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Merge branch 'kim-simulator-models' of github.com:ellio167/lammps into kim-simulator-models

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This commit is contained in:
Ellad Tadmor
2019-06-22 15:25:40 -05:00
parent 17fa2f787b 4a22e3bf70
commit 27d83b878d
5 changed files with 591 additions and 377 deletions
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27
src/KIM/README
View File

@ -1,29 +1,30 @@
This package provides a pair_style kim command which is a wrapper on
the Knowledge Base for Interatomic Models (KIM) repository of
interatomic potentials, so that they can be used by LAMMPS scripts.
This package provides the kim_init, kim_query, kim_interactions, and
the pair_style kim command which are wrappers on the Knowledgebase of
Interatomic Models (KIM) repository of interatomic potentials, so that
they can be used by LAMMPS scripts.
Information about the KIM project can be found at https://openkim.org.
The KIM project is lead by Ellad Tadmor and Ryan Elliott (U Minn) and
James Sethna (Cornell U). Ryan Elliott is the main developer for the
KIM API and he also maintains the code that implements the pair_style
kim command.
The KIM project is lead by Ellad B. Tadmor and Ryan S. Elliott (UMN).
Ryan Elliott is the main developer for the KIM API and he also
maintains the code that implements these commands.
Using this package requires the KIM library and its models
Using this package requires the KIM-API library and its models
(interatomic potentials) to be downloaded and installed on your
system. The library can be downloaded and built in lib/kim or
elsewhere on your system, which must be done before bulding LAMMPS
with this package. Details of the download, build, and install
process for KIM are given in the lib/kim/README file, and scripts
are provided to help automate the process. Also see the LAMMPS
manual for general information on building LAMMPS with external
process for the KIM-API are given in the lib/kim/README file, and
scripts are provided to help automate the process. Also see the
LAMMPS manual for general information on building LAMMPS with external
libraries. The settings in the Makefile.lammps file in lib/kim must
be correct for LAMMPS to build correctly with this package installed.
However, the default settings should be correct in most cases and the
Makefile.lammps file usually will not need to be changed.
Once you have successfully built LAMMPS with this package and the KIM
library you can test it using an input file from the examples dir:
library you can test it using an input files in the examples dir:
./lmp_serial -in lammps/examples/kim/in.kim.lj
This pair_style was written by Ryan S. Elliott (U Minn).
These commands were written by Ryan S. Elliott (UMN), Ellad B. Tadmor
(UMN) and Axel Kohlmeyer (Temple U).

423
src/KIM/kim_style.cpp → src/KIM/kim_init.cpp
View File

@ -14,6 +14,7 @@
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN)
Ellad B. Tadmor (UMN)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
@ -57,7 +58,8 @@
#include <cstring>
#include <string>
#include <sstream>
#include "kim_style.h"
#include <iomanip>
#include "kim_init.h"
#include "error.h"
#include "atom.h"
#include "comm.h"
@ -85,33 +87,26 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void KimStyle::command(int narg, char **arg)
void KimInit::command(int narg, char **arg)
{
if ((narg < 2) || (narg > 4)) error->all(FLERR,"Illegal kim_style command");
if ((narg < 2) || (narg > 3)) error->all(FLERR,"Illegal kim_init command");
if (strcmp(arg[0],"model") == 0) {
if (domain->box_exist)
error->all(FLERR,"Must use 'kim_style model' command before "
"simulation box is defined");
int len1 = strlen(arg[1])+1;
int len2 = strlen(arg[2])+1;
char *model_name = new char[len1]; strcpy(model_name,arg[1]);
char *user_units = new char[len2]; strcpy(user_units,arg[2]);
if (narg == 4) {
if (strcmp(arg[3],"unit_conversion_mode")==0) unit_conversion_mode = true;
else { error->all(FLERR,"Illegal kim_style command"); }
} else unit_conversion_mode = false;
if (domain->box_exist)
error->all(FLERR,"Must use 'kim_init' command before "
"simulation box is defined");
int len0 = strlen(arg[0])+1;
int len1 = strlen(arg[1])+1;
char *model_name = new char[len0]; strcpy(model_name,arg[0]);
