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Work on kim_style for latest definition prototype

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This commit is contained in:
Ryan S. Elliott
2019-06-20 16:45:45 -05:00
parent 128d021c10
commit 0613c10395
3 changed files with 217 additions and 112 deletions
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9
examples/kim/in.kim.lj.simulator_model
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@ -14,12 +14,11 @@ variable xx equal 20*$x
variable yy equal 20*$y
variable zz equal 20*$z
units metal
atom_style atomic
echo both
#kim_style model LennardJones_Ar metal
kim_style model Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu real unit_conversion_mode
newton on
kim_style init LennardJones_Ar
lattice fcc 4.4300
region box block 0 ${xx} 0 ${yy} 0 ${zz}
create_box 1 box
@ -28,7 +27,7 @@ create_atoms 1 box
#pair_style lj/cut 8.1500
#pair_coeff 1 1 0.0104 3.4000
kim_style define Ar
kim_style setup Au
mass 1 39.95
velocity all create 200.0 232345 loop geom

286
src/KIM/kim_style.cpp
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@ -51,7 +51,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Designed for use with the kim-api-2.0.2 (and newer) package
Designed for use with the kim-api-2.1.0 (and newer) package
------------------------------------------------------------------------- */
#include <cstring>
@ -68,6 +68,9 @@
#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"
//@@@@@
@ -78,42 +81,188 @@ using namespace LAMMPS_NS;
void KimStyle::command(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal kim_style command");
if ((narg < 2) || (narg > 4)) error->all(FLERR,"Illegal kim_style command");
units_from = NULL;
units_to = NULL;
if (strcmp(arg[0],"init") == 0) {
if (strcmp(arg[0],"model") == 0) {
if (domain->box_exist)
error->all(FLERR,"Must use 'kim_style init' command before "
error->all(FLERR,"Must use 'kim_style model' command before "
"simulation box is defined");
int len = strlen(arg[1])+1;
char *model = new char[len];
strcpy(model,arg[1]);
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;
int args_done = do_units(narg-2,arg-2);
if (narg > (args_done + 2))
error->all(FLERR,"Illegal kim_style command");
do_init(model);
do_variables();
} else if (strcmp(arg[0],"define") == 0) {
char *model_units;
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 define' command after "
error->all(FLERR,"Must use 'kim_style setup' command after "
"simulation box is defined");
int args_done = do_units(narg-1,arg-1);
do_defn(narg - (args_done+1),arg + (args_done+1));
} else if (strcmp(arg[0],"unit_variables") == 0) {
int args_done = do_units(narg,arg);
if (narg > args_done)
error->all(FLERR,"Illegal kim_style command");
do_variables();
do_setup(narg-1,++arg);
} else error->all(FLERR,"Illegal kim_style command");
}
/* ---------------------------------------------------------------------- */
namespace {
void get_kim_unit_names(
char const * const system,
KIM_LengthUnit & lengthUnit,
KIM_EnergyUnit & energyUnit,
KIM_ChargeUnit & chargeUnit,
KIM_TemperatureUnit & temperatureUnit,
KIM_TimeUnit & timeUnit,
Error * error)
{
if ((strcmp(system,"real")==0)) {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_kcal_mol;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if ((strcmp(system,"metal")==0)) {
lengthUnit = KIM_LENGTH_UNIT_A;
energyUnit = KIM_ENERGY_UNIT_eV;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_ps;
} else if ((strcmp(system,"si")==0)) {
lengthUnit = KIM_LENGTH_UNIT_m;
energyUnit = KIM_ENERGY_UNIT_J;
chargeUnit = KIM_CHARGE_UNIT_C;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(system,"cgs")==0)) {
lengthUnit = KIM_LENGTH_UNIT_cm;
energyUnit = KIM_ENERGY_UNIT_erg;
