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Merge pull request #1359 from martok/dynamical-matrix

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Updates and bugfixes to the dynamical_matrix command
This commit is contained in:
Axel Kohlmeyer
2019-03-20 21:34:34 -04:00
committed by GitHub
parent a626efbca0 7fe1cceb76
commit 76b9c0049d
2 changed files with 52 additions and 30 deletions
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76
src/USER-PHONON/dynamical_matrix.cpp
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@ -138,6 +138,9 @@ void DynamicalMatrix::command(int narg, char **arg)
else if (style == ESKM) options(narg-3,&arg[3]); //COME BACK
else if (comm->me == 0 && screen) fprintf(screen,"Illegal Dynamical Matrix command\n");
if (atom->map_style == 0)
error->all(FLERR,"Dynamical_matrix command requires an atom map, see atom_modify");
// move atoms by 3-vector or specified variable(s)
if (style == REGULAR) {
@ -240,7 +243,7 @@ void DynamicalMatrix::calculateMatrix()
int nlocal = atom->nlocal;
bigint natoms = atom->natoms;
int *type = atom->type;
int *gm = groupmap;
bigint *gm = groupmap;
double imass; // dynamical matrix element
double *m = atom->mass;
double **f = atom->f;
@ -256,20 +259,30 @@ void DynamicalMatrix::calculateMatrix()
//initialize dynmat to all zeros
dynmat_clear(dynmat);
if (comm->me == 0 && screen) fprintf(screen,"Calculating Dynamical Matrix...\n");
if (comm->me == 0 && screen) {
fprintf(screen,"Calculating Dynamical Matrix ...\n");
fprintf(screen," Total # of atoms = " BIGINT_FORMAT "\n", natoms);
fprintf(screen," Atoms in group = " BIGINT_FORMAT "\n", gcount);
fprintf(screen," Total dynamical matrix elements = " BIGINT_FORMAT "\n", (dynlen*dynlen) );
}
// emit dynlen rows of dimalpha*dynlen*dimbeta elements
update->nsteps = 0;
int prog = 0;
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
if (gm[i-1] < 0)
continue;
for (bigint alpha=0; alpha<3; alpha++){
displace_atom(local_idx, alpha, 1);
update_force();
for (bigint j=1; j<=natoms; j++){
local_jdx = atom->map(j);
if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
&& gm[i-1] >= 0 && gm[j-1] >= 0){
&& gm[j-1] >= 0){
for (int beta=0; beta<3; beta++){
dynmat[alpha][(gm[j-1])*3+beta] -= f[local_jdx][beta];
dynmat[alpha][gm[j-1]*3+beta] -= f[local_jdx][beta];
}
}
}
@ -278,15 +291,15 @@ void DynamicalMatrix::calculateMatrix()
for (bigint j=1; j<=natoms; j++){
local_jdx = atom->map(j);
if (local_idx >= 0 && local_jdx >= 0 && local_jdx < nlocal
&& gm[i-1] >= 0 && gm[j-1] >= 0){
&& gm[j-1] >= 0){
for (bigint beta=0; beta<3; beta++){
if (atom->rmass_flag == 1)
imass = sqrt(m[local_idx] * m[local_jdx]);
else
imass = sqrt(m[type[local_idx]] * m[type[local_jdx]]);
dynmat[alpha][(gm[j-1])*3+beta] -= -f[local_jdx][beta];
dynmat[alpha][(gm[j-1])*3+beta] /= (2 * del * imass);
dynmat[alpha][(gm[j-1])*3+beta] *= conversion;
dynmat[alpha][gm[j-1]*3+beta] -= -f[local_jdx][beta];
dynmat[alpha][gm[j-1]*3+beta] /= (2 * del * imass);
dynmat[alpha][gm[j-1]*3+beta] *= conversion;
}
}
}
@ -297,7 +310,16 @@ void DynamicalMatrix::calculateMatrix()
if (me == 0)
writeMatrix(fdynmat);
dynmat_clear(dynmat);
if (comm->me == 0 && screen) {
int p = 10 * gm[i-1] / gcount;
if (p > prog) {
prog = p;
