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lammps/src/USER-DPD/pair_multi_lucy_rx.cpp
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pair_multi_lucy_rx.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 authors:
James Larentzos and Joshua Moore (U.S. Army Research Laboratory)
Please cite the related publications:
J.D. Moore, B.C. Barnes, S. Izvekov, M. Lisal, M.S. Sellers, D.E. Taylor & J.K. Brennan
"A coarse-grain force field for RDX: Density dependent and energy conserving"
The Journal of Chemical Physics, 2016, 144, 104501.
------------------------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include "math_const.h"
#include <stdlib.h>
#include <string.h>
#include "pair_multi_lucy_rx.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "citeme.h"
#include "modify.h"
#include "fix.h"
using namespace LAMMPS_NS;
enum{NONE,RLINEAR,RSQ};
#define MAXLINE 1024
#ifdef DBL_EPSILON
#define MY_EPSILON (10.0*DBL_EPSILON)
#else
#define MY_EPSILON (10.0*2.220446049250313e-16)
#endif
#define oneFluidParameter (-1)
#define isOneFluid(_site) ( (_site) == oneFluidParameter )
static const char cite_pair_multi_lucy_rx[] =
"pair_style multi/lucy/rx command:\n\n"
"@Article{Moore16,\n"
" author = {J.D. Moore, B.C. Barnes, S. Izvekov, M. Lisal, M.S. Sellers, D.E. Taylor and J. K. Brennan},\n"
" title = {A coarse-grain force field for RDX: Density dependent and energy conserving},\n"
" journal = {J. Chem. Phys.},\n"
" year = 2016,\n"
" volume = 144\n"
" pages = {104501}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
PairMultiLucyRX::PairMultiLucyRX(LAMMPS *lmp) : Pair(lmp),
ntables(0), tables(NULL), tabindex(NULL), site1(NULL), site2(NULL)
{
if (lmp->citeme) lmp->citeme->add(cite_pair_multi_lucy_rx);
if (atom->rho_flag != 1) error->all(FLERR,"Pair multi/lucy/rx command requires atom_style with density (e.g. dpd, meso)");
ntables = 0;
tables = NULL;
comm_forward = 1;
comm_reverse = 1;
fractionalWeighting = true;
}
/* ---------------------------------------------------------------------- */
PairMultiLucyRX::~PairMultiLucyRX()
{
if (copymode) return;
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(tabindex);
}
}
/* ---------------------------------------------------------------------- */
void PairMultiLucyRX::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwlOld,fpair;
double rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;
int tlm1 = tablength - 1;
evdwlOld = 0.0;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int newton_pair = force->newton_pair;
double mixWtSite1old_i,mixWtSite1old_j;
double mixWtSite2old_i,mixWtSite2old_j;
double mixWtSite1_i;
double *uCG = atom->uCG;
double *uCGnew = atom->uCGnew;
double pi = MathConst::MY_PI;
double A_i, A_j;
double fraction_i,fraction_j;
int jtable;
double *rho = atom->rho;
double *mixWtSite1old = NULL;
double *mixWtSite2old = NULL;
double *mixWtSite1 = NULL;
double *mixWtSite2 = NULL;
{
const int ntotal = nlocal + nghost;
memory->create(mixWtSite1old, ntotal, "PairMultiLucyRX::mixWtSite1old");
memory->create(mixWtSite2old, ntotal, "PairMultiLucyRX::mixWtSite2old");
memory->create(mixWtSite1, ntotal, "PairMultiLucyRX::mixWtSite1");
memory->create(mixWtSite2, ntotal, "PairMultiLucyRX::mixWtSite2");
for (int i = 0; i < ntotal; ++i)
getMixingWeights(i, mixWtSite1old[i], mixWtSite2old[i], mixWtSite1[i], mixWtSite2[i]);
}
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
