Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F78000979
pair_table_rx.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Sat, Aug 17, 18:45
Size
36 KB
Mime Type
text/x-c
Expires
Mon, Aug 19, 18:45 (2 d)
Engine
blob
Format
Raw Data
Handle
19964792
Attached To
rLAMMPS lammps
pair_table_rx.cpp
View Options
/* ----------------------------------------------------------------------
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: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "pair_table_rx.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "modify.h"
#include "fix.h"
using namespace LAMMPS_NS;
enum{NONE,RLINEAR,RSQ,BMP};
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairTableRX::PairTableRX(LAMMPS *lmp) : Pair(lmp)
{
ntables = 0;
tables = NULL;
}
/* ---------------------------------------------------------------------- */
PairTableRX::~PairTableRX()
{
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 PairTableRX::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,factor_lj,fraction,value,a,b;
int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;
union_int_float_t rsq_lookup;
int tlm1 = tablength - 1;
fraction = double(0.0);
a = double(0.0);
b = double(0.0);
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;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double fractionOld1_i, fractionOld1_j;
double fractionOld2_i, fractionOld2_j;
double fraction1_i, fraction1_j;
double fraction2_i, fraction2_j;
double *uCG = atom->uCG;
double *uCGnew = atom->uCGnew;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// 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];
getParams(i,fractionOld1_i,fractionOld2_i,fraction1_i,fraction2_i);
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
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]) {
getParams(j,fractionOld1_j,fractionOld2_j,fraction1_j,fraction2_j);
tb = &tables[tabindex[itype][jtype]];
if (rsq < tb->innersq)
error->one(FLERR,"Pair distance < table inner cutoff");
if (tabstyle == LOOKUP) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
fpair = factor_lj * tb->f[itable];
} else if (tabstyle == LINEAR) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
value = tb->f[itable] + fraction*tb->df[itable];
fpair = factor_lj * value;
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((rsq - tb->innersq) * tb->invdelta);
if (itable >= tlm1)
error->one(FLERR,"Pair distance > table outer cutoff");
b = (rsq - tb->rsq[itable]) * tb->invdelta;
a = 1.0 - b;
value = a * tb->f[itable] + b * tb->f[itable+1] +
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
fpair = factor_lj * value;
} else {
rsq_lookup.f = rsq;
itable = rsq_lookup.i & tb->nmask;
itable >>= tb->nshiftbits;
fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
value = tb->f[itable] + fraction*tb->df[itable];
fpair = factor_lj * value;
}
if (strcmp(site1,site2) == 0) fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpair;
else fpair = (sqrt(fractionOld1_i*fractionOld2_j) + sqrt(fractionOld2_i*fractionOld1_j))*fpair;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (tabstyle == LOOKUP)
evdwl = tb->e[itable];
else if (tabstyle == LINEAR || tabstyle == BITMAP){
evdwl = tb->e[itable] + fraction*tb->de[itable];
}
else
evdwl = a * tb->e[itable] + b * tb->e[itable+1] +
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) *
tb->deltasq6;
if (strcmp(site1,site2) == 0){
evdwlOld = sqrt(fractionOld1_i*fractionOld2_j)*evdwl;
