325 lines
9.4 KiB
C++
325 lines
9.4 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: Carsten Svaneborg, science@zqex.dk
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------------------------------------------------------------------------- */
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#include "angle_cosine_shift_exp.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 "domain.h"
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#include "comm.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 "error.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
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AngleCosineShiftExp::AngleCosineShiftExp(LAMMPS *lmp) : Angle(lmp)
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{
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doExpansion = nullptr;
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umin = nullptr;
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a = nullptr;
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opt1 = nullptr;
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theta0 = nullptr;
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sint = nullptr;
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cost = nullptr;
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}
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/* ---------------------------------------------------------------------- */
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AngleCosineShiftExp::~AngleCosineShiftExp()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(umin);
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memory->destroy(a);
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memory->destroy(opt1);
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memory->destroy(cost);
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memory->destroy(sint);
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memory->destroy(theta0);
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memory->destroy(doExpansion);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleCosineShiftExp::compute(int eflag, int vflag)
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{
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int i1,i2,i3,n,type;
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double delx1,dely1,delz1,delx2,dely2,delz2;
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double eangle,f1[3],f3[3],ff;
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double rsq1,rsq2,r1,r2,c,s,a11,a12,a22;
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double exp2,aa,uumin,cccpsss,cssmscc;
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eangle = 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 **anglelist = neighbor->anglelist;
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int nanglelist = neighbor->nanglelist;
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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 < nanglelist; n++) {
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i1 = anglelist[n][0];
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i2 = anglelist[n][1];
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i3 = anglelist[n][2];
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type = anglelist[n][3];
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// 1st bond
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delx1 = x[i1][0] - x[i2][0];
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dely1 = x[i1][1] - x[i2][1];
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delz1 = x[i1][2] - x[i2][2];
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rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
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r1 = sqrt(rsq1);
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// 2nd bond
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delx2 = x[i3][0] - x[i2][0];
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dely2 = x[i3][1] - x[i2][1];
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delz2 = x[i3][2] - x[i2][2];
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rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
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r2 = sqrt(rsq2);
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// c = cosine of angle
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c = delx1*delx2 + dely1*dely2 + delz1*delz2;
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c /= r1*r2;
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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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// C= sine of angle
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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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aa=a[type];
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uumin=umin[type];
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cccpsss = c*cost[type]+s*sint[type];
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cssmscc = c*sint[type]-s*cost[type];
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if (doExpansion[type])
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{ // |a|<0.01 so use expansions relative precision <1e-5
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// std::cout << "Using expansion\n";
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if (eflag) eangle = -0.125*(1+cccpsss)*(4+aa*(cccpsss-1))*uumin;
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ff=0.25*uumin*cssmscc*(2+aa*cccpsss)/s;
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}
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else
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{
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// std::cout << "Not using expansion\n";
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exp2=exp(0.5*aa*(1+cccpsss));
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if (eflag) eangle = opt1[type]*(1-exp2);
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ff=0.5*a[type]*opt1[type]*exp2*cssmscc/s;
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}
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a11 = ff*c/ rsq1;
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a12 = -ff / (r1*r2);
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a22 = ff*c/ rsq2;
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f1[0] = a11*delx1 + a12*delx2;
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f1[1] = a11*dely1 + a12*dely2;
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f1[2] = a11*delz1 + a12*delz2;
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f3[0] = a22*delx2 + a12*delx1;
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f3[1] = a22*dely2 + a12*dely1;
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f3[2] = a22*delz2 + a12*delz1;
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// apply force to each of 3 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] -= f1[0] + f3[0];
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f[i2][1] -= f1[1] + f3[1];
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f[i2][2] -= f1[2] + f3[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 (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
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delx1,dely1,delz1,delx2,dely2,delz2);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleCosineShiftExp::allocate()
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{
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allocated = 1;
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int n = atom->nangletypes;
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memory->create(doExpansion, n+1, "angle:doExpansion");
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memory->create(umin , n+1, "angle:umin");
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memory->create(a , n+1, "angle:a");
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memory->create(sint , n+1, "angle:sint");
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memory->create(cost , n+1, "angle:cost");
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memory->create(opt1 , n+1, "angle:opt1");
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memory->create(theta0 , n+1, "angle:theta0");
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memory->create(setflag , n+1, "angle: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 AngleCosineShiftExp::coeff(int narg, char **arg)
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{
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if (narg != 4) error->all(FLERR,"Incorrect args for angle 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->nangletypes,ilo,ihi,error);
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double umin_ = utils::numeric(FLERR,arg[1],false,lmp);
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double theta0_ = utils::numeric(FLERR,arg[2],false,lmp);
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double a_ = utils::numeric(FLERR,arg[3],false,lmp);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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doExpansion[i]=(fabs(a_)<0.001);
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umin[i] = umin_;
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a[i] = a_;
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cost[i] = cos(theta0_*MY_PI / 180.0);
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sint[i] = sin(theta0_*MY_PI / 180.0);
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theta0[i]= theta0_*MY_PI / 180.0;
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if (!doExpansion[i]) opt1[i]=umin_/(exp(a_)-1);
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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 angle coefficients");
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}
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/* ---------------------------------------------------------------------- */
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double AngleCosineShiftExp::equilibrium_angle(int i)
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{
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return theta0[i];
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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 AngleCosineShiftExp::write_restart(FILE *fp)
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{
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fwrite(&umin[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&a[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&cost[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&sint[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&theta0[1],sizeof(double),atom->nangletypes,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 AngleCosineShiftExp::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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{
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utils::sfread(FLERR,&umin[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&a[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&cost[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&sint[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&theta0[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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}
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MPI_Bcast(&umin[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&a[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&cost[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&sint[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);
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for (int i = 1; i <= atom->nangletypes; i++)
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{
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setflag[i] = 1;
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doExpansion[i]=(fabs(a[i])<0.01);
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if (!doExpansion[i]) opt1[i]=umin[i]/(exp(a[i])-1);
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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 AngleCosineShiftExp::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->nangletypes; i++)
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fprintf(fp,"%d %g %g %g\n",i,umin[i],theta0[i]/MY_PI*180.0,a[i]);
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}
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/* ---------------------------------------------------------------------- */
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double AngleCosineShiftExp::single(int type, int i1, int i2, int i3)
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{
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double **x = atom->x;
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double delx1 = x[i1][0] - x[i2][0];
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double dely1 = x[i1][1] - x[i2][1];
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double delz1 = x[i1][2] - x[i2][2];
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domain->minimum_image(delx1,dely1,delz1);
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double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);
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double delx2 = x[i3][0] - x[i2][0];
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double dely2 = x[i3][1] - x[i2][1];
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double delz2 = x[i3][2] - x[i2][2];
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domain->minimum_image(delx2,dely2,delz2);
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double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);
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double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
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c /= r1*r2;
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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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double s=sqrt(1.0-c*c);
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double cccpsss=c*cost[type]+s*sint[type];
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if (doExpansion[type])
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{
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return -0.125*(1+cccpsss)*(4+a[type]*(cccpsss-1))*umin[type];
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}
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else
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{
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return opt1[type]*(1-exp(0.5*a[type]*(1+cccpsss)));
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}
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}
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