chargeUnit = KIM_CHARGE_UNIT_statC;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_s;
} else if ((strcmp(system,"electron")==0)) {
lengthUnit = KIM_LENGTH_UNIT_Bohr;
energyUnit = KIM_ENERGY_UNIT_Hartree;
chargeUnit = KIM_CHARGE_UNIT_e;
temperatureUnit = KIM_TEMPERATURE_UNIT_K;
timeUnit = KIM_TIME_UNIT_fs;
} else if ((strcmp(system,"lj")==0)) {
error->all(FLERR,"LAMMPS unit_style lj not supported by KIM models");
} else {
error->all(FLERR,"Unknown unit_style");
}
}
} // namespace
void KimStyle::determine_model_type_and_units(char * model_name,
char * user_units,
char ** model_units)
{
KIM_LengthUnit lengthUnit;
KIM_EnergyUnit energyUnit;
KIM_ChargeUnit chargeUnit;
KIM_TemperatureUnit temperatureUnit;
KIM_TimeUnit timeUnit;
int units_accepted;
KIM_Model * kim_MO;
void KimStyle::do_init(char *model)
get_kim_unit_names(user_units, lengthUnit, energyUnit,
chargeUnit, temperatureUnit, timeUnit, error);
int kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased,
lengthUnit,
energyUnit,
chargeUnit,
temperatureUnit,
timeUnit,
model_name,
&units_accepted,
&kim_MO);
if (!kim_error) // model is an MO
{
model_type = MO;
KIM_Model_Destroy(&kim_MO);
if (units_accepted)
{
int len=strlen(user_units);
*model_units = new char[len]; strcpy(*model_units,user_units);
return;
}
else if (unit_conversion_mode)
{
int const num_systems = 5;
char const * const systems[num_systems]
= {"metal", "real", "si", "cgs", "electron"};
for (int i=0; i < num_systems; ++i)
{
get_kim_unit_names(systems[i], lengthUnit, energyUnit,
chargeUnit, temperatureUnit, timeUnit, error);
kim_error = KIM_Model_Create(KIM_NUMBERING_zeroBased,
lengthUnit,
energyUnit,
chargeUnit,
temperatureUnit,
timeUnit,
model_name,
&units_accepted,
&kim_MO);
KIM_Model_Destroy(&kim_MO);
if (units_accepted)
{
int len=strlen(systems[i]);
*model_units = new char[len]; strcpy(*model_units,systems[i]);
return;
}
}
error->all(FLERR,"KIM Model does not support any lammps unit system");
}
else
{
error->all(FLERR,"KIM Model does not support the requested unit system");
}
}
KIM::SimulatorModel * kim_SM;
kim_error = KIM::SimulatorModel::Create(model_name, &kim_SM);
if (kim_error)
{
error->all(FLERR,"KIM model name not found");
}
model_type = SM;
int sim_fields;
int sim_lines;
std::string const * sim_field;
std::string const * sim_value;
kim_SM->GetNumberOfSimulatorFields(&sim_fields);
kim_SM->CloseTemplateMap();
for (int i=0; i < sim_fields; ++i) {
kim_SM->GetSimulatorFieldMetadata(i,&sim_lines,&sim_field);
if (*sim_field == "units") {
kim_SM->GetSimulatorFieldLine(i,0,&sim_value);
int len=(*sim_value).length();
*model_units = new char[len]; strcpy(*model_units,sim_value->c_str());
break;
}
}
KIM::SimulatorModel::Destroy(&kim_SM);
if ((! unit_conversion_mode) && (strcmp(*model_units, user_units)!=0))
{
error->all(FLERR,"Incompatible units for KIM Simulator Model");
}
}
/* ---------------------------------------------------------------------- */
void KimStyle::do_init(char *model_name, char *user_units, char* model_units)
{
// create storage proxy fix. delete existing fix, if needed.
@ -127,14 +276,20 @@ void KimStyle::do_init(char *model)
ifix = modify->find_fix("KIM_MODEL_STORE");
FixStoreKIM *fix_store = (FixStoreKIM *) modify->fix[ifix];
fix_store->setptr("model_name", (void *) model);
fix_store->setptr("units_from", (void *) units_from);
fix_store->setptr("units_to", (void *) units_to);
fix_store->setptr("model_name", (void *) model_name);
fix_store->setptr("user_units", (void *) user_units);
fix_store->setptr("model_units", (void *) 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,&simulatorModel);
kimerror = KIM::SimulatorModel::Create(model_name,&simulatorModel);
// not a Kim Simulator Model; nothing else to do here.
