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more bug fixes for new MDI classs

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This commit is contained in:
Steve Plimpton
2021-09-23 12:39:11 -06:00
parent 0029ed106b
commit dcfdddf83f
3 changed files with 91 additions and 73 deletions
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19
src/MDI/fix_mdi_engine2.cpp
View File

@ -40,18 +40,12 @@ int FixMDIEngine2::setmask()
mask |= POST_FORCE;
mask |= MIN_PRE_FORCE;
mask |= MIN_POST_FORCE;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixMDIEngine2::min_setup(int vflag)
{
mdi_engine->engine_node("@FORCES");
}
/* ---------------------------------------------------------------------- */
void FixMDIEngine2::post_integrate()
{
mdi_engine->engine_node("@COORDS");
@ -66,6 +60,13 @@ void FixMDIEngine2::min_pre_force(int vflag)
/* ---------------------------------------------------------------------- */
void FixMDIEngine2::post_force(int vflag)
{
mdi_engine->engine_node("@FORCES");
}
/* ---------------------------------------------------------------------- */
void FixMDIEngine2::min_post_force(int vflag)
{
mdi_engine->engine_node("@FORCES");
@ -73,7 +74,7 @@ void FixMDIEngine2::min_post_force(int vflag)
/* ---------------------------------------------------------------------- */
void FixMDIEngine2::post_force(int vflag)
void FixMDIEngine2::end_of_step()
{
mdi_engine->engine_node("@FORCES");
mdi_engine->engine_node("@ENDSTEP");
}

5
src/MDI/fix_mdi_engine2.h
View File

@ -32,12 +32,11 @@ class FixMDIEngine2 : public Fix {
~FixMDIEngine2() {}
int setmask();
void init() {}
void min_setup(int);
void post_integrate();
void post_force(int);
void min_pre_force(int);
void post_force(int);
void min_post_force(int);
void end_of_step();
};
} // namespace LAMMPS_NS

