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added a groupmap

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This commit is contained in:
charlie sievers
2019-02-03 09:13:37 -08:00
parent adebe90315
commit 5c3e3f381b
2 changed files with 85 additions and 41 deletions
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124
src/USER-PHONON/dynamical_matrix.cpp
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@ -40,6 +40,7 @@ DynamicalMatrix::DynamicalMatrix(LAMMPS *lmp) : Pointers(lmp), fp(NULL)
DynamicalMatrix::~DynamicalMatrix()
{
if (fp && me == 0) fclose(fp);
memory->destroy(groupmap);
memory->destroy(dynmat);
memory->destroy(final_dynmat);
fp = NULL;
@ -97,6 +98,13 @@ void DynamicalMatrix::setup()
//modify->setup_pre_reverse(eflag,vflag);
if (force->newton) comm->reverse_comm();
//if all then skip communication groupmap population
if (group->count(igroup) == atom->natoms)
for (int i=0; i<atom->natoms; i++)
groupmap[i] = i;
else
create_groupmap();
}
/* ---------------------------------------------------------------------- */
@ -126,6 +134,7 @@ void DynamicalMatrix::command(int narg, char **arg)
if (igroup == -1) error->all(FLERR,"Could not find dynamical matrix group ID");
groupbit = group->bitmask[igroup];
dynlen = (group->count(igroup))*3;
memory->create(groupmap,atom->natoms,"total_group_map:totalgm");
memory->create(dynmat,int(dynlen),int(dynlen),"dynamic_matrix:dynmat");
update->setupflag = 1;
@ -246,8 +255,8 @@ void DynamicalMatrix::calculateMatrix()
int local_jdx; // second local index
int nlocal = atom->nlocal;
bigint natoms = atom->natoms;
int *mask = atom->mask;
int *type = atom->type;
int *gm = groupmap;
double imass; // dynamical matrix element
double *m = atom->mass;
double **f = atom->f;
@ -263,16 +272,15 @@ 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 && local_idx < nlocal){
if (local_jdx >= 0 && local_idx < nlocal && gm[i-1] >= 0 && gm[j-1] >= 0){
for (int beta=0; beta<3; beta++){
dynmat[(i-1)*3+alpha][(j-1)*3+beta] += -f[j-1][beta];
dynmat[(gm[i-1])*3+alpha][(gm[j-1])*3+beta] += -f[j-1][beta];
}
}
}
@ -280,21 +288,15 @@ void DynamicalMatrix::calculateMatrix()
energy_force(0);
for (int j=1; j<=natoms; j++){
local_jdx = atom->map(j);
if (local_jdx >= 0 && local_idx < nlocal){
if (local_jdx >= 0 && local_idx < nlocal && gm[i-1] >= 0 && gm[j-1] >= 0){
for (int beta=0; beta<3; beta++){
if (atom->rmass_flag == 1)
imass = sqrt(m[i] * m[j]);
imass = sqrt(m[local_idx] * m[local_jdx]);
else
imass = sqrt(m[type[i]] * m[type[j]]);
//dynmat has length dynlen
//dynlen = (group->count(igroup))*3;
//currently dynmat is being called to natoms*3
//Also with this implementation
//I am not recovering the correct dynamical matrix
//if I have more than 1 core
dynmat[(i-1)*3+alpha][(j-1)*3+beta] -= -f[j-1][beta];
dynmat[(i-1)*3+alpha][(j-1)*3+beta] /= (2 * del * imass);
dynmat[(i-1)*3+alpha][(j-1)*3+beta] *= conversion;
imass = sqrt(m[type[local_idx]] * m[type[local_jdx]]);
dynmat[(gm[i-1])*3+alpha][(gm[j-1])*3+beta] -= -f[j-1][beta];
dynmat[(gm[i-1])*3+alpha][(gm[j-1])*3+beta] /= (2 * del * imass);
dynmat[(gm[i-1])*3+alpha][(gm[j-1])*3+beta] *= conversion;
}
}
}
@ -367,31 +369,6 @@ 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);
//}
force_clear();
if (pair_compute_flag) {
@ -489,3 +466,68 @@ void DynamicalMatrix::convert_units(const char *style)
} else error->all(FLERR,"Units Type Conversion Not Found");
}
/* ---------------------------------------------------------------------- */
void DynamicalMatrix::create_groupmap()
{
//Create a group map which maps atom order onto group
int local_idx; // local index
int gid = 0; //group index
int nlocal = atom->nlocal;
int *mask = atom->mask;
bigint natoms = atom->natoms;
int *recv = new int[comm->nprocs];
int *displs = new int[comm->nprocs];
int *temp_groupmap = new int[natoms];
//find number of local atoms in the group (final_gid)
for (int i=1; i<=natoms; i++){
local_idx = atom->map(i);
if (mask[local_idx] & groupbit && local_idx < nlocal)
gid += 1; // gid at the end of loop is final_Gid
}
//create an array of length final_gid
int *sub_groupmap = new int[gid];
gid = 0;
//create a map between global atom id and group atom id for each proc
for (int i=1; i<=natoms; i++){
local_idx = atom->map(i);
if (mask[local_idx] & groupbit && local_idx < nlocal){
sub_groupmap[gid] = i;
gid += 1;
}
}
//populate arrays for Allgatherv
for (int i=0; i<comm->nprocs; i++){
recv[i] = 0;
}
recv[comm->me] = gid;
MPI_Allreduce(recv,displs,4,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];
else displs[i] = 0;
}
//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+group->count(igroup));
//populate member groupmap based on temp groupmap
for (int i=0; i<natoms; i++){
if (i==temp_groupmap[i]-1)
groupmap[i] = temp_groupmap[i]-1;
else
groupmap[i] = -1;
}
//free that memory!
delete[] recv;
delete[] displs;
delete[] sub_groupmap;
delete[] temp_groupmap;
}