diff --git a/doc/doc2/Section_packages.html b/doc/doc2/Section_packages.html index 16186a05d..f6197d014 100644 --- a/doc/doc2/Section_packages.html +++ b/doc/doc2/Section_packages.html @@ -1,821 +1,850 @@ <HTML> <CENTER><A HREF = "Section_commands.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_accelerate.html">Next Section</A> </CENTER> <HR> <H3>4. Packages </H3> <P>This section gives a quick overview of the add-on packages that extend LAMMPS functionality. </P> 4.1 <A HREF = "#pkg_1">Standard packages</A><BR> 4.2 <A HREF = "#pkg_2">User packages</A> <BR> <P>LAMMPS includes many optional packages, which are groups of files that enable a specific set of features. For example, force fields for molecular systems or granular systems are in packages. You can see the list of all packages by typing "make package" from within the src directory of the LAMMPS distribution. </P> <P>See <A HREF = "Section_start.html#start_3">Section_start 3</A> of the manual for details on how to include/exclude specific packages as part of the LAMMPS build process, and for more details about the differences between standard packages and user packages. </P> <P>Unless otherwise noted below, every package is independent of all the others. I.e. any package can be included or excluded in a LAMMPS build, independent of all other packages. However, note that some packages include commands derived from commands in other packages. If the other package is not installed, the derived command from the new package will also not be installed when you include the new one. E.g. the pair lj/cut/coul/long/omp command from the USER-OMP package will not be installed as part of the USER-OMP package if the KSPACE package is not also installed, since it contains the pair lj/cut/coul/long command. If you later install the KSPACE pacakge and the USER-OMP package is already installed, both the pair lj/cut/coul/long and lj/cut/coul/long/omp commands will be installed. </P> <P>The two tables below list currently available packages in LAMMPS, with a one-line descriptions of each. The sections below give a few more details, including instructions for building LAMMPS with the package, either via the make command or the Make.py tool described in <A HREF = "Section_start.html#start_4">Section 2.4</A>. </P> <HR> <HR> <H4><A NAME = "pkg_1"></A>4.1 Standard packages </H4> <P>The current list of standard packages is as follows. </P> <DIV ALIGN=center><TABLE BORDER=1 > <TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Library</TD></TR> <TR ALIGN="center"><TD >ASPHERE</TD><TD > aspherical particles</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_14">Section_howto 6.14</A></TD><TD > ellipse</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >BODY</TD><TD > body-style particles</TD><TD > -</TD><TD > <A HREF = "body.html">body</A></TD><TD > body</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >CLASS2</TD><TD > class 2 force fields</TD><TD > -</TD><TD > <A HREF = "pair_class2.html">pair_style lj/class2</A></TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >COLLOID</TD><TD > colloidal particles</TD><TD > -</TD><TD > <A HREF = "atom_style.html">atom_style colloid</A></TD><TD > colloid</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >COMPRESS</TD><TD > I/O compression</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump.html">dump */gz</A></TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >CORESHELL</TD><TD > adiabatic core/shell model</TD><TD > Hendrik Heenen (Technical U of Munich)</TD><TD > <A HREF = "Section_howto.html#howto_25">Section_howto 6.25</A></TD><TD > coreshell</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >DIPOLE</TD><TD > point dipole particles</TD><TD > -</TD><TD > <A HREF = "pair_dipole.html">pair_style dipole/cut</A></TD><TD > dipole</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >FLD</TD><TD > Fast Lubrication Dynamics</TD><TD > Kumar & Bybee & Higdon (1)</TD><TD > <A HREF = "pair_lubricateU.html">pair_style lubricateU</A></TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >GPU</TD><TD > GPU-enabled styles</TD><TD > Mike Brown (ORNL)</TD><TD > <A HREF = "accelerate_gpu.html">Section accelerate</A></TD><TD > gpu</TD><TD > lib/gpu</TD></TR> <TR ALIGN="center"><TD >GRANULAR</TD><TD > granular systems</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_6">Section_howto 6.6</A></TD><TD > pour</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >KIM</TD><TD > openKIM potentials</TD><TD > Smirichinski & Elliot & Tadmor (3)</TD><TD > <A HREF = "pair_kim.html">pair_style kim</A></TD><TD > kim</TD><TD > KIM</TD></TR> <TR ALIGN="center"><TD >KOKKOS</TD><TD > Kokkos-enabled styles</TD><TD > Trott & Edwards (4)</TD><TD > <A HREF = "accelerate_kokkos.html">Section_accelerate</A></TD><TD > kokkos</TD><TD > lib/kokkos</TD></TR> <TR ALIGN="center"><TD >KSPACE</TD><TD > long-range Coulombic solvers</TD><TD > -</TD><TD > <A HREF = "kspace_style.html">kspace_style</A></TD><TD > peptide</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >MANYBODY</TD><TD > many-body potentials</TD><TD > -</TD><TD > <A HREF = "pair_tersoff.html">pair_style tersoff</A></TD><TD > shear</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >MEAM</TD><TD > modified EAM potential</TD><TD > Greg Wagner (Sandia)</TD><TD > <A HREF = "pair_meam.html">pair_style meam</A></TD><TD > meam</TD><TD > lib/meam</TD></TR> <TR ALIGN="center"><TD >MC</TD><TD > Monte Carlo options</TD><TD > -</TD><TD > <A HREF = "fix_gcmc.html">fix gcmc</A></TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >MOLECULE</TD><TD > molecular system force fields</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_3">Section_howto 6.3</A></TD><TD > peptide</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >OPT</TD><TD > optimized pair styles</TD><TD > Fischer & Richie & Natoli (2)</TD><TD > <A HREF = "accelerate_opt.