140
src/MDI/mdi_engine2.cpp
View File

@ -37,6 +37,7 @@
#include "modify.h"
#include "neighbor.h"
#include "output.h"
#include "thermo.h"
#include "timer.h"
#include "update.h"
#include "verlet.h"
@ -408,6 +409,10 @@ int MDIEngine2::execute_command(const char *command, MDI_Comm mdicomm)
strncpy(node_driver,"@FORCES",MDI_COMMAND_LENGTH);
node_match = false;
} else if (strcmp(command,"@ENDSTEP") == 0) {
strncpy(node_driver,"@ENDSTEP",MDI_COMMAND_LENGTH);
node_match = false;
// exit command
} else if (strcmp(command, "EXIT") == 0) {
@ -427,35 +432,35 @@ int MDIEngine2::execute_command(const char *command, MDI_Comm mdicomm)
// custom LAMMPS commands
// -------------------------------------------------------
} else if (strcmp(command, "NBYTES") == 0) {
} else if (strcmp(command,"NBYTES") == 0) {
nbytes_command();
} else if (strcmp(command, "COMMAND") == 0) {
} else if (strcmp(command,"COMMAND") == 0) {
single_command();
} else if (strcmp(command, "COMMANDS") == 0) {
} else if (strcmp(command,"COMMANDS") == 0) {
many_commands();
} else if (strcmp(command, "INFILE") == 0) {
} else if (strcmp(command,"INFILE") == 0) {
infile();
} else if (strcmp(command, "EVAL") == 0) {
} else if (strcmp(command,"EVAL") == 0) {
evaluate();
} else if (strcmp(command, "RESET_BOX") == 0) {
} else if (strcmp(command,"RESET_BOX") == 0) {
reset_box();
} else if (strcmp(command, "CREATE_ATOM") == 0) {
} else if (strcmp(command,"CREATE_ATOM") == 0) {
create_atoms(CREATE_ATOM);
} else if (strcmp(command, "CREATE_ID") == 0) {
} else if (strcmp(command,"CREATE_ID") == 0) {
create_atoms(CREATE_ID);
} else if (strcmp(command, "CREATE_TYPE") == 0) {
} else if (strcmp(command,"CREATE_TYPE") == 0) {
create_atoms(CREATE_TYPE);
} else if (strcmp(command, "CREATE_X") == 0) {
} else if (strcmp(command,"CREATE_X") == 0) {
create_atoms(CREATE_X);
} else if (strcmp(command, "CREATE_V") == 0) {
} else if (strcmp(command,"CREATE_V") == 0) {
create_atoms(CREATE_V);
} else if (strcmp(command, "CREATE_IMG") == 0) {
} else if (strcmp(command,"CREATE_IMG") == 0) {
create_atoms(CREATE_IMAGE);
} else if (strcmp(command, "CREATE_GO") == 0) {
} else if (strcmp(command,"CREATE_GO") == 0) {
create_atoms(CREATE_GO);
} else if (strcmp(command, "<PRESSURE") == 0) {
} else if (strcmp(command,"<PRESSURE") == 0) {
send_pressure();
} else if (strcmp(command, "<PTENSOR") == 0) {
} else if (strcmp(command,"<PTENSOR") == 0) {
send_ptensor();
// -------------------------------------------------------
@ -524,9 +529,10 @@ void MDIEngine2::mdi_commands()
MDI_Register_command("@INIT_MD", ">FORCES");
MDI_Register_command("@INIT_MD", ">+FORCES");
MDI_Register_command("@INIT_MD", "@");
MDI_Register_command("@INIT_MD", "@COORDS");
MDI_Register_command("@INIT_MD", "@DEFAULT");
MDI_Register_command("@INIT_MD", "@COORDS");
MDI_Register_command("@INIT_MD", "@FORCES");
MDI_Register_command("@INIT_MD", "@ENDSTEP");
MDI_Register_command("@INIT_MD", "EXIT");
// node for setting up and running a minimization
@ -551,11 +557,40 @@ void MDIEngine2::mdi_commands()
MDI_Register_command("@INIT_OPTG", ">FORCES");
MDI_Register_command("@INIT_OPTG", ">+FORCES");
MDI_Register_command("@INIT_OPTG", "@");
MDI_Register_command("@INIT_OPTG", "@COORDS");
MDI_Register_command("@INIT_OPTG", "@DEFAULT");
MDI_Register_command("@INIT_OPTG", "@COORDS");
MDI_Register_command("@INIT_OPTG", "@FORCES");
MDI_Register_command("@INIT_OPTG", "@ENDSTEP");
MDI_Register_command("@INIT_OPTG", "EXIT");
// node at POST_INTEGRATE location in timestep
MDI_Register_node("@COORDS");
MDI_Register_command("@COORDS", "<@");
MDI_Register_command("@COORDS", "<CELL");
MDI_Register_command("@COORDS", "<CELL_DISPL");
MDI_Register_command("@COORDS", "<CHARGES");
MDI_Register_command("@COORDS", "<COORDS");
MDI_Register_command("@COORDS", "<ENERGY");
MDI_Register_command("@COORDS", "<FORCES");
MDI_Register_command("@COORDS", "<KE");
MDI_Register_command("@COORDS", "<LABELS");
MDI_Register_command("@COORDS", "<MASSES");
MDI_Register_command("@COORDS", "<NATOMS");
MDI_Register_command("@COORDS", "<PE");
MDI_Register_command("@COORDS", "<TYPES");
MDI_Register_command("@COORDS", ">CELL");
MDI_Register_command("@COORDS", ">CELL_DISPL");
MDI_Register_command("@COORDS", ">COORDS");
MDI_Register_command("@COORDS", ">FORCES");
MDI_Register_command("@COORDS", ">+FORCES");
MDI_Register_command("@COORDS", "@");
MDI_Register_command("@COORDS", "@DEFAULT");
MDI_Register_command("@COORDS", "@COORDS");
MDI_Register_command("@COORDS", "@FORCES");
MDI_Register_command("@COORDS", "@ENDSTEP");
MDI_Register_command("@COORDS", "EXIT");
// node at POST_FORCE location in timestep
MDI_Register_node("@FORCES");
@ -580,37 +615,23 @@ void MDIEngine2::mdi_commands()
MDI_Register_command("@FORCES", ">FORCES");
MDI_Register_command("@FORCES", ">+FORCES");
