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Added code to define unit conversion factors

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This commit is contained in:
Ellad B. Tadmor
2019-06-21 18:39:18 -05:00
parent 88994d813a
commit 08cee18f32
4 changed files with 1596 additions and 95 deletions
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219
src/KIM/kim_style.cpp
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@ -56,6 +56,7 @@
#include <cstring>
#include <string>
#include <sstream>
#include "kim_style.h"
#include "error.h"
#include "atom.h"
@ -67,6 +68,7 @@
#include "input.h"
#include "variable.h"
#include "fix_store_kim.h"
#include "kim_units.h"
extern "C" {
#include "KIM_SimulatorHeaders.h"
@ -100,7 +102,6 @@ void KimStyle::command(int narg, char **arg)
determine_model_type_and_units(model_name, user_units, &model_units);
do_init(model_name, user_units, model_units);
if (unit_conversion_mode) do_variables(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 "
@ -255,7 +256,10 @@ void KimStyle::determine_model_type_and_units(char * model_name,
if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0))
{
error->all(FLERR,"Incompatible units for KIM Simulator Model");
std::stringstream mesg;
mesg << "Incompatible units for KIM Simulator Model, required units = "
<< *model_units;
error->all(FLERR,mesg.str().c_str());
}
}
@ -280,17 +284,43 @@ 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);
int kimerror;
// @@@@@ switch to c-bindings when they are available
KIM::SimulatorModel * simulatorModel;
kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel);
const std::string *sim_name, *sim_version;
simulatorModel->GetSimulatorNameAndVersion(&sim_name, &sim_version);
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 (screen) fputs(mesg.c_str(),screen);
if (logfile) fputs(mesg.c_str(),logfile);
}
// Define unit conversion factor variables and print to log
if (unit_conversion_mode) do_variables(user_units, model_units);
// set units
std::string cmd("units ");
cmd += model_units;
input->one(cmd.c_str());
int kimerror;
// @@@@@ switch to c-bindings when they are available
KIM::SimulatorModel * simulatorModel;
kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel);
// not a Kim Simulator Model; nothing else to do here.
if (kimerror) return;
@ -318,13 +348,36 @@ void KimStyle::do_init(char *model_name, char *user_units, char* model_units)
}
}
// reset template map.
// End output to log file
kim_style_log_delimiter("end","model");
// reset template map.
simulatorModel->OpenAndInitializeTemplateMap();
}
/* ---------------------------------------------------------------------- */
void KimStyle::kim_style_log_delimiter(std::string begin_end,
std::string model_setup)
{
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)
@ -345,30 +398,13 @@ void KimStyle::do_setup(int narg, char **arg)
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) {
const std::string *sim_name, *sim_version;
std::string atom_type_sym_list;
simulatorModel->GetSimulatorNameAndVersion(&sim_name, &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 = 0; i < narg; i++)
atom_type_sym_list += std::string(" ") + arg[i];
@ -455,6 +491,10 @@ void KimStyle::do_setup(int narg, char **arg)
input->one(cmd1.c_str());
input->one(cmd2.c_str());
}
// End output to log file
kim_style_log_delimiter("end","setup");
}
/* ---------------------------------------------------------------------- */
@ -464,85 +504,74 @@ void KimStyle::do_variables(char *user_units, char *model_units)
char *from = user_units, *to = model_units;
Variable *variable = input->variable;
// refuse convertion from or to reduced units
// refuse conversion from or to reduced units
if ((strcmp(from,"lj") == 0) || (strcmp(to,"lj") == 0))
error->all(FLERR,"Cannot set up conversion variables for 'lj' units");
// get index to internal style variables. create, if needed.
// default to conversion factor 1.0 for newly created variables
// @@@@@@ below needs to be updated to use Ellad's luc.