evdwl = sqrt(fraction1_i*fraction2_j)*evdwl;
} else {
evdwlOld = (sqrt(fractionOld1_i*fractionOld2_j) + sqrt(fractionOld2_i*fractionOld1_j))*evdwl;
evdwl = (sqrt(fraction1_i*fraction2_j) + sqrt(fraction2_i*fraction1_j))*evdwl;
}
evdwlOld *= factor_lj;
evdwl *= factor_lj;
uCG[i] += double(0.5)*evdwlOld;
uCG[j] += double(0.5)*evdwlOld;
uCGnew[i] += double(0.5)*evdwl;
uCGnew[j] += double(0.5)*evdwl;
evdwl = evdwlOld;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairTableRX::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 PairTableRX::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 if (strcmp(arg[0],"spline") == 0) tabstyle = SPLINE;
else if (strcmp(arg[0],"bitmap") == 0) tabstyle = BITMAP;
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
// assert the tabulation is compatible with a specific long-range solver
int iarg = 2;
while (iarg < narg) {
if (strcmp(arg[iarg],"ewald") == 0) ewaldflag = 1;
else if (strcmp(arg[iarg],"pppm") == 0) pppmflag = 1;
else if (strcmp(arg[iarg],"msm") == 0) msmflag = 1;
else if (strcmp(arg[iarg],"dispersion") == 0) dispersionflag = 1;
else if (strcmp(arg[iarg],"tip4p") == 0) tip4pflag = 1;
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 PairTableRX::coeff(int narg, char **arg)
{
if (narg != 6 && narg != 7) error->all(FLERR,"Illegal pair_coeff command");
if (!allocated) allocate();
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,"PairTableRX requires a fix rx command.");
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(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;
if(nspecies==0) error->all(FLERR,"There are no rx species specified.");
int n;
n = strlen(arg[3]) + 1;
site1 = new char[n];
strcpy(site1,arg[4]);
int ispecies;
for (ispecies = 0; ispecies < nspecies; ispecies++){
if (strcmp(site1,&atom->dname[ispecies][0]) == 0) break;
}
if (ispecies == nspecies && strcmp(site1,"1fluid") != 0)
error->all(FLERR,"Site1 name not recognized in pair coefficients");
n = strlen(arg[4]) + 1;
site2 = new char[n];
strcpy(site2,arg[5]);
for (ispecies = 0; ispecies < nspecies; ispecies++){
if (strcmp(site2,&atom->dname[ispecies][0]) == 0) break;
}
if (ispecies == nspecies && strcmp(site2,"1fluid") != 0)
error->all(FLERR,"Site2 name not recognized in pair coefficients");
// 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
// for BITMAP tables, file values can be in non-ascending order
if (tb->ninput <= 1) error->one(FLERR,"Invalid pair table length");
double rlo,rhi;
if (tb->rflag == 0) {
rlo = tb->rfile[0];
rhi = tb->rfile[tb->ninput-1];
} else {
rlo = tb->rlo;
rhi = tb->rhi;
}
if (tb->cut <= rlo || tb->cut > rhi)
error->all(FLERR,"Invalid pair table cutoff");
if (rlo <= 0.0) error->all(FLERR,"Invalid pair table cutoff");
// match = 1 if don't need to spline read-in tables
// this is only the case if r values needed by final tables
// exactly match r values read from file
// for tabstyle SPLINE, always need to build spline tables
tb->match = 0;
if (tabstyle == LINEAR && tb->ninput == tablength &&
tb->rflag == RSQ && tb->rhi == tb->cut) tb->match = 1;
if (tabstyle == BITMAP && tb->ninput == 1 << tablength &&
tb->rflag == BMP && tb->rhi == tb->cut) tb->match = 1;
if (tb->rflag == BMP && tb->match == 0)
error->all(FLERR,"Bitmapped table in file does not match requested table");
// 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++;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairTableRX::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,ntablebits
