mwlc angle potential
This commit is contained in:
farrelljd
2
src/.gitignore
vendored
2
src/.gitignore
vendored
@ -505,6 +505,8 @@
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/angle_harmonic.h
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/angle_mm3.cpp
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/angle_mm3.h
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/angle_mwlc.cpp
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/angle_mwlc.h
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/angle_quartic.cpp
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/angle_quartic.h
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/angle_spica.cpp
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311
src/EXTRA-MOLECULE/angle_mwlc.cpp
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311
src/EXTRA-MOLECULE/angle_mwlc.cpp
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@ -0,0 +1,311 @@
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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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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 author: James D. Farrell (IoP CAS)
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[ based on angle_cosine.cpp ]
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------------------------------------------------------------------------- */
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#include "angle_mwlc.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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#include <cstring>
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using namespace LAMMPS_NS;
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using MathConst::MY_PI;
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/* ---------------------------------------------------------------------- */
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AngleMWLC::AngleMWLC(LAMMPS *_lmp) : Angle(_lmp)
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{
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born_matrix_enable = 1;
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}
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/* ---------------------------------------------------------------------- */
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AngleMWLC::~AngleMWLC()
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{
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if (allocated && !copymode) {
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memory->destroy(setflag);
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memory->destroy(k1);
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memory->destroy(k2);
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memory->destroy(mu);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleMWLC::compute(int eflag, int vflag)
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{
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int i1, i2, i3, n, type;
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double delx1, dely1, delz1, delx2, dely2, delz2;
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double eangle, f1[3], f3[3];
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double rsq1, rsq2, r1, r2, c, a, a11, a12, a22;
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double q, qm, Q;
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eangle = 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 **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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for (n = 0; n < nanglelist; n++) {
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i1 = anglelist[n][0];
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i2 = anglelist[n][1];
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i3 = anglelist[n][2];
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type = anglelist[n][3];
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// 1st bond
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delx1 = x[i1][0] - x[i2][0];
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dely1 = x[i1][1] - x[i2][1];
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delz1 = x[i1][2] - x[i2][2];
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rsq1 = delx1 * delx1 + dely1 * dely1 + delz1 * delz1;
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r1 = sqrt(rsq1);
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// 2nd bond
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delx2 = x[i3][0] - x[i2][0];
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dely2 = x[i3][1] - x[i2][1];
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delz2 = x[i3][2] - x[i2][2];
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rsq2 = delx2 * delx2 + dely2 * dely2 + delz2 * delz2;
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r2 = sqrt(rsq2);
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// c = cosine of angle
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c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
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c /= r1 * r2;
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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// force & energy
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q = exp(-k1[type] * (1.0 + c));
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qm = exp(-k2[type] * (1.0 + c) - mu[type]);
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Q = q + qm;
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if (eflag) eangle = -log(Q);
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a = (k1[type] * q + k2[type] * qm) / Q;
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a11 = a * c / rsq1;
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a12 = -a / (r1 * r2);
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a22 = a * c / rsq2;
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f1[0] = a11 * delx1 + a12 * delx2;
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f1[1] = a11 * dely1 + a12 * dely2;
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f1[2] = a11 * delz1 + a12 * delz2;
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f3[0] = a22 * delx2 + a12 * delx1;
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f3[1] = a22 * dely2 + a12 * dely1;
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f3[2] = a22 * delz2 + a12 * delz1;
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// apply force to each of 3 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += f1[0];
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f[i1][1] += f1[1];
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f[i1][2] += f1[2];
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] -= f1[0] + f3[0];
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f[i2][1] -= f1[1] + f3[1];
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f[i2][2] -= f1[2] + f3[2];
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}
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if (newton_bond || i3 < nlocal) {
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f[i3][0] += f3[0];
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f[i3][1] += f3[1];
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f[i3][2] += f3[2];
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}
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if (evflag)
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ev_tally(i1, i2, i3, nlocal, newton_bond, eangle, f1, f3, delx1, dely1, delz1, delx2, dely2,
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delz2);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleMWLC::allocate()
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{
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allocated = 1;
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const int np1 = atom->nangletypes + 1;
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memory->create(k1, np1, "angle:k1");
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memory->create(k2, np1, "angle:k2");
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memory->create(mu, np1, "angle:mu");
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memory->create(setflag, np1, "angle:setflag");
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for (int i = 1; i < np1; i++) setflag[i] = 0;
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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 AngleMWLC::coeff(int narg, char **arg)
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{
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if (narg != 4) error->all(FLERR, "Incorrect args for angle 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->nangletypes, ilo, ihi, error);
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double k1_one = utils::numeric(FLERR, arg[1], false, lmp);
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double k2_one = utils::numeric(FLERR, arg[2], false, lmp);
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double mu_one = utils::numeric(FLERR, arg[3], false, lmp);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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k1[i] = k1_one;
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k2[i] = k2_one;
