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lammps/src/COLLOID/pair_lubricate.cpp
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pair_lubricate.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Randy Schunk (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lubricate.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "update.h"
#include "memory.h"
#include "random_mars.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
PairLubricate::PairLubricate(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
random = NULL;
}
/* ---------------------------------------------------------------------- */
PairLubricate::~PairLubricate()
{
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
memory->destroy_2d_double_array(cut);
memory->destroy_2d_double_array(cut_inner);
}
delete random;
}
/* ---------------------------------------------------------------------- */
void PairLubricate::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fpair,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,radi,tfmag;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3,w1,w2,w3,v_shear1,v_shear2,v_shear3;
double omega_t_1,omega_t_2,omega_t_3;
double n_cross_omega_t_1,n_cross_omega_t_2,n_cross_omega_t_3;
double wr1,wr2,wr3,wnnr,wn1,wn2,wn3,inv_inertia;
double P_dot_wrel_1,P_dot_wrel_2,P_dot_wrel_3;
double a_squeeze,a_shear,a_pump,a_twist;
int *ilist,*jlist,*numneigh,**firstneigh;
double PI = 4.0*atan(1.0);
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **angmom = atom->angmom;
double **torque = atom->torque;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
int omega_flag = atom->omega_flag;
double vxmu2f = force->vxmu2f;
double prethermostat = sqrt(2.0 * force->boltz * t_target / update->dt);
prethermostat *= sqrt(force->vxmu2f/force->ftm2v/force->mvv2e);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
a_squeeze = a_shear = a_pump = a_twist = 0.0;
// 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];
radi = atom->shape[itype][0];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
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]) {
r = sqrt(rsq);
// relative translational velocity
vr1 = v[i][0] - v[j][0];
vr2 = v[i][1] - v[j][1];
vr3 = v[i][2] - v[j][2];
// normal component N.(v1-v2) = nn.(v1-v2)
vnnr = vr1*delx + vr2*dely + vr3*delz;
vnnr /= r;
vn1 = delx*vnnr / r;
vn2 = dely*vnnr / r;
vn3 = delz*vnnr / r;
// tangential component -P.(v1-v2)
// P = (I - nn) where n is vector between centers
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// additive rotational velocity = omega_1 + omega_2
// use omega directly if it exists, else angmom
// angular momentum = I*omega = 2/5 * M*R^2 * omega
if (omega_flag) {
w1 = omega[i][0] + omega[j][0];
w2 = omega[i][1] + omega[j][1];
w3 = omega[i][2] + omega[j][2];
} else {
inv_inertia = 1.0 / (0.4*atom->mass[itype]*radi*radi);
w1 = inv_inertia * (angmom[i][0] + angmom[j][0]);
w2 = inv_inertia * (angmom[i][1] + angmom[j][1]);
w3 = inv_inertia * (angmom[i][2] + angmom[j][2]);
}
// relative velocities n X P . (v1-v2) = n X (I-nn) . (v1-v2)
v_shear1 = (dely*vt3 - delz*vt2) / r;
v_shear2 = -(delx*vt3 - delz*vt1) / r;
v_shear3 = (delx*vt2 - dely*vt1) / r;
// relative rotation rate P.(omega1 + omega2)
omega_t_1 = w1 - delx*(delx*w1) / rsq;
omega_t_2 = w2 - dely*(dely*w2) / rsq;