computeLocalDensity();
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
double fx_i = 0.0;
double fy_i = 0.0;
double fz_i = 0.0;
mixWtSite1old_i = mixWtSite1old[i];
mixWtSite2old_i = mixWtSite2old[i];
mixWtSite1_i = mixWtSite1[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
fpair = 0.0;
mixWtSite1old_j = mixWtSite1old[j];
mixWtSite2old_j = mixWtSite2old[j];
tb = &tables[tabindex[itype][jtype]];
if (rho[i]*rho[i] < tb->innersq || rho[j]*rho[j] < tb->innersq){
printf("Table inner cutoff = %lf\n",sqrt(tb->innersq));
printf("rho[%d]=%lf\n",i,rho[i]);
printf("rho[%d]=%lf\n",j,rho[j]);
error->one(FLERR,"Density < table inner cutoff");
}
if (tabstyle == LOOKUP) {
itable = static_cast<int> (((rho[i]*rho[i]) - tb->innersq) * tb->invdelta);
jtable = static_cast<int> (((rho[j]*rho[j]) - tb->innersq) * tb->invdelta);
if (itable >= tlm1 || jtable >= tlm1){
printf("Table outer index = %d\n",tlm1);
printf("itableIndex=%d rho[%d]=%lf\n",itable,i,rho[i]);
printf("jtableIndex=%d rho[%d]=%lf\n",jtable,j,rho[j]);
error->one(FLERR,"Density > table outer cutoff");
}
A_i = tb->f[itable];
A_j = tb->f[jtable];
const double rfactor = 1.0-sqrt(rsq/cutsq[itype][jtype]);
fpair = 0.5*(A_i + A_j)*(4.0-3.0*rfactor)*rfactor*rfactor*rfactor;
fpair /= sqrt(rsq);
} else if (tabstyle == LINEAR) {
itable = static_cast<int> ((rho[i]*rho[i] - tb->innersq) * tb->invdelta);
jtable = static_cast<int> (((rho[j]*rho[j]) - tb->innersq) * tb->invdelta);
if (itable >= tlm1 || jtable >= tlm1){
printf("Table outer index = %d\n",tlm1);
printf("itableIndex=%d rho[%d]=%lf\n",itable,i,rho[i]);
printf("jtableIndex=%d rho[%d]=%lf\n",jtable,j,rho[j]);
error->one(FLERR,"Density > table outer cutoff");
}
if(itable<0) itable=0;
if(itable>=tlm1) itable=tlm1;
if(jtable<0) jtable=0;
if(jtable>=tlm1)jtable=tlm1;
fraction_i = (((rho[i]*rho[i]) - tb->rsq[itable]) * tb->invdelta);
fraction_j = (((rho[j]*rho[j]) - tb->rsq[jtable]) * tb->invdelta);
if(itable==0) fraction_i=0.0;
if(itable==tlm1) fraction_i=0.0;
if(jtable==0) fraction_j=0.0;
if(jtable==tlm1) fraction_j=0.0;
A_i = tb->f[itable] + fraction_i*tb->df[itable];
A_j = tb->f[jtable] + fraction_j*tb->df[jtable];
const double rfactor = 1.0-sqrt(rsq/cutsq[itype][jtype]);
fpair = 0.5*(A_i + A_j)*(4.0-3.0*rfactor)*rfactor*rfactor*rfactor;
fpair /= sqrt(rsq);
} else error->one(FLERR,"Only LOOKUP and LINEAR table styles have been implemented for pair multi/lucy/rx");
if (isite1 == isite2) fpair = sqrt(mixWtSite1old_i*mixWtSite2old_j)*fpair;
else fpair = (sqrt(mixWtSite1old_i*mixWtSite2old_j) + sqrt(mixWtSite2old_i*mixWtSite1old_j))*fpair;
fx_i += delx*fpair;
fy_i += dely*fpair;
fz_i += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,0.0,0.0,fpair,delx,dely,delz);
}
}
f[i][0] += fx_i;
f[i][1] += fy_i;
f[i][2] += fz_i;
tb = &tables[tabindex[itype][itype]];
itable = static_cast<int> (((rho[i]*rho[i]) - tb->innersq) * tb->invdelta);
if (tabstyle == LOOKUP) evdwl = tb->e[itable];
else if (tabstyle == LINEAR){
if (itable >= tlm1){
printf("itableIndex=%d rho[%d]=%lf\n",itable,i,rho[i]);
error->one(FLERR,"Density > table outer cutoff");
}
if(itable==0) fraction_i=0.0;
else fraction_i = (((rho[i]*rho[i]) - tb->rsq[itable]) * tb->invdelta);
evdwl = tb->e[itable] + fraction_i*tb->de[itable];
} else error->one(FLERR,"Only LOOKUP and LINEAR table styles have been implemented for pair multi/lucy/rx");
evdwl *=(pi*cutsq[itype][itype]*cutsq[itype][itype])/84.0;
