convert from CR-LF to consistent line endings
This commit is contained in:
Axel Kohlmeyer
@ -1,280 +1,280 @@
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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 "bond_fene_nm_split.h"
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#include "atom.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 "math_const.h"
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#include "memory.h"
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#include "neighbor.h"
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#include "update.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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BondFENEnmSplit::BondFENEnmSplit(LAMMPS *lmp) : BondFENE(lmp) {}
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/* ---------------------------------------------------------------------- */
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BondFENEnmSplit::~BondFENEnmSplit()
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{
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if (allocated && !copymode) {
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memory->destroy(nn);
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memory->destroy(mm);
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}
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}
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/* ---------------------------------------------------------------------- */
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void BondFENEnmSplit::compute(int eflag, int vflag)
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{
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int i1, i2, n, type;
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double delx, dely, delz, ebond, fbond;
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double rsq, r0sq, rlogarg, sr2, sr6;
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double r;
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ebond = sr6 = 0.0;
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ev_init(eflag, vflag);
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double **x = atom->x;
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double **f = atom->f;
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int **bondlist = neighbor->bondlist;
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int nbondlist = neighbor->nbondlist;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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for (n = 0; n < nbondlist; n++) {
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i1 = bondlist[n][0];
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i2 = bondlist[n][1];
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type = bondlist[n][2];
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delx = x[i1][0] - x[i2][0];
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dely = x[i1][1] - x[i2][1];
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delz = x[i1][2] - x[i2][2];
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// force from log term
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rsq = delx * delx + dely * dely + delz * delz;
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r0sq = r0[type] * r0[type];
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rlogarg = 1.0 - rsq / r0sq;
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// if r -> r0, then rlogarg < 0.0 which is an error
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// issue a warning and reset rlogarg = epsilon
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// if r > 2*r0 something serious is wrong, abort
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// change cutuff from .1 to .02 so only bond lengths > 1.485 give the warning
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// and crash the run if rlogarg < -.21 rather than < -3
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// Don't print out warnings, only errors
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if (rlogarg < .02) {
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error->warning(FLERR, "fene/nm/split bond too long: {} {} {} {}", update->ntimestep,
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atom->tag[i1], atom->tag[i2], sqrt(rsq));
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if (rlogarg <= -.21) error->one(FLERR, "Bad FENE bond");
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rlogarg = 0.02;
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}
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fbond = -k[type] / rlogarg;
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// force from n-m term
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if (rsq < sigma[type]*sigma[type]) {
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r = sqrt(rsq);
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fbond += epsilon[type] * (nn[type] * mm[type] / (nn[type] - mm[type])) *
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(pow(sigma[type] / r, nn[type]) - pow(sigma[type] / r, mm[type])) / rsq;
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}
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// energy
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if (eflag) {
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ebond = -0.5 * k[type] * r0sq * log(rlogarg);
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if (rsq < sigma[type]*sigma[type])
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ebond += (epsilon[type] / (nn[type] - mm[type])) *
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(mm[type] * pow(sigma[type] / r, nn[type]) - nn[type] * pow(sigma[type] / r, mm[type]));
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}
