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Removed redundant element list from pair_coeff snap syntax

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This commit is contained in:
Aidan Thompson
2018-12-03 20:28:01 -07:00
parent 67041a5446
commit fa7e02ea71
19 changed files with 54 additions and 306 deletions
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68
src/SNAP/pair_snap.cpp
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@ -1416,11 +1416,7 @@ void PairSNAP::settings(int narg, char **arg)
void PairSNAP::coeff(int narg, char **arg)
{
// read SNAP element names between 2 filenames
// nelements = # of SNAP elements
// elements = list of unique element names
if (narg < 6) error->all(FLERR,"Incorrect args for pair coefficients");
if (narg < 5) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
if (nelements) {
@ -1432,30 +1428,17 @@ void PairSNAP::coeff(int narg, char **arg)
memory->destroy(coeffelem);
}
nelements = narg - 4 - atom->ntypes;
if (nelements < 1) error->all(FLERR,"Incorrect args for pair coefficients");
char* type1 = arg[0];
char* type2 = arg[1];
char* coefffilename = arg[2];
char** elemlist = &arg[3];
char* paramfilename = arg[3+nelements];
char** elemtypes = &arg[4+nelements];
char* paramfilename = arg[3];
char** elemtypes = &arg[4];
// insure I,J args are * *
if (strcmp(type1,"*") != 0 || strcmp(type2,"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
elements = new char*[nelements];
for (int i = 0; i < nelements; i++) {
char* elemname = elemlist[i];
int n = strlen(elemname) + 1;
elements[i] = new char[n];
strcpy(elements[i],elemname);
}
// read snapcoeff and snapparam files
read_files(coefffilename,paramfilename);
@ -1631,22 +1614,19 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
iword = 1;
words[iword] = strtok(NULL,"' \t\n\r\f");
int nelemfile = atoi(words[0]);
nelements = atoi(words[0]);
ncoeffall = atoi(words[1]);
// Set up element lists
// 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");
int *found = new int[nelements];
for (int ielem = 0; ielem < nelements; ielem++)
found[ielem] = 0;
// Loop over nelements blocks in the SNAP coefficient file
// Loop over elements in the SNAP coefficient file
for (int ielemfile = 0; ielemfile < nelemfile; ielemfile++) {
for (int ielem = 0; ielem < nelements; ielem++) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
@ -1673,33 +1653,12 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
words[iword] = strtok(NULL,"' \t\n\r\f");
char* elemtmp = words[0];
double radtmp = atof(words[1]);
double wjtmp = atof(words[2]);
int n = strlen(elemtmp) + 1;
elements[ielem] = new char[n];
strcpy(elements[ielem],elemtmp);
// skip if element name isn't in element list
int ielem;
for (ielem = 0; ielem < nelements; ielem++)
if (strcmp(elemtmp,elements[ielem]) == 0) break;
if (ielem == nelements) {
if (comm->me == 0)
for (int icoeff = 0; icoeff < ncoeffall; icoeff++)
ptr = fgets(line,MAXLINE,fpcoeff);
continue;
}
// skip if element already appeared
if (found[ielem]) {
if (comm->me == 0)
for (int icoeff = 0; icoeff < ncoeffall; icoeff++)
ptr = fgets(line,MAXLINE,fpcoeff);
continue;
}
found[ielem] = 1;
radelem[ielem] = radtmp;
wjelem[ielem] = wjtmp;
radelem[ielem] = atof(words[1]);
wjelem[ielem] = atof(words[2]);
if (comm->me == 0) {
@ -1821,7 +1780,6 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (rcutfacflag == 0 || twojmaxflag == 0)
error->all(FLERR,"Incorrect SNAP parameter file");
delete[] found;
}
/* ----------------------------------------------------------------------