537 lines
16 KiB
C++
537 lines
16 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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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 "angle.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.h"
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#include "math_const.h"
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#include "suffix.h"
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#include "atom_masks.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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using namespace MathConst;
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#define FOURTH 0.25
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/* ---------------------------------------------------------------------- */
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Angle::Angle(LAMMPS *lmp) : Pointers(lmp)
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{
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energy = 0.0;
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virial[0] = virial[1] = virial[2] = virial[3] = virial[4] = virial[5] = 0.0;
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writedata = 1;
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allocated = 0;
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suffix_flag = Suffix::NONE;
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maxeatom = maxvatom = maxcvatom = 0;
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eatom = nullptr;
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vatom = nullptr;
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cvatom = nullptr;
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setflag = nullptr;
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centroidstressflag = CENTROID_AVAIL;
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execution_space = Host;
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datamask_read = ALL_MASK;
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datamask_modify = ALL_MASK;
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copymode = 0;
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}
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/* ---------------------------------------------------------------------- */
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Angle::~Angle()
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{
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if (copymode) return;
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memory->destroy(eatom);
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memory->destroy(vatom);
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memory->destroy(cvatom);
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}
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/* ----------------------------------------------------------------------
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check if all coeffs are set
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------------------------------------------------------------------------- */
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void Angle::init()
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{
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if (!allocated && atom->nangletypes)
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error->all(FLERR,"Angle coeffs are not set");
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for (int i = 1; i <= atom->nangletypes; i++)
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if (setflag[i] == 0) error->all(FLERR,"All angle coeffs are not set");
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init_style();
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}
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/* ----------------------------------------------------------------------
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setup for energy, virial computation
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see integrate::ev_set() for bitwise settings of eflag/vflag
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set the following flags, values are otherwise set to 0:
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evflag != 0 if any bits of eflag or vflag are set
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eflag_global != 0 if ENERGY_GLOBAL bit of eflag set
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eflag_atom != 0 if ENERGY_ATOM bit of eflag set
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eflag_either != 0 if eflag_global or eflag_atom is set
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vflag_global != 0 if VIRIAL_PAIR or VIRIAL_FDOTR bit of vflag set
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vflag_atom != 0 if VIRIAL_ATOM bit of vflag set
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vflag_atom != 0 if VIRIAL_CENTROID bit of vflag set
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and centroidstressflag != CENTROID_AVAIL
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cvflag_atom != 0 if VIRIAL_CENTROID bit of vflag set
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and centroidstressflag = CENTROID_AVAIL
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vflag_either != 0 if any of vflag_global, vflag_atom, cvflag_atom is set
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------------------------------------------------------------------------- */
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void Angle::ev_setup(int eflag, int vflag, int alloc)
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{
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int i,n;
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evflag = 1;
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eflag_either = eflag;
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eflag_global = eflag & ENERGY_GLOBAL;
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eflag_atom = eflag & ENERGY_ATOM;
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vflag_global = vflag & (VIRIAL_PAIR | VIRIAL_FDOTR);
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vflag_atom = vflag & VIRIAL_ATOM;
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if (vflag & VIRIAL_CENTROID && centroidstressflag != CENTROID_AVAIL)
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vflag_atom = 1;
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cvflag_atom = 0;
