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@13983 f3b2605a-c512-4ea7-a41b-209d697bcdaa

Browse Source
This commit is contained in:
sjplimp
2015-09-02 20:39:55 +00:00
parent 3f79c91279
commit 047be536bc
35 changed files with 236 additions and 104 deletions
Download Patch File Download Diff File Expand all files Collapse all files

72
src/variable.cpp
View File

@ -262,8 +262,11 @@ void Variable::set(int narg, char **arg)
if (universe->me == 0) {
FILE *fp = fopen("tmp.lammps.variable","w");
if (fp == NULL)
error->one(FLERR,"Cannot open temporary file for world counter.");
fprintf(fp,"%d\n",universe->nworlds);
fclose(fp);
fp = NULL;
}
for (int jvar = 0; jvar < nvar; jvar++)
@ -518,7 +521,7 @@ int Variable::next(int narg, char **arg)
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
if (ivar == -1) error->all(FLERR,"Invalid variable in next command");
if (ivar < 0) error->all(FLERR,"Invalid variable in next command");
if (style[ivar] == ULOOP && style[find(arg[0])] == UNIVERSE) continue;
else if (style[ivar] == UNIVERSE && style[find(arg[0])] == ULOOP) continue;
else if (style[ivar] != style[find(arg[0])])
@ -614,6 +617,7 @@ int Variable::next(int narg, char **arg)
fprintf(fp,"%d\n",nextindex+1);
//printf("WRITE %d %d\n",universe->me,nextindex+1);
fclose(fp);
fp = NULL;
rename("tmp.lammps.variable.lock","tmp.lammps.variable");
if (universe->uscreen)
fprintf(universe->uscreen,
@ -716,7 +720,7 @@ int Variable::atomstyle(int ivar)
char *Variable::pythonstyle(char *name, char *funcname)
{
int ivar = find(name);
if (ivar == -1) return NULL;
if (ivar < 0) return NULL;
if (style[ivar] != PYTHON) return NULL;
if (strcmp(data[ivar][0],funcname) != 0) return NULL;
return data[ivar][1];
@ -739,7 +743,7 @@ char *Variable::pythonstyle(char *name, char *funcname)
char *Variable::retrieve(char *name)
{
int ivar = find(name);
if (ivar == -1) return NULL;
if (ivar < 0) return NULL;
if (which[ivar] >= num[ivar]) return NULL;
if (eval_in_progress[ivar])
@ -857,6 +861,11 @@ void Variable::compute_atom(int ivar, int igroup,
collapse_tree(tree);
} else vstore = reader[ivar]->fixstore->vstore;
if (result == NULL) {
eval_in_progress[ivar] = 0;
return;
}
int groupbit = group->bitmask[igroup];
int *mask = atom->mask;
int nlocal = atom->nlocal;
@ -1139,15 +1148,10 @@ double Variable::evaluate(char *str, Tree **tree)
error->all(FLERR,
"Variable evaluation before simulation box is defined");
n = strlen(word) - 2 + 1;
char *id = new char[n];
strcpy(id,&word[2]);
int icompute = modify->find_compute(id);
int icompute = modify->find_compute(word+2);
if (icompute < 0)
error->all(FLERR,"Invalid compute ID in variable formula");
Compute *compute = modify->compute[icompute];
delete [] id;
// parse zero or one or two trailing brackets
// point i beyond last bracket
@ -1366,14 +1370,9 @@ double Variable::evaluate(char *str, Tree **tree)
error->all(FLERR,
"Variable evaluation before simulation box is defined");
n = strlen(word) - 2 + 1;
char *id = new char[n];
strcpy(id,&word[2]);
int ifix = modify->find_fix(id);
int ifix = modify->find_fix(word+2);
if (ifix < 0) error->all(FLERR,"Invalid fix ID in variable formula");
Fix *fix = modify->fix[ifix];
delete [] id;
// parse zero or one or two trailing brackets
// point i beyond last bracket
@ -1545,11 +1544,8 @@ double Variable::evaluate(char *str, Tree **tree)
// ----------------
} else if (strncmp(word,"v_",2) == 0) {
n = strlen(word) - 2 + 1;
char *id = new char[n];
strcpy(id,&word[2]);
int ivar = find(id);
int ivar = find(word+2);
if (ivar < 0)
error->all(FLERR,"Invalid variable name in variable formula");
if (eval_in_progress[ivar])
