Merge pull request #872 from akohlmey/ave-correlate-long-bugfix (c5127eca) · Commits · 郑智淋 / lammps

src/USER-MISC/fix_ave_correlate_long.cpp

+30 −15

Original line number	Diff line number	Diff line
		@@ -31,6 +31,7 @@
		#include "compute.h"
		#include "input.h"
		#include "variable.h"
		#include "citeme.h"
		#include "memory.h"
		#include "error.h"
		#include "force.h"
		@@ -45,11 +46,24 @@ enum{AUTO,UPPER,LOWER,AUTOUPPER,AUTOLOWER,FULL};
		#define INVOKED_VECTOR 2
		#define INVOKED_ARRAY 4

		static const char cite_fix_ave_correlate_long[] =
		"fix ave/correlate/long command:\n\n"
		"@Article{Ramirez10,\n"
		" author = {Jorge Rami{\'}rez and Sathish K. Sukumaran and Bart Vorselaars and Alexei E. Likhtman},\n"
		" title = {Efficient on the fly calculation of time correlation functions in computer simulations},"
		" journal = {J.~Chem.~Phys.},\n"
		" year = 2010,\n"
		" volume = 133,\n"
		" pages = {154103}\n"
		"}\n\n";

		/* ---------------------------------------------------------------------- */

		FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
		Fix (lmp, narg, arg)
		{
		if (lmp->citeme) lmp->citeme->add(cite_fix_ave_correlate_long);

		// At least nevery nfrez and one value are needed
		if (narg < 6) error->all(FLERR,"Illegal fix ave/correlate/long command");

		@@ -321,6 +335,8 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
		nvalid_last = -1;
		nvalid = nextvalid();
		modify->addstep_compute_all(nvalid);
		last_accumulated_step = -1;

		}

		/* ---------------------------------------------------------------------- */
		@@ -479,7 +495,7 @@ void FixAveCorrelateLong::end_of_step()
		fprintf(fp,"# Timestep: " BIGINT_FORMAT "\n", ntimestep);
		for (unsigned int i=0;i<npcorr;++i) {
		fprintf(fp, "%lg ", t[i]*update->dt);
		for (unsigned int j=0;j<npair;++j) {
		for (int j=0;j<npair;++j) {
		fprintf(fp, "%lg ", f[j][i]);
		}
		fprintf(fp, "\n");
		@@ -499,7 +515,7 @@ void FixAveCorrelateLong::evaluate() {
		unsigned int jm=0;

		// First correlator
		for (unsigned int j=0;j<p;++j) {
		for (int j=0;j<p;++j) {
		if (ncorrelation[0][j] > 0) {
		t[jm] = j;
		for (int i=0;i<npair;++i)
		@@ -532,7 +548,7 @@ void FixAveCorrelateLong::accumulate()
		{
		int i,j,ipair;

		//printf("DEBUG %i %i\n", nvalues, npair);
		if (update->ntimestep <= last_accumulated_step) return;

		if (type == AUTO) {
		for (i=0; i<nvalues;i++) add(i,values[i]);
		@@ -566,13 +582,14 @@ void FixAveCorrelateLong::accumulate()
		else add(ipair++,values[i],values[j]);
		}
		}
		last_accumulated_step = update->ntimestep;
		}


