From a087813d01f0bb8673509008c59a4f7e97609bb5 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 18 Apr 2018 07:26:13 -0400
Subject: [PATCH] incorporate bugfix for fix ave/correlate/long from jorge
ramirez
---
src/USER-MISC/fix_ave_correlate_long.cpp | 45 ++++++++++++++++--------
src/USER-MISC/fix_ave_correlate_long.h | 14 ++++----
2 files changed, 37 insertions(+), 22 deletions(-)
diff --git a/src/USER-MISC/fix_ave_correlate_long.cpp b/src/USER-MISC/fix_ave_correlate_long.cpp
index f8d2e80352..e40447d859 100644
--- a/src/USER-MISC/fix_ave_correlate_long.cpp
+++ b/src/USER-MISC/fix_ave_correlate_long.cpp
@@ -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];
@@ -699,8 +716,8 @@ double FixAveCorrelateLong::memory_usage() {
// ncorrelation: numcorrelators x p
// naccumulator: numcorrelators
// insertindex: numcorrelators
- // t: numcorrelators x p
- // f: npair x numcorrelators x p
+ // t: numcorrelators x p
+ // f: npair x numcorrelators x p
double bytes = (4*npair*numcorrelators*p + 2*npair*numcorrelators
+ numcorrelators*p)*sizeof(double)
+ numcorrelators*p*sizeof(unsigned long int)
@@ -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))
diff --git a/src/USER-MISC/fix_ave_correlate_long.h b/src/USER-MISC/fix_ave_correlate_long.h
index d5354ebf5e..2823a5beb3 100644
--- a/src/USER-MISC/fix_ave_correlate_long.h
+++ b/src/USER-MISC/fix_ave_correlate_long.h
@@ -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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