diff --git a/doc/src/Section_tools.txt b/doc/src/Section_tools.txt
index 03611c7cd..d95c4f0cd 100644
--- a/doc/src/Section_tools.txt
+++ b/doc/src/Section_tools.txt
@@ -1,497 +1,500 @@
"Previous Section"_Section_perf.html - "LAMMPS WWW Site"_lws - "LAMMPS
Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Section_modify.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
9. Additional tools :h3
LAMMPS is designed to be a computational kernel for performing
molecular dynamics computations. Additional pre- and post-processing
steps are often necessary to setup and analyze a simulation. A
list of such tools can be found on the LAMMPS home page
at "http://lammps.sandia.gov/prepost.html"_http://lammps.sandia.gov/prepost.html
A few additional tools are provided with the LAMMPS distribution
and are described in this section.
Our group has also written and released a separate toolkit called
"Pizza.py"_pizza which provides tools for doing setup, analysis,
plotting, and visualization for LAMMPS simulations. Pizza.py is
written in "Python"_python and is available for download from "the
Pizza.py WWW site"_pizza.
:link(pizza,http://www.sandia.gov/~sjplimp/pizza.html)
:link(python,http://www.python.org)
Note that many users write their own setup or analysis tools or use
other existing codes and convert their output to a LAMMPS input format
or vice versa. The tools listed here are included in the LAMMPS
distribution as examples of auxiliary tools. Some of them are not
actively supported by Sandia, as they were contributed by LAMMPS
users. If you have problems using them, we can direct you to the
authors.
The source code for each of these codes is in the tools sub-directory
of the LAMMPS distribution. There is a Makefile (which you may need
to edit for your platform) which will build several of the tools which
reside in that directory. Most of them are larger packages in their
own sub-directories with their own Makefiles and/or README files.
"amber2lmp"_#amber
"binary2txt"_#binary
"ch2lmp"_#charmm
"chain"_#chain
"colvars"_#colvars
"createatoms"_#createatoms
"drude"_#drude
"eam database"_#eamdb
"eam generate"_#eamgn
"eff"_#eff
"emacs"_#emacs
"fep"_#fep
"i-pi"_#ipi
"ipp"_#ipp
"kate"_#kate
"lmp2arc"_#arc
"lmp2cfg"_#cfg
"matlab"_#matlab
"micelle2d"_#micelle
"moltemplate"_#moltemplate
"msi2lmp"_#msi
"phonon"_#phonon
"polybond"_#polybond
"pymol_asphere"_#pymol
"python"_#pythontools
"reax"_#reax_tool
"smd"_#smd
"vim"_#vim
"xmgrace"_#xmgrace
:line
amber2lmp tool :h4,link(amber)
The amber2lmp sub-directory contains two Python scripts for converting
files back-and-forth between the AMBER MD code and LAMMPS. See the
README file in amber2lmp for more information.
These tools were written by Keir Novik while he was at Queen Mary
University of London. Keir is no longer there and cannot support
these tools which are out-of-date with respect to the current LAMMPS
version (and maybe with respect to AMBER as well). Since we don't use
these tools at Sandia, you'll need to experiment with them and make
necessary modifications yourself.
:line
binary2txt tool :h4,link(binary)
The file binary2txt.cpp converts one or more binary LAMMPS dump file
into ASCII text files. The syntax for running the tool is
binary2txt file1 file2 ... :pre
which creates file1.txt, file2.txt, etc. This tool must be compiled
on a platform that can read the binary file created by a LAMMPS run,
since binary files are not compatible across all platforms.
:line
ch2lmp tool :h4,link(charmm)
The ch2lmp sub-directory contains tools for converting files
back-and-forth between the CHARMM MD code and LAMMPS.
They are intended to make it easy to use CHARMM as a builder and as a
post-processor for LAMMPS. Using charmm2lammps.pl, you can convert a
PDB file with associated CHARMM info, including CHARMM force field
data, into its LAMMPS equivalent. Using lammps2pdb.pl you can convert
LAMMPS atom dumps into PDB files.
See the README file in the ch2lmp sub-directory for more information.
