434 lines
12 KiB
C++
434 lines
12 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: James Larentzos (U.S. Army Research Laboratory)
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------------------------------------------------------------------------- */
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#include <stdlib.h>
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#include <string.h>
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#include "fix_eos_table.h"
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#include "atom.h"
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#include "error.h"
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#include "force.h"
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#include "memory.h"
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#define MAXLINE 1024
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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixEOStable::FixEOStable(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg != 7) error->all(FLERR,"Illegal fix eos/table command");
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restart_peratom = 1;
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nevery = 1;
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if (strcmp(arg[3],"linear") == 0) tabstyle = LINEAR;
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else error->all(FLERR,"Unknown table style in fix eos/table");
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tablength = force->inumeric(FLERR,arg[5]);
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if (tablength < 2) error->all(FLERR,"Illegal number of eos/table entries");
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ntables = 0;
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tables = NULL;
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int me;
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MPI_Comm_rank(world,&me);
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tables = (Table *)
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memory->srealloc(tables,(ntables+2)*sizeof(Table),"eos:tables");
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Table *tb = &tables[ntables];
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Table *tb2 = &tables[ntables+1];
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null_table(tb);
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null_table(tb2);
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if (me == 0) read_table(tb,tb2,arg[4],arg[6]);
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bcast_table(tb);
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bcast_table(tb2);
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// error check on table parameters
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if (tb->ninput <= 1) error->one(FLERR,"Invalid eos/table length");
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tb->lo = tb->rfile[0];
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tb->hi = tb->rfile[tb->ninput-1];
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if (tb->lo >= tb->hi) error->all(FLERR,"eos/table values are not increasing");
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if (tb2->ninput <= 1) error->one(FLERR,"Invalid eos/table length");
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tb2->lo = tb2->rfile[0];
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tb2->hi = tb2->rfile[tb2->ninput-1];
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if (tb2->lo >= tb2->hi) error->all(FLERR,"eos/table values are not increasing");
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// spline read-in and compute r,e,f vectors within table
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spline_table(tb);
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compute_table(tb);
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spline_table(tb2);
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compute_table(tb2);
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ntables++;
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}
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/* ---------------------------------------------------------------------- */
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FixEOStable::~FixEOStable()
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{
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for (int m = 0; m < 2*ntables; m++) free_table(&tables[m]);
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memory->sfree(tables);
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}
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/* ---------------------------------------------------------------------- */
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int FixEOStable::setmask()
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{
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int mask = 0;
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mask |= POST_INTEGRATE;
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mask |= END_OF_STEP;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixEOStable::init()
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{
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int nlocal = atom->nlocal;
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int *mask = atom->mask;
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double *uCond = atom->uCond;
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double *uMech = atom->uMech;
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double *dpdTheta = atom->dpdTheta;
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double tmp;
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if(this->restart_reset){
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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temperature_lookup(uCond[i]+uMech[i],dpdTheta[i]);
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} else {
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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energy_lookup(dpdTheta[i],tmp);
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uCond[i] = tmp / double(2.0);
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uMech[i] = tmp / double(2.0);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixEOStable::post_integrate()
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{
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int nlocal = atom->nlocal;
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int *mask = atom->mask;
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double *uCond = atom->uCond;
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double *uMech = atom->uMech;
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double *dpdTheta = atom->dpdTheta;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit){
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temperature_lookup(uCond[i]+uMech[i],dpdTheta[i]);
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if(dpdTheta[i] <= double(0.0))
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error->one(FLERR,"Internal temperature < zero");
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixEOStable::end_of_step()
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{
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int nlocal = atom->nlocal;
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int *mask = atom->mask;
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double *uCond = atom->uCond;
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double *uMech = atom->uMech;
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double *dpdTheta = atom->dpdTheta;
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for (int i = 0; i < nlocal; i++)
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if (mask[i] & groupbit){
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temperature_lookup(uCond[i]+uMech[i],dpdTheta[i]);
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if(dpdTheta[i] <= double(0.0))
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error->one(FLERR,"Internal temperature < zero");
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixEOStable::null_table(Table *tb)
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{
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tb->rfile = tb->efile = NULL;
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tb->e2file = NULL;
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tb->r = tb->e = tb->de = NULL;
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tb->e2 = NULL;
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}
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/* ---------------------------------------------------------------------- */
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void FixEOStable::free_table(Table *tb)
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{
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memory->destroy(tb->rfile);
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memory->destroy(tb->efile);
