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SNAP changes by Aidan

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This commit is contained in:
Steve Plimpton
2017-05-30 10:21:07 -06:00
parent 2225fce94e
commit 22fdb1fc14
15 changed files with 209 additions and 102 deletions
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194
src/SNAP/pair_snap.cpp
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@ -35,6 +35,10 @@ using namespace LAMMPS_NS;
#define MAXLINE 1024
#define MAXWORD 3
// Outstanding issues with quadratic term
// 1. there seems to a problem with compute_optimized energy calc
// it does not match compute_regular, even when quadratic coeffs = 0
/* ---------------------------------------------------------------------- */
PairSNAP::PairSNAP(LAMMPS *lmp) : Pair(lmp)
@ -232,10 +236,6 @@ void PairSNAP::compute_regular(int eflag, int vflag)
snaptr->compute_ui(ninside);
snaptr->compute_zi();
if (!gammaoneflag) {
snaptr->compute_bi();
snaptr->copy_bi2bvec();
}
// for neighbors of I within cutoff:
// compute dUi/drj and dBi/drj
@ -255,17 +255,41 @@ void PairSNAP::compute_regular(int eflag, int vflag)
fij[1] = 0.0;
fij[2] = 0.0;
// linear contributions
for (int k = 1; k <= ncoeff; k++) {
double bgb;
if (gammaoneflag)
bgb = coeffi[k];
else bgb = coeffi[k]*
gamma*pow(snaptr->bvec[k-1],gamma-1.0);
double bgb = coeffi[k];
fij[0] += bgb*snaptr->dbvec[k-1][0];
fij[1] += bgb*snaptr->dbvec[k-1][1];
fij[2] += bgb*snaptr->dbvec[k-1][2];
}
// quadratic contributions
if (quadraticflag) {
snaptr->compute_bi();
snaptr->copy_bi2bvec();
int k = ncoeff+1;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = snaptr->bvec[icoeff];
double fack = coeffi[k]*bveci;
double* dbveci = snaptr->dbvec[icoeff];
fij[0] += fack*snaptr->dbvec[icoeff][0];
fij[1] += fack*snaptr->dbvec[icoeff][1];
fij[2] += fack*snaptr->dbvec[icoeff][2];
k++;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double facki = coeffi[k]*bveci;
double fackj = coeffi[k]*snaptr->bvec[jcoeff];
double* dbvecj = snaptr->dbvec[jcoeff];
fij[0] += facki*dbvecj[0]+fackj*dbveci[0];
fij[1] += facki*dbvecj[1]+fackj*dbveci[1];
fij[2] += facki*dbvecj[2]+fackj*dbveci[2];
k++;
}
}
}
f[i][0] += fij[0];
f[i][1] += fij[1];
f[i][2] += fij[2];
@ -285,14 +309,33 @@ void PairSNAP::compute_regular(int eflag, int vflag)
// evdwl = energy of atom I, sum over coeffs_k * Bi_k
evdwl = coeffi[0];
if (gammaoneflag) {
snaptr->compute_bi();
snaptr->copy_bi2bvec();
for (int k = 1; k <= ncoeff; k++)
evdwl += coeffi[k]*snaptr->bvec[k-1];
} else
for (int k = 1; k <= ncoeff; k++)
evdwl += coeffi[k]*pow(snaptr->bvec[k-1],gamma);
if (!quadraticflag) {
snaptr->compute_bi();
snaptr->copy_bi2bvec();
}
// E = beta.B + 0.5*B^t.alpha.B
// coeff[k] = beta[k-1] or
// coeff[k] = alpha_ii or
// coeff[k] = alpha_ij = alpha_ji, j != i
// linear contributions
for (int k = 1; k <= ncoeff; k++)
evdwl += coeffi[k]*snaptr->bvec[k-1];
// quadratic contributions
if (quadraticflag) {
int k = ncoeff+1;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = snaptr->bvec[icoeff];
evdwl += 0.5*coeffi[k++]*bveci*bveci;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
evdwl += coeffi[k++]*bveci*snaptr->bvec[jcoeff];
}