char *user_units = new char[len1]; strcpy(user_units,arg[1]);
if (narg == 3) {
if (strcmp(arg[2],"unit_conversion_mode")==0) unit_conversion_mode = true;
else { error->all(FLERR,"Illegal kim_init command"); }
} else unit_conversion_mode = false;
char *model_units;
determine_model_type_and_units(model_name, user_units, &model_units);
char *model_units;
determine_model_type_and_units(model_name, user_units, &model_units);
do_init(model_name, user_units, model_units);
} else if (strcmp(arg[0],"setup") == 0) {
if (!domain->box_exist)
error->all(FLERR,"Must use 'kim_style setup' command after "
"simulation box is defined");
do_setup(narg-1,++arg);
} else error->all(FLERR,"Illegal kim_style command");
do_init(model_name, user_units, model_units);
}
@ -163,9 +158,9 @@ void get_kim_unit_names(
}
}
} // namespace
void KimStyle::determine_model_type_and_units(char * model_name,
char * user_units,
char ** model_units)
void KimInit::determine_model_type_and_units(char * model_name,
char * user_units,
char ** model_units)
{
KIM_LengthUnit lengthUnit;
KIM_EnergyUnit energyUnit;
@ -270,7 +265,7 @@ void KimStyle::determine_model_type_and_units(char * model_name,
/* ---------------------------------------------------------------------- */
void KimStyle::do_init(char *model_name, char *user_units, char* model_units)
void KimInit::do_init(char *model_name, char *user_units, char* model_units)
{
// create storage proxy fix. delete existing fix, if needed.
@ -288,32 +283,42 @@ void KimStyle::do_init(char *model_name, char *user_units, char* model_units)
fix_store->setptr("user_units", (void *) user_units);
fix_store->setptr("model_units", (void *) model_units);
// Begin output to log file
kim_init_log_delimiter("begin");
int kimerror;
// @@@@@ switch to c-bindings when they are available
KIM::SimulatorModel * simulatorModel;
kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel);
if (model_type == SM)
{
kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel);
const std::string *sim_name, *sim_version;
simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version);
const std::string *sim_name, *sim_version;
simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version);
if (*sim_name != "LAMMPS")
error->all(FLERR,"Incompatible KIM Simulator Model");
if (*sim_name != "LAMMPS")
error->all(FLERR,"Incompatible KIM Simulator Model");
// Begin output to log file
kim_style_log_delimiter("begin","model");
if (comm->me == 0) {
std::string mesg("# Using KIM Simulator Model : ");
mesg += model_name;
mesg += "\n";
mesg += "# For Simulator : ";
mesg += *sim_name + " " + *sim_version + "\n";
mesg += "# Running on : LAMMPS ";
mesg += universe->version;
mesg += "\n";
mesg += "#\n";
if (comm->me == 0) {
std::string mesg("# Using KIM Simulator Model : ");
mesg += model_name;
mesg += "\n";
mesg += "# For Simulator : ";
mesg += *sim_name + " " + *sim_version + "\n";
mesg += "# Running on : LAMMPS ";
mesg += universe->version;
mesg += "\n";
mesg += "#\n";
if (screen) fputs(mesg.c_str(),screen);
if (logfile) fputs(mesg.c_str(),logfile);
if (screen) fputs(mesg.c_str(),screen);
if (logfile) fputs(mesg.c_str(),logfile);
}
fix_store->setptr("simulator_model", (void *) simulatorModel);
// need to call this to have access to (some) simulator model init data.
simulatorModel->CloseTemplateMap();
}
// Define unit conversion factor variables and print to log
@ -325,192 +330,55 @@ void KimStyle::do_init(char *model_name, char *user_units, char* model_units)
cmd += model_units;
input->one(cmd.c_str());
// not a Kim Simulator Model; nothing else to do here.
if (kimerror) return;
fix_store->setptr("simulator_model", (void *) simulatorModel);
// need to call this to have access to (some) simulator model init data.
simulatorModel->CloseTemplateMap();
int sim_fields, sim_lines;
const std::string *sim_field, *sim_value;
simulatorModel->GetNumberOfSimulatorFields(&sim_fields);
// init model
for (int i=0; i < sim_fields; ++i) {
simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
if (*sim_field == "model-init") {
for (int j=0; j < sim_lines; ++j) {
simulatorModel->GetSimulatorFieldLine(i,j,&sim_value);
input->one(sim_value->c_str());
}
break;
}
}
// End output to log file
kim_style_log_delimiter("end","model");
// reset template map.
