonic 49.700 106.840 # SOURCE4 23 1.5653
angle_coeff @angle:cf-oh-ho harmonic 50.070 107.190 # SOURCE4 11 0.9954
angle_coeff @angle:c-oh-ho harmonic 51.190 107.370 # SOURCE3 34 1.6830
angle_coeff @angle:cl-oh-ho harmonic 43.560 102.400 # SOURCE2 1 0.0000
angle_coeff @angle:cx-oh-ho harmonic 49.640 106.170 # SOURCE3 3 0.0644
angle_coeff @angle:cy-oh-ho harmonic 47.620 107.320 # SOURCE4 5 0.4955
angle_coeff @angle:f-oh-ho harmonic 48.470 96.800 # SOURCE2 1 0.0000
angle_coeff @angle:ho-oh-ho harmonic 41.930 104.800 # SOURCE2 1 0.0000
angle_coeff @angle:ho-oh-i harmonic 35.670 107.980 # SOURCE3 2 0.0000
angle_coeff @angle:ho-oh-n1 harmonic 52.550 107.810 # HF/6-31G* 1
angle_coeff @angle:ho-oh-n2 harmonic 50.570 102.740 # SOURCE3 9 2.1286
angle_coeff @angle:ho-oh-n3 harmonic 50.610 102.330 # SOURCE3 5 1.2591
angle_coeff @angle:ho-oh-n4 harmonic 49.440 106.630 # SOURCE3 3 0.2770
angle_coeff @angle:ho-oh-n harmonic 50.460 101.030 # SOURCE3 6 1.4086
angle_coeff @angle:ho-oh-na harmonic 50.240 103.710 # SOURCE3 9 1.2590
angle_coeff @angle:ho-oh-nh harmonic 49.970 102.420 # SOURCE4 15 0.6819
angle_coeff @angle:ho-oh-no harmonic 50.310 102.170 # SOURCE3 1 0.0000
angle_coeff @angle:ho-oh-o harmonic 47.260 100.870 # SOURCE3 1
angle_coeff @angle:ho-oh-oh harmonic 49.340 98.720 # SOURCE3 2 0.0000
angle_coeff @angle:ho-oh-os harmonic 49.580 99.690 # SOURCE4 18 0.3384
angle_coeff @angle:ho-oh-p2 harmonic 44.140 109.450 # SOURCE3 8 3.3491
angle_coeff @angle:ho-oh-p3 harmonic 42.540 110.640 # SOURCE3 3 0.5191
angle_coeff @angle:ho-oh-p4 harmonic 43.670 110.190 # SOURCE3 4 0.2372
angle_coeff @angle:ho-oh-p5 harmonic 44.150 110.140 # SOURCE3 92 3.8033
angle_coeff @angle:ho-oh-py harmonic 44.390 110.730 # SOURCE3 79 1.7835
angle_coeff @angle:ho-oh-s4 harmonic 54.130 106.760 # SOURCE4 9 0.4035
angle_coeff @angle:ho-oh-s harmonic 51.720 100.150 # SOURCE3 2 0.0000
angle_coeff @angle:ho-oh-s6 harmonic 57.540 109.200 # SOURCE3 13 0.1856
angle_coeff @angle:ho-oh-sh harmonic 54.390 106.240 # SOURCE3 2 0.0661
angle_coeff @angle:ho-oh-ss harmonic 54.540 107.060 # SOURCE3 4 0.9967
angle_coeff @angle:ho-oh-sy harmonic 55.940 106.410 # SOURCE4 33 0.3729
angle_coeff @angle:br-os-br harmonic 65.080 110.630 # SOURCE3 1 0.0000
angle_coeff @angle:c1-os-c1 harmonic 66.990 115.020 # SOURCE3 1 0.0000
angle_coeff @angle:c1-os-c3 harmonic 64.470 113.390 # SOURCE3 1 0.0000
angle_coeff @angle:c2-os-c2 harmonic 65.950 113.140 # SOURCE3 6 2.1932
angle_coeff @angle:c2-os-c3 harmonic 64.210 112.090 # SOURCE3 7 4.1809
angle_coeff @angle:c2-os-ca harmonic 65.430 113.590 # SOURCE3 1 0.0000
angle_coeff @angle:c2-os-n2 harmonic 64.910 118.130 # SOURCE3 1 0.0000
angle_coeff @angle:c2-os-na harmonic 68.210 103.850 # SOURCE3 4 0.6297
angle_coeff @angle:c2-os-os harmonic 68.350 102.770 # SOURCE3 1 0.0000
angle_coeff @angle:c2-os-p5 harmonic 61.090 126.370 # SOURCE4 7 1.7939
angle_coeff @angle:c2-os-ss harmonic 79.830 108.130 # SOURCE3 1 0.0000
angle_coeff @angle:c3-os-c3 harmonic 62.390 112.450 # SOURCE4 1293 1.6468
angle_coeff @angle:c3-os-ca harmonic 62.270 117.970 # SOURCE4 2495 1.4576
angle_coeff @angle:c3-os-cc harmonic 62.430 117.580 # SOURCE4 118 1.0660
angle_coeff @angle:c3-os-cd harmonic 62.560 117.110 # SOURCE4 130 1.0230
angle_coeff @angle:c3-os-ce harmonic 62.850 115.700 # SOURCE4 31 2.2296
angle_coeff @angle:c3-os-cf harmonic 62.540 117.850 # SOURCE4 6 1.2514
angle_coeff @angle:c3-os-cl harmonic 60.430 110.500 # SOURCE2 1 0.0000
angle_coeff @angle:c3-os-cy harmonic 61.670 115.650 # SOURCE4 5 0.2390
angle_coeff @angle:c3-os-i harmonic 54.880 113.700 # SOURCE3 1 0.0000
angle_coeff @angle:c3-os-n1 harmonic 66.310 113.500 # HF/6-31G* 1
angle_coeff @angle:c3-os-n2 harmonic 65.920 108.120 # SOURCE3 7 0.3048
angle_coeff @angle:c3-os-n3 harmonic 64.520 110.280 # SOURCE4 14 1.9026
angle_coeff @angle:c3-os-n4 harmonic 64.880 110.500 # SOURCE3 3 0.5426
angle_coeff @angle:c3-os-n harmonic 65.400 109.520 # SOURCE4 14 0.6827
angle_coeff @angle:c3-os-na harmonic 64.540 109.910 # SOURCE3 9 1.8268
angle_coeff @angle:c3-os-nc harmonic 64.800 112.730 # SOURCE3 2 1.0358
angle_coeff @angle:c3-os-nd harmonic 64.800 112.730 # SOURCE3 2 same_as_c3-os-nc
angle_coeff @angle:c3-os-nh harmonic 65.220 109.690 # SOURCE4 8 0.1662
angle_coeff @angle:c3-os-no harmonic 63.890 113.800 # SOURCE4 42 0.2726
angle_coeff @angle:c3-os-o harmonic 65.620 103.000 # SOURCE3 1 0.0000
angle_coeff @angle:c3-os-oh harmonic 65.240 107.970 # SOURCE4 11 0.4333
angle_coeff @angle:c3-os-os harmonic 65.890 105.010 # SOURCE3 7 0.6328
angle_coeff @angle:c3-os-p2 harmonic 63.400 115.470 # SOURCE3 8 2.6374
angle_coeff @angle:c3-os-p3 harmonic 60.450 115.970 # SOURCE3 3 0.3597
angle_coeff @angle:c3-os-p4 harmonic 61.300 117.480 # SOURCE3 4 0.3850
angle_coeff @angle:c3-os-p5 harmonic 62.000 118.000 # SOURCE3 31 1.2882
angle_coeff @angle:c3-os-py harmonic 61.690 117.800 # SOURCE3 16 0.9654
angle_coeff @angle:c3-os-s4 harmonic 77.610 111.500 # SOURCE3 6 1.4240
angle_coeff @angle:c3-os-s6 harmonic 80.000 115.790 # SOURCE4 60 1.2588
angle_coeff @angle:c3-os-s harmonic 75.020 109.550 # SOURCE3 1 0.0000
angle_coeff @angle:c3-os-sh harmonic 78.050 112.820 # SOURCE3 1 0.0000
angle_coeff @angle:c3-os-ss harmonic 76.870 113.190 # SOURCE3 3 0.2455
angle_coeff @angle:ca-os-ca harmonic 63.310 119.950 # SOURCE4 107 1.6535
angle_coeff @angle:ca-os-cc harmonic 67.320 106.320 # SOURCE4 56 2.1614
angle_coeff @angle:ca-os-cd harmonic 66.250 109.770 # SOURCE3 6 5.0326
angle_coeff @angle:ca-os-n3 harmonic 65.390 112.190 # SOURCE3 1 0.0000
angle_coeff @angle:ca-os-na harmonic 66.470 108.240 # SOURCE3 1 0.0000
angle_coeff @angle:ca-os-nc harmonic 66.090 113.680 # SOURCE3 2
angle_coeff @angle:ca-os-nd harmonic 66.090 113.680 # SOURCE3 2
angle_coeff @angle:ca-os-p5 harmonic 61.600 123.420 # SOURCE4 54 1.1358
angle_coeff @angle:ca-os-s6 harmonic 80.940 116.970 # SOURCE4 15 0.9514
angle_coeff @angle:c-os-c2 harmonic 64.910 118.020 # SOURCE4 7 0.3666
angle_coeff @angle:c-os-c3 harmonic 63.630 115.140 # SOURCE3 17 1.8967
angle_coeff @angle:c-os-c harmonic 64.540 120.640 # SOURCE4 7 1.5114
angle_coeff @angle:c-os-ca harmonic 63.750 120.870 # SOURCE4 257 1.7209
angle_coeff @angle:c-os-cc harmonic 64.150 119.620 # SOURCE3 5 6.0675
angle_coeff @angle:cc-os-cc harmonic 67.250 106.760 # SOURCE4 192 0.6652
angle_coeff @angle:cc-os-cd harmonic 63.800 118.620 # SOURCE4 14 1.9764
angle_coeff @angle:c-os-cd harmonic 64.150 119.620 # SOURCE3 5 6.0675
angle_coeff @angle:cc-os-na harmonic 65.510 111.660 # SOURCE3 28 4.1343
angle_coeff @angle:cc-os-nc harmonic 68.120 107.230 # SOURCE3 6 2.7507
angle_coeff @angle:cc-os-os harmonic 66.270 108.470 # SOURCE3 2 0.0000
angle_coeff @angle:cc-os-ss harmonic 75.750 119.590 # SOURCE3 1 0.0000
angle_coeff @angle:c-os-cy harmonic 71.750 91.100 # SOURCE3 2 0.0155
angle_coeff @angle:cd-os-cd harmonic 67.350 106.450 # SOURCE4 60 0.9115
angle_coeff @angle:cd-os-na harmonic 65.510 111.660 # SOURCE3 28 4.1343
angle_coeff @angle:cd-os-nd harmonic 68.120 107.230 # SOURCE3 6 2.7507
angle_coeff @angle:cd-os-os harmonic 66.270 108.470 # SOURCE3 2 same_as_cc-os-os
angle_coeff @angle:cd-os-ss harmonic 75.750 119.590 # SOURCE3 1 same_as_cc-os-ss
angle_coeff @angle:cl-os-cl harmonic 60.450 110.760 # SOURCE3 2 0.0000
angle_coeff @angle:c-os-n2 harmonic 66.950 112.080 # SOURCE4 6 0.1154
angle_coeff @angle:c-os-n harmonic 66.830 112.100 # SOURCE4 6 0.6163
angle_coeff @angle:c-os-oh harmonic 66.500 110.500 # SOURCE3 1 0.0000
angle_coeff @angle:c-os-os harmonic 66.250 110.280 # SOURCE4 10 1.3612
angle_coeff @angle:c-os-p5 harmonic 62.330 122.100 # SOURCE4 5 0.5870
angle_coeff @angle:c-os-sy harmonic 78.280 113.490 # SOURCE3 1 0.0000
angle_coeff @angle:cx-os-cx harmonic 85.270 61.820 # SOURCE4 107 0.1793
angle_coeff @angle:cx-os-n harmonic 88.980 59.990 # SOURCE3 1 0.0000
angle_coeff @angle:cx-os-os harmonic 90.380 56.520 # SOURCE3 2 0.0000
angle_coeff @angle:cy-os-cy harmonic 68.810 93.400 # SOURCE2 2 1.4000
angle_coeff @angle:f-os-f harmonic 63.940 103.300 # SOURCE2 1 0.0000
angle_coeff @angle:f-os-os harmonic 63.940 109.500 # SOURCE2 1 0.0000
angle_coeff @angle:i-os-i harmonic 58.060 115.670 # SOURCE3 1 0.0000
angle_coeff @angle:n1-os-n1 harmonic 70.280 117.790 # HF/6-31G* 1
angle_coeff @angle:n2-os-n2 harmonic 68.760 106.830 # SOURCE3 1 0.0000
angle_coeff @angle:n2-os-s6 harmonic 84.320 111.300 # SOURCE4 7 0.5651
angle_coeff @angle:n3-os-n3 harmonic 67.760 104.880 # SOURCE3 1 0.0000
angle_coeff @angle:n4-os-n4 harmonic 65.660 114.680 # SOURCE3 1 0.0000
angle_coeff @angle:na-os-na harmonic 66.100 109.590 # SOURCE3 1 0.0000
angle_coeff @angle:na-os-ss harmonic 81.940 104.340 # SOURCE3 1 0.0000
angle_coeff @angle:nc-os-nc harmonic 68.170 110.400 # SOURCE2 1 0.0000
angle_coeff @angle:nc-os-ss harmonic 80.210 110.970 # SOURCE3 1 0.0000
angle_coeff @angle:nd-os-nd harmonic 68.170 110.400 # SOURCE2 1 same_as_nc-os-nc
angle_coeff @angle:nd-os-ss harmonic 80.210 110.970 # SOURCE3 1 same_as_nc-os-ss
angle_coeff @angle:nh-os-nh harmonic 67.810 108.290 # SOURCE3 1 0.0000
angle_coeff @angle:n-os-n harmonic 68.080 108.310 # SOURCE3 1 0.0000
angle_coeff @angle:no-os-no harmonic 66.400 111.860 # SOURCE3 1 0.0000
angle_coeff @angle:n-os-s6 harmonic 83.370 113.620 # SOURCE4 5 0.0928
angle_coeff @angle:o-os-o harmonic 62.760 114.680 # SOURCE3 1 0.0000
angle_coeff @angle:p2-os-p2 harmonic 64.670 120.020 # SOURCE3 1 0.0000
angle_coeff @angle:p2-os-p5 harmonic 67.590 107.860 # SOURCE3 1 0.0000
angle_coeff @angle:p3-os-p3 harmonic 60.040 121.220 # SOURCE3 1 0.0000
angle_coeff @angle:p3-os-py harmonic 65.620 105.580 # SOURCE3 1 0.0000
angle_coeff @angle:p5-os-p5 harmonic 61.920 126.250 # SOURCE3 1 0.0000
angle_coeff @angle:s4-os-s4 harmonic 99.450 111.630 # SOURCE3 1 0.0000
angle_coeff @angle:s6-os-s6 harmonic 103.740 119.070 # SOURCE3 2 0.4318
angle_coeff @angle:sh-os-sh harmonic 97.950 118.950 # SOURCE3 1 0.0000
angle_coeff @angle:s-os-s harmonic 91.270 118.080 # SOURCE3 1 0.0000
angle_coeff @angle:ss-os-ss harmonic 97.420 115.640 # SOURCE3 1 0.0000
angle_coeff @angle:br-p2-br harmonic 65.020 108.600 # SOURCE3 1
angle_coeff @angle:br-p2-c2 harmonic 63.020 102.320 # SOURCE3 2 0.0146
angle_coeff @angle:br-p2-n2 harmonic 64.590 103.330 # SOURCE3 1 0.0000
angle_coeff @angle:br-p2-o harmonic 63.020 110.870 # SOURCE3 1 0.0000
angle_coeff @angle:br-p2-p2 harmonic 63.350 115.460 # SOURCE3 4 7.8622
angle_coeff @angle:br-p2-s harmonic 82.100 110.520 # SOURCE3 1 0.0000
angle_coeff @angle:c1-p2-c1 harmonic 62.650 99.040 # SOURCE3 1
angle_coeff @angle:c1-p2-c2 harmonic 63.650 101.290 # SOURCE3 1
angle_coeff @angle:c1-p2-n2 harmonic 66.100 101.790 # SOURCE3 1
angle_coeff @angle:c1-p2-o harmonic 66.040 107.620 # SOURCE3 1
angle_coeff @angle:c1-p2-p2 harmonic 67.310 99.540 # SOURCE3 1
angle_coeff @angle:c1-p2-s harmonic 82.930 105.900 # SOURCE3 1
angle_coeff @angle:c2-p2-c2 harmonic 64.650 104.500 # SOURCE3 1
angle_coeff @angle:c2-p2-c3 harmonic 61.690 101.900 # SOURCE3 4 0.1132
angle_coeff @angle:c2-p2-ca harmonic 61.990 101.950 # SOURCE3 1
angle_coeff @angle:c2-p2-cl harmonic 61.200 102.720 # SOURCE3 2 0.0000
angle_coeff @angle:c2-p2-f harmonic 66.480 103.470 # SOURCE3 2 0.0136
angle_coeff @angle:c2-p2-hp harmonic 48.160 97.190 # SOURCE3 3 0.0216
angle_coeff @angle:c2-p2-i harmonic 54.100 101.940 # SOURCE3 2 0.0368
angle_coeff @angle:c2-p2-n2 harmonic 69.040 99.880 # SOURCE3 1
angle_coeff @angle:c2-p2-n3 harmonic 67.110 101.800 # SOURCE3 1
angle_coeff @angle:c2-p2-n4 harmonic 62.450 98.260 # SOURCE3 6 0.1522
angle_coeff @angle:c2-p2-n harmonic 65.340 103.280 # SOURCE3 4 3.3113
angle_coeff @angle:c2-p2-na harmonic 64.790 103.990 # SOURCE3 8 1.6834
angle_coeff @angle:c2-p2-nh harmonic 65.840 105.170 # SOURCE3 8 0.8263
angle_coeff @angle:c2-p2-no harmonic 66.990 97.970 # SOURCE3 3 0.4175
angle_coeff @angle:c2-p2-o harmonic 66.350 115.160 # SOURCE3 1
angle_coeff @angle:c2-p2-oh harmonic 67.930 102.890 # SOURCE3 3 0.8191
angle_coeff @angle:c2-p2-os harmonic 69.280 102.120 # SOURCE3 4 0.8783
angle_coeff @angle:c2-p2-p2 harmonic 69.100 99.560 # SOURCE3 1
angle_coeff @angle:c2-p2-p3 harmonic 60.750 99.270 # SOURCE3 4 1.1590
angle_coeff @angle:c2-p2-p4 harmonic 60.850 96.940 # SOURCE3 1
angle_coeff @angle:c2-p2-p5 harmonic 60.620 97.610 # SOURCE3 1
angle_coeff @angle:c2-p2-s4 harmonic 77.420 95.150 # SOURCE3 1
angle_coeff @angle:c2-p2-s6 harmonic 77.560 95.510 # SOURCE3 1
angle_coeff @angle:c2-p2-s harmonic 85.340 105.530 # SOURCE3 1
angle_coeff @angle:c2-p2-sh harmonic 81.290 101.490 # SOURCE3 3 0.0057
angle_coeff @angle:c2-p2-ss harmonic 81.300 101.810 # SOURCE3 4 0.5883
angle_coeff @angle:c3-p2-c3 harmonic 59.710 99.300 # SOURCE3 1
angle_coeff @angle:c3-p2-n2 harmonic 64.420 100.820 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p2-o harmonic 64.090 106.720 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p2-os harmonic 65.020 101.340 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p2-p2 harmonic 65.390 100.480 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p2-s harmonic 80.980 105.680 # SOURCE3 1 0.0000
angle_coeff @angle:ca-p2-ca harmonic 60.070 99.700 # SOURCE3 1
angle_coeff @angle:ca-p2-n2 harmonic 64.770 100.820 # SOURCE3 1
angle_coeff @angle:ca-p2-n harmonic 66.610 89.970 # SOURCE3 1
angle_coeff @angle:ca-p2-na harmonic 66.630 89.210 # SOURCE3 1
angle_coeff @angle:ca-p2-o harmonic 64.430 106.880 # SOURCE3 1
angle_coeff @angle:ca-p2-s harmonic 80.490 107.930 # SOURCE3 1
angle_coeff @angle:c-p2-c2 harmonic 62.160 97.300 # SOURCE3 1
angle_coeff @angle:c-p2-c harmonic 61.190 90.100 # SOURCE3 1
angle_coeff @angle:ce-p2-o harmonic 64.940 107.440 # SOURCE3 1
angle_coeff @angle:ce-p2-s harmonic 82.030 105.540 # SOURCE3 1
angle_coeff @angle:cf-p2-o harmonic 64.940 107.440 # SOURCE3 1 same_as_ce-p2-o
angle_coeff @angle:cf-p2-s harmonic 82.030 105.540 # SOURCE3 1 same_as_ce-p2-s
angle_coeff @angle:cl-p2-cl harmonic 59.120 108.700 # SOURCE3 1
angle_coeff @angle:cl-p2-n2 harmonic 63.020 103.380 # SOURCE3 1 0.0000
angle_coeff @angle:cl-p2-o harmonic 61.870 110.570 # SOURCE3 1 0.0000
angle_coeff @angle:cl-p2-p2 harmonic 64.880 103.110 # SOURCE3 1 0.0000
angle_coeff @angle:cl-p2-s harmonic 79.650 110.110 # SOURCE3 1 0.0000
angle_coeff @angle:f-p2-f harmonic 67.450 107.100 # SOURCE3 1
angle_coeff @angle:f-p2-n2 harmonic 69.660 103.570 # SOURCE3 1 0.0000
angle_coeff @angle:f-p2-o harmonic 70.010 110.610 # SOURCE3 1 0.0000
angle_coeff @angle:f-p2-p2 harmonic 68.870 103.480 # SOURCE3 1 0.0000
angle_coeff @angle:f-p2-s harmonic 83.240 114.710 # SOURCE3 2 5.2794
angle_coeff @angle:hp-p2-hp harmonic 36.510 98.760 # SOURCE3 1
angle_coeff @angle:hp-p2-n1 harmonic 49.670 95.180 # SOURCE3 2 1.5708
angle_coeff @angle:hp-p2-n2 harmonic 51.270 95.540 # SOURCE3 19 4.7352
angle_coeff @angle:hp-p2-ne harmonic 51.040 100.100 # SOURCE3 14 6.1290
angle_coeff @angle:hp-p2-nf harmonic 51.040 100.100 # SOURCE3 14 same_as_hp-p2-ne
angle_coeff @angle:hp-p2-o harmonic 51.210 105.580 # SOURCE3 1 0.0000
angle_coeff @angle:hp-p2-p2 harmonic 48.180 101.880 # SOURCE3 27 12.9535
angle_coeff @angle:hp-p2-p4 harmonic 41.290 94.510 # SOURCE3 1 0.0000
angle_coeff @angle:hp-p2-p5 harmonic 42.510 89.070 # SOURCE3 1 0.0000
angle_coeff @angle:hp-p2-pe harmonic 47.430 97.250 # SOURCE3 16 8.8916
angle_coeff @angle:hp-p2-pf harmonic 47.430 97.250 # SOURCE3 16 same_as_hp-p2-pe
angle_coeff @angle:hp-p2-s4 harmonic 53.260 89.990 # SOURCE3 1 0.0000
angle_coeff @angle:hp-p2-s harmonic 61.200 102.520 # SOURCE3 1 0.0000
angle_coeff @angle:hp-p2-s6 harmonic 54.080 88.130 # SOURCE3 1 0.0000
angle_coeff @angle:i-p2-i harmonic 57.140 104.160 # SOURCE3 1
angle_coeff @angle:i-p2-n2 harmonic 55.340 101.770 # SOURCE3 1 0.0000
angle_coeff @angle:i-p2-o harmonic 53.280 109.510 # SOURCE3 1 0.0000
angle_coeff @angle:i-p2-p2 harmonic 58.360 102.630 # SOURCE3 1 0.0000
angle_coeff @angle:i-p2-s harmonic 71.170 110.600 # SOURCE3 1 0.0000
angle_coeff @angle:n1-p2-n1 harmonic 74.350 86.220 # HF/6-31G* 1
angle_coeff @angle:n2-p2-n2 harmonic 72.910 98.000 # SOURCE3 1
angle_coeff @angle:n2-p2-n3 harmonic 70.540 100.420 # SOURCE3 1
angle_coeff @angle:n2-p2-n4 harmonic 66.370 93.420 # SOURCE3 1 0.0000
angle_coeff @angle:n2-p2-na harmonic 68.130 102.030 # SOURCE3 1 0.0000
angle_coeff @angle:n2-p2-nh harmonic 69.830 101.870 # SOURCE3 2 0.8491
angle_coeff @angle:n2-p2-no harmonic 69.740 98.120 # SOURCE3 1 0.0000
angle_coeff @angle:n2-p2-o harmonic 69.560 115.340 # SOURCE3 1
angle_coeff @angle:n2-p2-oh harmonic 68.760 109.720 # SOURCE3 1 0.0000
angle_coeff @angle:n2-p2-os harmonic 72.480 102.290 # SOURCE3 1 0.0000
angle_coeff @angle:n2-p2-p3 harmonic 62.580 99.510 # SOURCE3 1 0.0000
angle_coeff @angle:n2-p2-p4 harmonic 61.230 101.730 # SOURCE3 1
angle_coeff @angle:n2-p2-p5 harmonic 63.780 93.680 # SOURCE3 1
angle_coeff @angle:n2-p2-s4 harmonic 78.670 97.830 # SOURCE3 1
angle_coeff @angle:n2-p2-s6 harmonic 78.860 98.140 # SOURCE3 1
angle_coeff @angle:n2-p2-s harmonic 85.870 112.940 # SOURCE3 1
angle_coeff @angle:n2-p2-sh harmonic 84.460 100.820 # SOURCE3 1 0.0000
angle_coeff @angle:n2-p2-ss harmonic 84.230 101.760 # SOURCE3 1 0.0000
angle_coeff @angle:n3-p2-n3 harmonic 67.280 106.300 # SOURCE3 1
angle_coeff @angle:n3-p2-o harmonic 70.570 106.830 # SOURCE3 1
angle_coeff @angle:n3-p2-p2 harmonic 70.440 100.580 # SOURCE3 1
angle_coeff @angle:n3-p2-s harmonic 87.340 105.750 # SOURCE3 1
angle_coeff @angle:n4-p2-n4 harmonic 63.300 88.800 # SOURCE3 1
angle_coeff @angle:n4-p2-o harmonic 65.000 101.360 # SOURCE3 1 0.0000
angle_coeff @angle:n4-p2-p2 harmonic 66.570 96.530 # SOURCE3 1 0.0000
angle_coeff @angle:n4-p2-s harmonic 81.040 104.980 # SOURCE3 1 0.0000
angle_coeff @angle:na-p2-na harmonic 64.300 106.100 # SOURCE3 1
angle_coeff @angle:na-p2-o harmonic 68.270 107.460 # SOURCE3 1 0.0000
angle_coeff @angle:na-p2-s harmonic 84.570 108.150 # SOURCE3 1 0.0000
angle_coeff @angle:ne-p2-o harmonic 73.070 107.710 # SOURCE3 1
angle_coeff @angle:ne-p2-s harmonic 89.700 105.500 # SOURCE3 1
angle_coeff @angle:nf-p2-o harmonic 73.070 107.710 # SOURCE3 1 same_as_ne-p2-o
angle_coeff @angle:nf-p2-s harmonic 89.700 105.500 # SOURCE3 1 same_as_ne-p2-s
angle_coeff @angle:nh-p2-nh harmonic 67.650 104.000 # SOURCE3 1
angle_coeff @angle:nh-p2-o harmonic 69.920 108.110 # SOURCE3 2 0.6773
angle_coeff @angle:nh-p2-p2 harmonic 67.910 107.730 # SOURCE3 3 3.1678
angle_coeff @angle:nh-p2-s harmonic 85.580 109.620 # SOURCE3 2 1.7725
angle_coeff @angle:n-p2-n2 harmonic 69.610 98.850 # SOURCE3 1 0.0000
angle_coeff @angle:n-p2-o harmonic 69.470 105.080 # SOURCE3 1 0.0000
angle_coeff @angle:no-p2-no harmonic 67.260 98.200 # SOURCE3 1
angle_coeff @angle:no-p2-o harmonic 69.400 104.870 # SOURCE3 1 0.0000
angle_coeff @angle:no-p2-p2 harmonic 66.610 108.570 # SOURCE3 3 8.2121
angle_coeff @angle:no-p2-s harmonic 84.470 109.060 # SOURCE3 2 5.4074
angle_coeff @angle:n-p2-p2 harmonic 68.780 102.120 # SOURCE3 1 0.0000
angle_coeff @angle:n-p2-s harmonic 83.340 112.340 # SOURCE3 1 0.0000
angle_coeff @angle:oh-p2-oh harmonic 71.860 100.100 # SOURCE3 1
angle_coeff @angle:oh-p2-p2 harmonic 69.090 107.820 # SOURCE3 2 2.6708
angle_coeff @angle:oh-p2-s harmonic 87.090 109.750 # SOURCE3 1 0.0000
angle_coeff @angle:o-p2-o harmonic 70.950 119.960 # SOURCE3 1
angle_coeff @angle:o-p2-oh harmonic 70.850 110.460 # SOURCE3 1 0.0000
angle_coeff @angle:o-p2-os harmonic 72.860 108.810 # SOURCE3 1 0.0000
angle_coeff @angle:o-p2-p2 harmonic 68.910 114.230 # SOURCE3 1
angle_coeff @angle:o-p2-p3 harmonic 61.190 106.690 # SOURCE3 1 0.0000
angle_coeff @angle:o-p2-p4 harmonic 61.150 104.370 # SOURCE3 1
angle_coeff @angle:o-p2-p5 harmonic 61.090 104.490 # SOURCE3 1
angle_coeff @angle:o-p2-pe harmonic 59.000 145.960 # SOURCE3 1
angle_coeff @angle:o-p2-pf harmonic 59.000 145.960 # SOURCE3 1 same_as_o-p2-pe
angle_coeff @angle:o-p2-s4 harmonic 76.220 106.590 # SOURCE3 1
angle_coeff @angle:o-p2-s6 harmonic 77.110 105.040 # SOURCE3 1
angle_coeff @angle:o-p2-s harmonic 86.500 117.420 # SOURCE3 1
angle_coeff @angle:o-p2-sh harmonic 82.540 109.600 # SOURCE3 1 0.0000
angle_coeff @angle:os-p2-os harmonic 75.140 98.300 # SOURCE3 1
angle_coeff @angle:os-p2-p2 harmonic 72.150 101.460 # SOURCE3 1 0.0000
angle_coeff @angle:o-p2-ss harmonic 82.710 109.600 # SOURCE3 1 0.0000
angle_coeff @angle:os-p2-s harmonic 88.770 108.470 # SOURCE3 3 1.7065
angle_coeff @angle:p2-p2-n2 harmonic 72.700 97.400 # SOURCE3 1
angle_coeff @angle:p2-p2-p3 harmonic 63.950 101.730 # SOURCE3 1 0.0000
angle_coeff @angle:p2-p2-p4 harmonic 63.280 101.980 # SOURCE3 1
angle_coeff @angle:p2-p2-p5 harmonic 64.100 99.330 # SOURCE3 1
angle_coeff @angle:p2-p2-s4 harmonic 82.350 95.730 # SOURCE3 1
angle_coeff @angle:p2-p2-s6 harmonic 82.540 95.950 # SOURCE3 1
angle_coeff @angle:p2-p2-s harmonic 87.130 111.280 # SOURCE3 1
angle_coeff @angle:p2-p2-sh harmonic 81.160 113.940 # SOURCE3 3 8.5009
angle_coeff @angle:p3-p2-p3 harmonic 59.740 101.000 # SOURCE3 1
angle_coeff @angle:p3-p2-s harmonic 76.850 113.280 # SOURCE3 2 6.7035
angle_coeff @angle:p4-p2-s harmonic 79.510 103.890 # SOURCE3 1
angle_coeff @angle:p5-p2-p5 harmonic 62.680 89.400 # SOURCE3 1
angle_coeff @angle:p5-p2-s harmonic 80.520 101.210 # SOURCE3 1
angle_coeff @angle:pe-p2-s harmonic 87.030 106.350 # SOURCE3 1
angle_coeff @angle:pf-p2-s harmonic 87.030 106.350 # SOURCE3 1 same_as_pe-p2-s
angle_coeff @angle:s4-p2-s4 harmonic 102.320 85.300 # SOURCE3 1
angle_coeff @angle:s6-p2-s6 harmonic 95.800 98.200 # SOURCE3 1
angle_coeff @angle:sh-p2-sh harmonic 105.800 98.500 # SOURCE3 1
angle_coeff @angle:s-p2-s harmonic 113.120 106.600 # SOURCE3 1
angle_coeff @angle:s-p2-s4 harmonic 99.570 105.290 # SOURCE3 1
angle_coeff @angle:s-p2-s6 harmonic 99.150 106.930 # SOURCE3 1
angle_coeff @angle:s-p2-sh harmonic 104.500 110.730 # SOURCE3 2 0.0232
angle_coeff @angle:s-p2-ss harmonic 103.090 114.140 # SOURCE3 4 5.9223
angle_coeff @angle:ss-p2-ss harmonic 106.390 97.900 # SOURCE3 1
angle_coeff @angle:br-p3-br harmonic 65.960 103.540 # SOURCE3 1 0.0000
angle_coeff @angle:br-p3-hp harmonic 43.060 96.360 # SOURCE3 4 0.6701
angle_coeff @angle:c1-p3-c1 harmonic 61.500 100.500 # SOURCE3 1 0.0000
angle_coeff @angle:c1-p3-f harmonic 65.100 96.900 # SOURCE2 1 0.0000
angle_coeff @angle:c1-p3-hp harmonic 44.980 97.670 # SOURCE3 2 0.0000
angle_coeff @angle:c2-p3-c2 harmonic 59.650 101.770 # SOURCE3 3 0.0000
angle_coeff @angle:c2-p3-hp harmonic 44.060 97.850 # SOURCE3 4 0.0000
angle_coeff @angle:c3-p3-c3 harmonic 59.950 99.660 # SOURCE3 40 0.9854
angle_coeff @angle:c3-p3-ca harmonic 59.600 101.940 # SOURCE3 2 0.0000
angle_coeff @angle:c3-p3-cl harmonic 61.420 99.890 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p3-f harmonic 63.510 97.800 # SOURCE2 1 0.0000
angle_coeff @angle:c3-p3-hp harmonic 43.910 97.660 # SOURCE3 9 0.4096
angle_coeff @angle:c3-p3-n2 harmonic 63.720 96.550 # SOURCE3 2 0.0000
angle_coeff @angle:c3-p3-n3 harmonic 62.780 101.180 # SOURCE3 10 2.2338
angle_coeff @angle:c3-p3-n4 harmonic 61.660 96.940 # SOURCE3 6 0.4815
angle_coeff @angle:c3-p3-n harmonic 61.970 101.770 # SOURCE3 12 2.4449
angle_coeff @angle:c3-p3-na harmonic 62.590 100.170 # SOURCE3 4 0.0554
angle_coeff @angle:c3-p3-nh harmonic 61.770 104.500 # SOURCE3 2 0.0000
angle_coeff @angle:c3-p3-no harmonic 62.270 96.980 # SOURCE3 2 0.0000
angle_coeff @angle:c3-p3-o harmonic 62.860 111.670 # SOURCE3 28 5.3387
angle_coeff @angle:c3-p3-oh harmonic 64.890 98.210 # SOURCE3 2 0.0000
angle_coeff @angle:c3-p3-os harmonic 64.330 99.530 # SOURCE3 3 1.7678
angle_coeff @angle:c3-p3-p3 harmonic 57.790 100.310 # SOURCE3 18 2.1836
angle_coeff @angle:c3-p3-p5 harmonic 57.640 100.900 # SOURCE3 10 2.7070
angle_coeff @angle:c3-p3-s4 harmonic 76.740 98.880 # SOURCE3 8 6.2235
angle_coeff @angle:c3-p3-s6 harmonic 76.100 101.180 # SOURCE3 12 6.4536
angle_coeff @angle:c3-p3-sh harmonic 75.720 98.710 # SOURCE3 2 0.0000
angle_coeff @angle:c3-p3-ss harmonic 75.730 99.370 # SOURCE3 2 0.0000
angle_coeff @angle:ca-p3-ca harmonic 60.550 99.860 # SOURCE3 1 0.0000
angle_coeff @angle:ca-p3-hp harmonic 44.340 97.500 # SOURCE3 2 0.0000
angle_coeff @angle:c-p3-c3 harmonic 60.100 97.060 # SOURCE3 3 1.1490
angle_coeff @angle:c-p3-c harmonic 58.350 100.900 # SOURCE3 1 0.0000
angle_coeff @angle:c-p3-hp harmonic 43.390 96.550 # SOURCE3 6 0.5223
angle_coeff @angle:cl-p3-cl harmonic 62.670 102.820 # SOURCE3 1 0.0000
angle_coeff @angle:cl-p3-f harmonic 63.640 99.200 # SOURCE2 1 0.0000
angle_coeff @angle:cl-p3-hp harmonic 44.110 96.300 # SOURCE3 3 0.6203
angle_coeff @angle:c-p3-os harmonic 70.240 81.320 # SOURCE3 1 0.0000
angle_coeff @angle:cx-p3-hp harmonic 44.010 95.200 # SOURCE2 1 0.0000
angle_coeff @angle:f-p3-f harmonic 68.840 97.400 # SOURCE2 8 1.6636
angle_coeff @angle:f-p3-hp harmonic 48.850 96.410 # SOURCE3 2 0.0000
angle_coeff @angle:f-p3-n3 harmonic 66.890 100.600 # SOURCE2 1 0.0000
angle_coeff @angle:f-p3-os harmonic 67.790 102.200 # SOURCE2 1 0.0000
angle_coeff @angle:f-p3-p3 harmonic 59.520 97.200 # SOURCE2 1 0.0000
angle_coeff @angle:hp-p3-hp harmonic 35.200 95.520 # SOURCE3 44 2.4200
angle_coeff @angle:hp-p3-i harmonic 37.430 96.190 # SOURCE3 4 0.6454
angle_coeff @angle:hp-p3-n1 harmonic 49.970 92.980 # HF/6-31G* 1
angle_coeff @angle:hp-p3-n2 harmonic 46.470 98.280 # SOURCE3 10 1.8860
angle_coeff @angle:hp-p3-n3 harmonic 48.110 94.460 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-n4 harmonic 45.300 93.210 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-n harmonic 47.100 95.150 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-na harmonic 46.750 97.270 # SOURCE3 12 0.9318
angle_coeff @angle:hp-p3-nh harmonic 48.200 94.100 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-no harmonic 46.080 93.060 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-o harmonic 51.150 101.020 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-oh harmonic 49.120 95.950 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-os harmonic 48.580 97.350 # SOURCE3 6 2.8326
angle_coeff @angle:hp-p3-p2 harmonic 40.920 99.110 # SOURCE3 16 4.3022
angle_coeff @angle:hp-p3-p3 harmonic 40.500 95.520 # SOURCE3 4 0.0844
angle_coeff @angle:hp-p3-p4 harmonic 40.370 95.950 # SOURCE3 6 0.0489
angle_coeff @angle:hp-p3-p5 harmonic 40.510 95.540 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-s4 harmonic 54.390 95.490 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-s6 harmonic 55.380 92.950 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-sh harmonic 53.620 94.210 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p3-ss harmonic 53.780 94.610 # SOURCE3 2 0.0000
angle_coeff @angle:i-p3-i harmonic 58.550 105.250 # SOURCE3 1 0.0000
angle_coeff @angle:n1-p3-n1 harmonic 73.380 90.440 # HF/6-31G* 1
angle_coeff @angle:n2-p3-n2 harmonic 64.560 103.460 # SOURCE3 1 0.0000
angle_coeff @angle:n3-p3-n3 harmonic 62.770 113.800 # SOURCE3 1 0.0000
angle_coeff @angle:n3-p3-o harmonic 68.780 107.100 # SOURCE3 4 0.0000
angle_coeff @angle:n3-p3-oh harmonic 68.930 98.360 # SOURCE3 1
angle_coeff @angle:n4-p3-n4 harmonic 61.460 100.530 # SOURCE3 1 0.0000
angle_coeff @angle:na-p3-na harmonic 63.790 106.220 # SOURCE3 1
angle_coeff @angle:nh-p3-nh harmonic 64.100 109.110 # SOURCE3 1 0.0000
angle_coeff @angle:n-p3-n harmonic 64.000 104.580 # SOURCE3 1
angle_coeff @angle:n-p3-o harmonic 68.400 104.990 # SOURCE3 4 0.0000
angle_coeff @angle:no-p3-no harmonic 63.350 98.330 # SOURCE3 1 0.0000
angle_coeff @angle:oh-p3-oh harmonic 68.360 104.480 # SOURCE3 1 0.0000
angle_coeff @angle:o-p3-o harmonic 69.980 122.180 # SOURCE3 2 7.8556
angle_coeff @angle:o-p3-p3 harmonic 56.940 116.740 # SOURCE3 14 0.7525
angle_coeff @angle:o-p3-p5 harmonic 59.320 107.620 # SOURCE3 4 0.0000
angle_coeff @angle:o-p3-s4 harmonic 78.140 110.700 # SOURCE3 4 0.7259
angle_coeff @angle:o-p3-s6 harmonic 79.950 106.660 # SOURCE3 6 3.4017
angle_coeff @angle:os-p3-os harmonic 67.300 106.650 # SOURCE3 1 0.0000
angle_coeff @angle:p2-p3-p2 harmonic 58.990 103.580 # SOURCE3 1 0.0000
angle_coeff @angle:p3-p3-p3 harmonic 56.870 105.310 # SOURCE3 4 3.5864
angle_coeff @angle:p4-p3-p4 harmonic 58.570 99.090 # SOURCE3 1
angle_coeff @angle:p5-p3-p5 harmonic 58.650 99.100 # SOURCE3 1 0.0000
angle_coeff @angle:s4-p3-s4 harmonic 100.040 98.260 # SOURCE3 1 0.0000
angle_coeff @angle:s6-p3-s6 harmonic 100.770 97.780 # SOURCE3 1 0.0000
angle_coeff @angle:sh-p3-sh harmonic 93.590 107.580 # SOURCE3 1 0.0000
angle_coeff @angle:s-p3-s harmonic 87.250 131.320 # SOURCE3 1
angle_coeff @angle:ss-p3-ss harmonic 93.360 109.240 # SOURCE3 1 0.0000
angle_coeff @angle:br-p4-br harmonic 65.640 110.410 # SOURCE3 1
angle_coeff @angle:br-p4-o harmonic 60.420 124.800 # SOURCE3 1
angle_coeff @angle:c2-p4-c2 harmonic 59.340 104.210 # SOURCE3 1
angle_coeff @angle:c2-p4-hp harmonic 44.230 99.500 # SOURCE3 2 0.0000
angle_coeff @angle:c2-p4-o harmonic 63.010 113.590 # SOURCE3 1
angle_coeff @angle:c3-p4-c3 harmonic 59.460 102.550 # SOURCE3 4 0.0192
angle_coeff @angle:c3-p4-n2 harmonic 62.470 103.170 # SOURCE3 1
angle_coeff @angle:c3-p4-n3 harmonic 63.130 102.370 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p4-n4 harmonic 60.000 99.570 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p4-n harmonic 62.290 103.260 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p4-na harmonic 60.600 117.670 # SOURCE3 5 19.0404
angle_coeff @angle:c3-p4-nh harmonic 62.860 102.790 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p4-no harmonic 61.120 99.800 # SOURCE3 3 0.2151
angle_coeff @angle:c3-p4-o harmonic 61.960 116.440 # SOURCE3 25 2.6494
angle_coeff @angle:c3-p4-oh harmonic 65.550 98.560 # SOURCE3 2 0.4558
angle_coeff @angle:c3-p4-os harmonic 65.800 98.010 # SOURCE3 2 0.0931
angle_coeff @angle:c3-p4-p2 harmonic 56.110 109.270 # SOURCE3 1
angle_coeff @angle:c3-p4-p3 harmonic 56.940 103.530 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p4-p4 harmonic 60.790 102.120 # SOURCE3 1
angle_coeff @angle:c3-p4-p5 harmonic 56.380 104.150 # SOURCE3 1
angle_coeff @angle:c3-p4-sh harmonic 75.720 100.170 # SOURCE3 2 0.0815
angle_coeff @angle:c3-p4-ss harmonic 75.600 101.190 # SOURCE3 1
angle_coeff @angle:ca-p4-ca harmonic 58.870 107.770 # SOURCE3 1
angle_coeff @angle:ca-p4-o harmonic 63.970 111.640 # SOURCE3 1
angle_coeff @angle:cl-p4-cl harmonic 62.460 103.510 # SOURCE3 1 0.0000
angle_coeff @angle:cl-p4-o harmonic 61.910 116.530 # SOURCE3 2 0.0000
angle_coeff @angle:hp-p4-hp harmonic 36.070 99.210 # SOURCE3 4 6.4572
angle_coeff @angle:hp-p4-n1 harmonic 48.330 99.910 # HF/6-31G* 1
angle_coeff @angle:hp-p4-o harmonic 50.250 109.350 # SOURCE3 6 10.8284
angle_coeff @angle:hp-p4-p3 harmonic 39.650 98.960 # SOURCE3 4 0.0000
angle_coeff @angle:hp-p4-s harmonic 49.200 110.240 # SOURCE3 4 4.1081
angle_coeff @angle:i-p4-i harmonic 61.590 113.220 # SOURCE3 2 6.7916
angle_coeff @angle:i-p4-o harmonic 60.270 110.220 # SOURCE3 4 9.7726
angle_coeff @angle:n1-p4-n1 harmonic 68.740 100.610 # HF/6-31G* 1
angle_coeff @angle:n1-p4-o harmonic 67.970 114.590 # HF/6-31G* 1
angle_coeff @angle:n2-p4-n2 harmonic 66.360 102.540 # SOURCE3 1
angle_coeff @angle:n2-p4-o harmonic 65.230 120.280 # SOURCE3 1
angle_coeff @angle:n3-p4-o harmonic 67.920 113.270 # SOURCE3 1 0.0000
angle_coeff @angle:n4-p4-o harmonic 63.230 107.610 # SOURCE3 1 0.0000
angle_coeff @angle:na-p4-o harmonic 72.190 110.600 # SOURCE3 5 1.3133
angle_coeff @angle:nh-p4-nh harmonic 69.560 95.300 # SOURCE3 1 0.0000
angle_coeff @angle:nh-p4-o harmonic 66.920 115.860 # SOURCE3 3 3.2712
angle_coeff @angle:n-p4-o harmonic 65.600 117.990 # SOURCE3 1 0.0000
angle_coeff @angle:no-p4-o harmonic 63.000 114.690 # SOURCE3 3 0.1070
angle_coeff @angle:oh-p4-oh harmonic 72.990 95.710 # SOURCE3 1 0.0000
angle_coeff @angle:o-p4-o harmonic 72.010 117.220 # SOURCE3 6 2.7792
angle_coeff @angle:o-p4-oh harmonic 68.540 117.390 # SOURCE3 4 1.0083
angle_coeff @angle:o-p4-os harmonic 68.880 116.670 # SOURCE3 4 0.6923
angle_coeff @angle:o-p4-p2 harmonic 56.720 121.350 # SOURCE3 1
angle_coeff @angle:o-p4-p3 harmonic 57.580 114.000 # SOURCE3 3 0.6663
angle_coeff @angle:o-p4-p4 harmonic 61.640 116.430 # SOURCE3 1
angle_coeff @angle:o-p4-p5 harmonic 58.150 109.760 # SOURCE3 1
angle_coeff @angle:o-p4-s4 harmonic 72.350 112.190 # SOURCE3 1
angle_coeff @angle:o-p4-s6 harmonic 71.250 113.890 # SOURCE3 1
angle_coeff @angle:o-p4-s harmonic 75.540 112.780 # SOURCE3 2 0.0000
angle_coeff @angle:o-p4-sh harmonic 74.810 118.090 # SOURCE3 1
angle_coeff @angle:os-p4-os harmonic 71.510 100.340 # SOURCE3 1 0.0000
angle_coeff @angle:o-p4-ss harmonic 75.800 116.140 # SOURCE3 4 1.0636
angle_coeff @angle:p2-p4-p2 harmonic 56.350 110.710 # SOURCE3 1
angle_coeff @angle:p3-p4-p3 harmonic 54.380 114.980 # SOURCE3 1 0.0000
angle_coeff @angle:p4-p4-p4 harmonic 61.300 107.380 # SOURCE3 1
angle_coeff @angle:p5-p4-p5 harmonic 55.630 107.780 # SOURCE3 1
angle_coeff @angle:s4-p4-s4 harmonic 93.720 96.240 # SOURCE3 1
angle_coeff @angle:s6-p4-s6 harmonic 90.160 102.360 # SOURCE3 1
angle_coeff @angle:sh-p4-sh harmonic 98.440 98.810 # SOURCE3 1 0.0000
angle_coeff @angle:s-p4-s harmonic 93.540 106.300 # SOURCE3 2 25.0119
angle_coeff @angle:ss-p4-ss harmonic 96.270 104.410 # SOURCE3 1 0.0000
angle_coeff @angle:br-p5-br harmonic 67.070 103.380 # SOURCE3 1 0.0000
angle_coeff @angle:br-p5-o harmonic 62.390 114.650 # SOURCE3 3 1.0910
angle_coeff @angle:br-p5-oh harmonic 65.360 102.920 # SOURCE3 4 0.5468
angle_coeff @angle:c1-p5-c1 harmonic 62.070 102.890 # SOURCE3 1 0.0000
angle_coeff @angle:c1-p5-o harmonic 64.450 115.770 # SOURCE3 2 0.0000
angle_coeff @angle:c1-p5-oh harmonic 66.220 102.790 # SOURCE3 2 0.0000
angle_coeff @angle:c2-p5-c2 harmonic 57.300 106.560 # SOURCE3 1
angle_coeff @angle:c2-p5-o harmonic 63.330 109.240 # SOURCE4 7 2.2628
angle_coeff @angle:c2-p5-oh harmonic 64.000 101.690 # SOURCE3 1
angle_coeff @angle:c2-p5-os harmonic 63.780 103.340 # SOURCE3 1
angle_coeff @angle:c3-p5-c3 harmonic 59.060 106.230 # SOURCE3 14 2.6389
angle_coeff @angle:c3-p5-hp harmonic 43.230 103.620 # SOURCE4 7 1.1616
angle_coeff @angle:c3-p5-n3 harmonic 63.940 102.760 # SOURCE3 1 0.0000
angle_coeff @angle:c3-p5-o harmonic 63.790 112.500 # SOURCE3 23 4.4203
angle_coeff @angle:c3-p5-oh harmonic 65.260 101.560 # SOURCE3 17 2.1803
angle_coeff @angle:c3-p5-os harmonic 65.840 100.770 # SOURCE4 51 2.0928
angle_coeff @angle:c3-p5-p4 harmonic 55.960 106.270 # SOURCE3 1
angle_coeff @angle:c3-p5-s harmonic 75.870 113.400 # SOURCE3 4 2.0067
angle_coeff @angle:c3-p5-ss harmonic 74.660 103.760 # SOURCE3 1 0.0000
angle_coeff @angle:ca-p5-ca harmonic 59.290 107.530 # SOURCE3 1
angle_coeff @angle:ca-p5-o harmonic 63.850 113.980 # SOURCE3 1
angle_coeff @angle:ca-p5-oh harmonic 65.600 101.770 # SOURCE3 1
angle_coeff @angle:ca-p5-os harmonic 65.310 103.750 # SOURCE3 1
angle_coeff @angle:c-p5-c harmonic 57.470 104.160 # SOURCE3 1
angle_coeff @angle:cl-p5-cl harmonic 62.400 103.700 # SOURCE2 1 0.0000
angle_coeff @angle:cl-p5-o harmonic 62.360 115.320 # SOURCE3 2 0.0000
angle_coeff @angle:cl-p5-oh harmonic 65.050 102.440 # SOURCE3 2 0.0000
angle_coeff @angle:c-p5-o harmonic 63.510 107.190 # SOURCE4 16 0.5711
angle_coeff @angle:c-p5-oh harmonic 63.500 102.120 # SOURCE3 1
angle_coeff @angle:f-p5-f harmonic 67.910 99.960 # SOURCE2 4 0.9197
angle_coeff @angle:f-p5-o harmonic 69.070 112.030 # SOURCE4 7 0.5178
angle_coeff @angle:f-p5-oh harmonic 69.260 101.980 # SOURCE3 2 0.0000
angle_coeff @angle:f-p5-os harmonic 69.530 102.700 # SOURCE4 5 0.1524
angle_coeff @angle:f-p5-s harmonic 77.040 117.400 # SOURCE2 1 0.0000
angle_coeff @angle:hp-p5-hp harmonic 34.260 101.090 # SOURCE3 4 1.3036
angle_coeff @angle:hp-p5-n1 harmonic 49.690 101.320 # HF/6-31G* 1
angle_coeff @angle:hp-p5-o harmonic 48.280 116.580 # SOURCE3 7 1.3282
angle_coeff @angle:hp-p5-oh harmonic 48.850 101.450 # SOURCE3 5 0.9084
angle_coeff @angle:hp-p5-s harmonic 52.540 119.200 # SOURCE2 1 0.0000
angle_coeff @angle:i-p5-i harmonic 57.350 107.170 # SOURCE3 1 0.0000
angle_coeff @angle:i-p5-o harmonic 52.720 115.930 # SOURCE3 3 0.0415
angle_coeff @angle:i-p5-oh harmonic 56.650 102.260 # SOURCE3 4 1.9577
angle_coeff @angle:n1-p5-n1 harmonic 73.170 101.550 # HF/6-31G* 1
angle_coeff @angle:n1-p5-o harmonic 71.450 113.780 # HF/6-31G* 1
angle_coeff @angle:n2-p5-n2 harmonic 70.250 106.340 # SOURCE3 1
angle_coeff @angle:n2-p5-o harmonic 70.800 113.530 # SOURCE3 1
angle_coeff @angle:n2-p5-oh harmonic 71.420 102.400 # SOURCE3 1
angle_coeff @angle:n3-p5-n3 harmonic 68.510 103.370 # SOURCE4 47 2.1009
angle_coeff @angle:n3-p5-nh harmonic 68.130 104.020 # SOURCE4 5 1.8740
angle_coeff @angle:n3-p5-o harmonic 68.760 114.640 # SOURCE4 76 2.2728
angle_coeff @angle:n3-p5-oh harmonic 69.420 104.180 # SOURCE3 6 0.4373
angle_coeff @angle:n3-p5-os harmonic 70.640 101.940 # SOURCE4 34 2.3553
angle_coeff @angle:n3-p5-s harmonic 78.990 117.120 # SOURCE4 7 0.7109
angle_coeff @angle:n4-p5-n4 harmonic 62.620 102.200 # SOURCE3 1 0.0000
angle_coeff @angle:n4-p5-o harmonic 65.690 109.780 # SOURCE3 5 2.7519
angle_coeff @angle:n4-p5-oh harmonic 67.490 98.480 # SOURCE3 6 0.4104
angle_coeff @angle:n4-p5-os harmonic 69.210 94.550 # SOURCE3 2 0.0000
angle_coeff @angle:na-p5-na harmonic 64.830 108.570 # SOURCE3 1 0.0000
angle_coeff @angle:na-p5-o harmonic 67.730 113.430 # SOURCE3 11 0.8968
angle_coeff @angle:na-p5-oh harmonic 68.960 102.070 # SOURCE3 16 1.4144
angle_coeff @angle:na-p5-os harmonic 69.040 103.060 # SOURCE3 4 0.7463
angle_coeff @angle:nh-p5-nh harmonic 69.500 99.510 # SOURCE3 1 0.0000
angle_coeff @angle:nh-p5-o harmonic 67.300 118.910 # SOURCE3 3 1.3237
angle_coeff @angle:nh-p5-oh harmonic 69.360 103.810 # SOURCE3 2 0.0000
angle_coeff @angle:nh-p5-os harmonic 70.950 100.510 # SOURCE3 2 0.0000
angle_coeff @angle:n-p5-n3 harmonic 67.330 104.110 # SOURCE4 11 1.4088
angle_coeff @angle:n-p5-n harmonic 66.800 103.090 # SOURCE3 1 0.0000
angle_coeff @angle:n-p5-o harmonic 69.370 108.730 # SOURCE4 5 0.2571
angle_coeff @angle:n-p5-oh harmonic 68.990 102.440 # SOURCE3 4 0.0999
angle_coeff @angle:no-p5-no harmonic 64.570 95.680 # SOURCE3 1 0.0000
angle_coeff @angle:no-p5-o harmonic 64.720 112.750 # SOURCE3 4 3.3684
angle_coeff @angle:no-p5-oh harmonic 66.430 101.350 # SOURCE3 2 0.0000
angle_coeff @angle:no-p5-os harmonic 66.640 101.700 # SOURCE3 4 0.0565
angle_coeff @angle:n-p5-os harmonic 70.090 100.480 # SOURCE3 2 0.0000
angle_coeff @angle:oh-p5-oh harmonic 71.250 102.450 # SOURCE3 39 2.4223
angle_coeff @angle:oh-p5-os harmonic 71.770 102.370 # SOURCE3 8 1.5063
angle_coeff @angle:oh-p5-p2 harmonic 60.920 103.530 # SOURCE3 1
angle_coeff @angle:oh-p5-p3 harmonic 60.040 103.830 # SOURCE3 13 0.4303
angle_coeff @angle:oh-p5-p4 harmonic 60.070 101.790 # SOURCE3 1
angle_coeff @angle:oh-p5-p5 harmonic 64.950 100.450 # SOURCE3 1
angle_coeff @angle:oh-p5-s4 harmonic 81.520 103.240 # SOURCE3 1
angle_coeff @angle:oh-p5-s6 harmonic 82.230 101.480 # SOURCE3 1
angle_coeff @angle:oh-p5-s harmonic 85.370 102.880 # SOURCE3 3 1.6044
angle_coeff @angle:oh-p5-sh harmonic 80.940 101.410 # SOURCE3 2 0.0000
angle_coeff @angle:oh-p5-ss harmonic 78.780 104.330 # SOURCE3 6 2.0112
angle_coeff @angle:o-p5-o harmonic 73.530 115.800 # SOURCE3 17 5.7902
angle_coeff @angle:o-p5-oh harmonic 69.980 115.260 # SOURCE4 740 1.3004
angle_coeff @angle:o-p5-os harmonic 70.340 116.090 # SOURCE3 35 3.2062
angle_coeff @angle:o-p5-p2 harmonic 58.380 114.600 # SOURCE3 1
angle_coeff @angle:o-p5-p3 harmonic 57.310 115.480 # SOURCE3 9 2.1084
angle_coeff @angle:o-p5-p4 harmonic 56.910 114.660 # SOURCE3 1
angle_coeff @angle:o-p5-p5 harmonic 62.020 113.440 # SOURCE3 1
angle_coeff @angle:o-p5-s4 harmonic 80.110 110.230 # SOURCE3 1
angle_coeff @angle:o-p5-s6 harmonic 79.570 111.750 # SOURCE3 1
angle_coeff @angle:o-p5-s harmonic 81.840 116.940 # SOURCE3 3 2.9506
angle_coeff @angle:o-p5-sh harmonic 77.150 114.560 # SOURCE3 3 1.7645
angle_coeff @angle:os-p5-os harmonic 72.510 101.770 # SOURCE4 243 2.0816
angle_coeff @angle:os-p5-p3 harmonic 60.190 103.670 # SOURCE3 2 0.0000
angle_coeff @angle:os-p5-p5 harmonic 63.870 104.480 # SOURCE3 1
angle_coeff @angle:os-p5-s4 harmonic 82.050 102.520 # SOURCE3 1
angle_coeff @angle:os-p5-s6 harmonic 82.310 101.890 # SOURCE3 1
angle_coeff @angle:o-p5-ss harmonic 76.760 112.460 # SOURCE3 6 2.7392
angle_coeff @angle:os-p5-s harmonic 80.280 117.280 # SOURCE4 74 0.7542
angle_coeff @angle:os-p5-sh harmonic 79.910 104.590 # SOURCE3 2 0.0000
angle_coeff @angle:os-p5-ss harmonic 79.620 102.650 # SOURCE4 25 1.8093
angle_coeff @angle:p2-p5-p2 harmonic 57.260 107.140 # SOURCE3 1
angle_coeff @angle:p3-p5-p3 harmonic 56.920 105.230 # SOURCE3 3 5.1024
angle_coeff @angle:p4-p5-p4 harmonic 57.300 101.620 # SOURCE3 1
angle_coeff @angle:p5-p5-p5 harmonic 59.250 112.720 # SOURCE3 1
angle_coeff @angle:s6-p5-s6 harmonic 98.920 105.180 # SOURCE3 1
angle_coeff @angle:sh-p5-sh harmonic 97.210 104.560 # SOURCE3 1 0.0000
angle_coeff @angle:sh-p5-ss harmonic 95.280 107.130 # SOURCE3 1
angle_coeff @angle:s-p5-s harmonic 100.790 114.130 # SOURCE3 1 0.0000
angle_coeff @angle:ss-p5-ss harmonic 93.470 109.610 # SOURCE3 1 0.0000
angle_coeff @angle:cd-pc-n harmonic 68.330 90.800 # SOURCE3 3 2.3423
angle_coeff @angle:cd-pc-na harmonic 68.730 90.180 # SOURCE3 81 2.7619
angle_coeff @angle:cc-pd-n harmonic 68.330 90.800 # SOURCE3 3 same_as_cd-pc-n
angle_coeff @angle:cc-pd-na harmonic 68.730 90.180 # SOURCE3 81 same_as_cd-pc-na
angle_coeff @angle:c2-pe-ca harmonic 62.070 101.440 # SOURCE3 3 0.7177
angle_coeff @angle:c2-pe-ce harmonic 61.820 103.010 # SOURCE3 4 1.4470
angle_coeff @angle:c2-pe-cg harmonic 65.280 104.030 # SOURCE3 3 3.8740
angle_coeff @angle:c2-pe-n2 harmonic 71.820 94.140 # SOURCE3 1
angle_coeff @angle:c2-pe-ne harmonic 66.880 98.700 # SOURCE3 12 5.3383
angle_coeff @angle:c2-pe-o harmonic 65.620 115.160 # SOURCE3 2 0.0149
angle_coeff @angle:c2-pe-p2 harmonic 64.330 107.820 # SOURCE3 1
angle_coeff @angle:c2-pe-pe harmonic 60.830 102.990 # SOURCE3 9 8.2860
angle_coeff @angle:c2-pe-px harmonic 64.550 97.370 # SOURCE3 4 0.6655
angle_coeff @angle:c2-pe-py harmonic 64.310 96.710 # SOURCE3 4 1.2755
angle_coeff @angle:c2-pe-s harmonic 83.060 111.160 # SOURCE3 2 0.0000
angle_coeff @angle:c2-pe-sx harmonic 77.900 95.110 # SOURCE3 4 0.2676
angle_coeff @angle:c2-pe-sy harmonic 76.420 95.560 # SOURCE3 2 0.0462
angle_coeff @angle:ca-pe-n2 harmonic 65.480 102.030 # SOURCE3 1 0.0000
angle_coeff @angle:ca-pe-o harmonic 64.570 106.880 # SOURCE3 2 0.0018
angle_coeff @angle:ca-pe-p2 harmonic 64.350 100.790 # SOURCE3 1 0.0000
angle_coeff @angle:ca-pe-pf harmonic 61.170 99.700 # SOURCE3 2 0.0000
angle_coeff @angle:ca-pe-s harmonic 81.050 107.930 # SOURCE3 1 0.0000
angle_coeff @angle:c-pe-c2 harmonic 61.660 97.300 # SOURCE3 3 0.0335
angle_coeff @angle:ce-pe-n2 harmonic 66.250 100.550 # SOURCE3 1 0.0000
angle_coeff @angle:ce-pe-o harmonic 64.690 107.440 # SOURCE3 1 0.0000
angle_coeff @angle:ce-pe-p2 harmonic 64.930 99.560 # SOURCE3 1 0.0000
angle_coeff @angle:ce-pe-s harmonic 82.230 105.540 # SOURCE3 1 0.0000
angle_coeff @angle:cg-pe-n2 harmonic 70.820 101.790 # SOURCE3 1 0.0000
angle_coeff @angle:cg-pe-o harmonic 69.640 107.620 # SOURCE3 1 0.0000
angle_coeff @angle:cg-pe-p2 harmonic 66.260 104.680 # SOURCE3 2 5.1435
angle_coeff @angle:cg-pe-s harmonic 85.560 108.600 # SOURCE3 4 2.6981
angle_coeff @angle:n2-pe-n2 harmonic 72.340 108.140 # SOURCE3 1
angle_coeff @angle:n2-pe-ne harmonic 68.550 106.800 # SOURCE3 6 4.5981
angle_coeff @angle:n2-pe-o harmonic 70.860 115.390 # SOURCE3 1 0.0000
angle_coeff @angle:n2-pe-p2 harmonic 66.740 111.600 # SOURCE3 1
angle_coeff @angle:n2-pe-pe harmonic 61.500 109.400 # SOURCE3 1 0.0000
angle_coeff @angle:n2-pe-px harmonic 63.500 110.300 # SOURCE3 3 6.0548
angle_coeff @angle:n2-pe-py harmonic 68.340 93.680 # SOURCE3 1 0.0000
angle_coeff @angle:n2-pe-s harmonic 86.860 114.840 # SOURCE3 3 3.6512
angle_coeff @angle:n2-pe-sx harmonic 79.730 97.830 # SOURCE3 1 0.0000
angle_coeff @angle:n2-pe-sy harmonic 78.100 98.140 # SOURCE3 1 0.0000
angle_coeff @angle:ne-pe-o harmonic 68.170 110.240 # SOURCE3 3 3.8478
angle_coeff @angle:ne-pe-p2 harmonic 66.630 104.480 # SOURCE3 2 7.1207
angle_coeff @angle:ne-pe-s harmonic 85.380 109.190 # SOURCE3 5 3.6708
angle_coeff @angle:o-pe-o harmonic 70.340 119.960 # SOURCE3 1 0.0000
angle_coeff @angle:o-pe-p2 harmonic 66.560 114.230 # SOURCE3 1 0.0000
angle_coeff @angle:o-pe-pe harmonic 53.630 145.960 # SOURCE3 1 0.0000
angle_coeff @angle:o-pe-px harmonic 65.790 104.370 # SOURCE3 1 0.0000
angle_coeff @angle:o-pe-py harmonic 65.210 104.490 # SOURCE3 1 0.0000
angle_coeff @angle:o-pe-s harmonic 86.750 117.420 # SOURCE3 2 0.0426
angle_coeff @angle:o-pe-sx harmonic 76.900 106.590 # SOURCE3 1 0.0000
angle_coeff @angle:o-pe-sy harmonic 75.980 105.040 # SOURCE3 1 0.0000
angle_coeff @angle:p2-pe-pe harmonic 65.430 98.240 # SOURCE3 1 0.0000
angle_coeff @angle:p2-pe-px harmonic 63.970 108.280 # SOURCE3 2 6.2959
angle_coeff @angle:p2-pe-py harmonic 62.850 110.870 # SOURCE3 3 8.1645
angle_coeff @angle:p2-pe-s harmonic 85.370 111.280 # SOURCE3 1 0.0000
angle_coeff @angle:p2-pe-sx harmonic 81.920 95.730 # SOURCE3 1 0.0000
angle_coeff @angle:p2-pe-sy harmonic 80.670 95.950 # SOURCE3 1 0.0000
angle_coeff @angle:pe-pe-s harmonic 80.550 107.910 # SOURCE3 2 1.5577
angle_coeff @angle:px-pe-s harmonic 83.060 107.620 # SOURCE3 2 3.7266
angle_coeff @angle:py-pe-s harmonic 82.090 108.730 # SOURCE3 3 5.3201
angle_coeff @angle:s-pe-s harmonic 88.130 178.440 # SOURCE3 1 0.0000
angle_coeff @angle:s-pe-sx harmonic 99.120 108.320 # SOURCE3 2 3.0318
angle_coeff @angle:s-pe-sy harmonic 98.190 106.930 # SOURCE3 1 0.0000
angle_coeff @angle:c2-pf-ca harmonic 62.070 101.440 # SOURCE3 3 same_as_c2-pe-ca
angle_coeff @angle:c2-pf-cf harmonic 61.820 103.010 # SOURCE3 4 same_as_c2-pe-ce
angle_coeff @angle:c2-pf-ch harmonic 65.280 104.030 # SOURCE3 3 same_as_c2-pe-cg
angle_coeff @angle:c2-pf-n2 harmonic 71.820 94.140 # SOURCE3 1 same_as_c2-pe-n2
angle_coeff @angle:c2-pf-nf harmonic 66.880 98.700 # SOURCE3 12 same_as_c2-pe-ne
angle_coeff @angle:c2-pf-o harmonic 65.620 115.160 # SOURCE3 2 same_as_c2-pe-o
angle_coeff @angle:c2-pf-p2 harmonic 64.330 107.820 # SOURCE3 1 same_as_c2-pe-p2
angle_coeff @angle:c2-pf-pf harmonic 60.830 102.990 # SOURCE3 9 same_as_c2-pe-pe
angle_coeff @angle:c2-pf-px harmonic 64.550 97.370 # SOURCE3 4 same_as_c2-pe-px
angle_coeff @angle:c2-pf-py harmonic 64.310 96.710 # SOURCE3 4 same_as_c2-pe-py
angle_coeff @angle:c2-pf-s harmonic 83.060 111.160 # SOURCE3 2 same_as_c2-pe-s
angle_coeff @angle:c2-pf-sx harmonic 77.900 95.110 # SOURCE3 4 same_as_c2-pe-sx
angle_coeff @angle:c2-pf-sy harmonic 76.420 95.560 # SOURCE3 2 same_as_c2-pe-sy
angle_coeff @angle:ca-pf-n2 harmonic 65.480 102.030 # SOURCE3 1 same_as_ca-pe-n2
angle_coeff @angle:ca-pf-o harmonic 64.570 106.880 # SOURCE3 2 same_as_ca-pe-o
angle_coeff @angle:ca-pf-p2 harmonic 64.350 100.790 # SOURCE3 1 same_as_ca-pe-p2
angle_coeff @angle:ca-pf-pe harmonic 61.170 99.700 # SOURCE3 2 0.0000
angle_coeff @angle:ca-pf-s harmonic 81.050 107.930 # SOURCE3 1 same_as_ca-pe-s
angle_coeff @angle:c-pf-c2 harmonic 61.660 97.300 # SOURCE3 3 same_as_c-pe-c2
angle_coeff @angle:cf-pf-n2 harmonic 66.250 100.550 # SOURCE3 1 same_as_ce-pe-n2
angle_coeff @angle:cf-pf-o harmonic 64.690 107.440 # SOURCE3 1 same_as_ce-pe-o
angle_coeff @angle:cf-pf-p2 harmonic 64.930 99.560 # SOURCE3 1 same_as_ce-pe-p2
angle_coeff @angle:cf-pf-s harmonic 82.230 105.540 # SOURCE3 1 same_as_ce-pe-s
angle_coeff @angle:ch-pf-n2 harmonic 70.820 101.790 # SOURCE3 1 same_as_cg-pe-n2
angle_coeff @angle:ch-pf-o harmonic 69.640 107.620 # SOURCE3 1 same_as_cg-pe-o
angle_coeff @angle:ch-pf-p2 harmonic 66.260 104.680 # SOURCE3 2 same_as_cg-pe-p2
angle_coeff @angle:ch-pf-s harmonic 85.560 108.600 # SOURCE3 4 same_as_cg-pe-s
angle_coeff @angle:n2-pf-n2 harmonic 72.340 108.140 # SOURCE3 1 same_as_n2-pe-n2
angle_coeff @angle:n2-pf-nf harmonic 68.550 106.800 # SOURCE3 6 same_as_n2-pe-ne
angle_coeff @angle:n2-pf-o harmonic 70.860 115.390 # SOURCE3 1 same_as_n2-pe-o
angle_coeff @angle:n2-pf-p2 harmonic 66.740 111.600 # SOURCE3 1 same_as_n2-pe-p2
angle_coeff @angle:n2-pf-pf harmonic 61.500 109.400 # SOURCE3 1 same_as_n2-pe-pe
angle_coeff @angle:n2-pf-px harmonic 63.500 110.300 # SOURCE3 3 same_as_n2-pe-px
angle_coeff @angle:n2-pf-py harmonic 68.340 93.680 # SOURCE3 1 same_as_n2-pe-py
angle_coeff @angle:n2-pf-s harmonic 86.860 114.840 # SOURCE3 3 same_as_n2-pe-s
angle_coeff @angle:n2-pf-sx harmonic 79.730 97.830 # SOURCE3 1 same_as_n2-pe-sx
angle_coeff @angle:n2-pf-sy harmonic 78.100 98.140 # SOURCE3 1 same_as_n2-pe-sy
angle_coeff @angle:nf-pf-o harmonic 68.170 110.240 # SOURCE3 3 same_as_ne-pe-o
angle_coeff @angle:nf-pf-p2 harmonic 66.630 104.480 # SOURCE3 2 same_as_ne-pe-p2
angle_coeff @angle:nf-pf-s harmonic 85.380 109.190 # SOURCE3 5 same_as_ne-pe-s
angle_coeff @angle:o-pf-o harmonic 70.340 119.960 # SOURCE3 1 same_as_o-pe-o
angle_coeff @angle:o-pf-p2 harmonic 66.560 114.230 # SOURCE3 1 same_as_o-pe-p2
angle_coeff @angle:o-pf-pf harmonic 53.630 145.960 # SOURCE3 1 same_as_o-pe-pe
angle_coeff @angle:o-pf-px harmonic 65.790 104.370 # SOURCE3 1 same_as_o-pe-px
angle_coeff @angle:o-pf-py harmonic 65.210 104.490 # SOURCE3 1 same_as_o-pe-py
angle_coeff @angle:o-pf-s harmonic 86.750 117.420 # SOURCE3 2 same_as_o-pe-s
angle_coeff @angle:o-pf-sx harmonic 76.900 106.590 # SOURCE3 1 same_as_o-pe-sx
angle_coeff @angle:o-pf-sy harmonic 75.980 105.040 # SOURCE3 1 same_as_o-pe-sy
angle_coeff @angle:p2-pf-pf harmonic 65.430 98.240 # SOURCE3 1 same_as_p2-pe-pe
angle_coeff @angle:p2-pf-px harmonic 63.970 108.280 # SOURCE3 2 same_as_p2-pe-px
angle_coeff @angle:p2-pf-py harmonic 62.850 110.870 # SOURCE3 3 same_as_p2-pe-py
angle_coeff @angle:p2-pf-s harmonic 85.370 111.280 # SOURCE3 1 same_as_p2-pe-s
angle_coeff @angle:p2-pf-sx harmonic 81.920 95.730 # SOURCE3 1 same_as_p2-pe-sx
angle_coeff @angle:p2-pf-sy harmonic 80.670 95.950 # SOURCE3 1 same_as_p2-pe-sy
angle_coeff @angle:pf-pf-s harmonic 80.550 107.910 # SOURCE3 2 same_as_pe-pe-s
angle_coeff @angle:px-pf-s harmonic 83.060 107.620 # SOURCE3 2 same_as_px-pe-s
angle_coeff @angle:py-pf-s harmonic 82.090 108.730 # SOURCE3 3 same_as_py-pe-s
angle_coeff @angle:s-pf-s harmonic 88.130 178.440 # SOURCE3 1 same_as_s-pe-s
angle_coeff @angle:s-pf-sx harmonic 99.120 108.320 # SOURCE3 2 same_as_s-pe-sx
angle_coeff @angle:s-pf-sy harmonic 98.190 106.930 # SOURCE3 1 same_as_s-pe-sy
angle_coeff @angle:c3-px-ca harmonic 59.090 104.790 # SOURCE3 1 0.0000
angle_coeff @angle:c3-px-ce harmonic 59.140 104.860 # SOURCE3 4 0.6354
angle_coeff @angle:c3-px-cf harmonic 59.140 104.860 # SOURCE3 4 same_as_c3-px-ce
angle_coeff @angle:c3-px-ne harmonic 63.210 102.460 # SOURCE3 7 1.8685
angle_coeff @angle:c3-px-nf harmonic 63.210 102.460 # SOURCE3 7 same_as_c3-px-ne
angle_coeff @angle:c3-px-o harmonic 62.960 113.680 # SOURCE3 28 4.8990
angle_coeff @angle:c3-px-pe harmonic 60.390 105.730 # SOURCE3 10 4.4059
angle_coeff @angle:c3-px-pf harmonic 60.390 105.730 # SOURCE3 10 same_as_c3-px-pe
angle_coeff @angle:c3-px-py harmonic 57.460 103.110 # SOURCE3 3 0.8680
angle_coeff @angle:c3-px-sx harmonic 72.950 99.550 # SOURCE3 1 0.0000
angle_coeff @angle:c3-px-sy harmonic 71.410 103.410 # SOURCE3 1 0.0000
angle_coeff @angle:ca-px-ca harmonic 59.260 104.150 # SOURCE3 2 3.6168
angle_coeff @angle:ca-px-o harmonic 64.720 107.500 # SOURCE3 5 5.7355
angle_coeff @angle:c-px-c3 harmonic 58.650 101.720 # SOURCE3 1 0.0000
angle_coeff @angle:ce-px-ce harmonic 59.370 104.210 # SOURCE3 1 0.0000
angle_coeff @angle:ce-px-o harmonic 63.000 113.790 # SOURCE3 6 0.3877
angle_coeff @angle:cf-px-cf harmonic 59.370 104.210 # SOURCE3 1 same_as_ce-px-ce
angle_coeff @angle:cf-px-o harmonic 63.000 113.790 # SOURCE3 6 same_as_ce-px-o
angle_coeff @angle:c-px-o harmonic 60.710 114.470 # SOURCE3 1 0.0000
angle_coeff @angle:ne-px-ne harmonic 66.990 103.220 # SOURCE3 2 0.6807
angle_coeff @angle:ne-px-o harmonic 67.560 114.130 # SOURCE3 11 8.9737
angle_coeff @angle:nf-px-nf harmonic 66.990 103.220 # SOURCE3 2 same_as_ne-px-ne
angle_coeff @angle:nf-px-o harmonic 67.560 114.130 # SOURCE3 11 same_as_ne-px-o
angle_coeff @angle:o-px-pe harmonic 62.400 116.500 # SOURCE3 12 8.2925
angle_coeff @angle:o-px-pf harmonic 62.400 116.500 # SOURCE3 12 same_as_o-px-pe
angle_coeff @angle:o-px-py harmonic 57.960 114.200 # SOURCE3 5 1.7165
angle_coeff @angle:o-px-sx harmonic 72.440 112.810 # SOURCE3 3 0.8799
angle_coeff @angle:o-px-sy harmonic 71.990 113.540 # SOURCE3 3 0.5010
angle_coeff @angle:pe-px-pe harmonic 61.250 110.710 # SOURCE3 1 0.0000
angle_coeff @angle:pf-px-pf harmonic 61.250 110.710 # SOURCE3 1 same_as_pe-px-pe
angle_coeff @angle:py-px-py harmonic 56.600 107.780 # SOURCE3 1 0.0000
angle_coeff @angle:sx-px-sx harmonic 94.100 96.240 # SOURCE3 1 0.0000
angle_coeff @angle:sy-px-sy harmonic 90.960 102.360 # SOURCE3 1 0.0000
angle_coeff @angle:c3-py-n4 harmonic 59.670 103.830 # SOURCE3 4 0.0000
angle_coeff @angle:c3-py-na harmonic 61.950 106.890 # SOURCE3 2 0.0000
angle_coeff @angle:c3-py-o harmonic 62.250 117.870 # SOURCE3 13 2.3554
angle_coeff @angle:c3-py-oh harmonic 65.880 100.160 # SOURCE3 2 0.0000
angle_coeff @angle:c3-py-os harmonic 64.170 105.390 # SOURCE3 1 0.0000
angle_coeff @angle:c3-py-px harmonic 56.690 106.270 # SOURCE3 2 0.0000
angle_coeff @angle:c3-py-py harmonic 54.980 113.970 # SOURCE3 10 1.6346
angle_coeff @angle:c3-py-sx harmonic 70.270 106.360 # SOURCE3 4 0.0000
angle_coeff @angle:ca-py-ca harmonic 59.130 107.550 # SOURCE3 1 0.0000
angle_coeff @angle:ca-py-o harmonic 63.640 113.980 # SOURCE3 3 0.5309
angle_coeff @angle:ca-py-oh harmonic 65.370 102.680 # SOURCE4 5 1.2945
angle_coeff @angle:ca-py-os harmonic 64.980 103.750 # SOURCE3 2 0.0000
angle_coeff @angle:c-py-c3 harmonic 57.070 110.360 # SOURCE3 1 0.0000
angle_coeff @angle:c-py-c harmonic 57.910 104.200 # SOURCE3 1 0.0000
angle_coeff @angle:ce-py-ce harmonic 59.600 106.540 # SOURCE3 1 0.0000
angle_coeff @angle:ce-py-o harmonic 64.310 112.160 # SOURCE3 5 3.2594
angle_coeff @angle:ce-py-oh harmonic 64.850 104.770 # SOURCE3 6 2.1852
angle_coeff @angle:ce-py-os harmonic 65.240 103.340 # SOURCE3 2 0.0000
angle_coeff @angle:cf-py-cf harmonic 59.600 106.540 # SOURCE3 1 same_as_ce-py-ce
angle_coeff @angle:cf-py-o harmonic 64.310 112.160 # SOURCE3 5 same_as_ce-py-o
angle_coeff @angle:cf-py-oh harmonic 64.850 104.770 # SOURCE3 6 same_as_ce-py-oh
angle_coeff @angle:cf-py-os harmonic 65.240 103.340 # SOURCE3 2 same_as_ce-py-os
angle_coeff @angle:c-py-o harmonic 61.560 115.250 # SOURCE3 6 2.6519
angle_coeff @angle:c-py-oh harmonic 63.980 102.140 # SOURCE3 6 1.0654
angle_coeff @angle:c-py-os harmonic 66.040 95.740 # SOURCE3 3 9.0999
angle_coeff @angle:n3-py-ne harmonic 67.010 108.440 # SOURCE4 12 0.9498
angle_coeff @angle:n4-py-o harmonic 62.060 115.580 # SOURCE3 4 0.0000
angle_coeff @angle:n4-py-py harmonic 79.860 55.100 # SOURCE3 4 0.0000
angle_coeff @angle:na-py-o harmonic 65.180 122.400 # SOURCE3 2 0.0000
angle_coeff @angle:na-py-py harmonic 85.440 50.880 # SOURCE3 2 0.0000
angle_coeff @angle:ne-py-ne harmonic 69.540 106.290 # SOURCE3 1 0.0000
angle_coeff @angle:ne-py-o harmonic 70.320 113.210 # SOURCE3 15 3.8894
angle_coeff @angle:ne-py-oh harmonic 70.530 104.700 # SOURCE3 26 2.7513
angle_coeff @angle:ne-py-os harmonic 71.610 101.330 # SOURCE3 2 0.0000
angle_coeff @angle:nf-py-nf harmonic 69.540 106.290 # SOURCE3 1 same_as_ne-py-ne
angle_coeff @angle:nf-py-o harmonic 70.320 113.210 # SOURCE3 15 same_as_ne-py-o
angle_coeff @angle:nf-py-oh harmonic 70.530 104.700 # SOURCE3 26 same_as_ne-py-oh
angle_coeff @angle:nf-py-os harmonic 71.610 101.330 # SOURCE3 2 same_as_ne-py-os
angle_coeff @angle:oh-py-oh harmonic 72.010 101.780 # SOURCE3 35 2.2937
angle_coeff @angle:oh-py-pe harmonic 64.390 104.840 # SOURCE3 22 2.0337
angle_coeff @angle:oh-py-pf harmonic 64.390 104.840 # SOURCE3 22 same_as_oh-py-pe
angle_coeff @angle:oh-py-px harmonic 60.300 104.300 # SOURCE3 8 1.2772
angle_coeff @angle:oh-py-py harmonic 61.760 100.450 # SOURCE3 6 0.0000
angle_coeff @angle:oh-py-sx harmonic 75.730 100.940 # SOURCE3 4 0.0000
angle_coeff @angle:oh-py-sy harmonic 77.890 101.470 # SOURCE3 6 0.2490
angle_coeff @angle:o-py-oh harmonic 69.900 116.140 # SOURCE3 79 2.1455
angle_coeff @angle:o-py-os harmonic 69.600 116.790 # SOURCE3 17 1.3534
angle_coeff @angle:o-py-pe harmonic 62.460 114.560 # SOURCE3 12 3.6114
angle_coeff @angle:o-py-pf harmonic 62.460 114.560 # SOURCE3 12 same_as_o-py-pe
angle_coeff @angle:o-py-px harmonic 58.710 111.370 # SOURCE3 5 0.3803
angle_coeff @angle:o-py-py harmonic 56.790 120.430 # SOURCE3 16 6.0629
angle_coeff @angle:os-py-os harmonic 72.020 101.250 # SOURCE3 8 2.0860
angle_coeff @angle:os-py-py harmonic 60.540 104.480 # SOURCE3 4 0.0000
angle_coeff @angle:os-py-sx harmonic 74.640 103.860 # SOURCE3 2 0.0000
angle_coeff @angle:os-py-sy harmonic 77.620 102.120 # SOURCE3 2 0.0000
angle_coeff @angle:o-py-sx harmonic 70.140 118.560 # SOURCE3 7 6.2976
angle_coeff @angle:o-py-sy harmonic 74.750 111.710 # SOURCE3 5 1.1937
angle_coeff @angle:pe-py-pe harmonic 61.640 107.140 # SOURCE3 1 0.0000
angle_coeff @angle:pf-py-pf harmonic 61.640 107.140 # SOURCE3 1 same_as_pe-py-pe
angle_coeff @angle:py-py-py harmonic 55.680 112.700 # SOURCE3 1 0.0000
angle_coeff @angle:py-py-sx harmonic 93.740 61.540 # SOURCE3 4 0.0000
angle_coeff @angle:sy-py-sy harmonic 92.490 105.170 # SOURCE3 1 0.0000
angle_coeff @angle:c1-s2-o harmonic 41.150 117.250 # SOURCE3 1 0.0000
angle_coeff @angle:c2-s2-n2 harmonic 42.960 110.840 # SOURCE3 1 0.0000
angle_coeff @angle:c2-s2-o harmonic 41.410 114.700 # SOURCE2 1 0.0000
angle_coeff @angle:cl-s2-n1 harmonic 35.940 117.700 # SOURCE2 1 0.0000
angle_coeff @angle:f-s2-n1 harmonic 41.390 116.900 # SOURCE2 1 0.0000
angle_coeff @angle:n1-s2-o harmonic 45.710 108.460 # HF/6-31G* 1
angle_coeff @angle:n2-s2-o harmonic 42.500 121.200 # SOURCE2 2 0.8000
angle_coeff @angle:o-s2-o harmonic 42.540 116.170 # SOURCE3 1 0.0000
angle_coeff @angle:o-s2-s harmonic 50.510 118.300 # SOURCE2 1 0.0000
angle_coeff @angle:s-s2-s harmonic 63.640 115.040 # SOURCE3 1 0.0000
angle_coeff @angle:br-s4-br harmonic 40.430 98.020 # SOURCE3 1
angle_coeff @angle:br-s4-c3 harmonic 38.910 92.980 # SOURCE3 1 0.0000
angle_coeff @angle:br-s4-o harmonic 37.040 112.070 # SOURCE3 1 0.0000
angle_coeff @angle:c1-s4-c1 harmonic 40.890 93.550 # SOURCE3 1 0.0000
angle_coeff @angle:c1-s4-o harmonic 41.280 110.360 # SOURCE3 2 0.0000
angle_coeff @angle:c2-s4-c2 harmonic 38.790 102.290 # SOURCE3 1
angle_coeff @angle:c2-s4-c3 harmonic 39.720 94.950 # SOURCE3 1
angle_coeff @angle:c2-s4-o harmonic 41.680 107.090 # SOURCE3 1
angle_coeff @angle:c3-s4-c3 harmonic 38.840 96.820 # SOURCE3 11 1.5580
angle_coeff @angle:c3-s4-ca harmonic 39.410 95.000 # SOURCE3 1
angle_coeff @angle:c3-s4-f harmonic 41.500 91.700 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s4-hs harmonic 29.130 90.600 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s4-i harmonic 33.080 90.530 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s4-n2 harmonic 43.220 90.590 # SOURCE3 1
angle_coeff @angle:c3-s4-n3 harmonic 40.780 94.490 # SOURCE3 4 1.5570
angle_coeff @angle:c3-s4-n harmonic 40.220 96.070 # SOURCE3 4 1.0354
angle_coeff @angle:c3-s4-n4 harmonic 38.790 92.470 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s4-na harmonic 40.740 93.070 # SOURCE3 10 1.8813
angle_coeff @angle:c3-s4-nh harmonic 40.360 97.080 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s4-no harmonic 39.130 89.530 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s4-o harmonic 41.060 106.210 # SOURCE3 60 2.0426
angle_coeff @angle:c3-s4-oh harmonic 42.680 90.250 # SOURCE4 8 0.3023
angle_coeff @angle:c3-s4-os harmonic 42.690 90.060 # SOURCE3 4 0.4484
angle_coeff @angle:c3-s4-p2 harmonic 37.780 94.370 # SOURCE3 1
angle_coeff @angle:c3-s4-p3 harmonic 38.650 96.540 # SOURCE3 4 1.3634
angle_coeff @angle:c3-s4-p4 harmonic 36.430 97.400 # SOURCE3 1
angle_coeff @angle:c3-s4-p5 harmonic 38.720 99.180 # SOURCE3 1
angle_coeff @angle:c3-s4-s4 harmonic 50.930 89.500 # SOURCE3 1
angle_coeff @angle:c3-s4-s harmonic 48.550 98.720 # SOURCE3 2 0.0185
angle_coeff @angle:c3-s4-s6 harmonic 48.800 97.480 # SOURCE3 1
angle_coeff @angle:c3-s4-sh harmonic 48.100 94.660 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s4-ss harmonic 47.970 95.310 # SOURCE3 3 1.4101
angle_coeff @angle:ca-s4-ca harmonic 39.580 95.210 # SOURCE3 1
angle_coeff @angle:ca-s4-o harmonic 41.300 106.630 # SOURCE3 1
angle_coeff @angle:c-s4-c3 harmonic 38.500 95.070 # SOURCE3 1
angle_coeff @angle:c-s4-c harmonic 39.630 86.830 # SOURCE3 1
angle_coeff @angle:cl-s4-cl harmonic 38.990 97.680 # SOURCE3 1 0.0000
angle_coeff @angle:cl-s4-o harmonic 39.110 108.340 # SOURCE3 2 0.0000
angle_coeff @angle:c-s4-o harmonic 40.030 106.170 # SOURCE3 1
angle_coeff @angle:cx-s4-cx harmonic 54.250 48.800 # SOURCE2 1 0.0000
angle_coeff @angle:cx-s4-o harmonic 40.110 110.000 # SOURCE2 1 0.0000
angle_coeff @angle:f-s4-f harmonic 43.790 92.710 # SOURCE2 3 0.1490
angle_coeff @angle:f-s4-o harmonic 43.870 106.810 # SOURCE2 2 0.0100
angle_coeff @angle:f-s4-s harmonic 47.340 107.500 # SOURCE2 1 0.0000
angle_coeff @angle:hs-s4-hs harmonic 23.650 87.000 # SOURCE3 2 0.0202
angle_coeff @angle:hs-s4-n1 harmonic 32.050 90.510 # HF/6-31G* 1
angle_coeff @angle:hs-s4-o harmonic 31.160 110.270 # SOURCE3 5 0.1908
angle_coeff @angle:i-s4-i harmonic 34.070 97.290 # SOURCE3 1
angle_coeff @angle:i-s4-o harmonic 29.610 113.910 # SOURCE3 1 0.0000
angle_coeff @angle:n1-s4-n1 harmonic 45.300 94.020 # HF/6-31G* 1
angle_coeff @angle:n1-s4-o harmonic 43.950 110.090 # HF/6-31G* 1
angle_coeff @angle:n2-s4-n2 harmonic 47.410 90.170 # SOURCE3 1
angle_coeff @angle:n2-s4-o harmonic 45.130 107.570 # SOURCE3 1
angle_coeff @angle:n3-s4-n3 harmonic 43.100 91.190 # SOURCE3 1 0.0000
angle_coeff @angle:n3-s4-o harmonic 42.290 109.070 # SOURCE3 6 2.3605
angle_coeff @angle:n4-s4-n4 harmonic 37.790 94.610 # SOURCE3 1 0.0000
angle_coeff @angle:n4-s4-o harmonic 39.520 104.910 # SOURCE3 3 0.4370
angle_coeff @angle:na-s4-na harmonic 39.810 103.100 # SOURCE3 1
angle_coeff @angle:na-s4-o harmonic 41.620 109.750 # SOURCE3 10 2.6919
angle_coeff @angle:nh-s4-nh harmonic 43.150 92.240 # SOURCE3 1 0.0000
angle_coeff @angle:nh-s4-o harmonic 42.790 107.540 # SOURCE3 3 0.0401
angle_coeff @angle:n-s4-n harmonic 42.570 91.300 # SOURCE3 1
angle_coeff @angle:n-s4-o harmonic 42.600 105.700 # SOURCE3 4 1.6857
angle_coeff @angle:no-s4-no harmonic 39.760 83.400 # SOURCE3 1 0.0000
angle_coeff @angle:no-s4-o harmonic 39.370 103.580 # SOURCE3 3 1.5109
angle_coeff @angle:oh-s4-oh harmonic 43.170 100.340 # SOURCE3 1
angle_coeff @angle:o-s4-o harmonic 46.570 110.610 # SOURCE3 5 3.6413
angle_coeff @angle:o-s4-oh harmonic 43.430 110.130 # SOURCE4 10 0.5760
angle_coeff @angle:o-s4-os harmonic 43.590 109.020 # SOURCE3 8 1.5005
angle_coeff @angle:o-s4-p2 harmonic 37.660 106.770 # SOURCE3 1
angle_coeff @angle:o-s4-p3 harmonic 39.430 106.510 # SOURCE3 8 4.0943
angle_coeff @angle:o-s4-p4 harmonic 37.270 103.360 # SOURCE3 1
angle_coeff @angle:o-s4-p5 harmonic 42.180 96.950 # SOURCE3 1
angle_coeff @angle:o-s4-s4 harmonic 50.530 104.550 # SOURCE3 1
angle_coeff @angle:o-s4-s harmonic 48.850 112.220 # SOURCE3 4 2.8682
angle_coeff @angle:o-s4-s6 harmonic 50.940 102.840 # SOURCE3 1
angle_coeff @angle:o-s4-sh harmonic 47.960 107.510 # SOURCE3 3 0.7511
angle_coeff @angle:os-s4-os harmonic 44.590 93.680 # SOURCE3 2 2.4166
angle_coeff @angle:o-s4-ss harmonic 47.560 109.490 # SOURCE3 5 1.8509
angle_coeff @angle:p2-s4-p2 harmonic 38.360 92.620 # SOURCE3 1
angle_coeff @angle:p3-s4-p3 harmonic 39.590 95.710 # SOURCE3 2 1.2239
angle_coeff @angle:p5-s4-p5 harmonic 40.900 93.860 # SOURCE3 1
angle_coeff @angle:s4-s4-s4 harmonic 65.560 90.170 # SOURCE3 1
angle_coeff @angle:s4-s4-s6 harmonic 65.560 90.170 # SOURCE3 1
angle_coeff @angle:s6-s4-s6 harmonic 64.380 93.520 # SOURCE3 1
angle_coeff @angle:sh-s4-sh harmonic 58.920 102.760 # SOURCE3 1 0.0000
angle_coeff @angle:sh-s4-ss harmonic 58.980 102.640 # SOURCE3 1
angle_coeff @angle:s-s4-s harmonic 60.000 108.080 # SOURCE3 1 0.0000
angle_coeff @angle:ss-s4-ss harmonic 61.190 95.470 # SOURCE3 1 0.0000
angle_coeff @angle:br-s6-br harmonic 41.990 101.570 # SOURCE3 1 0.0000
angle_coeff @angle:br-s6-c3 harmonic 39.570 98.990 # SOURCE3 1 0.0000
angle_coeff @angle:br-s6-f harmonic 39.450 100.600 # SOURCE2 1 0.0000
angle_coeff @angle:br-s6-o harmonic 39.980 107.580 # SOURCE3 6 0.3000
angle_coeff @angle:c1-s6-c1 harmonic 40.100 99.990 # SOURCE3 1 0.0000
angle_coeff @angle:c1-s6-o harmonic 42.610 108.230 # SOURCE3 4 0.0000
angle_coeff @angle:c2-s6-c2 harmonic 38.710 102.750 # SOURCE3 1
angle_coeff @angle:c2-s6-c3 harmonic 38.310 104.050 # SOURCE3 1
angle_coeff @angle:c2-s6-o harmonic 42.250 106.580 # SOURCE3 1
angle_coeff @angle:c3-s6-c3 harmonic 38.390 102.830 # SOURCE3 7 1.2531
angle_coeff @angle:c3-s6-ca harmonic 38.480 103.170 # SOURCE3 1
angle_coeff @angle:c3-s6-cy harmonic 39.140 94.570 # SOURCE4 8 0.4183
angle_coeff @angle:c3-s6-f harmonic 41.130 97.110 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s6-hs harmonic 28.120 100.620 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s6-i harmonic 31.800 97.740 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s6-n2 harmonic 39.680 112.950 # SOURCE4 11 0.7920
angle_coeff @angle:c3-s6-n3 harmonic 41.120 101.380 # SOURCE4 60 0.9507
angle_coeff @angle:c3-s6-n harmonic 39.940 102.970 # SOURCE3 4 0.8785
angle_coeff @angle:c3-s6-n4 harmonic 38.370 99.400 # SOURCE3 3 0.4695
angle_coeff @angle:c3-s6-na harmonic 39.840 102.810 # SOURCE3 10 3.1256
angle_coeff @angle:c3-s6-nh harmonic 39.880 104.310 # SOURCE4 34 1.5848
angle_coeff @angle:c3-s6-no harmonic 37.590 99.570 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s6-o harmonic 41.660 108.320 # SOURCE3 112 1.8014
angle_coeff @angle:c3-s6-oh harmonic 42.370 98.600 # SOURCE4 42 0.8366
angle_coeff @angle:c3-s6-os harmonic 42.970 96.320 # SOURCE4 30 0.4539
angle_coeff @angle:c3-s6-p2 harmonic 35.860 106.470 # SOURCE3 1
angle_coeff @angle:c3-s6-p3 harmonic 37.690 103.400 # SOURCE3 3 0.8516
angle_coeff @angle:c3-s6-p4 harmonic 35.150 104.120 # SOURCE3 1
angle_coeff @angle:c3-s6-p5 harmonic 38.150 103.460 # SOURCE3 1
angle_coeff @angle:c3-s6-s4 harmonic 48.920 98.100 # SOURCE3 1
angle_coeff @angle:c3-s6-s harmonic 48.070 104.500 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s6-s6 harmonic 47.990 101.950 # SOURCE3 1
angle_coeff @angle:c3-s6-sh harmonic 47.570 101.840 # SOURCE3 1 0.0000
angle_coeff @angle:c3-s6-ss harmonic 47.260 102.470 # SOURCE3 3 1.7451
angle_coeff @angle:ca-s6-ca harmonic 38.670 103.080 # SOURCE3 1
angle_coeff @angle:ca-s6-o harmonic 42.780 104.070 # SOURCE4 59 0.5636
angle_coeff @angle:c-s6-c3 harmonic 37.620 101.240 # SOURCE3 1
angle_coeff @angle:c-s6-c harmonic 36.960 99.820 # SOURCE3 1
angle_coeff @angle:cc-s6-o harmonic 42.850 103.630 # SOURCE4 9 0.5934
angle_coeff @angle:cl-s6-cl harmonic 38.290 101.250 # SOURCE3 1 0.0000
angle_coeff @angle:cl-s6-f harmonic 38.940 99.000 # SOURCE2 1 0.0000
angle_coeff @angle:cl-s6-o harmonic 39.360 107.660 # SOURCE3 4 0.0000
angle_coeff @angle:c-s6-o harmonic 40.020 107.970 # SOURCE3 1
angle_coeff @angle:c-s6-os harmonic 40.270 102.120 # SOURCE3 1
angle_coeff @angle:cx-s6-cx harmonic 53.940 54.700 # SOURCE2 1 0.0000
angle_coeff @angle:cy-s6-o harmonic 39.940 110.220 # SOURCE4 20 1.1009
angle_coeff @angle:f-s6-f harmonic 44.300 94.700 # SOURCE2 3 0.9899
angle_coeff @angle:f-s6-o harmonic 45.290 106.480 # SOURCE3 2 0.0000
angle_coeff @angle:hs-s6-hs harmonic 22.430 99.020 # SOURCE3 2 0.0595
angle_coeff @angle:hs-s6-n1 harmonic 34.230 97.270 # HF/6-31G* 1
angle_coeff @angle:hs-s6-o harmonic 32.480 107.600 # SOURCE3 10 0.0343
angle_coeff @angle:i-s6-i harmonic 33.730 99.250 # SOURCE3 1
angle_coeff @angle:i-s6-o harmonic 29.870 109.740 # SOURCE3 2 0.0000
angle_coeff @angle:n1-s6-n1 harmonic 52.370 95.520 # HF/6-31G* 1
angle_coeff @angle:n1-s6-o harmonic 49.300 107.520 # HF/6-31G* 1
angle_coeff @angle:n2-s6-n2 harmonic 47.050 98.610 # SOURCE3 1
angle_coeff @angle:n2-s6-o harmonic 45.100 116.410 # SOURCE3 3 5.0830
angle_coeff @angle:n2-s6-oh harmonic 44.890 106.960 # SOURCE3 2 0.0000
angle_coeff @angle:n2-s6-os harmonic 45.860 103.250 # SOURCE3 1
angle_coeff @angle:n3-s6-n3 harmonic 44.730 98.570 # SOURCE4 7 0.2690
angle_coeff @angle:n3-s6-o harmonic 45.610 106.800 # SOURCE3 14 1.7908
angle_coeff @angle:n3-s6-os harmonic 45.580 99.260 # SOURCE4 8 0.5141
angle_coeff @angle:n4-s6-n4 harmonic 37.520 101.850 # SOURCE3 1 0.0000
angle_coeff @angle:n4-s6-o harmonic 41.190 102.920 # SOURCE3 10 1.5434
angle_coeff @angle:na-s6-na harmonic 42.390 98.040 # SOURCE3 1
angle_coeff @angle:na-s6-o harmonic 44.090 105.670 # SOURCE3 20 0.8019
angle_coeff @angle:nh-s6-nh harmonic 43.940 94.560 # SOURCE3 1 0.0000
angle_coeff @angle:nh-s6-o harmonic 43.940 109.120 # SOURCE3 6 0.9556
angle_coeff @angle:n-s6-n harmonic 41.410 104.160 # SOURCE3 1
angle_coeff @angle:n-s6-o harmonic 44.260 105.910 # SOURCE3 8 0.2953
angle_coeff @angle:no-s6-no harmonic 38.320 91.630 # SOURCE3 1 0.0000
angle_coeff @angle:no-s6-o harmonic 39.210 107.430 # SOURCE3 6 1.5494
angle_coeff @angle:n-s6-os harmonic 44.300 99.230 # SOURCE4 5 0.9794
angle_coeff @angle:oh-s6-oh harmonic 46.090 100.340 # SOURCE3 6 0.0076
angle_coeff @angle:oh-s6-os harmonic 47.130 96.620 # SOURCE4 26 0.6688
angle_coeff @angle:oh-s6-p2 harmonic 37.140 109.670 # SOURCE3 2 0.0000
angle_coeff @angle:o-s6-o harmonic 46.660 119.730 # SOURCE4 324 2.0530
angle_coeff @angle:o-s6-oh harmonic 46.380 108.210 # SOURCE3 18 0.7437
angle_coeff @angle:o-s6-os harmonic 46.660 107.840 # SOURCE3 12 0.7025
angle_coeff @angle:o-s6-p2 harmonic 37.890 106.610 # SOURCE3 1
angle_coeff @angle:o-s6-p3 harmonic 39.630 107.070 # SOURCE3 22 1.0550
angle_coeff @angle:o-s6-p4 harmonic 36.540 105.670 # SOURCE3 1
angle_coeff @angle:o-s6-p5 harmonic 40.380 106.640 # SOURCE3 1
angle_coeff @angle:o-s6-s4 harmonic 49.910 107.850 # SOURCE3 1
angle_coeff @angle:o-s6-s harmonic 50.300 110.290 # SOURCE3 6 2.2405
angle_coeff @angle:o-s6-s6 harmonic 50.330 106.070 # SOURCE3 1
