forked from lijiext/lammps
1533 lines
44 KiB
C++
1533 lines
44 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "atom_vec_body.h"
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#include "style_body.h"
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#include "body.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.h"
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#include "modify.h"
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#include "force.h"
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#include "fix.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp)
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{
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molecular = 0;
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// size_forward and size_border set in settings(), via Body class
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comm_x_only = comm_f_only = 0;
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size_forward = 0;
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size_reverse = 6;
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size_border = 0;
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size_velocity = 6;
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size_data_atom = 7;
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size_data_vel = 7;
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xcol_data = 5;
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atom->body_flag = 1;
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atom->rmass_flag = 1;
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atom->angmom_flag = atom->torque_flag = 1;
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nlocal_bonus = nghost_bonus = nmax_bonus = 0;
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bonus = NULL;
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bptr = NULL;
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if (sizeof(double) == sizeof(int)) intdoubleratio = 1;
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else if (sizeof(double) == 2*sizeof(int)) intdoubleratio = 2;
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else error->all(FLERR,"Internal error in atom_style body");
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}
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/* ---------------------------------------------------------------------- */
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AtomVecBody::~AtomVecBody()
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{
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int nall = nlocal_bonus + nghost_bonus;
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for (int i = 0; i < nall; i++) {
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icp->put(bonus[i].iindex);
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dcp->put(bonus[i].dindex);
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}
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memory->sfree(bonus);
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delete bptr;
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}
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/* ----------------------------------------------------------------------
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process additional args
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instantiate Body class
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set size_forward and size_border to max sizes
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------------------------------------------------------------------------- */
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void AtomVecBody::process_args(int narg, char **arg)
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{
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if (narg < 1) error->all(FLERR,"Invalid atom_style body command");
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if (0) bptr = NULL;
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#define BODY_CLASS
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#define BodyStyle(key,Class) \
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else if (strcmp(arg[0],#key) == 0) bptr = new Class(lmp,narg,arg);
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#include "style_body.h"
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#undef BodyStyle
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#undef BODY_CLASS
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else error->all(FLERR,"Unknown body style");
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bptr->avec = this;
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icp = bptr->icp;
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dcp = bptr->dcp;
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// max size of forward/border comm
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// 7,16 are packed in pack_comm/pack_border
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// bptr values = max number of additional ivalues/dvalues from Body class
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size_forward = 7 + bptr->size_forward;
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size_border = 16 + bptr->size_border;
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}
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/* ----------------------------------------------------------------------
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grow atom arrays
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n = 0 grows arrays by a chunk
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n > 0 allocates arrays to size n
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------------------------------------------------------------------------- */
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void AtomVecBody::grow(int n)
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{
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if (n == 0) grow_nmax();
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else nmax = n;
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atom->nmax = nmax;
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if (nmax < 0 || nmax > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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tag = memory->grow(atom->tag,nmax,"atom:tag");
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type = memory->grow(atom->type,nmax,"atom:type");
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mask = memory->grow(atom->mask,nmax,"atom:mask");
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image = memory->grow(atom->image,nmax,"atom:image");
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x = memory->grow(atom->x,nmax,3,"atom:x");
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v = memory->grow(atom->v,nmax,3,"atom:v");
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f = memory->grow(atom->f,nmax*comm->nthreads,3,"atom:f");
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rmass = memory->grow(atom->rmass,nmax,"atom:rmass");