omega_t_3 = w3 - delz*(delz*w3) / rsq;
// n X omega_t
n_cross_omega_t_1 = (dely*omega_t_3 - delz*omega_t_2) / r;
n_cross_omega_t_2 = -(delx*omega_t_3 - delz*omega_t_1) / r;
n_cross_omega_t_3 = (delx*omega_t_2 - dely*omega_t_1) / r;
// N.(w1-w2) and P.(w1-w2)
if (omega_flag) {
wr1 = omega[i][0] - omega[j][0];
wr2 = omega[i][1] - omega[j][1];
wr3 = omega[i][2] - omega[j][2];
} else {
wr1 = inv_inertia * (angmom[i][0] - angmom[j][0]);
wr2 = inv_inertia * (angmom[i][1] - angmom[j][1]);
wr3 = inv_inertia * (angmom[i][2] - angmom[j][2]);
}
wnnr = wr1*delx + wr2*dely + wr3*delz;
wn1 = delx*wnnr / rsq;
wn2 = dely*wnnr / rsq;
wn3 = delz*wnnr / rsq;
P_dot_wrel_1 = wr1 - delx*(delx*wr1)/rsq;
P_dot_wrel_2 = wr2 - dely*(dely*wr2)/rsq;
P_dot_wrel_3 = wr3 - delz*(delz*wr3)/rsq;
// compute components of pair-hydro
h_sep = r - 2.0*radi;
if (flag1)
a_squeeze = (3.0*PI*mu*2.0*radi/2.0) * (2.0*radi/4.0/h_sep);
if (flag2)
a_shear = (PI*mu*2.*radi/2.0) *
log(2.0*radi/2.0/h_sep)*(2.0*radi+h_sep)*(2.0*radi+h_sep)/4.0;
if (flag3)
a_pump = (PI*mu*pow(2.0*radi,4)/8.0) *
((3.0/20.0) * log(2.0*radi/2.0/h_sep) +
(63.0/250.0) * (h_sep/2.0/radi) * log(2.0*radi/2.0/h_sep));
if (flag4)
a_twist = (PI*mu*pow(2.0*radi,4)/4.0) *
(h_sep/2.0/radi) * log(2.0/(2.0*h_sep));
if (h_sep >= cut_inner[itype][jtype]) {
fx = -a_squeeze*vn1 - a_shear*(2.0/r)*(2.0/r)*vt1 +
(2.0/r)*a_shear*n_cross_omega_t_1;
fy = -a_squeeze*vn2 - a_shear*(2.0/r)*(2.0/r)*vt2 +
(2.0/r)*a_shear*n_cross_omega_t_2;
fz = -a_squeeze*vn3 - a_shear*(2.0/r)*(2.0/r)*vt3 +
(2.0/r)*a_shear*n_cross_omega_t_3;
fx *= vxmu2f;
fy *= vxmu2f;
fz *= vxmu2f;
// add in thermostat force
tfmag = prethermostat*sqrt(a_squeeze)*(random->uniform()-0.5);
fx -= tfmag * delx/r;
fy -= tfmag * dely/r;
fz -= tfmag * delz/r;
tx = -(2.0/r)*a_shear*v_shear1 - a_shear*omega_t_1 -
a_pump*P_dot_wrel_1 - a_twist*wn1;
ty = -(2.0/r)*a_shear*v_shear2 - a_shear*omega_t_2 -
a_pump*P_dot_wrel_2 - a_twist*wn2;
tz = -(2.0/r)*a_shear*v_shear3 - a_shear*omega_t_3 -
a_pump*P_dot_wrel_3 - a_twist*wn3;
torque[i][0] += vxmu2f * tx;
torque[i][1] += vxmu2f * ty;
torque[i][2] += vxmu2f * tz;
} else {
a_squeeze = (3.0*PI*mu*2.0*radi/2.0) *
(2.0*radi/4.0/cut_inner[itype][jtype]);
fpair = -a_squeeze*vnnr;
fpair *= vxmu2f;
// add in thermostat force
fpair -= prethermostat*sqrt(a_squeeze)*(random->uniform()-0.5);
fx = fpair * delx/r;
fy = fpair * dely/r;
fz = fpair * delz/r;
}
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 (h_sep >= cut_inner[itype][jtype]) {
tx = -(2.0/r)*a_shear*v_shear1 - a_shear*omega_t_1 +
a_pump*P_dot_wrel_1 + a_twist*wn1;
ty = -(2.0/r)*a_shear*v_shear2 - a_shear*omega_t_2 +
a_pump*P_dot_wrel_2 + a_twist*wn2;
tz = -(2.0/r)*a_shear*v_shear3 - a_shear*omega_t_3 +
a_pump*P_dot_wrel_3 + a_twist*wn3;
torque[j][0] += vxmu2f * tx;
torque[j][1] += vxmu2f * ty;
torque[j][2] += vxmu2f * tz;
}
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
0.0,0.0,fx,fy,fz,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLubricate::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");
cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
cut_inner = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLubricate::settings(int narg, char **arg)
{
if (narg != 9) error->all("Illegal pair_style command");
mu = atof(arg[0]);
flag1 = atoi(arg[1]);
flag2 = atoi(arg[2]);
