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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4192 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2010-05-24 17:10:50 +00:00
parent c3afad7de4
commit edbfa5caab
4 changed files with 165 additions and 33 deletions
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79
src/fix_ave_histo.cpp
View File

@ -95,11 +95,14 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
options(narg,arg);
// parse values until one isn't recognized
// if mode = VECTOR and value is a global array:
// expand it as if columns listed one by one
// adjust nvalues accordingly via maxvalues
which = new int[narg-9];
argindex = new int[narg-9];
ids = new char*[narg-9];
value2index = new int[narg-9];
which = argindex = value2index = NULL;
ids = NULL;
int maxvalues = nvalues;
allocate_values(maxvalues);
nvalues = 0;
iarg = 9;
@ -158,12 +161,52 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else break;
if (mode == VECTOR && which[nvalues] == COMPUTE &&
argindex[nvalues] == 0) {
int icompute = modify->find_compute(ids[nvalues]);
if (icompute < 0)
error->all("Compute ID for fix ave/histo does not exist");
if (modify->compute[icompute]->array_flag) {
int ncols = modify->compute[icompute]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols-1;
}
iarg++;
} else if (mode == VECTOR && which[nvalues] == FIX &&
argindex[nvalues] == 0) {
int ifix = modify->find_fix(ids[nvalues]);
if (ifix < 0)
error->all("Fix ID for fix ave/histo does not exist");
if (modify->fix[ifix]->array_flag) {
int ncols = modify->fix[ifix]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols-1;
}
}
nvalues++;
iarg++;
} else break;
}
// setup and error check
@ -430,11 +473,11 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
FixAveHisto::~FixAveHisto()
{
delete [] which;
delete [] argindex;
memory->sfree(which);
memory->sfree(argindex);
memory->sfree(value2index);
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
delete [] value2index;
memory->sfree(ids);
if (fp && me == 0) fclose(fp);
@ -901,3 +944,17 @@ void FixAveHisto::options(int narg, char **arg)
} else error->all("Illegal fix ave/histo command");
}
}
/* ----------------------------------------------------------------------
reallocate vectors for each input value, of length N
------------------------------------------------------------------------- */
void FixAveHisto::allocate_values(int n)
{
which = (int *) memory->srealloc(which,n*sizeof(int),"ave/time:which");
argindex = (int *) memory->srealloc(argindex,n*sizeof(int),
"ave/time:argindex");
value2index = (int *) memory->srealloc(value2index,n*sizeof(int),
"ave/time:value2index");
ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/time:ids");
}

1
src/fix_ave_histo.h
View File

@ -64,6 +64,7 @@ class FixAveHisto : public Fix {
void bin_vector(int, double *, int);
void bin_atoms(double *, int);
void options(int, char **);
void allocate_values(int);
};
}