evdwlOld = mixWtSite1old_i*evdwl;
evdwl = mixWtSite1_i*evdwl;
uCG[i] += evdwlOld;
uCGnew[i] += evdwl;
evdwl = evdwlOld;
if (evflag) ev_tally(0,0,nlocal,newton_pair,evdwl,0.0,0.0,0.0,0.0,0.0);
}
if (vflag_fdotr) virial_fdotr_compute();
memory->destroy(mixWtSite1old);
memory->destroy(mixWtSite2old);
memory->destroy(mixWtSite1);
memory->destroy(mixWtSite2);
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairMultiLucyRX::allocate()
{
allocated = 1;
const int nt = atom->ntypes + 1;
memory->create(setflag,nt,nt,"pair:setflag");
memory->create(cutsq,nt,nt,"pair:cutsq");
memory->create(tabindex,nt,nt,"pair:tabindex");
memset(&setflag[0][0],0,nt*nt*sizeof(int));
memset(&cutsq[0][0],0,nt*nt*sizeof(double));
memset(&tabindex[0][0],0,nt*nt*sizeof(int));
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairMultiLucyRX::settings(int narg, char **arg)
{
if (narg < 2) error->all(FLERR,"Illegal pair_style command");
// new settings
if (strcmp(arg[0],"lookup") == 0) tabstyle = LOOKUP;
else if (strcmp(arg[0],"linear") == 0) tabstyle = LINEAR;
else error->all(FLERR,"Unknown table style in pair_style command");
tablength = force->inumeric(FLERR,arg[1]);
if (tablength < 2) error->all(FLERR,"Illegal number of pair table entries");
// optional keywords
int iarg = 2;
while (iarg < narg) {
if (strcmp(arg[iarg],"fractional") == 0) fractionalWeighting = true;
else if (strcmp(arg[iarg],"molecular") == 0) fractionalWeighting = false;
else error->all(FLERR,"Illegal pair_style command");
iarg++;
}
// delete old tables, since cannot just change settings
for (int m = 0; m < ntables; m++) free_table(&tables[m]);
memory->sfree(tables);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(tabindex);
}
allocated = 0;
ntables = 0;
tables = NULL;
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairMultiLucyRX::coeff(int narg, char **arg)
{
if (narg != 6 && narg != 7) error->all(FLERR,"Illegal pair_coeff command");
bool rx_flag = false;
for (int i = 0; i < modify->nfix; i++)
if (strncmp(modify->fix[i]->style,"rx",2) == 0) rx_flag = true;
if (!rx_flag) error->all(FLERR,"PairMultiLucyRX requires a fix rx command.");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
int me;
MPI_Comm_rank(world,&me);
tables = (Table *)
memory->srealloc(tables,(ntables+1)*sizeof(Table),"pair:tables");
Table *tb = &tables[ntables];
null_table(tb);
if (me == 0) read_table(tb,arg[2],arg[3]);
bcast_table(tb);
nspecies = atom->nspecies_dpd;
int n;
n = strlen(arg[4]) + 1;
site1 = new char[n];
strcpy(site1,arg[4]);
n = strlen(arg[5]) + 1;
site2 = new char[n];
strcpy(site2,arg[5]);
// set table cutoff
if (narg == 7) tb->cut = force->numeric(FLERR,arg[6]);
else if (tb->rflag) tb->cut = tb->rhi;
else tb->cut = tb->rfile[tb->ninput-1];
// error check on table parameters
// insure cutoff is within table
if (tb->ninput <= 1) error->one(FLERR,"Invalid pair table length");
if (tb->rflag == 0) {
rho_0 = tb->rfile[0];
} else {
rho_0 = tb->rlo;
}
tb->match = 0;
if (tabstyle == LINEAR && tb->ninput == tablength &&
tb->rflag == RSQ) tb->match = 1;
// spline read-in values and compute r,e,f vectors within table
if (tb->match == 0) spline_table(tb);
compute_table(tb);
// store ptr to table in tabindex
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
tabindex[i][j] = ntables;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Illegal pair_coeff command");
ntables++;
// Match site* to isite values.