angle_coeff @angle:o-s6-sh harmonic 49.520 106.810 # SOURCE3 6 0.6292
angle_coeff @angle:os-s6-os harmonic 46.800 98.700 # SOURCE3 1 0.0000
angle_coeff @angle:o-s6-ss harmonic 49.150 107.430 # SOURCE3 10 1.1423
angle_coeff @angle:p3-s6-p3 harmonic 37.080 110.170 # SOURCE3 4 5.3678
angle_coeff @angle:p5-s6-p5 harmonic 38.770 104.490 # SOURCE3 1
angle_coeff @angle:s4-s6-s4 harmonic 61.650 101.990 # SOURCE3 1
angle_coeff @angle:s4-s6-s6 harmonic 65.560 90.170 # SOURCE3 1
angle_coeff @angle:s6-s6-s6 harmonic 61.260 103.290 # SOURCE3 1
angle_coeff @angle:sh-s6-sh harmonic 59.550 106.430 # SOURCE3 1 0.0000
angle_coeff @angle:sh-s6-ss harmonic 60.490 102.640 # SOURCE3 1
angle_coeff @angle:s-s6-s harmonic 60.770 109.340 # SOURCE3 1 0.0000
angle_coeff @angle:ss-s6-ss harmonic 60.590 101.820 # SOURCE3 1 0.0000
angle_coeff @angle:br-sh-hs harmonic 27.240 95.640 # SOURCE3 1 0.0000
angle_coeff @angle:c1-sh-hs harmonic 30.170 95.990 # calculated_based_on_C#C-SH 0
angle_coeff @angle:c2-sh-hs harmonic 28.660 97.080 # SOURCE4 5 0.3132
angle_coeff @angle:c3-sh-hs harmonic 28.120 96.600 # SOURCE3 12 0.8009
angle_coeff @angle:ca-sh-hs harmonic 28.980 94.840 # SOURCE4 13 0.4130
angle_coeff @angle:cc-sh-hs harmonic 29.040 95.380 # SOURCE4 8 1.1410
angle_coeff @angle:c-sh-hs harmonic 28.760 96.070 # SOURCE3 6 1.1164
angle_coeff @angle:f-sh-hs harmonic 30.090 96.500 # SOURCE3 1 0.0000
angle_coeff @angle:hs-sh-hs harmonic 23.430 93.720 # SOURCE3 3 0.4777
angle_coeff @angle:hs-sh-i harmonic 23.210 96.440 # SOURCE3 1 0.0000
angle_coeff @angle:hs-sh-n1 harmonic 32.340 93.510 # HF/6-31G* 1
angle_coeff @angle:hs-sh-n2 harmonic 30.110 95.820 # SOURCE3 5 3.1495
angle_coeff @angle:hs-sh-n harmonic 30.290 95.590 # SOURCE3 4 3.9065
angle_coeff @angle:hs-sh-n3 harmonic 30.070 95.980 # SOURCE3 3 1.1735
angle_coeff @angle:hs-sh-n4 harmonic 29.500 93.130 # SOURCE3 3 0.1675
angle_coeff @angle:hs-sh-na harmonic 30.110 97.380 # SOURCE3 9 1.0223
angle_coeff @angle:hs-sh-nh harmonic 29.730 101.110 # SOURCE3 1 0.0000
angle_coeff @angle:hs-sh-no harmonic 29.630 92.930 # SOURCE3 1 0.0000
angle_coeff @angle:hs-sh-o harmonic 30.170 109.230 # SOURCE3 2 0.0068
angle_coeff @angle:hs-sh-oh harmonic 30.500 98.640 # SOURCE3 2 0.0605
angle_coeff @angle:hs-sh-os harmonic 30.880 98.150 # SOURCE3 3 0.1661
angle_coeff @angle:hs-sh-p2 harmonic 27.940 99.120 # SOURCE3 10 5.4110
angle_coeff @angle:hs-sh-p3 harmonic 26.260 95.810 # SOURCE3 3 0.4396
angle_coeff @angle:hs-sh-p4 harmonic 26.700 94.220 # SOURCE3 4 0.7605
angle_coeff @angle:hs-sh-p5 harmonic 27.090 94.520 # SOURCE3 3 0.5589
angle_coeff @angle:hs-sh-s harmonic 32.420 102.870 # SOURCE3 2 0.0000
angle_coeff @angle:hs-sh-s4 harmonic 33.290 92.160 # SOURCE3 3 1.6519
angle_coeff @angle:hs-sh-s6 harmonic 33.980 93.830 # SOURCE3 3 1.2561
angle_coeff @angle:hs-sh-sh harmonic 33.890 99.070 # SOURCE3 2 0.0000
angle_coeff @angle:hs-sh-ss harmonic 33.730 99.170 # SOURCE3 3 0.2457
angle_coeff @angle:br-ss-br harmonic 41.920 102.920 # SOURCE3 1 0.0000
angle_coeff @angle:br-ss-c3 harmonic 39.460 99.030 # SOURCE3 1 0.0000
angle_coeff @angle:c1-ss-c1 harmonic 41.480 98.300 # SOURCE2 1 0.0000
angle_coeff @angle:c1-ss-c3 harmonic 39.350 99.900 # SOURCE2 1 0.0000
angle_coeff @angle:c2-ss-c2 harmonic 39.870 99.560 # SOURCE3 1 0.0000
angle_coeff @angle:c2-ss-c3 harmonic 38.710 100.370 # SOURCE4 100 2.3280
angle_coeff @angle:c2-ss-cy harmonic 40.860 88.610 # SOURCE4 27 0.4481
angle_coeff @angle:c2-ss-n2 harmonic 40.330 106.760 # SOURCE3 1 0.0000
angle_coeff @angle:c2-ss-na harmonic 40.680 100.510 # SOURCE3 6 6.9702
angle_coeff @angle:c2-ss-os harmonic 43.660 89.760 # SOURCE3 1 0.0000
angle_coeff @angle:c2-ss-ss harmonic 51.300 92.260 # SOURCE3 1 0.0000
angle_coeff @angle:c3-ss-c3 harmonic 37.940 99.920 # SOURCE3 14 2.0723
angle_coeff @angle:c3-ss-ca harmonic 38.040 102.120 # SOURCE4 161 1.3084
angle_coeff @angle:c3-ss-cc harmonic 38.610 100.850 # SOURCE4 74 1.3149
angle_coeff @angle:c3-ss-cd harmonic 38.730 100.210 # SOURCE4 13 1.3340
angle_coeff @angle:c3-ss-cl harmonic 37.940 99.400 # SOURCE2 1 0.0000
angle_coeff @angle:c3-ss-cy harmonic 38.750 94.320 # SOURCE4 62 0.3646
angle_coeff @angle:c3-ss-f harmonic 39.670 97.490 # SOURCE3 1 0.0000
angle_coeff @angle:c3-ss-i harmonic 35.060 100.000 # SOURCE3 1 0.0000
angle_coeff @angle:c3-ss-n1 harmonic 41.250 98.440 # HF/6-31G* 1
angle_coeff @angle:c3-ss-n2 harmonic 41.260 96.420 # SOURCE3 5 1.3604
angle_coeff @angle:c3-ss-n3 harmonic 40.110 98.830 # SOURCE3 3 0.2909
angle_coeff @angle:c3-ss-n harmonic 39.860 100.300 # SOURCE3 4 0.6579
angle_coeff @angle:c3-ss-n4 harmonic 39.380 97.790 # SOURCE3 3 0.2002
angle_coeff @angle:c3-ss-na harmonic 39.740 100.140 # SOURCE3 12 1.7415
angle_coeff @angle:c3-ss-nh harmonic 39.890 100.630 # SOURCE3 1 0.0000
angle_coeff @angle:c3-ss-no harmonic 39.050 98.620 # SOURCE3 1 0.0000
angle_coeff @angle:c3-ss-o harmonic 40.460 106.600 # SOURCE3 2 1.6714
angle_coeff @angle:c3-ss-oh harmonic 40.850 98.280 # SOURCE3 2 1.4326
angle_coeff @angle:c3-ss-os harmonic 40.650 98.210 # SOURCE3 4 1.7097
angle_coeff @angle:c3-ss-p2 harmonic 39.660 98.410 # SOURCE3 8 0.9454
angle_coeff @angle:c3-ss-p3 harmonic 37.720 98.700 # SOURCE3 3 0.0356
angle_coeff @angle:c3-ss-p4 harmonic 38.030 98.160 # SOURCE3 4 0.1361
angle_coeff @angle:c3-ss-p5 harmonic 37.500 100.220 # SOURCE4 23 1.1410
angle_coeff @angle:c3-ss-s4 harmonic 47.600 96.370 # SOURCE3 3 0.0202
angle_coeff @angle:c3-ss-s harmonic 47.470 101.900 # SOURCE3 1 0.0000
angle_coeff @angle:c3-ss-s6 harmonic 48.260 96.760 # SOURCE3 3 1.5680
angle_coeff @angle:c3-ss-sh harmonic 47.800 101.930 # SOURCE3 1 0.0000
angle_coeff @angle:c3-ss-ss harmonic 47.780 103.100 # SOURCE4 70 1.3377
angle_coeff @angle:ca-ss-ca harmonic 39.270 98.710 # SOURCE4 97 1.2321
angle_coeff @angle:ca-ss-cc harmonic 41.730 89.010 # SOURCE4 88 1.2324
angle_coeff @angle:ca-ss-cd harmonic 41.420 90.360 # SOURCE4 46 0.9833
angle_coeff @angle:ca-ss-cl harmonic 37.980 101.050 # SOURCE3 1 0.0000
angle_coeff @angle:ca-ss-n harmonic 41.150 97.160 # SOURCE3 1
angle_coeff @angle:ca-ss-na harmonic 40.520 99.320 # SOURCE3 1
angle_coeff @angle:ca-ss-nc harmonic 43.300 94.760 # SOURCE3 1 0.0000
angle_coeff @angle:ca-ss-nd harmonic 43.300 94.760 # SOURCE3 1 same_as_ca-ss-nc
angle_coeff @angle:ca-ss-ss harmonic 47.820 104.900 # SOURCE4 19 0.8743
angle_coeff @angle:c-ss-c2 harmonic 41.060 92.430 # SOURCE3 1 0.0000
angle_coeff @angle:c-ss-c3 harmonic 38.470 100.290 # SOURCE3 5 2.2127
angle_coeff @angle:c-ss-c harmonic 38.920 101.400 # SOURCE3 1 0.0000
angle_coeff @angle:c-ss-cc harmonic 41.050 92.430 # SOURCE4 14 2.3600
angle_coeff @angle:cc-ss-cc harmonic 41.930 89.910 # SOURCE3 11 2.2164
angle_coeff @angle:cc-ss-cd harmonic 41.970 89.740 # SOURCE4 49 0.7509
angle_coeff @angle:cc-ss-n harmonic 41.560 97.160 # SOURCE3 1 same_as_cd-ss-n
angle_coeff @angle:cc-ss-na harmonic 40.910 99.330 # SOURCE3 18 same_as_cd-ss-na
angle_coeff @angle:cc-ss-nc harmonic 44.100 93.610 # SOURCE4 10 0.8252
angle_coeff @angle:cc-ss-os harmonic 41.600 98.810 # SOURCE3 2 2.1583
angle_coeff @angle:cc-ss-ss harmonic 48.670 102.460 # SOURCE3 2 0.0000
angle_coeff @angle:cd-ss-cd harmonic 41.930 89.910 # SOURCE3 11 2.2164
angle_coeff @angle:cd-ss-n harmonic 41.560 97.160 # SOURCE3 1 0.0000
angle_coeff @angle:cd-ss-na harmonic 40.910 99.330 # SOURCE3 18 2.5847
angle_coeff @angle:cd-ss-nd harmonic 43.630 95.660 # SOURCE3 3 0.0000
angle_coeff @angle:cd-ss-os harmonic 41.600 98.810 # SOURCE3 2 same_as_cc-ss-os
angle_coeff @angle:cd-ss-ss harmonic 50.980 93.360 # SOURCE4 11 0.3795
angle_coeff @angle:cl-ss-cl harmonic 37.900 103.370 # SOURCE3 1 0.0000
angle_coeff @angle:cx-ss-cx harmonic 54.740 48.300 # SOURCE2 1 0.0000
angle_coeff @angle:f-ss-f harmonic 41.410 98.300 # SOURCE2 1 0.0000
angle_coeff @angle:f-ss-ss harmonic 47.400 108.300 # SOURCE2 1 0.0000
angle_coeff @angle:i-ss-i harmonic 36.380 106.290 # SOURCE3 1 0.0000
angle_coeff @angle:n1-ss-n1 harmonic 45.720 96.960 # HF/6-31G* 1
angle_coeff @angle:n2-ss-n2 harmonic 44.500 96.750 # SOURCE3 1 0.0000
angle_coeff @angle:n3-ss-n3 harmonic 41.610 102.340 # SOURCE3 1 0.0000
angle_coeff @angle:n4-ss-n4 harmonic 39.760 101.190 # SOURCE3 1 0.0000
angle_coeff @angle:na-ss-na harmonic 41.250 102.810 # SOURCE3 1 0.0000
angle_coeff @angle:nc-ss-nc harmonic 46.990 97.750 # SOURCE4 8 0.3345
angle_coeff @angle:nd-ss-nd harmonic 46.580 99.500 # SOURCE2 1 same_as_nc-ss-nc
angle_coeff @angle:nh-ss-nh harmonic 40.860 107.890 # SOURCE3 1 0.0000
angle_coeff @angle:n-ss-n harmonic 41.570 103.100 # SOURCE3 1 0.0000
angle_coeff @angle:no-ss-no harmonic 38.430 106.430 # SOURCE3 1 0.0000
angle_coeff @angle:oh-ss-oh harmonic 42.690 104.250 # SOURCE3 1 0.0000
angle_coeff @angle:o-ss-o harmonic 43.680 119.300 # SOURCE2 1 0.0000
angle_coeff @angle:o-ss-p5 harmonic 38.880 106.410 # SOURCE3 1 0.0000
angle_coeff @angle:o-ss-s6 harmonic 49.380 105.390 # SOURCE3 1
angle_coeff @angle:os-ss-os harmonic 42.400 102.990 # SOURCE3 1 0.0000
angle_coeff @angle:o-ss-ss harmonic 49.130 112.700 # SOURCE2 1 0.0000
angle_coeff @angle:p2-ss-p2 harmonic 41.220 99.520 # SOURCE3 1 0.0000
angle_coeff @angle:p3-ss-p3 harmonic 37.800 101.670 # SOURCE3 1
angle_coeff @angle:p5-ss-p5 harmonic 40.330 89.830 # SOURCE3 1 0.0000
angle_coeff @angle:s4-ss-s4 harmonic 60.990 96.080 # SOURCE3 1 0.0000
angle_coeff @angle:s4-ss-s6 harmonic 60.060 101.260 # SOURCE3 1
angle_coeff @angle:s6-ss-s6 harmonic 60.590 101.810 # SOURCE3 1 0.0000
angle_coeff @angle:sh-ss-sh harmonic 60.410 107.540 # SOURCE3 1 0.0000
angle_coeff @angle:sh-ss-ss harmonic 60.950 106.530 # SOURCE3 1
angle_coeff @angle:s-ss-s harmonic 57.790 115.040 # SOURCE3 1
angle_coeff @angle:ss-ss-ss harmonic 60.570 108.760 # SOURCE4 8 0.2385
angle_coeff @angle:c3-sx-ca harmonic 38.700 96.410 # SOURCE4 13 0.3130
angle_coeff @angle:c3-sx-cc harmonic 39.120 95.110 # SOURCE4 17 0.6557
angle_coeff @angle:c3-sx-ce harmonic 39.300 94.950 # SOURCE3 3 0.0007
angle_coeff @angle:c3-sx-cf harmonic 39.300 94.950 # SOURCE3 3 same_as_c3-sx-ce
angle_coeff @angle:c3-sx-ne harmonic 40.880 90.060 # SOURCE3 5 1.9627
angle_coeff @angle:c3-sx-nf harmonic 40.880 90.060 # SOURCE3 5 same_as_c3-sx-ne
angle_coeff @angle:c3-sx-o harmonic 40.630 107.880 # SOURCE3 30 0.8721
angle_coeff @angle:c3-sx-pe harmonic 38.060 94.320 # SOURCE3 7 0.5547
angle_coeff @angle:c3-sx-pf harmonic 38.060 94.320 # SOURCE3 7 same_as_c3-sx-pe
angle_coeff @angle:c3-sx-px harmonic 36.710 96.460 # SOURCE3 3 1.3351
angle_coeff @angle:c3-sx-py harmonic 36.650 95.670 # SOURCE3 1 0.0000
angle_coeff @angle:c3-sx-sx harmonic 45.310 91.470 # SOURCE3 4 1.9919
angle_coeff @angle:c3-sx-sy harmonic 46.490 95.470 # SOURCE3 3 2.8422
angle_coeff @angle:ca-sx-ca harmonic 38.770 95.210 # SOURCE3 1 0.0000
angle_coeff @angle:ca-sx-o harmonic 40.550 106.890 # SOURCE4 25 0.5562
angle_coeff @angle:c-sx-c3 harmonic 38.800 92.710 # SOURCE3 3 0.3095
angle_coeff @angle:c-sx-c harmonic 39.310 86.850 # SOURCE3 1 0.0000
angle_coeff @angle:cc-sx-o harmonic 41.250 104.490 # SOURCE4 17 1.7759
angle_coeff @angle:ce-sx-ce harmonic 39.430 94.960 # SOURCE3 1 0.0000
angle_coeff @angle:ce-sx-o harmonic 40.910 107.470 # SOURCE3 5 0.3128
angle_coeff @angle:cf-sx-cf harmonic 39.430 94.960 # SOURCE3 1 same_as_ce-sx-ce
angle_coeff @angle:cf-sx-o harmonic 40.910 107.470 # SOURCE3 5 same_as_ce-sx-o
angle_coeff @angle:c-sx-o harmonic 39.710 106.170 # SOURCE3 5 0.9477
angle_coeff @angle:ne-sx-ne harmonic 41.530 90.170 # SOURCE3 1 0.0000
angle_coeff @angle:ne-sx-o harmonic 40.900 109.200 # SOURCE3 7 1.4542
angle_coeff @angle:nf-sx-nf harmonic 41.530 90.170 # SOURCE3 1 same_as_ne-sx-ne
angle_coeff @angle:nf-sx-o harmonic 40.900 109.200 # SOURCE3 7 same_as_ne-sx-o
angle_coeff @angle:o-sx-pe harmonic 38.070 106.430 # SOURCE3 9 2.8345
angle_coeff @angle:o-sx-pf harmonic 38.070 106.430 # SOURCE3 9 same_as_o-sx-pe
angle_coeff @angle:o-sx-px harmonic 37.160 104.770 # SOURCE3 3 1.9810
angle_coeff @angle:o-sx-py harmonic 36.140 109.130 # SOURCE3 7 5.6840
angle_coeff @angle:o-sx-sx harmonic 44.100 104.650 # SOURCE3 6 3.0524
angle_coeff @angle:o-sx-sy harmonic 47.070 103.410 # SOURCE3 5 0.9618
angle_coeff @angle:pe-sx-pe harmonic 38.750 92.620 # SOURCE3 1 0.0000
angle_coeff @angle:pf-sx-pf harmonic 38.750 92.620 # SOURCE3 1 same_as_pe-sx-pe
angle_coeff @angle:py-sx-py harmonic 43.010 69.230 # SOURCE3 3 17.4143
angle_coeff @angle:sx-sx-sx harmonic 58.780 84.900 # SOURCE3 1 0.0000
angle_coeff @angle:sy-sx-sy harmonic 59.380 93.520 # SOURCE3 1 0.0000
angle_coeff @angle:c3-sy-ca harmonic 38.000 103.860 # SOURCE4 54 0.3180
angle_coeff @angle:c3-sy-cc harmonic 38.280 102.190 # SOURCE4 12 1.5324
angle_coeff @angle:c3-sy-ce harmonic 38.030 103.810 # SOURCE3 3 0.3368
angle_coeff @angle:c3-sy-cf harmonic 38.030 103.810 # SOURCE3 3 same_as_c3-sy-ce
angle_coeff @angle:c3-sy-ne harmonic 39.420 103.120 # SOURCE3 5 4.1882
angle_coeff @angle:c3-sy-nf harmonic 39.420 103.120 # SOURCE3 5 same_as_c3-sy-ne
angle_coeff @angle:c3-sy-o harmonic 41.280 108.480 # SOURCE3 62 0.8576
angle_coeff @angle:c3-sy-pe harmonic 35.490 106.030 # SOURCE3 6 2.6117
angle_coeff @angle:c3-sy-pf harmonic 35.490 106.030 # SOURCE3 6 same_as_c3-sy-pe
angle_coeff @angle:c3-sy-px harmonic 35.450 103.620 # SOURCE3 3 0.7078
angle_coeff @angle:c3-sy-py harmonic 36.330 103.390 # SOURCE3 3 0.4563
angle_coeff @angle:c3-sy-sx harmonic 44.560 104.640 # SOURCE3 3 4.6276
angle_coeff @angle:c3-sy-sy harmonic 45.480 100.780 # SOURCE3 4 1.1633
angle_coeff @angle:ca-sy-ca harmonic 37.950 104.040 # SOURCE4 25 2.0762
angle_coeff @angle:ca-sy-cc harmonic 37.720 105.090 # SOURCE4 5 0.3628
angle_coeff @angle:ca-sy-n3 harmonic 40.110 102.480 # SOURCE4 180 1.0802
angle_coeff @angle:ca-sy-n harmonic 39.350 105.450 # SOURCE4 51 1.1497
angle_coeff @angle:ca-sy-ne harmonic 39.330 103.470 # SOURCE4 11 1.6071
angle_coeff @angle:ca-sy-nh harmonic 39.330 105.590 # SOURCE4 78 1.5805
angle_coeff @angle:ca-sy-o harmonic 41.200 108.730 # SOURCE3 26 1.2638
angle_coeff @angle:ca-sy-oh harmonic 41.070 101.250 # SOURCE4 23 0.9100
angle_coeff @angle:ca-sy-os harmonic 42.320 92.980 # SOURCE3 1 0.0000
angle_coeff @angle:c-sy-c3 harmonic 37.600 101.250 # SOURCE3 3 1.1850
angle_coeff @angle:c-sy-c harmonic 37.060 99.810 # SOURCE3 1 0.0000
angle_coeff @angle:cc-sy-n3 harmonic 40.090 102.390 # SOURCE4 17 0.6395
angle_coeff @angle:cc-sy-o harmonic 41.420 107.270 # SOURCE4 62 0.9782
angle_coeff @angle:cd-sy-n3 harmonic 40.140 102.730 # SOURCE4 13 0.5722
angle_coeff @angle:cd-sy-nh harmonic 41.070 97.200 # SOURCE4 6 0.2429
angle_coeff @angle:cd-sy-o harmonic 41.360 108.420 # SOURCE4 38 0.6229
angle_coeff @angle:ce-sy-ce harmonic 38.220 102.780 # SOURCE3 1 0.0000
angle_coeff @angle:ce-sy-o harmonic 41.510 107.250 # SOURCE3 10 0.5477
angle_coeff @angle:cf-sy-cf harmonic 38.220 102.780 # SOURCE3 1 same_as_ce-sy-ce
angle_coeff @angle:cf-sy-o harmonic 41.510 107.250 # SOURCE3 10 same_as_ce-sy-o
angle_coeff @angle:c-sy-o harmonic 40.090 107.230 # SOURCE3 10 0.8425
angle_coeff @angle:f-sy-o harmonic 45.090 105.600 # SOURCE4 7 0.2000
angle_coeff @angle:n2-sy-o harmonic 43.410 123.530 # SOURCE4 6 1.2388
angle_coeff @angle:n3-sy-ne harmonic 41.520 102.400 # SOURCE4 5 1.3390
angle_coeff @angle:n3-sy-o harmonic 44.080 107.110 # SOURCE4 375 1.1257
angle_coeff @angle:na-sy-na harmonic 42.390 98.040 # SOURCE3 1
angle_coeff @angle:nc-sy-nc harmonic 47.080 98.040 # SOURCE3 2
angle_coeff @angle:nd-sy-nd harmonic 47.080 98.040 # SOURCE3 2
angle_coeff @angle:ne-sy-ne harmonic 41.660 98.620 # SOURCE3 1 0.0000
angle_coeff @angle:ne-sy-o harmonic 43.100 107.060 # SOURCE3 14 2.2705
angle_coeff @angle:nf-sy-nf harmonic 41.660 98.620 # SOURCE3 1 same_as_ne-sy-ne
angle_coeff @angle:nf-sy-o harmonic 43.100 107.060 # SOURCE3 14 same_as_ne-sy-o
angle_coeff @angle:nh-sy-o harmonic 43.910 106.380 # SOURCE4 123 1.6517
angle_coeff @angle:n-sy-o harmonic 43.660 107.500 # SOURCE4 61 1.8720
angle_coeff @angle:o-sy-o harmonic 45.300 121.880 # SOURCE3 46 0.9495
angle_coeff @angle:o-sy-oh harmonic 45.210 106.930 # SOURCE3 8 0.7424
angle_coeff @angle:o-sy-os harmonic 44.040 108.310 # SOURCE4 7 0.1222
angle_coeff @angle:o-sy-pe harmonic 37.280 106.900 # SOURCE3 12 1.4524
angle_coeff @angle:o-sy-pf harmonic 37.280 106.900 # SOURCE3 12 same_as_o-sy-pe
angle_coeff @angle:o-sy-px harmonic 36.810 106.170 # SOURCE3 6 0.7059
angle_coeff @angle:o-sy-py harmonic 37.840 106.670 # SOURCE3 10 0.6478
angle_coeff @angle:o-sy-sx harmonic 46.420 106.330 # SOURCE3 10 2.0456
angle_coeff @angle:o-sy-sy harmonic 46.560 106.190 # SOURCE3 12 0.1754
angle_coeff @angle:py-sy-py harmonic 36.250 104.490 # SOURCE3 1 0.0000
angle_coeff @angle:sx-sy-sx harmonic 56.860 101.990 # SOURCE3 1 0.0000
angle_coeff @angle:sy-sy-sy harmonic 56.630 103.290 # SOURCE3 1 0.0000
} # (end of angle_coeffs)
write_once("Data Angles By Type") {
@angle:hw-ow-hw @atom:hw @atom:ow @atom:hw
@angle:hw-hw-ow @atom:hw @atom:hw @atom:ow
@angle:br-c1-br @atom:br @atom:c1 @atom:br
@angle:br-c1-c1 @atom:br @atom:c1 @atom:c1
@angle:c1-c1-c1 @atom:c1 @atom:c1 @atom:c1
@angle:c1-c1-c2 @atom:c1 @atom:c1 @atom:c2
@angle:c1-c1-c3 @atom:c1 @atom:c1 @atom:c3
@angle:c1-c1-ca @atom:c1 @atom:c1 @atom:ca
@angle:c1-c1-cl @atom:c1 @atom:c1 @atom:cl
@angle:c1-c1-f @atom:c1 @atom:c1 @atom:f
@angle:c1-c1-ha @atom:c1 @atom:c1 @atom:ha
@angle:c1-c1-hc @atom:c1 @atom:c1 @atom:hc
@angle:c1-c1-i @atom:c1 @atom:c1 @atom:i
@angle:c1-c1-n1 @atom:c1 @atom:c1 @atom:n1
@angle:c1-c1-n2 @atom:c1 @atom:c1 @atom:n2
@angle:c1-c1-n3 @atom:c1 @atom:c1 @atom:n3
@angle:c1-c1-n4 @atom:c1 @atom:c1 @atom:n4
@angle:c1-c1-n @atom:c1 @atom:c1 @atom:n
@angle:c1-c1-na @atom:c1 @atom:c1 @atom:na
@angle:c1-c1-nh @atom:c1 @atom:c1 @atom:nh
@angle:c1-c1-no @atom:c1 @atom:c1 @atom:no
@angle:c1-c1-o @atom:c1 @atom:c1 @atom:o
@angle:c1-c1-oh @atom:c1 @atom:c1 @atom:oh
@angle:c1-c1-os @atom:c1 @atom:c1 @atom:os
@angle:c1-c1-p2 @atom:c1 @atom:c1 @atom:p2
@angle:c1-c1-p3 @atom:c1 @atom:c1 @atom:p3
@angle:c1-c1-p4 @atom:c1 @atom:c1 @atom:p4
@angle:c1-c1-p5 @atom:c1 @atom:c1 @atom:p5
@angle:c1-c1-s4 @atom:c1 @atom:c1 @atom:s4
@angle:c1-c1-s6 @atom:c1 @atom:c1 @atom:s6
@angle:c1-c1-s @atom:c1 @atom:c1 @atom:s
@angle:c1-c1-sh @atom:c1 @atom:c1 @atom:sh
@angle:c1-c1-ss @atom:c1 @atom:c1 @atom:ss
@angle:c2-c1-c2 @atom:c2 @atom:c1 @atom:c2
@angle:c2-c1-ce @atom:c2 @atom:c1 @atom:ce
@angle:c2-c1-n1 @atom:c2 @atom:c1 @atom:n1
@angle:c2-c1-o @atom:c2 @atom:c1 @atom:o
@angle:c2-c1-s2 @atom:c2 @atom:c1 @atom:s2
@angle:c3-c1-c3 @atom:c3 @atom:c1 @atom:c3
@angle:c3-c1-cg @atom:c3 @atom:c1 @atom:cg
@angle:c3-c1-n1 @atom:c3 @atom:c1 @atom:n1
@angle:ca-c1-ca @atom:ca @atom:c1 @atom:ca
@angle:c-c1-c1 @atom:c @atom:c1 @atom:c1
@angle:cg-c1-ha @atom:cg @atom:c1 @atom:ha
@angle:ch-c1-ha @atom:ch @atom:c1 @atom:ha
@angle:cl-c1-cl @atom:cl @atom:c1 @atom:cl
@angle:f-c1-f @atom:f @atom:c1 @atom:f
@angle:i-c1-i @atom:i @atom:c1 @atom:i
@angle:n1-c1-n1 @atom:n1 @atom:c1 @atom:n1
@angle:n1-c1-n3 @atom:n1 @atom:c1 @atom:n3
@angle:n1-c1-nh @atom:n1 @atom:c1 @atom:nh
@angle:n1-c1-os @atom:n1 @atom:c1 @atom:os
@angle:n1-c1-p3 @atom:n1 @atom:c1 @atom:p3
@angle:n1-c1-ss @atom:n1 @atom:c1 @atom:ss
@angle:n2-c1-n2 @atom:n2 @atom:c1 @atom:n2
@angle:n2-c1-o @atom:n2 @atom:c1 @atom:o
@angle:n2-c1-s @atom:n2 @atom:c1 @atom:s
@angle:n3-c1-n3 @atom:n3 @atom:c1 @atom:n3
@angle:n4-c1-n4 @atom:n4 @atom:c1 @atom:n4
@angle:na-c1-na @atom:na @atom:c1 @atom:na
@angle:ne-c1-o @atom:ne @atom:c1 @atom:o
@angle:ne-c1-s @atom:ne @atom:c1 @atom:s
@angle:nf-c1-o @atom:nf @atom:c1 @atom:o
@angle:nh-c1-nh @atom:nh @atom:c1 @atom:nh
@angle:n-c1-n @atom:n @atom:c1 @atom:n
@angle:no-c1-no @atom:no @atom:c1 @atom:no
@angle:oh-c1-oh @atom:oh @atom:c1 @atom:oh
@angle:o-c1-o @atom:o @atom:c1 @atom:o
@angle:os-c1-os @atom:os @atom:c1 @atom:os
@angle:p2-c1-p2 @atom:p2 @atom:c1 @atom:p2
@angle:p3-c1-p3 @atom:p3 @atom:c1 @atom:p3
@angle:p4-c1-p4 @atom:p4 @atom:c1 @atom:p4
@angle:p5-c1-p5 @atom:p5 @atom:c1 @atom:p5
@angle:s2-c1-s2 @atom:s2 @atom:c1 @atom:s2
@angle:s4-c1-s4 @atom:s4 @atom:c1 @atom:s4
@angle:s6-c1-s6 @atom:s6 @atom:c1 @atom:s6
@angle:sh-c1-sh @atom:sh @atom:c1 @atom:sh
@angle:s-c1-s @atom:s @atom:c1 @atom:s
@angle:ss-c1-ss @atom:ss @atom:c1 @atom:ss
@angle:br-c2-br @atom:br @atom:c2 @atom:br
@angle:br-c2-c2 @atom:br @atom:c2 @atom:c2
@angle:br-c2-c3 @atom:br @atom:c2 @atom:c3
@angle:br-c2-ce @atom:br @atom:c2 @atom:ce
@angle:br-c2-h4 @atom:br @atom:c2 @atom:h4
@angle:br-c2-ha @atom:br @atom:c2 @atom:ha
@angle:c1-c2-c1 @atom:c1 @atom:c2 @atom:c1
@angle:c1-c2-c2 @atom:c1 @atom:c2 @atom:c2
@angle:c1-c2-c3 @atom:c1 @atom:c2 @atom:c3
@angle:c1-c2-f @atom:c1 @atom:c2 @atom:f
@angle:c1-c2-ha @atom:c1 @atom:c2 @atom:ha
@angle:c2-c2-c2 @atom:c2 @atom:c2 @atom:c2
@angle:c2-c2-c3 @atom:c2 @atom:c2 @atom:c3
@angle:c2-c2-ca @atom:c2 @atom:c2 @atom:ca
@angle:c2-c2-cc @atom:c2 @atom:c2 @atom:cc
@angle:c2-c2-cd @atom:c2 @atom:c2 @atom:cd
@angle:c2-c2-cl @atom:c2 @atom:c2 @atom:cl
@angle:c2-c2-cx @atom:c2 @atom:c2 @atom:cx
@angle:c2-c2-cy @atom:c2 @atom:c2 @atom:cy
@angle:c2-c2-f @atom:c2 @atom:c2 @atom:f
@angle:c2-c2-h4 @atom:c2 @atom:c2 @atom:h4
@angle:c2-c2-ha @atom:c2 @atom:c2 @atom:ha
@angle:c2-c2-hc @atom:c2 @atom:c2 @atom:hc
@angle:c2-c2-hx @atom:c2 @atom:c2 @atom:hx
@angle:c2-c2-i @atom:c2 @atom:c2 @atom:i
@angle:c2-c2-n1 @atom:c2 @atom:c2 @atom:n1
@angle:c2-c2-n2 @atom:c2 @atom:c2 @atom:n2
@angle:c2-c2-n3 @atom:c2 @atom:c2 @atom:n3
@angle:c2-c2-n4 @atom:c2 @atom:c2 @atom:n4
@angle:c2-c2-n @atom:c2 @atom:c2 @atom:n
@angle:c2-c2-na @atom:c2 @atom:c2 @atom:na
@angle:c2-c2-nh @atom:c2 @atom:c2 @atom:nh
@angle:c2-c2-no @atom:c2 @atom:c2 @atom:no
@angle:c2-c2-o @atom:c2 @atom:c2 @atom:o
@angle:c2-c2-oh @atom:c2 @atom:c2 @atom:oh
@angle:c2-c2-os @atom:c2 @atom:c2 @atom:os
@angle:c2-c2-p2 @atom:c2 @atom:c2 @atom:p2
@angle:c2-c2-p3 @atom:c2 @atom:c2 @atom:p3
@angle:c2-c2-p4 @atom:c2 @atom:c2 @atom:p4
@angle:c2-c2-p5 @atom:c2 @atom:c2 @atom:p5
@angle:c2-c2-s4 @atom:c2 @atom:c2 @atom:s4
@angle:c2-c2-s6 @atom:c2 @atom:c2 @atom:s6
@angle:c2-c2-s @atom:c2 @atom:c2 @atom:s
@angle:c2-c2-sh @atom:c2 @atom:c2 @atom:sh
@angle:c2-c2-ss @atom:c2 @atom:c2 @atom:ss
@angle:c3-c2-c3 @atom:c3 @atom:c2 @atom:c3
@angle:c3-c2-cc @atom:c3 @atom:c2 @atom:cc
@angle:c3-c2-cd @atom:c3 @atom:c2 @atom:cd
@angle:c3-c2-ce @atom:c3 @atom:c2 @atom:ce
@angle:c3-c2-cf @atom:c3 @atom:c2 @atom:cf
@angle:c3-c2-h4 @atom:c3 @atom:c2 @atom:h4
@angle:c3-c2-ha @atom:c3 @atom:c2 @atom:ha
@angle:c3-c2-hc @atom:c3 @atom:c2 @atom:hc
@angle:c3-c2-n2 @atom:c3 @atom:c2 @atom:n2
@angle:c3-c2-n @atom:c3 @atom:c2 @atom:n
@angle:c3-c2-na @atom:c3 @atom:c2 @atom:na
@angle:c3-c2-ne @atom:c3 @atom:c2 @atom:ne
@angle:c3-c2-nf @atom:c3 @atom:c2 @atom:nf
@angle:c3-c2-nh @atom:c3 @atom:c2 @atom:nh
@angle:c3-c2-o @atom:c3 @atom:c2 @atom:o
@angle:c3-c2-oh @atom:c3 @atom:c2 @atom:oh
@angle:c3-c2-os @atom:c3 @atom:c2 @atom:os
@angle:c3-c2-p2 @atom:c3 @atom:c2 @atom:p2
@angle:c3-c2-s @atom:c3 @atom:c2 @atom:s
@angle:c3-c2-ss @atom:c3 @atom:c2 @atom:ss
@angle:ca-c2-ca @atom:ca @atom:c2 @atom:ca
@angle:ca-c2-hc @atom:ca @atom:c2 @atom:hc
@angle:c-c2-c2 @atom:c @atom:c2 @atom:c2
@angle:c-c2-c3 @atom:c @atom:c2 @atom:c3
@angle:c-c2-c @atom:c @atom:c2 @atom:c
@angle:cc-c2-h4 @atom:cc @atom:c2 @atom:h4
@angle:cc-c2-ha @atom:cc @atom:c2 @atom:ha
@angle:cc-c2-nh @atom:cc @atom:c2 @atom:nh
@angle:cc-c2-o @atom:cc @atom:c2 @atom:o
@angle:cd-c2-ha @atom:cd @atom:c2 @atom:ha
@angle:ce-c2-cl @atom:ce @atom:c2 @atom:cl
@angle:ce-c2-h4 @atom:ce @atom:c2 @atom:h4
@angle:ce-c2-ha @atom:ce @atom:c2 @atom:ha
@angle:ce-c2-na @atom:ce @atom:c2 @atom:na
@angle:ce-c2-nh @atom:ce @atom:c2 @atom:nh
@angle:ce-c2-no @atom:ce @atom:c2 @atom:no
@angle:ce-c2-o @atom:ce @atom:c2 @atom:o
@angle:ce-c2-oh @atom:ce @atom:c2 @atom:oh
@angle:ce-c2-os @atom:ce @atom:c2 @atom:os
@angle:cf-c2-ha @atom:cf @atom:c2 @atom:ha
@angle:c-c2-ha @atom:c @atom:c2 @atom:ha
@angle:c-c2-hc @atom:c @atom:c2 @atom:hc
@angle:cl-c2-cl @atom:cl @atom:c2 @atom:cl
@angle:cl-c2-h4 @atom:cl @atom:c2 @atom:h4
@angle:cl-c2-ha @atom:cl @atom:c2 @atom:ha
@angle:cx-c2-ha @atom:cx @atom:c2 @atom:ha
@angle:f-c2-f @atom:f @atom:c2 @atom:f
@angle:f-c2-ha @atom:f @atom:c2 @atom:ha
@angle:h4-c2-n2 @atom:h4 @atom:c2 @atom:n2
@angle:h4-c2-n @atom:h4 @atom:c2 @atom:n
@angle:h4-c2-na @atom:h4 @atom:c2 @atom:na
@angle:h4-c2-ne @atom:h4 @atom:c2 @atom:ne
@angle:h4-c2-nh @atom:h4 @atom:c2 @atom:nh
@angle:h4-c2-no @atom:h4 @atom:c2 @atom:no
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@angle:c3-ss-cy @atom:c3 @atom:ss @atom:cy
@angle:c3-ss-f @atom:c3 @atom:ss @atom:f
@angle:c3-ss-i @atom:c3 @atom:ss @atom:i
@angle:c3-ss-n1 @atom:c3 @atom:ss @atom:n1
@angle:c3-ss-n2 @atom:c3 @atom:ss @atom:n2
@angle:c3-ss-n3 @atom:c3 @atom:ss @atom:n3
@angle:c3-ss-n @atom:c3 @atom:ss @atom:n
@angle:c3-ss-n4 @atom:c3 @atom:ss @atom:n4
@angle:c3-ss-na @atom:c3 @atom:ss @atom:na
@angle:c3-ss-nh @atom:c3 @atom:ss @atom:nh
@angle:c3-ss-no @atom:c3 @atom:ss @atom:no
@angle:c3-ss-o @atom:c3 @atom:ss @atom:o
@angle:c3-ss-oh @atom:c3 @atom:ss @atom:oh
@angle:c3-ss-os @atom:c3 @atom:ss @atom:os
@angle:c3-ss-p2 @atom:c3 @atom:ss @atom:p2
@angle:c3-ss-p3 @atom:c3 @atom:ss @atom:p3
@angle:c3-ss-p4 @atom:c3 @atom:ss @atom:p4
@angle:c3-ss-p5 @atom:c3 @atom:ss @atom:p5
@angle:c3-ss-s4 @atom:c3 @atom:ss @atom:s4
@angle:c3-ss-s @atom:c3 @atom:ss @atom:s
@angle:c3-ss-s6 @atom:c3 @atom:ss @atom:s6
@angle:c3-ss-sh @atom:c3 @atom:ss @atom:sh
@angle:c3-ss-ss @atom:c3 @atom:ss @atom:ss
@angle:ca-ss-ca @atom:ca @atom:ss @atom:ca
@angle:ca-ss-cc @atom:ca @atom:ss @atom:cc
@angle:ca-ss-cd @atom:ca @atom:ss @atom:cd
@angle:ca-ss-cl @atom:ca @atom:ss @atom:cl
@angle:ca-ss-n @atom:ca @atom:ss @atom:n
@angle:ca-ss-na @atom:ca @atom:ss @atom:na
@angle:ca-ss-nc @atom:ca @atom:ss @atom:nc
@angle:ca-ss-nd @atom:ca @atom:ss @atom:nd
@angle:ca-ss-ss @atom:ca @atom:ss @atom:ss
@angle:c-ss-c2 @atom:c @atom:ss @atom:c2
@angle:c-ss-c3 @atom:c @atom:ss @atom:c3
@angle:c-ss-c @atom:c @atom:ss @atom:c
@angle:c-ss-cc @atom:c @atom:ss @atom:cc
@angle:cc-ss-cc @atom:cc @atom:ss @atom:cc
@angle:cc-ss-cd @atom:cc @atom:ss @atom:cd
@angle:cc-ss-n @atom:cc @atom:ss @atom:n
@angle:cc-ss-na @atom:cc @atom:ss @atom:na
@angle:cc-ss-nc @atom:cc @atom:ss @atom:nc
@angle:cc-ss-os @atom:cc @atom:ss @atom:os
@angle:cc-ss-ss @atom:cc @atom:ss @atom:ss
@angle:cd-ss-cd @atom:cd @atom:ss @atom:cd
@angle:cd-ss-n @atom:cd @atom:ss @atom:n
@angle:cd-ss-na @atom:cd @atom:ss @atom:na
@angle:cd-ss-nd @atom:cd @atom:ss @atom:nd
@angle:cd-ss-os @atom:cd @atom:ss @atom:os
@angle:cd-ss-ss @atom:cd @atom:ss @atom:ss
@angle:cl-ss-cl @atom:cl @atom:ss @atom:cl
@angle:cx-ss-cx @atom:cx @atom:ss @atom:cx
@angle:f-ss-f @atom:f @atom:ss @atom:f
@angle:f-ss-ss @atom:f @atom:ss @atom:ss
@angle:i-ss-i @atom:i @atom:ss @atom:i
@angle:n1-ss-n1 @atom:n1 @atom:ss @atom:n1
@angle:n2-ss-n2 @atom:n2 @atom:ss @atom:n2
@angle:n3-ss-n3 @atom:n3 @atom:ss @atom:n3
@angle:n4-ss-n4 @atom:n4 @atom:ss @atom:n4
@angle:na-ss-na @atom:na @atom:ss @atom:na
@angle:nc-ss-nc @atom:nc @atom:ss @atom:nc
@angle:nd-ss-nd @atom:nd @atom:ss @atom:nd
@angle:nh-ss-nh @atom:nh @atom:ss @atom:nh
@angle:n-ss-n @atom:n @atom:ss @atom:n
@angle:no-ss-no @atom:no @atom:ss @atom:no
@angle:oh-ss-oh @atom:oh @atom:ss @atom:oh
@angle:o-ss-o @atom:o @atom:ss @atom:o
@angle:o-ss-p5 @atom:o @atom:ss @atom:p5
@angle:o-ss-s6 @atom:o @atom:ss @atom:s6
@angle:os-ss-os @atom:os @atom:ss @atom:os
@angle:o-ss-ss @atom:o @atom:ss @atom:ss
@angle:p2-ss-p2 @atom:p2 @atom:ss @atom:p2
@angle:p3-ss-p3 @atom:p3 @atom:ss @atom:p3
@angle:p5-ss-p5 @atom:p5 @atom:ss @atom:p5
@angle:s4-ss-s4 @atom:s4 @atom:ss @atom:s4
@angle:s4-ss-s6 @atom:s4 @atom:ss @atom:s6
@angle:s6-ss-s6 @atom:s6 @atom:ss @atom:s6
@angle:sh-ss-sh @atom:sh @atom:ss @atom:sh
@angle:sh-ss-ss @atom:sh @atom:ss @atom:ss
@angle:s-ss-s @atom:s @atom:ss @atom:s
@angle:ss-ss-ss @atom:ss @atom:ss @atom:ss
@angle:c3-sx-ca @atom:c3 @atom:sx @atom:ca
@angle:c3-sx-cc @atom:c3 @atom:sx @atom:cc
@angle:c3-sx-ce @atom:c3 @atom:sx @atom:ce
@angle:c3-sx-cf @atom:c3 @atom:sx @atom:cf
@angle:c3-sx-ne @atom:c3 @atom:sx @atom:ne
@angle:c3-sx-nf @atom:c3 @atom:sx @atom:nf
@angle:c3-sx-o @atom:c3 @atom:sx @atom:o
@angle:c3-sx-pe @atom:c3 @atom:sx @atom:pe
@angle:c3-sx-pf @atom:c3 @atom:sx @atom:pf
@angle:c3-sx-px @atom:c3 @atom:sx @atom:px
@angle:c3-sx-py @atom:c3 @atom:sx @atom:py
@angle:c3-sx-sx @atom:c3 @atom:sx @atom:sx
@angle:c3-sx-sy @atom:c3 @atom:sx @atom:sy
@angle:ca-sx-ca @atom:ca @atom:sx @atom:ca
@angle:ca-sx-o @atom:ca @atom:sx @atom:o
@angle:c-sx-c3 @atom:c @atom:sx @atom:c3
@angle:c-sx-c @atom:c @atom:sx @atom:c
@angle:cc-sx-o @atom:cc @atom:sx @atom:o
@angle:ce-sx-ce @atom:ce @atom:sx @atom:ce
@angle:ce-sx-o @atom:ce @atom:sx @atom:o
@angle:cf-sx-cf @atom:cf @atom:sx @atom:cf
@angle:cf-sx-o @atom:cf @atom:sx @atom:o
@angle:c-sx-o @atom:c @atom:sx @atom:o
@angle:ne-sx-ne @atom:ne @atom:sx @atom:ne
@angle:ne-sx-o @atom:ne @atom:sx @atom:o
@angle:nf-sx-nf @atom:nf @atom:sx @atom:nf
@angle:nf-sx-o @atom:nf @atom:sx @atom:o
@angle:o-sx-pe @atom:o @atom:sx @atom:pe
@angle:o-sx-pf @atom:o @atom:sx @atom:pf
@angle:o-sx-px @atom:o @atom:sx @atom:px
@angle:o-sx-py @atom:o @atom:sx @atom:py
@angle:o-sx-sx @atom:o @atom:sx @atom:sx
@angle:o-sx-sy @atom:o @atom:sx @atom:sy
@angle:pe-sx-pe @atom:pe @atom:sx @atom:pe
@angle:pf-sx-pf @atom:pf @atom:sx @atom:pf
@angle:py-sx-py @atom:py @atom:sx @atom:py
@angle:sx-sx-sx @atom:sx @atom:sx @atom:sx
@angle:sy-sx-sy @atom:sy @atom:sx @atom:sy
@angle:c3-sy-ca @atom:c3 @atom:sy @atom:ca
@angle:c3-sy-cc @atom:c3 @atom:sy @atom:cc
@angle:c3-sy-ce @atom:c3 @atom:sy @atom:ce
@angle:c3-sy-cf @atom:c3 @atom:sy @atom:cf
@angle:c3-sy-ne @atom:c3 @atom:sy @atom:ne
@angle:c3-sy-nf @atom:c3 @atom:sy @atom:nf
@angle:c3-sy-o @atom:c3 @atom:sy @atom:o
@angle:c3-sy-pe @atom:c3 @atom:sy @atom:pe
@angle:c3-sy-pf @atom:c3 @atom:sy @atom:pf
@angle:c3-sy-px @atom:c3 @atom:sy @atom:px
@angle:c3-sy-py @atom:c3 @atom:sy @atom:py
@angle:c3-sy-sx @atom:c3 @atom:sy @atom:sx
@angle:c3-sy-sy @atom:c3 @atom:sy @atom:sy
@angle:ca-sy-ca @atom:ca @atom:sy @atom:ca
@angle:ca-sy-cc @atom:ca @atom:sy @atom:cc
@angle:ca-sy-n3 @atom:ca @atom:sy @atom:n3
@angle:ca-sy-n @atom:ca @atom:sy @atom:n
@angle:ca-sy-ne @atom:ca @atom:sy @atom:ne
@angle:ca-sy-nh @atom:ca @atom:sy @atom:nh
@angle:ca-sy-o @atom:ca @atom:sy @atom:o
@angle:ca-sy-oh @atom:ca @atom:sy @atom:oh
@angle:ca-sy-os @atom:ca @atom:sy @atom:os
@angle:c-sy-c3 @atom:c @atom:sy @atom:c3
@angle:c-sy-c @atom:c @atom:sy @atom:c
@angle:cc-sy-n3 @atom:cc @atom:sy @atom:n3
@angle:cc-sy-o @atom:cc @atom:sy @atom:o
@angle:cd-sy-n3 @atom:cd @atom:sy @atom:n3
@angle:cd-sy-nh @atom:cd @atom:sy @atom:nh
@angle:cd-sy-o @atom:cd @atom:sy @atom:o
@angle:ce-sy-ce @atom:ce @atom:sy @atom:ce
@angle:ce-sy-o @atom:ce @atom:sy @atom:o
@angle:cf-sy-cf @atom:cf @atom:sy @atom:cf
@angle:cf-sy-o @atom:cf @atom:sy @atom:o
@angle:c-sy-o @atom:c @atom:sy @atom:o
@angle:f-sy-o @atom:f @atom:sy @atom:o
@angle:n2-sy-o @atom:n2 @atom:sy @atom:o
@angle:n3-sy-ne @atom:n3 @atom:sy @atom:ne
@angle:n3-sy-o @atom:n3 @atom:sy @atom:o
@angle:na-sy-na @atom:na @atom:sy @atom:na
@angle:nc-sy-nc @atom:nc @atom:sy @atom:nc
@angle:nd-sy-nd @atom:nd @atom:sy @atom:nd
@angle:ne-sy-ne @atom:ne @atom:sy @atom:ne
@angle:ne-sy-o @atom:ne @atom:sy @atom:o
@angle:nf-sy-nf @atom:nf @atom:sy @atom:nf
@angle:nf-sy-o @atom:nf @atom:sy @atom:o
@angle:nh-sy-o @atom:nh @atom:sy @atom:o
@angle:n-sy-o @atom:n @atom:sy @atom:o
@angle:o-sy-o @atom:o @atom:sy @atom:o
@angle:o-sy-oh @atom:o @atom:sy @atom:oh
@angle:o-sy-os @atom:o @atom:sy @atom:os
@angle:o-sy-pe @atom:o @atom:sy @atom:pe
@angle:o-sy-pf @atom:o @atom:sy @atom:pf
@angle:o-sy-px @atom:o @atom:sy @atom:px
@angle:o-sy-py @atom:o @atom:sy @atom:py
@angle:o-sy-sx @atom:o @atom:sy @atom:sx
@angle:o-sy-sy @atom:o @atom:sy @atom:sy
@angle:py-sy-py @atom:py @atom:sy @atom:py
@angle:sx-sy-sx @atom:sx @atom:sy @atom:sx
@angle:sy-sy-sy @atom:sy @atom:sy @atom:sy
} # (end of Angles By Type)
write_once("In Settings") {
dihedral_coeff @dihedral:X-c-c-X fourier 1 0.3 2 180.0 #
dihedral_coeff @dihedral:X-c-c1-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c-cg-X fourier 1 0.0 2 180.0 # same as X-c-c1-X
dihedral_coeff @dihedral:X-c-ch-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c-c2-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-c-cu-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-c-cv-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-c-ce-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-c-cf-X fourier 1 2.175 2 180.0 # intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-c-c3-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230
dihedral_coeff @dihedral:X-c-cx-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230
dihedral_coeff @dihedral:X-c-cy-X fourier 1 0.0 2 180.0 # JCC, 7, (1986), 230
dihedral_coeff @dihedral:X-c-ca-X fourier 1 1.0 2 180.0 # optimized by Junmei Wang, Jan-2013
dihedral_coeff @dihedral:X-c-cc-X fourier 1 2.875 2 180.0 # statistic value
dihedral_coeff @dihedral:X-c-cd-X fourier 1 2.875 2 180.0 # statistic value
dihedral_coeff @dihedral:X-c-n-X fourier 1 2.5 2 180.0 # AA,NMA (no c-n3, c-n4, c-nh)
dihedral_coeff @dihedral:X-c-n2-X fourier 1 4.15 2 180.0 # double bond, same as X-c2-n2-X
dihedral_coeff @dihedral:X-c-nc-X fourier 1 4.0 2 180.0 # same as X-C-NC-X
dihedral_coeff @dihedral:X-c-nd-X fourier 1 4.0 2 180.0 # same as X-C-NC-X
dihedral_coeff @dihedral:X-c-ne-X fourier 1 0.2 2 180.0 # single bond
dihedral_coeff @dihedral:X-c-nf-X fourier 1 0.2 2 180.0 # single bond
dihedral_coeff @dihedral:X-c-na-X fourier 2 1.45 2 180.0 0.35 4 180.0 #
dihedral_coeff @dihedral:X-c-no-X fourier 1 0.45 2 180.0 #
dihedral_coeff @dihedral:X-c-oh-X fourier 1 2.3 2 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:X-c-os-X fourier 1 2.7 2 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:X-c-p2-X fourier 1 6.65 2 180.0 # double bond, same as X-c2-p2-X
dihedral_coeff @dihedral:X-c-pc-X fourier 1 2.0 2 180.0 # estimated
dihedral_coeff @dihedral:X-c-pd-X fourier 1 2.0 2 180.0 # estimated
dihedral_coeff @dihedral:X-c-pe-X fourier 1 0.0 2 180.0 # single bond
dihedral_coeff @dihedral:X-c-pf-X fourier 1 0.0 2 180.0 # single bond
dihedral_coeff @dihedral:X-c-p3-X fourier 1 1.55 2 180.0 #
dihedral_coeff @dihedral:X-c-p4-X fourier 1 1.35 2 180.0 #
dihedral_coeff @dihedral:X-c-px-X fourier 1 1.35 2 180.0 #
dihedral_coeff @dihedral:X-c-p5-X fourier 1 1.0 2 0.0 #
dihedral_coeff @dihedral:X-c-py-X fourier 1 1.0 2 0.0 #
dihedral_coeff @dihedral:X-c-sh-X fourier 1 2.25 2 180.0 #
dihedral_coeff @dihedral:X-c-ss-X fourier 1 3.1 2 180.0 #
dihedral_coeff @dihedral:X-c-s4-X fourier 1 0.2 2 180.0 #
dihedral_coeff @dihedral:X-c-sx-X fourier 1 0.2 2 180.0 #
dihedral_coeff @dihedral:X-c-s6-X fourier 1 0.5 2 0.0 #
dihedral_coeff @dihedral:X-c-sy-X fourier 1 0.5 2 0.0 #
dihedral_coeff @dihedral:X-c1-c1-X fourier 1 0.0 2 180.0 # for both triple and single bonds
dihedral_coeff @dihedral:X-c1-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds
dihedral_coeff @dihedral:X-c1-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds
dihedral_coeff @dihedral:X-cg-cg-X fourier 1 0.0 2 180.0 # for both triple and single bonds
dihedral_coeff @dihedral:X-ch-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds
dihedral_coeff @dihedral:X-cg-ch-X fourier 1 0.0 2 180.0 # for both triple and single bonds
dihedral_coeff @dihedral:X-c1-c2-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-c3-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-ca-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-cc-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-cd-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-ce-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-cf-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-cu-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-cv-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-cx-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-cy-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-n-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-n2-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-n3-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-n4-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-na-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-nb-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-nc-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-nd-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-ne-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-nf-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-nh-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-no-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-oh-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-os-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-p2-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-pb-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-pc-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-pd-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-pe-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-pf-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-p3-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-p4-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-px-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-p5-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-py-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-s2-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-sh-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-ss-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-s4-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-sx-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-s6-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c1-sy-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-c2-c2-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-c2-ce-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-c2-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-ce-cf-X fourier 1 6.65 2 180.0 # c2=c2 double bond, intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-ce-ce-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99
dihedral_coeff @dihedral:X-cf-cf-X fourier 1 1.0 2 180.0 # c2-c2 single bond, parm99
dihedral_coeff @dihedral:X-cc-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94
dihedral_coeff @dihedral:X-cc-cc-X fourier 1 4.0 2 180.0 # statistic value of parm94
dihedral_coeff @dihedral:X-cd-cd-X fourier 1 4.0 2 180.0 # statistic value of parm94
dihedral_coeff @dihedral:X-c2-c3-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c2-ca-X fourier 1 0.7 2 180.0 # optimized by Junmei Wang, March 2013
dihedral_coeff @dihedral:X-c2-n-X fourier 1 0.65 2 180.0 #
dihedral_coeff @dihedral:X-c2-n2-X fourier 1 4.15 2 180.0 # double bond, parm99
dihedral_coeff @dihedral:X-c2-ne-X fourier 1 4.15 2 180.0 # double bond, parm99
dihedral_coeff @dihedral:X-c2-nf-X fourier 1 4.15 2 180.0 # double bond, parm99
dihedral_coeff @dihedral:X-ce-ne-X fourier 1 0.8 2 180.0 # single bond
dihedral_coeff @dihedral:X-cf-nf-X fourier 1 0.8 2 180.0 # single bond
dihedral_coeff @dihedral:X-c2-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94
dihedral_coeff @dihedral:X-c2-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94
dihedral_coeff @dihedral:X-cc-nd-X fourier 1 4.75 2 180.0 # statistic value from parm94
dihedral_coeff @dihedral:X-cd-nc-X fourier 1 4.75 2 180.0 # statistiv value from parm94
dihedral_coeff @dihedral:X-cc-nc-X fourier 1 4.75 2 180.0 # statistic value from parm94
dihedral_coeff @dihedral:X-cd-nd-X fourier 1 4.75 2 180.0 # statistiv value from parm94
dihedral_coeff @dihedral:X-c2-n3-X fourier 1 0.3 2 180.0 # intrpol.
dihedral_coeff @dihedral:X-c2-n4-X fourier 1 0.0 3 180.0 # intrpol.
dihedral_coeff @dihedral:X-c2-na-X fourier 1 0.625 2 180.0 #
dihedral_coeff @dihedral:X-cc-na-X fourier 1 1.7 2 180.0 # statistic value from parm94
dihedral_coeff @dihedral:X-cd-na-X fourier 1 1.7 2 180.0 # statistic value from parm94
dihedral_coeff @dihedral:X-c2-nh-X fourier 1 0.675 2 180.0 #
dihedral_coeff @dihedral:X-c2-no-X fourier 1 0.75 2 180.0 #
dihedral_coeff @dihedral:X-c2-oh-X fourier 1 1.05 2 180.0 # parm99
dihedral_coeff @dihedral:X-c2-os-X fourier 1 1.05 2 180.0 # parm99
dihedral_coeff @dihedral:X-c2-p2-X fourier 1 6.65 2 180.0 # double bond
dihedral_coeff @dihedral:X-c2-pe-X fourier 1 6.65 2 180.0 # double bond
dihedral_coeff @dihedral:X-c2-pf-X fourier 1 6.65 2 180.0 # double bond
dihedral_coeff @dihedral:X-ce-pf-X fourier 1 6.65 2 180.0 # double bond
dihedral_coeff @dihedral:X-ce-pe-X fourier 1 0.95 2 180.0 # single bond
dihedral_coeff @dihedral:X-cf-pf-X fourier 1 0.95 2 180.0 # single bond
dihedral_coeff @dihedral:X-c2-pc-X fourier 1 4.75 2 180.0 # estimated
dihedral_coeff @dihedral:X-c2-pd-X fourier 1 4.75 2 180.0 # estimated
dihedral_coeff @dihedral:X-cc-pc-X fourier 1 4.75 2 180.0 # estimated
dihedral_coeff @dihedral:X-cc-pd-X fourier 1 4.75 2 180.0 # estimated
dihedral_coeff @dihedral:X-cd-pc-X fourier 1 4.75 2 180.0 # estimated
dihedral_coeff @dihedral:X-cd-pd-X fourier 1 4.75 2 180.0 # estimated
dihedral_coeff @dihedral:X-c2-p3-X fourier 1 0.45 2 180.0 #
dihedral_coeff @dihedral:X-c2-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!!
dihedral_coeff @dihedral:X-ce-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!!
dihedral_coeff @dihedral:X-cf-p4-X fourier 1 6.65 2 180.0 # c2=p4 double bond !!!
dihedral_coeff @dihedral:X-c2-px-X fourier 1 0.325 2 0.0 #
dihedral_coeff @dihedral:X-ce-px-X fourier 1 0.325 2 0.0 #
dihedral_coeff @dihedral:X-cf-px-X fourier 1 0.325 2 0.0 #
dihedral_coeff @dihedral:X-c2-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!!
dihedral_coeff @dihedral:X-ce-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!!
dihedral_coeff @dihedral:X-cf-p5-X fourier 1 6.65 2 180.0 # c2=p5 double bond !!!
dihedral_coeff @dihedral:X-c2-py-X fourier 1 1.43333333333 2 180.0 #
dihedral_coeff @dihedral:X-ce-py-X fourier 1 1.43333333333 2 180.0 #
dihedral_coeff @dihedral:X-cf-py-X fourier 1 1.43333333333 2 180.0 #
dihedral_coeff @dihedral:X-c2-sh-X fourier 1 0.5 2 180.0 #
dihedral_coeff @dihedral:X-c2-ss-X fourier 1 1.1 2 180.0 #
dihedral_coeff @dihedral:X-c2-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!!
dihedral_coeff @dihedral:X-ce-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!!
dihedral_coeff @dihedral:X-cf-s4-X fourier 1 6.65 2 180.0 # c2=s4 double bond !!!
dihedral_coeff @dihedral:X-c2-sx-X fourier 1 0.6 2 0.0 #
dihedral_coeff @dihedral:X-ce-sx-X fourier 1 0.6 2 0.0 #
dihedral_coeff @dihedral:X-cf-sx-X fourier 1 0.6 2 0.0 #
dihedral_coeff @dihedral:X-c2-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!!
dihedral_coeff @dihedral:X-ce-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!!
dihedral_coeff @dihedral:X-cf-s6-X fourier 1 6.65 2 180.0 # c2=s6 double bond !!!
dihedral_coeff @dihedral:X-c2-sy-X fourier 1 1.26666666667 2 180.0 #
dihedral_coeff @dihedral:X-ce-sy-X fourier 1 1.26666666667 2 180.0 #
dihedral_coeff @dihedral:X-cf-sy-X fourier 1 1.26666666667 2 180.0 #
dihedral_coeff @dihedral:X-c3-c3-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-cx-cx-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X
dihedral_coeff @dihedral:X-cy-cy-X fourier 1 0.155555555556 3 0.0 # same as X-c3-c3-X
dihedral_coeff @dihedral:X-c3-ca-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-n-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-cx-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X
dihedral_coeff @dihedral:X-cy-n-X fourier 1 0.0 2 0.0 # same as X-c3-n-X
dihedral_coeff @dihedral:X-c3-n2-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-ne-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-nf-X fourier 1 0.0 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-n3-X fourier 1 0.3 3 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:X-c3-n4-X fourier 1 0.155555555556 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-na-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-nh-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-no-X fourier 1 0.0 2 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-oh-X fourier 1 0.166666666667 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-os-X fourier 1 0.383333333333 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-p2-X fourier 1 0.266666666667 2 180.0 #
dihedral_coeff @dihedral:X-c3-pe-X fourier 1 0.266666666667 2 180.0 #
dihedral_coeff @dihedral:X-c3-pf-X fourier 1 0.266666666667 2 180.0 #
dihedral_coeff @dihedral:X-c3-p3-X fourier 1 0.133333333333 3 0.0 #
dihedral_coeff @dihedral:X-c3-p4-X fourier 1 0.133333333333 3 0.0 #
dihedral_coeff @dihedral:X-c3-px-X fourier 1 0.133333333333 3 0.0 #
dihedral_coeff @dihedral:X-c3-p5-X fourier 1 0.0222222222222 3 0.0 #
dihedral_coeff @dihedral:X-c3-py-X fourier 1 0.0222222222222 3 0.0 #
dihedral_coeff @dihedral:X-c3-sh-X fourier 1 0.25 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-ss-X fourier 1 0.333333333333 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:X-c3-s4-X fourier 1 0.2 3 0.0 #
dihedral_coeff @dihedral:X-c3-sx-X fourier 1 0.2 3 0.0 #
dihedral_coeff @dihedral:X-c3-s6-X fourier 1 0.144444444444 3 0.0 #
dihedral_coeff @dihedral:X-c3-sy-X fourier 1 0.144444444444 3 0.0 #
dihedral_coeff @dihedral:X-c3-cc-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X
dihedral_coeff @dihedral:X-c3-cd-X fourier 1 0.0 3 0.0 # same as X-c3-ca-X
dihedral_coeff @dihedral:X-ca-ca-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-ca-cp-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-ca-cq-X fourier 1 3.625 2 180.0 # intrpol.bsd.on C6H6
dihedral_coeff @dihedral:X-cp-cp-X fourier 1 1.0 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-cq-cq-X fourier 1 1.0 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-ca-n-X fourier 1 0.45 2 180.0 #
dihedral_coeff @dihedral:X-ca-n2-X fourier 1 0.0 3 180.0 #
dihedral_coeff @dihedral:X-ca-ne-X fourier 1 0.0 3 180.0 #
dihedral_coeff @dihedral:X-ca-nf-X fourier 1 0.0 3 180.0 #
dihedral_coeff @dihedral:X-ca-n4-X fourier 1 1.75 2 0.0 #
dihedral_coeff @dihedral:X-ca-na-X fourier 1 0.3 2 180.0 #
dihedral_coeff @dihedral:X-ca-nb-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X
dihedral_coeff @dihedral:X-ca-nc-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X
dihedral_coeff @dihedral:X-ca-nd-X fourier 1 4.8 2 180.0 # same as X-CA-NC-X
dihedral_coeff @dihedral:X-ca-nh-X fourier 1 1.05 2 180.0 #
dihedral_coeff @dihedral:X-cc-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X
dihedral_coeff @dihedral:X-cd-nh-X fourier 1 1.05 2 180.0 # same as X-ca-nh-X
dihedral_coeff @dihedral:X-ca-no-X fourier 1 0.6 2 180.0 #
dihedral_coeff @dihedral:X-ca-oh-X fourier 1 0.9 2 180.0 # Junmei et al, 99
dihedral_coeff @dihedral:X-ca-os-X fourier 1 0.9 2 180.0 # same as X-ca-oh-X
dihedral_coeff @dihedral:X-ca-p2-X fourier 1 0.6 2 180.0 #
dihedral_coeff @dihedral:X-ca-pe-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X
dihedral_coeff @dihedral:X-ca-pf-X fourier 1 0.6 2 180.0 # same as X-ca-p2-X
dihedral_coeff @dihedral:X-ca-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol
dihedral_coeff @dihedral:X-ca-pd-X fourier 1 4.8 2 180.0 # estimated, intrpol
dihedral_coeff @dihedral:X-ca-p3-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-ca-p4-X fourier 1 0.525 2 180.0 #
dihedral_coeff @dihedral:X-ca-px-X fourier 1 0.525 2 180.0 # estimated, same as X-ca-p4-X
dihedral_coeff @dihedral:X-ca-p5-X fourier 1 1.46666666667 2 180.0 #
dihedral_coeff @dihedral:X-ca-py-X fourier 1 1.46666666667 2 180.0 # estimated, same as X-ca-p5-X
dihedral_coeff @dihedral:X-ca-sh-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-ca-ss-X fourier 1 0.4 2 180.0 #
dihedral_coeff @dihedral:X-ca-s4-X fourier 1 0.3 2 0.0 #
dihedral_coeff @dihedral:X-ca-sx-X fourier 1 0.3 2 0.0 # estimated, same as X-ca-s4-X
dihedral_coeff @dihedral:X-ca-s6-X fourier 1 1.3 2 180.0 #
dihedral_coeff @dihedral:X-ca-sy-X fourier 1 1.3 2 180.0 # estimated, same as X-ca-s6-X
dihedral_coeff @dihedral:X-n-cc-X fourier 1 1.65 2 180.0 # statistic value from parm94
dihedral_coeff @dihedral:X-n-cd-X fourier 1 1.65 2 180.0 # statistic value from parm94
dihedral_coeff @dihedral:X-n-n-X fourier 1 1.15 2 0.0 #
dihedral_coeff @dihedral:X-n-n2-X fourier 1 0.4 2 0.0 #
dihedral_coeff @dihedral:X-n-ne-X fourier 1 0.4 2 0.0 #
dihedral_coeff @dihedral:X-n-nf-X fourier 1 0.4 2 0.0 #
dihedral_coeff @dihedral:X-n-n3-X fourier 1 1.075 2 0.0 #
dihedral_coeff @dihedral:X-n-n4-X fourier 1 0.95 2 0.0 #
dihedral_coeff @dihedral:X-n-na-X fourier 1 0.7 2 0.0 #
dihedral_coeff @dihedral:X-n-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n-nh-X fourier 1 1.1 2 0.0 #
dihedral_coeff @dihedral:X-n-no-X fourier 1 1.375 2 180.0 #
dihedral_coeff @dihedral:X-n-oh-X fourier 1 1.5 2 0.0 #
dihedral_coeff @dihedral:X-n-os-X fourier 1 1.1 2 0.0 #
dihedral_coeff @dihedral:X-n-p2-X fourier 1 1.0 2 180.0 #
dihedral_coeff @dihedral:X-n-pe-X fourier 1 1.0 2 180.0 #
dihedral_coeff @dihedral:X-n-pf-X fourier 1 4.8 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n-pc-X fourier 1 4.8 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n-pd-X fourier 1 1.0 2 180.0 #
dihedral_coeff @dihedral:X-n-p3-X fourier 1 2.25 2 0.0 #
dihedral_coeff @dihedral:X-n-p4-X fourier 1 0.325 2 0.0 #
dihedral_coeff @dihedral:X-n-px-X fourier 1 0.325 2 0.0 #
dihedral_coeff @dihedral:X-n-p5-X fourier 1 2.2 2 180.0 #
dihedral_coeff @dihedral:X-n-py-X fourier 1 2.2 2 180.0 #
dihedral_coeff @dihedral:X-n-sh-X fourier 1 1.1 2 0.0 #
dihedral_coeff @dihedral:X-n-ss-X fourier 1 1.5 2 0.0 #
dihedral_coeff @dihedral:X-n-s4-X fourier 1 1.5 3 0.0 #
dihedral_coeff @dihedral:X-n-sx-X fourier 1 1.5 3 0.0 #
dihedral_coeff @dihedral:X-n-s6-X fourier 1 1.1 2 180.0 #
dihedral_coeff @dihedral:X-n-sy-X fourier 1 1.1 2 180.0 #
dihedral_coeff @dihedral:X-n1-c2-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-c3-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-ca-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-cc-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-cd-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-ce-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-cf-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-cu-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-cv-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-cx-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-cy-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-n-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-n1-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-n2-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-n3-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-n4-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-na-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-nb-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-nc-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-nd-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-ne-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-nf-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-nh-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-no-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-oh-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-os-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-p2-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-pb-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-pc-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-pd-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-pe-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-pf-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-p3-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-p4-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-px-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-p5-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-py-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-s2-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-sh-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-ss-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-s4-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-sx-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-s6-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n1-sy-X fourier 1 0.0 2 180.0 #
dihedral_coeff @dihedral:X-n2-n2-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond
dihedral_coeff @dihedral:X-n2-ne-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond
dihedral_coeff @dihedral:X-n2-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond
dihedral_coeff @dihedral:X-ne-nf-X fourier 2 3.0 2 180.0 2.8 1 0.0 # double bond
dihedral_coeff @dihedral:X-ne-ne-X fourier 1 1.2 2 180.0 # single bond, intrpol
dihedral_coeff @dihedral:X-nf-nf-X fourier 1 1.2 2 180.0 # single bond, intrpol
dihedral_coeff @dihedral:X-nc-nc-X fourier 1 4.0 2 180.0 # estimated, intrpol
dihedral_coeff @dihedral:X-nd-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol
dihedral_coeff @dihedral:X-nc-nd-X fourier 1 4.0 2 180.0 # estimated, intrpol
dihedral_coeff @dihedral:X-n2-nc-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X
dihedral_coeff @dihedral:X-n2-nd-X fourier 2 3.0 2 180.0 2.8 1 0.0 # same as X-n2-n2-X
dihedral_coeff @dihedral:X-n2-n3-X fourier 1 6.1 2 180.0 #
dihedral_coeff @dihedral:X-ne-n3-X fourier 1 6.1 2 180.0 #
dihedral_coeff @dihedral:X-nf-n3-X fourier 1 6.1 2 180.0 #
dihedral_coeff @dihedral:X-n2-n4-X fourier 1 8.0 2 180.0 #
dihedral_coeff @dihedral:X-ne-n4-X fourier 1 8.0 2 180.0 #
dihedral_coeff @dihedral:X-nf-n4-X fourier 1 8.0 2 180.0 #
dihedral_coeff @dihedral:X-n2-na-X fourier 1 1.7 2 180.0 #
dihedral_coeff @dihedral:X-ne-na-X fourier 1 1.7 2 180.0 #
dihedral_coeff @dihedral:X-nf-na-X fourier 1 1.7 2 180.0 #
dihedral_coeff @dihedral:X-na-nc-X fourier 1 4.8 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-na-nd-X fourier 1 4.8 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n2-nh-X fourier 1 2.8 2 180.0 #
dihedral_coeff @dihedral:X-ne-nh-X fourier 1 2.8 2 180.0 #
dihedral_coeff @dihedral:X-nf-nh-X fourier 1 2.8 2 180.0 #
dihedral_coeff @dihedral:X-n2-no-X fourier 1 0.75 2 180.0 #
dihedral_coeff @dihedral:X-ne-no-X fourier 1 0.75 2 180.0 #
dihedral_coeff @dihedral:X-nf-no-X fourier 1 0.75 2 180.0 #
dihedral_coeff @dihedral:X-n2-oh-X fourier 1 3.2 2 180.0 #
dihedral_coeff @dihedral:X-ne-oh-X fourier 1 3.2 2 180.0 #
dihedral_coeff @dihedral:X-nf-oh-X fourier 1 3.2 2 180.0 #
dihedral_coeff @dihedral:X-n2-os-X fourier 1 3.0 2 180.0 #
dihedral_coeff @dihedral:X-ne-os-X fourier 1 3.0 2 180.0 #
dihedral_coeff @dihedral:X-nf-os-X fourier 1 3.0 2 180.0 #
dihedral_coeff @dihedral:X-nc-os-X fourier 1 4.8 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-nc-ss-X fourier 1 4.8 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n2-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n2-pe-X fourier 1 5.4 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n2-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-ne-pf-X fourier 1 5.4 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n2-pc-X fourier 1 5.4 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-n2-pd-X fourier 1 5.4 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-nc-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-nd-p2-X fourier 1 5.4 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-nc-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-nd-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-nd-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-nc-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-ne-pe-X fourier 1 0.6 1 0.0 # single bond
dihedral_coeff @dihedral:X-nf-pf-X fourier 1 0.6 1 0.0 # single bond
dihedral_coeff @dihedral:X-n2-p3-X fourier 1 2.1 2 180.0 #
dihedral_coeff @dihedral:X-n2-p4-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-ne-p4-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-nf-p4-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-n2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-ne-p5-X fourier 1 1.0 3 180.0 #
dihedral_coeff @dihedral:X-nf-p5-X fourier 1 1.0 3 180.0 #
dihedral_coeff @dihedral:X-ne-px-X fourier 1 1.0 3 180.0 #
dihedral_coeff @dihedral:X-nf-px-X fourier 1 1.0 3 180.0 #
dihedral_coeff @dihedral:X-n2-sh-X fourier 1 2.1 2 180.0 #
dihedral_coeff @dihedral:X-ne-sh-X fourier 1 2.1 2 180.0 #
dihedral_coeff @dihedral:X-nf-sh-X fourier 1 2.1 2 180.0 #
dihedral_coeff @dihedral:X-n2-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 #
dihedral_coeff @dihedral:X-ne-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 #
dihedral_coeff @dihedral:X-nf-ss-X fourier 2 2.8 2 180.0 1.3 1 180.0 #
dihedral_coeff @dihedral:X-n2-s4-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-ne-sx-X fourier 1 1.5 3 180.0 #
dihedral_coeff @dihedral:X-nf-sx-X fourier 1 1.5 3 180.0 #
dihedral_coeff @dihedral:X-n2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-ne-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 #
dihedral_coeff @dihedral:X-nf-sy-X fourier 2 0.5 3 180.0 6.8 1 180.0 #
dihedral_coeff @dihedral:X-n3-n3-X fourier 1 2.25 2 0.0 #
dihedral_coeff @dihedral:X-n3-n4-X fourier 1 0.25 3 0.0 #
dihedral_coeff @dihedral:X-n3-na-X fourier 1 1.6 2 0.0 #
dihedral_coeff @dihedral:X-n3-nh-X fourier 1 1.9 2 0.0 #
dihedral_coeff @dihedral:X-n3-no-X fourier 1 4.0 2 180.0 #
dihedral_coeff @dihedral:X-n3-oh-X fourier 1 2.2 2 0.0 #
dihedral_coeff @dihedral:X-n3-os-X fourier 1 1.8 2 0.0 #
dihedral_coeff @dihedral:X-n3-p2-X fourier 1 3.2 2 180.0 #
dihedral_coeff @dihedral:X-n3-pe-X fourier 1 3.2 2 180.0 #
dihedral_coeff @dihedral:X-n3-pf-X fourier 1 3.2 2 180.0 #
dihedral_coeff @dihedral:X-n3-p3-X fourier 1 2.35 2 0.0 #
dihedral_coeff @dihedral:X-n3-p4-X fourier 1 2.1 2 180.0 #
dihedral_coeff @dihedral:X-n3-px-X fourier 1 2.1 2 180.0 #
dihedral_coeff @dihedral:X-n3-p5-X fourier 1 3.0 2 180.0 #
dihedral_coeff @dihedral:X-n3-py-X fourier 1 3.0 2 180.0 #
dihedral_coeff @dihedral:X-n3-sh-X fourier 1 3.1 2 0.0 #
dihedral_coeff @dihedral:X-n3-ss-X fourier 1 2.6 2 0.0 #
dihedral_coeff @dihedral:X-n3-s4-X fourier 1 3.75 2 0.0 #
dihedral_coeff @dihedral:X-n3-sx-X fourier 1 3.75 2 0.0 #
dihedral_coeff @dihedral:X-n3-s6-X fourier 1 3.13333333333 2 0.0 #
dihedral_coeff @dihedral:X-n3-sy-X fourier 1 3.13333333333 2 0.0 #
dihedral_coeff @dihedral:X-n4-n4-X fourier 1 0.188888888889 3 0.0 #
dihedral_coeff @dihedral:X-n4-na-X fourier 1 0.233333333333 3 0.0 #
dihedral_coeff @dihedral:X-n4-nh-X fourier 1 0.183333333333 3 0.0 #
dihedral_coeff @dihedral:X-n4-no-X fourier 1 0.0833333333333 3 180.0 #
dihedral_coeff @dihedral:X-n4-oh-X fourier 1 0.333333333333 3 0.0 #
dihedral_coeff @dihedral:X-n4-os-X fourier 1 0.566666666667 3 0.0 #
dihedral_coeff @dihedral:X-n4-p2-X fourier 1 0.166666666667 3 180.0 #
dihedral_coeff @dihedral:X-n4-pe-X fourier 1 0.166666666667 3 180.0 #
dihedral_coeff @dihedral:X-n4-pf-X fourier 1 0.166666666667 3 180.0 #
dihedral_coeff @dihedral:X-n4-p3-X fourier 1 0.15 3 0.0 #
dihedral_coeff @dihedral:X-n4-p4-X fourier 1 0.05 3 0.0 #
dihedral_coeff @dihedral:X-n4-px-X fourier 1 0.05 3 0.0 #
dihedral_coeff @dihedral:X-n4-p5-X fourier 1 0.0888888888889 3 0.0 #
dihedral_coeff @dihedral:X-n4-py-X fourier 1 0.0888888888889 3 0.0 #
dihedral_coeff @dihedral:X-n4-sh-X fourier 1 0.666666666667 3 0.0 #
dihedral_coeff @dihedral:X-n4-ss-X fourier 1 0.333333333333 3 0.0 #
dihedral_coeff @dihedral:X-n4-s4-X fourier 1 0.283333333333 3 0.0 #
dihedral_coeff @dihedral:X-n4-sx-X fourier 1 0.283333333333 3 0.0 #
dihedral_coeff @dihedral:X-n4-s6-X fourier 1 0.133333333333 3 0.0 #
dihedral_coeff @dihedral:X-n4-sy-X fourier 1 0.133333333333 3 0.0 #
dihedral_coeff @dihedral:X-na-na-X fourier 1 0.9 2 0.0 #
dihedral_coeff @dihedral:X-na-nh-X fourier 1 1.2 2 0.0 #
dihedral_coeff @dihedral:X-na-no-X fourier 1 6.0 2 180.0 #
dihedral_coeff @dihedral:X-na-oh-X fourier 1 1.0 2 0.0 #
dihedral_coeff @dihedral:X-na-os-X fourier 1 0.65 2 0.0 #
dihedral_coeff @dihedral:X-na-p2-X fourier 1 1.0 2 180.0 #
dihedral_coeff @dihedral:X-na-pe-X fourier 1 1.0 2 180.0 #
dihedral_coeff @dihedral:X-na-pf-X fourier 1 1.0 2 180.0 #
dihedral_coeff @dihedral:X-na-p3-X fourier 1 1.45 2 0.0 #
dihedral_coeff @dihedral:X-na-p4-X fourier 1 1.1 3 0.0 #
dihedral_coeff @dihedral:X-na-px-X fourier 1 1.1 3 0.0 #
dihedral_coeff @dihedral:X-na-p5-X fourier 1 0.833333333333 2 180.0 #
dihedral_coeff @dihedral:X-na-py-X fourier 1 0.833333333333 2 180.0 #
dihedral_coeff @dihedral:X-na-sh-X fourier 1 1.8 2 0.0 #
dihedral_coeff @dihedral:X-na-ss-X fourier 1 7.8 2 0.0 #
dihedral_coeff @dihedral:X-na-s4-X fourier 1 1.05 2 0.0 #
dihedral_coeff @dihedral:X-na-sx-X fourier 1 1.05 2 0.0 #
dihedral_coeff @dihedral:X-na-s6-X fourier 1 3.66666666667 2 180.0 #
dihedral_coeff @dihedral:X-na-sy-X fourier 1 3.66666666667 2 180.0 #
dihedral_coeff @dihedral:X-nh-nh-X fourier 1 1.8 3 180.0 #
dihedral_coeff @dihedral:X-nh-no-X fourier 1 2.55 2 180.0 #
dihedral_coeff @dihedral:X-nh-oh-X fourier 1 1.5 2 0.0 #
dihedral_coeff @dihedral:X-nh-os-X fourier 1 1.5 1 0.0 #
dihedral_coeff @dihedral:X-nh-p2-X fourier 1 1.4 2 180.0 #
dihedral_coeff @dihedral:X-nh-pe-X fourier 1 1.4 2 180.0 #
dihedral_coeff @dihedral:X-nh-pf-X fourier 1 1.4 2 180.0 #
dihedral_coeff @dihedral:X-nh-p3-X fourier 1 2.35 2 0.0 #
dihedral_coeff @dihedral:X-nh-p4-X fourier 1 1.175 3 0.0 #
dihedral_coeff @dihedral:X-nh-px-X fourier 1 1.175 3 0.0 #
dihedral_coeff @dihedral:X-nh-p5-X fourier 1 0.8 2 0.0 #
dihedral_coeff @dihedral:X-nh-py-X fourier 1 0.8 2 0.0 #
dihedral_coeff @dihedral:X-nh-sh-X fourier 1 1.6 2 0.0 #
dihedral_coeff @dihedral:X-nh-ss-X fourier 1 2.1 2 0.0 #
dihedral_coeff @dihedral:X-nh-s4-X fourier 2 0.75 2 0.0 0.1 3 180.0 #
dihedral_coeff @dihedral:X-nh-sx-X fourier 2 0.75 2 0.0 0.1 3 180.0 #
dihedral_coeff @dihedral:X-nh-s6-X fourier 1 0.1 2 180.0 #
dihedral_coeff @dihedral:X-nh-sy-X fourier 1 0.1 2 180.0 #
dihedral_coeff @dihedral:X-no-no-X fourier 2 0.4 4 180.0 1.8 2 180.0 #
dihedral_coeff @dihedral:X-no-oh-X fourier 1 3.9 2 180.0 #
dihedral_coeff @dihedral:X-no-os-X fourier 1 3.0 2 180.0 #
dihedral_coeff @dihedral:X-no-p2-X fourier 1 0.3 2 180.0 #
dihedral_coeff @dihedral:X-no-pe-X fourier 1 0.3 2 180.0 #
dihedral_coeff @dihedral:X-no-pf-X fourier 1 0.3 2 180.0 #
dihedral_coeff @dihedral:X-no-p3-X fourier 1 1.9 2 180.0 #
dihedral_coeff @dihedral:X-no-p4-X fourier 1 0.575 2 180.0 #
dihedral_coeff @dihedral:X-no-px-X fourier 1 0.575 2 180.0 #
dihedral_coeff @dihedral:X-no-p5-X fourier 2 2.4 2 0.0 0.4 3 0.0 #
dihedral_coeff @dihedral:X-no-py-X fourier 2 2.4 2 0.0 0.4 3 0.0 #
dihedral_coeff @dihedral:X-no-sh-X fourier 1 2.3 2 180.0 #
dihedral_coeff @dihedral:X-no-ss-X fourier 1 2.7 2 180.0 #
dihedral_coeff @dihedral:X-no-s4-X fourier 1 2.6 2 180.0 #
dihedral_coeff @dihedral:X-no-sx-X fourier 1 2.6 2 180.0 #
dihedral_coeff @dihedral:X-no-s6-X fourier 1 0.333333333333 2 0.0 #
dihedral_coeff @dihedral:X-no-sy-X fourier 1 0.333333333333 2 0.0 #
dihedral_coeff @dihedral:X-oh-oh-X fourier 1 1.6 2 0.0 #
dihedral_coeff @dihedral:X-oh-os-X fourier 1 1.6 2 0.0 #
dihedral_coeff @dihedral:X-oh-p2-X fourier 1 1.5 2 180.0 #
dihedral_coeff @dihedral:X-oh-pe-X fourier 1 1.5 2 180.0 #
dihedral_coeff @dihedral:X-oh-pf-X fourier 1 1.5 2 180.0 #
dihedral_coeff @dihedral:X-oh-p3-X fourier 1 0.4 3 180.0 #
dihedral_coeff @dihedral:X-oh-p4-X fourier 1 0.7 1 0.0 #
dihedral_coeff @dihedral:X-oh-px-X fourier 1 0.7 1 0.0 #
dihedral_coeff @dihedral:X-oh-p5-X fourier 1 0.533333333333 3 0.0 #
dihedral_coeff @dihedral:X-oh-py-X fourier 1 0.533333333333 3 0.0 #
dihedral_coeff @dihedral:X-oh-sh-X fourier 1 2.4 2 0.0 #
dihedral_coeff @dihedral:X-oh-ss-X fourier 1 2.4 2 0.0 #
dihedral_coeff @dihedral:X-oh-s4-X fourier 1 5.0 1 0.0 #
dihedral_coeff @dihedral:X-oh-sx-X fourier 1 5.0 1 0.0 #
dihedral_coeff @dihedral:X-oh-s6-X fourier 1 9.5 1 180.0 #
dihedral_coeff @dihedral:X-oh-sy-X fourier 1 9.5 1 180.0 #
dihedral_coeff @dihedral:X-os-os-X fourier 1 1.0 1 0.0 #
dihedral_coeff @dihedral:X-os-ss-X fourier 1 2.2 2 0.0 #
dihedral_coeff @dihedral:X-os-sh-X fourier 1 1.8 2 0.0 #
dihedral_coeff @dihedral:X-os-s4-X fourier 1 1.65 3 0.0 #
dihedral_coeff @dihedral:X-os-sx-X fourier 1 1.65 3 0.0 #
dihedral_coeff @dihedral:X-os-s6-X fourier 1 1.2 2 180.0 #
dihedral_coeff @dihedral:X-os-sy-X fourier 1 1.2 2 180.0 #
dihedral_coeff @dihedral:X-os-p2-X fourier 2 3.0 2 180.0 2.0 1 180.0 #
dihedral_coeff @dihedral:X-os-pe-X fourier 2 3.0 2 180.0 2.0 1 180.0 #
dihedral_coeff @dihedral:X-os-pf-X fourier 2 3.0 2 180.0 2.0 1 180.0 #
dihedral_coeff @dihedral:X-os-p3-X fourier 1 2.2 2 0.0 #
dihedral_coeff @dihedral:X-os-p4-X fourier 1 1.05 2 180.0 #
dihedral_coeff @dihedral:X-os-px-X fourier 1 1.05 2 180.0 #
dihedral_coeff @dihedral:X-os-p5-X fourier 1 0.8 2 0.0 #
dihedral_coeff @dihedral:X-os-py-X fourier 1 0.8 2 0.0 #
dihedral_coeff @dihedral:X-p2-p2-X fourier 1 6.6 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-p2-pe-X fourier 1 6.6 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-p2-pf-X fourier 1 6.6 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-p2-pc-X fourier 1 6.6 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-p2-pd-X fourier 1 6.6 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-pe-pe-X fourier 1 1.2 2 180.0 # single bond
dihedral_coeff @dihedral:X-pf-pf-X fourier 1 1.2 2 180.0 # single bond
dihedral_coeff @dihedral:X-pc-pc-X fourier 1 7.2 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-pd-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-pc-pd-X fourier 1 7.2 2 180.0 # estimated, intrpol.
dihedral_coeff @dihedral:X-p2-p3-X fourier 1 1.2 1 0.0 #
dihedral_coeff @dihedral:X-pe-p3-X fourier 1 1.2 1 0.0 #
dihedral_coeff @dihedral:X-pf-p3-X fourier 1 1.2 1 0.0 #
dihedral_coeff @dihedral:X-p2-p4-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-pe-px-X fourier 1 2.45 2 0.0 #
dihedral_coeff @dihedral:X-pf-px-X fourier 1 2.45 2 0.0 #
dihedral_coeff @dihedral:X-p2-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-pe-py-X fourier 1 1.9 1 0.0 #
dihedral_coeff @dihedral:X-pf-py-X fourier 1 1.9 1 0.0 #
dihedral_coeff @dihedral:X-p2-sh-X fourier 1 1.4 2 180.0 #
dihedral_coeff @dihedral:X-pe-sh-X fourier 1 1.4 2 180.0 #
dihedral_coeff @dihedral:X-pf-sh-X fourier 1 1.4 2 180.0 #
dihedral_coeff @dihedral:X-p2-ss-X fourier 1 1.4 2 180.0 #
dihedral_coeff @dihedral:X-pe-ss-X fourier 1 1.4 2 180.0 #
dihedral_coeff @dihedral:X-pf-ss-X fourier 1 1.4 2 180.0 #
dihedral_coeff @dihedral:X-p2-s4-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-pe-sx-X fourier 1 1.5 2 0.0 #
dihedral_coeff @dihedral:X-pf-sx-X fourier 1 1.5 2 0.0 #
dihedral_coeff @dihedral:X-p2-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-pe-sy-X fourier 1 0.4 3 180.0 #
dihedral_coeff @dihedral:X-pf-sy-X fourier 1 0.4 3 180.0 #
dihedral_coeff @dihedral:X-p3-p3-X fourier 1 0.5 3 0.0 #
dihedral_coeff @dihedral:X-p3-p4-X fourier 1 0.9 1 0.0 #
dihedral_coeff @dihedral:X-p3-px-X fourier 1 0.9 1 0.0 #
dihedral_coeff @dihedral:X-p3-p5-X fourier 1 1.83333333333 2 180.0 #
dihedral_coeff @dihedral:X-p3-py-X fourier 1 1.83333333333 2 180.0 #
dihedral_coeff @dihedral:X-p3-sh-X fourier 1 4.6 2 0.0 #
dihedral_coeff @dihedral:X-p3-ss-X fourier 1 1.15 3 0.0 #
dihedral_coeff @dihedral:X-p3-s4-X fourier 1 3.85 2 0.0 #
dihedral_coeff @dihedral:X-p3-sx-X fourier 1 3.85 2 0.0 #
dihedral_coeff @dihedral:X-p3-s6-X fourier 1 0.266666666667 3 0.0 #
dihedral_coeff @dihedral:X-p3-sy-X fourier 1 0.266666666667 3 0.0 #
dihedral_coeff @dihedral:X-p4-p4-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-px-px-X fourier 1 1.45 2 180.0 #
dihedral_coeff @dihedral:X-p4-p5-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-px-py-X fourier 1 0.316666666667 2 180.0 #
dihedral_coeff @dihedral:X-p4-s4-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-px-sx-X fourier 1 0.85 1 0.0 #
dihedral_coeff @dihedral:X-p4-s6-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-px-sy-X fourier 1 0.116666666667 3 0.0 #
dihedral_coeff @dihedral:X-p4-sh-X fourier 1 0.25 1 180.0 #
dihedral_coeff @dihedral:X-px-sh-X fourier 1 0.25 1 180.0 #
dihedral_coeff @dihedral:X-p4-ss-X fourier 1 0.6 2 180.0 #
dihedral_coeff @dihedral:X-px-ss-X fourier 1 0.6 2 180.0 #
dihedral_coeff @dihedral:X-p5-p5-X fourier 1 6.66666666667 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-py-py-X fourier 1 0.6 2 0.0 #
dihedral_coeff @dihedral:X-p5-sh-X fourier 1 0.3 3 0.0 #
dihedral_coeff @dihedral:X-py-sh-X fourier 1 0.3 3 0.0 #
dihedral_coeff @dihedral:X-p5-ss-X fourier 1 3.8 2 180.0 #
dihedral_coeff @dihedral:X-py-ss-X fourier 1 3.8 2 180.0 #
dihedral_coeff @dihedral:X-p5-s4-X fourier 1 6.66666666667 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-py-sx-X fourier 1 0.266666666667 3 0.0 #
dihedral_coeff @dihedral:X-p5-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-py-sy-X fourier 1 0.277777777778 3 0.0 #
dihedral_coeff @dihedral:X-sh-sh-X fourier 1 5.6 3 0.0 #
dihedral_coeff @dihedral:X-sh-ss-X fourier 1 5.3 3 0.0 #
dihedral_coeff @dihedral:X-sh-s4-X fourier 1 0.7 3 0.0 #
dihedral_coeff @dihedral:X-sh-sx-X fourier 1 0.7 3 0.0 #
dihedral_coeff @dihedral:X-sh-s6-X fourier 1 4.66666666667 2 180.0 #
dihedral_coeff @dihedral:X-sh-sy-X fourier 1 4.66666666667 2 180.0 #
dihedral_coeff @dihedral:X-ss-ss-X fourier 1 0.0 3 0.0 #
dihedral_coeff @dihedral:X-ss-s4-X fourier 1 0.3 3 0.0 #
dihedral_coeff @dihedral:X-ss-sx-X fourier 1 0.3 3 0.0 #
dihedral_coeff @dihedral:X-ss-s6-X fourier 1 3.06666666667 2 180.0 #
dihedral_coeff @dihedral:X-ss-sy-X fourier 1 3.06666666667 2 180.0 #
dihedral_coeff @dihedral:X-s4-s4-X fourier 1 6.65 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-sx-sx-X fourier 1 0.625 3 0.0 #
dihedral_coeff @dihedral:X-s4-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-sx-sy-X fourier 1 4.33333333333 2 180.0 #
dihedral_coeff @dihedral:X-s6-s6-X fourier 1 6.66666666667 2 180.0 # estimated !!!
