342 lines
9.1 KiB
C++
342 lines
9.1 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://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 authors: Leo Silbert (SNL), Gary Grest (SNL)
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------------------------------------------------------------------------- */
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#include "pair_gran_hooke.h"
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#include <cmath>
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#include "atom.h"
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#include "force.h"
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#include "fix.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "comm.h"
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#include "memory.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairGranHooke::PairGranHooke(LAMMPS *lmp) : PairGranHookeHistory(lmp)
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{
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no_virial_fdotr_compute = 0;
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history = 0;
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}
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/* ---------------------------------------------------------------------- */
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void PairGranHooke::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum;
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double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
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double radi,radj,radsum,rsq,r,rinv,rsqinv;
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double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3;
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double wr1,wr2,wr3;
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double vtr1,vtr2,vtr3,vrel;
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double mi,mj,meff,damp,ccel,tor1,tor2,tor3;
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double fn,fs,ft,fs1,fs2,fs3;
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int *ilist,*jlist,*numneigh,**firstneigh;
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ev_init(eflag,vflag);
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// update rigid body info for owned & ghost atoms if using FixRigid masses
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// body[i] = which body atom I is in, -1 if none
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// mass_body = mass of each rigid body
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if (fix_rigid && neighbor->ago == 0) {
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int tmp;
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int *body = (int *) fix_rigid->extract("body",tmp);
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double *mass_body = (double *) fix_rigid->extract("masstotal",tmp);
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if (atom->nmax > nmax) {
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memory->destroy(mass_rigid);
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nmax = atom->nmax;
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memory->create(mass_rigid,nmax,"pair:mass_rigid");
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}
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++)
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if (body[i] >= 0) mass_rigid[i] = mass_body[body[i]];
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else mass_rigid[i] = 0.0;
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comm->forward_comm_pair(this);
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}
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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 **omega = atom->omega;
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double **torque = atom->torque;
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double *radius = atom->radius;
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double *rmass = atom->rmass;
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int *mask = atom->mask;
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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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// 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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radi = radius[i];
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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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j &= NEIGHMASK;
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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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radj = radius[j];
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radsum = radi + radj;
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if (rsq < radsum*radsum) {
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r = sqrt(rsq);
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rinv = 1.0/r;
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rsqinv = 1.0/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
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vnnr = vr1*delx + vr2*dely + vr3*delz;
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vn1 = delx*vnnr * rsqinv;
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vn2 = dely*vnnr * rsqinv;
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vn3 = delz*vnnr * rsqinv;
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// tangential component
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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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// relative rotational velocity
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wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
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wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
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wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
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// meff = effective mass of pair of particles
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// if I or J part of rigid body, use body mass
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// if I or J is frozen, meff is other particle
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mi = rmass[i];
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mj = rmass[j];
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if (fix_rigid) {
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if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
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if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
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}
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meff = mi*mj / (mi+mj);
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if (mask[i] & freeze_group_bit) meff = mj;
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if (mask[j] & freeze_group_bit) meff = mi;
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// normal forces = Hookian contact + normal velocity damping
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damp = meff*gamman*vnnr*rsqinv;
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ccel = kn*(radsum-r)*rinv - damp;
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if (limit_damping && (ccel < 0.0)) ccel = 0.0;
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// relative velocities
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vtr1 = vt1 - (delz*wr2-dely*wr3);
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vtr2 = vt2 - (delx*wr3-delz*wr1);
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vtr3 = vt3 - (dely*wr1-delx*wr2);
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vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
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vrel = sqrt(vrel);
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// force normalization
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fn = xmu * fabs(ccel*r);
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fs = meff*gammat*vrel;
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if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
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else ft = 0.0;
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// tangential force due to tangential velocity damping
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fs1 = -ft*vtr1;
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fs2 = -ft*vtr2;
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fs3 = -ft*vtr3;
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// forces & torques
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fx = delx*ccel + fs1;
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fy = dely*ccel + fs2;
