git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14220 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
118
src/variable.cpp
118
src/variable.cpp
@ -11,11 +11,11 @@
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "ctype.h"
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#include "unistd.h"
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#include <math.h>
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#include <stdlib.h>
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#include <string.h>
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#include <ctype.h>
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#include <unistd.h>
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#include "variable.h"
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#include "universe.h"
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#include "atom.h"
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@ -533,8 +533,8 @@ int Variable::next(int narg, char **arg)
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// invalid styles: STRING, EQUAL, WORLD, ATOM, GETENV, FORMAT, PYTHON
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int istyle = style[find(arg[0])];
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if (istyle == STRING || istyle == EQUAL || istyle == WORLD ||
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istyle == GETENV || istyle == ATOM || istyle == FORMAT ||
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if (istyle == STRING || istyle == EQUAL || istyle == WORLD ||
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istyle == GETENV || istyle == ATOM || istyle == FORMAT ||
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istyle == PYTHON)
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error->all(FLERR,"Invalid variable style with next command");
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@ -546,7 +546,7 @@ int Variable::next(int narg, char **arg)
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int iarg = 0;
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for (iarg = 0; iarg < narg; iarg++)
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if (strcmp(arg[iarg],names[i]) == 0) break;
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if (iarg == narg)
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if (iarg == narg)
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error->universe_one(FLERR,"Next command must list all "
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"universe and uloop variables");
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}
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@ -730,7 +730,7 @@ char *Variable::pythonstyle(char *name, char *funcname)
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/* ----------------------------------------------------------------------
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return ptr to the data text associated with a variable
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if INDEX or WORLD or UNIVERSE or STRING or SCALARFILE,
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if INDEX or WORLD or UNIVERSE or STRING or SCALARFILE,
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return ptr to stored string
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if LOOP or ULOOP, write int to data[0] and return ptr to string
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if EQUAL, evaluate variable and put result in str
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@ -748,13 +748,13 @@ char *Variable::retrieve(char *name)
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if (ivar < 0) return NULL;
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if (which[ivar] >= num[ivar]) return NULL;
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if (eval_in_progress[ivar])
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if (eval_in_progress[ivar])
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error->all(FLERR,"Variable has circular dependency");
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eval_in_progress[ivar] = 1;
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char *str = NULL;
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if (style[ivar] == INDEX || style[ivar] == WORLD ||
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style[ivar] == UNIVERSE || style[ivar] == STRING ||
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style[ivar] == UNIVERSE || style[ivar] == STRING ||
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style[ivar] == SCALARFILE) {
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str = data[ivar][which[ivar]];
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} else if (style[ivar] == LOOP || style[ivar] == ULOOP) {
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@ -793,7 +793,7 @@ char *Variable::retrieve(char *name)
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str = data[ivar][1];
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} else if (style[ivar] == PYTHON) {
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int ifunc = python->variable_match(data[ivar][0],names[ivar],0);
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if (ifunc < 0)
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if (ifunc < 0)
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error->all(FLERR,"Python variable does not match Python function");
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python->invoke_function(ifunc,data[ivar][1]);
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str = data[ivar][1];
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@ -813,7 +813,7 @@ char *Variable::retrieve(char *name)
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double Variable::compute_equal(int ivar)
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{
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if (eval_in_progress[ivar])
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if (eval_in_progress[ivar])
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error->all(FLERR,"Variable has circular dependency");
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eval_in_progress[ivar] = 1;
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@ -853,8 +853,8 @@ void Variable::compute_atom(int ivar, int igroup,
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{
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Tree *tree;
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double *vstore;
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if (eval_in_progress[ivar])
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if (eval_in_progress[ivar])
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error->all(FLERR,"Variable has circular dependency");
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eval_in_progress[ivar] = 1;
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@ -867,7 +867,7 @@ void Variable::compute_atom(int ivar, int igroup,
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eval_in_progress[ivar] = 0;
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return;
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}
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int groupbit = group->bitmask[igroup];
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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@ -991,7 +991,7 @@ void Variable::grow()
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memory->grow(which,maxvar,"var:which");
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memory->grow(pad,maxvar,"var:pad");
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reader = (VarReader **)
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reader = (VarReader **)
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memory->srealloc(reader,maxvar*sizeof(VarReader *),"var:reader");
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for (int i = old; i < maxvar; i++) reader[i] = NULL;
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@ -1151,7 +1151,7 @@ double Variable::evaluate(char *str, Tree **tree)
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"Variable evaluation before simulation box is defined");