dihedral_coeff @dihedral:X-sy-sy-X fourier 1 0.155555555556 2 180.0 #
dihedral_coeff @dihedral:c3-c-sh-hs fourier 2 2.25 2 180.0 1.3 1 180.0 #
dihedral_coeff @dihedral:c2-c2-ss-c3 fourier 2 1.1 2 180.0 0.7 3 180.0 #
dihedral_coeff @dihedral:c2-c2-n-c fourier 2 0.65 2 180.0 1.2 1 180.0 #
dihedral_coeff @dihedral:c-n-p2-c2 fourier 2 1.0 2 180.0 1.9 1 180.0 #
dihedral_coeff @dihedral:n-c3-c-n fourier 2 1.7 1 180.0 2.0 2 180.0 #
dihedral_coeff @dihedral:c-n-c3-c fourier 2 0.85 2 180.0 0.8 1 0.0 #
dihedral_coeff @dihedral:c3-c3-n-c fourier 3 0.5 4 180.0 0.15 3 180.0 0.53 1 0.0 # phi,psi,parm94
dihedral_coeff @dihedral:c3-c3-c-n fourier 2 0.1 4 0.0 0.07 2 0.0 # phi,psi,parm94
dihedral_coeff @dihedral:c2-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
dihedral_coeff @dihedral:c2-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
dihedral_coeff @dihedral:ce-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
dihedral_coeff @dihedral:ce-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
dihedral_coeff @dihedral:cf-ne-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
dihedral_coeff @dihedral:cf-nf-p5-o fourier 2 0.0 3 0.0 2.3 1 0.0 #
dihedral_coeff @dihedral:hn-n-c-o fourier 2 2.5 2 180.0 2.0 1 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:c3-ss-ss-c3 fourier 2 3.5 2 0.0 0.6 3 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:c3-n3-nh-ca fourier 2 1.9 2 0.0 1.9 3 0.0 #
dihedral_coeff @dihedral:c3-n3-p5-o fourier 2 3.0 2 180.0 2.3 3 0.0 #
dihedral_coeff @dihedral:ca-nh-oh-ho fourier 2 1.2 1 0.0 1.5 2 0.0 #
dihedral_coeff @dihedral:oh-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:os-p5-os-c3 fourier 2 0.25 3 0.0 1.2 2 0.0 # JCC,7,(1986),230
dihedral_coeff @dihedral:h1-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:hc-c3-c-o fourier 2 0.8 1 0.0 0.08 3 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:hc-c3-c3-hc fourier 1 0.15 3 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:hc-c3-c3-c3 fourier 1 0.16 3 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:hc-c3-c2-c2 fourier 2 0.38 3 180.0 1.15 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:ho-oh-c3-c3 fourier 2 0.16 3 0.0 0.25 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:ho-oh-c-o fourier 2 2.3 2 180.0 1.9 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:c2-c2-c-o fourier 2 2.175 2 180.0 0.3 3 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:c3-c2-c2-c3 fourier 2 6.65 2 180.0 1.9 1 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:c3-c3-c3-c3 fourier 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:c3-c3-n3-c3 fourier 2 0.3 3 0.0 0.48 2 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:c3-c3-os-c3 fourier 2 0.383 3 0.0 0.1 2 180.0 #
dihedral_coeff @dihedral:c3-c3-os-c fourier 2 0.383 3 0.0 0.8 1 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:c3-os-c3-os fourier 3 0.1 3 0.0 0.85 2 180.0 1.35 1 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:c3-os-c3-na fourier 2 0.383 3 0.0 0.65 2 0.0 # parm98.dat, TC,PC,PAK
dihedral_coeff @dihedral:o-c-os-c3 fourier 2 2.7 2 180.0 1.4 1 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:os-c3-na-c2 fourier 2 0.0 2 0.0 2.5 1 0.0 # parm98, TC,PC,PAK
dihedral_coeff @dihedral:os-c3-c3-os fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK
dihedral_coeff @dihedral:os-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK
dihedral_coeff @dihedral:oh-c3-c3-oh fourier 2 0.144 3 0.0 1.175 2 0.0 # parm98, TC,PC,PAK
dihedral_coeff @dihedral:f-c3-c3-f fourier 2 0.0 3 0.0 1.2 1 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:cl-c3-c3-cl fourier 2 0.0 3 0.0 0.45 1 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:br-c3-c3-br fourier 2 0.0 3 0.0 0.0 1 180.0 # Junmei et al, 1999
dihedral_coeff @dihedral:h1-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:h1-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:h1-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:h1-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:h1-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:hc-c3-c3-os fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:hc-c3-c3-oh fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:hc-c3-c3-f fourier 2 0.0 3 0.0 0.19 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:hc-c3-c3-cl fourier 2 0.0 3 0.0 0.25 1 0.0 # Junmei et al, 1999
dihedral_coeff @dihedral:hc-c3-c3-br fourier 2 0.0 3 0.0 0.55 1 0.0 # Junmei et al, 1999
} # (end of dihedral_coeffs)
write_once("Data Dihedrals By Type") {
@dihedral:X-c-c-X @atom:* @atom:c @atom:c @atom:*
@dihedral:X-c-c1-X @atom:* @atom:c @atom:c1 @atom:*
@dihedral:X-c-cg-X @atom:* @atom:c @atom:cg @atom:*
@dihedral:X-c-ch-X @atom:* @atom:c @atom:ch @atom:*
@dihedral:X-c-c2-X @atom:* @atom:c @atom:c2 @atom:*
@dihedral:X-c-cu-X @atom:* @atom:c @atom:cu @atom:*
@dihedral:X-c-cv-X @atom:* @atom:c @atom:cv @atom:*
@dihedral:X-c-ce-X @atom:* @atom:c @atom:ce @atom:*
@dihedral:X-c-cf-X @atom:* @atom:c @atom:cf @atom:*
@dihedral:X-c-c3-X @atom:* @atom:c @atom:c3 @atom:*
@dihedral:X-c-cx-X @atom:* @atom:c @atom:cx @atom:*
@dihedral:X-c-cy-X @atom:* @atom:c @atom:cy @atom:*
@dihedral:X-c-ca-X @atom:* @atom:c @atom:ca @atom:*
@dihedral:X-c-cc-X @atom:* @atom:c @atom:cc @atom:*
@dihedral:X-c-cd-X @atom:* @atom:c @atom:cd @atom:*
@dihedral:X-c-n-X @atom:* @atom:c @atom:n @atom:*
@dihedral:X-c-n2-X @atom:* @atom:c @atom:n2 @atom:*
@dihedral:X-c-nc-X @atom:* @atom:c @atom:nc @atom:*
@dihedral:X-c-nd-X @atom:* @atom:c @atom:nd @atom:*
@dihedral:X-c-ne-X @atom:* @atom:c @atom:ne @atom:*
@dihedral:X-c-nf-X @atom:* @atom:c @atom:nf @atom:*
@dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:*
@dihedral:X-c-na-X @atom:* @atom:c @atom:na @atom:*
@dihedral:X-c-no-X @atom:* @atom:c @atom:no @atom:*
@dihedral:X-c-oh-X @atom:* @atom:c @atom:oh @atom:*
@dihedral:X-c-os-X @atom:* @atom:c @atom:os @atom:*
@dihedral:X-c-p2-X @atom:* @atom:c @atom:p2 @atom:*
@dihedral:X-c-pc-X @atom:* @atom:c @atom:pc @atom:*
@dihedral:X-c-pd-X @atom:* @atom:c @atom:pd @atom:*
@dihedral:X-c-pe-X @atom:* @atom:c @atom:pe @atom:*
@dihedral:X-c-pf-X @atom:* @atom:c @atom:pf @atom:*
@dihedral:X-c-p3-X @atom:* @atom:c @atom:p3 @atom:*
@dihedral:X-c-p4-X @atom:* @atom:c @atom:p4 @atom:*
@dihedral:X-c-px-X @atom:* @atom:c @atom:px @atom:*
@dihedral:X-c-p5-X @atom:* @atom:c @atom:p5 @atom:*
@dihedral:X-c-py-X @atom:* @atom:c @atom:py @atom:*
@dihedral:X-c-sh-X @atom:* @atom:c @atom:sh @atom:*
@dihedral:X-c-ss-X @atom:* @atom:c @atom:ss @atom:*
@dihedral:X-c-s4-X @atom:* @atom:c @atom:s4 @atom:*
@dihedral:X-c-sx-X @atom:* @atom:c @atom:sx @atom:*
@dihedral:X-c-s6-X @atom:* @atom:c @atom:s6 @atom:*
@dihedral:X-c-sy-X @atom:* @atom:c @atom:sy @atom:*
@dihedral:X-c1-c1-X @atom:* @atom:c1 @atom:c1 @atom:*
@dihedral:X-c1-cg-X @atom:* @atom:c1 @atom:cg @atom:*
@dihedral:X-c1-ch-X @atom:* @atom:c1 @atom:ch @atom:*
@dihedral:X-cg-cg-X @atom:* @atom:cg @atom:cg @atom:*
@dihedral:X-ch-ch-X @atom:* @atom:ch @atom:ch @atom:*
@dihedral:X-cg-ch-X @atom:* @atom:cg @atom:ch @atom:*
@dihedral:X-c1-c2-X @atom:* @atom:c1 @atom:c2 @atom:*
@dihedral:X-c1-c3-X @atom:* @atom:c1 @atom:c3 @atom:*
@dihedral:X-c1-ca-X @atom:* @atom:c1 @atom:ca @atom:*
@dihedral:X-c1-cc-X @atom:* @atom:c1 @atom:cc @atom:*
@dihedral:X-c1-cd-X @atom:* @atom:c1 @atom:cd @atom:*
@dihedral:X-c1-ce-X @atom:* @atom:c1 @atom:ce @atom:*
@dihedral:X-c1-cf-X @atom:* @atom:c1 @atom:cf @atom:*
@dihedral:X-c1-cu-X @atom:* @atom:c1 @atom:cu @atom:*
@dihedral:X-c1-cv-X @atom:* @atom:c1 @atom:cv @atom:*
@dihedral:X-c1-cx-X @atom:* @atom:c1 @atom:cx @atom:*
@dihedral:X-c1-cy-X @atom:* @atom:c1 @atom:cy @atom:*
@dihedral:X-c1-n-X @atom:* @atom:c1 @atom:n @atom:*
@dihedral:X-c1-n2-X @atom:* @atom:c1 @atom:n2 @atom:*
@dihedral:X-c1-n3-X @atom:* @atom:c1 @atom:n3 @atom:*
@dihedral:X-c1-n4-X @atom:* @atom:c1 @atom:n4 @atom:*
@dihedral:X-c1-na-X @atom:* @atom:c1 @atom:na @atom:*
@dihedral:X-c1-nb-X @atom:* @atom:c1 @atom:nb @atom:*
@dihedral:X-c1-nc-X @atom:* @atom:c1 @atom:nc @atom:*
@dihedral:X-c1-nd-X @atom:* @atom:c1 @atom:nd @atom:*
@dihedral:X-c1-ne-X @atom:* @atom:c1 @atom:ne @atom:*
@dihedral:X-c1-nf-X @atom:* @atom:c1 @atom:nf @atom:*
@dihedral:X-c1-nh-X @atom:* @atom:c1 @atom:nh @atom:*
@dihedral:X-c1-no-X @atom:* @atom:c1 @atom:no @atom:*
@dihedral:X-c1-oh-X @atom:* @atom:c1 @atom:oh @atom:*
@dihedral:X-c1-os-X @atom:* @atom:c1 @atom:os @atom:*
@dihedral:X-c1-p2-X @atom:* @atom:c1 @atom:p2 @atom:*
@dihedral:X-c1-pb-X @atom:* @atom:c1 @atom:pb @atom:*
@dihedral:X-c1-pc-X @atom:* @atom:c1 @atom:pc @atom:*
@dihedral:X-c1-pd-X @atom:* @atom:c1 @atom:pd @atom:*
@dihedral:X-c1-pe-X @atom:* @atom:c1 @atom:pe @atom:*
@dihedral:X-c1-pf-X @atom:* @atom:c1 @atom:pf @atom:*
@dihedral:X-c1-p3-X @atom:* @atom:c1 @atom:p3 @atom:*
@dihedral:X-c1-p4-X @atom:* @atom:c1 @atom:p4 @atom:*
@dihedral:X-c1-px-X @atom:* @atom:c1 @atom:px @atom:*
@dihedral:X-c1-p5-X @atom:* @atom:c1 @atom:p5 @atom:*
@dihedral:X-c1-py-X @atom:* @atom:c1 @atom:py @atom:*
@dihedral:X-c1-s2-X @atom:* @atom:c1 @atom:s2 @atom:*
@dihedral:X-c1-sh-X @atom:* @atom:c1 @atom:sh @atom:*
@dihedral:X-c1-ss-X @atom:* @atom:c1 @atom:ss @atom:*
@dihedral:X-c1-s4-X @atom:* @atom:c1 @atom:s4 @atom:*
@dihedral:X-c1-sx-X @atom:* @atom:c1 @atom:sx @atom:*
@dihedral:X-c1-s6-X @atom:* @atom:c1 @atom:s6 @atom:*
@dihedral:X-c1-sy-X @atom:* @atom:c1 @atom:sy @atom:*
@dihedral:X-c2-c2-X @atom:* @atom:c2 @atom:c2 @atom:*
@dihedral:X-c2-ce-X @atom:* @atom:c2 @atom:ce @atom:*
@dihedral:X-c2-cf-X @atom:* @atom:c2 @atom:cf @atom:*
@dihedral:X-ce-cf-X @atom:* @atom:ce @atom:cf @atom:*
@dihedral:X-ce-ce-X @atom:* @atom:ce @atom:ce @atom:*
@dihedral:X-cf-cf-X @atom:* @atom:cf @atom:cf @atom:*
@dihedral:X-cc-cd-X @atom:* @atom:cc @atom:cd @atom:*
@dihedral:X-cc-cc-X @atom:* @atom:cc @atom:cc @atom:*
@dihedral:X-cd-cd-X @atom:* @atom:cd @atom:cd @atom:*
@dihedral:X-c2-c3-X @atom:* @atom:c2 @atom:c3 @atom:*
@dihedral:X-c2-ca-X @atom:* @atom:c2 @atom:ca @atom:*
@dihedral:X-c2-n-X @atom:* @atom:c2 @atom:n @atom:*
@dihedral:X-c2-n2-X @atom:* @atom:c2 @atom:n2 @atom:*
@dihedral:X-c2-ne-X @atom:* @atom:c2 @atom:ne @atom:*
@dihedral:X-c2-nf-X @atom:* @atom:c2 @atom:nf @atom:*
@dihedral:X-ce-ne-X @atom:* @atom:ce @atom:ne @atom:*
@dihedral:X-cf-nf-X @atom:* @atom:cf @atom:nf @atom:*
@dihedral:X-c2-nc-X @atom:* @atom:c2 @atom:nc @atom:*
@dihedral:X-c2-nd-X @atom:* @atom:c2 @atom:nd @atom:*
@dihedral:X-cc-nd-X @atom:* @atom:cc @atom:nd @atom:*
@dihedral:X-cd-nc-X @atom:* @atom:cd @atom:nc @atom:*
@dihedral:X-cc-nc-X @atom:* @atom:cc @atom:nc @atom:*
@dihedral:X-cd-nd-X @atom:* @atom:cd @atom:nd @atom:*
@dihedral:X-c2-n3-X @atom:* @atom:c2 @atom:n3 @atom:*
@dihedral:X-c2-n4-X @atom:* @atom:c2 @atom:n4 @atom:*
@dihedral:X-c2-na-X @atom:* @atom:c2 @atom:na @atom:*
@dihedral:X-cc-na-X @atom:* @atom:cc @atom:na @atom:*
@dihedral:X-cd-na-X @atom:* @atom:cd @atom:na @atom:*
@dihedral:X-c2-nh-X @atom:* @atom:c2 @atom:nh @atom:*
@dihedral:X-c2-no-X @atom:* @atom:c2 @atom:no @atom:*
@dihedral:X-c2-oh-X @atom:* @atom:c2 @atom:oh @atom:*
@dihedral:X-c2-os-X @atom:* @atom:c2 @atom:os @atom:*
@dihedral:X-c2-p2-X @atom:* @atom:c2 @atom:p2 @atom:*
@dihedral:X-c2-pe-X @atom:* @atom:c2 @atom:pe @atom:*
@dihedral:X-c2-pf-X @atom:* @atom:c2 @atom:pf @atom:*
@dihedral:X-ce-pf-X @atom:* @atom:ce @atom:pf @atom:*
@dihedral:X-ce-pe-X @atom:* @atom:ce @atom:pe @atom:*
@dihedral:X-cf-pf-X @atom:* @atom:cf @atom:pf @atom:*
@dihedral:X-c2-pc-X @atom:* @atom:c2 @atom:pc @atom:*
@dihedral:X-c2-pd-X @atom:* @atom:c2 @atom:pd @atom:*
@dihedral:X-cc-pc-X @atom:* @atom:cc @atom:pc @atom:*
@dihedral:X-cc-pd-X @atom:* @atom:cc @atom:pd @atom:*
@dihedral:X-cd-pc-X @atom:* @atom:cd @atom:pc @atom:*
@dihedral:X-cd-pd-X @atom:* @atom:cd @atom:pd @atom:*
@dihedral:X-c2-p3-X @atom:* @atom:c2 @atom:p3 @atom:*
@dihedral:X-c2-p4-X @atom:* @atom:c2 @atom:p4 @atom:*
@dihedral:X-ce-p4-X @atom:* @atom:ce @atom:p4 @atom:*
@dihedral:X-cf-p4-X @atom:* @atom:cf @atom:p4 @atom:*
@dihedral:X-c2-px-X @atom:* @atom:c2 @atom:px @atom:*
@dihedral:X-ce-px-X @atom:* @atom:ce @atom:px @atom:*
@dihedral:X-cf-px-X @atom:* @atom:cf @atom:px @atom:*
@dihedral:X-c2-p5-X @atom:* @atom:c2 @atom:p5 @atom:*
@dihedral:X-ce-p5-X @atom:* @atom:ce @atom:p5 @atom:*
@dihedral:X-cf-p5-X @atom:* @atom:cf @atom:p5 @atom:*
@dihedral:X-c2-py-X @atom:* @atom:c2 @atom:py @atom:*
@dihedral:X-ce-py-X @atom:* @atom:ce @atom:py @atom:*
@dihedral:X-cf-py-X @atom:* @atom:cf @atom:py @atom:*
@dihedral:X-c2-sh-X @atom:* @atom:c2 @atom:sh @atom:*
@dihedral:X-c2-ss-X @atom:* @atom:c2 @atom:ss @atom:*
@dihedral:X-c2-s4-X @atom:* @atom:c2 @atom:s4 @atom:*
@dihedral:X-ce-s4-X @atom:* @atom:ce @atom:s4 @atom:*
@dihedral:X-cf-s4-X @atom:* @atom:cf @atom:s4 @atom:*
@dihedral:X-c2-sx-X @atom:* @atom:c2 @atom:sx @atom:*
@dihedral:X-ce-sx-X @atom:* @atom:ce @atom:sx @atom:*
@dihedral:X-cf-sx-X @atom:* @atom:cf @atom:sx @atom:*
@dihedral:X-c2-s6-X @atom:* @atom:c2 @atom:s6 @atom:*
@dihedral:X-ce-s6-X @atom:* @atom:ce @atom:s6 @atom:*
@dihedral:X-cf-s6-X @atom:* @atom:cf @atom:s6 @atom:*
@dihedral:X-c2-sy-X @atom:* @atom:c2 @atom:sy @atom:*
@dihedral:X-ce-sy-X @atom:* @atom:ce @atom:sy @atom:*
@dihedral:X-cf-sy-X @atom:* @atom:cf @atom:sy @atom:*
@dihedral:X-c3-c3-X @atom:* @atom:c3 @atom:c3 @atom:*
@dihedral:X-cx-cx-X @atom:* @atom:cx @atom:cx @atom:*
@dihedral:X-cy-cy-X @atom:* @atom:cy @atom:cy @atom:*
@dihedral:X-c3-ca-X @atom:* @atom:c3 @atom:ca @atom:*
@dihedral:X-c3-n-X @atom:* @atom:c3 @atom:n @atom:*
@dihedral:X-cx-n-X @atom:* @atom:cx @atom:n @atom:*
@dihedral:X-cy-n-X @atom:* @atom:cy @atom:n @atom:*
@dihedral:X-c3-n2-X @atom:* @atom:c3 @atom:n2 @atom:*
@dihedral:X-c3-ne-X @atom:* @atom:c3 @atom:ne @atom:*
@dihedral:X-c3-nf-X @atom:* @atom:c3 @atom:nf @atom:*
@dihedral:X-c3-n3-X @atom:* @atom:c3 @atom:n3 @atom:*
@dihedral:X-c3-n4-X @atom:* @atom:c3 @atom:n4 @atom:*
@dihedral:X-c3-na-X @atom:* @atom:c3 @atom:na @atom:*
@dihedral:X-c3-nh-X @atom:* @atom:c3 @atom:nh @atom:*
@dihedral:X-c3-no-X @atom:* @atom:c3 @atom:no @atom:*
@dihedral:X-c3-oh-X @atom:* @atom:c3 @atom:oh @atom:*
@dihedral:X-c3-os-X @atom:* @atom:c3 @atom:os @atom:*
@dihedral:X-c3-p2-X @atom:* @atom:c3 @atom:p2 @atom:*
@dihedral:X-c3-pe-X @atom:* @atom:c3 @atom:pe @atom:*
@dihedral:X-c3-pf-X @atom:* @atom:c3 @atom:pf @atom:*
@dihedral:X-c3-p3-X @atom:* @atom:c3 @atom:p3 @atom:*
@dihedral:X-c3-p4-X @atom:* @atom:c3 @atom:p4 @atom:*
@dihedral:X-c3-px-X @atom:* @atom:c3 @atom:px @atom:*
@dihedral:X-c3-p5-X @atom:* @atom:c3 @atom:p5 @atom:*
@dihedral:X-c3-py-X @atom:* @atom:c3 @atom:py @atom:*
@dihedral:X-c3-sh-X @atom:* @atom:c3 @atom:sh @atom:*
@dihedral:X-c3-ss-X @atom:* @atom:c3 @atom:ss @atom:*
@dihedral:X-c3-s4-X @atom:* @atom:c3 @atom:s4 @atom:*
@dihedral:X-c3-sx-X @atom:* @atom:c3 @atom:sx @atom:*
@dihedral:X-c3-s6-X @atom:* @atom:c3 @atom:s6 @atom:*
@dihedral:X-c3-sy-X @atom:* @atom:c3 @atom:sy @atom:*
@dihedral:X-c3-cc-X @atom:* @atom:c3 @atom:cc @atom:*
@dihedral:X-c3-cd-X @atom:* @atom:c3 @atom:cd @atom:*
@dihedral:X-ca-ca-X @atom:* @atom:ca @atom:ca @atom:*
@dihedral:X-ca-cp-X @atom:* @atom:ca @atom:cp @atom:*
@dihedral:X-ca-cq-X @atom:* @atom:ca @atom:cq @atom:*
@dihedral:X-cp-cp-X @atom:* @atom:cp @atom:cp @atom:*
@dihedral:X-cq-cq-X @atom:* @atom:cq @atom:cq @atom:*
@dihedral:X-ca-n-X @atom:* @atom:ca @atom:n @atom:*
@dihedral:X-ca-n2-X @atom:* @atom:ca @atom:n2 @atom:*
@dihedral:X-ca-ne-X @atom:* @atom:ca @atom:ne @atom:*
@dihedral:X-ca-nf-X @atom:* @atom:ca @atom:nf @atom:*
@dihedral:X-ca-n4-X @atom:* @atom:ca @atom:n4 @atom:*
@dihedral:X-ca-na-X @atom:* @atom:ca @atom:na @atom:*
@dihedral:X-ca-nb-X @atom:* @atom:ca @atom:nb @atom:*
@dihedral:X-ca-nc-X @atom:* @atom:ca @atom:nc @atom:*
@dihedral:X-ca-nd-X @atom:* @atom:ca @atom:nd @atom:*
@dihedral:X-ca-nh-X @atom:* @atom:ca @atom:nh @atom:*
@dihedral:X-cc-nh-X @atom:* @atom:cc @atom:nh @atom:*
@dihedral:X-cd-nh-X @atom:* @atom:cd @atom:nh @atom:*
@dihedral:X-ca-no-X @atom:* @atom:ca @atom:no @atom:*
@dihedral:X-ca-oh-X @atom:* @atom:ca @atom:oh @atom:*
@dihedral:X-ca-os-X @atom:* @atom:ca @atom:os @atom:*
@dihedral:X-ca-p2-X @atom:* @atom:ca @atom:p2 @atom:*
@dihedral:X-ca-pe-X @atom:* @atom:ca @atom:pe @atom:*
@dihedral:X-ca-pf-X @atom:* @atom:ca @atom:pf @atom:*
@dihedral:X-ca-pc-X @atom:* @atom:ca @atom:pc @atom:*
@dihedral:X-ca-pd-X @atom:* @atom:ca @atom:pd @atom:*
@dihedral:X-ca-p3-X @atom:* @atom:ca @atom:p3 @atom:*
@dihedral:X-ca-p4-X @atom:* @atom:ca @atom:p4 @atom:*
@dihedral:X-ca-px-X @atom:* @atom:ca @atom:px @atom:*
@dihedral:X-ca-p5-X @atom:* @atom:ca @atom:p5 @atom:*
@dihedral:X-ca-py-X @atom:* @atom:ca @atom:py @atom:*
@dihedral:X-ca-sh-X @atom:* @atom:ca @atom:sh @atom:*
@dihedral:X-ca-ss-X @atom:* @atom:ca @atom:ss @atom:*
@dihedral:X-ca-s4-X @atom:* @atom:ca @atom:s4 @atom:*
@dihedral:X-ca-sx-X @atom:* @atom:ca @atom:sx @atom:*
@dihedral:X-ca-s6-X @atom:* @atom:ca @atom:s6 @atom:*
@dihedral:X-ca-sy-X @atom:* @atom:ca @atom:sy @atom:*
@dihedral:X-n-cc-X @atom:* @atom:n @atom:cc @atom:*
@dihedral:X-n-cd-X @atom:* @atom:n @atom:cd @atom:*
@dihedral:X-n-n-X @atom:* @atom:n @atom:n @atom:*
@dihedral:X-n-n2-X @atom:* @atom:n @atom:n2 @atom:*
@dihedral:X-n-ne-X @atom:* @atom:n @atom:ne @atom:*
@dihedral:X-n-nf-X @atom:* @atom:n @atom:nf @atom:*
@dihedral:X-n-n3-X @atom:* @atom:n @atom:n3 @atom:*
@dihedral:X-n-n4-X @atom:* @atom:n @atom:n4 @atom:*
@dihedral:X-n-na-X @atom:* @atom:n @atom:na @atom:*
@dihedral:X-n-nc-X @atom:* @atom:n @atom:nc @atom:*
@dihedral:X-n-nd-X @atom:* @atom:n @atom:nd @atom:*
@dihedral:X-n-nh-X @atom:* @atom:n @atom:nh @atom:*
@dihedral:X-n-no-X @atom:* @atom:n @atom:no @atom:*
@dihedral:X-n-oh-X @atom:* @atom:n @atom:oh @atom:*
@dihedral:X-n-os-X @atom:* @atom:n @atom:os @atom:*
@dihedral:X-n-p2-X @atom:* @atom:n @atom:p2 @atom:*
@dihedral:X-n-pe-X @atom:* @atom:n @atom:pe @atom:*
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@dihedral:X-pe-p3-X @atom:* @atom:pe @atom:p3 @atom:*
@dihedral:X-pf-p3-X @atom:* @atom:pf @atom:p3 @atom:*
@dihedral:X-p2-p4-X @atom:* @atom:p2 @atom:p4 @atom:*
@dihedral:X-pe-px-X @atom:* @atom:pe @atom:px @atom:*
@dihedral:X-pf-px-X @atom:* @atom:pf @atom:px @atom:*
@dihedral:X-p2-p5-X @atom:* @atom:p2 @atom:p5 @atom:*
@dihedral:X-pe-py-X @atom:* @atom:pe @atom:py @atom:*
@dihedral:X-pf-py-X @atom:* @atom:pf @atom:py @atom:*
@dihedral:X-p2-sh-X @atom:* @atom:p2 @atom:sh @atom:*
@dihedral:X-pe-sh-X @atom:* @atom:pe @atom:sh @atom:*
@dihedral:X-pf-sh-X @atom:* @atom:pf @atom:sh @atom:*
@dihedral:X-p2-ss-X @atom:* @atom:p2 @atom:ss @atom:*
@dihedral:X-pe-ss-X @atom:* @atom:pe @atom:ss @atom:*
@dihedral:X-pf-ss-X @atom:* @atom:pf @atom:ss @atom:*
@dihedral:X-p2-s4-X @atom:* @atom:p2 @atom:s4 @atom:*
@dihedral:X-pe-sx-X @atom:* @atom:pe @atom:sx @atom:*
@dihedral:X-pf-sx-X @atom:* @atom:pf @atom:sx @atom:*
@dihedral:X-p2-s6-X @atom:* @atom:p2 @atom:s6 @atom:*
@dihedral:X-pe-sy-X @atom:* @atom:pe @atom:sy @atom:*
@dihedral:X-pf-sy-X @atom:* @atom:pf @atom:sy @atom:*
@dihedral:X-p3-p3-X @atom:* @atom:p3 @atom:p3 @atom:*
@dihedral:X-p3-p4-X @atom:* @atom:p3 @atom:p4 @atom:*
@dihedral:X-p3-px-X @atom:* @atom:p3 @atom:px @atom:*
@dihedral:X-p3-p5-X @atom:* @atom:p3 @atom:p5 @atom:*
@dihedral:X-p3-py-X @atom:* @atom:p3 @atom:py @atom:*
@dihedral:X-p3-sh-X @atom:* @atom:p3 @atom:sh @atom:*
@dihedral:X-p3-ss-X @atom:* @atom:p3 @atom:ss @atom:*
@dihedral:X-p3-s4-X @atom:* @atom:p3 @atom:s4 @atom:*
@dihedral:X-p3-sx-X @atom:* @atom:p3 @atom:sx @atom:*
@dihedral:X-p3-s6-X @atom:* @atom:p3 @atom:s6 @atom:*
@dihedral:X-p3-sy-X @atom:* @atom:p3 @atom:sy @atom:*
@dihedral:X-p4-p4-X @atom:* @atom:p4 @atom:p4 @atom:*
@dihedral:X-px-px-X @atom:* @atom:px @atom:px @atom:*
@dihedral:X-p4-p5-X @atom:* @atom:p4 @atom:p5 @atom:*
@dihedral:X-px-py-X @atom:* @atom:px @atom:py @atom:*
@dihedral:X-p4-s4-X @atom:* @atom:p4 @atom:s4 @atom:*
@dihedral:X-px-sx-X @atom:* @atom:px @atom:sx @atom:*
@dihedral:X-p4-s6-X @atom:* @atom:p4 @atom:s6 @atom:*
@dihedral:X-px-sy-X @atom:* @atom:px @atom:sy @atom:*
@dihedral:X-p4-sh-X @atom:* @atom:p4 @atom:sh @atom:*
@dihedral:X-px-sh-X @atom:* @atom:px @atom:sh @atom:*
@dihedral:X-p4-ss-X @atom:* @atom:p4 @atom:ss @atom:*
@dihedral:X-px-ss-X @atom:* @atom:px @atom:ss @atom:*
@dihedral:X-p5-p5-X @atom:* @atom:p5 @atom:p5 @atom:*
@dihedral:X-py-py-X @atom:* @atom:py @atom:py @atom:*
@dihedral:X-p5-sh-X @atom:* @atom:p5 @atom:sh @atom:*
@dihedral:X-py-sh-X @atom:* @atom:py @atom:sh @atom:*
@dihedral:X-p5-ss-X @atom:* @atom:p5 @atom:ss @atom:*
@dihedral:X-py-ss-X @atom:* @atom:py @atom:ss @atom:*
@dihedral:X-p5-s4-X @atom:* @atom:p5 @atom:s4 @atom:*
@dihedral:X-py-sx-X @atom:* @atom:py @atom:sx @atom:*
@dihedral:X-p5-s6-X @atom:* @atom:p5 @atom:s6 @atom:*
@dihedral:X-py-sy-X @atom:* @atom:py @atom:sy @atom:*
@dihedral:X-sh-sh-X @atom:* @atom:sh @atom:sh @atom:*
@dihedral:X-sh-ss-X @atom:* @atom:sh @atom:ss @atom:*
@dihedral:X-sh-s4-X @atom:* @atom:sh @atom:s4 @atom:*
@dihedral:X-sh-sx-X @atom:* @atom:sh @atom:sx @atom:*
@dihedral:X-sh-s6-X @atom:* @atom:sh @atom:s6 @atom:*
@dihedral:X-sh-sy-X @atom:* @atom:sh @atom:sy @atom:*
@dihedral:X-ss-ss-X @atom:* @atom:ss @atom:ss @atom:*
@dihedral:X-ss-s4-X @atom:* @atom:ss @atom:s4 @atom:*
@dihedral:X-ss-sx-X @atom:* @atom:ss @atom:sx @atom:*
@dihedral:X-ss-s6-X @atom:* @atom:ss @atom:s6 @atom:*
@dihedral:X-ss-sy-X @atom:* @atom:ss @atom:sy @atom:*
@dihedral:X-s4-s4-X @atom:* @atom:s4 @atom:s4 @atom:*
@dihedral:X-sx-sx-X @atom:* @atom:sx @atom:sx @atom:*
@dihedral:X-s4-s6-X @atom:* @atom:s4 @atom:s6 @atom:*
@dihedral:X-sx-sy-X @atom:* @atom:sx @atom:sy @atom:*
@dihedral:X-s6-s6-X @atom:* @atom:s6 @atom:s6 @atom:*
@dihedral:X-sy-sy-X @atom:* @atom:sy @atom:sy @atom:*
@dihedral:c3-c-sh-hs @atom:c3 @atom:c @atom:sh @atom:hs
@dihedral:c3-c-sh-hs @atom:c3 @atom:c @atom:sh @atom:hs
@dihedral:c2-c2-ss-c3 @atom:c2 @atom:c2 @atom:ss @atom:c3
@dihedral:c2-c2-ss-c3 @atom:c2 @atom:c2 @atom:ss @atom:c3
@dihedral:c2-c2-n-c @atom:c2 @atom:c2 @atom:n @atom:c
@dihedral:c2-c2-n-c @atom:c2 @atom:c2 @atom:n @atom:c
@dihedral:c-n-p2-c2 @atom:c @atom:n @atom:p2 @atom:c2
@dihedral:c-n-p2-c2 @atom:c @atom:n @atom:p2 @atom:c2
@dihedral:n-c3-c-n @atom:n @atom:c3 @atom:c @atom:n
@dihedral:n-c3-c-n @atom:n @atom:c3 @atom:c @atom:n
@dihedral:c-n-c3-c @atom:c @atom:n @atom:c3 @atom:c
@dihedral:c-n-c3-c @atom:c @atom:n @atom:c3 @atom:c
@dihedral:c3-c3-n-c @atom:c3 @atom:c3 @atom:n @atom:c
@dihedral:c3-c3-n-c @atom:c3 @atom:c3 @atom:n @atom:c
@dihedral:c3-c3-n-c @atom:c3 @atom:c3 @atom:n @atom:c
@dihedral:c3-c3-c-n @atom:c3 @atom:c3 @atom:c @atom:n
@dihedral:c3-c3-c-n @atom:c3 @atom:c3 @atom:c @atom:n
@dihedral:c2-ne-p5-o @atom:c2 @atom:ne @atom:p5 @atom:o
@dihedral:c2-ne-p5-o @atom:c2 @atom:ne @atom:p5 @atom:o
@dihedral:c2-nf-p5-o @atom:c2 @atom:nf @atom:p5 @atom:o
@dihedral:c2-nf-p5-o @atom:c2 @atom:nf @atom:p5 @atom:o
@dihedral:ce-ne-p5-o @atom:ce @atom:ne @atom:p5 @atom:o
@dihedral:ce-ne-p5-o @atom:ce @atom:ne @atom:p5 @atom:o
@dihedral:ce-nf-p5-o @atom:ce @atom:nf @atom:p5 @atom:o
@dihedral:ce-nf-p5-o @atom:ce @atom:nf @atom:p5 @atom:o
@dihedral:cf-ne-p5-o @atom:cf @atom:ne @atom:p5 @atom:o
@dihedral:cf-ne-p5-o @atom:cf @atom:ne @atom:p5 @atom:o
@dihedral:cf-nf-p5-o @atom:cf @atom:nf @atom:p5 @atom:o
@dihedral:cf-nf-p5-o @atom:cf @atom:nf @atom:p5 @atom:o
@dihedral:hn-n-c-o @atom:hn @atom:n @atom:c @atom:o
@dihedral:hn-n-c-o @atom:hn @atom:n @atom:c @atom:o
@dihedral:c3-ss-ss-c3 @atom:c3 @atom:ss @atom:ss @atom:c3
@dihedral:c3-ss-ss-c3 @atom:c3 @atom:ss @atom:ss @atom:c3
@dihedral:c3-n3-nh-ca @atom:c3 @atom:n3 @atom:nh @atom:ca
@dihedral:c3-n3-nh-ca @atom:c3 @atom:n3 @atom:nh @atom:ca
@dihedral:c3-n3-p5-o @atom:c3 @atom:n3 @atom:p5 @atom:o
@dihedral:c3-n3-p5-o @atom:c3 @atom:n3 @atom:p5 @atom:o
@dihedral:ca-nh-oh-ho @atom:ca @atom:nh @atom:oh @atom:ho
@dihedral:ca-nh-oh-ho @atom:ca @atom:nh @atom:oh @atom:ho
@dihedral:oh-p5-os-c3 @atom:oh @atom:p5 @atom:os @atom:c3
@dihedral:oh-p5-os-c3 @atom:oh @atom:p5 @atom:os @atom:c3
@dihedral:os-p5-os-c3 @atom:os @atom:p5 @atom:os @atom:c3
@dihedral:os-p5-os-c3 @atom:os @atom:p5 @atom:os @atom:c3
@dihedral:h1-c3-c-o @atom:h1 @atom:c3 @atom:c @atom:o
@dihedral:h1-c3-c-o @atom:h1 @atom:c3 @atom:c @atom:o
@dihedral:hc-c3-c-o @atom:hc @atom:c3 @atom:c @atom:o
@dihedral:hc-c3-c-o @atom:hc @atom:c3 @atom:c @atom:o
@dihedral:hc-c3-c3-hc @atom:hc @atom:c3 @atom:c3 @atom:hc
@dihedral:hc-c3-c3-c3 @atom:hc @atom:c3 @atom:c3 @atom:c3
@dihedral:hc-c3-c2-c2 @atom:hc @atom:c3 @atom:c2 @atom:c2
@dihedral:hc-c3-c2-c2 @atom:hc @atom:c3 @atom:c2 @atom:c2
@dihedral:ho-oh-c3-c3 @atom:ho @atom:oh @atom:c3 @atom:c3
@dihedral:ho-oh-c3-c3 @atom:ho @atom:oh @atom:c3 @atom:c3
@dihedral:ho-oh-c-o @atom:ho @atom:oh @atom:c @atom:o
@dihedral:ho-oh-c-o @atom:ho @atom:oh @atom:c @atom:o
@dihedral:c2-c2-c-o @atom:c2 @atom:c2 @atom:c @atom:o
@dihedral:c2-c2-c-o @atom:c2 @atom:c2 @atom:c @atom:o
@dihedral:c3-c2-c2-c3 @atom:c3 @atom:c2 @atom:c2 @atom:c3
@dihedral:c3-c2-c2-c3 @atom:c3 @atom:c2 @atom:c2 @atom:c3
@dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3
@dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3
@dihedral:c3-c3-c3-c3 @atom:c3 @atom:c3 @atom:c3 @atom:c3
@dihedral:c3-c3-n3-c3 @atom:c3 @atom:c3 @atom:n3 @atom:c3
@dihedral:c3-c3-n3-c3 @atom:c3 @atom:c3 @atom:n3 @atom:c3
@dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3
@dihedral:c3-c3-os-c3 @atom:c3 @atom:c3 @atom:os @atom:c3
@dihedral:c3-c3-os-c @atom:c3 @atom:c3 @atom:os @atom:c
@dihedral:c3-c3-os-c @atom:c3 @atom:c3 @atom:os @atom:c
@dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os
@dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os
@dihedral:c3-os-c3-os @atom:c3 @atom:os @atom:c3 @atom:os
@dihedral:c3-os-c3-na @atom:c3 @atom:os @atom:c3 @atom:na
@dihedral:c3-os-c3-na @atom:c3 @atom:os @atom:c3 @atom:na
@dihedral:o-c-os-c3 @atom:o @atom:c @atom:os @atom:c3
@dihedral:o-c-os-c3 @atom:o @atom:c @atom:os @atom:c3
@dihedral:os-c3-na-c2 @atom:os @atom:c3 @atom:na @atom:c2
@dihedral:os-c3-na-c2 @atom:os @atom:c3 @atom:na @atom:c2
@dihedral:os-c3-c3-os @atom:os @atom:c3 @atom:c3 @atom:os
@dihedral:os-c3-c3-os @atom:os @atom:c3 @atom:c3 @atom:os
@dihedral:os-c3-c3-oh @atom:os @atom:c3 @atom:c3 @atom:oh
@dihedral:os-c3-c3-oh @atom:os @atom:c3 @atom:c3 @atom:oh
@dihedral:oh-c3-c3-oh @atom:oh @atom:c3 @atom:c3 @atom:oh
@dihedral:oh-c3-c3-oh @atom:oh @atom:c3 @atom:c3 @atom:oh
@dihedral:f-c3-c3-f @atom:f @atom:c3 @atom:c3 @atom:f
@dihedral:f-c3-c3-f @atom:f @atom:c3 @atom:c3 @atom:f
@dihedral:cl-c3-c3-cl @atom:cl @atom:c3 @atom:c3 @atom:cl
@dihedral:cl-c3-c3-cl @atom:cl @atom:c3 @atom:c3 @atom:cl
@dihedral:br-c3-c3-br @atom:br @atom:c3 @atom:c3 @atom:br
@dihedral:br-c3-c3-br @atom:br @atom:c3 @atom:c3 @atom:br
@dihedral:h1-c3-c3-os @atom:h1 @atom:c3 @atom:c3 @atom:os
@dihedral:h1-c3-c3-os @atom:h1 @atom:c3 @atom:c3 @atom:os
@dihedral:h1-c3-c3-oh @atom:h1 @atom:c3 @atom:c3 @atom:oh
@dihedral:h1-c3-c3-oh @atom:h1 @atom:c3 @atom:c3 @atom:oh
@dihedral:h1-c3-c3-f @atom:h1 @atom:c3 @atom:c3 @atom:f
@dihedral:h1-c3-c3-f @atom:h1 @atom:c3 @atom:c3 @atom:f
@dihedral:h1-c3-c3-cl @atom:h1 @atom:c3 @atom:c3 @atom:cl
@dihedral:h1-c3-c3-cl @atom:h1 @atom:c3 @atom:c3 @atom:cl
@dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br
@dihedral:h1-c3-c3-br @atom:h1 @atom:c3 @atom:c3 @atom:br
@dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os
@dihedral:hc-c3-c3-os @atom:hc @atom:c3 @atom:c3 @atom:os
@dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh
@dihedral:hc-c3-c3-oh @atom:hc @atom:c3 @atom:c3 @atom:oh
@dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f
@dihedral:hc-c3-c3-f @atom:hc @atom:c3 @atom:c3 @atom:f
@dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl
@dihedral:hc-c3-c3-cl @atom:hc @atom:c3 @atom:c3 @atom:cl
@dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br
@dihedral:hc-c3-c3-br @atom:hc @atom:c3 @atom:c3 @atom:br
} # (end of Dihedrals By Type)
write_once("In Settings") {
improper_coeff @improper:X-o-c-o cvff 1.1 -1 2 # JCC,7,(1986),230
improper_coeff @improper:X-X-c-o cvff 10.5 -1 2 # JCC,7,(1986),230
improper_coeff @improper:X-X-ca-ha cvff 1.1 -1 2 # bsd.on C6H6 nmodes
improper_coeff @improper:X-X-n-hn cvff 1.1 -1 2 # JCC,7,(1986),230
improper_coeff @improper:X-X-n2-hn cvff 1.1 -1 2 # JCC,7,(1986),230
improper_coeff @improper:X-X-na-hn cvff 1.1 -1 2 # JCC,7,(1986),230
improper_coeff @improper:X-c3-n-c3 cvff 1.1 -1 2 # JCC,7,(1986),230
improper_coeff @improper:X-n2-ca-n2 cvff 10.5 -1 2 # JCC,7,(1986),230
improper_coeff @improper:c-c2-c2-c3 cvff 1.1 -1 2 # dac guess, 9/94
improper_coeff @improper:c-ca-ca-c3 cvff 1.1 -1 2 # dac guess, 9/94
improper_coeff @improper:c-c3-n-hn cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:c-c3-n-o cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:c2-c2-na-c3 cvff 1.1 -1 2 #
improper_coeff @improper:c2-c-c2-c3 cvff 1.1 -1 2 #
improper_coeff @improper:c2-c3-c2-hc cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:c2-c3-ca-hc cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:c2-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:c3-o-c-oh cvff 1.1 -1 2 #
improper_coeff @improper:c3-c2-c2-n2 cvff 1.1 -1 2 #
improper_coeff @improper:c3-c2-c2-na cvff 1.1 -1 2 #
improper_coeff @improper:c3-ca-ca-n2 cvff 1.1 -1 2 #
improper_coeff @improper:c3-ca-ca-na cvff 1.1 -1 2 #
improper_coeff @improper:ca-ca-ca-c2 cvff 1.1 -1 2 #
improper_coeff @improper:ca-ca-ca-c3 cvff 1.1 -1 2 #
improper_coeff @improper:ca-ca-ca-f cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:ca-ca-ca-cl cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:ca-ca-ca-br cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:ca-ca-ca-i cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:ca-ca-c-oh cvff 1.1 -1 2 # (not used in tyr!)
improper_coeff @improper:ca-ca-na-c3 cvff 1.1 -1 2 #
improper_coeff @improper:ca-c-ca-c3 cvff 1.1 -1 2 #
improper_coeff @improper:ca-hc-c-o cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:ca-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94
improper_coeff @improper:hc-o-c-oh cvff 1.1 -1 2 # Junmei et al.1999
improper_coeff @improper:hc-o-c-os cvff 1.1 -1 2 #
improper_coeff @improper:n2-c2-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94
improper_coeff @improper:n2-ca-ca-n2 cvff 1.1 -1 2 # dac guess, 9/94
improper_coeff @improper:na-n2-ca-n2 cvff 1.1 -1 2 # dac, 10/94
} # (end of improper_coeffs)
write_once("Data Impropers By Type") {
@improper:X-o-c-o @atom:* @atom:o @atom:c @atom:o
@improper:X-X-c-o @atom:* @atom:* @atom:c @atom:o
@improper:X-X-ca-ha @atom:* @atom:* @atom:ca @atom:ha
@improper:X-X-n-hn @atom:* @atom:* @atom:n @atom:hn
@improper:X-X-n2-hn @atom:* @atom:* @atom:n2 @atom:hn
@improper:X-X-na-hn @atom:* @atom:* @atom:na @atom:hn
@improper:X-c3-n-c3 @atom:* @atom:c3 @atom:n @atom:c3
@improper:X-n2-ca-n2 @atom:* @atom:n2 @atom:ca @atom:n2
@improper:c-c2-c2-c3 @atom:c @atom:c2 @atom:c2 @atom:c3
@improper:c-ca-ca-c3 @atom:c @atom:ca @atom:ca @atom:c3
@improper:c-c3-n-hn @atom:c @atom:c3 @atom:n @atom:hn
@improper:c-c3-n-o @atom:c @atom:c3 @atom:n @atom:o
@improper:c2-c2-na-c3 @atom:c2 @atom:c2 @atom:na @atom:c3
@improper:c2-c-c2-c3 @atom:c2 @atom:c @atom:c2 @atom:c3
@improper:c2-c3-c2-hc @atom:c2 @atom:c3 @atom:c2 @atom:hc
@improper:c2-c3-ca-hc @atom:c2 @atom:c3 @atom:ca @atom:hc
@improper:c2-hc-c-o @atom:c2 @atom:hc @atom:c @atom:o
@improper:c3-o-c-oh @atom:c3 @atom:o @atom:c @atom:oh
@improper:c3-c2-c2-n2 @atom:c3 @atom:c2 @atom:c2 @atom:n2
@improper:c3-c2-c2-na @atom:c3 @atom:c2 @atom:c2 @atom:na
@improper:c3-ca-ca-n2 @atom:c3 @atom:ca @atom:ca @atom:n2
@improper:c3-ca-ca-na @atom:c3 @atom:ca @atom:ca @atom:na
@improper:ca-ca-ca-c2 @atom:ca @atom:ca @atom:ca @atom:c2
@improper:ca-ca-ca-c3 @atom:ca @atom:ca @atom:ca @atom:c3
@improper:ca-ca-ca-f @atom:ca @atom:ca @atom:ca @atom:f
@improper:ca-ca-ca-cl @atom:ca @atom:ca @atom:ca @atom:cl
@improper:ca-ca-ca-br @atom:ca @atom:ca @atom:ca @atom:br
@improper:ca-ca-ca-i @atom:ca @atom:ca @atom:ca @atom:i
@improper:ca-ca-c-oh @atom:ca @atom:ca @atom:c @atom:oh
@improper:ca-ca-na-c3 @atom:ca @atom:ca @atom:na @atom:c3
@improper:ca-c-ca-c3 @atom:ca @atom:c @atom:ca @atom:c3
@improper:ca-hc-c-o @atom:ca @atom:hc @atom:c @atom:o
@improper:ca-n2-ca-n2 @atom:ca @atom:n2 @atom:ca @atom:n2
@improper:hc-o-c-oh @atom:hc @atom:o @atom:c @atom:oh
@improper:hc-o-c-os @atom:hc @atom:o @atom:c @atom:os
@improper:n2-c2-ca-n2 @atom:n2 @atom:c2 @atom:ca @atom:n2
@improper:n2-ca-ca-n2 @atom:n2 @atom:ca @atom:ca @atom:n2
@improper:na-n2-ca-n2 @atom:na @atom:n2 @atom:ca @atom:n2
} # (end of Impropers By Type)
write_once("In Init") {
# Default styles and settings for AMBER based force-fields:
units real
atom_style full
bond_style hybrid harmonic
angle_style hybrid harmonic
dihedral_style hybrid fourier
improper_style hybrid cvff
- pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
- kspace_style pppm 0.0001
- # If long-range coulombic forces are not needed, replace the previous two
- # lines with "pair_style hybrid lj/charmm/coul/charmm 9.0 10.0 10.0"
+ pair_style hybrid lj/charmm/coul/charmm 9.0 10.0
+
+ # NOTE: Long-range coulombic forces were disabled intentionally. (See below)
+ # If you want to use long-range electrostatics, uncomment these lines:
+ #
+ #pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
+ #kspace_style pppm 0.0001
+ #
+ # Instead I use hybrid lj/charmm/coul/charmm by default, because
+ # LAMMPS complains if you attempt to use lj/charmm/coul/long on a
+ # system if it does not contain any charged particles.
+ # Currently, moltemplate does not assign atomic charge,
+ # so this problem occurs frequently.
+
pair_modify mix arithmetic
special_bonds amber
}
}
diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
index 1eb97e645..0d09e4d02 100755
--- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
+++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
@@ -1,34 +1,29 @@
#!/usr/bin/env python
# Calculate a table of pairwise energies and forces between "INT" atoms
# in the lipid membrane model described in
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
-# The previous version included the repulsive core term
def U(r, eps, sigma):
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
def F(r, eps, sigma):
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
-# We don't want to do that. Instead compute the core repulsion using a
-# different pair_style and add the attractive term on top of it using the table.
-# This way it the core repulsion acts as a default interaction with other atom
-# types (using the new repulsive mixing rules).
epsilon = 2.75/4.184 # kCal/mole
sigma = 7.5
Rmin = 0.02
Rmax = 22.6
rcut = 22.5
N = 1130
for i in range(0,N):
r = Rmin + i*(Rmax-Rmin)/(N-1)
U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
F_r = F(r, epsilon, sigma)
if r > rcut:
U_r = 0.0
F_r = 0.0
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt
index f5f117ece..2dc4bbe03 100644
--- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt
+++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.npt
@@ -1,60 +1,65 @@
+# PREREQUISITES:
+#
+# You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+#
# -------- REQUIREMENTS: ---------
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
# http://lammps.sandia.gov/doc/Section_start.html#start_3
# 2) It also may require additional features and bug fixes for LAMMPS.
# So, after typing "make yes-user-misc" in to the shell, ...
# be sure to download and copy the "additional_lammps_code" from
# http://moltemplate.org (upper-left corner menu)
# 3) Unpack it
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
# 5) Compile LAMMPS.
#
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
# then you made a mistake in the instructions above.
#
# -- Init Section --
include system.in.init
# -- Atom Definition Section --
read_data system.data
# -- Settings Section --
include system.in.settings
# -- Run Section --
#minimize 1.0e-5 1.0e-7 500 2000
timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
dump 1 all custom 10000 traj_npt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal vol epair ebond eangle
thermo 1000 # time interval for printing out "thermo" data
fix fxlan all langevin 300.0 300.0 120 48279
fix fxnph all nph x 0 0 1000 y 0 0 1000 couple xy
# Note: The temperature 300.0 K corresponds to 0.907033536873*epsilon
# (for the "epsilon" used by the coarse-grained lipid), and
# to 0.33*epsilon (for the "epsilon" used in the coarse-grained protein)
# Note: The langevin damping parameter "120" corresponds to
# the 0.12ps damping time used in Watson et. al JCP 2011.
# Note: We maintain the system system at constant (zero) tention
# using a barostat damping parameter Pdamp=1000 ("0 0 1000")
# optional (not sure if this helps):
# balance x uniform y uniform
-run 10000000
-
-write_restart system_after_npt.rst
+run 100000
+write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt
index 2ee9ae019..c9195b4e6 100644
--- a/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt
+++ b/tools/moltemplate/examples/CG_biomolecules/membrane+protein/run.in.nvt
@@ -1,67 +1,71 @@
-# -------- REQUIREMENTS: ---------
+# PREREQUISITES:
+#
+# 1) You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+# 2) You must equilibrate the system beforehand using "run.in.npt".
+# This will create the file "system_after_npt.data" which this file reads.
+# (Note: I have not verified that this equilibration protocol works well.)
+#
+# -------- LAMMPS REQUIREMENTS: ---------
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
# http://lammps.sandia.gov/doc/Section_start.html#start_3
# 2) It also may require additional features and bug fixes for LAMMPS.
# So, after typing "make yes-user-misc" in to the shell, ...
# be sure to download and copy the "additional_lammps_code" from
# http://moltemplate.org (upper-left corner menu)
# 3) Unpack it
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
# 5) Compile LAMMPS.
#
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
# then you made a mistake in the instructions above.
#
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
-# Normally, I would minimize the system and equilibrate the system at constant
-# pressure and temperature beforehand. If you run lammps with "run.in.npt",
-# it will generate a restart file "system_after_npt.rst" with reasonable
-# coordinates at that temperature and pressure. Then we could load it now:
-#
-#read_restart system_after_npt.rst
-#
-# Unfortunately the LAMMPS "read_restart" command has been undependable over
-# the past year (2012), and I feel it is safer to remove it from the examples.
-# Instead, for this example, I just read the raw coordinates generated by
-# moltemplate (and the default volume). (I get fewer questions this way.)
-# However you should never run any liquid simulations at constant volume without
-# pressure equilibration first. Hopefully in the future "read_restart" will
-# work. Until then, try "read_dump", "dump2data.py", or "restart2data".
+# Read the coordinates generated by an earlier NPT simulation
+
+read_data system_after_npt.data
+
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also. I prefer "write_data" and "read_data".)
-read_data system.data
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
dump 1 all custom 10000 traj_nvt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal vol epair ebond eangle
thermo 1000 # time interval for printing out "thermo" data
fix fxlan all langevin 300.0 300.0 120 48279
fix fxnve all nve
# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
# Note: The langevin damping parameter "120" corresponds to
# the 0.12ps damping time used in Watson et. al JCP 2011.
#restart 500000
run 10000000
-write_restart system_after_nvt.rst
+
+write_data system_after_nvt.data
+
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also.)
diff --git a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py
index 1eb97e645..0d09e4d02 100755
--- a/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py
+++ b/tools/moltemplate/examples/CG_biomolecules/membrane_BranniganPRE2005/moltemplate_files/calc_table/calc_table.py
@@ -1,34 +1,29 @@
#!/usr/bin/env python
# Calculate a table of pairwise energies and forces between "INT" atoms
# in the lipid membrane model described in
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
-# The previous version included the repulsive core term
def U(r, eps, sigma):
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
def F(r, eps, sigma):
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
-# We don't want to do that. Instead compute the core repulsion using a
-# different pair_style and add the attractive term on top of it using the table.
-# This way it the core repulsion acts as a default interaction with other atom
-# types (using the new repulsive mixing rules).
epsilon = 2.75/4.184 # kCal/mole
sigma = 7.5
Rmin = 0.02
Rmax = 22.6
rcut = 22.5
N = 1130
for i in range(0,N):
r = Rmin + i*(Rmax-Rmin)/(N-1)
U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
F_r = F(r, epsilon, sigma)
if r > rcut:
U_r = 0.0
F_r = 0.0
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
diff --git a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
index fcc6188f7..6300c4ce3 100644
--- a/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
+++ b/tools/moltemplate/examples/CG_biomolecules/protein_folding_examples/1beadProtSci2010/moltemplate_files/system.lt
@@ -1,25 +1,12 @@
import "1beadProtSci2010.lt"
using namespace 1beadProtSci2010
prot = new 4HelixBundle
write_once("Data Boundary") {
0 100 xlo xhi
0 100 ylo yhi
0 100 zlo zhi
}
-
-
-
-# ------------ Note: -------------
-#
-# If you want to try the version using "CHARMM" dihedrals, import this instead:
-#
-# import "versions_with_comments/1beadProtSci2010_charmm.lt"
-#
-# (The two versions should behave identically. However by overlaying
-# dihedral interactions on top of eachother, charmm allows you to construct
-# a Fourier series with an arbitrary number of terms. Class2 stops at 3.
-# This is useful if one day you want to use a more complex dihedral potential.)
diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
index 1eb97e645..0d09e4d02 100755
--- a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
+++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/moltemplate_files/calc_table/calc_CGLipidTableINTvsINT.py
@@ -1,34 +1,29 @@
#!/usr/bin/env python
# Calculate a table of pairwise energies and forces between "INT" atoms
# in the lipid membrane model described in
# Brannigan et al, Phys Rev E, 72, 011915 (2005)
# The energy of this interaction U(r) = eps*(0.4*(sigma/r)^12 - 3.0*(sigma/r)^2)
# However it is truncated at rc2 = 22.5 (shifted upwards to maintain continuity)
-# The previous version included the repulsive core term
def U(r, eps, sigma):
return eps* (0.4*pow((sigma/r),12) - 3.0*sigma*sigma/(r*r))
def F(r, eps, sigma):
return eps*(12*0.4*pow((sigma/r),13)/sigma - 2*3.0*sigma*sigma/(r*r*r))
-# We don't want to do that. Instead compute the core repulsion using a
-# different pair_style and add the attractive term on top of it using the table.
-# This way it the core repulsion acts as a default interaction with other atom
-# types (using the new repulsive mixing rules).
epsilon = 2.75/4.184 # kCal/mole
sigma = 7.5
Rmin = 0.02
Rmax = 22.6
rcut = 22.5
N = 1130
for i in range(0,N):
r = Rmin + i*(Rmax-Rmin)/(N-1)
U_r = U(r, epsilon, sigma) - U(rcut, epsilon, sigma)
F_r = F(r, epsilon, sigma)
if r > rcut:
U_r = 0.0
F_r = 0.0
print(str(i+1)+' '+str(r)+' '+str(U_r)+' '+str(F_r))
diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh
index f286193f0..8df6285ca 100755
--- a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh
+++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/packmol_files/README.sh
@@ -1,23 +1,18 @@
# Here we generate the starting coordinates of the simulation
# using PACKMOL
-
-
-# You must run each packmol commend one after the other
+# Running these three commands will probably take hours or even days.
+# (It depends on how dense and how uniformly you need the packing to be.)
# NOTE: If PACKMOL gets stuck in an endless loop, then edit the corresponding
# "inp" file. This should not happen. You can also usually interrupt
# packmol after 30 minutes, and the solution at that point should be good
# enough for use.
packmol < step1_proteins.inp # This step determines the protein's location
# It takes ~20 minutes (on an intel i7)
packmol < step2_innerlayer.inp # This step builds the inner monolayer
# It takes ~90 minutes
packmol < step3_outerlayer.inp # This step builds the outer monolayer
- # It takes at least ~4 hours
-
-# Running these three commands will probably take hours or even days.
-# (It depends on how dense and how uniformly you need the packing to be.)
-
-mv -f step3_outerlayer.xyz ../system.xyz
+ # It takes ~4 hours
+# This should create a file named "system.xyz" (which moltemplate will read).
diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min
index 7ef8e4c22..9cb2d9300 100644
--- a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min
+++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.min
@@ -1,53 +1,46 @@
# -------- REQUIREMENTS: ---------
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
# http://lammps.sandia.gov/doc/Section_start.html#start_3
# 2) It also may require additional features and bug fixes for LAMMPS.
# So, after typing "make yes-user-misc" in to the shell, ...
# be sure to download and copy the "additional_lammps_code" from
# http://moltemplate.org (upper-left corner menu)
# 3) Unpack it
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
# 5) Compile LAMMPS.
#
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
# then you made a mistake in the instructions above.
# -- Init section --
include system.in.init
# -- Atom definition section --
read_data system.data
-# If you repeat minimization later, you can skip the (slow) step above which
-# reads the coordinaes, by commenting it out and uncommenting this line below:
-#
-# read_restart system_t0.rst
-
# -- Settings Section --
include system.in.settings
# -- Run section --
-write_restart system_t0.rst
-
dump 1 all custom 50 traj_min.lammpstrj id mol type x y z ix iy iz
# minimize
minimize 1.0e-5 1.0e-7 5000 20000
# If minimization crashes, then instead try Langevin dynamics
# with a small timestep and a fast damping parameter. For example:
#
# timestep 0.05
# fix fxlan all langevin 300.0 300.0 100.0 48279
# fix fxnve all nve
#
# run 10000
-write_restart system_after_min.rst
+write_data system_after_min.data
diff --git a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt
index 3cb0e7067..253c04267 100644
--- a/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt
+++ b/tools/moltemplate/examples/CG_biomolecules/vesicle_Brannigan2005+Bellesia2010/run.in.nvt
@@ -1,70 +1,63 @@
# -------- REQUIREMENTS: ---------
# 1) This example requires the "USER-MISC" package. (Use "make yes-USER-MISC")
# http://lammps.sandia.gov/doc/Section_start.html#start_3
# 2) It also may require additional features and bug fixes for LAMMPS.
# So, after typing "make yes-user-misc" in to the shell, ...
# be sure to download and copy the "additional_lammps_code" from
# http://moltemplate.org (upper-left corner menu)
# 3) Unpack it
# 4) copy the .cpp and .h files to the src folding of your lammps installation.
# 5) Compile LAMMPS.
#
# If LAMMPS complains about an "Invalid pair_style", or "Invalid dihedral_style"
# then you made a mistake in the instructions above.
#
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
# Commenting out:
#
# read_data system.data
#
-# Instead read the restart file created by "run.in.min".
+# Instead read the data file created by "run.in.min".
-read_restart system_after_min.rst
-
-# WARNING: Unfortunately the LAMMPS "read_restart" command has been undependable
-# over the past year (2012). If this fails, then just move the minimization
-# steps in run.in.min into this script (into the "Run Section").
-# Alternately, try to extract the last frame of the dump file created
-# by run.in.min using "read_dump", "dump2data.py", and/or "restart2data".
+read_data system_after_min.data
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
# Just in case the previous minimization failed, try again.
-# (I don't know why this would help, but sometimes loading
-# up the restart file and trying again does help. Magic.)
+# (I don't know why this helps, but sometimes it does. Magic.)
minimize 1.0e-5 1.0e-7 5000 20000
# Run main simulation
timestep 10.0 # The time-step in Watson et. al 2011 was 0.002*3ps = 6fs
dump 1 all custom 2500 traj_nvt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal vol epair ebond eangle
thermo 100 # time interval for printing out "thermo" data
fix fxlan all langevin 300.0 300.0 120 48279
fix fxnve all nve
# Note: The energy scale "epsilon" = 2.75kJ/mole = 330.7485200981 Kelvin*kB.
# So a temperature of 300.0 Kelvin corresponds to 0.907033536873*epsilon.
# Note: The langevin damping parameter "120" corresponds to
# the 0.12ps damping time used in Watson et. al JCP 2011.
run 1000000
-write_restart system_after_nvt.rst
+write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt
index e3a37dfe3..c2e2e8de5 100644
--- a/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt
+++ b/tools/moltemplate/examples/CG_misc/translocation/run.in.nvt
@@ -1,43 +1,49 @@
+# PREREQUISITES:
+#
+# You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+
# -- Init Section --
include system.in.init
# -- Atom Definition Section --
read_data system.data
# -- Settings Section --
include system.in.settings
# -- Run Section --
timestep 1.0
dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal vol epair ebond eangle edihed
thermo 500 # time interval for printing out "thermo" data
# Optional: Improve efficiency by omitting the calcuation of interactions
# between immobile atoms. (Note: This is not optional under NPT conditions.)
neigh_modify exclude group groupB groupB
# Only the groupB atoms are immobile.
group mobile subtract all groupB
# The next two lines recalculate the temperature
# using only the mobile degrees of freedom:
compute tempMobile mobile temp
# Integrate the equations of motion:
fix fMoveStuff mobile nvt temp 300.0 300.0 100.0
fix_modify fMoveStuff temp tempMobile
run 100000
write_restart system_after_nvt.rst
diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt
index 59d5ce9f8..544daee70 100644
--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt
+++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.npt
@@ -1,58 +1,61 @@
# run.in.npt
#
# -- Usage --
#
-# lmp_g++ -i run.in.npt
-# (assuming lmp_g++ is the name of your lammps binary)
+# lmp_linux -i run.in.npt
+# (assuming lmp_linux is the name of your lammps binary)
#
# -- Prerequisite Input Files: --
# systen.data, system.in.init, system.in.settings, system.in.sw
#
# You can generate these files with this command:
# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt
# ---------------------------------
# ----- Init Section -----
include system.in.init
# ----- Atom Definition Section -----
read_data system.data
# ----- Settings Section -----
include system.in.settings
# ----- Run Section -----
# -- minimization protocol --
# Note: The minimization step is not necessary in this example. However
# in general, it's always a good idea to minimize the system beforehand.
minimize 1.0e-5 1.0e-7 100000 400000
# -- simulation protocol --
timestep 2.0 # <- This can be increased to 5.0 or 10.0 for bulk water
dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz
fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
thermo 500 # time interval for printing out "thermo" data
run 200000
-write_restart system_after_npt.rst
+write_data system_after_npt.data
+
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also.)
diff --git a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt
index 9d499517d..66334249b 100644
--- a/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt
+++ b/tools/moltemplate/examples/CG_solvent/cyclododecane+watMW/run.in.nvt
@@ -1,78 +1,81 @@
+# PREREQUISITES:
+#
+# 1) You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+# 2) You must equilibrate the system beforehand using "run.in.npt".
+# This will create the file "system_after_npt.data" which this file reads.
+# (Note: I have not verified that this equilibration protocol works well.)
+
# run.in.nvt
#
# -- Usage --
#
# lmp_g++ -i run.in.nvt
# (assuming lmp_g++ is the name of your lammps binary)
#
# -- Prerequisite Input Files: --
# systen.data, system.in.init, system.in.settings, system.in.sw
+# system_after_npt.data
+#
+# You can generate these files using this procedure
#
-# You can generate these files with this command:
# moltemplate.sh -a "@atom:/WatMW/mW 1" system.lt
+#
+# lmp_linux -i run.in.npt
+
# ---------------------------------
# -- init section --
include system.in.init
# -- atom definition section --
-# Normally, I would minimize the system and equilibrate the system at constant
-# pressure and temperature beforehand. If you run lammps with "run.in.npt",
-# it will generate a restart file "system_after_npt.rst" with reasonable
-# coordinates at that temperature and pressure. Then we could load it now:
-#
-#read_restart system_after_npt.rst
-#
-# Unfortunately the LAMMPS "read_restart" command has been undependable over
-# the past year (2012), and I feel it is safer to remove it from the examples.
-# Instead, for this example, I just read the raw coordinates generated by
-# moltemplate (and the default volume). (I get fewer questions this way.)
-# However you should never run any liquid simulations at constant volume without
-# pressure equilibration first. Hopefully in the future "read_restart" will
-# work. Otherwise try "read_dump", "dump2data.py", or "restart2data".
+# Read the coordinates generated by an earlier NPT simulation
-read_data system.data
+read_data system_after_npt.data
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also. I prefer "write_data" and "read_data".)
# -- settings section --
include system.in.settings
# -- run section --
timestep 2.0
dump 1 all custom 1000 traj_nvt.lammpstrj id mol type x y z ix iy iz
dump 2 TraPPE custom 1000 traj_alkane_nvt.lammpstrj id mol type x y z ix iy iz
fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
# The following commands are useful if you want to calculate the distribution
# of alkane-chain radius-of-gyration at a given temperature & pressure.
#compute cRg TraPPE gyration
#variable vRg equal c_cRg
#compute cPE all pe
#variable vPE equal c_cPE
#fix FprintPE all print 1000 "${vPE}" file U.dat
#fix FprintRg all print 1000 "${vRg}" file Rg.dat
thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
thermo 1000 # time interval for printing out "thermo" data
#thermo_modify flush yes
restart 100000 restart_nvt
run 1000000
-write_restart system_after_nvt.rst
+write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT
new file mode 100644
index 000000000..bafcbca1f
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/WARNING.TXT
@@ -0,0 +1,72 @@
+# -------- WARNING: --------
+
+This directory contains some examples of all-atom simulations using the GAFF
+force field, prepared using moltemplate.
+
+This software is experimental, and the force-fields and equilbration protocols
+have not been tested carefully by me. There is no gaurantee that simulations
+prepared using moltemplate will reproduce the behavior of AmberTools/AMBER.
+
+# -------- REQUEST FOR HELP: --------
+
+If you notice a problem with these examples, please report it.
+Peer-review is the only way to improve this software (or any software).
+Other suggestions are also welcome!
+
+(Contact jewett.aij@gmail.com, 2013-12-01)
+
+
+--- Charge ---
+
+This software does not assign charges to each atom.
+(AmberTools can do this.)
+
+For the purpose of demonstration, in the hydrocarbon examples located here,
+I am simply neglecting the partial charge of the carbon and hydrogen atoms.
+This approach is unlikely to be appropriate in most practical applications.
+
+
+--- Long-range electrostatics ---
+
+Furthermore long-range electrostatics (kspace_style pppm) are usually disabled
+by default. (Examples containing TIP3P water are an exception to this.)
+To enable long-range coulombics, make these modifications to the
+"system.in.init" and "system.in.settings" files AFTER running moltemplate:
+(enter these commands into the bash shell)
+
+echo "kspace_style pppm 0.0001" >> system.in.init
+echo "pair_style hybrid lj/charmm/coul/long 9.0 10.0" >> system.in.init
+sed -i 's/lj\/charmm\/coul\/charmm/lj\/charmm\/coul\/long/g' system.in.settings
+
+
+--- Improper angles ---
+
+I am also uncertain whether the improper angle interactions generated by
+moltemplate are equivalent to those generated by AmberTools. (I think they are,
+but I am worried that I might have listed the atom types in the wrong order.)
+
+
+--- Bloated lammps input scripts ---
+--- -> slow simulations ? ---
+
+As of 2013-12-01, LAMMPS input scripts prepared using moltemplate using the
+"gaff.lt" file contain the entire contents of the GAFF force-field,
+even if your simulation uses only a few of the atom types in GAFF.
+
+ Details:
+Moltemplate creates a file usually named "system.in.settings" containing all
+of the GAFF information. It is usually about 700kB large. This file is read
+by LAMMPS. This means that every interaction in GAFF is loaded
+into LAMMPS (for all ~72 atom types).
+This is true even if you only use a tiny subset of the atom types and bonded
+interactions defined in GAFF. Hopefully allocating the memory needed to store
+this extra information will not slow down your simulations noticably.
+
+However, in case it does, the "waterTIP3P+isobutane/README_setup.sh"
+contains detailed instructions how to strip this kind of junk from
+the "system.in.settings" file.
+
+(In the future I may modify moltemplate to do this automatically,
+however I may not remember to remove this warning from this file.
+Hopefully this issue will be fixed by the time you use moltemplate.)
+
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT
new file mode 100644
index 000000000..64ec594c6
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README.TXT
@@ -0,0 +1,44 @@
+This example is a simple simulation of 288 hexadecane molecules in a box at
+room temperature and atmospheric pressure. Please read the WARNING.TXT file.
+
+-------- REQUIREMENTS: ---------
+This example requires building LAMMPS with the "USER-MISC" package.
+(because it uses dihedral_style fourier)
+To do this, type "make yes-user-misc" before compiling LAMMPS.
+http://lammps.sandia.gov/doc/Section_start.html#start_3
+
+More detailed instructions on how to build LAMMPS input files and
+run a short simulation are provided in other README files:
+
+step 1) to setup the LAMMPS input files, run this file:
+README_setup.sh
+
+ (Currently there is a bug which makes this step slow.
+ I'll fix it later -Andrew 2013-10-15.)
+
+step 2) to run LAMMPS, follow the instructions in this file:
+README_run.sh
+
+------------ NOTE: There are two versions of this example. ----------------
+
+Both examples use the same force-field parameters.
+
+1)
+In this version, the force-field parameters are loaded from the "gaff.lt" file
+(located in the "common" subdirectory).
+This frees the user from the drudgery of manually specifying all of these
+force-field details for every molecule. (However, the user must be careful
+to choose @atom-type names which match AMBER GAFF conventions,
+such as the "c3" and "h1" atoms, in this example.)
+
+2)
+Alternately, there is another "hexadecane" example in the "all_atom_examples"
+directory. In that example, force-field parameters are loaded from a file
+named "alkanes.lt" (instead of "gaff.lt"). The "alkanes.lt" file contains
+only the excerpts from "gaff.lt" which are relevant to the hydrocarbon
+molcules used in that example. ("gaff.lt" contains parameters for most
+small organic molecules, not just hydrocarbons.)
+In this way, by editing "alkanes.lt", the user can manually control all of the
+force-field details in the simulation. (Without feeling as though they are
+relying on some kind of mysterious "black box" to do it for them.)
+
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh
new file mode 100755
index 000000000..8b01ab92d
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_run.sh
@@ -0,0 +1,39 @@
+# --- Running LAMMPS ---
+# -------- REQUIREMENTS: ---------
+# 1) This example requires building LAMMPS with the "USER-MISC" package.
+# (because it makes use of "gaff.lt" which uses dihedral_style fourier)
+# To do this, type "make yes-user-misc" before compiling LAMMPS.
+# http://lammps.sandia.gov/doc/Section_start.html#start_3
+# -------- PREREQUISITES: --------
+# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
+# input scripts which link to the input scripts and data files
+# you hopefully have created earlier with moltemplate.sh:
+# system.in.init, system.in.settings, system.data
+# If not, carry out the instructions in "README_setup.sh".
+#
+# -- Instructions: --
+# If "lmp_linux" is the name of the command you use to invoke lammps,
+# then you would run lammps on these files this way:
+
+
+lmp_linux -i run.in.npt # minimization and simulation at constant pressure
+lmp_linux -i run.in.nvt # minimization and simulation at constant volume
+
+#(Note: The constant volume simulation lacks pressure equilibration. These are
+# completely separate simulations. The results of the constant pressure
+# simulation might be ignored when beginning the simulation at constant
+# volume. (This is because restart files in LAMMPS don't always work,
+# and I was spending a lot of time trying to convince people it was a
+# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
+# Read the "run.in.nvt" file to find out how to use the "read_restart"
+# command to load the results of the pressure-equilibration simulation,
+# before beginning a constant-volume run.
+
+
+
+
+
+# If you have compiled the MPI version of lammps, you can run lammps in parallel
+#mpirun -np 4 lmp_linux -i run.in.npt
+#mpirun -np 4 lmp_linux -i run.in.nvt
+# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh
similarity index 62%
copy from tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
copy to tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh
index 3b867ae8a..3b7fb0990 100755
--- a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_setup.sh
@@ -1,89 +1,74 @@
# -------- REQUIREMENTS: ---------
# You must define your MOLTEMPLATE_PATH environment variable
# and set it to the "common" subdirectory of your moltemplate distribution.
# (See the "Installation" section in the moltemplate manual.)
# Create LAMMPS input files this way:
cd moltemplate_files
# run moltemplate
moltemplate.sh system.lt
# This will generate various files with names ending in *.in* and *.data.
# These files are the input files directly read by LAMMPS. Move them to
# the parent directory (or wherever you plan to run the simulation).
#cp -f system.data system.in* ../
# --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK ---------
- # --------- edit 2013-8-28 ---------
+ # --------- edit 2013-10-13 ---------
echo "-----------------------------------------------------------------" >&2
echo "OPTIONAL STEP: PRUNING THE RESULTING MOLTEMPLATE OUTPUT TO" >&2
echo " INCLUDE ONLY ATOMS AND TYPES WE ARE ACTUALLY USING." >&2
# Unfortunately, as of 2013-8-28, these files contain a lot of irrelevant
# information (for atom types not present in the current system).
# For now, we can strip this out using ltemplify.py to build a new .lt file.
# THIS IS AN UGLY WORKAROUND. HOPEFULLY IN THE FUTURE, WE CAN SKIP THESE STEPS
# do this in a temporary_directory
mkdir new_lt_file
cd new_lt_file/
# now run ltemplify.py
ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt
rm -rf ../system.data ../system.in* # these old lammps files no longer needed
# This creates a new .LT file named "system.lt" in the local directory.
- # Unfortunately, it may be missing some information because ltemplify.py
- # does not understand all the commands present in a LAMMPS input script.
- # If you define groups or use constraints, you must define them again. In this
- # case, we must add the SHAKE constraint for the "TIP3P_2004" water molecule.
- # So we have to remember the original name of the bond types and angle types.
- # (For this example, SHAKE is applied to the water molecule, which is defined
- # in "tip3p_2004.lt" file in the "common/" directory. Check this file.)
- ATOMTYPENUM_ow=`awk '{if ($1 == "@/atom:TIP3P_2004/ow") print $2}' < ../output_ttree/ttree_assignments.txt`
- ATOMTYPENUM_hw=`awk '{if ($1 == "@/atom:TIP3P_2004/hw") print $2}' < ../output_ttree/ttree_assignments.txt`
- BONDTYPENUM=`awk '{if ($1 == "@/bond:TIP3P_2004/OH") print $2}' < ../output_ttree/ttree_assignments.txt`
- ANGLETYPENUM=`awk '{if ($1 == "@/angle:TIP3P_2004/HOH") print $2}' < ../output_ttree/ttree_assignments.txt`
- echo "" >> system.lt
- echo "write_once(\"In Settings\") {" >> system.lt
- echo " group tip3p type @atom:type$ATOMTYPENUM_ow @atom:type$ATOMTYPENUM_hw" >> system.lt
- echo " fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:type$BONDTYPENUM a @angle:type$ANGLETYPENUM" >> system.lt
- echo "}" >> system.lt
- echo "" >> system.lt
+
# The ltemplify.py script also does not copy the boundary dimensions.
- # We must do this manually as well.
+ # We must do this manually.
echo "write_once(\"Data Boundary\") {" >> system.lt
cat "../output_ttree/Data Boundary" >> system.lt
echo "}" >> system.lt
echo "" >> system.lt
# Now, run moltemplate on this new .LT file.
moltemplate.sh system.lt
# This will create: "system.data" "system.in.init" "system.in.settings."
- # move the final DATA and INput scripts to the desired location,
+
+ # Move the final DATA and INput scripts to the desired location,
mv -f system.data system.in* ../../
# and clean up the mess
rm -rf output_ttree/
cd ..
rm -rf new_lt_file/
echo "---------------- DONE PRUNING MOLTEMPLATE OUTPUT ----------------" >&2
echo "-----------------------------------------------------------------" >&2
# --------- END OF OPTIONAL STEPS FOR STRIPPING OUT JUNK ---------
# Optional:
# The "./output_ttree/" directory is full of temporary files generated by
# moltemplate. They can be useful for debugging, but are usually thrown away.
rm -rf output_ttree/
cd ../
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt
new file mode 100644
index 000000000..019afc144
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/README_visualize.txt
@@ -0,0 +1,87 @@
+
+ ------- To view a lammps trajectory in VMD --------
+
+
+1) Build a PSF file for use in viewing with VMD.
+
+This step works with VMD 1.9 and topotools 1.2.
+(Older versions, like VMD 1.8.6, don't support this.)
+
+
+a) Start VMD
+b) Menu Extensions->Tk Console
+c) Enter:
+
+(I assume that the the DATA file is called "system.data")
+
+ topo readlammpsdata system.data full
+ animate write psf system.psf
+
+2)
+
+Later, to Load a trajectory in VMD:
+
+ Start VMD
+ Select menu: File->New Molecule
+ -Browse to select the PSF file you created above, and load it.
+ (Don't close the window yet.)
+ -Browse to select the trajectory file.
+ If necessary, for "file type" select: "LAMMPS Trajectory"
+ Load it.
+
+ ---- A note on trajectory format: -----
+If the trajectory is a DUMP file, then make sure the it contains the
+information you need for pbctools (see below. I've been using this
+command in my LAMMPS scripts to create the trajectories:
+
+ dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
+
+It's a good idea to use an atom_style which supports molecule-ID numbers
+so that you can assign a molecule-ID number to each atom. (I think this
+is needed to wrap atom coordinates without breaking molecules in half.)
+
+Of course, you don't have to save your trajectories in DUMP format,
+(other formats like DCD work fine) I just mention dump files
+because these are the files I'm familiar with.
+
+3) ----- Wrap the coordinates to the unit cell
+ (without cutting the molecules in half)
+
+a) Start VMD
+b) Load the trajectory in VMD (see above)
+c) Menu Extensions->Tk Console
+d) Try entering these commands:
+
+ pbc wrap -compound res -all
+ pbc box
+
+ ----- Optional ----
+ Sometimes the solvent or membrane obscures the view of the solute.
+ It can help to shift the location of the periodic boundary box
+ To shift the box in the y direction (for example) do this:
+
+ pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
+ pbc box -shiftcenterrel {0.0 0.15 0.0}
+
+ Distances are measured in units of box-length fractions, not Angstroms.
+
+ Alternately if you have a solute whose atoms are all of type 1,
+ then you can also try this to center the box around it:
+
+ pbc wrap -sel type=1 -all -centersel type=2 -center com
+
+4)
+ You should check if your periodic boundary conditions are too small.
+ To do that:
+ select Graphics->Representations menu option
+ click on the "Periodic" tab, and
+ click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
+
+5) Optional: If you like, change the atom types in the PSF file so
+ that VMD recognizes the atom types, use something like:
+
+sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
+sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
+sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
+
+(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT
new file mode 100644
index 000000000..def26ba76
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/WARNING.TXT
@@ -0,0 +1,16 @@
+# -------- WARNING: --------
+
+This software is experimental, and the force-fields and equilbration protocols
+have not been tested carefully by me. There is no gaurantee that the simulation
+will reproduce the behavior of real hexadecane molecules,
+(or even of hexadecane molecules simulated using AMBER, which should
+ be using the same force-field).
+
+# -------- REQUEST FOR HELP: --------
+
+However, if you notice a problem with this example, please report it.
+I confess I do not have a lot of experience running all-atom simulations.
+Peer-review is the only way to improve this software (or any software).
+Other suggestions are also welcome!
+
+(Contact jewett.aij@gmail.com, 2013-10-16)
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
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diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt
new file mode 100644
index 000000000..8cbfde6a5
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch2group.lt
@@ -0,0 +1,49 @@
+
+import "gaff.lt" # <-- defines the "GAFF" force field
+
+
+# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is
+# distributed with moltemplate. See the "Installation" section in the manual.)
+# It contains definitions of the atoms "c3", "h1", as well as the force-field
+# parameters for bonded and non-bonded interactions between them
+# (and many other atoms).
+
+# The charges for the atoms in this example are all set to zero.
+# In a realistic simulation, one must assign (partial) charges to each atom.
+
+
+CH2 inherits GAFF {
+
+ # atom-id mol-id atom-type charge x y z
+
+ write("Data Atoms") {
+ $atom:C $mol:... @atom:c3 0.00 0.00 0.000 0.000
+ $atom:H1 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 0.8924307629540046
+ $atom:H2 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 -0.8924307629540046
+ }
+
+ # Note: The "..." in "$mol:..." tells moltemplate that this molecule may
+ # be a part of a larger molecule, and (if so) to use the larger
+ # parent object's molecule id number as it's own.
+ # The CH2 group is part of the Hexadecane molecule.
+
+ # Now specify which pairs of atoms are bonded:
+ write('Data Bond List') {
+ $bond:CH1 $atom:C $atom:H1
+ $bond:CH2 $atom:C $atom:H2
+ }
+
+} # CH2
+
+
+
+
+######### (scratchwork calculations for the atomic coordinates) #########
+# Lcc = 1.5350 # length of the C-C bond (Sp3)
+# Lch = 1.0930 # length of the C-H bond
+# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
+# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
+# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
+# # 0.5*DeltaYc = 0.4431163316030377
+# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
+# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt
new file mode 100644
index 000000000..2be688c5f
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/ch3group.lt
@@ -0,0 +1,52 @@
+
+import "gaff.lt" # <-- defines the "GAFF" force field
+
+
+# The "gaff.lt" file is usually located in $MOLTEMPLATE_PATH (and is
+# distributed with moltemplate. See the "Installation" section in the manual.)
+# It contains definitions of the atoms "c3", "h1", as well as the force-field
+# parameters for bonded and non-bonded interactions between them
+# (and many other atoms).
+
+# The charges for the atoms in this example are all set to zero.
+# In a realistic simulation, one must assign (partial) charges to each atom.
+
+
+CH3 inherits GAFF {
+
+ # atom-id mol-id atom-type charge x y z
+
+ write("Data Atoms") {
+ $atom:C $mol:... @atom:c3 0.00 0.00 0.000 0.000
+ $atom:H1 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 0.8924307629540046
+ $atom:H2 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 -0.8924307629540046
+ $atom:H3 $mol:... @atom:h1 0.00 -0.8924307629540046 -0.6310438442242609 0.00
+ }
+
+ # Note: The "..." in "$mol:..." tells moltemplate that this molecule may
+ # be a part of a larger molecule, and (if so) to use the larger
+ # parent object's molecule id number as it's own.
+ # The CH3 group is part of the Hexadecane molecule.
+
+ # Now specify which pairs of atoms are bonded:
+ write('Data Bond List') {
+ $bond:CH1 $atom:C $atom:H1
+ $bond:CH2 $atom:C $atom:H2
+ $bond:CH3 $atom:C $atom:H3
+ }
+
+} # CH3
+
+
+
+
+######### (scratchwork calculations for the atomic coordinates) #########
+# Lcc = 1.5350 # length of the C-C bond (Sp3)
+# Lch = 1.0930 # length of the C-H bond
+# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
+# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
+# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
+# # 0.5*DeltaYc = 0.4431163316030377
+# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
+# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
+
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt
new file mode 100644
index 000000000..fa4a9ac25
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/hexadecane.lt
@@ -0,0 +1,84 @@
+# Define the "CH2" and "CH3" objects:
+
+import "ch2group.lt"
+import "ch3group.lt"
+
+
+
+Hexadecane inherits GAFF {
+
+ # Create an array of 16 "CH2" objects
+
+ monomers = new CH2.move(0,0.4431163,0) [16].rot(180,1,0,0).move(1.2533223,0,0)
+
+ # "monomers" is a 1-dimensional array containing 16 copies of the CH2 molecule
+ # Each copy is rotated 180 degrees and shifted along the x axix.
+ # (For an explanation, read sections 7.1-7.3 of the moltemplate manual.)
+ # Notes:
+ # 1.2533223 = DeltaXc = how far each CH2 group is shifted along the axis
+ # 0.4431163 = DeltaYc/2 = lateral displacement of carbons along axis
+
+ # ---- Now, modify the ends: ---
+ # Delete the CH2 groups at the beginning and end, and replace them with CH3.
+ # (Note: Alternately, instead of deleting the CH2 groups at each end, you
+ # could modify them by adding an extra hydrogen atom to those carbons.)
+
+ delete monomers[0]
+ delete monomers[15]
+ monomer_begin = new CH3
+ monomer_end = new CH3
+
+ # Move the CH3 groups to the correct location at either end of the chain:
+
+ monomer_begin.move(0,0.4431163,0)
+ monomer_end.move(0,0.4431163,0).rot(180,0,0,1).move(18.7998345,0,0)
+
+ # Note: 18.7998345 = (16-1) * DeltaXc
+
+
+ # Now add a list of bonds connecting the carbon atoms together:
+
+ write('Data Bond List') {
+ $bond:b1 $atom:monomer_begin/C $atom:monomers[1]/C
+ $bond:b2 $atom:monomers[1]/C $atom:monomers[2]/C
+ $bond:b3 $atom:monomers[2]/C $atom:monomers[3]/C
+ $bond:b4 $atom:monomers[3]/C $atom:monomers[4]/C
+ $bond:b5 $atom:monomers[4]/C $atom:monomers[5]/C
+ $bond:b6 $atom:monomers[5]/C $atom:monomers[6]/C
+ $bond:b7 $atom:monomers[6]/C $atom:monomers[7]/C
+ $bond:b8 $atom:monomers[7]/C $atom:monomers[8]/C
+ $bond:b9 $atom:monomers[8]/C $atom:monomers[9]/C
+ $bond:b10 $atom:monomers[9]/C $atom:monomers[10]/C
+ $bond:b11 $atom:monomers[10]/C $atom:monomers[11]/C
+ $bond:b12 $atom:monomers[11]/C $atom:monomers[12]/C
+ $bond:b13 $atom:monomers[12]/C $atom:monomers[13]/C
+ $bond:b14 $atom:monomers[13]/C $atom:monomers[14]/C
+ $bond:b15 $atom:monomers[14]/C $atom:monomer_end/C
+ }
+
+ create_var { $mol } # Define a molecule ID number for this polymer
+
+ # This causes monomer[0], monomer[1], ... to share the same molecule-ID.
+ # (because in the ch2group.lt file, the "..." in "$mol:..." looks for
+ # a counter of type "$mol" in a parent molecule or earlier ancestor.)
+
+} # Hexadecane
+
+
+
+
+
+
+
+
+
+
+######### (scratchwork calculations for the atomic coordinates) #########
+# Lcc = 1.5350 # length of the C-C bond (Sp3)
+# Lch = 1.0930 # length of the C-H bond
+# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
+# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
+# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
+# # 0.5*DeltaYc = 0.4431163316030377
+# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
+# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt
new file mode 100644
index 000000000..4e0cfaec6
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/moltemplate_files/system.lt
@@ -0,0 +1,18 @@
+import "hexadecane.lt" # <- defines the "Hexadecane" molecule type.
+
+# Periodic boundary conditions:
+write_once("Data Boundary") {
+ 0.0 62.4 xlo xhi
+ 0.0 62.4 ylo yhi
+ 0.0 62.4 zlo zhi
+}
+
+molecules = new Hexadecane [12].move(0, 0, 5.2)
+ [12].move(0, 5.2, 0)
+ [2].move(31.2, 0, 0)
+
+
+# NOTE: The spacing between molecules is large. There should be extra room to
+# move during the initial stages of equilibration. However, you will have to
+# run the simulation at NPT conditions later to compress the system to a
+# more realistic density.
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt
new file mode 100644
index 000000000..b1791c955
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.npt
@@ -0,0 +1,85 @@
+# PREREQUISITES:
+#
+# You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+
+# ------------------------------- Initialization Section --------------------
+
+include system.in.init
+
+# ------------------------------- Atom Definition Section -------------------
+
+read_data system.data
+
+# ------------------------------- Settings Section --------------------------
+
+include system.in.settings
+
+# ------------------------------- Run Section -------------------------------
+
+# To avvoid explosions, I have a 4-step equilibraion process (expand, minimize,
+# reorient, compress). The system (as defined in the "system.data" file)
+# is already expanded. That means there are 3 steps left:
+
+dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz
+thermo 50
+
+# -- Equilibration: part 1: initial minimization --
+
+# Note: In general, it's always a good idea to minimize the system at first.
+
+minimize 1.0e-5 1.0e-7 100000 400000
+undump dumpeq1
+
+write_data system_after_eq1_min.data
+
+# -- Equilibration part 2: reorienting the molecules (NVT) --
+
+timestep 1.0
+dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz
+
+# Run the system at high temperature (at constant volume) to reorient the
+# the molecules (which would otherwise be pointing in the same direction).
+
+# To speed it up, I randomize the atomic positions for a few thousand steps
+# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover).
+# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.)
+
+
+fix fxlan all langevin 900.0 900.0 120 48279
+fix fxnve all nve
+
+run 2000
+
+unfix fxlan
+unfix fxnve
+# Now continue the simulation at high temperature using fix nvt (Nose-Hoover).
+fix fxnvt all nvt temp 900.0 900.0 100.0
+
+run 5000
+undump dumpeq2
+
+
+write_data system_after_eq2_reorient.data
+
+unfix fxnvt
+
+# -- equilibration part 3: Equilibrating the density (NPT) --
+
+# Originally, the simulation box (in "system.data" and "system.lt") was
+# unrealistically large. The spacing between the molecules was large also.
+# I did this to enable the molecules to move freely and reorient themselves.
+# After doing that, we should run the simulation under NPT conditions to
+# allow the simulation box to contract to it's natural size. We do that here:
+# We begin the simulation at 100 barr (a relatively low pressure), and
+# slowly decrease it to 1 barr, maintianing the temperature at 300K.
+
+dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz
+fix fxnpt all npt temp 300.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0
+
+timestep 1.0
+run 30000
+
+write_data system_after_eq3_npt.data
+
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt
new file mode 100644
index 000000000..f8b2d31d0
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/hexadecane/run.in.nvt
@@ -0,0 +1,42 @@
+# PREREQUISITES:
+#
+# 1) You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+# 2) You must equilibrate the system beforehand using "run.in.npt".
+# This will create the file "system_after_npt.data" which this file reads.
+# (Note: I have not verified that this equilibration protocol works well.)
+
+# ------------------------------- Initialization Section --------------------
+
+include system.in.init
+
+# ------------------------------- Atom Definition Section -------------------
+
+
+# Read the coordinates generated by an earlier NPT simulation
+
+read_data system_after_eq3_npt.data
+
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also. I prefer "write_data" and "read_data".)
+
+
+# ------------------------------- Settings Section --------------------------
+
+include system.in.settings
+
+# ------------------------------- Run Section -------------------------------
+
+# -- simulation protocol --
+
+
+timestep 1.0
+dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
+fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1
+thermo 100
+#thermo_modify flush yes
+
+run 50000
+
+write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
index 3b867ae8a..3c7e07165 100755
--- a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/README_setup.sh
@@ -1,89 +1,116 @@
# -------- REQUIREMENTS: ---------
# You must define your MOLTEMPLATE_PATH environment variable
# and set it to the "common" subdirectory of your moltemplate distribution.
# (See the "Installation" section in the moltemplate manual.)
# Create LAMMPS input files this way:
cd moltemplate_files
# run moltemplate
moltemplate.sh system.lt
# This will generate various files with names ending in *.in* and *.data.
+
+ # FIX THE PAIR STYLES
+ # (Sorry, this is messy)
+ #
+ # I was forced to change the default pair-style for AMBER-force-fields (GAFF)
+ # from lj/charmm/coul/long to lj/charmm/coul/charmm. (This is because
+ # LAMMPS crashes when using lj/charmm/coul/long on a system without any
+ # charged particles, and users were complaining it was moltemplate's fault.
+ # I wish LAMMPS would not do this.)
+ #
+ # Unfortunately, this means that the "Isobutane" molecule (which uses
+ # AMBER's GAFF), and the "TIP3P_2004" molecule now use different pair styles.
+ #
+ # The cleanest way to fix this is to force the two molecules to use
+ # the same pair style.
+ # (Using a hybrid pair_style is not practical because that disables mixing
+ # rules. This would force us to add a huge list of pair_coeff commands to
+ # explain how TIP3P_2004 atoms interact with all of the various GAFF atoms.)
+
+ # Add a line to systems.in.init to override the pair_style.
+ # Change the pair_style to "lj/charmm/coul/long 10.0 10.5 10.5".