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if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL)
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cvflag_atom = 1;
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vflag_either = vflag_global || vflag_atom || cvflag_atom;
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// reallocate per-atom arrays if necessary
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if (eflag_atom && atom->nmax > maxeatom) {
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maxeatom = atom->nmax;
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if (alloc) {
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memory->destroy(eatom);
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memory->create(eatom,comm->nthreads*maxeatom,"angle:eatom");
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}
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}
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if (vflag_atom && atom->nmax > maxvatom) {
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maxvatom = atom->nmax;
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if (alloc) {
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memory->destroy(vatom);
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memory->create(vatom,comm->nthreads*maxvatom,6,"angle:vatom");
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}
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}
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if (cvflag_atom && atom->nmax > maxcvatom) {
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maxcvatom = atom->nmax;
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if (alloc) {
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memory->destroy(cvatom);
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memory->create(cvatom,comm->nthreads*maxcvatom,9,"angle:cvatom");
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}
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}
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// zero accumulators
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if (eflag_global) energy = 0.0;
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if (vflag_global) for (i = 0; i < 6; i++) virial[i] = 0.0;
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if (eflag_atom && alloc) {
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n = atom->nlocal;
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if (force->newton_bond) n += atom->nghost;
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for (i = 0; i < n; i++) eatom[i] = 0.0;
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}
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if (vflag_atom && alloc) {
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n = atom->nlocal;
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if (force->newton_bond) n += atom->nghost;
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for (i = 0; i < n; i++) {
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vatom[i][0] = 0.0;
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vatom[i][1] = 0.0;
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vatom[i][2] = 0.0;
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vatom[i][3] = 0.0;
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vatom[i][4] = 0.0;
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vatom[i][5] = 0.0;
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}
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}
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if (cvflag_atom && alloc) {
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n = atom->nlocal;
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if (force->newton_bond) n += atom->nghost;
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for (i = 0; i < n; i++) {
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cvatom[i][0] = 0.0;
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cvatom[i][1] = 0.0;
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cvatom[i][2] = 0.0;
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cvatom[i][3] = 0.0;
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cvatom[i][4] = 0.0;
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cvatom[i][5] = 0.0;
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cvatom[i][6] = 0.0;
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cvatom[i][7] = 0.0;
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cvatom[i][8] = 0.0;
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cvatom[i][9] = 0.0;
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}
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}
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}
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/* ----------------------------------------------------------------------
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tally energy and virial into global and per-atom accumulators
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virial = r1F1 + r2F2 + r3F3 = (r1-r2) F1 + (r3-r2) F3 = del1*f1 + del2*f3
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called by standard 3-body angles
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------------------------------------------------------------------------- */
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void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
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double eangle, double *f1, double *f3,
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double delx1, double dely1, double delz1,
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double delx2, double dely2, double delz2)
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{
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double eanglethird,v[6];
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if (eflag_either) {
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if (eflag_global) {
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if (newton_bond) energy += eangle;
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else {
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eanglethird = THIRD*eangle;
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if (i < nlocal) energy += eanglethird;
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if (j < nlocal) energy += eanglethird;
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if (k < nlocal) energy += eanglethird;
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}
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}