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angmom = memory->grow(atom->angmom,nmax,3,"atom:angmom");
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torque = memory->grow(atom->torque,nmax*comm->nthreads,3,"atom:torque");
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body = memory->grow(atom->body,nmax,"atom:body");
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
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}
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/* ----------------------------------------------------------------------
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reset local array ptrs
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------------------------------------------------------------------------- */
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void AtomVecBody::grow_reset()
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{
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tag = atom->tag; type = atom->type;
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mask = atom->mask; image = atom->image;
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x = atom->x; v = atom->v; f = atom->f;
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rmass = atom->rmass; angmom = atom->angmom; torque = atom->torque;
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body = atom->body;
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}
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/* ----------------------------------------------------------------------
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grow bonus data structure
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------------------------------------------------------------------------- */
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void AtomVecBody::grow_bonus()
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{
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nmax_bonus = grow_nmax_bonus(nmax_bonus);
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if (nmax_bonus < 0 || nmax_bonus > MAXSMALLINT)
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error->one(FLERR,"Per-processor system is too big");
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bonus = (Bonus *) memory->srealloc(bonus,nmax_bonus*sizeof(Bonus),
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"atom:bonus");
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}
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/* ----------------------------------------------------------------------
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copy atom I info to atom J
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if delflag and atom J has bonus data, then delete it
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------------------------------------------------------------------------- */
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void AtomVecBody::copy(int i, int j, int delflag)
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{
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tag[j] = tag[i];
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type[j] = type[i];
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mask[j] = mask[i];
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image[j] = image[i];
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x[j][0] = x[i][0];
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x[j][1] = x[i][1];
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x[j][2] = x[i][2];
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v[j][0] = v[i][0];
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v[j][1] = v[i][1];
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v[j][2] = v[i][2];
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rmass[j] = rmass[i];
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angmom[j][0] = angmom[i][0];
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angmom[j][1] = angmom[i][1];
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angmom[j][2] = angmom[i][2];
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// if deleting atom J via delflag and J has bonus data, then delete it
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if (delflag && body[j] >= 0) {
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icp->put(bonus[body[j]].iindex);
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dcp->put(bonus[body[j]].dindex);
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copy_bonus(nlocal_bonus-1,body[j]);
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nlocal_bonus--;
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}
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// if atom I has bonus data, reset I's bonus.ilocal to loc J
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// do NOT do this if self-copy (I=J) since I's bonus data is already deleted
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if (body[i] >= 0 && i != j) bonus[body[i]].ilocal = j;
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body[j] = body[i];
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j,delflag);
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}
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/* ----------------------------------------------------------------------
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copy bonus data from I to J, effectively deleting the J entry
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also reset body that points to I to now point to J
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------------------------------------------------------------------------- */
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void AtomVecBody::copy_bonus(int i, int j)
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{
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body[bonus[i].ilocal] = j;
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memcpy(&bonus[j],&bonus[i],sizeof(Bonus));
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}
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/* ----------------------------------------------------------------------
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clear ghost info in bonus data
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called before ghosts are recommunicated in comm and irregular
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------------------------------------------------------------------------- */
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void AtomVecBody::clear_bonus()
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{
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int nall = nlocal_bonus + nghost_bonus;
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for (int i = nlocal_bonus; i < nall; i++) {
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icp->put(bonus[i].iindex);
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dcp->put(bonus[i].dindex);
