349 lines
9.5 KiB
C++
349 lines
9.5 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://lammps.sandia.gov/, 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: Loukas D. Peristeras (Scienomics SARL)
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[ based on dihedral_helix.cpp Paul Crozier (SNL) ]
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------------------------------------------------------------------------- */
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#include "dihedral_quadratic.h"
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#include <cmath>
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#include "atom.h"
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#include "neighbor.h"
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#include "comm.h"
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#include "force.h"
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#include "update.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define TOLERANCE 0.05
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#define SMALL 0.001
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#define SMALLER 0.00001
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/* ---------------------------------------------------------------------- */
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DihedralQuadratic::DihedralQuadratic(LAMMPS *lmp) : Dihedral(lmp)
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{
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writedata = 1;
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}
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/* ---------------------------------------------------------------------- */
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DihedralQuadratic::~DihedralQuadratic()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(k);
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memory->destroy(phi0);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DihedralQuadratic::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,vb2xm,vb2ym,vb2zm;
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double edihedral,f1[3],f2[3],f3[3],f4[3];
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double sb1,sb2,sb3,rb1,rb3,c0,b1mag2,b1mag,b2mag2;
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double b2mag,b3mag2,b3mag,ctmp,r12c1,c1mag,r12c2;
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double c2mag,sc1,sc2,s1,s12,c,p,pd,a,a11,a22;
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double a33,a12,a13,a23,sx2,sy2,sz2;
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double s2,cx,cy,cz,cmag,dx,phi,si,siinv,sin2;
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edihedral = 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 **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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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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// c0 calculation
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sb1 = 1.0 / (vb1x*vb1x + vb1y*vb1y + vb1z*vb1z);
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sb2 = 1.0 / (vb2x*vb2x + vb2y*vb2y + vb2z*vb2z);
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sb3 = 1.0 / (vb3x*vb3x + vb3y*vb3y + vb3z*vb3z);
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rb1 = sqrt(sb1);
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rb3 = sqrt(sb3);
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c0 = (vb1x*vb3x + vb1y*vb3y + vb1z*vb3z) * rb1*rb3;
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// 1st and 2nd angle
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b1mag2 = vb1x*vb1x + vb1y*vb1y + vb1z*vb1z;
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b1mag = sqrt(b1mag2);
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b2mag2 = vb2x*vb2x + vb2y*vb2y + vb2z*vb2z;
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b2mag = sqrt(b2mag2);
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b3mag2 = vb3x*vb3x + vb3y*vb3y + vb3z*vb3z;
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b3mag = sqrt(b3mag2);
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ctmp = vb1x*vb2x + vb1y*vb2y + vb1z*vb2z;
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r12c1 = 1.0 / (b1mag*b2mag);
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c1mag = ctmp * r12c1;
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ctmp = vb2xm*vb3x + vb2ym*vb3y + vb2zm*vb3z;
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r12c2 = 1.0 / (b2mag*b3mag);
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c2mag = ctmp * r12c2;
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// cos and sin of 2 angles and final c
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sin2 = MAX(1.0 - c1mag*c1mag,0.0);
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sc1 = sqrt(sin2);
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if (sc1 < SMALL) sc1 = SMALL;
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sc1 = 1.0/sc1;
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sin2 = MAX(1.0 - c2mag*c2mag,0.0);
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sc2 = sqrt(sin2);
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if (sc2 < SMALL) sc2 = SMALL;
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sc2 = 1.0/sc2;
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s1 = sc1 * sc1;
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s2 = sc2 * sc2;
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s12 = sc1 * sc2;
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c = (c0 + c1mag*c2mag) * s12;
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cx = vb1y*vb2z - vb1z*vb2y;
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cy = vb1z*vb2x - vb1x*vb2z;
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cz = vb1x*vb2y - vb1y*vb2x;
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cmag = sqrt(cx*cx + cy*cy + cz*cz);
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dx = (cx*vb3x + cy*vb3y + cz*vb3z)/cmag/b3mag;
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// error check
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if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
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int me;
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MPI_Comm_rank(world,&me);
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if (screen) {
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char str[128];
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sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
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TAGINT_FORMAT " " TAGINT_FORMAT " "
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TAGINT_FORMAT " " TAGINT_FORMAT,
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me,update->ntimestep,
