348 lines
10 KiB
C++
348 lines
10 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 "angle_gaussian.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 SMAL 0.001
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#define SMALL 1.0e-8
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/* ---------------------------------------------------------------------- */
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AngleGaussian::AngleGaussian(LAMMPS *lmp)
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: Angle(lmp), nterms(nullptr), angle_temperature(nullptr),
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alpha(nullptr), width(nullptr), theta0(nullptr)
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{
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}
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/* ---------------------------------------------------------------------- */
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AngleGaussian::~AngleGaussian()
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{
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if (allocated && !copymode) {
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memory->destroy(setflag);
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memory->destroy(nterms);
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memory->destroy(angle_temperature);
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for (int i = 1; i <= atom->nangletypes; i++) {
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delete [] alpha[i];
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delete [] width[i];
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delete [] theta0[i];
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}
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delete [] alpha;
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delete [] width;
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delete [] theta0;
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleGaussian::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];
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double dtheta;
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double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
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double prefactor, exponent, g_i, sum_g_i, sum_numerator;
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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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// angle (cos and sin)
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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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s = sqrt(1.0 - c*c);
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if (s < SMAL) s = SMAL;
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s = 1.0/s;
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// force & energy
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double theta = acos(c);
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sum_g_i = 0.0;
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sum_numerator = 0.0;
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for (int i = 0; i < nterms[type]; i++) {
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dtheta = theta - theta0[type][i];
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prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
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exponent = -2*dtheta*dtheta/(width[type][i]*width[type][i]);
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g_i = prefactor*exp(exponent);
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sum_g_i += g_i;
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sum_numerator += g_i*dtheta/(width[type][i]*width[type][i]);
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}
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if (sum_g_i < SMALL) sum_g_i = SMALL;
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if (eflag) eangle = -(force->boltz*angle_temperature[type])*log(sum_g_i);
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// I should check about the sign of this expression
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a = -4.0*(force->boltz*angle_temperature[type])*(sum_numerator/sum_g_i)*s;
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a11 = a*c / rsq1;
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a12 = -a / (r1*r2);
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a22 = a*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 AngleGaussian::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(nterms,n+1,"angle:nterms");
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memory->create(angle_temperature,n+1,"angle:angle_temperature");
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alpha = new double *[n+1];
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width = new double *[n+1];
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theta0 = new double *[n+1];
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memset(alpha,0,sizeof(double)*(n+1));
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memset(width,0,sizeof(double)*(n+1));
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memset(theta0,0,sizeof(double)*(n+1));
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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 or more types
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------------------------------------------------------------------------- */
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void AngleGaussian::coeff(int narg, char **arg)
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{
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if (narg < 6) error->all(FLERR,"Incorrect args for angle coefficients");
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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 angle_temperature_one = utils::numeric(FLERR,arg[1],false,lmp);
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int n = utils::inumeric(FLERR,arg[2],false,lmp);
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if (narg != 3*n + 3)
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error->all(FLERR,"Incorrect args for angle coefficients");
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if (!allocated) allocate();
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// convert theta0 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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angle_temperature[i] = angle_temperature_one;
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nterms[i] = n;
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delete[] alpha[i];
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alpha[i] = new double [n];
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delete[] width[i];
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width[i] = new double [n];
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delete[] theta0[i];
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theta0[i] = new double [n];
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for (int j = 0; j < n; j++) {
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alpha[i][j] = utils::numeric(FLERR,arg[3+3*j],false,lmp);
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width[i][j] = utils::numeric(FLERR,arg[4+3*j],false,lmp);
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theta0[i][j] = utils::numeric(FLERR,arg[5+3*j],false,lmp)* MY_PI / 180.0;
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setflag[i] = 1;
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}
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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 AngleGaussian::equilibrium_angle(int i)
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{
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return theta0[i][0];
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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 AngleGaussian::write_restart(FILE *fp)
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{
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fwrite(&angle_temperature[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&nterms[1],sizeof(int),atom->nangletypes,fp);
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for (int i = 1; i <= atom->nangletypes; i++) {
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fwrite(alpha[i],sizeof(double),nterms[i],fp);
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fwrite(width[i],sizeof(double),nterms[i],fp);
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fwrite(theta0[i],sizeof(double),nterms[i],fp);
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}
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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 AngleGaussian::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,&angle_temperature[1],sizeof(double),atom->nangletypes,fp,nullptr,error);
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utils::sfread(FLERR,&nterms[1],sizeof(int),atom->nangletypes,fp,nullptr,error);
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}
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MPI_Bcast(&angle_temperature[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&nterms[1],atom->nangletypes,MPI_INT,0,world);
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// allocate
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for (int i = 1; i <= atom->nangletypes; i++) {
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alpha[i] = new double [nterms[i]];
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width[i] = new double [nterms[i]];
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theta0[i] = new double [nterms[i]];
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}
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if (comm->me == 0) {
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for (int i = 1; i <= atom->nangletypes; i++) {
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utils::sfread(FLERR,alpha[i],sizeof(double),nterms[i],fp,nullptr,error);
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utils::sfread(FLERR,width[i],sizeof(double),nterms[i],fp,nullptr,error);
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utils::sfread(FLERR,theta0[i],sizeof(double),nterms[i],fp,nullptr,error);
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}
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}
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for (int i = 1; i <= atom->nangletypes; i++) {
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MPI_Bcast(alpha[i],nterms[i],MPI_DOUBLE,0,world);
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MPI_Bcast(width[i],nterms[i],MPI_DOUBLE,0,world);
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MPI_Bcast(theta0[i],nterms[i],MPI_DOUBLE,0,world);
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}
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for (int i = 1; i <= atom->nangletypes; 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 AngleGaussian::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 %d",i,angle_temperature[i],nterms[i]);
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for (int j = 0; j < nterms[i]; j++) {
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fprintf(fp," %g %g %g",alpha[i][j],width[i][j],(theta0[i][j]/MY_PI)*180.0);
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}
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fprintf(fp, "\n");
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}
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}
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/* ---------------------------------------------------------------------- */
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double AngleGaussian::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 theta = acos(c) ;
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double sum_g_i = 0.0;
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for (int i = 0; i < nterms[type]; i++) {
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double dtheta = theta - theta0[type][i];
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double prefactor = (alpha[type][i]/(width[type][i]*sqrt(MY_PI2)));
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double exponent = -2*dtheta*dtheta/(width[type][i]*width[type][i]);
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double g_i = prefactor*exp(exponent);
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sum_g_i += g_i;
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}
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if (sum_g_i < SMALL) sum_g_i = SMALL;
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return -(force->boltz*angle_temperature[type])*log(sum_g_i);
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}
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