forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7148 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
c6d228775f
commit
89a39c7425
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@ -12,7 +12,9 @@ if (test $1 = 1) then
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cp fix_nve_tri.cpp ..
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cp fix_nvt_asphere.cpp ..
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cp pair_gayberne.cpp ..
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cp pair_line.cpp ..
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cp pair_resquared.cpp ..
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cp pair_tri.cpp ..
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cp compute_erotate_asphere.h ..
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cp compute_temp_asphere.h ..
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@ -24,7 +26,9 @@ if (test $1 = 1) then
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cp fix_nve_tri.h ..
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cp fix_nvt_asphere.h ..
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cp pair_gayberne.h ..
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cp pair_line.h ..
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cp pair_resquared.h ..
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cp pair_tri.h ..
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elif (test $1 = 0) then
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@ -38,7 +42,9 @@ elif (test $1 = 0) then
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rm -f ../fix_nve_tri.cpp
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rm -f ../fix_nvt_asphere.cpp
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rm -f ../pair_gayberne.cpp
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rm -f ../pair_line.cpp
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rm -f ../pair_resquared.cpp
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rm -f ../pair_tri.cpp
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rm -f ../compute_erotate_asphere.h
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rm -f ../compute_temp_asphere.h
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@ -50,6 +56,8 @@ elif (test $1 = 0) then
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rm -f ../fix_nve_tri.h
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rm -f ../fix_nvt_asphere.h
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rm -f ../pair_gayberne.h
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rm -f ../pair_line.h
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rm -f ../pair_resquared.h
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rm -f ../pair_tri.h
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fi
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@ -0,0 +1,444 @@
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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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#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_line.h"
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#include "atom.h"
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#include "atom_vec_line.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 "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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PairLine::PairLine(LAMMPS *lmp) : Pair(lmp)
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{
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avec = (AtomVecLine *) atom->style_match("line");
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if (!avec) error->all(FLERR,"Pair line requires atom style line");
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dmax = nmax = 0;
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discrete = NULL;
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dnum = dfirst = NULL;
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single_enable = 0;
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}
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/* ---------------------------------------------------------------------- */
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PairLine::~PairLine()
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{
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memory->sfree(discrete);
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memory->destroy(dnum);
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memory->destroy(dfirst);
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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memory->destroy(cut);
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memory->destroy(epsilon);
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memory->destroy(sigma);
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memory->destroy(lj1);