fprintf(screen," %d%%",p*10);
fflush(screen);
}
}
}
if (comm->me == 0 && screen) fprintf(screen,"\n");
for (int i=0; i < 3; i++)
delete [] dynmat[i];
@ -316,27 +338,24 @@ void DynamicalMatrix::calculateMatrix()
void DynamicalMatrix::writeMatrix(double **dynmat)
{
if (me != 0 || fp == NULL) return;
if (me != 0 || !fp)
return;
// print file comment lines
if (!binaryflag && fp) {
clearerr(fp);
if (binaryflag) {
for (int i=0; i<3; i++)
fwrite(dynmat[i], sizeof(double), dynlen, fp);
if (ferror(fp))
error->one(FLERR, "Error writing to binary file");
} else {
for (int i = 0; i < 3; i++) {
for (bigint j = 0; j < dynlen; j++) {
if ((j+1)%3==0) fprintf(fp, "%4.8f\n", dynmat[i][j]);
else fprintf(fp, "%4.8f ",dynmat[i][j]);
}
}
}
if (ferror(fp))
error->one(FLERR,"Error writing to file");
if (binaryflag && fp) {
clearerr(fp);
fwrite(&dynmat[0], sizeof(double), 3 * dynlen, fp);
if (ferror(fp))
error->one(FLERR, "Error writing to binary file");
}
}
@ -490,6 +509,7 @@ void DynamicalMatrix::convert_units(const char *style)
void DynamicalMatrix::create_groupmap()
{
//Create a group map which maps atom order onto group
// groupmap[global atom index-1] = output column/row
int local_idx; // local index
int gid = 0; //group index
@ -498,7 +518,7 @@ void DynamicalMatrix::create_groupmap()
bigint natoms = atom->natoms;
int *recv = new int[comm->nprocs];
int *displs = new int[comm->nprocs];
int *temp_groupmap = new int[natoms];
bigint *temp_groupmap = new bigint[natoms];
//find number of local atoms in the group (final_gid)
for (bigint i=1; i<=natoms; i++){
@ -507,7 +527,7 @@ void DynamicalMatrix::create_groupmap()
gid += 1; // gid at the end of loop is final_Gid
}
//create an array of length final_gid
int *sub_groupmap = new int[gid];
bigint *sub_groupmap = new bigint[gid];
gid = 0;
//create a map between global atom id and group atom id for each proc
@ -524,7 +544,7 @@ void DynamicalMatrix::create_groupmap()
recv[i] = 0;
}
recv[comm->me] = gid;
MPI_Allreduce(recv,displs,4,MPI_INT,MPI_SUM,world);
MPI_Allreduce(recv,displs,comm->nprocs,MPI_INT,MPI_SUM,world);
for (int i=0; i<comm->nprocs; i++){
recv[i]=displs[i];
if (i>0) displs[i] = displs[i-1]+recv[i-1];
@ -532,15 +552,17 @@ void DynamicalMatrix::create_groupmap()
}
//combine subgroup maps into total temporary groupmap
MPI_Allgatherv(sub_groupmap,gid,MPI_INT,temp_groupmap,recv,displs,MPI_INT,world);
MPI_Allgatherv(sub_groupmap,gid,MPI_LMP_BIGINT,temp_groupmap,recv,displs,MPI_LMP_BIGINT,world);
std::sort(temp_groupmap,temp_groupmap+gcount);
//populate member groupmap based on temp groupmap
for (bigint i=0; i<natoms; i++){
if (i==temp_groupmap[i]-1)
groupmap[i] = temp_groupmap[i]-1;
bigint j = 0;
for (bigint i=1; i<=natoms; i++){
// flag groupmap contents that are in temp_groupmap
if (j < gcount && i == temp_groupmap[j])
groupmap[i-1] = j++;
else
groupmap[i] = -1;
groupmap[i-1] = -1;
}
//free that memory!

2
src/USER-PHONON/dynamical_matrix.h
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@ -58,7 +58,7 @@ namespace LAMMPS_NS {
bigint dynlen; // rank of dynamical matrix
int scaleflag;
int me;
int *groupmap;
bigint *groupmap;
int compressed; // 1 if dump file is written compressed, 0 no
int binaryflag; // 1 if dump file is written binary, 0 no