forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1020 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
0c7a07e5da
commit
971a80f087
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@ -5,8 +5,10 @@ if ($1 == 1) then
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cp style_colloid.h ..
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cp pair_colloid.cpp ..
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cp pair_lubricate.cpp ..
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cp pair_colloid.h ..
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cp pair_lubricate.h ..
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else if ($1 == 0) then
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@ -14,7 +16,9 @@ else if ($1 == 0) then
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touch ../style_colloid.h
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rm ../pair_colloid.cpp
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rm ../pair_lubricate.cpp
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rm ../pair_colloid.h
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rm ../pair_lubricate.h
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endif
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@ -0,0 +1,474 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Randy Schunk (SNL)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "string.h"
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#include "pair_lubricate.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "update.h"
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#include "memory.h"
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#include "error.h"
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#include "domain.h"
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using namespace LAMMPS_NS;
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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/* ---------------------------------------------------------------------- */
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PairLubricate::PairLubricate(LAMMPS *lmp) : Pair(lmp)
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{
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single_enable = 0;
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}
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/* ---------------------------------------------------------------------- */
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PairLubricate::~PairLubricate()
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{
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if (allocated) {
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memory->destroy_2d_int_array(setflag);
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memory->destroy_2d_double_array(cutsq);
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memory->destroy_2d_double_array(cut);
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memory->destroy_2d_double_array(cut_inner);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLubricate::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz;
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double rsq,r,h_sep,radi,fforce,f1,f2,f3;
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double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
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double vt1,vt2,vt3,w1,w2,w3,v_shear1,v_shear2,v_shear3;
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double omega_t_1,omega_t_2,omega_t_3;
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double n_cross_omega_t_1,n_cross_omega_t_2,n_cross_omega_t_3;
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double wr1,wr2,wr3,wnnr,wn1,wn2,wn3;
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double P_dot_wrel_1,P_dot_wrel_2,P_dot_wrel_3;
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double a_squeeze,a_shear,a_pump,a_twist;
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int *ilist,*jlist,*numneigh,**firstneigh;
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double PI = 4.0*atan(1.0);
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eng_vdwl = 0.0;
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if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
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double **x = atom->x;
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double **v = atom->v;
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double **f = atom->f;
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double **angmom = atom->angmom;
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double **torque = atom->torque;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int newton_pair = force->newton_pair;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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a_squeeze = a_shear = a_pump = a_twist = 0.0;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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radi = atom->shape[itype][0];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r = sqrt(rsq);
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// relative translational velocity
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vr1 = v[i][0] - v[j][0];
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vr2 = v[i][1] - v[j][1];
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vr3 = v[i][2] - v[j][2];
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// normal component N.(v1-v2) = nn.(v1-v2)
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vnnr = vr1*delx + vr2*dely + vr3*delz;
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vnnr /= r;
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vn1 = delx*vnnr / r;
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vn2 = dely*vnnr / r;
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vn3 = delz*vnnr / r;
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// tangential component -P.(v1-v2)
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// P = (I - nn) where n is vector between centers
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vt1 = vr1 - vn1;
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vt2 = vr2 - vn2;
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vt3 = vr3 - vn3;
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// additive rotational velocity = omega_1 + omega_2 (if radi = radj)
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// angular momentum = I*omega = 2/5*M*R^2*omega
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w1 = angmom[i][0] + angmom[j][0];
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w2 = angmom[i][1] + angmom[j][1];
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w3 = angmom[i][2] + angmom[j][2];
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w1 *= 2.5/atom->mass[itype]/radi/radi;
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w2 *= 2.5/atom->mass[itype]/radi/radi;
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w3 *= 2.5/atom->mass[itype]/radi/radi;
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// relative velocities n X P . (v1-v2) = n X (I-nn) . (v1-v2)