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memory->destroy(lj2);
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memory->destroy(lj3);
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memory->destroy(lj4);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLine::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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int ni,nj,npi,npj,ifirst,jfirst;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,r2inv,r6inv,term1,term2,sig,sig3,forcelj;
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double xi[2],xj[2],fi[2],fj[2],dxi,dxj,dyi,dyj,ti,tj;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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double **x = atom->x;
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double **f = atom->f;
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double **torque = atom->torque;
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int *line = atom->line;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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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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// grow discrete list if necessary and initialize
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if (nall > nmax) {
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memory->destroy(dnum);
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memory->destroy(dfirst);
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memory->create(dnum,nall,"pair:dnum");
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memory->create(dfirst,nall,"pair:dfirst");
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}
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for (i = 0; i < nall; i++) dnum[i] = 0;
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ndiscrete = 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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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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jtype = type[j];
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if (rsq >= cutsq[itype][jtype]) continue;
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// line/line interactions = NxN particles
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evdwl = 0.0;
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if (line[i] >= 0 && line[j] >= 0) {
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if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
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npi = dnum[i];
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ifirst = dfirst[i];
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if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
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npj = dnum[j];
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jfirst = dfirst[j];
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for (ni = 0; ni < npi; ni++) {
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dxi = discrete[ifirst+ni].dx;
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dyi = discrete[ifirst+ni].dy;
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for (nj = 0; nj < npj; nj++) {
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dxj = discrete[jfirst+nj].dx;
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dyj = discrete[jfirst+nj].dy;
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xi[0] = x[i][0] + dxi;
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xi[1] = x[i][1] + dyi;
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xj[0] = x[j][0] + dxj;
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xj[1] = x[j][1] + dyj;
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delx = xi[0] - xj[0];
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dely = xi[1] - xj[1];
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rsq = delx*delx + dely*dely;
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sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
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sig3 = sig*sig*sig;
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term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
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term1 = 2.0 * term2 * sig3*sig3;
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (term1*r6inv - term2);
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fpair = forcelj*r2inv;
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if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
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fi[0] = delx*fpair;
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fi[1] = dely*fpair;
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f[i][0] += fi[0];
