448 lines
14 KiB
C++
448 lines
14 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: Paul Crozier (SNL)
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------------------------------------------------------------------------- */
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#include "dihedral_charmm.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 "pair.h"
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#include "respa.h"
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#include "update.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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static constexpr double TOLERANCE = 0.05;
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/* ---------------------------------------------------------------------- */
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DihedralCharmm::DihedralCharmm(LAMMPS *_lmp) : Dihedral(_lmp)
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{
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weightflag = 0;
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writedata = 1;
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}
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/* ---------------------------------------------------------------------- */
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DihedralCharmm::~DihedralCharmm()
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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(multiplicity);
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memory->destroy(shift);
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memory->destroy(cos_shift);
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memory->destroy(sin_shift);
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memory->destroy(weight);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DihedralCharmm::compute(int eflag, int vflag)
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{
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int i1, i2, i3, i4, i, m, n, type;
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double vb1x, vb1y, vb1z, vb2x, vb2y, vb2z, vb3x, vb3y, vb3z, vb2xm, vb2ym, vb2zm;
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double edihedral, f1[3], f2[3], f3[3], f4[3];
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double ax, ay, az, bx, by, bz, rasq, rbsq, rgsq, rg, rginv, ra2inv, rb2inv, rabinv;
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double df, df1, ddf1, fg, hg, fga, hgb, gaa, gbb;
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double dtfx, dtfy, dtfz, dtgx, dtgy, dtgz, dthx, dthy, dthz;
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double c, s, p, sx2, sy2, sz2;
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int itype, jtype;
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double delx, dely, delz, rsq, r2inv, r6inv;
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double forcecoul, forcelj, fpair, ecoul, evdwl;
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edihedral = evdwl = ecoul = 0.0;
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ev_init(eflag, vflag);
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// ensure pair->ev_tally() will use 1-4 virial contribution
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if (weightflag && vflag_global == VIRIAL_FDOTR)
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force->pair->vflag_either = force->pair->vflag_global = 1;
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double **x = atom->x;
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double **f = atom->f;
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double *q = atom->q;
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int *atomtype = atom->type;
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int **dihedrallist = neighbor->dihedrallist;
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int ndihedrallist = neighbor->ndihedrallist;
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int nlocal = atom->nlocal;
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int newton_bond = force->newton_bond;
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double qqrd2e = force->qqrd2e;
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for (n = 0; n < ndihedrallist; n++) {
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i1 = dihedrallist[n][0];
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i2 = dihedrallist[n][1];
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i3 = dihedrallist[n][2];
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i4 = dihedrallist[n][3];
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type = dihedrallist[n][4];
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// 1st bond
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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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// 2nd bond
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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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vb2xm = -vb2x;
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vb2ym = -vb2y;
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vb2zm = -vb2z;
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// 3rd bond
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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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ax = vb1y * vb2zm - vb1z * vb2ym;
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ay = vb1z * vb2xm - vb1x * vb2zm;
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az = vb1x * vb2ym - vb1y * vb2xm;
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bx = vb3y * vb2zm - vb3z * vb2ym;
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by = vb3z * vb2xm - vb3x * vb2zm;
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bz = vb3x * vb2ym - vb3y * vb2xm;
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rasq = ax * ax + ay * ay + az * az;
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rbsq = bx * bx + by * by + bz * bz;
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rgsq = vb2xm * vb2xm + vb2ym * vb2ym + vb2zm * vb2zm;
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rg = sqrt(rgsq);
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rginv = ra2inv = rb2inv = 0.0;
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if (rg > 0) rginv = 1.0 / rg;
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if (rasq > 0) ra2inv = 1.0 / rasq;
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if (rbsq > 0) rb2inv = 1.0 / rbsq;
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rabinv = sqrt(ra2inv * rb2inv);
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c = (ax * bx + ay * by + az * bz) * rabinv;
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s = rg * rabinv * (ax * vb3x + ay * vb3y + az * vb3z);
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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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m = multiplicity[type];
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p = 1.0;
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ddf1 = df1 = 0.0;
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for (i = 0; i < m; i++) {
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ddf1 = p * c - df1 * s;
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df1 = p * s + df1 * c;
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p = ddf1;
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}
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p = p * cos_shift[type] + df1 * sin_shift[type];