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}
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nghost_bonus = 0;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecBody::pack_comm(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz;
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double *quat;
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m = 0;
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if (pbc_flag == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0];
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buf[m++] = x[j][1];
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buf[m++] = x[j][2];
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if (body[j] >= 0) {
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quat = bonus[body[j]].quat;
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buf[m++] = quat[0];
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buf[m++] = quat[1];
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buf[m++] = quat[2];
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buf[m++] = quat[3];
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m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
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}
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}
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} else {
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if (domain->triclinic == 0) {
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dx = pbc[0]*domain->xprd;
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dy = pbc[1]*domain->yprd;
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dz = pbc[2]*domain->zprd;
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} else {
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dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
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dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
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dz = pbc[2]*domain->zprd;
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}
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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if (body[j] >= 0) {
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quat = bonus[body[j]].quat;
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buf[m++] = quat[0];
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buf[m++] = quat[1];
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buf[m++] = quat[2];
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buf[m++] = quat[3];
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m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
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}
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecBody::pack_comm_vel(int n, int *list, double *buf,
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int pbc_flag, int *pbc)
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{
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int i,j,m;
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double dx,dy,dz,dvx,dvy,dvz;
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double *quat;
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m = 0;
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if (pbc_flag == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0];
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buf[m++] = x[j][1];
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buf[m++] = x[j][2];
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if (body[j] >= 0) {
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quat = bonus[body[j]].quat;
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buf[m++] = quat[0];
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buf[m++] = quat[1];
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buf[m++] = quat[2];
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buf[m++] = quat[3];
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m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
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}
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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buf[m++] = angmom[j][0];
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buf[m++] = angmom[j][1];
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buf[m++] = angmom[j][2];
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}
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} else {
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if (domain->triclinic == 0) {
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dx = pbc[0]*domain->xprd;
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dy = pbc[1]*domain->yprd;
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dz = pbc[2]*domain->zprd;
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} else {
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dx = pbc[0]*domain->xprd + pbc[5]*domain->xy + pbc[4]*domain->xz;
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dy = pbc[1]*domain->yprd + pbc[3]*domain->yz;
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dz = pbc[2]*domain->zprd;
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}
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if (!deform_vremap) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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if (body[j] >= 0) {
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quat = bonus[body[j]].quat;
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buf[m++] = quat[0];
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buf[m++] = quat[1];
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buf[m++] = quat[2];
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buf[m++] = quat[3];
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m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
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}
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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buf[m++] = angmom[j][0];
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buf[m++] = angmom[j][1];
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buf[m++] = angmom[j][2];
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}
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} else {
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dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
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dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
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dvz = pbc[2]*h_rate[2];
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + dx;
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buf[m++] = x[j][1] + dy;
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buf[m++] = x[j][2] + dz;
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if (body[j] >= 0) {
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quat = bonus[body[j]].quat;
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buf[m++] = quat[0];
