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add support for recomputing normalization factors and finite size correction during

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This commit is contained in:
Axel Kohlmeyer
2017-07-07 15:39:25 -04:00
parent 4339379948
commit fe888e4622
3 changed files with 73 additions and 36 deletions
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96
src/compute_rdf.cpp
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@ -48,7 +48,6 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
array_flag = 1;
extarray = 0;
dynamic_group_allow = 0;
nbin = force->inumeric(FLERR,arg[3]);
if (nbin < 1) error->all(FLERR,"Illegal compute rdf command");
@ -125,6 +124,9 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
icount = new int[npairs];
jcount = new int[npairs];
duplicates = new int[npairs];
dynamic = 0;
natoms_old = 0;
}
/* ---------------------------------------------------------------------- */
@ -150,7 +152,6 @@ ComputeRDF::~ComputeRDF()
void ComputeRDF::init()
{
int i,j,m;
if (!force->pair && !cutflag)
error->all(FLERR,"Compute rdf requires a pair style be defined "
@ -184,40 +185,12 @@ void ComputeRDF::init()
for (int i = 0; i < nbin; i++)
array[i][0] = (i+0.5) * delr;
// count atoms of each type that are also in group
// initialize normalization, finite size correction, and changing atom counts
int *mask = atom->mask;
int *type = atom->type;
int nlocal = atom->nlocal;
int ntypes = atom->ntypes;
for (i = 1; i <= ntypes; i++) typecount[i] = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) typecount[type[i]]++;
// icount = # of I atoms participating in I,J pairs for each histogram
// jcount = # of J atoms participating in I,J pairs for each histogram
// duplicates = # of atoms in both groups I and J for each histogram
for (m = 0; m < npairs; m++) {
icount[m] = 0;
for (i = ilo[m]; i <= ihi[m]; i++) icount[m] += typecount[i];
jcount[m] = 0;
for (i = jlo[m]; i <= jhi[m]; i++) jcount[m] += typecount[i];
duplicates[m] = 0;
for (i = ilo[m]; i <= ihi[m]; i++)
for (j = jlo[m]; j <= jhi[m]; j++)
if (i == j) duplicates[m] += typecount[i];
}
int *scratch = new int[npairs];
MPI_Allreduce(icount,scratch,npairs,MPI_INT,MPI_SUM,world);
for (i = 0; i < npairs; i++) icount[i] = scratch[i];
MPI_Allreduce(jcount,scratch,npairs,MPI_INT,MPI_SUM,world);
for (i = 0; i < npairs; i++) jcount[i] = scratch[i];
MPI_Allreduce(duplicates,scratch,npairs,MPI_INT,MPI_SUM,world);
for (i = 0; i < npairs; i++) duplicates[i] = scratch[i];
delete [] scratch;
natoms_old = atom->natoms;
dynamic = group->dynamic[igroup];
if (dynamic_user) dynamic = 1;
init_norm();
// need an occasional half neighbor list
// if user specified, request a cutoff = cutoff_user + skin
@ -246,6 +219,48 @@ void ComputeRDF::init_list(int id, NeighList *ptr)
/* ---------------------------------------------------------------------- */
void ComputeRDF::init_norm()
{
int i,j,m;
// count atoms of each type that are also in group
const int nlocal = atom->nlocal;
const int ntypes = atom->ntypes;
const int * const mask = atom->mask;
const int * const type = atom->type;
for (i = 1; i <= ntypes; i++) typecount[i] = 0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) typecount[type[i]]++;
// icount = # of I atoms participating in I,J pairs for each histogram
// jcount = # of J atoms participating in I,J pairs for each histogram
// duplicates = # of atoms in both groups I and J for each histogram
for (m = 0; m < npairs; m++) {
icount[m] = 0;
for (i = ilo[m]; i <= ihi[m]; i++) icount[m] += typecount[i];
jcount[m] = 0;
for (i = jlo[m]; i <= jhi[m]; i++) jcount[m] += typecount[i];
duplicates[m] = 0;
for (i = ilo[m]; i <= ihi[m]; i++)
for (j = jlo[m]; j <= jhi[m]; j++)
if (i == j) duplicates[m] += typecount[i];
}
int *scratch = new int[npairs];
MPI_Allreduce(icount,scratch,npairs,MPI_INT,MPI_SUM,world);
for (i = 0; i < npairs; i++) icount[i] = scratch[i];
MPI_Allreduce(jcount,scratch,npairs,MPI_INT,MPI_SUM,world);
for (i = 0; i < npairs; i++) jcount[i] = scratch[i];
MPI_Allreduce(duplicates,scratch,npairs,MPI_INT,MPI_SUM,world);
for (i = 0; i < npairs; i++) duplicates[i] = scratch[i];
delete [] scratch;
}
/* ---------------------------------------------------------------------- */
void ComputeRDF::compute_array()
{
int i,j,m,ii,jj,inum,jnum,itype,jtype,ipair,jpair,ibin,ihisto;
@ -253,6 +268,17 @@ void ComputeRDF::compute_array()
int *ilist,*jlist,*numneigh,**firstneigh;
double factor_lj,factor_coul;
if (natoms_old != atom->natoms) {
dynamic = 1;
natoms_old = atom->natoms;
}
// if the number of atoms has changed or we have a dynamic group
// or dynamic updates are requested (e.g. when changing atom types)
// we need to recompute some normalization parameters
if (dynamic) init_norm();
invoked_array = update->ntimestep;
// invoke half neighbor list (will copy or build if necessary)