}
}
ev_tally_full(i,2.0*evdwl,0.0,0.0,delx,dely,delz);
}
@ -562,26 +605,46 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
sna[tid]->compute_dbidrj();
sna[tid]->copy_dbi2dbvec();
if (!gammaoneflag) {
sna[tid]->compute_bi();
sna[tid]->copy_bi2bvec();
}
fij[0] = 0.0;
fij[1] = 0.0;
fij[2] = 0.0;
// linear contributions
for (k = 1; k <= ncoeff; k++) {
double bgb;
if (gammaoneflag)
bgb = coeffi[k];
else bgb = coeffi[k]*
gamma*pow(sna[tid]->bvec[k-1],gamma-1.0);
double bgb = coeffi[k];
fij[0] += bgb*sna[tid]->dbvec[k-1][0];
fij[1] += bgb*sna[tid]->dbvec[k-1][1];
fij[2] += bgb*sna[tid]->dbvec[k-1][2];
}
// quadratic contributions
if (quadraticflag) {
sna[tid]->compute_bi();
sna[tid]->copy_bi2bvec();
int k = ncoeff+1;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = sna[tid]->bvec[icoeff];
double fack = coeffi[k]*bveci;
double* dbveci = sna[tid]->dbvec[icoeff];
fij[0] += fack*sna[tid]->dbvec[icoeff][0];
fij[1] += fack*sna[tid]->dbvec[icoeff][1];
fij[2] += fack*sna[tid]->dbvec[icoeff][2];
k++;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
double facki = coeffi[k]*bveci;
double fackj = coeffi[k]*sna[tid]->bvec[jcoeff];
double* dbvecj = sna[tid]->dbvec[jcoeff];
fij[0] += facki*dbvecj[0]+fackj*dbveci[0];
fij[1] += facki*dbvecj[1]+fackj*dbveci[1];
fij[2] += facki*dbvecj[2]+fackj*dbveci[2];
k++;
}
}
}
#if defined(_OPENMP)
#pragma omp critical
#endif
@ -606,15 +669,33 @@ void PairSNAP::compute_optimized(int eflag, int vflag)
if (eflag&&pairs[iijj][1] == 0) {
evdwl = coeffi[0];
if (gammaoneflag) {
sna[tid]->compute_bi();
sna[tid]->copy_bi2bvec();
for (int k = 1; k <= ncoeff; k++)
evdwl += coeffi[k]*sna[tid]->bvec[k-1];
} else
for (int k = 1; k <= ncoeff; k++)
evdwl += coeffi[k]*pow(sna[tid]->bvec[k-1],gamma);
sna[tid]->compute_bi();
sna[tid]->copy_bi2bvec();
// E = beta.B + 0.5*B^t.alpha.B
// coeff[k] = beta[k-1] or
// coeff[k] = alpha_ii or
// coeff[k] = alpha_ij = alpha_ji, j != i
// linear contributions
for (int k = 1; k <= ncoeff; k++)
evdwl += coeffi[k]*sna[tid]->bvec[k-1];
// quadratic contributions
if (quadraticflag) {
int k = ncoeff+1;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
double bveci = sna[tid]->bvec[icoeff];
evdwl += 0.5*coeffi[k++]*bveci*bveci;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
evdwl += coeffi[k++]*bveci*sna[tid]->bvec[jcoeff];
}
}
}
#if defined(_OPENMP)
#pragma omp critical
#endif
@ -1363,6 +1444,22 @@ void PairSNAP::coeff(int narg, char **arg)
read_files(coefffilename,paramfilename);
if (!quadraticflag)
ncoeff = ncoeffall - 1;
else {
// ncoeffall should be (ncoeff+2)*(ncoeff+1)/2
// so, ncoeff = floor(sqrt(2*ncoeffall))-1
ncoeff = sqrt(2*ncoeffall)-1;
ncoeffq = (ncoeff*(ncoeff+1))/2;
int ntmp = 1+ncoeff+ncoeffq;
if (ntmp != ncoeffall) {
printf("ncoeffall = %d ntmp = %d ncoeff = %d \n",ncoeffall,ntmp,ncoeff);
error->all(FLERR,"Incorrect SNAP coeff file");
}
}
// 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
@ -1416,6 +1513,7 @@ void PairSNAP::coeff(int narg, char **arg)
sna[tid]->grow_rij(nmax);
}
printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff);
if (ncoeff != sna[0]->ncoeff) {
printf("ncoeff = %d snancoeff = %d \n",ncoeff,sna[0]->ncoeff);