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >PERI</TD><TD > Peridynamics models</TD><TD > Mike Parks (Sandia)</TD><TD > <A HREF = "pair_peri.html">pair_style peri</A></TD><TD > peri</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >POEMS</TD><TD > coupled rigid body motion</TD><TD > Rudra Mukherjee (JPL)</TD><TD > <A HREF = "fix_poems.html">fix poems</A></TD><TD > rigid</TD><TD > lib/poems</TD></TR> <TR ALIGN="center"><TD >PYTHON</TD><TD > embed Python code in an input script</TD><TD > -</TD><TD > <A HREF = "python.html">python</A></TD><TD > python</TD><TD > lib/python</TD></TR> <TR ALIGN="center"><TD >REAX</TD><TD > ReaxFF potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_reax.html">pair_style reax</A></TD><TD > reax</TD><TD > lib/reax</TD></TR> <TR ALIGN="center"><TD >REPLICA</TD><TD > multi-replica methods</TD><TD > -</TD><TD > <A HREF = "Section_howto.html#howto_5">Section_howto 6.5</A></TD><TD > tad</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >RIGID</TD><TD > rigid bodies</TD><TD > -</TD><TD > <A HREF = "fix_rigid.html">fix rigid</A></TD><TD > rigid</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >SHOCK</TD><TD > shock loading methods</TD><TD > -</TD><TD > <A HREF = "fix_msst.html">fix msst</A></TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >SNAP</TD><TD > quantum-fit potential</TD><TD > Aidan Thompson (Sandia)</TD><TD > <A HREF = "pair_snap.html">pair snap</A></TD><TD > snap</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >SRD</TD><TD > stochastic rotation dynamics</TD><TD > -</TD><TD > <A HREF = "fix_srd.html">fix srd</A></TD><TD > srd</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >VORONOI</TD><TD > Voronoi tesselations</TD><TD > Daniel Schwen (LANL)</TD><TD > <A HREF = "compute_voronoi_atom.html">compute voronoi/atom</A></TD><TD > -</TD><TD > Voro++</TD></TR> <TR ALIGN="center"><TD >XTC</TD><TD > dumps in XTC format</TD><TD > -</TD><TD > <A HREF = "dump.html">dump</A></TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD > </TD></TR></TABLE></DIV> <P>The "Authors" column lists a name(s) if a specific person is responible for creating and maintaining the package. More details on multiple authors are give below. </P> <P>(1) The FLD package was created by Amit Kumar and Michael Bybee from Jonathan Higdon's group at UIUC. </P> <P>(2) The OPT package was created by James Fischer (High Performance Technologies), David Richie, and Vincent Natoli (Stone Ridge Technolgy). </P> <P>(3) The KIM package was created by Valeriu Smirichinski, Ryan Elliott, and Ellad Tadmor (U Minn). </P> <P>(4) The KOKKOS package was created primarily by Christian Trott (Sandia). It uses the Kokkos library which was developed by Carter Edwards, Christian, and collaborators at Sandia. </P> <P>The "Doc page" column links to either a portion of the <A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script command implemented as part of the package. </P> <P>The "Example" column is a sub-directory in the examples directory of the distribution which has an input script that uses the package. E.g. "peptide" refers to the examples/peptide directory. </P> <P>The "Library" column lists an external library which must be built first and which LAMMPS links to when it is built. If it is listed as lib/package, then the code for the library is under the lib directory of the LAMMPS distribution. See the lib/package/README file for info on how to build the library. If it is not listed as lib/package, then it is a third-party library not included in the LAMMPS distribution. See the src/package/README or src/package/Makefile.lammps file for info on where to download the library. <A HREF = "Section_start.html#start_3_3">Section start</A> of the manual also gives details on how to build LAMMPS with both kinds of auxiliary libraries. </P> <P>Except where explained below, all of these packages can be installed, and LAMMPS re-built, by issuing these commands from the src dir. </P> <PRE>make yes-package make machine or Make.py -p package -a machine </PRE> <P>To un-install the package and re-build LAMMPS without it: </P> <PRE>make no-package make machine or Make.py -p ^package -a machine </PRE> <P>"Package" is the name of the package in lower-case letters, e.g. asphere or rigid, and "machine" is the build target, e.g. mpi or serial. </P> <HR> <HR> <H4>Build instructions for COMPRESS package </H4> <HR> <H4>Build instructions for GPU package </H4> <HR> <H4>Build instructions for KIM package </H4> <HR> <H4>Build instructions for KOKKOS package </H4> <HR> <H4>Build instructions for KSPACE package </H4> <HR> <H4>Build instructions for MEAM package </H4> <HR> <H4>Build instructions for POEMS package </H4> <HR> <H4>Build instructions for PYTHON package </H4> <HR> <H4>Build instructions for REAX package </H4> <HR> <H4>Build instructions for VORONOI package </H4> <HR> <H4>Build instructions for XTC package </H4> <HR> <HR> <H4><A NAME = "pkg_2"></A>4.2 User packages </H4> <P>The current list of user-contributed packages is as follows: </P> <DIV ALIGN=center><TABLE BORDER=1 > <TR ALIGN="center"><TD >Package</TD><TD > Description</TD><TD > Author(s)</TD><TD > Doc page</TD><TD > Example</TD><TD > Pic/movie</TD><TD > Library</TD></TR> <TR ALIGN="center"><TD >USER-ATC</TD><TD > atom-to-continuum coupling</TD><TD > Jones & Templeton & Zimmerman (1)</TD><TD > <A HREF = "fix_atc.html">fix atc</A></TD><TD > USER/atc</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#atc">atc</A></TD><TD > lib/atc</TD></TR> <TR ALIGN="center"><TD >USER-AWPMD</TD><TD > wave-packet MD</TD><TD > Ilya Valuev (JIHT)</TD><TD > <A HREF = "pair_awpmd.html">pair_style awpmd/cut</A></TD><TD > USER/awpmd</TD><TD > -</TD><TD > lib/awpmd</TD></TR> <TR ALIGN="center"><TD >USER-CG-CMM</TD><TD > coarse-graining model</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "pair_sdk.html">pair_style lj/sdk</A></TD><TD > USER/cg-cmm</TD><TD > <A HREF = "http://lammps.sandia.gov/pictures.html#cg">cg</A></TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-COLVARS</TD><TD > collective variables</TD><TD > Fiorin & Henin & Kohlmeyer (2)</TD><TD > <A HREF = "fix_colvars.html">fix colvars</A></TD><TD > USER/colvars</TD><TD > <A HREF = "colvars">colvars</A></TD><TD > lib/colvars</TD></TR> <TR ALIGN="center"><TD >USER-CUDA</TD><TD > NVIDIA GPU styles</TD><TD > Christian Trott (U Tech Ilmenau)</TD><TD > <A HREF = "accelerate_cuda.html">Section accelerate</A></TD><TD > USER/cuda</TD><TD > -</TD><TD > lib/cuda</TD></TR> <TR ALIGN="center"><TD >USER-DIFFRACTION</TD><TD > virutal x-ray and electron diffraction</TD><TD > Shawn Coleman (ARL)</TD><TD ><A HREF = "compute_xrd.html">compute xrd</A></TD><TD > USER/diffraction</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-DRUDE</TD><TD > Drude oscillators</TD><TD > Dequidt & Devemy & Padua (3)</TD><TD > <A HREF = "tutorial_drude.html">tutorial</A></TD><TD > USER/drude</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-EFF</TD><TD > electron force field</TD><TD > Andres Jaramillo-Botero (Caltech)</TD><TD > <A HREF = "pair_eff.html">pair_style eff/cut</A></TD><TD > USER/eff</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#eff">eff</A></TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-FEP</TD><TD > free energy perturbation</TD><TD > Agilio Padua (U Blaise Pascal Clermont-Ferrand)</TD><TD > <A HREF = "compute_fep.html">compute fep</A></TD><TD > USER/fep</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-H5MD</TD><TD > dump output via HDF5</TD><TD > Pierre de Buyl (KU Leuven)</TD><TD > <A HREF = "dump_h5md.html">dump h5md</A></TD><TD > -</TD><TD > -</TD><TD > lib/h5md</TD></TR> <TR ALIGN="center"><TD >USER-INTEL</TD><TD > Vectorized CPU and Intel(R) coprocessor styles</TD><TD > W. Michael Brown (Intel)</TD><TD > <A HREF = "accelerate_intel.html">Section accelerate</A></TD><TD > examples/intel</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-LB</TD><TD > Lattice Boltzmann fluid</TD><TD > Colin Denniston (U Western Ontario)</TD><TD > <A HREF = "fix_lb_fluid.html">fix lb/fluid</A></TD><TD > USER/lb</TD><TD > -</TD><TD > -</TD></TR> +<TR ALIGN="center"><TD >USER-MGPT</TD><TD > Fast MGPT multi-ion potentials</TD><TD > Tomas Oppelstrup & John Moriarty (LLNL)</TD><TD > <A HREF = "pair_mgpt.html">pair_style mgpt</A></TD><TD > USER/mgpt</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-MISC</TD><TD > single-file contributions</TD><TD > USER-MISC/README</TD><TD > USER-MISC/README</TD><TD > -</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-MOLFILE</TD><TD > <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molfile plug-ins</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "dump_molfile.html">dump molfile</A></TD><TD > -</TD><TD > -</TD><TD > VMD-MOLFILE</TD></TR> <TR ALIGN="center"><TD >USER-OMP</TD><TD > OpenMP threaded styles</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "accelerate_omp.html">Section accelerate</A></TD><TD > -</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-PHONON</TD><TD > phonon dynamical matrix</TD><TD > Ling-Ti Kong (Shanghai Jiao Tong U)</TD><TD > <A HREF = "fix_phonon.html">fix phonon</A></TD><TD > USER/phonon</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-QMMM</TD><TD > QM/MM coupling</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "fix_qmmm.html">fix qmmm</A></TD><TD > USER/qmmm</TD><TD > -</TD><TD > lib/qmmm</TD></TR> <TR ALIGN="center"><TD >USER-QTB</TD><TD > quantum nuclear effects</TD><TD > Yuan Shen (Stanford)</TD><TD > <A HREF = "fix_qtb.html">fix qtb</A> <A HREF = "fix_qbmsst.html">fix_qbmsst</A></TD><TD > qtb</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-QUIP</TD><TD > QUIP/libatoms interface</TD><TD > Albert Bartok-Partay (U Cambridge)</TD><TD > <A HREF = "pair_quip.html">pair_style quip</A></TD><TD > USER/quip</TD><TD > -</TD><TD > lib/quip</TD></TR> <TR ALIGN="center"><TD >USER-REAXC</TD><TD > C version of ReaxFF</TD><TD > Metin Aktulga (LBNL)</TD><TD > <A HREF = "pair_reax_c.html">pair_style reaxc</A></TD><TD > reax</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-SMD</TD><TD > smoothed Mach dynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/smd</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-SPH</TD><TD > smoothed particle hydrodynamics</TD><TD > Georg Ganzenmuller (EMI)</TD><TD > <A HREF = "PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</A></TD><TD > USER/sph</TD><TD > <A HREF = "http://lammps.sandia.gov/movies.html#sph">sph</A></TD><TD > -</TD></TR> <TR ALIGN="center"><TD >USER-TALLY</TD><TD > Pairwise tallied computes</TD><TD > Axel Kohlmeyer (Temple U)</TD><TD > <A HREF = "compute_tally.html">compute <...>/tally</A></TD><TD > USER/tally</TD><TD > -</TD><TD > -</TD></TR> <TR ALIGN="center"><TD > </TD></TR></TABLE></DIV> <P>The "Authors" column lists a name(s) if a specific person is responible for creating and maintaining the package. </P> <P>(1) The ATC package was created by Reese Jones, Jeremy Templeton, and Jon Zimmerman (Sandia). </P> <P>(2) The COLVARS package was created by Axel Kohlmeyer (Temple U) using the colvars module library written by Giacomo Fiorin (Temple U) and Jerome Henin (LISM, Marseille, France). </P> <P>(3) The DRUDE package was created by Alain Dequidt (U Blaise Pascal Clermont-Ferrand) and co-authors Julien Devemy (CNRS) and Agilio Padua (U Blaise Pascal). </P> <P>If the Library is not listed as lib/package, then it is a third-party library not included in the LAMMPS distribution. See the src/package/Makefile.lammps file for info on where to download the library from. </P> <P>The "Doc page" column links to either a portion of the <A HREF = "Section_howto.html">Section_howto</A> of the manual, or an input script command implemented as part of the package, or to additional documentation provided within the package. </P> <P>The "Example" column is a sub-directory in the examples directory of the distribution which has an input script that uses the package. E.g. "peptide" refers to the examples/peptide directory. USER/cuda refers to the examples/USER/cuda directory. </P> <P>The "Library" column lists an external library which must be built first and which LAMMPS links to when it is built. If it is listed as lib/package, then the code for the library is under the lib directory of the LAMMPS distribution. See the lib/package/README file for info on how to build the library. If it is not listed as lib/package, then it is a third-party library not included in the LAMMPS distribution. See the src/package/Makefile.lammps file for info on where to download the library. <A HREF = "Section_start.html#start_3_3">Section start</A> of the manual also gives details on how to build LAMMPS with both kinds of auxiliary libraries. </P> <P>Except where explained below, all of these packages can be installed, and LAMMPS re-built, by issuing these commands from the src dir. </P> <PRE>make