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f[i][1] += fi[1];
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torque[i][2] += dxi*fi[1] - dyi*fi[0];
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if (newton_pair || j < nlocal) {
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fj[0] = -delx*fpair;
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fj[1] = -dely*fpair;
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f[j][0] += fj[0];
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f[j][1] += fj[1];
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torque[j][2] += dxj*fj[1] - dyj*fj[0];
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}
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}
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}
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// line/particle interaction = Nx1 particles
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// convert line into Np particles based on sigma and line length
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} else if (line[i] >= 0) {
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if (dnum[i] == 0) discretize(i,sigma[itype][itype]);
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npi = dnum[i];
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ifirst = dfirst[i];
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for (ni = 0; ni < npi; ni++) {
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dxi = discrete[ifirst+ni].dx;
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dyi = discrete[ifirst+ni].dy;
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xi[0] = x[i][0] + dxi;
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xi[1] = x[i][1] + dyi;
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xj[0] = x[j][0];
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xj[1] = x[j][1];
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delx = xi[0] - xj[0];
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dely = xi[1] - xj[1];
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rsq = delx*delx + dely*dely;
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sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
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sig3 = sig*sig*sig;
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term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
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term1 = 2.0 * term2 * sig3*sig3;
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (term1*r6inv - term2);
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fpair = forcelj*r2inv;
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if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
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fi[0] = delx*fpair;
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fi[1] = dely*fpair;
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f[i][0] += fi[0];
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f[i][1] += fi[1];
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torque[i][2] += dxi*fi[1] - dyi*fi[0];
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if (newton_pair || j < nlocal) {
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fj[0] = -delx*fpair;
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fj[1] = -dely*fpair;
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f[j][0] += fj[0];
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f[j][1] += fj[1];
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}
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}
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// particle/line interaction = Nx1 particles
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// convert line into Np particles based on sigma and line length
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} else if (line[j] >= 0) {
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if (dnum[j] == 0) discretize(j,sigma[jtype][jtype]);
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npj = dnum[j];
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jfirst = dfirst[j];
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for (nj = 0; nj < npj; nj++) {
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dxj = discrete[jfirst+nj].dx;
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dyj = discrete[jfirst+nj].dy;
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xi[0] = x[i][0];
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xi[1] = x[i][1];
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xj[0] = x[j][0] + dxj;
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xj[1] = x[j][1] + dyj;
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delx = xi[0] - xj[0];
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dely = xi[1] - xj[1];
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rsq = delx*delx + dely*dely;
