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add new 'kim_style' command as front end for KIM simulator (and regular) models

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This commit is contained in:
Axel Kohlmeyer
2019-05-24 10:23:26 -04:00
parent 1e2ceb88da
commit ce46d52c8a
7 changed files with 600 additions and 5 deletions
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4
examples/kim/in.kim.simulator-model
View File

@ -16,7 +16,6 @@ variable zz equal 20*$z
units metal
atom_style atomic
newton off
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
@ -26,8 +25,7 @@ create_atoms 1 box
#pair_style lj/cut 8.1500
#pair_coeff 1 1 0.0104 3.4000
pair_style kim ex_sim_model_Si_mod_tersoff
pair_coeff * * Si Si
kim_style define ex_sim_model_Si_mod_tersoff Si Si
mass * 39.95
velocity all create 200.0 232345 loop geom

127
src/KIM/fix_store_kim.cpp Normal file
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@ -0,0 +1,127 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (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-2.0.2 (and newer) package
------------------------------------------------------------------------- */
#include <cstring>
#include "fix_store_kim.h"
#include "KIM_SimulatorModel.hpp"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixStoreKIM::FixStoreKIM(LAMMPS *lmp, int narg, char **arg)
: Fix(lmp, narg, arg), simulator_model(NULL), model_name(NULL)
{
if (narg != 3) error->all(FLERR,"Illegal fix STORE/KIM command");
}
/* ---------------------------------------------------------------------- */
FixStoreKIM::~FixStoreKIM()
{
// free associated storage
if (simulator_model) {
KIM::SimulatorModel *sm = (KIM::SimulatorModel *)simulator_model;
KIM::SimulatorModel::Destroy(&sm);
simulator_model = NULL;
}
if (model_name) {
char *mn = (char *)model_name;
delete[] mn;
model_name = NULL;
}
}
/* ---------------------------------------------------------------------- */
int FixStoreKIM::setmask()
{
int mask = 0;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixStoreKIM::setptr(const char *name, void *ptr)
{
if (strcmp(name,"simulator_model") == 0) {
if (simulator_model) {
KIM::SimulatorModel *sm = (KIM::SimulatorModel *)simulator_model;
KIM::SimulatorModel::Destroy(&sm);
}
simulator_model = ptr;
} else if (strcmp(name,"model_name") == 0) {
if (model_name) {
char *mn = (char *)model_name;
delete[] mn;
}
model_name = ptr;
}
}
/* ---------------------------------------------------------------------- */
void *FixStoreKIM::getptr(const char *name)
{
if (strcmp(name,"simulator_model") == 0) return simulator_model;
else if (strcmp(name,"model_name") == 0) return model_name;
else return NULL;
}

98
src/KIM/fix_store_kim.h Normal file
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@ -0,0 +1,98 @@
/* -*- 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)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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-2.0.2 (and newer) package
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(STORE/KIM,FixStoreKIM)
#else
#ifndef LMP_FIX_STORE_KIM_H
#define LMP_FIX_STORE_KIM_H
#include <cstdio>
#include "fix.h"
namespace LAMMPS_NS {
class FixStoreKIM : public Fix {
public:
FixStoreKIM(class LAMMPS *, int, char **);
~FixStoreKIM();
int setmask();
void setptr(const char *, void *);
void *getptr(const char *);
private:
void *simulator_model; // pointer to KIM simulator model class
void *model_name; // string of KIM model name
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
*/

1
src/KIM/kim_query.cpp
View File

@ -11,7 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Axel Kohlmeyer (Temple U),
Ryan S. Elliott (UMN)