yes-user-package make machine or Make.py -p package -a machine </PRE> <P>To un-install the package and re-build LAMMPS without it: </P> <PRE>make no-user-package make machine or Make.py -p ^package -a machine </PRE> <P>"Package" is the name of the package (in this case without the user prefix) in lower-case letters, e.g. drude or phonon, and "machine" is the build target, e.g. mpi or serial. </P> <HR> <HR> <H4>USER-ATC package </H4> <P>This package implements a "fix atc" command which can be used in a LAMMPS input script. This fix can be employed to either do concurrent coupling of MD with FE-based physics surrogates or on-the-fly post-processing of atomic information to continuum fields. </P> <P>See the doc page for the fix atc command to get started. At the bottom of the doc page are many links to additional documentation contained in the doc/USER/atc directory. </P> <P>There are example scripts for using this package in examples/USER/atc. </P> <P>This package uses an external library in lib/atc which must be compiled before making LAMMPS. See the lib/atc/README file and the LAMMPS manual for information on building LAMMPS with external libraries. </P> <P>The primary people who created this package are Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl at sandia.gov) and Jon Zimmerman (jzimmer at sandia.gov) at Sandia. Contact them directly if you have questions. </P> <HR> <H4>USER-AWPMD package </H4> <P>This package contains a LAMMPS implementation of the Antisymmetrized Wave Packet Molecular Dynamics (AWPMD) method. </P> <P>See the doc page for the pair_style awpmd/cut command to get started. </P> <P>There are example scripts for using this package in examples/USER/awpmd. </P> <P>This package uses an external library in lib/awpmd which must be compiled before making LAMMPS. See the lib/awpmd/README file and the LAMMPS manual for information on building LAMMPS with external libraries. </P> <P>The person who created this package is Ilya Valuev at the JIHT in Russia (valuev at physik.hu-berlin.de). Contact him directly if you have questions. </P> <HR> <H4>USER-CG-CMM package </H4> <P>This package implements 3 commands which can be used in a LAMMPS input script: </P> <UL><LI>pair_style lj/sdk <LI>pair_style lj/sdk/coul/long <LI>angle_style sdk </UL> <P>These styles allow coarse grained MD simulations with the parametrization of Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007) (SDK), with extensions to simulate ionic liquids, electrolytes, lipids and charged amino acids. </P> <P>See the doc pages for these commands for details. </P> <P>There are example scripts for using this package in examples/USER/cg-cmm. </P> <P>This is the second generation implementation reducing the the clutter of the previous version. For many systems with electrostatics, it will be faster to use pair_style hybrid/overlay with lj/sdk and coul/long instead of the combined lj/sdk/coul/long style. since the number of charged atom types is usually small. For any other coulomb interactions this is now required. To exploit this property, the use of the kspace_style pppm/cg is recommended over regular pppm. For all new styles, input file backward compatibility is provided. The old implementation is still available through appending the /old suffix. These will be discontinued and removed after the new implementation has been fully validated. </P> <P>The current version of this package should be considered beta quality. The CG potentials work correctly for "normal" situations, but have not been testing with all kinds of potential parameters and simulation systems. </P> <P>The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. </P> <HR> <H4>USER-COLVARS package </H4> <P>This package implements the "fix colvars" command which can be used in a LAMMPS input script. </P> <P>This fix allows to use "collective variables" to implement Adaptive Biasing Force, Metadynamics, Steered MD, Umbrella Sampling and Restraints. This code consists of two parts: </P> <UL><LI>A portable collective variable module library written and maintained <LI>by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and <LI>Jerome Henin (LISM, CNRS, Marseille, France). This code is located in <LI>the directory lib/colvars and needs to be compiled first. The colvars <LI>fix and an interface layer, exchanges information between LAMMPS and <LI>the collective variable module. </UL> <P>See the doc page of <A HREF = "fix_colvars.html">fix colvars</A> for more details. </P> <P>There are example scripts for using this package in examples/USER/colvars </P> <P>This is a very new interface that does not yet support all features in the module and will see future optimizations and improvements. The colvars module library is also available in NAMD has been thoroughly used and tested there. Bugs and problems are likely due to the interface layers code. Thus the current version of this package should be considered beta quality. </P> <P>The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. </P> <HR> <H4>USER-CUDA package </H4> <P>This package provides acceleration of various LAMMPS pair styles, fix styles, compute styles, and long-range Coulombics via PPPM for NVIDIA GPUs. </P> <P>See this section of the manual to get started: </P> <P><A HREF = "Section_accelerate.html#acc_7">Section_accelerate</A> </P> <P>There are example scripts for using this package in examples/USER/cuda. </P> <P>This package uses an external library in lib/cuda which must be compiled before making LAMMPS. See the lib/cuda/README file and the LAMMPS manual for information on building LAMMPS with external libraries. </P> <P>The person who created this package is Christian Trott at the University of Technology Ilmenau, Germany (christian.trott at tu-ilmenau.de). Contact him directly if you have questions. </P> <HR> <H4>USER-DIFFRACTION package </H4> <P>This package contains the commands neeed to calculate x-ray and electron diffraction intensities based on kinematic diffraction theory. </P> <P>See these doc pages and their related commands to get started: </P> <UL><LI><A HREF = "compute_xrd.html">compute xrd</A> <LI><A HREF = "compute_saed.html">compute saed</A> <LI><A HREF = "fix_saed_vtk.html">fix saed/vtk</A> </UL> <P>The person who created this package is Shawn P. Coleman (shawn.p.coleman8.ctr at mail.mil) while at the University of Arkansas. Contact him directly if you have questions. </P> <HR> <H4>USER-DRUDE package </H4> <P>This package implements methods for simulating polarizable systems in LAMMPS using thermalized Drude oscillators. </P> <P>See these doc pages and their related commands to get started: </P> <UL><LI><A HREF = "tutorial_drude.html">Drude tutorial</A> <LI><A HREF = "fix_drude.html">fix drude</A> <LI><A HREF = "compute_temp_drude.html">compute temp/drude</A> <LI><A HREF = "fix_langevin_drude.html">fix langevin/drude</A> <LI><A HREF = "fix_drude_transform.html">fix drude/transform/...