angle_list.cpp

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   http://lammps.sandia.gov, Sandia National Laboratories
   Steve Plimpton, sjplimp@sandia.gov

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

#include "math.h"
#include "stdlib.h"
#include "angle_list.h"
#include "atom.h"
#include "neighbor.h"
#include "domain.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"

#include <stdio.h> 
#include <stdlib.h>
#include <string.h>     

using namespace LAMMPS_NS;
using namespace MathConst;

#define SMALL 0.001

/* ---------------------------------------------------------------------- */

AngleList::AngleList(LAMMPS *lmp) : Angle(lmp) {}

/* ---------------------------------------------------------------------- */

AngleList::~AngleList()
{
  if (allocated) {
    memory->destroy(setflag);
    memory->destroy(k);
    memory->destroy(theta0);
  }
}

/* ---------------------------------------------------------------------- */

void AngleList::compute(int eflag, int vflag)
{
  int i1,i2,i3,n,type;
  double delx1,dely1,delz1,delx2,dely2,delz2;
  double eangle,f1[3],f3[3];
  double dtheta,tk;
  double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22;

  eangle = 0.0;
  if (eflag || vflag) ev_setup(eflag,vflag);
  else evflag = 0;

  double **x = atom->x;
  int *tag = atom->tag;
  double **f = atom->f;
  int **anglelist = neighbor->anglelist;
  int nanglelist = neighbor->nanglelist;
  int nlocal = atom->nlocal;
  int newton_bond = force->newton_bond;

  for (n = 0; n < nanglelist; n++) {
    i1 = anglelist[n][0];
    i2 = anglelist[n][1];
    i3 = anglelist[n][2];
    type = tag[i1]+tag[i2] + tag[i3];

    // 1st bond

    delx1 = x[i1][0] - x[i2][0];
    dely1 = x[i1][1] - x[i2][1];
    delz1 = x[i1][2] - x[i2][2];

    rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;
    r1 = sqrt(rsq1);

    // 2nd bond

    delx2 = x[i3][0] - x[i2][0];
    dely2 = x[i3][1] - x[i2][1];
    delz2 = x[i3][2] - x[i2][2];

    rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;
    r2 = sqrt(rsq2);

    // angle (cos and sin)

    c = delx1*delx2 + dely1*dely2 + delz1*delz2;
    c /= r1*r2;

    if (c > 1.0) c = 1.0;
    if (c < -1.0) c = -1.0;

    s = sqrt(1.0 - c*c);
    if (s < SMALL) s = SMALL;
    s = 1.0/s;

    // force & energy

    dtheta = acos(c) - theta0[type];
    tk = k[type] * dtheta;
    //printf("%d(%d) %d(%d) %d(%d) %f\n", i1,tag[i1],i2,tag[i2],i3,tag[i3],dtheta);

    if (eflag) eangle = tk*dtheta;

    a = -2.0 * tk * s;
    a11 = a*c / rsq1;
    a12 = -a / (r1*r2);
    a22 = a*c / rsq2;

    f1[0] = a11*delx1 + a12*delx2;
    f1[1] = a11*dely1 + a12*dely2;
    f1[2] = a11*delz1 + a12*delz2;
    f3[0] = a22*delx2 + a12*delx1;
    f3[1] = a22*dely2 + a12*dely1;
    f3[2] = a22*delz2 + a12*delz1;

    // apply force to each of 3 atoms

    if (newton_bond || i1 < nlocal) {
      f[i1][0] += f1[0];
      f[i1][1] += f1[1];
      f[i1][2] += f1[2];
    }

    if (newton_bond || i2 < nlocal) {
      f[i2][0] -= f1[0] + f3[0];
      f[i2][1] -= f1[1] + f3[1];
      f[i2][2] -= f1[2] + f3[2];
    }

    if (newton_bond || i3 < nlocal) {
      f[i3][0] += f3[0];
      f[i3][1] += f3[1];
      f[i3][2] += f3[2];
    }

    if (evflag) ev_tally(i1,i2,i3,nlocal,newton_bond,eangle,f1,f3,
                         delx1,dely1,delz1,delx2,dely2,delz2);
  }
}

/* ---------------------------------------------------------------------- */

void AngleList::allocate()
{
  allocated = 1;
  int n = atom->nangletypes;

  //memory->create(k,n+1,"angle:k");
  //memory->create(theta0,n+1,"angle:theta0");

  memory->create(setflag,n+1,"angle:setflag");
  for (int i = 1; i <= n; i++) setflag[i] = 0;
}

/* ----------------------------------------------------------------------
   global settings
------------------------------------------------------------------------- */

void AngleList::settings(int narg, char **arg)
{
  if (narg != 1) error->all(FLERR,"Illegal angle_style command");

  FILE *fp = fopen(arg[0],"r");
  char line[1024];
  if (fp == NULL)
    error->all(FLERR,"Cannot open angle list file");

  // count lines in file for upper limit of storage needed
  int num = 1;
  char *ptr;
  int idx, id1, id2, id3;
  while(fgets(line,1024,fp)) {
    ptr = strtok(line," \t\n\r\f");

    // skip empty lines
    if (!ptr) continue;

    // skip comment lines starting with #
    if (*ptr == '#') continue;
    id1 = atoi(ptr);
    ptr = strtok(NULL," \t\n\r\f");