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// apply force to each of 2 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += delx * fbond;
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f[i1][1] += dely * fbond;
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f[i1][2] += delz * fbond;
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] -= delx * fbond;
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f[i2][1] -= dely * fbond;
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f[i2][2] -= delz * fbond;
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}
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if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
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}
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}
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/* ---------------------------------------------------------------------- */
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void BondFENEnmSplit::allocate()
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{
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BondFENE::allocate();
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int n = atom->nbondtypes + 1;
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memory->create(nn, n, "bond:nn");
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memory->create(mm, n, "bond:mm");
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}
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/* ----------------------------------------------------------------------
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set coeffs for one type
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------------------------------------------------------------------------- */
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void BondFENEnmSplit::coeff(int narg, char **arg)
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{
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if (narg != 7) error->all(FLERR, "Incorrect args for bond coefficients");
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if (!allocated) allocate();
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int ilo, ihi;
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utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
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double k_one = utils::numeric(FLERR, arg[1], false, lmp);
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double r0_one = utils::numeric(FLERR, arg[2], false, lmp);
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double epsilon_one = utils::numeric(FLERR, arg[3], false, lmp);
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double sigma_one = utils::numeric(FLERR, arg[4], false, lmp);
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double nn_one = utils::numeric(FLERR, arg[5], false, lmp);
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double mm_one = utils::numeric(FLERR, arg[6], false, lmp);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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k[i] = k_one;
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r0[i] = r0_one;
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epsilon[i] = epsilon_one;
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sigma[i] = sigma_one;
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nn[i] = nn_one;
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mm[i] = mm_one;
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setflag[i] = 1;
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count++;
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}
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if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
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}
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/* ----------------------------------------------------------------------
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check if special_bond settings are valid
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------------------------------------------------------------------------- */
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void BondFENEnmSplit::init_style()
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{
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// special bonds should be 0 1 1
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if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0) {
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if (comm->me == 0) error->warning(FLERR, "Use special bonds = 0,1,1 with bond style fene");
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}
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}
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/* ---------------------------------------------------------------------- */
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double BondFENEnmSplit::equilibrium_distance(int i)
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{
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return 0.97 * sigma[i];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void BondFENEnmSplit::write_restart(FILE *fp)
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{
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fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
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fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp);
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fwrite(&epsilon[1], sizeof(double), atom->nbondtypes, fp);
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fwrite(&sigma[1], sizeof(double), atom->nbondtypes, fp);