</A> <LI><A HREF = "pair_thole.html">pair thole</A> </UL> <P>There are auxiliary tools for using this package in tools/drude. </P> <P>The person who created this package is Alain Dequidt at Universite Blaise Pascal Clermont-Ferrand (alain.dequidt at univ-bpclermont.fr) Contact him directly if you have questions. Co-authors: Julien Devemy, Agilio Padua. </P> <HR> <H4>USER-EFF package </H4> <P>This package contains a LAMMPS implementation of the electron Force Field (eFF) currently under development at Caltech, as described in A. Jaramillo-Botero, J. Su, Q. An, and W.A. Goddard III, JCC, 2010. The eFF potential was first introduced by Su and Goddard, in 2007. </P> <P>eFF can be viewed as an approximation to QM wave packet dynamics and Fermionic molecular dynamics, combining the ability of electronic structure methods to describe atomic structure, bonding, and chemistry in materials, and of plasma methods to describe nonequilibrium dynamics of large systems with a large number of highly excited electrons. We classify it as a mixed QM-classical approach rather than a conventional force field method, which introduces QM-based terms (a spin-dependent repulsion term to account for the Pauli exclusion principle and the electron wavefunction kinetic energy associated with the Heisenberg principle) that reduce, along with classical electrostatic terms between nuclei and electrons, to the sum of a set of effective pairwise potentials. This makes eFF uniquely suited to simulate materials over a wide range of temperatures and pressures where electronically excited and ionized states of matter can occur and coexist. </P> <P>The necessary customizations to the LAMMPS core are in place to enable the correct handling of explicit electron properties during minimization and dynamics. </P> <P>See the doc page for the pair_style eff/cut command to get started. </P> <P>There are example scripts for using this package in examples/USER/eff. </P> <P>There are auxiliary tools for using this package in tools/eff. </P> <P>The person who created this package is Andres Jaramillo-Botero at CalTech (ajaramil at wag.caltech.edu). Contact him directly if you have questions. </P> <HR> <H4>USER-FEP package </H4> <P>This package provides methods for performing free energy perturbation simulations with soft-core pair potentials in LAMMPS. </P> <P>See these doc pages and their related commands to get started: </P> <UL><LI><A HREF = "fix_adapt_fep.html">fix adapt/fep</A> <LI><A HREF = "compute_fep.html">compute fep</A> <LI><A HREF = "pair_lj_soft.html">soft pair styles</A> </UL> <P>The person who created this package is Agilio Padua at Universite Blaise Pascal Clermont-Ferrand (agilio.padua at univ-bpclermont.fr) Contact him directly if you have questions. </P> <HR> <H4>USER-H5MD package </H4> <P>This package contains a <A HREF = "dump_h5md.html">dump h5md</A> command for performing a dump of atom properties in HDF5 format. <A HREF = "http://www.hdfgroup.org/HDF5/">HDF5 files</A> are binary, portable and self-describing and can be examined and used by a variety of auxiliary tools. The output HDF5 files are structured in a format called H5MD, which was designed to store molecular data, and can be used and produced by various MD and MD-related codes. The <A HREF = "doc/dump_h5md.html">dump h5md</A> command gives a citation to a paper describing the format. </P> <P>The person who created this package and the underlying H5MD format is Pierre de Buyl at KU Leuven (see http://pdebuyl.be). Contact him directly if you have questions. </P> <HR> <H4>USER-INTEL package </H4> <P>This package provides options for performing neighbor list and non-bonded force calculations in single, mixed, or double precision and also a capability for accelerating calculations with an Intel(R) Xeon Phi(TM) coprocessor. </P> <P>See this section of the manual to get started: </P> <P><A HREF = "Section_accelerate.html#acc_9">Section_accelerate</A> </P> <P>The person who created this package is W. Michael Brown at Intel (michael.w.brown at intel.com). Contact him directly if you have questions. </P> <HR> <H4>USER-LB package </H4> <P>This package contains a LAMMPS implementation of a background Lattice-Boltzmann fluid, which can be used to model MD particles influenced by hydrodynamic forces. </P> <P>See this doc page and its related commands to get started: </P> <P><A HREF = "fix_lb_fluid.html">fix lb/fluid</A> </P> <P>The people who created this package are Frances Mackay (fmackay at uwo.ca) and Colin (cdennist at uwo.ca) Denniston, University of Western Ontario. Contact them directly if you have questions. </P> <HR> +<H4>USER-MGPT package +</H4> +<P>This package contains a fast implementation for LAMMPS of +quantum-based MGPT multi-ion potentials. The MGPT or model GPT method +derives from first-principles DFT-based generalized pseudopotential +theory (GPT) through a series of systematic approximations valid for +mid-period transition metals with nearly half-filled d bands. The +MGPT method was originally developed by John Moriarty at Lawrence +Livermore National Lab (LLNL). +</P> +<P>In the general matrix representation of MGPT, which can also be +applied to f-band actinide metals, the multi-ion potentials are +evaluated on the fly during a simulation through d- or f-state matrix +multiplication, and the forces that move the ions are determined +analytically. The <I>mgpt</I> pair style in this package calculates forces +and energies using an optimized matrix-MGPT algorithm due to Tomas +Oppelstrup at LLNL. +</P> +<P>See this doc