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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12518 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2014-09-18 14:39:15 +00:00
parent c4241ba55c
commit bda37b7c98
1 changed files with 75 additions and 103 deletions
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178
src/QEQ/fix_qeq.cpp
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@ -41,6 +41,8 @@ using namespace LAMMPS_NS;
using namespace MathConst;
using namespace FixConst;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
FixQEq::FixQEq(LAMMPS *lmp, int narg, char **arg) :
@ -142,109 +144,6 @@ int FixQEq::setmask()
/* ---------------------------------------------------------------------- */
void FixQEq::read_file(char *arg)
{
int i,itype,ntypes;
double v1,v2,v3,v4,v5;
char units[20];
FILE *pf;
ntypes = atom->ntypes;
memory->create(chi,ntypes+1,"qeq:chi");
memory->create(eta,ntypes+1,"qeq:eta");
memory->create(gamma,ntypes+1,"qeq:gamma");
memory->create(zeta,ntypes+1,"qeq:zeta");
memory->create(zcore,ntypes+1,"qeq:zcore");
if (comm->me == 0) {
if ((pf = fopen(arg,"r")) == NULL)
error->one(FLERR,"Fix qeq parameter file could not be found");
fscanf(pf,"%s",units);
if ((strcmp(units,"real") != 0) && (strcmp(units,"metal") != 0))
error->one(FLERR,"Fix qeq param file must be in real or metal units");
for (i = 1; i <= ntypes && !feof(pf); i++) {
fscanf(pf,"%d %lg %lg %lg %lg %lg",&itype,&v1,&v2,&v3,&v4,&v5);
if (itype < 1 || itype > ntypes)
error->one(FLERR,"Fix qeq invalid atom type in param file");
chi[itype] = v1;
eta[itype] = v2;
gamma[itype] = v3;
zeta[itype] = v4;
zcore[itype] = v5;
// unit conversion
if (strcmp(units,"real") == 0) {
if (strcmp(update->unit_style,"metal") == 0) {
chi[itype] *= 0.0433634;
eta[itype] *= 0.0433634;
gamma[itype] *= 1.0;
zeta[itype] *= 1.0;
zcore[itype] *= 1.0;
} else if (strcmp(update->unit_style,"si") == 0) {
chi[itype] *= 6.95e-21;
eta[itype] *= 6.95e-21;
gamma[itype] *= 1.0e-10;
zeta[itype] *= 1.0e10;
zcore[itype] *= 1.6021765e-19;
} else if (strcmp(update->unit_style,"cgs") == 0) {
chi[itype] *= 6.95e-14;
eta[itype] *= 6.95e-14;
gamma[itype] *= 1.0e-8;
zeta[itype] *= 1.0e8;
zcore[itype] *= 4.8032044e-10;
} else if (strcmp(update->unit_style,"electron") == 0) {
chi[itype] *= 0.00159362;
eta[itype] *= 0.00159362;
gamma[itype] *= 1.8903;
zeta[itype] *= 0.5290;
zcore[itype] *= 1.0;
}
} else if (strcmp(units,"metal") == 0) {
if (strcmp(update->unit_style,"real") == 0) {
chi[itype] *= 23.0609;
eta[itype] *= 23.0609;
gamma[itype] *= 1.0;
zeta[itype] *= 1.0;
zcore[itype] *= 1.0;
} else if (strcmp(update->unit_style,"si") == 0) {
chi[itype] *= 1.6021e-19;
eta[itype] *= 1.6021e-19;
gamma[itype] *= 1.0e-10;
zeta[itype] *= 1.0e10;
zcore[itype] *= 1.6021765e-19;
} else if (strcmp(update->unit_style,"cgs") == 0) {
chi[itype] *= 1.6021e-12;
eta[itype] *= 1.6021e-12;
gamma[itype] *= 1.0e-8;
zeta[itype] *= 1.0e8;
zcore[itype] *= 4.8032044e-10;
} else if (strcmp(update->unit_style,"electron") == 0) {
chi[itype] *= 0.0367502;
eta[itype] *= 0.0367502;
gamma[itype] *= 1.8903;
zeta[itype] *= 0.5290;
zcore[itype] *= 1.0;
}
}
}
if (i <= ntypes) error->one(FLERR,"Invalid param file for fix qeq");
fclose(pf);
}
MPI_Bcast(&chi[1],ntypes+1,MPI_DOUBLE,0,world);
MPI_Bcast(&eta[1],ntypes+1,MPI_DOUBLE,0,world);
MPI_Bcast(&gamma[1],ntypes+1,MPI_DOUBLE,0,world);
MPI_Bcast(&zeta[1],ntypes+1,MPI_DOUBLE,0,world);
MPI_Bcast(&zcore[1],ntypes+1,MPI_DOUBLE,0,world);
}
/* ---------------------------------------------------------------------- */
void FixQEq::allocate_storage()
{
nmax = atom->nmax;
@ -793,3 +692,76 @@ void FixQEq::vector_add( double* dest, double c, double* v, int k )
}
/* ---------------------------------------------------------------------- */
void FixQEq::read_file(char *file)
{
int i,itype,ntypes;
int params_per_line = 6;
char **words = new char*[params_per_line+1];
ntypes = atom->ntypes;
memory->create(chi,ntypes+1,"qeq:chi");
memory->create(eta,ntypes+1,"qeq:eta");
memory->create(gamma,ntypes+1,"qeq:gamma");
memory->create(zeta,ntypes+1,"qeq:zeta");
memory->create(zcore,ntypes+1,"qeq:zcore");
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
int n,nwords,ielement,eof;
char line[MAXLINE],*ptr;
eof = ielement = 0;
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
ielement ++;
if (ielement > ntypes)
error->all(FLERR,"Invalid fix qeq parameter file");
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = atom->count_words(line);
if (nwords == 0) continue;
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
itype = atoi(words[0]);
chi[itype] = atof(words[1]);
eta[itype] = atof(words[2]);
gamma[itype] = atof(words[3]);
zeta[itype] = atof(words[4]);
zcore[itype] = atof(words[5]);
}
delete [] words;
}