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sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
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sig3 = sig*sig*sig;
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term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
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term1 = 2.0 * term2 * sig3*sig3;
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (term1*r6inv - term2);
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fpair = forcelj*r2inv;
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if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
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fi[0] = delx*fpair;
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fi[1] = dely*fpair;
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f[i][0] += fi[0];
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f[i][1] += fi[1];
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if (newton_pair || j < nlocal) {
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f[j][0] += fj[0];
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f[j][1] += fj[1];
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fj[0] = -delx*fpair;
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fj[1] = -dely*fpair;
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torque[j][2] += dxj*fj[1] - dyj*fj[0];
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}
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}
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// particle/particle interaction = 1x1 particles
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} else {
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
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fpair = forcelj*r2inv;
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if (eflag)
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evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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if (newton_pair || j < nlocal) {
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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}
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,fpair,delx,dely,delz);
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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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allocate all arrays
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------------------------------------------------------------------------- */
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void PairLine::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag,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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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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memory->create(cut,n+1,n+1,"pair:cut");
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memory->create(epsilon,n+1,n+1,"pair:epsilon");
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memory->create(sigma,n+1,n+1,"pair:sigma");
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memory->create(lj1,n+1,n+1,"pair:lj1");
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memory->create(lj2,n+1,n+1,"pair:lj2");
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memory->create(lj3,n+1,n+1,"pair:lj3");
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memory->create(lj4,n+1,n+1,"pair:lj4");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairLine::settings(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Illegal pair_style command");
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cut_global = force->numeric(arg[0]);
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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]) cut[i][j] = cut_global;
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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 PairLine::coeff(int narg, char **arg)
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{
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if (narg < 4 || narg > 5)
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error->all(FLERR,"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 epsilon_one = force->numeric(arg[2]);
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double sigma_one = force->numeric(arg[3]);
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double cut_one = cut_global;
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if (narg == 5) cut_one = force->numeric(arg[4]);
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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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epsilon[i][j] = epsilon_one;
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sigma[i][j] = sigma_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(FLERR,"Incorrect args for pair coefficients");