simulatorModel->OpenAndInitializeTemplateMap();
}
/* ---------------------------------------------------------------------- */
void KimStyle::kim_style_log_delimiter(std::string const begin_end,
std::string const model_setup) const
{
if (comm->me == 0) {
std::string mesg;
if ((begin_end == "begin") && (model_setup == "model")) mesg =
"#=== BEGIN kim-style MODEL ==================================\n";
else if ((begin_end == "begin") && (model_setup == "setup")) mesg =
"#=== BEGIN kim-style SETUP ==================================\n";
else if ((begin_end == "end") && (model_setup == "model")) mesg =
"#=== END kim-style MODEL ====================================\n\n";
else if ((begin_end == "end") && (model_setup == "setup")) mesg =
"#=== END kim-style SETUP ====================================\n\n";
if (screen) fputs(mesg.c_str(),screen);
if (logfile) fputs(mesg.c_str(),logfile);
}
}
/* ---------------------------------------------------------------------- */
void KimStyle::do_setup(int narg, char **arg)
{
if (narg != atom->ntypes)
error->all(FLERR,"Illegal kim_style command");
char *model = NULL;
KIM::SimulatorModel *simulatorModel(NULL);
// check if we had a kim_style init command by finding fix STORE/KIM
// retrieve model name and pointer to simulator model class instance.
// validate model name if not given as NULL.
// if kim_style init wasn't run try to initialize simulator model now.
int ifix = modify->find_fix("KIM_MODEL_STORE");
if (ifix >= 0) {
FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix];
model = (char *)fix_store->getptr("model_name");
simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model");
} else error->all(FLERR,"Must use 'kim_style model' before 'kim_style setup'");
// Begin output to log file
kim_style_log_delimiter("begin","setup");
if (simulatorModel) {
std::string delimiter("");
std::string atom_type_sym_list;
std::string atom_type_num_list;
for (int i = 0; i < narg; i++)
{
atom_type_sym_list += delimiter + arg[i];
atom_type_num_list += delimiter + SNUM(species_to_atomic_no(arg[i]));
delimiter = " ";
}
simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list);
simulatorModel->AddTemplateMap("atom-type-num-list",atom_type_num_list);
simulatorModel->CloseTemplateMap();
int len = strlen(atom_type_sym_list.c_str())+1;
char *strbuf = new char[len];
char *strword;
// validate species selection
int sim_num_species;
bool species_is_supported;
const std::string *sim_species;
simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species);
strcpy(strbuf,atom_type_sym_list.c_str());
strword = strtok(strbuf," \t");
while (strword) {
species_is_supported = false;
if (strcmp(strword,"NULL") == 0) continue;
for (int i=0; i < sim_num_species; ++i) {
simulatorModel->GetSupportedSpecies(i, &sim_species);
if (strcmp(sim_species->c_str(),strword) == 0)
species_is_supported = true;
}
if (!species_is_supported) {
std::string msg("Species '");
msg += strword;
msg += "' is not supported by this KIM Simulator Model";
error->all(FLERR,msg.c_str());
}
strword = strtok(NULL," \t");
}
delete[] strbuf;
// check if units are unchanged, and if kim_style init was required
if (model_type == SM)
{
int sim_fields, sim_lines;
const std::string *sim_field, *sim_value;
simulatorModel->GetNumberOfSimulatorFields(&sim_fields);
// init model
for (int i=0; i < sim_fields; ++i) {
simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
if (*sim_field == "units") {
simulatorModel->GetSimulatorFieldLine(i,0,&sim_value);
if (*sim_value != update->unit_style)
error->all(FLERR,"Incompatible units for KIM Simulator Model");
}
}
int sim_model_idx=-1;
for (int i=0; i < sim_fields; ++i) {
simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
if (*sim_field == "model-defn") {
sim_model_idx = i;
if (*sim_field == "model-init") {
for (int j=0; j < sim_lines; ++j) {
simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value);
simulatorModel->GetSimulatorFieldLine(i,j,&sim_value);
input->one(sim_value->c_str());
}
break;
}
}
if (sim_model_idx < 0)
error->all(FLERR,"KIM Simulator Model has no Model definition");
// reset template map.
simulatorModel->OpenAndInitializeTemplateMap();
} else {
// not a simulator model. issue pair_style and pair_coeff commands.
