Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/MANYBODY/pair_adp.cpp
354e20f43157efficient_neuronet

Last Change
Raw File

pair_adp.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 authors: Christopher Weinberger (SNL), Stephen Foiles (SNL),
Chandra Veer Singh (Cornell)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_adp.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
/* ---------------------------------------------------------------------- */
PairADP::PairADP(LAMMPS *lmp) : Pair(lmp)
{
restartinfo = 0;
nmax = 0;
rho = NULL;
fp = NULL;
mu = NULL;
lambda = NULL;
map = NULL;
setfl = NULL;
frho = NULL;
rhor = NULL;
z2r = NULL;
u2r = NULL;
w2r = NULL;
frho_spline = NULL;
rhor_spline = NULL;
z2r_spline = NULL;
u2r_spline = NULL;
w2r_spline = NULL;
// set comm size needed by this Pair
comm_forward = 10;
comm_reverse = 10;
single_enable = 0;
one_coeff = 1;
manybody_flag = 1;
}
/* ----------------------------------------------------------------------
check if allocated, since class can be destructed when incomplete
------------------------------------------------------------------------- */
PairADP::~PairADP()
{
memory->destroy(rho);
memory->destroy(fp);
memory->destroy(mu);
memory->destroy(lambda);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
delete [] map;
delete [] type2frho;
memory->destroy(type2rhor);
memory->destroy(type2z2r);
memory->destroy(type2u2r);
memory->destroy(type2w2r);
}
if (setfl) {
for (int i = 0; i < setfl->nelements; i++) delete [] setfl->elements[i];
delete [] setfl->elements;
delete [] setfl->mass;
memory->destroy(setfl->frho);
memory->destroy(setfl->rhor);
memory->destroy(setfl->z2r);
memory->destroy(setfl->u2r);
memory->destroy(setfl->w2r);
delete setfl;
}
memory->destroy(frho);
memory->destroy(rhor);
memory->destroy(z2r);
memory->destroy(u2r);
memory->destroy(w2r);
memory->destroy(frho_spline);
memory->destroy(rhor_spline);
memory->destroy(z2r_spline);
memory->destroy(u2r_spline);
memory->destroy(w2r_spline);
}
/* ---------------------------------------------------------------------- */
void PairADP::compute(int eflag, int vflag)
{
int i,j,ii,jj,m,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r,p,rhoip,rhojp,z2,z2p,recip,phip,psip,phi;
double u2,u2p,w2,w2p,nu;
double *coeff;
int *ilist,*jlist,*numneigh,**firstneigh;
double delmux,delmuy,delmuz,trdelmu,tradellam;
double adpx,adpy,adpz,fx,fy,fz;
double sumlamxx,sumlamyy,sumlamzz,sumlamyz,sumlamxz,sumlamxy;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
// grow local arrays if necessary
// need to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(rho);
memory->destroy(fp);
memory->destroy(mu);
memory->destroy(lambda);
nmax = atom->nmax;
memory->create(rho,nmax,"pair:rho");
memory->create(fp,nmax,"pair:fp");
memory->create(mu,nmax,3,"pair:mu");
memory->create(lambda,nmax,6,"pair:lambda");
}
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// zero out density
if (newton_pair) {
m = nlocal + atom->nghost;
for (i = 0; i < m; i++) {
rho[i] = 0.0;
mu[i][0] = 0.0; mu[i][1] = 0.0; mu[i][2] = 0.0;
lambda[i][0] = 0.0; lambda[i][1] = 0.0; lambda[i][2] = 0.0;
lambda[i][3] = 0.0; lambda[i][4] = 0.0; lambda[i][5] = 0.0;
}
} else {
for (i = 0; i < nlocal; i++) {
rho[i] = 0.0;
mu[i][0] = 0.0; mu[i][1] = 0.0; mu[i][2] = 0.0;
lambda[i][0] = 0.0; lambda[i][1] = 0.0; lambda[i][2] = 0.0;
lambda[i][3] = 0.0; lambda[i][4] = 0.0; lambda[i][5] = 0.0;
}
}
