Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/COLLOID/pair_colloid.cpp
659caee0ac0cefficient_neuronet

Last Change
Raw File

pair_colloid.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: Pieter in 't Veld (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_colloid.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
enum{SMALL_SMALL,SMALL_LARGE,LARGE_LARGE};
/* ---------------------------------------------------------------------- */
PairColloid::PairColloid(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairColloid::~PairColloid()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_int_array(form);
memory->destroy_2d_double_array(a12);
memory->destroy_2d_double_array(sigma);
memory->destroy_2d_double_array(d1);
memory->destroy_2d_double_array(d2);
memory->destroy_2d_double_array(a1);
memory->destroy_2d_double_array(a2);
memory->destroy_2d_double_array(diameter);
memory->destroy_2d_double_array(cut);
memory->destroy_2d_double_array(offset);
memory->destroy_2d_double_array(sigma3);
memory->destroy_2d_double_array(sigma6);
memory->destroy_2d_double_array(lj1);
memory->destroy_2d_double_array(lj2);
memory->destroy_2d_double_array(lj3);
memory->destroy_2d_double_array(lj4);
}
}
/* ---------------------------------------------------------------------- */
void PairColloid::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,r,forcelj,factor_lj;
double r2inv,r6inv,c1,c2,fR,dUR,dUA;
double K[9],h[4],g[4];
int *ilist,*jlist,*numneigh,**firstneigh;
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 nall = nlocal + atom->nghost;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
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];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_lj = 1.0;
else {
factor_lj = special_lj[j/nall];
j %= nall;
}
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]) continue;
switch (form[itype][jtype]) {
case SMALL_SMALL:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fpair = factor_lj*forcelj*r2inv;
if (eflag) evdwl = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
break;
case SMALL_LARGE:
c2 = a2[itype][jtype];
K[1] = c2*c2;
K[2] = rsq;
K[0] = K[1] - rsq;
K[4] = rsq*rsq;
K[3] = K[1] - K[2];
K[3] *= K[3]*K[3];
K[6] = K[3]*K[3];
fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
fpair = 4.0/15.0*fR*factor_lj *
(2.0*(K[1]+K[2]) * (K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
sigma6[itype][jtype]/K[6]-5.0) / K[0];
if (eflag)
evdwl = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
break;
case LARGE_LARGE:
r = sqrt(rsq);
c1 = a1[itype][jtype];
c2 = a2[itype][jtype];
K[0] = c1*c2;
K[1] = c1+c2;
K[2] = c1-c2;
K[3] = K[1]+r;
K[4] = K[1]-r;
K[5] = K[2]+r;
K[6] = K[2]-r;
K[7] = 1.0/(K[3]*K[4]);
K[8] = 1.0/(K[5]*K[6]);
g[0] = pow(K[3],-7.0);
g[1] = pow(K[4],-7.0);
g[2] = pow(K[5],-7.0);
g[3] = pow(K[6],-7.0);
h[0] = ((K[3]+5.0*K[1])*K[3]+30.0*K[0])*g[0];
h[1] = ((K[4]+5.0*K[1])*K[4]+30.0*K[0])*g[1];
h[2] = ((K[5]+5.0*K[2])*K[5]-30.0*K[0])*g[2];
h[3] = ((K[6]+5.0*K[2])*K[6]-30.0*K[0])*g[3];
g[0] *= 42.0*K[0]/K[3]+6.0*K[1]+K[3];
g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
evdwl = fR * (h[0]-h[1]-h[2]+h[3]);
dUR = evdwl/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
(2.0*K[0]*K[8]-1.0)*K[8]);
fpair = factor_lj * (dUR+dUA)/r;
if (eflag)
evdwl += a12[itype][jtype]/6.0 *
(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) - offset[itype][jtype];