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buf[m++] = quat[1];
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buf[m++] = quat[2];
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buf[m++] = quat[3];
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m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
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}
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if (mask[i] & deform_groupbit) {
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buf[m++] = v[j][0] + dvx;
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buf[m++] = v[j][1] + dvy;
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buf[m++] = v[j][2] + dvz;
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} else {
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buf[m++] = v[j][0];
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buf[m++] = v[j][1];
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buf[m++] = v[j][2];
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}
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buf[m++] = angmom[j][0];
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buf[m++] = angmom[j][1];
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buf[m++] = angmom[j][2];
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}
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecBody::pack_comm_hybrid(int n, int *list, double *buf)
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{
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int i,j,m;
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double *quat;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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if (body[j] >= 0) {
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quat = bonus[body[j]].quat;
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buf[m++] = quat[0];
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buf[m++] = quat[1];
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buf[m++] = quat[2];
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buf[m++] = quat[3];
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m += bptr->pack_comm_body(&bonus[body[j]],&buf[m]);
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecBody::unpack_comm(int n, int first, double *buf)
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{
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int i,m,last;
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double *quat;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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x[i][0] = buf[m++];
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x[i][1] = buf[m++];
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x[i][2] = buf[m++];
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if (body[i] >= 0) {
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quat = bonus[body[i]].quat;
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quat[0] = buf[m++];
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quat[1] = buf[m++];
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quat[2] = buf[m++];
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quat[3] = buf[m++];
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m += bptr->unpack_comm_body(&bonus[body[i]],&buf[m]);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecBody::unpack_comm_vel(int n, int first, double *buf)
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{
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int i,m,last;
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double *quat;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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x[i][0] = buf[m++];
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x[i][1] = buf[m++];
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x[i][2] = buf[m++];
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if (body[i] >= 0) {
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quat = bonus[body[i]].quat;
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quat[0] = buf[m++];
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quat[1] = buf[m++];
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quat[2] = buf[m++];
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quat[3] = buf[m++];
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m += bptr->unpack_comm_body(&bonus[body[i]],&buf[m]);
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}
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v[i][0] = buf[m++];
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v[i][1] = buf[m++];
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v[i][2] = buf[m++];
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angmom[i][0] = buf[m++];
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angmom[i][1] = buf[m++];
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angmom[i][2] = buf[m++];
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecBody::unpack_comm_hybrid(int n, int first, double *buf)
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{
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int i,m,last;
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double *quat;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++)
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if (body[i] >= 0) {
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quat = bonus[body[i]].quat;
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quat[0] = buf[m++];
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quat[1] = buf[m++];
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quat[2] = buf[m++];
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quat[3] = buf[m++];
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m += bptr->unpack_comm_body(&bonus[body[i]],&buf[m]);
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecBody::pack_reverse(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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buf[m++] = f[i][0];
|
|
buf[m++] = f[i][1];
|
|
buf[m++] = f[i][2];
|
|
buf[m++] = torque[i][0];
|
|
buf[m++] = torque[i][1];
|
|
buf[m++] = torque[i][2];
|
|
}
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::pack_reverse_hybrid(int n, int first, double *buf)
|
|
{
|
|
int i,m,last;
|
|
|
|
m = 0;
|
|
last = first + n;
|
|
for (i = first; i < last; i++) {
|
|
buf[m++] = torque[i][0];
|
|
buf[m++] = torque[i][1];
|
|
buf[m++] = torque[i][2];
|
|
}
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::unpack_reverse(int n, int *list, double *buf)
|
|
{
|
|
int i,j,m;
|
|
|
|
m = 0;
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
f[j][0] += buf[m++];
|
|
f[j][1] += buf[m++];
|
|
f[j][2] += buf[m++];
|
|
torque[j][0] += buf[m++];
|
|
torque[j][1] += buf[m++];
|
|
torque[j][2] += buf[m++];
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::unpack_reverse_hybrid(int n, int *list, double *buf)
|
|
{
|
|
int i,j,m;
|
|
|
|
m = 0;
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
torque[j][0] += buf[m++];
