817 lines
24 KiB
C++
817 lines
24 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, 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_tri.h"
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#include "atom.h"
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#include "domain.h"
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#include "error.h"
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#include "fix.h"
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#include "math_const.h"
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#include "math_eigen.h"
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#include "math_extra.h"
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#include "memory.h"
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#include "modify.h"
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#include <cmath>
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using namespace LAMMPS_NS;
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using MathConst::MY_PI;
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static constexpr double EPSILON = 0.001;
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/* ---------------------------------------------------------------------- */
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AtomVecTri::AtomVecTri(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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size_forward_bonus = 4;
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size_border_bonus = 17;
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size_restart_bonus_one = 17;
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size_data_bonus = 10;
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atom->tri_flag = 1;
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atom->molecule_flag = atom->rmass_flag = 1;
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atom->radius_flag = atom->omega_flag = atom->angmom_flag = 1;
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atom->torque_flag = 1;
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atom->sphere_flag = 1;
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nlocal_bonus = nghost_bonus = nmax_bonus = 0;
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bonus = nullptr;
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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 = {"molecule", "radius", "rmass", "omega", "angmom", "torque", "tri"};
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fields_copy = {"molecule", "radius", "rmass", "omega", "angmom"};
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fields_comm_vel = {"omega", "angmom"};
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fields_reverse = {"torque"};
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fields_border = {"molecule", "radius", "rmass"};
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fields_border_vel = {"molecule", "radius", "rmass", "omega"};
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fields_exchange = {"molecule", "radius", "rmass", "omega", "angmom"};
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fields_restart = {"molecule", "radius", "rmass", "omega", "angmom"};
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fields_create = {"molecule", "radius", "rmass", "omega", "angmom", "tri"};
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fields_data_atom = {"id", "molecule", "type", "tri", "rmass", "x"};
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fields_data_vel = {"id", "v", "omega", "angmom"};
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setup_fields();
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}
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/* ---------------------------------------------------------------------- */
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AtomVecTri::~AtomVecTri()
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{
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memory->sfree(bonus);
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecTri::init()
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{
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AtomVec::init();
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if (domain->dimension != 3)
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error->all(FLERR, "Atom_style tri can only be used in 3d simulations");
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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 AtomVecTri::grow_pointers()
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{
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tri = atom->tri;
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radius = atom->radius;
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rmass = atom->rmass;
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omega = atom->omega;
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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 AtomVecTri::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) error->one(FLERR, "Per-processor system is too big");
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bonus = (Bonus *) memory->srealloc(bonus, nmax_bonus * sizeof(Bonus), "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 AtomVecTri::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 && tri[j] >= 0) {
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copy_bonus_all(nlocal_bonus - 1, tri[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 (tri[i] >= 0 && i != j) bonus[tri[i]].ilocal = j;
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tri[j] = tri[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 tri that points to I to now point to J
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------------------------------------------------------------------------- */