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memory->destroy(tb->e2file);
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memory->destroy(tb->r);
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memory->destroy(tb->e);
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memory->destroy(tb->de);
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memory->destroy(tb->e2);
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}
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/* ----------------------------------------------------------------------
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read table file, only called by proc 0
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------------------------------------------------------------------------- */
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void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword)
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{
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char line[MAXLINE];
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// open file
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FILE *fp = fopen(file,"r");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open file %s",file);
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error->one(FLERR,str);
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}
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// loop until section found with matching keyword
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while (1) {
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if (fgets(line,MAXLINE,fp) == NULL)
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error->one(FLERR,"Did not find keyword in table file");
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if (strspn(line," \t\n\r") == strlen(line)) continue; // blank line
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if (line[0] == '#') continue; // comment
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char *word = strtok(line," \t\n\r");
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if (strcmp(word,keyword) == 0) break; // matching keyword
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fgets(line,MAXLINE,fp); // no match, skip section
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param_extract(tb,tb2,line);
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fgets(line,MAXLINE,fp);
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for (int i = 0; i < tb->ninput; i++) fgets(line,MAXLINE,fp);
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}
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// read args on 2nd line of section
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// allocate table arrays for file values
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fgets(line,MAXLINE,fp);
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param_extract(tb,tb2,line);
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memory->create(tb->rfile,tb->ninput,"eos:rfile");
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memory->create(tb->efile,tb->ninput,"eos:efile");
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memory->create(tb2->rfile,tb2->ninput,"eos:rfile2");
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memory->create(tb2->efile,tb2->ninput,"eos:efile2");
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// read r,e table values from file
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int itmp;
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fgets(line,MAXLINE,fp);
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for (int i = 0; i < tb->ninput; i++) {
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fgets(line,MAXLINE,fp);
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sscanf(line,"%d %lg %lg",&itmp,&tb->rfile[i],&tb->efile[i]);
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sscanf(line,"%d %lg %lg",&itmp,&tb2->efile[i],&tb2->rfile[i]);
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}
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fclose(fp);
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}
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/* ----------------------------------------------------------------------
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build spline representation of e,f over entire range of read-in table
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this function sets these values in e2file
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------------------------------------------------------------------------- */
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void FixEOStable::spline_table(Table *tb)
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{
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memory->create(tb->e2file,tb->ninput,"eos:e2file");
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}
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/* ----------------------------------------------------------------------
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compute r,e,f vectors from splined values
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------------------------------------------------------------------------- */
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void FixEOStable::compute_table(Table *tb)
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{
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// delta = table spacing for N-1 bins
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int tlm1 = tablength-1;
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tb->delta = (tb->hi - tb->lo)/ tlm1;
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tb->invdelta = 1.0/tb->delta;
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tb->deltasq6 = tb->delta*tb->delta / 6.0;
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// N-1 evenly spaced bins in r from min to max
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// r,e = value at lower edge of bin
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// de values = delta values of e,f
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// r,e are N in length so de arrays can compute difference
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memory->create(tb->r,tablength,"eos:r");
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memory->create(tb->e,tablength,"eos:e");
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memory->create(tb->de,tlm1,"eos:de");
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memory->create(tb->e2,tablength,"eos:e2");
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double a;
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for (int i = 0; i < tablength; i++) {
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a = tb->lo + i*tb->delta;
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tb->r[i] = a;
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tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,a);
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}
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for (int i = 0; i < tlm1; i++) {
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tb->de[i] = tb->e[i+1] - tb->e[i];
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}
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}
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/* ----------------------------------------------------------------------
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extract attributes from parameter line in table section
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format of line: N value
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N is required, other params are optional
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------------------------------------------------------------------------- */
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void FixEOStable::param_extract(Table *tb, Table *tb2, char *line)
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{
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tb->ninput = 0;
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tb2->ninput = 0;
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char *word = strtok(line," \t\n\r\f");
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while (word) {
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if (strcmp(word,"N") == 0) {
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word = strtok(NULL," \t\n\r\f");
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tb->ninput = atoi(word);
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tb2->ninput = atoi(word);
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} else {
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error->one(FLERR,"Invalid keyword in fix eos/table parameters");
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}
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word = strtok(NULL," \t\n\r\f");
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}
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if (tb->ninput == 0) error->one(FLERR,"fix eos/table parameters did not set N");
