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third order tensor calculator

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This commit is contained in:
casievers
2019-02-06 12:05:41 -08:00
parent 4226522e20
commit 490f67d332
3 changed files with 70 additions and 113 deletions
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14
src/USER-PHONON/dynamical_matrix.cpp
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@ -81,7 +81,7 @@ void DynamicalMatrix::setup()
//if all then skip communication groupmap population
if (gcount == atom->natoms)
for (int i=0; i<atom->natoms; i++)
for (bigint i=0; i<atom->natoms; i++)
groupmap[i] = i;
else
create_groupmap();
@ -268,7 +268,7 @@ void DynamicalMatrix::calculateMatrix()
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];
dynmat[alpha][(gm[j-1])*3+beta] -= f[local_jdx][beta];
}
}
}
@ -321,7 +321,7 @@ void DynamicalMatrix::writeMatrix(double **dynmat)
if (!binaryflag && fp) {
clearerr(fp);
for (int i = 0; i < 3; i++) {
for (int j = 0; j < dynlen; j++) {
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]);
}
@ -344,6 +344,8 @@ void DynamicalMatrix::writeMatrix(double **dynmat)
void DynamicalMatrix::displace_atom(int local_idx, int direction, int magnitude)
{
if (local_idx < 0) return;
double **x = atom->x;
int *sametag = atom->sametag;
int j = local_idx;
@ -496,7 +498,7 @@ void DynamicalMatrix::create_groupmap()
int *temp_groupmap = new int[natoms];
//find number of local atoms in the group (final_gid)
for (int i=1; i<=natoms; i++){
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit)
gid += 1; // gid at the end of loop is final_Gid
@ -506,7 +508,7 @@ void DynamicalMatrix::create_groupmap()
gid = 0;
//create a map between global atom id and group atom id for each proc
for (int i=1; i<=natoms; i++){
for (bigint i=1; i<=natoms; i++){
local_idx = atom->map(i);
if ((local_idx >= 0) && (local_idx < nlocal) && mask[local_idx] & groupbit){
sub_groupmap[gid] = i;
@ -531,7 +533,7 @@ void DynamicalMatrix::create_groupmap()
std::sort(temp_groupmap,temp_groupmap+gcount);
//populate member groupmap based on temp groupmap
for (int i=0; i<natoms; i++){
for (bigint i=0; i<natoms; i++){
if (i==temp_groupmap[i]-1)
groupmap[i] = temp_groupmap[i]-1;
else