git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@186 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
369
src/fix_deposit.cpp
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369
src/fix_deposit.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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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 "stdlib.h"
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#include "string.h"
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#include "fix_deposit.h"
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#include "atom.h"
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#include "force.h"
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#include "update.h"
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#include "comm.h"
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#include "domain.h"
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#include "lattice.h"
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#include "region.h"
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#include "random_park.h"
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#include "memory.h"
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#include "error.h"
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/* ---------------------------------------------------------------------- */
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FixDeposit::FixDeposit(int narg, char **arg) : Fix(narg, arg)
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{
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if (narg < 7) error->all("Illegal fix deposit command");
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// required args
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ninsert = atoi(arg[3]);
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ntype = atoi(arg[4]);
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nfreq = atoi(arg[5]);
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seed = atoi(arg[6]);
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// set defaults
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iregion = -1;
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globalflag = localflag = 0;
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lo = hi = deltasq = 0.0;
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nearsq = 0.0;
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maxattempt = 10;
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rateflag = 0;
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vxlo = vxhi = vylo = vyhi = vzlo = vzhi = 0.0;
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scaleflag = 1;
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// read options from end of input line
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options(narg-7,&arg[7]);
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// error check on region
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if (iregion == -1) error->all("Must specify a region in fix deposit");
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if (domain->regions[iregion]->interior == 0)
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error->all("Must use region with side = in with fix deposit");
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// store extent of region
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xlo = domain->regions[iregion]->extent_xlo;
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xhi = domain->regions[iregion]->extent_xhi;
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ylo = domain->regions[iregion]->extent_ylo;
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yhi = domain->regions[iregion]->extent_yhi;
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zlo = domain->regions[iregion]->extent_zlo;
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zhi = domain->regions[iregion]->extent_zhi;
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// setup scaling
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if (scaleflag && domain->lattice == NULL)
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error->all("Use of fix deposit with undefined lattice");
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double xscale,yscale,zscale;
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if (scaleflag) {
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xscale = domain->lattice->xlattice;
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yscale = domain->lattice->ylattice;
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zscale = domain->lattice->zlattice;
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}
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else xscale = yscale = zscale = 1.0;
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// apply scaling to all input parameters with dist/vel units
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if (force->dimension == 2) {
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lo *= yscale;
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hi *= yscale;
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rate *= yscale;
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} else {
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lo *= zscale;
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hi *= zscale;
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rate *= zscale;
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}
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deltasq *= xscale*xscale;
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nearsq *= xscale*xscale;
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vxlo *= xscale;
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vxhi *= xscale;
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vylo *= yscale;
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vyhi *= yscale;
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vzlo *= zscale;
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vzhi *= zscale;
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// store extent of region
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xlo = domain->regions[iregion]->extent_xlo;
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xhi = domain->regions[iregion]->extent_xhi;
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ylo = domain->regions[iregion]->extent_ylo;
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yhi = domain->regions[iregion]->extent_yhi;
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zlo = domain->regions[iregion]->extent_zlo;
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zhi = domain->regions[iregion]->extent_zhi;
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// random number generator, same for all procs
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random = new RanPark(seed);
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// set up reneighboring
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force_reneighbor = 1;
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next_reneighbor = update->ntimestep + 1;
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nfirst = next_reneighbor;
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ninserted = 0;
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}
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/* ---------------------------------------------------------------------- */
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FixDeposit::~FixDeposit()
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{
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delete random;
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}
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/* ---------------------------------------------------------------------- */
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int FixDeposit::setmask()
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{
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int mask = 0;
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mask |= PRE_EXCHANGE;
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return mask;
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}
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/* ----------------------------------------------------------------------
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perform particle insertion
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------------------------------------------------------------------------- */
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void FixDeposit::pre_exchange()
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{
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int flag,flagall;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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// just return if should not be called on this timestep
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if (next_reneighbor != update->ntimestep) return;
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// compute current offset = bottom of insertion volume
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double offset = 0.0;
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if (rateflag) offset = (update->ntimestep - nfirst) * update->dt * rate;
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// attempt an insertion until successful
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int success = 0;
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int attempt = 0;
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while (attempt < maxattempt) {
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attempt++;
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// choose random position for new atom within region
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xtmp = xlo + random->uniform() * (xhi-xlo);
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ytmp = ylo + random->uniform() * (yhi-ylo);
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ztmp = zlo + random->uniform() * (zhi-zlo);
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while (domain->regions[iregion]->match(xtmp,ytmp,ztmp) == 0) {
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xtmp = xlo + random->uniform() * (xhi-xlo);
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ytmp = ylo + random->uniform() * (yhi-ylo);
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ztmp = zlo + random->uniform() * (zhi-zlo);
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}
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// adjust vertical coord by offset
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if (force->dimension == 2) ytmp += offset;
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else ztmp += offset;
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// if global, reset vertical coord to be lo-hi above highest atom
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// if local, reset vertical coord to be lo-hi above highest "nearby" atom
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// local computation computes lateral distance between 2 particles w/ PBC
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if (globalflag || localflag) {
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int dim;
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double max,maxall,delx,dely,delz,rsq;
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if (force->dimension == 2) {
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dim = 1;
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max = domain->boxylo;
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} else {
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dim = 2;
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max = domain->boxzlo;
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}
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double **x = atom->x;
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++) {
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if (localflag) {
