288 lines
7.6 KiB
C++
288 lines
7.6 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://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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#include "lmptype.h"
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#include "mpi.h"
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#include "math.h"
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#include "stdlib.h"
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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 "neighbor.h"
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#include "domain.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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/* ---------------------------------------------------------------------- */
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ImproperHarmonic::ImproperHarmonic(LAMMPS *lmp) : Improper(lmp) {}
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/* ---------------------------------------------------------------------- */
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ImproperHarmonic::~ImproperHarmonic()
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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(chi);
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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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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 0;
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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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domain->minimum_image(vb1x,vb1y,vb1z);
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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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domain->minimum_image(vb2x,vb2y,vb2z);
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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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domain->minimum_image(vb3x,vb3y,vb3z);
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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)) {
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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,
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"Improper problem: %d " BIGINT_FORMAT " %d %d %d %d",
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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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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) - chi[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,
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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 ImproperHarmonic::allocate()
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{
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allocated = 1;
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int n = atom->nimpropertypes;
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memory->create(k,n+1,"improper:k");
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memory->create(chi,n+1,"improper:chi");
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memory->create(setflag,n+1,"improper: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 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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force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
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double k_one = force->numeric(arg[1]);
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double chi_one = force->numeric(arg[2]);
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// convert chi 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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chi[i] = chi_one/180.0 * MY_PI;
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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(&chi[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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fread(&k[1],sizeof(double),atom->nimpropertypes,fp);
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fread(&chi[1],sizeof(double),atom->nimpropertypes,fp);
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}
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MPI_Bcast(&k[1],atom->nimpropertypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&chi[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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