@ -150,19 +305,6 @@ void KimStyle::do_init(char *model)
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) {
@ -183,7 +325,7 @@ void KimStyle::do_init(char *model)
/* ---------------------------------------------------------------------- */
void KimStyle::do_defn(int narg, char **arg)
void KimStyle::do_setup(int narg, char **arg)
{
if (narg != atom->ntypes)
error->all(FLERR,"Illegal kim_style command");
@ -201,7 +343,7 @@ void KimStyle::do_defn(int narg, char **arg)
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 init' before 'kim_style define'");
} else error->all(FLERR,"Must use 'kim_style model' before 'kim_style setup'");
if (simulatorModel) {
@ -317,62 +459,11 @@ void KimStyle::do_defn(int narg, char **arg)
/* ---------------------------------------------------------------------- */
int KimStyle::do_units(int narg, char **arg)
void KimStyle::do_variables(char *user_units, char *model_units)
{
// retrieve custom units setting if kim_style had been called before
int ifix = modify->find_fix("KIM_MODEL_STORE");
FixStoreKIM *fix_store = NULL;
if (ifix >= 0) {
fix_store = (FixStoreKIM *) modify->fix[ifix];
units_from = (char *)fix_store->getptr("units_from");
units_to = (char *)fix_store->getptr("units_to");
}
if (narg < 2) return 0;
int iarg=0;
for (iarg = 0; iarg < narg; iarg += 2) {
if (strcmp(arg[iarg],"unit_variables") == 0) {
if (narg > iarg+2) error->all(FLERR,"Illegal kim_style command");
if (strcmp(arg[iarg+1],"NULL") == 0) {
delete[] units_to;
units_to = NULL;
} else {
int len = strlen(arg[iarg+1])+1;
delete[] units_to;
units_to = new char[len];
strcpy(units_to,arg[iarg+1]);
}
if (fix_store) fix_store->setptr("units_to",units_to);
} else if (strcmp(arg[iarg],"unit_from") == 0) {
if (narg > iarg+2) error->all(FLERR,"Illegal kim_style command");
if (strcmp(arg[iarg+1],"NULL") == 0) {
delete[] units_from;
units_from = NULL;
} else {
int len = strlen(arg[iarg+1])+1;
delete[] units_from;
units_from = new char[len];
strcpy(units_from,arg[iarg+1]);
}
if (fix_store) fix_store->setptr("units_from",units_from);
} else return iarg;
}
return iarg;
}
/* ---------------------------------------------------------------------- */
void KimStyle::do_variables()
{
char *from, *to;
char *from = user_units, *to = model_units;
Variable *variable = input->variable;
if (units_from) from = units_from;
else from = update->unit_style;
if (units_to) to = units_to;
else to = update->unit_style;
// refuse convertion from or to reduced units
if ((strcmp(from,"lj") == 0) || (strcmp(to,"lj") == 0))
@ -381,6 +472,7 @@ void KimStyle::do_variables()
// 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;
char *args[3];
args[1] = (char *)"internal";

34
src/KIM/kim_style.h
View File

@ -51,7 +51,7 @@
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Designed for use with the kim-api-2.0.2 (and newer) package
Designed for use with the kim-api-2.1.0 (and newer) package
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
@ -72,12 +72,14 @@ class KimStyle : protected Pointers {
KimStyle(class LAMMPS *lmp) : Pointers(lmp) {};
void command(int, char **);
private:
char *units_from;
char *units_to;
void do_init(char *);
void do_defn(int, char **);
int do_units(int, char **);
void do_variables();
enum model_type_enum {MO, SM};
model_type_enum model_type;
bool unit_conversion_mode;
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*);
};
}
@ -91,15 +93,27 @@ E: Illegal kim_style command
Incorrect number or kind of arguments to kim_style.
E: Must use 'kim_style init' command before simulation box is defined
E: Must use 'kim_style model' command before simulation box is defined
Self-explanatory.
E: Must use 'kim_style define' command after simulation box is defined
E: Must use 'kim_style setup' command after simulation box is defined
Self-explanatory.
E: Must use 'kim_style init' command before 'kim_style define'
E: Must use 'kim_style model' command before 'kim_style setup'
Self-explanatory.
E: KIM Model does not support the requested unit system
Self-explanatory.
E: KIM Model does not support any lammps unit system
Self-explanatory.
E: KIM model name not found
Self-explanatory.