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Tightened up the consistency checks on SNAP elements and LAMMPS types

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This commit is contained in:
Aidan Thompson
2021-03-09 18:38:47 -07:00
parent 6b3f0ddd3b
commit 115723a4d4
1 changed files with 93 additions and 47 deletions
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140
src/SNAP/pair_snap.cpp
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@ -381,17 +381,8 @@ void PairSNAP::settings(int narg, char ** /* arg */)
void PairSNAP::coeff(int narg, char **arg)
{
if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
if (nelements) {
for (int i = 0; i < nelements; i++)
delete[] elements[i];
delete[] elements;
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(coeffelem);
}
if (narg != 4 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients");
char* type1 = arg[0];
char* type2 = arg[1];
@ -404,6 +395,47 @@ void PairSNAP::coeff(int narg, char **arg)
if (strcmp(type1,"*") != 0 || strcmp(type2,"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// clean out old arrays
if (elements) {
for (int i = 0; i < nelements; i++)
delete[] elements[i];
delete[] elements;
memory->destroy(radelem);
memory->destroy(wjelem);
memory->destroy(coeffelem);
}
// nelements = # of unique elements declared
// elements = list of unique element names
// allocate as ntypes >= nelements
elements = new char*[atom->ntypes];
for (int i = 0; i < atom->ntypes; i++) elements[i] = nullptr;
// read args that map atom types to SNAP elements
// map[i] = which element the Ith atom type is, -1 if not mapped
// map[0] is not used
nelements = 0;
for (int i = 1; i <= atom->ntypes; i++) {
char* elemstring = elemtypes[i-1];
if (strcmp(elemstring,"NULL") == 0) {
map[i] = -1;
continue;
}
int j;
for (j = 0; j < nelements; j++)
if (strcmp(elemstring,elements[j]) == 0) break;
map[i] = j;
if (j == nelements) {
int n = strlen(elemstring) + 1;
elements[j] = new char[n];
strcpy(elements[j],elemstring);
nelements++;
}
}
// read snapcoeff and snapparam files
read_files(coefffilename,paramfilename);
@ -423,23 +455,6 @@ void PairSNAP::coeff(int narg, char **arg)
}
}
// read args that map atom types to SNAP elements
// map[i] = which element the Ith atom type is, -1 if not mapped
// map[0] is not used
for (int i = 1; i <= atom->ntypes; i++) {
char* elemname = elemtypes[i-1];
int jelem;
for (jelem = 0; jelem < nelements; jelem++)
if (strcmp(elemname,elements[jelem]) == 0)
break;
if (jelem < nelements)
map[i] = jelem;
else if (strcmp(elemname,"NULL") == 0) map[i] = -1;
else error->all(FLERR,"Incorrect args for pair coefficients");
}
// clear setflag since coeff() called once with I,J = * *
int n = atom->ntypes;
@ -559,19 +574,24 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
iword = 1;
words[iword] = strtok(nullptr,"' \t\n\r\f");
nelements = atoi(words[0]);
int nelemtmp = atoi(words[0]);
ncoeffall = atoi(words[1]);
// set up element lists
elements = new char*[nelements];
memory->create(radelem,nelements,"pair:radelem");
memory->create(wjelem,nelements,"pair:wjelem");
memory->create(coeffelem,nelements,ncoeffall,"pair:coeffelem");
// Loop over nelements blocks in the SNAP coefficient file
// initialize checklist for all required nelements
for (int ielem = 0; ielem < nelements; ielem++) {
int elementflags[nelements];
for (int jelem = 0; jelem < nelements; jelem++)
elementflags[jelem] = 0;
// loop over nelemtmp blocks in the SNAP coefficient file
for (int ielem = 0; ielem < nelemtmp; ielem++) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
@ -597,51 +617,77 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
iword = 2;
words[iword] = strtok(nullptr,"' \t\n\r\f");
char* elemtmp = words[0];
int n = strlen(elemtmp) + 1;
elements[ielem] = new char[n];
strcpy(elements[ielem],elemtmp);
int jelem;
for (jelem = 0; jelem < nelements; jelem++)
if (strcmp(words[0],elements[jelem]) == 0) break;
radelem[ielem] = atof(words[1]);
wjelem[ielem] = atof(words[2]);
// if this element not needed, skip this block
if (jelem == nelements) {
if (comm->me == 0) {
for (int icoeff = 0; icoeff < ncoeffall; icoeff++) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == nullptr) {
eof = 1;
fclose(fpcoeff);
}
}
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
continue;
}
if (elementflags[jelem] == 1)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
else
elementflags[jelem] = 1;
radelem[jelem] = atof(words[1]);
wjelem[jelem] = atof(words[2]);
if (comm->me == 0) {
if (screen) fprintf(screen,"SNAP Element = %s, Radius %g, Weight %g \n",
elements[ielem], radelem[ielem], wjelem[ielem]);
elements[jelem], radelem[jelem], wjelem[jelem]);
if (logfile) fprintf(logfile,"SNAP Element = %s, Radius %g, Weight %g \n",
elements[ielem], radelem[ielem], wjelem[ielem]);
elements[jelem], radelem[jelem], wjelem[jelem]);
}
for (int icoeff = 0; icoeff < ncoeffall; icoeff++) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == nullptr) {
eof = 1;
fclose(fpcoeff);
} else n = strlen(line) + 1;
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == nullptr) {
eof = 1;
fclose(fpcoeff);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
error->all(FLERR,"Incorrect format in SNAP coefficient file");
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
nwords = utils::trim_and_count_words(line);
if (nwords != 1)
error->all(FLERR,"Incorrect format in SNAP coefficient file");
error->all(FLERR,"Incorrect format in SNAP coefficient file");
iword = 0;
words[iword] = strtok(line,"' \t\n\r\f");
coeffelem[ielem][icoeff] = atof(words[0]);
coeffelem[jelem][icoeff] = atof(words[0]);
}
}
if (comm->me == 0) fclose(fpcoeff);
for (int jelem = 0; jelem < nelements; jelem++) {
if (elementflags[jelem] == 0)
error->all(FLERR,"Element not found in SNAP coefficient file");
}
// set flags for required keywords
rcutfacflag = 0;