		/* ----------------------------------------------------------------------
		Add a scalar value to the autocorrelator k of pair i
		------------------------------------------------------------------------- */
		void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k){
		void FixAveCorrelateLong::add(const int i, const double w, const int k){
		// If we exceed the correlator side, the value is discarded
		if (k == numcorrelators) return;
		if (k > kmax) kmax=k;
		@@ -593,7 +610,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k)
		unsigned int ind1=insertindex[k];
		if (k==0) { // First correlator is different
		int ind2=ind1;
		for (unsigned int j=0;j<p;++j) {
		for (int j=0;j<p;++j) {
		if (shift[i][k][ind2] > -1e10) {
		correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
		if (i==0) ++ncorrelation[k][j];
		@@ -603,7 +620,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k)
		}
		} else {
		int ind2=ind1-dmin;
		for (unsigned int j=dmin;j<p;++j) {
		for (int j=dmin;j<p;++j) {
		if (ind2<0) ind2+=p;
		if (shift[i][k][ind2] > -1e10) {
		correlation[i][k][j]+= shift[i][k][ind1]*shift[i][k][ind2];
		@@ -624,7 +641,7 @@ void FixAveCorrelateLong::add(const int i, const double w, const unsigned int k)
		Add 2 scalar values to the cross-correlator k of pair i
		------------------------------------------------------------------------- */
		void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
		const unsigned int k) {
		const int k) {
		if (k == numcorrelators) return;
		if (k > kmax) kmax=k;

		@@ -644,7 +661,7 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
		unsigned int ind1=insertindex[k];
		if (k==0) {
		int ind2=ind1;
		for (unsigned int j=0;j<p;++j) {
		for (int j=0;j<p;++j) {
		if (shift[i][k][ind2] > -1e10) {
		correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
		if (i==0) ++ncorrelation[k][j];
		@@ -655,7 +672,7 @@ void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
		}
		else {
		int ind2=ind1-dmin;
		for (unsigned int j=dmin;j<p;++j) {
		for (int j=dmin;j<p;++j) {
		if (ind2<0) ind2+=p;
		if (shift[i][k][ind2] > -1e10) {
		correlation[i][k][j]+= shift[i][k][ind1]*shift2[i][k][ind2];
		@@ -723,8 +740,7 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
		list[n++]=numcorrelators;
		list[n++]=p;
		list[n++]=m;
		list[n++]=nvalid;
		list[n++]=nvalid_last;
		list[n++] = last_accumulated_step;
		for (int i=0;i<npair;i++)
		for (int j=0;j<numcorrelators;j++) {
		for (int k=0;k<p;k++) {
		@@ -760,8 +776,7 @@ void FixAveCorrelateLong::restart(char *buf)
		int numcorrelatorsin = static_cast<int> (list[n++]);
		int pin = static_cast<int> (list[n++]);
		int min = static_cast<int> (list[n++]);
		nvalid = static_cast<int> (list[n++]);
		nvalid_last = static_cast<int> (list[n++]);
		last_accumulated_step = static_cast<int> (list[n++]);

		if ((npairin!=npair) \|\| (numcorrelatorsin!=numcorrelators)
		\|\| (pin!=p) \|\| (min!=m))

src/USER-MISC/fix_ave_correlate_long.h

+7 −7

Original line number	Diff line number	Diff line
		@@ -51,17 +51,17 @@ class FixAveCorrelateLong : public Fix {
		unsigned int *naccumulator;
		unsigned int *insertindex;

		unsigned int numcorrelators; // Recommended 20
		unsigned int p; // Points per correlator (recommended 16)
		int numcorrelators; // Recommended 20
		int p; // Points per correlator (recommended 16)
		unsigned int m; // Num points for average (recommended 2; p mod m = 0)
		unsigned int dmin; // Min distance between ponts for correlators k>0; dmin=p/m

		unsigned int length; // Length of result arrays
		unsigned int kmax; // Maximum correlator attained during simulation
		int length; // Length of result arrays
		int kmax; // Maximum correlator attained during simulation

		int me,nvalues;
		int nfreq;
		bigint nvalid,nvalid_last;
		bigint nvalid,nvalid_last,last_accumulated_step;
		int which,argindex,*value2index;
		char **ids;
		FILE *fp;
		@@ -76,8 +76,8 @@ class FixAveCorrelateLong : public Fix {
		void evaluate();
		bigint nextvalid();

		void add(const int i, const double w, const unsigned int k = 0);
		void add(const int i, const double wA, const double wB, const unsigned int k = 0);
		void add(const int i, const double w, const int k = 0);
		void add(const int i, const double wA, const double wB, const int k = 0);

		};

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