if (strcmp(site1, "1fluid") == 0)
isite1 = oneFluidParameter;
else {
isite1 = nspecies;
for (int ispecies = 0; ispecies < nspecies; ++ispecies)
if (strcmp(site1, atom->dname[ispecies]) == 0){
isite1 = ispecies;
break;
}
if (isite1 == nspecies)
error->all(FLERR,"Pair_multi_lucy_rx site1 is invalid.");
}
if (strcmp(site2, "1fluid") == 0)
isite2 = oneFluidParameter;
else {
isite2 = nspecies;
for (int ispecies = 0; ispecies < nspecies; ++ispecies)
if (strcmp(site2, atom->dname[ispecies]) == 0){
isite2 = ispecies;
break;
}
if (isite2 == nspecies)
error->all(FLERR,"Pair_multi_lucy_rx site2 is invalid.");
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairMultiLucyRX::init_one(int i, int j)
{
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
tabindex[j][i] = tabindex[i][j];
return tables[tabindex[i][j]].cut;
}
/* ----------------------------------------------------------------------
read a table section from a tabulated potential file
only called by proc 0
this function sets these values in Table:
ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi
------------------------------------------------------------------------- */
void PairMultiLucyRX::read_table(Table *tb, 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,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,line);
memory->create(tb->rfile,tb->ninput,"pair:rfile");
memory->create(tb->efile,tb->ninput,"pair:efile");
memory->create(tb->ffile,tb->ninput,"pair:ffile");
// read r,e,f table values from file
// if rflag set, compute r
// if rflag not set, use r from file
int itmp;
double rtmp;
fgets(line,MAXLINE,fp);
for (int i = 0; i < tb->ninput; i++) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %lg %lg",&itmp,&rtmp,&tb->efile[i],&tb->ffile[i]);
if (tb->rflag == RLINEAR)
rtmp = tb->rlo + (tb->rhi - tb->rlo)*i/(tb->ninput-1);
else if (tb->rflag == RSQ) {
rtmp = tb->rlo*tb->rlo +
(tb->rhi*tb->rhi - tb->rlo*tb->rlo)*i/(tb->ninput-1);
rtmp = sqrt(rtmp);
}
tb->rfile[i] = rtmp;
}
// close file
fclose(fp);
}
/* ----------------------------------------------------------------------
broadcast read-in table info from proc 0 to other procs
this function communicates these values in Table:
ninput,rfile,efile,ffile,rflag,rlo,rhi,fpflag,fplo,fphi
------------------------------------------------------------------------- */
void PairMultiLucyRX::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,"pair:rfile");
memory->create(tb->efile,tb->ninput,"pair:efile");
memory->create(tb->ffile,tb->ninput,"pair:ffile");
}
MPI_Bcast(tb->rfile,tb->ninput,MPI_DOUBLE,0,world);
MPI_Bcast(tb->efile,tb->ninput,MPI_DOUBLE,0,world);
MPI_Bcast(tb->ffile,tb->ninput,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->rflag,1,MPI_INT,0,world);
if (tb->rflag) {
MPI_Bcast(&tb->rlo,1,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->rhi,1,MPI_DOUBLE,0,world);
}
MPI_Bcast(&tb->fpflag,1,MPI_INT,0,world);
if (tb->fpflag) {
MPI_Bcast(&tb->fplo,1,MPI_DOUBLE,0,world);
MPI_Bcast(&tb->fphi,1,MPI_DOUBLE,0,world);
}
}
/* ----------------------------------------------------------------------
build spline representation of e,f over entire range of read-in table
this function sets these values in Table: e2file,f2file
------------------------------------------------------------------------- */
void PairMultiLucyRX::spline_table(Table *tb)
{
memory->create(tb->e2file,tb->ninput,"pair:e2file");
memory->create(tb->f2file,tb->ninput,"pair:f2file");
double ep0 = - tb->ffile[0];
double epn = - tb->ffile[tb->ninput-1];
spline(tb->rfile,tb->efile,tb->ninput,ep0,epn,tb->e2file);
if (tb->fpflag == 0) {
tb->fplo = (tb->ffile[1] - tb->ffile[0]) / (tb->rfile[1] - tb->rfile[0]);
