git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11160 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
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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 "molecule.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 "math_extra.h"
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#include "math_const.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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using namespace MathConst;
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enum{ATOM,MOLECULE};
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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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// read options from end of input line
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options(narg-7,&arg[7]);
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// error check on type
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if (mode == ATOM && (ntype <= 0 || ntype > atom->ntypes))
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error->all(FLERR,"Invalid atom type in fix deposit command");
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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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// error check and further setup for mode = MOLECULE
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if (atom->tag_enable == 0)
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error->all(FLERR,"Cannot use fix_deposit unless atoms have IDs");
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if (mode == MOLECULE) {
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if (atom->molecule_flag == 0)
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error->all(FLERR,"Fix deposit requires atom attribute molecule");
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if (onemol->xflag == 0)
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error->all(FLERR,"Fix deposit molecule must have coordinates");
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if (onemol->typeflag == 0)
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error->all(FLERR,"Fix deposit molecule must have atom types");
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if (ntype+onemol->maxtype <= 0 || ntype+onemol->maxtype > atom->ntypes)
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error->all(FLERR,"Invalid atom type in fix deposit mol command");
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// fix deposit uses geoemetric center of molecule for insertion
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onemol->compute_center();
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}
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if (rigidflag && mode == ATOM)
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error->all(FLERR,"Cannot use fix deposit rigid and not molecule");
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if (shakeflag && mode == ATOM)
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error->all(FLERR,"Cannot use fix deposit shake and not molecule");
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if (rigidflag && shakeflag)
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error->all(FLERR,"Cannot use fix deposit rigid and shake");
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// setup of coords and imageflags array
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if (mode == ATOM) natom = 1;
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else natom = onemol->natoms;
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memory->create(coords,natom,3,"deposit:coords");
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memory->create(imageflags,natom,"deposit:imageflags");
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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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// find current max atom and molecule IDs if necessary
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if (idnext) find_maxid();
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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 [] idrigid;
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delete [] idshake;
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delete [] idregion;
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memory->destroy(coords);
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memory->destroy(imageflags);
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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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// if rigidflag defined, check for rigid/small fix