// NOTE: all references to arg must appear before calls to input->one()
// as that will reset the argument vector.
std::string cmd1("pair_style kim ");
cmd1 += model;
std::string cmd2("pair_coeff * * ");
for (int i=0; i < narg; ++i) {
cmd2 += arg[i];
cmd2 += " ";
}
input->one(cmd1.c_str());
input->one(cmd2.c_str());
}
// End output to log file
kim_style_log_delimiter("end","setup");
kim_init_log_delimiter("end");
}
/* ---------------------------------------------------------------------- */
void KimStyle::do_variables(char *user_units, char *model_units)
void KimInit::kim_init_log_delimiter(std::string const begin_end) const
{
if (comm->me == 0) {
std::string mesg;
if (begin_end == "begin")
mesg =
"#=== BEGIN kim-init ==========================================\n";
else if (begin_end == "end")
mesg =
"#=== END kim-init ============================================\n\n";
if (screen) fputs(mesg.c_str(),screen);
if (logfile) fputs(mesg.c_str(),logfile);
}
}
/* ---------------------------------------------------------------------- */
void KimInit::do_variables(char *user_units, char *model_units)
{
char *from = user_units, *to = model_units;
Variable *variable = input->variable;
@ -576,7 +444,9 @@ void KimStyle::do_variables(char *user_units, char *model_units)
variable->internal_set(v_unit,conversion_factor);
if (comm->me == 0) {
std::stringstream mesg;
mesg << "variable " << var_str << " internal " << conversion_factor
mesg << "variable " << std::setw(15) << std::left << var_str
<< " internal "
<< std::setprecision(12) << std::scientific << conversion_factor
<< std::endl;
if (screen) fputs(mesg.str().c_str(),screen);
if (logfile) fputs(mesg.str().c_str(),logfile);
@ -587,128 +457,3 @@ void KimStyle::do_variables(char *user_units, char *model_units)
if (logfile) fputs("#\n",logfile);
}
}
/* ---------------------------------------------------------------------- */
int KimStyle::species_to_atomic_no(std::string const species) const
{
if (species == "H") return 1;
else if (species == "He") return 2;
else if (species == "Li") return 3;
else if (species == "Be") return 4;
else if (species == "B") return 5;
else if (species == "C") return 6;
else if (species == "N") return 7;
else if (species == "O") return 8;
else if (species == "F") return 9;
else if (species == "Ne") return 10;
else if (species == "Na") return 11;
else if (species == "Mg") return 12;
else if (species == "Al") return 13;
else if (species == "Si") return 14;
else if (species == "P") return 15;
else if (species == "S") return 16;
else if (species == "Cl") return 17;
else if (species == "Ar") return 18;
else if (species == "K") return 19;
else if (species == "Ca") return 20;
else if (species == "Sc") return 21;
else if (species == "Ti") return 22;
else if (species == "V") return 23;
else if (species == "Cr") return 24;
else if (species == "Mn") return 25;
else if (species == "Fe") return 26;
else if (species == "Co") return 27;
else if (species == "Ni") return 28;
else if (species == "Cu") return 29;
else if (species == "Zn") return 30;
else if (species == "Ga") return 31;
else if (species == "Ge") return 32;
else if (species == "As") return 33;
else if (species == "Se") return 34;
else if (species == "Br") return 35;
else if (species == "Kr") return 36;
else if (species == "Rb") return 37;
else if (species == "Sr") return 38;
else if (species == "Y") return 39;
else if (species == "Zr") return 40;
else if (species == "Nb") return 41;
else if (species == "Mo") return 42;
else if (species == "Tc") return 43;
else if (species == "Ru") return 44;
else if (species == "Rh") return 45;
else if (species == "Pd") return 46;
else if (species == "Ag") return 47;
else if (species == "Cd") return 48;
else if (species == "In") return 49;
else if (species == "Sn") return 50;
else if (species == "Sb") return 51;
else if (species == "Te") return 52;
else if (species == "I") return 53;
else if (species == "Xe") return 54;
else if (species == "Cs") return 55;
else if (species == "Ba") return 56;
else if (species == "La") return 57;
else if (species == "Ce") return 58;
else if (species == "Pr") return 59;
else if (species == "Nd") return 60;
else if (species == "Pm") return 61;
else if (species == "Sm") return 62;
else if (species == "Eu") return 63;
else if (species == "Gd") return 64;
else if (species == "Tb") return 65;
else if (species == "Dy") return 66;
else if (species == "Ho") return 67;
else if (species == "Er") return 68;
else if (species == "Tm") return 69;
