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lammps
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multiple small tweaks to compute entropy/atom 

- improve error detection and messages
- avoid sigma/cutoff to be zero (and thus division by zero)
- move new/delete of temporary storage outside of loop
This commit is contained in:
Axel Kohlmeyer 2018-06-29 06:48:11 -04:00
parent a3a2981cd2
commit 75a3968039
1 changed files with 9 additions and 10 deletions
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19
src/USER-MISC/compute_entropy_atom.cpp
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@ -59,11 +59,11 @@ ComputeEntropyAtom(LAMMPS *lmp, int narg, char **arg) :
// the g(r)
sigma = force->numeric(FLERR,arg[3]);
if (sigma < 0.0) error->all(FLERR,"Illegal compute entropy/atom"
" command; negative sigma");
if (sigma <= 0.0) error->all(FLERR,"Illegal compute entropy/atom"
" command; sigma must be positive");
cutoff = force->numeric(FLERR,arg[4]);
if (cutoff < 0.0) error->all(FLERR,"Illegal compute entropy/atom"
" command; negative cutoff");
if (cutoff <= 0.0) error->all(FLERR,"Illegal compute entropy/atom"
" command; cutoff must be positive");
avg_flag = 0;
local_flag = 0;
@ -121,7 +121,7 @@ ComputeEntropyAtom::~ComputeEntropyAtom()
void ComputeEntropyAtom::init()
{
if (force->pair == NULL)
error->all(FLERR,"Compute centro/atom requires a pair style be"
error->all(FLERR,"Compute entropy/atom requires a pair style be"
" defined");
if ( (cutoff+cutoff2) > (force->pair->cutforce + neighbor->skin) )
@ -208,6 +208,8 @@ void ComputeEntropyAtom::compute_peratom()
double **x = atom->x;
int *mask = atom->mask;
double *gofr = new double[nbin];
double *integrand = new double[nbin];
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
@ -236,7 +238,6 @@ void ComputeEntropyAtom::compute_peratom()
// loop over list of all neighbors within force cutoff
// initialize gofr
double *gofr = new double[nbin];
for(int k=0;k<nbin;++k) gofr[k]=0.;
for (jj = 0; jj < jnum; jj++) {
@ -266,7 +267,6 @@ void ComputeEntropyAtom::compute_peratom()
}
// Calculate integrand
double *integrand = new double[nbin];
for(int k=0;k<nbin;++k){
if (gofr[k]<1.e-10) {
integrand[k] = rbinsq[k];
@ -274,7 +274,6 @@ void ComputeEntropyAtom::compute_peratom()
integrand[k] = (gofr[k]*log(gofr[k])-gofr[k]+1)*rbinsq[k];
}
}
delete [] gofr;
// Integrate with trapezoid rule
double value = 0.;
@ -284,12 +283,12 @@ void ComputeEntropyAtom::compute_peratom()
value += 0.5*integrand[0];
value += 0.5*integrand[nbin-1];
value *= deltar;
delete [] integrand;
pair_entropy[i] = -2*MY_PI*density*value;
}
}
delete [] gofr;
delete [] integrand;
if (avg_flag) {
for (ii = 0; ii < inum; ii++) {