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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 PairLine::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
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sigma[i][i],sigma[j][j]);
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sigma[i][j] = mix_distance(sigma[i][i],sigma[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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lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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epsilon[j][i] = epsilon[i][j];
|
||||
sigma[j][i] = sigma[i][j];
|
||||
lj1[j][i] = lj1[i][j];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
lj4[j][i] = lj4[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
discretize line segment I into N sub-segments no more than sigma in length
|
||||
store new discrete particles in Discrete list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairLine::discretize(int i, double sigma)
|
||||
{
|
||||
AtomVecLine::Bonus *bonus = avec->bonus;
|
||||
double length = bonus[atom->line[i]].length;
|
||||
double theta = bonus[atom->line[i]].theta;
|
||||
int n = static_cast<int> (length/sigma) + 1;
|
||||
dnum[i] = n;
|
||||
dfirst[i] = ndiscrete;
|
||||
|
||||
if (ndiscrete + n > dmax) {
|
||||
dmax += DELTA;
|
||||
discrete = (Discrete *)
|
||||
memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
|
||||
}
|
||||
|
||||
double *x = atom->x[i];
|
||||
sigma = length/n;
|
||||
double delta;
|
||||
|
||||
for (int m = 0; m < n; m++) {
|
||||
delta = -0.5 + (2*m+1)/(2.0*n);
|
||||
discrete[ndiscrete].dx = delta*length*cos(theta);
|
||||
discrete[ndiscrete].dy = delta*length*sin(theta);
|
||||
discrete[ndiscrete].sigma = sigma;
|
||||
ndiscrete++;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,61 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(line,PairLine)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_LINE_H
|
||||
#define LMP_PAIR_LINE_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairLine : public Pair {
|
||||
public:
|
||||
PairLine(class LAMMPS *);
|
||||
~PairLine();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
class AtomVecLine *avec;
|
||||
|
||||
struct Discrete {
|
||||
double dx,dy;
|
||||
double sigma;
|
||||
};
|
||||
Discrete *discrete; // list of all discretes for all lines
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
void allocate();
|
||||
void discretize(int, double);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,637 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "pair_tri.h"
|
||||
#include "math_extra.h"
|
||||
#include "atom.h"
|
||||
#include "atom_vec_tri.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define DELTA 20
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairTri::PairTri(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
avec = (AtomVecTri *) atom->style_match("tri");
|
||||
if (!avec) error->all(FLERR,"Pair tri requires atom style tri");
|
||||
|
||||
dmax = nmax = 0;
|
||||
discrete = NULL;
|
||||
dnum = dfirst = NULL;
|
||||
|
||||
single_enable = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairTri::~PairTri()
|
||||
{
|
||||
memory->sfree(discrete);
|
||||
memory->destroy(dnum);
|
||||
memory->destroy(dfirst);
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut);
|
||||
memory->destroy(epsilon);
|
||||
memory->destroy(sigma);
|
||||
memory->destroy(lj1);
|
||||
memory->destroy(lj2);
|
||||
memory->destroy(lj3);
|
||||
memory->destroy(lj4);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairTri::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
int ni,nj,npi,npj,ifirst,jfirst;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,r2inv,r6inv,term1,term2,sig,sig3,forcelj;
|
||||
double dxi,dxj,dyi,dyj,dzi,dzj;
|
||||
double xi[3],xj[3],fi[3],fj[3],ti[3],tj[3],p[3][3];
|
||||
double dc1[3],dc2[3],dc3[3];
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
AtomVecTri::Bonus *bonus = avec->bonus;
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double **torque = atom->torque;
|
||||
int *tri = atom->tri;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int nall = nlocal + atom->nghost;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// grow discrete list if necessary and initialize
|
||||
|
||||
if (nall > nmax) {
|
||||
memory->destroy(dnum);
|
||||
memory->destroy(dfirst);
|
||||
memory->create(dnum,nall,"pair:dnum");
|
||||
memory->create(dfirst,nall,"pair:dfirst");
|
||||
}
|
||||
for (i = 0; i < nall; i++) dnum[i] = 0;
|
||||
ndiscrete = 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];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
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;
|
||||
|
||||
// tri/tri interactions = NxN particles
|
||||
// c1,c2,c3 = corner pts of triangle I or J
|