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void AtomVecTri::copy_bonus_all(int i, int j)
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{
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tri[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 AtomVecTri::clear_bonus()
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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 AtomVecTri::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 (tri[j] >= 0) {
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quat = bonus[tri[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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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecTri::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 (tri[i] >= 0) {
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quat = bonus[tri[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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}
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecTri::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, *c1, *c2, *c3, *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 (tri[j] < 0)
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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[tri[j]].quat;
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c1 = bonus[tri[j]].c1;
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c2 = bonus[tri[j]].c2;
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c3 = bonus[tri[j]].c3;
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inertia = bonus[tri[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++] = c1[0];
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buf[m++] = c1[1];
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buf[m++] = c1[2];
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buf[m++] = c2[0];
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buf[m++] = c2[1];
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buf[m++] = c2[2];
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buf[m++] = c3[0];
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buf[m++] = c3[1];
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buf[m++] = c3[2];
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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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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecTri::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, *c1, *c2, *c3, *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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tri[i] = (int) ubuf(buf[m++]).i;
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if (tri[i] == 0)
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tri[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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c1 = bonus[j].c1;
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c2 = bonus[j].c2;
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c3 = bonus[j].c3;
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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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c1[0] = buf[m++];
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c1[1] = buf[m++];
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c1[2] = buf[m++];
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c2[0] = buf[m++];
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c2[1] = buf[m++];
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c2[2] = buf[m++];
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c3[0] = buf[m++];
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c3[1] = buf[m++];
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c3[2] = 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].ilocal = i;
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tri[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 AtomVecTri::pack_exchange_bonus(int i, double *buf)
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{
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int m = 0;
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if (tri[i] < 0)
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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 = tri[i];
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double *quat = bonus[j].quat;
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double *c1 = bonus[j].c1;
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double *c2 = bonus[j].c2;
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double *c3 = bonus[j].c3;
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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++] = c1[0];
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buf[m++] = c1[1];
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buf[m++] = c1[2];
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buf[m++] = c2[0];
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buf[m++] = c2[1];
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buf[m++] = c2[2];
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buf[m++] = c3[0];
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buf[m++] = c3[1];
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buf[m++] = c3[2];
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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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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecTri::unpack_exchange_bonus(int ilocal, double *buf)
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{
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int m = 0;
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tri[ilocal] = (int) ubuf(buf[m++]).i;
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if (tri[ilocal] == 0)