112
src/fix_ave_time.cpp
View File

@ -71,11 +71,14 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
options(narg,arg);
// parse values until one isn't recognized
// if mode = VECTOR and value is a global array:
// expand it as if columns listed one by one
// adjust nvalues accordingly via maxvalues
which = new int[nvalues];
argindex = new int[nvalues];
ids = new char*[nvalues];
value2index = new int[nvalues];
which = argindex = value2index = offcol = NULL;
ids = NULL;
int maxvalues = nvalues;
allocate_values(maxvalues);
nvalues = 0;
iarg = 6;
@ -102,12 +105,60 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
nvalues++;
delete [] suffix;
} else break;
if (mode == VECTOR && which[nvalues] == COMPUTE &&
argindex[nvalues] == 0) {
int icompute = modify->find_compute(ids[nvalues]);
if (icompute < 0)
error->all("Compute ID for fix ave/time does not exist");
if (modify->compute[icompute]->array_flag) {
int ncols = modify->compute[icompute]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols;
}
iarg++;
} else if (mode == VECTOR && which[nvalues] == FIX &&
argindex[nvalues] == 0) {
int ifix = modify->find_fix(ids[nvalues]);
if (ifix < 0)
error->all("Fix ID for fix ave/time does not exist");
if (modify->fix[ifix]->array_flag) {
int ncols = modify->fix[ifix]->size_array_cols;
maxvalues += ncols-1;
allocate_values(maxvalues);
argindex[nvalues] = 1;
for (int icol = 1; icol < ncols; icol++) {
which[nvalues+icol] = which[nvalues];
argindex[nvalues+icol] = icol+1;
n = strlen(ids[nvalues]) + 1;
ids[nvalues+icol] = new char[n];
strcpy(ids[nvalues+icol],ids[nvalues]);
}
nvalues += ncols;
}
} else nvalues++;
iarg++;
} else break;
}
// set off columns now that nvalues is finalized
for (int i = 0; i < nvalues; i++) offcol[i] = 0;
for (int i = 0; i < noff; i++) {
if (offlist[i] < 1 || offlist[i] > nvalues)
error->all("Invalid fix ave/time off column");
offcol[offlist[i]-1] = 1;
}
// setup and error check
@ -203,6 +254,8 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
} else column = NULL;
// print file comment lines
// for mode = VECTOR, cannot use arg to print
// since array args may have been expanded to multiple vectors
if (fp && me == 0) {
if (title1) fprintf(fp,"%s\n",title1);
@ -216,7 +269,12 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (title3 && mode == VECTOR) fprintf(fp,"%s\n",title3);
else if (mode == VECTOR) {
fprintf(fp,"# Row");
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[6+i]);
for (int i = 0; i < nvalues; i++) {
if (which[i] == COMPUTE) fprintf(fp," c_%s",ids[i]);
else if (which[i] == FIX) fprintf(fp," f_%s",ids[i]);
else if (which[i] == VARIABLE) fprintf(fp," v_%s",ids[i]);
if (argindex[i]) fprintf(fp,"[%d]",argindex[i]);
}
fprintf(fp,"\n");
}
}
@ -376,13 +434,13 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
FixAveTime::~FixAveTime()
{
delete [] offcol;
delete [] which;
delete [] argindex;
memory->sfree(which);
memory->sfree(argindex);
memory->sfree(value2index);
memory->sfree(offcol);
for (int i = 0; i < nvalues; i++) delete [] ids[i];
delete [] ids;
delete [] value2index;
memory->sfree(ids);
delete [] extlist;
if (fp && me == 0) fclose(fp);
@ -763,8 +821,8 @@ void FixAveTime::options(int narg, char **arg)
ave = ONE;
startstep = 0;
mode = SCALAR;
offcol = new int[nvalues];
for (int i = 0; i < nvalues; i++) offcol[i] = 0;
noff = 0;
offlist = NULL;
title1 = NULL;
title2 = NULL;
title3 = NULL;
@ -809,10 +867,9 @@ void FixAveTime::options(int narg, char **arg)
iarg += 2;
} else if (strcmp(arg[iarg],"off") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/time command");
int ncolumn = atoi(arg[iarg+1]);
if (ncolumn <= 0 || ncolumn > nvalues)
error->all("Invalid fix ave/time off column");
offcol[ncolumn-1] = 1;
offlist = (int *)
memory->srealloc(offlist,(noff+1)*sizeof(int),"ave/time:offlist");
offlist[noff++] = atoi(arg[iarg+1]);
iarg += 2;
} else if (strcmp(arg[iarg],"title1") == 0) {
if (iarg+2 > narg) error->all("Illegal fix ave/spatial command");
@ -838,3 +895,18 @@ void FixAveTime::options(int narg, char **arg)
} else error->all("Illegal fix ave/time command");
}
}
/* ----------------------------------------------------------------------
reallocate vectors for each input value, of length N
------------------------------------------------------------------------- */
void FixAveTime::allocate_values(int n)
{
which = (int *) memory->srealloc(which,n*sizeof(int),"ave/time:which");
argindex = (int *) memory->srealloc(argindex,n*sizeof(int),
"ave/time:argindex");
value2index = (int *) memory->srealloc(value2index,n*sizeof(int),
"ave/time:value2index");
offcol = (int *) memory->srealloc(offcol,n*sizeof(int),"ave/time:offcol");
ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/time:ids");
}

6
src/fix_ave_time.h
View File

@ -40,13 +40,14 @@ class FixAveTime : public Fix {
private:
int me,nvalues;
int nrepeat,nfreq,nvalid,irepeat;
int *which,*argindex,*value2index;
int *which,*argindex,*value2index,*offcol;
char **ids;
FILE *fp;
int nrows;
int ave,nwindow,nsum,startstep,mode;
int *offcol;
int noff;
int *offlist;
char *title1,*title2,*title3;
int norm,iwindow,window_limit;
@ -61,6 +62,7 @@ class FixAveTime : public Fix {
void invoke_scalar(int);
void invoke_vector(int);
void options(int, char **);
void allocate_values(int);
};
}