tb->fphi = (tb->ffile[tb->ninput-1] - tb->ffile[tb->ninput-2]) /
(tb->rfile[tb->ninput-1] - tb->rfile[tb->ninput-2]);
}
double fp0 = tb->fplo;
double fpn = tb->fphi;
spline(tb->rfile,tb->ffile,tb->ninput,fp0,fpn,tb->f2file);
}
/* ----------------------------------------------------------------------
extract attributes from parameter line in table section
format of line: N value R/RSQ lo hi FP fplo fphi
N is required, other params are optional
------------------------------------------------------------------------- */
void PairMultiLucyRX::param_extract(Table *tb, char *line)
{
tb->ninput = 0;
tb->rflag = NONE;
tb->fpflag = 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);
} else if (strcmp(word,"R") == 0 || strcmp(word,"RSQ") == 0) {
if (strcmp(word,"R") == 0) tb->rflag = RLINEAR;
else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ;
word = strtok(NULL," \t\n\r\f");
tb->rlo = atof(word);
word = strtok(NULL," \t\n\r\f");
tb->rhi = atof(word);
} else if (strcmp(word,"FP") == 0) {
tb->fpflag = 1;
word = strtok(NULL," \t\n\r\f");
tb->fplo = atof(word);
word = strtok(NULL," \t\n\r\f");
tb->fphi = atof(word);
} else {
printf("WORD: %s\n",word);
error->one(FLERR,"Invalid keyword in pair table parameters");
}
word = strtok(NULL," \t\n\r\f");
}
if (tb->ninput == 0) error->one(FLERR,"Pair table parameters did not set N");
}
/* ----------------------------------------------------------------------
compute r,e,f vectors from splined values
------------------------------------------------------------------------- */
void PairMultiLucyRX::compute_table(Table *tb)
{
int tlm1 = tablength-1;
// inner = inner table bound
// cut = outer table bound
// delta = table spacing in rsq for N-1 bins
double inner;
if (tb->rflag) inner = tb->rlo;
else inner = tb->rfile[0];
tb->innersq = inner*inner;
tb->delta = (tb->rhi*tb->rhi - tb->innersq) / tlm1;
tb->invdelta = 1.0/tb->delta;
// direct lookup tables
// N-1 evenly spaced bins in rsq from inner to cut
// e,f = value at midpt of bin
// e,f are N-1 in length since store 1 value at bin midpt
// f is converted to f/r when stored in f[i]
// e,f are never a match to read-in values, always computed via spline interp
if (tabstyle == LOOKUP) {
memory->create(tb->e,tlm1,"pair:e");
memory->create(tb->f,tlm1,"pair:f");
double r,rsq;
for (int i = 0; i < tlm1; i++) {
rsq = tb->innersq + (i+0.5)*tb->delta;
r = sqrt(rsq);
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r);
}
}
// linear tables
// N-1 evenly spaced bins in rsq from inner to cut
// rsq,e,f = value at lower edge of bin
// de,df values = delta from lower edge to upper edge of bin
// rsq,e,f are N in length so de,df arrays can compute difference
// f is converted to f/r when stored in f[i]
// e,f can match read-in values, else compute via spline interp
if (tabstyle == LINEAR) {
memory->create(tb->rsq,tablength,"pair:rsq");
memory->create(tb->e,tablength,"pair:e");
memory->create(tb->f,tablength,"pair:f");
memory->create(tb->de,tlm1,"pair:de");
memory->create(tb->df,tlm1,"pair:df");
double r,rsq;
for (int i = 0; i < tablength; i++) {
rsq = tb->innersq + i*tb->delta;
r = sqrt(rsq);
tb->rsq[i] = rsq;
if (tb->match) {
tb->e[i] = tb->efile[i];
tb->f[i] = tb->ffile[i];
} else {
tb->e[i] = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
tb->f[i] = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r);
}
}
for (int i = 0; i < tlm1; i++) {
tb->de[i] = tb->e[i+1] - tb->e[i];
tb->df[i] = tb->f[i+1] - tb->f[i];
}
}
}
/* ----------------------------------------------------------------------
set all ptrs in a table to NULL, so can be freed safely