page to get started: +</P> +<P><A HREF = "pair_mgpt.html">pair_style mgpt</A> +</P> +<P>The persons who created the USER-MGPT package are Tomas Oppelstrup +(oppelstrup2@llnl.gov) and John Moriarty (moriarty2@llnl.gov) +Contact them directly if you have any questions. +</P> +<HR> + <H4>USER-MISC package </H4> <P>The files in this package are a potpourri of (mostly) unrelated features contributed to LAMMPS by users. Each feature is a single pair of files (*.cpp and *.h). </P> <P>More information about each feature can be found by reading its doc page in the LAMMPS doc directory. The doc page which lists all LAMMPS input script commands is as follows: </P> <P><A HREF = "Section_commands.html#cmd_5">Section_commands</A> </P> <P>User-contributed features are listed at the bottom of the fix, compute, pair, etc sections. </P> <P>The list of features and author of each is given in the src/USER-MISC/README file. </P> <P>You should contact the author directly if you have specific questions about the feature or its coding. </P> <HR> <H4>USER-MOLFILE package </H4> <P>This package contains a dump molfile command which uses molfile plugins that are bundled with the <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD</A> molecular visualization and analysis program, to enable LAMMPS to dump its information in formats compatible with various molecular simulation tools. </P> <P>The package only provides the interface code, not the plugins. These can be obtained from a VMD installation which has to match the platform that you are using to compile LAMMPS for. By adding plugins to VMD, support for new file formats can be added to LAMMPS (or VMD or other programs that use them) without having to recompile the application itself. </P> <P>See this doc page to get started: </P> <P><A HREF = "dump_molfile.html#acc_5">dump molfile</A> </P> <P>The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. </P> <HR> <H4>USER-OMP package </H4> <P>This package provides OpenMP multi-threading support and other optimizations of various LAMMPS pair styles, dihedral styles, and fix styles. </P> <P>See this section of the manual to get started: </P> <P><A HREF = "Section_accelerate.html#acc_5">Section_accelerate</A> </P> <P>The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. </P> <HR> <H4>USER-PHONON package </H4> <P>This package contains a fix phonon command that calculates dynamical matrices, which can then be used to compute phonon dispersion relations, directly from molecular dynamics simulations. </P> <P>See this doc page to get started: </P> <P><A HREF = "fix_phonon.html">fix phonon</A> </P> <P>The person who created this package is Ling-Ti Kong (konglt at sjtu.edu.cn) at Shanghai Jiao Tong University. Contact him directly if you have questions. </P> <HR> <H4>USER-QMMM package </H4> <P>This package provides a fix qmmm command which allows LAMMPS to be used in a QM/MM simulation, currently only in combination with pw.x code from the <A HREF = "http://www.quantum-espresso.org">Quantum ESPRESSO</A> package. </P> <P>The current implementation only supports an ONIOM style mechanical coupling to the Quantum ESPRESSO plane wave DFT package. Electrostatic coupling is in preparation and the interface has been written in a manner that coupling to other QM codes should be possible without changes to LAMMPS itself. </P> <P>See this doc page to get started: </P> <P><A HREF = "fix_qmmm.html">fix qmmm</A> </P> <P>as well as the lib/qmmm/README file. </P> <P>The person who created this package is Axel Kohlmeyer at Temple U (akohlmey at gmail.com). Contact him directly if you have questions. </P> <HR> <H4>USER-QTB package </H4> <P>This package provides a self-consistent quantum treatment of the vibrational modes in a classical molecular dynamics simulation. By coupling the MD simulation to a colored thermostat, it introduces zero point energy into the system, alter the energy power spectrum and the heat capacity towards their quantum nature. This package could be of interest if one wants to model systems at temperatures lower than their classical limits or when temperatures ramp up across the classical limits in the simulation. </P> <P>See these two doc pages to get started: </P> <P><A HREF = "fix_qtb.html">fix qtb</A> provides quantum nulcear correction through a colored thermostat and can be used with other time integration schemes like <A HREF = "fix_nve.html">fix nve</A> or <A HREF = "fix_nh.html">fix nph</A>. </P> <P><A HREF = "fix_qbmsst.html">fix qbmsst</A> enables quantum nuclear correction of a multi-scale shock technique simulation by coupling the quantum thermal bath with the shocked system. </P> <P>The person who created this package is Yuan Shen (sy0302 at stanford.edu) at Stanford University. Contact him directly if you have questions. </P> <HR> <H4>USER-REAXC package </H4> <P>This package contains a implementation for LAMMPS of the ReaxFF force field. ReaxFF uses distance-dependent bond-order functions to represent the contributions of chemical bonding to the potential energy. It was originally developed by Adri van Duin and the Goddard group at CalTech. </P> <P>The USER-REAXC version of ReaxFF (pair_style reax/c), implemented in C, should give identical or very similar results to pair_style reax, which is a ReaxFF implementation on top of a Fortran library, a version of which library was originally authored by Adri van Duin. </P> <P>The reax/c version should be somewhat faster and more scalable, particularly with respect to the charge equilibration calculation. It should also be easier to build and use since there are no complicating issues with Fortran memory allocation or linking to a Fortran library. </P> <P>For technical details about this implemention of ReaxFF, see this paper: </P> <P>Parallel and Scalable Reactive Molecular Dynamics: Numerical Methods and Algorithmic Techniques, H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama, Parallel Computing, in press (2011). </P> <P>See the doc page for the pair_style reax/c command for details of how to use it in LAMMPS. </P> <P>The person who created this package is Hasan Metin Aktulga (hmaktulga at lbl.gov), while at Purdue University. Contact him directly, or Aidan Thompson at Sandia (athomps at