/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   https://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: Christina Payne (Vanderbilt U)
                        Stan Moore (Sandia) for dipole terms
------------------------------------------------------------------------- */

#include "fix_efield_tip4p.h"  // TIP4P

#include <cmath> // TIP4P
#include <cstring>
#include "angle.h" // TIP4P
#include "atom.h"
#include "bond.h" // TIP4P
#include "comm.h"
#include "domain.h"
#include "update.h"
#include "force.h"
#include "neighbor.h" // TIP4P
#include "neigh_list.h" // TIP4P
#include "modify.h"
#include "respa.h"
#include "input.h"
#include "variable.h"
#include "region.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;
using namespace FixConst;

enum{NONE,CONSTANT,EQUAL,ATOM};

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

FixEfieldTIP4P::FixEfieldTIP4P(LAMMPS *lmp, int narg, char **arg) :  // TIP4P
  Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr),
  estr(nullptr), idregion(nullptr), efield(nullptr)
{

  if (narg < 11) error->all(FLERR,"Illegal fix efield TIP4P command");  //TIP4P

  dynamic_group_allow = 1;
  vector_flag = 1;
  scalar_flag = 1;
  size_vector = 3;
  global_freq = 1;
  extvector = 1;
  extscalar = 1;
  respa_level_support = 1;
  ilevel_respa = 0;
  virial_flag = 1;

  qe2f = force->qe2f;
  xstr = ystr = zstr = nullptr;

  if (strstr(arg[3],"v_") == arg[3]) {
    int n = strlen(&arg[3][2]) + 1;
    xstr = new char[n];
    strcpy(xstr,&arg[3][2]);
  } else {
    ex = qe2f * utils::numeric(FLERR,arg[3],false,lmp);
    xstyle = CONSTANT;
  }

  if (strstr(arg[4],"v_") == arg[4]) {
    int n = strlen(&arg[4][2]) + 1;
    ystr = new char[n];
    strcpy(ystr,&arg[4][2]);
  } else {
    ey = qe2f * utils::numeric(FLERR,arg[4],false,lmp);
    ystyle = CONSTANT;
  }

  if (strstr(arg[5],"v_") == arg[5]) {
    int n = strlen(&arg[5][2]) + 1;
    zstr = new char[n];
    strcpy(zstr,&arg[5][2]);
  } else {
    ez = qe2f * utils::numeric(FLERR,arg[5],false,lmp);
    zstyle = CONSTANT;
  }

  // optional args

  iregion = -1;
  idregion = nullptr;
  estr = nullptr;

  int iarg = 11;
  while (iarg < narg) {
    if (strcmp(arg[iarg],"region") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal fix efield TIP4P command"); // TIP4P
      iregion = domain->find_region(arg[iarg+1]);
      if (iregion == -1)
        error->all(FLERR,"Region ID for fix efield TIP4P does not exist"); // TIP4P
      int n = strlen(arg[iarg+1]) + 1;
      idregion = new char[n];
      strcpy(idregion,arg[iarg+1]);
      iarg += 2;
    } else if (strcmp(arg[iarg],"energy") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal fix efield TIP4P command"); // TIP4P
      if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
        int n = strlen(&arg[iarg+1][2]) + 1;
        estr = new char[n];
        strcpy(estr,&arg[iarg+1][2]);
      } else error->all(FLERR,"Illegal fix efield TIP4P command"); // TIP4P
      iarg += 2;
    } else error->all(FLERR,"Illegal fix efield TIP4P command"); // TIP4P
  }

  typeO = utils::inumeric(FLERR,arg[6],false,lmp);  //TIP4P
  typeH = utils::inumeric(FLERR,arg[7],false,lmp);  //TIP4P
  typeB = utils::inumeric(FLERR,arg[8],false,lmp);  //TIP4P
  typeA = utils::inumeric(FLERR,arg[9],false,lmp);  //TIP4P
  qdist = utils::numeric(FLERR,arg[10],false,lmp);  //TIP4P

  force_flag = 0;
  fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;

  maxatom = atom->nmax;
  memory->create(efield,maxatom,4,"efield:efield");
}

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

FixEfieldTIP4P::~FixEfieldTIP4P()  // TIP4P
{
  delete [] xstr;
  delete [] ystr;
  delete [] zstr;
  delete [] estr;
  delete [] idregion;
  memory->destroy(efield);
}

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

int FixEfieldTIP4P::setmask()  // TIP4P
{
  int mask = 0;
  mask |= THERMO_ENERGY;
  mask |= POST_FORCE;
  mask |= POST_FORCE_RESPA;
  mask |= MIN_POST_FORCE;
  return mask;
}

