154 lines
4.9 KiB
C++
154 lines
4.9 KiB
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.
|
|
------------------------------------------------------------------------- */
|
|
|
|
/* ----------------------------------------------------------------------
|
|
Contributing author: Mike Parks (SNL)
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "atom_vec_peri.h"
|
|
|
|
#include "atom.h"
|
|
#include "citeme.h"
|
|
#include "error.h"
|
|
|
|
#include <cfloat>
|
|
#include <cstring>
|
|
|
|
using namespace LAMMPS_NS;
|
|
|
|
static const char cite_peri_package[] =
|
|
"PERI package for Peridynamics:\n\n"
|
|
"@Article{Parks08,\n"
|
|
" author = {M. L. Parks, R. B. Lehoucq, S. J. Plimpton, S. A. Silling},\n"
|
|
" title = {Implementing peridynamics within a molecular dynamics code},\n"
|
|
" journal = {Comp.~Phys.~Comm.},\n"
|
|
" year = 2008,\n"
|
|
" volume = 179,\n"
|
|
" pages = {777--783}\n"
|
|
"}\n\n";
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
AtomVecPeri::AtomVecPeri(LAMMPS *lmp) : AtomVec(lmp)
|
|
{
|
|
if (lmp->citeme) lmp->citeme->add(cite_peri_package);
|
|
|
|
molecular = 0;
|
|
|
|
atom->rmass_flag = 1;
|
|
atom->peri_flag = 1;
|
|
atom->vfrac_flag = 1;
|
|
|
|
// strings with peratom variables to include in each AtomVec method
|
|
// strings cannot contain fields in corresponding AtomVec default strings
|
|
// order of fields in a string does not matter
|
|
// except: fields_data_atom & fields_data_vel must match data file
|
|
|
|
fields_grow = (char *) "rmass vfrac s0 x0";
|
|
fields_copy = (char *) "rmass vfrac s0 x0";
|
|
fields_comm = (char *) "s0";
|
|
fields_comm_vel = (char *) "s0";
|
|
fields_reverse = (char *) "";
|
|
fields_border = (char *) "rmass vfrac s0 x0";
|
|
fields_border_vel = (char *) "rmass vfrac s0 x0";
|
|
fields_exchange = (char *) "rmass vfrac s0 x0";
|
|
fields_restart = (char *) "rmass vfrac s0 x0";
|
|
fields_create = (char *) "rmass vfrac s0 x0";
|
|
fields_data_atom = (char *) "id type vfrac rmass x";
|
|
fields_data_vel = (char *) "id v";
|
|
|
|
setup_fields();
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set local copies of all grow ptrs used by this class, except defaults
|
|
needed in replicate when 2 atom classes exist and it calls pack_restart()
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecPeri::grow_pointers()
|
|
{
|
|
rmass = atom->rmass;
|
|
vfrac = atom->vfrac;
|
|
s0 = atom->s0;
|
|
x0 = atom->x0;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
initialize non-zero atom quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecPeri::create_atom_post(int ilocal)
|
|
{
|
|
vfrac[ilocal] = 1.0;
|
|
rmass[ilocal] = 1.0;
|
|
s0[ilocal] = DBL_MAX;
|
|
x0[ilocal][0] = x[ilocal][0];
|
|
x0[ilocal][1] = x[ilocal][1];
|
|
x0[ilocal][2] = x[ilocal][2];
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
modify what AtomVec::data_atom() just unpacked
|
|
or initialize other atom quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecPeri::data_atom_post(int ilocal)
|
|
{
|
|
s0[ilocal] = DBL_MAX;
|
|
x0[ilocal][0] = x[ilocal][0];
|
|
x0[ilocal][1] = x[ilocal][1];
|
|
x0[ilocal][2] = x[ilocal][2];
|
|
|
|
if (rmass[ilocal] <= 0.0)
|
|
error->one(FLERR,"Invalid mass in Atoms section of data file");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
assign an index to named atom property and return index
|
|
return -1 if name is unknown to this atom style
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecPeri::property_atom(char *name)
|
|
{
|
|
if (strcmp(name,"vfrac") == 0) return 0;
|
|
if (strcmp(name,"s0") == 0) return 1;
|
|
return -1;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack per-atom data into buf for ComputePropertyAtom
|
|
index maps to data specific to this atom style
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecPeri::pack_property_atom(int index, double *buf,
|
|
int nvalues, int groupbit)
|
|
{
|
|
int *mask = atom->mask;
|
|
int nlocal = atom->nlocal;
|
|
int n = 0;
|
|
|
|
if (index == 0) {
|
|
for (int i = 0; i < nlocal; i++) {
|
|
if (mask[i] & groupbit) buf[n] = vfrac[i];
|
|
else buf[n] = 0.0;
|
|
n += nvalues;
|
|
}
|
|
} else if (index == 1) {
|
|
for (int i = 0; i < nlocal; i++) {
|
|
if (mask[i] & groupbit) buf[n] = s0[i];
|
|
else buf[n] = 0.0;
|
|
n += nvalues;
|
|
}
|
|
}
|
|
}
|