+
+ echo "pair_style hybrid lj/charmm/coul/long 10.0 10.5 10.5" >> system.in.init
+
+ # Then use "sed" to replace "lj/charmm/coul/charmm" with "lj/charmm/coul/long"
+ sed -i 's/lj\/charmm\/coul\/charmm/lj\/charmm\/coul\/long/g' system.in.settings
+
# These files are the input files directly read by LAMMPS. Move them to
# the parent directory (or wherever you plan to run the simulation).
#cp -f system.data system.in* ../
# --------- OPTIONAL STEPS FOR STRIPPING OUT JUNK ---------
# --------- edit 2013-8-28 ---------
echo "-----------------------------------------------------------------" >&2
echo "OPTIONAL STEP: PRUNING THE RESULTING MOLTEMPLATE OUTPUT TO" >&2
echo " INCLUDE ONLY ATOMS AND TYPES WE ARE ACTUALLY USING." >&2
# Unfortunately, as of 2013-8-28, these files contain a lot of irrelevant
# information (for atom types not present in the current system).
# For now, we can strip this out using ltemplify.py to build a new .lt file.
# THIS IS AN UGLY WORKAROUND. HOPEFULLY IN THE FUTURE, WE CAN SKIP THESE STEPS
# do this in a temporary_directory
mkdir new_lt_file
cd new_lt_file/
# now run ltemplify.py
ltemplify.py ../system.in.init ../system.in.settings ../system.data > system.lt
rm -rf ../system.data ../system.in* # these old lammps files no longer needed
# This creates a new .LT file named "system.lt" in the local directory.
# Unfortunately, it may be missing some information because ltemplify.py
# does not understand all the commands present in a LAMMPS input script.
# If you define groups or use constraints, you must define them again. In this
# case, we must add the SHAKE constraint for the "TIP3P_2004" water molecule.
# So we have to remember the original name of the bond types and angle types.
# (For this example, SHAKE is applied to the water molecule, which is defined
# in "tip3p_2004.lt" file in the "common/" directory. Check this file.)
ATOMTYPENUM_ow=`awk '{if ($1 == "@/atom:TIP3P_2004/ow") print $2}' < ../output_ttree/ttree_assignments.txt`
ATOMTYPENUM_hw=`awk '{if ($1 == "@/atom:TIP3P_2004/hw") print $2}' < ../output_ttree/ttree_assignments.txt`
BONDTYPENUM=`awk '{if ($1 == "@/bond:TIP3P_2004/OH") print $2}' < ../output_ttree/ttree_assignments.txt`
ANGLETYPENUM=`awk '{if ($1 == "@/angle:TIP3P_2004/HOH") print $2}' < ../output_ttree/ttree_assignments.txt`
echo "" >> system.lt
echo "write_once(\"In Settings\") {" >> system.lt
echo " group tip3p type @atom:type$ATOMTYPENUM_ow @atom:type$ATOMTYPENUM_hw" >> system.lt
echo " fix fShakeTIP3P tip3p shake 0.0001 10 100 b @bond:type$BONDTYPENUM a @angle:type$ANGLETYPENUM" >> system.lt
echo "}" >> system.lt
echo "" >> system.lt
# The ltemplify.py script also does not copy the boundary dimensions.
# We must do this manually as well.
echo "write_once(\"Data Boundary\") {" >> system.lt
cat "../output_ttree/Data Boundary" >> system.lt
echo "}" >> system.lt
echo "" >> system.lt
# Now, run moltemplate on this new .LT file.
moltemplate.sh system.lt
# This will create: "system.data" "system.in.init" "system.in.settings."
# move the final DATA and INput scripts to the desired location,
mv -f system.data system.in* ../../
# and clean up the mess
rm -rf output_ttree/
cd ..
rm -rf new_lt_file/
echo "---------------- DONE PRUNING MOLTEMPLATE OUTPUT ----------------" >&2
echo "-----------------------------------------------------------------" >&2
# --------- END OF OPTIONAL STEPS FOR STRIPPING OUT JUNK ---------
# Optional:
# The "./output_ttree/" directory is full of temporary files generated by
# moltemplate. They can be useful for debugging, but are usually thrown away.
rm -rf output_ttree/
cd ../
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt
index c6b5584b7..50c539250 100644
--- a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/moltemplate_files/system.lt
@@ -1,31 +1,32 @@
import "tip3p_2004.lt"
# <- This defines the TIP3P water molecule. This file is
# located in the "common" directory. You can either copy it
# here, or (preferably), you can define a MOLTEMPLATE_PATH
# environment variable and point it to "common".
# (as explained in the installation section of the manual).
import "isobutane.lt" # <- defines the "Isobutane" molecule type.
# Periodic boundary conditions:
write_once("Data Boundary") {
0.0 41.50 xlo xhi
0.0 41.50 ylo yhi
0.0 41.50 zlo zhi
}
# The next command generates a (rather dense) cubic lattice with
# spacing 3.45 Angstroms. (The pressure must be equilibrated later.)
wat = new TIP3P_2004 [12].move(0.00, 0.00, 3.45)
[12].move(0.00, 3.45, 0.00)
[12].move(3.45, 0.00, 0.00)
isobutane = new Isobutane [4].move(0, 0, 10.35)
[4].move(0, 10.35, 0)
[4].move(10.35, 0, 0)
# move the isobutane molecules slightly to reduce overlap with the water
isobutane[*][*][*].move(1.725, 1.725, 1.725)
+
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt
index 652f13673..03127c1d6 100644
--- a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.npt
@@ -1,37 +1,43 @@
+# PREREQUISITES:
+#
+# You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
read_data system.data
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
# -- minimization protocol --
# Note: The minimization step is not necessary in this example. However
# in general, it's always a good idea to minimize the system beforehand.
# fShakeTIP3P was defined in system.in.settings. It is incompatible with "minimize".
unfix fShakeTIP3P
-minimize 1.0e-5 1.0e-7 100000 400000
+minimize 1.0e-4 1.0e-6 100000 400000
# Now read "system.in.settings" in order to redefine fShakeTIP3P again:
include system.in.settings
# -- simulation protocol --
timestep 1.0
dump 1 all custom 500 traj_npt.lammpstrj id mol type x y z ix iy iz
fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-thermo 500
+thermo 100
#thermo_modify flush yes
-run 50000
+run 2000
-write_restart system_after_npt.rst
+write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt
index 6cd2a0e16..24dd41da3 100644
--- a/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt
+++ b/tools/moltemplate/examples/all_atom_examples/AMBER_force_field_examples/waterTIP3P+isobutane/run.in.nvt
@@ -1,53 +1,51 @@
+# PREREQUISITES:
+#
+# 1) You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+# 2) You must equilibrate the system beforehand using "run.in.npt".
+# This will create the file "system_after_npt.data" which this file reads.
+# (Note: I have not verified that this equilibration protocol works well.)
+
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
-# Normally, I would minimize the system and equilibrate the system at constant
-# pressure and temperature beforehand. If you run lammps with "run.in.npt",
-# it will generate a restart file "system_after_npt.rst" with reasonable
-# coordinates at that temperature and pressure. Then we could load it now:
-#
-#read_restart system_after_npt.rst
-#
-# Unfortunately the LAMMPS "read_restart" command has been undependable over
-# the past year (2012), and I feel it is safer to remove it from the examples.
-# Instead, for this example, I just read the raw coordinates generated by
-# moltemplate (and the default volume). (I get fewer questions this way.)
-# However you should never run any liquid simulations at constant volume without
-# pressure equilibration first. Hopefully in the future "read_restart" will
-# work. Until then, try "read_dump", "dump2data.py", or "restart2data".
+# Read the coordinates generated by an earlier NPT simulation
+
+read_data system_after_npt.data
-read_data system.data
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also. I prefer "write_data" and "read_data".)
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
-
+# COMMENTING OUT MINIMIZATION STEPS:
+# If you are reading the coordinates generated by the NPT run
+# then you should not need to minimize the system beforehand.
# -- minimization protocol --
-# Note: If you are reading the restart file instead of the data file,
-# then you should not need to minimize the system beforehand..
-# fShakeTIP3P was defined in system.in.settings.
-# (It is incompatible with "minimize".)
-unfix fShakeTIP3P
-minimize 1.0e-5 1.0e-7 100000 400000
-# Now read "system.in.settings" in order to redefine fShakeTIP3P again:
-include system.in.settings
+## ("fix shake" is incompatible with "minimize".)
+#unfix fShakeTIP3P
+#minimize 1.0e-4 1.0e-6 100000 400000
+## Now read "system.in.settings" in order to redefine fShakeTIP3P again:
+#include system.in.settings
# -- simulation protocol --
timestep 1.0
dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
thermo 500
#thermo_modify flush yes
run 50000
-write_restart system_after_nvt.rst
+write_restart system_after_nvt.data
diff --git a/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt
new file mode 100644
index 000000000..5f53579d6
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt
@@ -0,0 +1,779 @@
+CNT {
+
+### LAMMPS commands for initialization
+### (These can be overridden later.)
+
+
+ write_once("In Init") {
+ units real
+ atom_style full
+ bond_style harmonic
+ angle_style charmm
+ dihedral_style charmm
+ pair_style lj/charmm/coul/charmm 8.0 10.0
+ pair_modify mix arithmetic
+ special_bonds charmm
+ }
+
+ write_once("In Settings") {
+ pair_coeff @atom:type1 @atom:type1 0.02 4.0
+ }
+
+### DATA sections
+
+
+ write_once("Data Masses") {
+ @atom:type1 10.0
+ }
+
+ write_once("Data Bond Coeffs") {
+ @bond:type1 2.0 1.4
+ }
+
+ write_once("Data Angle Coeffs") {
+ @angle:type1 0 120.0 0 2.0
+ }
+
+ write_once("Data Dihedral Coeffs") {
+ @dihedral:type1 0.0 2 180 1
+ }
+
+ write("Data Atoms") {
+ $atom:id1 $mol:id2 @atom:type1 0.000000 12.345 10.000 4.328
+ $atom:id2 $mol:id2 @atom:type1 0.000000 12.031 11.173 5.037
+ $atom:id3 $mol:id2 @atom:type1 0.000000 12.031 11.173 6.455
+ $atom:id4 $mol:id2 @atom:type1 0.000000 11.173 12.031 7.164
+ $atom:id5 $mol:id2 @atom:type1 0.000000 11.173 12.031 4.328
+ $atom:id6 $mol:id2 @atom:type1 0.000000 10.000 12.345 5.037
+ $atom:id7 $mol:id2 @atom:type1 0.000000 10.000 12.345 6.455
+ $atom:id8 $mol:id2 @atom:type1 0.000000 8.827 12.031 7.164
+ $atom:id9 $mol:id2 @atom:type1 0.000000 8.827 12.031 4.328
+ $atom:id10 $mol:id2 @atom:type1 0.000000 7.969 11.173 5.037
+ $atom:id11 $mol:id2 @atom:type1 0.000000 7.969 11.173 6.455
+ $atom:id12 $mol:id2 @atom:type1 0.000000 7.655 10.000 7.164
+ $atom:id13 $mol:id2 @atom:type1 0.000000 7.655 10.000 4.328
+ $atom:id14 $mol:id2 @atom:type1 0.000000 7.969 8.827 5.037
+ $atom:id15 $mol:id2 @atom:type1 0.000000 7.969 8.827 6.455
+ $atom:id16 $mol:id2 @atom:type1 0.000000 8.827 7.969 7.164
+ $atom:id17 $mol:id2 @atom:type1 0.000000 8.827 7.969 4.328
+ $atom:id18 $mol:id2 @atom:type1 0.000000 10.000 7.655 5.037
+ $atom:id19 $mol:id2 @atom:type1 0.000000 10.000 7.655 6.455
+ $atom:id20 $mol:id2 @atom:type1 0.000000 11.173 7.969 7.164
+ $atom:id21 $mol:id2 @atom:type1 0.000000 11.173 7.969 4.328
+ $atom:id22 $mol:id2 @atom:type1 0.000000 12.031 8.827 5.037
+ $atom:id23 $mol:id2 @atom:type1 0.000000 12.031 8.827 6.455
+ $atom:id24 $mol:id2 @atom:type1 0.000000 12.345 10.000 7.164
+ $atom:id25 $mol:id2 @atom:type1 0.000000 12.345 10.000 8.582
+ $atom:id26 $mol:id2 @atom:type1 0.000000 12.031 11.173 9.291
+ $atom:id27 $mol:id2 @atom:type1 0.000000 12.031 11.173 10.709
+ $atom:id28 $mol:id2 @atom:type1 0.000000 11.173 12.031 11.418
+ $atom:id29 $mol:id2 @atom:type1 0.000000 11.173 12.031 8.582
+ $atom:id30 $mol:id2 @atom:type1 0.000000 10.000 12.345 9.291
+ $atom:id31 $mol:id2 @atom:type1 0.000000 10.000 12.345 10.709
+ $atom:id32 $mol:id2 @atom:type1 0.000000 8.827 12.031 11.418
+ $atom:id33 $mol:id2 @atom:type1 0.000000 8.827 12.031 8.582
+ $atom:id34 $mol:id2 @atom:type1 0.000000 7.969 11.173 9.291
+ $atom:id35 $mol:id2 @atom:type1 0.000000 7.969 11.173 10.709
+ $atom:id36 $mol:id2 @atom:type1 0.000000 7.655 10.000 11.418
+ $atom:id37 $mol:id2 @atom:type1 0.000000 7.655 10.000 8.582
+ $atom:id38 $mol:id2 @atom:type1 0.000000 7.969 8.827 9.291
+ $atom:id39 $mol:id2 @atom:type1 0.000000 7.969 8.827 10.709
+ $atom:id40 $mol:id2 @atom:type1 0.000000 8.827 7.969 11.418
+ $atom:id41 $mol:id2 @atom:type1 0.000000 8.827 7.969 8.582
+ $atom:id42 $mol:id2 @atom:type1 0.000000 10.000 7.655 9.291
+ $atom:id43 $mol:id2 @atom:type1 0.000000 10.000 7.655 10.709
+ $atom:id44 $mol:id2 @atom:type1 0.000000 11.173 7.969 11.418
+ $atom:id45 $mol:id2 @atom:type1 0.000000 11.173 7.969 8.582
+ $atom:id46 $mol:id2 @atom:type1 0.000000 12.031 8.827 9.291
+ $atom:id47 $mol:id2 @atom:type1 0.000000 12.031 8.827 10.709
+ $atom:id48 $mol:id2 @atom:type1 0.000000 12.345 10.000 11.418
+ $atom:id49 $mol:id2 @atom:type1 0.000000 12.345 10.000 12.836
+ $atom:id50 $mol:id2 @atom:type1 0.000000 12.031 11.173 13.545
+ $atom:id51 $mol:id2 @atom:type1 0.000000 12.031 11.173 14.963
+ $atom:id52 $mol:id2 @atom:type1 0.000000 11.173 12.031 15.672
+ $atom:id53 $mol:id2 @atom:type1 0.000000 11.173 12.031 12.836
+ $atom:id54 $mol:id2 @atom:type1 0.000000 10.000 12.345 13.545
+ $atom:id55 $mol:id2 @atom:type1 0.000000 10.000 12.345 14.963
+ $atom:id56 $mol:id2 @atom:type1 0.000000 8.827 12.031 15.672
+ $atom:id57 $mol:id2 @atom:type1 0.000000 8.827 12.031 12.836
+ $atom:id58 $mol:id2 @atom:type1 0.000000 7.969 11.173 13.545
+ $atom:id59 $mol:id2 @atom:type1 0.000000 7.969 11.173 14.963
+ $atom:id60 $mol:id2 @atom:type1 0.000000 7.655 10.000 15.672
+ $atom:id61 $mol:id2 @atom:type1 0.000000 7.655 10.000 12.836
+ $atom:id62 $mol:id2 @atom:type1 0.000000 7.969 8.827 13.545
+ $atom:id63 $mol:id2 @atom:type1 0.000000 7.969 8.827 14.963
+ $atom:id64 $mol:id2 @atom:type1 0.000000 8.827 7.969 15.672
+ $atom:id65 $mol:id2 @atom:type1 0.000000 8.827 7.969 12.836
+ $atom:id66 $mol:id2 @atom:type1 0.000000 10.000 7.655 13.545
+ $atom:id67 $mol:id2 @atom:type1 0.000000 10.000 7.655 14.963
+ $atom:id68 $mol:id2 @atom:type1 0.000000 11.173 7.969 15.672
+ $atom:id69 $mol:id2 @atom:type1 0.000000 11.173 7.969 12.836
+ $atom:id70 $mol:id2 @atom:type1 0.000000 12.031 8.827 13.545
+ $atom:id71 $mol:id2 @atom:type1 0.000000 12.031 8.827 14.963
+ $atom:id72 $mol:id2 @atom:type1 0.000000 12.345 10.000 15.672
+ }
+
+ write("Data Bonds") {
+ $bond:id1 @bond:type1 $atom:id1 $atom:id2
+ $bond:id2 @bond:type1 $atom:id1 $atom:id22
+ $bond:id3 @bond:type1 $atom:id2 $atom:id3
+ $bond:id4 @bond:type1 $atom:id2 $atom:id5
+ $bond:id5 @bond:type1 $atom:id3 $atom:id24
+ $bond:id6 @bond:type1 $atom:id3 $atom:id4
+ $bond:id7 @bond:type1 $atom:id4 $atom:id7
+ $bond:id8 @bond:type1 $atom:id4 $atom:id29
+ $bond:id9 @bond:type1 $atom:id5 $atom:id6
+ $bond:id10 @bond:type1 $atom:id6 $atom:id7
+ $bond:id11 @bond:type1 $atom:id6 $atom:id9
+ $bond:id12 @bond:type1 $atom:id7 $atom:id8
+ $bond:id13 @bond:type1 $atom:id8 $atom:id33
+ $bond:id14 @bond:type1 $atom:id8 $atom:id11
+ $bond:id15 @bond:type1 $atom:id9 $atom:id10
+ $bond:id16 @bond:type1 $atom:id10 $atom:id13
+ $bond:id17 @bond:type1 $atom:id10 $atom:id11
+ $bond:id18 @bond:type1 $atom:id11 $atom:id12
+ $bond:id19 @bond:type1 $atom:id12 $atom:id15
+ $bond:id20 @bond:type1 $atom:id12 $atom:id37
+ $bond:id21 @bond:type1 $atom:id13 $atom:id14
+ $bond:id22 @bond:type1 $atom:id14 $atom:id17
+ $bond:id23 @bond:type1 $atom:id14 $atom:id15
+ $bond:id24 @bond:type1 $atom:id15 $atom:id16
+ $bond:id25 @bond:type1 $atom:id16 $atom:id19
+ $bond:id26 @bond:type1 $atom:id16 $atom:id41
+ $bond:id27 @bond:type1 $atom:id17 $atom:id18
+ $bond:id28 @bond:type1 $atom:id18 $atom:id21
+ $bond:id29 @bond:type1 $atom:id18 $atom:id19
+ $bond:id30 @bond:type1 $atom:id19 $atom:id20
+ $bond:id31 @bond:type1 $atom:id20 $atom:id23
+ $bond:id32 @bond:type1 $atom:id20 $atom:id45
+ $bond:id33 @bond:type1 $atom:id21 $atom:id22
+ $bond:id34 @bond:type1 $atom:id22 $atom:id23
+ $bond:id35 @bond:type1 $atom:id23 $atom:id24
+ $bond:id36 @bond:type1 $atom:id24 $atom:id25
+ $bond:id37 @bond:type1 $atom:id25 $atom:id26
+ $bond:id38 @bond:type1 $atom:id25 $atom:id46
+ $bond:id39 @bond:type1 $atom:id26 $atom:id27
+ $bond:id40 @bond:type1 $atom:id26 $atom:id29
+ $bond:id41 @bond:type1 $atom:id27 $atom:id48
+ $bond:id42 @bond:type1 $atom:id27 $atom:id28
+ $bond:id43 @bond:type1 $atom:id28 $atom:id31
+ $bond:id44 @bond:type1 $atom:id28 $atom:id53
+ $bond:id45 @bond:type1 $atom:id29 $atom:id30
+ $bond:id46 @bond:type1 $atom:id30 $atom:id31
+ $bond:id47 @bond:type1 $atom:id30 $atom:id33
+ $bond:id48 @bond:type1 $atom:id31 $atom:id32
+ $bond:id49 @bond:type1 $atom:id32 $atom:id57
+ $bond:id50 @bond:type1 $atom:id32 $atom:id35
+ $bond:id51 @bond:type1 $atom:id33 $atom:id34
+ $bond:id52 @bond:type1 $atom:id34 $atom:id37
+ $bond:id53 @bond:type1 $atom:id34 $atom:id35
+ $bond:id54 @bond:type1 $atom:id35 $atom:id36
+ $bond:id55 @bond:type1 $atom:id36 $atom:id39
+ $bond:id56 @bond:type1 $atom:id36 $atom:id61
+ $bond:id57 @bond:type1 $atom:id37 $atom:id38
+ $bond:id58 @bond:type1 $atom:id38 $atom:id41
+ $bond:id59 @bond:type1 $atom:id38 $atom:id39
+ $bond:id60 @bond:type1 $atom:id39 $atom:id40
+ $bond:id61 @bond:type1 $atom:id40 $atom:id43
+ $bond:id62 @bond:type1 $atom:id40 $atom:id65
+ $bond:id63 @bond:type1 $atom:id41 $atom:id42
+ $bond:id64 @bond:type1 $atom:id42 $atom:id45
+ $bond:id65 @bond:type1 $atom:id42 $atom:id43
+ $bond:id66 @bond:type1 $atom:id43 $atom:id44
+ $bond:id67 @bond:type1 $atom:id44 $atom:id47
+ $bond:id68 @bond:type1 $atom:id44 $atom:id69
+ $bond:id69 @bond:type1 $atom:id45 $atom:id46
+ $bond:id70 @bond:type1 $atom:id46 $atom:id47
+ $bond:id71 @bond:type1 $atom:id47 $atom:id48
+ $bond:id72 @bond:type1 $atom:id48 $atom:id49
+ $bond:id73 @bond:type1 $atom:id49 $atom:id50
+ $bond:id74 @bond:type1 $atom:id49 $atom:id70
+ $bond:id75 @bond:type1 $atom:id50 $atom:id51
+ $bond:id76 @bond:type1 $atom:id50 $atom:id53
+ $bond:id77 @bond:type1 $atom:id51 $atom:id72
+ $bond:id78 @bond:type1 $atom:id51 $atom:id52
+ $bond:id79 @bond:type1 $atom:id52 $atom:id55
+ $bond:id80 @bond:type1 $atom:id53 $atom:id54
+ $bond:id81 @bond:type1 $atom:id54 $atom:id55
+ $bond:id82 @bond:type1 $atom:id54 $atom:id57
+ $bond:id83 @bond:type1 $atom:id55 $atom:id56
+ $bond:id84 @bond:type1 $atom:id56 $atom:id59
+ $bond:id85 @bond:type1 $atom:id57 $atom:id58
+ $bond:id86 @bond:type1 $atom:id58 $atom:id61
+ $bond:id87 @bond:type1 $atom:id58 $atom:id59
+ $bond:id88 @bond:type1 $atom:id59 $atom:id60
+ $bond:id89 @bond:type1 $atom:id60 $atom:id63
+ $bond:id90 @bond:type1 $atom:id61 $atom:id62
+ $bond:id91 @bond:type1 $atom:id62 $atom:id65
+ $bond:id92 @bond:type1 $atom:id62 $atom:id63
+ $bond:id93 @bond:type1 $atom:id63 $atom:id64
+ $bond:id94 @bond:type1 $atom:id64 $atom:id67
+ $bond:id95 @bond:type1 $atom:id65 $atom:id66
+ $bond:id96 @bond:type1 $atom:id66 $atom:id69
+ $bond:id97 @bond:type1 $atom:id66 $atom:id67
+ $bond:id98 @bond:type1 $atom:id67 $atom:id68
+ $bond:id99 @bond:type1 $atom:id68 $atom:id71
+ $bond:id100 @bond:type1 $atom:id69 $atom:id70
+ $bond:id101 @bond:type1 $atom:id70 $atom:id71
+ $bond:id102 @bond:type1 $atom:id71 $atom:id72
+ }
+
+ write("Data Angles") {
+ $angle:id1 @angle:type1 $atom:id2 $atom:id1 $atom:id22
+ $angle:id2 @angle:type1 $atom:id1 $atom:id2 $atom:id3
+ $angle:id3 @angle:type1 $atom:id1 $atom:id2 $atom:id5
+ $angle:id4 @angle:type1 $atom:id3 $atom:id2 $atom:id5
+ $angle:id5 @angle:type1 $atom:id2 $atom:id3 $atom:id24
+ $angle:id6 @angle:type1 $atom:id2 $atom:id3 $atom:id4
+ $angle:id7 @angle:type1 $atom:id4 $atom:id3 $atom:id24
+ $angle:id8 @angle:type1 $atom:id3 $atom:id4 $atom:id7
+ $angle:id9 @angle:type1 $atom:id3 $atom:id4 $atom:id29
+ $angle:id10 @angle:type1 $atom:id7 $atom:id4 $atom:id29
+ $angle:id11 @angle:type1 $atom:id2 $atom:id5 $atom:id6
+ $angle:id12 @angle:type1 $atom:id5 $atom:id6 $atom:id7
+ $angle:id13 @angle:type1 $atom:id5 $atom:id6 $atom:id9
+ $angle:id14 @angle:type1 $atom:id7 $atom:id6 $atom:id9
+ $angle:id15 @angle:type1 $atom:id4 $atom:id7 $atom:id6
+ $angle:id16 @angle:type1 $atom:id4 $atom:id7 $atom:id8
+ $angle:id17 @angle:type1 $atom:id6 $atom:id7 $atom:id8
+ $angle:id18 @angle:type1 $atom:id7 $atom:id8 $atom:id33
+ $angle:id19 @angle:type1 $atom:id7 $atom:id8 $atom:id11
+ $angle:id20 @angle:type1 $atom:id11 $atom:id8 $atom:id33
+ $angle:id21 @angle:type1 $atom:id6 $atom:id9 $atom:id10
+ $angle:id22 @angle:type1 $atom:id9 $atom:id10 $atom:id13
+ $angle:id23 @angle:type1 $atom:id9 $atom:id10 $atom:id11
+ $angle:id24 @angle:type1 $atom:id11 $atom:id10 $atom:id13
+ $angle:id25 @angle:type1 $atom:id8 $atom:id11 $atom:id10
+ $angle:id26 @angle:type1 $atom:id8 $atom:id11 $atom:id12
+ $angle:id27 @angle:type1 $atom:id10 $atom:id11 $atom:id12
+ $angle:id28 @angle:type1 $atom:id11 $atom:id12 $atom:id15
+ $angle:id29 @angle:type1 $atom:id11 $atom:id12 $atom:id37
+ $angle:id30 @angle:type1 $atom:id15 $atom:id12 $atom:id37
+ $angle:id31 @angle:type1 $atom:id10 $atom:id13 $atom:id14
+ $angle:id32 @angle:type1 $atom:id13 $atom:id14 $atom:id17
+ $angle:id33 @angle:type1 $atom:id13 $atom:id14 $atom:id15
+ $angle:id34 @angle:type1 $atom:id15 $atom:id14 $atom:id17
+ $angle:id35 @angle:type1 $atom:id12 $atom:id15 $atom:id14
+ $angle:id36 @angle:type1 $atom:id12 $atom:id15 $atom:id16
+ $angle:id37 @angle:type1 $atom:id14 $atom:id15 $atom:id16
+ $angle:id38 @angle:type1 $atom:id15 $atom:id16 $atom:id19
+ $angle:id39 @angle:type1 $atom:id15 $atom:id16 $atom:id41
+ $angle:id40 @angle:type1 $atom:id19 $atom:id16 $atom:id41
+ $angle:id41 @angle:type1 $atom:id14 $atom:id17 $atom:id18
+ $angle:id42 @angle:type1 $atom:id17 $atom:id18 $atom:id21
+ $angle:id43 @angle:type1 $atom:id17 $atom:id18 $atom:id19
+ $angle:id44 @angle:type1 $atom:id19 $atom:id18 $atom:id21
+ $angle:id45 @angle:type1 $atom:id16 $atom:id19 $atom:id18
+ $angle:id46 @angle:type1 $atom:id16 $atom:id19 $atom:id20
+ $angle:id47 @angle:type1 $atom:id18 $atom:id19 $atom:id20
+ $angle:id48 @angle:type1 $atom:id19 $atom:id20 $atom:id23
+ $angle:id49 @angle:type1 $atom:id19 $atom:id20 $atom:id45
+ $angle:id50 @angle:type1 $atom:id23 $atom:id20 $atom:id45
+ $angle:id51 @angle:type1 $atom:id18 $atom:id21 $atom:id22
+ $angle:id52 @angle:type1 $atom:id1 $atom:id22 $atom:id21
+ $angle:id53 @angle:type1 $atom:id1 $atom:id22 $atom:id23
+ $angle:id54 @angle:type1 $atom:id21 $atom:id22 $atom:id23
+ $angle:id55 @angle:type1 $atom:id20 $atom:id23 $atom:id22
+ $angle:id56 @angle:type1 $atom:id20 $atom:id23 $atom:id24
+ $angle:id57 @angle:type1 $atom:id22 $atom:id23 $atom:id24
+ $angle:id58 @angle:type1 $atom:id3 $atom:id24 $atom:id23
+ $angle:id59 @angle:type1 $atom:id3 $atom:id24 $atom:id25
+ $angle:id60 @angle:type1 $atom:id23 $atom:id24 $atom:id25
+ $angle:id61 @angle:type1 $atom:id24 $atom:id25 $atom:id26
+ $angle:id62 @angle:type1 $atom:id24 $atom:id25 $atom:id46
+ $angle:id63 @angle:type1 $atom:id26 $atom:id25 $atom:id46
+ $angle:id64 @angle:type1 $atom:id25 $atom:id26 $atom:id27
+ $angle:id65 @angle:type1 $atom:id25 $atom:id26 $atom:id29
+ $angle:id66 @angle:type1 $atom:id27 $atom:id26 $atom:id29
+ $angle:id67 @angle:type1 $atom:id26 $atom:id27 $atom:id48
+ $angle:id68 @angle:type1 $atom:id26 $atom:id27 $atom:id28
+ $angle:id69 @angle:type1 $atom:id28 $atom:id27 $atom:id48
+ $angle:id70 @angle:type1 $atom:id27 $atom:id28 $atom:id31
+ $angle:id71 @angle:type1 $atom:id27 $atom:id28 $atom:id53
+ $angle:id72 @angle:type1 $atom:id31 $atom:id28 $atom:id53
+ $angle:id73 @angle:type1 $atom:id4 $atom:id29 $atom:id26
+ $angle:id74 @angle:type1 $atom:id4 $atom:id29 $atom:id30
+ $angle:id75 @angle:type1 $atom:id26 $atom:id29 $atom:id30
+ $angle:id76 @angle:type1 $atom:id29 $atom:id30 $atom:id31
+ $angle:id77 @angle:type1 $atom:id29 $atom:id30 $atom:id33
+ $angle:id78 @angle:type1 $atom:id31 $atom:id30 $atom:id33
+ $angle:id79 @angle:type1 $atom:id28 $atom:id31 $atom:id30
+ $angle:id80 @angle:type1 $atom:id28 $atom:id31 $atom:id32
+ $angle:id81 @angle:type1 $atom:id30 $atom:id31 $atom:id32
+ $angle:id82 @angle:type1 $atom:id31 $atom:id32 $atom:id57
+ $angle:id83 @angle:type1 $atom:id31 $atom:id32 $atom:id35
+ $angle:id84 @angle:type1 $atom:id35 $atom:id32 $atom:id57
+ $angle:id85 @angle:type1 $atom:id8 $atom:id33 $atom:id30
+ $angle:id86 @angle:type1 $atom:id8 $atom:id33 $atom:id34
+ $angle:id87 @angle:type1 $atom:id30 $atom:id33 $atom:id34
+ $angle:id88 @angle:type1 $atom:id33 $atom:id34 $atom:id37
+ $angle:id89 @angle:type1 $atom:id33 $atom:id34 $atom:id35
+ $angle:id90 @angle:type1 $atom:id35 $atom:id34 $atom:id37
+ $angle:id91 @angle:type1 $atom:id32 $atom:id35 $atom:id34
+ $angle:id92 @angle:type1 $atom:id32 $atom:id35 $atom:id36
+ $angle:id93 @angle:type1 $atom:id34 $atom:id35 $atom:id36
+ $angle:id94 @angle:type1 $atom:id35 $atom:id36 $atom:id39
+ $angle:id95 @angle:type1 $atom:id35 $atom:id36 $atom:id61
+ $angle:id96 @angle:type1 $atom:id39 $atom:id36 $atom:id61
+ $angle:id97 @angle:type1 $atom:id12 $atom:id37 $atom:id34
+ $angle:id98 @angle:type1 $atom:id12 $atom:id37 $atom:id38
+ $angle:id99 @angle:type1 $atom:id34 $atom:id37 $atom:id38
+ $angle:id100 @angle:type1 $atom:id37 $atom:id38 $atom:id41
+ $angle:id101 @angle:type1 $atom:id37 $atom:id38 $atom:id39
+ $angle:id102 @angle:type1 $atom:id39 $atom:id38 $atom:id41
+ $angle:id103 @angle:type1 $atom:id36 $atom:id39 $atom:id38
+ $angle:id104 @angle:type1 $atom:id36 $atom:id39 $atom:id40
+ $angle:id105 @angle:type1 $atom:id38 $atom:id39 $atom:id40
+ $angle:id106 @angle:type1 $atom:id39 $atom:id40 $atom:id43
+ $angle:id107 @angle:type1 $atom:id39 $atom:id40 $atom:id65
+ $angle:id108 @angle:type1 $atom:id43 $atom:id40 $atom:id65
+ $angle:id109 @angle:type1 $atom:id16 $atom:id41 $atom:id38
+ $angle:id110 @angle:type1 $atom:id16 $atom:id41 $atom:id42
+ $angle:id111 @angle:type1 $atom:id38 $atom:id41 $atom:id42
+ $angle:id112 @angle:type1 $atom:id41 $atom:id42 $atom:id45
+ $angle:id113 @angle:type1 $atom:id41 $atom:id42 $atom:id43
+ $angle:id114 @angle:type1 $atom:id43 $atom:id42 $atom:id45
+ $angle:id115 @angle:type1 $atom:id40 $atom:id43 $atom:id42
+ $angle:id116 @angle:type1 $atom:id40 $atom:id43 $atom:id44
+ $angle:id117 @angle:type1 $atom:id42 $atom:id43 $atom:id44
+ $angle:id118 @angle:type1 $atom:id43 $atom:id44 $atom:id47
+ $angle:id119 @angle:type1 $atom:id43 $atom:id44 $atom:id69
+ $angle:id120 @angle:type1 $atom:id47 $atom:id44 $atom:id69
+ $angle:id121 @angle:type1 $atom:id20 $atom:id45 $atom:id42
+ $angle:id122 @angle:type1 $atom:id20 $atom:id45 $atom:id46
+ $angle:id123 @angle:type1 $atom:id42 $atom:id45 $atom:id46
+ $angle:id124 @angle:type1 $atom:id25 $atom:id46 $atom:id45
+ $angle:id125 @angle:type1 $atom:id25 $atom:id46 $atom:id47
+ $angle:id126 @angle:type1 $atom:id45 $atom:id46 $atom:id47
+ $angle:id127 @angle:type1 $atom:id44 $atom:id47 $atom:id46
+ $angle:id128 @angle:type1 $atom:id44 $atom:id47 $atom:id48
+ $angle:id129 @angle:type1 $atom:id46 $atom:id47 $atom:id48
+ $angle:id130 @angle:type1 $atom:id27 $atom:id48 $atom:id47
+ $angle:id131 @angle:type1 $atom:id27 $atom:id48 $atom:id49
+ $angle:id132 @angle:type1 $atom:id47 $atom:id48 $atom:id49
+ $angle:id133 @angle:type1 $atom:id48 $atom:id49 $atom:id50
+ $angle:id134 @angle:type1 $atom:id48 $atom:id49 $atom:id70
+ $angle:id135 @angle:type1 $atom:id50 $atom:id49 $atom:id70
+ $angle:id136 @angle:type1 $atom:id49 $atom:id50 $atom:id51
+ $angle:id137 @angle:type1 $atom:id49 $atom:id50 $atom:id53
+ $angle:id138 @angle:type1 $atom:id51 $atom:id50 $atom:id53
+ $angle:id139 @angle:type1 $atom:id50 $atom:id51 $atom:id72
+ $angle:id140 @angle:type1 $atom:id50 $atom:id51 $atom:id52
+ $angle:id141 @angle:type1 $atom:id52 $atom:id51 $atom:id72
+ $angle:id142 @angle:type1 $atom:id51 $atom:id52 $atom:id55
+ $angle:id143 @angle:type1 $atom:id28 $atom:id53 $atom:id50
+ $angle:id144 @angle:type1 $atom:id28 $atom:id53 $atom:id54
+ $angle:id145 @angle:type1 $atom:id50 $atom:id53 $atom:id54
+ $angle:id146 @angle:type1 $atom:id53 $atom:id54 $atom:id55
+ $angle:id147 @angle:type1 $atom:id53 $atom:id54 $atom:id57
+ $angle:id148 @angle:type1 $atom:id55 $atom:id54 $atom:id57
+ $angle:id149 @angle:type1 $atom:id52 $atom:id55 $atom:id54
+ $angle:id150 @angle:type1 $atom:id52 $atom:id55 $atom:id56
+ $angle:id151 @angle:type1 $atom:id54 $atom:id55 $atom:id56
+ $angle:id152 @angle:type1 $atom:id55 $atom:id56 $atom:id59
+ $angle:id153 @angle:type1 $atom:id32 $atom:id57 $atom:id54
+ $angle:id154 @angle:type1 $atom:id32 $atom:id57 $atom:id58
+ $angle:id155 @angle:type1 $atom:id54 $atom:id57 $atom:id58
+ $angle:id156 @angle:type1 $atom:id57 $atom:id58 $atom:id61
+ $angle:id157 @angle:type1 $atom:id57 $atom:id58 $atom:id59
+ $angle:id158 @angle:type1 $atom:id59 $atom:id58 $atom:id61
+ $angle:id159 @angle:type1 $atom:id56 $atom:id59 $atom:id58
+ $angle:id160 @angle:type1 $atom:id56 $atom:id59 $atom:id60
+ $angle:id161 @angle:type1 $atom:id58 $atom:id59 $atom:id60
+ $angle:id162 @angle:type1 $atom:id59 $atom:id60 $atom:id63
+ $angle:id163 @angle:type1 $atom:id36 $atom:id61 $atom:id58
+ $angle:id164 @angle:type1 $atom:id36 $atom:id61 $atom:id62
+ $angle:id165 @angle:type1 $atom:id58 $atom:id61 $atom:id62
+ $angle:id166 @angle:type1 $atom:id61 $atom:id62 $atom:id65
+ $angle:id167 @angle:type1 $atom:id61 $atom:id62 $atom:id63
+ $angle:id168 @angle:type1 $atom:id63 $atom:id62 $atom:id65
+ $angle:id169 @angle:type1 $atom:id60 $atom:id63 $atom:id62
+ $angle:id170 @angle:type1 $atom:id60 $atom:id63 $atom:id64
+ $angle:id171 @angle:type1 $atom:id62 $atom:id63 $atom:id64
+ $angle:id172 @angle:type1 $atom:id63 $atom:id64 $atom:id67
+ $angle:id173 @angle:type1 $atom:id40 $atom:id65 $atom:id62
+ $angle:id174 @angle:type1 $atom:id40 $atom:id65 $atom:id66
+ $angle:id175 @angle:type1 $atom:id62 $atom:id65 $atom:id66
+ $angle:id176 @angle:type1 $atom:id65 $atom:id66 $atom:id69
+ $angle:id177 @angle:type1 $atom:id65 $atom:id66 $atom:id67
+ $angle:id178 @angle:type1 $atom:id67 $atom:id66 $atom:id69
+ $angle:id179 @angle:type1 $atom:id64 $atom:id67 $atom:id66
+ $angle:id180 @angle:type1 $atom:id64 $atom:id67 $atom:id68
+ $angle:id181 @angle:type1 $atom:id66 $atom:id67 $atom:id68
+ $angle:id182 @angle:type1 $atom:id67 $atom:id68 $atom:id71
+ $angle:id183 @angle:type1 $atom:id44 $atom:id69 $atom:id66
+ $angle:id184 @angle:type1 $atom:id44 $atom:id69 $atom:id70
+ $angle:id185 @angle:type1 $atom:id66 $atom:id69 $atom:id70
+ $angle:id186 @angle:type1 $atom:id49 $atom:id70 $atom:id69
+ $angle:id187 @angle:type1 $atom:id49 $atom:id70 $atom:id71
+ $angle:id188 @angle:type1 $atom:id69 $atom:id70 $atom:id71
+ $angle:id189 @angle:type1 $atom:id68 $atom:id71 $atom:id70
+ $angle:id190 @angle:type1 $atom:id68 $atom:id71 $atom:id72
+ $angle:id191 @angle:type1 $atom:id70 $atom:id71 $atom:id72
+ $angle:id192 @angle:type1 $atom:id51 $atom:id72 $atom:id71
+ }
+
+ write("Data Dihedrals") {
+ $dihedral:id1 @dihedral:type1 $atom:id22 $atom:id1 $atom:id2 $atom:id3
+ $dihedral:id2 @dihedral:type1 $atom:id22 $atom:id1 $atom:id2 $atom:id5
+ $dihedral:id3 @dihedral:type1 $atom:id2 $atom:id1 $atom:id22 $atom:id21
+ $dihedral:id4 @dihedral:type1 $atom:id2 $atom:id1 $atom:id22 $atom:id23
+ $dihedral:id5 @dihedral:type1 $atom:id1 $atom:id2 $atom:id3 $atom:id24
+ $dihedral:id6 @dihedral:type1 $atom:id1 $atom:id2 $atom:id3 $atom:id4
+ $dihedral:id7 @dihedral:type1 $atom:id5 $atom:id2 $atom:id3 $atom:id24
+ $dihedral:id8 @dihedral:type1 $atom:id5 $atom:id2 $atom:id3 $atom:id4
+ $dihedral:id9 @dihedral:type1 $atom:id1 $atom:id2 $atom:id5 $atom:id6
+ $dihedral:id10 @dihedral:type1 $atom:id3 $atom:id2 $atom:id5 $atom:id6
+ $dihedral:id11 @dihedral:type1 $atom:id2 $atom:id3 $atom:id24 $atom:id23
+ $dihedral:id12 @dihedral:type1 $atom:id2 $atom:id3 $atom:id24 $atom:id25
+ $dihedral:id13 @dihedral:type1 $atom:id4 $atom:id3 $atom:id24 $atom:id23
+ $dihedral:id14 @dihedral:type1 $atom:id4 $atom:id3 $atom:id24 $atom:id25
+ $dihedral:id15 @dihedral:type1 $atom:id2 $atom:id3 $atom:id4 $atom:id7
+ $dihedral:id16 @dihedral:type1 $atom:id2 $atom:id3 $atom:id4 $atom:id29
+ $dihedral:id17 @dihedral:type1 $atom:id24 $atom:id3 $atom:id4 $atom:id7
+ $dihedral:id18 @dihedral:type1 $atom:id24 $atom:id3 $atom:id4 $atom:id29
+ $dihedral:id19 @dihedral:type1 $atom:id3 $atom:id4 $atom:id7 $atom:id6
+ $dihedral:id20 @dihedral:type1 $atom:id3 $atom:id4 $atom:id7 $atom:id8
+ $dihedral:id21 @dihedral:type1 $atom:id29 $atom:id4 $atom:id7 $atom:id6
+ $dihedral:id22 @dihedral:type1 $atom:id29 $atom:id4 $atom:id7 $atom:id8
+ $dihedral:id23 @dihedral:type1 $atom:id3 $atom:id4 $atom:id29 $atom:id26
+ $dihedral:id24 @dihedral:type1 $atom:id3 $atom:id4 $atom:id29 $atom:id30
+ $dihedral:id25 @dihedral:type1 $atom:id7 $atom:id4 $atom:id29 $atom:id26
+ $dihedral:id26 @dihedral:type1 $atom:id7 $atom:id4 $atom:id29 $atom:id30
+ $dihedral:id27 @dihedral:type1 $atom:id2 $atom:id5 $atom:id6 $atom:id7
+ $dihedral:id28 @dihedral:type1 $atom:id2 $atom:id5 $atom:id6 $atom:id9
+ $dihedral:id29 @dihedral:type1 $atom:id5 $atom:id6 $atom:id7 $atom:id4
+ $dihedral:id30 @dihedral:type1 $atom:id5 $atom:id6 $atom:id7 $atom:id8
+ $dihedral:id31 @dihedral:type1 $atom:id9 $atom:id6 $atom:id7 $atom:id4
+ $dihedral:id32 @dihedral:type1 $atom:id9 $atom:id6 $atom:id7 $atom:id8
+ $dihedral:id33 @dihedral:type1 $atom:id5 $atom:id6 $atom:id9 $atom:id10
+ $dihedral:id34 @dihedral:type1 $atom:id7 $atom:id6 $atom:id9 $atom:id10
+ $dihedral:id35 @dihedral:type1 $atom:id4 $atom:id7 $atom:id8 $atom:id33
+ $dihedral:id36 @dihedral:type1 $atom:id4 $atom:id7 $atom:id8 $atom:id11
+ $dihedral:id37 @dihedral:type1 $atom:id6 $atom:id7 $atom:id8 $atom:id33
+ $dihedral:id38 @dihedral:type1 $atom:id6 $atom:id7 $atom:id8 $atom:id11
+ $dihedral:id39 @dihedral:type1 $atom:id7 $atom:id8 $atom:id33 $atom:id30
+ $dihedral:id40 @dihedral:type1 $atom:id7 $atom:id8 $atom:id33 $atom:id34
+ $dihedral:id41 @dihedral:type1 $atom:id11 $atom:id8 $atom:id33 $atom:id30
+ $dihedral:id42 @dihedral:type1 $atom:id11 $atom:id8 $atom:id33 $atom:id34
+ $dihedral:id43 @dihedral:type1 $atom:id7 $atom:id8 $atom:id11 $atom:id10
+ $dihedral:id44 @dihedral:type1 $atom:id7 $atom:id8 $atom:id11 $atom:id12
+ $dihedral:id45 @dihedral:type1 $atom:id33 $atom:id8 $atom:id11 $atom:id10
+ $dihedral:id46 @dihedral:type1 $atom:id33 $atom:id8 $atom:id11 $atom:id12
+ $dihedral:id47 @dihedral:type1 $atom:id6 $atom:id9 $atom:id10 $atom:id13
+ $dihedral:id48 @dihedral:type1 $atom:id6 $atom:id9 $atom:id10 $atom:id11
+ $dihedral:id49 @dihedral:type1 $atom:id9 $atom:id10 $atom:id13 $atom:id14
+ $dihedral:id50 @dihedral:type1 $atom:id11 $atom:id10 $atom:id13 $atom:id14
+ $dihedral:id51 @dihedral:type1 $atom:id9 $atom:id10 $atom:id11 $atom:id8
+ $dihedral:id52 @dihedral:type1 $atom:id9 $atom:id10 $atom:id11 $atom:id12
+ $dihedral:id53 @dihedral:type1 $atom:id13 $atom:id10 $atom:id11 $atom:id8
+ $dihedral:id54 @dihedral:type1 $atom:id13 $atom:id10 $atom:id11 $atom:id12
+ $dihedral:id55 @dihedral:type1 $atom:id8 $atom:id11 $atom:id12 $atom:id15
+ $dihedral:id56 @dihedral:type1 $atom:id8 $atom:id11 $atom:id12 $atom:id37
+ $dihedral:id57 @dihedral:type1 $atom:id10 $atom:id11 $atom:id12 $atom:id15
+ $dihedral:id58 @dihedral:type1 $atom:id10 $atom:id11 $atom:id12 $atom:id37
+ $dihedral:id59 @dihedral:type1 $atom:id11 $atom:id12 $atom:id15 $atom:id14
+ $dihedral:id60 @dihedral:type1 $atom:id11 $atom:id12 $atom:id15 $atom:id16
+ $dihedral:id61 @dihedral:type1 $atom:id37 $atom:id12 $atom:id15 $atom:id14
+ $dihedral:id62 @dihedral:type1 $atom:id37 $atom:id12 $atom:id15 $atom:id16
+ $dihedral:id63 @dihedral:type1 $atom:id11 $atom:id12 $atom:id37 $atom:id34
+ $dihedral:id64 @dihedral:type1 $atom:id11 $atom:id12 $atom:id37 $atom:id38
+ $dihedral:id65 @dihedral:type1 $atom:id15 $atom:id12 $atom:id37 $atom:id34
+ $dihedral:id66 @dihedral:type1 $atom:id15 $atom:id12 $atom:id37 $atom:id38
+ $dihedral:id67 @dihedral:type1 $atom:id10 $atom:id13 $atom:id14 $atom:id17
+ $dihedral:id68 @dihedral:type1 $atom:id10 $atom:id13 $atom:id14 $atom:id15
+ $dihedral:id69 @dihedral:type1 $atom:id13 $atom:id14 $atom:id17 $atom:id18
+ $dihedral:id70 @dihedral:type1 $atom:id15 $atom:id14 $atom:id17 $atom:id18
+ $dihedral:id71 @dihedral:type1 $atom:id13 $atom:id14 $atom:id15 $atom:id12
+ $dihedral:id72 @dihedral:type1 $atom:id13 $atom:id14 $atom:id15 $atom:id16
+ $dihedral:id73 @dihedral:type1 $atom:id17 $atom:id14 $atom:id15 $atom:id12
+ $dihedral:id74 @dihedral:type1 $atom:id17 $atom:id14 $atom:id15 $atom:id16
+ $dihedral:id75 @dihedral:type1 $atom:id12 $atom:id15 $atom:id16 $atom:id19
+ $dihedral:id76 @dihedral:type1 $atom:id12 $atom:id15 $atom:id16 $atom:id41
+ $dihedral:id77 @dihedral:type1 $atom:id14 $atom:id15 $atom:id16 $atom:id19
+ $dihedral:id78 @dihedral:type1 $atom:id14 $atom:id15 $atom:id16 $atom:id41
+ $dihedral:id79 @dihedral:type1 $atom:id15 $atom:id16 $atom:id19 $atom:id18
+ $dihedral:id80 @dihedral:type1 $atom:id15 $atom:id16 $atom:id19 $atom:id20
+ $dihedral:id81 @dihedral:type1 $atom:id41 $atom:id16 $atom:id19 $atom:id18
+ $dihedral:id82 @dihedral:type1 $atom:id41 $atom:id16 $atom:id19 $atom:id20
+ $dihedral:id83 @dihedral:type1 $atom:id15 $atom:id16 $atom:id41 $atom:id38
+ $dihedral:id84 @dihedral:type1 $atom:id15 $atom:id16 $atom:id41 $atom:id42
+ $dihedral:id85 @dihedral:type1 $atom:id19 $atom:id16 $atom:id41 $atom:id38
+ $dihedral:id86 @dihedral:type1 $atom:id19 $atom:id16 $atom:id41 $atom:id42
+ $dihedral:id87 @dihedral:type1 $atom:id14 $atom:id17 $atom:id18 $atom:id21
+ $dihedral:id88 @dihedral:type1 $atom:id14 $atom:id17 $atom:id18 $atom:id19
+ $dihedral:id89 @dihedral:type1 $atom:id17 $atom:id18 $atom:id21 $atom:id22
+ $dihedral:id90 @dihedral:type1 $atom:id19 $atom:id18 $atom:id21 $atom:id22
+ $dihedral:id91 @dihedral:type1 $atom:id17 $atom:id18 $atom:id19 $atom:id16
+ $dihedral:id92 @dihedral:type1 $atom:id17 $atom:id18 $atom:id19 $atom:id20
+ $dihedral:id93 @dihedral:type1 $atom:id21 $atom:id18 $atom:id19 $atom:id16
+ $dihedral:id94 @dihedral:type1 $atom:id21 $atom:id18 $atom:id19 $atom:id20
+ $dihedral:id95 @dihedral:type1 $atom:id16 $atom:id19 $atom:id20 $atom:id23
+ $dihedral:id96 @dihedral:type1 $atom:id16 $atom:id19 $atom:id20 $atom:id45
+ $dihedral:id97 @dihedral:type1 $atom:id18 $atom:id19 $atom:id20 $atom:id23
+ $dihedral:id98 @dihedral:type1 $atom:id18 $atom:id19 $atom:id20 $atom:id45
+ $dihedral:id99 @dihedral:type1 $atom:id19 $atom:id20 $atom:id23 $atom:id22
+ $dihedral:id100 @dihedral:type1 $atom:id19 $atom:id20 $atom:id23 $atom:id24
+ $dihedral:id101 @dihedral:type1 $atom:id45 $atom:id20 $atom:id23 $atom:id22
+ $dihedral:id102 @dihedral:type1 $atom:id45 $atom:id20 $atom:id23 $atom:id24
+ $dihedral:id103 @dihedral:type1 $atom:id19 $atom:id20 $atom:id45 $atom:id42
+ $dihedral:id104 @dihedral:type1 $atom:id19 $atom:id20 $atom:id45 $atom:id46
+ $dihedral:id105 @dihedral:type1 $atom:id23 $atom:id20 $atom:id45 $atom:id42
+ $dihedral:id106 @dihedral:type1 $atom:id23 $atom:id20 $atom:id45 $atom:id46
+ $dihedral:id107 @dihedral:type1 $atom:id18 $atom:id21 $atom:id22 $atom:id1
+ $dihedral:id108 @dihedral:type1 $atom:id18 $atom:id21 $atom:id22 $atom:id23
+ $dihedral:id109 @dihedral:type1 $atom:id1 $atom:id22 $atom:id23 $atom:id20
+ $dihedral:id110 @dihedral:type1 $atom:id1 $atom:id22 $atom:id23 $atom:id24
+ $dihedral:id111 @dihedral:type1 $atom:id21 $atom:id22 $atom:id23 $atom:id20
+ $dihedral:id112 @dihedral:type1 $atom:id21 $atom:id22 $atom:id23 $atom:id24
+ $dihedral:id113 @dihedral:type1 $atom:id20 $atom:id23 $atom:id24 $atom:id3
+ $dihedral:id114 @dihedral:type1 $atom:id20 $atom:id23 $atom:id24 $atom:id25
+ $dihedral:id115 @dihedral:type1 $atom:id22 $atom:id23 $atom:id24 $atom:id3
+ $dihedral:id116 @dihedral:type1 $atom:id22 $atom:id23 $atom:id24 $atom:id25
+ $dihedral:id117 @dihedral:type1 $atom:id3 $atom:id24 $atom:id25 $atom:id26
+ $dihedral:id118 @dihedral:type1 $atom:id3 $atom:id24 $atom:id25 $atom:id46
+ $dihedral:id119 @dihedral:type1 $atom:id23 $atom:id24 $atom:id25 $atom:id26
+ $dihedral:id120 @dihedral:type1 $atom:id23 $atom:id24 $atom:id25 $atom:id46
+ $dihedral:id121 @dihedral:type1 $atom:id24 $atom:id25 $atom:id26 $atom:id27
+ $dihedral:id122 @dihedral:type1 $atom:id24 $atom:id25 $atom:id26 $atom:id29
+ $dihedral:id123 @dihedral:type1 $atom:id46 $atom:id25 $atom:id26 $atom:id27
+ $dihedral:id124 @dihedral:type1 $atom:id46 $atom:id25 $atom:id26 $atom:id29
+ $dihedral:id125 @dihedral:type1 $atom:id24 $atom:id25 $atom:id46 $atom:id45
+ $dihedral:id126 @dihedral:type1 $atom:id24 $atom:id25 $atom:id46 $atom:id47
+ $dihedral:id127 @dihedral:type1 $atom:id26 $atom:id25 $atom:id46 $atom:id45
+ $dihedral:id128 @dihedral:type1 $atom:id26 $atom:id25 $atom:id46 $atom:id47
+ $dihedral:id129 @dihedral:type1 $atom:id25 $atom:id26 $atom:id27 $atom:id48
+ $dihedral:id130 @dihedral:type1 $atom:id25 $atom:id26 $atom:id27 $atom:id28
+ $dihedral:id131 @dihedral:type1 $atom:id29 $atom:id26 $atom:id27 $atom:id48
+ $dihedral:id132 @dihedral:type1 $atom:id29 $atom:id26 $atom:id27 $atom:id28
+ $dihedral:id133 @dihedral:type1 $atom:id25 $atom:id26 $atom:id29 $atom:id4
+ $dihedral:id134 @dihedral:type1 $atom:id25 $atom:id26 $atom:id29 $atom:id30
+ $dihedral:id135 @dihedral:type1 $atom:id27 $atom:id26 $atom:id29 $atom:id4
+ $dihedral:id136 @dihedral:type1 $atom:id27 $atom:id26 $atom:id29 $atom:id30
+ $dihedral:id137 @dihedral:type1 $atom:id26 $atom:id27 $atom:id48 $atom:id47
+ $dihedral:id138 @dihedral:type1 $atom:id26 $atom:id27 $atom:id48 $atom:id49
+ $dihedral:id139 @dihedral:type1 $atom:id28 $atom:id27 $atom:id48 $atom:id47
+ $dihedral:id140 @dihedral:type1 $atom:id28 $atom:id27 $atom:id48 $atom:id49
+ $dihedral:id141 @dihedral:type1 $atom:id26 $atom:id27 $atom:id28 $atom:id31
+ $dihedral:id142 @dihedral:type1 $atom:id26 $atom:id27 $atom:id28 $atom:id53
+ $dihedral:id143 @dihedral:type1 $atom:id48 $atom:id27 $atom:id28 $atom:id31
+ $dihedral:id144 @dihedral:type1 $atom:id48 $atom:id27 $atom:id28 $atom:id53
+ $dihedral:id145 @dihedral:type1 $atom:id27 $atom:id28 $atom:id31 $atom:id30
+ $dihedral:id146 @dihedral:type1 $atom:id27 $atom:id28 $atom:id31 $atom:id32
+ $dihedral:id147 @dihedral:type1 $atom:id53 $atom:id28 $atom:id31 $atom:id30
+ $dihedral:id148 @dihedral:type1 $atom:id53 $atom:id28 $atom:id31 $atom:id32
+ $dihedral:id149 @dihedral:type1 $atom:id27 $atom:id28 $atom:id53 $atom:id50
+ $dihedral:id150 @dihedral:type1 $atom:id27 $atom:id28 $atom:id53 $atom:id54
+ $dihedral:id151 @dihedral:type1 $atom:id31 $atom:id28 $atom:id53 $atom:id50
+ $dihedral:id152 @dihedral:type1 $atom:id31 $atom:id28 $atom:id53 $atom:id54
+ $dihedral:id153 @dihedral:type1 $atom:id4 $atom:id29 $atom:id30 $atom:id31
+ $dihedral:id154 @dihedral:type1 $atom:id4 $atom:id29 $atom:id30 $atom:id33
+ $dihedral:id155 @dihedral:type1 $atom:id26 $atom:id29 $atom:id30 $atom:id31
+ $dihedral:id156 @dihedral:type1 $atom:id26 $atom:id29 $atom:id30 $atom:id33
+ $dihedral:id157 @dihedral:type1 $atom:id29 $atom:id30 $atom:id31 $atom:id28
+ $dihedral:id158 @dihedral:type1 $atom:id29 $atom:id30 $atom:id31 $atom:id32
+ $dihedral:id159 @dihedral:type1 $atom:id33 $atom:id30 $atom:id31 $atom:id28
+ $dihedral:id160 @dihedral:type1 $atom:id33 $atom:id30 $atom:id31 $atom:id32
+ $dihedral:id161 @dihedral:type1 $atom:id29 $atom:id30 $atom:id33 $atom:id8
+ $dihedral:id162 @dihedral:type1 $atom:id29 $atom:id30 $atom:id33 $atom:id34
+ $dihedral:id163 @dihedral:type1 $atom:id31 $atom:id30 $atom:id33 $atom:id8
+ $dihedral:id164 @dihedral:type1 $atom:id31 $atom:id30 $atom:id33 $atom:id34
+ $dihedral:id165 @dihedral:type1 $atom:id28 $atom:id31 $atom:id32 $atom:id57
+ $dihedral:id166 @dihedral:type1 $atom:id28 $atom:id31 $atom:id32 $atom:id35
+ $dihedral:id167 @dihedral:type1 $atom:id30 $atom:id31 $atom:id32 $atom:id57
+ $dihedral:id168 @dihedral:type1 $atom:id30 $atom:id31 $atom:id32 $atom:id35
+ $dihedral:id169 @dihedral:type1 $atom:id31 $atom:id32 $atom:id57 $atom:id54
+ $dihedral:id170 @dihedral:type1 $atom:id31 $atom:id32 $atom:id57 $atom:id58
+ $dihedral:id171 @dihedral:type1 $atom:id35 $atom:id32 $atom:id57 $atom:id54
+ $dihedral:id172 @dihedral:type1 $atom:id35 $atom:id32 $atom:id57 $atom:id58
+ $dihedral:id173 @dihedral:type1 $atom:id31 $atom:id32 $atom:id35 $atom:id34
+ $dihedral:id174 @dihedral:type1 $atom:id31 $atom:id32 $atom:id35 $atom:id36
+ $dihedral:id175 @dihedral:type1 $atom:id57 $atom:id32 $atom:id35 $atom:id34
+ $dihedral:id176 @dihedral:type1 $atom:id57 $atom:id32 $atom:id35 $atom:id36
+ $dihedral:id177 @dihedral:type1 $atom:id8 $atom:id33 $atom:id34 $atom:id37
+ $dihedral:id178 @dihedral:type1 $atom:id8 $atom:id33 $atom:id34 $atom:id35
+ $dihedral:id179 @dihedral:type1 $atom:id30 $atom:id33 $atom:id34 $atom:id37
+ $dihedral:id180 @dihedral:type1 $atom:id30 $atom:id33 $atom:id34 $atom:id35
+ $dihedral:id181 @dihedral:type1 $atom:id33 $atom:id34 $atom:id37 $atom:id12
+ $dihedral:id182 @dihedral:type1 $atom:id33 $atom:id34 $atom:id37 $atom:id38
+ $dihedral:id183 @dihedral:type1 $atom:id35 $atom:id34 $atom:id37 $atom:id12
+ $dihedral:id184 @dihedral:type1 $atom:id35 $atom:id34 $atom:id37 $atom:id38
+ $dihedral:id185 @dihedral:type1 $atom:id33 $atom:id34 $atom:id35 $atom:id32
+ $dihedral:id186 @dihedral:type1 $atom:id33 $atom:id34 $atom:id35 $atom:id36
+ $dihedral:id187 @dihedral:type1 $atom:id37 $atom:id34 $atom:id35 $atom:id32
+ $dihedral:id188 @dihedral:type1 $atom:id37 $atom:id34 $atom:id35 $atom:id36
+ $dihedral:id189 @dihedral:type1 $atom:id32 $atom:id35 $atom:id36 $atom:id39
+ $dihedral:id190 @dihedral:type1 $atom:id32 $atom:id35 $atom:id36 $atom:id61
+ $dihedral:id191 @dihedral:type1 $atom:id34 $atom:id35 $atom:id36 $atom:id39
+ $dihedral:id192 @dihedral:type1 $atom:id34 $atom:id35 $atom:id36 $atom:id61
+ $dihedral:id193 @dihedral:type1 $atom:id35 $atom:id36 $atom:id39 $atom:id38
+ $dihedral:id194 @dihedral:type1 $atom:id35 $atom:id36 $atom:id39 $atom:id40
+ $dihedral:id195 @dihedral:type1 $atom:id61 $atom:id36 $atom:id39 $atom:id38
+ $dihedral:id196 @dihedral:type1 $atom:id61 $atom:id36 $atom:id39 $atom:id40
+ $dihedral:id197 @dihedral:type1 $atom:id35 $atom:id36 $atom:id61 $atom:id58
+ $dihedral:id198 @dihedral:type1 $atom:id35 $atom:id36 $atom:id61 $atom:id62
+ $dihedral:id199 @dihedral:type1 $atom:id39 $atom:id36 $atom:id61 $atom:id58
+ $dihedral:id200 @dihedral:type1 $atom:id39 $atom:id36 $atom:id61 $atom:id62
+ $dihedral:id201 @dihedral:type1 $atom:id12 $atom:id37 $atom:id38 $atom:id41
+ $dihedral:id202 @dihedral:type1 $atom:id12 $atom:id37 $atom:id38 $atom:id39
+ $dihedral:id203 @dihedral:type1 $atom:id34 $atom:id37 $atom:id38 $atom:id41
+ $dihedral:id204 @dihedral:type1 $atom:id34 $atom:id37 $atom:id38 $atom:id39
+ $dihedral:id205 @dihedral:type1 $atom:id37 $atom:id38 $atom:id41 $atom:id16
+ $dihedral:id206 @dihedral:type1 $atom:id37 $atom:id38 $atom:id41 $atom:id42
+ $dihedral:id207 @dihedral:type1 $atom:id39 $atom:id38 $atom:id41 $atom:id16
+ $dihedral:id208 @dihedral:type1 $atom:id39 $atom:id38 $atom:id41 $atom:id42
+ $dihedral:id209 @dihedral:type1 $atom:id37 $atom:id38 $atom:id39 $atom:id36
+ $dihedral:id210 @dihedral:type1 $atom:id37 $atom:id38 $atom:id39 $atom:id40
+ $dihedral:id211 @dihedral:type1 $atom:id41 $atom:id38 $atom:id39 $atom:id36
+ $dihedral:id212 @dihedral:type1 $atom:id41 $atom:id38 $atom:id39 $atom:id40
+ $dihedral:id213 @dihedral:type1 $atom:id36 $atom:id39 $atom:id40 $atom:id43
+ $dihedral:id214 @dihedral:type1 $atom:id36 $atom:id39 $atom:id40 $atom:id65
+ $dihedral:id215 @dihedral:type1 $atom:id38 $atom:id39 $atom:id40 $atom:id43
+ $dihedral:id216 @dihedral:type1 $atom:id38 $atom:id39 $atom:id40 $atom:id65
+ $dihedral:id217 @dihedral:type1 $atom:id39 $atom:id40 $atom:id43 $atom:id42
+ $dihedral:id218 @dihedral:type1 $atom:id39 $atom:id40 $atom:id43 $atom:id44
+ $dihedral:id219 @dihedral:type1 $atom:id65 $atom:id40 $atom:id43 $atom:id42
+ $dihedral:id220 @dihedral:type1 $atom:id65 $atom:id40 $atom:id43 $atom:id44
+ $dihedral:id221 @dihedral:type1 $atom:id39 $atom:id40 $atom:id65 $atom:id62
+ $dihedral:id222 @dihedral:type1 $atom:id39 $atom:id40 $atom:id65 $atom:id66
+ $dihedral:id223 @dihedral:type1 $atom:id43 $atom:id40 $atom:id65 $atom:id62
+ $dihedral:id224 @dihedral:type1 $atom:id43 $atom:id40 $atom:id65 $atom:id66
+ $dihedral:id225 @dihedral:type1 $atom:id16 $atom:id41 $atom:id42 $atom:id45
+ $dihedral:id226 @dihedral:type1 $atom:id16 $atom:id41 $atom:id42 $atom:id43
+ $dihedral:id227 @dihedral:type1 $atom:id38 $atom:id41 $atom:id42 $atom:id45
+ $dihedral:id228 @dihedral:type1 $atom:id38 $atom:id41 $atom:id42 $atom:id43
+ $dihedral:id229 @dihedral:type1 $atom:id41 $atom:id42 $atom:id45 $atom:id20
+ $dihedral:id230 @dihedral:type1 $atom:id41 $atom:id42 $atom:id45 $atom:id46
+ $dihedral:id231 @dihedral:type1 $atom:id43 $atom:id42 $atom:id45 $atom:id20
+ $dihedral:id232 @dihedral:type1 $atom:id43 $atom:id42 $atom:id45 $atom:id46
+ $dihedral:id233 @dihedral:type1 $atom:id41 $atom:id42 $atom:id43 $atom:id40
+ $dihedral:id234 @dihedral:type1 $atom:id41 $atom:id42 $atom:id43 $atom:id44
+ $dihedral:id235 @dihedral:type1 $atom:id45 $atom:id42 $atom:id43 $atom:id40
+ $dihedral:id236 @dihedral:type1 $atom:id45 $atom:id42 $atom:id43 $atom:id44
+ $dihedral:id237 @dihedral:type1 $atom:id40 $atom:id43 $atom:id44 $atom:id47
+ $dihedral:id238 @dihedral:type1 $atom:id40 $atom:id43 $atom:id44 $atom:id69
+ $dihedral:id239 @dihedral:type1 $atom:id42 $atom:id43 $atom:id44 $atom:id47
+ $dihedral:id240 @dihedral:type1 $atom:id42 $atom:id43 $atom:id44 $atom:id69
+ $dihedral:id241 @dihedral:type1 $atom:id43 $atom:id44 $atom:id47 $atom:id46
+ $dihedral:id242 @dihedral:type1 $atom:id43 $atom:id44 $atom:id47 $atom:id48
+ $dihedral:id243 @dihedral:type1 $atom:id69 $atom:id44 $atom:id47 $atom:id46
+ $dihedral:id244 @dihedral:type1 $atom:id69 $atom:id44 $atom:id47 $atom:id48
+ $dihedral:id245 @dihedral:type1 $atom:id43 $atom:id44 $atom:id69 $atom:id66
+ $dihedral:id246 @dihedral:type1 $atom:id43 $atom:id44 $atom:id69 $atom:id70
+ $dihedral:id247 @dihedral:type1 $atom:id47 $atom:id44 $atom:id69 $atom:id66
+ $dihedral:id248 @dihedral:type1 $atom:id47 $atom:id44 $atom:id69 $atom:id70
+ $dihedral:id249 @dihedral:type1 $atom:id20 $atom:id45 $atom:id46 $atom:id25
+ $dihedral:id250 @dihedral:type1 $atom:id20 $atom:id45 $atom:id46 $atom:id47
+ $dihedral:id251 @dihedral:type1 $atom:id42 $atom:id45 $atom:id46 $atom:id25
+ $dihedral:id252 @dihedral:type1 $atom:id42 $atom:id45 $atom:id46 $atom:id47
+ $dihedral:id253 @dihedral:type1 $atom:id25 $atom:id46 $atom:id47 $atom:id44
+ $dihedral:id254 @dihedral:type1 $atom:id25 $atom:id46 $atom:id47 $atom:id48
+ $dihedral:id255 @dihedral:type1 $atom:id45 $atom:id46 $atom:id47 $atom:id44
+ $dihedral:id256 @dihedral:type1 $atom:id45 $atom:id46 $atom:id47 $atom:id48
+ $dihedral:id257 @dihedral:type1 $atom:id44 $atom:id47 $atom:id48 $atom:id27
+ $dihedral:id258 @dihedral:type1 $atom:id44 $atom:id47 $atom:id48 $atom:id49
+ $dihedral:id259 @dihedral:type1 $atom:id46 $atom:id47 $atom:id48 $atom:id27
+ $dihedral:id260 @dihedral:type1 $atom:id46 $atom:id47 $atom:id48 $atom:id49
+ $dihedral:id261 @dihedral:type1 $atom:id27 $atom:id48 $atom:id49 $atom:id50
+ $dihedral:id262 @dihedral:type1 $atom:id27 $atom:id48 $atom:id49 $atom:id70
+ $dihedral:id263 @dihedral:type1 $atom:id47 $atom:id48 $atom:id49 $atom:id50
+ $dihedral:id264 @dihedral:type1 $atom:id47 $atom:id48 $atom:id49 $atom:id70
+ $dihedral:id265 @dihedral:type1 $atom:id48 $atom:id49 $atom:id50 $atom:id51
+ $dihedral:id266 @dihedral:type1 $atom:id48 $atom:id49 $atom:id50 $atom:id53
+ $dihedral:id267 @dihedral:type1 $atom:id70 $atom:id49 $atom:id50 $atom:id51
+ $dihedral:id268 @dihedral:type1 $atom:id70 $atom:id49 $atom:id50 $atom:id53
+ $dihedral:id269 @dihedral:type1 $atom:id48 $atom:id49 $atom:id70 $atom:id69
+ $dihedral:id270 @dihedral:type1 $atom:id48 $atom:id49 $atom:id70 $atom:id71
+ $dihedral:id271 @dihedral:type1 $atom:id50 $atom:id49 $atom:id70 $atom:id69
+ $dihedral:id272 @dihedral:type1 $atom:id50 $atom:id49 $atom:id70 $atom:id71
+ $dihedral:id273 @dihedral:type1 $atom:id49 $atom:id50 $atom:id51 $atom:id72
+ $dihedral:id274 @dihedral:type1 $atom:id49 $atom:id50 $atom:id51 $atom:id52
+ $dihedral:id275 @dihedral:type1 $atom:id53 $atom:id50 $atom:id51 $atom:id72
+ $dihedral:id276 @dihedral:type1 $atom:id53 $atom:id50 $atom:id51 $atom:id52
+ $dihedral:id277 @dihedral:type1 $atom:id49 $atom:id50 $atom:id53 $atom:id28
+ $dihedral:id278 @dihedral:type1 $atom:id49 $atom:id50 $atom:id53 $atom:id54
+ $dihedral:id279 @dihedral:type1 $atom:id51 $atom:id50 $atom:id53 $atom:id28
+ $dihedral:id280 @dihedral:type1 $atom:id51 $atom:id50 $atom:id53 $atom:id54
+ $dihedral:id281 @dihedral:type1 $atom:id50 $atom:id51 $atom:id72 $atom:id71
+ $dihedral:id282 @dihedral:type1 $atom:id52 $atom:id51 $atom:id72 $atom:id71
+ $dihedral:id283 @dihedral:type1 $atom:id50 $atom:id51 $atom:id52 $atom:id55
+ $dihedral:id284 @dihedral:type1 $atom:id72 $atom:id51 $atom:id52 $atom:id55
+ $dihedral:id285 @dihedral:type1 $atom:id51 $atom:id52 $atom:id55 $atom:id54
+ $dihedral:id286 @dihedral:type1 $atom:id51 $atom:id52 $atom:id55 $atom:id56
+ $dihedral:id287 @dihedral:type1 $atom:id28 $atom:id53 $atom:id54 $atom:id55
+ $dihedral:id288 @dihedral:type1 $atom:id28 $atom:id53 $atom:id54 $atom:id57
+ $dihedral:id289 @dihedral:type1 $atom:id50 $atom:id53 $atom:id54 $atom:id55
+ $dihedral:id290 @dihedral:type1 $atom:id50 $atom:id53 $atom:id54 $atom:id57
+ $dihedral:id291 @dihedral:type1 $atom:id53 $atom:id54 $atom:id55 $atom:id52
+ $dihedral:id292 @dihedral:type1 $atom:id53 $atom:id54 $atom:id55 $atom:id56
+ $dihedral:id293 @dihedral:type1 $atom:id57 $atom:id54 $atom:id55 $atom:id52
+ $dihedral:id294 @dihedral:type1 $atom:id57 $atom:id54 $atom:id55 $atom:id56
+ $dihedral:id295 @dihedral:type1 $atom:id53 $atom:id54 $atom:id57 $atom:id32
+ $dihedral:id296 @dihedral:type1 $atom:id53 $atom:id54 $atom:id57 $atom:id58
+ $dihedral:id297 @dihedral:type1 $atom:id55 $atom:id54 $atom:id57 $atom:id32
+ $dihedral:id298 @dihedral:type1 $atom:id55 $atom:id54 $atom:id57 $atom:id58
+ $dihedral:id299 @dihedral:type1 $atom:id52 $atom:id55 $atom:id56 $atom:id59
+ $dihedral:id300 @dihedral:type1 $atom:id54 $atom:id55 $atom:id56 $atom:id59
+ $dihedral:id301 @dihedral:type1 $atom:id55 $atom:id56 $atom:id59 $atom:id58
+ $dihedral:id302 @dihedral:type1 $atom:id55 $atom:id56 $atom:id59 $atom:id60
+ $dihedral:id303 @dihedral:type1 $atom:id32 $atom:id57 $atom:id58 $atom:id61
+ $dihedral:id304 @dihedral:type1 $atom:id32 $atom:id57 $atom:id58 $atom:id59
+ $dihedral:id305 @dihedral:type1 $atom:id54 $atom:id57 $atom:id58 $atom:id61
+ $dihedral:id306 @dihedral:type1 $atom:id54 $atom:id57 $atom:id58 $atom:id59
+ $dihedral:id307 @dihedral:type1 $atom:id57 $atom:id58 $atom:id61 $atom:id36
+ $dihedral:id308 @dihedral:type1 $atom:id57 $atom:id58 $atom:id61 $atom:id62
+ $dihedral:id309 @dihedral:type1 $atom:id59 $atom:id58 $atom:id61 $atom:id36
+ $dihedral:id310 @dihedral:type1 $atom:id59 $atom:id58 $atom:id61 $atom:id62
+ $dihedral:id311 @dihedral:type1 $atom:id57 $atom:id58 $atom:id59 $atom:id56
+ $dihedral:id312 @dihedral:type1 $atom:id57 $atom:id58 $atom:id59 $atom:id60
+ $dihedral:id313 @dihedral:type1 $atom:id61 $atom:id58 $atom:id59 $atom:id56
+ $dihedral:id314 @dihedral:type1 $atom:id61 $atom:id58 $atom:id59 $atom:id60
+ $dihedral:id315 @dihedral:type1 $atom:id56 $atom:id59 $atom:id60 $atom:id63
+ $dihedral:id316 @dihedral:type1 $atom:id58 $atom:id59 $atom:id60 $atom:id63
+ $dihedral:id317 @dihedral:type1 $atom:id59 $atom:id60 $atom:id63 $atom:id62
+ $dihedral:id318 @dihedral:type1 $atom:id59 $atom:id60 $atom:id63 $atom:id64
+ $dihedral:id319 @dihedral:type1 $atom:id36 $atom:id61 $atom:id62 $atom:id65
+ $dihedral:id320 @dihedral:type1 $atom:id36 $atom:id61 $atom:id62 $atom:id63
+ $dihedral:id321 @dihedral:type1 $atom:id58 $atom:id61 $atom:id62 $atom:id65
+ $dihedral:id322 @dihedral:type1 $atom:id58 $atom:id61 $atom:id62 $atom:id63
+ $dihedral:id323 @dihedral:type1 $atom:id61 $atom:id62 $atom:id65 $atom:id40
+ $dihedral:id324 @dihedral:type1 $atom:id61 $atom:id62 $atom:id65 $atom:id66
+ $dihedral:id325 @dihedral:type1 $atom:id63 $atom:id62 $atom:id65 $atom:id40
+ $dihedral:id326 @dihedral:type1 $atom:id63 $atom:id62 $atom:id65 $atom:id66
+ $dihedral:id327 @dihedral:type1 $atom:id61 $atom:id62 $atom:id63 $atom:id60
+ $dihedral:id328 @dihedral:type1 $atom:id61 $atom:id62 $atom:id63 $atom:id64
+ $dihedral:id329 @dihedral:type1 $atom:id65 $atom:id62 $atom:id63 $atom:id60
+ $dihedral:id330 @dihedral:type1 $atom:id65 $atom:id62 $atom:id63 $atom:id64
+ $dihedral:id331 @dihedral:type1 $atom:id60 $atom:id63 $atom:id64 $atom:id67
+ $dihedral:id332 @dihedral:type1 $atom:id62 $atom:id63 $atom:id64 $atom:id67
+ $dihedral:id333 @dihedral:type1 $atom:id63 $atom:id64 $atom:id67 $atom:id66
+ $dihedral:id334 @dihedral:type1 $atom:id63 $atom:id64 $atom:id67 $atom:id68
+ $dihedral:id335 @dihedral:type1 $atom:id40 $atom:id65 $atom:id66 $atom:id69
+ $dihedral:id336 @dihedral:type1 $atom:id40 $atom:id65 $atom:id66 $atom:id67
+ $dihedral:id337 @dihedral:type1 $atom:id62 $atom:id65 $atom:id66 $atom:id69
+ $dihedral:id338 @dihedral:type1 $atom:id62 $atom:id65 $atom:id66 $atom:id67
+ $dihedral:id339 @dihedral:type1 $atom:id65 $atom:id66 $atom:id69 $atom:id44
+ $dihedral:id340 @dihedral:type1 $atom:id65 $atom:id66 $atom:id69 $atom:id70
+ $dihedral:id341 @dihedral:type1 $atom:id67 $atom:id66 $atom:id69 $atom:id44
+ $dihedral:id342 @dihedral:type1 $atom:id67 $atom:id66 $atom:id69 $atom:id70
+ $dihedral:id343 @dihedral:type1 $atom:id65 $atom:id66 $atom:id67 $atom:id64
+ $dihedral:id344 @dihedral:type1 $atom:id65 $atom:id66 $atom:id67 $atom:id68
+ $dihedral:id345 @dihedral:type1 $atom:id69 $atom:id66 $atom:id67 $atom:id64
+ $dihedral:id346 @dihedral:type1 $atom:id69 $atom:id66 $atom:id67 $atom:id68
+ $dihedral:id347 @dihedral:type1 $atom:id64 $atom:id67 $atom:id68 $atom:id71
+ $dihedral:id348 @dihedral:type1 $atom:id66 $atom:id67 $atom:id68 $atom:id71
+ $dihedral:id349 @dihedral:type1 $atom:id67 $atom:id68 $atom:id71 $atom:id70
+ $dihedral:id350 @dihedral:type1 $atom:id67 $atom:id68 $atom:id71 $atom:id72
+ $dihedral:id351 @dihedral:type1 $atom:id44 $atom:id69 $atom:id70 $atom:id49
+ $dihedral:id352 @dihedral:type1 $atom:id44 $atom:id69 $atom:id70 $atom:id71
+ $dihedral:id353 @dihedral:type1 $atom:id66 $atom:id69 $atom:id70 $atom:id49
+ $dihedral:id354 @dihedral:type1 $atom:id66 $atom:id69 $atom:id70 $atom:id71
+ $dihedral:id355 @dihedral:type1 $atom:id49 $atom:id70 $atom:id71 $atom:id68
+ $dihedral:id356 @dihedral:type1 $atom:id49 $atom:id70 $atom:id71 $atom:id72
+ $dihedral:id357 @dihedral:type1 $atom:id69 $atom:id70 $atom:id71 $atom:id68
+ $dihedral:id358 @dihedral:type1 $atom:id69 $atom:id70 $atom:id71 $atom:id72
+ $dihedral:id359 @dihedral:type1 $atom:id68 $atom:id71 $atom:id72 $atom:id51
+ $dihedral:id360 @dihedral:type1 $atom:id70 $atom:id71 $atom:id72 $atom:id51
+ }
+
+} # end of "CNT" type definition
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT b/tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT
new file mode 100644
index 000000000..325cc95bd
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README.TXT
@@ -0,0 +1,38 @@
+This example is a simple simulation of 288 hexadecane molecules in a box at
+room temperature and atmospheric pressure. Please read the WARNING.TXT file.
+
+-------- REQUIREMENTS: ---------
+This example requires building LAMMPS with the "USER-MISC" package.
+(because it uses dihedral_style fourier)
+To do this, type "make yes-user-misc" before compiling LAMMPS.
+ http://lammps.sandia.gov/doc/Section_start.html#start_3
+
+More detailed instructions on how to build LAMMPS input files and
+run a short simulation are provided in other README files:
+
+step 1) to setup the LAMMPS input files, run this file:
+README_setup.sh
+
+step 2) to run LAMMPS, follow the instructions in this file:
+README_run.sh
+
+------------ NOTE: There are two versions of this example. ----------------
+
+Both examples use the same force-field parameters.
+
+1) In this directory, all of the force-field parameters are listed explicitly
+in the "alkanes.lt" file (located in the "moltemplate_files" directory).
+This allows the user to manually control all of the force-field details.
+
+2) However, there is an alternate version of this example in the
+"../AMBER_force_field_examples" directory.
+In that version, the force-fields are loaded from a much larger file named
+"gaff.lt" which contains all of the parameters in the AMBER GAFF force-field
+database. The "gaff.lt" is similar to the "alkanes.lt" file except that
+it is larger (because it contains information for nearly all small organic
+molecules). It is located in a different directory (in the "common" directory).
+
+Relying on "gaff.lt" frees the user from the drudgery of manually specifying
+all of these force-field details for every molecule. (However, the user must
+be careful to choose @atom-type names which match AMBER GAFF conventions,
+such as "c3" and "h1", in this example.)
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh
new file mode 100755
index 000000000..8b01ab92d
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_run.sh
@@ -0,0 +1,39 @@
+# --- Running LAMMPS ---
+# -------- REQUIREMENTS: ---------
+# 1) This example requires building LAMMPS with the "USER-MISC" package.
+# (because it makes use of "gaff.lt" which uses dihedral_style fourier)
+# To do this, type "make yes-user-misc" before compiling LAMMPS.
+# http://lammps.sandia.gov/doc/Section_start.html#start_3
+# -------- PREREQUISITES: --------
+# The 2 files "run.in.npt", and "run.in.nvt" are LAMMPS
+# input scripts which link to the input scripts and data files
+# you hopefully have created earlier with moltemplate.sh:
+# system.in.init, system.in.settings, system.data
+# If not, carry out the instructions in "README_setup.sh".
+#
+# -- Instructions: --
+# If "lmp_linux" is the name of the command you use to invoke lammps,
+# then you would run lammps on these files this way:
+
+
+lmp_linux -i run.in.npt # minimization and simulation at constant pressure
+lmp_linux -i run.in.nvt # minimization and simulation at constant volume
+
+#(Note: The constant volume simulation lacks pressure equilibration. These are
+# completely separate simulations. The results of the constant pressure
+# simulation might be ignored when beginning the simulation at constant
+# volume. (This is because restart files in LAMMPS don't always work,
+# and I was spending a lot of time trying to convince people it was a
+# LAMMPS bug, instead of a moltemplate bug, so I disabled restart files.)
+# Read the "run.in.nvt" file to find out how to use the "read_restart"
+# command to load the results of the pressure-equilibration simulation,
+# before beginning a constant-volume run.
+
+
+
+
+
+# If you have compiled the MPI version of lammps, you can run lammps in parallel
+#mpirun -np 4 lmp_linux -i run.in.npt
+#mpirun -np 4 lmp_linux -i run.in.nvt
+# (assuming you have 4 processors available)
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh
new file mode 100755
index 000000000..f632ada11
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_setup.sh
@@ -0,0 +1,25 @@
+# -------- REQUIREMENTS: ---------
+# You must define your MOLTEMPLATE_PATH environment variable
+# and set it to the "common" subdirectory of your moltemplate distribution.
+# (See the "Installation" section in the moltemplate manual.)
+
+
+# Create LAMMPS input files this way:
+cd moltemplate_files
+
+ # run moltemplate
+
+ moltemplate.sh system.lt
+
+ # This will generate various files with names ending in *.in* and *.data.
+ # These files are the input files directly read by LAMMPS. Move them to
+ # the parent directory (or wherever you plan to run the simulation).
+ mv -f system.data system.in* ../
+
+ # Optional:
+ # The "./output_ttree/" directory is full of temporary files generated by
+ # moltemplate. They can be useful for debugging, but are usually thrown away.
+ rm -rf output_ttree/
+
+
+cd ../
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt
new file mode 100644
index 000000000..019afc144
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/README_visualize.txt
@@ -0,0 +1,87 @@
+
+ ------- To view a lammps trajectory in VMD --------
+
+
+1) Build a PSF file for use in viewing with VMD.
+
+This step works with VMD 1.9 and topotools 1.2.
+(Older versions, like VMD 1.8.6, don't support this.)
+
+
+a) Start VMD
+b) Menu Extensions->Tk Console
+c) Enter:
+
+(I assume that the the DATA file is called "system.data")
+
+ topo readlammpsdata system.data full
+ animate write psf system.psf
+
+2)
+
+Later, to Load a trajectory in VMD:
+
+ Start VMD
+ Select menu: File->New Molecule
+ -Browse to select the PSF file you created above, and load it.
+ (Don't close the window yet.)
+ -Browse to select the trajectory file.
+ If necessary, for "file type" select: "LAMMPS Trajectory"
+ Load it.
+
+ ---- A note on trajectory format: -----
+If the trajectory is a DUMP file, then make sure the it contains the
+information you need for pbctools (see below. I've been using this
+command in my LAMMPS scripts to create the trajectories:
+
+ dump 1 all custom 5000 DUMP_FILE.lammpstrj id mol type x y z ix iy iz
+
+It's a good idea to use an atom_style which supports molecule-ID numbers
+so that you can assign a molecule-ID number to each atom. (I think this
+is needed to wrap atom coordinates without breaking molecules in half.)
+
+Of course, you don't have to save your trajectories in DUMP format,
+(other formats like DCD work fine) I just mention dump files
+because these are the files I'm familiar with.
+
+3) ----- Wrap the coordinates to the unit cell
+ (without cutting the molecules in half)
+
+a) Start VMD
+b) Load the trajectory in VMD (see above)
+c) Menu Extensions->Tk Console
+d) Try entering these commands:
+
+ pbc wrap -compound res -all
+ pbc box
+
+ ----- Optional ----
+ Sometimes the solvent or membrane obscures the view of the solute.
+ It can help to shift the location of the periodic boundary box
+ To shift the box in the y direction (for example) do this:
+
+ pbc wrap -compound res -all -shiftcenterrel {0.0 0.15 0.0}
+ pbc box -shiftcenterrel {0.0 0.15 0.0}
+
+ Distances are measured in units of box-length fractions, not Angstroms.
+
+ Alternately if you have a solute whose atoms are all of type 1,
+ then you can also try this to center the box around it:
+
+ pbc wrap -sel type=1 -all -centersel type=2 -center com
+
+4)
+ You should check if your periodic boundary conditions are too small.
+ To do that:
+ select Graphics->Representations menu option
+ click on the "Periodic" tab, and
+ click on the "+x", "-x", "+y", "-y", "+z", "-z" checkboxes.
+
+5) Optional: If you like, change the atom types in the PSF file so
+ that VMD recognizes the atom types, use something like:
+
+sed -e 's/ 1 1 / C C /g' < system.psf > temp1.psf
+sed -e 's/ 2 2 / H H /g' < temp1.psf > temp2.psf
+sed -e 's/ 3 3 / P P /g' < temp2.psf > system.psf
+
+(If you do this, it might effect step 2 above.)
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT b/tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT
new file mode 100644
index 000000000..def26ba76
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/WARNING.TXT
@@ -0,0 +1,16 @@
+# -------- WARNING: --------
+
+This software is experimental, and the force-fields and equilbration protocols
+have not been tested carefully by me. There is no gaurantee that the simulation
+will reproduce the behavior of real hexadecane molecules,
+(or even of hexadecane molecules simulated using AMBER, which should
+ be using the same force-field).
+
+# -------- REQUEST FOR HELP: --------
+
+However, if you notice a problem with this example, please report it.
+I confess I do not have a lot of experience running all-atom simulations.
+Peer-review is the only way to improve this software (or any software).
+Other suggestions are also welcome!
+
+(Contact jewett.aij@gmail.com, 2013-10-16)
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg b/tools/moltemplate/examples/all_atom_examples/hexadecane/images/hexadecane_12x12x2_t=0_LR.jpg
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diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt
new file mode 100644
index 000000000..5b6642b04
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/alkanes.lt
@@ -0,0 +1,84 @@
+
+Alkanes {
+
+ # LAMMPS offers many different force-field styles and atom-styles.
+ # We must select which kind of atoms and force fields we want to use.
+ # (This will effect the syntax of the "_coeff" commands below.)
+
+ write_once("In Init") {
+ # Default styles and settings for AMBER based force-fields:
+ units real
+ atom_style full
+ bond_style hybrid harmonic
+ angle_style hybrid harmonic
+ dihedral_style hybrid fourier
+ #improper_style hybrid cvff
+
+ pair_style hybrid lj/cut 9.0
+ pair_modify shift yes
+
+ # If you have charges on the atoms, then comment out the line above
+ # and use this instead:
+ #pair_style hybrid lj/charmm/coul/long 9.0 10.0 10.0
+ #kspace_style pppm 0.0001
+
+ pair_modify mix arithmetic
+ special_bonds amber
+ }
+
+ # The "Alkanes" object contains the definition of atoms, bonds, bond-angles,
+ # and all of the force-field parameters for simple n-Alkanes.
+ # (These parameters were taken from the January 2013 version of the
+ # AMBER GAFF force-field. See "common/gaff.lt" for details.)
+
+ # atom-type mass
+
+ write_once("Data Masses") {
+ @atom:c3 12.01
+ @atom:h1 1.008
+ }
+
+ # Pairwise (non-bonded) force-field parameters:
+
+ write_once("In Settings") {
+ pair_coeff @atom:c3 @atom:c3 lj/cut 0.1094 1.9080
+ pair_coeff @atom:h1 @atom:h1 lj/cut 0.0157 1.3870
+ }
+
+ # Rules for determining 3 and 4-body bonded interactions by type
+
+ # angle-type atomType1 atomType2 atomType3 bondType1 bondType2
+
+ write_once("Data Angles By Type") {
+ @angle:CCC @atom:c3 @atom:c3 @atom:c3 @bond:* @bond:*
+ @angle:CCH @atom:c3 @atom:c3 @atom:h1 @bond:* @bond:*
+ @angle:HCH @atom:h1 @atom:c3 @atom:h1 @bond:* @bond:*
+ }
+
+ # dihedral-type AtomType1 AtomType2 AtomType3 AtomType4 bondType1 btyp2 btyp3
+
+ write_once("Data Dihedrals By Type") {
+ @dihedral:XCCX @atom:* @atom:c3 @atom:c3 @atom:* @bond:* @bond:* @bond:*
+ @dihedral:CCCC @atom:c3 @atom:c3 @atom:c3 @atom:c3 @bond:* @bond:* @bond:*
+ }
+
+ # Parameters for these new angular interactions must be defined. (I recommend
+ # putting all force-field parameters (coeffs) in the "In Settings" section.)
+
+ write_once("In Settings") {
+
+ # bond-type k r0
+ bond_coeff @bond:CC harmonic 303.1 1.5350
+ bond_coeff @bond:CH harmonic 335.9 1.0930
+
+ # angle-type k theta0
+ angle_coeff @angle:CCC harmonic 63.210 110.630
+ angle_coeff @angle:CCH harmonic 46.360 110.070
+ angle_coeff @angle:HCH harmonic 39.180 109.550
+
+ # dihedral-type
+ dihedral_coeff @dihedral:XCCX fourier 1 0.155555555556 3 0.0
+ dihedral_coeff @dihedral:CCCC fourier 3 0.18 3 0.0 0.25 2 180.0 0.2 1 180.0
+ }
+
+} # Alkanes
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt
new file mode 100644
index 000000000..33051a0c1
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch2group.lt
@@ -0,0 +1,44 @@
+
+import "alkanes.lt" # <-- Defines the atoms and force-field used for Alkanes
+
+
+CH2 inherits Alkanes {
+
+ # atom-id mol-id atom-type charge x y z
+
+ write("Data Atoms") {
+ $atom:C $mol:... @atom:c3 0.00 0.00 0.000 0.000
+ $atom:H1 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 0.8924307629540046
+ $atom:H2 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 -0.8924307629540046
+ }
+
+ # Note: The "..." in "$mol:..." tells moltemplate that this molecule may
+ # be a part of a larger molecule, and (if so) to use the larger
+ # parent object's molecule id number as it's own.
+ # The CH2 group is part of the Hexadecane molecule.
+
+ # Now specify which pairs of atoms are bonded:
+ # bond-id bond-type atom-id1 atom-id2
+
+ write('Data Bonds') {
+ $bond:b1 @bond:CH $atom:C $atom:H1
+ $bond:b2 @bond:CH $atom:C $atom:H2
+ }
+
+} # CH2
+
+
+
+
+
+######### (scratchwork calculations for the atomic coordinates) #########
+# Lcc = 1.5350 # length of the C-C bond (Sp3)
+# Lch = 1.0930 # length of the C-H bond
+# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
+# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
+# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
+# # 0.5*DeltaYc = 0.4431163316030377
+# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
+# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
+
+
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt
new file mode 100644
index 000000000..b78d9947f
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/ch3group.lt
@@ -0,0 +1,44 @@
+
+import "alkanes.lt" # <-- Defines the atoms and force-field used for Alkanes
+
+
+CH3 inherits Alkanes {
+
+ # atom-id mol-id atom-type charge x y z
+
+ write("Data Atoms") {
+ $atom:C $mol:... @atom:c3 0.00 0.00 0.000 0.000
+ $atom:H1 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 0.8924307629540046
+ $atom:H2 $mol:... @atom:h1 0.00 0.00 0.6310438442242609 -0.8924307629540046
+ $atom:H3 $mol:... @atom:h1 0.00 -0.8924307629540046 -0.6310438442242609 0.00
+ }
+
+ # Note: The "..." in "$mol:..." tells moltemplate that this molecule may
+ # be a part of a larger molecule, and (if so) to use the larger
+ # parent object's molecule id number as it's own.
+ # The CH3 group is part of the Hexadecane molecule.
+
+ # Now specify which pairs of atoms are bonded:
+ # bond-id bond-type atom-id1 atom-id2
+
+ write('Data Bonds') {
+ $bond:b1 @bond:CH $atom:C $atom:H1
+ $bond:b2 @bond:CH $atom:C $atom:H2
+ $bond:b3 @bond:CH $atom:C $atom:H3
+ }
+
+} # CH3
+
+
+
+
+######### (scratchwork calculations for the atomic coordinates) #########
+# Lcc = 1.5350 # length of the C-C bond (Sp3)
+# Lch = 1.0930 # length of the C-H bond
+# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
+# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
+# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
+# # 0.5*DeltaYc = 0.4431163316030377
+# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
+# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
+
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt
new file mode 100644
index 000000000..c6af2a7a7
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/hexadecane.lt
@@ -0,0 +1,84 @@
+# Define the "CH2" and "CH3" objects:
+
+import "ch2group.lt"
+import "ch3group.lt"
+
+
+
+Hexadecane inherits Alkanes {
+
+ # Create an array of 16 "CH2" objects
+
+ monomers = new CH2.move(0,0.4431163,0) [16].rot(180,1,0,0).move(1.2533223,0,0)
+
+ # "monomers" is a 1-dimensional array containing 16 copies of the CH2 molecule
+ # Each copy is rotated 180 degrees and shifted along the x axix.
+ # (For an explanation, read sections 7.1-7.3 of the moltemplate manual.)
+ # Notes:
+ # 1.2533223 = DeltaXc = how far each CH2 group is shifted along the axis
+ # 0.4431163 = DeltaYc/2 = lateral displacement of carbons along axis
+
+ # ---- Now, modify the ends: ---
+ # Delete the CH2 groups at the beginning and end, and replace them with CH3.
+ # (Note: Alternately, instead of deleting the CH2 groups at each end, you
+ # could modify them by adding an extra hydrogen atom to those carbons.)
+
+ delete monomers[0]
+ delete monomers[15]
+ monomer_begin = new CH3
+ monomer_end = new CH3
+
+ # Move the CH3 groups to the correct location at either end of the chain:
+
+ monomer_begin.move(0,0.4431163,0)
+ monomer_end.move(0,0.4431163,0).rot(180,0,0,1).move(18.7998345,0,0)
+
+ # Note: 18.7998345 = (16-1) * DeltaXc
+
+
+ # Now add a list of bonds connecting the carbon atoms together:
+
+ write('Data Bonds') {
+ $bond:b1 @bond:CC $atom:monomer_begin/C $atom:monomers[1]/C
+ $bond:b2 @bond:CC $atom:monomers[1]/C $atom:monomers[2]/C
+ $bond:b3 @bond:CC $atom:monomers[2]/C $atom:monomers[3]/C
+ $bond:b4 @bond:CC $atom:monomers[3]/C $atom:monomers[4]/C
+ $bond:b5 @bond:CC $atom:monomers[4]/C $atom:monomers[5]/C
+ $bond:b6 @bond:CC $atom:monomers[5]/C $atom:monomers[6]/C
+ $bond:b7 @bond:CC $atom:monomers[6]/C $atom:monomers[7]/C
+ $bond:b8 @bond:CC $atom:monomers[7]/C $atom:monomers[8]/C
+ $bond:b9 @bond:CC $atom:monomers[8]/C $atom:monomers[9]/C
+ $bond:b10 @bond:CC $atom:monomers[9]/C $atom:monomers[10]/C
+ $bond:b11 @bond:CC $atom:monomers[10]/C $atom:monomers[11]/C
+ $bond:b12 @bond:CC $atom:monomers[11]/C $atom:monomers[12]/C
+ $bond:b13 @bond:CC $atom:monomers[12]/C $atom:monomers[13]/C
+ $bond:b14 @bond:CC $atom:monomers[13]/C $atom:monomers[14]/C
+ $bond:b15 @bond:CC $atom:monomers[14]/C $atom:monomer_end/C
+ }
+
+ create_var { $mol } # Define a molecule ID number for this polymer
+
+ # This causes monomer[0], monomer[1], ... to share the same molecule-ID.
+ # (because in the ch2group.lt file, the "..." in "$mol:..." looks for
+ # a counter of type "$mol" in a parent molecule or earlier ancestor.)
