278 lines
8.6 KiB
C++
278 lines
8.6 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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/* ----------------------------------------------------------------------
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Contributing authors: Mario Orsi & Wei Ding (QMUL), m.orsi@qmul.ac.uk
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------------------------------------------------------------------------- */
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#include "angle_dipole.h"
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#include "atom.h"
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#include "comm.h"
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#include "domain.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 <cmath>
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using namespace LAMMPS_NS;
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using namespace MathConst;
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static constexpr double SMALL = 1.0e-100;
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/* ---------------------------------------------------------------------- */
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AngleDipole::AngleDipole(LAMMPS *lmp) : Angle(lmp)
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{
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k = nullptr;
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gamma0 = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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AngleDipole::~AngleDipole()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(k);
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memory->destroy(gamma0);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleDipole::compute(int eflag, int vflag)
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{
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int iRef, iDip, iDummy, n, type;
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double delx, dely, delz;
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double eangle, tangle, fi[3], fj[3];
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double r, cosGamma, deltaGamma, kdg, rmu;
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eangle = 0.0;
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ev_init(eflag, vflag);
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double **x = atom->x; // position vector
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double **mu = atom->mu; // point-dipole components and moment magnitude
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double **torque = atom->torque;
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int **anglelist = neighbor->anglelist;
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int nanglelist = neighbor->nanglelist;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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double **f = atom->f;
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double delTx, delTy, delTz;
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double fx, fy, fz, fmod, fmod_len, len;
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if (!newton_bond) error->all(FLERR, "'newton' flag for bonded interactions must be 'on'");
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for (n = 0; n < nanglelist; n++) {
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iDip = anglelist[n][0]; // dipole whose orientation is to be restrained
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iRef = anglelist[n][1]; // reference atom toward which dipole will point
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iDummy = anglelist[n][2]; // dummy atom - irrelevant to the interaction
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type = anglelist[n][3];
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delx = x[iRef][0] - x[iDip][0];
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dely = x[iRef][1] - x[iDip][1];
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delz = x[iRef][2] - x[iDip][2];
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r = sqrt(delx * delx + dely * dely + delz * delz);
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if (r < SMALL) continue;
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rmu = r * mu[iDip][3];
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cosGamma = (mu[iDip][0] * delx + mu[iDip][1] * dely + mu[iDip][2] * delz) / rmu;
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deltaGamma = cosGamma - cos(gamma0[type]);
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kdg = k[type] * deltaGamma;
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if (eflag) eangle = kdg * deltaGamma; // energy
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tangle = 2.0 * kdg / rmu;
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delTx = tangle * (dely * mu[iDip][2] - delz * mu[iDip][1]);
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delTy = tangle * (delz * mu[iDip][0] - delx * mu[iDip][2]);
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delTz = tangle * (delx * mu[iDip][1] - dely * mu[iDip][0]);
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torque[iDip][0] += delTx;
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torque[iDip][1] += delTy;
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torque[iDip][2] += delTz;
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// Force couple that counterbalances dipolar torque
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fx = dely * delTz - delz * delTy; // direction (fi): - r x (-T)
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fy = delz * delTx - delx * delTz;
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fz = delx * delTy - dely * delTx;
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fmod = sqrt(delTx * delTx + delTy * delTy + delTz * delTz) / r; // magnitude
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len = sqrt(fx * fx + fy * fy + fz * fz);
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if (len < SMALL) continue;
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fmod_len = fmod / len;
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fi[0] = fx * fmod_len;
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fi[1] = fy * fmod_len;
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fi[2] = fz * fmod_len;
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fj[0] = -fi[0];
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fj[1] = -fi[1];
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fj[2] = -fi[2];
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f[iDip][0] += fj[0];
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f[iDip][1] += fj[1];
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f[iDip][2] += fj[2];
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f[iRef][0] += fi[0];
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f[iRef][1] += fi[1];
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f[iRef][2] += fi[2];
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if (evflag) // virial = rij.fi = 0 (fj = -fi & fk = 0)
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ev_tally(iRef, iDip, iDummy, nlocal, newton_bond, eangle, fj, fi, 0.0, 0.0, 0.0, 0.0, 0.0,
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0.0);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleDipole::allocate()
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{