MDI_Register_command("@FORCES", "@");
MDI_Register_command("@FORCES", "@COORDS");
MDI_Register_command("@FORCES", "@DEFAULT");
MDI_Register_command("@FORCES", "@COORDS");
MDI_Register_command("@FORCES", "@FORCES");
MDI_Register_command("@FORCES", "@ENDSTEP");
MDI_Register_command("@FORCES", "EXIT");
// node at POST_INTEGRATE location in timestep
// node at END_OF_STEP location in timestep
MDI_Register_node("@COORDS");
MDI_Register_command("@COORDS", "<@");
MDI_Register_command("@COORDS", "<CELL");
MDI_Register_command("@COORDS", "<CELL_DISPL");
MDI_Register_command("@COORDS", "<CHARGES");
MDI_Register_command("@COORDS", "<COORDS");
MDI_Register_command("@COORDS", "<ENERGY");
MDI_Register_command("@COORDS", "<FORCES");
MDI_Register_command("@COORDS", "<KE");
MDI_Register_command("@COORDS", "<LABELS");
MDI_Register_command("@COORDS", "<MASSES");
MDI_Register_command("@COORDS", "<NATOMS");
MDI_Register_command("@COORDS", "<PE");
MDI_Register_command("@COORDS", "<TYPES");
MDI_Register_command("@COORDS", ">CELL");
MDI_Register_command("@COORDS", ">CELL_DISPL");
MDI_Register_command("@COORDS", ">COORDS");
MDI_Register_command("@COORDS", ">FORCES");
MDI_Register_command("@COORDS", ">+FORCES");
MDI_Register_command("@COORDS", "@");
MDI_Register_command("@COORDS", "@COORDS");
MDI_Register_command("@COORDS", "@DEFAULT");
MDI_Register_command("@COORDS", "@FORCES");
MDI_Register_command("@COORDS", "EXIT");
MDI_Register_node("@ENDSTEP");
MDI_Register_command("@ENDSTEP", "<@");
MDI_Register_command("@ENDSTEP", "<ENERGY");
MDI_Register_command("@ENDSTEP", "@");
MDI_Register_command("@ENDSTEP", "@DEFAULT");
MDI_Register_command("@ENDSTEP", "@COORDS");
MDI_Register_command("@ENDSTEP", "@FORCES");
MDI_Register_command("@ENDSTEP", "@ENDSTEP");
MDI_Register_command("@ENDSTEP", "EXIT");
// ------------------------------------
// custom commands and nodes which LAMMPS supports
@ -637,20 +658,20 @@ void MDIEngine2::mdi_commands()
}
/* ----------------------------------------------------------------------
run an MD simulation under control of driver
run MD simulation under control of driver one step at a time
---------------------------------------------------------------------- */
void MDIEngine2::mdi_md()
{
// NOTE: create this fix only when @INIT_MD is triggered?
// if not needed, I dont think it should be defined,
// otherwise it will be be invoked in other use cases
// and switch engine out of DEFAULT node ?
//int ifix = modify->find_fix_by_style("mdi/engine2");
//bool added_mdi_engine_fix = false;
//if (ifix < 0) {
// NOTE: delete fix if already defined ?
// also delete in destructor if defined
// remove mdi/engine fix this method instantiated
//modify->delete_fix("MDI_ENGINE_INTERNAL");
modify->add_fix("MDI_ENGINE_INTERNAL all mdi/engine2");
int ifix = modify->find_fix_by_style("mdi/engine2");
mdi_fix = static_cast<FixMDIEngine2 *>(modify->fix[ifix]);
@ -670,6 +691,7 @@ void MDIEngine2::mdi_md()
lmp->init();
// engine is now at @INIT_MD node
// receive any commands driver may wish to send
engine_node("@INIT_MD");
if (strcmp(mdicmd,"@DEFAULT") == 0 || strcmp(mdicmd,"EXIT") == 0) return;
@ -678,10 +700,9 @@ void MDIEngine2::mdi_md()
update->integrate->setup(1);
engine_node("@FORCES");
if (strcmp(mdicmd,"@DEFAULT") == 0 || strcmp(mdicmd,"EXIT") == 0) return;
// run MD one step at a time
// run MD one step at a time until driver sends @DEFAULT or EXIT
// driver can communicate with LAMMPS within each timestep
// by sending a node command which matches a method in FixMDIEngine
while (1) {
update->whichflag = 1;
@ -695,14 +716,10 @@ void MDIEngine2::mdi_md()
update->integrate->run(1);
// done with MD if driver sends @DEFAULT or EXIT
// driver triggers end of MD loop by senging @DEFAULT or EXIT
if (strcmp(mdicmd,"@DEFAULT") == 0 || strcmp(mdicmd,"EXIT") == 0) return;
}
// remove mdi/engine fix this method instantiated
modify->delete_fix("MDI_ENGINE_INTERNAL");
}
/* ----------------------------------------------------------------------
@ -1054,8 +1071,6 @@ void MDIEngine2::send_labels()
void MDIEngine2::send_total_energy()
{
double convert = 1.0;
double potential_energy = pe->compute_scalar();
double kinetic_energy = ke->compute_scalar();
double total_energy = potential_energy + kinetic_energy;
@ -1326,12 +1341,13 @@ void MDIEngine2::evaluate()
update->whichflag = 1;
lmp->init();
update->integrate->setup(0);
update->integrate->setup(1);
} else {
// insure potential energy and virial are tallied on this step
update->ntimestep++;
pe->addstep(update->ntimestep);
press->addstep(update->ntimestep);
@ -1339,8 +1355,10 @@ void MDIEngine2::evaluate()
if (nflag == 0) {
comm->forward_comm();
update->integrate->setup_minimal(0);
output->thermo->compute(1);
} else {
update->integrate->setup_minimal(1);
output->thermo->compute(1);
}
}
}