------------------------------------------------------------------------- */
void PairMultiLucyRX::null_table(Table *tb)
{
tb->rfile = tb->efile = tb->ffile = NULL;
tb->e2file = tb->f2file = NULL;
tb->rsq = tb->drsq = tb->e = tb->de = NULL;
tb->f = tb->df = tb->e2 = tb->f2 = NULL;
}
/* ----------------------------------------------------------------------
free all arrays in a table
------------------------------------------------------------------------- */
void PairMultiLucyRX::free_table(Table *tb)
{
memory->destroy(tb->rfile);
memory->destroy(tb->efile);
memory->destroy(tb->ffile);
memory->destroy(tb->e2file);
memory->destroy(tb->f2file);
memory->destroy(tb->rsq);
memory->destroy(tb->drsq);
memory->destroy(tb->e);
memory->destroy(tb->de);
memory->destroy(tb->f);
memory->destroy(tb->df);
memory->destroy(tb->e2);
memory->destroy(tb->f2);
}
/* ----------------------------------------------------------------------
spline and splint routines modified from Numerical Recipes
------------------------------------------------------------------------- */
void PairMultiLucyRX::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 PairMultiLucyRX::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;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairMultiLucyRX::write_restart(FILE *fp)
{
write_restart_settings(fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairMultiLucyRX::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairMultiLucyRX::write_restart_settings(FILE *fp)
{
fwrite(&tabstyle,sizeof(int),1,fp);
fwrite(&tablength,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairMultiLucyRX::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&tabstyle,sizeof(int),1,fp);
fread(&tablength,sizeof(int),1,fp);
}
MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
MPI_Bcast(&tablength,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
void PairMultiLucyRX::computeLocalDensity()
{
double **x = atom->x;
const int *type = atom->type;
const int nlocal = atom->nlocal;
const int inum = list->inum;
const int *ilist = list->ilist;
const int *numneigh = list->numneigh;
int **firstneigh = list->firstneigh;
const double pi = MathConst::MY_PI;
const bool newton_pair = force->newton_pair;
const bool one_type = (atom->ntypes == 1);
// Special cut-off values for when there's only one type.
const double cutsq_type11 = cutsq[1][1];
const double rcut_type11 = sqrt(cutsq_type11);
const double factor_type11 = 84.0/(5.0*pi*rcut_type11*rcut_type11*rcut_type11);
double *rho = atom->rho;
// zero out density
if (newton_pair) {
const int m = nlocal + atom->nghost;
for (int i = 0; i < m; i++) rho[i] = 0.0;
}
else
for (int i = 0; i < nlocal; i++) rho[i] = 0.0;
// rho = density at each atom
// loop over neighbors of my atoms
for (int ii = 0; ii < inum; ii++){
const int i = ilist[ii];
const double xtmp = x[i][0];
const double ytmp = x[i][1];
const double ztmp = x[i][2];
double rho_i = rho[i];
const int itype = type[i];
const int *jlist = firstneigh[i];
const int jnum = numneigh[i];
for (int jj = 0; jj < jnum; jj++){
const int j = (jlist[jj] & NEIGHMASK);
const int jtype = type[j];
const double delx = xtmp - x[j][0];
const double dely = ytmp - x[j][1];
const double delz = ztmp - x[j][2];
const double rsq = delx*delx + dely*dely + delz*delz;
if (one_type) {
if (rsq < cutsq_type11) {
const double rcut = rcut_type11;
const double r_over_rcut = sqrt(rsq) / rcut;
const double tmpFactor = 1.0 - r_over_rcut;
const double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor;
const double factor = factor_type11*(1.0 + 1.5*r_over_rcut)*tmpFactor4;
rho_i += factor;
if (newton_pair || j < nlocal)
rho[j] += factor;
}
} else if (rsq < cutsq[itype][jtype]) {
const double rcut = sqrt(cutsq[itype][jtype]);
const double tmpFactor = 1.0-sqrt(rsq)/rcut;
const double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor;
const double factor = (84.0/(5.0*pi*rcut*rcut*rcut))*(1.0+3.0*sqrt(rsq)/(2.0*rcut))*tmpFactor4;
rho_i += factor;
if (newton_pair || j < nlocal)
rho[j] += factor;
}
}
rho[i] = rho_i;
}
if (newton_pair) comm->reverse_comm_pair(this);
comm->forward_comm_pair(this);
}
/* ---------------------------------------------------------------------- */
void PairMultiLucyRX::getMixingWeights(int id, double &mixWtSite1old, double &mixWtSite2old, double &mixWtSite1, double &mixWtSite2)
{
double fractionOFAold, fractionOFA;
double fractionOld1, fraction1;
double fractionOld2, fraction2;
double nMoleculesOFAold, nMoleculesOFA;
double nMoleculesOld1, nMolecules1;
double nMoleculesOld2, nMolecules2;
double nTotal, nTotalOld;
nTotal = 0.0;
nTotalOld = 0.0;
for (int ispecies = 0; ispecies < nspecies; ispecies++){
nTotal += atom->dvector[ispecies][id];
nTotalOld += atom->dvector[ispecies+nspecies][id];
}
if (isOneFluid(isite1) == false){
nMoleculesOld1 = atom->dvector[isite1+nspecies][id];
nMolecules1 = atom->dvector[isite1][id];
fractionOld1 = nMoleculesOld1/nTotalOld;
fraction1 = nMolecules1/nTotal;
}
if (isOneFluid(isite2) == false){
nMoleculesOld2 = atom->dvector[isite2+nspecies][id];
nMolecules2 = atom->dvector[isite2][id];
fractionOld2 = nMoleculesOld2/nTotalOld;
fraction2 = nMolecules2/nTotal;
}
if (isOneFluid(isite1) || isOneFluid(isite2)){
nMoleculesOFAold = 0.0;
nMoleculesOFA = 0.0;
fractionOFAold = 0.0;
fractionOFA = 0.0;
for (int ispecies = 0; ispecies < nspecies; ispecies++){
if (isite1 == ispecies || isite2 == ispecies) continue;
nMoleculesOFAold += atom->dvector[ispecies+nspecies][id];
nMoleculesOFA += atom->dvector[ispecies][id];
fractionOFAold += atom->dvector[ispecies+nspecies][id] / nTotalOld;
fractionOFA += atom->dvector[ispecies][id] / nTotal;
}
if (isOneFluid(isite1)){
nMoleculesOld1 = 1.0-(nTotalOld-nMoleculesOFAold);
nMolecules1 = 1.0-(nTotal-nMoleculesOFA);
fractionOld1 = fractionOFAold;
fraction1 = fractionOFA;
}
if (isOneFluid(isite2)){
nMoleculesOld2 = 1.0-(nTotalOld-nMoleculesOFAold);
nMolecules2 = 1.0-(nTotal-nMoleculesOFA);
fractionOld2 = fractionOFAold;
fraction2 = fractionOFA;
}
}
if(fractionalWeighting){
mixWtSite1old = fractionOld1;
mixWtSite1 = fraction1;
mixWtSite2old = fractionOld2;
mixWtSite2 = fraction2;
} else {
mixWtSite1old = nMoleculesOld1;
mixWtSite1 = nMolecules1;
mixWtSite2old = nMoleculesOld2;
mixWtSite2 = nMolecules2;
}
}
/* ---------------------------------------------------------------------- */
int PairMultiLucyRX::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
int i,j,m;
double *rho = atom->rho;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = rho[j];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairMultiLucyRX::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
double *rho = atom->rho;
m = 0;
last = first + n;
for (i = first; i < last; i++) rho[i] = buf[m++];
}
/* ---------------------------------------------------------------------- */
int PairMultiLucyRX::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
double *rho = atom->rho;
m = 0;
last = first + n;
for (i = first; i < last; i++) buf[m++] = rho[i];
return m;
}
/* ---------------------------------------------------------------------- */
void PairMultiLucyRX::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
double *rho = atom->rho;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
rho[j] += buf[m++];
}
}
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