// rho = density at each atom
// 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];
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;
if (rsq < cutforcesq) {
jtype = type[j];
p = sqrt(rsq)*rdr + 1.0;
m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rho[i] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[jtype][itype]][m];
u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
mu[i][0] += u2*delx;
mu[i][1] += u2*dely;
mu[i][2] += u2*delz;
coeff = w2r_spline[type2w2r[jtype][itype]][m];
w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
lambda[i][0] += w2*delx*delx;
lambda[i][1] += w2*dely*dely;
lambda[i][2] += w2*delz*delz;
lambda[i][3] += w2*dely*delz;
lambda[i][4] += w2*delx*delz;
lambda[i][5] += w2*delx*dely;
if (newton_pair || j < nlocal) {
// verify sign difference for mu and lambda
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rho[j] += ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[itype][jtype]][m];
u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
mu[j][0] -= u2*delx;
mu[j][1] -= u2*dely;
mu[j][2] -= u2*delz;
coeff = w2r_spline[type2w2r[itype][jtype]][m];
w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
lambda[j][0] += w2*delx*delx;
lambda[j][1] += w2*dely*dely;
lambda[j][2] += w2*delz*delz;
lambda[j][3] += w2*dely*delz;
lambda[j][4] += w2*delx*delz;
lambda[j][5] += w2*delx*dely;
}
}
}
}
// communicate and sum densities
if (newton_pair) comm->reverse_comm_pair(this);
// fp = derivative of embedding energy at each atom
// phi = embedding energy at each atom
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
p = rho[i]*rdrho + 1.0;
m = static_cast<int> (p);
m = MAX(1,MIN(m,nrho-1));
p -= m;
p = MIN(p,1.0);
coeff = frho_spline[type2frho[type[i]]][m];
fp[i] = (coeff[0]*p + coeff[1])*p + coeff[2];
if (eflag) {
phi = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
phi += 0.5*(mu[i][0]*mu[i][0]+mu[i][1]*mu[i][1]+mu[i][2]*mu[i][2]);
phi += 0.5*(lambda[i][0]*lambda[i][0]+lambda[i][1]*
lambda[i][1]+lambda[i][2]*lambda[i][2]);
phi += 1.0*(lambda[i][3]*lambda[i][3]+lambda[i][4]*
lambda[i][4]+lambda[i][5]*lambda[i][5]);
phi -= 1.0/6.0*(lambda[i][0]+lambda[i][1]+lambda[i][2])*
(lambda[i][0]+lambda[i][1]+lambda[i][2]);
if (eflag_global) eng_vdwl += phi;
if (eflag_atom) eatom[i] += phi;
}
}
// communicate derivative of embedding function
comm->forward_comm_pair(this);
// compute forces on each atom
// 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];
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;
if (rsq < cutforcesq) {
jtype = type[j];
r = sqrt(rsq);
p = r*rdr + 1.0;
m = static_cast<int> (p);
m = MIN(m,nr-1);
p -= m;
p = MIN(p,1.0);
// rhoip = derivative of (density at atom j due to atom i)
// rhojp = derivative of (density at atom i due to atom j)
// phi = pair potential energy
// phip = phi'
// z2 = phi * r
// z2p = (phi * r)' = (phi' r) + phi
// u2 = u
// u2p = u'
// w2 = w
// w2p = w'
// psip needs both fp[i] and fp[j] terms since r_ij appears in two
// terms of embed eng: Fi(sum rho_ij) and Fj(sum rho_ji)
// hence embed' = Fi(sum rho_ij) rhojp + Fj(sum rho_ji) rhoip
coeff = rhor_spline[type2rhor[itype][jtype]][m];
rhoip = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = rhor_spline[type2rhor[jtype][itype]][m];
rhojp = (coeff[0]*p + coeff[1])*p + coeff[2];
coeff = z2r_spline[type2z2r[itype][jtype]][m];
z2p = (coeff[0]*p + coeff[1])*p + coeff[2];