------------------------------------------------------------------------- */
void PairTableRX::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");
// setup bitmap parameters for table to read in
tb->ntablebits = 0;
int masklo,maskhi,nmask,nshiftbits;
if (tb->rflag == BMP) {
while (1 << tb->ntablebits < tb->ninput) tb->ntablebits++;
if (1 << tb->ntablebits != tb->ninput)
error->one(FLERR,"Bitmapped table is incorrect length in table file");
init_bitmap(tb->rlo,tb->rhi,tb->ntablebits,masklo,maskhi,nmask,nshiftbits);
}
// 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;
union_int_float_t rsq_lookup;
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);
} else if (tb->rflag == BMP) {
rsq_lookup.i = i << nshiftbits;
rsq_lookup.i |= masklo;
if (rsq_lookup.f < tb->rlo*tb->rlo) {
rsq_lookup.i = i << nshiftbits;
rsq_lookup.i |= maskhi;
}
rtmp = sqrtf(rsq_lookup.f);
}
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 PairTableRX::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 PairTableRX::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/BITMAP lo hi FP fplo fphi
N is required, other params are optional
------------------------------------------------------------------------- */
void PairTableRX::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 ||
strcmp(word,"BITMAP") == 0) {
if (strcmp(word,"R") == 0) tb->rflag = RLINEAR;
else if (strcmp(word,"RSQ") == 0) tb->rflag = RSQ;
else if (strcmp(word,"BITMAP") == 0) tb->rflag = BMP;
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 PairTableRX::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 = double(inner)*double(inner);
tb->delta = double(tb->cut*tb->cut - double(tb->innersq)) / double(tlm1);
tb->invdelta = double(1.0)/double(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)/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]/r;
} 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)/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];
}
}
// cubic spline tables
// N-1 evenly spaced bins in rsq from inner to cut
// rsq,e,f = value at lower edge of bin
// e2,f2 = spline coefficient for each bin
// rsq,e,f,e2,f2 are N in length so have N-1 spline bins
// f is converted to f/r after e is splined
// e,f can match read-in values, else compute via spline interp
if (tabstyle == SPLINE) {
memory->create(tb->rsq,tablength,"pair:rsq");
memory->create(tb->e,tablength,"pair:e");
memory->create(tb->f,tablength,"pair:f");
memory->create(tb->e2,tablength,"pair:e2");
memory->create(tb->f2,tablength,"pair:f2");
tb->deltasq6 = tb->delta*tb->delta / 6.0;
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]/r;
} 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);
}
}
// ep0,epn = dh/dg at inner and at cut
// h(r) = e(r) and g(r) = r^2
// dh/dg = (de/dr) / 2r = -f/2r
double ep0 = - tb->f[0] / (2.0 * sqrt(tb->innersq));
double epn = - tb->f[tlm1] / (2.0 * tb->cut);
spline(tb->rsq,tb->e,tablength,ep0,epn,tb->e2);
// fp0,fpn = dh/dg at inner and at cut
// h(r) = f(r)/r and g(r) = r^2
// dh/dg = (1/r df/dr - f/r^2) / 2r
// dh/dg in secant approx = (f(r2)/r2 - f(r1)/r1) / (g(r2) - g(r1))
double fp0,fpn;
double secant_factor = 0.1;
if (tb->fpflag) fp0 = (tb->fplo/sqrt(tb->innersq) - tb->f[0]/tb->innersq) /
(2.0 * sqrt(tb->innersq));
else {
double rsq1 = tb->innersq;
double rsq2 = rsq1 + secant_factor*tb->delta;
fp0 = (splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq2)) /
sqrt(rsq2) - tb->f[0] / sqrt(rsq1)) / (secant_factor*tb->delta);
}
if (tb->fpflag && tb->cut == tb->rfile[tb->ninput-1]) fpn =
(tb->fphi/tb->cut - tb->f[tlm1]/(tb->cut*tb->cut)) / (2.0 * tb->cut);
else {
double rsq2 = tb->cut * tb->cut;
double rsq1 = rsq2 - secant_factor*tb->delta;
fpn = (tb->f[tlm1] / sqrt(rsq2) -
splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,sqrt(rsq1)) /
sqrt(rsq1)) / (secant_factor*tb->delta);
}
for (int i = 0; i < tablength; i++) tb->f[i] /= sqrt(tb->rsq[i]);
spline(tb->rsq,tb->f,tablength,fp0,fpn,tb->f2);
}
// bitmapped linear tables
// 2^N bins from inner to cut, spaced in bitmapped manner
// 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 == BITMAP) {
double r;
union_int_float_t rsq_lookup;
int masklo,maskhi;
// linear lookup tables of length ntable = 2^n
// stored value = value at lower edge of bin
init_bitmap(inner,tb->cut,tablength,masklo,maskhi,tb->nmask,tb->nshiftbits);
int ntable = 1 << tablength;
int ntablem1 = ntable - 1;
memory->create(tb->rsq,ntable,"pair:rsq");
memory->create(tb->e,ntable,"pair:e");
memory->create(tb->f,ntable,"pair:f");
memory->create(tb->de,ntable,"pair:de");
memory->create(tb->df,ntable,"pair:df");
memory->create(tb->drsq,ntable,"pair:drsq");
union_int_float_t minrsq_lookup;
minrsq_lookup.i = 0 << tb->nshiftbits;
minrsq_lookup.i |= maskhi;
for (int i = 0; i < ntable; i++) {
rsq_lookup.i = i << tb->nshiftbits;
rsq_lookup.i |= masklo;
if (rsq_lookup.f < tb->innersq) {
rsq_lookup.i = i << tb->nshiftbits;
rsq_lookup.i |= maskhi;
}
r = sqrtf(rsq_lookup.f);
tb->rsq[i] = rsq_lookup.f;
if (tb->match) {
tb->e[i] = tb->efile[i];
tb->f[i] = tb->ffile[i]/r;
} 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)/r;
}
minrsq_lookup.f = MIN(minrsq_lookup.f,rsq_lookup.f);
}
tb->innersq = minrsq_lookup.f;
for (int i = 0; i < ntablem1; i++) {
tb->de[i] = tb->e[i+1] - tb->e[i];
tb->df[i] = tb->f[i+1] - tb->f[i];
tb->drsq[i] = 1.0/(tb->rsq[i+1] - tb->rsq[i]);
}
// get the delta values for the last table entries
// tables are connected periodically between 0 and ntablem1
tb->de[ntablem1] = tb->e[0] - tb->e[ntablem1];
tb->df[ntablem1] = tb->f[0] - tb->f[ntablem1];
tb->drsq[ntablem1] = 1.0/(tb->rsq[0] - tb->rsq[ntablem1]);
// get the correct delta values at itablemax
// smallest r is in bin itablemin
// largest r is in bin itablemax, which is itablemin-1,
// or ntablem1 if itablemin=0
// deltas at itablemax only needed if corresponding rsq < cut*cut
// if so, compute deltas between rsq and cut*cut
// if tb->match, data at cut*cut is unavailable, so we'll take
// deltas at itablemax-1 as a good approximation
double e_tmp,f_tmp;
int itablemin = minrsq_lookup.i & tb->nmask;
itablemin >>= tb->nshiftbits;
int itablemax = itablemin - 1;
if (itablemin == 0) itablemax = ntablem1;
int itablemaxm1 = itablemax - 1;
if (itablemax == 0) itablemaxm1 = ntablem1;
rsq_lookup.i = itablemax << tb->nshiftbits;
rsq_lookup.i |= maskhi;
if (rsq_lookup.f < tb->cut*tb->cut) {
if (tb->match) {
tb->de[itablemax] = tb->de[itablemaxm1];
tb->df[itablemax] = tb->df[itablemaxm1];
tb->drsq[itablemax] = tb->drsq[itablemaxm1];
} else {
rsq_lookup.f = tb->cut*tb->cut;
r = sqrtf(rsq_lookup.f);
e_tmp = splint(tb->rfile,tb->efile,tb->e2file,tb->ninput,r);
f_tmp = splint(tb->rfile,tb->ffile,tb->f2file,tb->ninput,r)/r;
tb->de[itablemax] = e_tmp - tb->e[itablemax];
tb->df[itablemax] = f_tmp - tb->f[itablemax];
tb->drsq[itablemax] = 1.0/(rsq_lookup.f - tb->rsq[itablemax]);
}
}
}
}
/* ----------------------------------------------------------------------
set all ptrs in a table to NULL, so can be freed safely
------------------------------------------------------------------------- */
void PairTableRX::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 PairTableRX::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 PairTableRX::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 PairTableRX::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 PairTableRX::write_restart(FILE *fp)
{
write_restart_settings(fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairTableRX::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairTableRX::write_restart_settings(FILE *fp)
{
fwrite(&tabstyle,sizeof(int),1,fp);
fwrite(&tablength,sizeof(int),1,fp);
fwrite(&ewaldflag,sizeof(int),1,fp);
fwrite(&pppmflag,sizeof(int),1,fp);
fwrite(&msmflag,sizeof(int),1,fp);
fwrite(&dispersionflag,sizeof(int),1,fp);
fwrite(&tip4pflag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairTableRX::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&tabstyle,sizeof(int),1,fp);
fread(&tablength,sizeof(int),1,fp);
fread(&ewaldflag,sizeof(int),1,fp);
fread(&pppmflag,sizeof(int),1,fp);
fread(&msmflag,sizeof(int),1,fp);
fread(&dispersionflag,sizeof(int),1,fp);
fread(&tip4pflag,sizeof(int),1,fp);
}
MPI_Bcast(&tabstyle,1,MPI_INT,0,world);
MPI_Bcast(&tablength,1,MPI_INT,0,world);
MPI_Bcast(&ewaldflag,1,MPI_INT,0,world);
MPI_Bcast(&pppmflag,1,MPI_INT,0,world);
MPI_Bcast(&msmflag,1,MPI_INT,0,world);
MPI_Bcast(&dispersionflag,1,MPI_INT,0,world);
MPI_Bcast(&tip4pflag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairTableRX::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
int itable;
double fraction,value,a,b,phi;
int tlm1 = tablength - 1;
Table *tb = &tables[tabindex[itype][jtype]];
double fraction1_i, fraction1_j;
double fraction2_i, fraction2_j;
double fractionOld1_i, fractionOld1_j;
double fractionOld2_i, fractionOld2_j;
fraction = double(0.0);
a = double(0.0);
b = double(0.0);
getParams(i,fractionOld1_i,fractionOld2_i,fraction1_i,fraction2_i);
getParams(j,fractionOld1_j,fractionOld2_j,fraction1_j,fraction2_j);
if (rsq < tb->innersq) error->one(FLERR,"Pair distance < table inner cutoff");
if (tabstyle == LOOKUP) {
itable = static_cast<int> ((rsq-tb->innersq) * tb->invdelta);
if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff");
fforce = factor_lj * tb->f[itable];
} else if (tabstyle == LINEAR) {
itable = static_cast<int> ((rsq-tb->innersq) * tb->invdelta);
if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff");
fraction = (rsq - tb->rsq[itable]) * tb->invdelta;
value = tb->f[itable] + fraction*tb->df[itable];
fforce = factor_lj * value;
} else if (tabstyle == SPLINE) {
itable = static_cast<int> ((rsq-tb->innersq) * tb->invdelta);
if (itable >= tlm1) error->one(FLERR,"Pair distance > table outer cutoff");
b = (rsq - tb->rsq[itable]) * tb->invdelta;
a = 1.0 - b;
value = a * tb->f[itable] + b * tb->f[itable+1] +
((a*a*a-a)*tb->f2[itable] + (b*b*b-b)*tb->f2[itable+1]) *
tb->deltasq6;
fforce = factor_lj * value;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & tb->nmask;
itable >>= tb->nshiftbits;
fraction = (rsq_lookup.f - tb->rsq[itable]) * tb->drsq[itable];
value = tb->f[itable] + fraction*tb->df[itable];
fforce = factor_lj * value;
}
if (strcmp(site1,site2) == 0) fforce = sqrt(fraction1_i*fraction2_j)*fforce;
else fforce = (sqrt(fraction1_i*fraction2_j) + sqrt(fraction2_i*fraction1_j))*fforce;
if (tabstyle == LOOKUP)
phi = tb->e[itable];
else if (tabstyle == LINEAR || tabstyle == BITMAP)
phi = tb->e[itable] + fraction*tb->de[itable];
else
phi = a * tb->e[itable] + b * tb->e[itable+1] +
((a*a*a-a)*tb->e2[itable] + (b*b*b-b)*tb->e2[itable+1]) * tb->deltasq6;
if (strcmp(site1,site2) == 0) phi = sqrt(fraction1_i*fraction2_j)*phi;
else phi = (sqrt(fraction1_i*fraction2_j) + sqrt(fraction2_i*fraction1_j))*phi;
return factor_lj*phi;
}
/* ----------------------------------------------------------------------
return the Coulomb cutoff for tabled potentials
called by KSpace solvers which require that all pairwise cutoffs be the same
loop over all tables not just those indexed by tabindex[i][j] since
no way to know which tables are active since pair::init() not yet called
------------------------------------------------------------------------- */
void *PairTableRX::extract(const char *str, int &dim)
{
if (strcmp(str,"cut_coul") != 0) return NULL;
if (ntables == 0) error->all(FLERR,"All pair coeffs are not set");
double cut_coul = tables[0].cut;
for (int m = 1; m < ntables; m++)
if (tables[m].cut != cut_coul)
error->all(FLERR,
"Pair table cutoffs must all be equal to use with KSpace");
dim = 0;
return &tables[0].cut;
}
/* ---------------------------------------------------------------------- */
void PairTableRX::getParams(int id, double &fractionOld1, double &fractionOld2, double &fraction1, double &fraction2)
{
double fractionOld, fraction;
double nTotal, nTotalOld;
fractionOld = double(0.0);
fraction = double(0.0);
fractionOld1 = double(0.0);
fractionOld2 = double(0.0);
fraction1 = double(0.0);
fraction2 = double(0.0);
nTotal = double(0.0);
nTotalOld = double(0.0);
for(int ispecies=0;ispecies<nspecies;ispecies++){
nTotal += atom->dvector[ispecies][id];
nTotalOld += atom->dvector[ispecies+nspecies][id];
}
if(nTotal < 1e-8 || nTotalOld < 1e-8)
error->all(FLERR,"The number of molecules in CG particle is less than 1e-8.");
for (int ispecies = 0; ispecies < nspecies; ispecies++) {
if (strcmp(site1,&atom->dname[ispecies][0]) == 0){
fractionOld1 = atom->dvector[ispecies+nspecies][id]/nTotalOld;
fraction1 = atom->dvector[ispecies][id]/nTotal;
}
if (strcmp(site2,&atom->dname[ispecies][0]) == 0){
fractionOld2 = atom->dvector[ispecies+nspecies][id]/nTotalOld;
fraction2 = atom->dvector[ispecies][id]/nTotal;
}
}
for (int ispecies = 0; ispecies < nspecies; ispecies++) {
if (strcmp(site1,&atom->dname[ispecies][0]) == 0){
fractionOld1 = atom->dvector[ispecies+nspecies][id]/nTotalOld;
fraction1 = atom->dvector[ispecies][id]/nTotal;
}
if (strcmp(site2,&atom->dname[ispecies][0]) == 0){
fractionOld2 = atom->dvector[ispecies+nspecies][id]/nTotalOld;
fraction2 = atom->dvector[ispecies][id]/nTotal;
}
if (strcmp(site1,"1fluid") == 0 || strcmp(site2,"1fluid") == 0) {
if (strcmp(site1,&atom->dname[ispecies][0]) == 0 || strcmp(site2,&atom->dname[ispecies][0]) == 0) continue;
fractionOld += atom->dvector[ispecies+nspecies][id]/nTotalOld;
fraction += atom->dvector[ispecies][id]/nTotal;
}
}
if(strcmp(site1,"1fluid") == 0){
fractionOld1 = fractionOld;
fraction1 = fraction;
}
if(strcmp(site2,"1fluid") == 0){
fractionOld2 = fractionOld;
fraction2 = fraction;
}
}
Event Timeline
Log In to Comment