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fwrite(&nn[1], sizeof(double), atom->nbondtypes, fp);
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fwrite(&mm[1], sizeof(double), atom->nbondtypes, fp);
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void BondFENEnmSplit::read_restart(FILE *fp)
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{
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allocate();
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if (comm->me == 0) {
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utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
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utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
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utils::sfread(FLERR, &epsilon[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
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utils::sfread(FLERR, &sigma[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
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utils::sfread(FLERR, &nn[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
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utils::sfread(FLERR, &mm[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
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}
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MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&epsilon[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&sigma[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&nn[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&mm[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
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for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void BondFENEnmSplit::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->nbondtypes; i++)
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fprintf(fp, "%d %g %g %g %g %g %g\n", i, k[i], r0[i], epsilon[i], sigma[i], nn[i], mm[i]);
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}
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/* ---------------------------------------------------------------------- */
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double BondFENEnmSplit::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
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{
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double r0sq = r0[type] * r0[type];
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double rlogarg = 1.0 - rsq / r0sq;
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double r;
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// if r -> r0, then rlogarg < 0.0 which is an error
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// issue a warning and reset rlogarg = epsilon
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// if r > 2*r0 something serious is wrong, abort
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// change cutuff from .1 to .02 so only bond lengths > 1.485 give the warning
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// and crash the run if rlogarg < -.21 rather than < -3
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// Don't print out warnings, only errors
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if (rlogarg < 0.02) {
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error->warning(FLERR, "FENE bond too long: {} {:.8}", update->ntimestep, sqrt(rsq));
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if (rlogarg <= -.21) error->one(FLERR, "Bad FENE bond");
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rlogarg = 0.02;
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}
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double eng = -0.5 * k[type] * r0sq * log(rlogarg);
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fforce = -k[type] / rlogarg;
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if (rsq < sigma[type]*sigma[type]) {
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r = sqrt(rsq);
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fforce += epsilon[type] * (nn[type] * mm[type] / (nn[type] - mm[type])) *
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(pow(sigma[type] / r, nn[type]) - pow(sigma[type] / r, mm[type])) / rsq;
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eng += (epsilon[type] / (nn[type] - mm[type])) *
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(mm[type] * pow(sigma[type] / r, nn[type]) - nn[type] * pow(sigma[type] / r, mm[type]));
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}
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return eng;
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}
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/* ---------------------------------------------------------------------- */
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void *BondFENEnmSplit::extract(const char *str, int &dim)
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{
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dim = 1;
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if (strcmp(str, "kappa") == 0) return (void *) k;
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if (strcmp(str, "r0") == 0) return (void *) r0;
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return nullptr;
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}
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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
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
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|
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "bond_fene_nm_split.h"
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#include "atom.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 "math_const.h"