flag3 = atoi(arg[3]);
flag4 = atoi(arg[4]);
cut_inner_global = atof(arg[5]);
cut_global = atof(arg[6]);
t_target = atof(arg[7]);
seed = atoi(arg[8]);
// 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_inner[i][j] = cut_inner_global;
cut[i][j] = cut_global;
}
}
// initialize Marsaglia RNG with processor-unique seed
delete random;
random = new RanMars(lmp,seed + comm->me);
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLubricate::coeff(int narg, char **arg)
{
if (narg != 2 && narg != 4)
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 cut_inner_one = cut_inner_global;
double cut_one = cut_global;
if (narg == 4) {
cut_inner_one = atof(arg[2]);
cut_one = atof(arg[3]);
}
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut_inner[i][j] = cut_inner_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all("Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLubricate::init_style()
{
if (!atom->torque_flag || atom->shape == NULL)
error->all("Pair lubricate requires atom attributes torque, shape");
// insure all particle shapes are spherical
for (int i = 1; i <= atom->ntypes; i++)
if ((atom->shape[i][0] != atom->shape[i][1]) ||
(atom->shape[i][0] != atom->shape[i][2]) ||
(atom->shape[i][1] != atom->shape[i][2]) )
error->all("Pair lubricate requires spherical particles");
// insure mono-dispersity
for (int i = 2; i <= atom->ntypes; i++)
if (atom->shape[i][0] != atom->shape[1][0])
error->all("Pair lubricate requires mono-disperse particles");
int irequest = neighbor->request(this);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLubricate::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
cut_inner[j][i] = cut_inner[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLubricate::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(&cut_inner[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLubricate::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (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 (me == 0) {
fread(&cut_inner[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLubricate::write_restart_settings(FILE *fp)
{
fwrite(&mu,sizeof(double),1,fp);
fwrite(&flag1,sizeof(int),1,fp);
fwrite(&flag2,sizeof(int),1,fp);
fwrite(&flag3,sizeof(int),1,fp);
fwrite(&flag4,sizeof(int),1,fp);
fwrite(&cut_inner_global,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&t_target,sizeof(double),1,fp);
fwrite(&seed,sizeof(int),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLubricate::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&mu,sizeof(double),1,fp);
fread(&flag1,sizeof(int),1,fp);
fread(&flag2,sizeof(int),1,fp);
fread(&flag3,sizeof(int),1,fp);
fread(&flag4,sizeof(int),1,fp);
fread(&cut_inner_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&t_target, sizeof(double),1,fp);
fread(&seed, sizeof(int),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
MPI_Bcast(&flag1,1,MPI_INT,0,world);
MPI_Bcast(&flag2,1,MPI_INT,0,world);
MPI_Bcast(&flag3,1,MPI_INT,0,world);
MPI_Bcast(&flag4,1,MPI_INT,0,world);
MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&t_target,1,MPI_DOUBLE,0,world);
MPI_Bcast(&seed,1,MPI_INT,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
// additional setup based on restart parameters
delete random;
random = new RanMars(lmp,seed + comm->me);
}
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