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// its molecule template must be same as this one
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fixrigid = NULL;
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if (rigidflag) {
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int ifix = modify->find_fix(idrigid);
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if (ifix < 0) error->all(FLERR,"Fix pour rigid fix does not exist");
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fixrigid = modify->fix[ifix];
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int tmp;
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if (onemol != (Molecule *) fixrigid->extract("onemol",tmp))
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error->all(FLERR,
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"Fix deposit and fix rigid/small not using same molecule ID");
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}
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// if shakeflag defined, check for SHAKE fix
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// its molecule template must be same as this one
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fixshake = NULL;
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if (shakeflag) {
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int ifix = modify->find_fix(idshake);
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if (ifix < 0) error->all(FLERR,"Fix deposit shake fix does not exist");
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fixshake = modify->fix[ifix];
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int tmp;
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if (onemol != (Molecule *) fixshake->extract("onemol",tmp))
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error->all(FLERR,"Fix deposit and fix shake not using same molecule ID");
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}
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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,m,n,nlocalprev,flag,flagall;
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double coord[3],lamda[3],delx,dely,delz,rsq;
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double alpha,beta,gamma;
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double r[3],vnew[3],rotmat[3][3],quat[4];
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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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// find current max atom and molecule IDs if necessary
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if (!idnext) find_maxid();
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// attempt an insertion until successful
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int dimension = domain->dimension;
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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 particle 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 (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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// when done, have final coord of atom or center pt of molecule
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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 (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 (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 (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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// coords = coords of all atoms
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// for molecule, perform random rotation around center pt
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// apply PBC so final coords are inside box
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// also store image flag modified due to PBC
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if (mode == ATOM) {
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coords[0][0] = coord[0];
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coords[0][1] = coord[1];
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coords[0][2] = coord[2];
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} else {
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if (dimension == 3) {
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r[0] = random->uniform() - 0.5;
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r[1] = random->uniform() - 0.5;
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r[2] = random->uniform() - 0.5;
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} else {