286
src/KIM/kim_style.cpp Normal file
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@ -0,0 +1,286 @@
/* ----------------------------------------------------------------------
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)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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-2.0.2 (and newer) package
------------------------------------------------------------------------- */
#include <cstring>
#include <string>
#include "kim_style.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 "fix_store_kim.h"
#include "KIM_SimulatorModel.hpp"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
void KimStyle::command(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal kim_style command");
if (strcmp(arg[0],"init") == 0) {
if (narg > 2) error->all(FLERR,"Illegal kim_style init command");
if (domain->box_exist)
error->all(FLERR,"Must use 'kim_style init' command before "
"simulation box is defined");
int len = strlen(arg[1])+1;
char *model = new char[len];
strcpy(model,arg[1]);
do_init(model);
} else if (strcmp(arg[0],"define") == 0) {
if (!domain->box_exist)
error->all(FLERR,"Must use 'kim_style define' command after "
"simulation box is defined");
do_defn(narg-1,arg+1);
} else error->all(FLERR,"Illegal kim_style command");
}
/* ---------------------------------------------------------------------- */
void KimStyle::do_init(char *model)
{
// create storage proxy fix. delete existing fix, if needed.
int ifix = modify->find_fix("KIM_MODEL_STORE");
if (ifix >= 0) modify->delete_fix(ifix);
input->one("fix KIM_MODEL_STORE all STORE/KIM");
ifix = modify->find_fix("KIM_MODEL_STORE");
FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix];
fix_store->setptr("model_name", (void *) model);
int kimerror;
KIM::SimulatorModel * simulatorModel;
kimerror = KIM::SimulatorModel::Create(model,&simulatorModel);
// 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);
// set units
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);
std::string cmd("units ");
cmd += *sim_value;
input->one(cmd.c_str());
break;
}
}
// 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;
}
}
// reset template map.
simulatorModel->ClearTemplateMap();
}
/* ---------------------------------------------------------------------- */
void KimStyle::do_defn(int narg, char **arg)
{
if (narg != atom->ntypes + 1)
error->all(FLERR,"Incorrect number of arguments for kim_style define command");
char *model = arg[0];
KIM::SimulatorModel *simulatorModel(NULL);
int kimerror;
// 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];
if (strcmp(model,"NULL") == 0)
model = (char *)fix_store->getptr("model_name");
else if (strcmp(model,(const char*)fix_store->getptr("model_name")) != 0)
error->all(FLERR,"Inconsistent KIM model name");
simulatorModel = (KIM::SimulatorModel *)fix_store->getptr("simulator_model");
} else {
kimerror = KIM::SimulatorModel::Create(model,&simulatorModel);
if (kimerror) simulatorModel = NULL;
}
if (simulatorModel) {
const std::string *sim_name, *sim_version;
std::string atom_type_sym_list;
simulatorModel->GetSimulatorName(&sim_name);
simulatorModel->GetSimulatorVersion(&sim_version);
if (comm->me == 0) {
std::string mesg("Using KIM Simulator Model : ");
mesg += model;
mesg += "\n";
mesg += "For Simulator : ";
mesg += *sim_name + " " + *sim_version + "\n";
mesg += "Running on : LAMMPS ";
mesg += universe->version;
mesg += "\n";
if (screen) fputs(mesg.c_str(),screen);
if (logfile) fputs(mesg.c_str(),logfile);
}
if (*sim_name != "LAMMPS")
error->all(FLERR,"Incompatible KIM Simulator Model");
for (int i = 1; i < narg; i++)
atom_type_sym_list += std::string(" ") + arg[i];
simulatorModel->AddTemplateMap("atom-type-sym-list",atom_type_sym_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;
const std::string *sim_species;
simulatorModel->GetNumberOfSupportedSpecies(&sim_num_species);
for (int i=0; i < sim_num_species; ++i) {
simulatorModel->GetSupportedSpecies(i, &sim_species);
strcpy(strbuf,atom_type_sym_list.c_str());
strword = strtok(strbuf," \t");
while (strword) {
if ((strcmp(strword,"NULL") != 0) && (strcmp(sim_species->c_str(),strword) != 0))
error->all(FLERR,"Species not supported by KIM Simulator Model");
strword = strtok(NULL," \t");
}
}
delete[] strbuf;
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");
break;
}
}
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");
} 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=1; i < narg; ++i) {
cmd2 += arg[i];
cmd2 += " ";
}
input->one(cmd1.c_str());
input->one(cmd2.c_str());
}
}

87
src/KIM/kim_style.h Normal file
View File

@ -0,0 +1,87 @@
/* -*- 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)
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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-2.0.2 (and newer) package
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(kim_style,KimStyle)
#else
#ifndef LMP_KIM_STYLE_H
#define LMP_KIM_STYLE_H
#include "pointers.h"
namespace LAMMPS_NS {
class KimStyle : protected Pointers {
public:
KimStyle(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **);
private:
void do_init(char *);
void do_defn(int, char **);
};
}
#endif
#endif
/* ERROR/WARNING messages:
*/

2
src/modify.cpp
View File

@ -793,7 +793,7 @@ void Modify::add_fix(int narg, char **arg, int trysuffix)
const char *exceptions[] =
{"GPU", "OMP", "INTEL", "property/atom", "cmap", "cmap3", "rx",
"deprecated", NULL};
"deprecated", "STORE/KIM", NULL};
if (domain->box_exist == 0) {
int m;