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fix_eos_table.cpp
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Thu, Oct 31, 16:37

fix_eos_table.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: James Larentzos (U.S. Army Research Laboratory)
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include "fix_eos_table.h"
#include "atom.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#define MAXLINE 1024
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixEOStable::FixEOStable(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), ntables(0), tables(NULL)
{
if (narg != 7) error->all(FLERR,"Illegal fix eos/table command");
nevery = 1;
if (strcmp(arg[3],"linear") == 0) tabstyle = LINEAR;
else error->all(FLERR,"Unknown table style in fix eos/table");
tablength = force->inumeric(FLERR,arg[5]);
if (tablength < 2) error->all(FLERR,"Illegal number of eos/table entries");
ntables = 0;
tables = NULL;
int me;
MPI_Comm_rank(world,&me);
tables = (Table *)
memory->srealloc(tables,(ntables+2)*sizeof(Table),"eos:tables");
Table *tb = &tables[ntables];
Table *tb2 = &tables[ntables+1];
null_table(tb);
null_table(tb2);
if (me == 0) read_table(tb,tb2,arg[4],arg[6]);
bcast_table(tb);
bcast_table(tb2);
// error check on table parameters
if (tb->ninput <= 1) error->one(FLERR,"Invalid eos/table length");
tb->lo = tb->rfile[0];
tb->hi = tb->rfile[tb->ninput-1];
if (tb->lo >= tb->hi) error->all(FLERR,"eos/table values are not increasing");
if (tb2->ninput <= 1) error->one(FLERR,"Invalid eos/table length");
tb2->lo = tb2->rfile[0];
tb2->hi = tb2->rfile[tb2->ninput-1];
if (tb2->lo >= tb2->hi) error->all(FLERR,"eos/table values are not increasing");
// spline read-in and compute r,e,f vectors within table
spline_table(tb);
compute_table(tb);
spline_table(tb2);
compute_table(tb2);
ntables++;
if (atom->dpd_flag != 1)
error->all(FLERR,"FixEOStable requires atom_style with internal temperature and energies (e.g. dpd)");
}
/* ---------------------------------------------------------------------- */
FixEOStable::~FixEOStable()
{
for (int m = 0; m < 2*ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
}
/* ---------------------------------------------------------------------- */
int FixEOStable::setmask()
{
int mask = 0;
mask |= POST_INTEGRATE;
mask |= END_OF_STEP;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixEOStable::init()
{
int nlocal = atom->nlocal;
int *mask = atom->mask;
double *uCond = atom->uCond;
double *uMech = atom->uMech;
double *dpdTheta = atom->dpdTheta;
double tmp;
if(this->restart_reset){
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
temperature_lookup(uCond[i]+uMech[i],dpdTheta[i]);
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if(dpdTheta[i] <= 0.0)
error->one(FLERR,"Internal temperature <= zero");
energy_lookup(dpdTheta[i],tmp);
uCond[i] = 0.0;
uMech[i] = tmp;
}
}
}
/* ---------------------------------------------------------------------- */
void FixEOStable::post_integrate()
{
int nlocal = atom->nlocal;
int *mask = atom->mask;
double *uCond = atom->uCond;
double *uMech = atom->uMech;
double *dpdTheta = atom->dpdTheta;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit){
temperature_lookup(uCond[i]+uMech[i],dpdTheta[i]);
if(dpdTheta[i] <= 0.0)
error->one(FLERR,"Internal temperature <= zero");
}
}
/* ---------------------------------------------------------------------- */
void FixEOStable::end_of_step()
{
int nlocal = atom->nlocal;
int *mask = atom->mask;
double *uCond = atom->uCond;
double *uMech = atom->uMech;
double *dpdTheta = atom->dpdTheta;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit){
temperature_lookup(uCond[i]+uMech[i],dpdTheta[i]);
if(dpdTheta[i] <= 0.0)
error->one(FLERR,"Internal temperature <= zero");
}
}
/* ---------------------------------------------------------------------- */