else if (species == "Yb") return 70;
else if (species == "Lu") return 71;
else if (species == "Hf") return 72;
else if (species == "Ta") return 73;
else if (species == "W") return 74;
else if (species == "Re") return 75;
else if (species == "Os") return 76;
else if (species == "Ir") return 77;
else if (species == "Pt") return 78;
else if (species == "Au") return 79;
else if (species == "Hg") return 80;
else if (species == "Tl") return 81;
else if (species == "Pb") return 82;
else if (species == "Bi") return 83;
else if (species == "Po") return 84;
else if (species == "At") return 85;
else if (species == "Rn") return 86;
else if (species == "Fr") return 87;
else if (species == "Ra") return 88;
else if (species == "Ac") return 89;
else if (species == "Th") return 90;
else if (species == "Pa") return 91;
else if (species == "U") return 92;
else if (species == "Np") return 93;
else if (species == "Pu") return 94;
else if (species == "Am") return 95;
else if (species == "Cm") return 96;
else if (species == "Bk") return 97;
else if (species == "Cf") return 98;
else if (species == "Es") return 99;
else if (species == "Fm") return 100;
else if (species == "Md") return 101;
else if (species == "No") return 102;
else if (species == "Lr") return 103;
else if (species == "Rf") return 104;
else if (species == "Db") return 105;
else if (species == "Sg") return 106;
else if (species == "Bh") return 107;
else if (species == "Hs") return 108;
else if (species == "Mt") return 109;
else if (species == "Ds") return 110;
else if (species == "Rg") return 111;
else if (species == "Cn") return 112;
else if (species == "Nh") return 113;
else if (species == "Fl") return 114;
else if (species == "Mc") return 115;
else if (species == "Lv") return 116;
else if (species == "Ts") return 117;
else if (species == "Og") return 118;
else return -1;
}

35
src/KIM/kim_style.h → src/KIM/kim_init.h
View File

@ -14,6 +14,7 @@
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN)
Ellad B. Tadmor (UMN)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
@ -56,20 +57,20 @@
#ifdef COMMAND_CLASS
CommandStyle(kim_style,KimStyle)
CommandStyle(kim_init,KimInit)
#else
#ifndef LMP_KIM_STYLE_H
#define LMP_KIM_STYLE_H
#ifndef LMP_KIM_INIT_H
#define LMP_KIM_INIT_H
#include "pointers.h"
namespace LAMMPS_NS {
class KimStyle : protected Pointers {
class KimInit : protected Pointers {
public:
KimStyle(class LAMMPS *lmp) : Pointers(lmp) {};
KimInit(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **);
private:
enum model_type_enum {MO, SM};
@ -78,11 +79,8 @@ class KimStyle : protected Pointers {
void determine_model_type_and_units(char *, char *, char **);
void do_init(char *, char *, char *);
void do_setup(int, char **);
void do_variables(char*, char*);
int species_to_atomic_no(std::string const species) const;
void kim_style_log_delimiter(std::string const begin_end,
std::string const model_setup) const;
void kim_init_log_delimiter(std::string const begin_end) const;
};
}
@ -92,19 +90,11 @@ class KimStyle : protected Pointers {
/* ERROR/WARNING messages:
E: Illegal kim_style command
E: Illegal kim_init command
Incorrect number or kind of arguments to kim_style.
Incorrect number or kind of arguments to kim_init.
E: Must use 'kim_style model' command before simulation box is defined
Self-explanatory.
E: Must use 'kim_style setup' command after simulation box is defined
Self-explanatory.
E: Must use 'kim_style model' command before 'kim_style setup'
E: Must use 'kim_init' command before simulation box is defined
Self-explanatory.
@ -125,11 +115,6 @@ E: Incompatible KIM Simulator Model
The requested KIM Simulator Model was defined for a different MD code
and thus is not compatible with LAMMPS.
E: Species XXX is not supported by this KIM Simulator Model
The kim_style define command was referencing a species that is not
present in the requested KIM Simulator Model.
E: Incompatible units for KIM Simulator Model
The selected unit style is not compatible with the requested KIM

367
src/KIM/kim_interactions.cpp Normal file
View File

@ -0,0 +1,367 @@
/* ----------------------------------------------------------------------
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: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN)
Ellad B. Tadmor (UMN)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation; either version 2 of the License, or (at your option)
any later version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
more details.
