#include "mpi.h"

#include "string.h"

#include "stdio.h"

#include "stdlib.h"

#include "math.h"

#include "pppm.h"

#include "atom.h"

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

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   www.cs.sandia.gov/~sjplimp/lammps.html

   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories

   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 "angle.h"

#include "atom.h"

#include "error.h"

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

Angle::Angle()

{

  allocated = 0;

  PI = 4.0*atan(1.0);

}

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

   check if all coeffs are set

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

void Angle::init()

{

  if (!allocated) error->all("Angle coeffs are not set");

  for (int i = 1; i <= atom->nangletypes; i++)

    if (setflag[i] == 0) error->all("All angle coeffs are not set");

}

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

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   www.cs.sandia.gov/~sjplimp/lammps.html

   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories

   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 "math.h"

#include "stdlib.h"

#include "angle_charmm.h"

#include "atom.h"

#include "neighbor.h"

#include "domain.h"

#include "comm.h"

#include "force.h"

#include "memory.h"

#include "error.h"

#define SMALL 0.001

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

   free all arrays 

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

AngleCharmm::~AngleCharmm()

{

  if (allocated) {

    memory->sfree(setflag);

    memory->sfree(k);

    memory->sfree(theta0);

    memory->sfree(k_ub);

    memory->sfree(r_ub);

  }

}

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

void AngleCharmm::compute(int eflag, int vflag)

{

  int i1,i2,i3,n,type,factor;

  double delx1,dely1,delz1,delx2,dely2,delz2,rfactor,dtheta,tk;

  double rsq1,rsq2,r1,r2,c,s,a,a11,a12,a22,vx1,vx2,vy1,vy2,vz1,vz2;

  double delxUB,delyUB,delzUB,rsqUB,rUB,dr,rk,forceUB;

  energy = 0.0;

  if (vflag) for (n = 0; n < 6; n++) virial[n] = 0.0;

  double **x = atom->x;

  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 = anglelist[n][3];

    if (newton_bond) factor = 3;

    else {

      factor = 0;

      if (i1 < nlocal) factor++;

      if (i2 < nlocal) factor++;

      if (i3 < nlocal) factor++;

      }

    rfactor = factor/3.0;

    // 1st bond

    delx1 = x[i1][0] - x[i2][0];

    dely1 = x[i1][1] - x[i2][1];

    delz1 = x[i1][2] - x[i2][2];

    domain->minimum_image(&delx1,&dely1,&delz1);

    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];

    domain->minimum_image(&delx2,&dely2,&delz2);

    rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;

    r2 = sqrt(rsq2);

    // Urey-Bradley bond

    delxUB = x[i3][0] - x[i1][0];

    delyUB = x[i3][1] - x[i1][1];

    delzUB = x[i3][2] - x[i1][2];

    domain->minimum_image(&delxUB,&delyUB,&delzUB);

    rsqUB = delxUB*delxUB + delyUB*delyUB + delzUB*delzUB;

    rUB = sqrt(rsqUB);

    // 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;

    // harmonic force & energy

    dtheta = acos(c) - theta0[type];

    tk = k[type] * dtheta;

    if (eflag) energy += rfactor * tk*dtheta;

    a = 2.0 * tk * s;

    a11 = a*c / rsq1;

    a12 = -a / (r1*r2);

    a22 = a*c / rsq2;

    vx1 = a11*delx1 + a12*delx2;

    vx2 = a22*delx2 + a12*delx1;

    vy1 = a11*dely1 + a12*dely2;

    vy2 = a22*dely2 + a12*dely1;

    vz1 = a11*delz1 + a12*delz2;

    vz2 = a22*delz2 + a12*delz1;

    // Urey-Bradley force & energy

    dr = rUB - r_ub[type];

    rk = k_ub[type] * dr;

    if (rUB > 0.0) forceUB = -2.0*rk/rUB;

    else forceUB = 0.0;

    if (eflag) energy += rfactor * rk*dr;

    // apply force to each of 3 atoms

    if (newton_bond || i1 < nlocal) {

      f[i1][0] -= vx1 + delxUB*forceUB;

      f[i1][1] -= vy1 + delyUB*forceUB;

      f[i1][2] -= vz1 + delzUB*forceUB;

    }

    if (newton_bond || i2 < nlocal) {

      f[i2][0] += vx1 + vx2;

      f[i2][1] += vy1 + vy2;

      f[i2][2] += vz1 + vz2;

    }

    if (newton_bond || i3 < nlocal) {

      f[i3][0] -= vx2 - delxUB*forceUB;

      f[i3][1] -= vy2 - delyUB*forceUB;

      f[i3][2] -= vz2 - delzUB*forceUB;

    }

    // virial contribution

    if (vflag) {

      virial[0] -= rfactor * (delx1*vx1 + delx2*vx2 - delxUB*delxUB*forceUB);

      virial[1] -= rfactor * (dely1*vy1 + dely2*vy2 - delyUB*delyUB*forceUB);

      virial[2] -= rfactor * (delz1*vz1 + delz2*vz2 - delzUB*delzUB*forceUB);

      virial[3] -= rfactor * (delx1*vy1 + delx2*vy2 - delxUB*delyUB*forceUB);

      virial[4] -= rfactor * (delx1*vz1 + delx2*vz2 - delxUB*delzUB*forceUB);

      virial[5] -= rfactor * (dely1*vz1 + dely2*vz2 - delyUB*delzUB*forceUB);

    }

  }

}

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

void AngleCharmm::allocate()

{

  allocated = 1;

  int n = atom->nangletypes;

  k = (double *) memory->smalloc((n+1)*sizeof(double),"angle:k");

  theta0 = (double *) memory->smalloc((n+1)*sizeof(double),"angle:theta0");

  k_ub = (double *) memory->smalloc((n+1)*sizeof(double),"angle:k_ub");

  r_ub = (double *) memory->smalloc((n+1)*sizeof(double),"angle:r_ub");

  setflag = (int *) memory->smalloc((n+1)*sizeof(int),"angle:setflag");

  for (int i = 1; i <= n; i++) setflag[i] = 0;

}

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

   set coeffs for one type

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

void AngleCharmm::coeff(int which, int narg, char **arg)

{

  if (which != 0) error->all("Invalid coeffs for this angle style");

  if (narg != 5) error->all("Incorrect args for angle coefficients");

  if (!allocated) allocate();

  int ilo,ihi;

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

  double k_one = atof(arg[1]);

  double theta0_one = atof(arg[2]);

  double k_ub_one = atof(arg[3]);

  double r_ub_one = atof(arg[4]);

  // convert theta0 from degrees to radians

  int count = 0;

  for (int i = ilo; i <= ihi; i++) {

    k[i] = k_one;

    theta0[i] = theta0_one/180.0 * PI;

    k_ub[i] = k_ub_one;

    r_ub[i] = r_ub_one;

    setflag[i] = 1;

    count++;

  }

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

}

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

double AngleCharmm::equilibrium_angle(int i)

{

  return theta0[i];

}

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

   proc 0 writes out coeffs to restart file

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

void AngleCharmm::write_restart(FILE *fp)

{

  fwrite(&k[1],sizeof(double),atom->nangletypes,fp);

  fwrite(&theta0[1],sizeof(double),atom->nangletypes,fp);

  fwrite(&k_ub[1],sizeof(double),atom->nangletypes,fp);

  fwrite(&r_ub[1],sizeof(double),atom->nangletypes,fp);

}

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

   proc 0 reads coeffs from restart file, bcasts them 

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

void AngleCharmm::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);

    fread(&k_ub[1],sizeof(double),atom->nangletypes,fp);

    fread(&r_ub[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);

  MPI_Bcast(&k_ub[1],atom->nangletypes,MPI_DOUBLE,0,world);

  MPI_Bcast(&r_ub[1],atom->nangletypes,MPI_DOUBLE,0,world);

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

}

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

double AngleCharmm::single(int type, int i1, int i2, int i3, double rfactor)

{

  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 delxUB = x[i3][0] - x[i1][0];

  double delyUB = x[i3][1] - x[i1][1];

  double delzUB = x[i3][2] - x[i1][2];

  domain->minimum_image(&delxUB,&delyUB,&delzUB);

  double rUB = sqrt(delxUB*delxUB + delyUB*delyUB + delzUB*delzUB);

  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;

  double dr = rUB - r_ub[type];

  double rk = k_ub[type] * dr;

  return (rfactor * (tk*dtheta + rk*dr));

}

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

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   www.cs.sandia.gov/~sjplimp/lammps.html

   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories

   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.

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

#ifndef ANGLE_CHARMM_H

#define ANGLE_CHARMM_H

#include "stdio.h"

#include "angle.h"

class AngleCharmm : public Angle {

 public:

  AngleCharmm() {}

  ~AngleCharmm();

  void compute(int, int);

  void coeff(int, int, char **);

  double equilibrium_angle(int);

  void write_restart(FILE *);

  void read_restart(FILE *);

  double single(int, int, int, int, double);

 private:

  double *k,*theta0,*k_ub,*r_ub;

  void allocate();

};

#endif

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

   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator

   www.cs.sandia.gov/~sjplimp/lammps.html

   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories

   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_cosine.h"

#include "atom.h"

#include "neighbor.h"

#include "domain.h"

#include "comm.h"

#include "force.h"

#include "memory.h"

#include "error.h"

#define SMALL 0.001

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

   free all arrays 

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

AngleCosine::~AngleCosine()

{

  if (allocated) {

    memory->sfree(setflag);

    memory->sfree(k);

  }

}

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

void AngleCosine::compute(int eflag, int vflag)

{

  int i1,i2,i3,n,type,factor;

  double delx1,dely1,delz1,delx2,dely2,delz2,rfactor;

  double rsq1,rsq2,r1,r2,c,a,a11,a12,a22,vx1,vx2,vy1,vy2,vz1,vz2;

  energy = 0.0;

  if (vflag) for (n = 0; n < 6; n++) virial[n] = 0.0;

  double **x = atom->x;

  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 = anglelist[n][3];

    if (newton_bond) factor = 3;

    else {

      factor = 0;

      if (i1 < nlocal) factor++;

      if (i2 < nlocal) factor++;

      if (i3 < nlocal) factor++;

      }

    rfactor = factor/3.0;

    // 1st bond

    delx1 = x[i1][0] - x[i2][0];

    dely1 = x[i1][1] - x[i2][1];

    delz1 = x[i1][2] - x[i2][2];

    domain->minimum_image(&delx1,&dely1,&delz1);

    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];

    domain->minimum_image(&delx2,&dely2,&delz2);

    rsq2 = delx2*delx2 + dely2*dely2 + delz2*delz2;

    r2 = sqrt(rsq2);

    // c = cosine of angle

    c = delx1*delx2 + dely1*dely2 + delz1*delz2;

    c /= r1*r2;

    if (c > 1.0) c = 1.0;

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

    // force & energy

    if (eflag) energy += rfactor * k[type]*(1.0+c);

    a = -k[type];

    a11 = a*c / rsq1;

    a12 = -a / (r1*r2);

    a22 = a*c / rsq2;

    vx1 = a11*delx1 + a12*delx2;

    vx2 = a22*delx2 + a12*delx1;

    vy1 = a11*dely1 + a12*dely2;

    vy2 = a22*dely2 + a12*dely1;

    vz1 = a11*delz1 + a12*delz2;

    vz2 = a22*delz2 + a12*delz1;

    // apply force to each of 3 atoms

    if (newton_bond || i1 < nlocal) {

      f[i1][0] -= vx1;

      f[i1][1] -= vy1;

      f[i1][2] -= vz1;

    }

    if (newton_bond || i2 < nlocal) {

      f[i2][0] += vx1 + vx2;

      f[i2][1] += vy1 + vy2;

      f[i2][2] += vz1 + vz2;

    }

    if (newton_bond || i3 < nlocal) {

      f[i3][0] -= vx2;

      f[i3][1] -= vy2;

      f[i3][2] -= vz2;

    }

    // virial contribution

    if (vflag) {

      virial[0] -= rfactor * (delx1*vx1 + delx2*vx2);

      virial[1] -= rfactor * (dely1*vy1 + dely2*vy2);

      virial[2] -= rfactor * (delz1*vz1 + delz2*vz2);

      virial[3] -= rfactor * (delx1*vy1 + delx2*vy2);

      virial[4] -= rfactor * (delx1*vz1 + delx2*vz2);

      virial[5] -= rfactor * (dely1*vz1 + dely2*vz2);

    }

  }

}

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

void AngleCosine::allocate()

{

  allocated = 1;

  int n = atom->nangletypes;

  k = (double *) memory->smalloc((n+1)*sizeof(double),"angle:k");

  setflag = (int *) memory->smalloc((n+1)*sizeof(int),"angle:setflag");

  for (int i = 1; i <= n; i++) setflag[i] = 0;

}

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

   set coeffs for one type

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

void AngleCosine::coeff(int which, int narg, char **arg)

{

  if (which != 0) error->all("Invalid coeffs for this angle style");

  if (narg != 2) error->all("Incorrect args for angle coefficients");

  if (!allocated) allocate();

  int ilo,ihi;

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

  double k_one = atof(arg[1]);

  int count = 0;

  for (int i = ilo; i <= ihi; i++) {

    k[i] = k_one;

    setflag[i] = 1;

    count++;

  }

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

}

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

double AngleCosine::equilibrium_angle(int i)

{

  return PI;

}

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

   proc 0 writes out coeffs to restart file 

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

void AngleCosine::write_restart(FILE *fp)

{

  fwrite(&k[1],sizeof(double),atom->nangletypes,fp);

}

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

   proc 0 reads coeffs from restart file, bcasts them 

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

void AngleCosine::read_restart(FILE *fp)

{

  allocate();

  if (comm->me == 0) fread(&k[1],sizeof(double),atom->nangletypes,fp);

  MPI_Bcast(&k[1],atom->nangletypes,MPI_DOUBLE,0,world);

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

}