These tools were created by Pieter in't Veld (pjintve at sandia.gov)
and Paul Crozier (pscrozi at sandia.gov) at Sandia.
:line
chain tool :h4,link(chain)
The file chain.f creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
containing chain definition parameters as an input. The created
chains and solvent atoms can strongly overlap, so LAMMPS needs to run
the system initially with a "soft" pair potential to un-overlap it.
The syntax for running the tool is
chain < def.chain > data.file :pre
See the def.chain or def.chain.ab files in the tools directory for
examples of definition files. This tool was used to create the
system for the "chain benchmark"_Section_perf.html.
:line
colvars tools :h4,link(colvars)
The colvars directory contains a collection of tools for postprocessing
data produced by the colvars collective variable library.
To compile the tools, edit the makefile for your system and run "make".
Please report problems and issues the colvars library and its tools
at: https://github.com/colvars/colvars/issues
abf_integrate:
MC-based integration of multidimensional free energy gradient
Version 20110511
Syntax: ./abf_integrate < filename > \[-n < nsteps >\] \[-t < temp >\] \[-m \[0|1\] (metadynamics)\] \[-h < hill_height >\] \[-f < variable_hill_factor >\] :pre
The LAMMPS interface to the colvars collective variable library, as
well as these tools, were created by Axel Kohlmeyer (akohlmey at
gmail.com) at ICTP, Italy.
:line
createatoms tool :h4,link(createatoms)
The tools/createatoms directory contains a Fortran program called
createAtoms.f which can generate a variety of interesting crystal
structures and geometries and output the resulting list of atom
coordinates in LAMMPS or other formats.
See the included Manual.pdf for details.
The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov.
:line
drude tool :h4,link(drude)
The tools/drude directory contains a Python script called
polarizer.py which can add Drude oscillators to a LAMMPS
data file in the required format.
See the header of the polarizer.py file for details.
The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
:line
eam database tool :h4,link(eamdb)
The tools/eam_database directory contains a Fortran program that will
generate EAM alloy setfl potential files for any combination of 16
elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
Zr. The files can then be used with the "pair_style
eam/alloy"_pair_eam.html command.
The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
and is based on his paper:
X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
144113 (2004).
:line
eam generate tool :h4,link(eamgn)
The tools/eam_generate directory contains several one-file C programs
that convert an analytic formula into a tabulated "embedded atom
method (EAM)"_pair_eam.html setfl potential file. The potentials they
produce are in the potentials directory, and can be used with the
"pair_style eam/alloy"_pair_eam.html command.
The source files and potentials were provided by Gerolf Ziegenhain
(gerolf at ziegenhain.com).
:line
eff tool :h4,link(eff)
The tools/eff directory contains various scripts for generating
structures and post-processing output for simulations using the
electron force field (eFF).
These tools were provided by Andres Jaramillo-Botero at CalTech
(ajaramil at wag.caltech.edu).
:line
emacs tool :h4,link(emacs)
The tools/emacs directory contains a Lips add-on file for Emacs that
enables a lammps-mode for editing of input scripts when using Emacs,
with various highlighting options setup.
These tools were provided by Aidan Thompson at Sandia
(athomps at sandia.gov).
:line
fep tool :h4,link(fep)
The tools/fep directory contains Python scripts useful for
post-processing results from performing free-energy perturbation
simulations using the USER-FEP package.
The scripts were contributed by Agilio Padua (Universite Blaise
Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
See README file in the tools/fep directory.
:line
i-pi tool :h4,link(ipi)
The tools/i-pi directory contains a version of the i-PI package, with
all the LAMMPS-unrelated files removed. It is provided so that it can
be used with the "fix ipi"_fix_ipi.html command to perform
path-integral molecular dynamics (PIMD).
The i-PI package was created and is maintained by Michele Ceriotti,
michele.ceriotti at gmail.com, to interface to a variety of molecular
dynamics codes.
See the tools/i-pi/manual.pdf file for an overview of i-PI, and the
"fix ipi"_fix_ipi.html doc page for further details on running PIMD
calculations with LAMMPS.