sandia.gov), if you have questions. </P> <HR> <H4>USER-SMD package </H4> <P>This package implements smoothed Mach dynamics (SMD) in LAMMPS. Currently, the package has the following features: </P> <P>* Does liquids via traditional Smooth Particle Hydrodynamics (SPH) </P> <P>* Also solves solids mechanics problems via a state of the art stabilized meshless method with hourglass control. </P> <P>* Can specify hydrostatic interactions independently from material strength models, i.e. pressure and deviatoric stresses are separated. </P> <P>* Many material models available (Johnson-Cook, plasticity with hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new material models. </P> <P>* Rigid boundary conditions (walls) can be loaded as surface geometries from *.STL files. </P> <P>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started. </P> <P>There are example scripts for using this package in examples/USER/smd. </P> <P>The person who created this package is Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if you have questions. </P> <H4>USER-SPH package </H4> <P>This package implements smoothed particle hydrodynamics (SPH) in LAMMPS. Currently, the package has the following features: </P> <P>* Tait, ideal gas, Lennard-Jones equation of states, full support for complete (i.e. internal-energy dependent) equations of state </P> <P>* Plain or Monaghans XSPH integration of the equations of motion </P> <P>* Density continuity or density summation to propagate the density field </P> <P>* Commands to set internal energy and density of particles from the input script </P> <P>* Output commands to access internal energy and density for dumping and thermo output </P> <P>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started. </P> <P>There are example scripts for using this package in examples/USER/sph. </P> <P>The person who created this package is Georg Ganzenmuller at the Fraunhofer-Institute for High-Speed Dynamics, Ernst Mach Institute in Germany (georg.ganzenmueller at emi.fhg.de). Contact him directly if you have questions. </P> </HTML> diff --git a/doc/doc2/pair_mgpt.html b/doc/doc2/pair_mgpt.html new file mode 100644 index 000000000..11ec3c2ff --- /dev/null +++ b/doc/doc2/pair_mgpt.html @@ -0,0 +1,221 @@ +<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 mgpt command +</H3> +<P><B>Syntax:</B> +</P> +<PRE>pair_style mgpt +</PRE> +<P><B>Examples:</B> +</P> +<PRE>pair_style mgpt +pair_coeff * * Ta6.8x.mgpt.parmin Ta6.8x.mgpt.potin Omega +cp ~/lammps/potentials/Ta6.8x.mgpt.parmin parmin +cp ~/lammps/potentials/Ta6.8x.mgpt.potin potin +pair_coeff * * parmin potin Omega volpress yes nbody 1234 precision double +pair_coeff * * parmin potin Omega volpress yes nbody 12 +</PRE> +<P><B>Description:</B> +</P> +<P>Within DFT quantum mechanics, generalized pseudopotential theory (GPT) +(<A HREF = "#Moriarty1">Moriarty1</A>) provides a first-principles approach to +multi-ion interatomic potentials in d-band transition metals, with a +volume-dependent, real-space total-energy functional for the N-ion +elemental bulk material in the form +</P> +<CENTER><IMG SRC = "Eqs/pair_mgpt.jpg"> +</CENTER> +<P>where the prime on each summation sign indicates the exclusion of all +self-interaction terms from the summation. The leading volume term +E_vol as well as the two-ion central-force pair potential v_2 and the +three- and four-ion angular-force potentials, v_3 and v_4, depend +explicitly on the atomic volume Omega, but are structure independent +and transferable to all bulk ion configurations, either ordered or +disordered, and with of without the presence of point and line +defects. The simplified model GPT or MGPT (<A HREF = "#Moriarty2">Moriarty2</A>, +<A HREF = "#Moriarty3">Moriarty3</A>), which retains the form of E_tot and permits +more efficient large-scale atomistic simulations, derives from the GPT +through a series of systematic approximations applied to E_vol and the +potentials v_n that are valid for mid-period transition metals with +nearly half-filled d bands. +</P> +<P>Both analytic (<A HREF = "#Moriarty2">Moriarty2</A>) and matrix +(<A HREF = "#Moriarty3">Moriarty3</A>) representations of MGPT have been developed. +In the more general matrix representation, which can also be applied +to f-band actinide metals and permits both canonical and non-canonical +d/f bands, the multi-ion potentials are evaluated on the fly during a +simulation through d- or f-state matrix multiplication, and the forces +that move the ions are determined analytically. Fast matrix-MGPT +algorithms have been developed independently by Glosli +(<A HREF = "#Glosi">Glosli</A>, <A HREF = "#Moriarty3">Moriarty3</A>) and by Oppelstrup +(<A HREF = "#Oppelstrup">Oppelstrup</A>) +</P> +<P>The <I>mgpt</I> pair style calculates forces, energies, and the total +energy per atom, E_tot/N, using the Oppelstrup matrix-MGPT algorithm. +Input potential and control data are entered through the +<A HREF = "pair_coeff.html">pair_coeff</A> command. Each material treated requires +input parmin and potin potential files, as shown in the above +examples, as well as specification by the user of the initial atomic +volume Omega through pair_coeff. At the beginning of a time step in +any simulation, the total volume of the simulation cell V should +always be equal to Omega*N, where N is the number of metal ions +present, taking into account the presence of any vacancies and/or +interstitials in the case of a solid. In a constant-volume +simulation, which is the normal mode of operation for the <I>mgpt</I> pair +style, Omega, V and N all remain constant throughout the simulation +and thus are equal to their initial values. In a constant-stress +simulation, the cell volume V will change (slowly) as the simulation +proceeds. After each time step, the atomic volume should be updated +by the code as Omega = V/N. In addition, the volume term E_vol and +the potentials v_2, v_3 and v_4 have to be removed at the end of the +time step, and then respecified at the new value of Omega. In all +smulations, Omega must remain within the defined volume range for +E_vol and the potentials for the given material. +</P> +<P>The default option volpress yes in the <A HREF = "pair_coeff.html">pair_coeff</A> +command