git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -21,10 +21,10 @@
|
||||
see J. Chem. Phys. 133, 154103 (2010)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "unistd.h"
|
||||
#include <math.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <unistd.h>
|
||||
#include "fix_ave_correlate_long.h"
|
||||
#include "update.h"
|
||||
#include "modify.h"
|
||||
@ -114,7 +114,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
|
||||
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"type") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal fix ave/correlate/long command");
|
||||
if (strcmp(arg[iarg+1],"auto") == 0) type = AUTO;
|
||||
else if (strcmp(arg[iarg+1],"upper") == 0) type = UPPER;
|
||||
@ -125,27 +125,27 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
|
||||
else error->all(FLERR,"Illegal fix ave/correlate/long command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"start") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal fix ave/correlate/long command");
|
||||
startstep = force->inumeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"ncorr") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal fix ave/correlate/long command");
|
||||
numcorrelators = force->inumeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"nlen") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal fix ave/correlate/long command");
|
||||
p = force->inumeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"ncount") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal fix ave/correlate/long command");
|
||||
m = force->inumeric(FLERR,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"file") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal fix ave/correlate/long command");
|
||||
if (me == 0) {
|
||||
fp = fopen(arg[iarg+1],"w");
|
||||
@ -160,7 +160,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
|
||||
overwrite = 1;
|
||||
iarg += 1;
|
||||
} else if (strcmp(arg[iarg],"title1") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal fix ave/correlate/long command");
|
||||
delete [] title1;
|
||||
int n = strlen(arg[iarg+1]) + 1;
|
||||
@ -168,7 +168,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
|
||||
strcpy(title1,arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"title2") == 0) {
|
||||
if (iarg+2 > narg)
|
||||
if (iarg+2 > narg)
|
||||
error->all(FLERR,"Illegal fix ave/correlate/long command");
|
||||
delete [] title2;
|
||||
int n = strlen(arg[iarg+1]) + 1;
|
||||
@ -309,7 +309,7 @@ FixAveCorrelateLong::FixAveCorrelateLong(LAMMPS * lmp, int narg, char **arg):
|
||||
}
|
||||
|
||||
for (int i=0;i<length;i++) t[i]=0.0;
|
||||
for (int i=0;i<npair;i++)
|
||||
for (int i=0;i<npair;i++)
|
||||
for (int j=0;j<length;j++) f[i][j]=0.0;
|
||||
|
||||
|
||||
@ -336,11 +336,11 @@ FixAveCorrelateLong::~FixAveCorrelateLong()
|
||||
memory->destroy(values);
|
||||
memory->destroy(shift);
|
||||
memory->destroy(shift2);
|
||||
memory->destroy(correlation);
|
||||
memory->destroy(accumulator);
|
||||
memory->destroy(accumulator2);
|
||||
memory->destroy(ncorrelation);
|
||||
memory->destroy(naccumulator);
|
||||
memory->destroy(correlation);
|
||||
memory->destroy(accumulator);
|
||||
memory->destroy(accumulator2);
|
||||
memory->destroy(ncorrelation);
|
||||
memory->destroy(naccumulator);
|
||||
memory->destroy(insertindex);
|
||||
memory->destroy(t);
|
||||
memory->destroy(f);
|
||||
@ -412,7 +412,7 @@ void FixAveCorrelateLong::end_of_step()
|
||||
// error check if timestep was reset in an invalid manner
|
||||
|
||||
bigint ntimestep = update->ntimestep;
|
||||
if (ntimestep < nvalid_last || ntimestep > nvalid)
|
||||
if (ntimestep < nvalid_last || ntimestep > nvalid)
|
||||
error->all(FLERR,"Invalid timestep reset for fix ave/correlate/long");
|
||||
if (ntimestep != nvalid) return;
|
||||
nvalid_last = nvalid;
|
||||
@ -622,7 +622,7 @@ 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,
|
||||
void FixAveCorrelateLong::add(const int i, const double wA, const double wB,
|
||||
const unsigned int k) {
|
||||
if (k == numcorrelators) return;
|
||||
if (k > kmax) kmax=k;
|
||||
@ -687,7 +687,7 @@ bigint FixAveCorrelateLong::nextvalid()
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory_usage
|
||||
memory_usage
|
||||
------------------------------------------------------------------------- */
|
||||
double FixAveCorrelateLong::memory_usage() {
|
||||
// shift: npair x numcorrelators x p
|
||||
@ -698,11 +698,11 @@ double FixAveCorrelateLong::memory_usage() {
|
||||
// ncorrelation: numcorrelators x p
|
||||
// naccumulator: numcorrelators
|
||||
// insertindex: numcorrelators
|
||||
// t: 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)
|
||||
+ numcorrelators*p*sizeof(unsigned long int)
|
||||
+ 2*numcorrelators*sizeof(unsigned int);
|
||||
return bytes;
|
||||
}
|
||||
@ -720,7 +720,7 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
|
||||
memory->create(list,nsize,"correlator:list");
|
||||
list[n++]=npair;
|
||||
list[n++]=numcorrelators;
|
||||
list[n++]=p;
|
||||
list[n++]=p;
|
||||
list[n++]=m;
|
||||
list[n++]=nvalid;
|
||||
list[n++]=nvalid_last;
|
||||
@ -740,7 +740,7 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
|
||||
list[n++]=insertindex[i];
|
||||
}
|
||||
|
||||
int size = n*sizeof(double);
|
||||
int size = n*sizeof(double);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
fwrite(list,sizeof(double),n,fp);
|
||||
memory->destroy(list);
|
||||
@ -754,17 +754,17 @@ void FixAveCorrelateLong::write_restart(FILE *fp) {
|
||||
void FixAveCorrelateLong::restart(char *buf)
|
||||
{
|
||||
int n = 0;
|
||||
double *list = (double *) buf;
|
||||
double *list = (double *) buf;
|
||||
int npairin = static_cast<int> (list[n++]);
|
||||
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++]);
|
||||
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++]);
|
||||
|
||||
if ((npairin!=npair) || (numcorrelatorsin!=numcorrelators)
|
||||
|| (pin!=p) || (min!=m))
|
||||
error->all(FLERR,"Fix ave/correlate/long: restart and input data are different");
|
||||
error->all(FLERR,"Fix ave/correlate/long: restart and input data are different");
|
||||
|
||||
for (int i=0;i<npair;i++)
|
||||
for (int j=0;j<numcorrelators;j++) {
|
||||
@ -777,7 +777,7 @@ void FixAveCorrelateLong::restart(char *buf)
|
||||
accumulator2[i][j] = list[n++];
|
||||
}
|
||||
for (int i=0;i<numcorrelators;i++) {
|
||||
for (int j=0;j<p;j++)
|
||||
for (int j=0;j<p;j++)
|
||||
ncorrelation[i][j] = static_cast<unsigned long int>(list[n++]);
|
||||
naccumulator[i] = static_cast<unsigned int> (list[n++]);
|
||||
insertindex[i] = static_cast<unsigned int> (list[n++]);
|
||||
|
||||
Reference in New Issue
Block a user