||||
|
||||
evdwl = 0.0;
|
||||
if (tri[i] >= 0 && tri[j] >= 0) {
|
||||
if (dnum[i] == 0) {
|
||||
MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
|
||||
MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
|
||||
MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
|
||||
MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
|
||||
dfirst[i] = ndiscrete;
|
||||
discretize(i,sigma[itype][itype],dc1,dc2,dc3);
|
||||
dnum[i] = ndiscrete - dfirst[i];
|
||||
}
|
||||
npi = dnum[i];
|
||||
ifirst = dfirst[i];
|
||||
|
||||
if (dnum[j] == 0) {
|
||||
MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
|
||||
MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
|
||||
MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
|
||||
MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
|
||||
dfirst[j] = ndiscrete;
|
||||
discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
|
||||
dnum[j] = ndiscrete - dfirst[j];
|
||||
}
|
||||
npj = dnum[j];
|
||||
jfirst = dfirst[j];
|
||||
|
||||
for (ni = 0; ni < npi; ni++) {
|
||||
dxi = discrete[ifirst+ni].dx;
|
||||
dyi = discrete[ifirst+ni].dy;
|
||||
dzi = discrete[ifirst+ni].dz;
|
||||
|
||||
for (nj = 0; nj < npj; nj++) {
|
||||
dxj = discrete[jfirst+nj].dx;
|
||||
dyj = discrete[jfirst+nj].dy;
|
||||
dzj = discrete[jfirst+nj].dz;
|
||||
|
||||
xi[0] = x[i][0] + dxi;
|
||||
xi[1] = x[i][1] + dyi;
|
||||
xi[2] = x[i][2] + dzi;
|
||||
xj[0] = x[j][0] + dxj;
|
||||
xj[1] = x[j][1] + dyj;
|
||||
xj[2] = x[j][2] + dzj;
|
||||
|
||||
delx = xi[0] - xj[0];
|
||||
dely = xi[1] - xj[1];
|
||||
delz = xi[2] - xj[2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
sig = 0.5 * (discrete[ifirst+ni].sigma+discrete[jfirst+nj].sigma);
|
||||
sig3 = sig*sig*sig;
|
||||
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
|
||||
term1 = 2.0 * term2 * sig3*sig3;
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (term1*r6inv - term2);
|
||||
fpair = forcelj*r2inv;
|
||||
|
||||
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
|
||||
|
||||
fi[0] = delx*fpair;
|
||||
fi[1] = dely*fpair;
|
||||
fi[2] = delz*fpair;
|
||||
f[i][0] += fi[0];
|
||||
f[i][1] += fi[1];
|
||||
f[i][2] += fi[2];
|
||||
ti[0] = dyi*fi[2] - dzi*fi[1];
|
||||
ti[1] = dzi*fi[0] - dxi*fi[2];
|
||||
ti[2] = dxi*fi[1] - dyi*fi[0];
|
||||
torque[i][0] += ti[0];
|
||||
torque[i][1] += ti[1];
|
||||
torque[i][2] += ti[2];
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
fj[0] = -delx*fpair;
|
||||
fj[1] = -dely*fpair;
|
||||
fj[2] = -delz*fpair;
|
||||
f[j][0] += fj[0];
|
||||
f[j][1] += fj[1];
|
||||
f[j][2] += fj[2];
|
||||
tj[0] = dyj*fj[2] - dzj*fj[1];
|
||||
tj[1] = dzj*fj[0] - dxj*fj[2];
|
||||
tj[2] = dxj*fj[1] - dyj*fj[0];
|
||||
torque[j][0] += tj[0];
|
||||
torque[j][1] += tj[1];
|
||||
torque[j][2] += tj[2];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// tri/particle interaction = Nx1 particles
|
||||
// c1,c2,c3 = corner pts of triangle I
|
||||
|
||||
} else if (tri[i] >= 0) {
|
||||
|
||||
if (dnum[i] == 0) {
|
||||
MathExtra::quat_to_mat(bonus[tri[i]].quat,p);
|
||||
MathExtra::matvec(p,bonus[tri[i]].c1,dc1);
|
||||
MathExtra::matvec(p,bonus[tri[i]].c2,dc2);
|
||||
MathExtra::matvec(p,bonus[tri[i]].c3,dc3);
|
||||
dfirst[i] = ndiscrete;
|
||||
discretize(i,sigma[itype][itype],dc1,dc2,dc3);
|
||||
dnum[i] = ndiscrete - dfirst[i];
|
||||
}
|
||||
npi = dnum[i];
|
||||
ifirst = dfirst[i];
|
||||
|
||||
for (ni = 0; ni < npi; ni++) {
|
||||
dxi = discrete[ifirst+ni].dx;
|
||||
dyi = discrete[ifirst+ni].dy;
|
||||
dzi = discrete[ifirst+ni].dz;
|
||||
|
||||
xi[0] = x[i][0] + dxi;
|
||||
xi[1] = x[i][1] + dyi;
|
||||
xi[2] = x[i][2] + dzi;
|
||||
xj[0] = x[j][0];
|
||||
xj[1] = x[j][1];
|
||||
xj[2] = x[j][2];
|
||||
|
||||
delx = xi[0] - xj[0];
|
||||
dely = xi[1] - xj[1];
|
||||
delz = xi[2] - xj[2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
sig = 0.5 * (discrete[ifirst+ni].sigma+sigma[jtype][jtype]);
|
||||
sig3 = sig*sig*sig;
|
||||
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
|
||||
term1 = 2.0 * term2 * sig3*sig3;
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (term1*r6inv - term2);
|
||||
fpair = forcelj*r2inv;
|
||||
|
||||
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
|
||||
|
||||
fi[0] = delx*fpair;
|
||||
fi[1] = dely*fpair;
|
||||
fi[2] = delz*fpair;
|
||||
f[i][0] += fi[0];
|
||||
f[i][1] += fi[1];
|
||||
f[i][2] += fi[2];
|
||||
ti[0] = dyi*fi[2] - dzi*fi[1];
|
||||
ti[1] = dzi*fi[0] - dxi*fi[2];
|
||||
ti[2] = dxi*fi[1] - dyi*fi[0];
|
||||
torque[i][2] += ti[0];
|
||||
torque[i][1] += ti[1];
|
||||
torque[i][2] += ti[2];
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
fj[0] = -delx*fpair;
|
||||
fj[1] = -dely*fpair;
|
||||
fj[2] = -delz*fpair;
|
||||
f[j][0] += fj[0];
|
||||
f[j][1] += fj[1];
|
||||
f[j][2] += fj[2];
|
||||
}
|
||||
}
|
||||
|
||||
// particle/tri interaction = Nx1 particles
|
||||
// c1,c2,c3 = corner pts of triangle J
