forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5034 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
2fbdda55e0
commit
c57a5e2af1
341
src/variable.cpp
341
src/variable.cpp
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@ -22,6 +22,7 @@
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#include "update.h"
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#include "group.h"
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#include "domain.h"
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#include "region.h"
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#include "modify.h"
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#include "compute.h"
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#include "fix.h"
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@ -44,13 +45,13 @@ using namespace LAMMPS_NS;
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enum{INDEX,LOOP,WORLD,UNIVERSE,ULOOP,STRING,EQUAL,ATOM};
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enum{ARG,OP};
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// customize by adding a math function
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// customize by adding a function
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enum{DONE,ADD,SUBTRACT,MULTIPLY,DIVIDE,CARAT,UNARY,
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EQ,NE,LT,LE,GT,GE,AND,OR,
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SQRT,EXP,LN,LOG,SIN,COS,TAN,ASIN,ACOS,ATAN,ATAN2,
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RANDOM,NORMAL,CEIL,FLOOR,ROUND,RAMP,STAGGER,LOGFREQ,
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VDISPLACE,SWIGGLE,CWIGGLE,
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VDISPLACE,SWIGGLE,CWIGGLE,GMASK,RMASK,GRMASK,
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VALUE,ATOMARRAY,TYPEARRAY,INTARRAY};
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// customize by adding a special function
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@ -1377,16 +1378,17 @@ double Variable::evaluate(char *str, Tree **tree)
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}
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/* ----------------------------------------------------------------------
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collapse an atom-style variable parse tree
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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 evaulate()
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only keep tree nodes that depend on ATOMARRAY, TYPEARRAY, INTARRAY
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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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customize by adding a math function:
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customize by adding a function:
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sqrt(),exp(),ln(),log(),sin(),cos(),tan(),asin(),acos(),atan(),
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atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(),
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ramp(x,y),stagger(x,y),logfreq(x,y,z),
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vdisplace(x,y),swiggle(x,y,z),cwiggle(x,y,z)
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vdisplace(x,y),swiggle(x,y,z),cwiggle(x,y,z),
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gmask(x),rmask(x),grmask(x,y)
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---------------------------------------------------------------------- */
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double Variable::collapse_tree(Tree *tree)
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@ -1631,7 +1633,7 @@ double Variable::collapse_tree(Tree *tree)
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return tree->value;
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}
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// random() or normal() never become a single collapsed value
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// random() or normal() do not become a single collapsed value
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if (tree->type == RANDOM) {
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double lower = collapse_tree(tree->left);
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@ -1763,17 +1765,24 @@ double Variable::collapse_tree(Tree *tree)
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return tree->value;
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}
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// mask functions do not become a single collapsed value
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if (tree->type == GMASK) return 0.0;
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if (tree->type == RMASK) return 0.0;
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if (tree->type == GRMASK) return 0.0;
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return 0.0;
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}
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/* ----------------------------------------------------------------------
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evaluate an atom-style variable parse tree for atom I
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tree was created by one-time parsing of formula string via evaulate()
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customize by adding a math function:
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customize by adding a function:
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sqrt(),exp(),ln(),log(),sin(),cos(),tan(),asin(),acos(),atan(),
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atan2(y,x),random(x,y,z),normal(x,y,z),ceil(),floor(),round(),
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ramp(x,y),stagger(x,y),logfreq(x,y,z),
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vdisplace(x,y),swiggle(x,y,z),cwiggle(x,y,z)
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vdisplace(x,y),swiggle(x,y,z),cwiggle(x,y,z),
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gmask(x),rmask(x),grmask(x,y)
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---------------------------------------------------------------------- */
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double Variable::eval_tree(Tree *tree, int i)
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@ -1801,8 +1810,7 @@ double Variable::eval_tree(Tree *tree, int i)
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if (exponent == 0.0) error->one("Power by 0 in variable formula");
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return pow(eval_tree(tree->left,i),exponent);
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}
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if (tree->type == UNARY)
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return -eval_tree(tree->left,i);
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if (tree->type == UNARY) return -eval_tree(tree->left,i);
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if (tree->type == EQ) {
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if (eval_tree(tree->left,i) == eval_tree(tree->right,i)) return 1.0;
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@ -1980,6 +1988,26 @@ double Variable::eval_tree(Tree *tree, int i)
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return arg;
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}
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if (tree->type == GMASK) {
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if (atom->mask[i] & tree->ivalue1) return 1.0;
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else return 0.0;
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}
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if (tree->type == RMASK) {
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if (domain->regions[tree->ivalue1]->inside(atom->x[i][0],
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atom->x[i][1],
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atom->x[i][2])) return 1.0;
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else return 0.0;
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}
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if (tree->type == GRMASK) {