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#include "memory.h"
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#include "neighbor.h"
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#include "update.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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BondFENEnmSplit::BondFENEnmSplit(LAMMPS *lmp) : BondFENE(lmp) {}
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/* ---------------------------------------------------------------------- */
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BondFENEnmSplit::~BondFENEnmSplit()
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{
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if (allocated && !copymode) {
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memory->destroy(nn);
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memory->destroy(mm);
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}
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}
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/* ---------------------------------------------------------------------- */
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void BondFENEnmSplit::compute(int eflag, int vflag)
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{
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int i1, i2, n, type;
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double delx, dely, delz, ebond, fbond;
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double rsq, r0sq, rlogarg, sr2, sr6;
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double r;
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ebond = sr6 = 0.0;
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ev_init(eflag, vflag);
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double **x = atom->x;
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double **f = atom->f;
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int **bondlist = neighbor->bondlist;
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int nbondlist = neighbor->nbondlist;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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for (n = 0; n < nbondlist; n++) {
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i1 = bondlist[n][0];
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i2 = bondlist[n][1];
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type = bondlist[n][2];
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delx = x[i1][0] - x[i2][0];
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dely = x[i1][1] - x[i2][1];
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delz = x[i1][2] - x[i2][2];
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// force from log term
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rsq = delx * delx + dely * dely + delz * delz;
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r0sq = r0[type] * r0[type];
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rlogarg = 1.0 - rsq / r0sq;
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// if r -> r0, then rlogarg < 0.0 which is an error
|
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// issue a warning and reset rlogarg = epsilon
|
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// if r > 2*r0 something serious is wrong, abort
|
||||
// change cutuff from .1 to .02 so only bond lengths > 1.485 give the warning
|
||||
// and crash the run if rlogarg < -.21 rather than < -3
|
||||
// Don't print out warnings, only errors
|
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if (rlogarg < .02) {
|
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error->warning(FLERR, "fene/nm/split bond too long: {} {} {} {}", update->ntimestep,
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atom->tag[i1], atom->tag[i2], sqrt(rsq));
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if (rlogarg <= -.21) error->one(FLERR, "Bad FENE bond");
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rlogarg = 0.02;
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}
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fbond = -k[type] / rlogarg;
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// force from n-m term
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if (rsq < sigma[type]*sigma[type]) {
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r = sqrt(rsq);
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fbond += epsilon[type] * (nn[type] * mm[type] / (nn[type] - mm[type])) *
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(pow(sigma[type] / r, nn[type]) - pow(sigma[type] / r, mm[type])) / rsq;
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}
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// energy
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||||
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if (eflag) {
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ebond = -0.5 * k[type] * r0sq * log(rlogarg);
|
||||
if (rsq < sigma[type]*sigma[type])
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||||
ebond += (epsilon[type] / (nn[type] - mm[type])) *
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(mm[type] * pow(sigma[type] / r, nn[type]) - nn[type] * pow(sigma[type] / r, mm[type]));
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||||
}
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||||
// apply force to each of 2 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += delx * fbond;
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f[i1][1] += dely * fbond;
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||||
f[i1][2] += delz * fbond;
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] -= delx * fbond;
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f[i2][1] -= dely * fbond;
