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changes to start to make atom style hybrid work

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This commit is contained in:
Steve Plimpton
2019-11-26 18:34:51 -07:00
parent 3736af0aaf
commit 6c18e366d7
24 changed files with 586 additions and 1432 deletions
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80
src/atom_vec_sphere.cpp
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@ -19,6 +19,7 @@
#include "fix_adapt.h"
#include "math_const.h"
#include "error.h"
#include "utils.h"
using namespace LAMMPS_NS;
using namespace MathConst;
@ -54,58 +55,61 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
setup_fields();
}
/* ----------------------------------------------------------------------
process sub-style args
optional arg = 0/1 for static/dynamic particle radii
------------------------------------------------------------------------- */
void AtomVecSphere::process_args(int narg, char **arg)
{
if (narg == 0) return;
if (narg != 1) error->all(FLERR,"Illegal atom_style sphere command");
radvary = utils::numeric(FLERR,arg[0],true,lmp);
if (radvary < 0 || radvary > 1)
error->all(FLERR,"Illegal atom_style sphere command");
if (radvary == 0) return;
// dynamic particle radius and mass must be communicated every step
fields_comm = (char *) "radius rmass";
fields_comm_vel = (char *) "radius rmass omega";
}
/* ---------------------------------------------------------------------- */
void AtomVecSphere::init()
{
AtomVec::init();
// set radvary if particle diameters are time-varying due to fix adapt
// NOTE: change this to a atom_style sphere optional arg
radvary = 0;
//comm_x_only = 1;
//size_forward = 3;
// check if optional radvary setting should have been set to 1
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"adapt") == 0) {
FixAdapt *fix = (FixAdapt *) modify->fix[i];
if (fix->diamflag) {
radvary = 1;
comm_x_only = 0;
size_forward = 5;
}
if (fix->diamflag && radvary == 0)
error->all(FLERR,"Fix adapt changes particle radii "
"but atom_style sphere is not dynamic");
}
//fields_comm = (char *) "radius rmass";
//fields_comm_vel = (char *) "radius rmass";
}
/* ----------------------------------------------------------------------
create one atom of itype at coord
modify what default AtomVec::create_atom() just created
initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecSphere::create_atom(int itype, double *coord)
void AtomVecSphere::create_atom_post(int ilocal)
{
AtomVec::create_atom(itype,coord);
int ilocal = atom->nlocal-1;
atom->radius[ilocal] = 0.5;
atom->rmass[ilocal] = 4.0*MY_PI/3.0 * 0.5*0.5*0.5;
}
/* ----------------------------------------------------------------------
unpack one line from Atoms section of data file
modify what default AtomVec::data_atom() just unpacked
modify what AtomVec::data_atom() just unpacked
or initialize other atom quantities
------------------------------------------------------------------------- */
void AtomVecSphere::data_atom(double *coord, imageint imagetmp, char **values)
void AtomVecSphere::data_atom_post(int ilocal)
{
AtomVec::data_atom(coord,imagetmp,values);
int ilocal = atom->nlocal-1;
double radius = 0.5 * atom->radius[ilocal];
atom->radius[ilocal] = radius;
if (radius > 0.0)
@ -115,3 +119,27 @@ void AtomVecSphere::data_atom(double *coord, imageint imagetmp, char **values)
if (atom->rmass[ilocal] <= 0.0)
error->one(FLERR,"Invalid mass in Atoms section of data file");
}
/* ----------------------------------------------------------------------
modify values for AtomVec::pack_data() to pack
------------------------------------------------------------------------- */
void AtomVecSphere::pack_data_pre(int ilocal)
{
radius = atom->radius[ilocal];
rmass = atom->rmass[ilocal];
atom->radius[ilocal] *= 2.0;
if (radius == 0.0)
atom->rmass[ilocal] = rmass / (4.0*MY_PI/3.0 * radius*radius*radius);
}
/* ----------------------------------------------------------------------
unmodify values packed by AtomVec::pack_data()
------------------------------------------------------------------------- */
void AtomVecSphere::pack_data_post(int ilocal)
{
atom->radius[ilocal] = radius;
atom->rmass[ilocal] = rmass;
}