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int icompute = modify->find_compute(word+2);
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if (icompute < 0)
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if (icompute < 0)
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error->all(FLERR,"Invalid compute ID in variable formula");
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Compute *compute = modify->compute[icompute];
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@ -1216,7 +1216,7 @@ double Variable::evaluate(char *str, Tree **tree)
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compute->invoked_flag |= INVOKED_VECTOR;
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}
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if (compute->size_vector_variable &&
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if (compute->size_vector_variable &&
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index1 > compute->size_vector) value1 = 0.0;
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else value1 = compute->vector[index1-1];
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if (tree) {
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@ -1248,7 +1248,7 @@ double Variable::evaluate(char *str, Tree **tree)
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compute->invoked_flag |= INVOKED_ARRAY;
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}
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if (compute->size_array_rows_variable &&
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if (compute->size_array_rows_variable &&
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index1 > compute->size_array_rows) value1 = 0.0;
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else value1 = compute->array[index1-1][index2-1];
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if (tree) {
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@ -1424,7 +1424,7 @@ double Variable::evaluate(char *str, Tree **tree)
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"accessed out-of-range");
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if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
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error->all(FLERR,"Fix in variable not computed at compatible time");
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value1 = fix->compute_vector(index1-1);
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if (tree) {
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Tree *newtree = new Tree();
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@ -1891,7 +1891,7 @@ double Variable::evaluate(char *str, Tree **tree)
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/* ----------------------------------------------------------------------
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one-time collapse of an atom-style variable parse tree
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tree was created by one-time parsing of formula string via evaluate()
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only keep tree nodes that depend on
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only keep tree nodes that depend on
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ATOMARRAY, TYPEARRAY, INTARRAY, BIGINTARRAY
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remainder is converted to single VALUE
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this enables optimal eval_tree loop over atoms
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@ -2321,8 +2321,8 @@ double Variable::collapse_tree(Tree *tree)
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int ivalue5 = static_cast<int> (collapse_tree(tree->extra[2]));
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int ivalue6 = static_cast<int> (collapse_tree(tree->extra[3]));
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if (tree->first->type != VALUE || tree->second->type != VALUE ||
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tree->extra[0]->type != VALUE || tree->extra[1]->type != VALUE ||
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tree->extra[2]->type != VALUE || tree->extra[3]->type != VALUE)
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tree->extra[0]->type != VALUE || tree->extra[1]->type != VALUE ||
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tree->extra[2]->type != VALUE || tree->extra[3]->type != VALUE)
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return 0.0;
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tree->type = VALUE;
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if (ivalue1 < 0 || ivalue2 < 0 || ivalue3 <= 0 || ivalue1 > ivalue2)
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@ -2337,7 +2337,7 @@ double Variable::collapse_tree(Tree *tree)
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if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) {
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int offset = update->ntimestep - ivalue1;
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istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
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if (update->ntimestep < ivalue2 && istep > ivalue4)
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if (update->ntimestep < ivalue2 && istep > ivalue4)
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tree->value = ivalue4;
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} else {
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int offset = update->ntimestep - ivalue4;
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@ -2657,7 +2657,7 @@ double Variable::eval_tree(Tree *tree, int i)
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if (update->ntimestep < ivalue4 || update->ntimestep > ivalue5) {
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int offset = update->ntimestep - ivalue1;
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istep = ivalue1 + (offset/ivalue3)*ivalue3 + ivalue3;
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if (update->ntimestep < ivalue2 && istep > ivalue4)
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if (update->ntimestep < ivalue2 && istep > ivalue4)
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tree->value = ivalue4;
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} else {
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int offset = update->ntimestep - ivalue4;
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@ -2859,7 +2859,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
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if (strcmp(word,"sqrt") && strcmp(word,"exp") &&
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strcmp(word,"ln") && strcmp(word,"log") &&
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strcmp(word,"abs") &&
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strcmp(word,"abs") &&
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strcmp(word,"sin") && strcmp(word,"cos") &&
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strcmp(word,"tan") && strcmp(word,"asin") &&
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strcmp(word,"acos") && strcmp(word,"atan") &&
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@ -2867,15 +2867,15 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
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strcmp(word,"normal") && strcmp(word,"ceil") &&
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strcmp(word,"floor") && strcmp(word,"round") &&
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strcmp(word,"ramp") && strcmp(word,"stagger") &&
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strcmp(word,"logfreq") && strcmp(word,"logfreq2") &&
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strcmp(word,"stride") && strcmp(word,"stride2") &&
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strcmp(word,"vdisplace") && strcmp(word,"swiggle") &&
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strcmp(word,"logfreq") && strcmp(word,"logfreq2") &&
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strcmp(word,"stride") && strcmp(word,"stride2") &&
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strcmp(word,"vdisplace") && strcmp(word,"swiggle") &&