break;
}
if (eflag) evdwl *= factor_lj;
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 (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
if (vflag_fdotr) virial_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairColloid::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
form = memory->create_2d_int_array(n+1,n+1,"pair:form");
a12 = memory->create_2d_double_array(n+1,n+1,"pair:a12");
sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");
d1 = memory->create_2d_double_array(n+1,n+1,"pair:d1");
d2 = memory->create_2d_double_array(n+1,n+1,"pair:d2");
a1 = memory->create_2d_double_array(n+1,n+1,"pair:a1");
a2 = memory->create_2d_double_array(n+1,n+1,"pair:a2");
diameter = memory->create_2d_double_array(n+1,n+1,"pair:diameter");
cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
sigma3 = memory->create_2d_double_array(n+1,n+1,"pair:sigma3");
sigma6 = memory->create_2d_double_array(n+1,n+1,"pair:sigma6");
lj1 = memory->create_2d_double_array(n+1,n+1,"pair:lj1");
lj2 = memory->create_2d_double_array(n+1,n+1,"pair:lj2");
lj3 = memory->create_2d_double_array(n+1,n+1,"pair:lj3");
lj4 = memory->create_2d_double_array(n+1,n+1,"pair:lj4");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairColloid::settings(int narg, char **arg)
{
if (narg != 1) error->all("Illegal pair_style command");
cut_global = force->numeric(arg[0]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairColloid::coeff(int narg, char **arg)
{
if (narg < 6 || narg > 7) error->all("Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double a12_one = force->numeric(arg[2]);
double sigma_one = force->numeric(arg[3]);
double d1_one = force->numeric(arg[4]);
double d2_one = force->numeric(arg[5]);
double cut_one = cut_global;
if (narg == 7) cut_one = force->numeric(arg[6]);
if (d1_one < 0.0 || d2_one < 0.0)
error->all("Invalid d1 or d2 value for pair colloid coeff");
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
a12[i][j] = a12_one;
sigma[i][j] = sigma_one;
if (i == j && d1_one != d2_one)
error->all("Invalid d1 or d2 value for pair colloid coeff");
d1[i][j] = d1_one;
d2[i][j] = d2_one;
diameter[i][j] = 0.5*(d1_one+d2_one);
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairColloid::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
a12[i][j] = mix_energy(a12[i][i],a12[j][j],sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
d1[i][j] = mix_distance(d1[i][i],d1[j][j]);
d2[i][j] = mix_distance(d2[i][i],d2[j][j]);
diameter[i][j] = 0.5 * (d1[i][j] + d2[i][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
sigma3[i][j] = sigma[i][j]*sigma[i][j]*sigma[i][j];
sigma6[i][j] = sigma3[i][j]*sigma3[i][j];
if (d1[i][j] == 0.0 && d2[i][j] == 0.0) form[i][j] = SMALL_SMALL;
else if (d1[i][j] == 0.0 || d2[i][j] == 0.0) form[i][j] = SMALL_LARGE;
else form[i][j] = LARGE_LARGE;
// for SMALL_SMALL, a1/a2 do not need to be set
// for SMALL_LARGE, a1 does not need to be set, a2 = radius for i,j and j,i
// for LARGE_LARGE, a1/a2 are radii, swap them for j,i
if (form[i][j] == SMALL_LARGE) {
if (d1[i][j] > 0.0) a2[i][j] = 0.5*d1[i][j];
else a2[i][j] = 0.5*d2[i][j];
a2[j][i] = a2[i][j];
} else if (form[i][j] == LARGE_LARGE) {
a2[j][i] = a1[i][j] = 0.5*d1[i][j];
a1[j][i] = a2[i][j] = 0.5*d2[i][j];
}
form[j][i] = form[i][j];
a12[j][i] = a12[i][j];
sigma[j][i] = sigma[i][j];
sigma3[j][i] = sigma3[i][j];
sigma6[j][i] = sigma6[i][j];
