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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14128 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-10-21 18:29:37 +00:00
parent ddfb996d8e
commit 9a878cdd67
53 changed files with 289 additions and 181 deletions
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41
src/compute_rdf.cpp
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@ -95,6 +95,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
typecount = new int[ntypes+1];
icount = new int[npairs];
jcount = new int[npairs];
duplicates = new int[npairs];
}
/* ---------------------------------------------------------------------- */
@ -113,13 +114,14 @@ ComputeRDF::~ComputeRDF()
delete [] typecount;
delete [] icount;
delete [] jcount;
delete [] duplicates;
}
/* ---------------------------------------------------------------------- */
void ComputeRDF::init()
{
int i,m;
int i,j,m;
if (force->pair) delr = force->pair->cutforce / nbin;
else error->all(FLERR,"Compute rdf requires a pair style be defined");
@ -143,12 +145,17 @@ void ComputeRDF::init()
// 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];
@ -156,6 +163,8 @@ void ComputeRDF::init()
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;
// need an occasional half neighbor list
@ -265,25 +274,28 @@ void ComputeRDF::compute_array()
MPI_Allreduce(hist[0],histall[0],npairs*nbin,MPI_DOUBLE,MPI_SUM,world);
// convert counts to g(r) and coord(r) and copy into output array
// nideal = # of J atoms surrounding single I atom in a single bin
// assuming J atoms are at uniform density
// vfrac = fraction of volume in shell m
// npairs = number of pairs, corrected for duplicates
// duplicates = pairs in which both atoms are the same
double constant,nideal,gr,ncoord,rlower,rupper;
double constant,vfrac,gr,ncoord,rlower,rupper,normfac;
if (domain->dimension == 3) {
constant = 4.0*MY_PI / (3.0*domain->xprd*domain->yprd*domain->zprd);
for (m = 0; m < npairs; m++) {
normfac = (icount[m] > 0) ? static_cast<double>(jcount[m])
- static_cast<double>(duplicates[m])/icount[m] : 0.0;
ncoord = 0.0;
for (ibin = 0; ibin < nbin; ibin++) {
rlower = ibin*delr;
rupper = (ibin+1)*delr;
nideal = constant *
(rupper*rupper*rupper - rlower*rlower*rlower) * jcount[m];
if (icount[m]*nideal != 0.0)
gr = histall[m][ibin] / (icount[m]*nideal);
vfrac = constant * (rupper*rupper*rupper - rlower*rlower*rlower);
if (vfrac * normfac != 0.0)
gr = histall[m][ibin] / (vfrac * normfac * icount[m]);
else gr = 0.0;
ncoord += gr*nideal;
if (icount[m] != 0)
ncoord += gr * vfrac * normfac;
array[ibin][1+2*m] = gr;
array[ibin][2+2*m] = ncoord;
}
@ -294,14 +306,17 @@ void ComputeRDF::compute_array()
for (m = 0; m < npairs; m++) {
ncoord = 0.0;
normfac = (icount[m] > 0) ? static_cast<double>(jcount[m])
- static_cast<double>(duplicates[m])/icount[m] : 0.0;
for (ibin = 0; ibin < nbin; ibin++) {
rlower = ibin*delr;
rupper = (ibin+1)*delr;
nideal = constant * (rupper*rupper - rlower*rlower) * jcount[m];
if (icount[m]*nideal != 0.0)
gr = histall[m][ibin] / (icount[m]*nideal);
vfrac = constant * (rupper*rupper - rlower*rlower);
if (vfrac * normfac != 0.0)
gr = histall[m][ibin] / (vfrac * normfac * icount[m]);
else gr = 0.0;
ncoord += gr*nideal;
if (icount[m] != 0)
ncoord += gr * vfrac * normfac;
array[ibin][1+2*m] = gr;
array[ibin][2+2*m] = ncoord;
}