z2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = u2r_spline[type2u2r[itype][jtype]][m];
u2p = (coeff[0]*p + coeff[1])*p + coeff[2];
u2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
coeff = w2r_spline[type2w2r[itype][jtype]][m];
w2p = (coeff[0]*p + coeff[1])*p + coeff[2];
w2 = ((coeff[3]*p + coeff[4])*p + coeff[5])*p + coeff[6];
recip = 1.0/r;
phi = z2*recip;
phip = z2p*recip - phi*recip;
psip = fp[i]*rhojp + fp[j]*rhoip + phip;
fpair = -psip*recip;
delmux = mu[i][0]-mu[j][0];
delmuy = mu[i][1]-mu[j][1];
delmuz = mu[i][2]-mu[j][2];
trdelmu = delmux*delx+delmuy*dely+delmuz*delz;
sumlamxx = lambda[i][0]+lambda[j][0];
sumlamyy = lambda[i][1]+lambda[j][1];
sumlamzz = lambda[i][2]+lambda[j][2];
sumlamyz = lambda[i][3]+lambda[j][3];
sumlamxz = lambda[i][4]+lambda[j][4];
sumlamxy = lambda[i][5]+lambda[j][5];
tradellam = sumlamxx*delx*delx+sumlamyy*dely*dely+
sumlamzz*delz*delz+2.0*sumlamxy*delx*dely+
2.0*sumlamxz*delx*delz+2.0*sumlamyz*dely*delz;
nu = sumlamxx+sumlamyy+sumlamzz;
adpx = delmux*u2 + trdelmu*u2p*delx*recip +
2.0*w2*(sumlamxx*delx+sumlamxy*dely+sumlamxz*delz) +
w2p*delx*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delx;
adpy = delmuy*u2 + trdelmu*u2p*dely*recip +
2.0*w2*(sumlamxy*delx+sumlamyy*dely+sumlamyz*delz) +
w2p*dely*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*dely;
adpz = delmuz*u2 + trdelmu*u2p*delz*recip +
2.0*w2*(sumlamxz*delx+sumlamyz*dely+sumlamzz*delz) +
w2p*delz*recip*tradellam - 1.0/3.0*nu*(w2p*r+2.0*w2)*delz;
adpx*=-1.0; adpy*=-1.0; adpz*=-1.0;
fx = delx*fpair+adpx;
fy = dely*fpair+adpy;
fz = delz*fpair+adpz;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
if (newton_pair || j < nlocal) {
f[j][0] -= fx;
f[j][1] -= fy;
f[j][2] -= fz;
}
if (eflag) evdwl = phi;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0.0,
fx,fy,fz,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairADP::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
map = new int[n+1];
for (int i = 1; i <= n; i++) map[i] = -1;
type2frho = new int[n+1];
memory->create(type2rhor,n+1,n+1,"pair:type2rhor");
memory->create(type2z2r,n+1,n+1,"pair:type2z2r");
memory->create(type2u2r,n+1,n+1,"pair:type2u2r");
memory->create(type2w2r,n+1,n+1,"pair:type2w2r");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairADP::settings(int narg, char **arg)
{
if (narg > 0) error->all(FLERR,"Illegal pair_style command");
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
read concatenated *.plt file
------------------------------------------------------------------------- */
void PairADP::coeff(int narg, char **arg)
{
int i,j;
if (!allocated) allocate();
if (narg != 3 + atom->ntypes)
error->all(FLERR,"Incorrect args for pair coefficients");
// insure I,J args are * *
if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
error->all(FLERR,"Incorrect args for pair coefficients");
// read ADP parameter file
if (setfl) {
for (i = 0; i < setfl->nelements; i++) delete [] setfl->elements[i];
delete [] setfl->elements;
delete [] setfl->mass;
memory->destroy(setfl->frho);
memory->destroy(setfl->rhor);
memory->destroy(setfl->z2r);
memory->destroy(setfl->u2r);
memory->destroy(setfl->w2r);
delete setfl;
}
setfl = new Setfl();
read_file(arg[2]);
// read args that map atom types to elements in potential file
// map[i] = which element the Ith atom type is, -1 if NULL
for (i = 3; i < narg; i++) {
if (strcmp(arg[i],"NULL") == 0) {
map[i-2] = -1;
continue;
}
for (j = 0; j < setfl->nelements; j++)
