forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10550 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
79a2a93f9c
commit
aff25bf586
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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 "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 "atom_vec.h"
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#include "force.h"
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#include "update.h"
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#include "modify.h"
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#include "fix.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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using namespace LAMMPS_NS;
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using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixDeposit::FixDeposit(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg)
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{
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if (narg < 7) error->all(FLERR,"Illegal fix deposit command");
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restart_global = 1;
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time_depend = 1;
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// required args
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ninsert = force->inumeric(FLERR,arg[3]);
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ntype = force->inumeric(FLERR,arg[4]);
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nfreq = force->inumeric(FLERR,arg[5]);
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seed = force->inumeric(FLERR,arg[6]);
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if (seed <= 0) error->all(FLERR,"Illegal fix deposit command");
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// set defaults
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iregion = -1;
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idregion = NULL;
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idnext = 0;
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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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targetflag = 0;
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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 checks on region and its extent being inside simulation box
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if (iregion == -1) error->all(FLERR,"Must specify a region in fix deposit");
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if (domain->regions[iregion]->bboxflag == 0)
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error->all(FLERR,"Fix deposit region does not support a bounding box");
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if (domain->regions[iregion]->dynamic_check())
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error->all(FLERR,"Fix deposit region cannot be dynamic");
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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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if (domain->triclinic == 0) {
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if (xlo < domain->boxlo[0] || xhi > domain->boxhi[0] ||
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ylo < domain->boxlo[1] || yhi > domain->boxhi[1] ||
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zlo < domain->boxlo[2] || zhi > domain->boxhi[2])
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error->all(FLERR,"Deposition region extends outside simulation box");
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} else {
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if (xlo < domain->boxlo_bound[0] || xhi > domain->boxhi_bound[0] ||
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ylo < domain->boxlo_bound[1] || yhi > domain->boxhi_bound[1] ||
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zlo < domain->boxlo_bound[2] || zhi > domain->boxhi_bound[2])
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error->all(FLERR,"Deposition region extends outside simulation box");
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}
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// setup scaling
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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 (domain->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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tx *= xscale;
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ty *= yscale;
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tz *= zscale;
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// maxtag_all = current max tag for all atoms
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if (idnext) {
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int *tag = atom->tag;
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int nlocal = atom->nlocal;
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int maxtag = 0;
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for (int i = 0; i < nlocal; i++) maxtag = MAX(maxtag,tag[i]);
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MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
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}
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// random number generator, same for all procs
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random = new RanPark(lmp,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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delete [] idregion;
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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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void FixDeposit::init()
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{
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// set index and check validity of region
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iregion = domain->find_region(idregion);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix deposit does not exist");
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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 i,j;
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int flag,flagall;
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double coord[3],lamda[3],delx,dely,delz,rsq;
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double *newcoord;
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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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double *sublo,*subhi;
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if (domain->triclinic == 0) {
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sublo = domain->sublo;
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subhi = domain->subhi;
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} else {
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sublo = domain->sublo_lamda;
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subhi = domain->subhi_lamda;
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}
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// attempt an insertion until successful
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int nfix = modify->nfix;
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Fix **fix = modify->fix;
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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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coord[0] = xlo + random->uniform() * (xhi-xlo);
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coord[1] = ylo + random->uniform() * (yhi-ylo);