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r[0] = r[1] = 0.0;
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r[2] = 1.0;
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}
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double theta = random->uniform() * MY_2PI;
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MathExtra::norm3(r);
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MathExtra::axisangle_to_quat(r,theta,quat);
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MathExtra::quat_to_mat(quat,rotmat);
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for (i = 0; i < natom; i++) {
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MathExtra::matvec(rotmat,onemol->dx[i],coords[i]);
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coords[i][0] += coord[0];
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coords[i][1] += coord[1];
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||||||
coords[i][2] += coord[2];
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||||||
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|
||||||
imageflags[i] = ((tagint) IMGMAX << IMG2BITS) |
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|
||||||
((tagint) IMGMAX << IMGBITS) | IMGMAX;
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|
||||||
domain->remap(coords[i],imageflags[i]);
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|
||||||
}
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|
||||||
}
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|
||||||
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|
||||||
// if distance to any inserted atom is less than near, try again
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|
||||||
// use minimum_image() to account for PBC
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|
||||||
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|
||||||
double **x = atom->x;
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|
||||||
int nlocal = atom->nlocal;
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|
||||||
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|
||||||
flag = 0;
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|
||||||
for (m = 0; m < natom; m++) {
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|
||||||
for (i = 0; i < nlocal; i++) {
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|
||||||
delx = coords[m][0] - x[i][0];
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|
||||||
dely = coords[m][1] - x[i][1];
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|
||||||
delz = coords[m][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;
|
|
||||||
if (rsq < nearsq) flag = 1;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
|
|
||||||
if (flagall) continue;
|
|
||||||
|
|
||||||
// proceed with insertion
|
|
||||||
|
|
||||||
nlocalprev = atom->nlocal;
|
|
||||||
|
|
||||||
// choose random velocity for new particle
|
|
||||||
// used for every atom in molecule
|
|
||||||
|
|
||||||
vnew[0] = vxlo + random->uniform() * (vxhi-vxlo);
|
|
||||||
vnew[1] = vylo + random->uniform() * (vyhi-vylo);
|
|
||||||
vnew[2] = vzlo + random->uniform() * (vzhi-vzlo);
|
|
||||||
|
|
||||||
// if target specified, change velocity vector accordingly
|
|
||||||
|
|
||||||
if (targetflag) {
|
|
||||||
double vel = sqrt(vnew[0]*vnew[0] + vnew[1]*vnew[1] + vnew[2]*vnew[2]);
|
|
||||||
delx = tx - coord[0];
|
|
||||||
dely = ty - coord[1];
|
|
||||||
delz = tz - coord[2];
|
|
||||||
double rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
if (rsq > 0.0) {
|
|
||||||
double rinv = sqrt(1.0/rsq);
|
|
||||||
vnew[0] = delx*rinv*vel;
|
|
||||||
vnew[1] = dely*rinv*vel;
|
|
||||||
vnew[2] = delz*rinv*vel;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// check if new atoms are in my sub-box or above it if I am highest proc
|
|
||||||
// if so, add atom to my list via create_atom()
|
|
||||||
// initialize additional info about the atoms
|
|
||||||
// set group mask to "all" plus fix group
|
|
||||||
|
|
||||||
for (m = 0; m < natom; m++) {
|
|
||||||
if (domain->triclinic) {
|
|
||||||
domain->x2lamda(coords[m],lamda);
|
|
||||||
newcoord = lamda;
|
|
||||||
} else newcoord = coords[m];
|
|
||||||
|
|
||||||
flag = 0;
|
|
||||||
if (newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
|
|
||||||
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1] &&
|
|
||||||
newcoord[2] >= sublo[2] && newcoord[2] < subhi[2]) flag = 1;
|
|
||||||
else if (dimension == 3 && newcoord[2] >= domain->boxhi[2] &&
|
|
||||||
comm->myloc[2] == comm->procgrid[2]-1 &&
|
|
||||||
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0] &&
|
|
||||||
newcoord[1] >= sublo[1] && newcoord[1] < subhi[1]) flag = 1;
