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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@254 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2007-01-30 00:22:05 +00:00
parent 9cdbeaf9f2
commit 209f169cbc
414 changed files with 6935 additions and 10462 deletions
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212
src/variable.cpp
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@ -1,7 +1,7 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
@ -14,6 +14,7 @@
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "unistd.h"
#include "variable.h"
#include "universe.h"
@ -21,18 +22,22 @@
#include "update.h"
#include "group.h"
#include "domain.h"
#include "modify.h"
#include "compute.h"
#include "output.h"
#include "thermo.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define VARDELTA 4
enum{INDEX,LOOP,EQUAL,WORLD,UNIVERSE,ULOOP};
/* ---------------------------------------------------------------------- */
Variable::Variable()
Variable::Variable(LAMMPS *lmp) : Pointers(lmp)
{
MPI_Comm_rank(world,&me);
@ -390,16 +395,26 @@ void Variable::copy(int narg, char **from, char **to)
}
/* ----------------------------------------------------------------------
recursive method to evaluate a string
string can be a number: 0.0, -5.45, etc
string can be a keyword: lx, ly, lz, vol, etc
string can be a vector: x[123], y[3], vx[34], etc
value inside brackets must be global ID from 1 to Natoms
string can be a function: div(x,y), mult(x,y), add(x,y), xcm(group,x), etc
function args can be combo of number, keyword, vector, fn(), group, etc
see lists of valid keywords, vectors, and functions below
recursive evaluation of a "string"
string is defined as one of several items:
number = 0.0, -5.45, 2.8e-4, ...
thermo keyword = ke, vol, atoms, ...
variable keyword = v_a, v_myvar, ...
math function = div(x,y), mult(x,y), add(x,y), ...
group function = mass(group), xcm(group,x), ...
atom vector = x[123], y[3], vx[34], ...
compute vector = c_mytemp[0], c_thermo_press[3], ...
functions contain ()
can have 1 or 2 args, each of which can be a "string"
vectors contain []
single arg must be integer
for atom vectors, it is global ID of atom
for compute vectors, 0 is the scalar value, 1-N are vector values
keywords start with a lowercase letter (no parens or brackets)
numbers start with a digit or "." or "-" (no parens or brackets)
see lists of valid functions, vectors, keywords below
when string is evaluated, put result in a newly allocated string
return address of result string (will be freed by caller)
return the address of result string (will be freed by caller)
------------------------------------------------------------------------- */
char *Variable::evaluate(char *str)
@ -409,7 +424,10 @@ char *Variable::evaluate(char *str)
char *result = new char[32];
double answer;
// if string is "function", grab one or two args, evaulate args recursively
// string is a "function" since contains ()
// grab one or two args, separated by ","
// evaulate args recursively
// then evaluate math or group function
if (strchr(str,'(')) {
if (str[strlen(str)-1] != ')')
@ -452,11 +470,9 @@ char *Variable::evaluate(char *str)
char *strarg1 = NULL;
char *strarg2 = NULL;
// customize by adding function to this list and to if statement
// math functions: add(x,y),sub(x,y),mult(x,y),div(x,y),
// neg(x),pow(x,y),exp(x),ln(x),sqrt(x)
// group functions: mass(group),charge(group),xcm(group,dim),
// vcm(group,dim),bound(group,xmin),gyration(group)
// customize by adding math function to this list and to if statement
// add(x,y),sub(x,y),mult(x,y),div(x,y),neg(x),
// pow(x,y),exp(x),ln(x),sqrt(x)
if (strcmp(func,"add") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
