ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Optimized Dynamical Matrix

Browse Source
This commit is contained in:
charlie sievers
2019-02-01 21:55:29 -08:00
parent 682b456aae
commit adebe90315
25 changed files with 7642 additions and 28 deletions
Download Patch File Download Diff File Expand all files Collapse all files

58
src/USER-PHONON/dynamical_matrix.cpp
View File

@ -244,7 +244,8 @@ void DynamicalMatrix::calculateMatrix()
{
int local_idx; // local index
int local_jdx; // second local index
int natoms = atom->natoms;
int nlocal = atom->nlocal;
bigint natoms = atom->natoms;
int *mask = atom->mask;
int *type = atom->type;
double imass; // dynamical matrix element
@ -262,13 +263,14 @@ void DynamicalMatrix::calculateMatrix()
for (int i=1; i<=natoms; i++){
local_idx = atom->map(i);
//if (screen) fprintf(screen, "local idx = %i on proc %i with %i local\n",local_idx, comm->me, nlocal);
if (local_idx >= 0){
for (int alpha=0; alpha<3; alpha++){
displace_atom(local_idx, alpha, 1);
energy_force(0);
for (int j=1; j<=natoms; j++){
local_jdx = atom->map(j);
if (local_jdx >= 0){
if (local_jdx >= 0 && local_idx < nlocal){
for (int beta=0; beta<3; beta++){
dynmat[(i-1)*3+alpha][(j-1)*3+beta] += -f[j-1][beta];
}
@ -278,7 +280,7 @@ void DynamicalMatrix::calculateMatrix()
energy_force(0);
for (int j=1; j<=natoms; j++){
local_jdx = atom->map(j);
if (local_jdx >= 0){
if (local_jdx >= 0 && local_idx < nlocal){
for (int beta=0; beta<3; beta++){
if (atom->rmass_flag == 1)
imass = sqrt(m[i] * m[j]);
@ -365,31 +367,31 @@ void DynamicalMatrix::displace_atom(int local_idx, int direction, int magnitude)
void DynamicalMatrix::energy_force(int resetflag)
{
// check for reneighboring
// always communicate since atoms move
int nflag = neighbor->check_distance();
if (nflag == 0) {
//if (comm->me == 0 && screen) fprintf(screen,"b\n");
timer->stamp();
comm->forward_comm();
timer->stamp(Timer::COMM);
//if (comm->me == 0 && screen) fprintf(screen,"c\n");
} else {
if (triclinic) domain->x2lamda(atom->nlocal);
domain->pbc();
if (domain->box_change) {
domain->reset_box();
comm->setup();
if (neighbor->style) neighbor->setup_bins();
}
timer->stamp();
comm->borders();
if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
timer->stamp(Timer::COMM);
neighbor->build(1);
timer->stamp(Timer::NEIGH);
}
//// check for reneighboring
//// always communicate since atoms move
//int nflag = neighbor->check_distance();
//
//if (nflag == 0) {
////if (comm->me == 0 && screen) fprintf(screen,"b\n");
// timer->stamp();
// comm->forward_comm();
// timer->stamp(Timer::COMM);
////if (comm->me == 0 && screen) fprintf(screen,"c\n");
//} else {
// if (triclinic) domain->x2lamda(atom->nlocal);
// domain->pbc();
// if (domain->box_change) {
// domain->reset_box();
// comm->setup();
// if (neighbor->style) neighbor->setup_bins();
// }
// timer->stamp();
// comm->borders();
// if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
// timer->stamp(Timer::COMM);
// neighbor->build(1);
// timer->stamp(Timer::NEIGH);
//}
force_clear();
if (pair_compute_flag) {