Homec4science
Diffusion lammps (lammm-master) Browse

lammps/src/create_box.cpp
fe17fe1eb6adlammm-master

Last Change
Raw File

create_box.cpp
View Options

/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "string.h"
#include "create_box.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "region.h"
#include "region_prism.h"
#include "comm.h"
#include "update.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
CreateBox::CreateBox(LAMMPS *lmp) : Pointers(lmp) {}
/* ---------------------------------------------------------------------- */
void CreateBox::command(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal create_box command");
if (domain->box_exist)
error->all(FLERR,"Cannot create_box after simulation box is defined");
if (domain->dimension == 2 && domain->zperiodic == 0)
error->all(FLERR,"Cannot run 2d simulation with nonperiodic Z dimension");
domain->box_exist = 1;
// region check
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all(FLERR,"Create_box region ID does not exist");
if (domain->regions[iregion]->bboxflag == 0)
error->all(FLERR,"Create_box region does not support a bounding box");
// if region not prism:
// setup orthogonal domain
// set simulation domain from region extent
// if region is prism:
// seutp triclinic domain
// set simulation domain params from prism params
if (strcmp(domain->regions[iregion]->style,"prism") != 0) {
domain->triclinic = 0;
domain->boxlo[0] = domain->regions[iregion]->extent_xlo;
domain->boxhi[0] = domain->regions[iregion]->extent_xhi;
domain->boxlo[1] = domain->regions[iregion]->extent_ylo;
domain->boxhi[1] = domain->regions[iregion]->extent_yhi;
domain->boxlo[2] = domain->regions[iregion]->extent_zlo;
domain->boxhi[2] = domain->regions[iregion]->extent_zhi;
} else {
domain->triclinic = 1;
RegPrism *region = (RegPrism *) domain->regions[iregion];
domain->boxlo[0] = region->xlo;
domain->boxhi[0] = region->xhi;
domain->boxlo[1] = region->ylo;
domain->boxhi[1] = region->yhi;
domain->boxlo[2] = region->zlo;
domain->boxhi[2] = region->zhi;
domain->xy = region->xy;
domain->xz = region->xz;
domain->yz = region->yz;
}
// if molecular, zero out topology info
if (atom->molecular) {
atom->bond_per_atom = 0;
atom->angle_per_atom = 0;
atom->dihedral_per_atom = 0;
atom->improper_per_atom = 0;
atom->nbonds = 0;
atom->nangles = 0;
atom->ndihedrals = 0;
atom->nimpropers = 0;
}
// set atom and topology type quantities
atom->ntypes = atoi(arg[0]);
atom->nbondtypes = 0;
atom->nangletypes = 0;
atom->ndihedraltypes = 0;
atom->nimpropertypes = 0;
// problem setup using info from header
// no call to atom->grow since create_atoms or fixes will do it
update->ntimestep = 0;
atom->allocate_type_arrays();
domain->print_box("Created ");
domain->set_initial_box();
domain->set_global_box();
comm->set_proc_grid();
domain->set_local_box();
}
c4science · Help