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tri[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 *c1 = bonus[nlocal_bonus].c1;
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double *c2 = bonus[nlocal_bonus].c2;
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double *c3 = bonus[nlocal_bonus].c3;
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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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c1[0] = buf[m++];
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c1[1] = buf[m++];
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c1[2] = buf[m++];
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c2[0] = buf[m++];
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c2[1] = buf[m++];
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c2[2] = buf[m++];
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c3[0] = buf[m++];
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c3[1] = buf[m++];
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c3[2] = 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].ilocal = ilocal;
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tri[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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size of restart data for all atoms owned by this proc
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include extra data stored by fixes
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------------------------------------------------------------------------- */
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int AtomVecTri::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 (tri[i] >= 0)
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n += size_restart_bonus_one;
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else
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n++;
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}
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return n;
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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 AtomVecTri::pack_restart_bonus(int i, double *buf)
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{
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int m = 0;
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if (tri[i] < 0)
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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 = tri[i];
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double *quat = bonus[j].quat;
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double *c1 = bonus[j].c1;
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double *c2 = bonus[j].c2;
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double *c3 = bonus[j].c3;
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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++] = c1[0];
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buf[m++] = c1[1];
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buf[m++] = c1[2];
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buf[m++] = c2[0];
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buf[m++] = c2[1];
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buf[m++] = c2[2];
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buf[m++] = c3[0];
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buf[m++] = c3[1];
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buf[m++] = c3[2];
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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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}
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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 AtomVecTri::unpack_restart_bonus(int ilocal, double *buf)
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{
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int m = 0;
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tri[ilocal] = (int) ubuf(buf[m++]).i;
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if (tri[ilocal] == 0)
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tri[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 *c1 = bonus[nlocal_bonus].c1;
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double *c2 = bonus[nlocal_bonus].c2;
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double *c3 = bonus[nlocal_bonus].c3;
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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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c1[0] = buf[m++];
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c1[1] = buf[m++];
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c1[2] = buf[m++];
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c2[0] = buf[m++];
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c2[1] = buf[m++];
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c2[2] = buf[m++];
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c3[0] = buf[m++];
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c3[1] = buf[m++];
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c3[2] = 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].ilocal = ilocal;
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tri[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 one line from Tris section of data file
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------------------------------------------------------------------------- */
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void AtomVecTri::data_atom_bonus(int m, const std::vector<std::string> &values)
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{
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if (tri[m]) error->one(FLERR, "Assigning tri parameters to non-tri atom");
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if (nlocal_bonus == nmax_bonus) grow_bonus();