if (strcmp(arg[i],setfl->elements[j]) == 0) break;
if (j < setfl->nelements) map[i-2] = j;
else error->all(FLERR,"No matching element in ADP potential file");
}
// clear setflag since coeff() called once with I,J = * *
int n = atom->ntypes;
for (i = 1; i <= n; i++)
for (j = i; j <= n; j++)
setflag[i][j] = 0;
// set setflag i,j for type pairs where both are mapped to elements
// set mass of atom type if i = j
int count = 0;
for (i = 1; i <= n; i++) {
for (j = i; j <= n; j++) {
if (map[i] >= 0 && map[j] >= 0) {
setflag[i][j] = 1;
if (i == j) atom->set_mass(i,setfl->mass[map[i]]);
count++;
}
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairADP::init_style()
{
// convert read-in file(s) to arrays and spline them
file2array();
array2spline();
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairADP::init_one(int i, int j)
{
// single global cutoff = max of cut from all files read in
// for funcfl could be multiple files
// for setfl or fs, just one file
if (setfl) cutmax = setfl->cut;
cutforcesq = cutmax*cutmax;
return cutmax;
}
/* ----------------------------------------------------------------------
read potential values from a DYNAMO single element funcfl file
------------------------------------------------------------------------- */
void PairADP::read_file(char *filename)
{
Setfl *file = setfl;
// open potential file
int me = comm->me;
FILE *fp;
char line[MAXLINE];
if (me == 0) {
fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open ADP potential file %s",filename);
error->one(FLERR,str);
}
}
// read and broadcast header
// extract element names from nelements line
int n;
if (me == 0) {
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
fgets(line,MAXLINE,fp);
n = strlen(line) + 1;
}
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
sscanf(line,"%d",&file->nelements);
int nwords = atom->count_words(line);
if (nwords != file->nelements + 1)
error->all(FLERR,"Incorrect element names in ADP potential file");
char **words = new char*[file->nelements+1];
nwords = 0;
strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
file->elements = new char*[file->nelements];
for (int i = 0; i < file->nelements; i++) {
n = strlen(words[i]) + 1;
file->elements[i] = new char[n];
strcpy(file->elements[i],words[i]);
}
delete [] words;
if (me == 0) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg %d %lg %lg",
&file->nrho,&file->drho,&file->nr,&file->dr,&file->cut);
}
MPI_Bcast(&file->nrho,1,MPI_INT,0,world);
MPI_Bcast(&file->drho,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->nr,1,MPI_INT,0,world);
MPI_Bcast(&file->dr,1,MPI_DOUBLE,0,world);
MPI_Bcast(&file->cut,1,MPI_DOUBLE,0,world);
file->mass = new double[file->nelements];
memory->create(file->frho,file->nelements,file->nrho+1,"pair:frho");
memory->create(file->rhor,file->nelements,file->nr+1,"pair:rhor");
memory->create(file->z2r,file->nelements,file->nelements,file->nr+1,
"pair:z2r");
memory->create(file->u2r,file->nelements,file->nelements,file->nr+1,
"pair:u2r");
memory->create(file->w2r,file->nelements,file->nelements,file->nr+1,
"pair:w2r");
int i,j,tmp;
for (i = 0; i < file->nelements; i++) {
if (me == 0) {
fgets(line,MAXLINE,fp);
sscanf(line,"%d %lg",&tmp,&file->mass[i]);
}
MPI_Bcast(&file->mass[i],1,MPI_DOUBLE,0,world);
if (me == 0) grab(fp,file->nrho,&file->frho[i][1]);
MPI_Bcast(&file->frho[i][1],file->nrho,MPI_DOUBLE,0,world);
if (me == 0) grab(fp,file->nr,&file->rhor[i][1]);
