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PairPACEActiveLearning: add flag is_dump_extrapolative_structures

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compute_pace: add compute_scalar
This commit is contained in:
Yury Lysogorskiy
2022-06-24 14:53:38 +02:00
parent edf40edfd9
commit 79c7a50ffc
4 changed files with 52 additions and 16 deletions
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17
src/ML-PACE/compute_pace.cpp
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@ -36,6 +36,8 @@ ComputePaceAtom::ComputePaceAtom(class LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg) {
if (narg < 3) error->all(FLERR, "Illegal compute pace/atom command");
peratom_flag = 1;
size_peratom_cols = 0;
scalar_flag = 1; // compute max of gamma
}
ComputePaceAtom::~ComputePaceAtom() {
@ -43,7 +45,7 @@ ComputePaceAtom::~ComputePaceAtom() {
void ComputePaceAtom::init() {
if (force->pair == nullptr)
error->all(FLERR, "Compute pace/atom requires a pair style be defined");
error->all(FLERR, "Compute pace/atom requires a pair style pace/al be defined");
int count = 0;
for (int i = 0; i < modify->ncompute; i++)
@ -53,14 +55,23 @@ void ComputePaceAtom::init() {
pair_pace_al = force->pair_match("pace/al", 1);
if (!pair_pace_al)
error->all(FLERR, "Compute pace/atom requires a `pace/al` pair style");
}
double ComputePaceAtom::compute_scalar() {
invoked_peratom = update->ntimestep;
auto pair = (PairPACEActiveLearning *) pair_pace_al;
if (invoked_peratom != pair->bevaluator_timestep)
error->all(FLERR, "PACE/gamma was not computed on needed timestep.\nIncrease `freq` in pair_style pace/al [gamma_lower_bound] [gamma_upper_bound] [freq] or reset timestep to 0");
scalar = pair->max_gamma_grade_per_structure;
return scalar;
}
void ComputePaceAtom::compute_peratom() {
invoked_peratom = update->ntimestep;
auto pair = (PairPACEActiveLearning *) pair_pace_al;
if (invoked_peratom != pair->bevaluator_timestep)
error->all(FLERR, "PACE/gamma was not computed on needed timestep");
error->all(FLERR, "PACE/gamma was not computed on needed timestep.\nIncrease `freq` in pair_style pace/al [gamma_lower_bound] [gamma_upper_bound] [freq] or reset timestep to 0");
vector_atom = pair->extrapolation_grade_gamma;
scalar = pair->max_gamma_grade_per_structure;
}

1
src/ML-PACE/compute_pace.h
View File

@ -35,6 +35,7 @@ namespace LAMMPS_NS {
ComputePaceAtom(class LAMMPS *, int, char **);
~ComputePaceAtom() override;
void init() override;
double compute_scalar() override;
void compute_peratom() override;
private:
int nmax;