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if ((atom->mask[i] & tree->ivalue1) &&
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(domain->regions[tree->ivalue2]->inside(atom->x[i][0],
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atom->x[i][1],
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atom->x[i][2]))) return 1.0;
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else return 0.0;
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}
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return 0.0;
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}
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@ -2600,7 +2628,7 @@ int Variable::region_function(char *id)
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{
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int iregion = domain->find_region(id);
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if (iregion == -1)
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error->all("Invalid region in group function in variable formula");
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error->all("Region ID in variable formula does not exist");
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return iregion;
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}
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@ -2611,7 +2639,7 @@ int Variable::region_function(char *id)
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contents = str between parentheses with one,two,three args
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return 0 if not a match, 1 if successfully processed
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customize by adding a special function:
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sum(x),min(x),max(x),ave(x),trap(x)
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sum(x),min(x),max(x),ave(x),trap(x),gmask(x),rmask(x),grmask(x,y)
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------------------------------------------------------------------------- */
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int Variable::special_function(char *word, char *contents, Tree **tree,
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@ -2621,7 +2649,8 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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// word not a match to any special function
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if (strcmp(word,"sum") && strcmp(word,"min") && strcmp(word,"max") &&
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strcmp(word,"ave") && strcmp(word,"trap"))
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strcmp(word,"ave") && strcmp(word,"trap") && strcmp(word,"gmask") &&
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strcmp(word,"rmask") && strcmp(word,"grmask"))
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return 0;
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// parse contents for arg1,arg2,arg3 separated by commas
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@ -2654,138 +2683,190 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
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narg = 3;
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} else arg3 = NULL;
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// match word to special function
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// special functions that operate on global vectors
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int method;
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if (strcmp(word,"sum") == 0) method = SUM;
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else if (strcmp(word,"min") == 0) method = XMIN;
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else if (strcmp(word,"max") == 0) method = XMAX;
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else if (strcmp(word,"ave") == 0) method = AVE;
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else if (strcmp(word,"trap") == 0) method = TRAP;
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if (strcmp(word,"sum") == 0 || strcmp(word,"min") == 0 ||
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strcmp(word,"max") == 0 || strcmp(word,"ave") == 0 ||
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strcmp(word,"trap") == 0) {
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if (narg != 1) error->all("Invalid special function in variable formula");
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int method;
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if (strcmp(word,"sum") == 0) method = SUM;
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else if (strcmp(word,"min") == 0) method = XMIN;
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else if (strcmp(word,"max") == 0) method = XMAX;
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else if (strcmp(word,"ave") == 0) method = AVE;
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else if (strcmp(word,"trap") == 0) method = TRAP;
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if (narg != 1) error->all("Invalid special function in variable formula");
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Compute *compute = NULL;
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Fix *fix = NULL;
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int index,nvec,nstride;
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Compute *compute = NULL;
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Fix *fix = NULL;
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int index,nvec,nstride;
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if (strstr(arg1,"c_") == arg1) {
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ptr1 = strchr(arg1,'[');
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if (ptr1) {
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ptr2 = ptr1;
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index = int_between_brackets(ptr2);
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*ptr1 = '\0';
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} else index = 0;
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if (strstr(arg1,"c_") == arg1) {
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ptr1 = strchr(arg1,'[');
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if (ptr1) {
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ptr2 = ptr1;
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index = int_between_brackets(ptr2);
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*ptr1 = '\0';
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} else index = 0;
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int icompute = modify->find_compute(&arg1[2]);
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if (icompute < 0) error->all("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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if (update->whichflag == 0) {
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if (compute->invoked_vector != update->ntimestep)
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error->all("Compute used in variable between runs is not current");
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} else if (!(compute->invoked_flag & INVOKED_VECTOR)) {
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compute->compute_vector();
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compute->invoked_flag |= INVOKED_VECTOR;
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}
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nvec = compute->size_vector;
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nstride = 1;
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} else if (index && compute->array_flag) {
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if (index > compute->size_array_cols)
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error->all("Variable formula compute array "
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"is accessed out-of-range");
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if (update->whichflag == 0) {
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if (compute->invoked_array != update->ntimestep)
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error->all("Compute used in variable between runs is not current");
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} else if (!(compute->invoked_flag & INVOKED_ARRAY)) {
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compute->compute_array();