|
|
torque[j][1] += buf[m++];
|
|
torque[j][2] += buf[m++];
|
|
}
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::pack_border(int n, int *list, double *buf,
|
|
int pbc_flag, int *pbc)
|
|
{
|
|
int i,j,m;
|
|
double dx,dy,dz;
|
|
double *quat,*inertia;
|
|
|
|
m = 0;
|
|
if (pbc_flag == 0) {
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
buf[m++] = x[j][0];
|
|
buf[m++] = x[j][1];
|
|
buf[m++] = x[j][2];
|
|
buf[m++] = ubuf(tag[j]).d;
|
|
buf[m++] = ubuf(type[j]).d;
|
|
buf[m++] = ubuf(mask[j]).d;
|
|
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
|
else {
|
|
buf[m++] = ubuf(1).d;
|
|
quat = bonus[body[j]].quat;
|
|
inertia = bonus[body[j]].inertia;
|
|
buf[m++] = quat[0];
|
|
buf[m++] = quat[1];
|
|
buf[m++] = quat[2];
|
|
buf[m++] = quat[3];
|
|
buf[m++] = inertia[0];
|
|
buf[m++] = inertia[1];
|
|
buf[m++] = inertia[2];
|
|
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
|
|
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
|
|
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
|
|
}
|
|
}
|
|
} else {
|
|
if (domain->triclinic == 0) {
|
|
dx = pbc[0]*domain->xprd;
|
|
dy = pbc[1]*domain->yprd;
|
|
dz = pbc[2]*domain->zprd;
|
|
} else {
|
|
dx = pbc[0];
|
|
dy = pbc[1];
|
|
dz = pbc[2];
|
|
}
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
buf[m++] = x[j][0] + dx;
|
|
buf[m++] = x[j][1] + dy;
|
|
buf[m++] = x[j][2] + dz;
|
|
buf[m++] = ubuf(tag[j]).d;
|
|
buf[m++] = ubuf(type[j]).d;
|
|
buf[m++] = ubuf(mask[j]).d;
|
|
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
|
else {
|
|
buf[m++] = ubuf(1).d;
|
|
quat = bonus[body[j]].quat;
|
|
inertia = bonus[body[j]].inertia;
|
|
buf[m++] = quat[0];
|
|
buf[m++] = quat[1];
|
|
buf[m++] = quat[2];
|
|
buf[m++] = quat[3];
|
|
buf[m++] = inertia[0];
|
|
buf[m++] = inertia[1];
|
|
buf[m++] = inertia[2];
|
|
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
|
|
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
|
|
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
|
|
}
|
|
}
|
|
}
|
|
|
|
if (atom->nextra_border)
|
|
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
|
|
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
|
|
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::pack_border_vel(int n, int *list, double *buf,
|
|
int pbc_flag, int *pbc)
|
|
{
|
|
int i,j,m;
|
|
double dx,dy,dz,dvx,dvy,dvz;
|
|
double *quat,*inertia;
|
|
|
|
m = 0;
|
|
if (pbc_flag == 0) {
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
buf[m++] = x[j][0];
|
|
buf[m++] = x[j][1];
|
|
buf[m++] = x[j][2];
|
|
buf[m++] = ubuf(tag[j]).d;
|
|
buf[m++] = ubuf(type[j]).d;
|
|
buf[m++] = ubuf(mask[j]).d;
|
|
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
|
else {
|
|
buf[m++] = ubuf(1).d;
|
|
quat = bonus[body[j]].quat;
|
|
inertia = bonus[body[j]].inertia;
|
|
buf[m++] = quat[0];
|
|
buf[m++] = quat[1];
|
|
buf[m++] = quat[2];
|
|
buf[m++] = quat[3];
|
|
buf[m++] = inertia[0];
|
|
buf[m++] = inertia[1];
|
|
buf[m++] = inertia[2];
|
|
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
|
|
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
|
|
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
|
|
}
|
|
buf[m++] = v[j][0];
|
|
buf[m++] = v[j][1];
|
|
buf[m++] = v[j][2];
|
|
buf[m++] = angmom[j][0];
|
|
buf[m++] = angmom[j][1];
|
|
buf[m++] = angmom[j][2];
|
|
}
|
|
} else {
|
|
if (domain->triclinic == 0) {
|
|
dx = pbc[0]*domain->xprd;
|
|
dy = pbc[1]*domain->yprd;
|
|
dz = pbc[2]*domain->zprd;
|
|
} else {
|
|
dx = pbc[0];
|
|
dy = pbc[1];
|
|
dz = pbc[2];
|
|
}
|
|
if (!deform_vremap) {
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
buf[m++] = x[j][0] + dx;
|
|
buf[m++] = x[j][1] + dy;
|
|
buf[m++] = x[j][2] + dz;
|
|
buf[m++] = ubuf(tag[j]).d;
|
|
buf[m++] = ubuf(type[j]).d;
|
|
buf[m++] = ubuf(mask[j]).d;
|
|
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
|
else {
|
|
buf[m++] = ubuf(1).d;
|
|
quat = bonus[body[j]].quat;
|
|
inertia = bonus[body[j]].inertia;
|
|
buf[m++] = quat[0];
|
|
buf[m++] = quat[1];
|
|
buf[m++] = quat[2];
|
|
buf[m++] = quat[3];
|
|
buf[m++] = inertia[0];
|
|
buf[m++] = inertia[1];
|
|
buf[m++] = inertia[2];
|
|
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
|
|
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
|
|
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
|
|
}
|
|
buf[m++] = v[j][0];
|
|
buf[m++] = v[j][1];
|
|
buf[m++] = v[j][2];
|
|
buf[m++] = angmom[j][0];
|
|
buf[m++] = angmom[j][1];
|
|
buf[m++] = angmom[j][2];
|
|
}
|
|
} else {
|
|
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
|
|
dvy = pbc[1]*h_rate[1] + pbc[3]*h_rate[3];
|
|
dvz = pbc[2]*h_rate[2];
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
buf[m++] = x[j][0] + dx;
|
|
buf[m++] = x[j][1] + dy;
|
|
buf[m++] = x[j][2] + dz;
|
|
buf[m++] = ubuf(tag[j]).d;
|
|
buf[m++] = ubuf(type[j]).d;
|
|
buf[m++] = ubuf(mask[j]).d;
|
|
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
|
else {
|
|
buf[m++] = ubuf(1).d;
|
|
quat = bonus[body[j]].quat;
|
|
inertia = bonus[body[j]].inertia;
|
|
buf[m++] = quat[0];
|
|
buf[m++] = quat[1];
|
|
buf[m++] = quat[2];
|
|
buf[m++] = quat[3];
|
|
buf[m++] = inertia[0];
|
|
buf[m++] = inertia[1];
|
|
buf[m++] = inertia[2];
|
|
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
|
|
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
|
|
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
|
|
}
|
|
if (mask[i] & deform_groupbit) {
|
|
buf[m++] = v[j][0] + dvx;
|
|
buf[m++] = v[j][1] + dvy;
|
|
buf[m++] = v[j][2] + dvz;
|
|
} else {
|
|
buf[m++] = v[j][0];
|
|
buf[m++] = v[j][1];
|
|
buf[m++] = v[j][2];
|
|
}
|
|
buf[m++] = angmom[j][0];
|
|
buf[m++] = angmom[j][1];
|
|
buf[m++] = angmom[j][2];
|
|
}
|
|
}
|
|
}
|
|
|
|
if (atom->nextra_border)
|
|
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
|
|
m += modify->fix[atom->extra_border[iextra]]->pack_border(n,list,&buf[m]);
|
|
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::pack_border_hybrid(int n, int *list, double *buf)
|
|
{
|
|
int i,j,m;
|
|
double *quat,*inertia;
|
|
|
|
m = 0;
|
|
for (i = 0; i < n; i++) {
|
|
j = list[i];
|
|
if (body[j] < 0) buf[m++] = ubuf(0).d;
|
|
else {
|
|
buf[m++] = ubuf(1).d;
|
|
quat = bonus[body[j]].quat;
|
|
inertia = bonus[body[j]].inertia;
|
|
buf[m++] = quat[0];
|
|
buf[m++] = quat[1];
|
|
buf[m++] = quat[2];
|
|
buf[m++] = quat[3];
|
|
buf[m++] = inertia[0];
|
|
buf[m++] = inertia[1];
|
|
buf[m++] = inertia[2];
|
|
buf[m++] = ubuf(bonus[body[j]].ninteger).d;
|
|
buf[m++] = ubuf(bonus[body[j]].ndouble).d;
|
|
m += bptr->pack_border_body(&bonus[body[j]],&buf[m]);
|
|
}
|
|
}
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::unpack_border(int n, int first, double *buf)
|
|
{
|
|
int i,j,m,last;
|
|
double *quat,*inertia;
|
|
|
|
m = 0;
|
|
last = first + n;
|
|
for (i = first; i < last; i++) {
|
|
if (i == nmax) grow(0);
|
|
x[i][0] = buf[m++];
|
|
x[i][1] = buf[m++];
|
|
x[i][2] = buf[m++];
|
|
tag[i] = (tagint) ubuf(buf[m++]).i;
|
|
type[i] = (int) ubuf(buf[m++]).i;
|
|
mask[i] = (int) ubuf(buf[m++]).i;
|
|
body[i] = (int) ubuf(buf[m++]).i;
|
|
if (body[i] == 0) body[i] = -1;
|
|
else {
|
|