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

void FixEfieldTIP4P::init()  // TIP4P
{
  qflag = muflag = 0;
  if (atom->q_flag) qflag = 1;
  if (atom->mu_flag && atom->torque_flag) muflag = 1;
  if (!qflag && !muflag)
    error->all(FLERR,"Fix efield TIP4P requires atom attribute q or mu");  // TIP4P

  // check variables

  if (xstr) {
    xvar = input->variable->find(xstr);
    if (xvar < 0)
      error->all(FLERR,"Variable name for fix efield TIP4P does not exist");  // TIP4P
    if (input->variable->equalstyle(xvar)) xstyle = EQUAL;
    else if (input->variable->atomstyle(xvar)) xstyle = ATOM;
    else error->all(FLERR,"Variable for fix efield TIP4P is invalid style");  // TIP4P
  }
  if (ystr) {
    yvar = input->variable->find(ystr);
    if (yvar < 0)
      error->all(FLERR,"Variable name for fix efield TIP4P does not exist");  // TIP4P
    if (input->variable->equalstyle(yvar)) ystyle = EQUAL;
    else if (input->variable->atomstyle(yvar)) ystyle = ATOM;
    else error->all(FLERR,"Variable for fix efield TIP4P is invalid style");  // TIP4P
  }
  if (zstr) {
    zvar = input->variable->find(zstr);
    if (zvar < 0)
      error->all(FLERR,"Variable name for fix efield TIP4P does not exist");  // TIP4P
    if (input->variable->equalstyle(zvar)) zstyle = EQUAL;
    else if (input->variable->atomstyle(zvar)) zstyle = ATOM;
    else error->all(FLERR,"Variable for fix efield TIP4P is invalid style");  // TIP4P
  }
  if (estr) {
    evar = input->variable->find(estr);
    if (evar < 0)
      error->all(FLERR,"Variable name for fix efield TIP4P does not exist");  // TIP4P
    if (input->variable->atomstyle(evar)) estyle = ATOM;
    else error->all(FLERR,"Variable for fix efield TIP4P is invalid style");  // TIP4P
  } else estyle = NONE;


  // set index and check validity of region

  if (iregion >= 0) {
    iregion = domain->find_region(idregion);
    if (iregion == -1)
      error->all(FLERR,"Region ID for fix aveforce does not exist");
  }

  if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
    varflag = ATOM;
  else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
    varflag = EQUAL;
  else varflag = CONSTANT;

  if (muflag && varflag == ATOM)
    error->all(FLERR,"Fix efield TIP4P with dipoles cannot use atom-style variables");  // TIP4P

  if (muflag && update->whichflag == 2 && comm->me == 0)
    error->warning(FLERR,
                   "The minimizer does not re-orient dipoles "
                   "when using fix efield TIP4P");  // TIP4P

  if (varflag == CONSTANT && estyle != NONE)
    error->all(FLERR,"Cannot use variable energy with "
               "constant efield in fix efield TIP4P");  // TIP4P
  if ((varflag == EQUAL || varflag == ATOM) &&
      update->whichflag == 2 && estyle == NONE)
    error->all(FLERR,"Must use variable energy with fix efield TIP4P");  // TIP4P

  if (strstr(update->integrate_style,"respa")) {
    ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
    if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
  }

  // TIP4P
  if (atom->tag_enable == 0)
    error->all(FLERR,"Pair style lj/cut/tip4p/long requires atom IDs");
  if (!force->newton_pair)
    error->all(FLERR,
               "Pair style lj/cut/tip4p/long requires newton pair on");
  if (!atom->q_flag)
    error->all(FLERR,
               "Pair style lj/cut/tip4p/long requires atom attribute q");
  if (force->bond == nullptr)
    error->all(FLERR,"Must use a bond style with TIP4P potential");
  if (force->angle == nullptr)
    error->all(FLERR,"Must use an angle style with TIP4P potential");

  // set alpha parameter
  // 根据qdist，theta，blen参数，计算alpha，进而用于计算虚拟电荷M点的位置。
  double theta = force->angle->equilibrium_angle(typeA);
  double blen = force->bond->equilibrium_distance(typeB);
  alpha = qdist / (cos(0.5*theta) * blen);
  // TIP4P
}

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

void FixEfieldTIP4P::setup(int vflag)  // TIP4P
{
  if (strstr(update->integrate_style,"verlet"))
    post_force(vflag);
  else {
    ((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);
    post_force_respa(vflag,ilevel_respa,0);
    ((Respa *) update->integrate)->copy_f_flevel(ilevel_respa);
  }
}


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

void FixEfieldTIP4P::min_setup(int vflag)  // TIP4P
{
  post_force(vflag);
}

/* ----------------------------------------------------------------------
   apply F = qE
------------------------------------------------------------------------- */

void FixEfieldTIP4P::post_force(int vflag)  // TIP4P
{
  double **f = atom->f;
  double *q = atom->q;
  int *mask = atom->mask;
  imageint *image = atom->image;
  int nlocal = atom->nlocal;