:line
ipp tool :h4,link(ipp)
The tools/ipp directory contains a Perl script ipp which can be used
to facilitate the creation of a complicated file (say, a lammps input
script or tools/createatoms input file) using a template file.
ipp was created and is maintained by Reese Jones (Sandia), rjones at
sandia.gov.
See two examples in the tools/ipp directory. One of them is for the
tools/createatoms tool's input file.
:line
kate tool :h4,link(kate)
The file in the tools/kate directory is an add-on to the Kate editor
in the KDE suite that allow syntax highlighting of LAMMPS input
scripts. See the README.txt file for details.
The file was provided by Alessandro Luigi Sellerio
(alessandro.sellerio at ieni.cnr.it).
:line
lmp2arc tool :h4,link(arc)
The lmp2arc sub-directory contains a tool for converting LAMMPS output
files to the format for Accelrys' Insight MD code (formerly
MSI/Biosym and its Discover MD code). See the README file for more
information.
This tool was written by John Carpenter (Cray), Michael Peachey
(Cray), and Steve Lustig (Dupont). John is now at the Mayo Clinic
(jec at mayo.edu), but still fields questions about the tool.
This tool was updated for the current LAMMPS C++ version by Jeff
Greathouse at Sandia (jagreat at sandia.gov).
:line
lmp2cfg tool :h4,link(cfg)
The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of *.cfg files which can be read into the
"AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A visualizer. See
the README file for more information.
This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
:line
matlab tool :h4,link(matlab)
The matlab sub-directory contains several "MATLAB"_matlabhome scripts for
post-processing LAMMPS output. The scripts include readers for log
and dump files, a reader for EAM potential files, and a converter that
reads LAMMPS dump files and produces CFG files that can be visualized
with the "AtomEye"_http://mt.seas.upenn.edu/Archive/Graphics/A
visualizer.
See the README.pdf file for more information.
These scripts were written by Arun Subramaniyan at Purdue Univ
(asubrama at purdue.edu).
:link(matlabhome,http://www.mathworks.com)
:line
micelle2d tool :h4,link(micelle)
The file micelle2d.f creates a LAMMPS data file containing short lipid
chains in a monomer solution. It uses a text file containing lipid
definition parameters as an input. The created molecules and solvent
atoms can strongly overlap, so LAMMPS needs to run the system
initially with a "soft" pair potential to un-overlap it. The syntax
for running the tool is
micelle2d < def.micelle2d > data.file :pre
See the def.micelle2d file in the tools directory for an example of a
definition file. This tool was used to create the system for the
"micelle example"_Section_example.html.
:line
moltemplate tool :h4,link(moltemplate)
The moltemplate sub-directory contains a Python-based tool for
building molecular systems based on a text-file description, and
creating LAMMPS data files that encode their molecular topology as
lists of bonds, angles, dihedrals, etc. See the README.TXT file for
more information.
This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
supports it. It has its own WWW page at
"http://moltemplate.org"_http://moltemplate.org.
:line
msi2lmp tool :h4,link(msi)
-The msi2lmp sub-directory contains a tool for creating LAMMPS input
-data files from BIOVIA's Materias Studio files (formerly Accelrys'
+The msi2lmp sub-directory contains a tool for creating LAMMPS template
+input and data files from BIOVIA's Materias Studio files (formerly Accelrys'
Insight MD code, formerly MSI/Biosym and its Discover MD code).
This tool was written by John Carpenter (Cray), Michael Peachey
(Cray), and Steve Lustig (Dupont). Several people contributed changes
to remove bugs and adapt its output to changes in LAMMPS.
-See the README file for more information.
+This tool has several known limitations and is no longer under active
+development, so there are no changes except for the occasional bugfix.
+
+See the README file in the tools/msi2lmp folder for more information.
:line
phonon tool :h4,link(phonon)
The phonon sub-directory contains a post-processing tool useful for
analyzing the output of the "fix phonon"_fix_phonon.html command in
the USER-PHONON package.
See the README file for instruction on building the tool and what
library it needs. And see the examples/USER/phonon directory
for example problems that can be post-processed with this tool.