@ -530,6 +546,10 @@ char *Variable::evaluate(char *str)
error->all("Cannot evaluate variable equal command");
answer = sqrt(value1);
// customize by adding group function to this list and to if statement
// mass(group),charge(group),xcm(group,dim),vcm(group,dim),
// bound(group,xmin),gyration(group)
} else if (strcmp(func,"mass") == 0) {
if (arg2) error->all("Cannot evaluate variable equal command");
int igroup = group->find(arg1);
@ -593,7 +613,7 @@ char *Variable::evaluate(char *str)
group->xcm(igroup,masstotal,xcm);
answer = group->gyration(igroup,masstotal,xcm);
} else error->all("Cannot evaluate variable equal command");
} else error->all("Invalid math/group function in variable equal command");
delete [] func;
delete [] arg1;
@ -604,13 +624,17 @@ char *Variable::evaluate(char *str)
}
sprintf(result,"%.10g",answer);
// if string is "vector", find which proc owns atom, grab vector value
// string is a "vector" since contains []
// index = everything between [] evaluated as integer
// if vector name starts with "c_", trailing chars are compute ID
// check if compute ID exists, invoke it with index as arg
// else is atom vector
// find which proc owns atom via atom->map()
// grab atom-based value with index as global atom ID
} else if (strchr(str,'[')) {
if (str[strlen(str)-1] != ']')
error->all("Cannot evaluate variable equal command");
if (atom->map_style == 0)
error->all("Cannot use vectors in variables unless atom map exists");
char *ptr = strchr(str,'[');
int n = ptr - str;
@ -625,77 +649,121 @@ char *Variable::evaluate(char *str)
arg = new char[n+1];
strncpy(arg,ptr,n);
arg[n] = '\0';
int i = atom->map(atoi(arg));
double mine;
if (i >= 0 && i < atom->nlocal) {
if (strncmp(vector,"c_",2) == 0) {
n = strlen(vector) - 2 + 1;
char *id = new char[n];
strcpy(id,&vector[2]);
// customize by adding vector to this list and to if statement
int icompute;
for (icompute = 0; icompute < modify->ncompute; icompute++)
if (strcmp(id,modify->compute[icompute]->id) == 0) break;
if (icompute == modify->ncompute)
error->all("Invalid compute ID in variable equal");
delete [] id;
modify->compute[icompute]->init();
// call compute() if index = 0, else compute_vector()
// make pre-call to Compute object's id_pre if it is defined
int index = atoi(arg);
if (index == 0) {
if (modify->compute[icompute]->scalar_flag == 0)
error->all("Variable compute ID does not compute scalar info");
if (modify->compute[icompute]->id_pre) {
int ipre = modify->find_compute(modify->compute[icompute]->id_pre);
if (ipre < 0) error->all("Could not pre-compute in variable equal");
answer = modify->compute[ipre]->compute_scalar();
}
answer = modify->compute[icompute]->compute_scalar();
} else if (index > 0) {
if (modify->compute[icompute]->vector_flag == 0)
error->all("Variable compute ID does not compute scalar info");
if (index > modify->compute[icompute]->size_vector)
error->all("Variable compute ID vector is not large enough");
if (modify->compute[icompute]->id_pre) {
int ipre = modify->find_compute(modify->compute[icompute]->id_pre);
if (ipre < 0) error->all("Could not pre-compute in variable equal");
modify->compute[ipre]->compute_vector();
}
modify->compute[icompute]->compute_vector();
answer = modify->compute[icompute]->vector[index-1];
} else error->all("Invalid compute ID index in variable equal");
} else {
if (atom->map_style == 0)
error->all("Cannot use atom vectors in variable "
"unless atom map exists");
int index = atom->map(atoi(arg));
// customize by adding atom vector to this list and to if statement
// x,y,z,vx,vy,vz,fx,fy,fz
if (strcmp(vector,"x") == 0) mine = atom->x[i][0];
else if (strcmp(vector,"y") == 0) mine = atom->x[i][1];
else if (strcmp(vector,"z") == 0) mine = atom->x[i][2];
else if (strcmp(vector,"vx") == 0) mine = atom->v[i][0];
else if (strcmp(vector,"vy") == 0) mine = atom->v[i][1];
else if (strcmp(vector,"vz") == 0) mine = atom->v[i][2];
else if (strcmp(vector,"fx") == 0) mine = atom->f[i][0];
else if (strcmp(vector,"fy") == 0) mine = atom->f[i][1];
else if (strcmp(vector,"fz") == 0) mine = atom->f[i][2];
double mine;
if (index >= 0 && index < atom->nlocal) {
else error->one("Invalid vector in variable equal command");
if (strcmp(vector,"x") == 0) mine = atom->x[index][0];
else if (strcmp(vector,"y") == 0) mine = atom->x[index][1];
else if (strcmp(vector,"z") == 0) mine = atom->x[index][2];
else if (strcmp(vector,"vx") == 0) mine = atom->v[index][0];
else if (strcmp(vector,"vy") == 0) mine = atom->v[index][1];
else if (strcmp(vector,"vz") == 0) mine = atom->v[index][2];
else if (strcmp(vector,"fx") == 0) mine = atom->f[index][0];
else if (strcmp(vector,"fy") == 0) mine = atom->f[index][1];
else if (strcmp(vector,"fz") == 0) mine = atom->f[index][2];
else error->one("Invalid atom vector in variable equal command");
} else mine = 0.0;
} else mine = 0.0;
MPI_Allreduce(&mine,&answer,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&mine,&answer,1,MPI_DOUBLE,MPI_SUM,world);
}
delete [] vector;
delete [] arg;
sprintf(result,"%.10g",answer);
// if string is "keyword", compute appropriate value via thermo
// string is "keyword" since starts with lowercase letter
// if keyword starts with "v_", trailing chars are variable name
// evaluate it via retrieve(), convert it to double
// else is thermo keyword
// evaluate it via evaluate_keyword()
} else if (str[0] - 'a' >= 0 && str[0] - 'a' < 26) {
// compute appropriate value via thermo
// customize by adding keyword to this list and to if statement
// keywords defined by thermo_style custom are passed to compute_value()
} else if (islower(str[0])) {
if (domain->box_exist == 0)
error->all("Using variable equal keyword before simulation box is defined");
if (strncmp(str,"v_",2) == 0) {
int n = strlen(str) - 2 + 1;
char *id = new char[n];
strcpy(id,&str[2]);
// process these keywords here, not in thermo
// they are allowed anytime after simulation box is defined
char *v = retrieve(id);
if (v == NULL)
error->all("Invalid variable name in variable equal command");
delete [] id;
if (strcmp(str,"step") == 0)
answer = update->ntimestep;
else if (strcmp(str,"atoms") == 0)
answer = atom->natoms;
else if (strcmp(str,"lx") == 0)
answer = domain->xprd;
else if (strcmp(str,"ly") == 0)
answer = domain->yprd;
else if (strcmp(str,"lz") == 0)
answer = domain->zprd;
else if (strcmp(str,"vol") == 0)
answer = domain->xprd * domain->yprd * domain->zprd;
answer = atof(v);
// process other keywords via thermo
// error if 1st run has not yet started
// warning if out-of-sync with thermo, since values can be bogus
else {
if (update->first_update == 0)
error->all("Using variable equal keyword before initial run");
if (update->ntimestep != output->next_thermo && me == 0)
error->warning("Using variable equal keyword with non-current thermo");
int flag = output->thermo->compute_value(str,&answer);
if (flag) error->all("Invalid keyword in variable equal command");
} else {
int flag = output->thermo->evaluate_keyword(str,&answer);
if (flag) error->all("Invalid thermo keyword in variable equal command");
}
sprintf(result,"%.10g",answer);
// string is a number, just copy to result
// string is a number since starts with digit or "." or "-"
// just copy to result
} else strcpy(result,str);
} else if (isdigit(str[0]) || str[0] == '.' || str[0] == '-') {
strcpy(result,str);
// string is an error
} else error->all("Cannot evaluate variable equal command");
// return newly allocated string