int v_length, v_mass, v_time;
// set conversion factors for newly created variables.
double conversion_factor;
int ier;
char *args[3];
std::string var_str;
args[1] = (char *)"internal";
args[2] = (char *)"1.0";
args[0] = (char *)"_u_length";
v_length = variable->find(args[0]);
if (v_length < 0) {
variable->set(3,args);
v_length = variable->find(args[0]);
int v_unit;
int const nunits = 14;
char *units[nunits] = {(char *)"mass",
(char *)"distance",
(char *)"time",
(char *)"energy",
(char *)"velocity",
(char *)"force",
(char *)"torque",
(char *)"temperature",
(char *)"pressure",
(char *)"viscosity",
(char *)"charge",
(char *)"dipole",
(char *)"efield",
(char *)"density"};
if (comm->me == 0) {
std::stringstream mesg;
mesg << "# Conversion factors from " << from << " to " << to
<< ":" << std::endl;
if (screen) fputs(mesg.str().c_str(),screen);
if (logfile) fputs(mesg.str().c_str(),logfile);
}
args[0] = (char *)"_u_mass";
v_mass = variable->find(args[0]);
if (v_mass < 0) {
variable->set(3,args);
v_mass = variable->find(args[0]);
}
args[0] = (char *)"_u_time";
v_time = variable->find(args[0]);
if (v_time < 0) {
variable->set(3,args);
v_time = variable->find(args[0]);
}
// special case: both unit styles are the same => conversion factor 1.0
if (strcmp(from,to) == 0) {
variable->internal_set(v_length,1.0);
variable->internal_set(v_mass,1.0);
variable->internal_set(v_time,1.0);
return;
}
if (strcmp(from,"real") == 0) {
if (strcmp(to,"metal") == 0) {
variable->internal_set(v_length,1.0);
variable->internal_set(v_mass,1.0);
variable->internal_set(v_time,0.001);
} else {
std::string err("Do not know how to set up conversion variables ");
err += "between '";
err += from;
err += "' and '";
err += to;
err += "' units";
for (int i = 0; i < nunits; i++)
{
var_str = std::string("_u_") + std::string(units[i]);
args[0] = (char *)var_str.c_str();
v_unit = variable->find(args[0]);
if (v_unit < 0) {
variable->set(3,args);
v_unit = variable->find(args[0]);
}
ier = lammps_unit_conversion(units[i],
from,
to,
conversion_factor);
if (ier != 0) {
std::string err = std::string("Unable to obtain conversion factor: ") +
"unit = " + units[i] + "; "
"from = " + from + "; "
"to = " + to + ".";
error->all(FLERR,err.c_str());
}
} else if (strcmp(from,"metal") == 0) {
if (strcmp(to,"real") == 0) {
variable->internal_set(v_length,1.0);
variable->internal_set(v_mass,1.0);
variable->internal_set(v_time,1000.0);
} else {
std::string err("Do not know how to set up conversion variables ");
err += "between '";
err += from;
err += "' and '";
err += to;
err += "' units";
error->all(FLERR,err.c_str());
variable->internal_set(v_unit,conversion_factor);
if (comm->me == 0) {
std::stringstream mesg;
mesg << "# " << var_str << " = " << conversion_factor << std::endl;
if (screen) fputs(mesg.str().c_str(),screen);
if (logfile) fputs(mesg.str().c_str(),logfile);
}
} else {
std::string err("Do not know how to set up conversion variables ");
err += "between '";
err += from;
err += "' and '";
err += to;
err += "' units";
error->all(FLERR,err.c_str());
}
if (comm->me == 0) {
if (screen) fputs("#\n",screen);
if (logfile) fputs("#\n",logfile);
}
}

2
src/KIM/kim_style.h
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@ -80,6 +80,8 @@ class KimStyle : protected Pointers {
void do_init(char *, char *, char *);
void do_setup(int, char **);
void do_variables(char*, char*);
void kim_style_log_delimiter(std::string begin_end,
std::string model_setup);
};
}

1411
src/KIM/kim_units.cpp Normal file
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59
src/KIM/kim_units.h Normal file
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@ -0,0 +1,59 @@
/* -*- 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: 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-2.0.2 (and newer) package
------------------------------------------------------------------------- */
int lammps_unit_conversion(std::string const &unit_type_str,
std::string const &from_system_str,
std::string const &to_system_str,
double &conversion_factor);