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df1 = df1 * cos_shift[type] - ddf1 * sin_shift[type];
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df1 *= -m;
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p += 1.0;
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if (m == 0) {
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p = 1.0 + cos_shift[type];
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df1 = 0.0;
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}
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if (eflag) edihedral = k[type] * p;
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fg = vb1x * vb2xm + vb1y * vb2ym + vb1z * vb2zm;
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hg = vb3x * vb2xm + vb3y * vb2ym + vb3z * vb2zm;
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fga = fg * ra2inv * rginv;
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hgb = hg * rb2inv * rginv;
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gaa = -ra2inv * rg;
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gbb = rb2inv * rg;
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dtfx = gaa * ax;
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dtfy = gaa * ay;
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dtfz = gaa * az;
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dtgx = fga * ax - hgb * bx;
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dtgy = fga * ay - hgb * by;
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dtgz = fga * az - hgb * bz;
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dthx = gbb * bx;
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dthy = gbb * by;
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dthz = gbb * bz;
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df = -k[type] * df1;
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sx2 = df * dtgx;
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sy2 = df * dtgy;
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sz2 = df * dtgz;
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f1[0] = df * dtfx;
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f1[1] = df * dtfy;
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f1[2] = df * dtfz;
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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] = df * dthx;
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f4[1] = df * dthy;
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f4[2] = df * dthz;
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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, edihedral, f1, f3, f4, vb1x, vb1y, vb1z, vb2x,
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vb2y, vb2z, vb3x, vb3y, vb3z);
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// 1-4 LJ and Coulomb interactions
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// tally energy/virial in pair, using newton_bond as newton flag
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if (weight[type] > 0.0) {
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itype = atomtype[i1];
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jtype = atomtype[i4];
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delx = x[i1][0] - x[i4][0];
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dely = x[i1][1] - x[i4][1];
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delz = x[i1][2] - x[i4][2];
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rsq = delx * delx + dely * dely + delz * delz;
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r2inv = 1.0 / rsq;
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r6inv = r2inv * r2inv * r2inv;
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if (implicit)
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forcecoul = qqrd2e * q[i1] * q[i4] * r2inv;
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else
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forcecoul = qqrd2e * q[i1] * q[i4] * sqrt(r2inv);
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forcelj = r6inv * (lj14_1[itype][jtype] * r6inv - lj14_2[itype][jtype]);
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fpair = weight[type] * (forcelj + forcecoul) * r2inv;
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if (eflag) {
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ecoul = weight[type] * forcecoul;
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evdwl = r6inv * (lj14_3[itype][jtype] * r6inv - lj14_4[itype][jtype]);
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evdwl *= weight[type];
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}
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += delx * fpair;
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f[i1][1] += dely * fpair;
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f[i1][2] += delz * fpair;
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}
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if (newton_bond || i4 < nlocal) {
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f[i4][0] -= delx * fpair;
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f[i4][1] -= dely * fpair;
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f[i4][2] -= delz * fpair;
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}
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if (evflag)
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force->pair->ev_tally(i1, i4, nlocal, newton_bond, evdwl, ecoul, fpair, delx, dely, delz);
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void DihedralCharmm::allocate()
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{
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allocated = 1;
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const int np1 = atom->ndihedraltypes + 1;
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memory->create(k, np1, "dihedral:k");
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memory->create(multiplicity, np1, "dihedral:multiplicity");
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memory->create(shift, np1, "dihedral:shift");
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memory->create(cos_shift, np1, "dihedral:cos_shift");
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memory->create(sin_shift, np1, "dihedral:sin_shift");
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memory->create(weight, np1, "dihedral:weight");
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memory->create(setflag, np1, "dihedral: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 DihedralCharmm::coeff(int narg, char **arg)
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{
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if (narg != 5) error->all(FLERR, "Incorrect args for dihedral 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->ndihedraltypes, ilo, ihi, error);
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// require integer values of shift for backwards compatibility
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// arbitrary phase angle shift could be allowed, but would break
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// backwards compatibility and is probably not needed
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double k_one = utils::numeric(FLERR, arg[1], false, lmp);
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int multiplicity_one = utils::inumeric(FLERR, arg[2], false, lmp);
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int shift_one = utils::inumeric(FLERR, arg[3], false, lmp);
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double weight_one = utils::numeric(FLERR, arg[4], false, lmp);