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delx = xtmp - x[i][0];
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dely = ytmp - x[i][1];
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delz = 0.0;
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domain->minimum_image(&delx,&dely,&delz);
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if (force->dimension == 2) rsq = delx*delx;
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else rsq = delx*delx + dely*dely;
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if (rsq > deltasq) continue;
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}
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if (x[i][dim] > max) max = x[i][dim];
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}
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MPI_Allreduce(&max,&maxall,1,MPI_DOUBLE,MPI_MAX,world);
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if (force->dimension == 2)
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ytmp = maxall + lo + random->uniform()*(hi-lo);
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else
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ztmp = maxall + lo + random->uniform()*(hi-lo);
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}
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// now have final xtmp,ytmp,ztmp
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// if distance to any atom is less than near, try again
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double **x = atom->x;
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int nlocal = atom->nlocal;
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flag = 0;
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for (int i = 0; i < nlocal; i++) {
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delx = xtmp - x[i][0];
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dely = ytmp - x[i][1];
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delz = ztmp - x[i][2];
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domain->minimum_image(&delx,&dely,&delz);
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < nearsq) flag = 1;
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}
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MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
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if (flagall) continue;
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// insertion will proceed
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// choose random velocity for new atom
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double vxtmp = vxlo + random->uniform() * (vxhi-vxlo);
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double vytmp = vylo + random->uniform() * (vyhi-vylo);
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double vztmp = vzlo + random->uniform() * (vzhi-vzlo);
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// check if new atom is in my sub-box or above it if I'm highest proc
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// if so, add to my list via create_one()
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// initialize info about the atoms
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// set group mask to "all" plus fix group
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flag = 0;
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if (xtmp >= domain->subxlo && xtmp < domain->subxhi &&
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ytmp >= domain->subylo && ytmp < domain->subyhi &&
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ztmp >= domain->subzlo && ztmp < domain->subzhi) flag = 1;
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else if (force->dimension == 3 && ztmp >= domain->boxzhi &&
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comm->myloc[2] == comm->procgrid[2]-1 &&
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xtmp >= domain->subxlo && xtmp < domain->subxhi &&
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ytmp >= domain->subylo && ytmp < domain->subyhi) flag = 1;
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else if (force->dimension == 2 && ytmp >= domain->boxyhi &&
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comm->myloc[1] == comm->procgrid[1]-1 &&
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xtmp >= domain->subxlo && xtmp < domain->subxhi) flag = 1;
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if (flag) {
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atom->create_one(ntype,xtmp,ytmp,ztmp);
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int m = atom->nlocal - 1;
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atom->type[m] = ntype;
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atom->mask[m] = 1 | groupbit;
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atom->v[m][0] = vxtmp;
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atom->v[m][1] = vytmp;
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atom->v[m][2] = vztmp;
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}
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MPI_Allreduce(&flag,&success,1,MPI_INT,MPI_MAX,world);
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break;
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}
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// warn if not successful b/c too many attempts or no proc owned particle
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if (comm->me == 0)
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if (success == 0)
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error->warning("Particle deposition was unsuccessful");
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// set tag # of new particle beyond all previous atoms
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// reset global natoms
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// if global map exists, reset it
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if (success && atom->tag_enable) {
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atom->tag_extend();
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atom->natoms += 1;
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if (atom->map_style) {
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atom->map_init();
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atom->map_set();
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}
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}
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// next timestep to insert
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if (ninserted < ninsert) next_reneighbor += nfreq;
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else next_reneighbor = 0;
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}
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/* ----------------------------------------------------------------------
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parse optional parameters at end of input line
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------------------------------------------------------------------------- */
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void FixDeposit::options(int narg, char **arg)
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{
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if (narg < 0) error->all("Illegal fix indent command");
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int iarg = 0;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"region") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix deposit command");
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for (iregion = 0; iregion < domain->nregion; iregion++)
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if (strcmp(arg[iarg+1],domain->regions[iregion]->id) == 0) break;
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if (iregion == domain->nregion)
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error->all("Fix deposit region ID does not exist");
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iarg += 2;
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} else if (strcmp(arg[iarg],"global") == 0) {
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if (iarg+3 > narg) error->all("Illegal fix deposit command");
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globalflag = 1;
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localflag = 0;
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lo = atof(arg[iarg+1]);
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hi = atof(arg[iarg+2]);
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iarg += 3;
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} else if (strcmp(arg[iarg],"local") == 0) {
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if (iarg+4 > narg) error->all("Illegal fix deposit command");
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localflag = 1;
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globalflag = 0;
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lo = atof(arg[iarg+1]);
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hi = atof(arg[iarg+2]);
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deltasq = atof(arg[iarg+3])*atof(arg[iarg+3]);
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iarg += 4;
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} else if (strcmp(arg[iarg],"near") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix deposit command");
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nearsq = atof(arg[iarg+1])*atof(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"attempt") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix deposit command");
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maxattempt = atoi(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"rate") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix deposit command");
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rateflag = 1;
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rate = atof(arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"vx") == 0) {
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if (iarg+3 > narg) error->all("Illegal fix deposit command");
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vxlo = atof(arg[iarg+1]);
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vxhi = atof(arg[iarg+2]);
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iarg += 3;
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} else if (strcmp(arg[iarg],"vy") == 0) {
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if (iarg+3 > narg) error->all("Illegal fix deposit command");
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vylo = atof(arg[iarg+1]);
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vyhi = atof(arg[iarg+2]);
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iarg += 3;
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} else if (strcmp(arg[iarg],"vz") == 0) {
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if (iarg+3 > narg) error->all("Illegal fix deposit command");
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vzlo = atof(arg[iarg+1]);
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vzhi = atof(arg[iarg+2]);
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iarg += 3;
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} else if (strcmp(arg[iarg],"units") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix deposit command");
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if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
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else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
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else error->all("Illegal fix deposit command");
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iarg += 2;
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} else error->all("Illegal fix deposit command");
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}
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}
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