j = nlocal_bonus + nghost_bonus;
|
|
if (j == nmax_bonus) grow_bonus();
|
|
quat = bonus[j].quat;
|
|
inertia = bonus[j].inertia;
|
|
quat[0] = buf[m++];
|
|
quat[1] = buf[m++];
|
|
quat[2] = buf[m++];
|
|
quat[3] = buf[m++];
|
|
inertia[0] = buf[m++];
|
|
inertia[1] = buf[m++];
|
|
inertia[2] = buf[m++];
|
|
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
|
|
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
|
|
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
|
|
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
|
|
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
|
|
bonus[j].ilocal = i;
|
|
body[i] = j;
|
|
nghost_bonus++;
|
|
}
|
|
}
|
|
|
|
if (atom->nextra_border)
|
|
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
|
|
m += modify->fix[atom->extra_border[iextra]]->
|
|
unpack_border(n,first,&buf[m]);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::unpack_border_vel(int n, int first, double *buf)
|
|
{
|
|
int i,j,m,last;
|
|
double *quat,*inertia;
|
|
|
|
m = 0;
|
|
last = first + n;
|
|
for (i = first; i < last; i++) {
|
|
if (i == nmax) grow(0);
|
|
x[i][0] = buf[m++];
|
|
x[i][1] = buf[m++];
|
|
x[i][2] = buf[m++];
|
|
tag[i] = (tagint) ubuf(buf[m++]).i;
|
|
type[i] = (int) ubuf(buf[m++]).i;
|
|
mask[i] = (int) ubuf(buf[m++]).i;
|
|
body[i] = (int) ubuf(buf[m++]).i;
|
|
if (body[i] == 0) body[i] = -1;
|
|
else {
|
|
j = nlocal_bonus + nghost_bonus;
|
|
if (j == nmax_bonus) grow_bonus();
|
|
quat = bonus[j].quat;
|
|
inertia = bonus[j].inertia;
|
|
quat[0] = buf[m++];
|
|
quat[1] = buf[m++];
|
|
quat[2] = buf[m++];
|
|
quat[3] = buf[m++];
|
|
inertia[0] = buf[m++];
|
|
inertia[1] = buf[m++];
|
|
inertia[2] = buf[m++];
|
|
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
|
|
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
|
|
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
|
|
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
|
|
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
|
|
bonus[j].ilocal = i;
|
|
body[i] = j;
|
|
nghost_bonus++;
|
|
}
|
|
v[i][0] = buf[m++];
|
|
v[i][1] = buf[m++];
|
|
v[i][2] = buf[m++];
|
|
angmom[i][0] = buf[m++];
|
|
angmom[i][1] = buf[m++];
|
|
angmom[i][2] = buf[m++];
|
|
}
|
|
|
|
if (atom->nextra_border)
|
|
for (int iextra = 0; iextra < atom->nextra_border; iextra++)
|
|
m += modify->fix[atom->extra_border[iextra]]->
|
|
unpack_border(n,first,&buf[m]);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::unpack_border_hybrid(int n, int first, double *buf)
|
|
{
|
|
int i,j,m,last;
|
|
double *quat,*inertia;
|
|
|
|
m = 0;
|
|
last = first + n;
|
|
for (i = first; i < last; i++) {
|
|
body[i] = (int) ubuf(buf[m++]).i;
|
|
if (body[i] == 0) body[i] = -1;
|
|
else {
|
|
j = nlocal_bonus + nghost_bonus;
|
|
if (j == nmax_bonus) grow_bonus();
|
|
quat = bonus[j].quat;
|
|
inertia = bonus[j].inertia;
|
|
quat[0] = buf[m++];
|
|
quat[1] = buf[m++];
|
|
quat[2] = buf[m++];
|
|
quat[3] = buf[m++];
|
|
inertia[0] = buf[m++];
|
|
inertia[1] = buf[m++];
|
|
inertia[2] = buf[m++];
|
|
bonus[j].ninteger = (int) ubuf(buf[m++]).i;
|
|
bonus[j].ndouble = (int) ubuf(buf[m++]).i;
|
|
bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
|
|
bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
|
|
m += bptr->unpack_border_body(&bonus[j],&buf[m]);
|
|
bonus[j].ilocal = i;
|
|
body[i] = j;
|
|
nghost_bonus++;
|
|
}
|
|
}
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack data for atom I for sending to another proc
|
|
xyz must be 1st 3 values, so comm::exchange() can test on them
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::pack_exchange(int i, double *buf)
|
|
{
|
|
int m = 1;
|
|
buf[m++] = x[i][0];
|
|
buf[m++] = x[i][1];
|
|
buf[m++] = x[i][2];
|
|
buf[m++] = v[i][0];
|
|
buf[m++] = v[i][1];
|
|
buf[m++] = v[i][2];
|
|
buf[m++] = ubuf(tag[i]).d;
|
|
buf[m++] = ubuf(type[i]).d;
|
|
buf[m++] = ubuf(mask[i]).d;
|
|
buf[m++] = ubuf(image[i]).d;
|
|
|
|
buf[m++] = rmass[i];
|
|
buf[m++] = angmom[i][0];
|
|
buf[m++] = angmom[i][1];
|
|
buf[m++] = angmom[i][2];
|
|
|
|
if (body[i] < 0) buf[m++] = ubuf(0).d;
|
|
else {
|
|
buf[m++] = ubuf(1).d;
|
|
int j = body[i];
|
|
double *quat = bonus[j].quat;
|
|
double *inertia = bonus[j].inertia;
|
|
buf[m++] = quat[0];
|
|
buf[m++] = quat[1];
|
|
buf[m++] = quat[2];
|
|
buf[m++] = quat[3];
|
|
buf[m++] = inertia[0];
|
|
buf[m++] = inertia[1];
|
|
buf[m++] = inertia[2];
|
|
buf[m++] = ubuf(bonus[j].ninteger).d;
|
|
buf[m++] = ubuf(bonus[j].ndouble).d;
|
|
memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
|
|
if (intdoubleratio == 1) m += bonus[j].ninteger;
|
|
else m += (bonus[j].ninteger+1)/2;
|
|
memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
|
|
m += bonus[j].ndouble;
|
|
}
|
|
|
|
if (atom->nextra_grow)
|
|
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
|
|
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
|
|
|
|
buf[0] = m;
|
|
return m;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::unpack_exchange(double *buf)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
if (nlocal == nmax) grow(0);
|
|
|
|
int m = 1;
|
|
x[nlocal][0] = buf[m++];
|
|
x[nlocal][1] = buf[m++];
|
|
x[nlocal][2] = buf[m++];
|
|
v[nlocal][0] = buf[m++];
|
|
v[nlocal][1] = buf[m++];
|
|
v[nlocal][2] = buf[m++];
|
|
tag[nlocal] = (tagint) ubuf(buf[m++]).i;
|
|
type[nlocal] = (int) ubuf(buf[m++]).i;
|
|
mask[nlocal] = (int) ubuf(buf[m++]).i;
|
|
image[nlocal] = (imageint) ubuf(buf[m++]).i;
|
|
|
|
rmass[nlocal] = buf[m++];
|
|
angmom[nlocal][0] = buf[m++];
|
|
angmom[nlocal][1] = buf[m++];
|
|
angmom[nlocal][2] = buf[m++];
|
|
|
|
body[nlocal] = (int) ubuf(buf[m++]).i;
|
|
if (body[nlocal] == 0) body[nlocal] = -1;
|
|
else {
|
|
if (nlocal_bonus == nmax_bonus) grow_bonus();
|
|
double *quat = bonus[nlocal_bonus].quat;
|
|
double *inertia = bonus[nlocal_bonus].inertia;
|
|
quat[0] = buf[m++];
|
|
quat[1] = buf[m++];
|
|
quat[2] = buf[m++];
|
|
quat[3] = buf[m++];
|
|
inertia[0] = buf[m++];
|
|
inertia[1] = buf[m++];
|
|
inertia[2] = buf[m++];
|
|
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
|
|
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
|
|
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
|
|
bonus[nlocal_bonus].iindex);
|
|
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
|
|
bonus[nlocal_bonus].dindex);
|
|
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
|
|
bonus[nlocal_bonus].ninteger*sizeof(int));
|
|
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
|
|
else m += (bonus[nlocal_bonus].ninteger+1)/2;
|
|
memcpy(bonus[nlocal_bonus].dvalue,&buf[m],
|
|
bonus[nlocal_bonus].ndouble*sizeof(double));
|
|
m += bonus[nlocal_bonus].ndouble;
|
|
|
|
bonus[nlocal_bonus].ilocal = nlocal;
|
|
body[nlocal] = nlocal_bonus++;
|
|
}
|
|
|
|
if (atom->nextra_grow)
|
|
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
|
|
m += modify->fix[atom->extra_grow[iextra]]->
|
|
unpack_exchange(nlocal,&buf[m]);
|
|
|
|
atom->nlocal++;
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
size of restart data for all atoms owned by this proc
|
|
include extra data stored by fixes
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::size_restart()