You should have received a copy of the GNU General Public License along with
this program; if not, see <https://www.gnu.org/licenses>.
Linking LAMMPS statically or dynamically with other modules is making a
combined work based on LAMMPS. Thus, the terms and conditions of the GNU
General Public License cover the whole combination.
In addition, as a special exception, the copyright holders of LAMMPS give
you permission to combine LAMMPS with free software programs or libraries
that are released under the GNU LGPL and with code included in the standard
release of the "kim-api" under the CDDL (or modified versions of such code,
with unchanged license). You may copy and distribute such a system following
the terms of the GNU GPL for LAMMPS and the licenses of the other code
concerned, provided that you include the source code of that other code
when and as the GNU GPL requires distribution of source code.
Note that people who make modified versions of LAMMPS are not obligated to
grant this special exception for their modified versions; it is their choice
whether to do so. The GNU General Public License gives permission to release
a modified version without this exception; this exception also makes it
possible to release a modified version which carries forward this exception.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Designed for use with the kim-api-2.1.0 (and newer) package
------------------------------------------------------------------------- */
#include <cstring>
#include <string>
#include <sstream>
#include "kim_interactions.h"
#include "error.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "update.h"
#include "universe.h"
#include "input.h"
#include "variable.h"
#include "fix_store_kim.h"
extern "C" {
#include "KIM_SimulatorHeaders.h"
}
//@@@@@ Need to switch to c-bindings when they are available.
#include "KIM_SimulatorModel.hpp"
//@@@@@
#define SNUM(x) \
static_cast<std::ostringstream const &>(std::ostringstream() \
<< std::dec << x).str()
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void KimInteractions::command(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal kim_interactions command");
if (!domain->box_exist)
error->all(FLERR,"Must use 'kim_interactions' command after "
"simulation box is defined");
do_setup(narg,arg);
}
/* ---------------------------------------------------------------------- */
void KimInteractions::kim_interactions_log_delimiter(
std::string const begin_end) const
{
if (comm->me == 0) {
std::string mesg;
if (begin_end == "begin")
mesg =
"#=== BEGIN kim_interactions ==================================\n";
else if (begin_end == "end")
mesg =
"#=== END kim_interactions ====================================\n\n";
if (screen) fputs(mesg.c_str(),screen);
if (logfile) fputs(mesg.c_str(),logfile);
}
}
/* ---------------------------------------------------------------------- */
void KimInteractions::do_setup(int narg, char **arg)
{
if (narg != atom->ntypes)
error->all(FLERR,"Illegal kim_interactions command");
char *model_name = NULL;
KIM::SimulatorModel *simulatorModel(NULL);
// check if we had a kim_init command by finding fix STORE/KIM
// retrieve model name and pointer to simulator model class instance.
// validate model name if not given as NULL.
int ifix = modify->find_fix("KIM_MODEL_STORE");
if (ifix >= 0) {
FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix];
model_name = (char *)fix_store->getptr("model_name");
simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model");
} else error->all(FLERR,"Must use 'kim_init' before 'kim_interactions'");
// Begin output to log file
kim_interactions_log_delimiter("begin");
if (simulatorModel) {
std::string delimiter("");
std::string atom_type_sym_list;
std::string atom_type_num_list;
for (int i = 0; i < narg; i++)
{
atom_type_sym_list += delimiter + arg[i];
atom_type_num_list += delimiter + SNUM(species_to_atomic_no(arg[i]));
delimiter = " ";
}
simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_list);
simulatorModel->AddTemplateMap("atom-type-num-list",atom_type_num_list);
simulatorModel->CloseTemplateMap();
int len = strlen(atom_type_sym_list.c_str())+1;
char *strbuf = new char[len];
char *strword;
// validate species selection
int sim_num_species;
bool species_is_supported;
const std::string *sim_species;
simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species);
strcpy(strbuf,atom_type_sym_list.c_str());
strword = strtok(strbuf," \t");
while (strword) {
species_is_supported = false;
if (strcmp(strword,"NULL") == 0) continue;
for (int i=0; i < sim_num_species; ++i) {
simulatorModel->GetSupportedSpecies(i, &sim_species);
if (strcmp(sim_species->c_str(),strword) == 0)
species_is_supported = true;
}
if (!species_is_supported) {
std::string msg("Species '");
msg += strword;
msg += "' is not supported by this KIM Simulator Model";
error->all(FLERR,msg.c_str());
}
strword = strtok(NULL," \t");
}
delete[] strbuf;
// check if units are unchanged
int sim_fields, sim_lines;
const std::string *sim_field, *sim_value;
simulatorModel->GetNumberOfSimulatorFields(&sim_fields);
for (int i=0; i < sim_fields; ++i) {
simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
if (*sim_field == "units") {
simulatorModel->GetSimulatorFieldLine(i,0,&sim_value);
if (*sim_value != update->unit_style)
error->all(FLERR,"Incompatible units for KIM Simulator Model");
}
}
int sim_model_idx=-1;
for (int i=0; i < sim_fields; ++i) {
simulatorModel->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
if (*sim_field == "model-defn") {
sim_model_idx = i;
for (int j=0; j < sim_lines; ++j) {
simulatorModel->GetSimulatorFieldLine(sim_model_idx,j,&sim_value);
input->one(sim_value->c_str());
}
}
}
if (sim_model_idx < 0)
error->all(FLERR,"KIM Simulator Model has no Model definition");
simulatorModel->OpenAndInitializeTemplateMap();
} else {
// not a simulator model. issue pair_style and pair_coeff commands.