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if (eflag_atom) {
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eanglethird = THIRD*eangle;
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if (newton_bond || i < nlocal) eatom[i] += eanglethird;
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if (newton_bond || j < nlocal) eatom[j] += eanglethird;
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if (newton_bond || k < nlocal) eatom[k] += eanglethird;
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}
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}
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if (vflag_either) {
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v[0] = delx1*f1[0] + delx2*f3[0];
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v[1] = dely1*f1[1] + dely2*f3[1];
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v[2] = delz1*f1[2] + delz2*f3[2];
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v[3] = delx1*f1[1] + delx2*f3[1];
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v[4] = delx1*f1[2] + delx2*f3[2];
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v[5] = dely1*f1[2] + dely2*f3[2];
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if (vflag_global) {
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if (newton_bond) {
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virial[0] += v[0];
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virial[1] += v[1];
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virial[2] += v[2];
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virial[3] += v[3];
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virial[4] += v[4];
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virial[5] += v[5];
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} else {
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double prefactor = 0.0;
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if (i < nlocal) prefactor += 1.0;
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if (j < nlocal) prefactor += 1.0;
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if (k < nlocal) prefactor += 1.0;
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virial[0] += prefactor*THIRD*v[0];
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virial[1] += prefactor*THIRD*v[1];
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virial[2] += prefactor*THIRD*v[2];
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virial[3] += prefactor*THIRD*v[3];
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virial[4] += prefactor*THIRD*v[4];
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virial[5] += prefactor*THIRD*v[5];
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}
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}
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if (vflag_atom) {
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if (newton_bond || i < nlocal) {
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vatom[i][0] += THIRD*v[0];
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vatom[i][1] += THIRD*v[1];
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vatom[i][2] += THIRD*v[2];
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vatom[i][3] += THIRD*v[3];
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vatom[i][4] += THIRD*v[4];
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vatom[i][5] += THIRD*v[5];
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}
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if (newton_bond || j < nlocal) {
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vatom[j][0] += THIRD*v[0];
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vatom[j][1] += THIRD*v[1];
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vatom[j][2] += THIRD*v[2];
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vatom[j][3] += THIRD*v[3];
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vatom[j][4] += THIRD*v[4];
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vatom[j][5] += THIRD*v[5];
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}
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if (newton_bond || k < nlocal) {
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vatom[k][0] += THIRD*v[0];
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vatom[k][1] += THIRD*v[1];
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vatom[k][2] += THIRD*v[2];
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vatom[k][3] += THIRD*v[3];
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vatom[k][4] += THIRD*v[4];
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vatom[k][5] += THIRD*v[5];
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}
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}
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}
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// per-atom centroid virial
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if (cvflag_atom) {
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// r0 = (r1+r2+r3)/3
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// rij = ri-rj
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// total virial = r10*f1 + r20*f2 + r30*f3
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// del1: r12
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// del2: r32
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if (newton_bond || i < nlocal) {
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double a1[3];
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// a1 = r10 = (2*r12 - r32)/3
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a1[0] = THIRD*(2*delx1-delx2);
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a1[1] = THIRD*(2*dely1-dely2);
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a1[2] = THIRD*(2*delz1-delz2);
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cvatom[i][0] += a1[0]*f1[0];
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cvatom[i][1] += a1[1]*f1[1];
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cvatom[i][2] += a1[2]*f1[2];
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cvatom[i][3] += a1[0]*f1[1];
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cvatom[i][4] += a1[0]*f1[2];
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cvatom[i][5] += a1[1]*f1[2];
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cvatom[i][6] += a1[1]*f1[0];
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cvatom[i][7] += a1[2]*f1[0];
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cvatom[i][8] += a1[2]*f1[1];
