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Added compute_rdf.cpp

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This commit is contained in:
Aidan Thompson
2018-10-19 18:43:04 -06:00
parent 04a4a29fcf
commit 3a735d15d4
1 changed files with 22 additions and 18 deletions
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40
src/compute_rdf.cpp
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@ -45,7 +45,7 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
hist(NULL), histall(NULL), typecount(NULL), icount(NULL), jcount(NULL), hist(NULL), histall(NULL), typecount(NULL), icount(NULL), jcount(NULL),
duplicates(NULL) duplicates(NULL)
{ {
if (narg < 4 || (narg-4) % 2) error->all(FLERR,"Illegal compute rdf command"); if (narg < 4) error->all(FLERR,"Illegal compute rdf command");
array_flag = 1; array_flag = 1;
extarray = 0; extarray = 0;
@ -77,7 +77,10 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
// pairwise args // pairwise args
if (nargpair == 0) npairs = 1; if (nargpair == 0) npairs = 1;
else npairs = nargpair/2; else {
if (nargpair % 2) error->all(FLERR,"Illegal compute rdf command");
npairs = nargpair/2;
}
size_array_rows = nbin; size_array_rows = nbin;
size_array_cols = 1 + 2*npairs; size_array_cols = 1 + 2*npairs;
@ -93,17 +96,13 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
if (nargpair == 0) { if (nargpair == 0) {
ilo[0] = 1; ihi[0] = ntypes; ilo[0] = 1; ihi[0] = ntypes;
jlo[0] = 1; jhi[0] = ntypes; jlo[0] = 1; jhi[0] = ntypes;
npairs = 1;
} else { } else {
npairs = 0;
iarg = 4; iarg = 4;
while (iarg < 4+nargpair) { for (int ipair = 0; ipair < npairs; ipair++) {
force->bounds(FLERR,arg[iarg],atom->ntypes,ilo[npairs],ihi[npairs]); force->bounds(FLERR,arg[iarg],atom->ntypes,ilo[ipair],ihi[ipair]);
force->bounds(FLERR,arg[iarg+1],atom->ntypes,jlo[npairs],jhi[npairs]); force->bounds(FLERR,arg[iarg+1],atom->ntypes,jlo[ipair],jhi[ipair]);
if (ilo[npairs] > ihi[npairs] || jlo[npairs] > jhi[npairs]) if (ilo[ipair] > ihi[ipair] || jlo[ipair] > jhi[ipair])
error->all(FLERR,"Illegal compute rdf command"); error->all(FLERR,"Illegal compute rdf command");
npairs++;
iarg += 2; iarg += 2;
} }
} }
@ -113,10 +112,13 @@ ComputeRDF::ComputeRDF(LAMMPS *lmp, int narg, char **arg) :
for (j = 1; j <= ntypes; j++) for (j = 1; j <= ntypes; j++)
nrdfpair[i][j] = 0; nrdfpair[i][j] = 0;
int ihisto;
for (int m = 0; m < npairs; m++) for (int m = 0; m < npairs; m++)
for (i = ilo[m]; i <= ihi[m]; i++) for (i = ilo[m]; i <= ihi[m]; i++)
for (j = jlo[m]; j <= jhi[m]; j++) for (j = jlo[m]; j <= jhi[m]; j++) {
rdfpair[nrdfpair[i][j]++][i][j] = m; ihisto = nrdfpair[i][j]++;
rdfpair[ihisto][i][j] = m;
}
memory->create(hist,npairs,nbin,"rdf:hist"); memory->create(hist,npairs,nbin,"rdf:hist");
memory->create(histall,npairs,nbin,"rdf:histall"); memory->create(histall,npairs,nbin,"rdf:histall");
@ -347,13 +349,15 @@ void ComputeRDF::compute_array()
ibin = static_cast<int> (r*delrinv); ibin = static_cast<int> (r*delrinv);
if (ibin >= nbin) continue; if (ibin >= nbin) continue;
if (ipair) for (ihisto = 0; ihisto < ipair; ihisto++) {
for (ihisto = 0; ihisto < ipair; ihisto++) m = rdfpair[ihisto][itype][jtype];
hist[rdfpair[ihisto][itype][jtype]][ibin] += 1.0; hist[m][ibin] += 1.0;
}
if (newton_pair || j < nlocal) { if (newton_pair || j < nlocal) {
if (jpair) for (ihisto = 0; ihisto < jpair; ihisto++) {
for (ihisto = 0; ihisto < jpair; ihisto++) m = rdfpair[ihisto][jtype][itype];
hist[rdfpair[ihisto][jtype][itype]][ibin] += 1.0; hist[m][ibin] += 1.0;
}
} }
} }
} }