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if (tb2->ninput == 0) error->one(FLERR,"fix eos/table parameters did not set N");
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}
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/* ----------------------------------------------------------------------
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broadcast read-in table info from proc 0 to other procs
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this function communicates these values in Table:
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ninput,rfile,efile
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------------------------------------------------------------------------- */
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void FixEOStable::bcast_table(Table *tb)
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{
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MPI_Bcast(&tb->ninput,1,MPI_INT,0,world);
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int me;
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MPI_Comm_rank(world,&me);
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if (me > 0) {
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memory->create(tb->rfile,tb->ninput,"eos:rfile");
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memory->create(tb->efile,tb->ninput,"eos:efile");
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}
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MPI_Bcast(tb->rfile,tb->ninput,MPI_DOUBLE,0,world);
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MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world);
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}
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/* ----------------------------------------------------------------------
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spline and splint routines modified from Numerical Recipes
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------------------------------------------------------------------------- */
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void FixEOStable::spline(double *x, double *y, int n,
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double yp1, double ypn, double *y2)
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{
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int i,k;
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double p,qn,sig,un;
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double *u = new double[n];
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if (yp1 > 0.99e30) y2[0] = u[0] = 0.0;
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else {
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y2[0] = -0.5;
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u[0] = (3.0/(x[1]-x[0])) * ((y[1]-y[0]) / (x[1]-x[0]) - yp1);
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}
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for (i = 1; i < n-1; i++) {
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sig = (x[i]-x[i-1]) / (x[i+1]-x[i-1]);
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p = sig*y2[i-1] + 2.0;
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y2[i] = (sig-1.0) / p;
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u[i] = (y[i+1]-y[i]) / (x[i+1]-x[i]) - (y[i]-y[i-1]) / (x[i]-x[i-1]);
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u[i] = (6.0*u[i] / (x[i+1]-x[i-1]) - sig*u[i-1]) / p;
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}
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if (ypn > 0.99e30) qn = un = 0.0;
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else {
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qn = 0.5;
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un = (3.0/(x[n-1]-x[n-2])) * (ypn - (y[n-1]-y[n-2]) / (x[n-1]-x[n-2]));
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}
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y2[n-1] = (un-qn*u[n-2]) / (qn*y2[n-2] + 1.0);
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for (k = n-2; k >= 0; k--) y2[k] = y2[k]*y2[k+1] + u[k];
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delete [] u;
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}
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/* ---------------------------------------------------------------------- */
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double FixEOStable::splint(double *xa, double *ya, double *y2a, int n, double x)
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{
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int klo,khi,k;
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double h,b,a,y;
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klo = 0;
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khi = n-1;
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while (khi-klo > 1) {
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k = (khi+klo) >> 1;
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if (xa[k] > x) khi = k;
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else klo = k;
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}
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h = xa[khi]-xa[klo];
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a = (xa[khi]-x) / h;
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b = (x-xa[klo]) / h;
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y = a*ya[klo] + b*ya[khi] +
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((a*a*a-a)*y2a[klo] + (b*b*b-b)*y2a[khi]) * (h*h)/6.0;
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return y;
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}
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/* ----------------------------------------------------------------------
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calculate internal energy u at temperature t
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insure t is between min/max
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------------------------------------------------------------------------- */
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void FixEOStable::energy_lookup(double t, double &u)
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{
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int itable;
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double fraction,a,b;
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Table *tb = &tables[0];
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if(t < tb->lo || t > tb->hi){
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printf("Temperature=%lf TableMin=%lf TableMax=%lf\n",t,tb->lo,tb->hi);
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error->one(FLERR,"Temperature is not within table cutoffs");
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}
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if (tabstyle == LINEAR) {
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itable = static_cast<int> ((t - tb->lo) * tb->invdelta);
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fraction = (t - tb->r[itable]) * tb->invdelta;
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u = tb->e[itable] + fraction*tb->de[itable];
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}
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}
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/* ----------------------------------------------------------------------
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calculate temperature t at energy u
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insure u is between min/max
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------------------------------------------------------------------------- */
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void FixEOStable::temperature_lookup(double u, double &t)
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{
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int itable;
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double fraction,a,b;
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Table *tb = &tables[1];
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if(u < tb->lo || u > tb->hi){
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printf("Energy=%lf TableMin=%lf TableMax=%lf\n",u,tb->lo,tb->hi);
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error->one(FLERR,"Energy is not within table cutoffs");
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}
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if (tabstyle == LINEAR) {
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itable = static_cast<int> ((u - tb->lo) * tb->invdelta);
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fraction = (u - tb->r[itable]) * tb->invdelta;
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t = tb->e[itable] + fraction*tb->de[itable];
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}
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}
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