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double c1[3], c2[3], c3[3];
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int ivalue = 1;
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c1[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
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c1[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
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c1[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
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c2[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
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c2[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
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c2[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
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c3[0] = utils::numeric(FLERR, values[ivalue++], true, lmp);
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c3[1] = utils::numeric(FLERR, values[ivalue++], true, lmp);
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c3[2] = utils::numeric(FLERR, values[ivalue++], true, lmp);
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// check for duplicate points
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if (c1[0] == c2[0] && c1[1] == c2[1] && c1[2] == c2[2])
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error->one(FLERR, "Invalid shape in Triangles section of data file");
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if (c1[0] == c3[0] && c1[1] == c3[1] && c1[2] == c3[2])
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error->one(FLERR, "Invalid shape in Triangles section of data file");
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if (c2[0] == c3[0] && c2[1] == c3[1] && c2[2] == c3[2])
|
|
error->one(FLERR, "Invalid shape in Triangles section of data file");
|
|
|
|
// size = length of one edge
|
|
|
|
double c2mc1[3], c3mc1[3];
|
|
MathExtra::sub3(c2, c1, c2mc1);
|
|
MathExtra::sub3(c3, c1, c3mc1);
|
|
double size = MAX(MathExtra::len3(c2mc1), MathExtra::len3(c3mc1));
|
|
|
|
// centroid = 1/3 of sum of vertices
|
|
|
|
double centroid[3];
|
|
centroid[0] = (c1[0] + c2[0] + c3[0]) / 3.0;
|
|
centroid[1] = (c1[1] + c2[1] + c3[1]) / 3.0;
|
|
centroid[2] = (c1[2] + c2[2] + c3[2]) / 3.0;
|
|
|
|
double dx = centroid[0] - x[m][0];
|
|
double dy = centroid[1] - x[m][1];
|
|
double dz = centroid[2] - x[m][2];
|
|
double delta = sqrt(dx * dx + dy * dy + dz * dz);
|
|
|
|
if (delta / size > EPSILON) error->one(FLERR, "Inconsistent triangle in data file");
|
|
|
|
x[m][0] = centroid[0];
|
|
x[m][1] = centroid[1];
|
|
x[m][2] = centroid[2];
|
|
|
|
// reset tri radius and mass
|
|
// rmass currently holds density
|
|
// tri area = 0.5 len(U x V), where U,V are edge vectors from one vertex
|
|
|
|
double c4[3];
|
|
MathExtra::sub3(c1, centroid, c4);
|
|
radius[m] = MathExtra::lensq3(c4);
|
|
MathExtra::sub3(c2, centroid, c4);
|
|
radius[m] = MAX(radius[m], MathExtra::lensq3(c4));
|
|
MathExtra::sub3(c3, centroid, c4);
|
|
radius[m] = MAX(radius[m], MathExtra::lensq3(c4));
|
|
radius[m] = sqrt(radius[m]);
|
|
|
|
double norm[3];
|
|
MathExtra::cross3(c2mc1, c3mc1, norm);
|
|
double area = 0.5 * MathExtra::len3(norm);
|
|
rmass[m] *= area;
|
|
|
|
// inertia = inertia tensor of triangle as 6-vector in Voigt ordering
|
|
|
|
double inertia[6];
|
|
MathExtra::inertia_triangle(c1, c2, c3, rmass[m], inertia);
|
|
|
|
// diagonalize inertia tensor via Jacobi rotations
|
|
// bonus[].inertia = 3 eigenvalues = principal moments of inertia
|
|
// evectors and exzy_space = 3 evectors = principal axes of triangle
|
|
|
|
double tensor[3][3], evectors[3][3];
|
|
tensor[0][0] = inertia[0];
|
|
tensor[1][1] = inertia[1];
|
|
tensor[2][2] = inertia[2];
|
|
tensor[1][2] = tensor[2][1] = inertia[3];
|
|
tensor[0][2] = tensor[2][0] = inertia[4];
|
|
tensor[0][1] = tensor[1][0] = inertia[5];
|
|
|
|
int ierror = MathEigen::jacobi3(tensor, bonus[nlocal_bonus].inertia, evectors);
|
|
if (ierror) error->one(FLERR, "Insufficient Jacobi rotations for triangle");
|
|
|
|
double ex_space[3], ey_space[3], ez_space[3];
|
|
ex_space[0] = evectors[0][0];
|
|
ex_space[1] = evectors[1][0];
|
|
ex_space[2] = evectors[2][0];
|
|
ey_space[0] = evectors[0][1];
|
|
ey_space[1] = evectors[1][1];
|
|
ey_space[2] = evectors[2][1];
|
|
ez_space[0] = evectors[0][2];
|
|
ez_space[1] = evectors[1][2];
|
|
ez_space[2] = evectors[2][2];
|
|
|
|
// enforce 3 orthogonal vectors as a right-handed coordinate system
|
|
// flip 3rd vector if needed
|
|
|
|
MathExtra::cross3(ex_space, ey_space, norm);
|
|
if (MathExtra::dot3(norm, ez_space) < 0.0) MathExtra::negate3(ez_space);
|
|
|
|
// create initial quaternion
|
|
|
|
MathExtra::exyz_to_q(ex_space, ey_space, ez_space, bonus[nlocal_bonus].quat);
|
|
|
|
// bonus c1,c2,c3 = displacement of c1,c2,c3 from centroid
|
|
// in basis of principal axes
|
|
|
|
double disp[3];
|
|
MathExtra::sub3(c1, centroid, disp);
|
|
MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c1);
|
|
MathExtra::sub3(c2, centroid, disp);
|
|
MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c2);
|
|
MathExtra::sub3(c3, centroid, disp);
|
|
MathExtra::transpose_matvec(ex_space, ey_space, ez_space, disp, bonus[nlocal_bonus].c3);
|
|
|
|
bonus[nlocal_bonus].ilocal = m;
|
|
tri[m] = nlocal_bonus++;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
return # of bytes of allocated bonus memory
|
|
------------------------------------------------------------------------- */
|
|
|
|
double AtomVecTri::memory_usage_bonus()
|
|
{
|
|
double bytes = 0;
|
|
bytes += (double) nmax_bonus * sizeof(Bonus);
|
|
return bytes;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
create one atom of itype at coord
|
|
set other values to defaults
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecTri::create_atom_post(int ilocal)
|
|
{
|
|
double radius_one = 0.5;
|
|
radius[ilocal] = radius_one;
