698 lines
21 KiB
C++
698 lines
21 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://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 "atom_vec_body.h"
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#include "style_body.h" // IWYU pragma: keep
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#include "atom.h"
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#include "body.h"
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#include "error.h"
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#include "fix.h"
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#include "memory.h"
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#include "modify.h"
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#include "my_pool_chunk.h"
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#include <cstring>
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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 = Atom::ATOMIC;
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bonus_flag = 1;
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// first 3 sizes do not include values from body itself
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// 1st,2nd body counts are added in process_args() via body style
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// 3rd body count is added in size_restart_bonus()
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// size_data_bonus is not used by Atom class for body style
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size_forward_bonus = 4;
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size_border_bonus = 10;
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size_restart_bonus_one = 10;
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size_data_bonus = 0;
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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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atom->radius_flag = 1;
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nlocal_bonus = nghost_bonus = nmax_bonus = 0;
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bonus = nullptr;
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bptr = nullptr;
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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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// strings with peratom variables to include in each AtomVec method
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// strings cannot contain fields in corresponding AtomVec default strings
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// order of fields in a string does not matter
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// except: fields_data_atom & fields_data_vel must match data file
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fields_grow = (char *) "radius rmass angmom torque body";
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fields_copy = (char *) "radius rmass angmom";
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fields_comm = (char *) "";
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fields_comm_vel = (char *) "angmom";
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fields_reverse = (char *) "torque";
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fields_border = (char *) "radius rmass";
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fields_border_vel = (char *) "radius rmass angmom";
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fields_exchange = (char *) "radius rmass angmom";
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fields_restart = (char *) "radius rmass angmom";
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fields_create = (char *) "radius rmass angmom body";
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fields_data_atom = (char *) "id type body rmass x";
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fields_data_vel = (char *) "id v angmom";
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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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// suppress unused parameter warning dependent on style_body.h
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(void)(arg);
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if (narg < 1) error->all(FLERR,"Invalid atom_style body command");
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if (0) bptr = nullptr;
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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,utils::
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check_packages_for_style("body",arg[0],lmp).c_str());
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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 and exchange comm
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// bptr values = max number of additional ivalues/dvalues from Body class
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size_forward_bonus += bptr->size_forward;
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size_border_bonus += bptr->size_border;
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maxexchange = bptr->maxexchange;
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setup_fields();
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}
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/* ----------------------------------------------------------------------
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set local copies of all grow ptrs used by this class, except defaults
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needed in replicate when 2 atom classes exist and it calls pack_restart()
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------------------------------------------------------------------------- */
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void AtomVecBody::grow_pointers()
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{
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body = atom->body;
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rmass = atom->rmass;
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radius = atom->radius;
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angmom = atom->angmom;
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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)
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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_bonus(int i, int j, int delflag)
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{
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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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int k = body[j];
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icp->put(bonus[k].iindex);
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dcp->put(bonus[k].dindex);
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copy_bonus_all(nlocal_bonus-1,k);
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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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}
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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_all(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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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]]->clear_bonus();
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecBody::pack_comm_bonus(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_bonus(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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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecBody::pack_border_bonus(int n, int *list, double *buf)
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{
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int i,j,m;
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double *quat,*inertia;
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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) buf[m++] = ubuf(0).d;
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else {
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buf[m++] = ubuf(1).d;
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quat = bonus[body[j]].quat;
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inertia = bonus[body[j]].inertia;
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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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buf[m++] = inertia[0];
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buf[m++] = inertia[1];
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buf[m++] = inertia[2];
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buf[m++] = ubuf(bonus[body[j]].ninteger).d;
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buf[m++] = ubuf(bonus[body[j]].ndouble).d;
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m += bptr->pack_border_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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int AtomVecBody::unpack_border_bonus(int n, int first, double *buf)
