312 lines
8.9 KiB
C++
312 lines
8.9 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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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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/* ----------------------------------------------------------------------
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Contributing author: Paul Crozier (SNL)
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------------------------------------------------------------------------- */
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#include "angle_charmm.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 MathConst::DEG2RAD;
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using MathConst::RAD2DEG;
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static constexpr double SMALL = 0.001;
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/* ---------------------------------------------------------------------- */
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AngleCharmm::AngleCharmm(LAMMPS *_lmp) : Angle(_lmp) {}
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/* ---------------------------------------------------------------------- */
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AngleCharmm::~AngleCharmm()
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{
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if (allocated && !copymode) {
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memory->destroy(setflag);
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memory->destroy(k);
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memory->destroy(theta0);
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memory->destroy(k_ub);
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memory->destroy(r_ub);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleCharmm::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 dtheta, tk;
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double rsq1, rsq2, r1, r2, c, s, a, a11, a12, a22;
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double delxUB, delyUB, delzUB, rsqUB, rUB, dr, rk, forceUB;
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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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// Urey-Bradley bond
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delxUB = x[i3][0] - x[i1][0];
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delyUB = x[i3][1] - x[i1][1];
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delzUB = x[i3][2] - x[i1][2];
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rsqUB = delxUB * delxUB + delyUB * delyUB + delzUB * delzUB;
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rUB = sqrt(rsqUB);
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// Urey-Bradley force & energy
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dr = rUB - r_ub[type];
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rk = k_ub[type] * dr;
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if (rUB > 0.0)
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forceUB = -2.0 * rk / rUB;
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else
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forceUB = 0.0;
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if (eflag) eangle = rk * dr;
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// angle (cos and sin)
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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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s = sqrt(1.0 - c * c);
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if (s < SMALL) s = SMALL;
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s = 1.0 / s;
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// harmonic force & energy
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dtheta = acos(c) - theta0[type];
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tk = k[type] * dtheta;
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if (eflag) eangle += tk * dtheta;
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a = -2.0 * tk * s;
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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 - delxUB * forceUB;
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f1[1] = a11 * dely1 + a12 * dely2 - delyUB * forceUB;
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f1[2] = a11 * delz1 + a12 * delz2 - delzUB * forceUB;
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f3[0] = a22 * delx2 + a12 * delx1 + delxUB * forceUB;
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f3[1] = a22 * dely2 + a12 * dely1 + delyUB * forceUB;
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f3[2] = a22 * delz2 + a12 * delz1 + delzUB * forceUB;
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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 AngleCharmm::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(k, np1, "angle:k");
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memory->create(theta0, np1, "angle:theta0");
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memory->create(k_ub, np1, "angle:k_ub");
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memory->create(r_ub, np1, "angle:r_ub");
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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 AngleCharmm::coeff(int narg, char **arg)
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{
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if (narg != 5) 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 k_one = utils::numeric(FLERR, arg[1], false, lmp);
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double theta0_one = utils::numeric(FLERR, arg[2], false, lmp);
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double k_ub_one = utils::numeric(FLERR, arg[3], false, lmp);
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double r_ub_one = utils::numeric(FLERR, arg[4], false, lmp);
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// convert theta0 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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theta0[i] = DEG2RAD * theta0_one;
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k_ub[i] = k_ub_one;
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r_ub[i] = r_ub_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 AngleCharmm::equilibrium_angle(int i)
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{
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return theta0[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 AngleCharmm::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(&theta0[1], sizeof(double), atom->nangletypes, fp);
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fwrite(&k_ub[1], sizeof(double), atom->nangletypes, fp);
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fwrite(&r_ub[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 AngleCharmm::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, &theta0[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
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utils::sfread(FLERR, &k_ub[1], sizeof(double), atom->nangletypes, fp, nullptr, error);
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utils::sfread(FLERR, &r_ub[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(&theta0[1], atom->nangletypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&k_ub[1], atom->nangletypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&r_ub[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 AngleCharmm::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->nangletypes; i++)
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fprintf(fp, "%d %g %g %g %g\n", i, k[i], RAD2DEG * theta0[i], k_ub[i], r_ub[i]);
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}
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/* ---------------------------------------------------------------------- */
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double AngleCharmm::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 delxUB = x[i3][0] - x[i1][0];
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double delyUB = x[i3][1] - x[i1][1];
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double delzUB = x[i3][2] - x[i1][2];
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domain->minimum_image(delxUB, delyUB, delzUB);
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double rUB = sqrt(delxUB * delxUB + delyUB * delyUB + delzUB * delzUB);
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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 dtheta = acos(c) - theta0[type];
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double tk = k[type] * dtheta;
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double dr = rUB - r_ub[type];
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double rk = k_ub[type] * dr;
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return (tk * dtheta + rk * dr);
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}
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