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}
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if (newton_bond || j < nlocal) {
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double a2[3];
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double f2[3];
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// a2 = r20 = ( -r12 - r32)/3
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a2[0] = THIRD*(-delx1-delx2);
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a2[1] = THIRD*(-dely1-dely2);
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a2[2] = THIRD*(-delz1-delz2);
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f2[0] = - f1[0] - f3[0];
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f2[1] = - f1[1] - f3[1];
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f2[2] = - f1[2] - f3[2];
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cvatom[j][0] += a2[0]*f2[0];
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cvatom[j][1] += a2[1]*f2[1];
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cvatom[j][2] += a2[2]*f2[2];
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cvatom[j][3] += a2[0]*f2[1];
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cvatom[j][4] += a2[0]*f2[2];
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cvatom[j][5] += a2[1]*f2[2];
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cvatom[j][6] += a2[1]*f2[0];
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cvatom[j][7] += a2[2]*f2[0];
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cvatom[j][8] += a2[2]*f2[1];
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}
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if (newton_bond || k < nlocal) {
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double a3[3];
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// a3 = r30 = ( -r12 + 2*r32)/3
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a3[0] = THIRD*(-delx1+2*delx2);
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a3[1] = THIRD*(-dely1+2*dely2);
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a3[2] = THIRD*(-delz1+2*delz2);
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cvatom[k][0] += a3[0]*f3[0];
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cvatom[k][1] += a3[1]*f3[1];
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cvatom[k][2] += a3[2]*f3[2];
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cvatom[k][3] += a3[0]*f3[1];
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cvatom[k][4] += a3[0]*f3[2];
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cvatom[k][5] += a3[1]*f3[2];
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cvatom[k][6] += a3[1]*f3[0];
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cvatom[k][7] += a3[2]*f3[0];
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cvatom[k][8] += a3[2]*f3[1];
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}
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}
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}
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/* ----------------------------------------------------------------------
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tally energy and virial into global and per-atom accumulators
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virial = r1F1 + r2F2 + r3F3 + r4F4
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called by AngleAmoeba for its 4-body angle term
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------------------------------------------------------------------------- */
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void Angle::ev_tally4(int i, int j, int k, int m, int nlocal, int newton_bond,
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double eangle,
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double *f1, double *f2, double *f3, double *f4)
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{
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double eanglefourth,v[6];
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if (eflag_either) {
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if (eflag_global) {
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if (newton_bond) energy += eangle;
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else {
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eanglefourth = FOURTH*eangle;
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if (i < nlocal) energy += eanglefourth;
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if (j < nlocal) energy += eanglefourth;
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if (k < nlocal) energy += eanglefourth;
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}
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}
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if (eflag_atom) {
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eanglefourth = FOURTH*eangle;
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if (newton_bond || i < nlocal) eatom[i] += eanglefourth;
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if (newton_bond || j < nlocal) eatom[j] += eanglefourth;
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if (newton_bond || k < nlocal) eatom[k] += eanglefourth;
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if (newton_bond || m < nlocal) eatom[m] += eanglefourth;
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}
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}
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if (vflag_either) {
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double **x = atom->x;
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v[0] = x[i][0]*f1[0] + x[j][0]*f2[0] + x[k][0]*f3[0] + x[m][0]*f4[0];
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v[1] = x[i][1]*f1[1] + x[j][1]*f2[1] + x[k][1]*f3[1] + x[m][1]*f4[1];
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v[2] = x[i][2]*f1[2] + x[j][2]*f2[2] + x[k][2]*f3[2] + x[m][2]*f4[2];
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v[3] = x[i][0]*f1[1] + x[j][0]*f2[1] + x[k][0]*f3[1] + x[m][0]*f4[1];
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v[4] = x[i][0]*f1[2] + x[j][0]*f2[2] + x[k][0]*f3[2] + x[m][0]*f4[2];
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v[5] = x[i][1]*f1[2] + x[j][1]*f2[2] + x[k][1]*f3[2] + x[m][1]*f4[2];
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if (vflag_global) {
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if (newton_bond) {
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virial[0] += v[0];
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virial[1] += v[1];
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virial[2] += v[2];
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virial[3] += v[3];
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virial[4] += v[4];
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virial[5] += v[5];
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} else {
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double prefactor = 0.0;
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if (i < nlocal) prefactor += 1.0;
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if (j < nlocal) prefactor += 1.0;
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if (k < nlocal) prefactor += 1.0;
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if (m < nlocal) prefactor += 1.0;
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virial[0] += prefactor*FOURTH*v[0];
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virial[1] += prefactor*FOURTH*v[1];
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virial[2] += prefactor*FOURTH*v[2];
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virial[3] += prefactor*FOURTH*v[3];
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virial[4] += prefactor*FOURTH*v[4];
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virial[5] += prefactor*FOURTH*v[5];
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}
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}
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if (vflag_atom) {
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if (newton_bond || i < nlocal) {
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vatom[i][0] += FOURTH*v[0];
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vatom[i][1] += FOURTH*v[1];
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vatom[i][2] += FOURTH*v[2];
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vatom[i][3] += FOURTH*v[3];
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vatom[i][4] += FOURTH*v[4];
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vatom[i][5] += FOURTH*v[5];
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}
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if (newton_bond || j < nlocal) {
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vatom[j][0] += FOURTH*v[0];
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vatom[j][1] += FOURTH*v[1];
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vatom[j][2] += FOURTH*v[2];
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vatom[j][3] += FOURTH*v[3];
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vatom[j][4] += FOURTH*v[4];
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vatom[j][5] += FOURTH*v[5];
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}
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if (newton_bond || k < nlocal) {
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vatom[k][0] += FOURTH*v[0];
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vatom[k][1] += FOURTH*v[1];
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vatom[k][2] += FOURTH*v[2];
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vatom[k][3] += FOURTH*v[3];
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vatom[k][4] += FOURTH*v[4];
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vatom[k][5] += FOURTH*v[5];
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}
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if (newton_bond || m < nlocal) {
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vatom[m][0] += FOURTH*v[0];
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vatom[m][1] += FOURTH*v[1];
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vatom[m][2] += FOURTH*v[2];
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vatom[m][3] += FOURTH*v[3];
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vatom[m][4] += FOURTH*v[4];
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vatom[m][5] += FOURTH*v[5];
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
/* ----------------------------------------------------------------------
|
|
tally energy and virial into global and per-atom accumulators
|
|
called by AngleAmoeba for its 2-body Urey-Bradley H-H bond term
|
|
identical to Bond:ev_tally()
|
|
------------------------------------------------------------------------- */
|
|
|
|
void Angle::ev_tally2(int i, int j, int nlocal, int newton_bond,
|
|
double ebond, double fbond,
|
|
double delx, double dely, double delz)
|
|
{
|
|
double ebondhalf,v[6];
|
|
|
|
if (eflag_either) {
|
|
if (eflag_global) {
|
|
if (newton_bond) energy += ebond;
|
|
else {
|
|
ebondhalf = 0.5*ebond;
|
|
if (i < nlocal) energy += ebondhalf;
|
|
if (j < nlocal) energy += ebondhalf;
|
|
}
|
|
}
|
|
if (eflag_atom) {
|
|
ebondhalf = 0.5*ebond;
|
|
if (newton_bond || i < nlocal) eatom[i] += ebondhalf;
|
|
if (newton_bond || j < nlocal) eatom[j] += ebondhalf;
|
|
}
|
|
}
|
|
|
|
if (vflag_either) {
|
|
v[0] = delx*delx*fbond;
|
|
v[1] = dely*dely*fbond;
|
|
v[2] = delz*delz*fbond;
|
|
v[3] = delx*dely*fbond;
|
|
v[4] = delx*delz*fbond;
|
|
v[5] = dely*delz*fbond;
|
|
|
|
if (vflag_global) {
|
|
if (newton_bond) {
|
|
virial[0] += v[0];
|
|
virial[1] += v[1];
|
|
virial[2] += v[2];
|
|
virial[3] += v[3];
|
|
virial[4] += v[4];
|
|
virial[5] += v[5];
|
|
} else {
|
|
if (i < nlocal) {
|
|
virial[0] += 0.5*v[0];
|
|
virial[1] += 0.5*v[1];
|
|
virial[2] += 0.5*v[2];
|
|
virial[3] += 0.5*v[3];
|
|
virial[4] += 0.5*v[4];
|
|
virial[5] += 0.5*v[5];
|
|
}
|
|
if (j < nlocal) {
|
|
virial[0] += 0.5*v[0];
|
|
virial[1] += 0.5*v[1];
|
|
virial[2] += 0.5*v[2];
|
|
virial[3] += 0.5*v[3];
|
|
virial[4] += 0.5*v[4];
|
|
virial[5] += 0.5*v[5];
|
|
}
|
|
}
|
|
}
|
|
|
|
if (vflag_atom) {
|
|
if (newton_bond || i < nlocal) {
|
|
vatom[i][0] += 0.5*v[0];
|
|
vatom[i][1] += 0.5*v[1];
|
|
vatom[i][2] += 0.5*v[2];
|
|
vatom[i][3] += 0.5*v[3];
|
|
vatom[i][4] += 0.5*v[4];
|
|
vatom[i][5] += 0.5*v[5];
|
|
}
|
|
if (newton_bond || j < nlocal) {
|
|
vatom[j][0] += 0.5*v[0];
|
|
vatom[j][1] += 0.5*v[1];
|
|
vatom[j][2] += 0.5*v[2];
|
|
vatom[j][3] += 0.5*v[3];
|
|
vatom[j][4] += 0.5*v[4];
|
|
vatom[j][5] += 0.5*v[5];
|
|
}
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double Angle::memory_usage()
|
|
{
|
|
double bytes = (double)comm->nthreads*maxeatom * sizeof(double);
|
|
bytes += (double)comm->nthreads*maxvatom*6 * sizeof(double);
|
|
bytes += (double)comm->nthreads*maxcvatom*9 * sizeof(double);
|
|
return bytes;
|
|
}
|