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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11250 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2014-01-17 18:43:09 +00:00
parent 961be6ee48
commit bad19033d0
172 changed files with 2523 additions and 2184 deletions
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27
src/variable.cpp
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@ -60,7 +60,7 @@ enum{DONE,ADD,SUBTRACT,MULTIPLY,DIVIDE,CARAT,MODULO,UNARY,
SQRT,EXP,LN,LOG,ABS,SIN,COS,TAN,ASIN,ACOS,ATAN,ATAN2,
RANDOM,NORMAL,CEIL,FLOOR,ROUND,RAMP,STAGGER,LOGFREQ,STRIDE,
VDISPLACE,SWIGGLE,CWIGGLE,GMASK,RMASK,GRMASK,
VALUE,ATOMARRAY,TYPEARRAY,INTARRAY};
VALUE,ATOMARRAY,TYPEARRAY,INTARRAY,BIGINTARRAY};
// customize by adding a special function
@ -1685,7 +1685,8 @@ double Variable::evaluate(char *str, Tree **tree)
/* ----------------------------------------------------------------------
one-time collapse of an atom-style variable parse tree
tree was created by one-time parsing of formula string via evaulate()
only keep tree nodes that depend on ATOMARRAY, TYPEARRAY, INTARRAY
only keep tree nodes that depend on
ATOMARRAY, TYPEARRAY, INTARRAY, BIGINTARRAY
remainder is converted to single VALUE
this enables optimal eval_tree loop over atoms
customize by adding a function:
@ -1704,6 +1705,7 @@ double Variable::collapse_tree(Tree *tree)
if (tree->type == ATOMARRAY) return 0.0;
if (tree->type == TYPEARRAY) return 0.0;
if (tree->type == INTARRAY) return 0.0;
if (tree->type == BIGINTARRAY) return 0.0;
if (tree->type == ADD) {
arg1 = collapse_tree(tree->left);
@ -2149,6 +2151,7 @@ double Variable::eval_tree(Tree *tree, int i)
if (tree->type == ATOMARRAY) return tree->array[i*tree->nstride];
if (tree->type == TYPEARRAY) return tree->array[atom->type[i]];
if (tree->type == INTARRAY) return (double) tree->iarray[i*tree->nstride];
if (tree->type == BIGINTARRAY) return (double) tree->barray[i*tree->nstride];
if (tree->type == ADD)
return eval_tree(tree->left,i) + eval_tree(tree->right,i);
@ -3510,9 +3513,14 @@ void Variable::atom_vector(char *word, Tree **tree,
treestack[ntreestack++] = newtree;
if (strcmp(word,"id") == 0) {
newtree->type = INTARRAY;
if (sizeof(tagint) == sizeof(smallint)) {
newtree->type = INTARRAY;
newtree->iarray = (int *) atom->tag;
} else {
newtree->type = BIGINTARRAY;
newtree->barray = (bigint *) atom->tag;
}
newtree->nstride = 1;
newtree->iarray = atom->tag;
} else if (strcmp(word,"mass") == 0) {
if (atom->rmass) {
newtree->nstride = 1;
@ -3998,7 +4006,8 @@ int VarReader::read_scalar(char *str)
int VarReader::read_peratom()
{
int i,m,n,tagdata,nchunk,eof;
int i,m,n,nchunk,eof;
tagint tag;
char *ptr,*next;
double value;
@ -4031,7 +4040,7 @@ int VarReader::read_peratom()
MPI_Bcast(str,n,MPI_CHAR,0,world);
bigint nlines = ATOBIGINT(str);
int map_tag_max = atom->map_tag_max;
tagint map_tag_max = atom->map_tag_max;
bigint nread = 0;
while (nread < nlines) {
@ -4043,10 +4052,10 @@ int VarReader::read_peratom()
for (i = 0; i < nchunk; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %lg",&tagdata,&value);
if (tagdata <= 0 || tagdata > map_tag_max)
sscanf(buf,TAGINT_FORMAT " %lg",&tag,&value);
if (tag <= 0 || tag > map_tag_max)
error->one(FLERR,"Invalid atom ID in variable file");
if ((m = atom->map(tagdata)) >= 0) vstore[m] = value;
if ((m = atom->map(tag)) >= 0) vstore[m] = value;
buf = next + 1;
}