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coord[2] = zlo + random->uniform() * (zhi-zlo);
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while (domain->regions[iregion]->match(coord[0],coord[1],coord[2]) == 0) {
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coord[0] = xlo + random->uniform() * (xhi-xlo);
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coord[1] = ylo + random->uniform() * (yhi-ylo);
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coord[2] = zlo + random->uniform() * (zhi-zlo);
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}
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// adjust vertical coord by offset
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if (domain->dimension == 2) coord[1] += offset;
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else coord[2] += 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 (domain->dimension == 2) {
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dim = 1;
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max = domain->boxlo[1];
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} else {
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dim = 2;
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max = domain->boxlo[2];
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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 (i = 0; i < nlocal; i++) {
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if (localflag) {
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delx = coord[0] - x[i][0];
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dely = coord[1] - 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 (domain->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 (domain->dimension == 2)
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coord[1] = maxall + lo + random->uniform()*(hi-lo);
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else
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coord[2] = maxall + lo + random->uniform()*(hi-lo);
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}
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// now have final coord
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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 (i = 0; i < nlocal; i++) {
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delx = coord[0] - x[i][0];
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dely = coord[1] - x[i][1];
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delz = coord[2] - 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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// if we have a sputter target change velocity vector accordingly
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if (targetflag) {
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double vel = sqrt(vxtmp*vxtmp + vytmp*vytmp + vztmp*vztmp);
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delx = tx - coord[0];
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dely = ty - coord[1];
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delz = tz - coord[2];
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double rsq = delx*delx + dely*dely + delz*delz;
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if (rsq > 0.0) {
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double rinv = sqrt(1.0/rsq);
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vxtmp = delx*rinv*vel;
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vytmp = dely*rinv*vel;
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vztmp = delz*rinv*vel;
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}
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}
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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_atom()
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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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if (domain->triclinic) {
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domain->x2lamda(coord,lamda);
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newcoord = lamda;
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} else newcoord = coord;
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flag = 0;
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if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
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newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
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newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
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else if (domain->dimension == 3 && newcoord[2] >= domain->boxhi[2] &&
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comm->myloc[2] == comm->procgrid[2]-1 &&
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newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
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newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
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else if (domain->dimension == 2 && newcoord[1] >= domain->boxhi[1] &&
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comm->myloc[1] == comm->procgrid[1]-1 &&
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newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
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if (flag) {
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atom->avec->create_atom(ntype,coord);
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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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for (j = 0; j < nfix; j++)
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if (fix[j]->create_attribute) fix[j]->set_arrays(m);
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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 (!success && comm->me == 0)
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error->warning(FLERR,"Particle deposition was unsuccessful",0);
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// reset global natoms
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// if idnext, set new atom ID to incremented maxtag_all
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// else set new atom ID to value beyond all current atoms
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// if global map exists, reset it now instead of waiting for comm
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// since adding an atom messes up ghosts
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if (success) {
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atom->natoms += 1;
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if (atom->tag_enable) {
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if (idnext) {
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maxtag_all++;
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if (atom->nlocal && atom->tag[atom->nlocal-1] == 0)
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atom->tag[atom->nlocal-1] = maxtag_all;
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} else atom->tag_extend();
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if (atom->map_style) {
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atom->nghost = 0;
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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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}
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// next timestep to insert
