Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F86873170
pair_colloid.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
Wed, Oct 9, 03:18
Size
15 KB
Mime Type
text/x-c
Expires
Fri, Oct 11, 03:18 (2 d)
Engine
blob
Format
Raw Data
Handle
21460450
Attached To
rLAMMPS lammps
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;
}
Event Timeline
Log In to Comment