325 lines
9.0 KiB
C++
325 lines
9.0 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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/* ----------------------------------------------------------------------
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Contributing author: Tod A Pascal (Caltech)
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------------------------------------------------------------------------- */
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#include "improper_umbrella.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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ImproperUmbrella::ImproperUmbrella(LAMMPS *_lmp) : Improper(_lmp)
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{
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writedata = 1;
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// the first and fourth atoms in the quadruplet are the atoms of symmetry
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symmatoms[0] = 1;
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symmatoms[3] = 2;
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}
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/* ---------------------------------------------------------------------- */
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ImproperUmbrella::~ImproperUmbrella()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(kw);
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memory->destroy(w0);
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memory->destroy(C);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ImproperUmbrella::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 eimproper, f1[3], f2[3], f3[3], f4[3];
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double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z;
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double domega, c, a, s, projhfg, dhax, dhay, dhaz, dahx, dahy, dahz, cotphi;
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double ax, ay, az, ra2, rh2, ra, rh, rar, rhr, arx, ary, arz, hrx, hry, hrz;
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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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// 1st bond
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vb1x = x[i2][0] - x[i1][0];
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vb1y = x[i2][1] - x[i1][1];
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vb1z = x[i2][2] - x[i1][2];
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// 2nd bond
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vb2x = x[i3][0] - x[i1][0];
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vb2y = x[i3][1] - x[i1][1];
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vb2z = x[i3][2] - x[i1][2];
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// 3rd bond
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vb3x = x[i4][0] - x[i1][0];
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vb3y = x[i4][1] - x[i1][1];
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vb3z = x[i4][2] - x[i1][2];
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// c0 calculation
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// A = vb1 X vb2 is perpendicular to IJK plane
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ax = vb1y * vb2z - vb1z * vb2y;
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ay = vb1z * vb2x - vb1x * vb2z;
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az = vb1x * vb2y - vb1y * vb2x;
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ra2 = ax * ax + ay * ay + az * az;
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rh2 = vb3x * vb3x + vb3y * vb3y + vb3z * vb3z;
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ra = sqrt(ra2);
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rh = sqrt(rh2);
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if (ra < SMALL) ra = SMALL;
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if (rh < SMALL) rh = SMALL;
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rar = 1 / ra;
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rhr = 1 / rh;
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arx = ax * rar;
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ary = ay * rar;
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arz = az * rar;
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hrx = vb3x * rhr;
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hry = vb3y * rhr;
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hrz = vb3z * rhr;
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c = arx * hrx + ary * hry + arz * hrz;
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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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cotphi = c / s;
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projhfg =
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(vb3x * vb1x + vb3y * vb1y + vb3z * vb1z) / sqrt(vb1x * vb1x + vb1y * vb1y + vb1z * vb1z);
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projhfg +=
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(vb3x * vb2x + vb3y * vb2y + vb3z * vb2z) / sqrt(vb2x * vb2x + vb2y * vb2y + vb2z * vb2z);
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if (projhfg > 0.0) {
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s *= -1.0;
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cotphi *= -1.0;
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}
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// force and energy
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// if w0 = 0: E = k * (1 - cos w)
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// if w0 != 0: E = 0.5 * C (cos w - cos w0)^2, C = k/(sin(w0)^2
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if (w0[type] == 0.0) {
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if (eflag) eimproper = kw[type] * (1.0 - s);
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a = -kw[type];
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} else {
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domega = s - cos(w0[type]);
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a = 0.5 * C[type] * domega;
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if (eflag) eimproper = a * domega;
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a *= 2.0;
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}
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// dhax = diffrence between H and A in X direction, etc
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a = a * cotphi;
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dhax = hrx - c * arx;
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dhay = hry - c * ary;
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dhaz = hrz - c * arz;
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dahx = arx - c * hrx;
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dahy = ary - c * hry;
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dahz = arz - c * hrz;
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f2[0] = (dhay * vb1z - dhaz * vb1y) * rar * a;
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f2[1] = (dhaz * vb1x - dhax * vb1z) * rar * a;
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f2[2] = (dhax * vb1y - dhay * vb1x) * rar * a;
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f3[0] = (-dhay * vb2z + dhaz * vb2y) * rar * a;
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f3[1] = (-dhaz * vb2x + dhax * vb2z) * rar * a;
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f3[2] = (-dhax * vb2y + dhay * vb2x) * rar * a;
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f4[0] = dahx * rhr * a;
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f4[1] = dahy * rhr * a;
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f4[2] = dahz * rhr * a;
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f1[0] = -(f2[0] + f3[0] + f4[0]);
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f1[1] = -(f2[1] + f3[1] + f4[1]);
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f1[2] = -(f2[2] + f3[2] + 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] += f3[0];
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f[i2][1] += f3[1];
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f[i2][2] += f3[2];
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}
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if (newton_bond || i3 < nlocal) {
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f[i3][0] += f2[0];
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f[i3][1] += f2[1];
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f[i3][2] += f2[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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// get correct 4-body geometry for virial tally
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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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ev_tally(i1, i2, i3, i4, nlocal, newton_bond, eimproper, f1, f2, 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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/* ---------------------------------------------------------------------- */
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void ImproperUmbrella::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(kw, np1, "improper:kw");
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memory->create(w0, np1, "improper:w0");
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memory->create(C, np1, "improper:C");
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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 ImproperUmbrella::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 w_one = utils::numeric(FLERR, arg[2], false, lmp);
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// convert w0 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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kw[i] = k_one;
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w0[i] = DEG2RAD * w_one;
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if (w_one == 0)
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C[i] = 1.0;
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else
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C[i] = kw[i] / (pow(sin(w0[i]), 2.0));
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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 ImproperUmbrella::write_restart(FILE *fp)
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{
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fwrite(&kw[1], sizeof(double), atom->nimpropertypes, fp);
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fwrite(&w0[1], sizeof(double), atom->nimpropertypes, fp);
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fwrite(&C[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 ImproperUmbrella::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, &kw[1], sizeof(double), atom->nimpropertypes, fp, nullptr, error);
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utils::sfread(FLERR, &w0[1], sizeof(double), atom->nimpropertypes, fp, nullptr, error);
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utils::sfread(FLERR, &C[1], sizeof(double), atom->nimpropertypes, fp, nullptr, error);
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}
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MPI_Bcast(&kw[1], atom->nimpropertypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&w0[1], atom->nimpropertypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&C[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 ImproperUmbrella::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, kw[i], RAD2DEG * w0[i]);
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}
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