void FixEOStable::null_table(Table *tb)
{
tb->rfile = tb->efile = NULL;
tb->e2file = NULL;
tb->r = tb->e = tb->de = NULL;
tb->e2 = NULL;
}
/* ---------------------------------------------------------------------- */
void FixEOStable::free_table(Table *tb)
{
memory->destroy(tb->rfile);
memory->destroy(tb->efile);
memory->destroy(tb->e2file);
memory->destroy(tb->r);
memory->destroy(tb->e);
memory->destroy(tb->de);
memory->destroy(tb->e2);
}
/* ----------------------------------------------------------------------
read table file, only called by proc 0
------------------------------------------------------------------------- */
void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword)
{
char line[MAXLINE];
// open file
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);
error->one(FLERR,str);
}
// loop until section found with matching keyword
while (1) {
if (fgets(line,MAXLINE,fp) == NULL)
error->one(FLERR,"Did not find keyword in table file");
if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
if (line[0] == '#') continue; // comment
char *word = strtok(line," \t\n\r");
if (strcmp(word,keyword) == 0) break; // matching keyword
fgets(line,MAXLINE,fp); // no match, skip section
param_extract(tb,tb2,line);
fgets(line,MAXLINE,fp);
for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
}
// read args on 2nd line of section
// allocate table arrays for file values
fgets(line,MAXLINE,fp);
param_extract(tb,tb2,line);
memory->create(tb->rfile,tb->ninput,"eos:rfile");
memory->create(tb->efile,tb->ninput,"eos:efile");
memory->create(tb2->rfile,tb2->ninput,"eos:rfile2");
memory->create(tb2->efile,tb2->ninput,"eos:efile2");
// read r,e table values from file
int itmp;
fgets(line,MAXLINE,fp);
for (int i = 0; i < tb->ninput; i++) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %lg",&itmp,&tb->rfile[i],&tb->efile[i]);
sscanf(line,"%d %lg %lg",&itmp,&tb2->efile[i],&tb2->rfile[i]);
}
fclose(fp);
}
/* ----------------------------------------------------------------------
build spline representation of e,f over entire range of read-in table
this function sets these values in e2file
------------------------------------------------------------------------- */
void FixEOStable::spline_table(Table *tb)
{
memory->create(tb->e2file,tb->ninput,"eos:e2file");
double ep0 = 0.0;
double epn = 0.0;
spline(tb->rfile,tb->efile,tb->ninput,ep0,epn,tb->e2file);
}
/* ----------------------------------------------------------------------
compute r,e,f vectors from splined values
------------------------------------------------------------------------- */
void FixEOStable::compute_table(Table *tb)
{
// delta = table spacing for N-1 bins
int tlm1 = tablength-1;
tb->delta = (tb->hi - tb->lo)/ tlm1;
tb->invdelta = 1.0/tb->delta;
tb->deltasq6 = tb->delta*tb->delta / 6.0;
// N-1 evenly spaced bins in r from min to max
// r,e = value at lower edge of bin
// de values = delta values of e,f
// r,e are N in length so de arrays can compute difference
memory->create(tb->r,tablength,"eos:r");
memory->create(tb->e,tablength,"eos:e");
memory->create(tb->de,tlm1,"eos:de");
memory->create(tb->e2,tablength,"eos:e2");
double a;
for (int i = 0; i < tablength; i++) {
a = tb->lo + i*tb->delta;
tb->r[i] = a;
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,a);
}
for (int i = 0; i < tlm1; i++) {
tb->de[i] = tb->e[i+1] - tb->e[i];
}
}
/* ----------------------------------------------------------------------
extract attributes from parameter line in table section
format of line: N value
N is required, other params are optional
------------------------------------------------------------------------- */
void FixEOStable::param_extract(Table *tb, Table *tb2, char *line)
{
tb->ninput = 0;
tb2->ninput = 0;