includes all volume derivatives of E_tot required to calculate +the stress tensor and pressure correctly. The option volpress no +disregards the pressure contribution resulting from the volume term +E_vol, and can be used for testing and analysis purposes. The +additional optional variable nbody controls the specific terms in +E_tot that are calculated. The default option and the normal option +for mid-period transition and actinide metals is nbody 1234 for which +all four terms in E_tot are retained. The option nbody 12, for +example, retains only the volume term and the two-ion pair potential +term and can be used for GPT series-end transition metals that can be +well described without v_3 and v_4. The nbody option can also be used +to test or analyze the contribution of any of the four terms in E_tot +to a given calculated property. +</P> +<P>The <I>mgpt</I> pair style makes extensive use of matrix algebra and +includes optimized kernels for the BlueGene/Q architecture and the +Intel/AMD (x86) architectures. When compiled with the appropriate +compiler and compiler switches (-msse3 on x86, and using the IBM XL +compiler on BG/Q), these optimized routines are used automatically. +For BG/Q machines, building with the default Makefile for that +architecture (e.g., "make bgq") should enable the optimized algebra +routines. For x-86 machines, the here provided Makefile.mpi_fastmgpt +(build with "make mpi_fastmgpt") enables the fast algebra routines. +The user will be informed in the output files of the matrix kernels in +use. To further improve speed, on x86 the option precision single can +be added to the <A HREF = "pair_coeff.html">pair_coeff</A> command line, which +improves speed (up to a factor of two) at the cost of doing matrix +calculations with 7 digit precision instead of the default 16. For +consistency the default option can be specified explicitly by the +option precision double. +</P> +<P>All remaining potential and control data are contained with the parmin +and potin files, including cutoffs, atomic mass, and other basic MGPT +variables. Specific MGPT potential data for the transition metals +tantalum (Ta4 and Ta6.8x potentials), molybdenum (Mo5.2 potentials), +and vanadium (V6.1 potentials) are contained in the LAMMPS potentials +directory. The stored files are, respectively, Ta4.mgpt.parmin, +Ta4.mgpt.potin, Ta6.8x.mgpt.parmin, Ta6.8x.mgpt.potin, +Mo5.2.mgpt.parmin, Mo5.2.mgpt.potin, V6.1.mgpt.parmin, and +V6.1.mgpt.potin . Useful corresponding informational "README" files +on the Ta4, Ta6.8x, Mo5.2 and V6.1 potentials are also included in the +potentials directory. These latter files indicate the volume mesh and +range for each potential and give appropriate references for the +potentials. It is expected that MGPT potentials for additional +materials will be added over time. +</P> +<P>Useful example MGPT scripts are given in the examples/USER/mgpt +directory. These scripts show the necessary steps to perform +constant-volume calculations and simulations. It is strongly +recommended that the user work through and understand these examples +before proceeding to more complex simulations. +</P> +<HR> + +<P><B>Mixing, shift, table tail correction, restart</B>: +</P> +<P>The (mgpt) pair style does not support the +<A HREF = "pair_modify.html">pair_modify</A> mix, shift, table, and tail options. +</P> +<P>This pair style does not write its information to <A HREF = "restart.html">binary restart +files</A>, since it is stored in potential files. Thus, you +needs to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. +</P> +<P>This pair style 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>The <I>mgpt</I> pair style is part of the USER-MGPT package and is only +enabled if LAMMPS is built with that package. +</P> +<P>The MGPT potentials require the <A HREF = "newton.html">newtion</A> setting to be +"on" for pair style interactions. +</P> +<P>The stored parmin and potin potential files provided with LAMMPS in +the "potentials" directory are written in Rydberg atomic units, with +energies in Rydbergs and distances in Bohr radii. The <I>mgpt</I> pair +style converts Rydbergs to Hartrees to make the potential files +compatible with LAMMPS electron <A HREF = "units.html">units</A>. +</P> +<P>The form of E_tot used in the <I>mgpt</I> pair style is only appropriate +for elemental bulk solids and liquids. This includes solids with +point and extended defects such as vacancies, interstitials, grain +boundaries and dislocations. Alloys and free surfaces, however, +require significant modifications, which are not included in the +<I>mgpt</I> pair style. Likewise, the <I>hybrid</I> pair style is not allowed, +where MGPT would be used for some atoms but not for others. +</P> +<P>Electron-thermal effects are not included in the standard MGPT +potentials provided in the "potentials" directory, where the +potentials have been constructed at zero electron temperature. +Physically, electron-thermal effects may be important in 3d (e.g., V) +and 4d (e.g., Mo) transition metals at high temperatures near melt and +above. It is expected that temperature-dependent MGPT potentials for +such cases will be added over time. +</P> +<P><B>Related commands:</B> +</P> +<P><A HREF = "pair_coeff.html">pair_coeff</A> +</P> +<P><B>Default:</B> +</P> +<P>The options defaults for the <A HREF = "pair_coeff.html">pair_coeff</A> command are +volpress yes, nbody 1234, and precision double. +</P> +<HR> + +<A NAME = "Moriarty1"></A> + +<P><B>(Moriarty1)</B> Moriarty, Physical Review B, 38, 3199 (1988). +</P> +<A NAME = "Moriarty2"></A> + +<P><B>(Moriarty2)</B> Moriarty, Physical Review B, 42, 1609 (1990). +Moriarty, Physical Review B 49, 12431 (1994). +</P> +<A NAME = "Moriarty3"></A> + +<P><B>(Moriarty3)</B> Moriarty, Benedict, Glosli, Hood, Orlikowski, Patel, Soderlind, Streitz, Tang, and Yang, +Journal of Materials Research, 21, 563 (2006). +</P> +<A NAME = "Glosli"></A> + +<P><B>(Glosli)</B> Glosli, unpublished, 2005. +Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference +Series, 46, 254 (2006). +</P> +<A NAME = "Oppelstrup"></A> + +<P><B>(Oppelstrup)</B> Oppelstrup, unpublished, 2015. +Oppelstrup and Moriarty, to be published. +</P> +</HTML>