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This commit is contained in:
Aidan Thompson
2022-03-11 14:14:45 -07:00
parent 3f9cc03fc0
commit 8323c4fe45
4 changed files with 73 additions and 18 deletions
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53
src/ML-SNAP/pair_snap.cpp
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@ -46,6 +46,8 @@ PairSNAP::PairSNAP(LAMMPS *lmp) : Pair(lmp)
radelem = nullptr;
wjelem = nullptr;
coeffelem = nullptr;
rinnerelem = nullptr;
drinnerelem = nullptr;
beta_max = 0;
beta = nullptr;
@ -62,6 +64,8 @@ PairSNAP::~PairSNAP()
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(coeffelem);
memory->destroy(rinnerelem);
memory->destroy(drinnerelem);
memory->destroy(beta);
memory->destroy(bispectrum);
@ -151,6 +155,12 @@ void PairSNAP::compute(int eflag, int vflag)
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jelem];
snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac;
if (switchinnerflag) {
snaptr->rinnerij[ninside] = 0.5*(rinnerelem[ielem]+rinnerelem[jelem]);
snaptr->rinnerij[ninside] = 0.5*(drinnerelem[ielem]+drinnerelem[jelem]);
// snaptr->rinnerij[ninside] = 0.0;
// snaptr->drinnerij[ninside] = 1.5;
}
if (chemflag) snaptr->element[ninside] = jelem;
ninside++;
}
@ -179,8 +189,7 @@ void PairSNAP::compute(int eflag, int vflag)
else
snaptr->compute_duidrj(snaptr->rij[jj], snaptr->wj[jj],
snaptr->rcutij[jj], jj, 0,
// snaptr->rinnerij[jj], snaptr->drinnerij[jj],jj);
0.0, 1.0);
snaptr->rinnerij[jj], snaptr->drinnerij[jj]);
snaptr->compute_deidrj(fij);
@ -328,6 +337,12 @@ void PairSNAP::compute_bispectrum()
snaptr->inside[ninside] = j;
snaptr->wj[ninside] = wjelem[jelem];
snaptr->rcutij[ninside] = (radi + radelem[jelem])*rcutfac;
if (switchinnerflag) {
snaptr->rinnerij[ninside] = 0.5*(rinnerelem[ielem]+rinnerelem[jelem]);
snaptr->rinnerij[ninside] = 0.5*(drinnerelem[ielem]+drinnerelem[jelem]);
// snaptr->rinnerij[ninside] = 0.0;
// snaptr->drinnerij[ninside] = 1.5;
}
if (chemflag) snaptr->element[ninside] = jelem;
ninside++;
}
@ -512,9 +527,13 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(coeffelem);
memory->destroy(rinnerelem);
memory->destroy(drinnerelem);
memory->create(radelem,nelements,"pair:radelem");
memory->create(wjelem,nelements,"pair:wjelem");
memory->create(coeffelem,nelements,ncoeffall,"pair:coeffelem");
memory->create(rinnerelem,nelements,"pair:rinnerelem");
memory->create(drinnerelem,nelements,"pair:drinnerelem");
// initialize checklist for all required nelements
@ -630,10 +649,15 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
switchinnerflag = 1;
switchinnerflag = 0;
chunksize = 32768;
parallel_thresh = 8192;
// set local input checks
int rinnerflag = 0;
int drinnerflag = 0;
// open SNAP parameter file on proc 0
FILE *fpparam;
@ -667,7 +691,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
}
if (words.size() == 0) continue;
if (words.size() != 2)
if (words.size() < 2)
error->all(FLERR,"Incorrect format in SNAP parameter file");
auto keywd = words[0];
@ -698,11 +722,25 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
bnormflag = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "wselfallflag")
wselfallflag = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "switchinnerflag")
switchinnerflag = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "chunksize")
chunksize = utils::inumeric(FLERR,keyval,false,lmp);
else if (keywd == "parallelthresh")
parallel_thresh = utils::inumeric(FLERR,keyval,false,lmp);
else
else if (keywd == "rinner") {
for (int ielem = 0; ielem < nelements; ielem++) {
rinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp);
keyval = strtok(nullptr,"' \t\n\r\f");
}
rinnerflag = 1;
} else if (keywd == "drinner") {
for (int ielem = 0; ielem < nelements; ielem++) {
drinnerelem[ielem] = utils::numeric(FLERR,keyval,false,lmp);
keyval = strtok(nullptr,"' \t\n\r\f");
}
drinnerflag = 1;
} else
error->all(FLERR,"Unknown parameter '{}' in SNAP parameter file", keywd);
}
@ -712,6 +750,11 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (chemflag && nelemtmp != nelements)
error->all(FLERR,"Incorrect SNAP parameter file");
if (switchinnerflag && !(rinnerflag && drinnerflag))
error->all(FLERR,"Incorrect SNAP parameter file");
if (!switchinnerflag && (rinnerflag || drinnerflag))
error->all(FLERR,"Incorrect SNAP parameter file");
}
/* ----------------------------------------------------------------------