char *word = strtok(line," \t\n\r\f");
while (word) {
if (strcmp(word,"N") == 0) {
word = strtok(NULL," \t\n\r\f");
tb->ninput = atoi(word);
tb2->ninput = atoi(word);
} else {
error->one(FLERR,"Invalid keyword in fix eos/table parameters");
}
word = strtok(NULL," \t\n\r\f");
}
if (tb->ninput == 0) error->one(FLERR,"fix eos/table parameters did not set N");
if (tb2->ninput == 0) error->one(FLERR,"fix eos/table parameters did not set N");
}
/* ----------------------------------------------------------------------
broadcast read-in table info from proc 0 to other procs
this function communicates these values in Table:
ninput,rfile,efile
------------------------------------------------------------------------- */
void FixEOStable::bcast_table(Table *tb)
{
MPI_Bcast(&tb->ninput,1,MPI_INT,0,world);
int me;
MPI_Comm_rank(world,&me);
if (me > 0) {
memory->create(tb->rfile,tb->ninput,"eos:rfile");
memory->create(tb->efile,tb->ninput,"eos:efile");
}
MPI_Bcast(tb->rfile,tb->ninput,MPI_DOUBLE,0,world);
MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
spline and splint routines modified from Numerical Recipes
------------------------------------------------------------------------- */
void FixEOStable::spline(double *x, double *y, int n,
double yp1, double ypn, double *y2)
{
int i,k;
double p,qn,sig,un;
double *u = new double[n];
if (yp1 > 0.99e30) y2[0] = u[0] = 0.0;
else {
y2[0] = -0.5;
u[0] = (3.0/(x[1]-x[0])) * ((y[1]-y[0]) / (x[1]-x[0]) - yp1);
}
for (i = 1; i < n-1; i++) {
sig = (x[i]-x[i-1]) / (x[i+1]-x[i-1]);
p = sig*y2[i-1] + 2.0;
y2[i] = (sig-1.0) / p;
u[i] = (y[i+1]-y[i]) / (x[i+1]-x[i]) - (y[i]-y[i-1]) / (x[i]-x[i-1]);
u[i] = (6.0*u[i] / (x[i+1]-x[i-1]) - sig*u[i-1]) / p;
}
if (ypn > 0.99e30) qn = un = 0.0;
else {
qn = 0.5;
un = (3.0/(x[n-1]-x[n-2])) * (ypn - (y[n-1]-y[n-2]) / (x[n-1]-x[n-2]));
}
y2[n-1] = (un-qn*u[n-2]) / (qn*y2[n-2] + 1.0);
for (k = n-2; k >= 0; k--) y2[k] = y2[k]*y2[k+1] + u[k];
delete [] u;
}
/* ---------------------------------------------------------------------- */
double FixEOStable::splint(double *xa, double *ya, double *y2a, int n, double x)
{
int klo,khi,k;
double h,b,a,y;
klo = 0;
khi = n-1;
while (khi-klo > 1) {
k = (khi+klo) >> 1;
if (xa[k] > x) khi = k;
else klo = k;
}
h = xa[khi]-xa[klo];
a = (xa[khi]-x) / h;
b = (x-xa[klo]) / h;
y = a*ya[klo] + b*ya[khi] +
((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
return y;
}
/* ----------------------------------------------------------------------
calculate internal energy u at temperature t
insure t is between min/max
------------------------------------------------------------------------- */
void FixEOStable::energy_lookup(double t, double &u)
{
int itable;
double fraction;
Table *tb = &tables[0];
if(t < tb->lo || t > tb->hi){
printf("Temperature=%lf TableMin=%lf TableMax=%lf\n",t,tb->lo,tb->hi);
error->one(FLERR,"Temperature is not within table cutoffs");
}
if (tabstyle == LINEAR) {
itable = static_cast<int> ((t - tb->lo) * tb->invdelta);
fraction = (t - tb->r[itable]) * tb->invdelta;
u = tb->e[itable] + fraction*tb->de[itable];
}
}
/* ----------------------------------------------------------------------
calculate temperature t at energy u
insure u is between min/max
------------------------------------------------------------------------- */
void FixEOStable::temperature_lookup(double u, double &t)
{
int itable;
double fraction;
Table *tb = &tables[1];
if(u < tb->lo || u > tb->hi){
printf("Energy=%lf TableMin=%lf TableMax=%lf\n",u,tb->lo,tb->hi);
error->one(FLERR,"Energy is not within table cutoffs");
}
if (tabstyle == LINEAR) {
itable = static_cast<int> ((u - tb->lo) * tb->invdelta);
fraction = (u - tb->r[itable]) * tb->invdelta;
t = tb->e[itable] + fraction*tb->de[itable];
}
}

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