git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6647 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/USER-MISC/angle_cosine_shift.cpp
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263
src/USER-MISC/angle_cosine_shift.cpp
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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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/* ----------------------------------------------------------------------
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Contributing author: Carsten Svaneborg, science@zqex.dk
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "angle_cosineshift.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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#define SMALL 0.001
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/* ---------------------------------------------------------------------- */
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AngleCosineShift::AngleCosineShift(LAMMPS *lmp) : Angle(lmp) {}
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/* ---------------------------------------------------------------------- */
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AngleCosineShift::~AngleCosineShift()
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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(kcost);
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memory->destroy(ksint);
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memory->destroy(theta);
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleCosineShift::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 rsq1,rsq2,r1,r2,c,s,cps,kcos,ksin,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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domain->minimum_image(delx1,dely1,delz1);
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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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domain->minimum_image(delx2,dely2,delz2);
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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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if (eflag) eangle = -k[type]-kcos*c-ksin*s;
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kcos=kcost[type];
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ksin=ksint[type];
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cps = c/s; // NOTE absorbed one c
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a11 = (-kcos +ksin*cps )*c/ rsq1;
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a12 = ( kcos -ksin*cps ) / (r1*r2);
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a22 = (-kcos +ksin*cps )*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 AngleCosineShift::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(ksint ,n+1,"Angle:ksint");
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memory->create(kcost ,n+1,"Angle:kcost");
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memory->create(theta ,n+1,"Angle:theta");
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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 AngleCosineShift::coeff(int narg, char **arg)
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{
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if (narg != 3) error->all("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(arg[0],atom->nangletypes,ilo,ihi);
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double umin = force->numeric(arg[1]);
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double theta0 = force->numeric(arg[2]);
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// k=Umin/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] = umin/2;
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kcost[i] = umin/2*cos(theta0*3.14159265/180);
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ksint[i] = umin/2*sin(theta0*3.14159265/180);
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theta[i] = theta0*3.14159265/180;
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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("Incorrect args for angle coefficients");
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}
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/* ---------------------------------------------------------------------- */
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double AngleCosineShift::equilibrium_angle(int i)
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{
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return theta[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 AngleCosineShift::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(&kcost[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&ksint[1],sizeof(double),atom->nangletypes,fp);
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fwrite(&theta[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 AngleCosineShift::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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fread(&k[1],sizeof(double),atom->nangletypes,fp);
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fread(&kcost[1],sizeof(double),atom->nangletypes,fp);
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fread(&ksint[1],sizeof(double),atom->nangletypes,fp);
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fread(&theta[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(&kcost[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&ksint[1],atom->nangletypes,MPI_DOUBLE,0,world);
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MPI_Bcast(&theta[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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double AngleCosineShift::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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return -k[type]-kcost[type]*c-ksint[type]*s;
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}
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