|
|
{
|
|
int i;
|
|
|
|
int n = 0;
|
|
int nlocal = atom->nlocal;
|
|
for (i = 0; i < nlocal; i++)
|
|
if (body[i] >= 0) {
|
|
n += 25;
|
|
if (intdoubleratio == 1) n += bonus[body[i]].ninteger;
|
|
else n += (bonus[body[i]].ninteger+1)/2;
|
|
n += bonus[body[i]].ndouble;
|
|
} else n += 16;
|
|
|
|
if (atom->nextra_restart)
|
|
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
|
|
for (i = 0; i < nlocal; i++)
|
|
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
|
|
|
|
return n;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack atom I's data for restart file including extra quantities
|
|
xyz must be 1st 3 values, so that read_restart can test on them
|
|
molecular types may be negative, but write as positive
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::pack_restart(int i, double *buf)
|
|
{
|
|
int m = 1;
|
|
buf[m++] = x[i][0];
|
|
buf[m++] = x[i][1];
|
|
buf[m++] = x[i][2];
|
|
buf[m++] = ubuf(tag[i]).d;
|
|
buf[m++] = ubuf(type[i]).d;
|
|
buf[m++] = ubuf(mask[i]).d;
|
|
buf[m++] = ubuf(image[i]).d;
|
|
buf[m++] = v[i][0];
|
|
buf[m++] = v[i][1];
|
|
buf[m++] = v[i][2];
|
|
|
|
buf[m++] = rmass[i];
|
|
buf[m++] = angmom[i][0];
|
|
buf[m++] = angmom[i][1];
|
|
buf[m++] = angmom[i][2];
|
|
|
|
if (body[i] < 0) buf[m++] = ubuf(0).d;
|
|
else {
|
|
buf[m++] = ubuf(1).d;
|
|
int j = body[i];
|
|
double *quat = bonus[j].quat;
|
|
double *inertia = bonus[j].inertia;
|
|
buf[m++] = quat[0];
|
|
buf[m++] = quat[1];
|
|
buf[m++] = quat[2];
|
|
buf[m++] = quat[3];
|
|
buf[m++] = inertia[0];
|
|
buf[m++] = inertia[1];
|
|
buf[m++] = inertia[2];
|
|
buf[m++] = ubuf(bonus[j].ninteger).d;
|
|
buf[m++] = ubuf(bonus[j].ndouble).d;
|
|
memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
|
|
if (intdoubleratio == 1) m += bonus[j].ninteger;
|
|
else m += (bonus[j].ninteger+1)/2;
|
|
memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
|
|
m += bonus[j].ndouble;
|
|
}
|
|
|
|
if (atom->nextra_restart)
|
|
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
|
|
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
|
|
|
|
buf[0] = m;
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack data for one atom from restart file including extra quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::unpack_restart(double *buf)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
if (nlocal == nmax) {
|
|
grow(0);
|
|
if (atom->nextra_store)
|
|
memory->grow(atom->extra,nmax,atom->nextra_store,"atom:extra");
|
|
}
|
|
|
|
int m = 1;
|
|
x[nlocal][0] = buf[m++];
|
|
x[nlocal][1] = buf[m++];
|
|
x[nlocal][2] = buf[m++];
|
|
tag[nlocal] = (tagint) ubuf(buf[m++]).i;
|
|
type[nlocal] = (int) ubuf(buf[m++]).i;
|
|
mask[nlocal] = (int) ubuf(buf[m++]).i;
|
|
image[nlocal] = (imageint) ubuf(buf[m++]).i;
|
|
v[nlocal][0] = buf[m++];
|
|
v[nlocal][1] = buf[m++];
|
|
v[nlocal][2] = buf[m++];
|
|
|
|
rmass[nlocal] = buf[m++];
|
|
angmom[nlocal][0] = buf[m++];
|
|
angmom[nlocal][1] = buf[m++];
|
|
angmom[nlocal][2] = buf[m++];
|
|
|
|
body[nlocal] = (int) ubuf(buf[m++]).i;
|
|
if (body[nlocal] == 0) body[nlocal] = -1;
|
|
else {
|
|
if (nlocal_bonus == nmax_bonus) grow_bonus();
|
|
double *quat = bonus[nlocal_bonus].quat;
|
|
double *inertia = bonus[nlocal_bonus].inertia;
|
|
quat[0] = buf[m++];
|
|
quat[1] = buf[m++];
|
|
quat[2] = buf[m++];
|
|
quat[3] = buf[m++];
|
|
inertia[0] = buf[m++];
|
|
inertia[1] = buf[m++];
|
|
inertia[2] = buf[m++];
|
|
bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
|
|
bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
|
|
bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
|
|
bonus[nlocal_bonus].iindex);
|
|
bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
|
|
bonus[nlocal_bonus].dindex);
|
|
memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
|
|
bonus[nlocal_bonus].ninteger*sizeof(int));
|
|
if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
|
|
else m += (bonus[nlocal_bonus].ninteger+1)/2;
|
|
memcpy(bonus[nlocal_bonus].dvalue,&buf[m],
|
|
bonus[nlocal_bonus].ndouble*sizeof(double));
|
|
m += bonus[nlocal_bonus].ndouble;
|
|
bonus[nlocal_bonus].ilocal = nlocal;
|
|
body[nlocal] = nlocal_bonus++;
|
|
}
|
|
|
|
double **extra = atom->extra;
|
|
if (atom->nextra_store) {
|
|
int size = static_cast<int> (buf[0]) - m;
|
|
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
|
|
}
|
|
|
|
atom->nlocal++;
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
create one atom of itype at coord
|
|
set other values to defaults
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::create_atom(int itype, double *coord)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
if (nlocal == nmax) grow(0);
|
|
|
|
tag[nlocal] = 0;
|
|
type[nlocal] = itype;
|
|
x[nlocal][0] = coord[0];
|
|
x[nlocal][1] = coord[1];
|
|
x[nlocal][2] = coord[2];
|
|
mask[nlocal] = 1;
|
|
image[nlocal] = ((imageint) IMGMAX << IMG2BITS) |
|
|
((imageint) IMGMAX << IMGBITS) | IMGMAX;
|
|
v[nlocal][0] = 0.0;
|
|
v[nlocal][1] = 0.0;
|
|
v[nlocal][2] = 0.0;
|
|
|
|
rmass[nlocal] = 1.0;
|
|
angmom[nlocal][0] = 0.0;
|
|
angmom[nlocal][1] = 0.0;
|
|
angmom[nlocal][2] = 0.0;
|
|
body[nlocal] = -1;
|
|
|
|
atom->nlocal++;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack one line from Atoms section of data file
|
|
initialize other atom quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::data_atom(double *coord, imageint imagetmp, char **values)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
if (nlocal == nmax) grow(0);
|
|
|
|
tag[nlocal] = ATOTAGINT(values[0]);
|
|
type[nlocal] = atoi(values[1]);
|
|
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
|
|
error->one(FLERR,"Invalid atom type in Atoms section of data file");
|
|
|
|
body[nlocal] = atoi(values[2]);
|
|
if (body[nlocal] == 0) body[nlocal] = -1;
|
|
else if (body[nlocal] == 1) body[nlocal] = 0;
|
|
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
|
|
|
|
rmass[nlocal] = atof(values[3]);
|
|
if (rmass[nlocal] <= 0.0)
|
|
error->one(FLERR,"Invalid density in Atoms section of data file");
|
|
|
|
x[nlocal][0] = coord[0];
|
|
x[nlocal][1] = coord[1];
|
|
x[nlocal][2] = coord[2];
|
|
|
|
image[nlocal] = imagetmp;
|
|
|
|
mask[nlocal] = 1;
|
|
v[nlocal][0] = 0.0;
|
|
v[nlocal][1] = 0.0;
|
|
v[nlocal][2] = 0.0;
|
|
angmom[nlocal][0] = 0.0;
|
|
angmom[nlocal][1] = 0.0;
|
|
angmom[nlocal][2] = 0.0;
|
|
|
|
atom->nlocal++;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack hybrid quantities from one line in Atoms section of data file
|
|
initialize other atom quantities for this sub-style
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::data_atom_hybrid(int nlocal, char **values)
|
|
{
|
|
body[nlocal] = atoi(values[0]);
|
|
if (body[nlocal] == 0) body[nlocal] = -1;
|
|
else if (body[nlocal] == 1) body[nlocal] = 0;
|
|
else error->one(FLERR,"Invalid atom type in Atoms section of data file");
|
|
|
|
rmass[nlocal] = atof(values[1]);
|
|
if (rmass[nlocal] <= 0.0)
|
|
error->one(FLERR,"Invalid density in Atoms section of data file");
|
|
|
|
return 2;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack one body from Bodies section of data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::data_body(int m, int ninteger, int ndouble,
