271 lines
8.1 KiB
C++
271 lines
8.1 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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/* ----------------------------------------------------------------------
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Contributing author: Paolo Raiteri (Curtin University)
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------------------------------------------------------------------------- */
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#include <mpi.h>
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#include <cmath>
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#include <cstdlib>
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#include "improper_distance.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 "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define TOLERANCE 0.05
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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
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ImproperDistance::ImproperDistance(LAMMPS *lmp) : Improper(lmp) {}
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/* ---------------------------------------------------------------------- */
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ImproperDistance::~ImproperDistance()
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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 ImproperDistance::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 xab, yab, zab; // bond 1-2
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double xac, yac, zac; // bond 1-3
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double xad, yad, zad; // bond 1-4
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double xbc, ybc, zbc; // bond 2-3
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double xbd, ybd, zbd; // bond 2-4
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double xna, yna, zna, rna; // normal
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double da;
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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 domega,a;
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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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// 1 is the central atom
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// 2-3-4 are ment to be equivalent
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// I need the bonds between 2-3 and 2-4 to get the plane normal
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// Then I need the bond 1-2 to project it onto the normal to the plane
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// bond 1->2
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xab = x[i2][0] - x[i1][0];
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yab = x[i2][1] - x[i1][1];
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zab = x[i2][2] - x[i1][2];
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domain->minimum_image(xab,yab,zab);
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// bond 1->3
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xac = x[i3][0] - x[i1][0];
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yac = x[i3][1] - x[i1][1];
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zac = x[i3][2] - x[i1][2];
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domain->minimum_image(xac,yac,zac);
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// bond 1->4
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xad = x[i4][0] - x[i1][0];
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yad = x[i4][1] - x[i1][1];
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zad = x[i4][2] - x[i1][2];
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domain->minimum_image(xad,yad,zad);
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// bond 2-3
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xbc = x[i3][0] - x[i2][0];
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ybc = x[i3][1] - x[i2][1];
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zbc = x[i3][2] - x[i2][2];
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domain->minimum_image(xbc,ybc,zbc);
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// bond 2-4
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xbd = x[i4][0] - x[i2][0];
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ybd = x[i4][1] - x[i2][1];
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zbd = x[i4][2] - x[i2][2];
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domain->minimum_image(xbd,ybd,zbd);
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xna = ybc*zbd - zbc*ybd;
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yna = -(xbc*zbd - zbc*xbd);
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zna = xbc*ybd - ybc*xbd;
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rna = 1.0 / sqrt(xna*xna+yna*yna+zna*zna);
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xna *= rna;
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yna *= rna;
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zna *= rna;
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da = xna*xab + yna*yab + zna*zab;
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domega = k[type]*da*da + chi[type]*da*da*da*da;
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//printf("%3i %3i %3i %3i %10.5f %10.5f \n",i1,i2,i3,i4,da,domega);
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a = 2.0* (k[type]*da + 2.0*chi[type]*da*da*da);
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if (eflag) eimproper = domega;
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f1[0] = a*( xna);
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f1[1] = a*( yna);
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f1[2] = a*( zna);
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f2[0] = a*( -xna -yab*(zbd-zbc)*rna +zab*(ybd-ybc)*rna -da*( -yna*(zbd-zbc) + zna*(ybd-ybc) )*rna);
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f2[1] = a*( +xab*(zbd-zbc)*rna -yna +zab*(xbc-xbd)*rna -da*( +xna*(zbd-zbc) + zna*(xbc-xbd) )*rna);
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f2[2] = a*( -xab*(ybd-ybc)*rna -yab*(xbc-xbd)*rna -zna -da*( +xna*(ybc-ybd) - yna*(xbc-xbd) )*rna);
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f3[0] = a*( ( yab*zbd -zab*ybd ) *rna +da*( -yna*zbd +zna*ybd )*rna);
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f3[1] = a*( ( -xab*zbd +zab*xbd ) *rna +da*( +xna*zbd -zna*xbd )*rna);
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f3[2] = a*( ( +xab*ybd -yab*xbd ) *rna +da*( -xna*ybd +yna*xbd )*rna);
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f4[0] = a*( ( -yab*zbc +zab*ybc ) *rna -da*( -yna*zbc +zna*ybc )*rna);
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f4[1] = a*( ( +xab*zbc -zab*xbc ) *rna -da*( +xna*zbc -zna*xbc )*rna);
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f4[2] = a*( ( -xab*ybc +yab*xbc ) *rna -da*( -xna*ybc +yna*xbc )*rna);
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//printf("%10.5f %10.5f %10.5f \n",f1[0],f1[1],f1[2]);
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//printf("%10.5f %10.5f %10.5f \n",f2[0],f2[1],f2[2]);
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//printf("%10.5f %10.5f %10.5f \n",f3[0],f3[1],f3[2]);
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//printf("%10.5f %10.5f %10.5f \n",f4[0],f4[1],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,f2,f3,f4,
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xab,yab,zab,xac,yac,zac,xad-xac,yad-yac,zad-zac);
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}
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}
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/* ---------------------------------------------------------------------- */
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void ImproperDistance::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 ImproperDistance::coeff(int narg, char **arg)
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{
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// if (which > 0) return;
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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(FLERR,arg[0],atom->nimpropertypes,ilo,ihi);
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double k_one = force->numeric(FLERR,arg[1]);
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double chi_one = force->numeric(FLERR,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;
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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 ImproperDistance::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 ImproperDistance::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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/* ----------------------------------------------------------------------
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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void ImproperDistance::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->nimpropertypes; i++)
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fprintf(fp,"%d %g %g\n",i,k[i],chi[i]);
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}
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