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strcmp(word,"cwiggle"))
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return 0;
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// parse contents for comma-separated args
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// narg = number of args, args = strings between commas
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char *args[MAXFUNCARG];
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int narg = parse_args(contents,args);
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@ -2909,7 +2909,7 @@ int Variable::math_function(char *word, char *contents, Tree **tree,
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if (narg > 1) {
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value2 = evaluate(args[1],NULL);
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if (narg > 2) {
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for (int i = 2; i < narg; i++)
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for (int i = 2; i < narg; i++)
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values[i-2] = evaluate(args[i],NULL);
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}
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}
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@ -3264,7 +3264,7 @@ int Variable::group_function(char *word, char *contents, Tree **tree,
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// parse contents for comma-separated args
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// narg = number of args, args = strings between commas
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char *args[MAXFUNCARG];
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int narg = parse_args(contents,args);
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@ -3501,7 +3501,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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if (strcmp(word,"sum") && strcmp(word,"min") && strcmp(word,"max") &&
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strcmp(word,"ave") && strcmp(word,"trap") && strcmp(word,"slope") &&
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strcmp(word,"gmask") && strcmp(word,"rmask") &&
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strcmp(word,"gmask") && strcmp(word,"rmask") &&
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strcmp(word,"grmask") && strcmp(word,"next") &&
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strcmp(word,"is_active") && strcmp(word,"is_defined") &&
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strcmp(word,"is_available"))
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@ -3509,7 +3509,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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// parse contents for comma-separated args
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// narg = number of args, args = strings between commas
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char *args[MAXFUNCARG];
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int narg = parse_args(contents,args);
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@ -3527,7 +3527,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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else if (strcmp(word,"trap") == 0) method = TRAP;
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else if (strcmp(word,"slope") == 0) method = SLOPE;
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if (narg != 1)
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if (narg != 1)
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error->all(FLERR,"Invalid special function in variable formula");
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Compute *compute = NULL;
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@ -3544,7 +3544,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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} else index = 0;
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int icompute = modify->find_compute(&args[0][2]);
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if (icompute < 0)
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if (icompute < 0)
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error->all(FLERR,"Invalid compute ID in variable formula");
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compute = modify->compute[icompute];
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if (index == 0 && compute->vector_flag) {
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@ -3654,9 +3654,9 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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}
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}
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if (method == TRAP) {
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if (index) value -= 0.5*fix->compute_array(0,index-1) +
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if (index) value -= 0.5*fix->compute_array(0,index-1) +
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0.5*fix->compute_array(nvec-1,index-1);
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else value -= 0.5*fix->compute_vector(0) +
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else value -= 0.5*fix->compute_vector(0) +
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0.5*fix->compute_vector(nvec-1);
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}
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}
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@ -3686,7 +3686,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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} else if (strcmp(word,"gmask") == 0) {
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if (tree == NULL)
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error->all(FLERR,"Gmask function in equal-style variable formula");
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if (narg != 1)
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if (narg != 1)
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error->all(FLERR,"Invalid special function in variable formula");
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int igroup = group->find(args[0]);
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@ -3703,7 +3703,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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} else if (strcmp(word,"rmask") == 0) {
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if (tree == NULL)
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error->all(FLERR,"Rmask function in equal-style variable formula");
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if (narg != 1)
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if (narg != 1)
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error->all(FLERR,"Invalid special function in variable formula");
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int iregion = region_function(args[0]);
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@ -3719,7 +3719,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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} else if (strcmp(word,"grmask") == 0) {
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if (tree == NULL)
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error->all(FLERR,"Grmask function in equal-style variable formula");
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if (narg != 2)
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if (narg != 2)
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error->all(FLERR,"Invalid special function in variable formula");
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int igroup = group->find(args[0]);
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@ -3739,7 +3739,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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// special function for file-style or atomfile-style variables
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} else if (strcmp(word,"next") == 0) {
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if (narg != 1)