|
||||
|
||||
} else if (tri[j] >= 0) {
|
||||
if (dnum[j] == 0) {
|
||||
MathExtra::quat_to_mat(bonus[tri[j]].quat,p);
|
||||
MathExtra::matvec(p,bonus[tri[j]].c1,dc1);
|
||||
MathExtra::matvec(p,bonus[tri[j]].c2,dc2);
|
||||
MathExtra::matvec(p,bonus[tri[j]].c3,dc3);
|
||||
dfirst[j] = ndiscrete;
|
||||
discretize(j,sigma[jtype][jtype],dc1,dc2,dc3);
|
||||
dnum[j] = ndiscrete - dfirst[j];
|
||||
}
|
||||
npj = dnum[j];
|
||||
jfirst = dfirst[j];
|
||||
|
||||
for (nj = 0; nj < npj; nj++) {
|
||||
dxj = discrete[jfirst+nj].dx;
|
||||
dyj = discrete[jfirst+nj].dy;
|
||||
dzj = discrete[jfirst+nj].dz;
|
||||
|
||||
xi[0] = x[i][0];
|
||||
xi[1] = x[i][1];
|
||||
xi[2] = x[i][2];
|
||||
xj[0] = x[j][0] + dxj;
|
||||
xj[1] = x[j][1] + dyj;
|
||||
xj[2] = x[j][2] + dzj;
|
||||
|
||||
delx = xi[0] - xj[0];
|
||||
dely = xi[1] - xj[1];
|
||||
delz = xi[2] - xj[2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
|
||||
sig = 0.5 * (sigma[itype][itype]+discrete[jfirst+nj].sigma);
|
||||
sig3 = sig*sig*sig;
|
||||
term2 = 24.0*epsilon[itype][jtype] * sig3*sig3;
|
||||
term1 = 2.0 * term2 * sig3*sig3;
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (term1*r6inv - term2);
|
||||
fpair = forcelj*r2inv;
|
||||
|
||||
if (eflag) evdwl += r6inv*(term1/12.0*r6inv-term2/6.0);
|
||||
|
||||
fi[0] = delx*fpair;
|
||||
fi[1] = dely*fpair;
|
||||
fi[2] = delz*fpair;
|
||||
f[i][0] += fi[0];
|
||||
f[i][1] += fi[1];
|
||||
f[i][2] += fi[2];
|
||||
|
||||
if (newton_pair || j < nlocal) {
|
||||
fj[0] = -delx*fpair;
|
||||
fj[1] = -dely*fpair;
|
||||
fj[2] = -delz*fpair;
|
||||
f[j][0] += fj[0];
|
||||
f[j][1] += fj[1];
|
||||
f[j][2] += fj[2];
|
||||
tj[0] = dyj*fj[2] - dzj*fj[1];
|
||||
tj[1] = dzj*fj[0] - dxj*fj[2];
|
||||
tj[2] = dxj*fj[1] - dyj*fj[0];
|
||||
torque[j][0] += tj[0];
|
||||
torque[j][1] += tj[1];
|
||||
torque[j][2] += tj[2];
|
||||
}
|
||||
}
|
||||
|
||||
// particle/particle interaction = 1x1 particles
|
||||
|
||||
} else {
|
||||
r2inv = 1.0/rsq;
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||
fpair = forcelj*r2inv;
|
||||
|
||||
if (eflag)
|
||||
evdwl += r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
|
||||
|
||||
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_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairTri::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut,n+1,n+1,"pair:cut");
|
||||
memory->create(epsilon,n+1,n+1,"pair:epsilon");
|
||||
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||
memory->create(lj4,n+1,n+1,"pair:lj4");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairTri::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR,"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 PairTri::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 4 || narg > 5)
|
||||
error->all(FLERR,"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 epsilon_one = force->numeric(arg[2]);
|
||||
double sigma_one = force->numeric(arg[3]);
|
||||
|
||||
double cut_one = cut_global;
|
||||
if (narg == 5) cut_one = force->numeric(arg[4]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairTri::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
|
||||
sigma[i][i],sigma[j][j]);
|
||||
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
|
||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
||||
}
|
||||
|
||||
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
|
||||
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
|
||||
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
|
||||
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
|
||||
|
||||
epsilon[j][i] = epsilon[i][j];
|
||||
sigma[j][i] = sigma[i][j];
|
||||
lj1[j][i] = lj1[i][j];
|
||||
lj2[j][i] = lj2[i][j];
|
||||
lj3[j][i] = lj3[i][j];
|
||||
lj4[j][i] = lj4[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
recursively discretize triangle I with displaced corners c1,c2,c3
|
||||
into N sub-tris no more than sigma in size
|
||||
recurse by making 2 tris via bisecting longest side
|
||||
store new discrete particles in Discrete list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairTri::discretize(int i, double sigma,
|
||||
double *c1, double *c2, double *c3)
|
||||
{
|
||||
double c1c2[3],c2c3[3],c1c3[3];
|
||||
|
||||
double centroid[3],dc1[3],dc2[3],dc3[3];
|
||||
|
||||
centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0;
|
||||
centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0;
|
||||
centroid[2] = (c1[2] + c2[2] + c3[2]) / 3.0;
|
||||
|
||||
MathExtra::sub3(c1,centroid,dc1);
|
||||
MathExtra::sub3(c2,centroid,dc2);
|
||||
MathExtra::sub3(c3,centroid,dc3);
|
||||
|
||||
double sigmasq = 0.25 * sigma*sigma;
|
||||
double len1sq = MathExtra::lensq3(dc1);
|
||||
double len2sq = MathExtra::lensq3(dc2);
|
||||
double len3sq = MathExtra::lensq3(dc3);
|
||||
|
||||
// if sigma sphere overlaps all corner points, add particle at centroid
|
