291 lines
8.0 KiB
C++
291 lines
8.0 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "improper_harmonic.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 <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 TOLERANCE = 0.05;
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static constexpr double SMALL = 0.001;
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/* ---------------------------------------------------------------------- */
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ImproperHarmonic::ImproperHarmonic(LAMMPS *_lmp) : Improper(_lmp)
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{
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writedata = 1;
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// the first atom in the quadruplet is the atom of symmetry
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symmatoms[0] = 1;
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}
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/* ---------------------------------------------------------------------- */
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ImproperHarmonic::~ImproperHarmonic()
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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(chi0);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ImproperHarmonic::compute(int eflag, int vflag)
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{
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int i1, i2, i3, i4, n, type;
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double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z;
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double eimproper, f1[3], f2[3], f3[3], f4[3];
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double ss1, ss2, ss3, r1, r2, r3, c0, c1, c2, s1, s2;
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double s12, c, s, domega, a, a11, a22, a33, a12, a13, a23;
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double sx2, sy2, sz2;
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eimproper = 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 **improperlist = neighbor->improperlist;
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int nimproperlist = neighbor->nimproperlist;
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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 < nimproperlist; n++) {
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i1 = improperlist[n][0];
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i2 = improperlist[n][1];
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i3 = improperlist[n][2];
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i4 = improperlist[n][3];
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type = improperlist[n][4];
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// geometry of 4-body
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vb1x = x[i1][0] - x[i2][0];
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vb1y = x[i1][1] - x[i2][1];
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vb1z = x[i1][2] - x[i2][2];
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vb2x = x[i3][0] - x[i2][0];
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vb2y = x[i3][1] - x[i2][1];
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vb2z = x[i3][2] - x[i2][2];
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vb3x = x[i4][0] - x[i3][0];
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vb3y = x[i4][1] - x[i3][1];
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vb3z = x[i4][2] - x[i3][2];
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ss1 = 1.0 / (vb1x * vb1x + vb1y * vb1y + vb1z * vb1z);
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ss2 = 1.0 / (vb2x * vb2x + vb2y * vb2y + vb2z * vb2z);
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ss3 = 1.0 / (vb3x * vb3x + vb3y * vb3y + vb3z * vb3z);
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r1 = sqrt(ss1);
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r2 = sqrt(ss2);
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r3 = sqrt(ss3);
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// sin and cos of angle
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c0 = (vb1x * vb3x + vb1y * vb3y + vb1z * vb3z) * r1 * r3;
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c1 = (vb1x * vb2x + vb1y * vb2y + vb1z * vb2z) * r1 * r2;
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c2 = -(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) * r3 * r2;
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s1 = 1.0 - c1 * c1;
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if (s1 < SMALL) s1 = SMALL;
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s1 = 1.0 / s1;
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s2 = 1.0 - c2 * c2;
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if (s2 < SMALL) s2 = SMALL;
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s2 = 1.0 / s2;
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s12 = sqrt(s1 * s2);
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c = (c1 * c2 + c0) * s12;
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// error check
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if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) problem(FLERR, i1, i2, i3, i4);
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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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// force & energy
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domega = acos(c) - chi0[type];
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a = k[type] * domega;
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if (eflag) eimproper = a * domega;
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a = -a * 2.0 / s;
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c = c * a;
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s12 = s12 * a;
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a11 = c * ss1 * s1;
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a22 = -ss2 * (2.0 * c0 * s12 - c * (s1 + s2));
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a33 = c * ss3 * s2;
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a12 = -r1 * r2 * (c1 * c * s1 + c2 * s12);
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a13 = -r1 * r3 * s12;
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a23 = r2 * r3 * (c2 * c * s2 + c1 * s12);
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sx2 = a22 * vb2x + a23 * vb3x + a12 * vb1x;
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sy2 = a22 * vb2y + a23 * vb3y + a12 * vb1y;
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sz2 = a22 * vb2z + a23 * vb3z + a12 * vb1z;
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f1[0] = a12 * vb2x + a13 * vb3x + a11 * vb1x;
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f1[1] = a12 * vb2y + a13 * vb3y + a11 * vb1y;
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f1[2] = a12 * vb2z + a13 * vb3z + a11 * vb1z;
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f2[0] = -sx2 - f1[0];
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f2[1] = -sy2 - f1[1];
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f2[2] = -sz2 - f1[2];
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f4[0] = a23 * vb2x + a33 * vb3x + a13 * vb1x;
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f4[1] = a23 * vb2y + a33 * vb3y + a13 * vb1y;
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f4[2] = a23 * vb2z + a33 * vb3z + a13 * vb1z;
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f3[0] = sx2 - f4[0];
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f3[1] = sy2 - f4[1];
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f3[2] = sz2 - f4[2];
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// apply force to each of 4 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] += f2[0];
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f[i2][1] += f2[1];
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f[i2][2] += f2[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 (newton_bond || i4 < nlocal) {
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f[i4][0] += f4[0];
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f[i4][1] += f4[1];
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f[i4][2] += f4[2];
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}
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if (evflag)
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ev_tally(i1, i2, i3, i4, nlocal, newton_bond, eimproper, f1, f3, f4, vb1x, vb1y, vb1z, vb2x,
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vb2y, vb2z, vb3x, vb3y, vb3z);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ImproperHarmonic::allocate()
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{
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allocated = 1;
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const int np1 = atom->nimpropertypes + 1;
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memory->create(k, np1, "improper:k");
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memory->create(chi0, np1, "improper:chi0");
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memory->create(setflag, np1, "improper: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 ImproperHarmonic::coeff(int narg, char **arg)
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{
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if (narg != 3) error->all(FLERR, "Incorrect args for improper 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->nimpropertypes, ilo, ihi, error);
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double k_one = utils::numeric(FLERR, arg[1], false, lmp);
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double chi_one = utils::numeric(FLERR, arg[2], false, lmp);
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// convert chi0 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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chi0[i] = DEG2RAD * chi_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 improper coefficients");
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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 ImproperHarmonic::write_restart(FILE *fp)
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{
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fwrite(&k[1], sizeof(double), atom->nimpropertypes, fp);
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fwrite(&chi0[1], sizeof(double), atom->nimpropertypes, 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 ImproperHarmonic::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->nimpropertypes, fp, nullptr, error);
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utils::sfread(FLERR, &chi0[1], sizeof(double), atom->nimpropertypes, fp, nullptr, error);
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}
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MPI_Bcast(&k[1], atom->nimpropertypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&chi0[1], atom->nimpropertypes, MPI_DOUBLE, 0, world);
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for (int i = 1; i <= atom->nimpropertypes; 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 ImproperHarmonic::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->nimpropertypes; i++)
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fprintf(fp, "%d %g %g\n", i, k[i], RAD2DEG * chi0[i]);
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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 *ImproperHarmonic::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, "chi0") == 0) return (void *) chi0;
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return nullptr;
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}
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