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f[i2][2] -= delz * fbond;
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}
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||||
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if (evflag) ev_tally(i1, i2, nlocal, newton_bond, ebond, fbond, delx, dely, delz);
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}
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}
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|
||||
/* ---------------------------------------------------------------------- */
|
||||
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void BondFENEnmSplit::allocate()
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{
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BondFENE::allocate();
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int n = atom->nbondtypes + 1;
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||||
memory->create(nn, n, "bond:nn");
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||||
memory->create(mm, n, "bond:mm");
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||||
}
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||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one type
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondFENEnmSplit::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 7) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo, ihi;
|
||||
utils::bounds(FLERR, arg[0], 1, atom->nbondtypes, ilo, ihi, error);
|
||||
|
||||
double k_one = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
double r0_one = utils::numeric(FLERR, arg[2], false, lmp);
|
||||
double epsilon_one = utils::numeric(FLERR, arg[3], false, lmp);
|
||||
double sigma_one = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
double nn_one = utils::numeric(FLERR, arg[5], false, lmp);
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||||
double mm_one = utils::numeric(FLERR, arg[6], false, lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = k_one;
|
||||
r0[i] = r0_one;
|
||||
epsilon[i] = epsilon_one;
|
||||
sigma[i] = sigma_one;
|
||||
nn[i] = nn_one;
|
||||
mm[i] = mm_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR, "Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check if special_bond settings are valid
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondFENEnmSplit::init_style()
|
||||
{
|
||||
// special bonds should be 0 1 1
|
||||
|
||||
if (force->special_lj[1] != 0.0 || force->special_lj[2] != 1.0 || force->special_lj[3] != 1.0) {
|
||||
if (comm->me == 0) error->warning(FLERR, "Use special bonds = 0,1,1 with bond style fene");
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondFENEnmSplit::equilibrium_distance(int i)
|
||||
{
|
||||
return 0.97 * sigma[i];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondFENEnmSplit::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&r0[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&epsilon[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&sigma[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&nn[1], sizeof(double), atom->nbondtypes, fp);
|
||||
fwrite(&mm[1], sizeof(double), atom->nbondtypes, fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondFENEnmSplit::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR, &k[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &r0[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &epsilon[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &sigma[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &nn[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
utils::sfread(FLERR, &mm[1], sizeof(double), atom->nbondtypes, fp, nullptr, error);
|
||||
}
|
||||
MPI_Bcast(&k[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&r0[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&epsilon[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&sigma[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&nn[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
MPI_Bcast(&mm[1], atom->nbondtypes, MPI_DOUBLE, 0, world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondFENEnmSplit::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp, "%d %g %g %g %g %g %g\n", i, k[i], r0[i], epsilon[i], sigma[i], nn[i], mm[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondFENEnmSplit::single(int type, double rsq, int /*i*/, int /*j*/, double &fforce)
|
||||
{
|
||||
double r0sq = r0[type] * r0[type];
|
||||
double rlogarg = 1.0 - rsq / r0sq;
|
||||
double r;
|
||||
// if r -> r0, then rlogarg < 0.0 which is an error
|
||||
// issue a warning and reset rlogarg = epsilon
|
||||
// if r > 2*r0 something serious is wrong, abort
|
||||
|
||||
// change cutuff from .1 to .02 so only bond lengths > 1.485 give the warning
|
||||
// and crash the run if rlogarg < -.21 rather than < -3
|
||||
// Don't print out warnings, only errors
|
||||
if (rlogarg < 0.02) {
|
||||
error->warning(FLERR, "FENE bond too long: {} {:.8}", update->ntimestep, sqrt(rsq));
|
||||
if (rlogarg <= -.21) error->one(FLERR, "Bad FENE bond");
|
||||
rlogarg = 0.02;
|
||||
}
|
||||
|
||||
double eng = -0.5 * k[type] * r0sq * log(rlogarg);
|
||||
fforce = -k[type] / rlogarg;
|
||||
|
||||
if (rsq < sigma[type]*sigma[type]) {
|
||||
r = sqrt(rsq);
|
||||
fforce += epsilon[type] * (nn[type] * mm[type] / (nn[type] - mm[type])) *
|
||||
(pow(sigma[type] / r, nn[type]) - pow(sigma[type] / r, mm[type])) / rsq;
|
||||
eng += (epsilon[type] / (nn[type] - mm[type])) *
|
||||
(mm[type] * pow(sigma[type] / r, nn[type]) - nn[type] * pow(sigma[type] / r, mm[type]));
|
||||
}
|
||||
|
||||
return eng;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *BondFENEnmSplit::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 1;
|
||||
if (strcmp(str, "kappa") == 0) return (void *) k;
|
||||