|
|
||||||
else if (dimension == 2 && newcoord[1] >= domain->boxhi[1] &&
|
|
||||||
comm->myloc[1] == comm->procgrid[1]-1 &&
|
|
||||||
newcoord[0] >= sublo[0] && newcoord[0] < subhi[0]) flag = 1;
|
|
||||||
|
|
||||||
if (flag) {
|
|
||||||
if (mode == ATOM) atom->avec->create_atom(ntype,coords[m]);
|
|
||||||
else atom->avec->create_atom(ntype+onemol->type[m],coords[m]);
|
|
||||||
n = atom->nlocal - 1;
|
|
||||||
atom->tag[n] = maxtag_all + m+1;
|
|
||||||
if (mode == MOLECULE) atom->molecule[n] = maxmol_all;
|
|
||||||
atom->mask[n] = 1 | groupbit;
|
|
||||||
atom->image[n] = imageflags[m];
|
|
||||||
atom->v[n][0] = vnew[0];
|
|
||||||
atom->v[n][1] = vnew[1];
|
|
||||||
atom->v[n][2] = vnew[2];
|
|
||||||
if (mode == MOLECULE) atom->add_molecule_atom(onemol,m,n,maxtag_all);
|
|
||||||
for (j = 0; j < nfix; j++)
|
|
||||||
if (fix[j]->create_attribute) fix[j]->set_arrays(n);
|
|
||||||
}
|
|
||||||
|
|
||||||
// FixRigidSmall::set_molecule stores rigid body attributes
|
|
||||||
// coord is new position of geometric center of mol, not COM
|
|
||||||
// FixShake::set_molecule stores shake info for molecule
|
|
||||||
|
|
||||||
if (rigidflag)
|
|
||||||
fixrigid->set_molecule(nlocalprev,maxtag_all,coord,vnew,quat);
|
|
||||||
else if (shakeflag)
|
|
||||||
fixshake->set_molecule(nlocalprev,maxtag_all,coord,vnew,quat);
|
|
||||||
}
|
|
||||||
|
|
||||||
// old code: unsuccessful if no proc performed insertion of an atom
|
|
||||||
// don't think that check is necessary
|
|
||||||
// if get this far, should always be succesful
|
|
||||||
// would be hard to undo partial insertion for a molecule
|
|
||||||
// better to check how many atoms could be inserted (w/out inserting)
|
|
||||||
// then sum to insure all are inserted, before doing actual insertion
|
|
||||||
// MPI_Allreduce(&flag,&success,1,MPI_INT,MPI_MAX,world);
|
|
||||||
|
|
||||||
success = 1;
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
|
|
||||||
// warn if not successful b/c too many attempts
|
|
||||||
|
|
||||||
if (!success && comm->me == 0)
|
|
||||||
error->warning(FLERR,"Particle deposition was unsuccessful",0);
|
|
||||||
|
|
||||||
// reset global natoms,nbonds,etc
|
|
||||||
// increment maxtag_all and maxmol_all if necessary
|
|
||||||
// if global map exists, reset it now instead of waiting for comm
|
|
||||||
// since adding atoms messes up ghosts
|
|
||||||
|
|
||||||
if (success) {
|
|
||||||
atom->natoms += natom;
|
|
||||||
if (mode == MOLECULE) {
|
|
||||||
atom->nbonds += onemol->nbonds;
|
|
||||||
atom->nangles += onemol->nangles;
|
|
||||||
atom->ndihedrals += onemol->ndihedrals;
|
|
||||||
atom->nimpropers += onemol->nimpropers;
|
|
||||||
}
|
|
||||||
if (idnext) {
|
|
||||||
maxtag_all += natom;
|
|
||||||
if (mode == MOLECULE) maxmol_all++;
|
|
||||||
}
|
|
||||||
if (atom->map_style) {
|
|
||||||
atom->nghost = 0;
|
|
||||||
atom->map_init();
|
|
||||||
atom->map_set();
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// next timestep to insert
|
|
||||||
// next_reneighbor = 0 if done
|
|
||||||
|
|
||||||
if (success) ninserted++;
|
|
||||||
if (ninserted < ninsert) next_reneighbor += nfreq;
|
|
||||||
else next_reneighbor = 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
maxtag_all = current max atom ID for all atoms
|
|
||||||
maxmol_all = current max molecule ID for all atoms
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixDeposit::find_maxid()
|
|
||||||
{
|
|
||||||
int *tag = atom->tag;
|
|
||||||
int *molecule = atom->molecule;
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
|
|
||||||
int max = 0;
|
|
||||||
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
|
|
||||||
MPI_Allreduce(&max,&maxtag_all,1,MPI_INT,MPI_MAX,world);
|
|
||||||
|
|
||||||
if (mode == MOLECULE) {
|
|
||||||
max = 0;
|
|
||||||
for (int i = 0; i < nlocal; i++) max = MAX(max,molecule[i]);
|
|
||||||
MPI_Allreduce(&max,&maxmol_all,1,MPI_INT,MPI_MAX,world);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
parse optional parameters at end of input line
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void FixDeposit::options(int narg, char **arg)
|
|
||||||
{
|
|
||||||
// defaults
|
|
||||||
|
|
||||||
iregion = -1;
|
|
||||||
idregion = NULL;
|
|
||||||
mode = ATOM;
|
|
||||||
rigidflag = 0;
|
|
||||||
idrigid = NULL;
|
|
||||||
shakeflag = 0;
|
|
||||||
idshake = NULL;
|
|
||||||
idnext = 0;
|
|
||||||
globalflag = localflag = 0;
|
|
||||||
lo = hi = deltasq = 0.0;
|
|
||||||
nearsq = 0.0;
|
|
||||||
maxattempt = 10;
|
|
||||||
rateflag = 0;
|
|
||||||
vxlo = vxhi = vylo = vyhi = vzlo = vzhi = 0.0;
|
|
||||||
scaleflag = 1;
|
|
||||||
targetflag = 0;
|
|