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atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
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error->warning(FLERR,str,0);
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fprintf(screen," 1st atom: %d %g %g %g\n",
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me,x[i1][0],x[i1][1],x[i1][2]);
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fprintf(screen," 2nd atom: %d %g %g %g\n",
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me,x[i2][0],x[i2][1],x[i2][2]);
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fprintf(screen," 3rd atom: %d %g %g %g\n",
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me,x[i3][0],x[i3][1],x[i3][2]);
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fprintf(screen," 4th atom: %d %g %g %g\n",
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me,x[i4][0],x[i4][1],x[i4][2]);
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}
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}
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if (c > 1.0) c = 1.0;
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if (c < -1.0) c = -1.0;
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// force & energy
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// p = k ( phi- phi0)^2
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// pd = dp/dc
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phi = acos(c);
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if (dx > 0.0) phi *= -1.0;
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si = sin(phi);
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if (fabs(si) < SMALLER) si = SMALLER;
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siinv = 1.0/si;
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double dphi = phi-phi0[type];
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if (dphi > MY_PI) dphi -= 2*MY_PI;
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else if (dphi < -MY_PI) dphi += 2*MY_PI;
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p = k[type]*dphi;
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pd = - 2.0 * p * siinv;
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p = p * dphi;
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if (eflag) edihedral = p;
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a = pd;
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c = c * a;
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s12 = s12 * a;
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a11 = c*sb1*s1;
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a22 = -sb2 * (2.0*c0*s12 - c*(s1+s2));
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a33 = c*sb3*s2;
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a12 = -r12c1 * (c1mag*c*s1 + c2mag*s12);
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a13 = -rb1*rb3*s12;
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a23 = r12c2 * (c2mag*c*s2 + c1mag*s12);
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sx2 = a12*vb1x + a22*vb2x + a23*vb3x;
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sy2 = a12*vb1y + a22*vb2y + a23*vb3y;
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sz2 = a12*vb1z + a22*vb2z + a23*vb3z;
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f1[0] = a11*vb1x + a12*vb2x + a13*vb3x;
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f1[1] = a11*vb1y + a12*vb2y + a13*vb3y;
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f1[2] = a11*vb1z + a12*vb2z + a13*vb3z;
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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] = a13*vb1x + a23*vb2x + a33*vb3x;
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f4[1] = a13*vb1y + a23*vb2y + a33*vb3y;
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f4[2] = a13*vb1z + a23*vb2z + a33*vb3z;
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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,
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vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
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}
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}
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/* ---------------------------------------------------------------------- */
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void DihedralQuadratic::allocate()
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{
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allocated = 1;
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int n = atom->ndihedraltypes;
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memory->create(k,n+1,"dihedral:k");
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memory->create(phi0,n+1,"dihedral:phi0");
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memory->create(setflag,n+1,"dihedral:setflag");
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for (int i = 1; i <= n; 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 DihedralQuadratic::coeff(int narg, char **arg)
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{
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if (narg != 3) error->all(FLERR,"Incorrect args for dihedral 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->ndihedraltypes,ilo,ihi,error);
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double k_one = utils::numeric(FLERR,arg[1],false,lmp);
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double phi0_one= utils::numeric(FLERR,arg[2],false,lmp);
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// require k >= 0
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if (k_one < 0.0)
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error->all(FLERR,"Incorrect coefficient arg for dihedral coefficients");
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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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phi0[i] = phi0_one*MY_PI/180.0;
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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 dihedral 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 DihedralQuadratic::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(&phi0[1],sizeof(double),atom->ndihedraltypes,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 DihedralQuadratic::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,&phi0[1],sizeof(double),atom->ndihedraltypes,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(&phi0[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
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for (int i = 1; i <= atom->ndihedraltypes; 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 DihedralQuadratic::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 %g \n",i,k[i],phi0[i]*180.0/MY_PI);
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}
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