// NOTE: all references to arg must appear before calls to input->one()
// as that will reset the argument vector.
std::string cmd1("pair_style kim ");
cmd1 += model_name;
std::string cmd2("pair_coeff * * ");
for (int i=0; i < narg; ++i) {
cmd2 += arg[i];
cmd2 += " ";
}
input->one(cmd1.c_str());
input->one(cmd2.c_str());
}
// End output to log file
kim_interactions_log_delimiter("end");
}
/* ---------------------------------------------------------------------- */
int KimInteractions::species_to_atomic_no(std::string const species) const
{
if (species == "H") return 1;
else if (species == "He") return 2;
else if (species == "Li") return 3;
else if (species == "Be") return 4;
else if (species == "B") return 5;
else if (species == "C") return 6;
else if (species == "N") return 7;
else if (species == "O") return 8;
else if (species == "F") return 9;
else if (species == "Ne") return 10;
else if (species == "Na") return 11;
else if (species == "Mg") return 12;
else if (species == "Al") return 13;
else if (species == "Si") return 14;
else if (species == "P") return 15;
else if (species == "S") return 16;
else if (species == "Cl") return 17;
else if (species == "Ar") return 18;
else if (species == "K") return 19;
else if (species == "Ca") return 20;
else if (species == "Sc") return 21;
else if (species == "Ti") return 22;
else if (species == "V") return 23;
else if (species == "Cr") return 24;
else if (species == "Mn") return 25;
else if (species == "Fe") return 26;
else if (species == "Co") return 27;
else if (species == "Ni") return 28;
else if (species == "Cu") return 29;
else if (species == "Zn") return 30;
else if (species == "Ga") return 31;
else if (species == "Ge") return 32;
else if (species == "As") return 33;
else if (species == "Se") return 34;
else if (species == "Br") return 35;
else if (species == "Kr") return 36;
else if (species == "Rb") return 37;
else if (species == "Sr") return 38;
else if (species == "Y") return 39;
else if (species == "Zr") return 40;
else if (species == "Nb") return 41;
else if (species == "Mo") return 42;
else if (species == "Tc") return 43;
else if (species == "Ru") return 44;
else if (species == "Rh") return 45;
else if (species == "Pd") return 46;
else if (species == "Ag") return 47;
else if (species == "Cd") return 48;
else if (species == "In") return 49;
else if (species == "Sn") return 50;
else if (species == "Sb") return 51;
else if (species == "Te") return 52;
else if (species == "I") return 53;
else if (species == "Xe") return 54;
else if (species == "Cs") return 55;
else if (species == "Ba") return 56;
else if (species == "La") return 57;
else if (species == "Ce") return 58;
else if (species == "Pr") return 59;
else if (species == "Nd") return 60;
else if (species == "Pm") return 61;
else if (species == "Sm") return 62;
else if (species == "Eu") return 63;
else if (species == "Gd") return 64;
else if (species == "Tb") return 65;
else if (species == "Dy") return 66;
else if (species == "Ho") return 67;
else if (species == "Er") return 68;
else if (species == "Tm") return 69;
else if (species == "Yb") return 70;
else if (species == "Lu") return 71;
else if (species == "Hf") return 72;
else if (species == "Ta") return 73;
else if (species == "W") return 74;
else if (species == "Re") return 75;
else if (species == "Os") return 76;
else if (species == "Ir") return 77;
else if (species == "Pt") return 78;
else if (species == "Au") return 79;
else if (species == "Hg") return 80;
else if (species == "Tl") return 81;
else if (species == "Pb") return 82;
else if (species == "Bi") return 83;
else if (species == "Po") return 84;
else if (species == "At") return 85;
else if (species == "Rn") return 86;
else if (species == "Fr") return 87;
else if (species == "Ra") return 88;
else if (species == "Ac") return 89;
else if (species == "Th") return 90;
else if (species == "Pa") return 91;
else if (species == "U") return 92;
else if (species == "Np") return 93;
else if (species == "Pu") return 94;
else if (species == "Am") return 95;
else if (species == "Cm") return 96;
else if (species == "Bk") return 97;