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compute->invoked_flag |= INVOKED_ARRAY;
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}
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nvec = compute->size_array_rows;
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nstride = compute->size_array_cols;
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} else error->all("Mismatched compute in variable formula");
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int icompute = modify->find_compute(&arg1[2]);
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if (icompute < 0) error->all("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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if (update->whichflag == 0) {
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if (compute->invoked_vector != update->ntimestep)
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error->all("Compute used in variable between runs is not current");
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} else if (!(compute->invoked_flag & INVOKED_VECTOR)) {
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compute->compute_vector();
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compute->invoked_flag |= INVOKED_VECTOR;
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}
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nvec = compute->size_vector;
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nstride = 1;
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} else if (index && compute->array_flag) {
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if (index > compute->size_array_cols)
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error->all("Variable formula compute array "
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"is accessed out-of-range");
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if (update->whichflag == 0) {
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if (compute->invoked_array != update->ntimestep)
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error->all("Compute used in variable between runs is not current");
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} else if (!(compute->invoked_flag & INVOKED_ARRAY)) {
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compute->compute_array();
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compute->invoked_flag |= INVOKED_ARRAY;
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}
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nvec = compute->size_array_rows;
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nstride = compute->size_array_cols;
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} else error->all("Mismatched compute in variable formula");
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} else if (strstr(arg1,"f_") == arg1) {
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ptr1 = strchr(arg1,'[');
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if (ptr1) {
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ptr2 = ptr1;
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index = int_between_brackets(ptr2);
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*ptr1 = '\0';
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} else index = 0;
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int ifix = modify->find_fix(&arg1[2]);
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if (ifix < 0) error->all("Invalid fix ID in variable formula");
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fix = modify->fix[ifix];
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if (index == 0 && fix->vector_flag) {
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if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
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error->all("Fix in variable not computed at compatible time");
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nvec = fix->size_vector;
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nstride = 1;
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} else if (index && fix->array_flag) {
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if (index > fix->size_array_cols)
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error->all("Variable formula fix array is accessed out-of-range");
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if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
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error->all("Fix in variable not computed at compatible time");
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nvec = fix->size_array_rows;
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nstride = fix->size_array_cols;
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} else error->all("Mismatched fix in variable formula");
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} else error->all("Invalid special function in variable formula");
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} else if (strstr(arg1,"f_") == arg1) {
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ptr1 = strchr(arg1,'[');
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if (ptr1) {
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ptr2 = ptr1;
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index = int_between_brackets(ptr2);
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*ptr1 = '\0';
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} else index = 0;
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double value = 0.0;
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if (method == XMIN) value = BIG;
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if (method == XMAX) value = -BIG;
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int ifix = modify->find_fix(&arg1[2]);
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if (ifix < 0) error->all("Invalid fix ID in variable formula");
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fix = modify->fix[ifix];
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if (index == 0 && fix->vector_flag) {
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if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
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error->all("Fix in variable not computed at compatible time");
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nvec = fix->size_vector;
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nstride = 1;
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} else if (index && fix->array_flag) {
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if (index > fix->size_array_cols)
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error->all("Variable formula fix array is accessed out-of-range");
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if (update->whichflag > 0 && update->ntimestep % fix->global_freq)
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error->all("Fix in variable not computed at compatible time");
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nvec = fix->size_array_rows;
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nstride = fix->size_array_cols;
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} else error->all("Mismatched fix in variable formula");
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} else error->all("Invalid special function in variable formula");
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double value = 0.0;
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if (method == XMIN) value = BIG;
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if (method == XMAX) value = -BIG;
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if (compute) {
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double *vec;
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if (index) vec = &compute->array[0][index];
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else vec = compute->vector;
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int j = 0;
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for (int i = 0; i < nvec; i++) {
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if (method == SUM) value += vec[j];
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else if (method == XMIN) value = MIN(value,vec[j]);
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else if (method == XMAX) value = MAX(value,vec[j]);
