From 278b9f7fba477da3cc235cefb09151330ef2c5b7 Mon Sep 17 00:00:00 2001 From: Axel Kohlmeyer Date: Wed, 17 May 2017 14:59:46 -0400 Subject: [PATCH] move pair gw and gw/zbl to USER-MISC package --- doc/src/Section_commands.txt | 2 + doc/src/lammps.book | 1 + doc/src/pair_gw.txt | 118 ++++++++++++++++++++ doc/src/pairs.txt | 1 + src/USER-MISC/README | 2 + src/{MANYBODY => USER-MISC}/pair_gw.cpp | 0 src/{MANYBODY => USER-MISC}/pair_gw.h | 0 src/{MANYBODY => USER-MISC}/pair_gw_zbl.cpp | 0 src/{MANYBODY => USER-MISC}/pair_gw_zbl.h | 0 9 files changed, 124 insertions(+) create mode 100644 doc/src/pair_gw.txt rename src/{MANYBODY => USER-MISC}/pair_gw.cpp (100%) rename src/{MANYBODY => USER-MISC}/pair_gw.h (100%) rename src/{MANYBODY => USER-MISC}/pair_gw_zbl.cpp (100%) rename src/{MANYBODY => USER-MISC}/pair_gw_zbl.h (100%) diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 771e830841..bf7b48f32b 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -931,6 +931,8 @@ KOKKOS, o = USER-OMP, t = OPT. "gran/hertz/history (o)"_pair_gran.html, "gran/hooke (o)"_pair_gran.html, "gran/hooke/history (o)"_pair_gran.html, +"gw"_pair_gw.html, +"gw/zbl"_pair_gw.html, "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, "hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, "kim"_pair_kim.html, diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 6b3ca8aa07..2fd953ffaf 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -432,6 +432,7 @@ pair_gauss.html pair_gayberne.html pair_gran.html pair_gromacs.html +pair_gw.html pair_hbond_dreiding.html pair_hybrid.html pair_kim.html diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt new file mode 100644 index 0000000000..2240dca6f7 --- /dev/null +++ b/doc/src/pair_gw.txt @@ -0,0 +1,118 @@ +"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 gw command :h3 +pair_style gw/zbl command :h3 + +[Syntax:] + +pair_style gw :pre + +[Examples:] + +pair_style gw +pair_coeff * * SiC.gw Si C C + +pair_style gw/zbl +pair_coeff * * SiC.gw.zbl C Si :pre + +[Description:] + +The {gw} style computes a 3-body "Gao-Weber"_#Gao potential; +similarly {gw/zbl} combines this potential with a modified +repulsive ZBL core function in a similar fashion as implemented +in the "tersoff/zbl"_pair_tersoff_zbl.html pair style. + +Unfortunately the author of this contributed code has not been +able to submit a suitable documentation explaining the details +of the potentials. The LAMMPS developers thus have finally decided +to release the code anyway with only the technical explanations. +For details of the model and the parameters, please refer to the +linked publication. + +Only a single pair_coeff command is used with the {gw} and {gw/zbl} +styles which specifies a Gao-Weber potential file with parameters +for all needed elements. These are mapped to LAMMPS atom types by +specifying N additional arguments after the filename in the pair_coeff +command, where N is the number of LAMMPS atom types: + +filename +N element names = mapping of GW elements to atom types :ul + +See the "pair_coeff"_pair_coeff.html doc page for alternate ways +to specify the path for the potential file. + +As an example, imagine a file SiC.gw has Gao-Weber values for Si and C. +If your LAMMPS simulation has 4 atoms types and you want the first 3 to +be Si, and the 4th to be C, you would use the following pair_coeff command: + +pair_coeff * * SiC.gw Si Si Si C :pre + +The first 2 arguments must be * * so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1,2,3 to the Si +element in the GW file. The final C argument maps LAMMPS atom type 4 +to the C element in the GW file. If a mapping value is specified as +NULL, the mapping is not performed. This can be used when a {gw} +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. + +Gao-Weber files in the {potentials} directory of the LAMMPS +distribution have a ".gw" suffix. Gao-Weber with ZBL files +have a ".gz.zbl" suffix. The structure of the potential files +is similar to other many-body potentials supported by LAMMPS. +You have to refer to the comments in the files and the literature +to learn more details. + +: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. + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does 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 and pair_coeff commands in an input +script that reads a restart file. + +This pair style 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:] + +This pair style is part of the USER-MISC 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. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. + +The Gao-Weber potential files provided with LAMMPS (see the +potentials directory) are parameterized for metal "units"_units.html. +You can use the GW potential with any LAMMPS units, but you would need +to create your own GW potential file with coefficients listed in the +appropriate units if your simulation doesn't use "metal" units. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + +:link(Gao) +[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504. diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 0898906e7c..369c942280 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -36,6 +36,7 @@ Pair Styles :h1 pair_gayberne pair_gran pair_gromacs + pair_gw pair_hbond_dreiding pair_hybrid pair_kim diff --git a/src/USER-MISC/README b/src/USER-MISC/README index cacee41e0c..1e927fdfab 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -60,6 +60,8 @@ pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 +pair_style gw, German Samolyuk, samolyuk at gmail.com, 17 May 17 +pair_style gw/zbl, German Samolyuk, samolyuk at gmail.com, 17 May 17 pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13 pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 diff --git a/src/MANYBODY/pair_gw.cpp b/src/USER-MISC/pair_gw.cpp similarity index 100% rename from src/MANYBODY/pair_gw.cpp rename to src/USER-MISC/pair_gw.cpp diff --git a/src/MANYBODY/pair_gw.h b/src/USER-MISC/pair_gw.h similarity index 100% rename from src/MANYBODY/pair_gw.h rename to src/USER-MISC/pair_gw.h diff --git a/src/MANYBODY/pair_gw_zbl.cpp b/src/USER-MISC/pair_gw_zbl.cpp similarity index 100% rename from src/MANYBODY/pair_gw_zbl.cpp rename to src/USER-MISC/pair_gw_zbl.cpp diff --git a/src/MANYBODY/pair_gw_zbl.h b/src/USER-MISC/pair_gw_zbl.h similarity index 100% rename from src/MANYBODY/pair_gw_zbl.h rename to src/USER-MISC/pair_gw_zbl.h