+
+} # Hexadecane
+
+
+
+
+
+
+
+
+
+
+######### (scratchwork calculations for the atomic coordinates) #########
+# Lcc = 1.5350 # length of the C-C bond (Sp3)
+# Lch = 1.0930 # length of the C-H bond
+# theta=2*atan(sqrt(2)) # ~= 109.5 degrees = tetrahedronal angle (C-C-C angle)
+# DeltaXc = Lcc*sin(theta/2) # = 1.2533222517240594
+# DeltaYc = Lcc*cos(theta/2) # = 0.8862326632060754
+# # 0.5*DeltaYc = 0.4431163316030377
+# DeltaZh = Lch*sin(theta/2) # = 0.8924307629540046
+# DeltaYh = Lch*cos(theta/2) # = 0.6310438442242609
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt
new file mode 100644
index 000000000..4e0cfaec6
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/moltemplate_files/system.lt
@@ -0,0 +1,18 @@
+import "hexadecane.lt" # <- defines the "Hexadecane" molecule type.
+
+# Periodic boundary conditions:
+write_once("Data Boundary") {
+ 0.0 62.4 xlo xhi
+ 0.0 62.4 ylo yhi
+ 0.0 62.4 zlo zhi
+}
+
+molecules = new Hexadecane [12].move(0, 0, 5.2)
+ [12].move(0, 5.2, 0)
+ [2].move(31.2, 0, 0)
+
+
+# NOTE: The spacing between molecules is large. There should be extra room to
+# move during the initial stages of equilibration. However, you will have to
+# run the simulation at NPT conditions later to compress the system to a
+# more realistic density.
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt
new file mode 100644
index 000000000..b1791c955
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.npt
@@ -0,0 +1,85 @@
+# PREREQUISITES:
+#
+# You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+
+# ------------------------------- Initialization Section --------------------
+
+include system.in.init
+
+# ------------------------------- Atom Definition Section -------------------
+
+read_data system.data
+
+# ------------------------------- Settings Section --------------------------
+
+include system.in.settings
+
+# ------------------------------- Run Section -------------------------------
+
+# To avvoid explosions, I have a 4-step equilibraion process (expand, minimize,
+# reorient, compress). The system (as defined in the "system.data" file)
+# is already expanded. That means there are 3 steps left:
+
+dump dumpeq1 all custom 50 traj_eq1_min.lammpstrj id mol type x y z ix iy iz
+thermo 50
+
+# -- Equilibration: part 1: initial minimization --
+
+# Note: In general, it's always a good idea to minimize the system at first.
+
+minimize 1.0e-5 1.0e-7 100000 400000
+undump dumpeq1
+
+write_data system_after_eq1_min.data
+
+# -- Equilibration part 2: reorienting the molecules (NVT) --
+
+timestep 1.0
+dump dumpeq2 all custom 200 traj_eq2_reorient.lammpstrj id mol type x y z ix iy iz
+
+# Run the system at high temperature (at constant volume) to reorient the
+# the molecules (which would otherwise be pointing in the same direction).
+
+# To speed it up, I randomize the atomic positions for a few thousand steps
+# using fix langevin (and fix nve). Then I switch to fix nvt (Nose-Hoover).
+# (If I start with fix nvt (Nose-Hoover), it seems to get "stuck" for a while.)
+
+
+fix fxlan all langevin 900.0 900.0 120 48279
+fix fxnve all nve
+
+run 2000
+
+unfix fxlan
+unfix fxnve
+# Now continue the simulation at high temperature using fix nvt (Nose-Hoover).
+fix fxnvt all nvt temp 900.0 900.0 100.0
+
+run 5000
+undump dumpeq2
+
+
+write_data system_after_eq2_reorient.data
+
+unfix fxnvt
+
+# -- equilibration part 3: Equilibrating the density (NPT) --
+
+# Originally, the simulation box (in "system.data" and "system.lt") was
+# unrealistically large. The spacing between the molecules was large also.
+# I did this to enable the molecules to move freely and reorient themselves.
+# After doing that, we should run the simulation under NPT conditions to
+# allow the simulation box to contract to it's natural size. We do that here:
+# We begin the simulation at 100 barr (a relatively low pressure), and
+# slowly decrease it to 1 barr, maintianing the temperature at 300K.
+
+dump dumpeq3 all custom 200 traj_eq3_npt.lammpstrj id mol type x y z ix iy iz
+fix fxnpt all npt temp 300.0 300.0 100.0 iso 100.0 1.0 1000.0 drag 2.0
+
+timestep 1.0
+run 30000
+
+write_data system_after_eq3_npt.data
+
diff --git a/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt
new file mode 100644
index 000000000..f8b2d31d0
--- /dev/null
+++ b/tools/moltemplate/examples/all_atom_examples/hexadecane/run.in.nvt
@@ -0,0 +1,42 @@
+# PREREQUISITES:
+#
+# 1) You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+# 2) You must equilibrate the system beforehand using "run.in.npt".
+# This will create the file "system_after_npt.data" which this file reads.
+# (Note: I have not verified that this equilibration protocol works well.)
+
+# ------------------------------- Initialization Section --------------------
+
+include system.in.init
+
+# ------------------------------- Atom Definition Section -------------------
+
+
+# Read the coordinates generated by an earlier NPT simulation
+
+read_data system_after_eq3_npt.data
+
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also. I prefer "write_data" and "read_data".)
+
+
+# ------------------------------- Settings Section --------------------------
+
+include system.in.settings
+
+# ------------------------------- Run Section -------------------------------
+
+# -- simulation protocol --
+
+
+timestep 1.0
+dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
+fix fxnvt all nvt temp 350.0 350.0 500.0 tchain 1
+thermo 100
+#thermo_modify flush yes
+
+run 50000
+
+write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
index 02d7dd762..ee6786d7c 100644
--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
+++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/moltemplate_files/nanotube.lt
@@ -1,24 +1,96 @@
import "graphene.lt"
# ------------------ nanotube ---------------
# Now use this to build a simple ("zigzag") nanotube where the long-axis of each
# hexagon is aligned with the tube axis (along the Z direction). If the
# cicumference of a "zigzag" nanotube contains N hexagons, then the radius of
# the tube, R=(W/4)/tan((2*pi)/(4*N)), where W=2*d*sqrt(3)/2, and d = the carbon
# bond length. If N=14 and d=1.42 Ansgroms then R=5.457193512764 Angstroms
# In the Joly 2011 paper, the tube radii varied between 5.14 and 18.7 Angstroms.
+
+
nanotube = new Graphene/2AtomCellAlignXZ.move(0, 5.457193512764, 0) # 5.45 = R
[14].rot(25.7142857,0,0,1) #25.7=360/14
[12].rot(12.8571429,0,0,1).move(0, 0, 2.13) #12.9=180/14
#2.13= d*1.5
+
# Note: The length is 12 hexegons, the circumference is
# 14 hexegons (~=25.56 and 34.43 Angstroms, respectively).
+
# Move all of the unit-cells in the nanotube between the two graphene sheets.
nanotube[*][*].move(0, 0, 33.42)
+
+
+
+
+# ---------- BUILDING CHIRAL NANOTUBES USING EXTERNAL SOFTWARE -------------
+#
+# The approach shown here works well for "zig-zag" nanotubes.
+# Nanotubes with other chiralities are more difficult to make this way
+# (because the tube axis is no longer perpendicular to graphene basis vectors).
+# For those nanotubes, I recommend using an external program to generate
+# a LAMMPS data file for the nanotube. If you want to combine the tube
+# with other molecules created by moltemplate, you can then import it into
+# moltemplate as a molecule object using the "ltemplify.py" utility. Details:
+#
+# --- VMD plugins (by Axel Kohlmeyer and Robert R. Johnson) ---
+#
+# The nanotube-builder for VMD can generate nanotubes (with smooth tips)
+# for any chirality. These tubes also have explicit bonds between carbons:
+# http://www.ks.uiuc.edu/Research/vmd/plugins/nanotube/
+#
+# The resulting nanotube can be converted to a data file using topotools:
+# https://sites.google.com/site/akohlmey/software/topotools
+# To do that, select the "Extensions"->"Tk Console" menu and enter
+#
+# topo writelammpsdata nanotube.data full
+#
+# --- ltemplify.py ---
+#
+# That data file can be converted to moltemplate format (an .LT file)
+# using the "ltemplify.py" utility.
+#
+# The first step is to create a short input script containing the atom_style
+# command (ltemplify.py will read this script. Presumably atom_style is "full").
+#
+# echo "atom_style full" > nanotube.in
+#
+# Then run ltemplify to convert nanotube.data into a moltemplate file:
+# ltemplify.py -name Nanotube nanotube.in nanotube.data > nanotube.lt
+#
+# You will need to edit the "nanotuble.lt" file to replace all of the
+# "@atom:type1" atoms types file to match the carbon atom types in the other lt
+# files (ie "@atom:../C"). If you don't plan on defining bonded interactions
+# between carbon atoms, then be sure to remove the write("Data Bonds") section
+# of the "nanotube.lt" file (if it is present).
+#
+# Finally make sure the "system.lt" contains these lines:
+#
+# import "nanotube.lt"
+# nanotube = new Nanotube.move(?,?,?)
+#
+# (Replace ?,?,? with the location where you want the nanotube to go.
+# You can also rotate it using .rot(angle,axisx,axisy,axiz).)
+#
+# ... and then run moltemplate the normal way
+#
+# Let me know if you run into trouble with this approach,
+# and I will make note of that in this file.
+#
+# --- links ---
+# Note: there are numerous programs for specifying the coordinates
+# of the atoms in a nanotube, some of which are below.
+# http://www.nanotube.msu.edu/tubeASP/
+# http://turin.nss.udel.edu/research/tubegenonline.html
+# http://www.ugr.es/~gmdm/java/contub/contub.html
+# (You can load coordinates into moltemplate using the "-xyz" or "-pdb"
+# arguments. However currently (2013-12-01), the file must contain coordinates
+# for all of the atoms in your sytem, not just the nanotube.)
+# -------------------------------------------------------------------------
diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt
index 2261f99ac..6bd4fd8a1 100644
--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt
+++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.npt
@@ -1,98 +1,102 @@
# THIS EXAMPLE HAS NOT BEEN RIGOROUSLY TESTED.
# (This simulation may fail.
# However the "run.in.nvt" example in this directory should work.)
#
# Requirements:
# To run this system at constant pressure, it might help to compile LAMMPS with
# the optional RIGID package, and use "fix rigid" on the carbon. (Optional.)
# The use of fix rigid is controversial. This method is demonstrated below.
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
read_data system.data
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
# Only the Cgraphene atoms are immobile.
group mobile subtract all Cgraphene
# Unfortunately you can not use the LAMMPS "minimize" command on this system
# because there is no way to immobilize the carbon graphene & nanotube atoms
# during minimization. Instead, we can use langevin dynamics with a large
# damping parameter and a small timestep.
print "--------- beginning minimization (using fix langevin) ---------"
timestep 0.1
fix fxlan mobile langevin 1.0 1.0 100.0 48279
fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation)
thermo 100
run 2500
unfix fxlan
unfix fxnve
# -- simulation protocol --
print "--------- beginning simulation (using fix nvt) ---------"
timestep 0.25
dump 1 all custom 1000 traj_npt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
thermo 1000 # time interval for printing out "thermo" data
# ------------------------- NPT ---------------------------
# Set temp=300K, pressure=100bar, and equilibrate volume only in the z direction
fix fxMoveStuff mobile npt temp 300 300 100 z 100 100 1000.0 dilate mobile
# ------ QUESTIONABLE (see below): ------
fix Ffreezestuff Cgraphene rigid/npt single temp 300 300 100 z 100 100 1000.0 force * off off off torque * off off off dilate mobile
# -- Alternate npt rigid method --
# I'm not sure which way is more correct, however
# this also seems to behave in a reasonable-looking way:
#fix Ffreezestuff Cgraphene rigid single force * off off off torque * off off off
#
# The use of either "fix rigid" or "fix rigid/npt" to immobilize
# an object is somewhat controversial. Feel free to omit it.
#(Neither Trung or Steve Plimpton use rigid or rigid/npt for immobilizing
#molecules, but I noticed that at NPT, it does a better job of maintaining
# the correct volume. However "fix rigid" has changed since then (2011),
# so this may no longer be true. Please use this example with caution.)
# ----------------------------------------
# IMPORTANT for NPT: You must use "neigh_modify" to turn off calculation of the
# forces between immobilized atoms.
neigh_modify exclude group Cgraphene Cgraphene
# The next two lines recalculate the temperature
# using only the mobile degrees of freedom:
compute tempMobile mobile temp
compute pressMobile all pressure tempMobile
thermo_style custom step c_tempMobile c_pressMobile temp press vol
fix_modify fxMoveStuff temp tempMobile
run 100000
-write_restart system_after_npt.rst
+write_data system_after_npt.data
+
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also.)
+
diff --git a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
index f4fd0bbc1..59c847c07 100644
--- a/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
+++ b/tools/moltemplate/examples/all_atom_examples/nanotube+water/run.in.nvt
@@ -1,71 +1,79 @@
+# PREREQUISITES:
+#
+# You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+# (You do not need to run LAMMPS to equilibrate the system before
+# using this file.)
+
# ----------------------------- Initialization Section --------------------
include system.in.init
# ----------------------------- Atom Definition Section -------------------
read_data system.data
# ----------------------------- Settings Section --------------------------
include system.in.settings
# ----------------------------- Run Section -------------------------------
# Optional: Improve efficiency by omitting the calcuation of interactions
# between immobile atoms. (Note: This is not optional under NPT conditions.)
neigh_modify exclude group Cgraphene Cgraphene
# Only the Cgraphene atoms are immobile.
group mobile subtract all Cgraphene
# -- minimization protocol --
# Unfortunately you can not use the LAMMPS "minimize" command on this system
# because there is no way to immobilize the carbon graphene & nanotube atoms
# during minimization. Instead, we can use langevin dynamics with a large
# damping parameter and a small timestep.
print "--------- beginning minimization (using fix langevin) ---------"
timestep 0.1
fix fxlan mobile langevin 1.0 1.0 100.0 48279
fix fxnve mobile nve # <-- needed by fix langevin (see lammps documentation)
thermo 100
run 2500
unfix fxlan
unfix fxnve
# -- simulation protocol --
print "--------- beginning simulation (using fix nvt) ---------"
timestep 1.0
dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pe etotal press vol epair #ebond eangle edihed
thermo 500 # time interval for printing out "thermo" data
# Integrate the equations of motion:
fix fxMoveStuff mobile nvt temp 300.0 300.0 100.0
# The next two lines recalculate the temperature
# using only the mobile degrees of freedom:
compute tempMobile mobile temp
fix_modify fxMoveStuff temp tempMobile
restart 5000000 restart_nvt
run 10000000
-write_restart system_after_nvt.rst
+write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
index 3ea3c2ff3..4d8af42b5 100644
--- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
+++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.npt
@@ -1,52 +1,48 @@
-##################################################
-# Box of water
-##################################################
+# PREREQUISITES:
#
-# define the system being simulated:
+# You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
-# ----- init section -----
+# ------------------------------- Initialization Section --------------------
-include system.in.init
+include system.in.init
+# ------------------------------- Atom Definition Section -------------------
-# ----- atom definition section -----
+read_data system.data
-read_data system.data
+# ------------------------------- Settings Section --------------------------
+include system.in.settings
-# ----- settings section -----
-
-include system.in.settings
-
-
-# ----- run section -----
+# ------------------------------- Run Section -------------------------------
# -- minimization protocol --
-# In general, it's always a good idea to minimize the system beforehand.
-# fShakeSPCE was defined in system.in.settings. It is incompatible with minimize
+
+# Note: The minimization step is not necessary in this example. However
+# in general, it's always a good idea to minimize the system beforehand.
+# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize".
unfix fShakeSPCE
-minimize 1.0e-5 1.0e-7 100000 400000
+minimize 1.0e-3 1.0e-5 100000 400000
# Now read "system.in.settings" in order to redefine fShakeSPCE again:
include system.in.settings
# -- simulation protocol --
timestep 1.0
-
-dump 1 all custom 100 traj_npt.lammpstrj id mol type x y z ix iy iz
-fix fxnpt all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 1.0
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle edihed
+dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz
+fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
thermo 100
run 10000
# Now that the system's temperature has become more equilibrated,
# we can increase the timestep:
timestep 2.0
run 50000
-write_restart system_after_npt.rst
+write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
index 0bde0eb93..22fb1f271 100644
--- a/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
+++ b/tools/moltemplate/examples/all_atom_examples/read_PDB_file_examples/waterSPCE_from_PDBfile/run.in.nvt
@@ -1,67 +1,58 @@
-##################################################
-# Box of water
-##################################################
+# PREREQUISITES:
#
-# define the system being simulated:
+# 1) You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+# 2) You must equilibrate the system beforehand using "run.in.npt".
+# This will create the file "system_after_npt.data" which this file reads.
+# (Note: I have not verified that this equilibration protocol works well.)
-# -- init section --
-include system.in.init
+# ------------------------------- Initialization Section --------------------
-# ------------------------ Atom Definition Section --------------
+include system.in.init
-# Normally, I would minimize the system and equilibrate the system at constant
-# pressure and temperature beforehand. If you run lammps with "run.in.npt",
-# it will generate a restart file "system_after_npt.rst" with reasonable
-# coordinates at that temperature and pressure. Then we could load it now:
-#
-#read_restart system_after_npt.rst
-#
-# Unfortunately the LAMMPS "read_restart" command has been undependable over
-# the past year (2012), and I feel it is safer to remove it from the examples.
-# Instead, for this example, I just read the raw coordinates generated by
-# moltemplate (and the default volume). (I get fewer questions this way.)
-# However you should never run any liquid simulations at constant volume without
-# pressure equilibration first. Hopefully in the future "read_restart" will
-# work. Otherwise try "read_dump", "dump2data.py", or "restart2data".
+# ------------------------------- Atom Definition Section -------------------
-read_data system.data
+# Read the coordinates generated by an earlier NPT simulation
-# ------------------------ Settings section ---------------------
+read_data system_after_npt.data
-include system.in.settings
-# ------------------------ Run section -------------------------
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also. I prefer "write_data" and "read_data".)
+# ------------------------------- Settings Section --------------------------
-# -- minimization protocol --
+include system.in.settings
-# In general, it's always a good idea to minimize the system beforehand.
-# fShakeSPCE was defined in system.in.settings. It is incompatible with minimize
+# ------------------------------- Run Section -------------------------------
+
+
+# -- minimization protocol --
+# Note: If you are reading the restart file instead of the data file,
+# then you should not need to minimize the system beforehand..
+# fShakeSPCE was defined in system.in.settings.
+# (It is incompatible with "minimize".)
unfix fShakeSPCE
minimize 1.0e-5 1.0e-7 100000 400000
# Now read "system.in.settings" in order to redefine fShakeSPCE again:
include system.in.settings
# -- simulation protocol --
-timestep 1.0
+timestep 1.0
dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
-
-thermo_style custom step temp pe etotal press vol epair ebond eangle
-thermo 500 # time interval for printing out "thermo" data
-#thermo_modify flush yes
+thermo 500
run 10000
# Now that the system's temperature has become more equilibrated,
# we can increase the timestep:
timestep 2.0
run 50000
-write_restart system_after_nvt.rst
-
-
+write_data system_after_nvt.data
diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
index b5a4eb54f..4d8af42b5 100644
--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
+++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.npt
@@ -1,44 +1,48 @@
+# PREREQUISITES:
+#
+# You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
read_data system.data
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
# -- minimization protocol --
# Note: The minimization step is not necessary in this example. However
# in general, it's always a good idea to minimize the system beforehand.
# fShakeSPCE was defined in system.in.settings. It is incompatible with "minimize".
unfix fShakeSPCE
-minimize 1.0e-5 1.0e-7 100000 400000
+minimize 1.0e-3 1.0e-5 100000 400000
# Now read "system.in.settings" in order to redefine fShakeSPCE again:
include system.in.settings
# -- simulation protocol --
timestep 1.0
-dump 1 all custom 100 traj_npt.lammpstrj id mol type x y z ix iy iz
+dump 1 all custom 200 traj_npt.lammpstrj id mol type x y z ix iy iz
fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0
-
thermo 100
-#thermo_modify flush yes
run 10000
# Now that the system's temperature has become more equilibrated,
# we can increase the timestep:
timestep 2.0
run 50000
-write_restart system_after_npt.rst
+write_data system_after_npt.data
diff --git a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
index 1f4110204..22fb1f271 100644
--- a/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
+++ b/tools/moltemplate/examples/all_atom_examples/waterSPCE+Na+Cl/run.in.nvt
@@ -1,61 +1,58 @@
+# PREREQUISITES:
+#
+# 1) You must use moltemplate.sh to create 3 files:
+# system.data system.in.init system.in.settings
+# (Follow the instructions in README_setup.sh, or run it using ./README_sh.)
+# 2) You must equilibrate the system beforehand using "run.in.npt".
+# This will create the file "system_after_npt.data" which this file reads.
+# (Note: I have not verified that this equilibration protocol works well.)
+
# ------------------------------- Initialization Section --------------------
include system.in.init
# ------------------------------- Atom Definition Section -------------------
+# Read the coordinates generated by an earlier NPT simulation
-# Normally, I would minimize the system and equilibrate the system at constant
-# pressure and temperature beforehand. If you run lammps with "run.in.npt",
-# it will generate a restart file "system_after_npt.rst" with reasonable
-# coordinates at that temperature and pressure. Then we could load it now:
-#
-#read_restart system_after_npt.rst
-#
-# Unfortunately the LAMMPS "read_restart" command has been undependable over
-# the past year (2012), and I feel it is safer to remove it from the examples.
-# Instead, for this example, I just read the raw coordinates generated by
-# moltemplate (and the default volume). (I get fewer questions this way.)
-# However you should never run any liquid simulations at constant volume without
-# pressure equilibration first. Hopefully in the future "read_restart" will
-# work. Until then, try "read_dump", "dump2data.py", or "restart2data".
+read_data system_after_npt.data
-read_data system.data
+
+# (The "write_restart" and "read_restart" commands were buggy in 2012,
+# but they should work also. I prefer "write_data" and "read_data".)
# ------------------------------- Settings Section --------------------------
include system.in.settings
# ------------------------------- Run Section -------------------------------
# -- minimization protocol --
# Note: If you are reading the restart file instead of the data file,
# then you should not need to minimize the system beforehand..
# fShakeSPCE was defined in system.in.settings.
# (It is incompatible with "minimize".)
unfix fShakeSPCE
minimize 1.0e-5 1.0e-7 100000 400000
# Now read "system.in.settings" in order to redefine fShakeSPCE again:
include system.in.settings
# -- simulation protocol --
timestep 1.0
dump 1 all custom 500 traj_nvt.lammpstrj id mol type x y z ix iy iz
fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1
thermo 500
run 10000
# Now that the system's temperature has become more equilibrated,
# we can increase the timestep:
timestep 2.0
run 50000
-write_restart system_after_nvt.rst
-
-
+write_data system_after_nvt.data
diff --git a/tools/moltemplate/src/dump2data.py b/tools/moltemplate/src/dump2data.py
index b79934701..604a69fa4 100755
--- a/tools/moltemplate/src/dump2data.py
+++ b/tools/moltemplate/src/dump2data.py
@@ -1,1263 +1,1262 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
dump2data.py
Extract dynamical degrees of freedom from a lammps DUMP file (from the stdin)
and construct a new DATA file (to the stdout).
A reference DATA file is needed (argument).
basic usage
./dump2data.py orig_file.data < dump.lammpstrj > new_file.data
(This extract last frame, uses "full" atom_style.)
options:
-./dump2data.py [-time t -atomstyle style] orig.data < dump.lammpstrj > new.data
+./dump2data.py [-t t -atomstyle style] orig.data < dump.lammpstrj > new.data
"""
# Authors: Andrew Jewett, Lieberman-Aiden group
# License: New BSD License
# Copyright (c) 2013
# All rights reserved.
import sys
from collections import defaultdict
from operator import itemgetter, attrgetter
class InputError(Exception):
def __init__(self, err_msg):
self.err_msg = err_msg
def __str__(self):
return self.err_msg
def ErrorLeader(infile, lineno):
return '\"'+infile+'\", line '+str(lineno)+': '
class MiscSettings(object):
def __init__(self):
self.tstart = None
self.tstop = None
self.timestep_str = ''
self.last_frame = False
self.center_frame = False
self.output_format = 'data'
self.input_format = 'dump'
self.multi = True
self.skip_interval = 1
self.scale = None
class AtomStyleSettings(object):
def __init__(self):
# The following new member data indicate which columns store
# LAMMPS-specific information.
# The next 6 members store keep track of the different columns
# of the "Atoms" section of a LAMMPS data file:
self.column_names = [] #<--A list of column names (optional)
self.i_coords=[] #<--A triplet of integers indicating which columns store coordinate data
#self.ii_coords= [] #<--A list of triplets of column indexes storing coordinate data
self.ii_vects=[] #<--A list of triplets of column indexes storing directional data
# (such as dipole or ellipsoid orientations)
self.i_atomid=None #<--An integer indicating which column has the atomid
self.i_atomtype=None #<--An integer indicating which column has the atomtype
self.i_molid=None #<--An integer indicating which column has the molid, if applicable
class DataSettings(AtomStyleSettings):
def __init__(self):
AtomStyleSettings.__init__(self)
self.contents = ''
self.file_name = ''
# Atom Styles in LAMMPS as of 2011-7-29
g_style_map = {'angle': ['atom-ID','molecule-ID','atom-type','x','y','z'],
'atomic': ['atom-ID','atom-type','x','y','z'],
'bond': ['atom-ID','molecule-ID','atom-type','x','y','z'],
'charge': ['atom-ID','atom-type','q','x','y','z'],
'colloid': ['atom-ID','atom-type','x','y','z'],
'dipole': ['atom-ID','atom-type','q','x','y','z','mux','muy','muz'],
'electron': ['atom-ID','atom-type','q','spin','eradius','x','y','z'],
'ellipsoid':['atom-ID','atom-type','x','y','z','quatw','quati','quatj','quatk'],
'full': ['atom-ID','molecule-ID','atom-type','q','x','y','z'],
'granular': ['atom-ID','atom-type','diameter','density','x','y','z'],
'molecular':['atom-ID','molecule-ID','atom-type','x','y','z'],
'peri': ['atom-ID','atom-type','volume','density','x','y','z'],
'hybrid': ['atom-ID','atom-type','x','y','z']}
def AtomStyle2ColNames(atom_style_string):
atom_style_string = atom_style_string.strip()
if len(atom_style_string) == 0:
raise InputError('Error(dump2data): Invalid atom_style\n'
' (The atom_style command was followed by an empty string.)\n')
atom_style_args = atom_style_string.split()
atom_style = atom_style_args[0]
hybrid_args = atom_style_args[1:]
if (atom_style not in g_style_map):
if (len(atom_style_args) >= 2):
# If the atom_style_string includes at least 2 words, then we
# interpret this as a list of the individual column names
return atom_style_args
else:
raise InputError('Error(dump2data): Unrecognized atom_style: \"'+atom_style+'\"\n')
if (atom_style != 'hybrid'):
return g_style_map[atom_style]
else:
column_names = ['atom-ID','atom-type','x','y','z']
if (len(hybrid_args)==0):
raise InputError('Error(dump2data): atom_style hybrid must be followed by a sub_style.\n')
for sub_style in hybrid_args:
if (sub_style not in g_style_map):
raise InputError('Error(dump2data): Unrecognized atom_style: \"'+sub_style+'\"\n')
for cname in g_style_map[sub_style]:
if cname not in column_names:
column_names.append(cname)
return column_names
def ColNames2AidAtypeMolid(column_names):
# Because of the diversity of ways that these
# numbers are referred to in the LAMMPS documentation,
# we have to be flexible and allow the user to refer
# to these quantities in a variety of ways.
# Hopefully this covers everything:
i_atomid = None
if 'atom-ID' in column_names:
i_atomid = column_names.index('atom-ID')
elif 'atom−ID' in column_names: # (− is the character used in the manual)
i_atomid = column_names.index('atom−ID')
elif 'atomID' in column_names:
i_atomid = column_names.index('atomID')
elif 'atomid' in column_names:
i_atomid = column_names.index('atomid')
elif 'id' in column_names:
i_atomid = column_names.index('id')
elif 'atom' in column_names:
i_atomid = column_names.index('atom')
elif '$atom' in column_names:
i_atomid = column_names.index('$atom')
else:
raise InputError('Error(dump2data): List of column names lacks an \"atom-ID\"\n')
i_atomtype = None
if 'atom-type' in column_names:
i_atomtype = column_names.index('atom-type')
elif 'atom−type' in column_names: # (− hyphen character used in manual)
i_atomtype = column_names.index('atom−type')
elif 'atomtype' in column_names:
i_atomtype = column_names.index('atomtype')
elif 'type' in column_names:
i_atomtype = column_names.index('type')
elif '@atom' in column_names:
i_atomtype = column_names.index('@atom')
else:
raise InputError('Error(dump2data): List of column names lacks an \"atom-type\"\n')
i_molid = None
if 'molecule-ID' in column_names:
i_molid = column_names.index('molecule-ID')
elif 'molecule−ID' in column_names: # (− hyphen character used in manual)
i_molid = column_names.index('molecule−ID')
elif 'moleculeID' in column_names:
i_molid = column_names.index('moleculeID')
elif 'moleculeid' in column_names:
i_molid = column_names.index('moleculeid')
elif 'molecule' in column_names:
i_molid = column_names.index('molecule')
elif 'molID' in column_names:
i_molid = column_names.index('molID')
elif 'molid' in column_names:
i_molid = column_names.index('molid')
elif 'mol' in column_names:
i_molid = column_names.index('mol')
elif '$mol' in column_names:
i_molid = column_names.index('$mol')
else:
pass # some atom_types do not have a valid molecule-ID
return i_atomid, i_atomtype, i_molid
def ColNames2Coords(column_names):
""" Which of the columns correspond to coordinates
which must be transformed using rigid-body
(affine: rotation + translation) transformations?
This function outputs a list of lists of triplets of integers.
"""
i_x = None
i_y = None
i_z = None
if 'x' in column_names:
i_x = column_names.index('x')
if 'y' in column_names:
i_y = column_names.index('y')
if 'z' in column_names:
i_z = column_names.index('z')
if (((i_x != None) != (i_y != None)) or
((i_y != None) != (i_z != None)) or
((i_z != None) != (i_x != None))):
raise InputError('Error(dump2data): columns must include \"x\", \"y\", and \"z\".\n')
return [[i_x, i_y, i_z]]
def ColNames2Vects(column_names):
""" Which of the columns correspond to coordinates
which must be transformed using rotations?
Some coordinates like dipole moments and
ellipsoid orientations should only be rotated
(not translated).
This function outputs a list of lists of triplets of integers.
"""
vects = []
i_mux = None
i_muy = None
i_muz = None
if 'mux' in column_names:
i_mux = column_names.index('mux')
if 'muy' in column_names:
i_muy = column_names.index('muy')
if 'muz' in column_names:
i_muz = column_names.index('muz')
if (((i_mux != None) != (i_muy != None)) or
((i_muy != None) != (i_muz != None)) or
((i_muz != None) != (i_mux != None))):
raise InputError('Error(dump2data): custom atom_style list must define mux, muy, and muz or none.\n')
if i_mux != None:
vects.append([i_mux, i_muy, i_muz])
i_quati = None
i_quatj = None
i_quatk = None
if 'quati' in column_names:
i_quati = column_names.index('quati')
if 'quatj' in column_names:
i_quatj = column_names.index('quatj')
if 'quatk' in column_names:
i_quatk = column_names.index('quatk')
if (((i_quati != None) != (i_quatj != None)) or
((i_quatj != None) != (i_quatk != None)) or
((i_quatk != None) != (i_quati != None))):
raise InputError('Error(dump2data): custom atom_style list must define quati, quatj, and quatk or none.\n')
if i_quati != None:
vects.append([i_quati, i_quatj, i_quatk])
return vects
def ParseArgs(argv,
misc_settings,
data_settings,
warning_strings=None):
# Loop over the remaining arguments not processed yet.
# These arguments are specific to the lttree.py program
# and are not understood by this program.
i = 1
while i < len(argv):
#sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
if ((argv[i].lower() == '-atomstyle') or
(argv[i].lower() == '-atom_style') or
(argv[i].lower() == '-atom-style')):
in_init = []
if i+1 >= len(argv):
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by a an atom_style name.\n'
' (Or single quoted string which includes a space-separated\n'
' list of column names.)\n')
data_settings.column_names = AtomStyle2ColNames(argv[i+1])
sys.stderr.write(' \"Atoms\" column format:\n')
sys.stderr.write(' '+(' '.join(data_settings.column_names))+'\n')
# ColNames2Coords() and ColNames2Vects() generate lists of
# triplets of integers, storing the column numbers containing
# x, y, and z coordinate values, and vx,vy,vz direction vectors.
data_settings.ii_vects = ColNames2Vects(data_settings.column_names)
ii_coords = ColNames2Coords(data_settings.column_names)
# This program assumes that there is only one coordinate triplet
# (x,y,z) for each atom. Hence we assume that len(ii_coords)==1
assert(len(ii_coords) == 1)
data_settings.i_coords = ii_coords[0]
# Now figure out which columns correspond to atomid, atomtype, molid
data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid(data_settings.column_names)
del(argv[i:i+2])
elif (argv[i].lower() == '-icoord'):
if i+1 >= len(argv):
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers\n'
' corresponding to column numbers for coordinates in\n'
' the \"Atoms\" section of a LAMMPS data file.\n')
ilist = argv[i+1].split()
if (len(ilist) % 3) != 0:
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers.\n'
' This is usually a list of 3 intebers, but it can contain more.\n'
' The number of cooridnate columns must be divisible by 3,\n'
' (even if the simulation is in 2 dimensions)\n')
#ii_coords = []
#for i in range(0, len(ilist)/3):
# cols = [ilist[3*i]+1, ilist[3*i+1]+1, ilist[3*i+2]+1]
# ii_coords.append(cols)
#if ((len(ii_coords) != 0) or (len(ii_coords[0]) != 3)):
# raise InputError('Error(dump2data): Argument \"'+argv[i]+'\" must be followed by exactly 3 integers.\n')
data_settings.i_coords = ilist
if (len(i_coords) != 3):
raise InputError('Error(dump2data): Argument \"'+argv[i]+'\" must be followed by exactly 3 integers.\n')
data_settings.i_coords = ii_coords[0]
del(argv[i:i+2])
elif (argv[i].lower() == '-ivect'):
if i+1 >= len(argv):
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers\n'
' corresponding to column numbers for direction vectors in\n'
' the \"Atoms\" section of a LAMMPS data file.\n')
ilist = argv[i+1].split()
if (len(ilist) % 3) != 0:
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by list of integers.\n'
' This is usually a list of 3 intebers, but it can contain more.\n'
' The number of cooridnate columns must be divisible by 3,\n'
' (even if the simulation is in 2 dimensions)\n')
data_settings.ii_vects = []
for i in range(0, len(ilist)/3):
cols = [ilist[3*i]+1, ilist[3*i+1]+1, ilist[3*i+2]+1]
setting.ii_vects.append(cols)
# This should override any earlier settings as a result of the
# -atomstyle argument. So you can specify a custom list of column
# names using -atomstyle "list of column names", and then afterwards
# specify which of these columns correspond to direction vectors
# using the "-ivect" command line argument later on.
# This way, in theory you should be able to read columns from
# new custom atom-styles that have not been invented yet.
# (Although I haven't tested this.)
del(argv[i:i+2])
# i_atomid is not really needed for this program, but I load it anyway
elif ((argv[i].lower() == '-iatomid') or
(argv[i].lower() == '-iid') or
(argv[i].lower() == '-iatom-id')):
if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n'
' (>=1) indicating which column in the \"Atoms\" section of a\n'
' LAMMPS data file contains the atom id number (typically 1).\n'
' (This argument is unnecessary if you use the -atomstyle argument.)\n')
i_atomid = int(argv[i+1])-1
del(argv[i:i+2])
# i_atomtype is not really needed for this program, but I load it anyway
elif ((argv[i].lower() == '-iatomtype') or
(argv[i].lower() == '-itype') or
(argv[i].lower() == '-iatom-type')):
if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n'
' (>=1) indicating which column in the \"Atoms\" section of a\n'
' LAMMPS data file contains the atom type.\n'
' (This argument is unnecessary if you use the -atomstyle argument.)\n')
i_atomtype = int(argv[i+1])-1
del(argv[i:i+2])
# i_molid is not really needed for this program, but I load it anyway
elif ((argv[i].lower() == '-imolid') or
(argv[i].lower() == '-imol') or
(argv[i].lower() == '-imol-id') or
(argv[i].lower() == '-imoleculeid') or
(argv[i].lower() == '-imolecule-id')):
if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer\n'
' (>=1) indicating which column in the \"Atoms\" section of a\n'
' LAMMPS data file contains the molecule id number.\n'
' (This argument is unnecessary if you use the -atomstyle argument.)\n')
del(argv[i:i+2])
# Which frame do we want?
elif (argv[i].lower() == '-t'):
if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer indicating\n'
' the frame you want to extract from the dump file (trajectory).\n'
' This integer should match the timestep corresponding to the frame\n'
' whose coordinates you wish to extract.\n')
misc_settings.timestep_str = argv[i+1]
del(argv[i:i+2])
misc_settings.multi = False
+ misc_settings.last_frame = False
elif (argv[i].lower() == '-tstart'):
if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an integer indicating\n'
' the first frame you want to extract from the dump file (trajectory).\n'
' This integer should match the timestep corresponding to the frame\n'
' (after which) you wish to extract coordinates.\n')
misc_settings.tstart = float(argv[i+1])
del(argv[i:i+2])
misc_settings.multi = True
elif (argv[i].lower() == '-tstop'):
if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
raise InputError('Error(dump2data): '+argv[i]+' flag should be followed by an number indicating\n'
' the first frame you want to extract from the dump file (trajectory).\n'
' Frames after this timestep will be ignored.\n')
misc_settings.tstop = float(argv[i+1])
del(argv[i:i+2])
misc_settings.multi = True
elif (argv[i].lower() == '-center'):
misc_settings.center_frame = True
del(argv[i:i+1])
elif ((argv[i].lower() == '-raw') or (argv[i].lower() == '-rawout')):
misc_settings.output_format = 'raw'
del(argv[i:i+1])
elif (argv[i].lower() == '-rawin'):
misc_settings.input_format = 'raw'
misc_settings.multi = False
del(argv[i:i+1])
elif ((argv[i].lower() == '-xyz') or (argv[i].lower() == '-xyzout')):
misc_settings.output_format = 'xyz'
del(argv[i:i+1])
elif (argv[i].lower() == '-xyzin'):
misc_settings.input_format = 'xyz'
misc_settings.multi = False
del(argv[i:i+1])
elif (argv[i].lower() == '-multi'):
- # This is usually not necessary for the user
- # because "-multi" is on by default
misc_settings.multi = True
del(argv[i:i+1])
elif (argv[i].lower() == '-last'):
misc_settings.last_frame = True
misc_settings.multi = False
del(argv[i:i+1])
elif (argv[i].lower() == '-interval'):
misc_settings.skip_interval = int(argv[i+1])
del(argv[i:i+2])
elif (argv[i].lower() == '-scale'):
misc_settings.scale = float(argv[i+1])
del(argv[i:i+2])
elif ((argv[i][0] == '-') and (__name__ == "__main__")):
raise InputError('Error(dump2data): Unrecogized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
usage_examples = \
""" Typical usage:
dump2data.py orig_file.data < dump.lammpstrj > new_file.data
(This extracts last frame, uses "full" atom_style.)
Additional options:
-dump2data.py -time t -atomstyle style orig.data < dump.lammpstrj > new.data
+dump2data.py -t t -atomstyle style orig.data < dump.lammpstrj > new.data
"""
#if __name__ == "__main__":
if (len(argv) > 2):
# if there are more than 2 remaining arguments,
# AND
# no other function will process the remaining argument list
# (ie. if __name__ == "__main__")
# THEN
raise InputError(' ----\n'
'ERROR(dump2data): You have too many arguments (or unrecognized arguments):\n'
' \"'+(' '.join(argv))+'\"\n'
' ----\n'
+usage_examples)
elif (len(argv) < 2):
if misc_settings.output_format == 'data':
raise InputError(' ----\n'
'ERROR(dump2data): Problem with argument list:\n'
' Expected a LAMMPS .data file as an argument.\n'
' ----\n'
+usage_examples)
else:
in_data_file = open(argv[1], 'r')
data_settings.file_name = argv[1];
data_settings.contents = in_data_file.readlines()
in_data_file.close()
#end of if-then statement for "if __name__ == "__main__""
if len(data_settings.i_coords) == 0:
if warning_strings != None:
warning_strings.append('WARNING(dump2data): atom_style unknown. (Use -atomstyle style. Assuming \"full\")')
warn_atom_style_unspecified = True
# The default atom_style is "full"
data_settings.column_names = AtomStyle2ColNames('full')
ii_coords = ColNames2Coords(data_settings.column_names)
# This program assumes that there is only one coordinate triplet
# (x,y,z) for each atom. Hence we assume that len(ii_coords)==1
assert(len(ii_coords) == 1)
data_settings.i_coords = ii_coords[0]
data_settings.ii_vects = ColNames2Vects(data_settings.column_names)
data_settings.i_atomid, data_settings.i_atomtype, data_settings.i_molid = ColNames2AidAtypeMolid(data_settings.column_names)
### sys.stderr.write('########################################################\n'
### '## WARNING: atom_style unspecified ##\n'
### '## --> \"Atoms\" column data has an unknown format. ##\n'
### '## Assuming atom_style = \"full\" ##\n'
### '########################################################\n'
### '## To specify the \"Atoms\" column format you can: ##\n'
### '## 1) Use the -atom_style \"STYLE\" argument ##\n'
### '## where \"STYLE\" is a string indicating a LAMMPS ##\n'
### '## atom_style, including hybrid styles.(Standard ##\n'
### '## atom styles defined in 2011 are supported.) ##\n'
### '## 2) Use the -atom_style \"COL_LIST\" argument ##\n'
### '## where \"COL_LIST" is a quoted list of strings ##\n'
### '## indicating the name of each column. ##\n'
### '## Names \"x\",\"y\",\"z\" are interpreted as ##\n'
### '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n'
### '## and \"quati\",\"quatj\",\"quatk\" are ##\n'
### '## interpreted as direction vectors. ##\n'
### '## 3) Use the -icoord \"cx cy cz...\" argument ##\n'
### '## where \"cx cy cz\" is a list of integers ##\n'
### '## indicating the column numbers for the x,y,z ##\n'
### '## coordinates of each atom. ##\n'
### '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n'
### '## where \"cmux cmuy cmuz...\" is a list of ##\n'
### '## integers indicating the column numbers for ##\n'
### '## the vector that determines the direction of a ##\n'
### '## dipole or ellipsoid (ie. a rotateable vector).##\n'
### '## (More than one triplet can be specified. The ##\n'
### '## number of entries must be divisible by 3.) ##\n'
### '## 5) Include a ##\n'
### '## write(\"in_init.txt\"){atom_style ...} ##\n'
### '## statement in your .ttree file. ##\n'
### '########################################################\n')
def GetIntAtomID(pair):
return int(pair[0])
def WriteFrameToData(out_file,
descr_str,
misc_settings,
data_settings,
natoms,
coords,
coords_ixiyiz,
vects,
velocities,
xlo_str, xhi_str,
ylo_str, yhi_str,
zlo_str, zhi_str,
xy_str, xz_str, yz_str):
"""
Open a data file. Read the LAMMPS DATA file line by line.
When the line contains information which is also in the dump file,
replace that information with information from the dump file.
(Information from a dump file is stored in the arguments to this function.)
The resulting file also has LAMMPS DATA format.
"""
section = ''
firstline = True
for line in data_settings.contents:
line = line.strip()
ic = line.find('#')
if ic != -1:
line = line[:ic]
if firstline: # Construct a new descriptive header line:
if descr_str != None:
line = descr_str
firstline = False
if (len(line) > 0):
# The initial section (section='') is assumed to be
# the "LAMMPS Description" section. This is where the
# box boundaries are specified.
if section == '':
tokens = line.split()
if ((len(tokens) >= 2) and
((tokens[-2] == 'xlo') and (tokens[-1] == 'xhi')) and
((xlo_str != None) and (xhi_str != None))):
tokens[0] = xlo_str
tokens[1] = xhi_str
line = ' '.join(tokens)
elif ((len(tokens) >= 2) and
((tokens[-2] == 'ylo') and (tokens[-1] == 'yhi')) and
((ylo_str != None) and (yhi_str != None))):
tokens[0] = ylo_str
tokens[1] = yhi_str
line = ' '.join(tokens)
elif ((len(tokens) >= 2) and
((tokens[-2] == 'zlo') and (tokens[-1] == 'zhi')) and
((zlo_str != None) and (zhi_str != None))):
tokens[0] = zlo_str
tokens[1] = zhi_str
line = ' '.join(tokens)
elif ((len(tokens) >= 3) and
((tokens[-3] == 'xy') and
(tokens[-2] == 'xz') and
(tokens[-1] == 'yz')) and
((xy_str != None) and
(xz_str != None) and
(yz_str != None))):
tokens[0] = xy_str
tokens[1] = xz_str
tokens[2] = yz_str
line = ' '.join(tokens)
if (line in set(['Masses', 'Velocities', 'Atoms',
'Bond Coeffs', 'Angle Coeffs',
'Dihedral Coeffs', 'Improper Coeffs',
'Bonds', 'Angles', 'Dihedrals', 'Impropers'])):
section = line
else:
if (section == 'Atoms'):
tokens = line.split()
atomid = tokens[0]
if atomid in coords:
# Loop over all of the vector degrees of
# freedom of the particle, excluding coords
# (for example: mu_x, mu_y, mu_z,
# or quat_i, quat_j, quat_k)
# In principle, depending on the atom_style,
# there could be multiple vectors per atom.
for I in range(0,len(data_settings.ii_vects)):
vxvyvz = vects[atomid][I]
i_vx = data_settings.ii_vects[I][0]
i_vy = data_settings.ii_vects[I][1]
i_vz = data_settings.ii_vects[I][2]
if ((i_vx >= len(tokens)) or
(i_vy >= len(tokens)) or
(i_vz >= len(tokens))):
raise InputError('Error(dump2data): Atom style incompatible with data file.\n'
' Specify the atom_style using -atomstyle style.\n')
if ((vxvyvz == None) or
(type(vxvyvz) is not tuple)):
assert(data_settings.column_names[i_vx] not in dump_column_names)
raise InputError('Error(dump2data): You have a vector coordinate in your DATA file named \"'+data_settings.column_names[i_vx]+'\"\n'
' However there are no columns with this name in your DUMP file\n'
' (or the column was not in the expected place).\n'
' Hence, the atom styles in the dump and data files do not match.')
# Replace the vector components with numbers
# from the dump file
tokens[i_vx] = vxvyvz[0]
tokens[i_vy] = vxvyvz[1]
tokens[i_vz] = vxvyvz[2]
# Now loop over the coordinates of each atom.
#for I in range(0,len(data_settings.ii_coords)):
# xyz = coords[atomid][I]
# THIS LOOP IS SILLY.
# EACH ATOM ONLY HAS ONE SET OF X,Y,Z
# COORDINATES. COMMENTING OUT THIS LOOP:
# i_x = data_settings.ii_coords[I][0]
# i_y = data_settings.ii_coords[I][1]
# i_z = data_settings.ii_coords[I][2]
# USING THIS INSTEAD:
xyz = coords[atomid]
i_x = data_settings.i_coords[0]
i_y = data_settings.i_coords[1]
i_z = data_settings.i_coords[2]
if ((i_x >= len(tokens)) or
(i_y >= len(tokens)) or
(i_z >= len(tokens))):
raise InputError('Error(dump2data): Atom style incompatible with data file.\n'
' Specify the atom_style using -atomstyle style.\n')
# Replace the coordinates with coordinates from
# the dump file into tokens[i_x]...
tokens[i_x] = str(xyz[0])
tokens[i_y] = str(xyz[1])
tokens[i_z] = str(xyz[2])
# Are there there any integer coords
# (ix, iy, iz) in the dump file?
if coords_ixiyiz[atomid]:
assert(len(coords_ixiyiz[atomid]) == 3)
# Integer coords stored in the DATA file too?
if len(tokens)==(len(data_settings.column_names)+3):
# Then replace the last 3 columns of the
# line in the data file with: ix iy iz
tokens[-3] = coords_ixiyiz[atomid][0]
tokens[-2] = coords_ixiyiz[atomid][1]
tokens[-1] = coords_ixiyiz[atomid][2]
else:
if (not misc_settings.center_frame):
# Append them to the end of the line:
tokens.append(coords_ixiyiz[atomid][0])
tokens.append(coords_ixiyiz[atomid][1])
tokens.append(coords_ixiyiz[atomid][2])
# Now finally paste all the tokens together:
line = ' '.join(tokens)
elif (section == 'Velocities'):
tokens = line.split()
atomid = tokens[0]
if atomid in velocities:
vxvyvz = velocities[atomid]
if len(tokens) < 4:
raise InputError('Error(dump2data): Not enough columns in the \"Velocities\" file.\n')
# Replace the coordinates with coordinates from
# the dump file into tokens[i_x]...
tokens[1] = str(vxvyvz[0])
tokens[2] = str(vxvyvz[1])
tokens[3] = str(vxvyvz[2])
# Now finally paste all the tokens together:
line = ' '.join(tokens)
out_file.write(line+'\n')
if __name__ == "__main__":
g_program_name = 'dump2data.py'
- g_date_str = '2013-9-19'
- g_version_str = 'v0.42'
+ g_date_str = '2013-10-30'
+ g_version_str = 'v0.43'
####### Main Code Below: #######
sys.stderr.write(g_program_name+' '+g_version_str+' '+g_date_str+' ')
#if sys.version < '3':
# sys.stderr.write(' (python version < 3)\n')
#else:
sys.stderr.write('\n')
try:
data_settings = DataSettings()
misc_settings = MiscSettings()
warning_strings = []
ParseArgs(sys.argv,
misc_settings,
data_settings,
warning_strings)
# Open the lammps dump file (trajectory file)
# Skip to the line containing the correct frame/timestep.
# (this is the last frame by default).
# Read the "BOX BOUNDS" and the "ATOMS" sections.
# Store the x,y,z coordinates in the "coords" associative array
# (indexed by atom id, which could be non-numeric in general).
section = ''
#coords = defaultdict(list)
#coords_ixiyiz = defaultdict(list)
#vects = defaultdict(list)
#xlo_str = xhi_str = ylo_str = yhi_str = zlo_str = zhi_str = None
#xy_str = xz_str = yz_str = None
#natoms = -1
#timestep_str = ''
frame_coords = defaultdict(list)
frame_coords_ixiyiz = defaultdict(list)
frame_vects = defaultdict(list)
frame_velocities = defaultdict(list)
frame_xlo_str = frame_xhi_str = None
frame_ylo_str = frame_yhi_str = None
frame_zlo_str = frame_zhi_str = None
frame_xy_str = frame_xz_str = frame_yz_str = None
frame_natoms = -1
frame_timestep_str = ''
i_atomid = i_atomtype = i_molid = -1
i_x = i_y = i_z = i_xu = i_yu = i_zu = -1
i_xs = i_ys = i_zs = i_xsu = i_ysu = i_zsu = -1
dump_column_names = []
#num_frames_in = -1
num_frames_out = 0
finished_reading_frame = False
read_last_frame = False
#in_coord_file = open('traj_nvt.lammpstrj','r')
#in_coord_file = open('deleteme.lammpstrj','r')
in_coord_file = sys.stdin
while True:
line = in_coord_file.readline()
if line == '': # if EOF
if len(frame_coords) > 0:
finished_reading_frame = True
read_last_frame = True
line = line.strip()
if (line.find('ITEM:') == 0):
section = line
if (section.find('ITEM: ATOMS ') == 0):
dump_column_names = line[12:].split()
i_atomid, i_atomtype, i_molid = \
ColNames2AidAtypeMolid(dump_column_names)
#ii_coords = ColNames2Coords(dump_column_names)
if 'x' in dump_column_names:
i_x = dump_column_names.index('x')
elif 'xu' in dump_column_names:
i_xu = dump_column_names.index('xu')
elif 'xs' in dump_column_names:
i_xs = dump_column_names.index('xs')
elif 'xsu' in dump_column_names:
i_xsu = dump_column_names.index('xsu')
else:
raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"x\" column.\n'+
' (excerpt below)\n' + line)
if 'y' in dump_column_names:
i_y = dump_column_names.index('y')
elif 'yu' in dump_column_names:
i_yu = dump_column_names.index('yu')
elif 'ys' in dump_column_names:
i_ys = dump_column_names.index('ys')
elif 'ysu' in dump_column_names:
i_ysu = dump_column_names.index('ysu')
else:
raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"y\" column.\n'+
' (excerpt below)\n' + line)
if 'z' in dump_column_names:
i_z = dump_column_names.index('z')
elif 'zu' in dump_column_names:
i_zu = dump_column_names.index('zu')
elif 'zs' in dump_column_names:
i_zs = dump_column_names.index('zs')
elif 'zsu' in dump_column_names:
i_zsu = dump_column_names.index('zsu')
else:
raise InputError('Error(dump2data): \"ATOMS\" section of dump file lacks a \"z\" column.\n'+
' (excerpt below)\n' + line)
ii_vects = ColNames2Vects(dump_column_names)
if (len(ii_vects) != len(data_settings.ii_vects)):
raise InputError('Error(dump2data): atom styles in data and dump files differ.\n'
' Some needed columns from the atom_styles are missing in the dump file.')
i_ix = i_iy = i_iz = -1
if 'ix' in dump_column_names:
i_ix = dump_column_names.index('ix')
if 'iy' in dump_column_names:
i_iy = dump_column_names.index('iy')
if 'iz' in dump_column_names:
i_iz = dump_column_names.index('iz')
i_vx = i_vy = i_vz = -1
if 'vx' in dump_column_names:
i_vx = dump_column_names.index('vx')
if 'vy' in dump_column_names:
i_vy = dump_column_names.index('vy')
if 'vz' in dump_column_names:
i_vz = dump_column_names.index('vz')
elif (section.find('ITEM: BOX BOUNDS') == 0):
avec=[1.0, 0.0, 0.0]
bvec=[0.0, 1.0, 0.0]
cvec=[0.0, 0.0, 1.0]
elif (section.find('ITEM: TIMESTEP') == 0):
if len(frame_coords) > 0:
finished_reading_frame = True
elif ((len(line) > 0) and (line[0] != '#')):
if (section.find('ITEM: TIMESTEP') == 0):
finished_reading_frame = False
frame_timestep_str = line
frame_coords = defaultdict(list)
frame_coords_ixiyiz = defaultdict(list)
frame_vects = defaultdict(list)
frame_velocities = defaultdict(list)
frame_xlo_str = frame_xhi_str = None
frame_ylo_str = frame_yhi_str = None
frame_zlo_str = frame_zhi_str = None
frame_xy_str = frame_xz_str = frame_yz_str = None
elif (section == 'ITEM: NUMBER OF ATOMS'):
frame_natoms = int(line)
elif (section.find('ITEM: BOX BOUNDS') == 0):
is_triclinic = (section.find('xy xz yz') == 0)
tokens = line.split()
if not frame_xlo_str:
assert(not frame_xhi_str)
frame_xlo_str = tokens[0]
frame_xhi_str = tokens[1]
avec[0] = float(frame_xhi_str) - float(frame_xlo_str)
if (is_triclinic and (len(tokens) > 2)):
frame_xy_str = tokens[2]
bvec[0] = float(frame_xy_str)
#See http://lammps.sandia.gov/doc/Section_howto.html#howto_12
#sys.stderr.write('avec='+str(avec)+'\n')
elif not frame_ylo_str:
assert(not frame_yhi_str)
frame_ylo_str = tokens[0]
frame_yhi_str = tokens[1]
bvec[1] = float(frame_yhi_str) - float(frame_ylo_str)
if (is_triclinic and (len(tokens) > 2)):
frame_xz_str = tokens[2]
cvec[0] = float(frame_xz_str)
#See http://lammps.sandia.gov/doc/Section_howto.html#howto_12
#sys.stderr.write('bvec='+str(bvec)+'\n')
elif not frame_zlo_str:
assert(not frame_zhi_str)
frame_zlo_str = tokens[0]
frame_zhi_str = tokens[1]
cvec = [0.0, 0.0, float(frame_zhi_str) - float(frame_zlo_str)]
if (is_triclinic and (len(tokens) > 2)):
frame_yz_str = tokens[2]
cvec[1] = float(frame_yz_str)
#See http://lammps.sandia.gov/doc/Section_howto.html#howto_12
#sys.stderr.write('cvec='+str(cvec)+'\n')
elif (section.find('ITEM: ATOMS') == 0):
tokens = line.split()
atomid = tokens[i_atomid]
if ((i_x != -1) and (i_y != -1) and (i_z != -1)):
x = float(tokens[i_x]) #i_x determined above
y = float(tokens[i_y])
z = float(tokens[i_z])
elif ((i_xu != -1) and (i_yu != -1) and (i_zu != -1)):
x = float(tokens[i_xu]) #i_x determined above
y = float(tokens[i_yu])
z = float(tokens[i_zu])
elif ((i_xs != -1) and (i_ys != -1) and (i_zs != -1)):
xs = float(tokens[i_xs]) #i_xs determined above
ys = float(tokens[i_ys])
zs = float(tokens[i_zs])
x = float(xlo_str) + xs*avec[0] + ys*bvec[0] + zs*cvec[0]
y = float(ylo_str) + xs*avec[1] + ys*bvec[1] + zs*cvec[1]
z = float(zlo_str) + xs*avec[2] + ys*bvec[2] + zs*cvec[2]
# avec, bvec, cvec described here:
#http://lammps.sandia.gov/doc/Section_howto.html#howto_12
elif ((i_xsu != -1) and (i_ysu != -1) and (i_zsu != -1)):
xsu = float(tokens[i_xsu]) #i_xs determined above
ysu = float(tokens[i_ysu])
zsu = float(tokens[i_zsu])
x = float(xlo_str) + xsu*avec[0] + ysu*bvec[0] + zsu*cvec[0]
y = float(ylo_str) + xsu*avec[1] + ysu*bvec[1] + zsu*cvec[1]
z = float(zlo_str) + xsu*avec[2] + ysu*bvec[2] + zsu*cvec[2]
# Now deal with ix, iy, iz
if i_ix != -1:
ix = int(tokens[i_ix])
if (misc_settings.center_frame or
(misc_settings.output_format != 'data')):
#sys.stderr.write('ix = '+str(ix)+', avec='+str(avec)+'\n')
x += ix*avec[0]
y += ix*avec[1]
z += ix*avec[2]
else:
if atomid not in frame_coords_ixiyiz:
frame_coords_ixiyiz[atomid] = ["0", "0", "0"]
else:
frame_coords_ixiyiz[atomid][0] = str(ix)
if i_iy != -1:
iy = int(tokens[i_iy])
if (misc_settings.center_frame or
(misc_settings.output_format != 'data')):
#sys.stderr.write('iy = '+str(iy)+', bvec='+str(bvec)+'\n')
x += iy*bvec[0]
y += iy*bvec[1]
z += iy*bvec[2]
else:
if atomid not in frame_coords_ixiyiz:
frame_coords_ixiyiz[atomid] = ["0", "0", "0"]
else:
frame_coords_ixiyiz[atomid][1] = str(iy)
if i_iz != -1:
iz = int(tokens[i_iz])
if (misc_settings.center_frame or
(misc_settings.output_format != 'data')):
#sys.stderr.write('iz = '+str(iz)+', cvec='+str(cvec)+'\n')
x += iz*cvec[0]
y += iz*cvec[1]
z += iz*cvec[2]
else:
if atomid not in frame_coords_ixiyiz:
frame_coords_ixiyiz[atomid] = ["0", "0", "0"]
else:
frame_coords_ixiyiz[atomid][2] = str(iz)
#frame_coords[atomid] = [str(x), str(y), str(z)]
frame_coords[atomid] = [x, y, z]
vx = 0.0
vy = 0.0
vz = 0.0
if i_vx != -1:
vx = float(tokens[i_vx])
if i_vy != -1:
vy = float(tokens[i_vy])
if i_vz != -1:
vz = float(tokens[i_vz])
frame_velocities[atomid] = [vx, vy, vz]
# Ugly detail:
# There can be multiple "vects" associated with each atom
# (for example, dipole moments, ellipsoid directions, etc..)
if atomid not in frame_vects:
frame_vects[atomid] = [None for I in range(0,len(ii_vects))]
for I in range(0, len(ii_vects)):
i_vx = ii_vects[I][0]
i_vy = ii_vects[I][1]
i_vz = ii_vects[I][2]
vx_str = tokens[i_vx]
vy_str = tokens[i_vy]
vz_str = tokens[i_vz]
# Now the annoying part:
# Which vect is it (mux,muy,muz) or (quati,quatj,quatk)?
# The columns could be listed in a different order
# in the data file and in the dump file.
# Figure out which vector it is in the data file (stored
# in the integer "I_data") so that column names match.
name_vx = dump_column_names[i_vx]
name_vy = dump_column_names[i_vy]
name_vz = dump_column_names[i_vz]
i_vx_data = 0
I_data = -1
# This code is ugly and inneficient.
# I never want to touch this code again. (Hope it works)
while i_vx_data < len(data_settings.column_names):
if name_vx == data_settings.column_names[i_vx_data]:
I_data = 0
while I_data < len(data_settings.ii_vects):
if ii_vects[I] == data_settings.ii_vects[I_data]:
break
I_data += 1
if (0<I_data) and (I_data < len(data_settings.ii_vects)):
break
i_vx_data += 1
if (0 <= I_data) and (I_data < len(data_settings.ii_vects)):
frame_vects[atomid][I_data] = (vx_str,vy_str,vz_str)
else:
raise InputError('Error(dump2data): You have a vector coordinate in your dump file named \"'+name_vx+'\"\n'
' However there are no columns with this name in your data file\n'
' (or the column was not in the expected place).\n'
' Hence, the atom styles in the dump and data files do not match.')
if finished_reading_frame:
if misc_settings.scale != None:
for atomid in frame_coords:
for d in range(0,3):
crd = float(frame_coords[atomid][d])
frame_coords[atomid][d] = str(crd*misc_settings.scale)
if len(frame_coords) != frame_natoms:
err_msg = 'Number of lines in \"ITEM: ATOMS\" section disagrees with\n' \
+ ' \"ITEM: NUMBER OF ATOMS\" declared earlier in this file.\n'
raise InputError(err_msg)
if misc_settings.center_frame:
cm = [0.0, 0.0, 0.0]
for atomid in frame_coords:
for d in range(0,3):
cm[d] += float(frame_coords[atomid][d])
for d in range(0,3):
cm[d] /= float(len(frame_coords))
for atomid in frame_coords:
for d in range(0,3):
frame_coords[atomid][d] = "%.7g" % (float(frame_coords[atomid][d]) - cm[d])
frame_coords_ixiyiz[atomid] = ["0","0","0"]
if misc_settings.output_format != 'data':
frame_coords_ixiyiz[atomid] = ["0","0","0"]
#if (num_frames_in == -1):
# if (misc_settings.timestep_str != ''):
# if (float(frame_timestep_str) >=
# float(misc_settings.timestep_str)):
# num_frames_in = 1
# if not misc_settings.multi:
# read_last_frame = True
# else:
# num_frames_in = 1
# Should we write out the coordinates in this frame?
write_this_frame = False
if misc_settings.multi:
write_this_frame = True
if (misc_settings.tstart and
(int(frame_timestep_str) < misc_settings.tstart)):
write_this_frame = False
if (misc_settings.tstop and
(int(frame_timestep_str) > misc_settings.tstop)):
write_this_frame = False
read_last_frame = True
if misc_settings.tstart:
tstart = misc_settings.tstart
else:
tstart = 0
if ((int(frame_timestep_str) - tstart)
%
misc_settings.skip_interval) != 0:
write_this_frame = False
else:
if misc_settings.last_frame:
if read_last_frame:
write_this_frame = True
else:
assert(misc_settings.timestep_str)
if (int(frame_timestep_str) >=
int(misc_settings.timestep_str)):
write_this_frame = True
read_last_frame = True
if write_this_frame:
num_frames_out += 1
sys.stderr.write(' (writing frame '+str(num_frames_out)+
' at timestep '+frame_timestep_str+')\n')
# Print the frame
# First check which format to output the data:
if misc_settings.output_format == 'raw':
# Print out the coordinates in simple 3-column text format
for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)):
if misc_settings.scale == None:
sys.stdout.write(str(xyz[0])+' '+str(xyz[1])+' '+str(xyz[2])+'\n')
else:
# Only convert to float and back if misc_settings.scale != None
sys.stdout.write(str(misc_settings.scale*float(xyz[0]))+' '+
str(misc_settings.scale*float(xyz[1]))+' '+
str(misc_settings.scale*float(xyz[2]))+'\n')
sys.stdout.write('\n')
elif misc_settings.output_format == 'xyz':
# Print out the coordinates in simple 3-column text format
sys.stdout.write(str(len(frame_coords))+'\n')
descr_str = 'LAMMPS data from timestep '+frame_timestep_str
sys.stdout.write(descr_str+'\n')
for atomid, xyz in iter(sorted(frame_coords.items(), key=GetIntAtomID)):
if misc_settings.scale == None:
sys.stdout.write(str(atomid)+' '+
str(xyz[0])+' '+
str(xyz[1])+' '+
str(xyz[2])+'\n')
else:
# Only convert to float and back if misc_settings.scale != None
sys.stdout.write(str(atomid)+' '+
str(misc_settings.scale*float(xyz[0]))+' '+
str(misc_settings.scale*float(xyz[1]))+' '+
str(misc_settings.scale*float(xyz[2]))+'\n')
else:
# Parse the DATA file specified by the user
# and replace appropriate lines or fields with
# the corresponding text from the DUMP file.
descr_str = 'LAMMPS data from timestep '+frame_timestep_str
- if misc_settings.multi:
+ if misc_settings.multi and (misc_settings.output_format == 'data'):
out_file_name = data_settings.file_name + '.'\
+ str(num_frames_out)
sys.stderr.write(' (creating file \"'+out_file_name+'\")\n')
out_file = open(out_file_name, 'w')
else:
out_file = sys.stdout
WriteFrameToData(out_file,
descr_str,
misc_settings,
data_settings,
frame_natoms,
frame_coords,
frame_coords_ixiyiz,
frame_vects,
frame_velocities,
frame_xlo_str, frame_xhi_str,
frame_ylo_str, frame_yhi_str,
frame_zlo_str, frame_zhi_str,
frame_xy_str, frame_xz_str, frame_yz_str)
#if misc_settings.multi:
# out_file.close()
#if num_frames_in >= 0:
# num_frames_in += 1
if read_last_frame:
exit(0)
for warning_str in warning_strings:
sys.stderr.write(warning_str+'\n')
except (ValueError, InputError) as err:
sys.stderr.write('\n'+str(err)+'\n')
sys.exit(-1)
diff --git a/tools/moltemplate/src/lttree.py b/tools/moltemplate/src/lttree.py
index 4a9f3fad9..5d1b34b7b 100755
--- a/tools/moltemplate/src/lttree.py
+++ b/tools/moltemplate/src/lttree.py
@@ -1,745 +1,745 @@
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
lttree.py
lttree.py is an extension of the generic ttree.py program.
This version can understand and manipulate ttree-style templates which
are specialized for storing molecule-specific data for use in LAMMPS.
The main difference between lttree.py and ttree.py is:
Unlike ttree.py, lttree.py understands rigid-body movement commands like
"rot()" and "move()" which allows it to reorient and move each copy
of a molecule to a new location. (ttree.py just ignores these commands.
Consequently LAMMPS input file (fragments) created with ttree.py have
invalid (overlapping) atomic coordinates and must be modified or aguemted
later (by loading atomic coordinates from a PDB file or an XYZ file).
lttree.py understands the "Data Atoms" section of a LAMMPS
data file (in addition to the various "atom_styles" which effect it).
Additional LAMMPS-specific features may be added in the future.
"""
import sys
from ttree import *
from lttree_styles import *
from ttree_matrix_stack import *
try:
unicode
except NameError:
# Python 3
basestring = unicode = str
class LttreeSettings(BasicUISettings):
def __init__(self,
user_bindings_x=None,
user_bindings=None,
order_method='by_command'):
BasicUISettings.__init__(self,
user_bindings_x,
user_bindings,
order_method)
# The following new member data indicate which columns store
# LAMMPS-specific information.
# The next 6 members store keep track of the different columns
# of the "Data Atoms" section of a LAMMPS data file:
self.column_names = [] #<--A list of column names (optional)
self.ii_coords=[] #<--A list of triplets of column indexes storing coordinate data
self.ii_vects=[] #<--A list of triplets of column indexes storing directional data
# (such as dipole or ellipsoid orientations)
self.i_atomid=None #<--An integer indicating which column has the atomid
self.i_atomtype=None #<--An integer indicating which column has the atomtype
self.i_molid=None #<--An integer indicating which column has the molid, if applicable
self.infile=None # Name of the outermost file. This is the file
# which was read at the moment parsing begins.
def LttreeParseArgs(argv, settings):
BasicUIParseArgs(argv, settings)
# Loop over the remaining arguments not processed yet.
# These arguments are specific to the lttree.py program
# and are not understood by ttree.py:
i = 1
while i < len(argv):
#sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
if ((argv[i].lower() == '-atomstyle') or
(argv[i].lower() == '-atom-style') or
(argv[i].lower() == '-atom_style')):
if i+1 >= len(argv):
raise InputError('Error('+g_program_name+'): The '+argv[i]+' flag should be followed by a LAMMPS\n'
' atom_style name (or single quoted string containing a space-separated\n'
' list of column names such as: atom-ID atom-type q x y z molecule-ID.)\n')
settings.column_names = AtomStyle2ColNames(argv[i+1])
sys.stderr.write('\n \"'+data_atoms+'\" column format:\n')
sys.stderr.write(' '+(' '.join(settings.column_names))+'\n\n')
settings.ii_coords = ColNames2Coords(settings.column_names)
settings.ii_vects = ColNames2Vects(settings.column_names)
settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names)
del(argv[i:i+2])
elif (argv[i].lower() == '-icoord'):
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n'
' corresponding to column numbers for coordinates in\n'
' the \"'+data_atoms+'\" section of a LAMMPS data file.\n')
ilist = argv[i+1].split()
if (len(ilist) % 3) != 0:
raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n'
' This is usually a list of 3 integers, but it can contain more.\n'
' The number of cooridnate columns must be divisible by 3,\n'
' (even if the simulation is in 2 dimensions)\n')
settings.iaffinevects = []
for i in range(0, len(ilist)/3):
cols = [int(ilist[3*i])+1,
int(ilist[3*i+1])+1,
int(ilist[3*i+2])+1]
settings.iaffinevects.append(cols)
del(argv[i:i+2])
elif (argv[i].lower() == '-ivect'):
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by list of integers\n'
' corresponding to column numbers for direction vectors in\n'
' the \"'+data_atoms+'\" section of a LAMMPS data file.\n')
ilist = argv[i+1].split()
if (len(ilist) % 3) != 0:
raise InputError('Error: '+argv[i]+' flag should be followed by list of integers.\n'
' This is usually a list of 3 integers, but it can contain more.\n'
' The number of cooridnate columns must be divisible by 3,\n'
' (even if the simulation is in 2 dimensions)\n')
settings.ivects = []
for i in range(0, len(ilist)/3):
cols = [int(ilist[3*i])+1,
int(ilist[3*i+1])+1,
int(ilist[3*i+2])+1]
settings.ivects.append(cols)
del(argv[i:i+2])
elif ((argv[i].lower() == '-iatomid') or
(argv[i].lower() == '-iid') or
(argv[i].lower() == '-iatom-id')):
if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n'
' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n'
' LAMMPS data file contains the atom id number (typically 1).\n'
' (This argument is unnecessary if you use the -atomstyle argument.)\n')
i_atomid = int(argv[i+1])-1
del(argv[i:i+2])
elif ((argv[i].lower() == '-iatomtype') or
(argv[i].lower() == '-itype') or
(argv[i].lower() == '-iatom-type')):
if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n'
' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n'
' LAMMPS data file contains the atom type.\n'
' (This argument is unnecessary if you use the -atomstyle argument.)\n')
i_atomtype = int(argv[i+1])-1
del(argv[i:i+2])
elif ((argv[i].lower() == '-imolid') or
(argv[i].lower() == '-imol') or
(argv[i].lower() == '-imol-id') or
(argv[i].lower() == '-imoleculeid') or
(argv[i].lower() == '-imolecule-id')):
if ((i+1 >= len(argv)) or (not str.isdigit(argv[i+1]))):
raise InputError('Error: '+argv[i]+' flag should be followed by an integer\n'
' (>=1) indicating which column in the \"'+data_atoms+'\" section of a\n'
' LAMMPS data file contains the molecule id number.\n'
' (This argument is unnecessary if you use the -atomstyle argument.)\n')
i_molid = int(argv[i+1])-1
del(argv[i:i+2])
elif ((argv[i][0] == '-') and (__name__ == "__main__")):
#elif (__name__ == "__main__"):
raise InputError('Error('+g_program_name+'):\n'
'Unrecogized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
if __name__ == "__main__":
# Instantiate the lexer we will be using.
# (The lexer's __init__() function requires an openned file.
# Assuming __name__ == "__main__", then the name of that file should
# be the last remaining (unprocessed) argument in the argument list.
# Otherwise, then name of that file will be determined later by the
# python script which imports this module, so we let them handle it.)
if len(argv) == 1:
raise InputError('Error: This program requires at least one argument\n'
' the name of a file containing ttree template commands\n')
elif len(argv) == 2:
try:
settings.lex = TemplateLexer(open(argv[1], 'r'), argv[1]) # Parse text from file
except IOError:
sys.stderr.write('Error: unable to open file\n'
' \"'+argv[1]+'\"\n'
' for reading.\n')
sys.exit(1)
del(argv[1:2])
else:
# if there are more than 2 remaining arguments,
problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
raise InputError('Syntax Error('+g_program_name+'):\n\n'
' Problem with argument list.\n'
' The remaining arguments are:\n\n'
' '+(' '.join(problem_args))+'\n\n'
' (The actual problem may be earlier in the argument list.\n'
' If these arguments are source files, then keep in mind\n'
' that this program can not parse multiple source files.)\n'
' Check the syntax of the entire argument list.\n')
if len(settings.ii_coords) == 0:
sys.stderr.write('########################################################\n'
'## WARNING: atom_style unspecified ##\n'
'## --> \"'+data_atoms+'\" column data has an unknown format ##\n'
'## Assuming atom_style = \"full\" ##\n'
# '########################################################\n'
# '## To specify the \"'+data_atoms+'\" column format you can: ##\n'
# '## 1) Use the -atomstyle \"STYLE\" argument ##\n'
# '## where \"STYLE\" is a string indicating a LAMMPS ##\n'
# '## atom_style, including hybrid styles.(Standard ##\n'
# '## atom styles defined in 2011 are supported.) ##\n'
# '## 2) Use the -atomstyle \"COL_LIST\" argument ##\n'
# '## where \"COL_LIST" is a quoted list of strings ##\n'
# '## indicating the name of each column. ##\n'
# '## Names \"x\",\"y\",\"z\" are interpreted as ##\n'
# '## atomic coordinates. \"mux\",\"muy\",\"muz\" ##\n'
# '## are interpreted as direction vectors. ##\n'
# '## 3) Use the -icoord \"cx cy cz...\" argument ##\n'
# '## where \"cx cy cz\" is a list of integers ##\n'
# '## indicating the column numbers for the x,y,z ##\n'
# '## coordinates of each atom. ##\n'
# '## 4) Use the -ivect \"cmux cmuy cmuz...\" argument ##\n'
# '## where \"cmux cmuy cmuz...\" is a list of ##\n'
# '## integers indicating the column numbers for ##\n'
# '## the vector that determines the direction of a ##\n'
# '## dipole or ellipsoid (ie. a rotateable vector).##\n'
# '## (More than one triplet can be specified. The ##\n'
# '## number of entries must be divisible by 3.) ##\n'
'########################################################\n')
# The default atom_style is "full"
settings.column_names = AtomStyle2ColNames('full')
settings.ii_coords = ColNames2Coords(settings.column_names)
settings.ii_vects = ColNames2Vects(settings.column_names)
settings.i_atomid, settings.i_atomtype, settings.i_molid = ColNames2AidAtypeMolid(settings.column_names)
def TransformAtomText(text, matrix):
""" Apply transformations to the coordinates and other vector degrees
of freedom stored in the \"Data Atoms\" section of a LAMMPS data file.
This is the \"text\" argument.
The \"matrix\" stores the aggregate sum of combined transformations
to be applied.
"""
#sys.stderr.write('matrix_stack.M = \n'+ MatToStr(matrix) + '\n')
lines = text.split('\n')
for i in range(0, len(lines)):
line_orig = lines[i]
ic = line_orig.find('#')
if ic != -1:
line = line_orig[:ic]
comment = ' '+line_orig[ic:].rstrip('\n')
else:
line = line_orig.rstrip('\n')
comment = ''
columns = line.split()
if len(columns) > 0:
if len(columns) == len(settings.column_names)+3:
raise InputError('Error: lttree.py does not yet support integer unit-cell counters \n'
' within the \"'+data_atoms+'\" section of a LAMMPS data file.\n'
' Instead please add the appropriate offsets (these offsets\n'
' should be multiples of the cell size) to the atom coordinates\n'
' in the data file, and eliminate the extra columns. Then try again.\n'
' (If you get this message often, email me and I\'ll fix this limitation.)')
if len(columns) < len(settings.column_names):
raise InputError('Error: The number of columns in your data file does not\n'
' match the LAMMPS atom_style you selected.\n'
' Use the -atomstyle <style> command line argument.\n')
x0 = [0.0, 0.0, 0.0]
x = [0.0, 0.0, 0.0]
# Atomic coordinates transform using "affine" transformations
# (translations plus rotations [or other linear transformations])
for cxcycz in settings.ii_coords:
for d in range(0,3):
x0[d] = float(columns[cxcycz[d]])
AffineTransform(x, matrix, x0) # x = matrix * x0 + b
for d in range(0,3): #("b" is part of "matrix")
columns[cxcycz[d]] = str(x[d])
# Dipole moments and other direction-vectors
# are not effected by translational movement
for cxcycz in settings.ii_vects:
for d in range(0,3):
x0[d] = float(columns[cxcycz[d]])
LinearTransform(x, matrix, x0) # x = matrix * x0
for d in range(0,3):
columns[cxcycz[d]] = str(x[d])
lines[i] = ' '.join(columns) + comment
return '\n'.join(lines)
def CalcCM(text_Atoms,
text_Masses=None,
settings=None):
types2masses = None
# Loop through the "Masses" section: what is the mass of each atom type?
if text_Masses != None:
types2masses = {}
lines = text_Masses.split('\n')
for i in range(0, len(lines)):
line = lines[i]
columns = line.split()
if len(columns) == 2:
atomtype = columns[0]
m = float(columns[1])
types2masses[atomtype] = m
lines = text_Atoms.split('\n')
# Pass 1 through the "Data Atoms" section: Determine each atom's mass
if text_Masses != None:
assert(settings != None)
for i in range(0, len(lines)):
line = lines[i]
columns = line.split()
atomid = columns[settings.i_atomid]
atomtype = columns[settings.i_atomtype]
if atomtype not in types2masses[atomtype]:
raise InputError('Error(lttree): You have neglected to define the mass of atom type: \"'+atomtype+'\"\n'
'Did you specify the mass of every atom type using write(\"Masses\"){}?')
atomid2mass[atomid] = atomtype2mass[atomtype]
# Pass 2 through the "Data Atoms" section: Find the center of mass.
for i in range(0, len(lines)):
line = lines[i]
columns = line.split()
if len(columns) > 0:
if len(columns) == len(settings.column_names)+3:
raise InputError('Error: lttree.py does not yet support integer unit-cell counters (ix, iy, iz)\n'
' within the \"'+data_atoms+'\" section of a LAMMPS data file.\n'
' Instead please add the appropriate offsets (these offsets\n'
' should be multiples of the cell size) to the atom coordinates\n'
' in the data file, and eliminate the extra columns. Then try again.\n'
' (If you get this message often, email me and I\'ll fix this limitation.)')
if len(columns) != len(settings.column_names):
raise InputError('Error: The number of columns in your data file does not\n'
' match the LAMMPS atom_style you selected.\n'
' Use the -atomstyle <style> command line argument.\n')
x = [0.0, 0.0, 0.0]
if atomids2masses != None:
m = atomids2masses[atomid]
else:
m = 1.0
tot_m += m
for cxcycz in settings.ii_coords:
for d in range(0,3):
x[d] = float(columns[cxcycz[d]])
tot_x[d] += x[d]
# Note: dipole moments and other direction vectors don't effect
# the center of mass. So I commented out the loop below.
#for cxcycz in settings.ii_vects:
# for d in range(0,3):
# v[d] = float(columns[cxcycz[d]])
lines[i] = ' '.join(columns)
xcm = [0.0, 0.0, 0.0]
for d in range(0,3):
xcm[d] = tot_x[d] / tot_m
return xcm
def _ExecCommands(command_list,
index,
global_files_content,
settings,
matrix_stack,
current_scope_id=None,
substitute_vars=True):
"""
_ExecCommands():
The argument "commands" is a nested list of lists of
"Command" data structures (defined in ttree.py).
Carry out the write() and write_once() commands (which
write out the contents of the templates contain inside them).
Instead of writing the files, save their contents in a string.
The argument "global_files_content" should be of type defaultdict(list)
It is an associative array whose key is a string (a filename)
and whose value is a lists of strings (of rendered templates).
"""
files_content = defaultdict(list)
postprocessing_commands = []
while index < len(command_list):
command = command_list[index]
index += 1
# For debugging only
if ((not isinstance(command, StackableCommand)) and
(not isinstance(command, ScopeCommand)) and
(not isinstance(command, WriteFileCommand))):
sys.stderr.write(str(command)+'\n')
if isinstance(command, PopCommand):
assert(current_scope_id != None)
if command.context_node == None:
command.context_node = current_scope_id
if isinstance(command, PopRightCommand):
matrix_stack.PopRight(which_stack = command.context_node)
elif isinstance(command, PopLeftCommand):
matrix_stack.PopLeft(which_stack = command.context_node)
else:
assert(False)
elif isinstance(command, PushCommand):
assert(current_scope_id != None)
if command.context_node == None:
command.context_node = current_scope_id
# Some commands are post-processing commands, and must be
# carried out AFTER all the text has been rendered. For example
# the "movecm(0,0,0)" waits until all of the coordinates have
# been rendered, calculates the center-of-mass, and then applies
# a translation moving the center of mass to the origin (0,0,0).
# We need to figure out which of these commands need to be
# postponed, and which commands can be carried out now.
# ("now"=pushing transformation matrices onto the matrix stack).
# UNFORTUNATELY POSTPONING SOME COMMANDS MAKES THE CODE UGLY
transform_list = command.contents.split('.')
transform_blocks = []
i_post_process = -1
# Example: Suppose:
#command.contents = '.rot(30,0,0,1).movecm(0,0,0).rot(45,1,0,0).scalecm(2.0).move(-2,1,0)'
# then
#transform_list = ['rot(30,0,0,1)', 'movecm(0,0,0)', 'rot(45,1,0,0)', 'scalecm(2.0)', 'move(-2,1,0)']
# Note: the first command 'rot(30,0,0,1)' is carried out now.
# The remaining commands are carried out during post-processing,
# (when processing the "ScopeEnd" command.
#
# We break up the commands into "blocks" separated by center-
# of-mass transformations ('movecm', 'rotcm', or 'scalecm')
#
# transform_blocks = ['.rot(30,0,0,1)',
# '.movecm(0,0,0).rot(45,1,0,0)',
# '.scalecm(2.0).move(-2,1,0)']
i = 0
while i < len(transform_list):
transform_block = ''
while i < len(transform_list):
transform = transform_list[i]
i += 1
if transform != '':
transform_block += '.' + transform
transform = transform.split('(')[0]
if ((transform == 'movecm') or
(transform == 'rotcm') or
(transform == 'scalecm')):
break
transform_blocks.append(transform_block)
if len(postprocessing_commands) == 0:
# The first block (before movecm, rotcm, or scalecm)
# can be executed now by modifying the matrix stack.
if isinstance(command, PushRightCommand):
matrix_stack.PushCommandsRight(transform_blocks[0].strip('.'),
command.srcloc,
which_stack=command.context_node)
elif isinstance(command, PushLeftCommand):
matrix_stack.PushCommandsLeft(transform_blocks[0].strip('.'),
command.srcloc,
which_stack=command.context_node)
# Everything else must be saved for later.
postprocessing_blocks = transform_blocks[1:]
else:
# If we already encountered a "movecm" "rotcm" or "scalecm"
# then all of the command blocks must be handled during
# postprocessing.
postprocessing_blocks = transform_blocks
for transform_block in postprocessing_blocks:
assert(isinstance(block, basestring))
if isinstance(command, PushRightCommand):
postprocessing_commands.append(PushRightCommand(transform_block,
command.srcloc,
command.context_node))
elif isinstance(command, PushLeftCommand):
postprocessing_commands.append(PushLeftCommand(transform_block,
command.srcloc,
command.context_node))
elif isinstance(command, WriteFileCommand):
# --- Throw away lines containin references to deleted variables:---
# First: To edit the content of a template,
# you need to make a deep local copy of it
tmpl_list = []
for entry in command.tmpl_list:
if isinstance(entry, TextBlock):
tmpl_list.append(TextBlock(entry.text,
entry.srcloc)) #, entry.srcloc_end))
else:
tmpl_list.append(entry)
# Now throw away lines with deleted variables
DeleteLinesWithBadVars(tmpl_list)
# --- Now render the text ---
text = Render(tmpl_list,
substitute_vars)
# ---- Coordinates of the atoms, must be rotated
# and translated after rendering.
# In addition, other vectors (dipoles, ellipsoid orientations)
# must be processed.
# This requires us to re-parse the contents of this text
# (after it has been rendered), and apply these transformations
# before passing them on to the caller.
if command.filename == data_atoms:
text = TransformAtomText(text, matrix_stack.M)
files_content[command.filename].append(text)
elif isinstance(command, ScopeBegin):
if isinstance(command.node, InstanceObj):
if ((command.node.children != None) and
(len(command.node.children) > 0)):
matrix_stack.PushStack(command.node)
# "command_list" is a long list of commands.
# ScopeBegin and ScopeEnd are (usually) used to demarcate/enclose
# the commands which are issued for a single class or
# class instance. _ExecCommands() carries out the commands for
# a single class/instance. If we reach a ScopeBegin(),
# then recursively process the commands belonging to the child.
index = _ExecCommands(command_list,
index,
files_content,
settings,
matrix_stack,
command.node,
substitute_vars)
elif isinstance(command, ScopeEnd):
if data_atoms in files_content:
for ppcommand in postprocessing_commands:
if data_masses in files_content:
xcm = CalcCM(files_content[data_atoms],
files_content[data_masses],
settings)
else:
xcm = CalcCM(files_content[data_atoms])
if isinstance(ppcommand, PushRightCommand):
matrix_stack.PushCommandsRight(ppcommand.contents,
ppcommand.srcloc,
xcm,
which_stack=command.context_node)
elif isinstance(ppcommand, PushLeftCommand):
matrix_stack.PushCommandsLeft(ppcommand.contents,
ppcommand.srcloc,
xcm,
which_stack=command.context_node)
files_content[data_atoms] = \
TransformAtomText(files_content[data_atoms],
matrix_stack.M)
for ppcommand in postprocessing_commands:
matrix_stack.Pop(which_stack = command.context_node)
#(same as PopRight())
if isinstance(command.node, InstanceObj):
if ((command.node.children != None) and
(len(command.node.children) > 0)):
matrix_stack.PopStack()
# "ScopeEnd" means we're done with this class/instance.
break
else:
assert(False)
# no other command types allowed at this point
# After processing the commands in this list,
# merge the templates with the callers template list
for filename, tmpl_list in files_content.items():
global_files_content[filename] += \
files_content[filename]
return index
def ExecCommands(commands,
files_content,
settings,
substitute_vars=True):
matrix_stack = MultiAffineStack()
index = _ExecCommands(commands,
0,
files_content,
settings,
matrix_stack,
None,
substitute_vars)
assert(index == len(commands))
def WriteFiles(files_content, suffix='', write_to_stdout=True):
for filename, str_list in files_content.items():
if filename != None:
out_file = None
if filename == '':
if write_to_stdout:
out_file = sys.stdout
else:
out_file = open(filename+suffix, 'a')
if out_file != None:
out_file.write(''.join(str_list))
if filename != '':
out_file.close()
if __name__ == "__main__":
"""
This is is a "main module" wrapper for invoking lttree.py
as a stand alone program. This program:
1)reads a ttree file,
2)constructs a tree of class definitions (g_objectdefs)
3)constructs a tree of instantiated class objects (g_objects),
4)automatically assigns values to the variables,
5)and carries out the "write" commands to write the templates a file(s).
"""
g_program_name = __file__.split('/')[-1] # ='lttree.py'
g_date_str = '2013-9-19'
g_version_str = '0.73'
####### Main Code Below: #######
sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
sys.stderr.write('\n(python version '+str(sys.version)+')\n')
- if sys.version < '2.7':
- raise InputError('Error: Alas, you must upgrade to a newever version of python.')
+ if sys.version < '2.6':
+ raise InputError('Error: Alas, you must upgrade to a newer version of python.')
try:
#settings = BasicUISettings()
#BasicUIParseArgs(sys.argv, settings)
settings = LttreeSettings()
LttreeParseArgs(sys.argv, settings)
# Data structures to store the class definitionss and instances
g_objectdefs = StaticObj('', None) # The root of the static tree
# has name '' (equivalent to '/')
g_objects = InstanceObj('', None) # The root of the instance tree
# has name '' (equivalent to '/')
# A list of commands to carry out
g_static_commands = []
g_instance_commands = []
BasicUI(settings,
g_objectdefs,
g_objects,
g_static_commands,
g_instance_commands)
# Interpret the the commands. (These are typically write() or
# write_once() commands, rendering templates into text.
# This step also handles coordinate transformations and delete commands.
# Coordinate transformations can be applied to the rendered text
# as a post-processing step.
sys.stderr.write(' done\nbuilding templates...')
files_content = defaultdict(list)
ExecCommands(g_static_commands,
files_content,
settings,
False)
ExecCommands(g_instance_commands,
files_content,
settings,
False)
# Finally: write the rendered text to actual files.
# Erase the files that will be written to:
sys.stderr.write(' done\nwriting templates...')
EraseTemplateFiles(g_static_commands)
EraseTemplateFiles(g_instance_commands)
# Write the files as templates
# (with the original variable names present)
WriteFiles(files_content, suffix=".template", write_to_stdout=False)
# Write the files with the variables substituted by values
sys.stderr.write(' done\nbuilding and rendering templates...')
files_content = defaultdict(list)
ExecCommands(g_static_commands, files_content, settings, True)
ExecCommands(g_instance_commands, files_content, settings, True)
sys.stderr.write(' done\nwriting rendered templates...\n')
WriteFiles(files_content)
sys.stderr.write(' done\n')
# Step 11: Now write the variable bindings/assignments table.
# Now write the variable bindings/assignments table.
sys.stderr.write('writing \"ttree_assignments.txt\" file...')
open('ttree_assignments.txt', 'w').close() # <-- erase previous version.
WriteVarBindingsFile(g_objectdefs)
WriteVarBindingsFile(g_objects)
sys.stderr.write(' done\n')
except (ValueError, InputError) as err:
sys.stderr.write('\n\n'+str(err)+'\n')
sys.exit(-1)
diff --git a/tools/moltemplate/src/lttree_check.py b/tools/moltemplate/src/lttree_check.py
index ad526b2f0..9a6edf111 100755
--- a/tools/moltemplate/src/lttree_check.py
+++ b/tools/moltemplate/src/lttree_check.py
@@ -1,2211 +1,2211 @@
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
lttree_check.py
The original template file format supports any variable types or file names.
However if you plan to process template files using lttree.py to create
LAMMPS-readable input/data files, then variables and file names obey certain
naming conventions. This code attempts to insure these conventions are obeyed
and to make sure that necessary variables are defined.
-- This code checks static variables (@) and basic LAMMPS syntax --
This program makes an attempt to check that the variables and file names
which appear in an "lttree" file are not mispelled (or miscapitlised).
It also attempts to check that LAMMPS syntax conventions are obeyed.
(It checks that the appropriate type of variable is located in each column).
It also attempts to check that all of the needed coeffs are defined.
-- This code does NOT check instance variables ($) --
This code does not check to make sure that all references to instance variables
(such as $atom, $bond, $angle, $dihedral, $improper or $mol variables) are valid
This means a user's input script command (like the "group" command) could refer
to an $atom or $mol which was never defined, and this code would not detect it.
(Why: Checking for instance variables requires building the entire instance tree
and checking references uses up additional memory after that. I do not do this
because memory is often very scarce after building the instance tree.)
Instead, we could check for these kinds of errors when post-processing of
the files generated by lttree.py or moltemplate.sh.
-- This is not the pretiest code I've ever written. --
"""
import sys
#from ttree import *
from lttree_styles import *
from lttree import *
from ttree_lex import InputError
-if sys.version < '2.7':
- raise InputError('Error: Alas, you must upgrade to a newever version of python.')
+if sys.version < '2.6':
+ raise InputError('Error: Alas, you must upgrade to a newer version of python.')
#g_no_check_msg = \
# "(If this error message is wrong, and/or you would like to continue anyway,\n"+\
# "try running moltemplate again using the \"-nocheck\" command-line-argument.)\n"
g_no_check_msg = \
'(To continue anyway, run moltemplate using the \"-nocheck\" argument.)\n'
def CheckCommonVarNames(prefix, descr_str, suffix, srcloc):
""" Check the name of variables in a lttree-file to confirm
that they follow the conventions used by lttree.
Almost any variable/category name is permitted, except for
names which closely match those reserved by lttree.
"""
cat_name, cat_ptkns, leaf_ptkns = \
DescrToCatLeafPtkns(descr_str,
srcloc)
if (cat_name.lower()=='mol'):
if (cat_name != 'mol'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
'closely with a reserved lttree variable category.\n'
'Perhaps you meant \"mol\"?')
elif (cat_name.lower()=='group'):
if (cat_name != 'group'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
'closely with a reserved lttree variable category.\n'
'Perhaps you meant \"group\"?')
elif (cat_name.lower()=='fix'):
if (cat_name != 'fix'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
'closely with a reserved lttree variable category.\n'
'Use \"fix\" instead.')
elif (cat_name.lower()=='atom'):
if (cat_name != 'atom'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Illegal lttree variable category: \"'+cat_name+'\"\n'+
'Use \"atom\" instead.')
elif (cat_name.lower()=='bond'):
if (cat_name != 'bond'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
'closely with a reserved lttree variable category.\n'
'Use \"bond\" instead.')
elif (cat_name.lower()=='angle'):
if (cat_name != 'angle'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
'closely with a reserved lttree variable category.\n'
'Use \"angle\" instead.')
elif (cat_name.lower()=='dihedral'):
if (cat_name != 'dihedral'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
'closely with a reserved lttree variable category.\n'
'Use \"dihedral\" instead.')
elif (cat_name.lower()=='improper'):
if (cat_name != 'improper'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Variable category: \"'+cat_name+'\" does not match, yet overlaps\n'+
'closely with a reserved lttree variable category.\n'
'Use \"improper\" instead.')
else:
sys.stderr.write('-----------------------------------------------------\n'+
'WARNING: in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
' Unrecognised template variable category: \"'+cat_name+'\"\n'+
'-----------------------------------------------------\n')
def CheckDataFileNames(filename,
srcloc,
write_command,
fnames_found):
N_data_prefix = len(data_prefix)
#data_prefix_no_space = data_prefix.rstrip()
N_data_prefix_no_space = len(data_prefix)
section_name = filename[N_data_prefix:]
if ((section_name.lower() == 'atom') or
(section_name.lower() == 'atoms')):
if (filename != data_atoms):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_atoms+'\"?')
elif (write_command == 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'velocities') or
(section_name.lower() == 'velocity')):
if (filename != data_velocities):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_velocities+'\"?')
elif (write_command == 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'mass') or
(section_name.lower() == 'masses')):
if (filename != data_masses):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_masses+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'ellipsoids') or
(section_name.lower() == 'ellipsoid') or
(section_name.lower() == 'elipsoids') or
(section_name.lower() == 'elipsoid')):
if (filename != data_ellipsoids):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_ellipsoids+'\"?')
elif (write_command == 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'triangle') or
(section_name.lower() == 'triangles')):
if (filename != data_triangles):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_triangles+'\"?')
elif (write_command == 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'line') or
(section_name.lower() == 'lines')):
if (filename != data_lines):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_lines+'\"?')
elif (write_command == 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('pair coef') == 0) or
(section_name.lower().find('pair_coef') == 0) or
(section_name.lower().find('paircoef') == 0) or
(section_name.lower().find('pair by type') == 0) or
(section_name.lower().find('pair bytype') == 0) or
(section_name.lower().find('pair_by_type') == 0) or
(section_name.lower().find('pair_bytype') == 0) or
(section_name.lower().find('pairbytype') == 0)):
if (filename != data_pair_coeffs):
err_msg = 'Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+\
'Output file name (\"'+filename+'\") does not match,\n'+\
'yet overlaps closely with reserved lttree-file name.\n'+\
'Perhaps you meant \"'+data_pair_coeffs+'\"?'
if ((section_name.lower().find('by type') != -1) or
(section_name.lower().find('by_type') != -1) or
(section_name.lower().find('bytype') != -1)):
err_msg += '\n (Note: "pair" parameters are always assigned by type.\n'+\
' There\'s no need to specify \"by type\")'
raise InputError(err_msg)
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('bond coef') == 0) or
(section_name.lower().find('bond_coef') == 0) or
(section_name.lower().find('bondcoef') == 0)):
if (filename != data_bond_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_bond_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('angle coef') == 0) or
(section_name.lower().find('angle_coef') == 0) or
(section_name.lower().find('anglecoef') == 0)):
if (filename != data_angle_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_angle_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('dihedral coef') == 0) or
(section_name.lower().find('dihedral_coef') == 0) or
(section_name.lower().find('dihedralcoef') == 0)):
if (filename != data_dihedral_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_dihedral_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('improper coef') == 0) or
(section_name.lower().find('improper_coef') == 0) or
(section_name.lower().find('impropercoef') == 0)):
if (filename != data_improper_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_improper_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
# -- class2 data sections --
elif ((section_name.lower().find('bondbond coef') == 0) or
(section_name.lower().find('bondbond_coef') == 0) or
(section_name.lower().find('bondbondcoef') == 0)):
if (filename != data_bondbond_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_bondbond_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('bondangle coef') == 0) or
(section_name.lower().find('bondangle_coef') == 0) or
(section_name.lower().find('bondanglecoef') == 0)):
if (filename != data_bondangle_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_bondangle_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('middlebondtorsion coef') == 0) or
(section_name.lower().find('middlebondtorsion_coef') == 0) or
(section_name.lower().find('middlebondtorsioncoef') == 0) or
(section_name.lower().find('middlebondtorision coef') == 0) or
(section_name.lower().find('middlebondtorision_coef') == 0) or
(section_name.lower().find('middlebondtorisioncoef') == 0)):
if (filename != data_middlebondtorsion_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_middlebondtorsion_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('endbondtorsion coef') == 0) or
(section_name.lower().find('endbondtorsion_coef') == 0) or
(section_name.lower().find('endbondtorsioncoef') == 0) or
(section_name.lower().find('endbondtorision coef') == 0) or
(section_name.lower().find('endbondtorision_coef') == 0) or
(section_name.lower().find('endbondtorisioncoef') == 0)):
if (filename != data_endbondtorsion_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_endbondtorsion_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('angletorsion coef') == 0) or
(section_name.lower().find('angletorsion_coef') == 0) or
(section_name.lower().find('angletorsioncoef') == 0) or
(section_name.lower().find('angletorision coef') == 0) or
(section_name.lower().find('angletorision_coef') == 0) or
(section_name.lower().find('angletorisioncoef') == 0)):
if (filename != data_angletorsion_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_angletorsion_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('angleangletorsion coef') == 0) or
(section_name.lower().find('angleangletorsion_coef') == 0) or
(section_name.lower().find('angleangletorsioncoef') == 0) or
(section_name.lower().find('angleangletorision coef') == 0) or
(section_name.lower().find('angleangletorision_coef') == 0) or
(section_name.lower().find('angleangletorisioncoef') == 0)):
if (filename != data_angleangletorsion_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_angleangletorsion_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('bondbond13 coef') == 0) or
(section_name.lower().find('bondbond13_coef') == 0) or
(section_name.lower().find('bondbond13coef') == 0)):
if (filename != data_bondbond13_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_bondbond13_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('angleangle coef') == 0) or
(section_name.lower().find('angleangle_coef') == 0) or
(section_name.lower().find('angleanglecoef') == 0)):
if (filename != data_angleangle_coeffs):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_angleangle_coeffs+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'bonds by type') or
(section_name.lower() == 'bonds bytype') or
(section_name.lower() == 'bonds_by_type') or
(section_name.lower() == 'bonds_bytype') or
(section_name.lower() == 'bondsbytype') or
(section_name.lower() == 'bond by type') or
(section_name.lower() == 'bond bytype') or
(section_name.lower() == 'bond_by_type') or
(section_name.lower() == 'bond_bytype') or
(section_name.lower() == 'bondbytype')):
if (filename != data_bonds_by_type):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_bonds_by_type+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'angles by type') or
(section_name.lower() == 'angles bytype') or
(section_name.lower() == 'angles_by_type') or
(section_name.lower() == 'angles_bytype') or
(section_name.lower() == 'anglesbytype') or
(section_name.lower() == 'angle by type') or
(section_name.lower() == 'angle bytype') or
(section_name.lower() == 'angle_by_type') or
(section_name.lower() == 'angle_bytype') or
(section_name.lower() == 'anglebytype')):
if (filename != data_angles_by_type):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_angles_by_type+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'dihedrals by type') or
(section_name.lower() == 'dihedrals bytype') or
(section_name.lower() == 'dihedrals_by_type') or
(section_name.lower() == 'dihedrals_bytype') or
(section_name.lower() == 'dihedralsbytype') or
(section_name.lower() == 'dihedral by type') or
(section_name.lower() == 'dihedral bytype') or
(section_name.lower() == 'dihedral_by_type') or
(section_name.lower() == 'dihedral_bytype') or
(section_name.lower() == 'dihedralbytype')):
if (filename != data_dihedrals_by_type):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_dihedrals_by_type+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'impropers by type') or
(section_name.lower() == 'impropers bytype') or
(section_name.lower() == 'impropers_by_type') or
(section_name.lower() == 'impropers_bytype') or
(section_name.lower() == 'impropersbytype') or
(section_name.lower() == 'improper by type') or
(section_name.lower() == 'improper bytype') or
(section_name.lower() == 'improper_by_type') or
(section_name.lower() == 'improper_bytype') or
(section_name.lower() == 'improperbytype')):
if (filename != data_impropers_by_type):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_impropers_by_type+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'bonds') or
(section_name.lower() == 'bond')):
if (filename != data_bonds):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_bonds+'\"?')
elif (write_command == 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower().find('bond list') == 0) or
(section_name.lower().find('bonds list') == 0) or
(section_name.lower().find('bond_list') == 0) or
(section_name.lower().find('bonds_list') == 0)):
if (filename != data_bond_list):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_bonds_by_type+'\"?')
elif (write_command != 'write'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'angles') or
(section_name.lower() == 'angle')):
if (filename != data_angles):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_angles+'\"?')
elif (write_command == 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'dihedrals') or
(section_name.lower() == 'dihedral')):
if (filename != data_dihedrals):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_dihedrals+'\"?')
elif (write_command == 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'impropers') or
(section_name.lower() == 'improper')):
if (filename != data_impropers):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_impropers+'\"?')
elif (write_command == 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write(\"'+filename+'\") instead.\n')
elif ((section_name.lower() == 'box boundaries') or
(section_name.lower() == 'box boundary') or
(section_name.lower() == 'boundaries') or
(section_name.lower() == 'boundary') or
(section_name.lower() == 'boundary conditions') or
(section_name.lower() == 'periodic boundaries') or
(section_name.lower() == 'periodic boundary conditions') or
(section_name.lower() == 'periodic_boundaries') or
(section_name.lower() == 'periodic_boundary_conditions') or
(section_name.lower() == 'pbc')):
if ((filename != data_boundary) and
(filename != data_pbc)):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_boundary+'\"?\n'
'(Specify periodic boundary conditions this way.)')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif (filename == data_pbc):
sys.stderr.write('WARNING: write_once(\"'+data_pbc+'\") is depreciated.\n'
' Use write_once(\"'+data_boundary+'\") instead.\n')
def CheckCommonFileNames(filename,
srcloc,
write_command,
filenames_found):
"""
Check the write() or write_once() statements in a
lttree-file to make sure that the files being written
follow the conventions used by lttree.