  // energy and virial setup

  if (vflag) v_setup(vflag);
  else evflag = 0;

  // reallocate efield array if necessary

  if (varflag == ATOM && atom->nmax > maxatom) {
    maxatom = atom->nmax;
    memory->destroy(efield);
    memory->create(efield,maxatom,4,"efield:efield");
  }

  // update region if necessary

  Region *region = nullptr;
  if (iregion >= 0) {
    region = domain->regions[iregion];
    region->prematch();
  }

  // fsum[0] = "potential energy" for added force
  // fsum[123] = extra force added to atoms

  fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
  force_flag = 0;

  double **x = atom->x;
  double fx,fy,fz;
  double v[6];

  // constant efield

  if (varflag == CONSTANT) {

    int iH1,iH2,itype;
    int *type = atom->type;
    tagint *tag = atom->tag;
    double unwrap[3];
    double unwrapH1[3];
    double unwrapH2[3];
    double fO[3],fH[3];

    // charge interactions
    // force = qE, potential energy = F dot x in unwrapped coords

    if (qflag) {
      for (int i = 0; i < nlocal; i++)
        if (mask[i] & groupbit) {

          if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;

          itype = type[i];
          fx = q[i]*ex;
          fy = q[i]*ey;
          fz = q[i]*ez;

/* ------------------------------TIP4P----------------------------------- */

          if (itype != typeO) {
            f[i][0] += fx;
            f[i][1] += fy;
            f[i][2] += fz;

            domain->unmap(x[i],image[i],unwrap);
            fsum[0] -= fx*unwrap[0]+fy*unwrap[1]+fz*unwrap[2];
            fsum[1] += fx;
            fsum[2] += fy;
            fsum[3] += fz;

            if (evflag) {
              v[0] = fx*unwrap[0];
              v[1] = fy*unwrap[1];
              v[2] = fz*unwrap[2];
              v[3] = fx*unwrap[1];
              v[4] = fx*unwrap[2];
              v[5] = fy*unwrap[2];
              v_tally(i, v);
            }

          } else {
            iH1 = atom->map(tag[i] + 1);
            iH2 = atom->map(tag[i] + 2);
            if (iH1 == -1 || iH2 == -1)
             error->one(FLERR,"TIP4P hydrogen is missing");
            if (atom->type[iH1] != typeH || atom->type[iH2] != typeH)
             error->one(FLERR,"TIP4P hydrogen has incorrect atom type");
            //iH1 = domain->closest_image(i,iH1);
            //iH2 = domain->closest_image(i,iH2);

            fO[0] = fx*(1 - alpha);
            fO[1] = fy*(1 - alpha);
            fO[2] = fz*(1 - alpha);

            fH[0] = 0.5 * alpha * fx;
            fH[1] = 0.5 * alpha * fy;
            fH[2] = 0.5 * alpha * fz;

            f[i][0] += fO[0];
            f[i][1] += fO[1];
            f[i][2] += fO[2];


            f[iH1][0] += fH[0];
            f[iH1][1] += fH[1];
            f[iH1][2] += fH[2];

            f[iH2][0] += fH[0];
            f[iH2][1] += fH[1];
            f[iH2][2] += fH[2];

            domain->unmap(x[iH1],image[iH1],unwrapH1);
            domain->unmap(x[iH2],image[iH2],unwrapH2);


            fsum[0] -= fO[0]*unwrap[0]+fO[1]*unwrap[1]+fO[2]*unwrap[2]+fH[0]*unwrapH1[0]+fH[1]*unwrapH1[1]+fH[2]*unwrapH1[2]+fH[0]*unwrapH2[0]+fH[1]*unwrapH2[1]+fH[2]*unwrapH2[2];
            fsum[1] += fx;
            fsum[2] += fy;
            fsum[3] += fz;

            if (evflag) {

              v[0] = fO[0]*unwrap[0]+fH[0]*unwrapH1[0]+fH[0]*unwrapH2[0];
              v[1] = fO[1]*unwrap[1]+fH[1]*unwrapH1[1]+fH[1]*unwrapH2[1];
              v[2] = fO[2]*unwrap[2]+fH[2]*unwrapH1[2]+fH[2]*unwrapH2[2];
              v[3] = fO[0]*unwrap[1]+fH[0]*unwrapH1[1]+fH[0]*unwrapH2[1];
              v[4] = fO[0]*unwrap[2]+fH[0]*unwrapH1[2]+fH[0]*unwrapH2[2];
              v[5] = fO[1]*unwrap[2]+fH[1]*unwrapH1[2]+fH[1]*unwrapH2[2];
              v_tally(i, v);
            }