    // The second site
    if (!ptr)
      error->all(FLERR,"Incorrectly formatted angle list file");
    id2 = atoi(ptr);

    // The third site
    ptr = strtok(NULL," \t\n\r\f");
    if (!ptr)
      error->all(FLERR,"Incorrectly formatted angle list file");
    id3 = atoi(ptr);

    // Setting the idx in the base array
    if (id1>num) num=id1;
    if (id2>num) num=id2;
    if (id3>num) num=id3;

  }

  //while(fgets(line,1024,fp)) ++num;
  rewind(fp);
  int array_size = 10*(num+2); 
  // Allocate arrays that *should* contain all angles
  memory->create(k,array_size,"angle:k");
  memory->create(theta0,array_size,"angle:theta0");

  // Read the first line


  // Loop through the rest of the lines
  while(fgets(line,1024,fp)) { 
    ptr = strtok(line," \t\n\r\f");

    // skip empty lines
    if (!ptr) continue;
    
    // skip comment lines starting with #
    if (*ptr == '#') continue;

    id1 = atoi(ptr);

    // The second site
    ptr = strtok(NULL," \t\n\r\f");
    if (!ptr)
      error->all(FLERR,"Incorrectly formatted angle list file");
    id2 = atoi(ptr);

    // The third site
    ptr = strtok(NULL," \t\n\r\f");
    if (!ptr)
      error->all(FLERR,"Incorrectly formatted angle list file");
    id3 = atoi(ptr);
    
    // Setting the idx in the base array
    idx = id1 + id2 + id3;
    if ((idx-1) > array_size)
        error->all(FLERR,"Parameter array in angle_list.cpp is too short!");

    // theta0
    ptr = strtok(NULL," \t\n\r\f");
    if (!ptr)
      error->all(FLERR,"Incorrectly formatted angle list file");
    theta0[idx] = force->numeric(FLERR,ptr);
    theta0[idx] = theta0[idx] /180.0 * MY_PI;

    // k
    ptr = strtok(NULL," \t\n\r\f");
    if (!ptr)
      error->all(FLERR,"Incorrectly formatted angle list file");
    k[idx] = force->numeric(FLERR,ptr);
    //printf("%d %f %f\n",idx,k[idx],theta0[idx]);
  }

  fclose(fp);

}




/* ----------------------------------------------------------------------
   there are no coeffs to be set, but we need to update setflag and pretend
------------------------------------------------------------------------- */

void AngleList::coeff(int narg, char **arg)
{
  if (narg < 1) error->all(FLERR,"Incorrect args for angle coefficients");
  if (!allocated) allocate();

  int ilo,ihi;
  force->bounds(FLERR,arg[0],atom->nangletypes,ilo,ihi);

  // convert theta0 from degrees to radians

  int count = 0;
  for (int i = ilo; i <= ihi; i++) {
    setflag[i] = 1;
    count++;
  }

  if (count == 0) error->all(FLERR,"Incorrect args for angle coefficients");
}

/* ---------------------------------------------------------------------- */

double AngleList::equilibrium_angle(int i)
{
  return theta0[i];
}

/* ----------------------------------------------------------------------
   proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */

void AngleList::write_restart(FILE *fp)
{
  fwrite(&k[1],sizeof(double),atom->nangletypes,fp);
  fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);
}

/* ----------------------------------------------------------------------
   proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */

void AngleList::read_restart(FILE *fp)
{
  allocate();

  if (comm->me == 0) {
    fread(&k[1],sizeof(double),atom->nangletypes,fp);
    fread(&theta0[1],sizeof(double),atom->nangletypes,fp);
  }
  MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);
  MPI_Bcast(&theta0[1],atom->nangletypes,MPI_DOUBLE,0,world);

  for (int i = 1; i <= atom->nangletypes; i++) setflag[i] = 1;
}

/* ----------------------------------------------------------------------
   proc 0 writes to data file
------------------------------------------------------------------------- */

void AngleList::write_data(FILE *fp)
{
  for (int i = 1; i <= atom->nangletypes; i++)
    fprintf(fp,"%d %g %g\n",i,k[i],theta0[i]/MY_PI*180.0);
}

/* ---------------------------------------------------------------------- */

double AngleList::single(int type, int i1, int i2, int i3)
{
  double **x = atom->x;

  double delx1 = x[i1][0] - x[i2][0];
  double dely1 = x[i1][1] - x[i2][1];
  double delz1 = x[i1][2] - x[i2][2];
  domain->minimum_image(delx1,dely1,delz1);
  double r1 = sqrt(delx1*delx1 + dely1*dely1 + delz1*delz1);

  double delx2 = x[i3][0] - x[i2][0];
  double dely2 = x[i3][1] - x[i2][1];
  double delz2 = x[i3][2] - x[i2][2];
  domain->minimum_image(delx2,dely2,delz2);
  double r2 = sqrt(delx2*delx2 + dely2*dely2 + delz2*delz2);

  double c = delx1*delx2 + dely1*dely2 + delz1*delz2;
  c /= r1*r2;
  if (c > 1.0) c = 1.0;
  if (c < -1.0) c = -1.0;

  double dtheta = acos(c) - theta0[type];
  double tk = k[type] * dtheta;
  return tk*dtheta;
}