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{
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int i,j,m,last;
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double *quat,*inertia;
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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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body[i] = (int) ubuf(buf[m++]).i;
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if (body[i] == 0) body[i] = -1;
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else {
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j = nlocal_bonus + nghost_bonus;
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if (j == nmax_bonus) grow_bonus();
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quat = bonus[j].quat;
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inertia = bonus[j].inertia;
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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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inertia[0] = buf[m++];
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inertia[1] = buf[m++];
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inertia[2] = buf[m++];
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bonus[j].ninteger = (int) ubuf(buf[m++]).i;
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bonus[j].ndouble = (int) ubuf(buf[m++]).i;
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// corresponding put() calls are in clear_bonus()
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bonus[j].ivalue = icp->get(bonus[j].ninteger,bonus[j].iindex);
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bonus[j].dvalue = dcp->get(bonus[j].ndouble,bonus[j].dindex);
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m += bptr->unpack_border_body(&bonus[j],&buf[m]);
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bonus[j].ilocal = i;
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body[i] = j;
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nghost_bonus++;
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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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pack data for atom I for sending to another proc
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xyz must be 1st 3 values, so comm::exchange() can test on them
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------------------------------------------------------------------------- */
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int AtomVecBody::pack_exchange_bonus(int i, double *buf)
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{
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int m = 0;
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if (body[i] < 0) buf[m++] = ubuf(0).d;
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else {
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buf[m++] = ubuf(1).d;
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int j = body[i];
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double *quat = bonus[j].quat;
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double *inertia = bonus[j].inertia;
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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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buf[m++] = inertia[0];
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buf[m++] = inertia[1];
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buf[m++] = inertia[2];
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buf[m++] = ubuf(bonus[j].ninteger).d;
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buf[m++] = ubuf(bonus[j].ndouble).d;
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memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
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if (intdoubleratio == 1) m += bonus[j].ninteger;
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else m += (bonus[j].ninteger+1)/2;
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memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
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m += bonus[j].ndouble;
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecBody::unpack_exchange_bonus(int ilocal, double *buf)
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{
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int m = 0;
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body[ilocal] = (int) ubuf(buf[m++]).i;
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if (body[ilocal] == 0) body[ilocal] = -1;
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else {
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if (nlocal_bonus == nmax_bonus) grow_bonus();
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double *quat = bonus[nlocal_bonus].quat;
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double *inertia = bonus[nlocal_bonus].inertia;
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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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inertia[0] = buf[m++];
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inertia[1] = buf[m++];
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inertia[2] = buf[m++];
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bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
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bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
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// corresponding put() calls are in copy()
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bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
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bonus[nlocal_bonus].iindex);
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bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
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bonus[nlocal_bonus].dindex);
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memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
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bonus[nlocal_bonus].ninteger*sizeof(int));
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if (intdoubleratio == 1) m += bonus[nlocal_bonus].ninteger;
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else m += (bonus[nlocal_bonus].ninteger+1)/2;
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memcpy(bonus[nlocal_bonus].dvalue,&buf[m],
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bonus[nlocal_bonus].ndouble*sizeof(double));
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m += bonus[nlocal_bonus].ndouble;
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bonus[nlocal_bonus].ilocal = ilocal;
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body[ilocal] = nlocal_bonus++;
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}
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return m;
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}
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/* ----------------------------------------------------------------------
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unpack data for one atom from restart file including bonus data
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------------------------------------------------------------------------- */
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int AtomVecBody::size_restart_bonus()
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{
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int i;
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int n = 0;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++) {
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if (body[i] >= 0) {
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n += size_restart_bonus_one;
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if (intdoubleratio == 1) n += bonus[body[i]].ninteger;
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else n += (bonus[body[i]].ninteger+1)/2;
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n += bonus[body[i]].ndouble;
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} else n++;
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}
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return n;
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}
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/* ----------------------------------------------------------------------
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pack atom I's data for restart file including extra quantities
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xyz must be 1st 3 values, so that read_restart can test on them
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molecular types may be negative, but write as positive
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------------------------------------------------------------------------- */