if (strcmp(str, "r0") == 0) return (void *) r0;
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
@ -1,156 +1,156 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing Author: Julien Devemy (ICCF), Robert S. Hoy (USF), Joseph D. Dietz (USF)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_nm_cut_split.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "math_special.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using MathSpecial::powint;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
PairNMCutSplit::PairNMCutSplit(LAMMPS *lmp) : PairNMCut(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
|
||||
void PairNMCutSplit::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,r2inv,factor_lj;
|
||||
double r,forcenm,rminv,rninv;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
r = sqrt(rsq);
|
||||
|
||||
// r < r0 --> use generalized LJ
|
||||
if (rsq < r0[itype][jtype]*r0[itype][jtype]) {
|
||||
forcenm = e0nm[itype][jtype]*nm[itype][jtype]*
|
||||
(r0n[itype][jtype]/pow(r,nn[itype][jtype])
|
||||
-r0m[itype][jtype]/pow(r,mm[itype][jtype]));
|
||||
}
|
||||
// r > r0 --> use standard LJ (m = 6 n = 12)
|
||||
else forcenm =(e0[itype][jtype]/6.0)*72.0*(4.0/powint(r,12)-2.0/powint(r,6));
|
||||
|
||||
fpair = factor_lj*forcenm*r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < r0[itype][jtype]*r0[itype][jtype]) {
|
||||
rminv = pow(r2inv,mm[itype][jtype]/2.0);
|
||||
rninv = pow(r2inv,nn[itype][jtype]/2.0);
|
||||
|
||||
evdwl = e0nm[itype][jtype]*(mm[itype][jtype]*r0n[itype][jtype]*rninv -
|
||||
nn[itype][jtype]*r0m[itype][jtype]*rminv) -
|
||||
offset[itype][jtype];
|
||||
} else evdwl = (e0[itype][jtype]/6.0)*(24.0*powint(r2inv,6) - 24.0*pow(r2inv,3));
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairNMCutSplit::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double /*factor_coul*/, double factor_lj, double &fforce)
|
||||
{
|
||||
double r2inv,rminv,rninv,r,forcenm,phinm;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
r = sqrt(rsq);
|
||||
rminv = pow(r2inv,mm[itype][jtype]/2.0);
|
||||
rninv = pow(r2inv,nn[itype][jtype]/2.0);
|
||||
// r < 2^1/6, use generalized LJ
|
||||
if (rsq < r0[itype][jtype]*r0[itype][jtype]) { // note the addition of the r0 factor
|
||||
forcenm = e0nm[itype][jtype]*nm[itype][jtype]*
|
||||
(r0n[itype][jtype]/pow(r,nn[itype][jtype])-r0m[itype][jtype]/pow(r,mm[itype][jtype]));
|
||||
phinm = e0nm[itype][jtype]*(mm[itype][jtype]*r0n[itype][jtype]*rninv
|
||||
-nn[itype][jtype]*r0m[itype][jtype]*rminv)-offset[itype][jtype];
|
||||
|
||||
}
|
||||
// r > 2^1/6 --> use standard LJ (m = 6 n = 12)
|
||||
else{forcenm = (e0[itype][jtype]/6.0)*72.0*(4.0/powint(r,12)-2.0/powint(r,6));
|
||||
phinm = (e0[itype][jtype]/6.0)*(24.0*powint(r2inv,6)-24.0*powint(r2inv,3));
|
||||
}
|
||||
|
||||
fforce = factor_lj*forcenm*r2inv;
|
||||
return factor_lj*phinm;
|
||||
}
|
||||
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing Author: Julien Devemy (ICCF), Robert S. Hoy (USF), Joseph D. Dietz (USF)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "pair_nm_cut_split.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "math_special.h"
|
||||
#include "memory.h"
|
||||
#include "neigh_list.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using MathSpecial::powint;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
PairNMCutSplit::PairNMCutSplit(LAMMPS *lmp) : PairNMCut(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
|
||||
void PairNMCutSplit::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double rsq,r2inv,factor_lj;
|
||||
double r,forcenm,rminv,rninv;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
r = sqrt(rsq);
|
||||
|
||||
// r < r0 --> use generalized LJ
|
||||
if (rsq < r0[itype][jtype]*r0[itype][jtype]) {
|
||||
forcenm = e0nm[itype][jtype]*nm[itype][jtype]*
|
||||
(r0n[itype][jtype]/pow(r,nn[itype][jtype])
|
||||
-r0m[itype][jtype]/pow(r,mm[itype][jtype]));
|
||||
}
|
||||
// r > r0 --> use standard LJ (m = 6 n = 12)
|
||||
else forcenm =(e0[itype][jtype]/6.0)*72.0*(4.0/powint(r,12)-2.0/powint(r,6));
|
||||
|
||||
fpair = factor_lj*forcenm*r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < r0[itype][jtype]*r0[itype][jtype]) {
|
||||
rminv = pow(r2inv,mm[itype][jtype]/2.0);
|
||||
rninv = pow(r2inv,nn[itype][jtype]/2.0);
|
||||
|
||||
evdwl = e0nm[itype][jtype]*(mm[itype][jtype]*r0n[itype][jtype]*rninv -
|
||||
nn[itype][jtype]*r0m[itype][jtype]*rminv) -
|
||||
offset[itype][jtype];
|
||||
} else evdwl = (e0[itype][jtype]/6.0)*(24.0*powint(r2inv,6) - 24.0*pow(r2inv,3));
|
||||
evdwl *= factor_lj;
|
||||
}
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairNMCutSplit::single(int /*i*/, int /*j*/, int itype, int jtype, double rsq, double /*factor_coul*/, double factor_lj, double &fforce)
|
||||
{
|
||||
double r2inv,rminv,rninv,r,forcenm,phinm;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
r = sqrt(rsq);
|
||||
rminv = pow(r2inv,mm[itype][jtype]/2.0);
|
||||
rninv = pow(r2inv,nn[itype][jtype]/2.0);
|
||||
// r < 2^1/6, use generalized LJ
|
||||
if (rsq < r0[itype][jtype]*r0[itype][jtype]) { // note the addition of the r0 factor
|
||||
forcenm = e0nm[itype][jtype]*nm[itype][jtype]*
|
||||
(r0n[itype][jtype]/pow(r,nn[itype][jtype])-r0m[itype][jtype]/pow(r,mm[itype][jtype]));
|
||||
phinm = e0nm[itype][jtype]*(mm[itype][jtype]*r0n[itype][jtype]*rninv
|
||||
-nn[itype][jtype]*r0m[itype][jtype]*rminv)-offset[itype][jtype];
|
||||
|
||||
}
|
||||
// r > 2^1/6 --> use standard LJ (m = 6 n = 12)
|
||||
else{forcenm = (e0[itype][jtype]/6.0)*72.0*(4.0/powint(r,12)-2.0/powint(r,6));
|
||||
phinm = (e0[itype][jtype]/6.0)*(24.0*powint(r2inv,6)-24.0*powint(r2inv,3));
|
||||
}
|
||||
|
||||
fforce = factor_lj*forcenm*r2inv;
|
||||
return factor_lj*phinm;
|
||||
}
|
||||
|
||||
|
||||
Reference in New Issue
Block a user