|
|
char **ivalues, char **dvalues)
|
|
{
|
|
if (body[m]) error->one(FLERR,"Assigning body parameters to non-body atom");
|
|
if (nlocal_bonus == nmax_bonus) grow_bonus();
|
|
bptr->data_body(nlocal_bonus,ninteger,ndouble,ivalues,dvalues);
|
|
bonus[nlocal_bonus].ilocal = m;
|
|
body[m] = nlocal_bonus++;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack one tri from Velocities section of data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::data_vel(int m, char **values)
|
|
{
|
|
v[m][0] = atof(values[0]);
|
|
v[m][1] = atof(values[1]);
|
|
v[m][2] = atof(values[2]);
|
|
angmom[m][0] = atof(values[3]);
|
|
angmom[m][1] = atof(values[4]);
|
|
angmom[m][2] = atof(values[5]);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack hybrid quantities from one body in Velocities section of data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::data_vel_hybrid(int m, char **values)
|
|
{
|
|
angmom[m][0] = atof(values[0]);
|
|
angmom[m][1] = atof(values[1]);
|
|
angmom[m][2] = atof(values[2]);
|
|
return 3;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack atom info for data file including 3 image flags
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::pack_data(double **buf)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
for (int i = 0; i < nlocal; i++) {
|
|
buf[i][0] = ubuf(tag[i]).d;
|
|
buf[i][1] = ubuf(type[i]).d;
|
|
if (body[i] < 0) buf[i][2] = ubuf(0).d;
|
|
else buf[i][2] = ubuf(1).d;
|
|
buf[i][3] = rmass[i];
|
|
buf[i][4] = x[i][0];
|
|
buf[i][5] = x[i][1];
|
|
buf[i][6] = x[i][2];
|
|
buf[i][7] = ubuf((image[i] & IMGMASK) - IMGMAX).d;
|
|
buf[i][8] = ubuf((image[i] >> IMGBITS & IMGMASK) - IMGMAX).d;
|
|
buf[i][9] = ubuf((image[i] >> IMG2BITS) - IMGMAX).d;
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack hybrid atom info for data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::pack_data_hybrid(int i, double *buf)
|
|
{
|
|
if (body[i] < 0) buf[0] = ubuf(0).d;
|
|
else buf[0] = ubuf(1).d;
|
|
buf[1] = rmass[i];
|
|
return 2;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
write atom info to data file including 3 image flags
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::write_data(FILE *fp, int n, double **buf)
|
|
{
|
|
for (int i = 0; i < n; i++)
|
|
fprintf(fp,TAGINT_FORMAT " %d %d %g %g %g %g %d %d %d\n",
|
|
(tagint) ubuf(buf[i][0]).i,(int) ubuf(buf[i][1]).i,
|
|
(int) ubuf(buf[i][2]).i,
|
|
buf[i][3],buf[i][4],buf[i][5],buf[i][6],
|
|
(int) ubuf(buf[i][7]).i,(int) ubuf(buf[i][8]).i,
|
|
(int) ubuf(buf[i][9]).i);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
write hybrid atom info to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::write_data_hybrid(FILE *fp, double *buf)
|
|
{
|
|
fprintf(fp," %d %g",(int) ubuf(buf[0]).i,buf[1]);
|
|
return 2;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack velocity info for data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::pack_vel(double **buf)
|
|
{
|
|
int nlocal = atom->nlocal;
|
|
for (int i = 0; i < nlocal; i++) {
|
|
buf[i][0] = ubuf(tag[i]).d;
|
|
buf[i][1] = v[i][0];
|
|
buf[i][2] = v[i][1];
|
|
buf[i][3] = v[i][2];
|
|
buf[i][4] = angmom[i][0];
|
|
buf[i][5] = angmom[i][1];
|
|
buf[i][6] = angmom[i][2];
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack hybrid velocity info for data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::pack_vel_hybrid(int i, double *buf)
|
|
{
|
|
buf[0] = angmom[i][0];
|
|
buf[1] = angmom[i][1];
|
|
buf[2] = angmom[i][2];
|
|
return 3;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
write velocity info to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::write_vel(FILE *fp, int n, double **buf)
|
|
{
|
|
for (int i = 0; i < n; i++)
|
|
fprintf(fp,TAGINT_FORMAT " %g %g %g %g %g %g\n",
|
|
(tagint) ubuf(buf[i][0]).i,buf[i][1],buf[i][2],buf[i][3],
|
|
buf[i][4],buf[i][5],buf[i][6]);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
write hybrid velocity info to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::write_vel_hybrid(FILE *fp, double *buf)
|
|
{
|
|
fprintf(fp," %g %g %g",buf[0],buf[1],buf[2]);
|
|
return 3;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
return # of bytes of allocated memory
|
|
------------------------------------------------------------------------- */
|
|
|
|
bigint AtomVecBody::memory_usage()
|
|
{
|
|
bigint bytes = 0;
|
|
|
|
if (atom->memcheck("tag")) bytes += memory->usage(tag,nmax);
|
|
if (atom->memcheck("type")) bytes += memory->usage(type,nmax);
|
|
if (atom->memcheck("mask")) bytes += memory->usage(mask,nmax);
|
|
if (atom->memcheck("image")) bytes += memory->usage(image,nmax);
|
|
if (atom->memcheck("x")) bytes += memory->usage(x,nmax,3);
|
|
if (atom->memcheck("v")) bytes += memory->usage(v,nmax,3);
|
|
if (atom->memcheck("f")) bytes += memory->usage(f,nmax*comm->nthreads,3);
|
|
|
|
if (atom->memcheck("rmass")) bytes += memory->usage(rmass,nmax);
|
|
if (atom->memcheck("angmom")) bytes += memory->usage(angmom,nmax,3);
|
|
if (atom->memcheck("torque")) bytes +=
|
|
memory->usage(torque,nmax*comm->nthreads,3);
|
|
if (atom->memcheck("body")) bytes += memory->usage(body,nmax);
|
|
|
|
bytes += nmax_bonus*sizeof(Bonus);
|
|
bytes += icp->size + dcp->size;
|
|
|
|
int nall = nlocal_bonus + nghost_bonus;
|
|
for (int i = 0; i < nall; i++) {
|
|
bytes += bonus[i].ninteger * sizeof(int);
|
|
bytes += bonus[i].ndouble * sizeof(double);
|
|
}
|
|
|
|
return bytes;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
debug method for sanity checking of own/bonus data pointers
|
|
------------------------------------------------------------------------- */
|
|
|
|
/*
|
|
void AtomVecBody::check(int flag)
|
|
{
|
|
for (int i = 0; i < atom->nlocal; i++) {
|
|
if (atom->body[i] >= 0 && atom->body[i] >= nlocal_bonus) {
|
|
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
|
|
errorx->one(FLERR,"BAD AAA");
|
|
}
|
|
}
|
|
for (int i = atom->nlocal; i < atom->nlocal+atom->nghost; i++) {
|
|
if (atom->body[i] >= 0 &&
|
|
(atom->body[i] < nlocal_bonus ||
|
|
atom->body[i] >= nlocal_bonus+nghost_bonus)) {
|
|
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
|
|
errorx->one(FLERR,"BAD BBB");
|
|
}
|
|
}
|
|
for (int i = 0; i < nlocal_bonus; i++) {
|
|
if (bonus[i].ilocal < 0 || bonus[i].ilocal >= atom->nlocal) {
|
|
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
|
|
errorx->one(FLERR,"BAD CCC");
|
|
}
|
|
}
|
|
for (int i = 0; i < nlocal_bonus; i++) {
|
|
if (atom->body[bonus[i].ilocal] != i) {
|
|
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
|
|
errorx->one(FLERR,"BAD DDD");
|
|
}
|
|
}
|
|
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
|
|
if (bonus[i].ilocal < atom->nlocal ||
|
|
bonus[i].ilocal >= atom->nlocal+atom->nghost) {
|
|
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
|
|
errorx->one(FLERR,"BAD EEE");
|
|
}
|
|
}
|
|
for (int i = nlocal_bonus; i < nlocal_bonus+nghost_bonus; i++) {
|
|
if (atom->body[bonus[i].ilocal] != i) {
|
|
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
|
|
errorx->one(FLERR,"BAD FFF");
|
|
}
|
|
}
|
|
}
|
|
*/
|