This tool was written by Ling-Ti Kong at Shanghai Jiao Tong
University.
:line
polybond tool :h4,link(polybond)
The polybond sub-directory contains a Python-based tool useful for
performing "programmable polymer bonding". The Python file
lmpsdata.py provides a "Lmpsdata" class with various methods which can
be invoked by a user-written Python script to create data files with
complex bonding topologies.
See the Manual.pdf for details and example scripts.
This tool was written by Zachary Kraus at Georgia Tech.
:line
pymol_asphere tool :h4,link(pymol)
The pymol_asphere sub-directory contains a tool for converting a
LAMMPS dump file that contains orientation info for ellipsoidal
particles into an input file for the "PyMol visualization
package"_pymolhome or its "open source variant"_pymolopen.
:link(pymolhome,http://www.pymol.org)
:link(pymolopen,http://sourceforge.net/scm/?type=svn&group_id=4546)
Specifically, the tool triangulates the ellipsoids so they can be
viewed as true ellipsoidal particles within PyMol. See the README and
examples directory within pymol_asphere for more information.
This tool was written by Mike Brown at Sandia.
:line
python tool :h4,link(pythontools)
The python sub-directory contains several Python scripts
that perform common LAMMPS post-processing tasks, such as:
extract thermodynamic info from a log file as columns of numbers
plot two columns of thermodynamic info from a log file using GnuPlot
sort the snapshots in a dump file by atom ID
convert multiple "NEB"_neb.html dump files into one dump file for viz
convert dump files into XYZ, CFG, or PDB format for viz by other packages :ul
These are simple scripts built on "Pizza.py"_pizza modules. See the
README for more info on Pizza.py and how to use these scripts.
:line
reax tool :h4,link(reax_tool)
The reax sub-directory contains stand-alond codes that can
post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
command from a LAMMPS simulation using "ReaxFF"_pair_reax.html. See
the README.txt file for more info.
These tools were written by Aidan Thompson at Sandia.
:line
smd tool :h4,link(smd)
The smd sub-directory contains a C++ file dump2vtk_tris.cpp and
Makefile which can be compiled and used to convert triangle output
files created by the Smooth-Mach Dynamics (USER-SMD) package into a
VTK-compatible unstructured grid file. It could then be read in and
visualized by VTK.
See the header of dump2vtk.cpp for more details.
This tool was written by the USER-SMD package author, Georg
Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics,
Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de).
:line
vim tool :h4,link(vim)
The files in the tools/vim directory are add-ons to the VIM editor
that allow easier editing of LAMMPS input scripts. See the README.txt
file for details.
These files were provided by Gerolf Ziegenhain (gerolf at
ziegenhain.com)
:line
xmgrace tool :h4,link(xmgrace)
The files in the tools/xmgrace directory can be used to plot the
thermodynamic data in LAMMPS log files via the xmgrace plotting
package. There are several tools in the directory that can be used in
post-processing mode. The lammpsplot.cpp file can be compiled and
used to create plots from the current state of a running LAMMPS
simulation.
See the README file for details.
These files were provided by Vikas Varshney (vv0210 at gmail.com)
diff --git a/tools/msi2lmp/README b/tools/msi2lmp/README
index a20f6e893..db9b1aca5 100644
--- a/tools/msi2lmp/README
+++ b/tools/msi2lmp/README
@@ -1,227 +1,240 @@
-Axel Kohlmeyer is the current maintainer of the msi2lmp tool.
-Please send any inquiries about msi2lmp to the lammps-users mailing list.
-06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>
-
-Improved whitespace handling in parsing topology and force field
-files to avoid bogus warnings about type name truncation.
-
-24 Oct 2015 Axel Kohlmeyer <akohlmey@gmail.com>
-
-Added check to make certain that force field files
-are consistent with the notation of non-bonded parameters
-that the msi2lmp code expects. For Class 1 and OPLS-AA
-the A-B notation with geometric mixing is expected and for
-Class 2 the r-eps notation with sixthpower mixing.
-
-11 Sep 2014 Axel Kohlmeyer <akohlmey@gmail.com>
-
-Refactored ReadMdfFile.c so it more consistently honors
-the MAX_NAME and MAX_STRING string length defines and
-potentially handles inputs with long names better.