MPI_Bcast(&file->rhor[i][1],file->nr,MPI_DOUBLE,0,world);
}
for (i = 0; i < file->nelements; i++)
for (j = 0; j <= i; j++) {
if (me == 0) grab(fp,file->nr,&file->z2r[i][j][1]);
MPI_Bcast(&file->z2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
for (i = 0; i < file->nelements; i++)
for (j = 0; j <= i; j++) {
if (me == 0) grab(fp,file->nr,&file->u2r[i][j][1]);
MPI_Bcast(&file->u2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
for (i = 0; i < file->nelements; i++)
for (j = 0; j <= i; j++) {
if (me == 0) grab(fp,file->nr,&file->w2r[i][j][1]);
MPI_Bcast(&file->w2r[i][j][1],file->nr,MPI_DOUBLE,0,world);
}
// close the potential file
if (me == 0) fclose(fp);
}
/* ----------------------------------------------------------------------
convert read-in funcfl potential(s) to standard array format
interpolate all file values to a single grid and cutoff
------------------------------------------------------------------------- */
void PairADP::file2array()
{
int i,j,m,n;
int ntypes = atom->ntypes;
// set function params directly from setfl file
nrho = setfl->nrho;
nr = setfl->nr;
drho = setfl->drho;
dr = setfl->dr;
// ------------------------------------------------------------------
// setup frho arrays
// ------------------------------------------------------------------
// allocate frho arrays
// nfrho = # of setfl elements + 1 for zero array
nfrho = setfl->nelements + 1;
memory->destroy(frho);
memory->create(frho,nfrho,nrho+1,"pair:frho");
// copy each element's frho to global frho
for (i = 0; i < setfl->nelements; i++)
for (m = 1; m <= nrho; m++) frho[i][m] = setfl->frho[i][m];
// add extra frho of zeroes for non-ADP types to point to (pair hybrid)
// this is necessary b/c fp is still computed for non-ADP atoms
for (m = 1; m <= nrho; m++) frho[nfrho-1][m] = 0.0;
// type2frho[i] = which frho array (0 to nfrho-1) each atom type maps to
// if atom type doesn't point to element (non-ADP atom in pair hybrid)
// then map it to last frho array of zeroes
for (i = 1; i <= ntypes; i++)
if (map[i] >= 0) type2frho[i] = map[i];
else type2frho[i] = nfrho-1;
// ------------------------------------------------------------------
// setup rhor arrays
// ------------------------------------------------------------------
// allocate rhor arrays
// nrhor = # of setfl elements
nrhor = setfl->nelements;
memory->destroy(rhor);
memory->create(rhor,nrhor,nr+1,"pair:rhor");
// copy each element's rhor to global rhor
for (i = 0; i < setfl->nelements; i++)
for (m = 1; m <= nr; m++) rhor[i][m] = setfl->rhor[i][m];
// type2rhor[i][j] = which rhor array (0 to nrhor-1) each type pair maps to
// for setfl files, I,J mapping only depends on I
// OK if map = -1 (non-APD atom in pair hybrid) b/c type2rhor not used
for (i = 1; i <= ntypes; i++)
for (j = 1; j <= ntypes; j++)
type2rhor[i][j] = map[i];
// ------------------------------------------------------------------
// setup z2r arrays
// ------------------------------------------------------------------
// allocate z2r arrays
// nz2r = N*(N+1)/2 where N = # of setfl elements
nz2r = setfl->nelements * (setfl->nelements+1) / 2;
memory->destroy(z2r);
memory->create(z2r,nz2r,nr+1,"pair:z2r");
// copy each element pair z2r to global z2r, only for I >= J
n = 0;
for (i = 0; i < setfl->nelements; i++)
for (j = 0; j <= i; j++) {
for (m = 1; m <= nr; m++) z2r[n][m] = setfl->z2r[i][j][m];
n++;
}
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
// set of z2r arrays only fill lower triangular Nelement matrix
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
// swap indices when irow < icol to stay lower triangular
// OK if map = -1 (non-ADP atom in pair hybrid) b/c type2z2r not used
int irow,icol;
for (i = 1; i <= ntypes; i++) {
for (j = 1; j <= ntypes; j++) {
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) continue;
if (irow < icol) {
irow = map[j];
icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
n += icol;
type2z2r[i][j] = n;
}
}
// ------------------------------------------------------------------
// setup u2r arrays
// ------------------------------------------------------------------
// allocate u2r arrays
// nu2r = N*(N+1)/2 where N = # of setfl elements
nu2r = setfl->nelements * (setfl->nelements+1) / 2;
memory->destroy(u2r);
memory->create(u2r,nu2r,nr+1,"pair:u2r");
// copy each element pair z2r to global z2r, only for I >= J
n = 0;
for (i = 0; i < setfl->nelements; i++)
for (j = 0; j <= i; j++) {
for (m = 1; m <= nr; m++) u2r[n][m] = setfl->u2r[i][j][m];
n++;
}
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
// set of z2r arrays only fill lower triangular Nelement matrix
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
// swap indices when irow < icol to stay lower triangular
// OK if map = -1 (non-ADP atom in pair hybrid) b/c type2z2r not used
for (i = 1; i <= ntypes; i++) {
for (j = 1; j <= ntypes; j++) {
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) continue;
if (irow < icol) {
irow = map[j];
icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
n += icol;
type2u2r[i][j] = n;
}
}
// ------------------------------------------------------------------
// setup w2r arrays
// ------------------------------------------------------------------
// allocate w2r arrays
// nw2r = N*(N+1)/2 where N = # of setfl elements
nw2r = setfl->nelements * (setfl->nelements+1) / 2;
memory->destroy(w2r);
memory->create(w2r,nw2r,nr+1,"pair:w2r");
// copy each element pair z2r to global z2r, only for I >= J
n = 0;
for (i = 0; i < setfl->nelements; i++)
for (j = 0; j <= i; j++) {
for (m = 1; m <= nr; m++) w2r[n][m] = setfl->w2r[i][j][m];
n++;
}
// type2z2r[i][j] = which z2r array (0 to nz2r-1) each type pair maps to
// set of z2r arrays only fill lower triangular Nelement matrix
// value = n = sum over rows of lower-triangular matrix until reach irow,icol
// swap indices when irow < icol to stay lower triangular
// OK if map = -1 (non-ADP atom in pair hybrid) b/c type2z2r not used
for (i = 1; i <= ntypes; i++) {
for (j = 1; j <= ntypes; j++) {
irow = map[i];
icol = map[j];
if (irow == -1 || icol == -1) continue;
if (irow < icol) {
irow = map[j];
icol = map[i];
}
n = 0;
for (m = 0; m < irow; m++) n += m + 1;
n += icol;
type2w2r[i][j] = n;
}
}
}
/* ---------------------------------------------------------------------- */
void PairADP::array2spline()
{
rdr = 1.0/dr;
rdrho = 1.0/drho;
memory->destroy(frho_spline);
memory->destroy(rhor_spline);
memory->destroy(z2r_spline);
memory->destroy(u2r_spline);
memory->destroy(w2r_spline);
memory->create(frho_spline,nfrho,nrho+1,7,"pair:frho");
memory->create(rhor_spline,nrhor,nr+1,7,"pair:rhor");
memory->create(z2r_spline,nz2r,nr+1,7,"pair:z2r");
memory->create(u2r_spline,nz2r,nr+1,7,"pair:u2r");
memory->create(w2r_spline,nz2r,nr+1,7,"pair:w2r");
for (int i = 0; i < nfrho; i++)
interpolate(nrho,drho,frho[i],frho_spline[i]);
for (int i = 0; i < nrhor; i++)
interpolate(nr,dr,rhor[i],rhor_spline[i]);
for (int i = 0; i < nz2r; i++)
interpolate(nr,dr,z2r[i],z2r_spline[i]);
for (int i = 0; i < nu2r; i++)
interpolate(nr,dr,u2r[i],u2r_spline[i]);
for (int i = 0; i < nw2r; i++)
interpolate(nr,dr,w2r[i],w2r_spline[i]);
}
/* ---------------------------------------------------------------------- */
void PairADP::interpolate(int n, double delta, double *f, double **spline)
{
for (int m = 1; m <= n; m++) spline[m][6] = f[m];
spline[1][5] = spline[2][6] - spline[1][6];
spline[2][5] = 0.5 * (spline[3][6]-spline[1][6]);
spline[n-1][5] = 0.5 * (spline[n][6]-spline[n-2][6]);
spline[n][5] = spline[n][6] - spline[n-1][6];
for (int m = 3; m <= n-2; m++)
spline[m][5] = ((spline[m-2][6]-spline[m+2][6]) +
8.0*(spline[m+1][6]-spline[m-1][6])) / 12.0;
for (int m = 1; m <= n-1; m++) {
spline[m][4] = 3.0*(spline[m+1][6]-spline[m][6]) -
2.0*spline[m][5] - spline[m+1][5];
spline[m][3] = spline[m][5] + spline[m+1][5] -
2.0*(spline[m+1][6]-spline[m][6]);
}
spline[n][4] = 0.0;
spline[n][3] = 0.0;
for (int m = 1; m <= n; m++) {
spline[m][2] = spline[m][5]/delta;
spline[m][1] = 2.0*spline[m][4]/delta;
spline[m][0] = 3.0*spline[m][3]/delta;
}
}
/* ----------------------------------------------------------------------
grab n values from file fp and put them in list
values can be several to a line
only called by proc 0
------------------------------------------------------------------------- */
void PairADP::grab(FILE *fp, int n, double *list)
{
char *ptr;
char line[MAXLINE];
int i = 0;
while (i < n) {
fgets(line,MAXLINE,fp);
ptr = strtok(line," \t\n\r\f");
list[i++] = atof(ptr);
while ((ptr = strtok(NULL," \t\n\r\f"))) list[i++] = atof(ptr);
}
}
/* ---------------------------------------------------------------------- */
int PairADP::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = fp[j];
buf[m++] = mu[j][0];
buf[m++] = mu[j][1];
buf[m++] = mu[j][2];
buf[m++] = lambda[j][0];
buf[m++] = lambda[j][1];
buf[m++] = lambda[j][2];
buf[m++] = lambda[j][3];
buf[m++] = lambda[j][4];
buf[m++] = lambda[j][5];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairADP::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
fp[i] = buf[m++];
mu[i][0] = buf[m++];
mu[i][1] = buf[m++];
mu[i][2] = buf[m++];
lambda[i][0] = buf[m++];
lambda[i][1] = buf[m++];
lambda[i][2] = buf[m++];
lambda[i][3] = buf[m++];
lambda[i][4] = buf[m++];
lambda[i][5] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int PairADP::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = rho[i];
buf[m++] = mu[i][0];
buf[m++] = mu[i][1];
buf[m++] = mu[i][2];
buf[m++] = lambda[i][0];
buf[m++] = lambda[i][1];
buf[m++] = lambda[i][2];
buf[m++] = lambda[i][3];
buf[m++] = lambda[i][4];
buf[m++] = lambda[i][5];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairADP::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
rho[j] += buf[m++];
mu[j][0] += buf[m++];
mu[j][1] += buf[m++];
mu[j][2] += buf[m++];
lambda[j][0] += buf[m++];
lambda[j][1] += buf[m++];
lambda[j][2] += buf[m++];
lambda[j][3] += buf[m++];
lambda[j][4] += buf[m++];
lambda[j][5] += buf[m++];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based arrays
------------------------------------------------------------------------- */
double PairADP::memory_usage()
{
double bytes = Pair::memory_usage();
bytes += 21 * nmax * sizeof(double);
return bytes;
}
c4science · Help