error->all(FLERR,"Incorrect SNAP parameter file");
@ -1470,7 +1568,7 @@ double PairSNAP::init_one(int i, int j)
void PairSNAP::read_files(char *coefffilename, char *paramfilename)
{
// open SNAP ceofficient file on proc 0
// open SNAP coefficient file on proc 0
FILE *fpcoeff;
if (comm->me == 0) {
@ -1518,13 +1616,13 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
words[iword] = strtok(NULL,"' \t\n\r\f");
int nelemfile = atoi(words[0]);
ncoeff = atoi(words[1])-1;
ncoeffall = atoi(words[1]);
// Set up element lists
memory->create(radelem,nelements,"pair:radelem");
memory->create(wjelem,nelements,"pair:wjelem");
memory->create(coeffelem,nelements,ncoeff+1,"pair:coeffelem");
memory->create(coeffelem,nelements,ncoeffall,"pair:coeffelem");
int *found = new int[nelements];
for (int ielem = 0; ielem < nelements; ielem++)
@ -1569,7 +1667,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (strcmp(elemtmp,elements[ielem]) == 0) break;
if (ielem == nelements) {
if (comm->me == 0)
for (int icoeff = 0; icoeff <= ncoeff; icoeff++)
for (int icoeff = 0; icoeff < ncoeffall; icoeff++)
ptr = fgets(line,MAXLINE,fpcoeff);
continue;
}
@ -1578,7 +1676,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (found[ielem]) {
if (comm->me == 0)
for (int icoeff = 0; icoeff <= ncoeff; icoeff++)
for (int icoeff = 0; icoeff < ncoeffall; icoeff++)
ptr = fgets(line,MAXLINE,fpcoeff);
continue;
}
@ -1595,7 +1693,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
elements[ielem], radelem[ielem], wjelem[ielem]);
}
for (int icoeff = 0; icoeff <= ncoeff; icoeff++) {
for (int icoeff = 0; icoeff < ncoeffall; icoeff++) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fpcoeff);
if (ptr == NULL) {
@ -1629,13 +1727,12 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
// Set defaults for optional keywords
gamma = 1.0;
gammaoneflag = 1;
rfac0 = 0.99363;
rmin0 = 0.0;
diagonalstyle = 3;
switchflag = 1;
bzeroflag = 1;
quadraticflag = 0;
// open SNAP parameter file on proc 0
@ -1689,9 +1786,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
} else if (strcmp(keywd,"twojmax") == 0) {
twojmax = atoi(keyval);
twojmaxflag = 1;
} else if (strcmp(keywd,"gamma") == 0)
gamma = atof(keyval);
else if (strcmp(keywd,"rfac0") == 0)
} else if (strcmp(keywd,"rfac0") == 0)
rfac0 = atof(keyval);
else if (strcmp(keywd,"rmin0") == 0)
rmin0 = atof(keyval);
@ -1701,6 +1796,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
switchflag = atoi(keyval);
else if (strcmp(keywd,"bzeroflag") == 0)
bzeroflag = atoi(keyval);
else if (strcmp(keywd,"quadraticflag") == 0)
quadraticflag = atoi(keyval);
else
error->all(FLERR,"Incorrect SNAP parameter file");
}
@ -1708,9 +1805,6 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
if (rcutfacflag == 0 || twojmaxflag == 0)
error->all(FLERR,"Incorrect SNAP parameter file");
if (gamma == 1.0) gammaoneflag = 1;
else gammaoneflag = 0;
delete[] found;
}
@ -1726,7 +1820,7 @@ double PairSNAP::memory_usage()
bytes += n*n*sizeof(double);
bytes += 3*nmax*sizeof(double);
bytes += nmax*sizeof(int);
bytes += (2*ncoeff+1)*sizeof(double);
bytes += (2*ncoeffall)*sizeof(double);
bytes += (ncoeff*3)*sizeof(double);
bytes += sna[0]->memory_usage()*nthreads;
return bytes;