-
-27 May 2014 Axel Kohlmeyer <akohlmey@gmail.com>
-
-Added TopoTools style type hints as comments to all Mass, PairCoeff,
-BondCoeff, AngleCoeff, DihedralCoeff, ImproperCoeff entries.
-This should make it easier to identify force field entries with
-the structure and force field map in the data file later.
-
-06 Mar 2014 Axel Kohlmeyer <akohlmey@gmail.com>
-
-Fixed a bug in handling of triclinic cells, where the matrices to
-convert to and from fractional coordinates were incorrectly built.
-
-26 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
-
-Implemented writing out force field style hints in generated data
-files for improved consistency checking when reading those files.
-Also added writing out CGCMM style comments to identify atom types.
+ msi2lmp.exe
-08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+This code has several known limitations listed below under "LIMITATIONS"
+(and possibly some unknown ones, too) and is no longer under active
+development. Only the occasional bugfix is applied.
-Fixed a memory access violation with Class 2 force fields.
-Free all allocated memory to better detection of memory errors.
-Print out version number and data with all print levels > 0.
-Added valgrind checks to the regression tests
+Please send any inquiries about msi2lmp to the lammps-users
+mailing list and not to individual people.
-08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+------------------------------------------------------------------------
-Fixed a memory access violation with Class 2 force fields.
-Free all allocated memory to better detection of memory errors.
-Print out version number and data with all print levels > 0.
-Added valgrind checks to the regression tests
+OVERVIEW
-02 Aug 2013 Axel Kohlmeyer <akohlmey@gmail.com>
-
-Added rudimentary support for OPLS-AA based on
-input provided by jeff greathouse.
+This is the third version of a program that generates a LAMMPS data file
+based on the information in MSI .car (atom coordinates), .mdf (molecular
+topology) and .frc (forcefield) files. The .car and .mdf files are
+specific to a molecular system while the .frc file is specific to a
+forcefield version. The only coherency needed between .frc and
+.car/.mdf files are the atom types.
-18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
-
-Added support for writing out image flags
-Improved accuracy of atom masses
-Added flag for shifting the entire system
-Fixed some minor logic bugs and prepared
-for supporting other force fields and morse style bonds.
-
-12 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
-
-Fixed the bug that caused improper coefficients to be wrong
-Cleaned up the handling of box parameters and center the box
-by default around the system/molecule. Added a flag to make
-this step optional and center the box around the origin instead.
-Added a regression test script with examples.
-
-1 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+The first version was written by Steve Lustig at Dupont, but required
+using Discover to derive internal coordinates and forcefield parameters
-Cleanup and improved port to windows.
-Removed some more static string limits.
-Added print level 3 for additional output.
-Make code stop at missing force field parameters
-and added -i flag to override this.
-Safer argument checking.
-Provide short versions for all flags.
+The second version was written by Michael Peachey while an intern in the
+Cray Chemistry Applications Group managed by John Carpenter. This
+version derived internal coordinates from the mdf file and looked up
+parameters in the frc file thus eliminating the need for Discover.
-23 Sep 2011
+The third version was written by John Carpenter to optimize the
+performance of the program for large molecular systems (the original
+code for deriving atom numbers was quadratic in time) and to make the
+program fully dynamic. The second version used fixed dimension arrays
+for the internal coordinates.
-added support for triclinic boxes
-see msi2lmp/TriclinicModification.pdf doc for details
+The third version was revised in Fall 2011 by Stephanie Teich-McGoldrick
+to add support non-orthogonal cells.
------------------------------
+The next revision was started in Summer/Fall 2013 by Axel Kohlmeyer to
+improve portability to Windows compilers, clean up command line parsing
+and improve compatibility with the then current LAMMPS versions. This
+revision removes compatibility with the obsolete LAMMPS version written
+in Fortran 90.
- msi2lmp V3.6 4/10/2005
+INSTALLATION & USAGE
- This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
+This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
program to produce a LAMMPS data file.
