125 lines
3.9 KiB
C++
125 lines
3.9 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.
|
|
------------------------------------------------------------------------- */
|
|
|
|
#include "atom_vec_mdpd.h"
|
|
#include <cstring>
|
|
#include "atom.h"
|
|
#include "update.h"
|
|
#include "error.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
AtomVecMDPD::AtomVecMDPD(LAMMPS *lmp) : AtomVec(lmp)
|
|
{
|
|
molecular = 0;
|
|
mass_type = 1;
|
|
forceclearflag = 1;
|
|
|
|
atom->rho_flag = 1;
|
|
atom->vest_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 *) "rho drho vest";
|
|
fields_copy = (char *) "rho drho vest";
|
|
fields_comm = (char *) "rho vest";
|
|
fields_comm_vel = (char *) "rho vest";
|
|
fields_reverse = (char *) "drho";
|
|
fields_border = (char *) "rho vest";
|
|
fields_border_vel = (char *) "rho vest";
|
|
fields_exchange = (char *) "rho vest";
|
|
fields_restart = (char * ) "rho vest";
|
|
fields_create = (char *) "rho drho vest";
|
|
fields_data_atom = (char *) "id type rho x";
|
|
fields_data_vel = (char *) "id v";
|
|
|
|
setup_fields();
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AtomVecMDPD::init()
|
|
{
|
|
if (strcmp(update->unit_style,"lj") != 0)
|
|
error->all(FLERR,"Atom style mdpd requires lj units");
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
clear extra forces starting at atom N
|
|
nbytes = # of bytes to clear for a per-atom vector
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecMDPD::force_clear(int n, size_t nbytes)
|
|
{
|
|
memset(&atom->drho[n],0,nbytes);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
modify what AtomVec::data_atom() just unpacked
|
|
or initialize other atom quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecMDPD::data_atom_post(int ilocal)
|
|
{
|
|
atom->drho[ilocal] = 0.0;
|
|
atom->vest[ilocal][0] = 0.0;
|
|
atom->vest[ilocal][1] = 0.0;
|
|
atom->vest[ilocal][2] = 0.0;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
assign an index to named atom property and return index
|
|
return -1 if name is unknown to this atom style
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecMDPD::property_atom(char *name)
|
|
{
|
|
if (strcmp(name,"rho") == 0) return 0;
|
|
if (strcmp(name,"drho") == 0) return 1;
|
|
return -1;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack per-atom data into buf for ComputePropertyAtom
|
|
index maps to data specific to this atom style
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecMDPD::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) {
|
|
double *rho = atom->rho;
|
|
for (int i = 0; i < nlocal; i++) {
|
|
if (mask[i] & groupbit) buf[n] = rho[i];
|
|
else buf[n] = 0.0;
|
|
n += nvalues;
|
|
}
|
|
} else if (index == 1) {
|
|
double *drho = atom->drho;
|
|
for (int i = 0; i < nlocal; i++) {
|
|
if (mask[i] & groupbit) buf[n] = drho[i];
|
|
else buf[n] = 0.0;
|
|
n += nvalues;
|
|
}
|
|
}
|
|
}
|