4
src/ML-SNAP/pair_snap.h
View File

@ -59,7 +59,9 @@ class PairSNAP : public Pair {
double **scale; // for thermodynamic integration
int twojmax, switchflag, bzeroflag, bnormflag;
int chemflag, wselfallflag;
int switchinnerflag;
int switchinnerflag; // inner cutoff switch
double *rinnerelem; // element inner cutoff
double *drinnerelem; // element inner cutoff range
int chunksize,parallel_thresh;
double rfac0, rmin0, wj1, wj2;
int rcutfacflag, twojmaxflag; // flags for required parameters

5
src/ML-SNAP/sna.cpp
View File

@ -178,7 +178,7 @@ SNA::~SNA()
memory->destroy(rinnerij);
memory->destroy(drinnerij);
}
if (chem_flag) memory->destroy(element);
if (chem_flag) memory->destroy(element);
memory->destroy(ulist_r_ij);
memory->destroy(ulist_i_ij);
delete[] idxz;
@ -376,8 +376,7 @@ void SNA::compute_ui(int jnum, int ielem)
if (chem_flag)
add_uarraytot(r, wj[j], rcutij[j], j, element[j], rinnerij[j], drinnerij[j]);
else
// add_uarraytot(r, wj[j], rcutij[j], j, 0, rinnerij[j], drinnerij[j]);
add_uarraytot(r, wj[j], rcutij[j], j, 0, 0.0, 1.0);
add_uarraytot(r, wj[j], rcutij[j], j, 0, rinnerij[j], drinnerij[j]);
}
}

29
src/ML-SNAP/sna.h
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@ -61,23 +61,31 @@ class SNA : protected Pointers {
double compute_sfac_inner(double, double, double);
double compute_dsfac_inner(double, double, double);
// public bispectrum data
int twojmax;
double *blist;
double **dblist;
// short neighbor list data
void grow_rij(int);
int nmax; // allocated size of short lists
double **rij; // short rij list
int *inside; // short neighbor list
double *wj; // short weight list
double *rcutij; // short cutoff list
double *rcutij; // short cutoff list
// only allocated for switch_inner_flag=1
double *rinnerij; // short inner cutoff list
double *drinnerij;// short inner range list
// only allocated for chem_flag=1
int *element; // short element list [0,nelements)
int nmax; // allocated size of short lists
void grow_rij(int);
int twojmax;
double *ylist_r, *ylist_i;
int idxcg_max, idxu_max, idxz_max, idxb_max;
private:
double rmin0, rfac0;
@ -103,6 +111,9 @@ class SNA : protected Pointers {
double **dulist_r, **dulist_i;
int elem_duarray; // element of j in derivative
double *ylist_r, *ylist_i;
int idxcg_max, idxu_max, idxz_max, idxb_max;
void create_twojmax_arrays();
void destroy_twojmax_arrays();
void init_clebsch_gordan();