Almost any file name is permitted, except for file names
which closely match those reserved by lttree.
"""
filenames_found.add(filename)
N_data_prefix = len(data_prefix)
#data_prefix_no_space = data_prefix.rstrip()
N_data_prefix_no_space = len(data_prefix_no_space)
if ((filename[:N_data_prefix].lower() == data_prefix.lower()) and
(filename[:N_data_prefix] != data_prefix)):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'The beginning of output file (\"'+filename+'\")\n'
'does not match yet overlaps closely with a reserved lttree-file name prefix.\n'
'(\"'+data_prefix+'\"). Perhaps you meant \"'+data_prefix+filename[N_data_prefix:]+'\"?')
# check did they forget the space?
if (filename[:N_data_prefix_no_space] == data_prefix_no_space):
if (filename[:N_data_prefix] == data_prefix):
CheckDataFileNames(filename,
srcloc,
write_command,
filenames_found)
else:
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'The beginning of output file (\"'+filename+'\")\n'
'does not match yet overlaps closely with a reserved lttree-file name prefix.\n'
'(\"'+data_prefix+'\"). Perhaps you meant \"'+data_prefix+filename[N_data_prefix_no_space:]+'\"?')
elif ((filename.lower() == 'box boundaries') or
(filename.lower() == 'box boundary') or
(filename.lower() == 'boundaries') or
(filename.lower() == 'boundary') or
(filename.lower() == 'boundary conditions') or
(filename.lower() == 'periodic boundaries') or
(filename.lower() == 'periodic boundary conditions') or
(filename.lower() == 'periodic_boundaries') or
(filename.lower() == 'periodic_boundary_conditions') or
(filename.lower() == 'pbc')):
# In that case (for one thing) they forgot the data_prefix
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+data_boundary+'\"?\n'
'(Specify periodic boundary conditions this way.)')
elif ((filename.lower() == 'init') or
(filename.lower() == 'in init') or
(filename.lower() == 'ininit') or
(filename.lower() == 'initialize') or
(filename.lower() == 'in initialize') or
(filename.lower() == 'ininitialize')):
if (filename != in_init):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+in_init+'\"?')
elif (write_command != 'write_once'):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'When using moltemplate.sh to build LAMMPS input files, you probably do not\n'
'want to use the '+write_command+'() command with \"'+filename+'\".\n'
'You should probably use write_once(\"'+filename+'\") instead.\n')
elif ((filename.lower() == 'settings') or
(filename.lower() == 'in settings') or
(filename.lower() == 'insettings')):
if (filename != in_settings):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+in_settings+'\"?')
elif ((filename.lower() == 'set_coords') or
(filename.lower() == 'set coords') or
(filename.lower() == 'setcoords') or
(filename.lower() == 'in set_coords') or
(filename.lower() == 'in set coords') or
(filename.lower() == 'in setcoords')):
if (filename != in_set_coords):
raise InputError('Probable typo in '+ErrorLeader(srcloc.infile,srcloc.lineno)+'\n\n'+
'Output file name (\"'+filename+'\") does not match,\n'
'yet overlaps closely with reserved lttree-file name.\n'
'Perhaps you meant \"'+in_set_coords+'\"?')
def CheckSyntaxCheap(lex):
""" Parse() builds a static tree of StaticObjs by parsing text file.
-The "lex" argument is afile or input stream which has been converted
to a "TemplateLexer" object (similar to the python's built-in shlex lexer).
"""
fnames_found = set([])
prematurely_read_token = None
while True:
if prematurely_read_token == None:
command = lex.get_token()
else:
command = prematurely_read_token
prematurely_read_token = None
#print('Parse(): token = \"'+command+'\", '+lex.error_leader())
if command == lex.eof:
#print('Parse(): EOF encountered\n')
break
if ((command == 'write') or (command == 'write_once')):
open_paren = lex.get_token()
#print('Parse(): open_paren=\"'+open_paren+'\"')
if open_paren=='{':
# ..then the user neglected to specify the "filename" file-name
# argument. In that case, supply the default, ''.
# (which is shorthand for the standard out in this case)
open_curly = open_paren[0]
open_paren = ''
close_paren = ''
filename = ''
srcloc = lex.GetSrcLoc()
else:
filename = lex.get_token()
if filename == ')':
filename == ''
close_paren = ')'
else:
close_paren = lex.get_token()
open_curly = lex.get_token()
srcloc = lex.GetSrcLoc()
if ((open_curly != '{') or
((open_paren == '') and (close_paren != '')) or
((open_paren == '(') and (close_paren != ')'))):
raise InputError('Error: in '+lex.error_leader()+'\n\n'
'Syntax error at beginning of '+command+' command.')
filename = RemoveOuterQuotes(filename, lex.quotes)
# The previous line is similar to:
#filename = filename.strip(lex.quotes)
CheckCommonFileNames(filename, lex.GetSrcLoc(), command, fnames_found)
tmpl_contents = lex.ReadTemplate()
StaticObj.CleanupReadTemplate(tmpl_contents, lex)
for entry in tmpl_contents:
if (type(entry) is VarRef):
CheckCommonVarNames(entry.prefix,
entry.descr_str,
entry.suffix,
entry.srcloc)
#if (data_velocities not in fnames_found):
# sys.stderr.write('-------------------------------------------------\n'
# 'WARNING: \"'+data_velocities+'\" file not found\n'
# '-------------------------------------------------\n')
#if (data_pair_coeffs not in fnames_found):
# sys.stderr.write('-------------------------------------------------\n'
# 'WARNING: \"'+data_pair_coeffs+'\" file not found\n'
# '-------------------------------------------------\n')
if (data_atoms not in fnames_found):
sys.stderr.write('WARNING: \"'+data_atoms+'\" file not found\n')
if (data_masses not in fnames_found):
sys.stderr.write('WARNING: \"'+data_masses+'\" file not found\n')
#if (data_bonds not in fnames_found):
# sys.stderr.write('--------------------------------------------------\n'
# 'WARNING: \"'+data_bonds+'\" file not found\n'
# '--------------------------------------------------\n')
#if (data_angles not in fnames_found):
# sys.stderr.write('--------------------------------------------------\n'
# 'WARNING: \"'+data_angles+'\" file not found\n'
# '--------------------------------------------------\n')
#if (data_dihedrals not in fnames_found):
# sys.stderr.write('--------------------------------------------------\n'
# 'WARNING: \"'+data_dihedrals+'\" file not found\n'
# '--------------------------------------------------\n')
#if (data_impropers not in fnames_found):
# sys.stderr.write('--------------------------------------------------\n'
# 'WARNING: \"'+data_impropers+'\" file not found\n'
# '--------------------------------------------------\n')
#if (data_bond_coeffs not in fnames_found):
# sys.stderr.write('--------------------------------------------------\n'
# 'WARNING: \"'+data_bond_coeffs+'\" file not found\n'
# '--------------------------------------------------\n')
#if (data_angle_coeffs not in fnames_found):
# sys.stderr.write('--------------------------------------------------\n'
# 'WARNING: \"'+data_angle_coeffs+'\" file not found\n'
# '--------------------------------------------------\n')
#if (data_dihedral_coeffs not in fnames_found):
# sys.stderr.write('--------------------------------------------------\n'
# 'WARNING: \"'+data_dihedral_coeffs+'\" file not found\n'
# '--------------------------------------------------\n')
#if (data_improper_coeffs not in fnames_found):
# sys.stderr.write('--------------------------------------------------\n'
# 'WARNING: \"'+data_imrpoper_coeffs+'\" file not found\n'
# '--------------------------------------------------\n')
if (in_init not in fnames_found):
sys.stderr.write('WARNING: \"'+in_init+'\" file not found\n')
if (in_settings not in fnames_found):
sys.stderr.write('WARNING: \"'+in_settings+'\" file not found\n')
def CheckSyntaxStatic(context_node,
root_node,
atom_column_names,
data_pair_coeffs_defined,
data_bond_coeffs_defined,
data_angle_coeffs_defined,
data_dihedral_coeffs_defined,
data_improper_coeffs_defined,
in_pair_coeffs_defined,
in_bond_coeffs_defined,
in_angle_coeffs_defined,
in_dihedral_coeffs_defined,
in_improper_coeffs_defined,
search_instance_commands):
if search_instance_commands:
assert(isinstance(context_node, StaticObj))
commands = context_node.instance_commands
else:
# Note: Leaf nodes contain no commands, so skip them
if (not hasattr(context_node, 'commands')):
return
# Otherwise process their commands
commands = context_node.commands
for command in commands:
if isinstance(command, WriteFileCommand):
filename = command.filename
if filename == None: # (The "create_var" command causes this)
pass
elif (filename.find(in_prefix) == 0): #if filename begins with "In "
CheckInFileSyntax(command.tmpl_list,
root_node,
in_pair_coeffs_defined,
in_bond_coeffs_defined,
in_angle_coeffs_defined,
in_dihedral_coeffs_defined,
in_improper_coeffs_defined)
elif filename == 'Data Atoms':
table = TableFromTemplate(command.tmpl_list,
[[' ', '\t', '\r'], '\n'],
[True, False])
for i in range(0, len(table)):
assert(hasattr(table[i], '__len__'))
if len(table[i]) == 0:
pass # skip blank lines
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass # skip comment lines
else:
syntax_err = False
if len(table[i]) < len(atom_column_names):
syntax_err = True
else:
syntax_err = False
for j in range(0, len(atom_column_names)):
if ((atom_column_names[j].lower() == 'atom-id') and
(not ((j < len(table[i])) and
isinstance(table[i][j], VarRef) and
(table[i][j].prefix in ('$','${')) and
(ExtractCatName(table[i][j].descr_str) == 'atom')))):
syntax_err = True
elif ((atom_column_names[j].lower() == 'molecule-id') and
(not ((j < len(table[i])) and
isinstance(table[i][j], VarRef) and
(table[i][j].prefix in ('$','${')) and
(ExtractCatName(table[i][j].descr_str) == 'mol')))):
syntax_err = True
elif ((atom_column_names[j].lower() == 'atom-type') and
(not ((j < len(table[i])) and
(isinstance(table[i][j], VarRef)) and
(table[i][j].prefix in ('@', '@{')) and
(table[i][j].nptr.cat_name == 'atom') and
(table[i][j].nptr.cat_node == root_node)))):
syntax_err = True
if syntax_err:
correct_rows_list = [s for s in atom_column_names]
for j in range(0, len(correct_rows_list)):
if correct_rows_list[j].lower() == 'atom-id':
correct_rows_list[j] = '$atom:id'
elif correct_rows_list[j].lower() == 'atom-type':
correct_rows_list[j] = '@atom:type'
elif correct_rows_list[j].lower() == 'molecule-id':
correct_rows_list[j] = '$mol:id'
correct_rows_msg = ' '.join(correct_rows_list)
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Invalid "Data Atoms" syntax.\n'+
'Each line of the \"Data Atoms\" section should have this format:\n\n'
' '+correct_rows_msg+'\n\n'
'You may have forgotten to specify the LAMMPS atom_style.\n'+
'(You can do this running moltemplate with the -atom-style _style_ argument.)\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
elif filename == 'Data Bonds':
table = TableFromTemplate(command.tmpl_list,
[[' ', '\t', '\r'], '\n'],
[True, False])
for i in range(0, len(table)):
syntax_err = False
assert(hasattr(table[i], '__len__'))
if len(table[i]) > 0:
if ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass
else:
if len(table[i]) < 4:
syntax_err = True
table_entry = table[i][0]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'bond'))):
syntax_err = True
if len(table[i]) > 1:
table_entry = table[i][1]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('@', '@{')) and
(table_entry.nptr.cat_name == 'bond') and
(table_entry.nptr.cat_node == root_node))):
syntax_err = True
if len(table[i]) > 2:
table_entry = table[i][2]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 3:
table_entry = table[i][3]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if syntax_err:
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Bonds" syntax.\n'+
'Each line of the \"Data Bonds\" section should have this format:\n\n'
' $bond:id @bond:type $atom:id1 $atom:id2\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
elif filename == 'Data Bond List':
table = TableFromTemplate(command.tmpl_list,
[[' ', '\t', '\r'], '\n'],
[True, False])
for i in range(0, len(table)):
syntax_err = False
assert(hasattr(table[i], '__len__'))
if len(table[i]) > 0:
if ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass
else:
if len(table[i]) < 3:
syntax_err = True
table_entry = table[i][0]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'bond'))):
syntax_err = True
if len(table[i]) > 1:
table_entry = table[i][1]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 2:
table_entry = table[i][2]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if syntax_err:
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Bond List" syntax.\n'+
'Each lines in this section should have this format:\n\n'
' $bond:id $atom:id1 $atom:id2\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
elif filename == 'Data Angles':
table = TableFromTemplate(command.tmpl_list,
[[' ', '\t', '\r'], '\n'],
[True, False])
for i in range(0, len(table)):
syntax_err = False
assert(hasattr(table[i], '__len__'))
if len(table[i]) > 0:
if ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass
else:
if len(table[i]) < 5:
syntax_err = True
table_entry = table[i][0]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'angle'))):
syntax_err = True
if len(table[i]) > 1:
table_entry = table[i][1]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('@', '@{')) and
(table_entry.nptr.cat_name == 'angle') and
(table_entry.nptr.cat_node == root_node))):
syntax_err = True
if len(table[i]) > 2:
table_entry = table[i][2]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 3:
table_entry = table[i][3]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 4:
table_entry = table[i][4]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if syntax_err:
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Angles" syntax.\n'+
'Each line of the \"Data Angles\" section should have this format:\n\n'
' $angle:id @angle:type $atom:id1 $atom:id2 $atom:id3\n'+
'----------------------------------------------------\n\n'+
g_no_check_msg)
elif filename == 'Data Dihedrals':
table = TableFromTemplate(command.tmpl_list,
[[' ', '\t', '\r'], '\n'],
[True, False])
for i in range(0, len(table)):
syntax_err = False
assert(hasattr(table[i], '__len__'))
if len(table[i]) > 0:
if ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass
else:
if len(table[i]) < 6:
syntax_err = True
table_entry = table[i][0]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'dihedral'))):
syntax_err = True
if len(table[i]) > 1:
table_entry = table[i][1]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('@', '@{')) and
(table_entry.nptr.cat_name == 'dihedral') and
(table_entry.nptr.cat_node == root_node))):
syntax_err = True
if len(table[i]) > 2:
table_entry = table[i][2]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 3:
table_entry = table[i][3]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 4:
table_entry = table[i][4]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 5:
table_entry = table[i][5]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if syntax_err:
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Dihedrals" syntax.\n'+
'Each line of the \"Data Dihedrals\" section should have this format:\n\n'
' $dihedral:id @dihedral:type $atom:id1 $atom:id2 $atom:id3 $atom:id4\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
elif filename == 'Data Impropers':
table = TableFromTemplate(command.tmpl_list,
[[' ', '\t', '\r'], '\n'],
[True, False])
for i in range(0, len(table)):
syntax_err = False
assert(hasattr(table[i], '__len__'))
if len(table[i]) > 0:
if ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass
else:
if len(table[i]) < 6:
syntax_err = True
table_entry = table[i][0]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'improper'))):
syntax_err = True
if len(table[i]) > 1:
table_entry = table[i][1]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('@', '@{')) and
(table_entry.nptr.cat_name == 'improper') and
(table_entry.nptr.cat_node == root_node))):
syntax_err = True
if len(table[i]) > 2:
table_entry = table[i][2]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 3:
table_entry = table[i][3]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 4:
table_entry = table[i][4]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if len(table[i]) > 5:
table_entry = table[i][5]
if (not ((isinstance(table_entry, VarRef)) and
(table_entry.prefix in ('$','${')) and
(ExtractCatName(table_entry.descr_str) == 'atom'))):
syntax_err = True
if syntax_err:
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Impropers" syntax.\n'+
'Each line of the \"Data Impropers\" section should have this format:\n\n'
' $improper:id @improper:type $atom:id1 $atom:id2 $atom:id3 $atom:id4\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
# A simple wildcard is the character "*" on its own.
# These are okay.
# A "compound" wildcard expression is something like
# 5*7 or
# 5* or
# *7 or
# @{bond:A}*@bond:B or
# @{bond:A}* or
# *@bond:B
# LAMMPS allows this but in moltemplate this causes
# unintended side-effects. Check for these now.
if filename in set(['Data Bond Coeffs',
'Data Angle Coeffs',
'Data Dihedral Coeffs',
'Data Improper Coeffs',
'Data Pair Coeffs']):
table = TableFromTemplate(command.tmpl_list,
[[' ','\t','\r'], '\n'],
[True, False])
for i in range(0, len(table)):
assert(hasattr(table[i], '__len__'))
if len(table[i]) > 0:
if (isinstance(table[i][0], TextBlock) and
table[i][0].text == '*'):
if filename == 'Data Bond Coeffs':
data_bond_coeffs_defined.add('*')
elif filename == 'Data Angle Coeffs':
data_angle_coeffs_defined.add('*')
elif filename == 'Data Dihedral Coeffs':
data_dihedral_coeffs_defined.add('*')
elif filename == 'Data Improper Coeffs':
data_improper_coeffs_defined.add('*')
elif filename == 'Data Pair Coeffs':
data_pair_coeffs_defined.add(('*','*'))
else:
compound_wildcard = False
if (len(table[i]) > 1):
if hasattr(table[i][0],'__len__'):
ltmpl = table[i][0]
else:
ltmpl = [table[i][0]]
for entry in ltmpl:
if (isinstance(entry, TextBlock) and
('*' in entry.text)):
compound_wildcard = True
elif (isinstance(entry, VarRef) and
('*' in entry.descr_str)):
compound_wildcard = True
if compound_wildcard:
raise InputError('--- Paranoid checking: ---\n'
' Possible error near '+
ErrorLeader(entry.srcloc.infile,
entry.srcloc.lineno)+'\n'
'The wildcard symbol, \"*\", is not recommended within \"'+filename+'\".\n'
'It is safer to specify the parameters for each type explicitly.\n'
'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n'
'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n')
if filename == 'Data Bond Coeffs':
# Commenting the next line out. We did this already:
#table = TableFromTemplate(command.tmpl_list,
# [[' ','\t','\r'], '\n'],
# [True, False])
for i in range(0, len(table)):
if len(table[i]) == 0:
pass
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(table[i][0].text == '*')):
pass # we dealt with this case earlier
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass #Ignore comment lines (postprocessing removes them)
elif (not (isinstance(table[i][0], VarRef) and
(table[i][0].prefix in ('@', '@{')) and
(table[i][0].nptr.cat_name == 'bond') and
(table[i][0].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Bond Coeffs" syntax.\n'
' Each line of the \"Data Bond Coeffs\" section\n'
' should have the following syntax:\n\n'+
' @bond:type list-of-parameters...\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
else:
data_bond_coeffs_defined.add(table[i][0].binding)
elif filename == 'Data Angle Coeffs':
# Commenting the next line out. We did this already:
#table = TableFromTemplate(command.tmpl_list,
# [[' ','\t','\r'], '\n'],
# [True, False])
for i in range(0, len(table)):
if len(table[i]) == 0:
pass
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(table[i][0].text == '*')):
pass # we dealt with this case earlier
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass #Ignore comment lines (postprocessing removes them)
elif (not (isinstance(table[i][0], VarRef) and
(table[i][0].prefix in ('@', '@{')) and
(table[i][0].nptr.cat_name == 'angle') and
(table[i][0].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Angle Coeffs" syntax.\n'
' Each line of the \"Data Angle Coeffs\" section\n'
' should have the following syntax:\n\n'+
' @angle:type list-of-parameters...\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
else:
data_angle_coeffs_defined.add(table[i][0].binding)
elif filename == 'Data Dihedral Coeffs':
# Commenting the next line out. We did this already:
#table = TableFromTemplate(command.tmpl_list,
# [[' ','\t','\r'], '\n'],
# [True, False])
for i in range(0, len(table)):
if len(table[i]) == 0:
pass
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(table[i][0].text == '*')):
pass # we dealt with this case earlier
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass #Ignore comment lines (postprocessing removes them)
elif (not (isinstance(table[i][0], VarRef) and
(table[i][0].prefix in ('@', '@{')) and
(table[i][0].nptr.cat_name == 'dihedral') and
(table[i][0].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Dihedral Coeffs" syntax.\n'
' Each line of the \"Data Dihedral Coeffs\" section\n'
' should have the following syntax:\n\n'+
' @dihedral:type list-of-parameters...\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
else:
data_dihedral_coeffs_defined.add(table[i][0].binding)
elif filename == 'Data Improper Coeffs':
# Commenting the next line out. We did this already:
#table = TableFromTemplate(command.tmpl_list,
# [[' ','\t','\r'], '\n'],
# [True, False])
for i in range(0, len(table)):
if len(table[i]) == 0:
pass
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(table[i][0].text == '*')):
pass # we dealt with this case earlier
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass #Ignore comment lines (postprocessing removes them)
elif (not (isinstance(table[i][0], VarRef) and
(table[i][0].prefix in ('@', '@{')) and
(table[i][0].nptr.cat_name == 'improper') and
(table[i][0].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Improper Coeffs" syntax.\n'
' Each line of the \"Data Improper Coeffs\" section\n'
' should have the following syntax:\n\n'+
' @improper:type list-of-parameters...\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
else:
data_improper_coeffs_defined.add(table[i][0].binding)
elif filename == 'Data Pair Coeffs':
# Commenting the next line out. We did this already:
#table = TableFromTemplate(command.tmpl_list,
# [[' ','\t','\r'], '\n'],
# [True, False])
for i in range(0, len(table)):
if len(table[i]) == 0:
pass
elif ((len(table[i]) > 0) and
isinstance(table[i][0], TextBlock) and
(table[i][0].text == '*')):
pass # we dealt with this case earlier
elif ((len(table[i]) > 0) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass #Ignore comment lines (postprocessing removes them)
elif (not ((len(table[i]) > 0) and
isinstance(table[i][0], VarRef) and
(table[i][0].prefix in ('@', '@{')) and
(table[i][0].nptr.cat_name == 'atom') and
(table[i][0].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect "Data Pair Coeffs" syntax.\n'
' Each line of the \"Data Pair Coeffs\" section\n'
' should have the following syntax:\n\n'+
' @atom:type list-of-parameters...\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
else:
data_pair_coeffs_defined.add((table[i][0].binding,
table[i][0].binding))
elif filename == 'Data Bonds By Type':
table = TableFromTemplate(command.tmpl_list,
[[' ','\t','\r'], '\n'],
[True, False])
for i in range(0, len(table)):
if len(table[i]) == 0:
pass
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass #Ignore comment lines (postprocessing removes them)
elif (not ((len(table[i]) >= 3) and
isinstance(table[i][0], VarRef) and
(table[i][0].prefix in ('@', '@{')) and
(table[i][0].nptr.cat_name == 'bond') and
(table[i][0].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect \"Data Bonds By Type\" syntax.\n'
' Each line of the \"Data Bonds By Type\" section should begin with an\n'
' @bond:type variable followed by 2 atom types.\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
elif filename == 'Data Angles By Type':
table = TableFromTemplate(command.tmpl_list,
[[' ','\t','\r'], '\n'],
[True, False])
for i in range(0, len(table)):
if len(table[i]) == 0:
pass
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass #Ignore comment lines (postprocessing removes them)
elif (not ((len(table[i]) >= 4) and
isinstance(table[i][0], VarRef) and
(table[i][0].prefix in ('@', '@{')) and
(table[i][0].nptr.cat_name == 'angle') and
(table[i][0].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect \"Data Angles By Type\" syntax.\n'
' Each line of the \"Data Angles By Type\" section should begin with an\n'
' @angle:type variable followed by 3 atom types (and 2 optional bond types).\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
elif filename == 'Data Dihedrals By Type':
table = TableFromTemplate(command.tmpl_list,
[[' ','\t','\r'], '\n'],
[True, False])
for i in range(0, len(table)):
if len(table[i]) == 0:
pass
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass #Ignore comment lines (postprocessing removes them)
elif (not ((len(table[i]) >= 5) and
isinstance(table[i][0], VarRef) and
(table[i][0].prefix in ('@', '@{')) and
(table[i][0].nptr.cat_name == 'dihedral') and
(table[i][0].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect \"Data Dihedrals By Type\" syntax.\n'
' Each line of the \"Data Dihedrals By Type\" section should begin with a\n\n'
' @dihedral:type variable followed by 4 atom types (and 3 optional bond types).\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
elif filename == 'Data Impropers By Type':
table = TableFromTemplate(command.tmpl_list,
[[' ','\t','\r'], '\n'],
[True, False])
for i in range(0, len(table)):
if len(table[i]) == 0:
pass
elif ((len(table[i]) > 1) and
isinstance(table[i][0], TextBlock) and
(len(table[i][0].text) > 0) and
(table[i][0].text == '#')):
pass #Ignore comment lines (postprocessing removes them)
elif (not ((len(table[i]) >= 5) and
isinstance(table[i][0], VarRef) and
(table[i][0].prefix in ('@', '@{')) and
(table[i][0].nptr.cat_name == 'improper') and
(table[i][0].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Incorrect \"Data Impropers By Type\" syntax.\n'
' Each line of the \"Data Impropers By Type\" section should begin with an\n\n'
' @improper:type variable followed by 4 atom types (and 3 optional bond types).\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
# Recursively invoke AssignVarPtrs() on all (non-leaf) child nodes:
for child in context_node.children:
CheckSyntaxStatic(child,
root_node,
atom_column_names,
data_pair_coeffs_defined,
data_bond_coeffs_defined,
data_angle_coeffs_defined,
data_dihedral_coeffs_defined,
data_improper_coeffs_defined,
in_pair_coeffs_defined,
in_bond_coeffs_defined,
in_angle_coeffs_defined,
in_dihedral_coeffs_defined,
in_improper_coeffs_defined,
search_instance_commands)
def CheckInFileSyntax(tmpl_list,
root_node,
pair_coeffs_defined,
bond_coeffs_defined,
angle_coeffs_defined,
dihedral_coeffs_defined,
improper_coeffs_defined):
table = TableFromTemplate(tmpl_list,
[[' ','\t','\r'], '\n'],
[True, False])
for i in range(0, len(table)):
assert(hasattr(table[i], '__len__'))
if len(table[i]) > 0:
if ((isinstance(table[i][0], TextBlock)) and
(table[i][0].text in set(['bond_coeff',
'angle_coeff',
'dihedral_coeff',
'improper_coeff']))):
if len(table[i]) > 1: # if not deal with error later
if (isinstance(table[i][1], TextBlock) and
table[i][1].text == '*'):
if table[i][0].text == 'bond_coeff':
bond_coeffs_defined.add('*')
elif table[i][0].text == 'angle_coeff':
angle_coeffs_defined.add('*')
elif table[i][0].text == 'dihedral_coeff':
dihedral_coeffs_defined.add('*')
elif table[i][0].text == 'improper_coeff':
improper_coeffs_defined.add('*')
else:
compound_wildcard = False
if (len(table[i]) > 1):
if hasattr(table[i][1], '__len__'):
ltmpl = table[i][1]
else:
ltmpl = [table[i][1]]
for entry in ltmpl:
if (isinstance(entry, TextBlock) and
('*' in entry.text)):
compound_wildcard = True
elif (isinstance(entry, VarRef) and
('*' in entry.descr_str)):
compound_wildcard = True
if compound_wildcard:
raise InputError('---- Paranoid checking: ---\n'
' Possible error near '+
ErrorLeader(entry.srcloc.infile,
entry.srcloc.lineno)+'\n'
'The wildcard symbol, \"*\", is not recommended within a \"'+table[i][0].text+'\".\n'
'command. It is safer to specify the parameters for each bond type explicitly.\n'
'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n'
'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n')
if ((isinstance(table[i][0], TextBlock)) and
((table[i][0].text.lower() == 'bondcoeff') or
(table[i][0].text.lower() == 'bond_coeff'))):
if table[i][0].text != 'bond_coeff':
raise InputError('----------------------------------------------------\n'+
' Spelling error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Use \"bond_coeff\", not \"'+table[i][0].text+'\"\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
if ((len(table[i]) > 1) and
isinstance(table[i][1], TextBlock) and
(table[i][1].text == '*')):
pass # we dealt with this case earlier
elif (not ((len(table[i]) > 1) and
(isinstance(table[i][1], VarRef)) and
(table[i][1].prefix in ('@', '@{')) and
(table[i][1].nptr.cat_name == 'bond') and
(table[i][1].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Invalid \"bond_coeff\" command.\n\n'+
' Each \"bond_coeff\" command should have the following syntax:\n\n'+
' bond_coeff @bond:type [optional style] list-of-parameters...\n'+
'----------------------------------------------------\n\n'+
g_no_check_msg)
else:
bond_coeffs_defined.add(table[i][1].binding)
if ((isinstance(table[i][0], TextBlock)) and
((table[i][0].text.lower() == 'anglecoeff') or
(table[i][0].text.lower() == 'angle_coeff'))):
if table[i][0].text != 'angle_coeff':
raise InputError('----------------------------------------------------\n'+
' Spelling error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Use \"angle_coeff\", not \"'+table[i][0].text+'\"\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
if ((len(table[i]) > 1) and
isinstance(table[i][1], TextBlock) and
(table[i][1].text == '*')):
pass # we dealt with this case earlier
elif (not ((len(table[i]) > 1) and
(isinstance(table[i][1], VarRef)) and
(table[i][1].prefix in ('@', '@{')) and
(table[i][1].nptr.cat_name == 'angle') and
(table[i][1].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Invalid \"angle_coeff\" command.\n\n'+
' Each \"angle_coeff\" command should have the following syntax:\n\n'+
' angle_coeff @angle:type [optional style] list-of-parameters...\n'+
'----------------------------------------------------\n\n'+
g_no_check_msg)
else:
angle_coeffs_defined.add(table[i][1].binding)
if ((isinstance(table[i][0], TextBlock)) and
((table[i][0].text.lower() == 'dihedralcoeff') or
(table[i][0].text.lower() == 'dihedral_coeff'))):
if table[i][0].text != 'dihedral_coeff':
raise InputError('----------------------------------------------------\n'+
' Spelling error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Use \"dihedral_coeff\", not \"'+table[i][0].text+'\"\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
if ((len(table[i]) > 1) and
isinstance(table[i][1], TextBlock) and
(table[i][1].text == '*')):
pass # we dealt with this case earlier
elif (not ((len(table[i]) > 1) and
(isinstance(table[i][1], VarRef)) and
(table[i][1].prefix in ('@', '@{')) and
(table[i][1].nptr.cat_name == 'dihedral') and
(table[i][1].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Invalid \"dihedral_coeff\" command.\n\n'+
' Each \"dihedral_coeff\" command should have the following syntax:\n\n'+
' dihedral_coeff @dihedral:type [optional style] list-of-parameters...\n'+
'----------------------------------------------------\n\n'+
g_no_check_msg)
else:
dihedral_coeffs_defined.add(table[i][1].binding)
if ((isinstance(table[i][0], TextBlock)) and
((table[i][0].text.lower() == 'impropercoeff') or
(table[i][0].text.lower() == 'improper_coeff'))):
if table[i][0].text != 'improper_coeff':
raise InputError('----------------------------------------------------\n'+
' Spelling error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Use \"improper_coeff\", not \"'+table[i][0].text+'\"\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
if ((len(table[i]) > 1) and
isinstance(table[i][1], TextBlock) and
(table[i][1].text == '*')):
pass # we dealt with this case earlier
elif (not ((len(table[i]) > 1) and
(isinstance(table[i][1], VarRef)) and
(table[i][1].prefix in ('@', '@{')) and
(table[i][1].nptr.cat_name == 'improper') and
(table[i][1].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Invalid \"improper_coeff\" command.\n\n'+
' Each \"improper_coeff\" command should have the following syntax:\n\n'+
' improper_coeff @improper:type [optional style] list-of-parameters...\n'+
'----------------------------------------------------\n\n'+
g_no_check_msg)
else:
improper_coeffs_defined.add(table[i][1].binding)
elif ((isinstance(table[i][0], TextBlock)) and
((table[i][0].text.lower() == 'paircoeff') or
(table[i][0].text.lower() == 'pair_coeff'))):
if table[i][0].text != 'pair_coeff':
raise InputError('----------------------------------------------------\n'+
' Spelling error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Use \"pair_coeff\", not \"'+table[i][0].text+'\"\n'+
'----------------------------------------------------\n'+
g_no_check_msg)
if len(table[i]) > 2: # if not, deal with error later
if ((isinstance(table[i][1], TextBlock) and
(table[i][1].text == '*')) and
(isinstance(table[i][1], TextBlock) and
(table[i][1].text == '*'))):
pair_coeffs_defined.add(('*','*'))
else:
compound_wildcard = False
assert(len(table[i]) > 1)
if hasattr(table[i][1], '__len__'):
ltmpl = table[i][1]
else:
ltmpl = [table[i][1]]
for entry in ltmpl:
if (isinstance(entry, TextBlock) and
('*' in entry.text)):
compound_wildcard = True
elif (isinstance(entry, VarRef) and
('*' in entry.descr_str)):
compound_wildcard = True
if hasattr(table[i][2], '__len__'):
ltmpl = table[i][2]
else:
ltmpl = [table[i][2]]
for entry in ltmpl:
if (isinstance(entry, TextBlock) and
('*' in entry.text)):
compound_wildcard = True
elif (isinstance(entry, VarRef) and
('*' in entry.descr_str)):
compound_wildcard = True
if compound_wildcard:
raise InputError('---- Paranoid checking: ---\n'
' Possible error near '+
ErrorLeader(entry.srcloc.infile,
entry.srcloc.lineno)+'\n'
'The wildcard symbol, \"*\", is not recommended within a \"pair_coeff\" command.\n'
'It is safer to specify the parameters for each bond type explicitly.\n'
'You CAN use \"*\" wildcards, but you must disable syntax checking. To get\n'
'past this error message, run moltemplate.sh using the \"-nocheck\" option.\n')
if ((len(table[i]) > 2) and
(isinstance(table[i][1], TextBlock) and
(table[i][1].text == '*')) and
(isinstance(table[i][2], TextBlock) and
(table[i][2].text == '*'))):
pass # we dealt with this case earlier
elif (not ((len(table[i]) > 2) and
(isinstance(table[i][1], VarRef)) and
(table[i][1].prefix in ('@', '@{')) and
(table[i][1].nptr.cat_name == 'atom') and
(table[i][1].nptr.cat_node == root_node) and
(isinstance(table[i][2], VarRef)) and
(table[i][2].prefix in ('@', '@{')) and
(table[i][2].nptr.cat_name == 'atom') and
(table[i][2].nptr.cat_node == root_node))):
raise InputError('----------------------------------------------------\n'+
' Syntax error near '+
ErrorLeader(table[i][0].srcloc.infile,
table[i][0].srcloc.lineno)+'\n'
' Invalid \"pair_coeff\" command.\n\n'+
' Each \"pair_coeff\" command should have the following syntax:\n\n'+
' pair_coeff @atom:typeI @atom:typeJ [optional style] list-of-parameters...\n'+
'----------------------------------------------------\n\n'+
g_no_check_msg)
else:
pair_coeffs_defined.add((table[i][1].binding, table[i][2].binding))
def LttreeCheckParseArgs(argv, settings):
LttreeParseArgs(argv, settings)
if __name__ == "__main__":
# Instantiate the lexer we will be using.
# (The lexer's __init__() function requires an openned file.
# Assuming __name__ == "__main__", then the name of that file should
# be the last remaining (unprocessed) argument in the argument list.)
if len(argv) == 1:
raise InputError('Error: This program requires at least one argument\n'
' the name of a file containing ttree template commands\n')
elif len(argv) == 2:
settings.infile = argv[1]
try:
settings.lex = TemplateLexer(open(settings.infile, 'r'),
settings.infile) # Parse text from file
except IOError:
sys.stderr.write('Error: unable to open file\n'
' \"'+settings.infile+'\"\n'
' for reading.\n')
sys.exit(1)
del(argv[1:2])
else:
# if there are more than 2 remaining arguments,
problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
raise InputError('Syntax Error('+g_program_name+'):\n\n'
' Unrecognized argument.\n'
' (That or there is some other problem with the argument list.)\n'
' The problem begins with these arguments:\n'
' '+(' '.join(problem_args))+'\n\n'
' (The actual problem may be earlier in the argument list.\n'
' If these arguments are source files, then keep in mind\n'
' that this program can not parse multiple source files.)\n'
' Check the syntax of the entire argument list.\n')
####### control flow begins here: #######
if __name__ == "__main__":
g_program_name = __file__.split('/')[-1] # = 'lttree_check.py'
g_version_str = '0.73'
g_date_str = '2013-8-06'
sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+'\n')
try:
# Parse the argument list and instantiate the lexer we will be using:
#settings = BasicUISettings()
#BasicUIParseArgs(sys.argv, settings)
settings = LttreeSettings()
LttreeCheckParseArgs(sys.argv, settings)
# Invoke syntax checker pass:
# This first check only checks for very simple mistakes
# (mispelled versions of standard files or variable names).
CheckSyntaxCheap(settings.lex)
settings.lex.instream.close()
# Now read the file again.
# This time parse it using StaticObj.ReadTemplate().
# (This will allow us to check for deeper problems.)
del settings.lex
settings.lex = TemplateLexer(open(settings.infile, 'r'),
settings.infile)
static_tree_root = StaticObj('', None) # The root of the static tree
# has name '' (equivalent to '/')
sys.stderr.write(g_program_name+': parsing the class definitions...')
static_tree_root.Parse(settings.lex)
sys.stderr.write(' done\n'+g_program_name+': looking up classes...')
static_tree_root.LookupStaticRefs()
sys.stderr.write(' done\n'+g_program_name+': looking up @variables...')
AssignVarPtrs(static_tree_root,
search_instance_commands=False)
AssignVarPtrs(static_tree_root,
search_instance_commands=True)
sys.stderr.write(' done\n')
#sys.stderr.write(' done\n\nclass_def_tree = ' + str(static_tree_root) + '\n\n')
data_pair_coeffs_defined = set([])
data_bond_coeffs_defined = set([])
data_angle_coeffs_defined = set([])
data_dihedral_coeffs_defined = set([])
data_improper_coeffs_defined = set([])
in_pair_coeffs_defined = set([])
in_bond_coeffs_defined = set([])
in_angle_coeffs_defined = set([])
in_dihedral_coeffs_defined = set([])
in_improper_coeffs_defined = set([])
# Now check the static syntax
# Here we check the contents of the the "write_once()" commands:
CheckSyntaxStatic(static_tree_root,
static_tree_root,
settings.column_names,
data_pair_coeffs_defined,
data_bond_coeffs_defined,
data_angle_coeffs_defined,
data_dihedral_coeffs_defined,
data_improper_coeffs_defined,
in_pair_coeffs_defined,
in_bond_coeffs_defined,
in_angle_coeffs_defined,
in_dihedral_coeffs_defined,
in_improper_coeffs_defined,
search_instance_commands=False)
# Here we check the contents of the the "write()" commands:
CheckSyntaxStatic(static_tree_root,
static_tree_root,
settings.column_names,
data_pair_coeffs_defined,
data_bond_coeffs_defined,
data_angle_coeffs_defined,
data_dihedral_coeffs_defined,
data_improper_coeffs_defined,
in_pair_coeffs_defined,
in_bond_coeffs_defined,
in_angle_coeffs_defined,
in_dihedral_coeffs_defined,
in_improper_coeffs_defined,
search_instance_commands=True)
if 'bond' in static_tree_root.categories:
if ((len(data_bond_coeffs_defined) > 0) and
(len(in_bond_coeffs_defined) > 0)):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: You can EITHER use \"bond_coeff\" commands\n'+
' OR you can have a \"Data Bond Coeffs\" section.\n'+
' LAMMPS will not allow both (...as of late 2012)\n'+
'---------------------------------------------------------------------\n'+
g_no_check_msg)
#' If this is no longer true, to override this error message you must\n'+
#' disable error checking by running moltemplate with the -nocheck option.\n')
if len(data_bond_coeffs_defined) > 0:
bond_coeffs_defined = data_bond_coeffs_defined
else:
bond_coeffs_defined = in_bond_coeffs_defined
bond_bindings = static_tree_root.categories['bond'].bindings
for nd,bond_binding in bond_bindings.items():
if not nd.IsDeleted():
if ((not (bond_binding in bond_coeffs_defined)) and
(not HasWildCard(bond_binding.full_name)) and
(not ('*' in bond_coeffs_defined))):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: Missing bond coeff.\n\n'+
' No coeffs for the \"'+bond_binding.full_name+'\" bond type have been\n'+
'defined, but a reference to that bond type was discovered\n'+
'near '+ErrorLeader(bond_binding.refs[0].srcloc.infile,
bond_binding.refs[0].srcloc.lineno)+'. Check this file and also check\n'
'your \"bond_coeff\" commands or your \"Data Bond Coeffs" section.\n'
'---------------------------------------------------------------------\n'+
g_no_check_msg)
if 'angle' in static_tree_root.categories:
if ((len(data_angle_coeffs_defined) > 0) and
(len(in_angle_coeffs_defined) > 0)):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: You can EITHER use \"angle_coeff\" commands\n'+
' OR you can have a \"Data Angle Coeffs\" section.\n'+
' LAMMPS will not allow both (...as of late 2012)\n'+
'---------------------------------------------------------------------\n'+
g_no_check_msg)
#' If this is no longer true, to override this error message you must\n'+
#' disable error checking by running moltemplate with the -nocheck option.\n')
if len(data_angle_coeffs_defined) > 0:
angle_coeffs_defined = data_angle_coeffs_defined
else:
angle_coeffs_defined = in_angle_coeffs_defined
angle_bindings = static_tree_root.categories['angle'].bindings
for nd,angle_binding in angle_bindings.items():
if not nd.IsDeleted():
if ((not (angle_binding in angle_coeffs_defined)) and
#(not HasWildCard(angle_binding.full_name)) and
(not ('*' in angle_coeffs_defined))):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: Missing angle coeff.\n\n'+
' No coeffs for the \"'+angle_binding.full_name+'\" angle type have been\n'+
'defined, but a reference to that angle type was discovered\n'+
'near '+ErrorLeader(angle_binding.refs[0].srcloc.infile,
angle_binding.refs[0].srcloc.lineno)+'. Check this file and\n'
'also check your \"angle_coeff\" commands or your \"Data Angle Coeffs" section.\n'+
'---------------------------------------------------------------------\n'+
g_no_check_msg)
if 'dihedral' in static_tree_root.categories:
if ((len(data_dihedral_coeffs_defined) > 0) and
(len(in_dihedral_coeffs_defined) > 0)):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: You can EITHER use \"dihedral_coeff\" commands\n'+
' OR you can have a \"Data Dihedral Coeffs\" section.\n'+
' LAMMPS will not allow both (...as of late 2012)\n'+
'---------------------------------------------------------------------\n'+
g_no_check_msg)
#' If this is no longer true, to override this error message you must\n'+
#' disable error checking by running moltemplate with the -nocheck option.\n')
if len(data_dihedral_coeffs_defined) > 0:
dihedral_coeffs_defined = data_dihedral_coeffs_defined
else:
dihedral_coeffs_defined = in_dihedral_coeffs_defined
dihedral_bindings = static_tree_root.categories['dihedral'].bindings
for nd,dihedral_binding in dihedral_bindings.items():
if not nd.IsDeleted():
if ((not (dihedral_binding in dihedral_coeffs_defined)) and
#(not HasWildCard(dihedral_binding.full_name)) and
(not ('*' in dihedral_coeffs_defined))):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: Missing dihedral coeff.\n\n'+
' No coeffs for the \"'+dihedral_binding.full_name+'\" dihedral type have been\n'+
'defined, but a reference to that dihedral type was discovered\n'+
'near '+ErrorLeader(dihedral_binding.refs[0].srcloc.infile,
dihedral_binding.refs[0].srcloc.lineno)+'. Check this file and\n'
'also check your \"dihedral_coeff\" commands or your \"Data Dihedral Coeffs" section.\n'+
'---------------------------------------------------------------------\n'+
g_no_check_msg)
if 'improper' in static_tree_root.categories:
if ((len(data_improper_coeffs_defined) > 0) and
(len(in_improper_coeffs_defined) > 0)):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: You can EITHER use \"improper_coeff\" commands\n'+
' OR you can have a \"Data Improper Coeffs\" section.\n'+
' LAMMPS will not allow both (...as of late 2012)\n'+
'---------------------------------------------------------------------\n'+
g_no_check_msg)
#' If this is no longer true, to override this error message you must\n'+
#' disable error checking by running moltemplate with the -nocheck option.\n')
if len(data_improper_coeffs_defined) > 0:
improper_coeffs_defined = data_improper_coeffs_defined
else:
improper_coeffs_defined = in_improper_coeffs_defined
improper_bindings = static_tree_root.categories['improper'].bindings
for nd,improper_binding in improper_bindings.items():
if not nd.IsDeleted():
if ((not (improper_binding in improper_coeffs_defined)) and
#(not HasWildCard(improper_binding.full_name)) and
(not ('*' in improper_coeffs_defined))):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: Missing improper coeff.\n\n'+
' No coeffs for the \"'+improper_binding.full_name+'\" improper type have been\n'+
'defined, but a reference to that improper type was discovered\n'+
'near '+ErrorLeader(improper_binding.refs[0].srcloc.infile,
improper_binding.refs[0].srcloc.lineno)+'. Check this file and\n'
'also check your \"improper_coeff\" commands or your \"Data Improper Coeffs" section.\n'+
'---------------------------------------------------------------------\n'+
g_no_check_msg)
if 'atom' in static_tree_root.categories:
if ((len(data_pair_coeffs_defined) > 0) and
(len(in_pair_coeffs_defined) > 0)):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: You can EITHER use \"pair_coeff\" commands\n'+
' OR you can have a \"Data Pair Coeffs\" section.\n'+
' LAMMPS will not allow both (...as of late 2012)\n'+
'---------------------------------------------------------------------\n'+
g_no_check_msg)
#' If this is no longer true, to override this error message you must\n'+
#' disable error checking by running moltemplate with the -nocheck option.\n')
if len(data_pair_coeffs_defined) > 0:
pair_coeffs_defined = data_pair_coeffs_defined
else:
pair_coeffs_defined = in_pair_coeffs_defined
atom_bindings = static_tree_root.categories['atom'].bindings
for nd,atom_binding in atom_bindings.items():
if not nd.IsDeleted():
if ((not ((atom_binding,atom_binding)
in
pair_coeffs_defined)) and
(not HasWildCard(atom_binding.full_name)) and
(not (('*','*') in pair_coeffs_defined))):
raise InputError('---------------------------------------------------------------------\n'+
' Syntax error: Missing pair coeff.\n\n'+
' No pair coeffs for the \"'+atom_binding.full_name+'\" atom type have been\n'+
'defined, but a reference to that atom type was discovered\n'+
'near '+ErrorLeader(atom_binding.refs[0].srcloc.infile,
atom_binding.refs[0].srcloc.lineno)+'. Check this file and\n'
'also check your \"pair_coeff\" commands or your \"Data Pair Coeffs" section.\n\n'+
g_no_check_msg)
#else:
# raise InputError('Error: No atom types (@atom) have been defined.\n')
sys.stderr.write(g_program_name+': -- No errors detected. --\n')
exit(0)
except (ValueError, InputError) as err:
sys.stderr.write('\n'+str(err)+'\n')
sys.exit(1)
diff --git a/tools/moltemplate/src/moltemplate.sh b/tools/moltemplate/src/moltemplate.sh
index f08691651..43dea70da 100755
--- a/tools/moltemplate/src/moltemplate.sh
+++ b/tools/moltemplate/src/moltemplate.sh
@@ -1,1775 +1,1781 @@
#!/usr/bin/env bash
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2012, Regents of the University of California
# All rights reserved.
G_PROGRAM_NAME="moltemplate.sh"
-G_VERSION="1.14"
-G_DATE="2013-10-08"
+G_VERSION="1.17"
+G_DATE="2013-12-23"
echo "${G_PROGRAM_NAME} v${G_VERSION} ${G_DATE}" >&2
echo "" >&2
# Check for python:
# I prefer python over python3 because python3 requires
# more memory. Use regular python (ie 2.7) when available.
if which python > /dev/null; then
PYTHON_COMMAND='python'
elif which python3 > /dev/null; then
PYTHON_COMMAND='python3'
else
echo "Error: $G_PROGRAM_NAME requires python or python3" >&2
exit 1
fi
# First, determine the directory in which this shell script is located.
# (The python script files should also be located here as well.)
#SCRIPT_DIR=$(dirname $0)
SCRIPT_DIR=`dirname "$0"`
MSG_BAD_INSTALL=$(cat <<EOF
INSTALLATION ERROR:
Follow the instructions in the "Installation" chapter of the moltemplate manual.
(Note: You may need to log out and log in again before the changes take effect.)
EOF
)
ERR_BAD_INSTALL()
{
echo "$MSG_BAD_INSTALL" >&2
exit 1
}
ERR_INTERNAL()
{
- echo " --- Possible internal error. ---" >&2
+ echo " !!!!!! Possible internal error !!!!!!" >&2
echo "This could be a bug in moltemplate." >&2
echo "Please report this error." >&2
echo "(And please include the last few lines of moltemplate output preceeding this.)" >&2
echo " Thank you." >&2
exit 100
}
MOLTEMPLATE_FILES_NEEDED=$(cat <<EOF
ttree.py
lttree.py
lttree_check.py
lttree_postprocess.py
nbody_by_type.py
nbody_fix_ttree_assignments.py
nbody_reorder_atoms.py
pdbsort.py
postprocess_input_script.py
remove_duplicate_atoms.py
remove_duplicates_nbody.py
renumber_DATA_first_column.py
ttree_render.py
dump2data.py
raw2data.py
EOF
)
OIFS=$IFS
#IFS=$'\n'
IFS="
"
for f in $MOLTEMPLATE_FILES_NEEDED; do
if [ ! -s "${SCRIPT_DIR}/$f" ]; then
echo "Error: Missing file \"${SCRIPT_DIR}/$f\"" >&2
ERR_BAD_INSTALL
fi
done
IFS=$OIFS
IMOLPATH=""
if [ -n "${MOLTEMPLATE_PATH}" ]; then
IMOLPATH="-importpath \"${MOLTEMPLATE_PATH}\""
fi
# command that invokes lttree.py
LTTREE_COMMAND="$PYTHON_COMMAND \"${SCRIPT_DIR}/lttree.py\" ${IMOLPATH}"
# command that invokes lttree_check.py
LTTREE_CHECK_COMMAND="$PYTHON_COMMAND \"${SCRIPT_DIR}/lttree_check.py\" ${IMOLPATH}"
# command that invokes lttree_postprocess.py
LTTREE_POSTPROCESS_COMMAND="$PYTHON_COMMAND \"${SCRIPT_DIR}/lttree_postprocess.py\" ${IMOLPATH}"
# -----------------------------------------------------------
# If everything worked, then running ttree usually
# generates the following files:
#
# Users of lttree typically generate the following files:
# The variable below refer to file names generated by
# write() and write_once() commands in a lttree-file.
# (I keep changing my mind what I want these names to be.)
data_prefix="Data "
data_prefix_no_space="Data"
data_header="Data Header"
data_atoms="Data Atoms"
data_masses="Data Masses"
data_velocities="Data Velocities"
data_bonds="Data Bonds"
data_bond_list="Data Bond List"
data_angles="Data Angles"
data_dihedrals="Data Dihedrals"
data_impropers="Data Impropers"
data_bond_coeffs="Data Bond Coeffs"
data_angle_coeffs="Data Angle Coeffs"
data_dihedral_coeffs="Data Dihedral Coeffs"
data_improper_coeffs="Data Improper Coeffs"
data_pair_coeffs="Data Pair Coeffs"
# interactions-by-type (not id. This is not part of the LAMMPS standard.)
data_bonds_by_type="Data Bonds By Type"
data_angles_by_type="Data Angles By Type"
data_dihedrals_by_type="Data Dihedrals By Type"
data_impropers_by_type="Data Impropers By Type"
# class2 data sections
data_bondbond_coeffs="Data BondBond Coeffs"
data_bondangle_coeffs="Data BondAngle Coeffs"
data_middlebondtorsion_coeffs="Data MiddleBondTorsion Coeffs"
data_endbondtorsion_coeffs="Data EndBondTorsion Coeffs"
data_angletorsion_coeffs="Data AngleTorsion Coeffs"
data_angleangletorsion_coeffs="Data AngleAngleTorsion Coeffs"
data_bondbond13_coeffs="Data BondBond13 Coeffs"
data_angleangle_coeffs="Data AngleAngle Coeffs"
# sections for non-point-like particles:
data_ellipsoids="Data Ellipsoids"
data_lines="Data Lines"
data_triangles="Data Triangles"
# periodic boundary conditions
data_boundary="Data Boundary"
# (for backward compatibility), an older version of this file was named:
data_pbc="Data PBC"
# ---------------------------------------------------------------
# Note: The files above are fragments of a LAMMPS data file.
# In addition, moltemplate will probably also generate the following files:
# (These files represent different sections of the LAMMPS input script.)
# ---------------------------------------------------------------
in_prefix="In "
in_prefix_no_space="In"
in_init="In Init"
in_settings="In Settings"
in_coords="In Coords"
# If present, the various "In " files contain commands which should be
# included by the user in their LAMMPS input script. (This task is left
# to the user.) However, the "Data " files are processed and pasted together
# automatically in order to build a LAMMPS data file.
# ---------------------------------------------------------------
tmp_atom_coords="tmp_atom_coords.dat" #<-temporary file for storing coordinates
MOLTEMPLATE_TEMP_FILES=$(cat <<EOF
*.template
ttree_assignments.txt
$tmp_atom_coords
$data_masses
$data_pair_coeffs
$data_bond_coeffs
$data_angle_coeffs
$data_dihedral_coeffs
$data_improper_coeffs
$data_atoms
$data_velocities
$data_bonds
$data_bond_list
$data_angles
$data_dihedrals
$data_impropers
$data_bondbond_coeffs
$data_bondangle_coeffs
$data_middlebondtorsion_coeffs
$data_endbondtorsion_coeffs
$data_angletorsion_coeffs
$data_angleangletorsion_coeffs
$data_bondbond13_coeffs
$data_angleangle_coeffs
$data_ellipsoids
$data_lines
$data_triangles
$data_boundary
$data_bonds_by_type
$data_angles_by_type
$data_dihedrals_by_type
$data_impropers_by_type
$in_init
$in_settings
EOF
)
OIFS=$IFS
#IFS=$'\n'
IFS="
"
for f in $MOLTEMPLATE_TEMP_FILES; do
#echo "removing [$f]"
rm -f "$f"
done
IFS=$OIFS
rm -rf output_ttree
SYNTAX_MSG=$(cat <<EOF
Syntax example:
Usage:
moltemplate.sh [-atomstyle style] \
[-pdb/-xyz coord_file] \
[-a assignments.txt] file.lt
Optional arguments:
-atomstyle style By default, moltemplate.sh assumes you are using the "full"
atom style in LAMMPS. You can change the atom style to "dipole"
using -atomstyle dipole. If you are using a hybrid style,
you must enclose the list of styles in quotes. For example:
-atomstyle "hybrid full dipole"
For custom atom styles, you can also specify the
list of column names manually (enclosed in quotes):
-atomstyle "molid x y z atomid atomtype mux muy muz"
-xyz xyz_file An optional xyz_file argument can be supplied as an argument
following "-xyz".
This file should contain the atomic coordinates in xyz format.
(The atoms must appear in the same order in the data file.)
-pdb pdb_file An optional pdb_file argument can be supplied as an argument
following "-pdb".
This should be a PDB file (with ATOM or HETATM records) with
the coordinates you wish to appear in the LAMMPS data file.
(The atoms must appear in the same order in the data file.)
If the PDB file contains periodic boundary box information
(ie., a "CRYST1" record), this information is also copied
to the LAMMPS data file.
(Support for triclinic cells is experimental as of 2012-2-13.
Other molecular structure formats may be supported later.)
-a "@atom:x 1"
-a assignments.txt
The user can customize the numbers assigned to atom, bond,
angle, dihedral, and improper types or id numbers by using
-a "VARIABLE_NAME VALUE"
for each variable you want to modify. If there are many
variables you want to modify, you can save them in a file
(one variable per line). For an example of the file format
run moltemplat.sh once and search for a file named
"ttree_assignments.txt". (This file is often located in
the "output_ttree/" directory.) Once assigned, the remaining
variables in the same category will be automatically assigned
to values which do not overlap with your chosen values.
-b assignments.txt
"-b" is similar to "-a". However, in this case, no attempt
is made to assign exclusive (unique) values to each variable.
-nocheck
Normally moltemplate.sh checks for common errors and typos and
halts if it thinks it has found one. This forces the variables
and categories as well as write(file) and write_once(file)
commands to obey standard naming conventions. The "-nocheck"
argument bypasses these checks and eliminates these restrictions.
EOF
)
# --- Periodic boundary box information (default) ---
# We will determine these numbers later.
TRICLINIC=""
BOXSIZE_MINX=0.0
BOXSIZE_MINY=0.0
BOXSIZE_MINZ=0.0
BOXSIZE_MAXX=""
BOXSIZE_MAXY=""
BOXSIZE_MAXZ=""
BOXSIZE_XY=0.0
BOXSIZE_XZ=0.0
BOXSIZE_YZ=0.0
if [ "$1" = "--help" ]; then
echo "$SYNTAX_MSG" >&2
exit 0
fi
# --- Did the user specify a file containing atomic coordinates?
rm -f "$tmp_atom_coords"
# Optional files containing atom coordinates:
PDB_FILE=""
XYZ_FILE=""
RAW_FILE=""
LT_FILE=""
OUT_FILE_BASE="system"
# REMOVE_DUPLICATE variables:
# ...If true (default), then any duplicate entries in the lists of bonds
# bonds, angles, dihedrals, or impropers in the LAMMPS DATA file
# are removed, giving priority to the most recent entry in the list.
# (This might not be necessary, but I want to be careful.)
REMOVE_DUPLICATE_BONDS="true"
REMOVE_DUPLICATE_ANGLES="true"
REMOVE_DUPLICATE_DIHEDRALS="true"
REMOVE_DUPLICATE_IMPROPERS="true"
ARGC=0
for A in "$@"; do
ARGC=$((ARGC+1))
eval ARGV${ARGC}=\"$A\"
done
TTREE_ARGS=""
ATOM_STYLE=""
i=0
while [ "$i" -lt "$ARGC" ]; do
i=$((i+1))
eval A=\${ARGV${i}}
if [ "$A" == "-nocheck" ]; then
# Disable syntax checking by undefining LTTREE_CHECK_COMMAND
unset LTTREE_CHECK_COMMAND
unset LTTREE_POSTPROCESS_COMMAND
elif [ "$A" == "-overlay-bonds" ]; then
# In that case, do not remove duplicate bond interactions
unset REMOVE_DUPLICATE_BONDS
elif [ "$A" == "-overlay-angles" ]; then
# In that case, do not remove duplicate angle interactions
unset REMOVE_DUPLICATE_ANGLES
- elif [ "$A" == "-overlay-dihdedrals" ]; then
+ elif [ "$A" == "-overlay-dihedrals" ]; then
# In that case, do not remove duplicate dihedral interactions
unset REMOVE_DUPLICATE_DIHEDRALS
elif [ "$A" == "-overlay-impropers" ]; then
# In that case, do not remove duplicate improper interactions
unset REMOVE_DUPLICATE_IMPROPERS
elif [ "$A" == "-raw" ]; then
if [ "$i" -eq "$ARGC" ]; then
echo "$SYNTAX_MSG" >&2
exit 7
fi
i=$((i+1))
eval A=\${ARGV${i}}
RAW_FILE=$A
if [ ! -s "$RAW_FILE" ]; then
echo "$SYNTAX_MSG" >&2
echo "-----------------------" >&2
echo "" >&2
echo "Error: Unable to open RAW-file \"$RAW_FILE\"." >&2
echo " (File is empty or does not exist.)" >&2
exit 8
fi
#echo " (extracting coordinates from \"$RAW_FILE\")" >&2
awk '{if (NF==3) {print $0}}' < "$RAW_FILE" > "$tmp_atom_coords"
elif [ "$A" == "-xyz" ]; then
if [ "$i" -eq "$ARGC" ]; then
echo "$SYNTAX_MSG" >&2
exit 7
fi
i=$((i+1))
eval A=\${ARGV${i}}
XYZ_FILE=$A
if [ ! -s "$XYZ_FILE" ]; then
echo "$SYNTAX_MSG" >&2
echo "-----------------------" >&2
echo "" >&2
echo "Error: Unable to open XYZ-file \"$XYZ_FILE\"." >&2
echo " (File is empty or does not exist.)" >&2
exit 8
fi
#echo " (extracting coordinates from \"$XYZ_FILE\")" >&2
# "isnum(x)" returns 1 or 0 depending upon whether or not
# a string is numeric.
#http://rosettacode.org/wiki/Determine_if_a_string_is_numeric#AWK
awk 'function isnum(x){return(x==x+0)} BEGIN{targetframe=1;framecount=0} {if (isnum($0)) {framecount++} else{if (framecount==targetframe){ if (NF>0) { if ((NF==3) && isnum($1)) {print $1" "$2" "$3} else if ((NF==4) && isnum($2)) {print $2" "$3" "$4} }}}}' < "$XYZ_FILE" > "$tmp_atom_coords"
elif [ "$A" == "-pdb" ]; then
if [ "$i" -eq "$ARGC" ]; then
echo "$SYNTAX_MSG" >&2
exit 9
fi
i=$((i+1))
eval A=\${ARGV${i}}
PDB_FILE=$A
if [ ! -s "$PDB_FILE" ]; then
echo "$SYNTAX_MSG" >&2
echo "-----------------------" >&2
echo "" >&2
echo "Error: Unable to open PDB-file \"$PDB_FILE\"." >&2
echo " (File is empty or does not exist.)" >&2
exit 10
fi
#echo " (extracting coordinates from \"$PDB_FILE\")" >&2
if grep -q '^ATOM \|^HETATM' "$PDB_FILE"; then
# Extract the coords from the "ATOM" records in the PDB file
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/pdbsort.py" < "$PDB_FILE" \
| awk '/^ATOM |^HETATM/{print substr($0,31,8)" "substr($0,39,8)" "substr($0,47,8)}' > "$tmp_atom_coords"; then
ERR_INTERNAL
fi
else
echo "$SYNTAX_MSG" >&2
echo "-----------------------" >&2
echo "" >&2
echo "Error: File \"$PDB_FILE\" is not a valid PDB file." >&2
exit 11
fi
# Now extract the periodic bounding-box informatio from the PDB file
# The CRYST1 records are described at:
# http://deposit.rcsb.org/adit/docs/pdb_atom_format.html
BOXSIZE_A=-1.0
BOXSIZE_B=-1.0
BOXSIZE_C=-1.0
ALPHA=" 90.00" #Note: The space before the number in " 90.00" is intentional.
BETA=" 90.00" # Later we will check to see if the system is triclinic
GAMMA=" 90.00" # by comparing these strings for equality with " 90.00"
if grep -qF "CRYST1" "$PDB_FILE"; then
BOXSIZE_A=`awk '/CRYST1/{print substr($0,8,8)}' < "$PDB_FILE"`
BOXSIZE_B=`awk '/CRYST1/{print substr($0,17,8)}' < "$PDB_FILE"`
BOXSIZE_C=`awk '/CRYST1/{print substr($0,26,8)}' < "$PDB_FILE"`
ALPHA=`awk '/CRYST1/{print substr($0,35,6)}' < "$PDB_FILE"`
BETA=`awk '/CRYST1/{print substr($0,42,6)}' < "$PDB_FILE"`
GAMMA=`awk '/CRYST1/{print substr($0,49,6)}' < "$PDB_FILE"`
fi
if [ `echo "$ALPHA!=90.0"|bc` -eq 1 ] || [ `echo "$BETA!=90.0"|bc` -eq 1 ] || [ `echo "$GAMMA!=90.0"|bc` -eq 1 ]; then
# I transform the parameters from one format to the other by inverting
# the transformation formula from the LAMMPS documentation (which matches
# http://www.ccl.net/cca/documents/molecular-modeling/node4.html)
# Disclaimer:
# As of September 2012, I have not tested the code below. I think the
# equations are correct, but I don't know if their are special cases
# that require the coordinates to be rotated or processed beforehand.
# This is an experimental feature.
TRICLINIC="True"
PI=3.1415926535897931
BOXSIZE_X=$BOXSIZE_A
BOXSIZE_Y=`awk "BEGIN{print $BOXSIZE_B*sin($GAMMA*$PI/180.0)}"`
BOXSIZE_XY=`awk "BEGIN{print $BOXSIZE_B*cos($GAMMA*$PI/180.0)}"`
BOXSIZE_XZ=`awk "BEGIN{print $BOXSIZE_C*cos($BETA*$PI/180.0)}"`
BOXSIZE_YZ=`awk "BEGIN{ca=cos($ALPHA*$PI/180.0); cb=cos($BETA*$PI/180.0); cg=cos($GAMMA*$PI/180.0); sg=sin($GAMMA*$PI/180.0); c=$BOXSIZE_C; print c*(ca-(cg*cb))/sg}"`
BOXSIZE_Z=`awk "BEGIN{print sqrt(($BOXSIZE_C**2)-(($BOXSIZE_XZ**2)+($BOXSIZE_YZ**2)))}"`
else
BOXSIZE_X=$BOXSIZE_A
BOXSIZE_Y=$BOXSIZE_B
BOXSIZE_Z=$BOXSIZE_C
BOXSIZE_XY=0.0
BOXSIZE_XZ=0.0
BOXSIZE_YZ=0.0
fi
BOXSIZE_MINX=0.0
BOXSIZE_MINY=0.0
BOXSIZE_MINZ=0.0
BOXSIZE_MAXX=$BOXSIZE_X
BOXSIZE_MAXY=$BOXSIZE_Y
BOXSIZE_MAXZ=$BOXSIZE_Z
elif [ "$A" == "-atomstyle" ] || [ "$A" == "-atom-style" ] || [ "$A" == "-atom_style" ]; then
if [ "$i" -eq "$ARGC" ]; then
echo "$SYNTAX_MSG" >&2
exit 7
fi
i=$((i+1))
eval A=\${ARGV${i}}
if [ -z "$A" ]; then
echo "$SYNTAX_MSG" >&2
echo "-----------------------" >&2
echo "" >&2
echo "Error: The \"-atomstyle\" argument should be followed by an atom style." >&2
echo " (See the \"atom_style\" command in the LAMMPS documentation.\n" >&2
echo " Note: hybrid atom styles are allowed but should be enclosed in quotes.)\n" >&2
exit 8
fi
#echo " (atom_style=\"$A\")" >&2
#echo "" >&2
ATOM_STYLE="-atomstyle \"$A\""
# (minor detail: $ATOM_STYLE should also be appended to TTREE_ARGS)
if [ -z "$TTREE_ARGS" ]; then
TTREE_ARGS="$ATOM_STYLE"
else
TTREE_ARGS="${TTREE_ARGS} $ATOM_STYLE"
fi
#else: If the arguments are not understood in this script, then
# pass them on to "lttree.py"
else
if [ -z "$TTREE_ARGS" ]; then
TTREE_ARGS="\"$A\""
else
TTREE_ARGS="${TTREE_ARGS} \"$A\""
fi
# Check to see if this string ($A) ends in .lt or .LT
# If so, then set the base name of the output files
# to equal the base name of the .LT file being read.
# (Being careful here.
# Sometimes the last argument is not the .lt or .LT file.
# Sometimes that file appears earlier in the argument list.
# I want to supply a default value.)
#
# Note, in bash you can use:
# if [ "${LAST_ARG/%.lt/}" -neq "$LAST_ARG" ]; then
# OUT_FILE_BASE="${LAST_ARG/%.lt/}"
# But in the original bourn shell (sh), this does not work.
# Instead we use a hack involving basename and dirname:
A_FIRSTCHAR="$(echo $A| cut -c 1)"
if [ "$A_FIRSTCHAR" != "-" ]; then
DN=`dirname "$A"`
if [ "$DN" == "." ]; then
DN=""
else
DN="${DN}/"
fi
BN=`basename "$A" .lt`
if [ "${DN}${BN}" != "$A" ]; then
OUT_FILE_BASE="$BN"
else
BN=`basename "$A" .LT`
if [ "${DN}${BN}" != "$A" ]; then
OUT_FILE_BASE="$BN"
fi
fi
fi
fi
done
+
+
OUT_FILE_INPUT_SCRIPT="${OUT_FILE_BASE}.in"
OUT_FILE_INIT="${OUT_FILE_BASE}.in.init"
OUT_FILE_SETTINGS="${OUT_FILE_BASE}.in.settings"
OUT_FILE_DATA="${OUT_FILE_BASE}.data"
OUT_FILE_COORDS="${OUT_FILE_BASE}.in.coords"
rm -f "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_INIT" "$OUT_FILE_SETTINGS" "$OUT_FILE_DATA" "$OUT_FILE_COORDS"
# --------------------------------------------------------------------
# --- Now run ttree/lttree to generate the file fragments we need. ---
# ------ (Afterwards, we will paste these fragments together.) -----
# --------------------------------------------------------------------
# If checking is not disabled, then first check for common spelling errors.
if [ -n "$LTTREE_CHECK_COMMAND" ]; then
if ! eval $LTTREE_CHECK_COMMAND $TTREE_ARGS; then
exit 1
fi
fi
# --- Run ttree. ---
#
# 3, 2, 1, ...
if ! eval $LTTREE_COMMAND $TTREE_ARGS; then
exit 2
fi
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# > Traceback (most recent call last):
# > File "./lttree.py", line...
# .-.
# (0.0)
# '=.|m|.='
# .='`"``=.
#
# Hopefully this does not happen.
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
echo "" >&2
if [ -s "${data_atoms}" ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \
< "${data_atoms}" \
> "${data_atoms}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_atoms}.tmp" "${data_atoms}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \
< "${data_atoms}.template" \
> "${data_atoms}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_atoms}.tmp" "${data_atoms}.template"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_atoms}" \
> "${data_atoms}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_atoms}.tmp" "${data_atoms}"
else
echo "Error: There are no atoms in your system." >&2
echo "" >&2
echo " Make sure that the object(s) you created are indeed molecules." >&2
echo " (Molecule objects must contain at least one" >&2
echo " write(\"${data_atoms}\") command.)" >&2
echo "" >&2
echo " (This error often occurs if you instantiated an object" >&2
echo " which you thought was a molecule, but it is actually" >&2
echo " only a namespace, a force-field name or category" >&2
echo " containing the definitions of other molecules.)" >&2
echo "" >&2
exit 200
fi
# ---------------- Interactions By Type -----------------
# At the time of writing, bonded-interactions-by-atom-type were not
# understood by LAMMPS. These features require auxilliary python scripts.
# These data sections must be processed before everything else (because
# they effect the other data sections, and the ttree_assignments.txt file.)
# -------------------------------------------------------
if [ -s "${data_bond_list}.template" ]; then
if [ ! -s "$data_bonds_by_type" ]; then
echo "Error: You have a \"Data Bond List\", section somewhere\n"
echo " without a \"Data Bonds By Type\" section to support it.\n"
echo " (Did you mean to use \"Data Bonds\" instead?)\n"
echo "Details:"
echo " Unlike the \"Data Bonds\" section, the \"Data Bond List\" section\n"
echo " allows the user to omit the bond types. Instead moltemplate attempts\n"
echo " to infer the type of bond by considering the pair of atom types.\n"
echo " However you must define a \"Data Bonds By Type\" section\n"
echo " to make this feature work (or use \"Data Bonds\" instead).\n"
exit 15
fi
echo "Looking up bond types according to atom type" >&2
#-- Generate a file containing bondid bondtype atomid1 atomid2 --
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/bonds_by_type.py" \
-atoms "${data_atoms}.template" \
-bond-list "${data_bond_list}.template" \
-bondsbytype "${data_bonds_by_type}.template" \
-prefix '$/bond:bytype' > gen_Bonds.template.tmp; then
exit 4
#WARNING: DO NOT REPLACE THIS WITH
#if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
fi
# ---- cleanup: ----
# ---- Create or re-build the "${data_bonds}.template" file ----
# Instert these lines into the "${data_bonds}.template" file which includes
# the newly generated interactions. (Note: these are in .template format)
cp gen_Bonds.template.tmp new_Bonds.template.tmp
if [ -s "${data_bonds}.template" ]; then
# Then append existing "Bonds" to the end of the generated interactions
# (Hopefully this way they will override those interactions.)
cat "${data_bonds}.template" >> new_Bonds.template.tmp
fi
mv -f new_Bonds.template.tmp "${data_bonds}.template"
# ------ THE NEXT STEP IS NOT CURRENTLY NEEDED ------
# All of the $bond variables have already been created, they just lack types
# However we will need to do this if the user wants to omits the bond-ids.
# In case I plan to allow the user to omit bond-ids, I leave this code here.
#
#echo "(Repairing ttree_assignments.txt file after bonds added.)" >&2
#
## ---- Repair the ttree_assignments.txt file ----
## The next 2 lines extract the variable names from data_new.template.tmp
## and instert them into the appropriate place in ttree_assignments.txt
## (renumbering the relevant variable-assignments to avoid clashes).
#if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
# '/bond' gen_Bonds.template.tmp \
# < ttree_assignments.txt \
# > ttree_assignments.tmp; then
# exit 5
#fi
#
#echo "(Rendering ttree_assignments.tmp file after bonds added.)" >&2
#mv -f ttree_assignments.tmp ttree_assignments.txt
# ----------------------------------------------------
# ---- Re-build (render) the "$data_bonds" file ----
# Now substitute these variable values (assignments) into the variable
# names present in the .template file. (We want to convert the file from
# a .template format into an ordinary (numeric) LAMMPS data-section format.)
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
ttree_assignments.txt \
< "${data_bonds}.template" \
> "$data_bonds"; then
exit 6
fi
echo "" >&2
rm -f gen_Bonds.template.tmp new_Bonds.template.tmp
fi
if [ -s "$data_angles_by_type" ]; then
echo "Generating 3-body angle interactions by atom/bond type" >&2
#-- Generate a file containing the list of interactions on separate lines --
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_by_type.py" \
-subgraph nbody_Angles.py \
-section "Angles" \
-sectionbytype "Angles By Type" \
-atoms "${data_atoms}.template" \
-bonds "${data_bonds}.template" \
-nbodybytype "${data_angles_by_type}.template" \
-prefix '$/angle:bytype' > gen_Angles.template.tmp; then
exit 4
#WARNING: DO NOT REPLACE THIS WITH
#if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
fi
# ---- cleanup: ----
# ---- Re-build the "${data_angles}.template" file ----
# Instert these lines into the "${data_angles}.template" file which includes
# the newly generated interactions. (Note: these are in .template format)
cp gen_Angles.template.tmp new_Angles.template.tmp
if [ -s "${data_angles}.template" ]; then
# Then append existing "Angles" to the end of the generated interactions
# (Hopefully this way they will override those interactions.)
cat "${data_angles}.template" >> new_Angles.template.tmp
fi
mv -f new_Angles.template.tmp "${data_angles}.template"
echo "(Repairing ttree_assignments.txt file after angles added.)" >&2
# ---- Repair the ttree_assignments.txt file ----
# The next 2 lines extract the variable names from data_new.template.tmp
# and instert them into the appropriate place in ttree_assignments.txt
# (renumbering the relevant variable-assignments to avoid clashes).
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
'/angle' gen_Angles.template.tmp \
< ttree_assignments.txt \
> ttree_assignments.tmp; then
exit 5
fi
echo "(Rendering ttree_assignments.tmp file after angles added.)" >&2
# ---- Re-build (render) the "$data_angles" file ----
# Now substitute these variable values (assignments) into the variable
# names present in the .template file. (We want to convert the file from
# a .template format into an ordinary (numeric) LAMMPS data-section format.)
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
ttree_assignments.tmp \
< "${data_angles}.template" \
> "$data_angles"; then
exit 6
fi
echo "" >&2
mv -f ttree_assignments.tmp ttree_assignments.txt
rm -f gen_Angles.template.tmp new_Angles.template.tmp
fi
if [ -s "$data_dihedrals_by_type" ]; then
echo "Generating 4-body dihedral interactions by atom/bond type" >&2
#-- Generate a file containing the list of interactions on separate lines --
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_by_type.py" \
-subgraph nbody_Dihedrals.py \
-section "Dihedrals" \
-sectionbytype "Dihedrals By Type" \
-atoms "${data_atoms}.template" \
-bonds "${data_bonds}.template" \
-nbodybytype "${data_dihedrals_by_type}.template" \
-prefix '$/dihedral:bytype' > gen_Dihedrals.template.tmp; then
exit 4
#WARNING: DO NOT REPLACE THIS WITH
#if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
fi
# ---- cleanup: ----
# ---- Re-build the "${data_dihedrals}.template" file ----
# Instert these lines into the "${data_dihedrals}.template" file which includes
# the newly generated interactions. (Note: these are in .template format)
cp gen_Dihedrals.template.tmp new_Dihedrals.template.tmp
if [ -s "${data_dihedrals}.template" ]; then
# Then append existing "Dihedrals" to the end of the generated interactions
# (Hopefully this way they will override those interactions.)
cat "${data_dihedrals}.template" >> new_Dihedrals.template.tmp
fi
mv -f new_Dihedrals.template.tmp "${data_dihedrals}.template"
echo "(Repairing ttree_assignments.txt file after dihedrals added.)" >&2
# ---- Repair the ttree_assignments.txt file ----
# The next 2 lines extract the variable names from data_new.template.tmp
# and instert them into the appropriate place in ttree_assignments.txt
# (renumbering the relevant variable-assignments to avoid clashes).
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
'/dihedral' gen_Dihedrals.template.tmp \
< ttree_assignments.txt \
> ttree_assignments.tmp; then
exit 5
fi
echo "(Rendering ttree_assignments.tmp file after dihedrals added.)" >&2
# ---- Re-build (render) the "$data_dihedrals" file ----
# Now substitute these variable values (assignments) into the variable
# names present in the .template file. (We want to convert the file from
# a .template format into an ordinary (numeric) LAMMPS data-section format.)
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
ttree_assignments.tmp \
< "${data_dihedrals}.template" \
> "$data_dihedrals"; then
exit 6
fi
echo "" >&2
mv -f ttree_assignments.tmp ttree_assignments.txt
rm -f gen_Dihedrals.template.tmp new_Dihedrals.template.tmp
fi
if [ -s "$data_impropers_by_type" ]; then
echo "Generating 4-body improper interactions by atom/bond type" >&2
#-- Generate a file containing the list of interactions on separate lines --
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_by_type.py" \
-subgraph nbody_Impropers.py \
-section "Impropers" \
-sectionbytype "Impropers By Type" \
-atoms "${data_atoms}.template" \
-bonds "${data_bonds}.template" \
-nbodybytype "${data_impropers_by_type}.template" \
-prefix '$/improper:bytype' > gen_Impropers.template.tmp; then
exit 4
#WARNING: DO NOT REPLACE THIS WITH
#if ! $NBODY_COMMAND ...<-this sometimes causes a shell quotes-related error
fi
# ---- cleanup: ----
# ---- Re-build the "${data_impropers}.template" file ----
# Instert these lines into the "${data_impropers}.template" file which includes
# the newly generated interactions. (Note: these are in .template format)
cp gen_Impropers.template.tmp new_Impropers.template.tmp
if [ -s "${data_impropers}.template" ]; then
# Then append existing "Impropers" to the end of the generated interactions
# (Hopefully this way they will override those interactions.)
cat "${data_impropers}.template" >> new_Impropers.template.tmp
fi
mv -f new_Impropers.template.tmp "${data_impropers}.template"
echo "(Repairing ttree_assignments.txt file after impropers added.)" >&2
# ---- Repair the ttree_assignments.txt file ----
# The next 2 lines extract the variable names from data_new.template.tmp
# and instert them into the appropriate place in ttree_assignments.txt
# (renumbering the relevant variable-assignments to avoid clashes).
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_fix_ttree_assignments.py" \
'/improper' gen_Impropers.template.tmp \
< ttree_assignments.txt \
> ttree_assignments.tmp; then
exit 5
fi
echo "(Rendering ttree_assignments.tmp file after impropers added.)" >&2
# ---- Re-build (render) the "$data_impropers" file ----
# Now substitute these variable values (assignments) into the variable
# names present in the .template file. (We want to convert the file from
# a .template format into an ordinary (numeric) LAMMPS data-section format.)
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/ttree_render.py" \
ttree_assignments.tmp \
< "${data_impropers}.template" \
> "$data_impropers"; then
exit 6
fi
echo "" >&2
mv -f ttree_assignments.tmp ttree_assignments.txt
rm -f gen_Impropers.template.tmp new_Impropers.template.tmp
fi
if [ -n "$LTTREE_POSTPROCESS_COMMAND" ]; then
echo "" >&2
if ! eval $LTTREE_POSTPROCESS_COMMAND $TTREE_ARGS; then
exit 3
fi
echo "" >&2
fi
# -------------------------------------------------------
# If present, then remove duplicate bonds, angles, dihedrals, and impropers
# (unless overridden by the user).
# -------------------------------------------------------
if [ -s "${data_masses}" ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicate_atoms.py" \
< "${data_masses}" \
> "${data_masses}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_masses}.tmp" "${data_masses}"
fi
if [ -s "${data_bonds}" ]; then
if [ ! -z $REMOVE_DUPLICATE_BONDS ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
Bonds \
< "${data_bonds}" \
> "${data_bonds}.tmp"; then
ERR_INTERNAL
fi
cp -f "${data_bonds}.tmp" "${data_bonds}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 2 \
< "${data_bonds}" \
> "${data_bonds}.tmp"; then
ERR_INTERNAL
fi
mv "${data_bonds}.tmp" "${data_bonds}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 2 \
< "${data_bonds}.template" \
> "${data_bonds}.tmp"; then
ERR_INTERNAL
fi
mv "${data_bonds}.tmp" "${data_bonds}.template"
fi
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_bonds}" \
> "${data_bonds}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_bonds}.tmp" "${data_bonds}"
fi
if [ -s "${data_angles}" ]; then
if [ ! -z $REMOVE_DUPLICATE_ANGLES ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
Angles \
< "${data_angles}" \
> "${data_angles}.tmp"; then
ERR_INTERNAL
fi
cp -f "${data_angles}.tmp" "${data_angles}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 3 \
< "${data_angles}" \
> "${data_angles}.tmp"; then
ERR_INTERNAL
fi
mv "${data_angles}.tmp" "${data_angles}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 3 \
< "${data_angles}.template" \
> "${data_angles}.tmp"; then
ERR_INTERNAL
fi
mv "${data_angles}.tmp" "${data_angles}".template
fi
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_angles}" \
> "${data_angles}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_angles}.tmp" "${data_angles}"
fi
if [ -s "${data_dihedrals}" ]; then
if [ ! -z $REMOVE_DUPLICATE_DIHEDRALS ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
Dihedrals \
< "${data_dihedrals}" \
> "${data_dihedrals}.tmp"; then
ERR_INTERNAL
fi
cp -f "${data_dihedrals}.tmp" "${data_dihedrals}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
< "${data_dihedrals}" \
> "${data_dihedrals}.tmp"; then
ERR_INTERNAL
fi
mv "${data_dihedrals}.tmp" "${data_dihedrals}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
< "${data_dihedrals}.template" \
> "${data_dihedrals}.tmp"; then
ERR_INTERNAL
fi
mv "${data_dihedrals}.tmp" "${data_dihedrals}.template"
fi
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_dihedrals}" \
> "${data_dihedrals}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_dihedrals}.tmp" "${data_dihedrals}"
fi
if [ -s "${data_impropers}" ]; then
if [ ! -z $REMOVE_DUPLICATE_IMPROPERS ]; then
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/nbody_reorder_atoms.py" \
Impropers \
< "${data_impropers}" \
> "${data_impropers}.tmp"; then
ERR_INTERNAL
fi
cp -f "${data_impropers}.tmp" "${data_impropers}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
< "${data_impropers}" \
> "${data_impropers}.tmp"; then
ERR_INTERNAL
fi
mv "${data_impropers}.tmp" "${data_impropers}"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/remove_duplicates_nbody.py" 4 \
< "${data_impropers}.template" \
> "${data_impropers}.tmp"; then
ERR_INTERNAL
fi
mv "${data_impropers}.tmp" "${data_impropers}.template"
fi
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/renumber_DATA_first_column.py" \
< "${data_impropers}" \
> "${data_impropers}.tmp"; then
ERR_INTERNAL
fi
mv -f "${data_impropers}.tmp" "${data_impropers}"
fi
# -------------------------------------------------------
NATOMTYPES=`awk '/^@\/atom:/{n++}END{print n}' < ttree_assignments.txt`
NBONDTYPES=`awk '/^@\/bond:/{n++}END{print n}' < ttree_assignments.txt`
NANGLETYPES=`awk '/^@\/angle:/{n++}END{print n}' < ttree_assignments.txt`
NDIHEDRALTYPES=`awk '/^@\/dihedral:/{n++}END{print n}' < ttree_assignments.txt`
NIMPROPERTYPES=`awk '/^@\/improper:/{n++}END{print n}' < ttree_assignments.txt`
#NATOMS=`awk '/^\$\/atom:/{n++}END{print n}' < ttree_assignments.txt`
#NBONDS=`awk '/^\$\/bond:/{n++}END{print n}' < ttree_assignments.txt`
#NANGLES=`awk '/^\$\/angle:/{n++}END{print n}' < ttree_assignments.txt`
#NDIHEDRALS=`awk '/^\$\/dihedral:/{n++}END{print n}' < ttree_assignments.txt`
#NIMPROPERS=`awk '/^\$\/improper:/{n++}END{print n}' < ttree_assignments.txt`
NATOMS="0"
NBONDS="0"
NANGLES="0"
NDIHEDRALS="0"
NIMPROPERS="0"
if [ -s "${data_atoms}" ]; then
NATOMS=`awk 'END{print NR}' < "${data_atoms}"`
fi
if [ -s "${data_bonds}" ]; then
NBONDS=`awk 'END{print NR}' < "${data_bonds}"`
fi
if [ -s "${data_angles}" ]; then
NANGLES=`awk 'END{print NR}' < "${data_angles}"`
fi
if [ -s "${data_dihedrals}" ]; then
NDIHEDRALS=`awk 'END{print NR}' < "${data_dihedrals}"`
fi
if [ -s "${data_impropers}" ]; then
NIMPROPERS=`awk 'END{print NR}' < "${data_impropers}"`
fi
rm -f "$OUT_FILE_DATA"
echo "LAMMPS Description" > "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
echo " $NATOMS atoms" >> "$OUT_FILE_DATA"
if [ -n "$NBONDS" ]; then
echo " $NBONDS bonds" >> "$OUT_FILE_DATA"
fi
if [ -n "$NANGLES" ]; then
echo " $NANGLES angles" >> "$OUT_FILE_DATA"
fi
if [ -n "$NDIHEDRALS" ]; then
echo " $NDIHEDRALS dihedrals" >> "$OUT_FILE_DATA"
fi
if [ -n "$NIMPROPERS" ]; then
echo " $NIMPROPERS impropers" >> "$OUT_FILE_DATA"
fi
echo "" >> "$OUT_FILE_DATA"
echo " $NATOMTYPES atom types" >> "$OUT_FILE_DATA"
if [ -n "$NBONDTYPES" ]; then
echo " $NBONDTYPES bond types" >> "$OUT_FILE_DATA"
fi
if [ -n "$NANGLETYPES" ]; then
echo " $NANGLETYPES angle types" >> "$OUT_FILE_DATA"
fi
if [ -n "$NDIHEDRALTYPES" ]; then
echo " $NDIHEDRALTYPES dihedral types" >> "$OUT_FILE_DATA"
fi
if [ -n "$NIMPROPERTYPES" ]; then
echo " $NIMPROPERTYPES improper types" >> "$OUT_FILE_DATA"
fi
echo "" >> "$OUT_FILE_DATA"
# --- PERIODIC BOUNDARY CONDITIONS ---
# Note: If there is a "$data_boundary" file present, it overrides any settings
# which may have been stored in a pdb file or other external file.
if [ -s "$data_pbc" ] && [ ! -s "$data_boundary" ]; then
mv -f "$data_pbc" "$data_boundary"
echo "WARNING: write_once(\"$data_pbc\") is depreciated" >&2
echo " Use write_once(\"$data_boundary\") instead" >&2
fi
if [ -s "$data_boundary" ]; then
# Copy the boundary conditions from the "$data_boundary" file.
# Don't assume there is only one line containing "xlo xhi", for example.
# It's possible the user wrote the boundary conditions multiple times.
# As always, the most recent setting overrides the earlier settings.
BOXSIZE_MINX=`awk '{if ($3=="xlo") {xlo=$1}} END{print xlo}' < "$data_boundary"`
BOXSIZE_MAXX=`awk '{if ($4=="xhi") {xhi=$2}} END{print xhi}' < "$data_boundary"`
BOXSIZE_MINY=`awk '{if ($3=="ylo") {ylo=$1}} END{print ylo}' < "$data_boundary"`
BOXSIZE_MAXY=`awk '{if ($4=="yhi") {yhi=$2}} END{print yhi}' < "$data_boundary"`
BOXSIZE_MINZ=`awk '{if ($3=="zlo") {zlo=$1}} END{print zlo}' < "$data_boundary"`
BOXSIZE_MAXZ=`awk '{if ($4=="zhi") {zhi=$2}} END{print zhi}' < "$data_boundary"`
if [ -z "$BOXSIZE_MINX" ] || [ -z "$BOXSIZE_MAXX" ]; then
echo "Error: Problem with box boundary format (\"xlo xhi\") in \"$data_boundary\"" >&2
exit 12
fi
if [ -z "$BOXSIZE_MINY" ] || [ -z "$BOXSIZE_MAXY" ]; then
echo "Error: Problem with box boundary format (\"ylo yhi\") in \"$data_boundary\"" >&2
exit 12
fi
if [ -z "$BOXSIZE_MINZ" ] || [ -z "$BOXSIZE_MAXZ" ]; then
echo "Error: Problem with box boundary format (\"zlo zhi\") in \"$data_boundary\"" >&2
exit 12
fi
BOXSIZE_XY=`awk '{if ($4=="xy") {xy=$1}} END{print xy}' < "$data_boundary"`
BOXSIZE_XZ=`awk '{if ($5=="xz") {xz=$2}} END{print xz}' < "$data_boundary"`
BOXSIZE_YZ=`awk '{if ($6=="yz") {yz=$3}} END{print yz}' < "$data_boundary"`
if [ -n "$BOXSIZE_XY" ] || [ -n "$BOXSIZE_XZ" ] || [ -n "$BOXSIZE_YZ" ]; then
if [ -n "$BOXSIZE_XY" ] && [ -n "$BOXSIZE_XZ" ] && [ -n "$BOXSIZE_YZ" ]; then
#echo "triclinic_parameters: XY XZ YZ = $BOXSIZE_XY $BOXSIZE_XZ $BOXSIZE_YZ" >&2
TRICLINIC="True"
else
echo "Error: Problem with triclinic format (\"xy xz yz\") in \"$data_boundary\"" >&2
exit 13
fi
fi
fi
if [ -z "$BOXSIZE_MINX" ] || [ -z "$BOXSIZE_MAXX" ] || [ -z "$BOXSIZE_MINY" ] || [ -z "$BOXSIZE_MAXY" ] || [ -z "$BOXSIZE_MINZ" ] || [ -z "$BOXSIZE_MAXZ" ]; then
echo "Periodic boundary conditions unspecified. Attempting to generate automatically." >&2
# By default, disable triclinic
BOXSIZE_XY=""
BOXSIZE_XZ=""
BOXSIZE_YZ=""
TRICLINIC=""
if [ -s "$tmp_atom_coords" ]; then
# Estimate the minimimum, maximum x,y,z values
# from the coordinate data.
MINMAX_BOUNDS=`awk 'BEGIN{first=1}{if (NF>=3){x=$1; y=$2; z=$3; if (first) {first=0; xmin=x; xmax=x; ymin=y; ymax=y; zmin=z; zmax=z;} else {if (x<xmin) xmin=x; if (x>xmax) xmax=x; if (y<ymin) ymin=y; if (y>ymax) ymax=y; if (z<zmin) zmin=z; if (z>zmax) zmax=z;}}} END{print xmin" "xmax" "ymin" "ymax" "zmin" "zmax;}' < "$tmp_atom_coords"`
# ...and add a narrow margin (10%) around the boundaries:
BOXSIZE_MINX=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$2-$1; print $1-0.5*margin*width}"`
BOXSIZE_MAXX=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$2-$1; print $2+0.5*margin*width}"`
BOXSIZE_MINY=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$4-$3; print $3-0.5*margin*width}"`
BOXSIZE_MAXY=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$4-$3; print $4+0.5*margin*width}"`
BOXSIZE_MINZ=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$6-$5; print $5-0.5*margin*width}"`
BOXSIZE_MAXZ=`echo $MINMAX_BOUNDS | awk "{margin=0.1; width=$6-$5; print $6+0.5*margin*width}"`
else
# By default, choose some reasonably large box:
BOXSIZE_MINX="-100.0"
BOXSIZE_MAXX="100.0"
BOXSIZE_MINY="-100.0"
BOXSIZE_MAXY="100.0"
BOXSIZE_MINZ="-100.0"
BOXSIZE_MAXZ="100.0"
# ...and print message scolding the user for being lazy
echo "----------------------------------------------------------------------" >&2
echo "---- WARNING: Unable to determine periodic boundary conditions. ----" >&2
echo "---- (A default cube of volume=(200.0)^3 was used. ----" >&2
echo "---- This is probably not what you want!) ----" >&2
echo "---- It is recommended that you specify your periodic boundary ----" >&2
echo "---- by adding a write_once(\"Boundary\") command to your .lt file. ----" >&2
echo "---- For example: ----" >&2
#echo "----------------------------------------------------------------------" >&2
echo "---- ----" >&2
echo "---- write_once(\"Boundary\") { ----" >&2
echo "---- 2.51 46.79 xlo xhi ----" >&2
echo "---- -4.38 35.824 ylo yhi ----" >&2
echo "---- 0.3601 42.95 zlo zhi ----" >&2
echo "---- } ----" >&2
echo "----------------------------------------------------------------------" >&2
fi
fi
if [ -z "$TRICLINIC" ]; then
echo " $BOXSIZE_MINX $BOXSIZE_MAXX xlo xhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_MINY $BOXSIZE_MAXY ylo yhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_MINZ $BOXSIZE_MAXZ zlo zhi" >> "$OUT_FILE_DATA"
else
echo "triclinic parameters: XY XZ YZ = $BOXSIZE_XY $BOXSIZE_XZ $BOXSIZE_YZ" >&2
echo "" >&2
# Otherwise, this is a triclinic (non orthoganal) crystal basis.
# LAMMPS represents triclinic symmetry using a different set of parameters
# (lx,ly,lz,xy,xz,yz) than the PDB file format (alpha,beta,gamma).
echo " $BOXSIZE_MINX $BOXSIZE_MAXX xlo xhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_MINY $BOXSIZE_MAXY ylo yhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_MINZ $BOXSIZE_MAXZ zlo zhi" >> "$OUT_FILE_DATA"
#echo " 0.000000 $BOXSIZE_X xlo xhi" >> "$OUT_FILE_DATA"
#echo " 0.000000 $BOXSIZE_Y ylo yhi" >> "$OUT_FILE_DATA"
#echo " 0.000000 $BOXSIZE_Z zlo zhi" >> "$OUT_FILE_DATA"
echo " $BOXSIZE_XY $BOXSIZE_XZ $BOXSIZE_YZ xy xz yz" >> "$OUT_FILE_DATA"
#echo "a,b,c,alpha,beta,gamma = $BOXSIZE_A,$BOXSIZE_B,$BOXSIZE_C,$ALPHA,$BETA,$GAMMA"
fi
echo "" >> "$OUT_FILE_DATA"
if [ -s "$data_header" ]; then
cat "$data_header" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_masses" ]; then
echo "Masses" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_masses" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
echo "WARNING: missing file \"$data_masses\"" >&2
fi
if [ -s "$data_pair_coeffs" ]; then
echo "Pair Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_pair_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ ! -s "$in_settings" ] || (! grep -q pair_coeff "$in_settings"); then
echo "WARNING: no pair coeffs have been set!" >&2
fi
fi
if [ -s "$data_bond_coeffs" ]; then
echo "Bond Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bond_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ -n "$NBONDTYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q bond_coeff "$in_settings") ); then
echo "WARNING: no bond coeff have been set!" >&2
fi
fi
if [ -s "$data_angle_coeffs" ]; then
echo "Angle Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angle_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ -n "$NANGLETYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q angle_coeff "$in_settings") ); then
echo "WARNING: no angle coeffs have been set!" >&2
fi
fi
if [ -s "$data_dihedral_coeffs" ]; then
echo "Dihedral Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_dihedral_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ -n "$NDIHEDRALTYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q dihedral_coeff "$in_settings") ); then
echo "WARNING: no dihedral coeffs have been set!" >&2
fi
fi
if [ -s "$data_improper_coeffs" ]; then
echo "Improper Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_improper_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
if [ -n "$NIMPROPERTYPES" ] && ( [ ! -s "$in_settings" ] || (! grep -q improper_coeff "$in_settings") ); then
echo "WARNING: no improper coeffs have been set!" >&2
fi
fi
# data file sections specific to class2 force-fields:
if [ -s "$data_bondbond_coeffs" ]; then
echo "BondBond Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bondbond_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_bondangle_coeffs" ]; then
echo "BondAngle Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bondangle_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_middlebondtorsion_coeffs" ]; then
echo "MiddleBondTorsion Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_middlebondtorsion_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_endbondtorsion_coeffs" ]; then
echo "EndBondTorsion Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_endbondtorsion_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_angletorsion_coeffs" ]; then
echo "AngleTorsion Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angletorsion_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_angleangletorsion_coeffs" ]; then
echo "AngleAngleTorsion Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angleangletorsion_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_bondbond13_coeffs" ]; then
echo "BondBond13 Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bondbond13_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_angleangle_coeffs" ]; then
echo "AngleAngle Coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angleangle_coeffs" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_atoms" ]; then
echo "Atoms" >> "$OUT_FILE_DATA"
if [ -s "$tmp_atom_coords" ]; then
echo "# (Note: x,y,z coordinates may overlap and can be modified later.)" >> "$OUT_FILE_DATA"
else
echo "" >> "$OUT_FILE_DATA"
fi
cat "$data_atoms" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
else
echo "WARNING: missing file \"$data_atoms\"" >&2
fi
if [ -s "$data_ellipsoids" ]; then
echo "Ellipsoids" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_ellipsoids" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_triangles" ]; then
echo "Triangles" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_triangles" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_lines" ]; then
echo "Lines" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_lines" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_velocities" ]; then
echo "Velocities" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_velocities" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "Velocities" >> "$OUT_FILE_DATA"
# echo "" >> "$OUT_FILE_DATA"
# awk '{print $1 " 0.0 0.0 0.0"}' < "$data_atoms" >> "$OUT_FILE_DATA"
# echo "" >> "$OUT_FILE_DATA"
fi
if [ -s "$data_bonds" ]; then
echo "Bonds" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_bonds" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "WARNING: missing file \"$data_bonds\"" >&2
fi
if [ -s "$data_angles" ]; then
echo "Angles" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_angles" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "WARNING: missing file \"$data_angles\"" >&2
fi
if [ -s "$data_dihedrals" ]; then
echo "Dihedrals" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_dihedrals" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "WARNING: missing file \"$data_dihedrals\"" >&2
fi
if [ -s "$data_impropers" ]; then
echo "Impropers" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$data_impropers" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
#else
# echo "WARNING: missing file \"$data_impropers\"" >&2
fi
rm -f $OUT_FILE_INPUT_SCRIPT
if [ -s "$in_init" ]; then
echo "" >> $OUT_FILE_INPUT_SCRIPT
cp -f "$in_init" $OUT_FILE_INIT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- Init Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "include \"$OUT_FILE_INIT\"" >> $OUT_FILE_INPUT_SCRIPT
#echo "# \"$in_init\" typically contains various styles, dimensions, and units:" >> $OUT_FILE_INPUT_SCRIPT
#echo "include \"$in_init\"" >> $OUT_FILE_INPUT_SCRIPT
#cat "$in_init" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
fi
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- Atom Definition Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "read_data \"$OUT_FILE_DATA\"" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- Settings Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
if [ -s "$in_settings" ]; then
#echo "# \"$in_settings\" typically contains coeffs, fixes, groups & modify commands:" >> $OUT_FILE_INPUT_SCRIPT
#echo "include \"$in_settings\"" >> $OUT_FILE_INPUT_SCRIPT
#cat "$in_settings" >> $OUT_FILE_INPUT_SCRIPT
cp -f "$in_settings" $OUT_FILE_SETTINGS
echo "include \"$OUT_FILE_SETTINGS\"" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
fi
if [ -s "$tmp_atom_coords" ]; then
NATOMS=`awk '/^\\\$\/atom:/{n++}END{print n}' < ttree_assignments.txt`
NATOMCRDS=`awk '{if (NF>=3) natom+=1} END{print(natom)}' < "$tmp_atom_coords"`
if [ $NATOMS -ne $NATOMCRDS ]; then
echo "Error: Number of atoms in coordinate file provided by user ($NATOMCRDS)" >&2
echo "does not match the number of atoms generated in ttree file ($NATOMS)" >&2
exit 14
fi
# Copy the coordinates in $tmp_atom_coords into $OUT_FILE_DATA
rm -f "$OUT_FILE_COORDS"
if ! $PYTHON_COMMAND "${SCRIPT_DIR}/raw2data.py" $ATOM_STYLE "$OUT_FILE_DATA" < "$tmp_atom_coords" > "$OUT_FILE_COORDS"; then
ERR_INTERNAL
fi
mv -f "$OUT_FILE_COORDS" "$OUT_FILE_DATA"
# Previously, in earlier versions of moltemplate, we used to
# create a new input script containing "set" commands which the
# user was supposed to tell LAMMPS to read using an "include" command.
# If for some reason, you want to go back to doing it that way, then
# uncomment the following 6 lines:
#
#rm -f "$OUT_FILE_COORDS"
#awk '{if (NF>=3) {natom++; print "set atom "natom" x "$1" y "$2" z "$3" image 0 0 0"}}' < "$tmp_atom_coords" >> "$OUT_FILE_COORDS"
#echo "# Load the atom coordinates:" >> $OUT_FILE_INPUT_SCRIPT
#echo "" >> $OUT_FILE_INPUT_SCRIPT
#echo "include \"$OUT_FILE_COORDS\"" >> $OUT_FILE_INPUT_SCRIPT
#echo "" >> $OUT_FILE_INPUT_SCRIPT
else
rm -f "$OUT_FILE_COORDS"
# echo "Warning: (moltemplate.sh)" >&2
# echo " Atomic coordinates were not supplied externally" >&2
# echo " (for example using the \"-pdb\" or \"-xyz\" arguments)." >&2
# echo " Hopefully you used rot(), trans() lttree commands to move" >&2
# echo " molecules to non-overlapping positions." >&2
fi
# ############## CLEAN UP ################
# A lot of files have been created along the way.
# However only a few of them are actually useful.
#
# Optional: clean up some non-essential temporary
# files created by running ttree
# We move the non-essential files into a different directory
# (but we don't delete them).
if [ ! -d output_ttree ]; then
mkdir output_ttree
fi
# Move temporary files into the "output_ttree/" directory:
OIFS=$IFS
#IFS=$'\n'
IFS="
"
for file in $MOLTEMPLATE_TEMP_FILES; do
#echo "file=\"$file\""
rm -f "output_ttree/$file" >/dev/null 2>&1 || true
if [ -e "$file" ]; then
#mv "$file" output_ttree/ >/dev/null 2>&1 || true
#dos2unix < "$file" > "output_ttree/$file"
tr -d '\r' < "$file" > "output_ttree/$file"
rm -f "$file" >/dev/null 2>&1 || true
fi
done
IFS=$OIFS
# ############## DEAL WITH CUSTOM NON-STANDARD SECTIONS ################
N_data_prefix=`expr length "$data_prefix"`
ls "${data_prefix}"* 2> /dev/null | while read file_name; do
#If using bash:
#section_name="${file_name:$N_data_prefix}"
#If using sh:
section_name=`expr substr "$file_name" $(($N_data_prefix+1)) 1000000`
# Create a new section in the data file
# matching the portion of the name of
# the file after the data_prefix.
echo "" >> "$OUT_FILE_DATA"
echo "$section_name" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
cat "$file_name" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
mv -f "$file_name" output_ttree/
done
if [ -e "$data_prefix_no_space" ]; then
echo "" >> "$OUT_FILE_DATA"
cat "$data_prefix_no_space" >> "$OUT_FILE_DATA"
echo "" >> "$OUT_FILE_DATA"
mv -f "$data_prefix_no_space" output_ttree/
fi
if [ -e "$OUT_FILE_DATA" ]; then
mv -f "$OUT_FILE_DATA" "$OUT_FILE_DATA.tmp" >/dev/null 2>&1 || true
#dos2unix < "$OUT_FILE_DATA.tmp" > "$OUT_FILE_DATA"
tr -d '\r' < "$OUT_FILE_DATA.tmp" > "$OUT_FILE_DATA"
rm -f "$OUT_FILE_DATA.tmp" >/dev/null 2>&1 || true
fi
N_in_prefix=`expr length "$in_prefix"`
ls "${in_prefix}"* 2> /dev/null | while read file_name; do
#If using bash:
#section_name="${file_name:$N_in_prefix}"
#If using sh:
section_name=`expr substr "$file_name" $(($N_in_prefix+1)) 1000000`
# Create a new section in the lammps input script
# matching the portion of the name of
# the file after the in_prefix.
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- $section_name Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
cat "$file_name" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
mv -f "$file_name" output_ttree/
done
if [ -e "$in_prefix_no_space" ]; then
echo "" >> $OUT_FILE_INPUT_SCRIPT
cat "$in_prefix_no_space" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
mv -f "$in_prefix_no_space" output_ttree/
fi
# Swap the order of atom types I, J in all "pair_coeff I J ..." commands
# whenever I > J. Do this for every input script file generated by moltemplate.
# (Perhaps later I'll check to make sure the user did not specify contradictory
# "pair_coeff I J ..." and "pair_coeff J I ..." commands, but I won't do it
# here, because at this point we've thrown away the original atom type names,
# so there's no easy way to explain the problem to the user if there is one.)
echo "" > input_scripts_so_far.tmp
for file_name in "$OUT_FILE_INIT" "$OUT_FILE_INPUT_SCRIPT" "$OUT_FILE_SETTINGS"; do
if [ -s "$file_name" ]; then
echo "postprocessing file \"$file_name\"" >&2
- $PYTHON_COMMAND "${SCRIPT_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp
+ if ! $PYTHON_COMMAND "${SCRIPT_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp; then
+ ERR_INTERNAL
+ fi
echo "" >&2
mv "$file_name".tmp "$file_name"
#cat "$file_name" >> input_scripts_so_far.tmp
#dos2unix < "$file_name" >> input_scripts_so_far.tmp
tr -d '\r' < "$file_name" >> input_scripts_so_far.tmp
fi
done
ls "${in_prefix}"* 2> /dev/null | while read file_name; do
echo "postprocessing file \"$file_name\"" >&2
- $PYTHON_COMMAND "${SCRIPT_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp
+ if ! $PYTHON_COMMAND "${SCRIPT_DIR}/postprocess_input_script.py" input_scripts_so_far.tmp < "$file_name" > "$file_name".tmp; then
+ ERR_INTERNAL
+ fi
echo "" >&2
mv "$file_name".tmp "$file_name"
cat "$file_name" >> input_scripts_so_far.tmp
done
rm -f input_scripts_so_far.tmp
# ############ Optional: Add a fake run section as an example ############
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# ----------------- Run Section -----------------" >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
echo "# The lines above define the system you want to simulate." >> $OUT_FILE_INPUT_SCRIPT
echo "# What you do next is up to you." >> $OUT_FILE_INPUT_SCRIPT
echo "# Typically a user would minimize and equilibrate" >> $OUT_FILE_INPUT_SCRIPT
echo "# the system using commands similar to the following:" >> $OUT_FILE_INPUT_SCRIPT
echo "# ---- examples ----" >> $OUT_FILE_INPUT_SCRIPT
echo "#" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- minimize --" >> $OUT_FILE_INPUT_SCRIPT
echo "# minimize 1.0e-5 1.0e-7 1000 10000" >> $OUT_FILE_INPUT_SCRIPT
echo "# (Note: Some fixes, for example \"shake\", interfere with the minimize command," >> $OUT_FILE_INPUT_SCRIPT
echo "# You can use the \"unfix\" command to disable them before minimization.)" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- declare time step for normal MD --" >> $OUT_FILE_INPUT_SCRIPT
echo "# timestep 1.0" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- run at constant pressure (Nose-Hoover)--" >> $OUT_FILE_INPUT_SCRIPT
#echo "# timestep 1.0" >> $OUT_FILE_INPUT_SCRIPT
echo "# fix fxnpt all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 1.0">>$OUT_FILE_INPUT_SCRIPT
echo "# -- ALTERNATELY, run at constant volume (Nose-Hoover) --" >> $OUT_FILE_INPUT_SCRIPT
echo "# fix fxnvt all nvt temp 300.0 300.0 500.0 tchain 1" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- ALTERNATELY, run at constant volume using Langevin dynamics. --" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- (This is good for sparse CG polymers in implicit solvent.) --" >> $OUT_FILE_INPUT_SCRIPT
echo "fix fxlan all langevin 300.0 300.0 5000 48279" >> $OUT_FILE_INPUT_SCRIPT
echo "# -- Now, finally run the simulation --" >> $OUT_FILE_INPUT_SCRIPT
echo "# run 50000" >> $OUT_FILE_INPUT_SCRIPT
#echo "# write_restart system_after_nvt.rst" >> $OUT_FILE_INPUT_SCRIPT
#echo "# run 50000" >> $OUT_FILE_INPUT_SCRIPT
#echo "# write_restart system_after_npt.rst" >> $OUT_FILE_INPUT_SCRIPT
echo "# ---- (end of examples) ----">> $OUT_FILE_INPUT_SCRIPT
#echo "# It is the responsibility of the user to learn LAMMPS and specify these">>$OUT_FILE_INPUT_SCRIPT
#echo "# these commands." >> $OUT_FILE_INPUT_SCRIPT
echo "" >> $OUT_FILE_INPUT_SCRIPT
diff --git a/tools/moltemplate/src/nbody_by_type.py b/tools/moltemplate/src/nbody_by_type.py
index 96d59661b..486844c23 100755
--- a/tools/moltemplate/src/nbody_by_type.py
+++ b/tools/moltemplate/src/nbody_by_type.py
@@ -1,639 +1,639 @@
#!/usr/bin/env python
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
man_page_text = """
nbody_by_type.py reads a LAMMPS data file (or an excerpt of a LAMMPS)
data file containing bonded many-body interactions by atom type
(and bond type), and generates a list of additional interactions
in LAMMPS format consistent with those type (to the standard out).
Typical Usage:
nbody_by_type.py X < old.data > new.data
--or--
nbody_by_type.py X \\
-atoms atoms.data \\
-bonds bonds.data \\
-nbody X.data \\
-nbodybytype X_by_type.data \\
> new_X.data
In both cases "X" denotes the interaction type, which
is either "Angles", "Dihedrals", or "Impropers".
(Support for other interaction types can be added by the user. See below.)
-------- Example 1 -------
nbody_by_type.py X < old.data > new.data
In this example, nbody_by_type.py reads a LAMMPS data file
"orig.data", and extracts the relevant section ("Angles",
"Dihedrals", or "Impropers"). It also looks a section named "X By Type",
(eg. "Angles By type", "Impropers By type", "Impropers By type")
which contains a list of criteria for automatically defining additional
interactions of that type. For example, this file might contain:
Angle By Type
7 1 2 1 * *
8 2 2 * * *
9 3 4 3 * *
The first column is an interaction type ID.
The next 3 columns are atom type identifiers.
The final 2 columns are bond type identifiers.
The * is a wildcard symbol indicating there is no preference for bond types
in this example. (Optionally, regular expressions can also be used to
define a type match, by enclosing the atom or bond type in / slashes.)
The first line tells us to that there should be a 3-body "Angle"
interaction of type "7" whenever an atom of type 1 is bonded to an atom
of type "2", which is bonded to another atom of type "1" again.
The second line tells us that an angle is defined whenever three atoms
are bonded together and the first two are of type "2".
(Redundant angle interactions are filtered.)
New interactions are created for every group of bonded
atoms which match these criteria if they are bonded together
in the relevant way for that interaction type (as determined by
nbody_X.py), and printed to the standard output. For example,
suppose you are automatically generating 3-body "Angle" interactions using:
nbody_by_type Angles < old.data > new.data
The file "new.data" will be identical to "old.data", however the
"Angles By Type" section will be deleted, and the following lines of
text will be added to the "Angles" section:
394 7 5983 5894 5895
395 7 5984 5895 5896
396 7 5985 5896 5897
: : : : :
847 9 14827 14848 14849
The numbers in the first column are counters which assign a ID to
every interaction of that type, and start where the original "Angles"
data left off (New angle ID numbers do not overlap with old ID numbers).
The text in the second column ("7", "9", ...) matches the text from the
first column of the "Angle By Type" section of the input file.
-------- Example 2 -------
nbody_by_type.py X \\
-atoms atoms.data \\
-bonds bonds.data \\
-nbody X.data \\
-nbodybytype X_by_type.data \\
-prefix "SOMESTRING" -suffix "ANOTHERSTRING" \\
> new_X.data
In particular, for Angle interactions:
nbody_by_type.py Angles \\
-atoms atoms.data \\
-bonds bonds.data \\
-nbody angles.data \\
-nbodybytype angles_by_type.data \\
> new_Angles.data
When run this way, nbody_by_type.py behaves exactly the same way
as in Example 1, however only the lines of text corresponding to
the new generated interactions are printed, (not the entire data file).
Also note, that when run this way, nbody_by_type.py does not read the
LAMMPS data from the standard input. Instead, it reads each section of
the data file from a different file indicated by the arguments following
the "-atoms", "-bonds", "-nbody", and "-nbodybytype" flags.
"Angles" is a 3-body interaction style. So when run this way,
nbody_by_type.py will create a 5 (=3+2) column file (new_Angles.data).
Note: the atom, bond and other IDs/types in need not be integers.
Note: This program must be distributed with several python modules, including:
nbody_Angles.py, nbody_Dihedrals.py, and nbody_Impropers.py. These
contain bond definitions for angular, dihedral, and improper interactions.
(In case any new interaction types are ever added to LAMMPS, with only
a few lines of python it is easy to edit to define new bonded
interaction types by supplying new "nbody_X.py" python module.
Refer to the modules listed above for examples.)
Note: Optional "-prefix" and "-suffix" arguments can be included to decorate
the interaction IDs (first column). For example, -prefix "auto_" and
-suffix "_angle", causes "new_Angles.data" to contain the following text:
auto_394_angle 7 5983 5894 5895
auto_395_angle 7 5984 5895 5896
auto_396_angle 7 5985 5896 5897
: : : : :
auto_847_angle 9 14827 14848 14849
"""
import sys
from extract_lammps_data import *
from nbody_by_type_lib import GenInteractions_str
from ttree_lex import *
from lttree_styles import AtomStyle2ColNames, ColNames2AidAtypeMolid
if sys.version < '2.6':
raise InputError('Error: Using python '+sys.version+'\n'
- ' Alas, you must upgrade to a newever version of python (2.7 or later).')
+ ' Alas, you must upgrade to a newer version of python (2.6 or later).')
elif sys.version < '2.7':
sys.stderr.write('--------------------------------------------------------\n'
'----------------- WARNING: OLD PYTHON VERSION ----------\n'
' This program is untested on your python version ('+sys.version+').\n'
' PLEASE LET ME KNOW IF THIS PROGRAM CRASHES (and upgrade python).\n'
- ' -Andrew 2012-4-16\n'
+ ' -Andrew 2013-10-25\n'
'--------------------------------------------------------\n'
'--------------------------------------------------------\n')
from ordereddict import OrderedDict
else:
from collections import OrderedDict
def GenInteractions_lines(lines_atoms,
lines_bonds,
lines_nbody,
lines_nbodybytype,
atom_style,
g_bond_pattern,
canonical_order, #function to sort atoms and bonds
prefix='',
suffix='',
report_progress = False):
column_names = AtomStyle2ColNames(atom_style)
i_atomid, i_atomtype, i_molid = ColNames2AidAtypeMolid(column_names)
atomids_str = []
atomtypes_str = []
for iv in range(0, len(lines_atoms)):
line = lines_atoms[iv].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) > 0:
tokens = SplitQuotedString(line)
if ((len(tokens) <= i_atomid) or (len(tokens) <= i_atomtype)):
raise(InputError('Error not enough columns on line '+str(iv+1)+' of \"Atoms\" section.'))
tokens = SplitQuotedString(line)
atomids_str.append(EscCharStrToChar(tokens[i_atomid]))
atomtypes_str.append(EscCharStrToChar(tokens[i_atomtype]))
bondids_str = []
bondtypes_str = []
bond_pairs = []
for ie in range(0, len(lines_bonds)):
line = lines_bonds[ie].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) > 0:
tokens = SplitQuotedString(line)
if len(tokens) < 4:
raise(InputError('Error not enough columns on line '+str(ie+1)+' of \"Bonds\" section.'))
bondids_str.append(EscCharStrToChar(tokens[0]))
bondtypes_str.append(EscCharStrToChar(tokens[1]))
bond_pairs.append( (EscCharStrToChar(tokens[2]),
EscCharStrToChar(tokens[3])) )
typepattern_to_coefftypes = []
for i in range(0, len(lines_nbodybytype)):
line = lines_nbodybytype[i].strip()
if '#' in line:
icomment = line.find('#')
line = (line[:icomment]).strip()
if len(line) > 0:
tokens = SplitQuotedString(line)
if ((len(tokens) != 1 + g_bond_pattern.GetNumVerts()) and
(len(tokens) != 1 + g_bond_pattern.GetNumVerts()
+ g_bond_pattern.GetNumEdges())):
raise(InputError('Error: Wrong number of columns in \"By Type\" section of data file.\n'
'Offending line:\n'+
'\"'+line+'\"\n'
'Expected either '+
str(1 + g_bond_pattern.GetNumVerts()) + ' or ' +
str(1 + g_bond_pattern.GetNumVerts() +
g_bond_pattern.GetNumEdges())
+ ' colunms.'))
coefftype = EscCharStrToChar(tokens[0])
typepattern = []
for typestr in tokens[1:]:
if ((len(typestr) >= 2) and
(typestr[0] == '/') and (typestr[-1] == '/')):
regex_str = typestr[1:-1]
typepattern.append( re.compile(regex_str) )
else:
typepattern.append(EscCharStrToChar(typestr))
# If the user neglected to specify the bond types, assume '*'
if len(tokens) == 1 + g_bond_pattern.GetNumVerts():
typepattern += ['*'] * g_bond_pattern.GetNumEdges()
typepattern_to_coefftypes.append([typepattern, coefftype])
coefftype_to_atomids_str = GenInteractions_str(bond_pairs,
g_bond_pattern,
typepattern_to_coefftypes,
canonical_order,
atomids_str,
atomtypes_str,
bondids_str,
bondtypes_str,
report_progress)
lines_nbody_new = []
for coefftype, atomids_list in coefftype_to_atomids_str.items():
for atomids_found in atomids_list:
n = len(lines_nbody) + len(lines_nbody_new) + 1
line = prefix+str(n)+suffix+' '+ \
coefftype+' '+(' '.join(atomids_found))+'\n'
lines_nbody_new.append(line)
return lines_nbody_new
def GenInteractions_files(lines_data,
src_bond_pattern,
fname_atoms,
fname_bonds,
fname_nbody,
fname_nbodybytype,
section_name,
section_name_bytype,
atom_style,
prefix='',
suffix='',
report_progress = False):
if fname_atoms == None:
lines_atoms = [line for line in ExtractDataSection(lines_data, 'Atoms')]
else:
try:
f = open(fname_atoms, 'r')
except:
sys.stderr.write('Error: Unable to open file \"'+fname_atoms+'\" for reading.\n')
sys.exit(-1)
lines_atoms = [line for line in f.readlines()
if ((len(line.strip())>0) and (line.strip()[0] != '#'))]
f.close()
if fname_bonds == None:
lines_bonds = [line for line in ExtractDataSection(lines_data, 'Bonds')]
else:
try:
f = open(fname_bonds, 'r')
except IOError:
sys.stderr.write('Error: Unable to open file \"'+fname_bonds+'\" for reading.\n')
sys.exit(-1)
lines_bonds = [line for line in f.readlines()
if ((len(line.strip())>0) and (line.strip()[0] != '#'))]
f.close()
if fname_nbody == None:
lines_nbody = [line for line in ExtractDataSection(lines_data, section_name)]
else:
try:
f = open(fname_nbody, 'r')
lines_nbody = [line for line in f.readlines()
if ((len(line.strip())>0) and (line.strip()[0] != '#'))]
f.close()
except IOError:
#sys.stderr.write(' (omitting optional file \"'+fname_nbody+'\")\n')
lines_nbody = []
if fname_nbodybytype == None:
lines_nbodybytype=[line for
line in ExtractDataSection(lines_data,
section_name_bytype)]
else:
try:
f = open(fname_nbodybytype, 'r')
except:
sys.stderr.write('Error: Unable to open file \"'+fname_nbodybytype+'\" for reading.\n')
sys.exit(-1)
lines_nbodybytype = [line for line in f.readlines()
if((len(line.strip())>0)and(line.strip()[0]!='#'))]
f.close()
g = __import__(src_bond_pattern) #defines g.bond_pattern, g.canonical_order
return GenInteractions_lines(lines_atoms,
lines_bonds,
lines_nbody,
lines_nbodybytype,
atom_style,
g.bond_pattern,
g.canonical_order,
prefix,
suffix,
report_progress)
if __name__ == "__main__":
g_program_name = __file__.split('/')[-1] # = 'nbody_by_type.py'
g_date_str = '2013-8-06'
g_version_str = '0.15'
####### Main Code Below: #######
sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
if sys.version < '3':
sys.stderr.write(' (python version < 3)\n')
else:
sys.stderr.write('\n')
try:
fname_atoms = None
fname_bonds = None
fname_nbody = None
fname_nbodybytype = None
atom_style = 'full'
prefix=''
suffix=''
argv = [arg for arg in sys.argv]
if len(argv) == 1:
raise InputError('Error: Missing argument required.\n'
' The \"'+g_program_name+'\" program requires an argument containing the\n'
' name of a section from a LAMMPS data file storing bonded interactions.\n'
' (For example: "Angles", "Dihedrals", or "Impropers".)\n'
#' Note: The first letter of each section is usually capitalized.)\n'
'\n'
'--------------- general documentation -------------\n'
'\n' + man_page_text + '\n')
section_name = '' # (This will be replaced later.)
section_name_bytype = '' # (This will be replaced later.)
# Loop over the remaining arguments not processed yet.
# These arguments are specific to the lttree.py program
# and are not understood by ttree.py:
i = 1
while i < len(argv):
#sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
if ((argv[i].lower() == '-?') or
(argv[i].lower() == '--?') or
(argv[i].lower() == '-help') or
(argv[i].lower() == '-help')):
if i+1 >= len(argv):
sys.stdout.write(man_page_text+'\n')
sys.exit(0)
elif argv[i].lower() == '-atoms':
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
' text which might appear in the "Atoms" section of a LAMMPS data file.\n')
fname_atoms = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-bonds':
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
' text which might appear in the "Bonds" section of a LAMMPS data file.\n')
fname_bonds = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-nbody':
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
#raise InputError('Error: '+argv[i]+' flag should be followed by a file name containing lines of\n'
# ' text which might appear in the "'+section_name+' section of a LAMMPS data file.\n')
fname_nbody = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-nbodybytype':
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a file name\n')
#raise InputError('Error: '+argv[i]+' flag should be followed by a file name containing\n'
# ' text which might appear in the "'+section_name+' By Type" section\n'
# ' of a LAMMPS data file.\n')
fname_nbodybytype = argv[i+1]
del(argv[i:i+2])
elif ((argv[i].lower() == '-atom-style') or
(argv[i].lower() == '-atom_style')):
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a an atom_style name.\n'
' (Or single quoted string which includes a space-separated\n'
' list of column names.)\n')
atom_style = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-prefix':
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a prefix string\n'
' (a string you want to appear to the left of the integer\n'
' which counts the bonded interactions you have generated.)\n')
prefix = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-suffix':
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by a suffix string\n'
' (a string you want to appear to the right of the integer\n'
' which counts the bonded interactions you have generated.)\n')
prefix = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-subgraph':
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by the name of a python file\n'
' containing the definition of the subgraph you are searching for\n'
' and it\'s symmetry properties.\n'
' (See nbody_Dihedrals.py for example.)\n')
bond_pattern_module_name = argv[i+1]
# If the file name ends in ".py", then strip off this suffix.
bond_pattern_module_name=bond_pattern_module_name.rstrip('.py')
del(argv[i:i+2])
elif argv[i].lower() == '-section':
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by the name of the LAMMPS\n'
' Data section describing the type of interaction being generated.\n'
' (For example: \"Angles\", \"Dihedrals\", \"Impropers\", etc...)\n')
section_name = argv[i+1]
del(argv[i:i+2])
elif argv[i].lower() == '-sectionbytype':
if i+1 >= len(argv):
raise InputError('Error: '+argv[i]+' flag should be followed by the name of the\n'
' write_once(\"???? By Type\") section describing how to create the\n'
' interactions. (For example: \"Angles By Type\", \"Dihedrals By Type\",\n'
' \"Impropers By Type\", etc... Note that this argument\n'
' will contain spaces, so surround it with quotes.)\n')
section_name_bytype = argv[i+1]
del(argv[i:i+2])
elif argv[i][0] == '-':
raise InputError('Error('+g_program_name+'):\n'
'Unrecogized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
#if len(argv) == 1:
# raise InputError('Error: Missing argument required.\n'
# ' The \"'+g_program_name+'\" program requires an argument containing the\n'
# ' name of a section from a LAMMPS data file storing bonded interactions.\n'
# ' (For example: "Angles", "Dihedrals", or "Impropers".)\n')
# #' Note: The first letter of each section is usually capitalized.)\n'
if len(argv) == 1:
pass
elif len(argv) == 2:
section_name = argv[1]
section_name_bytype = section_name + ' By Type'
bond_pattern_module_name = 'nbody_'+section_name
del(argv[1:2])
else:
# if there are more than 2 remaining arguments,
problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
raise InputError('Syntax Error('+g_program_name+'):\n\n'
' Problem with argument list.\n'
' The remaining arguments are:\n\n'
' '+(' '.join(problem_args))+'\n\n'
' (The actual problem may be earlier in the argument list.)\n')
if ((section_name == '') or
(section_name_bytype == '') or
(bond_pattern_module_name == '')):
raise InputError('Syntax Error('+g_program_name+'):\n\n'
' You have not defined the following arguments:\n'
' -section name\n'
' -sectionbytype namebytype\n'
' -subgraph pythonfile.py\n')
# ------------ Done parsing argument list ----------
if (fname_atoms or fname_bonds or fname_nbody or fname_nbodybytype):
output_full_DATA_file = False
lines_data = []
else:
output_full_DATA_file = True
lines_data = sys.stdin.readlines()
# Calculate the interactions and generate a list of lines of text
lines_new_interactions = \
GenInteractions_files(lines_data,
bond_pattern_module_name,
fname_atoms,
fname_bonds,
fname_nbody,
fname_nbodybytype,
section_name,
section_name_bytype,
atom_style,
prefix,
suffix,
report_progress=True)
# Print this text to the standard out.
# Question: Do we write out the entire DATA file,
# or just the portion that was generated by this program?
if not output_full_DATA_file:
# ...then only print out the interactions which were generated
# by this program, omitting any lines from the original data file:
# (This is the way I usually run this program.)
for line in lines_new_interactions:
sys.stdout.write(line)
else:
# ...then print out the entire data file, deleting the "By Type"
# section, and adding the generated lines of text to the corresponding
# If present, update the interaction counter at the beginning
# of the LAMMPS data file. (For example, if if 100 new "Angles"
# interactions were generated, replace "2 Angles" with "102 Angles")
#
for i in range(0, len(lines_data)):
line = lines_data[i].strip()
tokens = SplitQuotedString(line)
# updating the interaction counter
if ((len(tokens) == 2) and (tokens[1] == (section_name).lower())):
tokens[0] = str(int(tokens[0]) + len(lines_new_interactions))
lines_data[i] = ' '.join(tokens) + '\n'
# stop when you come to a section header
elif line in lammps_data_sections:
#"lammps_data_sections" is defined in "extract_lammps_data.py"
break
# locate the appropriate section of the data file
# (storing the type of interactions we just created)
i_nbody_a, i_nbody_b = \
FindDataSection(lines_data, section_name)
if i_nbody_a == -1:
if len(lines_new_interactions) > 0:
# If not found, create a new section at the end of the file,
# containing a section name followed by the list of lines
lines_data += ['\n', section_name+'\n', '\n'] + \
lines_new_interactions + ['\n']
else:
# Insert the new lines into the existing section
lines_data[i_nbody_b:i_nbody_b] = lines_new_interactions
# Figure out where the "By Type" section is located
# (so we skip over it)
i_bytype_a, i_bytype_b = \
FindDataSection(lines_data, section_name_bytype)
in_bytype_section = False
for i in range(0, len(lines_data)):
line = lines_data[i].strip()
# Omit all lines of text in the 'By Type' section (including the
# header and commments or blank lines which immediately follow it.)
if line == section_name_bytype:
in_bytype_section = True
elif i == i_bytype_b:
in_bytype_section = False
if not in_bytype_section:
sys.stdout.write(lines_data[i])
except (ValueError, InputError) as err:
sys.stderr.write('\n'+str(err)+'\n')
sys.exit(-1)
diff --git a/tools/moltemplate/src/nbody_by_type_lib_old.py b/tools/moltemplate/src/nbody_by_type_lib_old.py
deleted file mode 100644
index 431172d9b..000000000
--- a/tools/moltemplate/src/nbody_by_type_lib_old.py
+++ /dev/null
@@ -1,312 +0,0 @@
-#!/usr/bin/env python
-
-# Author: Andrew Jewett (jewett.aij at g mail)
-# http://www.chem.ucsb.edu/~sheagroup
-# License: 3-clause BSD License (See LICENSE.TXT)
-# Copyright (c) 2012, Regents of the University of California
-# All rights reserved.
-
-
-import sys
-from nbody_graph_search import *
-#from collections import namedtuple
-from collections import defaultdict, OrderedDict
-from ttree_lex import MatchesPattern, MatchesAll, InputError
-#import gc
-
-
-def GenInteractions_int(G_system,
- g_bond_pattern,
- typepattern_to_coefftype,
- canonical_order, #function to sort atoms and bonds
- atomtypes_int2str,
- bondtypes_int2str,
- report_progress = False): #print messages to sys.stderr?
- """
- GenInteractions() automatically determines a list of interactions
- present in a system of bonded atoms (argument "G_system"),
- which satisfy the bond topology present in "g_bond_pattern", and
- satisfy the atom and bond type requirements in "typepattern_to_coefftype".
-
- Whenever a set of atoms in "G_system" are bonded together in a way which
- matches "g_bond_pattern", and when the atom and bond types is consistent
- with one of the entries in "typepattern_to_coefftype", the corresponding
- list of atoms from G_system is appended to the list of results.
-
- These results (the list of lists of atoms participating in an interaction)
- are organized according their corresponding "coefftype", a string
- which identifies the type of interaction they obey as explained above.
- results are returned as a dictionary using "coefftype" as the lookup key.
-
- Arguments:
-
- -- typepattern_to_coefftype is a list of 2-tuples --
- The first element of the 2-tuple is the "typepattern".
- It contains a string describing a list of atom types and bond types.
- The typepattern is associated with a "coefftype",
- which is the second element of the 2-tuple. This is a string
- which identifies the type of interaction between the atoms.
- Later on, this string can be used to lookup the force field
- parameters for this interaction elsewhere.)
-
- -- Arguments: G_system, g_bond_pattern, atomtypes_int2str, bondtypes_int2str --
-
- G_system stores a list of atoms and bonds, and their attributes in
- "Ugraph" format. In this format:
- Atom ID numbers are represented by indices into the G_system.verts[] list.
- Bond ID numbers are represented by indices into the G_system.edges[] list.
- Atom types are represented as integers in the G_system.verts[i].attr list.
- Bond types are represented as integers in the G_system.edges[i].attr list.
- They are converted into strings using
- atomtypes_int2str, and bondtypes_int2str.
-
- g_bond_pattern is a graph which specifies the type of bonding between
- the atoms required for a match. It is in Ugraph format (however the
- atom and bond types are left blank.)
-
- Atom and bond types are supplied by the user in string format. (These
- strings typically encode integers, but could be any string in principle.)
- The string-version of the ith atom type is stored in
- atomtypes_int2str[ G_system.verts[i].attr ]
- The string-version of the ith bond type is stored in
- bondtypes_int2str[ G_system.edges[i].attr ]
-
- -- The "canonical_order" argument: --
-
- The search for atoms with a given bond pattern often yields
- redundant matches. There is no difference for example
- between the angle formed between three consecutively
- bonded atoms (named, 1, 2, 3, for example), and the
- angle between the same atoms in reverse order (3, 2, 1).
- However both triplets of atoms will be returned by the subgraph-
- matching algorithm when searching for ALL 3-body interactions.)
-
- To eliminate this redundancy, the caller must supply a "canonical_order"
- argument. This is a function which sorts the atoms and bonds in a way
- which is consistent with the type of N-body interaction being considered.
- The atoms (and bonds) in a candidate match are rearranged by the
- canonical_order(). Then the re-ordered list of atom and bond ids is
- tested against the list of atom/bond ids in the matches-found-so-far,
- before it is added.
-
- """
-
- if report_progress:
- startatomid = 0
- sys.stderr.write(' Searching for matching bond patterns:\n')
- sys.stderr.write(' 0%')
-
- # Figure out which atoms from "G_system" bond together in a way which
- # matches the "g_bond_pattern" argument. Organize these matches by
- # atom and bond types and store all of the non-redundant ones in
- # the "interactions_by_type" variable.
-
- gm = GraphMatcher(G_system, g_bond_pattern)
-
- interactions_by_type = defaultdict(list)
-
- for atombondids in gm.Matches():
- # "atombondids" is a tuple.
- # atombondids[0] has atomIDs from G_system corresponding to g_bond_pattern
- # (These atomID numbers are indices into the G_system.verts[] list.)
- # atombondids[1] has bondIDs from G_system corresponding to g_bond_pattern
- # (These bondID numbers are indices into the G_system.edges[] list.)
-
- # It's convenient to organize the list of interactions-between-
- # atoms in a dictionary indexed by atomtypes and bondtypes.
- # (Because many atoms and bonds typically share the same type,
- # organizing the results this way makes it faster to check
- # whether a given interaction matches a "typepattern" defined
- # by the user. We only have to check once for the whole group.)
-
- atombondtypes = \
- (tuple([G_system.GetVert(Iv).attr for Iv in atombondids[0]]),
- tuple([G_system.GetEdge(Ie).attr for Ie in atombondids[1]]))
-
- interactions_by_type[atombondtypes].append(atombondids)
-
- if report_progress:
- # GraphMatcher.Matches() searches for matches in an order
- # that selects a different atomid number from G_system,
- # starting at 0, and continuing up to the number of atoms (-1)
- # in the system (G_system.nv-1), and using this as the first
- # atom in the match (ie match[0][0]). This number can be used
- # to guess much progress has been made so far.
- oldatomid = startatomid
- startatomid = atombondids[0][0]
- percent_complete = (100 * startatomid) // G_system.GetNumVerts()
- # report less often as more progress made
- if percent_complete <= 4:
- old_pc = (100 * oldatomid) // G_system.GetNumVerts()
- if percent_complete > old_pc:
- sys.stderr.write(' '+str(percent_complete)+'%')
- elif percent_complete <= 8:
- pc_d2 = (100 * startatomid) // (2*G_system.GetNumVerts())
- oldpc_d2 = (100 * oldatomid) // (2*G_system.GetNumVerts())
- if pc_d2 > oldpc_d2:
- sys.stderr.write(' '+str(percent_complete)+'%')
- elif percent_complete <= 20:
- pc_d4 = (100 * startatomid) // (4*G_system.GetNumVerts())
- oldpc_d4 = (100 * oldatomid) // (4*G_system.GetNumVerts())
- if pc_d4 > oldpc_d4:
- sys.stderr.write(' '+str(percent_complete)+'%')
- else:
- pc_d10 = (100 * startatomid) // (10*G_system.GetNumVerts())
- oldpc_d10 = (100 * oldatomid) // (10*G_system.GetNumVerts())
- if pc_d10 > oldpc_d10:
- sys.stderr.write(' '+str(percent_complete)+'%')
-
- if report_progress:
- sys.stderr.write(' 100%\n')
- sys.stderr.write(' Looking up atom and bond types...')
-
- # Now test each match to see if the types of atoms and bonds involved match
- # any of the type-patterns in the "typepattern_to_coefftype" argument.
- # If so, store them in the out_topo list
-
- #coefftype_to_atomids = defaultdict(list)
- #abids_to_coefftypes = defaultdict(list)
- coefftype_to_atomids = OrderedDict()
- abids_to_coefftypes = OrderedDict()
-
- count = 0
-
- for typepattern, coefftype in typepattern_to_coefftype:
- if report_progress:
- sys.stderr.write(' Checking (atom-types,bond-types) against \n '+str(typepattern)+'-->'+coefftype+'\n')
- for atombondtypes, abidslist in interactions_by_type.items():
- # express atom & bond types in a tuple of the original string format
- types_atoms = [atomtypes_int2str[Iv] for Iv in atombondtypes[0]]
- types_bonds = [bondtypes_int2str[Ie] for Ie in atombondtypes[1]]
- type_strings = types_atoms + types_bonds
- # use string comparisons to check for a match with typepattern
- if MatchesAll(type_strings, typepattern): #<-see "ttree_lex.py"
- for abids in abidslist:
-
- # Re-order the atoms (and bonds) in a "canonical" way.
- # Only add new interactions to the list after re-ordering
- # them and checking that they have not been added earlier.
- # (...well not when using the same coefftype at least.
- # This prevents the same triplet of atoms from
- # being used to calculate the bond-angle twice:
- # once for 1-2-3 and 3-2-1, for example.)
- abids = canonical_order(abids)
- redundant = False
- if abids in abids_to_coefftypes:
- coefftypes = abids_to_coefftypes[abids]
- if coefftype in coefftypes:
- redundant = True
-
- if not redundant:
- # (It's too bad python does not
- # have an Ordered defaultdict)
- if coefftype in coefftype_to_atomids:
- coefftype_to_atomids[coefftype].append(abids[0])
- else:
- coefftype_to_atomids[coefftype]=[abids[0]]
- if abids in abids_to_coefftypes:
- abids_to_coefftypes[abids].append(coefftype)
- else:
- abids_to_coefftypes[abids] = [coefftype]
- count += 1
-
- if report_progress:
- sys.stderr.write(' done\n (found '+
- str(count)+' non-redundant matches)\n')
-
- return coefftype_to_atomids
-
-
-
-
-
-
-
-
-def GenInteractions_str(bond_pairs,
- g_bond_pattern,
- typepattern_to_coefftype,
- canonical_order, #function to sort atoms and bonds
- atomids_str,
- atomtypes_str,
- bondids_str,
- bondtypes_str,
- report_progress = False): #print messages to sys.stderr?
-
-
- assert(len(atomids_str) == len(atomtypes_str))
- assert(len(bondids_str) == len(bondtypes_str))
- # The atomids and atomtypes and bondtypes are strings.
- # First we assign a unique integer id to each string.
-
- atomids_str2int = {}
- atomtypes_str2int = {}
- atomtypes_int2str = []
- atomtype_int = 0
- for i in range(0, len(atomids_str)):
- if atomids_str[i] in atomids_str2int:
- raise InputError('Error: multiple atoms have the same id ('+
- str(atomids_str[i])+')')
- atomids_str2int[atomids_str[i]] = i
- #atomtypes_int = len(atomtypes_int)+1
- if (not (atomtypes_str[i] in atomtypes_str2int)):
- atomtypes_str2int[atomtypes_str[i]] = atomtype_int
- atomtypes_int2str.append(atomtypes_str[i])
- atomtype_int += 1
- #atomtypes_int.append(atomtype_int)
-
- bondids_str2int = {}
- bondtypes_str2int = {}
- bondtypes_int2str = []
- bondtype_int = 0
- for i in range(0, len(bondids_str)):
- if bondids_str[i] in bondids_str2int:
- raise InputError('Error: multiple bonds have the same id ('+
- str(bondids_str[i])+')')
- bondids_str2int[bondids_str[i]] = i
- #bondtype_int = len(bondtypes_int)+1
- if (not (bondtypes_str[i] in bondtypes_str2int)):
- bondtypes_str2int[bondtypes_str[i]] = bondtype_int
- bondtypes_int2str.append(bondtypes_str[i])
- bondtype_int += 1
-
- # Now convert "bond_pairs" into the UGraph format
- G_system = Ugraph()
- for iv in range(0, len(atomtypes_str)):
- G_system.AddVertex(iv, atomtypes_str2int[atomtypes_str[iv]])
-
- for ie in range(0, len(bond_pairs)):
- atomid1_str = bond_pairs[ie][0]
- atomid2_str = bond_pairs[ie][1]
- if (atomid1_str not in atomids_str2int):
- raise InputError('Error in Bonds Section:\n'
- ' '+atomid1_str+' is not defined in Atoms section\n')
- if (atomid2_str not in atomids_str2int):
- raise InputError('Error in Bonds Section:\n'
- ' '+atomid2_str+' is not defined in Atoms section\n')
- G_system.AddEdge(atomids_str2int[atomid1_str],
- atomids_str2int[atomid2_str],
- bondtypes_str2int[bondtypes_str[ie]])
-
- coefftype_to_atomids_int = GenInteractions_int(G_system,
- g_bond_pattern,
- typepattern_to_coefftype,
- canonical_order,
- atomtypes_int2str,
- bondtypes_int2str,
- report_progress)
- coefftype_to_atomids_str = OrderedDict()
- for coefftype, atomidss_int in coefftype_to_atomids_int.items():
- sys.stderr.write(' processing coefftype='+str(coefftype)+'\n')
- for atomids_int in atomidss_int:
- if coefftype in coefftype_to_atomids_str:
- coefftype_to_atomids_str[coefftype].append(
- [atomids_str[iv] for iv in atomids_int])
- else:
- coefftype_to_atomids_str[coefftype] = \
- [[atomids_str[iv] for iv in atomids_int]]
- #gc.collect()
-
- return coefftype_to_atomids_str
-
-
diff --git a/tools/moltemplate/src/postprocess_input_script.py b/tools/moltemplate/src/postprocess_input_script.py
index 5733aa224..7600358b9 100755
--- a/tools/moltemplate/src/postprocess_input_script.py
+++ b/tools/moltemplate/src/postprocess_input_script.py
@@ -1,146 +1,145 @@
#!/usr/bin/env python
"""
Reorder the integer arguments to the commands in a LAMMPS input
file if these arguments violate LAMMPS order requirements.
We have to do this because the moltemplate.sh script will automatically
assign these integers in a way which may violate these restrictions
and the user has little control over this.
Right now, the only thing this script does is swap the I and J integers in
"pair_coeff I J ..." commands. Later changes may be added.
"""
import sys
lines_orig = []
-in_stream = sys.stdin
f = None
fname = None
num_lines_ignore = 0
# Lines from files passed as arguments are read and processed silently.
# (Why? Sometimes it's necessary to read the contents of previous input scripts
# in order to be able to understand a script command which appears later.
# I'm assuming these files will be processed by lammps in the same order. So I
# must insure that moltemplate.sh passes them to this program in that order.
# I'm too lazy to read the "include" commands in input scripts correctly.)
if len(sys.argv) > 1:
for fname in sys.argv[1:]:
f = open(fname, 'r')
in_stream = f
lines_orig += in_stream.readlines()
num_lines_ignore += len(lines_orig)
f.close()
# Lines read from the standard input are read, processed, and printed to stdout
in_stream = sys.stdin
lines_orig += in_stream.readlines()
pair_style_list=[]
swap_occured = False
warn_wildcard = False
i=0
while i < len(lines_orig):
# Read the next logical line
# Any lines ending in '&' should be merged with the next line before breaking
line_orig = ''
while i < len(lines_orig):
line_counter = 1 + i - num_lines_ignore
line_orig += lines_orig[i]
if ((len(line_orig) < 2) or (line_orig[-2:] != '&\n')):
break
i += 1
line = line_orig.replace('&\n','\n').rstrip('\n')
comment = ''
if '#' in line_orig:
ic = line.find('#')
line = line_orig[:ic]
comment = line_orig[ic:] # keep track of comments (put them back later)
tokens = line.strip().split()
if ((len(tokens) >= 2) and (tokens[0] == 'pair_style')):
pair_style_list = tokens[1:]
if ((len(tokens) >= 3) and (tokens[0] == 'pair_coeff')):
if ((tokens[1].isdigit() and (tokens[2].isdigit())) and
(int(tokens[1]) > int(tokens[2]))):
swap_occured = True
tmp = tokens[2]
tokens[2] = tokens[1]
tokens[1] = tmp
if i >= num_lines_ignore:
# polite warning:
sys.stderr.write('swapped pair_coeff order on line '+str(line_counter))
#if (fname != None):
# sys.stderr.write(' of file \"'+fname+'\"')
sys.stderr.write('\n')
# Deal with the "hbond/" pair coeffs.
#
# The hbond/dreiding pair style designates one of the two atom types
# as a donor, and the other as an acceptor (using the 'i','j' flags)
# If swapped atom types eariler, we also need to swap 'i' with 'j'.
#
# If "hbond/dreiding.." pair style is used with "hybrid" or
# "hybrid/overlay" then tokens[3] is the name of the pair style
# and tokens[5] is either 'i' or 'j'.
if len(pair_style_list) > 0:
if ((pair_style_list[0] == 'hybrid') or
(pair_style_list[0] == 'hybrid/overlay')):
- if ((tokens[5] == 'i') and (tokens[3][0:6]=='hbond/')):
+ if ((len(tokens) > 5) and (tokens[5] == 'i') and (tokens[3][0:6]=='hbond/')):
tokens[5] = 'j'
sys.stderr.write(' (and replaced \"i\" with \"j\")\n')
- elif ((tokens[5] == 'j') and (tokens[3][0:6]=='hbond/')):
+ elif ((len(tokens) > 5) and (tokens[5] == 'j') and (tokens[3][0:6]=='hbond/')):
tokens[5] = 'i'
sys.stderr.write(' (and replaced \"j\" with \"i\")\n')
elif (pair_style_list[0][0:6] == 'hbond/'):
- if (tokens[4] == 'i'):
+ if ((len(tokens) > 4) and (tokens[4] == 'i')):
tokens[4] = 'j'
sys.stderr.write(' (and replaced \"i\" with \"j\")\n')
- elif (tokens[4] == 'j'):
+ elif ((len(tokens) > 4) and (tokens[4] == 'j')):
tokens[4] = 'i'
sys.stderr.write(' (and replaced \"j\" with \"i\")\n')
sys.stdout.write((' '.join(tokens)+comment).replace('\n','&\n')+'\n')
else:
if ((('*' in tokens[1]) or ('*' in tokens[2]))
and
(not (('*' == tokens[1]) and ('*' == tokens[2])))):
warn_wildcard = True
if i >= num_lines_ignore:
sys.stdout.write(line_orig)
else:
if i >= num_lines_ignore:
sys.stdout.write(line_orig)
i += 1
if swap_occured:
sys.stderr.write('\n'
' WARNING: Atom order in some pair_coeff commands was swapped to pacify LAMMPS.\n'
' For some exotic pair_styles such as hbond/dreiding, this is not enough. If you\n'
' use exotic pair_styles, please verify the \"pair_coeff\" commands are correct.\n')
if warn_wildcard:
sys.stderr.write('\n'
' WARNING: The use of wildcard characters (\"*\") in your \"pair_coeff\"\n'
' commands is not recommended.\n'
' (It is safer to specify each interaction pair manually.\n'
' Check every pair_coeff command. Make sure that every atom type in\n'
' the first group is <= atom types in the second group.\n'
' Moltemplate does NOT do this when wildcards are used.)\n'
' If you are using a many-body pair style then ignore this warning.\n')
diff --git a/tools/moltemplate/src/raw2data.py b/tools/moltemplate/src/raw2data.py
index 9e6035f35..a987f59b4 100755
--- a/tools/moltemplate/src/raw2data.py
+++ b/tools/moltemplate/src/raw2data.py
@@ -1,99 +1,96 @@
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from dump2data import *
g_program_name = 'raw2data.py'
g_date_str = '2013-9-19'
g_version_str = 'v0.42'
####### Main Code Below: #######
sys.stderr.write(g_program_name+' '+g_version_str+' '+g_date_str)
-#if sys.version < '3':
-# sys.stderr.write(' (python version < 3)\n')
-#else:
sys.stderr.write('\n')
try:
data_settings = DataSettings()
misc_settings = MiscSettings()
misc_settings.multi = False
warning_strings = []
ParseArgs(sys.argv,
misc_settings,
data_settings,
warning_strings)
frame_coords = defaultdict(list)
frame_coords_ixiyiz = defaultdict(list)
frame_vects = defaultdict(list)
frame_velocities = defaultdict(list)
frame_xlo_str = frame_xhi_str = None
frame_ylo_str = frame_yhi_str = None
frame_zlo_str = frame_zhi_str = None
frame_xy_str = frame_xz_str = frame_yz_str = None
frame_natoms = -1
frame_timestep_str = ''
i_atomid = i_atomtype = i_molid = -1
i_x = i_y = i_z = i_xu = i_yu = i_zu = -1
i_xs = i_ys = i_zs = i_xsu = i_ysu = i_zsu = -1
dump_column_names = []
#num_frames_in = -1
num_frames_out = 0
finished_reading_frame = False
read_last_frame = False
#in_coord_file = open('traj.raw','r')
#in_coord_file = open('tmp_atom_coords.dat','r')
in_coord_file = sys.stdin
read_last_frame = False
while True:
line = '\n'
while (line != '') and (line.strip() == ''):
line = in_coord_file.readline()
if line == '': # if EOF
break
frame_coords = defaultdict(list)
while line.strip() != '':
n_crds = len(frame_coords)
#sys.stdout.write("n_crds="+str(n_crds)+": \""+line.strip()+"\"\n")
frame_coords[str(n_crds+1)] = line.split()
line = in_coord_file.readline()
while (line != '') and (line.strip() == ''):
line = in_coord_file.readline()
# Parse the DATA file specified by the user
# and replace appropriate lines or fields with
# the corresponding text from the input file.
if misc_settings.multi:
out_file_name = data_settings.file_name + '.'\
+ str(num_frames_out)
sys.stderr.write(' (creating file \"'+out_file_name+'\")\n')
out_file = open(out_file_name, 'w')
else:
out_file = sys.stdout
WriteFrameToData(out_file,
None,
misc_settings,
data_settings,
frame_natoms,
frame_coords,
frame_coords_ixiyiz,
frame_vects,
frame_velocities,
frame_xlo_str, frame_xhi_str,
frame_ylo_str, frame_yhi_str,
frame_zlo_str, frame_zhi_str,
frame_xy_str, frame_xz_str, frame_yz_str)
except (ValueError, InputError) as err:
sys.stderr.write('\n'+str(err)+'\n')
sys.exit(-1)
diff --git a/tools/moltemplate/src/ttree.py b/tools/moltemplate/src/ttree.py
index 3f4e3bb49..3b9546b45 100755
--- a/tools/moltemplate/src/ttree.py
+++ b/tools/moltemplate/src/ttree.py
@@ -1,4762 +1,4762 @@
#!/usr/bin/env python
# Authors: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2011, Regents of the University of California
# All rights reserved.
"""
ttree Ttree is a simple program for recursively composing and generating
large redundant text files from small template files.
By default, the large number of unique template variables generated
in the process are automatically substituted with integers
(or other numeric counters, all of which can be overridden),
rendered, and the rendered templates are written to a file.
ttree was designed to be useful for generating input files for
molecular simulation software like LAMMPS or NAMD.
BasicUI This section of the code contains the user interface for ttree
when run as a stand-alone program, as described above. (This
section of code contains the "if __name__ == __main__:" code block.)
-- Data Types --
StaticObj Static nodes are data structures used to store ttree class definitions.
(Static nodes are useful for defining molecule types or
namespaces in LAMMPS or other molecular simulation programs.)
The nodes themselves are stored in a tree of nested class definitions.
Static variables (such as "@atom:C") are also associated with
StaticObjs.
InstanceObj Instance nodes are created when a user creates one (or many)
copies of a class, using the "new" command.
These classes in turn may instantiate other classes.
(Example: A user may manually instantiate several copies of a
molecule, such as a protein, however each of those
molecules may contain molecular subunits, such as
amino acids, which are automatically instantiated.)
Instance variables (such as "$atom:CA") are also associated with
InstanceObjs.
"""
import sys
from collections import defaultdict
import operator
import random
#import gc
try:
unicode
except NameError:
# Python 3
basestring = unicode = str
# -- ttree_lex.py --
# TtreeShlex is a backwards-compatible version of python's standard shlex module.
# It has the additional member: "self.wordterminators", which overrides
# the "self.wordchars" member. This enables better handling of unicode
# characters by allowing a much larger variety of characters to appear
# in words or tokens parsed by TtreeShlex. Otherwise it is identical to shlex.
from ttree_lex import *
if sys.version < '2.6':
raise InputError('Error: Using python '+sys.version+'\n'
- ' Alas, you must upgrade to a newever version of python (2.7 or later).')
+ ' Alas, you must upgrade to a newer version of python (2.7 or later).')
elif sys.version < '2.7':
sys.stderr.write('--------------------------------------------------------\n'
'----------------- WARNING: OLD PYTHON VERSION ----------\n'
' This program is untested on your python version ('+sys.version+').\n'
' PLEASE LET ME KNOW IF THIS PROGRAM CRASHES (and upgrade python).\n'
- ' -Andrew 2012-4-16\n'
+ ' -Andrew 2013-10-25\n'
'--------------------------------------------------------\n'
'--------------------------------------------------------\n')
from ordereddict import OrderedDict
else:
from collections import OrderedDict
if sys.version > '3':
import io
else:
import cStringIO
# We keep track of the program name and version.
# (This is only used for generating error messages.)
#g_filename = 'ttree.py'
g_filename = __file__.split('/')[-1]
g_module_name = g_filename
if g_filename.rfind('.py') != -1:
g_module_name = g_filename[:g_filename.rfind('.py')]
g_date_str = '2013-9-12'
g_version_str = '0.76'
class ClassReference(object):
""" Every class defined by the user (stored in an StaticObj data structure)
may contain references to other classes (ie. other StaticObjs).
(Note: All of these StaticObjs are stored in the same tree, the
global static tree.)
Examples:
Whenever an instance of a class is created, this may automatically spawn
the creation of additional classes (which are instantiated because a 'new'
command appeared within the first class's definition). These are stored in
the "StaticObj.instance_commands[i].class_ref" attribute.
Similarly, each class (StaticObj) can optionally inherit some of its
traits (consisting of write() and new commands) from one or more
"class_parents" (also StaticObjs). A list of these parents is stored in the
"StaticObj.class_parents" attribute. In both cases (self.instance_commands
or self.class_parents) we need to storea pointer to the StaticObj(s)
corresponding to the instance-childen or class-parents.
(This stored in self.statobj).
However, for the purposes of debugging and interactivity, it is also
convenient to permanently keep track of the string that the user used to
specify the name/location of that class/StaticObj
(stored in self.statobj_str), in addition to the location
in the file where that string occurs (stored in self.srcloc)."""
__slots__=["statobj_str","srcloc","statobj"]
def __init__(self,
statobj_str=None,
srcloc=None,
statobj=None):
self.statobj_str = statobj_str
if srcloc is None:
self.srcloc = OSrcLoc('', -1)
else:
self.srcloc = srcloc
self.statobj = statobj
#def __repr__(self):
# return repr((self.statobj_str, self.srcloc))
# "Command"s are tasks to carry out.
# (...either immediately, or later during instantiation)
# Commands are used to write to files, create new instances, delete instances,
# or custom commands to modify an instance of a class.
# (For example "instance = new Class.move(1,0,0).rot(45,0,0,1)"
# The ".move(1,0,0)" and ".rot(45,0,0,1)" commands are "stackable" and
# have similar syntax to member functions in C++, JAVA, Python.)
class Command(object):
__slots__=["srcloc"]
def __init__(self, srcloc=None):
self.srcloc = srcloc
# COMMENTING OUT: "COUNT" AND "ORDER" ARE NO LONGER NEEDED
#count = 0
#def __init__(self, srcloc=None):
# self.srcloc = srcloc
# # The "order" member is a counter that keeps track of the order
# # in which the Command data types are created (issued by the user).
# Command.count += 1
# self.order = Command.count
#def __lt__(self, x):
# return self.order < x.order
class WriteFileCommand(Command):
""" WriteFileCommand
filename This is the name of the file that will be written to
when the command is executed.
tmpl_list This is the contents of what will be written to the file.
Text strings are often simple strings, however more
generally, they can be strings which include other variables
(ie templates). In general, templates are lists of alternating
TextBlocks and VarRefs, (with additional tags and data to
identify where they occur in in the original user's files).
"""
__slots__=["filename", "tmpl_list"]
def __init__(self,
filename = None,
tmpl_list = None,
srcloc = None):
self.filename = filename
if tmpl_list is None:
self.tmpl_list = []
else:
Command.__init__(self, srcloc)
self.tmpl_list = tmpl_list
def __str__(self):
if self.filename:
return 'WriteFileCommand(\"'+self.filename+'\")'
else:
return 'WriteFileCommand(NULL)'
def __copy__(self):
tmpl_list = []
CopyTmplList(self.tmpl_list, tmpl_list) #CHECK:IS_MEMORY_WASTED_HERE?
return WriteFileCommand(self.filename, tmpl_list, self.srcloc)
class InstantiateCommand(Command):
""" InstantiateCommand is a simple tuple-like datatype used to
store pairs of names (strings, stored in self.name),
and ClassReferences (see above, stored in self.class_ref).n
The "suffix" argument is an optional string which may contain
additional instructions how to instantiate the object.
"""
__slots__=["name", "class_ref"]
def __init__(self,
name = None,
class_ref = None,
srcloc = None):
Command.__init__(self, srcloc)
self.name = name
#if class_ref is None:
# self.class_ref = ClassReference()
#else:
self.class_ref = class_ref
def __str__(self):
return 'InstantiateCommand('+self.name+')'
def __copy__(self):
return InstantiateCommand(self.name, self.class_ref, self.srcloc)
class DeleteCommand(Command):
__slots__=[]
def __init__(self,
srcloc = None):
Command.__init__(self, srcloc)
def __str__(self):
return 'DeleteCommand()'
def __copy__(self):
return DeleteCommand(self.srcloc)
class StackableCommand(Command):
""" StackableCommand is a class for storing commands
that effect the environment of the object being created.
The combined effect of these commands can be thought of as a "stack"
Commands can be pushed on the stack, or popped off
The actual commands themselves are represented by the "contents" member
which is usually a text string.
ttree.py does not attempt to understand the content of these commands.
That job is left up to the __main___ module. (IE. whatever script that
happens to be importing ttree.py. If there is no script, and
ttree.py IS the main module, then it simply ignores these commands.)
"""
__slots__=["context_node"]
def __init__(self,
srcloc,
context_node=None):
Command.__init__(self, srcloc)
self.context_node = context_node # if multiple stacks are present, then use "context_node"
# as a key to identify which stack you want
# the command to modify
class PushCommand(StackableCommand):
__slots__=["contents"]
def __init__(self,
contents,
srcloc,
context_node=None):
StackableCommand.__init__(self, srcloc, context_node)
self.contents = contents
def __copy__(self):
return PushCommand(self.contents, self.srcloc, self.context_node)
def __str__(self):
return 'PushCommand('+str(self.contents)+')'
class PushRightCommand(PushCommand):
__slots__=[]
def __init__(self,
contents,
srcloc,
context_node=None):
PushCommand.__init__(self, contents, srcloc, context_node)
def __copy__(self):
return PushRightCommand(self.contents, self.srcloc, self.context_node)
def __str__(self):
return 'PushRightCommand('+str(self.contents)+')'
class PushLeftCommand(PushCommand):
__slots__=[]
def __init__(self,
contents,
srcloc,
context_node=None):
PushCommand.__init__(self, contents, srcloc, context_node)
def __copy__(self):
return PushLeftCommand(self.contents, self.srcloc, self.context_node)
def __str__(self):
return 'PushLeftCommand('+str(self.contents)+')'
class PopCommand(StackableCommand):
__slots__=["partner"]
def __init__(self,
partner,
srcloc,
context_node=None):
StackableCommand.__init__(self, srcloc, context_node)
self.partner = partner
def __copy__(self):
return PopCommand(self.partner, self.srcloc, self.context_node)
def __str__(self):
return 'PopCommand('+str(self.partner.contents)+')'
class PopRightCommand(PopCommand):
__slots__=[]
def __init__(self,
partner,
srcloc,
context_node=None):
PopCommand.__init__(self, partner, srcloc, context_node)
assert((partner is None) or isinstance(partner, PushRightCommand))
def __copy__(self):
return PopRightCommand(self.partner, self.srcloc, self.context_node)
def __str__(self):
return 'PopRightCommand('+str(self.partner.contents)+')'
class PopLeftCommand(PopCommand):
__slots__=[]
def __init__(self,
partner,
srcloc,
context_node=None):
PopCommand.__init__(self, partner, srcloc, context_node)
assert((partner is None) or isinstance(partner, PushLeftCommand))
def __copy__(self):
return PopLeftCommand(self.partner, self.srcloc, self.context_node)
def __str__(self):
return 'PopLeftCommand('+str(self.partner.contents)+')'
# The ScopeCommand, ScopeBegin, and ScopeEnd commands are useful to designate
# which commands belong to a particular class definition (or class instance).
# (This is useful later on, when a linear list of commands has been created.)
# They are simply markers an do not do anything. These classes can be ignored.
class ScopeCommand(Command):
__slots__=["node"]
def __init__(self,
node,
srcloc):
Command.__init__(self, srcloc)
self.node = node
#self.srcloc = srcloc
def __copy__(self):
return ScopeCommand(self.node, self.srcloc)
def __str__(self):
if self.node:
return 'ScopeCommand('+self.node.name+')'
else:
return 'ScopeCommand(None)'
class ScopeBegin(ScopeCommand):
__slots__=[]
def __init__(self, node, srcloc):
ScopeCommand.__init__(self, node, srcloc)
def __copy__(self):
return ScopeBegin(self.node, self.srcloc)
def __str__(self):
if self.node:
return 'ScopeBegin('+NodeToStr(self.node)+')'
else:
return 'ScopeBegin(None)'
class ScopeEnd(ScopeCommand):
__slots__=[]
def __init__(self, node, srcloc):
ScopeCommand.__init__(self, node, srcloc)
def __copy__(self):
return ScopeEnd(self.node, self.srcloc)
def __str__(self):
if self.node:
return 'ScopeEnd('+NodeToStr(self.node)+')'
else:
return 'ScopeEnd(None)'
# COMMENTING OUT: NOT NEEDED AT THE MOMENT
#class VarAssignCommand(Command):
# """ VarAssignCommand
#
# This class is used whenever the user makes an explicit request to assign
# a variable to a value (values are text strings).
#
# var_ref The variable name (tecnically speaking, I call this
# a variable descriptor string and it includes at least one of
# the following: the name of a leaf node, a category node name,
# and category name)
# the location in the file where variable appears, and (eventually
# after subsequent lookup), references to the leaf_node, cat_node,
# "Category", and "VarBinding" data structures associated with it.
# text_tmpl Text strings are often simple strings, however more
# generally, they can be strings which include other variables
# (ie templates). In general, templates are lists of alternating
# TextBlocks and VarRefs, (with additional tags and data to
# identify where they occur in in the original user's files).
#
# """
# __slots__=["var_ref","text_tmpl"]
#
# def __init__(self,
# #command_name = '=', <-- ?!?
# var_ref = None,
# text_tmpl=None):
# Command.__init__(self, srcloc)
# self.var_ref = var_ref
# self.text_tmpl = text_tmpl
class ModCommand(object):
__slots__=["command","multi_descr_str"]
def __init__(self,
command,
multi_descr_str):
self.command = command
self.multi_descr_str = multi_descr_str
def __str__(self):
return 'ModCommand('+str(self.command)+')'
def __copy__(self):
return ModCommand(self.command.__copy__(), self.multi_descr_str)
def CopyTmplList(source_tmpl_list, dest_cpy):
for entry in source_tmpl_list:
if isinstance(entry, TextBlock):
dest_cpy.append(entry) # Then make a shallow copy
# (pointer assignment) to the text
# block (Text blocks do not change
# during instantiation.)
elif isinstance(entry, VarRef):
assert(len(entry.prefix)>0)
if entry.prefix[0] == '@': # '@' vars refer to static data
dest_cpy.append(entry) # Then make a shallow copy
# pointer assignment) to the static
# variable. (Static variables do
# not change during instantiation.)
elif entry.prefix[0] == '$': # new '$' vars are created
# during every instantiation.
# var_refs do change when you instantiate them. So
# create a new VarRef object, and copy the attributes.
var_ref = VarRef(entry.prefix,
entry.descr_str,
entry.suffix,
entry.srcloc)
# Note: for instance variables ('$' vars)
# "entry.nptr" should not contain
# any data yet, so we just ignore it.
# I assert this below:
assert((entry.nptr.cat_node is None) and
(entry.nptr.leaf_node is None))
dest_cpy.append(var_ref)
else:
assert(False) # prefix[0] should be either '@' or '$'
else:
assert(False) # type(entry) should be either TextBlock or VarRef
def RecursiveJoin(tokens_expr, delimiter = ''):
""" RecursiveJoin() converts a tree-like list/tuple of tokens, for example:
['a ', ('tree', '-', ['like', 'container']), [[' '], 'of'], ' strings']
to an ordinary string, eg:
'a tree-like container of strings'
This behavees similarly to "reduce(lambda a, b: a+b, tokens)",
except that it works with arbitrarily nested lists/tuples."""
text = ''
if isinstance(tokens_expr, basestring):
return tokens_expr
else:
text_lstr = []
for i in range(0, len(tokens_expr)):
text.append( TokensToStr(tokens_expr[i]) )
return ''.join(text_lstr, delimiter)
#----------------------------------------------------------
#----------------------------------------------------------
# The following code is specific to ttree.
#
# (Up until this point, we have only defined
# a few simple general text parsing routines.)
#----------------------------------------------------------
#----------------------------------------------------------
def PtknsToStr(path_tokens):
"""
There are three ways to store paths:
As a single string: '/Protein/Phe/Ca' <- the format entered by the user
As a list of tokens ['Protein', 'Phe', 'Ca'] <- split into tokens
As a list of nodes in a tree (pointers to nodes in a tree hierarchy)
This function converts between the first two formats.
"""
text = ''
if len(path_tokens) > 0:
text = path_tokens[0]
for i in range(1, len(path_tokens)):
text += '/' + path_tokens[i]
else:
text = ''
return text
def StrToPtkns(path_string):
""" The inverse of PtknsToStr(), this function splits a string like
'/usr/local/../bin/awk' into ['usr','local','..','bin','awk'].
For illustrative purposes only. Use text.split('/') directly instead."""
return orig_text.split('/')
def FindChild(name, node, dbg_loc):
""" FindChild looks over the list of node.children to find a child
which matches the name given in the first argument.
If it is not found, it returns None.
Note: I have not yet specified what kind of nodes FindChild() operates
on. Both StaticObjs and InstanceObjs have self.children and self.parent.
However only StaticObjs have "self.class_parents".
("class_parents" are "parents" in the object-oriented sense.)
If "node" (2nd argument) happens t be an StaticObj, this means it also
We must search over the children of these class_parents as well.
Terminology used here differs from Object Oriented Programming
Children in node.children are not children in the object-oriented
programming sense. However, in OOP, "children" are objects that share all
of the traits of their ancestors (and may have additionl traits as well).
I have implemented OOP style children and parents, but this informtion
is stored in "node.class_parents", instead of "node.parents".
For comparison, instantiated nodes (InstanceObjs) are different. Altough
instantiated classes (InstanceObjs) have access to the attributes of the
class_parents of the StaticObjs that define them, they do not remember the
ownership of that data. (It just gets merged with their own member data,
including their .children.)
Hence we must treat StaticObjs carefully because their are two ways we can
access child data. We should loop over both of them. We do that below:
"""
for child in node.children:
if child.name == name:
return child
# The object-oriented inheritance stuff appears here.
# If you don't care about OOP or inheritance,
# then comment out the loop that follows:
if isinstance(node, StaticObj):
#CONTINUEHERE: DEBUG THIS FEATURE AND EXTEND NAMESPACES TO INSTOBJS
# Search recursively over the "children" (ie attributes or members)
# belonging to any OOP ancestors of this node.
for class_parent in node.class_parents:
for child in class_parent.children:
child = FindChild(name, class_parent, dbg_loc)
if child != None:
return child
for namespace_node in node.namespaces:
for child in namespace_node.children:
child = FindChild(name, namespace_node, dbg_loc)
if child != None:
return child
# Otherwise, a child name match was not found
return None
def FollowPath(path_tokens, starting_node, dbg_loc):
""" FollowPath() returns the "last_node", a node whose position in the
tree is indicated by a list of path_tokens, describing the names
of nodes connecting "starting_node" to "last_node".
If it one of the strings in the list of path_tokens turns out
not to match then names of classes in the tree, then this function
returns the last_node that did match before the error occurred,
as well as an integer which stores the number of tokens in
the path_tokens list which were successfully processed.
In other words, the list of node naes is not a full path, but the
relative path that takes you from one node (not necessarily the root)
to another. Return Value:
Ideally, each node in the list should be a parent or a child of the
previous node. (See comment for PathTokensToStr(), for more details.)
This function returns the number of path_tokens successfully
parsed. Under normal termination, this is len(path_tokens).
If the path can not be followed (because at some point, a child
or parent does not exist), then this function returns a number
smaller than len(path_tokens).
We let the caller handle undefined paths. """
#print(' FollowPath() invoked on: ', path_tokens)
if len(path_tokens) == 0:
return 0, starting_node
node = starting_node
# Is this path a relative path, or a full path?
# If the path-string began with '/', then it's a full path. This means
# that after processing by split('/'), the first token will be ''
# Example: path_tokens='/Prot/Alanine'.split('/')
# --> path_tokens[0] == ''
if path_tokens[0] == '':
# In that case, then take us to the root node:
while node.parent != None:
node = node.parent
#sys.stdout.write('FollowPath(): Retreating to node \"'+node.name+'\"\n')
i0 = 1 # <- We've just processed the first token. Skip over it later.
else:
i0 = 0
i = i0
while i < len(path_tokens):
if path_tokens[i] == '..':
if node.parent is None:
return i, node # <-return the index into the token list
# Caller will know that something went awry
# if the return value is not equal to the
# length of the token list
else:
node = node.parent
i += 1
elif path_tokens[i] == '...':
node_before_ellipsis = node
if i == len(path_tokens)-1:
return i, node_before_ellipsis
search_target = path_tokens[i+1]
# Now search over the "children" of this node
# for one who's name matches path_tokens[i].
# If not found, then move up to the parent node's children.
# (This is not an exhaustive tree search. Only the nodes which
# are immediate children of this node's parents are searched.)
while node != None:
child = FindChild(search_target, node, dbg_loc)
if child is None:
node = node.parent
else:
node = child
break
if node is None:
# Caller will know that something went awry if the return
# value is not equal to the length of the token list.
return i, node_before_ellipsis
i += 2
elif path_tokens[i] in ('','.'): # <-Note we ignore empty tokens from now on.
# (Same convention is used in specifying a
# directory in a filesystem, eg. using /usr/local
# or /usr//local or /usr/./local. These are equivalent.)
i += 1
else:
# Now search over the "children" of this
# node for one who's name matches path_tokens[i].
child = FindChild(path_tokens[i], node, dbg_loc)
if child is None:
# In that case, return with the node_list incomplete.
# Let the caller check to see if something went wrong.
return i, node # <-return the index into the token list (i)
# Caller will know that something went awry
# if the return value is not equal to the
# length of the token list
else:
node = child
i += 1
if node.IsDeleted():
#sys.stderr.write('(debug_msg: encountered deleted node: \"'+node.name+'\")\n')
break
return len(path_tokens), node
def PtknsToNode(path_tokens, starting_node, dbg_loc):
""" PtknsToNode() is identical to def FollowPath() except
that it raises syntax-error exceptions if the path is undefined."""
i_last_ptkn, last_node = FollowPath(path_tokens, starting_node, dbg_loc)
if i_last_ptkn < len(path_tokens):
#assert(isinstance(last_node,StaticObj)) <--why did I assert this? seems wrong
if (last_node.parent is None) and (path_tokens[i_last_ptkn] == '..'):
#In that case, we tried to back out beyond the root of the tree.
raise InputError('Error('+g_module_name+'.PtknsToNode()):\n'
' Invalid variable/class name:\n'
' \"'+PtknsToStr(path_tokens)+'\" located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
' There are too many \"..\" tokens in the path string.')
elif path_tokens[i_last_ptkn] == '...':
if i_last_ptkn+1 == len(path_tokens):
raise InputError('Error('+g_module_name+'.PtknsToNode()):\n'
' Error in '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
' Expected name following \"...\"\n')
else:
search_target = path_tokens[i_last_ptkn+1]
#In that case, we were unable to find the node referenced by "..."
raise InputError('Error('+g_module_name+'.PtknsToNode()):\n'
' Class or variable \"'+search_target+'\" not found\n'
' in this context: \"'+PtknsToStr(path_tokens)+'\"\n'
' located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno))
else:
#Then the reason is: The string in path_tokens[i_last_ptkn]
#was supposed to be a child of last_node but a child
#of that name was not found.
err_msg = 'Error('+g_module_name+'.PtknsToNode()):\n'+\
' Undefined variable/class name:\n'+\
' \"'+PtknsToStr(path_tokens)+'\",\n'+\
' This occured near or before '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'+\
' (Specifically \"'+path_tokens[i_last_ptkn]+\
'\" is not a subordinate of \"'+MaxLenStr(last_node.name,'/')+'\".)\n'+\
' This may be due to a typo located here or earlier.\n'+\
' It may also occur if you deleted the object earlier. (Referring to a\n'+\
' deleted object is only forgiven when using [0-9] or [0:10] notation.)\n'+\
' If this object refers to an array you must use brackets []\n'+\
' to explicitly specify the element(s) you want from that array.\n'+\
' (To select multiple elements, you can use [*] or [0-9] or [0:10].)\n'
if (path_tokens[i_last_ptkn] in NodeToPtkns(last_node)):
err_msg += '\nIn this case:\n'+\
' It seems like you may have omitted a } character somewhere before:\n'+\
' '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)
raise InputError(err_msg)
assert(False) # One of the two conditions above should be true.
return last_node
def StrToNode(obj_name, starting_node, dbg_loc):
path_tokens = obj_name.split('/')
return PtknsToNode(path_tokens, starting_node, dbg_loc)
def NodeListToPtkns(node_list, dbg_loc=None):
assert(len(node_list) > 0) #The path must contain at least the starting node
path_tokens = [node_list[0].name]
for i in range(1, len(node_list)):
if node_list[i] == node_list[i-1].parent:
path_tokens.append('..')
else:
path_tokens.append(node_list[i].name)
# Now check to make sure the user supplied consistent information:
if (node_list[i] not in node_list[i-1].children):
raise InputError('Error('+g_module_name+'.NodeListToPtkns()):\n'
' Undefined variable/class name:\n'
' \"'+PtknsToStr(path_tokens)+'\" located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
' (\"'+path_tokens[i]+'\" is not subordinate to \"'+MaxLenStr(node_list[i-1].name,'/')+'\")\n'
' This could be an internal error.')
return path_tokens
def NodeListToStr(node_list, dbg_loc=None):
assert(len(node_list) > 0) #The path must contain at least the starting node
path_str = node_list[0].name
for i in range(1, len(node_list)):
if node_list[i] == node_list[i-1].parent:
path_str += '/..'
else:
path_str += '/' + node_list[i].name
# Now check to make sure the user supplied consistent information:
if (node_list[i] not in node_list[i-1].children):
err_msg = 'Error('+g_module_name+'.NodeListToStr()):\n'+\
' Invalid variable/class name:\n' +\
' \"'+PtknsToStr(path_tokens)+'\"'
if dbg_loc != None:
err_msg += ' located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)
err_msg += '\n' +\
' (\"'+node_list[i].name+'\" is not a subordinate of \"'+MaxLenStr(node_list[i-1].name,'/')+'\")\n'+\
' This could be an internal error.'
raise InputError(err_msg)
return path_str
def NodeToPtkns(node):
ptkns = []
nd = node
while nd != None:
ptkns.append(nd.name)
nd = nd.parent
ptkns.reverse()
return ptkns
def NodeToStr(node):
ptkns = NodeToPtkns(node)
assert(len(ptkns) > 0)
if node.parent is None:
assert(node.name == '')
return '/'
path_str = ptkns[0]
i = 1
while i < len(ptkns):
path_str += '/'+ptkns[i]
i += 1
return path_str
def CatLeafNodesToTkns(cat_name, cat_node, leaf_node, dbg_loc):
assert((cat_node != None) and (leaf_node != None))
assert((cat_name != None) and (cat_name != ''))
# Determine the path of the cat node
cat_node_ptkns = NodeToPtkns(cat_node)
cat_node_ptkns.append(cat_name+':')
# Determine the path of the leaf node (which should inherit from cat)
deleted = False
leaf_node_ptkns = []
if cat_node != leaf_node:
node = leaf_node
while node.parent != None:
if node.IsDeleted():
deleted = True
leaf_node_ptkns.append('DELETED_'+node.name)
break
leaf_node_ptkns.append(node.name)
if node.parent == cat_node:
break
node = node.parent
leaf_node_ptkns.reverse()
if not deleted:
# Check that leaf inherits from cat. If not, print error.
if ((node.parent != cat_node) and (node != cat_node)):
err_msg = 'Error('+g_module_name+'.CatLeafNodesToPtkns()):\n'+\
' Invalid variable (category:leaf) pair\n'
if dbg_loc != None:
cat_node_str = NodeToStr(cat_node)
leaf_node_str = NodeToStr(leaf_node)
err_msg += ' located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'+\
' (\"'+leaf_node.name+'\" is not in the scope of \"'+cat_node_str+'/'+cat_name+':\")\n'+\
' This will happen if you used the \"category\" command to manually\n'+\
' create a category/counter which is not defined globally.\n'+\
'\n'+\
' Note: Using the analogy of a unix style file system, \n'+\
' the problem is that \"'+leaf_node_str+'\"\n'+\
' is not a subdirectory of \"'+cat_node_str+'\".\n'+\
'\n'+\
' Note: This often occurs when \".../\" is used. In that case, you may\n'+\
' be able to avoid this error by referring to your variable explicitly\n'+\
' by using chains of \"../\" tokens in the path instead of \".../\".\n'
#' Make sure that your variable you are using is defined in \n'+\
#' an environment (currently \"'+leaf_node_str+'\")\n'+\
#' which lies WITHIN the environment where the category was defined.\n'+\
#' (currently \"'+cat_node_str+'\").\n'
raise InputError(err_msg)
else:
err_msg = 'Warning: Strange variable path'
if dbg_loc != None:
err_msg += ' near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)
err_msg += '\n' +\
' The category and leaf nodes for variable \"'+cat_name+':'+leaf_node.name+'\" are the same.\n'+\
' Check to see that this variable is behaving the way you intended.\n'+\
' (It\'s possible this could be an internal error in the program.)\n'
sys.stderr.write(err_msg)
# Merge the list of strings together into a single string:
return cat_node_ptkns + leaf_node_ptkns
def CanonicalCatName(cat_name, cat_node, dbg_loc=None):
# Determine the path of the cat node
tkns = NodeToPtkns(cat_node)
tkns.append(cat_name)
#full_cat_name = tkns[0]
#for i in range(1,len(tkns)):
# full_cat_name += '/'+tkns[i]
# better way:
return '/'.join(tkns)
def CanonicalDescrStr(cat_name, cat_node, leaf_node, dbg_loc=None):
tkns = CatLeafNodesToTkns(cat_name, cat_node, leaf_node, dbg_loc)
descr_str = tkns[0]
for i in range(1, len(tkns)):
if (len(descr_str)>0) and (descr_str[-1] == ':'):
descr_str += tkns[i]
else:
descr_str += '/'+tkns[i]
return descr_str
def CollapsePath(path_tokens):
"""
CollapsePath() takes a list of Strings argument representing a
directory-like path string
(for example '/SUB1A/Sub2A/../Sub2B/sub3b/../sub3c/entry'),
and replaces it with a version which should contain no '..' patterns.
(In the example above, it returns /SUB1A/Sub2B/sub3c/entry')
"""
new_ptkns = []
ndelete = 0
i = len(path_tokens)-1
while i >= 0:
if path_tokens[i] == '..':
ndelete += 1
else:
if (ndelete > 0) and (path_tokens[i] != ''):
# Note: "path_tokens[i] != '')" means "/a/b//c" <-> "/a/b/c"
ndelete -= 1
else:
if len(path_tokens[i]) > 0:
new_ptkns.append(path_tokens[i])
i -= 1
new_ptkns.reverse()
if ndelete > 0:
return ndelete # <-- useful to let caller know an error ocurred
return new_ptkns
def FindCatNode(category_name, current_node, srcloc):
""" Search upwards (toward the ancester nodes), looking for a node
containing a category matching category_name (first argument).
Useful when the user specifies a category name, but neglects to
specify which node it was defined in.
Note: there is no gaurantee that the category node returned by this function
contains an entry in it's "categories" list corresponding to this
category name. You must check for this condition and handle it."""
cat_node = None
node = current_node
while True:
if category_name in node.categories:
cat_node = node
break
elif node.parent != None:
node = node.parent
else:
# node.parent is None, ... we're done
break
if cat_node is None:
assert(node.parent is None)
#sys.stderr.write('Warning near ' +
# ErrorLeader(srcloc.infile,
# srcloc.lineno)+'\n'+
# ' no category named \"'+category_name+'\" found.\n'+
# ' Creating a new global category: /'+
# category_name+':\n')
cat_node = node # the global node
assert(cat_node != None)
return cat_node
def RemoveNullTokens(in_ptkns):
"""This function just gets rid of useless empty tokens in the path ('', '.')
(However if '' appears at the beginning of a path, we leave it alone.)
"""
out_ptkns = []
for i in range(0,len(in_ptkns)):
if ((in_ptkns[i] != '.') and
((in_ptkns[i] != '') or (i==0))):
out_ptkns.append(in_ptkns[i])
# (I'm sure there are ways to write this in python
# using fewer lines of code. Sigh.)
return out_ptkns
def DescrToCatLeafPtkns(descr_str, dbg_loc):
"""
Review: Variables in this program have three parts:
1) A variable category name (designating the type of variable).
2) A variable category path, which consists of a node which is an ancestor
of the variable leaf (1) in the tree
3) A variable name ("leaf"), which refers to a node in the tree
(either a static type tree or instance tree)
DescrToCatLeafPtkns() takes a string describing a variable,
as it appears in a template (ie, a write() command, once it has been
stripped of it's '$' or '@' prefix, and surrounding {} brackets)
...and divides it into strings which specify the location of that leaf in
a static or instance tree, in addition to the name and location of the
category node. Descriptor examples for atoms in water:
"AtomType:/Water/O", There are only 2 --types-- of atoms in
"AtomType:/Water/H", a water molecule. We identify them this way.
"AtomID:O" However each water molecule has 3 atoms, and we
"AtomID:H1" can give each atom in each water molecule a unique
"AtomID:H2" AtomID number. "AtomID:H2" is the id number of the
second hydrogen atom in the current water molecule.
---- Output: This function returns a 3-tuple: ----
leaf_ptkns The name of the variable's leaf node, as well as the list of
tokens denoting the path (named list of nodes) which lead to it.
cat_name The name of the variable category (no path information)
cat_ptkns A --suggestion-- for where to find the node containing the
category mentioned in "cat_name". Same format as leaf_ptkns.
Examples:
"AtomType:/Water/O" cat_name='AtomType', cat_path=[], leaf_ptkns=['','Water','O']
"AtomType:/Water/H" cat_name='AtomType', cat_path=[], leaf_ptkns=['','Water','H']
"AtomID:O" cat_name='AtomID', cat_path=[], leaf_ptkns=['O']
"AtomID:H1" cat_name='AtomID', cat_path=[], leaf_ptkns=['H1']
"AtomID:H2" cat_name='AtomID', cat_path=[], leaf_ptkns=['H2']
"mol:/" cat_name='mol', cat_path=[], leaf_ptkns=['']
"mol:" cat_name='mol', cat_path=[], leaf_ptkns=[]
"mol:../" cat_name='mol', cat_path=[], leaf_ptkns=['..']
"../mol" cat_name='mol', cat_path=[], leaf_ptkns=['..']
"$/peptide[3]/ResID:res[25]" cat_name='ResID', cat_path=['', 'peptide[3]'], leaf_ptkns=['res[25]']
"""
split_colon = descr_str.split(':')
if len(split_colon) > 2:
raise InputError('Error('+g_module_name+'.DescrToCatLeafPtkns())\n'
' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n\n'
' Bad variable descriptor: \"'+descr_str+'\"\n'+
' There can be at most one \':\' character in a variable descriptor.\n')
# ---- Are we using colon syntax (example '$atom:H1')?
elif len(split_colon) == 2:
# The category name = text after the last '/' (if present)and before ':'
cat_ptkns = split_colon[0].split('/')
cat_name = cat_ptkns[-1]
# The text before that is the suggested (category) path
cat_ptkns = cat_ptkns[:-1]
# if len(cat_ptkns) == 0:
# cat_ptkns.append('.')
# The remaining text is the path leading to the leaf node.
if split_colon[1] != '':
leaf_ptkns = split_colon[1].split('/')
else:
leaf_ptkns = []
if (cat_name == ''):
raise InputError('Error('+g_module_name+'.DescrToCatLeafPtkns()):\n'
' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n\n'
' Bad variable descriptor: \"'+descr_str+'\"\n')
else:
# ---- Are we using colon-less syntax (example: "$../mol") ?
ptkns = split_colon[0].split('/')
cat_name = ptkns[-1] # last token (eg. "mol") is the cat_name
leaf_ptkns = ptkns[:-1] # the rest is the leaf's path ("..")
if len(leaf_ptkns) == 0:
leaf_ptkns.append('.')
#cat_ptkns = ptkns[:-1] # the same goes for the cat path suggestion
#if len(cat_ptkns) == 0:
# cat_ptkns.append('.')
cat_ptkns = []
# On 2012-8-22, I commented out this line:
#return cat_name, RemoveNullTokens(cat_ptkns), RemoveNullTokens(leaf_ptkns)
# and replaced it with:
return cat_name, RemoveNullTokens(cat_ptkns), leaf_ptkns
def DescrToCatLeafNodes(descr_str,
context_node,
dbg_loc,
create_missing_nodes=False):
"""
Variables in ttree correspond to nodes in a tree
(and also categories to which they belong).
DescrToCatLeafNodes() reads the name of a variable,
(its descriptor) and determines where in the tree
does this variable reside, and what is it's category?
This function is the heart of ttree because it is
the function used to interpret ttree variable syntax.
(It is very messy right now. I will clean up the code later. AJ 2011-9-06)
Arguments:
descr_str The complete name that the user gave
to the variable. (Excluding '$' or '@')
context_node The class (node) in which the variable
was used. descr_str is interpeted
relative to this context. (This argument
is similar to the current directory
in which a command was issued in unix.)
dbg_loc The location in the user's input file(s)
where this variable is referred to.
create_missing_nodes
If we lookup a variable whose leaf node
does not exist yet, should we create it?
Setting this argument to "True" allows
us to augment the tree to add nodes
corresponding to variables.
-- Here is a greatly simplified version of DescrToCatLeafNodes(): --
def DescrToCatLeafNodes(descr_str, context_node, dbg_loc):
cat_name, cat_ptkns, leaf_ptkns = DescrToCatLeafPtkns(descr_str, dbg_loc)
cat_node = PtknsToNode(cat_ptkns, context_node, dbg_loc)
if len(cat_ptkns) > 0:
leaf_node = PtknsToNode(leaf_ptkns, cat_node, dbg_loc)
else:
leaf_node = PtknsToNode(leaf_ptkns, context_node, dbg_loc)
return cat_name, cat_node, leaf_node
(This version works, but it does not handle "..." corectly,
and it does not create missing nodes when needed.)
-- Here is a (probably unnecessary) review of terminology: --
Descriptor String:
The first argument ("descr_str") is a descriptor string.
A descriptor string typically contains ":" and "/"
characters to to divide the string into pieces in order
to identify a category name, category node, and leaf node.
Conceptually, the variable's NAME is the leaf node.
The variable's TYPE is the category (node and name).
Node:
Nodes are used to represent both class objects and variable names
1) class objects
Each type of class objects is represented by an StaticObj.
Each instantiated object is represented by an InstanceObj.
2) variable names (leaf nodes)
However variable names are also represented using either
StaticObjs (for @ static variables) or
InstanceObjs (for $ instance variables)
Again, all variables in ttree are members of a class object.
In this case, the name of the node corresponds to the variable's
name, and it's position in the tree refers to the class to which
it belongs.
However "leaf nodes" do not uniquely identify the
actual variable itself. A single node can refer to two different
variables if they are in different categories.
All 3 identifiers (leaf node, category node, category name)
are needed to uniquely identify a ttree variable. See below.
Ptkn (Path Token)
Strings containing multiple '/' characters are typically used
to identify the location of the category and leaf nodes in the
tree (ie the path to the node). The '/' characters are
delimiters which break up the string into small pieces, (which
are usually the names of classes).
These pieces are called "path tokens" or "ptkns"
Leaf Node:
It exists as a node in a tree (instead of a simple string)
because, just like member variables in a class in an
object oriented programming language (or in a C struct)
language, variables in ttree belong to the class in
which they are defined. The node's location in the
tree represents which class it belongs to.
If a variable's leaf node name
refers to a node which does no exist yet, then we create it
(assuming the "create_missing_nodes" argument is "True").
Category Node/Name:
Categories are a peculiar feature of ttree. Categories
are groups of variables that share the same counter when
numeric values are automatically given to each variable.
So you can think of a category as a counter with a name.
Variables in different categories have different counters,
and are assigned numeric values independently.
Consequently two variables in different categories
may be assigned the same number. But two variables
in the same category are always given unique values.
Counters are typically global, but can have local scope.
(ie, only defined within a Class, or an instantiated
class, and whatever other classes are nested or
instantiated beneath it.)
Therefore to identify a counter/category you must specify
both a name AND a node. The node identifies the class where
the scope is defined. It is assumed that the Leaf Node
(see above) lies within this scope (ie. somewhere after
it in the tree).
Example: local counters are used to keep track of the
residues within in a protein chain. If we use a class to
represent the protein, we can create a local residue-
counter (category) within that protein. Then when we
instantiate the protein multiple times, this counter
is reset for every new instance of of the protein.
"""
cat_name, cat_ptkns, leaf_ptkns = DescrToCatLeafPtkns(descr_str, dbg_loc)
# ---- ellipsis hack ----
#
# Search for class:
# Most users expect ttree.py to behave like a
# standard programming language: If the class they are
# instantiating was not defined in this specific
# location, they expect ttree.py to search for
# it outwards, first in the parent's environment,
# and then in the parent's parent's environment,
# and so on, until the object is found.
# For example, most users expect this to work:
# class Res{
# write("Atoms") {
# $atom:CA @atom:CA 0.123 1.234 2.345
# $atom:CB @atom:CB 1.234 2.345 3.456
# }
# }
# class Protein{
# write_once("AnglesByType") {
# @angle:backbone @atom:Res/CA @atom:Res/CA @atom:Res/CA
# }
# Notice that in class Protein, we did not have to specify
# where "Res" was defined because it is defined in the parent
# environment (ie. immediately outside Proteins's environment).
# The general way to do this in ttree.py, is to
# use ellipsis syntax "@atom:.../Res/CA" symbol. The
# ellipsis ".../" tells ttree.py to search upwards
# for the object to the right of it ("Res")
# In order to make ttree.py behave the way
# most users are expecting, we artificially insert a
# ".../" before the class name here. (Later on, the
# code that processes the ".../" symbol will take
# care of finding A. We don't have to worry about
# about doing that now.)
#
# I think we only want to do this for variables with path information
# such as "@atom:Res/CA" (which means that leaf_ptkns = ['Res', 'CA']).
# For simple variables like "@atom:CA", we don't automatically look upwards
# unless the user eplicitly requests it.
# (That's why we check to make sure that len(leaf_ptkns) > 1 below
# before we insert '...' into the leaf_ptkns.)
# In other words, the two variables "@atom:CA" below are treated differently
#
# A {
# write("Atoms") {
# @atom:CA
# }
# class B {
# write("Atoms") {
# @atom:CA
# }
# }
# }
#
if ((descr_str.find(':') != -1) and
#(not ((len(leaf_ptkns) == 1) and
# (leaf_ptkns[0] == context_node.name))) and
#(len(leaf_ptkns) > 0) and
(len(leaf_ptkns) > 1) and
(len(leaf_ptkns[0]) > 0) and
(leaf_ptkns[0][0] not in ('.','*','?'))):
leaf_ptkns.insert(0, '...')
# ---- Done with "ellipsis hack" -----
#sys.stderr.write(' DescrToCatLeafNodes(): (cat_ptkns, cat_name, lptkns) = ('+
# str(cat_ptkns)+', \"'+cat_name+'\", '+str(leaf_ptkns)+')\n')
cat_node = None
cat_start_node = context_node
leaf_start_node = context_node
if (len(cat_ptkns) > 0):
if cat_ptkns[-1] == '...':
# The "..." in this position means trace the path from the
# current node (context_node) up to cat_ptkns[:-1].
cat_start_node = PtknsToNode(cat_ptkns[:-1], context_node, dbg_loc)
# Later on, we will search upwards until we find an ancestor
# node containing a category matching cat_name. This will
# be taken care of later. (See "if cat_node is None:" below.)
else:
# In this case, the user supplied an explicit path
# for the category node. Find it now.
cat_node = PtknsToNode(cat_ptkns, context_node, dbg_loc)
# Whenever the user supplies an explicit path, then
# the cat node should be the starting location from
# which the leaf path is interpreted. This nearly
# insures that the leaf node will be an ancestor
# of the category node, which is what we want.
leaf_start_node = cat_node
if cat_node is None:
# Otherwise, the user did not indicate where the category
# node is defined, but only supplied the category name.
# (This is the most common scenario.)
# In this case, climb up the tree to the parent
# until you find an ancestor with a category whose
# name matches cat_name.
cat_node = FindCatNode(cat_name, cat_start_node, dbg_loc)
if (cat_name not in cat_node.categories):
if create_missing_nodes:
# If this is the first time we encountered a variable in this
# category (ie if it's the first time we encountered a variable
# with this category's name and node), then we must create a
# new entry in the cat_node.categories associative container
# (using cat_name as the dictionary key).
cat_node.categories[cat_name] = Category(cat_name)
else:
raise InputError('Error('+g_module_name+'.DescrToCatLeafNodes()):\n'
' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
' Category named \"'+cat_name+'\" not found at\n'
' position '+NodeToStr(cat_node)+'\n')
# ---------- Now look up the leaf node -----------
if (len(leaf_ptkns) > 0) and (leaf_ptkns[-1] == 'query()'):
# Special case: "query()"
# Variables named "query()" are not really variables.
# (They are a way for users to query a category's counter.)
# But we treat them as such internally. Consequently we
# give them unique names to avoid clashes (just in case
# "query()" appears multiple times in the same context).
leaf_ptkns[-1] = '__query__'+str(dbg_loc.order)
# Lookup the path for the leaf:
#
# Often, the leaf that the path refers to does not
# exist yet. For example, it is common for a template to
# contain a reference to "$atom:CA". If the current context_node
# is "/protein1/res22", this means that the leaf should be
# at "/protein1/res22/CA". (However in this example, "CA"
# is not a class that has been defined yet. It is the name
# of a variable which which may not have even been mentioned
# before. Think of "CA" as a variable placeholder.
#
# So we follow the path tokens as far as we can:
i_last_ptkn, last_node = FollowPath(leaf_ptkns,
leaf_start_node,
dbg_loc)
# Did we find the node?
if i_last_ptkn == len(leaf_ptkns):
leaf_node = last_node
else:
# If we are here, then we did not find the node.
# The unrecognized token is stored in
# leaf_ptkns[i_last_ptkn]
if leaf_ptkns[i_last_ptkn] == '...':
# ----------------------------------------------
# ---- UGHH I hate dealing with '...' ----
# ----(Messy code to follow in this section)----
# ----------------------------------------------
# The "..." means different things depending on
# whether or not it is the last token in leaf_ptkns.
if i_last_ptkn+1 < len(leaf_ptkns):
# If "..." is NOT the last token in leaf_ptkns, we
# should search for an ancestor of this node who has
# a child whose name matches a the requested target
# string (located in leaf_ptkns[i_last_ptkn+1])
search_target = leaf_ptkns[i_last_ptkn+1]
# If such an ancestor exists, then FollowPath()
# should have already found it for us.
# This means it was not found.
# So if there is only one more token in the
# list of tokens, then create the needed node
if (create_missing_nodes and
(i_last_ptkn+1 == len(leaf_ptkns)-1)):
# Create a new leaf node and link it:
new_leaf_name = leaf_ptkns[-1]
parent_node = last_node
# Is this parent_node an StaticObj? (..or inherit from StaticObj?)
if isinstance(parent_node, StaticObj):
parent_node.children.append(StaticObj(new_leaf_name, parent_node))
elif isinstance(parent_node, InstanceObj):
parent_node.children.append(InstanceObjBasic(new_leaf_name, parent_node))
else:
assert(False) # (only 2 types of nodes are possible)
# Now assign the pointer
leaf_node = parent_node.children[-1]
else:
#In that case, we were unable to find the node referenced by "..."
raise InputError('Error('+g_module_name+'.DescrToCatLeafNodes()):\n'
' Broken path.\n' # containing ellipsis (...)\n'
' class/variable \"'+search_target+'\" not found in this\n'
' context: \"'
#+var_ref.prefix + var_ref.descr_str + var_ref.suffix+'\"\n'
+descr_str+'\"\n'
' located near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno))
else: # if i_last_ptkn+1 < len(leaf_ptkns):
# If "..." IS the last token, then it means:
# we want to search for the CATEGORY NAME,
# This is very different.
# It means we need to:
# search backwards up the ancestor tree until
# we find an ancestor variable (of last_node)
# which has the right category, (ie until you
# find an ancestor node with a variable (VarRef)
# pointing to it with belonging to the correct
# category node and name (determined above).)
# If not found, then use the current context_node.
assert(cat_name in cat_node.categories)
var_bindings = cat_node.categories[cat_name].bindings
node = last_node
while (node != None):
# Recall that cat_node.categories[cat_name]
# is a dictionary whose keys are leaf nodes
# corresponding to the variables in this category.
if node in var_bindings:
# then we found it, and we're done
break
else:
node = node.parent
if node != None:
leaf_node = node
else:
# If not found, have it point to the
# current (context) node.
leaf_node = context_node
# -----------------------------------------------
# -- Finished dealing with '...' in leaf_ptkns --
# -----------------------------------------------
elif (create_missing_nodes and
((i_last_ptkn == len(leaf_ptkns)-1) or
HasWildCard('/'.join(leaf_ptkns)))):
#elif (create_missing_nodes and
# (i_last_ptkn == len(leaf_ptkns)-1)):
# Again, another reason the leaf-node was not found is
# that it refers to a leaf node which has not yet been
# created. If the path was valid until up to the last
# token, then we sould create a new node with this name.
# -- This is a common scenario. --
# -- This is how all new variables are created. --
# Anyway, we handle that here:
# Create a new leaf node and link it:
new_leaf_name = leaf_ptkns[-1]
new_leaf_name = '/'.join(leaf_ptkns[i_last_ptkn:])
parent_node = last_node
# Is this parent_node an StaticObj? (..or does it inherit from StaticObj?)
if isinstance(parent_node, StaticObj):
parent_node.children.append(StaticObj(new_leaf_name, parent_node))
elif isinstance(parent_node, InstanceObj):
parent_node.children.append(InstanceObjBasic(new_leaf_name, parent_node))
else:
assert(False) # (only 2 types of nodes are possible)
# Now assign the pointer
leaf_node = parent_node.children[-1]
else:
# Otherwise, the user made a mistake in the path.
# Figure out which kind of mistake and print an error.
if (last_node.parent is None) and (leaf_ptkns[i_last_ptkn] == '..'):
#In that case, we tried to back out beyond the root of the tree.
raise InputError('Error('+g_module_name+'.DescrToCatLeafNodes()):\n'
' Broken path in variable:\n'
#' \"'+var_ref.prefix + var_ref.descr_str + var_ref.suffix+'\"\n'
' \"'+ descr_str + '\"\n'
' located near '+
ErrorLeader(dbg_loc.infile,
dbg_loc.lineno)+'\n'
' There are too many \"..\" tokens in the path string.')
else:
#Then the reason is: The string in leaf_ptkns[i_last_ptkn]
#was supposed to be a child of last_node but a child
#of that name was not found.
raise InputError('Error('+g_module_name+'.DescrToCatLeafNodes()):\n'
' Broken path / Undefined variable:\n'
#' \"'+var_ref.prefix + var_ref.descr_str + var_ref.suffix+'\"\n'
' \"'+ descr_str + '\"\n'
' located near '+
ErrorLeader(dbg_loc.infile,
dbg_loc.lineno)+'\n'
' Undefined: \"'+PtknsToStr(leaf_ptkns)+'\"\n'
' (Specifically \"'+leaf_ptkns[i_last_ptkn]+
'\" is not a subordinate of \"'+MaxLenStr(last_node.name,'/')+'\")')
#'\n This could be a typo or spelling error.')
return cat_name, cat_node, leaf_node
def DescrToVarBinding(descr_str, context_node, dbg_loc):
""" DescrToVarBinding() is identical to LookupVar(), but it has a name
that is harder to remember. See comment for LookupVar() below.
"""
cat_name, cat_node, leaf_node = DescrToCatLeafNodes(descr_str,
context_node,
dbg_loc)
if cat_name in cat_node.categories:
category = cat_node.categories[cat_name]
var_bindings = category.bindings
if leaf_node in var_bindings:
var_binding = var_bindings[leaf_node]
else:
raise InputError('Error('+g_module_name+'.DescrToVarBinding()):\n'
' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
' Bad variable reference: \"'+descr_str+'\". There is\n'
' There no category named \"'+cat_name+'\" defined for "'+NodeToStr(cat_node)+'\".\n')
else:
raise InputError('Error('+g_module_name+'.DescrToVarBinding()):\n'
' Error near '+ErrorLeader(dbg_loc.infile, dbg_loc.lineno)+'\n'
' Bad variable reference: \"'+descr_str+'\". There is\n'
' no category named \"'+cat_name+'\" defined for "'+NodeToStr(cat_node)+'\".\n')
return var_binding
# Wrappers:
def LookupVar(descr_str, context_node, dbg_loc):
""" LookupVar() looks up a string (a variable descriptor, which is the
variable's name, excluding the '$', '@' prefixes and any '{}' brackets.)
This function returns the variable's "VarBinding" (the variable-name:value
pair). This is useful for querying or changing the value of a variable.
Because nearly all variables are local, you must specify the starting
node (ie. the node corresponding to the class in which this class
or variable was referred to). This is typically the global node.
"""
return DescrToVarBinding(descr_str, context_node, dbg_loc)
def LookupNode(obj_name, starting_node, dbg_loc):
""" LookupNode() parses through a string like
'../ClassA/NestedClassB'
and returns the corresponding node.
Nodes are data types used for representing a class or class instance.
They are also used for storing variables.
'ClassA/NestedClassB/VariableC'
Because nearly all variables are local, you must specify the starting
node (ie. the node corresponding to the class in which this class
or variable was referred to). This is typically the global node.
"""
return StrToNode(obj_name, starting_node, dbg_loc)
class SimpleCounter(object):
__slots__=["n","nincr"]
def __init__(self, n0 = 1, nincr = 1):
self.n = n0 - nincr
self.nincr = nincr
def query(self):
return self.n
def incr(self):
self.n += self.nincr
def __copy__(self): #makes a (deep) copy of the counter in its current state
return SimpleCounter(self.n + self.nincr, self.nincr)
class Category(object):
"""
Category contains a list of all of the variables which belong
to the same category, as well as some supporting information.
Attributes:
name The name of the category (a string)
bindings An OrderedDict() containing leaf_node:VarBinding
(key:value) pairs. Variables are looked up by their leaf node.
The actual variable name (which simply refers to the leaf node)
and values are both stored in the VarBinding data structure.
counter A counter object like "SimpleCounter". Each time counter.incr()
is invoked it should return a unique string (typically this is
simply a string representing an integer which is incremented).
"""
__slots__=["name","bindings","counter","manual_assignments","reserved_values"]
def __init__(self,
name = '',
bindings = None,
counter = None,
manual_assignments = None,
reserved_values = None):
self.name = name
if bindings is None:
self.bindings = OrderedDict()
else:
self.bindings = bindings
if counter is None:
self.counter = SimpleCounter(1,1)
else:
self.counter = counter
if manual_assignments is None:
self.manual_assignments = OrderedDict()
else:
self.manual_assignments = manual_assignments
if reserved_values is None:
self.reserved_values = OrderedDict()
else:
self.reserved_values = reserved_values
class StaticObj(object):
""" StaticObjs and InstanceObjs:
The state of the system is stored in two different trees:
1) The static tree:
StaticObj trees are similar "class" definitions in an OOP language.
These trees contains class definitions, and their nested classes,
and instructions for how to create new instances (copies) of this class.
Nodes in this tree are stored using StaticObjs:
2) The instance tree:
This tree contains classes that have been instantiated, and any sub-
classes (members or attributes) that are instantiated as a result.
This tree is automatically generated by instantiating the root
StaticObj. Nodes in this tree are stored using InstanceObjs.
StaticObjs and InstanceObjs both contain
"commands" (commands which usually involve instructions
for writing templates)
"categories" (local counters used to assign variables. See below.)
"children" (branches in the tree. -Not- OOP class children. See below.)
StaticObjs also contain
"instance_commands"
"instance_categories"
These three members contain information to create a new instance/copy
of this class (how to construct an InstanceObj from an StaticObj).
StaticObj contains the member function Parse() which builds the global static
tree by parsing the contents of a text file supplied by the user.
The external function BuildInstanceTree(), creates the global instance tree
from the global static tree (a tree of StaticObjs).
----- CLASS MEMBERS OF StaticObj: ----
0) Name:
Every class (object type) has a name. It is stored in self.name.
To make it easier to distinguish the names of classes from the names of
individual instances of that class, I recommend using a capital letter
for the name of a class type (and lower-case letters for instances).
1) Commands
Commands are usually instructions for writing templates.
Templates are blocks of ordinary text which contain variables.
(Variables in this program consist of variable names, categories,
and (eventually) bound values (usually generated automatically),
which will be substituted into the template to generate a text file.)
A class can contain multiple templates, each one having a unique name
which also happens to be the name of the file that will be created when
the template is written.
Variants:
self.commands:
Some templates are written immediate after the class is defined
(stored in "self.commands").
Example: The "write_once()" command.
self.instance_commands:
Other templates are written when an instance/copy of the class is created
(stored in "self.instance_commands".
Example: The "write()" command.
2) Children
self.children:
Class definitions can be defined from within the definition of other
("parent") classes. These nested classes are referred to as "children".
These sub-classes are not "children" in the OOP sense of the word at
all (they do not have any of the the traits of their "parents").
However in the source code I refer to them as "children" because here
they are implemented as "child" nodes (branches) in the tree-like
data-structure used to store class definitions (the static tree).
3) Categories
This is a new concept and is difficult to explain.
Recall that each class contains a list of templates containing raw text,
interspersed with variables (whose values will determined later).
In most cases, variables are assigned to integer values which are
automatically generated by incrementing a counter. Simply put,
"categories" are collections of variables which share the same counter.
Within a category, the goal is to assign a unique integer (or other
symbol) to each distinct variable in this category.
To avoid name-clashes, variable names have local "scope".
This scope is the "leaf_token"
Categories can be specific to a particular class (node), and any of the
classes (nodes) which are nested within it, but by default are global.
(This means they "belong" to the global (outermost) node by default.)
All the various categories which are defined within a particular
StaticObj are stored in self.categories.
Static variables (ie. variables with a '@' prefix) are stored this way.
"self.categories"
If a class contains a new category, it means that if any nested
classes defined within that class definition contain (static, '@')
variables whose categories match the category name, their values will
be determined by looking up the couter associated with this category
stored locally (here) in self.categories. All variables belonging
to this category are stored in "self.categories[category_name]".
"self.instance_categories"
Recall that creating a new copy (instance) of a class automatically
creates an InstanceObj in the instance-tree. InstanceObj's have a
".categories" attribute of their own, the contents of which are
copied from this StaticObj's "self.instance_categories" attribute.
Instantiating a new class also spawns the instantiation of any
sub-classes.
If any of these "instance children" contain variables whose category
names match a category stored in the parent InstanceObj's .categories
dictionary, then their values will be determined by that InstanceObj's
counter for that category name.
4) Parent:
A link to the parent StaticObj is stored in self.parent.
"""
# sigh
__slots__=["name",
"parent",
"children",
"categories",
"commands",
"srcloc_begin",
"srcloc_end",
"deleted",
"class_parents",
"namespaces",
"instname_refs",
"instance_categories",
"instance_commands_push",
"instance_commands",
"instance_commands_pop"]
def __init__(self,
name='',
parent=None):
"""
The members/attributes of StaticObj are defined in the comment
for StaticObj above. """
# The following members are shared by both InstanceObj and StaticObj:
self.name = name
self.parent = parent #For traversing the global static template tree
self.children = [] # Nested class definitions.
self.categories=OrderedDict() #<- new variable categories that are only defined
# in the context of this molecule's type definition
self.commands=[] # Commands to carry out (only once)
##vb##self.var_bindings=[] # List of variables assigned to this object.
self.srcloc_begin = None # Keep track of location in user files
self.srcloc_end = None # (useful for error message reporting)
self.deleted = False # Users can delete static objects?
# (why not?)
# The following members are not shared with InstanceObj:
self.class_parents = [] # classes we inherit traits from (this is
# similar to the parent/child relationship
# in an object-oriented-programming language)
self.namespaces = [] # A list of classes we also look in when searching
# for other static nodes or variables. (similar to
# class_parents, but only used for searches.)
self.instname_refs = {} # <-- used for debugging to insure that
# two instances do not have the same name
self.instance_categories=OrderedDict()#<-new variable categories that are defined
#within the scope of this molecule's instance
self.instance_commands_push=[] #1)process these commands first by adding
# these commands to InstanceObj.commands
# (before you deal with class_parents)
self.instance_commands=[] #2) then add this to InstanceObj.commands
self.instance_commands_pop=[] #3) finally add these commands
def DeleteSelf(self):
self.deleted = True
def IsDeleted(self):
return self.deleted
##vb##def AddVarBinding(self, var_binding):
##vb## if self.var_bindings is None:
##vb## self.var_bindings = [var_binding]
##vb## else:
##vb## self.var_bindings.append(var_binding)
def Parse(self, lex):
""" Parse() builds a static tree of StaticObjs by parsing text file.
-The "lex" argument is a file or input stream which has been converted
to a "TemplateLexer" object (similar to the python's built-in shlex lexer).
"""
#sys.stdout.write(' -- Parse() invoked --\n')
# Keep track of the location in the users' input files where this
# class object is first defined. (Keep in mind that the user might
# augment their original class definition, adding new content to an
# existing class. In that case self.srcloc_begin will have already
# been assigned. We don't want to overwrite it in that case.)
if self.srcloc_begin is None: # <-- not defined yet?
self.srcloc_begin = lex.GetSrcLoc()
while True:
cmd_token = lex.get_token()
#print('Parse(): token = \"'+cmd_token+'\", '+lex.error_leader())
if cmd_token == lex.eof:
#print('Parse(): EOF encountered\n')
break
if ((cmd_token == 'write') or
(cmd_token == 'write_once') or
(cmd_token == 'create_var') or
(cmd_token == 'create_vars')):
open_paren = lex.get_token()
#print('Parse(): open_paren=\"'+open_paren+'\"')
if open_paren=='{':
# ..then the user neglected to specify the "dest" file-name
# argument. In that case, supply the default, ''.
# (which is shorthand for the standard out in this case)
open_curly = open_paren[0]
open_paren = ''
close_paren = ''
tmpl_filename = ''
srcloc = lex.GetSrcLoc()
else:
tmpl_filename = lex.get_token()
if tmpl_filename == ')':
tmpl_filename = ''
close_paren = ')'
else:
close_paren = lex.get_token()
open_curly = lex.get_token()
srcloc = lex.GetSrcLoc()
if ((cmd_token == 'create_var') or
(cmd_token == 'create_vars')):
tmpl_filename = None
# This means: define the template without attaching
# a file name to it. (IE., don't write the contents
# of what's enclosed in the curly brackets { } to a file.)
if ((open_curly != '{') or
((open_paren == '') and (close_paren != '')) or
((open_paren == '(') and (close_paren != ')'))):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error in '+lex.error_leader()+'\n\n'
'Syntax error at the beginning of the \"'+cmd_token+'\" command.')
if tmpl_filename != None:
tmpl_filename = RemoveOuterQuotes(tmpl_filename, lex.quotes)
# ( The previous line is similar to:
# tmpl_filename = tmpl_filename.strip(lex.quotes) )
tmpl_contents = lex.ReadTemplate()
StaticObj.CleanupReadTemplate(tmpl_contents, lex)
#sys.stdout.write(' Parse() after ReadTemplate, tokens:\n\n')
#print(tmpl_contents)
#sys.stdout.write('\n----------------\n')
if cmd_token == 'write_once':
# Check for a particular bug:
# Ordinary instance variables (preceded by a '$')
# should never appear in a write_once() statement.
for entry in tmpl_contents:
if (isinstance(entry, VarRef) and
(entry.prefix[0]=='$')):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+ErrorLeader(entry.srcloc.infile,
entry.srcloc.lineno)+'\n'
' Illegal variable: \"'+entry.prefix+entry.descr_str+entry.suffix+'\"\n'
' All variables in a \"write_once()\" statement must be statically\n'
' defined, and hence they must begin with a \'@\' prefix character.\n'
' (not a \'$\' character).\n'
' Suggestion: Use the \"write()\" command instead.\n')
if cmd_token == 'write':
commands = self.instance_commands
elif cmd_token == 'write_once':
commands = self.commands
elif ((cmd_token == 'create_var') or
(cmd_token == 'create_vars')):
commands = self.instance_commands
else:
assert(False)
command = WriteFileCommand(tmpl_filename,
tmpl_contents,
srcloc)
commands.append(command)
# end of "if (cmd_token == 'write') or (cmd_token == 'write_once'):"
elif cmd_token == 'delete':
instobj_descr_str = lex.get_token()
instobj_srcloc = lex.GetSrcLoc()
delete_command = DeleteCommand(instobj_srcloc)
mod_command = ModCommand(delete_command,
instobj_descr_str)
self.instance_commands.append(mod_command)
elif cmd_token == 'using':
namespacecom_str = lex.get_token()
if namespacecom_str != 'namespace':
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' The \"'+cmd_token+'\" command must be followed by the \"namespace\" keyword.')
namespace_str = lex.get_token()
stnode = StrToNode(namespace_str,
self,
lex.GetSrcLoc())
self.namespaces.append(stnode)
elif cmd_token == 'category':
cat_name = lex.get_token()
cat_count_start = 1
cat_count_incr = 1
open_paren = lex.get_token()
if (open_paren == '('):
token = lex.get_token()
if token == ',':
token = lex.get_token()
if token != ')':
# Interpret token as an integer, float, or string
try:
cat_count_start = int(token)
except ValueError:
try:
cat_count_start = float(token)
except ValueError:
cat_count_start = RemoveOuterQuotes(token, '\'\"')
token = lex.get_token()
if token == ',':
token = lex.get_token()
if token != ')':
# Interpret token as an integer,float,or string
try:
cat_count_incr = int(token)
except ValueError:
try:
cat_count_incr = float(token)
except ValueError:
cat_count_incr = RemoveOuterQuotes(token, '\'\"')
token = lex.get_token()
if token != ')':
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' \"'+cmd_token+' '+cat_name+'...\" has too many arguments,\n'
' or lacks a close-paren \')\'.\n')
else:
lex.push_token(open_paren)
if (isinstance(cat_count_start, basestring) or
isinstance(cat_count_incr, basestring)):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' \"'+cmd_token+' '+cat_name+'('+
str(cat_count_start)+','+
str(cat_count_incr)+')\"\n'
' Only numeric counters are currently supported.\n')
# check for really stupid and unlikely errors:
if type(cat_count_start) is not type(cat_count_incr):
if ((isinstance(cat_count_start, int) or
isinstance(cat_count_start, float))
and
(isinstance(cat_count_incr, int) or
isinstance(cat_count_incr, float))):
cat_count_start = float(cat_count_start)
cat_count_incr = float(cat_count_incr)
else:
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' Problem with \"'+cmd_token+'\" command.\n')
prefix = cat_name[0]
cat_name = cat_name[1:]
# Add this category to the list.
if prefix == '@':
self.categories[cat_name] = Category(cat_name)
self.categories[cat_name].counter=SimpleCounter(cat_count_start,
cat_count_incr)
elif prefix == '$':
self.instance_categories[cat_name] = Category(cat_name)
self.instance_categories[cat_name].counter=SimpleCounter(cat_count_start,
cat_count_incr)
else:
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' category name = \"'+cat_name+'\" lacks a \'$\' or \'&\' prefix.\n'
' This one-character prefix indicates whether the variables in this\n'
' new category will be static or dynamics variables\n')
elif (cmd_token == '}') or (cmd_token == ''):
# a '}' character means we have reached the end of our scope.
# Stop parsing and let the caller deal with the remaining text.
# (And a '' means we reached the end of the file... I think.)
break
#elif (cmd_token == 'include'):
# "include filename" loads a file (adds it to the file stack)
# The "TtreeShlex" class (from which "lex" inherits) handles
# "include" statements (ie. "source" statements) automatically.
else:
# Otherwise, 'cmd_token' is not a command at all.
# Instead it's the name of an object which needs to be
# defined or instantiated.
# First, let's figure out which.
# (small detail: The "class" keyword is optional
# and can be skipped.)
if cmd_token == 'class':
object_name = lex.get_token()
else:
object_name = cmd_token
next_symbol = lex.get_token()
#print('Parse(): next_token=\"'+next_symbol+'\"')
class_parents = []
if next_symbol == 'inherits':
# Then read in the list of classes which are parents of
# of this class. (Multiple inheritance is allowed.)
# (We don't yet check to insure that these are valid class
# names. We'll do this later in LookupStaticRefs().)
syntax_err_inherits = False
while True:
next_symbol = lex.get_token()
if ((next_symbol == '{') or
(next_symbol == lex.eof)):
break
elif (next_symbol == '='):
syntax_err_inherits = True
break
else:
class_parents.append(StrToNode(next_symbol,
self,
lex.GetSrcLoc()))
if len(class_parents) == 0:
syntax_err_inherits = True
if syntax_err_inherits:
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' \"inherits\" should be followed by one or more class names.\n')
if next_symbol == '{':
child_name = object_name
# Check to see if this class has already been defined.
# (IE. check if it present in the list of children.)
# If the name (child_name) matches another class (child),
# then the contents of the new class will be appended to
# the old. This way, class definitions can be augmented
# later. (This is the way "namespaces" work in C++.)
child = None
for child in self.children:
if child.name == child_name:
break
# If found, we refer to it as "child".
# If not, then we create a new StaticObj named "child".
if (child is None) or (child.name != child_name):
child = StaticObj(child_name, self)
self.children.append(child)
assert(child in self.children)
# Either way we invoke child.Parse(), to
# add contents (class commands) to child.
child.Parse(lex)
child.class_parents += class_parents
elif next_symbol == '=':
next_symbol = lex.get_token()
if next_symbol == 'new':
base_name = object_name
base_srcloc = lex.GetSrcLoc()
if base_name.find('/') != -1:
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+ErrorLeader(base_srcloc.infile,
base_srcloc.lineno)+'\n'
' (You can not instantiate some other class\'s members.)\n'
' Invalid instance name: \"'+base_name+'\"\n')
elif base_name in self.instname_refs:
ref_srcloc = self.instname_refs[base_name]
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Duplicate class/array \"'+base_name+'\"\n'
' This occurs near:\n'
' '+ErrorLeader(ref_srcloc.infile,
ref_srcloc.lineno)+'\n'
' and also near:\n'
' '+ErrorLeader(base_srcloc.infile,
base_srcloc.lineno)+'\n')
else:
self.instname_refs[base_name] = base_srcloc
# If the statobj_str token contains a ']' character
# then this means the user wants us to make multiple
# copies of this template. The number of copies
# to instantiate is enclosed in the [] characters
# (Example wat = new Water[3000] creates
# 3000 instantiations of the Water template
# named wat[1], wat[2], wat[3], ... wat[3000]).
# Note: Here '[' and ']' have a special meaning.
# So lex.get_token() should not treat them as
# ordinary word characters. To prevent this:
orig_wordterminators = lex.wordterminators
lex.wordterminators += '[],'
class_name_str = lex.get_token()
if ((class_name_str == lex.eof) or
(class_name_str == '}')):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
'Class ends prematurely. (Incomplete \"new\" statement.)')
assert(len(class_name_str) > 0)
if (class_name_str[0] == '['):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' new'+class_name_str+'\n'
'Bracketed number should be preceeded by a class name.')
class_names = []
weights = []
if class_name_str == 'random':
class_names, weights = self._ParseRandom(lex)
tmp_token = lex.get_token()
if len(tmp_token)>0:
if tmp_token[0]=='.':
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' \"'+tmp_token+'\" should not follow random()\n'
'\n'
' Coordinate transformations and other commands (such as \"'+tmp_token+'\")\n'
' should appear after each class name inside the random() statement,\n'
' not after it. For example, do not use:\n'
' \"lipids=new random([DPPC,DLPC],[0.5,0.5]).move(0,0,23.6)\"\n'
' Use this instead:\n'
' \"lipids=new random([DPPC.move(0,0,23.6),DLPC.move(0,0,23.6)],[0.5,0.5])\"\n')
lex.push_token(tmp_token)
else:
class_name, class_suffix, class_suffix_srcloc = \
self._ProcessClassName(class_name_str, lex)
array_size = []
array_suffixes = []
array_srclocs = []
# A general "new" statement could look like this:
# "m = new Mol.scale(3) [2].trans(0,4.5,0).rotate(30,0,0,1)
# [3].trans(0,0,4.5)"
# So far we have processed "m = new Mol.scale(3)".
# Now, we need to deal with:
# "[2].trans(0,4.5,0).rotate(30,0,0,1) [3].trans(0,0,4.5)"
while True:
new_token = lex.get_token()
#if ((new_token == '') or (new_token == lex.eof)):
# break
if new_token == '[':
number_str = lex.get_token()
close_bracket = lex.get_token()
if ((not str.isdigit(number_str)) or
(close_bracket != ']')):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error in new statement near '+lex.error_leader()+'\n'
' A \'[\' character should be followed by a number and a \']\' character.')
array_size.append(int(number_str))
suffix = lex.get_token()
if ((suffix == '') or (suffix == lex.eof)):
array_suffixes.append('')
array_srclocs.append(base_srcloc)
break
if suffix[0] == '.':
lex.push_token(suffix[1:])
suffix_func = lex.GetParenExpr()
suffix = '.' + suffix_func
array_suffixes.append(suffix)
array_srclocs.append(lex.GetSrcLoc())
else:
array_suffixes.append('')
array_srclocs.append(base_srcloc)
lex.push_token(suffix)
if suffix != '[':
break
else:
lex.push_token(new_token)
break
srcloc_final = lex.GetSrcLoc()
lex.wordterminators = orig_wordterminators
assert(len(array_size) == len(array_suffixes))
# If the user wants us to instantiate a
# multidimensional array of class instances
# then we must loop through this multidimensional
# array and create a new instance for each entry.
# For example fill a 3 dimensional volume
# with 1000 water molecules
# Example 1:
# solvent = new Water [10][10][10]
# (The coordinates must be read separately.)
# In this example array_size = [10,10,10]
# array_suffixes = ['','','']
# Example 2:
# solvent = new Water.transcm(0,0,0)
# [10].trans(0,0,4)
# [10].trans(0,4,0).rot(45,0,0,1)
# [10].trans(4,0,0)
# (This command generates a 10x10x10 lattice
# simple cubic lattice of regularly spaced
# water molecules pointing the same direction.)
# In this example array_size = [10,10,10]
# and
# class_suffix = 'transcm(0,0,0)'
# and
# array_suffixes = ['trans(0,0,4)',
# 'trans(0,4,0).rot(45,0,0,1)',
# 'trans(4,0,0)']
# Note that tree ignores the "trans()"
# commands, it stores them so that inherited
# classes can attempt to process them.
D = len(array_size)
if D > 0:
digits = [0 for d in range(0, D)]
table_filled = False
pushed_commands = []
while (not table_filled):
instance_name = base_name
for d in range(0, D):
i = digits[d]
instance_name += '['+str(i)+']'
# Does the user want us to select
# a class at random?
if len(class_names) > 0:
class_name_str = RandomSelect(class_names,
weights)
class_name, class_suffix, class_suffix_srcloc= \
self._ProcessClassName(class_name_str, lex)
if class_suffix != '':
class_suffix_command = \
PushRightCommand(class_suffix.lstrip('.'),
class_suffix_srcloc)
self.instance_commands.append(class_suffix_command)
command = \
InstantiateCommand(instance_name,
ClassReference(class_name,
base_srcloc),
base_srcloc)
self.instance_commands.append(command)
if class_suffix != '':
command = \
PopRightCommand(class_suffix_command,
srcloc_final)
self.instance_commands.append(command)
# Now go to the next entry in the table.
# The indices of this table are similar to
# a D-digit integer. We increment this d-digit number now.
d_carry = D-1
while True:
digits[d_carry] += 1
if digits[d_carry] >= array_size[d_carry]:
digits[d_carry] = 0
if array_suffixes[d_carry] != '':
for i in range(0, array_size[d_carry]-1):
partner = pushed_commands.pop()
command = PopRightCommand(partner,
srcloc_final)
self.instance_commands.append(command)
d_carry -= 1
else:
if array_suffixes[d_carry] != '':
command = PushRightCommand(array_suffixes[d_carry].lstrip('.'),
array_srclocs[d_carry])
pushed_commands.append(command)
self.instance_commands.append(command)
break
if d_carry < 0:
table_filled = True
break
pass
else:
if len(class_names) > 0:
class_name_str = RandomSelect(class_names,
weights)
class_name, class_suffix, class_suffix_srcloc= \
self._ProcessClassName(class_name_str, lex)
if class_suffix != '':
class_suffix_command = \
PushRightCommand(class_suffix.lstrip('.'),
class_suffix_srcloc)
self.instance_commands.append(class_suffix_command)
command = \
InstantiateCommand(base_name,
ClassReference(class_name,
base_srcloc),
base_srcloc)
self.instance_commands.append(command)
if class_suffix != '':
command = \
PopRightCommand(class_suffix_command,
srcloc_final)
self.instance_commands.append(command)
else:
# Now check for commands using this syntax:
#
# "MolNew = MolOld.rot(45,1,0,0).scale(100.0)"
# /|\ /|\ `-----------.------------'
# | | |
# child_name parent_name optional suffix
child_name = object_name
parent_name_str = next_symbol
child = StaticObj(child_name, self)
parent_name, suffix, suffix_srcloc = \
self._ProcessClassName(parent_name_str, lex)
child.class_parents.append(StrToNode(parent_name,
self,
lex.GetSrcLoc()))
if suffix != '':
# Assume the command is a StackableCommand. (This
# way it will enclose the commands of the parents.)
# Stackable commands come in (Push...Pop) pairs.
push_command = PushLeftCommand(suffix,
suffix_srcloc)
pop_command = PopLeftCommand(push_command,
suffix_srcloc)
push_mod_command = ModCommand(push_command, './')
pop_mod_command = ModCommand(pop_command, './')
child.instance_commands_push.append(push_mod_command)
child.instance_commands_pop.insert(0,pop_mod_command)
#sys.stderr.write('child.instance_commands_push = '+str(child.instance_commands_push)+'\n')
#sys.stderr.write('child.instance_commands_pop = '+str(child.instance_commands_pop)+'\n')
# Check to see if this class has already been defined.
# (IE. check if it present in the list of children.)
for i in range(0, len(self.children)):
if self.children[i].name == child_name:
if self.children[i].IsDeleted():
del self.children[i]
else:
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' The name \"'+child_name+'\" is already in use.')
self.children.append(child)
else:
# Otherwise hopefully this is a post-instance command
# (a command applied to a class which has been instantiated)
# In that case, the object_name would be followed by
# a dot and a function-call containing a '(' paren (which
# would have ended up stored in the next_symbol variable).
open_paren_encountered = False
if (next_symbol == '('):
open_paren_encountered = True
lex.push_token(next_symbol) #put '(' back in the stream
i_dot = object_name.rfind('.')
i_slash = object_name.rfind('/')
dot_encountered = ((i_dot != -1) and
((i_slash == -1) or (i_slash < i_dot)))
if (open_paren_encountered and dot_encountered and
(object_name[:1] != '[')):
obj_descr_str, suffix, suffix_srcloc = \
self._ExtractSuffix(object_name, lex)
path_tokens = obj_descr_str.split('/')
i_last_ptkn, staticobj = FollowPath(path_tokens,
self,
lex.GetSrcLoc())
instobj_descr_str = './'+'/'.join(path_tokens[i_last_ptkn:])
# I still support the "object_name.delete()" syntax for
# backwards compatibility. (However newer input files
# use this equivalent syntax: "delete object_name")
if suffix == 'delete()':
delete_command = DeleteCommand(suffix_srcloc)
mod_command = ModCommand(delete_command,
instobj_descr_str)
staticobj.instance_commands.append(mod_command)
else:
push_command = PushLeftCommand(suffix,
suffix_srcloc,
'.')
pop_command = PopLeftCommand(push_command,
suffix_srcloc,
'.')
push_mod_command = ModCommand(push_command,
instobj_descr_str)
pop_mod_command = ModCommand(pop_command,
instobj_descr_str)
if instobj_descr_str != './':
#sys.stderr.write('DEBUG: Adding '+str(push_command)+' to '+
# staticobj.name+'.instance_commands\n')
staticobj.instance_commands.append(push_mod_command)
staticobj.instance_commands.append(pop_mod_command)
else:
#sys.stderr.write('DEBUG: Adding '+str(push_command)+' to '+
# staticobj.name+'.instance_commands_push\n')
# CONTINUEHERE: should I make these PushRight commands and
# append them in the opposite order?
# If so I also have to worry about the case above.
staticobj.instance_commands_push.append(push_mod_command)
staticobj.instance_commands_pop.insert(0,pop_mod_command)
else:
# Otherwise, the cmd_token is not any of these:
# "write", "write_once", "create_vars"
# "delete", or "category".
# ... and it is ALSO not any of these:
# the name of a class (StaticObj), or
# the name of an instance (InstanceObj)
# followed by either a '.' or "= new"
#
# In that case, it is a syntax error:
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Syntax error at or before '+lex.error_leader()+'\n'
' \"'+object_name+' '+next_symbol+'\".')
# Keep track of the location in the user's input files
# where the definition of this object ends.
self.srcloc_end = lex.GetSrcLoc()
@staticmethod
def CleanupReadTemplate(tmpl_contents, lex):
#1) Remove any newlines at the beginning of the first text block
# in tmpl_content.(Sometimes they cause ugly extra blank lines)
assert(len(tmpl_contents) > 0)
if isinstance(tmpl_contents[0], TextBlock):
first_token_strip = tmpl_contents[0].text.lstrip(' ')
if ((len(first_token_strip) > 0) and
(first_token_strip[0] in lex.newline)):
tmpl_contents[0].text = first_token_strip[1:]
tmpl_contents[0].srcloc.lineno += 1
#2) Remove any trailing '}' characters, and complain if absent.
# The last token
assert(isinstance(tmpl_contents[-1], TextBlock))
assert(tmpl_contents[-1].text in ['}',''])
if tmpl_contents[-1].text == '}':
del tmpl_contents[-1]
else:
tmpl_begin = None
if isinstance(tmpl_contents[0], TextBlock):
tmpl_begin = tmpl_contents[0].srcloc
elif isinstance(tmpl_contents[0], VarRef):
tmpl_begin = tmpl_contents[0].srcloc
else:
assert(False)
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n\n'
' Premature end to template.\n'
'(Missing terminator character, usually a \'}\'.) The\n'
'incomplete template begins near '+ErrorLeader(tmpl_begin.infile, tmpl_begin.lineno)+'\n')
#3) Finally, if there is nothing but whitespace between the
# last newline and the end, then strip that off too.
if isinstance(tmpl_contents[-1], TextBlock):
i = len(tmpl_contents[-1].text)-1
if i >= 0:
while ((i >= 0) and
(tmpl_contents[-1].text[i] in lex.whitespace) and
(tmpl_contents[-1].text[i] not in lex.newline)):
i -= 1
if (tmpl_contents[-1].text[i] in lex.newline):
tmpl_contents[-1].text = tmpl_contents[-1].text[0:i+1]
def LookupStaticRefs(self):
""" Whenever the user requests to instantiate a new copy of a class,
the name of that class is stored in self.instance_commands.
This name is stored as a string. After all of the classes have been
defined, then we go back through the tree and replace these names
with pointers to actual StaticObjs which correspond to those classes.
(This was deferred until all of the classes have been defined so
that users can refer to classes that they will define later on.)
"""
# Now do the same for any children which
# are created during instantiation:
for command in self.instance_commands:
# Does this command create/instantiate a new copy of a class?
if isinstance(command, InstantiateCommand):
# If so, figure out which statobj is referred to by statobj_str.
assert(isinstance(command.class_ref.statobj_str, basestring))
command.class_ref.statobj = StrToNode(command.class_ref.statobj_str,
self,
command.class_ref.srcloc)
# Now recursively resolve StaticObj pointers for the "children"
# (in this case, "children" refers to classes whose definitions
# are nested within this one).
for child in self.children:
child.LookupStaticRefs()
def _ExtractSuffix(self, class_name_str, lex):
"""
This ugly function helps process "new" commands such as:
mola = new ForceFieldA/../MoleculeA.move(30,0,0).rot(45,0,0,1)
This function expects a string,
(such as "ForceFieldA/../MoleculeA.move(30,0,0).rot(45,0,0,1)")
It extracts the class name "ForceFieldA/../MoleculeA"
and suffix "move(30,0,0).rot(45,0,0,1)"
"""
# Dots in class names can appear for 2 reasons:
# 1) as part of a path like "../" describing the location
# where this class was defined relative to the caller.
# In that case it will be preceeded or followed by
# either another dot '.', or a slash '/'
# 2) as part of a "suffix" which appears after the name
# containing instructions which modify how to
# instantiate that class.
# Case 1 is handled elsewhere. Case 2 is handled here.
i_dot = 0
while i_dot < len(class_name_str):
i_dot = class_name_str.find('.', i_dot)
if i_dot == -1:
break
# Is the '.' character followed by another '.', as in ".."?
# If so, it's part of a path such as "../Parent/Mol', (if
# so, it's not what we're looking for, so keep searching)
if i_dot < len(class_name_str)-1:
if class_name_str[i_dot+1] == '.':
i_dot += 1
#otherwise, check to see if it is followed by a '/'?
elif class_name_str[i_dot+1] != '/':
# if not, then it must be part of a function name
break;
class_suffix = ''
class_name = class_name_str
class_suffix_srcloc = None
if ((i_dot != -1) and
(i_dot < len(class_name_str))):
class_suffix = class_name_str[i_dot:]
class_name = class_name_str[:i_dot]
if class_name_str[-1] != ')':
# If it does not already contains the parenthesis?
class_suffix += lex.GetParenExpr()
class_suffix_srcloc = lex.GetSrcLoc()
#sys.stderr.write(' splitting class name into class_name.suffix\n'
# ' class_name=\"'+class_name+'\"\n'
# ' suffix=\"'+class_suffix+'\"\n')
return class_name, class_suffix.lstrip('.'), class_suffix_srcloc
def _ProcessClassName(self, class_name_str, lex):
"""
This function does some additional
processing (occasionaly inserting "..." before class_name).
"""
class_name, class_suffix, class_suffix_srcloc = \
self._ExtractSuffix(class_name_str, lex)
# ---- ellipsis hack ----
# (Note-to-self 2012-4-15)
# Most users expect ttree.py to behave like a
# standard programming language: If the class they are
# instantiating was not defined in this specific
# location, they expect ttree.py to search for
# it outwards, first in the parent's environment,
# and then in the parent's parent's environment,
# and so on, until the object is found.
# For example, most users expect this to work:
# class A{
# <definition_of_a_goes_here...>
# }
# class B{
# a = new A
# }
# Notice in the example above we did not have to specify where "A"
# was defined, because it is defined in the parent's
# environment (ie. immediately outside B's environment).
#
# One can obtain the equivalent behavior in ttree.py
# using ellipsis syntax: "a = new .../A" symbol.
# The ellipsis ".../" tells ttree.py to search upwards
# for the object to the right of it ("A")
# In order to make ttree.py behave the way
# most users are expecting, we artificially insert a
# ".../" before the class name here. (Later on, the
# code that processes the ".../" symbol will take
# care of finding A.)
if (len(class_name)>0) and (class_name[0] not in ('.','/','*','?')):
class_name = '.../' + class_name
return class_name, class_suffix, class_suffix_srcloc
def _ParseRandom(self, lex):
bracket1 = lex.get_token()
bracket2 = lex.get_token()
if ((bracket1 != '(') and (bracket1 != '[')):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
'Expected a \"([\" following '+class_name+'.')
class_names = []
token = ''
prev_token = '['
while True:
token = lex.get_token()
if (token == '('):
lex.push_token(token)
token = lex.GetParenExpr()
if (prev_token not in (',','[','(')):
assert(len(class_names) > 0)
class_names[-1] = prev_token + token
prev_token = prev_token + token
else:
class_names.append(token)
prev_token = token
else:
if ((token == ']') or
(token == lex.eof) or
(token == '}') or
((token in lex.wordterminators) and
(token != ','))):
if (prev_token in (',','[','(')):
class_names.append('')
break
if token != ',':
class_names.append(token)
elif (prev_token in (',','[','(')):
class_names.append('')
prev_token = token
token_comma = lex.get_token()
bracket1 = lex.get_token()
if ((token != ']') or
(token_comma != ',') or
(bracket1 != '[')):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
'Expected a list of class names enclosed in [] brackets, followed by\n'
'a comma, and then a list of probabilities also enclosed in [] brackets.\n'
'(A random-seed following another comma is optional.)')
weights = []
while True:
token = lex.get_token()
if ((token == ']') or
(token == lex.eof) or
(token == '}') or
((token in lex.wordterminators) and
(token != ','))):
break
if token != ',':
try:
weight = float(token)
except ValueError:
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' \"'+token+'\"\n'
'Expected a list of numbers enclosed in [] brackets.')
if (weight < 0.0):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' Negative numbers are not allowed in \"random(\" argument list.\n')
weights.append(weight)
bracket2 = lex.get_token()
if ((token != ']') or
(bracket2 not in (')',','))):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
'Expected a \")\" or a \",\" following the list of numeric weights.')
if len(class_names) != len(weights):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
'Unequal number of entries in object list and probability list.\n')
tot_weight = sum(weights)
if (tot_weight <= 0.0):
if (weight < 0.0):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' The numbers in the \"random(\" argument list can not all be zero.\n')
for i in range(0,len(weights)):
weights[i] /= tot_weight
if bracket2 == ',':
try:
token = lex.get_token()
seed = int(token)
random.seed(seed)
except ValueError:
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' \"'+token+'\"\n'
'Expected an integer (a seed) following the list of weights.')
bracket2 = lex.get_token()
if (bracket2 != ')'):
raise InputError('Error('+g_module_name+'.StaticObj.Parse()):\n'
' Error near '+lex.error_leader()+'\n'
' \"'+token+'\"\n'
'Expected a \")\".')
else:
random.seed()
return (class_names, weights)
def BuildCommandList(self, command_list):
"""
Search the commands in the tree and make a linear list of commands
in the order they should be carried out.
"""
if self.IsDeleted():
return
# Add a special note to the list of commands to indicate which object
# the commands refer to. (This might be useful one day.)
# Later we can loop through this command list and still be able to tell
# whether or not we are within the scope of a particular class or instance
# (by seeing if we are between a "ScopeBegin" and "ScopeEnd" pair).
command_list.append(ScopeBegin(self, self.srcloc_begin))
# We want to append commands to the command_list in the same order
# that these commands appear in the user's input files.
# Unfortunately the commands may be interspersed with the creation of
# new StaticObjs which have their own commands which we have to explore
# recursively.
# Fortunately each child (StaticObj) has a srcloc_begin member, so we
# can infer the correct order of all the commands belonging to the
# children and correctly insert them into the correct place in between
# the commands of the parent.
srcloc2command_or_child = {}
for command in self.commands:
srcloc2command_or_child[command.srcloc] = command
for child in self.children:
srcloc = child.srcloc_begin
# special case: Some children do not have a srcloc because
# they were generated automatically. These children should
# not have any commands either so we can ignore them.
if srcloc != None:
srcloc2command_or_child[srcloc] = child
else:
assert(len(child.commands) == 0)
for srcloc in sorted(srcloc2command_or_child.keys()):
entry = srcloc2command_or_child[srcloc]
if isinstance(entry, StaticObj):
child = entry
child_commands = []
child.BuildCommandList(child_commands)
command_list += child_commands
else:
command_list.append(entry)
command_list.append(ScopeEnd(self, self.srcloc_end))
def __str__(self):
out_str = self.name
if len(self.children) > 0:
out_str += '('
for i in range(0,len(self.children)):
if i+1 < len(self.children):
out_str += str(self.children[i])+', '
else:
out_str += str(self.children[i])+')'
return out_str
def RandomSelect(entries, weights):
""" Return an entry from a list at random using
a (normalized) list of probabilities. """
assert(len(entries) == len(weights))
x = random.random()
i = 0
tot_probability = 0.0
while i < len(weights)-1:
tot_probability += weights[i]
if x <= tot_probability:
break
i += 1
return entries[i]
class InstanceObjBasic(object):
""" A simplified version of InstanceObj.
See the documentation/comments for InstanceObj for more details.
(Leaf nodes (variables) are typically stored as InstanceObjBasic objects
More general, non-leaf nodes are stored using InstanceObj objects.)
"""
__slots__=["name","parent"]
def __init__(self,
name = '',
parent = None):
self.parent = parent # the environment/object which created this object
# Example:
# Suppose this "molecule" is an amino acid monomer
# belonging to a protein. The "parent" refers to
# the InstanceObj for the protein. ".parent" is
# useful for traversing the global instance tree.
# (use InstanceObj.statobj.parent for
# traversing the global static tree)
self.name = name # A string uniquely identifying this object in
# in it's "parent" environment.
# (It is always the same for every instance
# of the parent object. It would save memory to
# get rid of this member. Andrew 2012/9/13)
##vb##self.var_bindings=None # List of variables assigned to this object
##vb## # or None (None takes up less space than an
##vb## # empty list.)
##vb##def AddVarBinding(self, var_binding):
##vb## if self.var_bindings is None:
##vb## self.var_bindings = [var_binding]
##vb## else:
##vb## self.var_bindings.append(var_binding)
def Dealloc(self):
pass
##vb##if self.var_bindings is None:
##vb## return
##vb##N = len(self.var_bindings)-1
##vb##for i in range(0,len(self.var_bindings)):
##vb## vb = self.var_bindings[N-i]
##vb## cat = vb.category
##vb## assert(self in cat.bindings)
##vb## del cat.bindings[self]
##vb## del self.var_bindings[N-i]
##vb##self.var_bindings = None
def DeleteSelf(self):
self.Dealloc()
self.parent = self # This condition (normally never true)
# flags the node as "deleted". (Nodes are never
# actually deleted, just flagged.)
# I used to have a separate boolean member variable
# which was set True when deleted, but I started
# eliminated unnecessary data members to save space.
def IsDeleted(self):
# Return true if self.parent == self
# for this node (or for any ancestor node).
node = self
while node.parent != None:
if node.parent == node:
return True
node = node.parent
return False
class InstanceObj(InstanceObjBasic):
""" InstanceObjs are used to store nodes in the global
"instance tree", the tree of all classes (molecules) which have
been instantiated. Recall that whenever a class is instantiated,
it's members will be instantiated as well. Since these
members can also be classes, this relationship is hierarchical,
and can be represented as a tree.
"InstanceObjs" are the data type used to store the nodes in that tree."""
__slots__=["statobj",
"children",
"categories",
"commands",
"commands_push",
"commands_pop",
"srcloc_begin",
"srcloc_end"]
def __init__(self,
name = '',
parent = None):
InstanceObjBasic.__init__(self, name, parent)
self.statobj = None # The statobj node refered to by this instance
self.children = [] # A list of statobjs corresponding to
# constituent parts (members) of the
# current class instance.
# The typical example is to consider the
# multiple amino acids (child-molecules)
# which must be created in order to create a
# new protein (instance) to which they belong
# (which would be "self" in this example)
self.categories = OrderedDict() # This member stores the same data as the
# Instance variables (ie. variables
# with a '$' prefix) are stored in a
# category belonging to node.categories
# where "node" is of type InstanceObj.
# (There is a long explanation of
# "categories" in the comments
# of class StaticObj.)
# always equal self.statobj.categories.
# It may seem redundant to make a
# new member to store the same data,
# but I do it because then the two
# types of trees (StaticObjs, InstanceObjs) have
# the same member names (although different
# connectivity). This way I can write
# simple functions (eg FindCatNode())
# which can traverse through either
# type of tree.
self.commands = [] # An ordered list of commands to carry out
# during instantiation
self.commands_push = [] # Stackable commands to carry out (first, before children)
self.commands_pop = [] # Stackable commands to carry out (last, after children)
self.srcloc_begin = None # Keep track of location in user files
self.srcloc_end = None # (useful for error message reporting)
def LookupMultiDescrStr(self,
multi_descr_str,
srcloc,
null_list_warning=False,
null_list_error=False):
"""
Post-Instance (PI) modifiers/commands are commands which modify
an instance of a class after it has already been instantiated.
Simple Example:
class A {
...
}
class B {
a = new A.command_1()
a.command_2()
}
In the example above "command_2()" is a ModCommand, and
"a" is the multi_descr_str (string describing the correspond InstanceObj).
The "command_2()" command will be retroactively pushed onto the
list of commands to execute once "a" is instantiated.
(This is somewhat counter-intuitive.)
When array brackets [] and wildcards are used, a single ModCommand
can modify many different instances, for example suppose:
a = new A [2][5][3]
then "a[1][2][*].command_3()" is equivalent to
a[0][2][0].command_3()
a[0][2][1].command_3()
a[0][2][2].command_3()
In this example "a[1][2][*]" is the multi_descr_str
"a[*][3][*].command_4()" is equivalent to
a[0][3][0].command_4()
a[0][3][1].command_4()
a[1][3][0].command_4()
a[1][3][1].command_4()
In this function, we interpret strings like "a" and "a[*][3][*]"
in the examples above, and figure out which InstanceObjs they refer to,
and push the corresponding command into that InstanceObjs instance
command stack retroactively.
In addition to [*], you can use [a-b] and [a:b] syntax. For example:
"a[0][1-2][0-1].command_3()" and
"a[0][1:3][0:2].command_3()" are both equivalent to:
a[0][1][0].command_3()
a[0][1][1].command_3()
a[0][2][0].command_3()
a[0][2][1].command_3()
"""
pattern_str = multi_descr_str
# Suppose pattern_str = 'a[1][*][3]/b[**][2]'
# We want to split this string into a list of string fragments
# which omits the '*' characters: [ 'a[', '][3]/b', '][2]' ]
# However, we only want to do this when * is enclosed in [].
pattern_fragments = []
ranges_ab = []
i_close_prev = 0
i_close = 0
i_open = 0
while True:
i_open = pattern_str.find('[', i_open+1)
if i_open == -1:
pattern_fragments.append(pattern_str[i_close_prev:])
break
else:
i_close = pattern_str.find(']', i_open+1)
if i_close == -1:
pattern_fragments.append(pattern_str[i_close_prev:])
break
# If there is a '*' or a ':' character between
# the [] brackets, then split the string at '['
# (at i_open) and resume reading again at ']'
# (at i_close) (and create a new entry in the
# pattern_fragments[] and ranges_ab[] lists)
wildcard_here = True
range_ab = [0,-1]
for j in range(i_open+1, i_close):
if ((pattern_str[j] == ':') or
((pattern_str[j] == '-') and (j > i_open+1)) or
(pattern_str[j] == '*')):
i_wildcard = len(pattern_fragments)
range_a_str = pattern_str[i_open+1 : j]
range_b_str = pattern_str[j+1 : i_close]
if (range_a_str != ''):
if str.isdigit(range_a_str):
range_ab[0] = int(range_a_str)
else:
raise InputError('Error near '+
ErrorLeader(srcloc.infile,
srcloc.lineno)+'\n'
' Expected colon-separated integers.\n')
if (range_b_str != ''):
if str.isdigit(range_b_str):
range_ab[1] = int(range_b_str)
# special case: When [a-b] type syntax is
# used, it selects from a to b inclusive.
# (IE. b is not a strict upper bound.)
if pattern_str[j] == '-':
range_ab[1] += 1
else:
raise InputError('Error near '+
ErrorLeader(srcloc.infile,
srcloc.lineno)+'\n'
' Expected colon-separated integers.\n')
break
elif j == i_close-1:
wildcard_here = False
if wildcard_here:
pattern_fragments.append(pattern_str[i_close_prev:i_open+1])
ranges_ab.append(range_ab)
i_close_prev = i_close
assert(len(pattern_fragments)-1==len(ranges_ab))
# Now figure out which InstanceObj or InstanceObjs correspond to
# the name or set of names suggested by the multi_descr_str,
# (after wildcard characters have been substituted with integers).
instobj_list = []
if len(pattern_fragments) == 1:
# commenting out:
# instobj_list.append(StrToNode(pattern_str, self, srcloc))
#
# Line above will print an error message if the node is not found.
# However sometimes we don't want this. Use this code instead:
path_tokens = pattern_str.split('/')
i_last_ptkn, instobj = FollowPath(path_tokens,
self,
srcloc)
# If found add to instobj_list
if ((i_last_ptkn == len(path_tokens))
and (not instobj.IsDeleted())): # (make sure not "deleted")
instobj_list.append(instobj)
else:
# num_counters equals the number of bracket-enclosed wildcards
num_counters= len(pattern_fragments)-1
multi_counters = [ranges_ab[i][0] for i in range(0, num_counters)]
all_matches_found = False
d_carry = 0
while d_carry < num_counters:
# Find the next InstanceObj in the set of InstanceObjs which
# satisfy the wild-card pattern in pattern_fragments.
while d_carry < num_counters:
candidate_descr_str = ''.join([pattern_fragments[i] +
str(multi_counters[i])
for i in range(0,num_counters)] \
+ \
[pattern_fragments[num_counters]])
#sys.stderr.write('DEBUG: /'+self.name+
# '.LookupMultiDescrStr()\n'
# ' looking up \"'+
# candidate_descr_str+'\"\n')
path_tokens = candidate_descr_str.split('/')
i_last_ptkn, instobj = FollowPath(path_tokens,
self,
srcloc)
# If there is an InstanceObj with that name,
# then add it to the list of InstanceObjs to
# which we will apply this modifier function,
# and increment the counters
# If found (and if the counter is within the range)...
if ((i_last_ptkn == len(path_tokens)) and
((ranges_ab[d_carry][1] == -1) or
(multi_counters[d_carry]<ranges_ab[d_carry][1]))):
# (make sure it has not yet been "deleted")
if (not instobj.IsDeleted()):
instobj_list.append(instobj)
d_carry = 0
multi_counters[0] += 1
#sys.stderr.write('DEBUG: InstanceObj found.\n')
break
# If there is no InstanceObj with that name,
# then perhaps it is because we have incremented
# the counter too high. If there are multiple
# counters, increment the next most significant
# counter, and reset this counter to 0.
# Keep looking
# (We only do this if the user neglected to explicitly
# specify an upper bound --> ranges_ab[d_carry[1]==-1)
elif ((ranges_ab[d_carry][1] == -1) or
(multi_counters[d_carry]>=ranges_ab[d_carry][1])):
#sys.stderr.write('DEBUG: InstanceObj not found.\n')
multi_counters[d_carry] = ranges_ab[d_carry][0]
d_carry += 1
if d_carry >= num_counters:
break
multi_counters[d_carry] += 1
else:
# Object was not found but we keep going. Skip
# to the next entry in the multi-dimensional list.
d_carry = 0
multi_counters[0] += 1
break
if (null_list_warning and (len(instobj_list) == 0)):
sys.stderr.write('WARNING('+g_module_name+'.LookupMultiDescrStr()):\n'
' Potential problem near '+
ErrorLeader(srcloc.infile,
srcloc.lineno)+'\n'
' No objects (yet) matching name \"'+pattern_str+'\".\n')
if (null_list_error and
(len(instobj_list) == 0)):
if len(pattern_fragments) == 1:
raise InputError('Error('+g_module_name+'.LookupMultiDescrStr()):\n'
' Syntax error near '+
ErrorLeader(srcloc.infile,
srcloc.lineno)+'\n'
' No objects matching name \"'+pattern_str+'\".')
else:
sys.stderr.write('WARNING('+g_module_name+'.LookupMultiDescrStr()):\n'
' Potential problem near '+
ErrorLeader(srcloc.infile,
srcloc.lineno)+'\n'
' No objects (yet) matching name \"'+pattern_str+'\".\n')
return instobj_list
def __str__(self):
if len(self.children) > 0:
out_str = self.name + '('
for i in range(0,len(self.children)):
if i+1 < len(self.children):
out_str += str(self.children[i])+', '
else:
out_str += str(self.children[i])+')'
else:
out_str = self.name
return out_str
def Dealloc(self):
InstanceObjBasic.Dealloc(self)
# Trying to remove pointers and variables.
# Hope I'm doing it correctly
#sys.stderr.write(self.name+'.Dealloc() invoked.\n')
N = len(self.commands)-1
for i in range(0, len(self.commands)):
del self.commands[N-i]
N = len(self.children)-1
for i in range(0, len(self.children)):
child = self.children[N-i]
child.Dealloc()
del self.children[N-i]
#def __del__(self):
# sys.stderr.write(self.name+'.__del__() invoked.\n')
def DeleteSelf(self):
# Modification: Don't get rid of pointers to yourself. Knowing which
# objects you instantiated and destroyed might be useful
# in case you want to apply multiple delete [*] commands
# Commenting out:
#assert(parent != None)
#i = 0
#while i < len(parent.children):
# if command.instobj == parent.children[i]:
# del parent.children[i]
# else:
# i += 1
self.Dealloc()
InstanceObjBasic.DeleteSelf(self)
def BuildInstanceTree(self,
statobj,
class_parents_in_use):
"""
This takes care of the details of copying relevant data from an StaticObj
into a newly-created InstanceObj. It allocates space for and performs
a deep-copy of any instance variables (and new instance categories), but
it performs a shallow copy of everything else (template text, etc..).
This is done recursively for every child that this class instantiates.
"""
if self.IsDeleted():
return
#sys.stderr.write(' DEBUG: '+self.name+
# '.BuildInstanceTree('+statobj.name+')\n')
#instance_refs = {}
# Keep track of which line in the file (and which file) we were
# in when we began parsing the class which defines this instance,
# as well as when we stopped parsing.
# (Don't do this if you are recusively searching class_parents because
# in that case you would be overwritting .statobj with with the parent.)
if len(class_parents_in_use) == 0:
self.statobj = statobj
self.srcloc_begin = statobj.srcloc_begin
self.srcloc_end = statobj.srcloc_end
# Make copies of the class_parents' StaticObj data.
# First deal with the "self.instance_commands_push"
# These commands should be carried out before any of the commands
# in "self.instance_commands".
for command in statobj.instance_commands_push:
self.ProcessCommand(command)
# Then deal with class parents
for class_parent in statobj.class_parents:
# Avoid the "Diamond of Death" multiple inheritance problem
if class_parent not in class_parents_in_use:
#sys.stderr.write(' DEBUG: '+self.name+'.class_parent = '+
# class_parent.name+'\n')
self.BuildInstanceTree(class_parent,
class_parents_in_use)
class_parents_in_use.add(class_parent)
# Now, deal with the data in THIS object and its children
assert((self.commands != None) and (self.categories != None))
# "instance_categories" contains a list of new "categories" (ie new
# types of variables) to create whenever this class is instantiated.
# (This is used whenever we create a local counter variable: Suppose we
# want to count the residues within a particular protein, when there
# are multiple copies of the same protein in the simulation.)
for cat_name, cat in statobj.instance_categories.items():
assert(len(cat.bindings) == 0)
self.categories[cat_name] = Category(cat_name)
self.categories[cat_name].counter = cat.counter.__copy__()
# Note: Later on we will generate leaf nodes corresponding to
# variables, and put references to them in this category.
# Deal with the "instance_commands",
for command in statobj.instance_commands:
self.ProcessCommand(command)
# Finally deal with the "self.instance_commands_pop"
# These commands should be carried out after all of the commands
# in "self.instance_commands".
for command in statobj.instance_commands_pop:
self.ProcessCommand(command)
def ProcessCommand(self, command):
if isinstance(command, ModCommand):
sys.stderr.write(' processing command \"'+str(command)+'\"\n')
mod_command = command
instobj_list = self.LookupMultiDescrStr(mod_command.multi_descr_str,
mod_command.command.srcloc)
if len(instobj_list) == 0:
if isinstance(mod_command.command, DeleteCommand):
# It's possible that some nodes we want to delete have
# not yet been created yet. Deal with these later.
# (See InvokeAllDeletes().)
self.commands.append(mod_command.__copy__())
else:
raise InputError('Error('+g_module_name+'.ProcessCommand()):\n'
' Syntax error at or before '+
ErrorLeader(mod_command.command.srcloc.infile,
mod_command.command.srcloc.lineno)+'\n'
' No objects matching name \"'+
mod_command.multi_descr_str+'\"\n'
' (If the object is an array, include brackets. Eg. \"molecules[*][*][*]\")')
else:
for instobj in instobj_list:
if isinstance(mod_command.command, DeleteCommand):
# We need the instance tree to be fully defined after
# this function is called, so carry out the deletion now
instobj.DeleteSelf()
else:
command = mod_command.command.__copy__()
self.ProcessContextNodes(command)
if isinstance(command, PushCommand):
instobj.commands_push.append(command)
elif isinstance(mod_command.command, PopCommand):
instobj.commands_pop.insert(0, command)
else:
# I don't know if any other types commands will ever
# occur but I handle them below, just in case...
assert(not isinstance(command, InstantiateCommand))
instobj.commands.append(command.__copy__())
return
# Not needed:
#if isinstance(command, DeleteCommand):
# self.DeleteSelf()
# return # (Note: we do not append this command to self.commands)
# Otherwise:
command = command.__copy__()
self.ProcessContextNodes(command)
if isinstance(command, InstantiateCommand):
sys.stderr.write(' processing command \"'+str(command)+'\"\n')
self.commands.append(command) # <- useful later to keep track of the
# order that children were created
child = InstanceObj(command.name, self)
if command.class_ref.statobj_str == '':
child.DeleteSelf()
# Why? This if-then check handles the case when the user
# wants to create an array of molecules with random vacancies.
# When this happens, some of the instance commands will
# contain instructions to create a copy of a molecule with
# an empty molecule-type-string (class_ref.statobj_str).
# Counter-intuitively, ...
# ...we DO want to create something here so that the user can
# safely loop over the array without generating an error.
# (Such as to delete elements, or move the remaining
# members in the array.) We just want to mark it as
# 'deleted'. (That's what "DeleteSelf()" does.)
else:
# This is the heart of "BuildInstanceTree()"
# (which implements object composition)
new_class_parents_in_use = set([])
child.BuildInstanceTree(command.class_ref.statobj,
new_class_parents_in_use)
self.children.append(child)
else:
# Otherwise, we don't know what this command is yet.
# Append it to the list of commands and process it/ignore it later.
self.commands.append(command)
def ProcessContextNodes(self, command):
if hasattr(command, 'context_node'):
# Lookup any nodes pointers to instobjs
if command.context_node != None:
if type(command.context_node) is str:
command.context_node = StrToNode(command.context_node,
self,
command.srcloc)
# (Otherwise, just leave it as None)
def BuildCommandList(self, command_list):
"""
Search the commands in the tree and make a linear list of commands
in the order they should be carried out.
"""
if self.IsDeleted():
return
if (len(self.commands) == 0):
# To save memory don't generate any commands
# for trivial (leaf) nodes
assert(len(self.children) == 0)
return
# Add a special note to the list of commands to indicate which object
# the commands refer to. (This might be useful one day.)
# Later we can loop through this command list and still be able to tell
# whether or not we are within the scope of a particular class or instance
# (by seeing if we are between a "ScopeBegin" and "ScopeEnd" pair).
command_list.append(ScopeBegin(self, self.srcloc_begin))
# Note:
# The previous version looped over all commands in this node, and then
# recursively invoke BuildCommandList() on all the children of this node
# We don't do that anymore because it does not take into account the
# order that various child objects were created/instantiated
# which potentially could occur in-between other commands. Instead,
# now we loop through the command_list and recursively visit child
# nodes only when we encounter them in the command list.
for command in self.commands_push:
assert(isinstance(command, InstantiateCommand) == False)
command_list.append(command)
i_child = 0
for command in self.commands:
if isinstance(command, InstantiateCommand):
child = self.children[i_child]
child.BuildCommandList(command_list)
i_child += 1
else:
command_list.append(command)
for command in self.commands_pop:
assert(isinstance(command, InstantiateCommand) == False)
command_list.append(command)
command_list.append(ScopeEnd(self, self.srcloc_begin))
def AssignVarPtrs(context_node, search_instance_commands = False):
"""
Now scan through all the variables within the templates defined
for this context_node (either static or dynamic depending on var_filter).
Each reference to a variable in the template has a descriptor which
indicates the variable's type, and in which molecule it is defined (ie
where it is located in the molecule instance tree or type definition tree).
(See comments for "class VarNPtr(object):" above for details.)
Also check to see the nodes in the tree that are refered to by the
descriptor exist, and, if so, assign pointers to these nodes.
If not, then (in some cases), create new node whose names match the
variable descriptor names (and assign pointers to them).
Also figure out the category node and name which specify the type of
variable. These three pieces of information
This node (it's name and location in the tree) essentially identifies the
variable, (like a variable name) but it does not store anything.
Also: Eventually we want to assign a value to each variable.
This same variable (node) may appear multiple times in diffent templates.
So we also create a place to store this variable's value, and also assign
(two-way) pointers from the VarRef in the template, to this storage area
so that later on when we write out the contents of the template to a file,
we can substitute this variable with it's value.
"""
#sys.stdout.write('AssignVarPtrs() invoked on node: \"'+NodeToStr(context_node)+'\"\n')
if search_instance_commands:
assert(isinstance(context_node, StaticObj))
commands = context_node.instance_commands
else:
# Note: Leaf nodes contain no commands, so skip them
if (not hasattr(context_node, 'commands')):
return
# Otherwise process their commands
commands = context_node.commands
for command in commands:
if isinstance(command, WriteFileCommand):
for var_ref in command.tmpl_list:
# Process the VarRef entries in the tmpl_list,
# (and check they have the correct prefix: either '$' or '@')
# Ignore other entries (for example, ignore TextBlocks).
if (isinstance(var_ref, VarRef) and
((isinstance(context_node, StaticObj) and (var_ref.prefix[0] == '@')) or
(isinstance(context_node, InstanceObjBasic) and (var_ref.prefix[0] == '$')))):
var_ref.nptr.cat_name, var_ref.nptr.cat_node, var_ref.nptr.leaf_node = \
DescrToCatLeafNodes(var_ref.descr_str,
context_node,
var_ref.srcloc,
True)
categories = var_ref.nptr.cat_node.categories
# "categories" is a dictionary storing "Category" objects
# indexed by category names.
# Note to self: Always use the ".categories" member,
# (never the ".instance_categories" member.
# ".instance_categories" are only used temporarilly before
# we instantiate, ie. before we build the tree of InstanceObjs.)
category = categories[var_ref.nptr.cat_name]
# "category" is a Category object containing a
# dictionary of VarBinding objects, and an internal counter.
var_bindings = category.bindings
# "var_bindings" is a dictionary storing "VarBinding"
# objects, indexed by leaf nodes. Each leaf node
# corresponds to a unique variable in this category.
# --- Now update "var_bindings" ---
# Search for the "VarBinding" object that
# corresponds to this leaf node.
# If not found, then create one.
if var_ref.nptr.leaf_node in var_bindings:
var_binding = var_bindings[var_ref.nptr.leaf_node]
# "var_binding" stores the information for a variable,
# including pointers to all of the places the variable
# is rerefenced, the variable's (full) name, and value.
#
# Keep track of all the places that varible is
# referenced by updating the ".refs" member
var_binding.refs.append(var_ref)
else:
# Not found, so we create a new binding.
var_binding = VarBinding()
# var_binding.refs contains a list of all the places
# this variable is referenced. Start with this var_ref:
var_binding.refs = [var_ref]
# keep track of the cat_node, cat_name, leaf_node:
var_binding.nptr = var_ref.nptr
# "var_binding.full_name" stores a unique string like
# '@/atom:Water/H' or '$/atom:water[1423]/H2',
# which contains the full path for the category and leaf
# nodes, and uniquely identifies this variable globally.
# Thus these strings correspond uniquely (ie. in a
# one-to-one fashion) with the nodes they represent.
var_binding.full_name = var_ref.prefix[0] + \
CanonicalDescrStr(var_ref.nptr.cat_name,
var_ref.nptr.cat_node,
var_ref.nptr.leaf_node,
var_ref.srcloc)
# (These names can always be generated later when needed
# but it doesn't hurt to keep track of it here too.)
# Now add this binding to the other
# bindings in this category:
var_bindings[var_ref.nptr.leaf_node] = var_binding
##vb## var_ref.nptr.leaf_node.AddVarBinding(var_binding)
var_binding.category = category
# It's convenient to add a pointer in the opposite direction
# so that later if we find the var_ref, we can find its
# binding and visa-versa. (Ie. two-way pointers)
var_ref.binding = var_binding
assert(var_ref.nptr.leaf_node in var_bindings)
# Recursively invoke AssignVarPtrs() on all (non-leaf) child nodes:
for child in context_node.children:
AssignVarPtrs(child, search_instance_commands)
def AssignVarOrderByFile(context_node, search_instance_commands=False):
"""
For each category in context_node, and each variable in that category,
set the order of each variable equal to the position of that variable
in the user's input file.
"""
if search_instance_commands:
assert(isinstance(context_node, StaticObj))
commands = context_node.instance_commands_push + \
context_node.instance_commands + \
context_node.instance_commands_pop
else:
commands = context_node.commands
for command in commands:
if isinstance(command, WriteFileCommand):
tmpl_list = command.tmpl_list
for var_ref in tmpl_list:
if isinstance(var_ref, VarRef):
if (((var_ref.prefix == '@') and
isinstance(context_node, StaticObj)) or
((var_ref.prefix == '$') and
isinstance(context_node, InstanceObjBasic))):
#if ((var_ref.prefix == '@') or
# (not search_instance_commands)):
if ((var_ref.binding.order is None) or
(var_ref.binding.order > var_ref.srcloc.order)):
var_ref.binding.order = var_ref.srcloc.order
for child in context_node.children:
AssignVarOrderByFile(child, search_instance_commands)
def AssignVarOrderByCommand(command_list, prefix_filter):
"""
For each category in context_node, and each variable in that category,
set the order of each variable according to the position of the
write(), write_once(), or other command that created it.
Only variables with the correct prefix ('$' or '@') are affected.
"""
count = 0
for command in command_list:
if isinstance(command, WriteFileCommand):
tmpl_list = command.tmpl_list
for var_ref in tmpl_list:
if isinstance(var_ref, VarRef):
if var_ref.prefix in prefix_filter:
count += 1
if ((var_ref.binding.order is None) or
(var_ref.binding.order > count)):
var_ref.binding.order = count
def AutoAssignVals(cat_node,
sort_variables,
reserved_values = None,
ignore_prior_values = False):
"""
This function automatically assigns all the variables
belonging to all the categories in cat_node.categories.
Each category has its own internal counter. For every variable in that
category, query the counter (which usually returns an integer),
and assign the variable to it. Exceptions can be made if the integer
is reserved by some other variable, or if it has been already assigned.
Afterwards, we recursively search the child nodes recursively
(in a depth-first-search order).
sort_variables: Sorting the variables according to their "binding.order"
counters is optional.
"""
if (not hasattr(cat_node, 'categories')):
# (sometimes leaf nodes lack a 'categories' member, to save memory)
return
# Search the tree in a depth-first-search manner.
# For each node, examine the "categories" associated with that node
# (ie the list of variables whose counters lie within that node's scope).
for cat_name, cat in cat_node.categories.items():
# Loop through all the variables in this category.
if sort_variables:
# Sort the list of variables according to var_binding.order
# First, print a progress indicator (this could be slow)
prefix = '$'
# Is this parent_node an StaticObj? (..or inherit from StaticObj?)
if isinstance(cat_node, StaticObj):
prefix = '@'
sys.stderr.write(' sorting variables in category: '+prefix+
CanonicalCatName(cat_name, cat_node)+':\n')
var_bind_iter = iter(sorted(cat.bindings.items(),
key=operator.itemgetter(1)))
else:
# Just iterate through them in the order that they were added
# to the category list. (This happens to be the same order as
# we found it earlier when searching the tree.)
var_bind_iter = iter(cat.bindings.items())
for leaf_node,var_binding in var_bind_iter:
if ((var_binding.value is None) or ignore_prior_values):
if var_binding.nptr.leaf_node.name[:9] == '__query__':
# -- THE "COUNT" HACK --
# '__query__...' variables are not really variables.
# They are a mechanism to allow the user to query the
# category counter without incrementing it.
var_binding.value = str(cat.counter.query())
elif HasWildCard(var_binding.full_name):
# -- The wildcard hack ---
# Variables containing * or ? characters in their names
# are not allowed. These are not variables, but patterns
# to match with other variables. Represent them by the
# (full-path-expanded) string containing the * or ?.
var_binding.value = var_binding.full_name
else:
if (not var_binding.nptr.leaf_node.IsDeleted()):
# For each (regular) variable, query this category's counter
# (convert it to a string), and see if it is already in use
# (in this category). If not, then set this variable's value
# to the counter's value. Either way, increment the counter.
while True:
cat.counter.incr()
value = str(cat.counter.query())
if ((reserved_values is None) or
((cat, value) not in reserved_values)):
break
var_binding.value = value
# Recursively invoke AssignVarValues() on all child nodes
for child in cat_node.children:
AutoAssignVals(child,
sort_variables,
reserved_values,
ignore_prior_values)
def InvokeAllDeletes(node,
null_list_warning=False,
null_list_error=True):
""" This is a short simple function to carry out any remaining delete
statements which have not yet been processed. """
i_child = 0
i = 0
while i < len(node.commands):
command = node.commands[i]
if isinstance(command, ModCommand):
mod_command = command
if isinstance(mod_command.command, DeleteCommand):
instobj_list = node.LookupMultiDescrStr(mod_command.multi_descr_str,
mod_command.command.srcloc,
null_list_warning,
null_list_error)
for instobj in instobj_list:
instobj.DeleteSelf()
del node.commands[i]
else:
assert(False)
elif isinstance(command, DeleteCommand):
node.DeleteSelf()
del node.commands[i]
elif isinstance(command, InstantiateCommand):
child = node.children[i_child]
InvokeAllDeletes(child,
null_list_warning,
null_list_error)
i_child += 1
i += 1
else:
i += 1
# Did the user ask us to reformat the output string?
# This information is encoded in the variable's suffix.
def ExtractFormattingCommands(suffix):
if (len(suffix) <= 1):
return None, None
if suffix[-1] == '}': # Get rid of any trailing '}' characters
suffix = suffix[:-1]
if suffix[-1] != ')': # Format functions are always followed by parens
return None, None
else:
idot = suffix.find('.') # Format functions usually preceeded by '.'
ioparen = suffix.find('(')
icparen = suffix.find(')')
format_fname = suffix[idot+1:ioparen]
args = suffix[ioparen+1:icparen]
args = args.split(',')
for i in range(0, len(args)):
args[i] = RemoveOuterQuotes(args[i].strip(), '\"\'')
return format_fname, args
def Render(tmpl_list, substitute_vars=True):
"""
This function converts a TextBlock,VarRef list into a string.
It is invoked by WriteTemplatesValue() in order to print
out the templates stored at each node of the tree.
"""
out_str_list = []
i = 0
while i < len(tmpl_list):
entry = tmpl_list[i]
if isinstance(entry, VarRef):
var_ref = entry
var_bindings = var_ref.nptr.cat_node.categories[var_ref.nptr.cat_name].bindings
#if var_ref.nptr.leaf_node not in var_bindings:
#assert(var_ref.nptr.leaf_node in var_bindings)
if var_ref.nptr.leaf_node.IsDeleted():
raise InputError('Error near '+
ErrorLeader(var_ref.srcloc.infile,
var_ref.srcloc.lineno)+'\n'
' The variable you referred to does not exist:\n'
' '+var_ref.prefix+var_ref.descr_str+var_ref.suffix+'\n'
' (You probably deleted it or something it belonged to earlier.)\n')
else:
if substitute_vars:
value = var_bindings[var_ref.nptr.leaf_node].value
format_fname, args = ExtractFormattingCommands(var_ref.suffix)
if format_fname == 'ljust':
if len(args) == 1:
value = value.ljust(int(args[0]))
else:
value = value.ljust(int(args[0]), args[1])
elif format_fname == 'rjust':
if len(args) == 1:
value = value.rjust(int(args[0]))
else:
value = value.rjust(int(args[0]), args[1])
out_str_list.append(value)
else:
out_str_list.append(var_ref.prefix +
SafelyEncodeString(var_bindings[var_ref.nptr.leaf_node].full_name[1:]) +
var_ref.suffix)
else:
assert(isinstance(entry, TextBlock))
out_str_list.append(entry.text)
i += 1
return ''.join(out_str_list)
def MergeWriteCommands(command_list):
""" Write commands are typically to the same file.
We can improve performance by appending all of
commands that write to the same file together before
carrying out the write commands.
"""
file_templates = defaultdict(list)
for command in command_list:
if isinstance(command, WriteFileCommand):
if command.filename != None:
file_templates[command.filename] += \
command.tmpl_list
return file_templates
def WriteTemplatesValue(file_templates):
""" Carry out the write() and write_once() commands (which
write out the contents of the templates contain inside them).
"""
for filename, tmpl_list in file_templates.items():
if filename == '':
out_file = sys.stdout
else:
out_file = open(filename, 'a')
out_file.write(Render(tmpl_list, substitute_vars=True))
if filename != '':
out_file.close()
# Alternate (old method):
#for command in command_list:
# if isinstance(command, WriteFileCommand):
# if command.filename != None:
# if command.filename == '':
# out_file = sys.stdout
# else:
# out_file = open(command.filename, 'a')
#
# out_file.write(Render(command.tmpl_list))
#
# if command.filename != '':
# out_file.close()
def WriteTemplatesVarName(file_templates):
""" Carry out the write() and write_once() commands (which
write out the contents of the templates contain inside them).
However variables within the templates are represented by their
full name instead of their assigned value.
"""
for filename, tmpl_list in file_templates.items():
if filename != '':
out_file = open(filename + '.template', 'a')
out_file.write(Render(tmpl_list, substitute_vars=False))
out_file.close()
def EraseTemplateFiles(command_list):
filenames = set([])
for command in command_list:
if isinstance(command, WriteFileCommand):
if (command.filename != None) and (command.filename != ''):
if command.filename not in filenames:
filenames.add(command.filename)
# Openning the files (in mode 'w') and closing them again
# erases their contents.
out_file = open(command.filename, 'w')
out_file.close()
out_file = open(command.filename + '.template', 'w')
out_file.close()
#def ClearTemplates(file_templates):
# for filename in file_templates:
# if filename != '':
# out_file = open(filename, 'w')
# out_file.close()
# out_file = open(filename + '.template', 'w')
# out_file.close()
def WriteVarBindingsFile(node):
""" Write out a single file which contains a list of all
of the variables defined (regardless of which class they
were defined in). Next to each variable name is the corresponding
information stored in that variable (a number) that variable.
"""
if (not hasattr(node, 'categories')):
# (sometimes leaf nodes lack a 'categories' member, to save memory)
return
out = open('ttree_assignments.txt', 'a')
for cat_name in node.categories:
var_bindings = node.categories[cat_name].bindings
for nd, var_binding in var_bindings.items():
if nd.IsDeleted():
continue # In that case, skip this variable
#if type(node) is type(nd):
if ((isinstance(node, InstanceObjBasic) and isinstance(nd, InstanceObjBasic))
or
(isinstance(node, StaticObj) and isinstance(nd, StaticObj))):
# Now omit variables whos names contain "*" or "?"
# (these are actually not variables, but wildcard patterns)
if not HasWildCard(var_binding.full_name):
if len(var_binding.refs) > 0:
usage_example = ' #'+\
ErrorLeader(var_binding.refs[0].srcloc.infile, \
var_binding.refs[0].srcloc.lineno)
else:
usage_example = ''
out.write(SafelyEncodeString(var_binding.full_name) +' '+
SafelyEncodeString(var_binding.value)
+usage_example+'\n')
out.close()
for child in node.children:
WriteVarBindingsFile(child)
def CustomizeBindings(bindings,
g_objectdefs,
g_objects):
var_assignments = set()
for name,vlpair in bindings.items():
prefix = name[0]
var_descr_str = name[1:]
value = vlpair.val
dbg_loc = vlpair.loc
if prefix == '@':
var_binding = LookupVar(var_descr_str,
g_objectdefs,
dbg_loc)
elif prefix == '$':
var_binding = LookupVar(var_descr_str,
g_objects,
dbg_loc)
else:
# If the user neglected a prefix, this should have generated
# an error earlier on.
assert(False)
# Change the assignment:
var_binding.value = value
var_assignments.add((var_binding.category, value))
#sys.stderr.write(' CustomizeBindings: descr=' + var_descr_str +
# ', value=' + value + '\n')
return var_assignments
##############################################################
##################### BasicUI functions #####################
# These functions are examples of how to use the StaticObj
# and InstanceObj data structures above, and to read a ttree file.
# These are examples only. New programs based on ttree_lib.py
# will probably require their own settings and functions.
##############################################################
def BasicUIReadBindingsFile(bindings_so_far, filename):
try:
f = open(filename, 'r')
except IOError:
sys.stderr.write('Error('+g_filename+'):\n'' : unable to open file\n'
'\n'
' \"'+bindings_filename+'\"\n'
' for reading.\n'
'\n'
' (If you were not trying to open a file with this name, then this could\n'
' occur if you forgot to enclose your command-line-argument in quotes,\n'
' For example, use: \'$atom:wat[2]/H1 20\' or "\$atom:wat[2]/H1 to 20"\n'
' to set the variable $atom:wat[2]/H1 to 20.)\n')
sys.exit(1)
BasicUIReadBindingsStream(bindings_so_far, f, filename)
f.close()
def BasicUIReadBindingsText(bindings_so_far, text, source_name=''):
if sys.version > '3':
in_stream = io.StringIO(text)
else:
in_stream = cStringIO.StringIO(text)
return BasicUIReadBindingsStream(bindings_so_far, in_stream, source_name)
class ValLocPair(object):
__slots__=["val","loc"]
def __init__(self,
val = None,
loc = None):
self.val = val
self.loc = loc
def BasicUIReadBindingsStream(bindings_so_far, in_stream, source_name=''):
# EXAMPLE (simple version)
# The simple version of this function commented out below
# does not handle variable whose names or values
# contain strange or escaped characters, quotes or whitespace.
# But I kept it in for illustrative purposes:
#
#for line in f:
# line = line.strip()
# tokens = line.split()
# if len(tokens) == 2:
# var_name = tokens[0]
# var_value = tokens[1]
# var_assignments[var_name] = var_value
#f.close()
lex = TemplateLexer(in_stream, source_name)
tmpllist = lex.ReadTemplate()
i = 0
if isinstance(tmpllist[0], TextBlock):
i += 1
while i+1 < len(tmpllist):
# process one line at a time (2 entries per line)
var_ref = tmpllist[i]
text_block = tmpllist[i+1]
assert(isinstance(var_ref, VarRef))
if (not isinstance(text_block, TextBlock)):
raise InputError('Error('+g_filename+'):\n'
' This is not a valid name-value pair:\n'
' \"'+var_ref.prefix+var_ref.descr_str+' '+text_block.text.rstrip()+'\"\n'
' Each variable asignment should contain a variable name (beginning with\n'
' @ or $) followed by a space, and then a string you want to assign to it.\n'
' (Surrounding quotes are optional and will be removed.)\n')
# Variables in the ttree_assignments.txt file use "full-path" style.
# In other words, the full name of the variable, (including all
# path information) is stored var_ref.descr_str,
# and the first character of the prefix stores either a @ or $
var_name = var_ref.prefix[:1] + var_ref.descr_str
text = SplitQuotedString(text_block.text.strip())
var_value = EscCharStrToChar(RemoveOuterQuotes(text, '\'\"'))
bindings_so_far[var_name] = ValLocPair(var_value, lex.GetSrcLoc())
i += 2
class BasicUISettings(object):
"""
BasicUISettings() contains several run-time user customisations
for ttree. (These effect the order and values assigned to variables
in a ttreee file).
This object, along with the other "UI" functions below are examples only.
(New programs based on ttree_lib.py will probably have their own settings
and functions.)
Members:
user_bindings
user_bindings_x
These are lists containing pairs of variable names,
and the string values they are bound to (which are typically numeric).
Values specified in the "user_bindings_x" list are "exclusive".
This means their values are reserved, so that later on, when other
variables (in the same category) are automatically assigned to values, care
care will be taken to avoid duplicating the values in user_bindings_x.
However variables in the "user_bindings" list are assigned without regard
to the values assigned to other variables, and may or may not be unique.
order_method
The order_method specifies the order in which values will be automatically
assigned to variables. (In the context of building molecular simulation
input files, this helps the user to insure that the order of the atoms
created by the ttree file matches the order they appear in other files
created by other programs.)
"""
def __init__(self,
user_bindings_x=None,
user_bindings=None,
order_method='by_command',
lex=None):
if user_bindings_x:
self.user_bindings_x = user_bindings_x
else:
self.user_bindings_x = OrderedDict()
if user_bindings:
self.user_bindings = user_bindings
else:
self.user_bindings = OrderedDict()
self.order_method = order_method
self.lex = lex
def BasicUIParseArgs(argv, settings):
"""
BasicUIParseArgs()
The following function contains part of the user interface for a
typical ttree-based program. This function processes an argument list
and extracts the common ttree user settings.
This function, along with the other "UI" functions below are examples only.
(New programs based on ttree_lib.py will probably have their own UI.)
"""
#argv = [arg for arg in orig_argv] # (make a deep copy of "orig_argv")
# This error message is used in multiple places:
bind_err_msg = 'should either be followed by a 2-column\n'+\
' file (containing variable-value pairs on each line).\n'+\
' --OR-- a quoted string (such as \"@atom:x 2\")\n'+\
' with the full variable name and its desired value.'
bind_err_msg_var = 'Missing value, or space needed separating variable\n'+\
' and value. (Remember to use quotes to surround the argument\n'+\
' containing the variable name, and it\'s assigned value.)'
i = 1
while i < len(argv):
#sys.stderr.write('argv['+str(i)+'] = \"'+argv[i]+'\"\n')
if argv[i] == '-a':
if ((i+1 >= len(argv)) or (argv[i+1][:1] == '-')):
raise InputError('Error('+g_filename+'):\n'
' Error in -a \"'+argv[i+1]+' argument.\"\n'
' The -a flag '+bind_err_msg)
if (argv[i+1][0] in '@$'):
#tokens = argv[i+1].strip().split(' ')
tokens = SplitQuotedString(argv[i+1].strip())
if len(tokens) < 2:
raise InputError('Error('+g_filename+'):\n'
' Error in -a \"'+argv[i+1]+'\" argument.\n'
' '+bind_err_msg_var)
BasicUIReadBindingsText(settings.user_bindings_x,
argv[i+1],
'__command_line_argument__')
else:
BasicUIReadBindingsFile(settings.user_bindings_x,
argv[i+1])
#i += 2
del(argv[i:i+2])
elif argv[i] == '-b':
if ((i+1 >= len(argv)) or (argv[i+1][:1] == '-')):
raise InputError('Error('+g_filename+'):\n'
' Error in -b \"'+argv[i+1]+' argument.\"\n'
' The -b flag '+bind_err_msg)
if (argv[i+1][0] in '@$'):
#tokens = argv[i+1].strip().split(' ')
tokens = SplitQuotedString(argv[i+1].strip())
if len(tokens) < 2:
raise InputError('Error('+g_filename+'):\n'
' Error in -b \"'+argv[i+1]+'\" argument.\n'
' '+bind_err_msg_var)
BasicUIReadBindingsText(settings.user_bindings,
argv[i+1],
'__command_line_argument__')
else:
BasicUIReadBindingsFile(settings.user_bindings,
argv[i+1])
#i += 2
del(argv[i:i+2])
elif argv[i] == '-order-command':
settings.order_method = 'by_command'
#i += 1
del(argv[i:i+1])
elif argv[i] == '-order-file':
settings.order_method = 'by_file'
#i += 1
del(argv[i:i+1])
elif ((argv[i] == '-order-tree') or (argv[i] == '-order-dfs')):
settings.order_method = 'by_tree'
del(argv[i:i+1])
elif ((argv[i] == '-importpath') or
(argv[i] == '-import-path') or
(argv[i] == '-import_path')):
if ((i+1 >= len(argv)) or (argv[i+1][:1] == '-')):
raise InputError('Error('+g_filename+'):\n'
' Error in \"'+argv[i]+'\" argument.\"\n'
' The \"'+argv[i]+'\" argument should be followed by the name of\n'
' an environment variable storing a path for including/importing files.\n')
TtreeShlex.custom_path = RemoveOuterQuotes(argv[i+1])
del(argv[i:i+2])
elif ((argv[i][0] == '-') and (__name__ == "__main__")):
#elif (__name__ == "__main__"):
raise InputError('Error('+g_filename+'):\n'
'Unrecogized command line argument \"'+argv[i]+'\"\n')
else:
i += 1
if __name__ == "__main__":
# Instantiate the lexer we will be using.
# (The lexer's __init__() function requires an openned file.
# Assuming __name__ == "__main__", then the name of that file should
# be the last remaining (unprocessed) argument in the argument list.
# Otherwise, then name of that file will be determined later by the
# python script which imports this module, so we let them handle it.)
if len(argv) == 1:
raise InputError('Error('+g_filename+'):\n'
' This program requires at least one argument\n'
' the name of a file containing ttree template commands\n')
elif len(argv) == 2:
try:
settings.lex = TemplateLexer(open(argv[1], 'r'), argv[1]) # Parse text from file
except IOError:
sys.stderr.write('Error('+g_filename+'):\n'
' unable to open file\n'
' \"'+argv[1]+'\"\n'
' for reading.\n')
sys.exit(1)
del(argv[1:2])
else:
# if there are more than 2 remaining arguments,
problem_args = ['\"'+arg+'\"' for arg in argv[1:]]
raise InputError('Syntax Error ('+g_filename+'):\n'
' Problem with argument list.\n'
' The remaining arguments are:\n\n'
' '+(' '.join(problem_args))+'\n\n'
' (The actual problem may be earlier in the argument list.\n'
' If these arguments are source files, then keep in mind\n'
' that this program can not parse multiple source files.)\n'
' Check the syntax of the entire argument list.\n')
def BasicUI(settings,
static_tree_root,
instance_tree_root,
static_commands,
instance_commands):
"""
BasicUI()
This function loads a ttree file and optional custom bindings for it,
creates a "static" tree (of defined ttree classes),
creates an "instance" tree (of instantiated ttree objects),
automatically assigns values to unbound variables,
substitutes them into text templates (renders the template).
The actual writing of the templates to a file is not handled here.
"""
# Parsing, and compiling is a multi-pass process.
# Step 1: Read in the StaticObj (class) defintions, without checking
# whether or not the instance_children refer to valid StaticObj types.
sys.stderr.write('parsing the class definitions...')
static_tree_root.Parse(settings.lex)
#gc.collect()
#sys.stderr.write('static = ' + str(static_tree_root) + '\n')
# Step 2: Now that the static tree has been constructed, lookup
# any references to classes (StaticObjs), contained within
# the instance_children or class_parents of each node in
# static_tree_root. Replace them with (pointers to)
# the StaticObjs they refer to (and check validity).
# (Note: Variables stored within the templates defined by write()
# and write_once() statements may also refer to StaticObjs in
# the tree, but we leave these references alone. We handle
# these assignments later using "AssignVarPtrs()" below.)
sys.stderr.write(' done\nlooking up classes...')
static_tree_root.LookupStaticRefs()
#gc.collect()
# Step 3: Now scan through all the (static) variables within the templates
# and replace the (static) variable references to pointers
# to nodes in the StaticObj tree:
sys.stderr.write(' done\nlooking up @variables...')
# Here we assign pointers for variables in "write_once(){text}" templates:
AssignVarPtrs(static_tree_root, search_instance_commands=False)
# Here we assign pointers for variables in "write(){text}" templates:
AssignVarPtrs(static_tree_root, search_instance_commands=True)
sys.stderr.write(' done\nconstructing the tree of class definitions...')
sys.stderr.write(' done\n\nclass_def_tree = ' + str(static_tree_root) + '\n\n')
#gc.collect()
# Step 4: Construct the instance tree (the tree of instantiated
# classes) from the static tree of type definitions.
sys.stderr.write('constructing the instance tree...\n')
class_parents_in_use = set([])
instance_tree_root.BuildInstanceTree(static_tree_root, class_parents_in_use)
#sys.stderr.write('done\n garbage collection...')
#gc.collect()
sys.stderr.write(' done\n')
#sys.stderr.write('instance_tree = ' + str(instance_tree_root) + '\n')
# Step 5: Now scan through all the (instance) variables within the templates
# and replace the (instance) variable references to pointers
# to nodes in the InstanceObj tree:
sys.stderr.write(' done\nlooking up $variables...')
AssignVarPtrs(instance_tree_root, search_instance_commands=False)
#sys.stderr.write('done\n garbage collection...')
#gc.collect()
# Step 6: Now carry out all of the "delete" commands (deferred earlier).
# (These were deferred because the instance tree must be complete before any
# references to target nodes (with non-trivial paths) can be understood.)
InvokeAllDeletes(instance_tree_root,
null_list_warning=False,
null_list_error=True)
sys.stderr.write(' done\n')
#sys.stderr.write('instance_v = ' + str(instance_tree_root) + '\n')
#gc.collect()
# Step 7: The commands must be carried out in a specific order.
# (for example, the "write()" and "new" commands).
# Search through the tree, and append commands to a command list.
# Then re-order the list in the order the commands should have
# been executed in. (We don't carry out the commands yet,
# we just store them and sort them.)
class_parents_in_use = set([])
static_tree_root.BuildCommandList(static_commands)
instance_tree_root.BuildCommandList(instance_commands)
#sys.stderr.write('static_commands = '+str(static_commands)+'\n')
#sys.stderr.write('instance_commands = '+str(instance_commands)+'\n')
# Step 8: We are about to assign numbers to the variables.
# We need to decide the order in which to assign them.
# By default static variables (@) are assigned in the order
# they appear in the file.
# And, by default instance variables ($)
# are assigned in the order they are created during instantiation.
#sys.stderr.write(' done\ndetermining variable count order...')
AssignVarOrderByFile(static_tree_root, search_instance_commands=False)
AssignVarOrderByFile(static_tree_root, search_instance_commands=True)
AssignVarOrderByCommand(instance_commands, '$')
# Step 9: Assign the variables.
# (If the user requested any customized variable bindings,
# load those now.)
if len(settings.user_bindings_x) > 0:
reserved_values = CustomizeBindings(settings.user_bindings_x,
static_tree_root,
instance_tree_root)
else:
reserved_values = None
sys.stderr.write('sorting variables...\n')
AutoAssignVals(static_tree_root,
(settings.order_method != 'by_tree'),
reserved_values)
AutoAssignVals(instance_tree_root,
(settings.order_method != 'by_tree'),
reserved_values)
if len(settings.user_bindings) > 0:
CustomizeBindings(settings.user_bindings,
static_tree_root,
instance_tree_root)
sys.stderr.write(' done\n')
if __name__ == "__main__":
"""
This is is a "main module" wrapper for invoking ttree.py
as a stand alone program. This program:
1)reads a ttree file,
2)constructs a tree of class definitions (g_objectdefs)
3)constructs a tree of instantiated class objects (g_objects),
4)automatically assigns values to the variables,
5)and carries out the "write" commands to write the templates a file(s).
"""
####### Main Code Below: #######
g_program_name = g_filename
sys.stderr.write(g_program_name+' v'+g_version_str+' '+g_date_str+' ')
sys.stderr.write('\n(python version '+str(sys.version)+')\n')
try:
settings = BasicUISettings()
BasicUIParseArgs(sys.argv, settings)
# Data structures to store the class definitionss and instances
g_objectdefs = StaticObj('', None) # The root of the static tree
# has name '' (equivalent to '/')
g_objects = InstanceObj('', None) # The root of the instance tree
# has name '' (equivalent to '/')
# A list of commands to carry out
g_static_commands = []
g_instance_commands = []
BasicUI(settings,
g_objectdefs,
g_objects,
g_static_commands,
g_instance_commands)
# Now write the files
# (Finally carry out the "write()" and "write_once()" commands.)
# Optional: Multiple commands to write to the same file can be merged to
# reduce the number of times the file is openned and closed.
sys.stderr.write('writing templates...\n')
# Erase the files that will be written to:
EraseTemplateFiles(g_static_commands)
EraseTemplateFiles(g_instance_commands)
g_static_commands = MergeWriteCommands(g_static_commands)
g_instance_commands = MergeWriteCommands(g_instance_commands)
# Write the files with the original variable names present
WriteTemplatesVarName(g_static_commands)
WriteTemplatesVarName(g_instance_commands)
# Write the files with the variable names substituted by values
WriteTemplatesValue(g_static_commands)
WriteTemplatesValue(g_instance_commands)
sys.stderr.write(' done\n')
# Step 11: Now write the variable bindings/assignments table.
sys.stderr.write('writing \"ttree_assignments.txt\" file...')
open('ttree_assignments.txt', 'w').close() # <-- erase previous version.
WriteVarBindingsFile(g_objectdefs)
WriteVarBindingsFile(g_objects)
except (ValueError, InputError) as err:
sys.stderr.write('\n\n'+str(err)+'\n')
sys.exit(-1)

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