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else if (method == AVE) value += vec[j];
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else if (method == TRAP) {
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if (i > 0 && i < nvec-1) value += vec[j];
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else value += 0.5*vec[j];
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}
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j += nstride;
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}
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}
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if (fix) {
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double one;
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for (int i = 0; i < nvec; i++) {
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if (index) one = fix->compute_array(i,index-1);
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else one = fix->compute_vector(i);
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if (method == SUM) value += one;
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else if (method == XMIN) value = MIN(value,one);
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else if (method == XMAX) value = MAX(value,one);
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else if (method == AVE) value += one;
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else if (method == TRAP) {
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if (i > 1 && i < nvec) value += one;
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else value += 0.5*one;
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if (compute) {
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double *vec;
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if (index) vec = &compute->array[0][index];
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else vec = compute->vector;
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int j = 0;
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for (int i = 0; i < nvec; i++) {
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if (method == SUM) value += vec[j];
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else if (method == XMIN) value = MIN(value,vec[j]);
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else if (method == XMAX) value = MAX(value,vec[j]);
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else if (method == AVE) value += vec[j];
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else if (method == TRAP) {
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if (i > 0 && i < nvec-1) value += vec[j];
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else value += 0.5*vec[j];
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}
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j += nstride;
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}
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}
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}
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if (method == AVE) value /= nvec;
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delete [] arg1;
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delete [] arg2;
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delete [] arg3;
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if (fix) {
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double one;
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for (int i = 0; i < nvec; i++) {
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if (index) one = fix->compute_array(i,index-1);
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else one = fix->compute_vector(i);
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if (method == SUM) value += one;
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else if (method == XMIN) value = MIN(value,one);
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else if (method == XMAX) value = MAX(value,one);
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else if (method == AVE) value += one;
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else if (method == TRAP) {
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if (i > 1 && i < nvec) value += one;
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else value += 0.5*one;
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}
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}
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}
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if (method == AVE) value /= nvec;
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delete [] arg1;
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delete [] arg2;
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delete [] arg3;
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// save value in tree or on argstack
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if (tree) {
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Tree *newtree = new Tree();
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newtree->type = VALUE;
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newtree->value = value;
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newtree->left = newtree->middle = newtree->right = NULL;
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treestack[ntreestack++] = newtree;
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} else argstack[nargstack++] = value;
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// save value in tree or on argstack
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// mask special functions
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if (tree) {
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} else if (strcmp(word,"gmask") == 0) {
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if (tree == NULL)
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error->all("Gmask function in equal-style variable formula");
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if (narg != 1) error->all("Invalid special function in variable formula");
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int igroup = group->find(arg1);
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if (igroup == -1)
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error->all("Group ID in variable formula does not exist");
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Tree *newtree = new Tree();
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newtree->type = VALUE;
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newtree->value = value;
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newtree->type = GMASK;
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newtree->ivalue1 = group->bitmask[igroup];
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newtree->left = newtree->middle = newtree->right = NULL;
|
||||
treestack[ntreestack++] = newtree;
|
||||
} else argstack[nargstack++] = value;
|
||||
|
||||
} else if (strcmp(word,"rmask") == 0) {
|
||||
if (tree == NULL)
|
||||
error->all("Rmask function in equal-style variable formula");
|
||||
if (narg != 1) error->all("Invalid special function in variable formula");
|
||||
|
||||
int iregion = region_function(arg1);
|
||||
|
||||
Tree *newtree = new Tree();
|
||||
newtree->type = RMASK;
|
||||
newtree->ivalue1 = iregion;
|
||||
newtree->left = newtree->middle = newtree->right = NULL;
|
||||
treestack[ntreestack++] = newtree;
|
||||
|
||||
} else if (strcmp(word,"grmask") == 0) {
|
||||
if (tree == NULL)
|
||||
error->all("Grmask function in equal-style variable formula");
|
||||
if (narg != 2) error->all("Invalid special function in variable formula");
|
||||
|
||||
int igroup = group->find(arg1);
|
||||
if (igroup == -1)
|
||||
error->all("Group ID in variable formula does not exist");
|
||||
int iregion = region_function(arg2);
|
||||
|
||||
Tree *newtree = new Tree();
|
||||
newtree->type = RMASK;
|
||||
newtree->ivalue1 = group->bitmask[igroup];
|
||||
newtree->ivalue2 = iregion;
|
||||
newtree->left = newtree->middle = newtree->right = NULL;
|
||||
treestack[ntreestack++] = newtree;
|
||||
}
|
||||
|
||||
return 1;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -54,6 +54,7 @@ class Variable : protected Pointers {
|
|||
double value;
|
||||
double *array;
|
||||
int *iarray;
|
||||
int ivalue1,ivalue2;
|
||||
int nstride;
|
||||
int type;
|
||||
Tree *left,*middle,*right;
|
||||
|
|
|
|||
Loading…
Reference in New Issue