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mu[i] = mu_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 angle coefficients");
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}
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/* ---------------------------------------------------------------------- */
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double AngleMWLC::equilibrium_angle(int /*i*/)
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{
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return MY_PI;
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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 AngleMWLC::write_restart(FILE *fp)
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{
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fwrite(&k1[1], sizeof(double), atom->nangletypes, fp);
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fwrite(&k2[1], sizeof(double), atom->nangletypes, fp);
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fwrite(&mu[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 AngleMWLC::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, &k1[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
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utils::sfread(FLERR, &k2[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
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utils::sfread(FLERR, &mu[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
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}
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MPI_Bcast(&k1[1], atom->nangletypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&k2[1], atom->nangletypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&mu[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 AngleMWLC::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 %g\n", i, k1[i], k2[i], mu[i]);
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}
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/* ---------------------------------------------------------------------- */
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double AngleMWLC::single(int type, int i1, int i2, int i3)
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{
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double **x = atom->x;
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double delx1 = x[i1][0] - x[i2][0];
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double dely1 = x[i1][1] - x[i2][1];
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double delz1 = x[i1][2] - x[i2][2];
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domain->minimum_image(delx1, dely1, delz1);
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double r1 = sqrt(delx1 * delx1 + dely1 * dely1 + delz1 * delz1);
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double delx2 = x[i3][0] - x[i2][0];
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double dely2 = x[i3][1] - x[i2][1];
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double delz2 = x[i3][2] - x[i2][2];
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domain->minimum_image(delx2, dely2, delz2);
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double r2 = sqrt(delx2 * delx2 + dely2 * dely2 + delz2 * delz2);
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double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
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c /= r1 * r2;
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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double q = exp(-k1[type] * (1.0 + c));
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double qm = exp(-k2[type] * (1.0 + c) - mu[type]);
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return -log(q + qm);
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}
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/* ---------------------------------------------------------------------- */
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void AngleMWLC::born_matrix(int type, int i1, int i2, int i3, double &du, double &du2)
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{
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double **x = atom->x;
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double delx1 = x[i1][0] - x[i2][0];
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double dely1 = x[i1][1] - x[i2][1];
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double delz1 = x[i1][2] - x[i2][2];
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domain->minimum_image(delx1, dely1, delz1);
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double delx2 = x[i3][0] - x[i2][0];
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double dely2 = x[i3][1] - x[i2][1];
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double delz2 = x[i3][2] - x[i2][2];
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domain->minimum_image(delx2, dely2, delz2);
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double c = delx1 * delx2 + dely1 * dely2 + delz1 * delz2;
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c /= sqrt((delx1 * delx1 + dely1 * dely1 + delz1 * delz1) *
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(delx2 * delx2 + dely2 * dely2 + delz2 * delz2));
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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const double q = exp(-k1[type] * (1.0 + c));
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const double qm = exp(-k2[type] * (1.0 + c) - mu[type]);
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const double Q = q + qm;
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du = (k1[type] * q + k2[type] * qm) / Q;
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du2 = (k1[type] - k2[type]) / Q;
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du2 *= -du2 * q * qm;
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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 *AngleMWLC::extract(const char *str, int &dim)
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{
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dim = 1;
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if (strcmp(str, "k1") == 0) return (void *) k1;
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if (strcmp(str, "k2") == 0) return (void *) k2;
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if (strcmp(str, "mu") == 0) return (void *) mu;
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return nullptr;
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}
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52
src/EXTRA-MOLECULE/angle_mwlc.h
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52
src/EXTRA-MOLECULE/angle_mwlc.h
Normal file
@ -0,0 +1,52 @@
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/* -*- 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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#ifdef ANGLE_CLASS
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// clang-format off
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AngleStyle(mwlc,AngleMWLC);
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// clang-format on
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#else
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#ifndef LMP_ANGLE_MWLC_H
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#define LMP_ANGLE_MWLC_H
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#include "angle.h"
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namespace LAMMPS_NS {
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class AngleMWLC : public Angle {
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public:
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AngleMWLC(class LAMMPS *);
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~AngleMWLC() override;
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void compute(int, int) override;
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void coeff(int, char **) override;
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double equilibrium_angle(int) override;
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void write_restart(FILE *) override;
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void read_restart(FILE *) override;
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void write_data(FILE *) override;
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double single(int, int, int, int) override;
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void born_matrix(int type, int i1, int i2, int i3, double &du, double &du2) override;
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void *extract(const char *, int &) override;
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protected:
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double *k1;
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double *k2;
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double *mu;
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virtual void allocate();
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};
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} // namespace LAMMPS_NS
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#endif
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#endif
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