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Make dB/dR indices start at zero in compute snap array.

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This commit is contained in:
rohskopf
2022-06-14 16:31:31 -06:00
parent 880382e26a
commit 5060a8b8a5
1 changed files with 52 additions and 25 deletions
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77
src/ML-SNAP/compute_snap.cpp
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@ -220,20 +220,26 @@ ComputeSnap::~ComputeSnap()
{
memory->destroy(snap);
//printf("---------------- 1\n");
memory->destroy(snapall);
//printf("---------------- 2\n");
memory->destroy(snap_peratom);
//printf("---------------- 3\n");
memory->destroy(radelem);
//printf("---------------- 4\n");
memory->destroy(wjelem);
//printf("---------------- 5\n");
memory->destroy(cutsq);
//printf("---------------- 6\n");
delete snaptr;
//printf("---------------- 7\n");
if (chemflag) memory->destroy(map);
if (switchinnerflag) {
memory->destroy(sinnerelem);
memory->destroy(dinnerelem);
}
//printf("---------------- 8\n");
if (dbirjflag){
//printf("dbirj_rows: %d\n", dbirj_rows);
//printf("----- destroy dbirj\n");
@ -248,6 +254,7 @@ ComputeSnap::~ComputeSnap()
memory->destroy(dbiri);
//printf("----- 5-1-1-1-1-1\n");
}
//printf("---------------- 9\n");
}
/* ---------------------------------------------------------------------- */
@ -529,14 +536,14 @@ void ComputeSnap::compute_array()
dbirj[dbirj_row_indx+1][icoeff] = snaptr->dblist[icoeff][1];
dbirj[dbirj_row_indx+2][icoeff] = snaptr->dblist[icoeff][2];
if (icoeff==(ncoeff-1)){
dbirj[dbirj_row_indx+0][ncoeff] = atom->tag[i];
dbirj[dbirj_row_indx+0][ncoeff+1] = atom->tag[j];
dbirj[dbirj_row_indx+0][ncoeff] = atom->tag[i]-1;
dbirj[dbirj_row_indx+0][ncoeff+1] = atom->tag[j]-1;
dbirj[dbirj_row_indx+0][ncoeff+2] = 0;
dbirj[dbirj_row_indx+1][ncoeff] = atom->tag[i];
dbirj[dbirj_row_indx+1][ncoeff+1] = atom->tag[j];
dbirj[dbirj_row_indx+1][ncoeff] = atom->tag[i]-1;
dbirj[dbirj_row_indx+1][ncoeff+1] = atom->tag[j]-1;
dbirj[dbirj_row_indx+1][ncoeff+2] = 1;
dbirj[dbirj_row_indx+2][ncoeff] = atom->tag[i];
dbirj[dbirj_row_indx+2][ncoeff+1] = atom->tag[j];
dbirj[dbirj_row_indx+2][ncoeff] = atom->tag[i]-1;
dbirj[dbirj_row_indx+2][ncoeff+1] = atom->tag[j]-1;
dbirj[dbirj_row_indx+2][ncoeff+2] = 2;
}
// Accumulate dBi/dRi = sum (-dBi/dRj) for neighbors j of if i.
@ -545,16 +552,16 @@ void ComputeSnap::compute_array()
dbiri[3*(atom->tag[i]-1)+2][icoeff] -= snaptr->dblist[icoeff][2];
// Get last columns
if (icoeff==(ncoeff-1)){
dbiri[3*(atom->tag[i]-1)+0][ncoeff] = atom->tag[i];
dbiri[3*(atom->tag[i]-1)+0][ncoeff+1] = atom->tag[i];
dbiri[3*(atom->tag[i]-1)+0][ncoeff] = atom->tag[i]-1;
dbiri[3*(atom->tag[i]-1)+0][ncoeff+1] = atom->tag[i]-1;
dbiri[3*(atom->tag[i]-1)+0][ncoeff+2] = 0;
dbiri[3*(atom->tag[i]-1)+1][ncoeff] = atom->tag[i];
dbiri[3*(atom->tag[i]-1)+1][ncoeff+1] = atom->tag[i];
dbiri[3*(atom->tag[i]-1)+1][ncoeff] = atom->tag[i]-1;
dbiri[3*(atom->tag[i]-1)+1][ncoeff+1] = atom->tag[i]-1;
dbiri[3*(atom->tag[i]-1)+1][ncoeff+2] = 1;
dbiri[3*(atom->tag[i]-1)+2][ncoeff] = atom->tag[i];
dbiri[3*(atom->tag[i]-1)+2][ncoeff+1] = atom->tag[i];
dbiri[3*(atom->tag[i]-1)+2][ncoeff] = atom->tag[i]-1;
dbiri[3*(atom->tag[i]-1)+2][ncoeff+1] = atom->tag[i]-1;
dbiri[3*(atom->tag[i]-1)+2][ncoeff+2] = 2;
}
}
@ -821,7 +828,15 @@ void ComputeSnap::compute_array()
*/
// accumulate forces to global array
if (dbirjflag){
for (int i=0; i<atom->nlocal; i++){
int iglobal = atom->tag[i];
snap[iglobal-1][ncoeff+0] = atom->f[i][0];
snap[iglobal-1][ncoeff+1] = atom->f[i][1];
snap[iglobal-1][ncoeff+2] = atom->f[i][2];
}
}
else{
for (int i = 0; i < atom->nlocal; i++) {
@ -838,13 +853,22 @@ void ComputeSnap::compute_array()
// accumulate bispectrum virial contributions to global array
//dbdotr_compute();
if (dbirjflag){
}
else{
dbdotr_compute();
}
// sum up over all processes
MPI_Allreduce(&snap[0][0],&snapall[0][0],size_array_rows*size_array_cols,MPI_DOUBLE,MPI_SUM,world);
// assign energy to last column
if (dbirjflag){
// Assign reference energy right after the dbirj rows, first column.
int irow = bik_rows + dbirj_rows + 3*natoms; // add 3N for the dBi/dRi rows
//printf("irow bik_rows dbirj_rows: %d %d %d\n", irow, bik_rows, dbirj_rows);
double reference_energy = c_pe->compute_scalar();
snapall[irow][0] = reference_energy;
}
else{
for (int i = 0; i < bik_rows; i++) snapall[i][lastcol] = 0;
@ -857,15 +881,18 @@ void ComputeSnap::compute_array()
// switch to Voigt notation
c_virial->compute_vector();
/*
irow += 3*natoms+bik_rows;
snapall[irow++][lastcol] = c_virial->vector[0];
snapall[irow++][lastcol] = c_virial->vector[1];
snapall[irow++][lastcol] = c_virial->vector[2];
snapall[irow++][lastcol] = c_virial->vector[5];
snapall[irow++][lastcol] = c_virial->vector[4];
snapall[irow][lastcol] = c_virial->vector[3];
*/
if (dbirjflag){
}
else{
int irow = 3*natoms+bik_rows;
snapall[irow++][lastcol] = c_virial->vector[0];
snapall[irow++][lastcol] = c_virial->vector[1];
snapall[irow++][lastcol] = c_virial->vector[2];
snapall[irow++][lastcol] = c_virial->vector[5];
snapall[irow++][lastcol] = c_virial->vector[4];
snapall[irow][lastcol] = c_virial->vector[3];
}
//}// else
}