@ -1574,7 +1570,7 @@ double Variable::evaluate(char *str, Tree **tree)
if (nbracket == 0 && style[ivar] != ATOM && style[ivar] != ATOMFILE) {
char *var = retrieve(id);
char *var = retrieve(word+2);
if (var == NULL)
error->all(FLERR,"Invalid variable evaluation in variable formula");
if (tree) {
@ -1636,8 +1632,6 @@ double Variable::evaluate(char *str, Tree **tree)
} else error->all(FLERR,"Mismatched variable in variable formula");
delete [] id;
// ----------------
// math/group/special function or atom value/vector or
// constant or thermo keyword
@ -3745,7 +3739,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
error->all(FLERR,"Invalid special function in variable formula");
int ivar = find(args[0]);
if (ivar == -1)
if (ivar < 0)
error->all(FLERR,"Variable ID in variable formula does not exist");
// SCALARFILE has single current value, read next one
@ -3981,23 +3975,25 @@ void Variable::atom_vector(char *word, Tree **tree,
/* ----------------------------------------------------------------------
check if word matches a constant
return 1 if yes, else 0
customize by adding a constant: PI
customize by adding a constant: PI, version
------------------------------------------------------------------------- */
int Variable::is_constant(char *word)
{
if (strcmp(word,"PI") == 0) return 1;
if (strcmp(word,"version") == 0) return 1;
return 0;
}
/* ----------------------------------------------------------------------
process a constant in formula
customize by adding a constant: PI
customize by adding a constant: PI, version
------------------------------------------------------------------------- */
double Variable::constant(char *word)
{
if (strcmp(word,"PI") == 0) return MY_PI;
if (strcmp(word,"version") == 0) return atof(universe->num_ver);
return 0.0;
}
@ -4344,17 +4340,11 @@ unsigned int Variable::data_mask(char *str)
error->all(FLERR,
"Variable evaluation before simulation box is defined");
n = strlen(word) - 2 + 1;
char *id = new char[n];
strcpy(id,&word[2]);
int icompute = modify->find_compute(id);
int icompute = modify->find_compute(word+2);
if (icompute < 0)
error->all(FLERR,"Invalid compute ID in variable formula");
datamask &= modify->compute[icompute]->data_mask();
delete [] id;
}
if ((strncmp(word,"f_",2) == 0) && (i>0) && (!isalnum(str[i-1]))) {
@ -4362,19 +4352,15 @@ unsigned int Variable::data_mask(char *str)
error->all(FLERR,
"Variable evaluation before simulation box is defined");
n = strlen(word) - 2 + 1;
char *id = new char[n];
strcpy(id,&word[2]);
int ifix = modify->find_fix(id);
int ifix = modify->find_fix(word+2);
if (ifix < 0) error->all(FLERR,"Invalid fix ID in variable formula");
datamask &= modify->fix[ifix]->data_mask();
delete [] id;
}
if ((strncmp(word,"v_",2) == 0) && (i>0) && (!isalnum(str[i-1]))) {
int ivar = find(word);
int ivar = find(word+2);
if (ivar < 0) error->all(FLERR,"Invalid variable name in variable formula");
datamask &= data_mask(ivar);
}
@ -4395,6 +4381,7 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
{
me = comm->me;
style = flag;
fp = NULL;
if (me == 0) {
fp = fopen(file,"r");
@ -4403,7 +4390,7 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
sprintf(str,"Cannot open file variable file %s",file);
error->one(FLERR,str);
}
} else fp = NULL;
}
// if atomfile-style variable, must store per-atom values read from file
// allocate a new fix STORE, so they persist
@ -4441,7 +4428,10 @@ VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
VarReader::~VarReader()
{
if (me == 0) fclose(fp);
if (me == 0) {
fclose(fp);
fp = NULL;
}
// check modify in case all fixes have already been deleted