49
src/ML-PACE/pair_pace_al.cpp
View File

@ -71,6 +71,8 @@ using namespace MathConst;
#define MAXLINE 1024
#define DELTA 4
#define PACE_AL_EXTRAPOLATION_GRADE_FNAME "grade.dat"
#define EXTRAPOLATIVE_STRUCTURES_FNAME "extrapolative_structures.dat"
#define SPECIES_TYPE_FNAME "species_types.dat"
//added YL
@ -144,8 +146,12 @@ PairPACEActiveLearning::~PairPACEActiveLearning() {
memory->destroy(extrapolation_grade_gamma);
}
if (dump)
if (dump) {
delete dump;
dump = nullptr;
}
//computePaceAtom will be deleted by lmp->modify, as it was registered there
}
/* ---------------------------------------------------------------------- */
@ -315,8 +321,9 @@ void PairPACEActiveLearning::compute(int eflag, int vflag) {
MPI_Comm_rank(world, &mpi_rank);
if (max_gamma_grade_per_structure > gamma_upper_bound) {
if (mpi_rank == 0) dump_extrapolation_grade(update->ntimestep, max_gamma_grade_per_structure);
dump->write();
if (mpi_rank == 0)
dump_extrapolation_grade(update->ntimestep, max_gamma_grade_per_structure);
if (is_dump_extrapolative_structures) dump->write();
MPI_Barrier(world);
if (mpi_rank == 0) {
@ -326,8 +333,10 @@ void PairPACEActiveLearning::compute(int eflag, int vflag) {
MPI_Abort(world, 1); //abort properly with error code '1' if not using 4 processes
exit(EXIT_FAILURE);
} else if (max_gamma_grade_per_structure > gamma_lower_bound) {
if (mpi_rank == 0) dump_extrapolation_grade(update->ntimestep, max_gamma_grade_per_structure);
dump->write();
if (mpi_rank == 0)
dump_extrapolation_grade(update->ntimestep, max_gamma_grade_per_structure);
if (is_dump_extrapolative_structures)
dump->write();
}
}
@ -351,9 +360,10 @@ void PairPACEActiveLearning::allocate() {
------------------------------------------------------------------------- */
void PairPACEActiveLearning::settings(int narg, char **arg) {
if (narg > 3) {
//TODO: make keyword base interface: pair_style pace/al freq 100 gamma_lo 1.5 gamma_hi 10 dump yes
if (narg > 4) {
error->all(FLERR,
"Illegal pair_style command. Correct form:\n\tpair_style pace/al [gamma_lower_bound] [gamma_upper_bound]");
"Illegal pair_style command. Correct form:\n\tpair_style pace/al [gamma_lower_bound] [gamma_upper_bound] [freq] [nodump]");
}
if (narg > 0) {
@ -381,12 +391,23 @@ void PairPACEActiveLearning::settings(int narg, char **arg) {
"Illegal gamma_grade_eval_freq value: it should be integer number >= 1");
}
if (narg > 3) {
if (strcmp(arg[3], "nodump") == 0) is_dump_extrapolative_structures = false;
if (strcmp(arg[3], "dump") == 0) is_dump_extrapolative_structures = true;
}
if (comm->me == 0) {
if (screen) {
utils::logmesg(lmp, "ACE/AL version: {}.{}.{}\n", VERSION_YEAR, VERSION_MONTH, VERSION_DAY);
utils::logmesg(lmp, "Extrapolation grade thresholds (lower/upper): {}/{}\n", gamma_lower_bound,
gamma_upper_bound);
utils::logmesg(lmp, "Extrapolation grade evaluation frequency: {}\n", gamma_grade_eval_freq);
if (is_dump_extrapolative_structures)
utils::logmesg(lmp, "Extrapolative structures will be dumped into {}\n",
EXTRAPOLATIVE_STRUCTURES_FNAME);
else
utils::logmesg(lmp, "No extrapolative structures will be dumped\n");
}
}
}
@ -448,7 +469,10 @@ void PairPACEActiveLearning::coeff(int narg, char **arg) {
aceimpl->rec_ace->element_type_mapping.init(atom->ntypes + 1);
aceimpl->rec_ace->element_type_mapping.fill(-1); //-1 means atom not included into potential
FILE *species_type_file = fopen("species_types.dat", "w");
FILE *species_type_file = nullptr;
if (is_dump_extrapolative_structures)
species_type_file = fopen(SPECIES_TYPE_FNAME, "w");
const int n = atom->ntypes;
for (int i = 1; i <= n; i++) {
char *elemname = elemtypes[i - 1];
@ -459,9 +483,8 @@ void PairPACEActiveLearning::coeff(int narg, char **arg) {
map[i] = -1;
if (comm->me == 0) utils::logmesg(lmp, "Skipping LAMMPS atom type #{}(NULL)\n", i);
} else {
// dump species types for reconstruction of atomic configurations
fprintf(species_type_file, "%s ", elemname);
if (is_dump_extrapolative_structures) fprintf(species_type_file, "%s ", elemname);
int atomic_number = AtomicNumberByName_pace_al(elemname);
if (atomic_number == -1) error->all(FLERR, "'{}' is not a valid element\n", elemname);
SPECIES_TYPE mu = aceimpl->basis_set->get_species_index_by_name(elemname);
@ -479,7 +502,7 @@ void PairPACEActiveLearning::coeff(int narg, char **arg) {
}
}
}
fclose(species_type_file);
if (is_dump_extrapolative_structures) fclose(species_type_file);
aceimpl->ace->set_basis(*aceimpl->basis_set);
aceimpl->rec_ace->set_basis(*aceimpl->ctilde_basis_set);
@ -508,14 +531,14 @@ void PairPACEActiveLearning::coeff(int narg, char **arg) {
}
// prepare dump class
if (!dump) {
if (is_dump_extrapolative_structures && !dump) {
// dump pace all custom freq extrapolation.dat id type mass x y z
char **dumpargs = new char *[12];
dumpargs[0] = (char *) "pace"; // dump id
dumpargs[1] = (char *) "all"; // group
dumpargs[2] = (char *) "custom"; // dump style
dumpargs[3] = (char *) "1"; // dump frequency
dumpargs[4] = (char *) "extrapolative_structures.dat"; // fname
dumpargs[4] = (char *) EXTRAPOLATIVE_STRUCTURES_FNAME; // fname
dumpargs[5] = (char *) "id";
dumpargs[6] = (char *) "type";
dumpargs[7] = (char *) "mass";

1
src/ML-PACE/pair_pace_al.h
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@ -59,6 +59,7 @@ namespace LAMMPS_NS {
struct ACEALImpl *aceimpl;
int gamma_grade_eval_freq = 1;
bool is_dump_extrapolative_structures = true;
DumpCustom *dump = nullptr;
Compute *computePaceAtom = nullptr;
int natoms; //total number of atoms