|
|
rmass[ilocal] = 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
|
|
tri[ilocal] = -1;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
modify what AtomVec::data_atom() just unpacked
|
|
or initialize other atom quantities
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecTri::data_atom_post(int ilocal)
|
|
{
|
|
tri_flag = tri[ilocal];
|
|
if (tri_flag == 0)
|
|
tri_flag = -1;
|
|
else if (tri_flag == 1)
|
|
tri_flag = 0;
|
|
else
|
|
error->one(FLERR, "Invalid tri flag in Atoms section of data file");
|
|
tri[ilocal] = tri_flag;
|
|
|
|
if (rmass[ilocal] <= 0.0) error->one(FLERR, "Invalid density in Atoms section of data file");
|
|
|
|
if (tri_flag < 0) {
|
|
double radius_one = 0.5;
|
|
radius[ilocal] = radius_one;
|
|
rmass[ilocal] *= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
|
|
} else
|
|
radius[ilocal] = 0.0;
|
|
|
|
omega[ilocal][0] = 0.0;
|
|
omega[ilocal][1] = 0.0;
|
|
omega[ilocal][2] = 0.0;
|
|
angmom[ilocal][0] = 0.0;
|
|
angmom[ilocal][1] = 0.0;
|
|
angmom[ilocal][2] = 0.0;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
modify values for AtomVec::pack_data() to pack
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecTri::pack_data_pre(int ilocal)
|
|
{
|
|
tri_flag = tri[ilocal];
|
|
rmass_one = rmass[ilocal];
|
|
|
|
if (tri_flag < 0)
|
|
tri[ilocal] = 0;
|
|
else
|
|
tri[ilocal] = 1;
|
|
|
|
if (tri_flag < 0) {
|
|
double radius_one = radius[ilocal];
|
|
rmass[ilocal] /= 4.0 * MY_PI / 3.0 * radius_one * radius_one * radius_one;
|
|
} else {
|
|
double c2mc1[3], c3mc1[3], norm[3];
|
|
MathExtra::sub3(bonus[tri_flag].c2, bonus[tri_flag].c1, c2mc1);
|
|
MathExtra::sub3(bonus[tri_flag].c3, bonus[tri_flag].c1, c3mc1);
|
|
MathExtra::cross3(c2mc1, c3mc1, norm);
|
|
double area = 0.5 * MathExtra::len3(norm);
|
|
rmass[ilocal] /= area;
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
unmodify values packed by AtomVec::pack_data()
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecTri::pack_data_post(int ilocal)
|
|
{
|
|
tri[ilocal] = tri_flag;
|
|
rmass[ilocal] = rmass_one;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
pack bonus tri info for writing to data file
|
|
if buf is nullptr, just return buffer size
|
|
------------------------------------------------------------------------- */
|
|
|
|
int AtomVecTri::pack_data_bonus(double *buf, int /*flag*/)
|
|
{
|
|
int i, j;
|
|
double xc, yc, zc;
|
|
double dc1[3], dc2[3], dc3[3];
|
|
double p[3][3];
|
|
|
|
double **x = atom->x;
|
|
tagint *tag = atom->tag;
|
|
int nlocal = atom->nlocal;
|
|
|
|
int m = 0;
|
|
for (i = 0; i < nlocal; i++) {
|
|
if (tri[i] < 0) continue;
|
|
if (buf) {
|
|
buf[m++] = ubuf(tag[i]).d;
|
|
j = tri[i];
|
|
MathExtra::quat_to_mat(bonus[j].quat, p);
|
|
MathExtra::matvec(p, bonus[j].c1, dc1);
|
|
MathExtra::matvec(p, bonus[j].c2, dc2);
|
|
MathExtra::matvec(p, bonus[j].c3, dc3);
|
|
xc = x[i][0];
|
|
yc = x[i][1];
|
|
zc = x[i][2];
|
|
buf[m++] = xc + dc1[0];
|
|
buf[m++] = yc + dc1[1];
|
|
buf[m++] = zc + dc1[2];
|
|
buf[m++] = xc + dc2[0];
|
|
buf[m++] = yc + dc2[1];
|
|
buf[m++] = zc + dc2[2];
|
|
buf[m++] = xc + dc3[0];
|
|
buf[m++] = yc + dc3[1];
|
|
buf[m++] = zc + dc3[2];
|
|
} else
|
|
m += size_data_bonus;
|
|
}
|
|
return m;
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
write bonus tri info to data file
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecTri::write_data_bonus(FILE *fp, int n, double *buf, int /*flag*/)
|
|
{
|
|
int i = 0;
|
|
while (i < n) {
|
|
fmt::print(fp, "{} {} {} {} {} {} {} {} {} {}\n", ubuf(buf[i]).i, buf[i + 1], buf[i + 2],
|
|
buf[i + 3], buf[i + 4], buf[i + 5], buf[i + 6], buf[i + 7], buf[i + 8], buf[i + 9]);
|
|
i += size_data_bonus;
|
|
}
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
set equilateral tri of size in bonus data for particle I
|
|
oriented symmetrically in xy plane
|
|
this may create or delete entry in bonus data
|
|
------------------------------------------------------------------------- */
|
|
|
|
void AtomVecTri::set_equilateral(int i, double size)
|
|
{
|
|
// also set radius = distance from center to corner-pt = len(c1)
|
|
// unless size = 0.0, then set diameter = 1.0
|
|
|
|
if (tri[i] < 0) {
|
|
if (size == 0.0) return;
|
|
if (nlocal_bonus == nmax_bonus) grow_bonus();
|
|
double *quat = bonus[nlocal_bonus].quat;
|
|
double *c1 = bonus[nlocal_bonus].c1;
|
|
double *c2 = bonus[nlocal_bonus].c2;
|
|
double *c3 = bonus[nlocal_bonus].c3;
|
|
double *inertia = bonus[nlocal_bonus].inertia;
|
|
quat[0] = 1.0;
|
|
quat[1] = 0.0;
|
|
quat[2] = 0.0;
|
|
quat[3] = 0.0;
|
|
c1[0] = -size / 2.0;
|
|
c1[1] = -sqrt(3.0) / 2.0 * size / 3.0;
|
|
c1[2] = 0.0;
|
|
c2[0] = size / 2.0;
|
|
c2[1] = -sqrt(3.0) / 2.0 * size / 3.0;
|
|
c2[2] = 0.0;
|
|
c3[0] = 0.0;
|
|
c3[1] = sqrt(3.0) / 2.0 * size * 2.0 / 3.0;
|
|
c3[2] = 0.0;
|
|
inertia[0] = sqrt(3.0) / 96.0 * size * size * size * size;
|
|
inertia[1] = sqrt(3.0) / 96.0 * size * size * size * size;
|
|
inertia[2] = sqrt(3.0) / 48.0 * size * size * size * size;
|
|
radius[i] = MathExtra::len3(c1);
|
|
bonus[nlocal_bonus].ilocal = i;
|
|
tri[i] = nlocal_bonus++;
|
|
} else if (size == 0.0) {
|
|
radius[i] = 0.5;
|
|
copy_bonus_all(nlocal_bonus - 1, tri[i]);
|
|
nlocal_bonus--;
|
|
tri[i] = -1;
|
|
} else {
|
|
double *c1 = bonus[tri[i]].c1;
|
|
double *c2 = bonus[tri[i]].c2;
|
|
double *c3 = bonus[tri[i]].c3;
|
|
double *inertia = bonus[tri[i]].inertia;
|
|
c1[0] = -size / 2.0;
|
|
c1[1] = -sqrt(3.0) / 2.0 * size / 3.0;
|
|
c1[2] = 0.0;
|
|
c2[0] = size / 2.0;
|
|
c2[1] = -sqrt(3.0) / 2.0 * size / 3.0;
|
|
c2[2] = 0.0;
|
|
c3[0] = 0.0;
|
|
c3[1] = sqrt(3.0) / 2.0 * size * 2.0 / 3.0;
|
|
c3[2] = 0.0;
|
|
inertia[0] = sqrt(3.0) / 96.0 * size * size * size * size;
|
|
inertia[1] = sqrt(3.0) / 96.0 * size * size * size * size;
|
|
inertia[2] = sqrt(3.0) / 48.0 * size * size * size * size;
|
|
radius[i] = MathExtra::len3(c1);
|
|
}
|
|
}
|