forked from lijiext/lammps
removed harmonic bond and angle from repo
This commit is contained in:
cdt1802
parent
331fff0613
commit
902d772b85
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@ -1,264 +0,0 @@
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/* ----------------------------------------------------------------------
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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 <cmath>
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#include <cstdlib>
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#include "angle_harmonic.h"
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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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AngleHarmonic::AngleHarmonic(LAMMPS *lmp) : Angle(lmp)
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{
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k = NULL;
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theta0 = NULL;
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}
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/* ---------------------------------------------------------------------- */
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AngleHarmonic::~AngleHarmonic()
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{
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if (allocated && !copymode) {
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memory->destroy(setflag);
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memory->destroy(k);
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memory->destroy(theta0);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleHarmonic::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,tk;
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double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;
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eangle = 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 **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 < SMALL) s = SMALL;
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s = 1.0/s;
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// force & energy
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dtheta = acos(c) - theta0[type];
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tk = k[type] * dtheta;
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if (eflag) eangle = tk*dtheta;
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a = -2.0 * tk * 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 AngleHarmonic::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(k,n+1,"angle:k");
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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 or more types
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------------------------------------------------------------------------- */
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void AngleHarmonic::coeff(int narg, char **arg)
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{
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if (narg != 3) 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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force->bounds(FLERR,arg[0],atom->nangletypes,ilo,ihi);
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double k_one = force->numeric(FLERR,arg[1]);
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double theta0_one = force->numeric(FLERR,arg[2]);
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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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k[i] = k_one;
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theta0[i] = theta0_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 angle coefficients");
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}
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/* ---------------------------------------------------------------------- */
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double AngleHarmonic::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 AngleHarmonic::write_restart(FILE *fp)
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{
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fwrite(&k[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 AngleHarmonic::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->nangletypes,fp);
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fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
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}
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MPI_Bcast(&k[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++) 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 AngleHarmonic::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\n",i,k[i],theta0[i]/MY_PI*180.0);
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}
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/* ---------------------------------------------------------------------- */
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double AngleHarmonic::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 dtheta = acos(c) - theta0[type];
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double tk = k[type] * dtheta;
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return tk*dtheta;
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}
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@ -1,215 +0,0 @@
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/* ----------------------------------------------------------------------
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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 <cmath>
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#include <cstdlib>
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#include <cstring>
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#include "bond_harmonic.h"
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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 "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp)
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{
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reinitflag = 1;
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}
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/* ---------------------------------------------------------------------- */
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BondHarmonic::~BondHarmonic()
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{
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if (allocated && !copymode) {
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memory->destroy(setflag);
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memory->destroy(k);
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memory->destroy(r0);
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}
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}
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/* ---------------------------------------------------------------------- */
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void BondHarmonic::compute(int eflag, int vflag)
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{
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int i1,i2,n,type;
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double delx,dely,delz,ebond,fbond;
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double rsq,r,dr,rk;
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ebond = 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 **bondlist = neighbor->bondlist;
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int nbondlist = neighbor->nbondlist;
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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 < nbondlist; n++) {
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i1 = bondlist[n][0];
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i2 = bondlist[n][1];
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type = bondlist[n][2];
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delx = x[i1][0] - x[i2][0];
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dely = x[i1][1] - x[i2][1];
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delz = x[i1][2] - x[i2][2];
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rsq = delx*delx + dely*dely + delz*delz;
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r = sqrt(rsq);
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dr = r - r0[type];
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rk = k[type] * dr;
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// force & energy
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if (r > 0.0) fbond = -2.0*rk/r;
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else fbond = 0.0;
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if (eflag) ebond = rk*dr;
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// apply force to each of 2 atoms
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if (newton_bond || i1 < nlocal) {
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f[i1][0] += delx*fbond;
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f[i1][1] += dely*fbond;
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f[i1][2] += delz*fbond;
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}
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if (newton_bond || i2 < nlocal) {
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f[i2][0] -= delx*fbond;
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f[i2][1] -= dely*fbond;
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f[i2][2] -= delz*fbond;
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}
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if (evflag) ev_tally(i1,i2,nlocal,newton_bond,ebond,fbond,delx,dely,delz);
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}
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}
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/* ---------------------------------------------------------------------- */
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void BondHarmonic::allocate()
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{
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allocated = 1;
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int n = atom->nbondtypes;
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memory->create(k,n+1,"bond:k");
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memory->create(r0,n+1,"bond:r0");
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memory->create(setflag,n+1,"bond: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 BondHarmonic::coeff(int narg, char **arg)
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{
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if (narg != 3) error->all(FLERR,"Incorrect args for bond 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->nbondtypes,ilo,ihi);
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double k_one = force->numeric(FLERR,arg[1]);
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double r0_one = force->numeric(FLERR,arg[2]);
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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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r0[i] = r0_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 bond coefficients");
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}
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/* ----------------------------------------------------------------------
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return an equilbrium bond length
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------------------------------------------------------------------------- */
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double BondHarmonic::equilibrium_distance(int i)
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{
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return r0[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 BondHarmonic::write_restart(FILE *fp)
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{
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fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
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fwrite(&r0[1],sizeof(double),atom->nbondtypes,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 BondHarmonic::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->nbondtypes,fp);
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fread(&r0[1],sizeof(double),atom->nbondtypes,fp);
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}
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MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&r0[1],atom->nbondtypes,MPI_DOUBLE,0,world);
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for (int i = 1; i <= atom->nbondtypes; 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 BondHarmonic::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->nbondtypes; i++)
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fprintf(fp,"%d %g %g\n",i,k[i],r0[i]);
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}
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/* ---------------------------------------------------------------------- */
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double BondHarmonic::single(int type, double rsq, int /*i*/, int /*j*/,
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double &fforce)
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{
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double r = sqrt(rsq);
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double dr = r - r0[type];
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double rk = k[type] * dr;
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fforce = 0;
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if (r > 0.0) fforce = -2.0*rk/r;
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return rk*dr;
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}
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/* ----------------------------------------------------------------------
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Return ptr to internal members upon request.
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------------------------------------------------------------------------ */
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void *BondHarmonic::extract( char *str, int &dim )
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{
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dim = 1;
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if( strcmp(str,"kappa")==0) return (void*) k;
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if( strcmp(str,"r0")==0) return (void*) r0;
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return NULL;
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}
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