||||||
|
|
||||||
int iarg = 0;
|
|
||||||
while (iarg < narg) {
|
|
||||||
if (strcmp(arg[iarg],"region") == 0) {
|
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
iregion = domain->find_region(arg[iarg+1]);
|
|
||||||
if (iregion == -1)
|
|
||||||
error->all(FLERR,"Region ID for fix deposit does not exist");
|
|
||||||
int n = strlen(arg[iarg+1]) + 1;
|
|
||||||
idregion = new char[n];
|
|
||||||
strcpy(idregion,arg[iarg+1]);
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg],"mol") == 0) {
|
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
int imol = atom->find_molecule(arg[iarg+1]);
|
|
||||||
if (imol == -1)
|
|
||||||
error->all(FLERR,"Molecule ID for fix deposit does not exist");
|
|
||||||
mode = MOLECULE;
|
|
||||||
onemol = atom->molecules[imol];
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg],"rigid") == 0) {
|
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
int n = strlen(arg[iarg+1]) + 1;
|
|
||||||
delete [] idrigid;
|
|
||||||
idrigid = new char[n];
|
|
||||||
strcpy(idrigid,arg[iarg+1]);
|
|
||||||
rigidflag = 1;
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg],"shake") == 0) {
|
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
int n = strlen(arg[iarg+1]) + 1;
|
|
||||||
delete [] idshake;
|
|
||||||
idshake = new char[n];
|
|
||||||
strcpy(idshake,arg[iarg+1]);
|
|
||||||
shakeflag = 1;
|
|
||||||
iarg += 2;
|
|
||||||
|
|
||||||
} else if (strcmp(arg[iarg],"id") == 0) {
|
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
if (strcmp(arg[iarg+1],"max") == 0) idnext = 0;
|
|
||||||
else if (strcmp(arg[iarg+1],"next") == 0) idnext = 1;
|
|
||||||
else error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg],"global") == 0) {
|
|
||||||
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
globalflag = 1;
|
|
||||||
localflag = 0;
|
|
||||||
lo = force->numeric(FLERR,arg[iarg+1]);
|
|
||||||
hi = force->numeric(FLERR,arg[iarg+2]);
|
|
||||||
iarg += 3;
|
|
||||||
} else if (strcmp(arg[iarg],"local") == 0) {
|
|
||||||
if (iarg+4 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
localflag = 1;
|
|
||||||
globalflag = 0;
|
|
||||||
lo = force->numeric(FLERR,arg[iarg+1]);
|
|
||||||
hi = force->numeric(FLERR,arg[iarg+2]);
|
|
||||||
deltasq = force->numeric(FLERR,arg[iarg+3]) *
|
|
||||||
force->numeric(FLERR,arg[iarg+3]);
|
|
||||||
iarg += 4;
|
|
||||||
|
|
||||||
} else if (strcmp(arg[iarg],"near") == 0) {
|
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
nearsq = force->numeric(FLERR,arg[iarg+1]) *
|
|
||||||
force->numeric(FLERR,arg[iarg+1]);
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg],"attempt") == 0) {
|
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
maxattempt = force->inumeric(FLERR,arg[iarg+1]);
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg],"rate") == 0) {
|
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
rateflag = 1;
|
|
||||||
rate = force->numeric(FLERR,arg[iarg+1]);
|
|
||||||
iarg += 2;
|
|
||||||
} else if (strcmp(arg[iarg],"vx") == 0) {
|
|
||||||
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
vxlo = force->numeric(FLERR,arg[iarg+1]);
|
|
||||||
vxhi = force->numeric(FLERR,arg[iarg+2]);
|
|
||||||
iarg += 3;
|
|
||||||
} else if (strcmp(arg[iarg],"vy") == 0) {
|
|
||||||
if (iarg+3 > narg) error->all(FLERR,"Illegal fix deposit command");
|
|
||||||
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);
|
|
||||||
}
|
|
||||||
@ -1,110 +0,0 @@
|
|||||||
/* -*- 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;
|
|
||||||
int mode,rigidflag,shakeflag,idnext;
|
|
||||||
double lo,hi,deltasq,nearsq,rate;
|
|
||||||
double vxlo,vxhi,vylo,vyhi,vzlo,vzhi;
|
|
||||||
double xlo,xhi,ylo,yhi,zlo,zhi;
|
|
||||||
double tx,ty,tz;
|
|
||||||
char *idregion;
|
|
||||||
char *idrigid,*idshake;
|
|
||||||
|
|
||||||
class Molecule *onemol;
|
|
||||||
int natom;
|
|
||||||
double **coords;
|
|
||||||
int *imageflags;
|
|
||||||
class Fix *fixrigid,*fixshake;
|
|
||||||
|
|
||||||
int nfirst,ninserted;
|
|
||||||
int maxtag_all,maxmol_all;
|
|
||||||
class RanPark *random;
|
|
||||||
|
|
||||||
void find_maxid();
|
|
||||||
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.
|
|
||||||
|
|
||||||
*/
|
|
||||||
2578
src/fix_shake.cpp
2578
src/fix_shake.cpp
File diff suppressed because it is too large
Load Diff
242
src/fix_shake.h
242
src/fix_shake.h
@ -1,242 +0,0 @@
|
|||||||
/* ----------------------------------------------------------------------
|
|
||||||
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(shake,FixShake)
|
|
||||||
|
|
||||||
#else
|
|
||||||
|
|
||||||
#ifndef LMP_FIX_SHAKE_H
|
|
||||||
#define LMP_FIX_SHAKE_H
|
|
||||||
|
|
||||||
#include "fix.h"
|
