ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #17 from akohlmey/mdi_update

Browse Source 
MDI formatting updates and MPI STUBS handling
This commit is contained in:
taylor-a-barnes
2021-05-13 14:41:51 -04:00
committed by GitHub
parent 50de35c41a 44ed6f1896
commit d02e09baaa
5 changed files with 266 additions and 315 deletions
Download Patch File Download Diff File Expand all files Collapse all files

468
src/USER-MDI/fix_mdi_engine.cpp
View File

File diff suppressed because it is too large Load Diff

43
src/USER-MDI/fix_mdi_engine.h
View File

@ -11,11 +11,10 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(mdi/engine,FixMDIEngine)
// clang-format off
FixStyle(mdi/engine, FixMDIEngine);
// clang-format on
#else
#ifndef LMP_FIX_MDI_ENGINE_H
@ -42,12 +41,12 @@ class FixMDIEngine : public Fix {
void min_setup(int);
void post_integrate();
void post_force(int);
void min_pre_force(int); //@COORDS
void min_post_force(int); //@FORCES
void min_pre_force(int); //@COORDS
void min_post_force(int); //@FORCES
double *add_force; // stores forces added using +FORCE command
double potential_energy; // stores potential energy
double kinetic_energy; // stores kinetic energy
double *add_force; // stores forces added using +FORCE command
double potential_energy; // stores potential energy
double kinetic_energy; // stores kinetic energy
// current command
@ -57,23 +56,23 @@ class FixMDIEngine : public Fix {
void exchange_forces();
private:
int lmpunits; // REAL or METAL
int lmpunits; // REAL or METAL
int master, ierr;
int driver_socket;
int most_recent_init; // which MDI init command was most recently received?
// 0 - none
// 1 - MD
// 2 - OPTG
int most_recent_init; // which MDI init command was most recently received?
// 0 - none
// 1 - MD
// 2 - OPTG
bool exit_flag;
bool local_exit_flag;
char *current_node;
char *target_node; // is the code supposed to advance to a particular node?
// 0 - none
// 1 - @COORDS (before pre-force calculation)
// 2 - @PRE-FORCES (before final force calculation)
// 3 - @FORCES (before time integration)
// -1 - after MD_INIT command
// -2 - after MD_INIT command followed by @PRE-FORCES (actually @INIT_OPTG?)
char *target_node; // is the code supposed to advance to a particular node?
// 0 - none
// 1 - @COORDS (before pre-force calculation)
// 2 - @PRE-FORCES (before final force calculation)
// 3 - @FORCES (before time integration)
// -1 - after MD_INIT command
// -2 - after MD_INIT command followed by @PRE-FORCES (actually @INIT_OPTG?)
// command to be executed at the target node
@ -103,7 +102,7 @@ class FixMDIEngine : public Fix {
void receive_celldispl(Error *);
};
}
} // namespace LAMMPS_NS
#endif
#endif

6
src/USER-MDI/library_mdi.cpp
View File

@ -82,7 +82,11 @@ int MDI_Plugin_init_lammps()
if (!found_filename) MPI_Abort(MPI_COMM_WORLD, 1);
// create and run a LAMMPS instance
auto lmp = lammps_open(mdi_argc, mdi_argv, mpi_world_comm, NULL);
void *lmp = nullptr;
if (lammps_config_has_mpi_support() > 0)
lmp = lammps_open(mdi_argc, mdi_argv, mpi_world_comm, nullptr);
else
lmp = lammps_open_no_mpi(mdi_argc, mdi_argv, nullptr);
lammps_file(lmp, filename);
lammps_close(lmp);