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int AtomVecBody::pack_restart_bonus(int i, double *buf)
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{
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int m = 0;
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if (body[i] < 0) buf[m++] = ubuf(0).d;
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else {
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buf[m++] = ubuf(1).d;
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int j = body[i];
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double *quat = bonus[j].quat;
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double *inertia = bonus[j].inertia;
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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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buf[m++] = inertia[0];
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buf[m++] = inertia[1];
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buf[m++] = inertia[2];
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buf[m++] = ubuf(bonus[j].ninteger).d;
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buf[m++] = ubuf(bonus[j].ndouble).d;
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memcpy(&buf[m],bonus[j].ivalue,bonus[j].ninteger*sizeof(int));
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if (intdoubleratio == 1) m += bonus[j].ninteger;
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else m += (bonus[j].ninteger+1)/2;
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memcpy(&buf[m],bonus[j].dvalue,bonus[j].ndouble*sizeof(double));
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m += bonus[j].ndouble;
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}
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return m;
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}
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/* ----------------------------------------------------------------------
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unpack data for one atom from restart file including bonus data
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------------------------------------------------------------------------- */
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int AtomVecBody::unpack_restart_bonus(int ilocal, double *buf)
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{
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int m = 0;
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body[ilocal] = (int) ubuf(buf[m++]).i;
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if (body[ilocal] == 0) body[ilocal] = -1;
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else {
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if (nlocal_bonus == nmax_bonus) grow_bonus();
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double *quat = bonus[nlocal_bonus].quat;
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double *inertia = bonus[nlocal_bonus].inertia;
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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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inertia[0] = buf[m++];
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inertia[1] = buf[m++];
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inertia[2] = buf[m++];
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bonus[nlocal_bonus].ninteger = (int) ubuf(buf[m++]).i;
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bonus[nlocal_bonus].ndouble = (int) ubuf(buf[m++]).i;
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bonus[nlocal_bonus].ivalue = icp->get(bonus[nlocal_bonus].ninteger,
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bonus[nlocal_bonus].iindex);
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bonus[nlocal_bonus].dvalue = dcp->get(bonus[nlocal_bonus].ndouble,
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bonus[nlocal_bonus].dindex);
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memcpy(bonus[nlocal_bonus].ivalue,&buf[m],
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bonus[nlocal_bonus].ninteger*sizeof(int));
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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 = ilocal;
|
|
body[ilocal] = nlocal_bonus++;
|
|
}
|
|
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
create one atom of itype at coord
|
|
set other values to defaults
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::create_atom_post(int ilocal)
|
|
{
|
|
radius[ilocal] = 0.5;
|
|
rmass[ilocal] = 1.0;
|
|
body[ilocal] = -1;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
modify what AtomVec::data_atom() just unpacked
|
|
or initialize other atom quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::data_atom_post(int ilocal)
|
|
{
|
|
body_flag = body[ilocal];
|
|
if (body_flag == 0) body_flag = -1;
|
|
else if (body_flag == 1) body_flag = 0;
|
|
else error->one(FLERR,"Invalid body flag in Atoms section of data file");
|
|
body[ilocal] = body_flag;
|
|
|
|
if (rmass[ilocal] <= 0.0)
|
|
error->one(FLERR,"Invalid density in Atoms section of data file");
|
|
|
|
radius[ilocal] = 0.5;
|
|
angmom[ilocal][0] = 0.0;
|
|
angmom[ilocal][1] = 0.0;
|
|
angmom[ilocal][2] = 0.0;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unpack one body from Bodies section of data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::data_body(int m, int ninteger, int ndouble,
|
|
int *ivalues, double *dvalues)
|
|
{
|
|
if (body[m])
|
|
error->one(FLERR,"Assigning body parameters to non-body atom");
|
|
if (nlocal_bonus == nmax_bonus) grow_bonus();
|
|
bonus[nlocal_bonus].ilocal = m;
|
|
bptr->data_body(nlocal_bonus,ninteger,ndouble,ivalues,dvalues);
|
|
body[m] = nlocal_bonus++;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
return # of bytes of allocated memory
|
|
------------------------------------------------------------------------- */
|
|
|
|
double AtomVecBody::memory_usage_bonus()
|
|
{
|
|
double bytes = 0;
|
|
bytes += (double)nmax_bonus*sizeof(Bonus);
|
|
bytes += icp->size() + dcp->size();
|
|
|
|
int nall = nlocal_bonus + nghost_bonus;
|
|
for (int i = 0; i < nall; i++) {
|
|
if (body[i] >= 0) {
|
|
bytes += (double)bonus[body[i]].ninteger * sizeof(int);
|
|
bytes += (double)bonus[body[i]].ndouble * sizeof(double);
|
|
}
|
|
}
|
|
|
|
return bytes;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
modify values for AtomVec::pack_data() to pack
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::pack_data_pre(int ilocal)
|
|
{
|
|
body_flag = body[ilocal];
|
|
|
|
if (body_flag < 0) body[ilocal] = 0;
|
|
else body[ilocal] = 1;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack bonus body info for writing to data file
|
|
if buf is nullptr, just return buffer size
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecBody::pack_data_bonus(double *buf, int /*flag*/)
|
|
{
|
|
int i;
|
|
|
|
tagint *tag = atom->tag;
|
|
int nlocal = atom->nlocal;
|
|
|
|
int m = 0;
|
|
for (i = 0; i < nlocal; i++) {
|
|
if (body[i] < 0) continue;
|
|
int n = bptr->pack_data_body(tag[i],body[i],buf);
|
|
m += n;
|
|
if (buf) buf += n;
|
|
}
|
|
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
write bonus body info to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
|
|
{
|
|
int i = 0;
|
|
while (i < n) {
|
|
i += bptr->write_data_body(fp,&buf[i]);
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unmodify values packed by AtomVec::pack_data()
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::pack_data_post(int ilocal)
|
|
{
|
|
body[ilocal] = body_flag;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
body computes its size based on ivalues/dvalues and returns it
|
|
------------------------------------------------------------------------- */
|
|
|
|
double AtomVecBody::radius_body(int ninteger, int ndouble,
|
|
int *ivalues, double *dvalues)
|
|
{
|
|
return bptr->radius_body(ninteger,ndouble,ivalues,dvalues);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
reset quat orientation for atom M to quat_external
|
|
called by Atom:add_molecule_atom()
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecBody::set_quat(int m, double *quat_external)
|
|
{
|
|
if (body[m] < 0) error->one(FLERR,"Assigning quat to non-body atom");
|
|
double *quat = bonus[body[m]].quat;
|
|
quat[0] = quat_external[0]; quat[1] = quat_external[1];
|
|
quat[2] = quat_external[2]; quat[3] = quat_external[3];
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
debug method for sanity checking of own/bonus data pointers
|
|
------------------------------------------------------------------------- */
|
|
|
|
/*
|
|
void AtomVecBody::check(int flag)
|
|
{
|
|
for (int i = 0; i < atom->nlocal; i++) {
|
|
if (body[i] >= 0 && 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 (body[i] >= 0 &&
|
|
(body[i] < nlocal_bonus ||
|
|
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 (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 (body[bonus[i].ilocal] != i) {
|
|
printf("Proc %d, step %ld, flag %d\n",comm->me,update->ntimestep,flag);
|
|
errorx->one(FLERR,"BAD FFF");
|
|
}
|
|
}
|
|
}
|
|
*/
|