          }
     }
}

/* ------------------------------TIP4P----------------------------------- */


    // dipole interactions
    // no force, torque = mu cross E, potential energy = -mu dot E

    if (muflag) {
      double **mu = atom->mu;
      double **t = atom->torque;
      double tx,ty,tz;
      for (int i = 0; i < nlocal; i++)
        if (mask[i] & groupbit) {
          if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
          tx = ez*mu[i][1] - ey*mu[i][2];
          ty = ex*mu[i][2] - ez*mu[i][0];
          tz = ey*mu[i][0] - ex*mu[i][1];
          t[i][0] += tx;
          t[i][1] += ty;
          t[i][2] += tz;
          fsum[0] -= mu[i][0]*ex + mu[i][1]*ey + mu[i][2]*ez;
        }
    }

  // variable efield, wrap with clear/add
  // potential energy = evar if defined, else 0.0

  } else {

    modify->clearstep_compute();

    if (xstyle == EQUAL) ex = qe2f * input->variable->compute_equal(xvar);
    else if (xstyle == ATOM)
      input->variable->compute_atom(xvar,igroup,&efield[0][0],4,0);
    if (ystyle == EQUAL) ey = qe2f * input->variable->compute_equal(yvar);
    else if (ystyle == ATOM)
      input->variable->compute_atom(yvar,igroup,&efield[0][1],4,0);
    if (zstyle == EQUAL) ez = qe2f * input->variable->compute_equal(zvar);
    else if (zstyle == ATOM)
      input->variable->compute_atom(zvar,igroup,&efield[0][2],4,0);
    if (estyle == ATOM)
      input->variable->compute_atom(evar,igroup,&efield[0][3],4,0);

    modify->addstep_compute(update->ntimestep + 1);

    // charge interactions
    // force = qE

    if (qflag) {
      for (int i = 0; i < nlocal; i++)
        if (mask[i] & groupbit) {
          if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
          if (xstyle == ATOM) fx = qe2f * q[i]*efield[i][0];
          else fx = q[i]*ex;
          f[i][0] += fx;
          fsum[1] += fx;
          if (ystyle == ATOM) fy = qe2f * q[i]*efield[i][1];
          else fy = q[i]*ey;
          f[i][1] += fy;
          fsum[2] += fy;
          if (zstyle == ATOM) fz = qe2f * q[i]*efield[i][2];
          else fz = q[i]*ez;
          f[i][2] += fz;
          fsum[3] += fz;
          if (estyle == ATOM) fsum[0] += efield[0][3];
        }
    }

    // dipole interactions
    // no force, torque = mu cross E

    if (muflag) {
      double **mu = atom->mu;
      double **t = atom->torque;
      double tx,ty,tz;
      for (int i = 0; i < nlocal; i++)
        if (mask[i] & groupbit) {
          if (region && !region->match(x[i][0],x[i][1],x[i][2])) continue;
          tx = ez*mu[i][1] - ey*mu[i][2];
          ty = ex*mu[i][2] - ez*mu[i][0];
          tz = ey*mu[i][0] - ex*mu[i][1];
          t[i][0] += tx;
          t[i][1] += ty;
          t[i][2] += tz;
        }
    }
  }
}

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

void FixEfieldTIP4P::post_force_respa(int vflag, int ilevel, int /*iloop*/)  // TIP4P
{
  if (ilevel == ilevel_respa) post_force(vflag);
}

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

void FixEfieldTIP4P::min_post_force(int vflag)  // TIP4P
{
  post_force(vflag);
}

/* ----------------------------------------------------------------------
   memory usage of local atom-based array
------------------------------------------------------------------------- */

double FixEfieldTIP4P::memory_usage()  // TIP4P
{
  double bytes = 0.0;
  if (varflag == ATOM) bytes = atom->nmax*4 * sizeof(double);
  return bytes;
}

/* ----------------------------------------------------------------------
   return energy added by fix
------------------------------------------------------------------------- */

double FixEfieldTIP4P::compute_scalar(void)  // TIP4P
{
  if (force_flag == 0) {
    MPI_Allreduce(fsum,fsum_all,4,MPI_DOUBLE,MPI_SUM,world);
    force_flag = 1;
  }
  return fsum_all[0];
}

/* ----------------------------------------------------------------------
   return total extra force due to fix
------------------------------------------------------------------------- */

double FixEfieldTIP4P::compute_vector(int n)  // TIP4P
{
  if (force_flag == 0) {
    MPI_Allreduce(fsum,fsum_all,4,MPI_DOUBLE,MPI_SUM,world);
    force_flag = 1;
  }
  return fsum_all[n+1];
}