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minor dynmat changes and start of third order changes

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This commit is contained in:
casievers
2019-02-05 17:52:28 -08:00
parent 8ec9b6fb64
commit 4226522e20
4 changed files with 180 additions and 104 deletions
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76
src/USER-PHONON/dynamical_matrix.cpp
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@ -80,7 +80,7 @@ void DynamicalMatrix::setup()
update_force();
//if all then skip communication groupmap population
if (ngatoms == atom->natoms)
if (gcount == atom->natoms)
for (int i=0; i<atom->natoms; i++)
groupmap[i] = i;
else
@ -113,8 +113,8 @@ void DynamicalMatrix::command(int narg, char **arg)
igroup = group->find(arg[0]);
if (igroup == -1) error->all(FLERR,"Could not find dynamical matrix group ID");
groupbit = group->bitmask[igroup];
ngatoms = group->count(igroup);
dynlen = (ngatoms)*3;
gcount = group->count(igroup);
dynlen = (gcount)*3;
memory->create(groupmap,atom->natoms,"total_group_map:totalgm");
update->setupflag = 1;
@ -260,44 +260,42 @@ void DynamicalMatrix::calculateMatrix()
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
if (local_idx >= 0){
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_jdx >= 0 && local_jdx < nlocal
&& gm[i-1] >= 0 && gm[j-1] >= 0){
for (int beta=0; beta<3; beta++){
dynmat[alpha][(gm[j-1])*3+beta] = -f[local_jdx][beta];
}
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){
for (int beta=0; beta<3; beta++){
dynmat[alpha][(gm[j-1])*3+beta] = -f[local_jdx][beta];
}
}
displace_atom(local_idx,alpha,-2);
update_force();
for (bigint j=1; j<=natoms; j++){
local_jdx = atom->map(j);
if (local_jdx >= 0 && local_jdx < nlocal
&& gm[i-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;
}
}
}
displace_atom(local_idx,alpha,1);
}
for (int k=0; k<3; k++)
MPI_Reduce(dynmat[k],fdynmat[k],dynlen,MPI_DOUBLE,MPI_SUM,0,world);
if (me == 0)
writeMatrix(fdynmat);
dynmat_clear(dynmat);
displace_atom(local_idx,alpha,-2);
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){
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;
}
}
}
displace_atom(local_idx,alpha,1);
}
for (int k=0; k<3; k++)
MPI_Reduce(dynmat[k],fdynmat[k],dynlen,MPI_DOUBLE,MPI_SUM,0,world);
if (me == 0)
writeMatrix(fdynmat);
dynmat_clear(dynmat);
}
for (int i=0; i < 3; i++)
@ -530,7 +528,7 @@ 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);
std::sort(temp_groupmap,temp_groupmap+ngatoms);
std::sort(temp_groupmap,temp_groupmap+gcount);
//populate member groupmap based on temp groupmap
for (int i=0; i<natoms; i++){
@ -545,4 +543,4 @@ void DynamicalMatrix::create_groupmap()
delete[] displs;
delete[] sub_groupmap;
delete[] temp_groupmap;
}
}