pair_entropy_atom workin - avg missing (4e6188cf) · Commits · 郑智淋 / lammps

src/compute_pair_entropy_atom.cpp

+49 −29

Original line number	Diff line number	Diff line
		@@ -40,9 +40,9 @@ using namespace MathConst;

		ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS lmp, int narg, char *arg) :
		Compute(lmp, narg, arg),
		gofr(NULL), pair_entropy(NULL)
		list(NULL), pair_entropy(NULL)
		{
		if (narg < 5 \|\| narg > 7)
		if (narg < 5 \|\| narg > 5)
		error->all(FLERR,"Illegal compute pentropy/atom command");

		sigma = force->numeric(FLERR,arg[3]);
		@@ -52,7 +52,6 @@ ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS lmp, int narg, char *arg
		avg_flag = 0;

		// optional keywords

		int iarg = 5;
		while (iarg < narg) {
		if (strcmp(arg[iarg],"avg") == 0) {
		@@ -60,12 +59,12 @@ ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS lmp, int narg, char *arg
		error->all(FLERR,"Illegal compute pentropy/atom missing arguments after avg");
		if (strcmp(arg[iarg+1],"yes") == 0) avg_flag = 1;
		else if (strcmp(arg[iarg+1],"no") == 0) avg_flag = 0;
		else error->all(FLERR,"Illegal compute centro/atom argument after avg should be yes or no");
		else error->all(FLERR,"Illegal compute pentropy/atom argument after avg should be yes or no");
		cutoff2 = force->numeric(FLERR,arg[iarg+2]);
		if (cutoff2 < 0.0) error->all(FLERR,"Illegal compute pentropy/atom command; negative cutoff2");
		cutsq2 = cutoff2*cutoff2;
		iarg += 2;
		} else error->all(FLERR,"Illegal compute centro/atom argument after sigma and cutoff should be avg");
		} else error->all(FLERR,"Illegal compute pentropy/atom argument after sigma and cutoff should be avg");
		}

		peratom_flag = 1;
		@@ -74,14 +73,8 @@ ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS lmp, int narg, char *arg
		nbin = static_cast<int>(cutoff / sigma) + 1;
		nmax = 0;
		maxneigh = 0;
		deltabin = 2;
		deltabin = 1;
		deltar = sigma;
		rbin = new double(nbin);
		rbinsq = new double(nbin);
		for (int i = 0; i < nbin; i++) {
		rbin[i] = i*deltar;
		rbinsq[i] = rbin[i]*rbin[i];
		}
		}

		/* ---------------------------------------------------------------------- */
		@@ -89,7 +82,6 @@ ComputePairEntropyAtom::ComputePairEntropyAtom(LAMMPS lmp, int narg, char *arg
		ComputePairEntropyAtom::~ComputePairEntropyAtom()
		{
		memory->destroy(pair_entropy);
		memory->destroy(gofr);
		}

		/* ---------------------------------------------------------------------- */
		@@ -141,9 +133,16 @@ void ComputePairEntropyAtom::compute_peratom()
		int i,j,k,ii,jj,kk,n,inum,jnum;
		double xtmp,ytmp,ztmp,delx,dely,delz,rsq,value;
		int ilist,jlist,numneigh,*firstneigh;
		double rbin[nbin], rbinsq[nbin];

		invoked_peratom = update->ntimestep;

		// Initialize distance vectors
		for (int i = 0; i < nbin; i++) {
		rbin[i] = i*deltar;
		rbinsq[i] = rbin[i]*rbin[i];
		}

		// grow pair_entropy array if necessary

		if (atom->nmax > nmax) {
		@@ -162,6 +161,11 @@ void ComputePairEntropyAtom::compute_peratom()
		numneigh = list->numneigh;
		firstneigh = list->firstneigh;

		// Compute some constants
		double nlist_cutoff = force->pair->cutforce;
		double sigmasq2=2sigmasigma;
		double volume = (4./3.)MY_PInlist_cutoffnlist_cutoffnlist_cutoff;

		// compute pair entropy for each atom in group
		// use full neighbor list

		@@ -179,18 +183,16 @@ void ComputePairEntropyAtom::compute_peratom()


		// calculate kernel normalization
		double nlist_cutoff = force->pair->cutforce;
		double density = jnum/((4./3.)MY_PIcutoffnlist_cutoffnlist_cutoff*nlist_cutoff);
		double density = jnum/volume;
		double normConstantBase = 2MY_PIdensity; // Normalization of g(r)
		normConstantBase = sqrt(2.MY_PI)*sigma; // Normalization of gaussian
		double invNormConstantBase = 1./normConstantBase;
		double sigmasq2=2sigmasigma;

		// loop over list of all neighbors within force cutoff

		// re-initialize gofr
		delete [] gofr;
		gofr = new double(nbin);
		// initialize gofr
		double gofr[nbin];
		for(int k=0;k<nbin;++k) gofr[k]=0.;

		for (jj = 0; jj < jnum; jj++) {
		j = jlist[jj];
		@@ -219,20 +221,38 @@ void ComputePairEntropyAtom::compute_peratom()
		}
		}

		//value = 0.0;
		//for (j = 0; j < nhalf; j++) value += pairs[j];
		pair_entropy[i] = gofr[0];

		/*
		if (ii==500) {
		for(int k=0;k<nbin;++k) {
		fprintf(screen,"%f %f \n",rbin[k], gofr[k]);
		}
		}
		*/

		// Calculate integrand
		double integrand[nbin];
		for(int k=0;k<nbin;++k){
		if (gofr[k]<1.e-10) {
		integrand[k] = rbinsq[k];
		} else {
		integrand[k] = (gofr[k]log(gofr[k])-gofr[k]+1)rbinsq[k];
		}
		}

		//delete [] pairs;
		// Integrate with trapezoid rule
		double value = 0.;
		for(int k=1;k<nbin-1;++k){
		value += integrand[k];
		}
		value += 0.5*integrand[0];
		value += 0.5*integrand[nbin-1];
		value *= deltar;

		for (ii = 0; ii < inum; ii++) {
		i = ilist[ii];
		if (mask[i] & groupbit)
		array_atom[i][0] = pair_entropy[i];
		pair_entropy[i] = -2MY_PIdensity*value;

		}
		}

		}

src/compute_pair_entropy_atom.h

+0 −2

Original line number	Diff line number	Diff line
		@@ -39,8 +39,6 @@ class ComputePairEntropyAtom : public Compute {
		double *pair_entropy;
		double sigma, cutoff, cutoff2;
		double cutsq, cutsq2;
		double rbin, rbinsq;
		double *gofr;
		double deltar;
		int deltabin;
		double invNormConstantBase;

Admin message