1. Building msi2lmp
Use the Makefile in the src directory. It is
currently set up for gcc. You will have to modify
it to use a different compiler.
2. Testing the program
There are several pairs of input test files in the format generated
by materials studio or compatible programs (one .car and one .mdf
file each) in the test directory. There is also a LAMMPS input to
run a minimization for each and write out the resulting system as
a data file. With the runtests.sh script all of those inputs are
converted via msi2lmp, then the minimization with LAMMPS is run
and the generated data files are compared with the corresponding
files in the reference folder. This script assumes you are on a
unix/linux system and that you have compile a serial LAMMPS executable
called lmp_serial with make serial. The tests are groups by the
force fields they use.
3. To run the program
The program is started by supplying information at the command prompt
according to the usage described below.
USAGE: msi2lmp.exe <ROOTNAME> {-print #} {-class #} {-frc FRC_FILE}
{-ignore} {-nocenter} {-shift # # #}
-- msi2lmp.exe is the name of the executable
-- <ROOTNAME> is the base name of the .car and .mdf files
-- -2001
Output lammps files for LAMMPS version 2001 (F90 version)
Default is to write output for the C++ version of LAMMPS
-- -print (or -p)
# is the print level 0 - silent except for error messages
1 - minimal (default)
2 - verbose (usual for developing and
checking new data files for consistency)
3 - even more verbose (additional debug info)
-- -ignore (or -i) ignore errors about missing force field parameters
and treat them as warnings instead.
-- -nocenter (or -n) do not recenter the simulation box around the
geometrical center of the provided geometry but
rather around the origin
-- -oldstyle (or -o) write out a data file without style hints
(to be compatible with older LAMMPS versions)
-- -shift (or -s) translate the entire system (box and coordinates)
by a vector (default: 0.0 0.0 0.0)
-- -class (or -c)
# is the class of forcefield to use (I or 1 = Class I e.g., CVFF)
(O or 0 = OPLS-AA)
(II or 2 = Class II e.g., CFFx)
default is -class I
-- -frc (or -f) specifies name of the forcefield file (e.g., cff91)
If the file name includes a directory component (or drive letter
on Windows), then the name is used as is. Otherwise, the program
looks for the forcefield file in $MSI2LMP_LIBRARY (or %MSI2LMP_LIBRARY%
on Windows). If $MSI2LMP_LIBRARY is not set, ../frc_files is used
(for testing). If the file name does not end in .frc, then .frc
is appended to the name.
For example, -frc cvff (assumes cvff.frc is in $MSI2LMP_LIBRARY
or ../frc_files)
-frc cff/cff91 (assumes cff91.frc is in cff)
-frc /usr/local/forcefields/cff95
(assumes cff95.frc is in /usr/local/forcefields/)
By default, the program uses $MSI2LMP_LIBRARY/cvff.frc or
../frc_files/cvff.frc depending on whether MSI2LMP_LIBRARY is set.
-- the LAMMPS data file is written to <ROOTNAME>.data
protocol and error information is written to the screen.
-****************************************************************
-*
-* msi2lmp
-*
-* This is the third version of a program that generates a LAMMPS
-* data file based on the information in MSI .car (atom
-* coordinates), .mdf (molecular topology) and .frc (forcefield)
-* files. The .car and .mdf files are specific to a molecular
-* system while the .frc file is specific to a forcefield version.
-* The only coherency needed between .frc and .car/.mdf files are
-* the atom types.
-*
-* The first version was written by Steve Lustig at Dupont, but
-* required using Discover to derive internal coordinates and
-* forcefield parameters
-*
-* The second version was written by Michael Peachey while an
-* intern in the Cray Chemistry Applications Group managed
-* by John Carpenter. This version derived internal coordinates
-* from the mdf file and looked up parameters in the frc file
-* thus eliminating the need for Discover.
-*
-* The third version was written by John Carpenter to optimize
-* the performance of the program for large molecular systems
-* (the original code for deriving atom numbers was quadratic in time)
-* and to make the program fully dynamic. The second version used
-* fixed dimension arrays for the internal coordinates.
-*
-* The current maintainer is only reluctantly doing so because John Mayo no longer
-* needs this code.
