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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5066 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2010-10-18 19:27:50 +00:00
parent 29dad0d827
commit 42fc29e43a
2 changed files with 21 additions and 10 deletions
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30
src/compute_atom_molecule.cpp
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@ -164,9 +164,15 @@ ComputeAtomMolecule(LAMMPS *lmp, int narg, char **arg) :
ComputeAtomMolecule::~ComputeAtomMolecule()
{
delete [] which;
delete [] argindex;
for (int m = 0; m < nvalues; m++) delete [] ids[m];
delete [] ids;
delete [] value2index;
memory->sfree(vone);
memory->sfree(vector);
memory->sfree(aone);
memory->destroy_2d_double_array(aone);
memory->destroy_2d_double_array(array);
memory->sfree(scratch);
}
@ -224,11 +230,13 @@ void ComputeAtomMolecule::compute_vector()
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
vone[imol] = scratch[j];
vone[imol] += peratom[j];
}
j += nstride;
}
int me;
MPI_Comm_rank(world,&me);
MPI_Allreduce(vone,vector,nmolecules,MPI_DOUBLE,MPI_SUM,world);
}
@ -245,7 +253,7 @@ void ComputeAtomMolecule::compute_array()
int nlocal = atom->nlocal;
for (n = 0; n < nvalues; n++) {
for (m = 0; m < nmolecules; m++) aone[n][m] = 0.0;
for (m = 0; m < nmolecules; m++) aone[m][n] = 0.0;
compute_one(n);
j = 0;
@ -254,7 +262,7 @@ void ComputeAtomMolecule::compute_array()
imol = molecule[i];
if (molmap) imol = molmap[imol-idlo];
else imol--;
aone[n][imol] = scratch[j];
aone[imol][n] += peratom[j];
}
j += nstride;
}
@ -267,7 +275,7 @@ void ComputeAtomMolecule::compute_array()
/* ----------------------------------------------------------------------
calculate per-atom values for one input M
invoke the appropriate compute,fix,variable
reallocate scratch vector if necessary
reallocate scratch if necessary for per-atom variable scratch space
------------------------------------------------------------------------- */
void ComputeAtomMolecule::compute_one(int m)
@ -286,10 +294,10 @@ void ComputeAtomMolecule::compute_one(int m)
}
if (aidx == 0) {
scratch = compute->vector_atom;
peratom = compute->vector_atom;
nstride = 1;
} else {
scratch = &compute->array_atom[0][aidx-1];
peratom = &compute->array_atom[0][aidx-1];
nstride = compute->size_array_cols;
}
@ -302,10 +310,10 @@ void ComputeAtomMolecule::compute_one(int m)
Fix *fix = modify->fix[vidx];
if (aidx == 0) {
scratch = fix->vector_atom;
peratom = fix->vector_atom;
nstride = 1;
} else {
scratch = &fix->array_atom[0][aidx-1];
peratom = &fix->array_atom[0][aidx-1];
nstride = fix->size_array_cols;
}
@ -317,9 +325,11 @@ void ComputeAtomMolecule::compute_one(int m)
memory->sfree(scratch);
scratch = (double *)
memory->smalloc(maxatom*sizeof(double),"atom/molecule:scratch");
peratom = scratch;
}
input->variable->compute_atom(vidx,igroup,scratch,1,0);
input->variable->compute_atom(vidx,igroup,peratom,1,0);
nstride = 1;
}
}