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v_shear1 = (dely*vt3 - delz*vt2) / r;
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v_shear2 = -(delx*vt3 - delz*vt1) / r;
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v_shear3 = (delx*vt2 - dely*vt1) / r;
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// relative rotation rate P.(omega1 + omega2)
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omega_t_1 = w1 - delx*(delx*w1) / rsq;
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omega_t_2 = w2 - dely*(dely*w2) / rsq;
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omega_t_3 = w3 - delz*(delz*w3) / rsq;
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// n x omega_t
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n_cross_omega_t_1 = (dely*omega_t_3 - delz*omega_t_2) / r;
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n_cross_omega_t_2 = -(delx*omega_t_3 - delz*omega_t_1) / r;
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n_cross_omega_t_3 = (delx*omega_t_2 - dely*omega_t_1) / r;
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// N.(w1-w2) and P.(w1-w2)
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wr1 = angmom[i][0] - angmom[j][0];
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wr2 = angmom[i][1] - angmom[j][1];
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wr3 = angmom[i][2] - angmom[j][2];
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wr1 *= 5./2./atom->mass[itype]/radi/radi;
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wr2 *= 5./2./atom->mass[itype]/radi/radi;
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wr3 *= 5./2./atom->mass[itype]/radi/radi;
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wnnr = wr1*delx + wr2*dely + wr3*delz;
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wn1 = delx*wnnr / rsq;
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wn2 = dely*wnnr / rsq;
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wn3 = delz*wnnr / rsq;
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P_dot_wrel_1 = wr1 - delx*(delx*wr1)/rsq;
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P_dot_wrel_2 = wr2 - dely*(dely*wr2)/rsq;
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P_dot_wrel_3 = wr3 - delz*(delz*wr3)/rsq;
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// compute components of pair-hydro
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h_sep = r - 2.0*radi;
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if (flag1)
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a_squeeze = (3.0*PI*mu*2.0*radi/2.0) * (2.0*radi/4.0/h_sep);
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if (flag2)
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a_shear = (PI*mu*2.*radi/2.0) *
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log(2.0*radi/2.0/h_sep)*(2.0*radi+h_sep)*(2.0*radi+h_sep)/4.0;
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if (flag3)
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a_pump = (PI*mu*pow(2.0*radi,4)/8.0) *
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((3.0/20.0) * log(2.0*radi/2.0/h_sep) +
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(63.0/250.0) * (h_sep/2.0/radi) * log(2.0*radi/2.0/h_sep));
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if (flag4)
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a_twist = (PI*mu*pow(2.0*radi,4)/4.0) *
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(h_sep/2.0/radi) * log(2.0/(2.0*h_sep));
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if (h_sep >= cut_inner[itype][jtype]) {
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f1 = -a_squeeze*vn1 - a_shear*(2.0/r)*(2.0/r)*vt1 +
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(2.0/r)*a_shear*n_cross_omega_t_1;
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f2 = -a_squeeze*vn2 - a_shear*(2.0/r)*(2.0/r)*vt2 +
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(2.0/r)*a_shear*n_cross_omega_t_2;
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f3 = -a_squeeze*vn3 - a_shear*(2.0/r)*(2.0/r)*vt3 +
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(2.0/r)*a_shear*n_cross_omega_t_3;
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torque[i][0] += -(2.0/r)*a_shear*v_shear1 - a_shear*omega_t_1 -
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a_pump*P_dot_wrel_1 - a_twist*wn1;
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torque[i][1] += -(2.0/r)*a_shear*v_shear2 - a_shear*omega_t_2 -
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a_pump*P_dot_wrel_2 - a_twist*wn2;
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torque[i][2] += -(2.0/r)*a_shear*v_shear3 - a_shear*omega_t_3 -
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a_pump*P_dot_wrel_3 - a_twist*wn3;
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} else {
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fforce = -vnnr*(3.0*PI*mu*radi/2.0)*radi/4.0/cut_inner[itype][jtype];
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f1 = fforce*delx/r;
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f2 = fforce*dely/r;
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f3 = fforce*delz/r;
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}
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f[i][0] += f1;
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f[i][1] += f2;
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f[i][2] += f3;
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if (newton_pair || j < nlocal) {
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f[j][0] -= f1;
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f[j][1] -= f2;
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f[j][2] -= f3;
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if (h_sep >= cut_inner[itype][jtype]) {
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torque[j][0] += -(2.0/r)*a_shear*v_shear1 - a_shear*omega_t_1 +
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a_pump*P_dot_wrel_1 + a_twist*wn1;
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torque[j][1] += -(2.0/r)*a_shear*v_shear2 - a_shear*omega_t_2 +
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a_pump*P_dot_wrel_2 + a_twist*wn2;
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torque[j][2] += -(2.0/r)*a_shear*v_shear3 - a_shear*omega_t_3 +
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a_pump*P_dot_wrel_3 + a_twist*wn3;
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}
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}
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if (vflag == 1) {
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if (newton_pair == 0 && j >= nlocal) {
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f1 *= 0.5;
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f2 *= 0.5;
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f3 *= 0.5;
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}
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virial[0] += delx*f1;
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virial[1] += dely*f2;