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if (narg != 1)
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error->all(FLERR,"Invalid special function in variable formula");
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int ivar = find(args[0]);
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@ -3768,7 +3768,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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// set selfalloc = 1 so result will be deleted by free_tree() after eval
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} else if (style[ivar] == ATOMFILE) {
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if (tree == NULL)
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if (tree == NULL)
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error->all(FLERR,"Atomfile variable in equal-style variable formula");
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double *result;
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@ -3790,7 +3790,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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} else error->all(FLERR,"Invalid variable style in special function next");
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} else if (strcmp(word,"is_active") == 0) {
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if (narg != 2)
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if (narg != 2)
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error->all(FLERR,"Invalid is_active() function in variable formula");
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Info info(lmp);
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@ -3808,7 +3808,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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} else argstack[nargstack++] = value;
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} else if (strcmp(word,"is_available") == 0) {
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if (narg != 2)
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if (narg != 2)
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error->all(FLERR,"Invalid is_available() function in variable formula");
|
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|
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Info info(lmp);
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@ -3826,7 +3826,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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} else argstack[nargstack++] = value;
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} else if (strcmp(word,"is_defined") == 0) {
|
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if (narg != 2)
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if (narg != 2)
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error->all(FLERR,"Invalid is_defined() function in variable formula");
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|
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Info info(lmp);
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@ -3892,7 +3892,7 @@ void Variable::peratom2global(int flag, char *word,
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}
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else if (strcmp(word,"type") == 0) mine = atom->type[index];
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else if (strcmp(word,"mol") == 0) {
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if (!atom->molecule_flag)
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if (!atom->molecule_flag)
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error->one(FLERR,"Variable uses atom property that isn't allocated");
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mine = atom->molecule[index];
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}
|
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@ -3906,7 +3906,7 @@ void Variable::peratom2global(int flag, char *word,
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else if (strcmp(word,"fy") == 0) mine = atom->f[index][1];
|
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else if (strcmp(word,"fz") == 0) mine = atom->f[index][2];
|
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else if (strcmp(word,"q") == 0) {
|
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if (!atom->q_flag)
|
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if (!atom->q_flag)
|
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error->one(FLERR,"Variable uses atom property that isn't allocated");
|
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mine = atom->q[index];
|
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}
|
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@ -4002,7 +4002,7 @@ void Variable::atom_vector(char *word, Tree **tree,
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newtree->iarray = atom->type;
|
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|
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} else if (strcmp(word,"mol") == 0) {
|
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if (!atom->molecule_flag)
|
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if (!atom->molecule_flag)
|
||||
error->one(FLERR,"Variable uses atom property that isn't allocated");
|
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if (sizeof(tagint) == sizeof(smallint)) {
|
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newtree->type = INTARRAY;
|
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@ -4169,7 +4169,7 @@ double Variable::evaluate_boolean(char *str)
|
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// ----------------
|
||||
|
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else if (onechar == '(') {
|
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if (expect == OP)
|
||||
if (expect == OP)
|
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error->all(FLERR,"Invalid Boolean syntax in if command");
|
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expect = OP;
|
||||
|
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@ -4190,7 +4190,7 @@ double Variable::evaluate_boolean(char *str)
|
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// ----------------
|
||||
|
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} else if (isdigit(onechar) || onechar == '.' || onechar == '-') {
|
||||
if (expect == OP)
|
||||
if (expect == OP)
|
||||
error->all(FLERR,"Invalid Boolean syntax in if command");
|
||||
expect = OP;
|
||||
|
||||
@ -4216,7 +4216,7 @@ double Variable::evaluate_boolean(char *str)
|
||||
// ----------------
|
||||
|
||||
} else if (isalpha(onechar)) {
|
||||
if (expect == OP)
|
||||
if (expect == OP)
|
||||
error->all(FLERR,"Invalid Boolean syntax in if command");
|
||||
expect = OP;
|
||||
|
||||
@ -4280,7 +4280,7 @@ double Variable::evaluate_boolean(char *str)
|
||||
continue;
|
||||
}
|
||||
|
||||
if (expect == ARG)
|
||||
if (expect == ARG)
|
||||
error->all(FLERR,"Invalid Boolean syntax in if command");
|
||||
expect = ARG;
|
||||
|
||||
@ -4411,7 +4411,7 @@ unsigned int Variable::data_mask(char *str)
|
||||
"Variable evaluation before simulation box is defined");
|
||||
|
||||
int icompute = modify->find_compute(word+2);
|
||||
if (icompute < 0)
|
||||
if (icompute < 0)
|
||||
error->all(FLERR,"Invalid compute ID in variable formula");
|
||||
|
||||
datamask &= modify->compute[icompute]->data_mask();
|
||||
@ -4421,13 +4421,13 @@ unsigned int Variable::data_mask(char *str)
|
||||
if (domain->box_exist == 0)
|
||||
error->all(FLERR,
|
||||
"Variable evaluation before simulation box is defined");
|
||||
|
||||
|
||||
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();
|
||||
}
|
||||
|
||||
|
||||
if ((strncmp(word,"v_",2) == 0) && (i>0) && (!isalnum(str[i-1]))) {
|
||||
int ivar = find(word+2);
|
||||
if (ivar < 0) error->all(FLERR,"Invalid variable name in variable formula");
|
||||
@ -4446,7 +4446,7 @@ unsigned int Variable::data_mask(char *str)
|
||||
for flag = ATOMFILE, reads set of one value per atom
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
|
||||
VarReader::VarReader(LAMMPS *lmp, char *name, char *file, int flag) :
|
||||
Pointers(lmp)
|
||||
{
|
||||
me = comm->me;
|
||||
|
||||
Reference in New Issue
Block a user