54
src/USER-MDI/mdi_engine.cpp
View File

@ -31,8 +31,8 @@
#include "update.h"
#include "verlet.h"
#include <string.h>
#include <limits>
#include <string.h>
using namespace LAMMPS_NS;
@ -188,17 +188,15 @@ void MDIEngine::command(int narg, char **arg)
// identify the mdi_engine fix
ifix = modify->find_fix_by_style("mdi/engine");
mdi_fix = static_cast<FixMDIEngine*>(modify->fix[ifix]);
mdi_fix = static_cast<FixMDIEngine *>(modify->fix[ifix]);
// check that LAMMPS is setup as a compatible MDI engine
if (narg > 0) error->all(FLERR,"Illegal mdi/engine command");
if (narg > 0) error->all(FLERR, "Illegal mdi/engine command");
if (atom->tag_enable == 0)
error->all(FLERR,"Cannot use mdi/engine without atom IDs");
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use mdi/engine without atom IDs");
if (atom->tag_consecutive() == 0)
error->all(FLERR,"mdi/engine requires consecutive atom IDs");
if (atom->tag_consecutive() == 0) error->all(FLERR, "mdi/engine requires consecutive atom IDs");
// endless engine loop, responding to driver commands
@ -213,21 +211,22 @@ void MDIEngine::command(int narg, char **arg)
// MDI commands for dynamics or minimization
if (strcmp(command,"@INIT_MD") == 0 ) {
if (strcmp(command, "@INIT_MD") == 0) {
command = mdi_md();
if (strcmp(command,"EXIT")) break;
if (strcmp(command, "EXIT")) break;
} else if (strcmp(command,"@INIT_OPTG") == 0 ) {
} else if (strcmp(command, "@INIT_OPTG") == 0) {
command = mdi_optg();
if (strcmp(command,"EXIT")) break;
if (strcmp(command, "EXIT")) break;
} else if (strcmp(command,"EXIT") == 0) {
} else if (strcmp(command, "EXIT") == 0) {
break;
} else
error->all(FLERR,
fmt::format("MDI node exited with "
"invalid command: {}",command));
"invalid command: {}",
command));
}
// remove mdi/engine fix that mdi/engine instantiated
@ -256,11 +255,10 @@ char *MDIEngine::mdi_md()
// engine is now at @INIT_MD node
char *command = NULL;
char *command = nullptr;
command = mdi_fix->engine_mode("@INIT_MD");
if (strcmp(command,"@DEFAULT") == 0 || strcmp(command,"EXIT") == 0)
return command;
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
// setup the MD simulation
@ -268,8 +266,7 @@ char *MDIEngine::mdi_md()
command = mdi_fix->engine_mode("@FORCES");
if (strcmp(command,"@DEFAULT") == 0 || strcmp(command,"EXIT") == 0)
return command;
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
// run MD one step at a time
@ -289,11 +286,10 @@ char *MDIEngine::mdi_md()
command = mdi_fix->command;
if (strcmp(command,"@DEFAULT") == 0 || strcmp(command,"EXIT") == 0)
return command;
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
}
return NULL;
return nullptr;
}
/* ----------------------------------------------------------------------
@ -322,11 +318,10 @@ char *MDIEngine::mdi_optg()
// engine is now at @INIT_OPTG node
char *command = NULL;
char *command = nullptr;
command = mdi_fix->engine_mode("@INIT_OPTG");
if (strcmp(command,"@DEFAULT") == 0 || strcmp(command,"EXIT") == 0)
return command;
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
// setup the minimization
@ -336,8 +331,7 @@ char *MDIEngine::mdi_optg()
command = mdi_fix->command;
if (strcmp(command,"@DEFAULT") == 0 || strcmp(command,"EXIT") == 0)
return command;
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
// Start a minimization, which is configured to run (essentially)
// infinite steps. When the driver sends the EXIT command,
@ -350,11 +344,11 @@ char *MDIEngine::mdi_optg()
command = mdi_fix->command;
if (strcmp(command,"@DEFAULT") == 0 || strcmp(command,"EXIT") == 0)
return command;
if (strcmp(command, "@DEFAULT") == 0 || strcmp(command, "EXIT") == 0) return command;
error->all(FLERR,
fmt::format("MDI reached end of OPTG simulation "
"with invalid command: {}",command));
return NULL;
"with invalid command: {}",
command));
return nullptr;
}

10
src/USER-MDI/mdi_engine.h
View File

@ -12,9 +12,9 @@
------------------------------------------------------------------------- */
#ifdef COMMAND_CLASS
CommandStyle(mdi/engine,MDIEngine)
// clang-format off
CommandStyle(mdi/engine, MDIEngine);
// clang-format on
#else
#ifndef LMP_MDI_ENGINE_H
@ -30,14 +30,14 @@ class MDIEngine : public Command {
virtual ~MDIEngine() {}
void command(int, char **);
private:
private:
class FixMDIEngine *mdi_fix;
char *mdi_md();
char *mdi_optg();
};
}
} // namespace LAMMPS_NS
#endif
#endif