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lammps/src/create_box.cpp
Axel Kohlmeyer 719a64d9dd apply clang-format
2024-10-05 22:25:07 -04:00

272 lines
9.6 KiB
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS development team: developers@lammps.org
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 "create_box.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "lattice.h"
#include "region.h"
#include "region_prism.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
CreateBox::CreateBox(LAMMPS *lmp) : Command(lmp) {}
/* ---------------------------------------------------------------------- */
void CreateBox::command(int narg, char **arg)
{
if (narg < 2) utils::missing_cmd_args(FLERR, "create_box", error);
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
Region *region = nullptr;
int triclinic_general = 0;
if (strcmp(arg[1], "NULL") == 0)
triclinic_general = 1;
else {
region = domain->get_region_by_id(arg[1]);
if (!region) error->all(FLERR, "Create_box region {} does not exist", arg[1]);
if (region->bboxflag == 0)
error->all(FLERR, "Create_box region does not support a bounding box");
region->init();
}
// setup simulation box
// 3 options: orthogonal, restricted triclinic, general triclinic
int iarg = 2;
if (region) {
// region is not prism
// setup orthogonal box
// set simulation domain from region extent
if (strcmp(region->style, "prism") != 0) {
domain->triclinic = 0;
domain->boxlo[0] = region->extent_xlo;
domain->boxhi[0] = region->extent_xhi;
domain->boxlo[1] = region->extent_ylo;
domain->boxhi[1] = region->extent_yhi;
domain->boxlo[2] = region->extent_zlo;
domain->boxhi[2] = region->extent_zhi;
// region is prism
// seutp restricted triclinic box
// set simulation domain from prism params
} else {
domain->triclinic = 1;
auto prism = dynamic_cast<RegPrism *>(region);
domain->boxlo[0] = prism->xlo;
domain->boxhi[0] = prism->xhi;
domain->boxlo[1] = prism->ylo;
domain->boxhi[1] = prism->yhi;
domain->boxlo[2] = prism->zlo;
domain->boxhi[2] = prism->zhi;
domain->xy = prism->xy;
domain->xz = prism->xz;
domain->yz = prism->yz;
}
if (domain->dimension == 2) {
if (domain->boxlo[2] >= 0.0 || domain->boxhi[2] <= 0.0)
error->all(FLERR, "Create_box region zlo/zhi for 2d simulation must straddle 0.0");
}
// setup general triclinic box (with no region)
// read next box extent arguments to create ABC edge vectors + origin
// define_general_triclinic() converts
// ABC edge vectors + origin to restricted triclinic
} else if (triclinic_general) {
if (!domain->lattice->is_general_triclinic())
error->all(FLERR, "Create_box for general triclinic requires triclnic/general lattice");
if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "create_box general triclinic", error);
double alo = utils::numeric(FLERR, arg[iarg + 0], false, lmp);
double ahi = utils::numeric(FLERR, arg[iarg + 1], false, lmp);
double blo = utils::numeric(FLERR, arg[iarg + 2], false, lmp);
double bhi = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
double clo = utils::numeric(FLERR, arg[iarg + 4], false, lmp);
double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp);
iarg += 6;
if (domain->dimension == 2)
if (clo != -0.5 || chi != 0.5)
error->all(FLERR, "Create_box for general triclinic requires clo = -0.5 and chi = 0.5");
// use lattice2box() to generate origin and ABC vectors
// origin = abc lo
// ABC vectors = hi in one dim - origin
double avec[3], bvec[3], cvec[3], origin[3];
double px, py, pz;
px = alo;
py = blo;
pz = clo;
domain->lattice->lattice2box(px, py, pz);
origin[0] = px;
origin[1] = py;
origin[2] = pz;
px = ahi;
py = blo;
pz = clo;
domain->lattice->lattice2box(px, py, pz);
avec[0] = px - origin[0];
avec[1] = py - origin[1];
avec[2] = pz - origin[2];
px = alo;
py = bhi;
pz = clo;
domain->lattice->lattice2box(px, py, pz);
bvec[0] = px - origin[0];
bvec[1] = py - origin[1];
bvec[2] = pz - origin[2];
px = alo;
py = blo;
pz = chi;
domain->lattice->lattice2box(px, py, pz);
cvec[0] = px - origin[0];
cvec[1] = py - origin[1];
cvec[2] = pz - origin[2];
// define general triclinic box within Domain class
domain->define_general_triclinic(avec, bvec, cvec, origin);
}
// if molecular, zero out topology info
if (atom->molecular != Atom::ATOMIC) {
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 = utils::inumeric(FLERR, arg[0], false, lmp);
atom->nbondtypes = 0;
atom->nangletypes = 0;
atom->ndihedraltypes = 0;
atom->nimpropertypes = 0;
// process optional args that can overwrite default settings
while (iarg < narg) {
if (strcmp(arg[iarg], "bond/types") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box bond/type", error);
if (!atom->avec->bonds_allow)
error->all(FLERR, "No bonds allowed with atom style {}", atom->get_style());
atom->nbondtypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "angle/types") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box angle/types", error);
if (!atom->avec->angles_allow)
error->all(FLERR, "No angles allowed with atom style {}", atom->get_style());
atom->nangletypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "dihedral/types") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box dihedral/types", error);
if (!atom->avec->dihedrals_allow)
error->all(FLERR, "No dihedrals allowed with atom style {}", atom->get_style());
atom->ndihedraltypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "improper/types") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box improper/types", error);
if (!atom->avec->impropers_allow)
error->all(FLERR, "No impropers allowed with atom style {}", atom->get_style());
atom->nimpropertypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/bond/per/atom") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/bond/per/atom", error);
if (!atom->avec->bonds_allow)
error->all(FLERR, "No bonds allowed with atom style {}", atom->get_style());
atom->bond_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/angle/per/atom") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/angle/per/atom", error);
if (!atom->avec->angles_allow)
error->all(FLERR, "No angles allowed with atom style {}", atom->get_style());
atom->angle_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/dihedral/per/atom") == 0) {
if (iarg + 2 > narg)
utils::missing_cmd_args(FLERR, "create_box extra/dihedral/per/atom", error);
if (!atom->avec->dihedrals_allow)
error->all(FLERR, "No dihedrals allowed with atom style {}", atom->get_style());
atom->dihedral_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/improper/per/atom") == 0) {
if (iarg + 2 > narg)
utils::missing_cmd_args(FLERR, "create_box extra/improper/per/atom", error);
if (!atom->avec->impropers_allow)
error->all(FLERR, "No impropers allowed with atom style {}", atom->get_style());
atom->improper_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2;
} else if (strcmp(arg[iarg], "extra/special/per/atom") == 0) {
if (iarg + 2 > narg)
utils::missing_cmd_args(FLERR, "create_box extra/special/per/atom", error);
force->special_extra = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
atom->maxspecial += force->special_extra;
iarg += 2;
} else
error->all(FLERR, "Unknown create_box keyword: {}", arg[iarg]);
}
// setup the simulation box and initial system
// deallocate/grow ensures any extra settings are used for topology arrays
// necessary in case no create_atoms is performed
update->ntimestep = 0;
atom->allocate_type_arrays();
atom->deallocate_topology();
atom->avec->grow(1);
domain->print_box("Created ");
domain->set_initial_box();
domain->set_global_box();
comm->set_proc_grid();
domain->set_local_box();
}
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