-*
-* V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
-* systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
-* for number_of_dihedrals, etc. could be unpredictable in these systems.
-*
-* V3.3 was generated in response to a strange error reading a MDF file generated by
-* Accelys' Materials Studio GUI. Simply rewriting the input part of ReadMdfFile.c
-* seems to have fixed the problem.
-*
-* V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car and .mdf files
-* written by Accelys' Materials Studio GUI.
-*
-* V3.6 outputs to LAMMPS 2005 (C++ version).
-*
-* Contact: Kelly L. Anderson, kelly.anderson@cantab.net
-*
-* April 2005
+------------------------------------------------------------------------
+
+LIMITATIONS
+
+msi2lmp has the following known limitations:
+
+- there is no support to select morse bonds over harmonic bonds
+- there is no support for auto-equivalences to supplement fully
+ parameterized interactions with heuristic ones
+- there is no support for bond increments
+
+------------------------------------------------------------------------
+
+CHANGELOG
+
+06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Improved whitespace handling in parsing topology and force field
+files to avoid bogus warnings about type name truncation.
+
+24 Oct 2015 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Added check to make certain that force field files are consistent with
+the notation of non-bonded parameters that the msi2lmp code expects.
+For Class 1 and OPLS-AA the A-B notation with geometric mixing is
+expected and for Class 2 the r-eps notation with sixthpower mixing.
+
+11 Sep 2014 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Refactored ReadMdfFile.c so it more consistently honors the MAX_NAME
+and MAX_STRING string length defines and potentially handles inputs
+with long names better.
+
+27 May 2014 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Added TopoTools style type hints as comments to all Mass, PairCoeff,
+BondCoeff, AngleCoeff, DihedralCoeff, ImproperCoeff entries.
+This should make it easier to identify force field entries with
+the structure and force field map in the data file later.
+
+06 Mar 2014 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Fixed a bug in handling of triclinic cells, where the matrices to
+convert to and from fractional coordinates were incorrectly built.
+
+26 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Implemented writing out force field style hints in generated data
+files for improved consistency checking when reading those files.
+Also added writing out CGCMM style comments to identify atom types.
+
+08 Oct 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Fixed a memory access violation with Class 2 force fields. Free all
+allocated memory to better detection of memory errors. Print out
+version number and data with all print levels > 0. Added valgrind
+checks to the regression tests.
+
+02 Aug 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Added rudimentary support for OPLS-AA based on input provided
+by jeff greathouse.
+
+18 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Added support for writing out image flags. Improved accuracy of atom
+masses. Added flag for shifting the entire system. Fixed some minor
+logic bugs and prepared for supporting other force fields and morse
+style bonds.
+
+12 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Fixed the bug that caused improper coefficients to be wrong. Cleaned up
+the handling of box parameters and center the box by default around the
+system/molecule. Added a flag to make this step optional and center the
+box around the origin instead. Added a regression test script with
+examples.
+
+1 Jul 2013 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Cleanup and improved port to windows. Removed some more static string
+limits. Added print level 3 for additional output. Make code stop at
+missing force field parameters and added -i flag to override this.
+Safer argument checking. Provide short versions for all flags.
+
+23 Sep 2011
+
+added support for triclinic boxes
+
+V3.6 outputs to LAMMPS 2005 (C++ version).
+
+Contact: Kelly L. Anderson, kelly.anderson@cantab.net
+
+V3.4 and V3.5 are minor upgrades to fix bugs associated mostly with .car
+ and .mdf files written by Accelys' Materials Studio GUI. April 2005
+
+V3.3 was generated in response to a strange error reading a MDF file
+generated by Accelys' Materials Studio GUI. Simply rewriting the input
+part of ReadMdfFile.c seems to have fixed the problem.
+
+V3.2 corresponds to adding code to MakeLists.c to gracefully deal with
+systems that may only be molecules of 1 to 3 atoms. In V3.1, the values
+for number_of_dihedrals, etc. could be unpredictable in these systems.
+
+-----------------------------
+
+ msi2lmp v3.9.8 6/10/2016
+