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if (multiplicity_one < 0)
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error->all(FLERR, "Incorrect multiplicity arg for dihedral coefficients");
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if (weight_one < 0.0 || weight_one > 1.0)
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error->all(FLERR, "Incorrect weight arg for dihedral coefficients");
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if (weight_one > 0.0) weightflag = 1;
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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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shift[i] = shift_one;
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cos_shift[i] = cos(DEG2RAD * shift_one);
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sin_shift[i] = sin(DEG2RAD * shift_one);
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multiplicity[i] = multiplicity_one;
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weight[i] = weight_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 dihedral coefficients" + utils::errorurl(21));
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}
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/* ----------------------------------------------------------------------
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error check and initialize all values needed for force computation
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------------------------------------------------------------------------- */
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void DihedralCharmm::init_style()
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{
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if (utils::strmatch(update->integrate_style, "^respa")) {
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auto r = dynamic_cast<Respa *>(update->integrate);
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if (r->level_pair >= 0 && (r->level_pair != r->level_dihedral))
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error->all(FLERR, "Dihedral style charmm must be set to same r-RESPA level as 'pair'");
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if (r->level_outer >= 0 && (r->level_outer != r->level_dihedral))
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error->all(FLERR, "Dihedral style charmm must be set to same r-RESPA level as 'outer'");
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}
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// ensure use of CHARMM pair_style if any weight factors are non-zero
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// set local ptrs to LJ 14 arrays setup by Pair
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// also verify that the correct 1-4 scaling is set
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if (weightflag) {
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if ((force->special_lj[3] != 0.0) || (force->special_coul[3] != 0.0))
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error->all(FLERR,
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"Must use 'special_bonds charmm' with dihedral "
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"style charmm for use with CHARMM pair styles");
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int itmp;
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if (force->pair == nullptr)
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error->all(FLERR, "Dihedral charmm is incompatible with Pair style");
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lj14_1 = (double **) force->pair->extract("lj14_1", itmp);
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lj14_2 = (double **) force->pair->extract("lj14_2", itmp);
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lj14_3 = (double **) force->pair->extract("lj14_3", itmp);
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lj14_4 = (double **) force->pair->extract("lj14_4", itmp);
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int *ptr = (int *) force->pair->extract("implicit", itmp);
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if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
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error->all(FLERR, "Dihedral charmm is incompatible with Pair style");
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implicit = *ptr;
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}
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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 DihedralCharmm::write_restart(FILE *fp)
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{
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fwrite(&k[1], sizeof(double), atom->ndihedraltypes, fp);
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fwrite(&multiplicity[1], sizeof(int), atom->ndihedraltypes, fp);
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fwrite(&shift[1], sizeof(int), atom->ndihedraltypes, fp);
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fwrite(&weight[1], sizeof(double), atom->ndihedraltypes, fp);
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fwrite(&weightflag, sizeof(int), 1, 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 DihedralCharmm::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->ndihedraltypes, fp, nullptr, error);
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utils::sfread(FLERR, &multiplicity[1], sizeof(int), atom->ndihedraltypes, fp, nullptr, error);
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utils::sfread(FLERR, &shift[1], sizeof(int), atom->ndihedraltypes, fp, nullptr, error);
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utils::sfread(FLERR, &weight[1], sizeof(double), atom->ndihedraltypes, fp, nullptr, error);
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utils::sfread(FLERR, &weightflag, sizeof(int), 1, fp, nullptr, error);
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}
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MPI_Bcast(&k[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&multiplicity[1], atom->ndihedraltypes, MPI_INT, 0, world);
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MPI_Bcast(&shift[1], atom->ndihedraltypes, MPI_INT, 0, world);
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MPI_Bcast(&weight[1], atom->ndihedraltypes, MPI_DOUBLE, 0, world);
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MPI_Bcast(&weightflag, 1, MPI_INT, 0, world);
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for (int i = 1; i <= atom->ndihedraltypes; i++) {
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setflag[i] = 1;
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cos_shift[i] = cos(DEG2RAD * shift[i]);
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sin_shift[i] = sin(DEG2RAD * shift[i]);
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}
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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 DihedralCharmm::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->ndihedraltypes; i++)
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fprintf(fp, "%d %g %d %d %g\n", i, k[i], multiplicity[i], shift[i], weight[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 *DihedralCharmm::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, "n") == 0) return (void *) multiplicity;
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if (strcmp(str, "d") == 0) return (void *) shift;
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return nullptr;
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}
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