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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2006-09-27 19:51:33 +00:00
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "string.h"
#include "unistd.h"
#include "variable.h"
#include "universe.h"
#include "atom.h"
#include "update.h"
#include "group.h"
#include "domain.h"
#include "output.h"
#include "thermo.h"
#include "memory.h"
#include "error.h"
#define VARDELTA 4
enum{INDEX,LOOP,EQUAL,WORLD,UNIVERSE};
/* ---------------------------------------------------------------------- */
Variable::Variable()
{
MPI_Comm_rank(world,&me);
nvar = maxvar = 0;
names = NULL;
style = NULL;
num = NULL;
index = NULL;
data = NULL;
}
/* ---------------------------------------------------------------------- */
Variable::~Variable()
{
for (int i = 0; i < nvar; i++) {
delete [] names[i];
for (int j = 0; j < num[i]; j++) delete [] data[i][j];
delete [] data[i];
}
memory->sfree(names);
memory->sfree(style);
memory->sfree(num);
memory->sfree(index);
memory->sfree(data);
}
/* ----------------------------------------------------------------------
called by variable command in input script
------------------------------------------------------------------------- */
void Variable::set(int narg, char **arg)
{
if (narg < 3) error->all("Illegal variable command");
// if var already exists, just skip (except EQUAL vars)
if (find(arg[0]) >= 0 && strcmp(arg[1],"equal") != 0) return;
// make space for new variable
if (nvar == maxvar) {
maxvar += VARDELTA;
names = (char **)
memory->srealloc(names,maxvar*sizeof(char *),"var:names");
style = (int *) memory->srealloc(style,maxvar*sizeof(int),"var:style");
num = (int *) memory->srealloc(num,maxvar*sizeof(int),"var:num");
index = (int *) memory->srealloc(index,maxvar*sizeof(int),"var:index");
data = (char ***)
memory->srealloc(data,maxvar*sizeof(char **),"var:data");
}
// INDEX
// num = listed args, index = 1st value, data = copied args
if (strcmp(arg[1],"index") == 0) {
style[nvar] = INDEX;
num[nvar] = narg - 2;
index[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(num[nvar],&arg[2],data[nvar]);
// LOOP
// num = N, index = 1st value, data = list of NULLS since never used
} else if (strcmp(arg[1],"loop") == 0) {
style[nvar] = LOOP;
num[nvar] = atoi(arg[2]);
index[nvar] = 0;
data[nvar] = new char*[num[nvar]];
for (int i = 0; i < num[nvar]; i++) data[nvar][i] = NULL;
// EQUAL
// remove pre-existing var if also style EQUAL (allows it to be reset)
// num = 2, index = 1st value
// data = 2 values, 1st is string to eval, 2nd is filled on retrieval
} else if (strcmp(arg[1],"equal") == 0) {
if (find(arg[0]) >= 0) {
if (style[find(arg[0])] != EQUAL)
error->all("Cannot redefine variable as a different style");
remove(find(arg[0]));
}
style[nvar] = EQUAL;
num[nvar] = 2;
index[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(1,&arg[2],data[nvar]);
data[nvar][1] = NULL;
// WORLD
// num = listed args, index = partition this proc is in, data = copied args
// error check that num = # of worlds in universe
} else if (strcmp(arg[1],"world") == 0) {
style[nvar] = WORLD;
num[nvar] = narg - 2;
if (num[nvar] != universe->nworlds)
error->all("World variable count doesn't match # of partitions");
index[nvar] = universe->iworld;
data[nvar] = new char*[num[nvar]];
copy(num[nvar],&arg[2],data[nvar]);
// UNIVERSE
// num = listed args, index = partition this proc is in, data = copied args
// universe proc 0 creates lock file
// error check that all other universe variables are same length
} else if (strcmp(arg[1],"universe") == 0) {
style[nvar] = UNIVERSE;
num[nvar] = narg - 2;
if (num[nvar] < universe->nworlds)
error->all("Universe variable count < # of partitions");
index[nvar] = universe->iworld;
data[nvar] = new char*[num[nvar]];
copy(num[nvar],&arg[2],data[nvar]);
if (universe->me == 0) {
FILE *fp = fopen("tmp.lammps.variable","w");
fprintf(fp,"%d\n",universe->nworlds);
fclose(fp);
}
for (int jvar = 0; jvar < nvar; jvar++)
if (num[jvar] && style[jvar] == UNIVERSE && num[nvar] != num[jvar])
error->all("All universe variables must have same # of values");
if (me == 0) {
if (universe->uscreen)
fprintf(universe->uscreen,
"Initial ${%s} setting: value %d on partition %d\n",
arg[0],index[nvar]+1,universe->iworld);
if (universe->ulogfile)
fprintf(universe->ulogfile,
"Initial ${%s} setting: value %d on partition %d\n",
