ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15414 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2016-08-01 20:35:57 +00:00
parent 6ff87be849
commit ce5f174281
9 changed files with 347 additions and 200 deletions
Download Patch File Download Diff File Expand all files Collapse all files

130
src/fix_ave_time.cpp
View File

@ -73,89 +73,46 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (nvalues == 0) error->all(FLERR,"No values in fix ave/time command");
options(narg,arg);
options(iarg,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
// expand args if any have wildcard character "*"
// this can reset nvalues
int expand = 0;
char **earg,**arghold;
nvalues = input->expand_args(nvalues,&arg[6],mode,earg);
if (earg != &arg[6]) expand = 1;
arghold = arg;
arg = earg;
// parse values
which = argindex = value2index = offcol = varlen = NULL;
ids = NULL;
int maxvalues = nvalues;
allocate_values(maxvalues);
nvalues = 0;
allocate_values(nvalues);
iarg = 6;
while (iarg < narg) {
if (strncmp(arg[iarg],"c_",2) == 0 ||
strncmp(arg[iarg],"f_",2) == 0 ||
strncmp(arg[iarg],"v_",2) == 0) {
if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE;
else if (arg[iarg][0] == 'f') which[nvalues] = FIX;
else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE;
for (int i = 0; i < nvalues; i++) {
if (arg[i][0] == 'c') which[i] = COMPUTE;
else if (arg[i][0] == 'f') which[i] = FIX;
else if (arg[i][0] == 'v') which[i] = VARIABLE;
int n = strlen(arg[iarg]);
char *suffix = new char[n];
strcpy(suffix,&arg[iarg][2]);
int n = strlen(arg[i]);
char *suffix = new char[n];
strcpy(suffix,&arg[i][2]);
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal fix ave/time command");
argindex[nvalues] = atoi(ptr+1);
*ptr = '\0';
} else argindex[nvalues] = 0;
n = strlen(suffix) + 1;
ids[nvalues] = new char[n];
strcpy(ids[nvalues],suffix);
delete [] suffix;
if (mode == VECTOR && which[nvalues] == COMPUTE &&
argindex[nvalues] == 0) {
int icompute = modify->find_compute(ids[nvalues]);
if (icompute < 0)
error->all(FLERR,"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-1;
}
} else if (mode == VECTOR && which[nvalues] == FIX &&
argindex[nvalues] == 0) {
int ifix = modify->find_fix(ids[nvalues]);
if (ifix < 0)
error->all(FLERR,"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-1;
}
}
nvalues++;
iarg++;
} else break;
char *ptr = strchr(suffix,'[');
if (ptr) {
if (suffix[strlen(suffix)-1] != ']')
error->all(FLERR,"Illegal fix ave/time command");
argindex[i] = atoi(ptr+1);
*ptr = '\0';
} else argindex[i] = 0;
n = strlen(suffix) + 1;
ids[i] = new char[n];
strcpy(ids[i],suffix);
delete [] suffix;
}
// set off columns now that nvalues is finalized
@ -311,18 +268,13 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
if (title2) fprintf(fp,"%s\n",title2);
else if (mode == SCALAR) {
fprintf(fp,"# TimeStep");
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",arg[6+i]);
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",earg[i]);
fprintf(fp,"\n");
} else fprintf(fp,"# TimeStep Number-of-rows\n");
if (title3 && mode == VECTOR) fprintf(fp,"%s\n",title3);
else if (mode == VECTOR) {
fprintf(fp,"# Row");
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]);
}
for (int i = 0; i < nvalues; i++) fprintf(fp," %s",earg[i]);
fprintf(fp,"\n");
}
if (ferror(fp))
@ -335,6 +287,15 @@ FixAveTime::FixAveTime(LAMMPS *lmp, int narg, char **arg) :
delete [] title2;
delete [] title3;
// if wildcard expansion occurred, free earg memory from expand_args()
// wait to do this after file comment lines are printed
if (expand) {
for (int i = 0; i < nvalues; i++) delete [] earg[i];
memory->sfree(earg);
arg = arghold;
}
// allocate memory for averaging
vector = vector_total = NULL;
@ -1049,7 +1010,7 @@ double FixAveTime::compute_array(int i, int j)
parse optional args
------------------------------------------------------------------------- */
void FixAveTime::options(int narg, char **arg)
void FixAveTime::options(int iarg, int narg, char **arg)
{
// option defaults
@ -1068,7 +1029,6 @@ void FixAveTime::options(int narg, char **arg)
// optional args
int iarg = 6 + nvalues;
while (iarg < narg) {
if (strcmp(arg[iarg],"file") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/time command");