else if (species == "Cf") return 98;
else if (species == "Es") return 99;
else if (species == "Fm") return 100;
else if (species == "Md") return 101;
else if (species == "No") return 102;
else if (species == "Lr") return 103;
else if (species == "Rf") return 104;
else if (species == "Db") return 105;
else if (species == "Sg") return 106;
else if (species == "Bh") return 107;
else if (species == "Hs") return 108;
else if (species == "Mt") return 109;
else if (species == "Ds") return 110;
else if (species == "Rg") return 111;
else if (species == "Cn") return 112;
else if (species == "Nh") return 113;
else if (species == "Fl") return 114;
else if (species == "Mc") return 115;
else if (species == "Lv") return 116;
else if (species == "Ts") return 117;
else if (species == "Og") return 118;
else return -1;
}

116
src/KIM/kim_interactions.h Normal file
View File

@ -0,0 +1,116 @@
/* -*- 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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN)
Ellad B. Tadmor (UMN)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
This program is free software; you can redistribute it and/or modify it
under the terms of the GNU General Public License as published by the Free
Software Foundation; either version 2 of the License, or (at your option)
any later version.
This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for
more details.
You should have received a copy of the GNU General Public License along with
this program; if not, see <https://www.gnu.org/licenses>.
Linking LAMMPS statically or dynamically with other modules is making a
combined work based on LAMMPS. Thus, the terms and conditions of the GNU
General Public License cover the whole combination.
In addition, as a special exception, the copyright holders of LAMMPS give
you permission to combine LAMMPS with free software programs or libraries
that are released under the GNU LGPL and with code included in the standard
release of the "kim-api" under the CDDL (or modified versions of such code,
with unchanged license). You may copy and distribute such a system following
the terms of the GNU GPL for LAMMPS and the licenses of the other code
concerned, provided that you include the source code of that other code
when and as the GNU GPL requires distribution of source code.
Note that people who make modified versions of LAMMPS are not obligated to
grant this special exception for their modified versions; it is their choice
whether to do so. The GNU General Public License gives permission to release
a modified version without this exception; this exception also makes it
possible to release a modified version which carries forward this exception.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Designed for use with the kim-api-2.1.0 (and newer) package
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(kim_interactions,KimInteractions)
#else
#ifndef LMP_KIM_INTERACTIONS_H
#define LMP_KIM_INTERACTIONS_H
#include "pointers.h"
namespace LAMMPS_NS {
class KimInteractions : protected Pointers {
public:
KimInteractions(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **);
private:
void do_setup(int, char **);
int species_to_atomic_no(std::string const species) const;
void kim_interactions_log_delimiter(std::string const begin_end) const;
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal kim_interactions command
Incorrect number or kind of arguments to kim_interactions.
E: Must use 'kim_interactions' command after simulation box is defined
Self-explanatory.
E: Must use 'kim_init' command before 'kim_interactions'
Self-explanatory.
E: Species XXX is not supported by this KIM Simulator Model
The kim_interactions command was referencing a species that is not
present in the requested KIM Simulator Model.
E: Incompatible units for KIM Simulator Model
The selected unit style is not compatible with the requested KIM
Simulator Model.
E: KIM Simulator Model has no Model definition
There is no model definition (key: model-defn) in the KIM Simulator
Model. Please contact the OpenKIM database maintainers to verify
and potentially correct this.
*/