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make new/incremental quantum trigger more robust, including fix GCMC and atom/swap

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This commit is contained in:
Steve Plimpton
2023-02-13 11:10:50 -07:00
parent 4f4a67fb45
commit f1fde259e7
6 changed files with 173 additions and 70 deletions
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21
src/MC/fix_atom_swap.cpp
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@ -103,6 +103,8 @@ FixAtomSwap::FixAtomSwap(LAMMPS *lmp, int narg, char **arg) :
// zero out counters
mc_active = 0;
nswap_attempts = 0.0;
nswap_successes = 0.0;
@ -304,6 +306,8 @@ void FixAtomSwap::pre_exchange()
if (next_reneighbor != update->ntimestep) return;
mc_active = 1;
// ensure current system is ready to compute energy
if (domain->triclinic) domain->x2lamda(atom->nlocal);
@ -336,6 +340,8 @@ void FixAtomSwap::pre_exchange()
nswap_successes += nsuccess;
next_reneighbor = update->ntimestep + nevery;
mc_active = 0;
}
/* ----------------------------------------------------------------------
@ -815,3 +821,18 @@ void FixAtomSwap::restart(char *buf)
if (ntimestep_restart != update->ntimestep)
error->all(FLERR, "Must not reset timestep when restarting fix atom/swap");
}
/* ----------------------------------------------------------------------
extract variable which stores whether MC is active or not
active = MC moves are taking place
not active = normal MD is taking place
------------------------------------------------------------------------- */
void *FixAtomSwap::extract(const char *name, int &dim)
{
if (strcmp(name,"mc_active") == 0) {
dim = 0;
return (void *) &mc_active;
}
return nullptr;
}

1
src/MC/fix_atom_swap.h
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@ -37,6 +37,7 @@ class FixAtomSwap : public Fix {
double memory_usage() override;
void write_restart(FILE *) override;
void restart(char *) override;
void *extract(const char *, int &) override;
private:
int nevery, seed;

14
src/MC/fix_gcmc.cpp
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@ -220,6 +220,8 @@ FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
// zero out counters
mc_active = 0;
ntranslation_attempts = 0.0;
ntranslation_successes = 0.0;
nrotation_attempts = 0.0;
@ -718,6 +720,8 @@ void FixGCMC::pre_exchange()
if (next_reneighbor != update->ntimestep) return;
mc_active = 1;
xlo = domain->boxlo[0];
xhi = domain->boxhi[0];
ylo = domain->boxlo[1];
@ -795,7 +799,10 @@ void FixGCMC::pre_exchange()
}
}
}
next_reneighbor = update->ntimestep + nevery;
mc_active = 0;
}
/* ----------------------------------------------------------------------
@ -2583,11 +2590,18 @@ void FixGCMC::grow_molecule_arrays(int nmolatoms) {
/* ----------------------------------------------------------------------
extract variable which stores whether MC is active or not
active = MC moves are taking place
not active = normal MD is taking place
extract variable which stores index of exclusion group
------------------------------------------------------------------------- */
void *FixGCMC::extract(const char *name, int &dim)
{
if (strcmp(name,"mc_active") == 0) {
dim = 0;
return (void *) &mc_active;
}
if (strcmp(name,"exclusion_group") == 0) {
dim = 0;
return (void *) &exclusion_group;

2
src/MC/fix_gcmc.h
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@ -74,6 +74,8 @@ class FixGCMC : public Fix {
double ninsertion_attempts;
double ninsertion_successes;
int mc_active; // 1 during MC trials, otherwise 0
int gcmc_nmax;
int max_region_attempts;
double gas_mass;