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// next_reneighbor = 0 if done
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if (success) ninserted++;
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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(FLERR,"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(FLERR,"Illegal fix deposit command");
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iregion = domain->find_region(arg[iarg+1]);
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if (iregion == -1)
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error->all(FLERR,"Region ID for fix deposit does not exist");
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int n = strlen(arg[iarg+1]) + 1;
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idregion = new char[n];
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strcpy(idregion,arg[iarg+1]);
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iarg += 2;
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} else if (strcmp(arg[iarg],"id") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
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if (strcmp(arg[iarg+1],"max") == 0) idnext = 0;
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else if (strcmp(arg[iarg+1],"next") == 0) idnext = 1;
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else error->all(FLERR,"Illegal fix deposit command");
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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(FLERR,"Illegal fix deposit command");
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globalflag = 1;
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localflag = 0;
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lo = force->numeric(FLERR,arg[iarg+1]);
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hi = force->numeric(FLERR,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(FLERR,"Illegal fix deposit command");
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localflag = 1;
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globalflag = 0;
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lo = force->numeric(FLERR,arg[iarg+1]);
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hi = force->numeric(FLERR,arg[iarg+2]);
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deltasq = force->numeric(FLERR,arg[iarg+3])*force->numeric(FLERR,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(FLERR,"Illegal fix deposit command");
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nearsq = force->numeric(FLERR,arg[iarg+1])*force->numeric(FLERR,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(FLERR,"Illegal fix deposit command");
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maxattempt = force->inumeric(FLERR,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(FLERR,"Illegal fix deposit command");
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rateflag = 1;
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rate = force->numeric(FLERR,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(FLERR,"Illegal fix deposit command");
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vxlo = force->numeric(FLERR,arg[iarg+1]);
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vxhi = force->numeric(FLERR,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(FLERR,"Illegal fix deposit command");
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vylo = force->numeric(FLERR,arg[iarg+1]);
|
||||
vyhi = force->numeric(FLERR,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg],"vz") == 0) {
|
||||
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
|
||||
vzlo = force->numeric(FLERR,arg[iarg+1]);
|
||||
vzhi = force->numeric(FLERR,arg[iarg+2]);
|
||||
iarg += 3;
|
||||
} else if (strcmp(arg[iarg],"units") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
|
||||
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
|
||||
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = 1;
|
||||
else error->all(FLERR,"Illegal fix deposit command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"target") == 0) {
|
||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
|
||||
tx = force->numeric(FLERR,arg[iarg+1]);
|
||||
ty = force->numeric(FLERR,arg[iarg+2]);
|
||||
tz = force->numeric(FLERR,arg[iarg+3]);
|
||||
targetflag = 1;
|
||||
iarg += 4;
|
||||
} else error->all(FLERR,"Illegal fix deposit command");
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack entire state of Fix into one write
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixDeposit::write_restart(FILE *fp)
|
||||
{
|
||||
int n = 0;
|
||||
double list[4];
|
||||
list[n++] = random->state();
|
||||
list[n++] = ninserted;
|
||||
list[n++] = nfirst;
|
||||
list[n++] = next_reneighbor;
|
||||
|
||||
if (comm->me == 0) {
|
||||
int size = n * sizeof(double);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
fwrite(list,sizeof(double),n,fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
use state info from restart file to restart the Fix
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixDeposit::restart(char *buf)
|
||||
{
|
||||
int n = 0;
|
||||
double *list = (double *) buf;
|
||||
|
||||
seed = static_cast<int> (list[n++]);
|
||||
ninserted = static_cast<int> (list[n++]);
|
||||
nfirst = static_cast<int> (list[n++]);
|
||||
next_reneighbor = static_cast<int> (list[n++]);
|
||||
|
||||
random->reset(seed);
|
||||
}
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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 FIX_CLASS
|
||||
|
||||
FixStyle(deposit,FixDeposit)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_DEPOSIT_H
|
||||
#define LMP_FIX_DEPOSIT_H
|
||||
|
||||
#include "stdio.h"
|
||||
#include "fix.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixDeposit : public Fix {
|
||||
public:
|
||||
int ntype; // type of deposited atom, visible to PairGran
|
||||
|
||||
FixDeposit(class LAMMPS *, int, char **);
|
||||
~FixDeposit();
|
||||
int setmask();
|
||||
void init();
|
||||
void pre_exchange();
|
||||
void write_restart(FILE *);
|
||||
void restart(char *);
|
||||
|
||||
private:
|
||||
int ninsert,nfreq,seed;
|
||||
int iregion,globalflag,localflag,maxattempt,rateflag,scaleflag,targetflag;
|
||||
char *idregion;
|
||||
double lo,hi,deltasq,nearsq,rate;
|
||||
double vxlo,vxhi,vylo,vyhi,vzlo,vzhi;
|
||||
double xlo,xhi,ylo,yhi,zlo,zhi;
|
||||
double tx,ty,tz;
|
||||
int nfirst,ninserted;
|
||||
int idnext,maxtag_all;
|
||||
class RanPark *random;
|
||||
|
||||
void options(int, char **);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Must specify a region in fix deposit
|
||||
|
||||
The region keyword must be specified with this fix.
|
||||
|
||||
E: Fix deposit region does not support a bounding box
|
||||
|
||||
Not all regions represent bounded volumes. You cannot use
|
||||
such a region with the fix deposit command.
|
||||
|
||||
E: Fix deposit region cannot be dynamic
|
||||
|
||||
Only static regions can be used with fix deposit.
|
||||
|
||||
E: Deposition region extends outside simulation box
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Region ID for fix deposit does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
W: Particle deposition was unsuccessful
|
||||
|
||||
The fix deposit command was not able to insert as many atoms as
|
||||
needed. The requested volume fraction may be too high, or other atoms
|
||||
may be in the insertion region.
|
||||
|
||||
U: Use of fix deposit with undefined lattice
|
||||
|
||||
Must use lattice command with compute fix deposit command if units
|
||||
option is set to lattice.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue