444 lines
14 KiB
C++
444 lines
14 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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LAMMPS development team: developers@lammps.org
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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 "dihedral.h"
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#include "atom.h"
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#include "atom_masks.h"
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#include "comm.h"
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#include "error.h"
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#include "force.h"
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#include "info.h"
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#include "memory.h"
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#include "suffix.h"
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#include "update.h"
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using namespace LAMMPS_NS;
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/* ----------------------------------------------------------------------
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set dihedral contribution to Vdwl and Coulombic energy to 0.0
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DihedralCharmm will override this
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------------------------------------------------------------------------- */
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Dihedral::Dihedral(LAMMPS *_lmp) : Pointers(_lmp)
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{
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energy = 0.0;
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writedata = 0;
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reinitflag = 1;
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allocated = 0;
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suffix_flag = Suffix::NONE;
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born_matrix_enable = 0;
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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 = kokkosable = 0;
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}
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/* ---------------------------------------------------------------------- */
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Dihedral::~Dihedral()
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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 Dihedral::init()
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{
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if (!allocated && atom->ndihedraltypes)
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error->all(FLERR, Error::NOLASTLINE,
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"Dihedral coeffs are not set. Status:\n" + Info::get_dihedral_coeff_status(lmp));
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for (int i = 1; i <= atom->ndihedraltypes; i++)
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if (setflag[i] == 0)
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error->all(FLERR, Error::NOLASTLINE,
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"All dihedral coeffs are not set. Status:\n"
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+ Info::get_dihedral_coeff_status(lmp));
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init_style();
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}
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/* ----------------------------------------------------------------------
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check that there are no arguments
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------------------------------------------------------------------------- */
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void Dihedral::settings(int narg, char **args)
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{
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if (narg > 0)
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error->all(FLERR, "Illegal dihedral_style {} argument: {}", force->dihedral_style, args[0]);
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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 Dihedral::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) vflag_atom = 1;
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cvflag_atom = 0;
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if (vflag & VIRIAL_CENTROID && centroidstressflag == CENTROID_AVAIL) 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, "dihedral: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, "dihedral: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, "dihedral: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)
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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 + r4F4 = (r1-r2) F1 + (r3-r2) F3 + (r4-r2) F4
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= (r1-r2) F1 + (r3-r2) F3 + (r4-r3 + r3-r2) F4
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= vb1*f1 + vb2*f3 + (vb3+vb2)*f4
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------------------------------------------------------------------------- */
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void Dihedral::ev_tally(int i1, int i2, int i3, int i4, int nlocal, int newton_bond,
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double edihedral, double *f1, double *f3, double *f4, double vb1x,
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double vb1y, double vb1z, double vb2x, double vb2y, double vb2z,
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double vb3x, double vb3y, double vb3z)
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{
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double edihedralquarter, v[6];
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if (eflag_either) {
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if (eflag_global) {
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if (newton_bond)
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energy += edihedral;
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else {
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edihedralquarter = 0.25 * edihedral;
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if (i1 < nlocal) energy += edihedralquarter;
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if (i2 < nlocal) energy += edihedralquarter;
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if (i3 < nlocal) energy += edihedralquarter;
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if (i4 < nlocal) energy += edihedralquarter;
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}
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}
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if (eflag_atom) {
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edihedralquarter = 0.25 * edihedral;
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if (newton_bond || i1 < nlocal) eatom[i1] += edihedralquarter;
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if (newton_bond || i2 < nlocal) eatom[i2] += edihedralquarter;
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if (newton_bond || i3 < nlocal) eatom[i3] += edihedralquarter;
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if (newton_bond || i4 < nlocal) eatom[i4] += edihedralquarter;
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}
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}
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if (vflag_either) {
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v[0] = vb1x * f1[0] + vb2x * f3[0] + (vb3x + vb2x) * f4[0];
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v[1] = vb1y * f1[1] + vb2y * f3[1] + (vb3y + vb2y) * f4[1];
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v[2] = vb1z * f1[2] + vb2z * f3[2] + (vb3z + vb2z) * f4[2];
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v[3] = vb1x * f1[1] + vb2x * f3[1] + (vb3x + vb2x) * f4[1];
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v[4] = vb1x * f1[2] + vb2x * f3[2] + (vb3x + vb2x) * f4[2];
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v[5] = vb1y * f1[2] + vb2y * f3[2] + (vb3y + vb2y) * 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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if (i1 < nlocal) {
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virial[0] += 0.25 * v[0];
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virial[1] += 0.25 * v[1];
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virial[2] += 0.25 * v[2];
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virial[3] += 0.25 * v[3];
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virial[4] += 0.25 * v[4];
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virial[5] += 0.25 * v[5];
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}
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if (i2 < nlocal) {
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virial[0] += 0.25 * v[0];
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virial[1] += 0.25 * v[1];
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virial[2] += 0.25 * v[2];
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virial[3] += 0.25 * v[3];
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virial[4] += 0.25 * v[4];
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virial[5] += 0.25 * v[5];
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}
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if (i3 < nlocal) {
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virial[0] += 0.25 * v[0];
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virial[1] += 0.25 * v[1];
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virial[2] += 0.25 * v[2];
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virial[3] += 0.25 * v[3];
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virial[4] += 0.25 * v[4];
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virial[5] += 0.25 * v[5];
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}
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if (i4 < nlocal) {
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virial[0] += 0.25 * v[0];
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virial[1] += 0.25 * v[1];
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virial[2] += 0.25 * v[2];
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virial[3] += 0.25 * v[3];
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virial[4] += 0.25 * v[4];
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virial[5] += 0.25 * v[5];
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}
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}
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}
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if (vflag_atom) {
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if (newton_bond || i1 < nlocal) {
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vatom[i1][0] += 0.25 * v[0];
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vatom[i1][1] += 0.25 * v[1];
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vatom[i1][2] += 0.25 * v[2];
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vatom[i1][3] += 0.25 * v[3];
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vatom[i1][4] += 0.25 * v[4];
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vatom[i1][5] += 0.25 * v[5];
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}
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if (newton_bond || i2 < nlocal) {
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vatom[i2][0] += 0.25 * v[0];
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vatom[i2][1] += 0.25 * v[1];
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vatom[i2][2] += 0.25 * v[2];
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vatom[i2][3] += 0.25 * v[3];
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vatom[i2][4] += 0.25 * v[4];
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vatom[i2][5] += 0.25 * v[5];
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}
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if (newton_bond || i3 < nlocal) {
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vatom[i3][0] += 0.25 * v[0];
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vatom[i3][1] += 0.25 * v[1];
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vatom[i3][2] += 0.25 * v[2];
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vatom[i3][3] += 0.25 * v[3];
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vatom[i3][4] += 0.25 * v[4];
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vatom[i3][5] += 0.25 * v[5];
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}
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if (newton_bond || i4 < nlocal) {
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vatom[i4][0] += 0.25 * v[0];
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vatom[i4][1] += 0.25 * v[1];
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vatom[i4][2] += 0.25 * v[2];
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vatom[i4][3] += 0.25 * v[3];
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vatom[i4][4] += 0.25 * v[4];
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vatom[i4][5] += 0.25 * 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+r4)/4
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// rij = ri-rj
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// total virial = r10*f1 + r20*f2 + r30*f3 + r40*f4
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// vb1: r12
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// vb2: r32
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// vb3: r43
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if (newton_bond || i1 < nlocal) {
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double a1[3];
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// a1 = r10 = (3*r12 - 2*r32 - r43)/4
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a1[0] = 0.25 * (3 * vb1x - 2 * vb2x - vb3x);
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a1[1] = 0.25 * (3 * vb1y - 2 * vb2y - vb3y);
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a1[2] = 0.25 * (3 * vb1z - 2 * vb2z - vb3z);
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cvatom[i1][0] += a1[0] * f1[0];
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cvatom[i1][1] += a1[1] * f1[1];
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cvatom[i1][2] += a1[2] * f1[2];
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cvatom[i1][3] += a1[0] * f1[1];
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cvatom[i1][4] += a1[0] * f1[2];
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cvatom[i1][5] += a1[1] * f1[2];
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cvatom[i1][6] += a1[1] * f1[0];
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cvatom[i1][7] += a1[2] * f1[0];
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cvatom[i1][8] += a1[2] * f1[1];
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}
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if (newton_bond || i2 < nlocal) {
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double a2[3];
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double f2[3];
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// a2 = r20 = ( -r12 - 2*r32 - r43)/4
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a2[0] = 0.25 * (-vb1x - 2 * vb2x - vb3x);
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a2[1] = 0.25 * (-vb1y - 2 * vb2y - vb3y);
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a2[2] = 0.25 * (-vb1z - 2 * vb2z - vb3z);
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f2[0] = -f1[0] - f3[0] - f4[0];
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f2[1] = -f1[1] - f3[1] - f4[1];
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f2[2] = -f1[2] - f3[2] - f4[2];
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cvatom[i2][0] += a2[0] * f2[0];
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cvatom[i2][1] += a2[1] * f2[1];
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cvatom[i2][2] += a2[2] * f2[2];
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cvatom[i2][3] += a2[0] * f2[1];
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cvatom[i2][4] += a2[0] * f2[2];
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cvatom[i2][5] += a2[1] * f2[2];
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cvatom[i2][6] += a2[1] * f2[0];
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cvatom[i2][7] += a2[2] * f2[0];
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cvatom[i2][8] += a2[2] * f2[1];
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}
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if (newton_bond || i3 < nlocal) {
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double a3[3];
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// a3 = r30 = ( -r12 + 2*r32 - r43)/4
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a3[0] = 0.25 * (-vb1x + 2 * vb2x - vb3x);
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a3[1] = 0.25 * (-vb1y + 2 * vb2y - vb3y);
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a3[2] = 0.25 * (-vb1z + 2 * vb2z - vb3z);
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cvatom[i3][0] += a3[0] * f3[0];
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cvatom[i3][1] += a3[1] * f3[1];
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cvatom[i3][2] += a3[2] * f3[2];
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cvatom[i3][3] += a3[0] * f3[1];
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cvatom[i3][4] += a3[0] * f3[2];
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cvatom[i3][5] += a3[1] * f3[2];
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cvatom[i3][6] += a3[1] * f3[0];
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cvatom[i3][7] += a3[2] * f3[0];
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cvatom[i3][8] += a3[2] * f3[1];
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}
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if (newton_bond || i4 < nlocal) {
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double a4[3];
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// a4 = r40 = ( -r12 + 2*r32 + 3*r43)/4
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a4[0] = 0.25 * (-vb1x + 2 * vb2x + 3 * vb3x);
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a4[1] = 0.25 * (-vb1y + 2 * vb2y + 3 * vb3y);
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a4[2] = 0.25 * (-vb1z + 2 * vb2z + 3 * vb3z);
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cvatom[i4][0] += a4[0] * f4[0];
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cvatom[i4][1] += a4[1] * f4[1];
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cvatom[i4][2] += a4[2] * f4[2];
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cvatom[i4][3] += a4[0] * f4[1];
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cvatom[i4][4] += a4[0] * f4[2];
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cvatom[i4][5] += a4[1] * f4[2];
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cvatom[i4][6] += a4[1] * f4[0];
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cvatom[i4][7] += a4[2] * f4[0];
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cvatom[i4][8] += a4[2] * f4[1];
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void Dihedral::problem(const char *filename, int lineno, int i1, int i2, int i3, int i4)
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{
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const auto x = atom->x;
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auto warn = fmt::format("Dihedral problem: {} {} {} {} {} {}\n", comm->me, update->ntimestep,
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atom->tag[i1], atom->tag[i2], atom->tag[i3], atom->tag[i4]);
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warn += fmt::format("WARNING: 1st atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i1][0], x[i1][1],
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x[i1][2]);
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warn += fmt::format("WARNING: 2nd atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i2][0], x[i2][1],
|
|
x[i2][2]);
|
|
warn += fmt::format("WARNING: 3rd atom: {} {:.8} {:.8} {:.8}\n", comm->me, x[i3][0], x[i3][1],
|
|
x[i3][2]);
|
|
warn += fmt::format("WARNING: 4th atom: {} {:.8} {:.8} {:.8}", comm->me, x[i4][0], x[i4][1],
|
|
x[i4][2]);
|
|
error->warning(filename, lineno, warn);
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double Dihedral::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;
|
|
}
|
|
|
|
/* -----------------------------------------------------------------------
|
|
reset all type-based dihedral params via init()
|
|
-------------------------------------------------------------------------- */
|
|
|
|
void Dihedral::reinit()
|
|
{
|
|
if (!reinitflag)
|
|
error->all(FLERR, "Fix adapt interface to this dihedral style not supported");
|
|
|
|
init();
|
|
}
|