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
|
||||||
|
|
||||||
class FixShake : public Fix {
|
|
||||||
public:
|
|
||||||
FixShake(class LAMMPS *, int, char **);
|
|
||||||
~FixShake();
|
|
||||||
int setmask();
|
|
||||||
void init();
|
|
||||||
void setup(int);
|
|
||||||
void pre_neighbor();
|
|
||||||
void post_force(int);
|
|
||||||
void post_force_respa(int, int, int);
|
|
||||||
|
|
||||||
double memory_usage();
|
|
||||||
void grow_arrays(int);
|
|
||||||
void copy_arrays(int, int, int);
|
|
||||||
void set_arrays(int);
|
|
||||||
void update_arrays(int, int);
|
|
||||||
void set_molecule(int, int, double *, double *, double *);
|
|
||||||
|
|
||||||
int pack_exchange(int, double *);
|
|
||||||
int unpack_exchange(int, double *);
|
|
||||||
int pack_comm(int, int *, double *, int, int *);
|
|
||||||
void unpack_comm(int, int, double *);
|
|
||||||
|
|
||||||
int dof(int);
|
|
||||||
void reset_dt();
|
|
||||||
void *extract(const char *, int &);
|
|
||||||
|
|
||||||
private:
|
|
||||||
int me,nprocs;
|
|
||||||
double tolerance; // SHAKE tolerance
|
|
||||||
int max_iter; // max # of SHAKE iterations
|
|
||||||
int output_every; // SHAKE stat output every so often
|
|
||||||
bigint next_output; // timestep for next output
|
|
||||||
|
|
||||||
// settings from input command
|
|
||||||
int *bond_flag,*angle_flag; // bond/angle types to constrain
|
|
||||||
int *type_flag; // constrain bonds to these types
|
|
||||||
double *mass_list; // constrain bonds to these masses
|
|
||||||
int nmass; // # of masses in mass_list
|
|
||||||
|
|
||||||
double *bond_distance,*angle_distance; // constraint distances
|
|
||||||
|
|
||||||
int ifix_respa; // rRESPA fix needed by SHAKE
|
|
||||||
int nlevels_respa; // copies of needed rRESPA variables
|
|
||||||
int *loop_respa;
|
|
||||||
double *step_respa;
|
|
||||||
|
|
||||||
double **x,**v,**f; // local ptrs to atom class quantities
|
|
||||||
double *mass,*rmass;
|
|
||||||
int *type;
|
|
||||||
int nlocal;
|
|
||||||
// atom-based arrays
|
|
||||||
int *shake_flag; // 0 if atom not in SHAKE cluster
|
|
||||||
// 1 = size 3 angle cluster
|
|
||||||
// 2,3,4 = size of bond-only cluster
|
|
||||||
int **shake_atom; // global IDs of atoms in cluster
|
|
||||||
// central atom is 1st
|
|
||||||
// lowest global ID is 1st for size 2
|
|
||||||
int **shake_type; // bondtype of each bond in cluster
|
|
||||||
// for angle cluster, 3rd value
|
|
||||||
// is angletype
|
|
||||||
double **xshake; // unconstrained atom coords
|
|
||||||
int *nshake; // count
|
|
||||||
|
|
||||||
double dtv,dtfsq; // timesteps for trial move
|
|
||||||
double dtf_inner,dtf_innerhalf; // timesteps for rRESPA trial move
|
|
||||||
|
|
||||||
int *list; // list of clusters to SHAKE
|
|
||||||
int nlist,maxlist; // size and max-size of list
|
|
||||||
|
|
||||||
// stat quantities
|
|
||||||
int *b_count,*b_count_all; // counts for each bond type
|
|
||||||
double *b_ave,*b_max,*b_min; // ave/max/min dist for each bond type
|
|
||||||
double *b_ave_all,*b_max_all,*b_min_all; // MPI summing arrays
|
|
||||||
int *a_count,*a_count_all; // ditto for angle types
|
|
||||||
double *a_ave,*a_max,*a_min;
|
|
||||||
double *a_ave_all,*a_max_all,*a_min_all;
|
|
||||||
|
|
||||||
// molecules added on-the-fly with SHAKE constraints
|
|
||||||
|
|
||||||
class Molecule *onemol;
|
|
||||||
|
|
||||||
void find_clusters();
|
|
||||||
int masscheck(double);
|
|
||||||
void unconstrained_update();
|
|
||||||
void unconstrained_update_respa(int);
|
|
||||||
void shake(int);
|
|
||||||
void shake3(int);
|
|
||||||
void shake4(int);
|
|
||||||
void shake3angle(int);
|
|
||||||
void stats();
|
|
||||||
int bondfind(int, int, int);
|
|
||||||
int anglefind(int, int, int);
|
|
||||||
|
|
||||||
// static variable for ring communication callback to access class data
|
|
||||||
// callback functions for ring communication
|
|
||||||
|
|
||||||
static FixShake *fsptr;
|
|
||||||
static void ring_bonds(int, char *);
|
|
||||||
static void ring_nshake(int, char *);
|
|
||||||
static void ring_shake(int, char *);
|
|
||||||
};
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
#endif
|
|
||||||
#endif
|
|
||||||
|
|
||||||
/* ERROR/WARNING messages:
|
|
||||||
|
|
||||||
E: Cannot use fix shake with non-molecular system
|
|
||||||
|
|
||||||
Your choice of atom style does not have bonds.
|
|
||||||
|
|
||||||
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: Invalid bond type index for fix shake
|
|
||||||
|
|
||||||
Self-explanatory. Check the fix shake command in the input script.
|
|
||||||
|
|
||||||
E: Invalid angle type index for fix shake
|
|
||||||
|
|
||||||
Self-explanatory.