arg[0],index[nvar]+1,universe->iworld);
}
} else error->all("Illegal variable command");
// set variable name (after possible EQUAL remove)
names[nvar] = new char[strlen(arg[0]) + 1];
strcpy(names[nvar],arg[0]);
nvar++;
}
/* ----------------------------------------------------------------------
single-value INDEX variable created by command-line argument
------------------------------------------------------------------------- */
void Variable::set(char *name, char *value)
{
int ivar = find(name);
if (ivar >= 0) error->all("Command-line variable already exists");
if (nvar == maxvar) {
maxvar += VARDELTA;
names = (char **)
memory->srealloc(style,maxvar*sizeof(char *),"var:names");
style = (int *) memory->srealloc(style,maxvar*sizeof(int),"var:style");
num = (int *) memory->srealloc(num,maxvar*sizeof(int),"var:num");
index = (int *) memory->srealloc(index,maxvar*sizeof(int),"var:index");
data = (char ***)
memory->srealloc(data,maxvar*sizeof(char **),"var:data");
}
names[nvar] = new char[strlen(name) + 1];
strcpy(names[nvar],name);
style[nvar] = INDEX;
num[nvar] = 1;
index[nvar] = 0;
data[nvar] = new char*[num[nvar]];
copy(1,&value,data[nvar]);
nvar++;
}
/* ----------------------------------------------------------------------
increment variable(s)
return 0 if OK if successfully incremented
return 1 if any variable is exhausted, free the variable to allow re-use
------------------------------------------------------------------------- */
int Variable::next(int narg, char **arg)
{
int ivar;
if (narg == 0) error->all("Illegal next command");
// check that variables exist and are all the same style
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
if (ivar == -1) error->all("Invalid variable in next command");
if (style[ivar] != style[find(arg[0])])
error->all("All variables in next command must be same style");
}
// check for invalid styles EQUAL or WORLD
int istyle = style[find(arg[0])];
if (istyle == EQUAL || istyle == WORLD)
error->all("Invalid variable style with next command");
// increment all variables in list
// if any variable is exhausted, set flag = 1 and remove var to allow re-use
int flag = 0;
if (istyle == INDEX || istyle == LOOP) {
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
index[ivar]++;
if (index[ivar] >= num[ivar]) {
flag = 1;
remove(ivar);
}
}
} else if (istyle == UNIVERSE) {
// wait until lock file can be created and owned by proc 0 of this world
// read next available index and Bcast it within my world
// set all variables in list to nextindex
int nextindex;
if (me == 0) {
while (1) {
if (!rename("tmp.lammps.variable","tmp.lammps.variable.lock")) break;
usleep(100000);
}
FILE *fp = fopen("tmp.lammps.variable.lock","r");
fscanf(fp,"%d",&nextindex);
fclose(fp);
fp = fopen("tmp.lammps.variable.lock","w");
fprintf(fp,"%d\n",nextindex+1);
fclose(fp);
rename("tmp.lammps.variable.lock","tmp.lammps.variable");
if (universe->uscreen)
fprintf(universe->uscreen,
"Increment via next: value %d on partition %d\n",
nextindex+1,universe->iworld);
if (universe->ulogfile)
fprintf(universe->ulogfile,
"Increment via next: value %d on partition %d\n",
nextindex+1,universe->iworld);
}
MPI_Bcast(&nextindex,1,MPI_INT,0,world);
for (int iarg = 0; iarg < narg; iarg++) {
ivar = find(arg[iarg]);
index[ivar] = nextindex;
if (index[ivar] >= num[ivar]) {
flag = 1;
remove(ivar);
}
}
}
return flag;
}
/* ----------------------------------------------------------------------
return ptr to the data text associated with a variable
return NULL if no variable or index is bad, caller must respond
------------------------------------------------------------------------- */
char *Variable::retrieve(char *name)
{
int ivar = find(name);
if (ivar == -1) return NULL;
if (index[ivar] >= num[ivar]) return NULL;
char *str;
if (style[ivar] == INDEX) {
str = data[ivar][index[ivar]];
} else if (style[ivar] == LOOP) {
char *value = new char[16];
sprintf(value,"%d",index[ivar]+1);
int n = strlen(value) + 1;
if (data[ivar][0]) delete [] data[ivar][0];
data[ivar][0] = new char[n];
strcpy(data[ivar][0],value);
delete [] value;
str = data[ivar][0];
} else if (style[ivar] == EQUAL) {
char *value = evaluate(data[ivar][0]);
int n = strlen(value) + 1;
if (data[ivar][1]) delete [] data[ivar][1];
data[ivar][1] = new char[n];
strcpy(data[ivar][1],value);
delete [] value;
str = data[ivar][1];
} else if (style[ivar] == WORLD) {
str = data[ivar][index[ivar]];
} else if (style[ivar] == UNIVERSE) {
str = data[ivar][index[ivar]];
}
return str;
}
/* ----------------------------------------------------------------------
search for name in list of variables names
return index or -1 if not found
------------------------------------------------------------------------- */
int Variable::find(char *name)
{
for (int i = 0; i < nvar; i++)
if (strcmp(name,names[i]) == 0) return i;
return -1;
}
/* ----------------------------------------------------------------------
remove Nth variable from list and compact list
------------------------------------------------------------------------- */
void Variable::remove(int n)
{
delete [] names[n];
for (int i = 0; i < num[n]; i++) delete [] data[n][i];
delete [] data[n];
for (int i = n+1; i < nvar; i++) {
names[i-1] = names[i];
style[i-1] = style[i];
num[i-1] = num[i];
index[i-1] = index[i];
data[i-1] = data[i];
}
nvar--;
}
/* ----------------------------------------------------------------------
copy narg strings from **from to **to
------------------------------------------------------------------------- */
void Variable::copy(int narg, char **from, char **to)
{
int n;
for (int i = 0; i < narg; i++) {
n = strlen(from[i]) + 1;
to[i] = new char[n];
strcpy(to[i],from[i]);
}
}
/* ----------------------------------------------------------------------
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
when string is evaluated, put result in a newly allocated string
return address of result string (will be freed by caller)
------------------------------------------------------------------------- */
char *Variable::evaluate(char *str)
{
// allocate a new string for the eventual result
char *result = new char[32];
double answer;
// if string is "function", grab one or two args, evaulate args recursively
if (strchr(str,'(')) {
if (str[strlen(str)-1] != ')')
error->all("Cannot evaluate variable equal command");
char *ptr = strchr(str,'(');
int n = ptr - str;
char *func = new char[n+1];
strncpy(func,str,n);
func[n] = '\0';
char *comma = ++ptr;
int level = 0;
while (1) {
if (*comma == '\0')
error->all("Cannot evaluate variable equal command");
else if (*comma == ',' && level == 0) break;
else if (*comma == ')' && level == 0) break;
else if (*comma == '(') level++;
else if (*comma == ')') level--;
comma++;
}
char *arg1,*arg2;
n = comma - ptr;
arg1 = new char[n+1];
strncpy(arg1,ptr,n);
arg1[n] = '\0';
if (*comma == ',') {
ptr = comma + 1;
comma = &str[strlen(str)-1];
n = comma - ptr;
arg2 = new char[n+1];
strncpy(arg2,ptr,n);
arg2[n] = '\0';
} else arg2 = NULL;
double value1,value2;
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)
if (strcmp(func,"add") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
strarg1 = evaluate(arg1);
strarg2 = evaluate(arg2);
value1 = atof(strarg1);
value2 = atof(strarg2);
answer = value1 + value2;
} else if (strcmp(func,"sub") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
strarg1 = evaluate(arg1);
strarg2 = evaluate(arg2);
value1 = atof(strarg1);
value2 = atof(strarg2);
answer = value1 - value2;
} else if (strcmp(func,"mult") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
strarg1 = evaluate(arg1);
strarg2 = evaluate(arg2);
value1 = atof(strarg1);
value2 = atof(strarg2);
answer = value1 * value2;
} else if (strcmp(func,"div") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
strarg1 = evaluate(arg1);
strarg2 = evaluate(arg2);
value1 = atof(strarg1);
value2 = atof(strarg2);
if (value2 == 0.0)
error->all("Cannot evaluate variable equal command");
answer = value1 / value2;
} else if (strcmp(func,"neg") == 0) {
if (arg2) error->all("Cannot evaluate variable equal command");
strarg1 = evaluate(arg1);
value1 = atof(strarg1);
answer = -value1;
} else if (strcmp(func,"pow") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
strarg1 = evaluate(arg1);
strarg2 = evaluate(arg2);
value1 = atof(strarg1);
value2 = atof(strarg2);
if (value2 == 0.0)
error->all("Cannot evaluate variable equal command");
answer = pow(value1,value2);
} else if (strcmp(func,"exp") == 0) {
if (arg2) error->all("Cannot evaluate variable equal command");
strarg1 = evaluate(arg1);
value1 = atof(strarg1);
answer = exp(value1);
} else if (strcmp(func,"ln") == 0) {
if (arg2) error->all("Cannot evaluate variable equal command");
strarg1 = evaluate(arg1);
value1 = atof(strarg1);
if (value1 == 0.0)
error->all("Cannot evaluate variable equal command");
answer = log(value1);
} else if (strcmp(func,"sqrt") == 0) {
if (arg2) error->all("Cannot evaluate variable equal command");
strarg1 = evaluate(arg1);
value1 = atof(strarg1);
if (value1 == 0.0)
error->all("Cannot evaluate variable equal command");
answer = sqrt(value1);
} else if (strcmp(func,"mass") == 0) {
if (arg2) error->all("Cannot evaluate variable equal command");
int igroup = group->find(arg1);
if (igroup == -1) error->all("Variable equal group ID does not exist");
atom->check_mass();
answer = group->mass(igroup);
} else if (strcmp(func,"charge") == 0) {
if (arg2) error->all("Cannot evaluate variable equal command");
int igroup = group->find(arg1);
if (igroup == -1) error->all("Variable equal group ID does not exist");
answer = group->charge(igroup);
} else if (strcmp(func,"xcm") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
int igroup = group->find(arg1);
if (igroup == -1) error->all("Variable equal group ID does not exist");
atom->check_mass();
double masstotal = group->mass(igroup);
double xcm[3];
group->xcm(igroup,masstotal,xcm);
if (strcmp(arg2,"x") == 0) answer = xcm[0];
else if (strcmp(arg2,"y") == 0) answer = xcm[1];
else if (strcmp(arg2,"z") == 0) answer = xcm[2];
else error->all("Cannot evaluate variable equal command");
} else if (strcmp(func,"vcm") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
int igroup = group->find(arg1);
if (igroup == -1) error->all("Variable equal group ID does not exist");
atom->check_mass();
double masstotal = group->mass(igroup);
double vcm[3];
group->vcm(igroup,masstotal,vcm);
if (strcmp(arg2,"x") == 0) answer = vcm[0];
else if (strcmp(arg2,"y") == 0) answer = vcm[1];
else if (strcmp(arg2,"z") == 0) answer = vcm[2];
else error->all("Cannot evaluate variable equal command");
} else if (strcmp(func,"bound") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
int igroup = group->find(arg1);
if (igroup == -1) error->all("Variable equal group ID does not exist");
double minmax[6];
group->bounds(igroup,minmax);
if (strcmp(arg2,"xmin") == 0) answer = minmax[0];
else if (strcmp(arg2,"xmax") == 0) answer = minmax[1];
if (strcmp(arg2,"ymin") == 0) answer = minmax[2];
else if (strcmp(arg2,"ymax") == 0) answer = minmax[3];
if (strcmp(arg2,"zmin") == 0) answer = minmax[4];
else if (strcmp(arg2,"zmax") == 0) answer = minmax[5];
else error->all("Cannot evaluate variable equal command");
} else if (strcmp(func,"gyration") == 0) {
if (!arg2) error->all("Cannot evaluate variable equal command");
int igroup = group->find(arg1);
if (igroup == -1) error->all("Variable equal group ID does not exist");
atom->check_mass();
double masstotal = group->mass(igroup);
double xcm[3];
group->xcm(igroup,masstotal,xcm);
answer = group->gyration(igroup,masstotal,xcm);
} else error->all("Cannot evaluate variable equal command");
delete [] func;
delete [] arg1;
delete [] strarg1;
if (arg2) {
delete [] arg2;
delete [] strarg2;
}
sprintf(result,"%g",answer);
// if string is "vector", find which proc owns atom, grab vector value
} 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;
char *vector = new char[n+1];
strncpy(vector,str,n);
vector[n] = '\0';
char *arg;
ptr++;
char *ptr2 = &str[strlen(str)-1];
n = ptr2 - ptr;
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) {
// customize by adding 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];
else error->one("Invalid vector in variable equal command");
} else mine = 0.0;
MPI_Allreduce(&mine,&answer,1,MPI_DOUBLE,MPI_SUM,world);
delete [] vector;
delete [] arg;
sprintf(result,"%g",answer);
// if string is "keyword", compute appropriate value via thermo
} else if (str[0] - 'a' >= 0 && str[0] - 'a' < 26) {
// customize by adding keyword to this list and to if statement
// keywords defined by thermo_style custom are passed to compute_value()
if (domain->box_exist == 0)
error->all("Using variable equal keyword before simulation box is defined");
// process these keywords here, not in thermo
// they are allowed anytime after simulation box is defined
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;
// 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");
}
sprintf(result,"%g",answer);
// string is a number, just copy to result
} else strcpy(result,str);
// return newly allocated string
return result;
}