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support for >ELEMENTS MDI command

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This commit is contained in:
Steve Plimpton
2022-06-24 15:09:15 -06:00
parent f4342ea7e4
commit 7a5410a085
5 changed files with 149 additions and 27 deletions
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10
examples/mdi/Run.sh
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@ -3,7 +3,7 @@
# -------------------------------------------------
# -------------------------------------------------
# Example 1
# Example 1 = run ab initio MD (AIMD)
# ---
@ -56,7 +56,7 @@ mv log.aimd.engine.plugin log.aimd.engine.plugin.3
# -------------------------------------------------
# -------------------------------------------------
# Example 2
# Example 2 = run LAMMPS, compute QM forces on snapshots from a long run
# ---
@ -116,7 +116,7 @@ mv dump.snapshot.driver.plugin dump.snapshot.driver.plugin.3
# -------------------------------------------------
# -------------------------------------------------
# Example 3
# Example 3 = run LAMMPS, compute QM forces on series of independent systems
# ---
@ -176,7 +176,7 @@ mv dump.series.driver.plugin dump.series.driver.plugin.3
# -------------------------------------------------
# -------------------------------------------------
# Example 4
# Example 4 = Python driver runs a sequence of unrelated LAMMPS calculations
# ---
@ -221,7 +221,7 @@ mpirun -np 3 python3 sequence_driver.py -plugin lammps -mdi "-role DRIVER -name
# -------------------------------------------------
# -------------------------------------------------
# Example 5
# Example 5 = run AIMD with Python driver code and 2 LAMMPS instances as engines
# ---

51
src/MDI/fix_mdi_qm.cpp
View File

@ -25,6 +25,8 @@ using namespace FixConst;
enum { NATIVE, REAL, METAL }; // LAMMPS units which MDI supports
#define MAXELEMENT 103 // used elsewhere in MDI package
/* ---------------------------------------------------------------------- */
FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
@ -49,6 +51,7 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
addflag = 1;
every = 1;
connectflag = 1;
elements = nullptr;
int iarg = 3;
while (iarg < narg) {
@ -75,6 +78,17 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
else if (strcmp(arg[iarg+1],"no") == 0) connectflag = 0;
else error->all(FLERR,"Illegal fix mdi/qm command");
iarg += 2;
} else if (strcmp(arg[iarg],"elements") == 0) {
int ntypes = atom->ntypes;
if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal fix mdi/qm command");
delete [] elements;
elements = new int[ntypes+1];
for (int i = 1; i <= ntypes; i++) {
elements[i] = utils::inumeric(FLERR,arg[iarg+i],false,lmp);
if (elements[i] < 1 || elements[i] > MAXELEMENT)
error->all(FLERR,"Illegal fix mdi/qm command");
}
iarg += ntypes+1;
} else error->all(FLERR,"Illegal fix mdi/qm command");
}
@ -154,6 +168,8 @@ FixMDIQM::~FixMDIQM()
// clean up
delete[] elements;
memory->destroy(fqm);
memory->destroy(ibuf1);
@ -220,7 +236,7 @@ void FixMDIQM::init()
}
}
// send natoms, atom types, and simulation box to engine
// send natoms, atom types or elements, and simulation box to engine
// this will trigger setup of a new system
// subsequent calls in post_force() will be for same system until new init()
@ -232,7 +248,8 @@ void FixMDIQM::init()
ierr = MDI_Send(&n, 1, MDI_INT, mdicomm);
if (ierr) error->all(FLERR, "MDI: >NATOMS data");
send_types();
if (elements) send_elements();
else send_types();
send_box();
}
@ -420,7 +437,7 @@ void FixMDIQM::reallocate()
}
/* ----------------------------------------------------------------------
send numeric atom types to MDI engine
send LAMMPS atom types to MDI engine
------------------------------------------------------------------------- */
void FixMDIQM::send_types()
@ -448,6 +465,34 @@ void FixMDIQM::send_types()
if (ierr) error->all(FLERR, "MDI: >TYPES data");
}
/* ----------------------------------------------------------------------
send elements to MDI engine = atomic numbers for each type
------------------------------------------------------------------------- */
void FixMDIQM::send_elements()
{
int n = static_cast<int> (atom->natoms);
memset(ibuf1, 0, n * sizeof(int));
// use local atomID to index into ordered ibuf1
tagint *tag = atom->tag;
int *type = atom->type;
int nlocal = atom->nlocal;
int index;
for (int i = 0; i < nlocal; i++) {
index = static_cast<int>(tag[i]) - 1;
ibuf1[index] = elements[type[i]];
}
MPI_Reduce(ibuf1, ibuf1all, n, MPI_INT, MPI_SUM, 0, world);
int ierr = MDI_Send_command(">ELEMENTS", mdicomm);
if (ierr) error->all(FLERR, "MDI: >ELEMENTS command");
ierr = MDI_Send(ibuf1all, n, MDI_INT, mdicomm);
if (ierr) error->all(FLERR, "MDI: >ELEMETNS data");
}
/* ----------------------------------------------------------------------
send simulation box size and shape to MDI engine

2
src/MDI/fix_mdi_qm.h
View File

@ -44,6 +44,7 @@ class FixMDIQM : public Fix {
int plugin;
int maxlocal;
int sumflag;
int *elements;
double qm_energy;
int lmpunits;
@ -70,6 +71,7 @@ class FixMDIQM : public Fix {
void reallocate();
void send_types();
void send_elements();
void send_box();
void unit_conversions();
};

110
src/MDI/mdi_engine.cpp
View File

@ -54,6 +54,8 @@ enum { DEFAULT, MD, OPT }; // top-level MDI engine modes
enum { TYPE, CHARGE, MASS, COORD, VELOCITY, FORCE, ADDFORCE };
#define MAXELEMENT 103 // used elsewhere in MDI package
/* ----------------------------------------------------------------------
trigger LAMMPS to start acting as an MDI engine
either in standalone mode or plugin mode
@ -63,17 +65,47 @@ enum { TYPE, CHARGE, MASS, COORD, VELOCITY, FORCE, ADDFORCE };
when EXIT command is received, mdi engine command exits
---------------------------------------------------------------------- */
MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char ** /*arg*/) : Pointers(_lmp)
MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char ** arg) : Pointers(_lmp)
{
if (narg) error->all(FLERR, "Illegal mdi engine command");
// check requirements for LAMMPS to work with MDI as an engine
if (atom->tag_enable == 0) error->all(FLERR, "Cannot use MDI engine without atom IDs");
if (atom->tag_enable == 0) error->all(FLERR, "MDI engine requires atom IDs");
if (atom->natoms && atom->tag_consecutive() == 0)
error->all(FLERR, "MDI engine requires consecutive atom IDs");
// optional args
elements = nullptr;
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"elements") == 0) {
int ntypes = atom->ntypes;
delete [] elements;
elements = new int[ntypes+1];
if (iarg+ntypes+1 > narg) error->all(FLERR,"Illegal mdi engine command");
for (int i = 1; i <= ntypes; i++) {
elements[i] = utils::inumeric(FLERR,arg[iarg+i],false,lmp);
if (elements[i] < 0 || elements[i] > MAXELEMENT)
error->all(FLERR,"Illegal mdi engine command");
}
iarg += ntypes+1;
} else error->all(FLERR,"Illegal mdi engine command");
}
// error check an MDI element does not map to multiple atom types
if (elements) {
int ntypes = atom->ntypes;
for (int i = 1; i < ntypes; i++)
for (int j = i+1; j <= ntypes; j++) {
if (elements[i] == 0 || elements[j] == 0) continue;
if (elements[i] == elements[j])
error->all(FLERR,"MDI engine element cannot map to multiple types");
}
}
// confirm LAMMPS is being run as an engine
int role;
@ -194,6 +226,8 @@ MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char ** /*arg*/) : Pointers(_lmp)
// clean up
delete[] elements;
delete[] mdicmd;
delete[] node_engine;
delete[] node_driver;
@ -299,6 +333,11 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm)
} else if (strcmp(command, ">COORDS") == 0) {
receive_coords();
} else if (strcmp(command, ">ELEMENTS") == 0) {
if (!elements)
error->all(FLERR,"MDI engine command did not define element list");
receive_elements();
} else if (strcmp(command, ">FORCES") == 0) {
receive_double3(FORCE);
@ -323,7 +362,7 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm)
else
receive_double3(VELOCITY);
// -----------------------------------------------
// -----------------------------------------------
} else if (strcmp(command, "<@") == 0) {
ierr = MDI_Send(node_engine, MDI_NAME_LENGTH, MDI_CHAR, mdicomm);
@ -372,9 +411,9 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm)
} else if (strcmp(command, "<VELOCITIES") == 0) {
send_double3(VELOCITY);
// -----------------------------------------------
// -----------------------------------------------
// MDI action commands at @DEFAULT node
// MDI action commands at @DEFAULT node
} else if (strcmp(command, "MD") == 0) {
md();
@ -382,9 +421,9 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm)
} else if (strcmp(command, "OPTG") == 0) {
optg();
// -----------------------------------------------
// -----------------------------------------------
// MDI node commands
// MDI node commands
} else if (strcmp(command, "@INIT_MD") == 0) {
if (mode != DEFAULT) error->all(FLERR, "MDI: MDI engine is already performing a simulation");
@ -419,14 +458,14 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm)
strncpy(node_driver, command, MDI_COMMAND_LENGTH);
node_match = false;
// exit command
// exit command
} else if (strcmp(command, "EXIT") == 0) {
exit_command = true;
// -------------------------------------------------------
// custom LAMMPS commands
// -------------------------------------------------------
// -------------------------------------------------------
// custom LAMMPS commands
// -------------------------------------------------------
} else if (strcmp(command, "NBYTES") == 0) {
nbytes_command();
@ -439,9 +478,9 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm)
} else if (strcmp(command, "<KE") == 0) {
send_ke();
// -------------------------------------------------------
// unknown command
// -------------------------------------------------------
// -------------------------------------------------------
// unknown command
// -------------------------------------------------------
} else {
error->all(FLERR, "MDI: Unknown command {} received from driver", command);
@ -479,6 +518,7 @@ void MDIEngine::mdi_commands()
MDI_Register_command("@DEFAULT", ">CELL_DISPL");
MDI_Register_command("@DEFAULT", ">CHARGES");
MDI_Register_command("@DEFAULT", ">COORDS");
MDI_Register_command("@DEFAULT", ">ELEMENTS");
MDI_Register_command("@DEFAULT", ">NATOMS");
MDI_Register_command("@DEFAULT", ">NSTEPS");
MDI_Register_command("@DEFAULT", ">TOLERANCE");
@ -914,7 +954,7 @@ void MDIEngine::evaluate()
/* ----------------------------------------------------------------------
create a new system
>CELL, >NATOMS, >TYPES, >COORDS commands are required
>CELL, >NATOMS, >TYPES or >ELEMENTS, >COORDS commands are required
>CELL_DISPL, >CHARGES, >VELOCITIES commands are optional
---------------------------------------------------------------------- */
@ -924,8 +964,8 @@ void MDIEngine::create_system()
if (flag_cell == 0 || flag_natoms == 0 || flag_types == 0 || flag_coords == 0)
error->all(FLERR,
"MDI create_system requires >CELL, >NATOMS, >TYPES, >COORDS "
"MDI commands");
"MDI create_system requires >CELL, >NATOMS, "
">TYPES or >ELEMENTS, >COORDS MDI commands");
// remove all existing atoms via delete_atoms command
@ -1160,6 +1200,38 @@ void MDIEngine::receive_coords()
for (int i = 0; i < n; i++) sys_coords[i] *= mdi2lmp_length;
}
/* ----------------------------------------------------------------------
>ELEMENTS command
receive elements for each atom = atomic numbers
convert to LAMMPS atom types and store in sys_types
---------------------------------------------------------------------- */
void MDIEngine::receive_elements()
{
actionflag = 0;
flag_types = 1;
int ierr = MDI_Recv(sys_types, sys_natoms, MDI_INT, mdicomm);
if (ierr) error->all(FLERR, "MDI: >ELEMENTS data");
MPI_Bcast(sys_types, sys_natoms, MPI_INT, 0, world);
// convert from element atomic numbers to LAMMPS atom types
// use maping provided by mdi engine command
int ntypes = atom->ntypes;
int itype;
for (int i = 0; i < sys_natoms; i++) {
for (itype = 1; itype <= ntypes; itype++) {
if (sys_types[i] == elements[itype]) {
sys_types[i] = itype;
break;
}
}
if (itype > ntypes)
error->all(FLERR,"MDI element not found in element list");
}
}
/* ----------------------------------------------------------------------
>NATOMS command
natoms cannot exceed 32-bit int for use with MDI

3
src/MDI/mdi_engine.h
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@ -70,6 +70,8 @@ class MDIEngine : protected Pointers {
int actionflag; // 1 if MD or OPTG just completed, else 0
int *elements;
// buffers for MDI comm
int maxatom;
@ -106,6 +108,7 @@ class MDIEngine : protected Pointers {
void receive_cell_displ();
void receive_charges();
void receive_coords();
void receive_elements();
void receive_natoms();
void receive_nsteps();
void receive_tolerance();