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allocated = 1;
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int n = atom->nangletypes;
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memory->create(k, n + 1, "angle:k");
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memory->create(gamma0, n + 1, "angle:gamma0");
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memory->create(setflag, n + 1, "angle:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more types
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------------------------------------------------------------------------- */
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void AngleDipole::coeff(int narg, char **arg)
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{
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if (narg != 3) error->all(FLERR, "Incorrect args for angle coefficients" + utils::errorurl(21));
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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->nangletypes, ilo, ihi, error);
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double k_one = utils::numeric(FLERR, arg[1], false, lmp);
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double gamma0_one = utils::numeric(FLERR, arg[2], false, lmp);
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// convert gamma0 from degrees to radians
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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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gamma0[i] = gamma0_one / 180.0 * MY_PI;
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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 angle coefficients" + utils::errorurl(21));
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more types
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------------------------------------------------------------------------- */
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void AngleDipole::init_style()
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{
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if (!atom->mu_flag || !atom->torque_flag)
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error->all(FLERR, "Angle style dipole requires atom attributes mu and torque");
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}
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/* ----------------------------------------------------------------------
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used by SHAKE
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------------------------------------------------------------------------- */
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double AngleDipole::equilibrium_angle(int i)
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{
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return gamma0[i];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes out coeffs to restart file
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------------------------------------------------------------------------- */
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void AngleDipole::write_restart(FILE *fp)
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{
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fwrite(&k[1], sizeof(double), atom->nangletypes, fp);
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fwrite(&gamma0[1], sizeof(double), atom->nangletypes, fp);
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}
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/* ----------------------------------------------------------------------
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proc 0 reads coeffs from restart file, bcasts them
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------------------------------------------------------------------------- */
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void AngleDipole::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->nangletypes, fp, nullptr, error);
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utils::sfread(FLERR, &gamma0[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
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}
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MPI_Bcast(&k[1], atom->nangletypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&gamma0[1], atom->nangletypes, MPI_DOUBLE, 0, world);
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for (int i = 1; i <= atom->nangletypes; 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 AngleDipole::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->nangletypes; i++) fprintf(fp, "%d %g %g\n", i, k[i], gamma0[i]);
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}
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/* ----------------------------------------------------------------------
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used by ComputeAngleLocal
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------------------------------------------------------------------------- */
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double AngleDipole::single(int type, int iRef, int iDip, int /*iDummy*/)
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{
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double **x = atom->x; // position vector
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double **mu = atom->mu; // point-dipole components and moment magnitude
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double delx = x[iRef][0] - x[iDip][0];
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double dely = x[iRef][1] - x[iDip][1];
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double delz = x[iRef][2] - x[iDip][2];
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domain->minimum_image(FLERR, delx, dely, delz);
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double r = sqrt(delx * delx + dely * dely + delz * delz);
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if (r < SMALL) return 0.0;
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double rmu = r * mu[iDip][3];
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double cosGamma = (mu[iDip][0] * delx + mu[iDip][1] * dely + mu[iDip][2] * delz) / rmu;
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double deltaGamma = cosGamma - cos(gamma0[type]);
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double kdg = k[type] * deltaGamma;
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return kdg * deltaGamma; // energy
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}
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/* ----------------------------------------------------------------------
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return ptr to internal members upon request
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------------------------------------------------------------------------ */
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void *AngleDipole::extract(const char *str, int &dim)
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{
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dim = 1;
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if (strcmp(str, "k") == 0) return (void *) k;
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if (strcmp(str, "gamma0") == 0) return (void *) gamma0;
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return nullptr;
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}
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