196
src/MDI/fix_mdi_qm.cpp
View File

@ -58,8 +58,8 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
addflag = 1;
every = 1;
connectflag = 1;
exclude = 0;
id_exclude = nullptr;
mcflag = 0;
id_mcfix = nullptr;
elements = nullptr;
int iarg = 3;
@ -96,11 +96,11 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
else
error->all(FLERR, "Illegal fix mdi/qm command");
iarg += 2;
} else if (strcmp(arg[iarg],"exclude") == 0) {
} else if (strcmp(arg[iarg],"mc") == 0) {
if (iarg+2 > narg) error->all(FLERR, "Illegal fix mdi/qm command");
exclude = 1;
delete[] id_exclude;
id_exclude = utils::strdup(arg[iarg+1]);
mcflag = 1;
delete[] id_mcfix;
id_mcfix = utils::strdup(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg], "elements") == 0) {
@ -230,7 +230,7 @@ FixMDIQM::~FixMDIQM()
// clean up
delete[] id_exclude;
delete[] id_mcfix;
delete[] elements;
memory->destroy(qmIDs);
@ -324,48 +324,90 @@ void FixMDIQM::init()
MPI_Bcast(&types_exists, 1, MPI_INT, 0, world);
}
// extract pointer to exclusion_group variable from id_exclude
// exclusion_group = index of a group the Fix defines
// the group flags atoms to be excluded from QM calculation
// extract pointers to MC variables from id_mcfix
// mc_active = 1/0 for MC moves on/off (required)
// exclusion_group = index of a group the Fix defines to exclude atoms (optional)
if (exclude) {
Fix *f_exclude = modify->get_fix_by_id(id_exclude);
if (!f_exclude) error->all(FLERR,"Fix mdi/qm could not find exclude fix ID {}", id_exclude);
if (mcflag) {
Fix *f_mc = modify->get_fix_by_id(id_mcfix);
if (!f_mc) error->all(FLERR,"Fix mdi/qm could not find Monte Carlo fix ID {}", id_mcfix);
int dim;
exclusion_group_ptr = (int *) f_exclude->extract("exclusion_group", dim);
if (!exclusion_group_ptr || dim != 0)
error->all(FLERR,"Fix mdi/qm could not query exclude_group of fix ID {}", id_exclude);
mc_active_ptr = (int *) f_mc->extract("mc_active", dim);
if (!mc_active_ptr || dim != 0)
error->all(FLERR,"Fix mdi/qm could not query mc_active from Monte Carlo fix ID {}", id_mcfix);
exclusion_group_ptr = (int *) f_mc->extract("exclusion_group", dim);
}
// nqm = # of QM atoms
// if hasn't changed, then continuing previous simulation
// else setup new simulation with MDI engine
// determine whether a new vs incremental QM calc is needed
// new when first run or when
// atom count or elements/types or box has changed between runs
// otherwise incremental = subsequent run of same system
int new_system = 0;
// check if quantum atom count has changed
// on first run, old count is 0
int nqm_old = nqm;
nqm = set_nqm();
if (nqm != nqm_last) {
if (nqm != nqm_old) {
if (nqm > max_nqm) reallocate();
// create list of QM atom IDs in sorted order
// set mapping of my local atoms into global list
create_qm_list();
set_qm2owned();
// initial send of info to MDI engine
// values that often won't change for AIMD simulations
// if not sending elements or types, assume engine initialized itself
send_box();
send_natoms();
new_system = 1;
}
if (elements && elements_exists) {
// check if box has changed
if (new_system) set_box();
else {
double old_cell[9],old_cell_displ[3];
memcpy(old_cell,qm_cell,9*sizeof(double));
memcpy(old_cell_displ,qm_cell_displ,3*sizeof(double));
set_box();
for (int i = 0; i < 9; i++)
if (qm_cell[i] != old_cell[i]) new_system = 1;
for (int i = 0; i < 3; i++)
if (qm_cell_displ[i] != old_cell_displ[i]) new_system = 1;
}
// check if atom elements or types have changed
if (elements && elements_exists) {
if (new_system) set_eqm();
else {
int *eqm_old;
memory->create(eqm_old,nqm,"mdi/qm:eqm_old");
memcpy(eqm_old,eqm,nqm*sizeof(int));
set_eqm();
send_elements();
} else if (types_exists) {
set_tqm();
send_types();
for (int i = 0; i < nqm; i++)
if (eqm[i] != eqm_old[i]) new_system = 1;
memory->destroy(eqm_old);
}
} else if (types_exists) {
if (new_system) set_tqm();
else {
int *tqm_old;
memory->create(tqm_old,nqm,"mdi/qm:tqm_old");
memcpy(tqm_old,tqm,nqm*sizeof(int));
set_tqm();
for (int i = 0; i < nqm; i++)
if (tqm[i] != tqm_old[i]) new_system = 1;
memory->destroy(tqm_old);
}
}
// new system, so send setup info to MDI engine
// values that often won't change for AIMD simulations
// if not sending elements or types, assume engine initialized itself
if (new_system) {
send_natoms();
send_box();
if (elements && elements_exists) send_elements();
else if (types_exists) send_types();
nqm_last = nqm;
}
}
@ -408,17 +450,27 @@ void FixMDIQM::post_force(int vflag)
memory->create(array_atom,nmax,3,"mdi/qm:array_atom");
}
// check count of QM atoms, could be different due to exclusions
// if so, need to reset QM data structures
// determine whether a new vs incremental QM calc is needed
// new when atom count has changed (deposit, evaporate)
// or when MC fix is active (insertion, deletion, large moves)
// incremental when a system is slowly evolving (AIMD)
nqm = set_nqm();
int new_system = 0;
if (nqm != nqm_last) new_system = 1;
else if (mcflag && *mc_active_ptr) new_system = 1;
if (nqm != nqm_last) {
nqm_last = nqm;
// send new system info to MDI engine: atom count and elements/types
// reset QM data structures if atom count has changed
if (new_system) {
nqm = set_nqm();
if (nqm > max_nqm) reallocate();
create_qm_list();
set_qm2owned();
send_natoms();
set_box();
send_box();
if (elements && elements_exists) {
set_eqm();
send_elements();
@ -426,11 +478,16 @@ void FixMDIQM::post_force(int vflag)
set_tqm();
send_types();
}
}
nqm_last = nqm;
// incremental system
// if simulation box dynamically changes, send current box to MDI engine
if (domain->box_change_size || domain->box_change_shape) send_box();
} else if (domain->box_change_size || domain->box_change_shape) {
set_box();
send_box();
}
// send current coords of QM atoms to MDI engine
@ -476,9 +533,9 @@ void FixMDIQM::post_force(int vflag)
}
// array_atom = fix output for peratom QM forces
// if exclude, some atoms may not be QM atoms, so zero array_atom first
// if nexclude, some atoms are not QM atoms, zero array_atom first
if (exclude) {
if (nexclude) {
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++) {
array_atom[i][0] = 0.0;
@ -626,7 +683,7 @@ void FixMDIQM::reallocate()
/* ----------------------------------------------------------------------
ncount = # of QM atoms
can be less than all atoms if exclude flag is set
can be less than all atoms if MC flag is set
return ncount to set nqm
------------------------------------------------------------------------- */
@ -635,7 +692,7 @@ int FixMDIQM::set_nqm()
int ncount = atom->natoms;
nexclude = 0;
if (exclude) {
if (mcflag && exclusion_group_ptr) {
int nexclude_mine = 0;
int exclusion_group = *exclusion_group_ptr;
@ -756,6 +813,29 @@ void FixMDIQM::set_qm2owned()
/* ---------------------------------------------------------------------- */
void FixMDIQM::set_box()
{
qm_cell_displ[0] = domain->boxlo[0] * lmp2mdi_length;
qm_cell_displ[1] = domain->boxlo[1] * lmp2mdi_length;
qm_cell_displ[2] = domain->boxlo[2] * lmp2mdi_length;
qm_cell[0] = domain->boxhi[0] - domain->boxlo[0];
qm_cell[1] = 0.0;
qm_cell[2] = 0.0;
qm_cell[3] = domain->xy;
qm_cell[4] = domain->boxhi[1] - domain->boxlo[1];
qm_cell[5] = 0.0;
qm_cell[6] = domain->xz;
qm_cell[7] = domain->yz;
qm_cell[8] = domain->boxhi[2] - domain->boxlo[2];
// convert cell units to bohr
for (int icell = 0; icell < 9; icell++) qm_cell[icell] *= lmp2mdi_length;
}
/* ---------------------------------------------------------------------- */
void FixMDIQM::set_xqm()
{
for (int i = 0; i < nqm; i++) {
@ -883,35 +963,17 @@ void FixMDIQM::send_elements()
void FixMDIQM::send_box()
{
int ierr;
double cell[9];
if (celldispl_exists) {
ierr = MDI_Send_command(">CELL_DISPL", mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command");
cell[0] = domain->boxlo[0] * lmp2mdi_length;
cell[1] = domain->boxlo[1] * lmp2mdi_length;
cell[2] = domain->boxlo[2] * lmp2mdi_length;
ierr = MDI_Send(cell, 3, MDI_DOUBLE, mdicomm);
ierr = MDI_Send(qm_cell_displ, 3, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL_DISPL data");
}
ierr = MDI_Send_command(">CELL", mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL command");
cell[0] = domain->boxhi[0] - domain->boxlo[0];
cell[1] = 0.0;
cell[2] = 0.0;
cell[3] = domain->xy;
cell[4] = domain->boxhi[1] - domain->boxlo[1];
cell[5] = 0.0;
cell[6] = domain->xz;
cell[7] = domain->yz;
cell[8] = domain->boxhi[2] - domain->boxlo[2];
// convert cell units to bohr
for (int icell = 0; icell < 9; icell++) cell[icell] *= lmp2mdi_length;
ierr = MDI_Send(cell, 9, MDI_DOUBLE, mdicomm);
ierr = MDI_Send(qm_cell, 9, MDI_DOUBLE, mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL data");
}

9
src/MDI/fix_mdi_qm.h
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@ -50,11 +50,13 @@ class FixMDIQM : public Fix {
int nprocs;
int every, virialflag, addflag, connectflag;
int plugin;
int sumflag,exclude;
char *id_exclude;
int *exclusion_group_ptr;
int sumflag,mcflag;
char *id_mcfix;
int *mc_active_ptr,*exclusion_group_ptr;
int *elements;
double qm_cell[9],qm_cell_displ[3];
double qm_energy;
double qm_virial[9], qm_virial_symmetric[6];
@ -92,6 +94,7 @@ class FixMDIQM : public Fix {
int set_nqm();
void create_qm_list();
void set_qm2owned();
void set_box();
void set_xqm();
void set_eqm();
void set_tqm();