||||
|
||||
if (len1sq <= sigmasq && len2sq <= sigmasq & len3sq <= sigmasq) {
|
||||
if (ndiscrete == dmax) {
|
||||
dmax += DELTA;
|
||||
discrete = (Discrete *)
|
||||
memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
|
||||
}
|
||||
discrete[ndiscrete].dx = centroid[0];
|
||||
discrete[ndiscrete].dy = centroid[1];
|
||||
discrete[ndiscrete].dz = centroid[2];
|
||||
sigmasq = MAX(len1sq,len2sq);
|
||||
sigmasq = MAX(sigmasq,len3sq);
|
||||
discrete[ndiscrete].sigma = 2.0 * sqrt(sigmasq);
|
||||
ndiscrete++;
|
||||
return;
|
||||
}
|
||||
|
||||
// else break triangle into 2 sub-triangles and recurse
|
||||
|
||||
double c12[3],c23[3],c13[3],mid[3];
|
||||
|
||||
MathExtra::sub3(c2,c3,c23);
|
||||
len1sq = MathExtra::lensq3(c23);
|
||||
MathExtra::sub3(c1,c3,c13);
|
||||
len2sq = MathExtra::lensq3(c13);
|
||||
MathExtra::sub3(c1,c2,c12);
|
||||
len3sq = MathExtra::lensq3(c12);
|
||||
|
||||
double maxsq = MAX(len1sq,len2sq);
|
||||
maxsq = MAX(maxsq,len3sq);
|
||||
|
||||
if (len1sq == maxsq) {
|
||||
MathExtra::add3(c2,c3,mid);
|
||||
MathExtra::scale3(0.5,mid);
|
||||
discretize(i,sigma,c1,c2,mid);
|
||||
discretize(i,sigma,c1,c3,mid);
|
||||
} else if (len2sq == maxsq) {
|
||||
MathExtra::add3(c1,c3,mid);
|
||||
MathExtra::scale3(0.5,mid);
|
||||
discretize(i,sigma,c2,c1,mid);
|
||||
discretize(i,sigma,c2,c3,mid);
|
||||
} else {
|
||||
MathExtra::add3(c1,c2,mid);
|
||||
MathExtra::scale3(0.5,mid);
|
||||
discretize(i,sigma,c3,c1,mid);
|
||||
discretize(i,sigma,c3,c2,mid);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
recursively discretize triangle I with displaced corners c1,c2,c3
|
||||
into N sub-tris no more than sigma in size
|
||||
recurse by making 6 tris via centroid
|
||||
store new discrete particles in Discrete list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/*
|
||||
void PairTri::discretize(int i, double sigma,
|
||||
double *c1, double *c2, double *c3)
|
||||
{
|
||||
double centroid[3],dc1[3],dc2[3],dc3[3];
|
||||
|
||||
centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0;
|
||||
centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0;
|
||||
centroid[2] = (c1[2] + c2[2] + c3[2]) / 3.0;
|
||||
|
||||
MathExtra::sub3(c1,centroid,dc1);
|
||||
MathExtra::sub3(c2,centroid,dc2);
|
||||
MathExtra::sub3(c3,centroid,dc3);
|
||||
|
||||
double sigmasq = 0.25 * sigma*sigma;
|
||||
double len1sq = MathExtra::lensq3(dc1);
|
||||
double len2sq = MathExtra::lensq3(dc2);
|
||||
double len3sq = MathExtra::lensq3(dc3);
|
||||
|
||||
// if sigma sphere overlaps all corner points, add particle at centroid
|
||||
|
||||
if (len1sq <= sigmasq && len2sq <= sigmasq & len3sq <= sigmasq) {
|
||||
if (ndiscrete == dmax) {
|
||||
dmax += DELTA;
|
||||
discrete = (Discrete *)
|
||||
memory->srealloc(discrete,dmax*sizeof(Discrete),"pair:discrete");
|
||||
}
|
||||
discrete[ndiscrete].dx = centroid[0];
|
||||
discrete[ndiscrete].dy = centroid[1];
|
||||
discrete[ndiscrete].dz = centroid[2];
|
||||
sigmasq = MAX(len1sq,len2sq);
|
||||
sigmasq = MAX(sigmasq,len3sq);
|
||||
discrete[ndiscrete].sigma = 2.0 * sqrt(sigmasq);
|
||||
ndiscrete++;
|
||||
return;
|
||||
}
|
||||
|
||||
// else break triangle into 6 sub-triangles and recurse
|
||||
|
||||
double c1c2mid[3],c2c3mid[3],c1c3mid[3];
|
||||
|
||||
MathExtra::add3(c1,c2,c1c2mid);
|
||||
MathExtra::scale3(0.5,c1c2mid);
|
||||
MathExtra::add3(c2,c3,c2c3mid);
|
||||
MathExtra::scale3(0.5,c2c3mid);
|
||||
MathExtra::add3(c1,c3,c1c3mid);
|
||||
MathExtra::scale3(0.5,c1c3mid);
|
||||
|
||||
discretize(i,sigma,c1,c1c2mid,centroid);
|
||||
discretize(i,sigma,c1,c1c3mid,centroid);
|
||||
discretize(i,sigma,c2,c2c3mid,centroid);
|
||||
discretize(i,sigma,c2,c1c2mid,centroid);
|
||||
discretize(i,sigma,c3,c1c3mid,centroid);
|
||||
discretize(i,sigma,c3,c2c3mid,centroid);
|
||||
}
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,61 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(tri,PairTri)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_TRI_H
|
||||
#define LMP_PAIR_TRI_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairTri : public Pair {
|
||||
public:
|
||||
PairTri(class LAMMPS *);
|
||||
~PairTri();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **epsilon,**sigma;
|
||||
double **lj1,**lj2,**lj3,**lj4;
|
||||
class AtomVecTri *avec;
|
||||
|
||||
struct Discrete {
|
||||
double dx,dy,dz;
|
||||
double sigma;
|
||||
};
|
||||
Discrete *discrete; // list of all discretes for all lines
|
||||
int ndiscrete; // number of discretes in list
|
||||
int dmax; // allocated size of discrete list
|
||||
int *dnum; // number of discretes per line, 0 if uninit
|
||||
int *dfirst; // index of first discrete per each line
|
||||
int nmax; // allocated size of dnum,dfirst vectors
|
||||
|
||||
void allocate();
|
||||
void discretize(int, double, double *, double *, double *);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue