text: /* ----------------------------------------------------------------------
     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.
  ------------------------------------------------------------------------- */
  
  /* ----------------------------------------------------------------------
     Contributing author: Paul Crozier (SNL)
  ------------------------------------------------------------------------- */
  
  #include <mpi.h>
  #include <math.h>
  #include <stdlib.h>
  #include "dihedral_harmonic.h"
  #include "atom.h"
  #include "comm.h"
  #include "neighbor.h"
  #include "domain.h"
  #include "force.h"
  #include "update.h"
  #include "memory.h"
  #include "error.h"
  
  using namespace LAMMPS_NS;
  
  #define TOLERANCE 0.05
  #define SMALL     0.001
  
  /* ---------------------------------------------------------------------- */
  
  DihedralHarmonic::DihedralHarmonic(LAMMPS *lmp) : Dihedral(lmp)
  {
    writedata = 1;
  }
  
  /* ---------------------------------------------------------------------- */
  
  DihedralHarmonic::~DihedralHarmonic()
  {
    if (allocated) {
      memory->destroy(setflag);
      memory->destroy(k);
      memory->destroy(sign);
      memory->destroy(multiplicity);
      memory->destroy(cos_shift);
      memory->destroy(sin_shift);
    }
  }
  
  /* ---------------------------------------------------------------------- */
  
  void DihedralHarmonic::compute(int eflag, int vflag)
  {
    int i1,i2,i3,i4,i,m,n,type;
    double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
    double edihedral,f1[3],f2[3],f3[3],f4[3];
    double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
    double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
    double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
    double c,s,p,sx2,sy2,sz2;
  
    edihedral = 0.0;
    if (eflag || vflag) ev_setup(eflag,vflag);
    else evflag = 0;
  
    double **x = atom->x;
    double **f = atom->f;
    int **dihedrallist = neighbor->dihedrallist;
    int ndihedrallist = neighbor->ndihedrallist;
    int nlocal = atom->nlocal;
    int newton_bond = force->newton_bond;
  
    for (n = 0; n < ndihedrallist; n++) {
      i1 = dihedrallist[n][0];
      i2 = dihedrallist[n][1];
      i3 = dihedrallist[n][2];
      i4 = dihedrallist[n][3];
      type = dihedrallist[n][4];
  
      // 1st bond
  
      vb1x = x[i1][0] - x[i2][0];
      vb1y = x[i1][1] - x[i2][1];
      vb1z = x[i1][2] - x[i2][2];
  
      // 2nd bond
  
      vb2x = x[i3][0] - x[i2][0];
      vb2y = x[i3][1] - x[i2][1];
      vb2z = x[i3][2] - x[i2][2];
  
      vb2xm = -vb2x;
      vb2ym = -vb2y;
      vb2zm = -vb2z;
  
      // 3rd bond
  
      vb3x = x[i4][0] - x[i3][0];
      vb3y = x[i4][1] - x[i3][1];
      vb3z = x[i4][2] - x[i3][2];
  
      // c,s calculation
  
      ax = vb1y*vb2zm - vb1z*vb2ym;
      ay = vb1z*vb2xm - vb1x*vb2zm;
      az = vb1x*vb2ym - vb1y*vb2xm;
      bx = vb3y*vb2zm - vb3z*vb2ym;
      by = vb3z*vb2xm - vb3x*vb2zm;
      bz = vb3x*vb2ym - vb3y*vb2xm;
  
      rasq = ax*ax + ay*ay + az*az;
      rbsq = bx*bx + by*by + bz*bz;
      rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
      rg = sqrt(rgsq);
  
      rginv = ra2inv = rb2inv = 0.0;
      if (rg > 0) rginv = 1.0/rg;
      if (rasq > 0) ra2inv = 1.0/rasq;
      if (rbsq > 0) rb2inv = 1.0/rbsq;
      rabinv = sqrt(ra2inv*rb2inv);
  
      c = (ax*bx + ay*by + az*bz)*rabinv;
      s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
  
      // error check
  
      if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
        int me;
        MPI_Comm_rank(world,&me);
        if (screen) {
          char str[128];
          sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
                  TAGINT_FORMAT " " TAGINT_FORMAT " "
                  TAGINT_FORMAT " " TAGINT_FORMAT,
                  me,update->ntimestep,
                  atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
          error->warning(FLERR,str,0);
          fprintf(screen,"  1st atom: %d %g %g %g\n",
                  me,x[i1][0],x[i1][1],x[i1][2]);
          fprintf(screen,"  2nd atom: %d %g %g %g\n",
                  me,x[i2][0],x[i2][1],x[i2][2]);
          fprintf(screen,"  3rd atom: %d %g %g %g\n",
                  me,x[i3][0],x[i3][1],x[i3][2]);
          fprintf(screen,"  4th atom: %d %g %g %g\n",
                  me,x[i4][0],x[i4][1],x[i4][2]);
        }
      }
  
      if (c > 1.0) c = 1.0;
      if (c < -1.0) c = -1.0;
  
      m = multiplicity[type];
      p = 1.0;
      ddf1 = df1 = 0.0;
  
      for (i = 0; i < m; i++) {
        ddf1 = p*c - df1*s;
        df1 = p*s + df1*c;
        p = ddf1;
      }
  
      p = p*cos_shift[type] + df1*sin_shift[type];
      df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
      df1 *= -m;
      p += 1.0;
  
      if (m == 0) {
        p = 1.0 + cos_shift[type];
        df1 = 0.0;
      }
  
      if (eflag) edihedral = k[type] * p;
  
      fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
      hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
      fga = fg*ra2inv*rginv;
      hgb = hg*rb2inv*rginv;
      gaa = -ra2inv*rg;
      gbb = rb2inv*rg;
  
      dtfx = gaa*ax;
      dtfy = gaa*ay;
      dtfz = gaa*az;
      dtgx = fga*ax - hgb*bx;
      dtgy = fga*ay - hgb*by;
      dtgz = fga*az - hgb*bz;
      dthx = gbb*bx;
      dthy = gbb*by;
      dthz = gbb*bz;
  
      df = -k[type] * df1;
  
      sx2 = df*dtgx;
      sy2 = df*dtgy;
      sz2 = df*dtgz;
  
      f1[0] = df*dtfx;
      f1[1] = df*dtfy;
      f1[2] = df*dtfz;
  
      f2[0] = sx2 - f1[0];
      f2[1] = sy2 - f1[1];
      f2[2] = sz2 - f1[2];
  
      f4[0] = df*dthx;
      f4[1] = df*dthy;
      f4[2] = df*dthz;
  
      f3[0] = -sx2 - f4[0];
      f3[1] = -sy2 - f4[1];
      f3[2] = -sz2 - f4[2];
  
      // apply force to each of 4 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] += f2[0];
        f[i2][1] += f2[1];
        f[i2][2] += f2[2];
      }
  
      if (newton_bond || i3 < nlocal) {
        f[i3][0] += f3[0];
        f[i3][1] += f3[1];
        f[i3][2] += f3[2];
      }
  
      if (newton_bond || i4 < nlocal) {
        f[i4][0] += f4[0];
        f[i4][1] += f4[1];
        f[i4][2] += f4[2];
      }
  
      if (evflag)
        ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
                 vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
    }
  }
  
  /* ---------------------------------------------------------------------- */
  
  void DihedralHarmonic::allocate()
  {
    allocated = 1;
    int n = atom->ndihedraltypes;
  
    memory->create(k,n+1,"dihedral:k");
    memory->create(sign,n+1,"dihedral:sign");
    memory->create(multiplicity,n+1,"dihedral:multiplicity");
    memory->create(cos_shift,n+1,"dihedral:cos_shift");
    memory->create(sin_shift,n+1,"dihedral:sin_shift");
  
    memory->create(setflag,n+1,"dihedral:setflag");
    for (int i = 1; i <= n; i++) setflag[i] = 0;
  }
  
  /* ----------------------------------------------------------------------
     set coeffs for one type
  ------------------------------------------------------------------------- */
  
  void DihedralHarmonic::coeff(int narg, char **arg)
  {
    if (narg != 4) error->all(FLERR,"Incorrect args for dihedral coefficients");
    if (!allocated) allocate();
  
    int ilo,ihi;
    force->bounds(FLERR,arg[0],atom->ndihedraltypes,ilo,ihi);
  
    double k_one = force->numeric(FLERR,arg[1]);
    int sign_one = force->inumeric(FLERR,arg[2]);
    int multiplicity_one = force->inumeric(FLERR,arg[3]);
  
    // require sign = +/- 1 for backwards compatibility
    // arbitrary phase angle shift could be allowed, but would break
    //   backwards compatibility and is probably not needed
  
    if (sign_one != -1 && sign_one != 1)
      error->all(FLERR,"Incorrect sign arg for dihedral coefficients");
    if (multiplicity_one < 0)
      error->all(FLERR,"Incorrect multiplicity arg for dihedral coefficients");
  
    int count = 0;
    for (int i = ilo; i <= ihi; i++) {
      k[i] = k_one;
      sign[i] = sign_one;
      if (sign[i] == 1) {
        cos_shift[i] = 1;
        sin_shift[i] = 0;
      } else {
        cos_shift[i] = -1;
        sin_shift[i] = 0;
      }
      multiplicity[i] = multiplicity_one;
      setflag[i] = 1;
      count++;
    }
  
    if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
  }
  
  /* ----------------------------------------------------------------------
     proc 0 writes out coeffs to restart file
  ------------------------------------------------------------------------- */
  
  void DihedralHarmonic::write_restart(FILE *fp)
  {
    fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
    fwrite(&sign[1],sizeof(int),atom->ndihedraltypes,fp);
    fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
  }
  
  /* ----------------------------------------------------------------------
     proc 0 reads coeffs from restart file, bcasts them
  ------------------------------------------------------------------------- */
  
  void DihedralHarmonic::read_restart(FILE *fp)
  {
    allocate();
  
    if (comm->me == 0) {
      fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
      fread(&sign[1],sizeof(int),atom->ndihedraltypes,fp);
      fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
    }
    MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
    MPI_Bcast(&sign[1],atom->ndihedraltypes,MPI_INT,0,world);
    MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
  
    for (int i = 1; i <= atom->ndihedraltypes; i++) {
      setflag[i] = 1;
      if (sign[i] == 1) {
        cos_shift[i] = 1;
        sin_shift[i] = 0;
      } else {
        cos_shift[i] = -1;
        sin_shift[i] = 0;
      }
    }
  }
  
  /* ----------------------------------------------------------------------
     proc 0 writes to data file
  ------------------------------------------------------------------------- */
  
  void DihedralHarmonic::write_data(FILE *fp)
  {
    for (int i = 1; i <= atom->ndihedraltypes; i++)
      fprintf(fp,"%d %g %d %d\n",i,k[i],sign[i],multiplicity[i]);
  }
  
  