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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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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() 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(vone);
memory->sfree(vector); memory->sfree(vector);
memory->sfree(aone); memory->destroy_2d_double_array(aone);
memory->destroy_2d_double_array(array); memory->destroy_2d_double_array(array);
memory->sfree(scratch); memory->sfree(scratch);
} }
@ -224,11 +230,13 @@ void ComputeAtomMolecule::compute_vector()
imol = molecule[i]; imol = molecule[i];
if (molmap) imol = molmap[imol-idlo]; if (molmap) imol = molmap[imol-idlo];
else imol--; else imol--;
vone[imol] = scratch[j]; vone[imol] += peratom[j];
} }
j += nstride; j += nstride;
} }
int me;
MPI_Comm_rank(world,&me);
MPI_Allreduce(vone,vector,nmolecules,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(vone,vector,nmolecules,MPI_DOUBLE,MPI_SUM,world);
} }
@ -245,7 +253,7 @@ void ComputeAtomMolecule::compute_array()
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
for (n = 0; n < nvalues; n++) { 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); compute_one(n);
j = 0; j = 0;
@ -254,7 +262,7 @@ void ComputeAtomMolecule::compute_array()
imol = molecule[i]; imol = molecule[i];
if (molmap) imol = molmap[imol-idlo]; if (molmap) imol = molmap[imol-idlo];
else imol--; else imol--;
aone[n][imol] = scratch[j]; aone[imol][n] += peratom[j];
} }
j += nstride; j += nstride;
} }
@ -267,7 +275,7 @@ void ComputeAtomMolecule::compute_array()
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
calculate per-atom values for one input M calculate per-atom values for one input M
invoke the appropriate compute,fix,variable 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) void ComputeAtomMolecule::compute_one(int m)
@ -286,10 +294,10 @@ void ComputeAtomMolecule::compute_one(int m)
} }
if (aidx == 0) { if (aidx == 0) {
scratch = compute->vector_atom; peratom = compute->vector_atom;
nstride = 1; nstride = 1;
} else { } else {
scratch = &compute->array_atom[0][aidx-1]; peratom = &compute->array_atom[0][aidx-1];
nstride = compute->size_array_cols; nstride = compute->size_array_cols;
} }
@ -302,10 +310,10 @@ void ComputeAtomMolecule::compute_one(int m)
Fix *fix = modify->fix[vidx]; Fix *fix = modify->fix[vidx];
if (aidx == 0) { if (aidx == 0) {
scratch = fix->vector_atom; peratom = fix->vector_atom;
nstride = 1; nstride = 1;
} else { } else {
scratch = &fix->array_atom[0][aidx-1]; peratom = &fix->array_atom[0][aidx-1];
nstride = fix->size_array_cols; nstride = fix->size_array_cols;
} }
@ -317,9 +325,11 @@ void ComputeAtomMolecule::compute_one(int m)
memory->sfree(scratch); memory->sfree(scratch);
scratch = (double *) scratch = (double *)
memory->smalloc(maxatom*sizeof(double),"atom/molecule:scratch"); 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;
} }
} }

1
src/compute_atom_molecule.h
View File

@ -44,6 +44,7 @@ class ComputeAtomMolecule : public Compute {
double *vone; double *vone;
double **aone; double **aone;
double *scratch; double *scratch;
double *peratom;
void compute_one(int); void compute_one(int);
}; };