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virial[2] += delz*f3;
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virial[3] += delx*f2;
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virial[4] += delx*f3;
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virial[5] += dely*f3;
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}
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}
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}
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}
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if (vflag == 2) virial_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairLubricate::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
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cut = memory->create_2d_double_array(n+1,n+1,"pair:cut");
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cut_inner = memory->create_2d_double_array(n+1,n+1,"pair:cut_inner");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairLubricate::settings(int narg, char **arg)
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{
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if (narg != 7) error->all("Illegal pair_style command");
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mu = atof(arg[0]);
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flag1 = atoi(arg[1]);
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flag2 = atoi(arg[2]);
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flag3 = atoi(arg[3]);
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flag4 = atoi(arg[4]);
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cut_inner_global = atof(arg[5]);
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cut_global = atof(arg[6]);
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// reset cutoffs that have been explicitly set
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if (allocated) {
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i+1; j <= atom->ntypes; j++)
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if (setflag[i][j]) {
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cut_inner[i][j] = cut_inner_global;
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cut[i][j] = cut_global;
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}
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}
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairLubricate::coeff(int narg, char **arg)
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{
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if (narg != 2 && narg != 4)
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error->all("Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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force->bounds(arg[0],atom->ntypes,ilo,ihi);
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force->bounds(arg[1],atom->ntypes,jlo,jhi);
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double cut_inner_one = cut_inner_global;
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double cut_one = cut_global;
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if (narg == 4) {
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cut_inner_one = atof(arg[2]);
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cut_one = atof(arg[3]);
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}
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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cut_inner[i][j] = cut_inner_one;
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cut[i][j] = cut_one;
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setflag[i][j] = 1;
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count++;
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}
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}
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if (count == 0) error->all("Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairLubricate::init_style()
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{
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if (!atom->angmom_flag || !atom->torque_flag)
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error->all("Pair lubricate requires atom attributes omega, torque");
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for (int i = 1; i <= atom->ntypes; i++)
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if ((atom->shape[i][0] != atom->shape[i][1]) ||
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(atom->shape[i][0] != atom->shape[i][2]) ||
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(atom->shape[i][1] != atom->shape[i][2]) )
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error->all("Pair lubricate requires spherical particles");
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if (domain->dimension != 3)
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error->all("Pair lubricate only available for 3d");
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int irequest = neighbor->request(this);
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairLubricate::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
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}
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cut_inner[j][i] = cut_inner[i][j];
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return cut[i][j];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairLubricate::write_restart(FILE *fp)
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{
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write_restart_settings(fp);
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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fwrite(&setflag[i][j],sizeof(int),1,fp);
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if (setflag[i][j]) {
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fwrite(&cut_inner[i][j],sizeof(double),1,fp);
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fwrite(&cut[i][j],sizeof(double),1,fp);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
|
||||
|
||||
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(&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(&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(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
|
@ -0,0 +1,47 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef PAIR_LUBRICATE_H
|
||||
#define PAIR_LUBRICATE_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLubricate : public Pair {
|
||||
public:
|
||||
PairLubricate(class LAMMPS *);
|
||||
~PairLubricate();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
void init_style();
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
|
||||
protected:
|
||||
double cut_inner_global,cut_global;
|
||||
double **cut_inner,**cut;
|
||||
double mu;
|
||||
int flag1,flag2,flag3,flag4;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
|
||||
|
|
@ -13,8 +13,10 @@
|
|||
|
||||
#ifdef PairInclude
|
||||
#include "pair_colloid.h"
|
||||
#include "pair_lubricate.h"
|
||||
#endif
|
||||
|
||||
#ifdef PairClass
|
||||
PairStyle(colloid,PairColloid)
|
||||
PairStyle(lubricate,PairLubricate)
|
||||
#endif
|
||||
|
|
|
|||
Loading…
Reference in New Issue