diff --git a/src/USER-MISC/compute_pentropy_atom.cpp b/src/USER-MISC/compute_pentropy_atom.cpp index ccdeb6d31e48a32964c82a7bd8b3abb5a4ce80da..271648e3c53ed37594169e3916cdfc4f72277d3b 100644 --- a/src/USER-MISC/compute_pentropy_atom.cpp +++ b/src/USER-MISC/compute_pentropy_atom.cpp @@ -50,10 +50,10 @@ ComputePairEntropyAtom(LAMMPS *lmp, int narg, char **arg) : " of arguments"); // Arguments are: sigma cutoff avg yes/no cutoff2 local yes/no - // sigma is the gaussian width - // cutoff is the cutoff for the calculation of g(r) + // sigma is the gaussian width + // cutoff is the cutoff for the calculation of g(r) // avg is optional and allows averaging the pair entropy over neighbors - // the next argument should be yes or no + // the next argument should be yes or no // cutoff2 is the cutoff for the averaging // local is optional and allows using the local density to normalize // the g(r) @@ -102,8 +102,8 @@ ComputePairEntropyAtom(LAMMPS *lmp, int narg, char **arg) : // Number of bins above and below the central one that will be // considered as affected by the gaussian kernel // 2 seems a good compromise between speed and good mollification - deltabin = 2; - deltar = sigma; + deltabin = 2; + deltar = sigma; peratom_flag = 1; size_peratom_cols = 0; } @@ -124,9 +124,9 @@ void ComputePairEntropyAtom::init() error->all(FLERR,"Compute centro/atom requires a pair style be" " defined"); - if ( (cutoff+cutoff2) > (force->pair->cutforce + neighbor->skin) ) + if ( (cutoff+cutoff2) > (force->pair->cutforce + neighbor->skin) ) { - error->all(FLERR,"Compute pentropy/atom cutoff is longer than the" + error->all(FLERR,"Compute pentropy/atom cutoff is longer than the" " pairwise cutoff. Increase the neighbor list skin" " distance."); } @@ -220,16 +220,16 @@ void ComputePairEntropyAtom::compute_peratom() // If local density is used, calculate it if (local_flag) { double neigh_cutoff = force->pair->cutforce + neighbor->skin; - double volume = + double volume = (4./3.)*MY_PI*neigh_cutoff*neigh_cutoff*neigh_cutoff; density = jnum / volume; } // calculate kernel normalization // Normalization of g(r) - double normConstantBase = 4*MY_PI*density; + double normConstantBase = 4*MY_PI*density; // Normalization of gaussian - normConstantBase *= sqrt(2.*MY_PI)*sigma; + normConstantBase *= sqrt(2.*MY_PI)*sigma; double invNormConstantBase = 1./normConstantBase; // loop over list of all neighbors within force cutoff @@ -259,7 +259,7 @@ void ComputePairEntropyAtom::compute_peratom() for(int k=minbin;k<maxbin+1;k++) { double invNormKernel=invNormConstantBase/rbinsq[k]; double distance = r - rbin[k]; - gofr[k] += invNormKernel*exp(-distance*distance/sigmasq2); + gofr[k] += invNormKernel*exp(-distance*distance/sigmasq2); } } } @@ -298,7 +298,7 @@ void ComputePairEntropyAtom::compute_peratom() ztmp = x[i][2]; jlist = firstneigh[i]; jnum = numneigh[i]; - + pair_entropy_avg[i] = pair_entropy[i]; double counter = 1; @@ -306,7 +306,7 @@ void ComputePairEntropyAtom::compute_peratom() for (jj = 0; jj < jnum; jj++) { j = jlist[jj]; j &= NEIGHMASK; - + delx = xtmp - x[j][0]; dely = ytmp - x[j][1]; delz = ztmp - x[j][2];