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fz = delz*ccel + fs3;
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f[i][0] += fx;
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f[i][1] += fy;
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f[i][2] += fz;
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tor1 = rinv * (dely*fs3 - delz*fs2);
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tor2 = rinv * (delz*fs1 - delx*fs3);
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tor3 = rinv * (delx*fs2 - dely*fs1);
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torque[i][0] -= radi*tor1;
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torque[i][1] -= radi*tor2;
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torque[i][2] -= radi*tor3;
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if (newton_pair || j < nlocal) {
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f[j][0] -= fx;
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f[j][1] -= fy;
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f[j][2] -= fz;
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torque[j][0] -= radj*tor1;
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torque[j][1] -= radj*tor2;
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torque[j][2] -= radj*tor3;
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}
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if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
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0.0,0.0,fx,fy,fz,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ---------------------------------------------------------------------- */
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double PairGranHooke::single(int i, int j, int /*itype*/, int /*jtype*/, double rsq,
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double /*factor_coul*/, double /*factor_lj*/,
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double &fforce)
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{
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double radi,radj,radsum,r,rinv,rsqinv;
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double delx,dely,delz;
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double vr1,vr2,vr3,vnnr,vn1,vn2,vn3,vt1,vt2,vt3,wr1,wr2,wr3;
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double vtr1,vtr2,vtr3,vrel;
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double mi,mj,meff,damp,ccel;
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double fn,fs,ft;
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double *radius = atom->radius;
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radi = radius[i];
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radj = radius[j];
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radsum = radi + radj;
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// zero out forces if caller requests non-touching pair outside cutoff
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if (rsq >= radsum*radsum) {
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fforce = 0.0;
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for (int m = 0; m < single_extra; m++) svector[m] = 0.0;
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return 0.0;
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}
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r = sqrt(rsq);
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rinv = 1.0/r;
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rsqinv = 1.0/rsq;
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// relative translational velocity
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double **v = atom->v;
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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
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double **x = atom->x;
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delx = x[i][0] - x[j][0];
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dely = x[i][1] - x[j][1];
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delz = x[i][2] - x[j][2];
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vnnr = vr1*delx + vr2*dely + vr3*delz;
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vn1 = delx*vnnr * rsqinv;
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vn2 = dely*vnnr * rsqinv;
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vn3 = delz*vnnr * rsqinv;
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// tangential component
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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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// relative rotational velocity
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double **omega = atom->omega;
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wr1 = (radi*omega[i][0] + radj*omega[j][0]) * rinv;
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wr2 = (radi*omega[i][1] + radj*omega[j][1]) * rinv;
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wr3 = (radi*omega[i][2] + radj*omega[j][2]) * rinv;
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// meff = effective mass of pair of particles
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// if I or J part of rigid body, use body mass
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// if I or J is frozen, meff is other particle
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double *rmass = atom->rmass;
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int *mask = atom->mask;
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mi = rmass[i];
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mj = rmass[j];
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if (fix_rigid) {
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// NOTE: insure mass_rigid is current for owned+ghost atoms?
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if (mass_rigid[i] > 0.0) mi = mass_rigid[i];
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if (mass_rigid[j] > 0.0) mj = mass_rigid[j];
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}
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meff = mi*mj / (mi+mj);
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if (mask[i] & freeze_group_bit) meff = mj;
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if (mask[j] & freeze_group_bit) meff = mi;
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// normal forces = Hookian contact + normal velocity damping
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damp = meff*gamman*vnnr*rsqinv;
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ccel = kn*(radsum-r)*rinv - damp;
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if (limit_damping && (ccel < 0.0)) ccel = 0.0;
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// relative velocities
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vtr1 = vt1 - (delz*wr2-dely*wr3);
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vtr2 = vt2 - (delx*wr3-delz*wr1);
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vtr3 = vt3 - (dely*wr1-delx*wr2);
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vrel = vtr1*vtr1 + vtr2*vtr2 + vtr3*vtr3;
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vrel = sqrt(vrel);
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// force normalization
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fn = xmu * fabs(ccel*r);
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fs = meff*gammat*vrel;
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if (vrel != 0.0) ft = MIN(fn,fs) / vrel;
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else ft = 0.0;
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// set force and return no energy
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fforce = ccel;
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// set single_extra quantities
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svector[0] = -ft*vtr1;
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svector[1] = -ft*vtr2;
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svector[2] = -ft*vtr3;
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svector[3] = sqrt(svector[0]*svector[0] +
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svector[1]*svector[1] +
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svector[2]*svector[2]);
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svector[4] = vn1;
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svector[5] = vn2;
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svector[6] = vn3;
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svector[7] = vt1;
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svector[8] = vt2;
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svector[9] = vt3;
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return 0.0;
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}
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