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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8723 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-08-28 14:21:55 +00:00
parent 8972165b3a
commit dba019f3e4
28 changed files with 737 additions and 245 deletions
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116
src/variable.cpp
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@ -30,6 +30,7 @@
#include "thermo.h"
#include "random_mars.h"
#include "math_const.h"
#include "atom_masks.h"
#include "memory.h"
#include "error.h"
@ -78,6 +79,8 @@ Variable::Variable(LAMMPS *lmp) : Pointers(lmp)
pad = NULL;
data = NULL;
eval_in_progress = NULL;
randomequal = NULL;
randomatom = NULL;
@ -109,6 +112,8 @@ Variable::~Variable()
memory->destroy(pad);
memory->sfree(data);
memory->destroy(eval_in_progress);
delete randomequal;
delete randomatom;
}
@ -135,7 +140,7 @@ void Variable::set(int narg, char **arg)
} else if (strcmp(arg[1],"index") == 0) {
if (narg < 3) error->all(FLERR,"Illegal variable command");
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) extend();
if (nvar == maxvar) grow();
style[nvar] = INDEX;
num[nvar] = narg - 2;
which[nvar] = 0;
@ -149,7 +154,7 @@ void Variable::set(int narg, char **arg)
} else if (strcmp(arg[1],"loop") == 0) {
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) extend();
if (nvar == maxvar) grow();
style[nvar] = LOOP;
int nfirst,nlast;
if (narg == 3 || (narg == 4 && strcmp(arg[3],"pad") == 0)) {
@ -184,7 +189,7 @@ void Variable::set(int narg, char **arg)
} else if (strcmp(arg[1],"world") == 0) {
if (narg < 3) error->all(FLERR,"Illegal variable command");
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) extend();
if (nvar == maxvar) grow();
style[nvar] = WORLD;
num[nvar] = narg - 2;
if (num[nvar] != universe->nworlds)
@ -205,7 +210,7 @@ void Variable::set(int narg, char **arg)
if (strcmp(arg[1],"universe") == 0) {
if (narg < 3) error->all(FLERR,"Illegal variable command");
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) extend();
if (nvar == maxvar) grow();
style[nvar] = UNIVERSE;
num[nvar] = narg - 2;
pad[nvar] = 0;
@ -215,7 +220,7 @@ void Variable::set(int narg, char **arg)
if (narg < 3 || narg > 4 || (narg == 4 && strcmp(arg[3],"pad") != 0))
error->all(FLERR,"Illegal variable command");
if (find(arg[0]) >= 0) return;
if (nvar == maxvar) extend();
if (nvar == maxvar) grow();
style[nvar] = ULOOP;
num[nvar] = atoi(arg[2]);
data[nvar] = new char*[1];
@ -254,7 +259,7 @@ void Variable::set(int narg, char **arg)
error->all(FLERR,"Cannot redefine variable as a different style");
remove(find(arg[0]));
}
if (nvar == maxvar) extend();
if (nvar == maxvar) grow();
style[nvar] = STRING;
num[nvar] = 1;
which[nvar] = 0;
@ -274,7 +279,7 @@ void Variable::set(int narg, char **arg)
error->all(FLERR,"Cannot redefine variable as a different style");
remove(find(arg[0]));
}
if (nvar == maxvar) extend();
if (nvar == maxvar) grow();
style[nvar] = EQUAL;
num[nvar] = 2;
which[nvar] = 0;
@ -295,7 +300,7 @@ void Variable::set(int narg, char **arg)
error->all(FLERR,"Cannot redefine variable as a different style");
remove(find(arg[0]));
}
if (nvar == maxvar) extend();
if (nvar == maxvar) grow();
style[nvar] = ATOM;
num[nvar] = 1;
which[nvar] = 0;
@ -475,7 +480,13 @@ char *Variable::retrieve(char *name)
double Variable::compute_equal(int ivar)
{
return evaluate(data[ivar][0],NULL);
// eval_in_progress used to detect circle dependencies
// could extend this later to check v_a = c_b + v_a constructs?
eval_in_progress[ivar] = 1;
double value = evaluate(data[ivar][0],NULL);
eval_in_progress[ivar] = 0;
return value;
}
/* ----------------------------------------------------------------------
@ -573,17 +584,18 @@ void Variable::remove(int n)
make space in arrays for new variable
------------------------------------------------------------------------- */
void Variable::extend()
void Variable::grow()
{
maxvar += VARDELTA;
names = (char **)
memory->srealloc(names,maxvar*sizeof(char *),"var:names");
memory->srealloc(names,maxvar*sizeof(char *),"var:names");
memory->grow(style,maxvar,"var:style");
memory->grow(num,maxvar,"var:num");
memory->grow(which,maxvar,"var:which");
memory->grow(pad,maxvar,"var:pad");
data = (char ***)
memory->srealloc(data,maxvar*sizeof(char **),"var:data");
data = (char ***) memory->srealloc(data,maxvar*sizeof(char **),"var:data");
memory->grow(eval_in_progress,maxvar,"var:eval_in_progress");
for (int i = 0; i < maxvar; i++) eval_in_progress[i] = 0;
}
/* ----------------------------------------------------------------------
@ -1113,6 +1125,8 @@ double Variable::evaluate(char *str, Tree **tree)
int ivar = find(id);
if (ivar < 0)
error->all(FLERR,"Invalid variable name in variable formula");
if (eval_in_progress[ivar])
error->all(FLERR,"Variable has circular dependency");
// parse zero or one trailing brackets
// point i beyond last bracket
@ -3426,3 +3440,79 @@ double Variable::evaluate_boolean(char *str)
if (nargstack != 1) error->all(FLERR,"Invalid Boolean syntax in if command");
return argstack[0];
}
/* ---------------------------------------------------------------------- */
unsigned int Variable::data_mask(int ivar)
{
if (eval_in_progress[ivar]) return EMPTY_MASK;
eval_in_progress[ivar] = 1;
unsigned int datamask = data_mask(data[ivar][0]);
eval_in_progress[ivar] = 0;
return datamask;
}
/* ---------------------------------------------------------------------- */
unsigned int Variable::data_mask(char *str)
{
unsigned int datamask = EMPTY_MASK;
for (unsigned int i=0; i < strlen(str)-2; i++) {
int istart = i;
while (isalnum(str[i]) || str[i] == '_') i++;
int istop = i-1;
int n = istop - istart + 1;
char *word = new char[n+1];
strncpy(word,&str[istart],n);
word[n] = '\0';
// ----------------
// compute
// ----------------
if ((strncmp(word,"c_",2) == 0) && (i>0) && (not isalnum(str[i-1]))){
if (domain->box_exist == 0)
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);
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) && (not isalnum(str[i-1]))) {
if (domain->box_exist == 0)
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);
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) && (not isalnum(str[i-1]))) {
int ivar = find(word);
datamask &= data_mask(ivar);
}
delete [] word;
}
return datamask;
}