|
|
||||||
|
|
||||||
E: Invalid atom type index for fix shake
|
|
||||||
|
|
||||||
Atom types must range from 1 to Ntypes inclusive.
|
|
||||||
|
|
||||||
E: Invalid atom mass for fix shake
|
|
||||||
|
|
||||||
Mass specified in fix shake command must be > 0.0.
|
|
||||||
|
|
||||||
E: Too many masses for fix shake
|
|
||||||
|
|
||||||
The fix shake command cannot list more masses than there are atom
|
|
||||||
types.
|
|
||||||
|
|
||||||
E: More than one fix shake
|
|
||||||
|
|
||||||
Only one fix shake can be defined.
|
|
||||||
|
|
||||||
E: Fix shake cannot be used with minimization
|
|
||||||
|
|
||||||
Cannot use fix shake while doing an energy minimization since
|
|
||||||
it turns off bonds that should contribute to the energy.
|
|
||||||
|
|
||||||
E: Shake fix must come before NPT/NPH fix
|
|
||||||
|
|
||||||
NPT fix must be defined in input script after SHAKE fix, else the
|
|
||||||
SHAKE fix contribution to the pressure virial is incorrect.
|
|
||||||
|
|
||||||
E: Bond potential must be defined for SHAKE
|
|
||||||
|
|
||||||
Cannot use fix shake unless bond potential is defined.
|
|
||||||
|
|
||||||
E: Angle potential must be defined for SHAKE
|
|
||||||
|
|
||||||
When shaking angles, an angle_style potential must be used.
|
|
||||||
|
|
||||||
E: Shake angles have different bond types
|
|
||||||
|
|
||||||
All 3-atom angle-constrained SHAKE clusters specified by the fix shake
|
|
||||||
command that are the same angle type, must also have the same bond
|
|
||||||
types for the 2 bonds in the angle.
|
|
||||||
|
|
||||||
E: Shake atoms %d %d missing on proc %d at step %ld
|
|
||||||
|
|
||||||
The 2 atoms in a single shake cluster specified by the fix shake
|
|
||||||
command are not all accessible to a processor. This probably means
|
|
||||||
an atom has moved too far.
|
|
||||||
|
|
||||||
E: Shake atoms %d %d %d missing on proc %d at step %ld
|
|
||||||
|
|
||||||
The 3 atoms in a single shake cluster specified by the fix shake
|
|
||||||
command are not all accessible to a processor. This probably means
|
|
||||||
an atom has moved too far.
|
|
||||||
|
|
||||||
E: Shake atoms %d %d %d %d missing on proc %d at step %ld
|
|
||||||
|
|
||||||
The 4 atoms in a single shake cluster specified by the fix shake
|
|
||||||
command are not all accessible to a processor. This probably means
|
|
||||||
an atom has moved too far.
|
|
||||||
|
|
||||||
E: Did not find fix shake partner info
|
|
||||||
|
|
||||||
Could not find bond partners implied by fix shake command. This error
|
|
||||||
can be triggered if the delete_bonds command was used before fix
|
|
||||||
shake, and it removed bonds without resetting the 1-2, 1-3, 1-4
|
|
||||||
weighting list via the special keyword.
|
|
||||||
|
|
||||||
E: Shake cluster of more than 4 atoms
|
|
||||||
|
|
||||||
A single cluster specified by the fix shake command can have no more
|
|
||||||
than 4 atoms.
|
|
||||||
|
|
||||||
E: Shake clusters are connected
|
|
||||||
|
|
||||||
A single cluster specified by the fix shake command must have a single
|
|
||||||
central atom with up to 3 other atoms bonded to it.
|
|
||||||
|
|
||||||
W: Shake determinant < 0.0
|
|
||||||
|
|
||||||
The determinant of the quadratic equation being solved for a single
|
|
||||||
cluster specified by the fix shake command is numerically suspect. LAMMPS
|
|
||||||
will set it to 0.0 and continue.
|
|
||||||
|
|
||||||
E: Shake determinant = 0.0
|
|
||||||
|
|
||||||
The determinant of the matrix being solved for a single cluster
|
|
||||||
specified by the fix shake command is numerically invalid.
|
|
||||||
|
|
||||||
*/
|
|
||||||
Reference in New Issue
Block a user