diameter[j][i] = diameter[i][j];
cut[j][i] = cut[i][j];
cutsq[j][i] = cutsq[i][j] = cut[i][j] * cut[i][j];
double epsilon = a12[i][j]/144.0;
lj1[j][i] = lj1[i][j] = 48.0 * epsilon * sigma6[i][j] * sigma6[i][j];
lj2[j][i] = lj2[i][j] = 24.0 * epsilon * sigma6[i][j];
lj3[j][i] = lj3[i][j] = 4.0 * epsilon * sigma6[i][j] * sigma6[i][j];
lj4[j][i] = lj4[i][j] = 4.0 * epsilon * sigma6[i][j];
offset[j][i] = offset[i][j] = 0.0;
if (offset_flag) {
double tmp;
offset[j][i] = offset[i][j] = single(0,0,i,j,cutsq[i][j],0.0,1.0,tmp);
}
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairColloid::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&a12[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&d1[i][j],sizeof(double),1,fp);
fwrite(&d2[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairColloid::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (comm->me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (comm->me == 0) {
fread(&a12[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&d1[i][j],sizeof(double),1,fp);
fread(&d2[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&a12[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&d1[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&d2[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairColloid::write_restart_settings(FILE *fp)
{
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairColloid::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairColloid::single(int i, int j, int itype, int jtype, double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double K[9],h[4],g[4];
double r,r2inv,r6inv,forcelj,c1,c2,phi,fR,dUR,dUA;
switch (form[itype][jtype]) {
case SMALL_SMALL:
r2inv = 1.0/rsq;
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
fforce = factor_lj*forcelj*r2inv;
phi = r6inv*(r6inv*lj3[itype][jtype]-lj4[itype][jtype]) -
offset[itype][jtype];
break;
case SMALL_LARGE:
r = sqrt(rsq);
c2 = a2[itype][jtype];
K[1] = c2*c2;
K[2] = rsq;
K[4] = rsq*rsq;
K[3] = K[1] - K[2];
K[3] *= K[3]*K[3];
K[6] = K[3]*K[3];
fR = sigma3[itype][jtype]*a12[itype][jtype]*c2*K[1]/K[3];
fforce = 4.0/15.0*r*fR*factor_lj *
(2.0*(K[1]+K[2])*(K[1]*(5.0*K[1]+22.0*K[2])+5.0*K[4]) *
sigma6[itype][jtype]/K[6] - 5.0)/K[0];
phi = 2.0/9.0*fR *
(1.0-(K[1]*(K[1]*(K[1]/3.0+3.0*K[2])+4.2*K[4])+K[2]*K[4]) *
sigma6[itype][jtype]/K[6]) - offset[itype][jtype];
break;
case LARGE_LARGE:
r = sqrt(rsq);
c1 = a1[itype][jtype];
c2 = a2[itype][jtype];
K[0] = c1*c2;
K[1] = c1+c2;
K[2] = c1-c2;
K[3] = K[1]+r;
K[4] = K[1]-r;
K[5] = K[2]+r;
K[6] = K[2]-r;
K[7] = 1.0/(K[3]*K[4]);
K[8] = 1.0/(K[5]*K[6]);
g[0] = pow(K[3],-7.0);
g[1] = pow(K[4],-7.0);
g[2] = pow(K[5],-7.0);
g[3] = pow(K[6],-7.0);
h[0] = ((K[3]+5.0*K[1])*K[3]+30.0*K[0])*g[0];
h[1] = ((K[4]+5.0*K[1])*K[4]+30.0*K[0])*g[1];
h[2] = ((K[5]+5.0*K[2])*K[5]-30.0*K[0])*g[2];
h[3] = ((K[6]+5.0*K[2])*K[6]-30.0*K[0])*g[3];
g[0] *= 42.0*K[0]/K[3]+6.0*K[1]+K[3];
g[1] *= 42.0*K[0]/K[4]+6.0*K[1]+K[4];
g[2] *= -42.0*K[0]/K[5]+6.0*K[2]+K[5];
g[3] *= -42.0*K[0]/K[6]+6.0*K[2]+K[6];
fR = a12[itype][jtype]*sigma6[itype][jtype]/r/37800.0;
phi = fR * (h[0]-h[1]-h[2]+h[3]);
dUR = phi/r + 5.0*fR*(g[0]+g[1]-g[2]-g[3]);
dUA = -a12[itype][jtype]/3.0*r*((2.0*K[0]*K[7]+1.0)*K[7] +
(2.0*K[0]*K[8]-1.0)*K[8]);
fforce = factor_lj*(dUR+dUA)/r;
phi += a12[itype][jtype]/6.0*(2.0*K[0]*(K[7]+K[8])-log(K[8]/K[7])) -
offset[itype][jtype];
break;
}
return factor_lj*phi;
}
c4science · Help