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: Hendrik Heenen (Technical University of Munich)
                          (hendrik.heenen at mytum.com)
  ------------------------------------------------------------------------- */
  
  #include <mpi.h>
  #include <stdlib.h>
  #include <string.h>
  #include <math.h>
  #include "compute_temp_cs.h"
  #include "atom.h"
  #include "atom_vec.h"
  #include "domain.h"
  #include "update.h"
  #include "force.h"
  #include "group.h"
  #include "modify.h"
  #include "fix.h"
  #include "fix_store.h"
  #include "comm.h"
  #include "memory.h"
  #include "error.h"
  
  using namespace LAMMPS_NS;
  
  /* ---------------------------------------------------------------------- */
  
  ComputeTempCS::ComputeTempCS(LAMMPS *lmp, int narg, char **arg) :
    Compute(lmp, narg, arg), vint(NULL), id_fix(NULL), fix(NULL)
  {
    if (narg != 5) error->all(FLERR,"Illegal compute temp/cs command");
  
    if (atom->avec->bonds_allow == 0)
      error->all(FLERR,"Compute temp/cs used when bonds are not allowed");
  
    scalar_flag = vector_flag = 1;
    size_vector = 6;
    extscalar = 0;
    extvector = 1;
    tempflag = 1;
    tempbias = 1;
    extarray = 0;
  
    // find and define groupbits for core and shell groups
  
    cgroup = group->find(arg[3]);
    if (cgroup == -1)
      error->all(FLERR,"Cannot find specified group ID for core particles");
    groupbit_c = group->bitmask[cgroup];
  
    sgroup = group->find(arg[4]);
    if (sgroup == -1)
      error->all(FLERR,"Cannot find specified group ID for shell particles");
    groupbit_s = group->bitmask[sgroup];
  
    // create a new fix STORE style
    // id = compute-ID + COMPUTE_STORE, fix group = compute group
  
    int n = strlen(id) + strlen("_COMPUTE_STORE") + 1;
    id_fix = new char[n];
    strcpy(id_fix,id);
    strcat(id_fix,"_COMPUTE_STORE");
  
    char **newarg = new char*[6];
    newarg[0] = id_fix;
    newarg[1] = group->names[igroup];
    newarg[2] = (char *) "STORE";
    newarg[3] = (char *) "peratom";
    newarg[4] = (char *) "0";
    newarg[5] = (char *) "1";
    modify->add_fix(6,newarg);
    fix = (FixStore *) modify->fix[modify->nfix-1];
    delete [] newarg;
  
    // set fix store values = 0 for now
    // fill them in via setup() once Comm::borders() has been called
    // skip if resetting from restart file
  
    if (fix->restart_reset) {
      fix->restart_reset = 0;
      firstflag = 0;
    } else {
      double *partner = fix->vstore;
      int nlocal = atom->nlocal;
      for (int i = 0; i < nlocal; i++) partner[i] = ubuf(0).d;
      firstflag = 1;
    }
  
    // allocate memory
  
    vector = new double[6];
    maxatom = 0;
    vint = NULL;
  
    // set comm size needed by this Compute
  
    comm_reverse = 1;
  }
  
  /* ---------------------------------------------------------------------- */
  
  ComputeTempCS::~ComputeTempCS()
  {
    // check nfix in case all fixes have already been deleted
  
    if (modify->nfix) modify->delete_fix(id_fix);
  
    delete [] id_fix;
    delete [] vector;
    memory->destroy(vint);
  }
  
  /* ---------------------------------------------------------------------- */
  
  void ComputeTempCS::init()
  {
    if (comm->ghost_velocity == 0)
      error->all(FLERR,"Compute temp/cs requires ghost atoms store velocity");
  }
  
  /* ---------------------------------------------------------------------- */
  
  void ComputeTempCS::setup()
  {
    if (firstflag) {
      firstflag = 0;
  
      // insure # of core atoms = # of shell atoms
  
      int ncores = group->count(cgroup);
      nshells = group->count(sgroup);
      if (ncores != nshells)
        error->all(FLERR,"Number of core atoms != number of shell atoms");
  
      // for each C/S pair:
      // set partner IDs of both atoms if this atom stores bond between them
      // will set partner IDs for ghost atoms if needed by another proc
      // nall loop insures all ghost atom partner IDs are set before reverse comm
  
      int *num_bond = atom->num_bond;
      tagint **bond_atom = atom->bond_atom;
      tagint *tag = atom->tag;
      int *mask = atom->mask;
      int nlocal = atom->nlocal;
  
      double *partner = fix->vstore;
      tagint partnerID;
  
      int nall = nlocal + atom->nghost;
      for (int i = nlocal; i < nall; i++) partner[i] = ubuf(0).d;
  
      int i,j,m,match;
      for (i = 0; i < nlocal; i++) {
        if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
          for (m = 0; m < num_bond[i]; m++) {
            partnerID = bond_atom[i][m];
            j = atom->map(partnerID);
            if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
            match = 0;
            if (mask[i] & groupbit_c && mask[j] & groupbit_s) match = 1;
            if (mask[i] & groupbit_s && mask[j] & groupbit_c) match = 1;
            if (match) {
              partner[i] = ubuf(partnerID).d;
              partner[j] = ubuf(tag[i]).d;
            }
          }
        }
      }
  
      // reverse comm to acquire unknown partner IDs from ghost atoms
      // only needed if newton_bond = on
  
      if (force->newton_bond) comm->reverse_comm_compute(this);
  
      // check that all C/S partners were found
  
      int flag = 0;
      for (i = 0; i < nlocal; i++) {
        if (mask[i] & groupbit_c || mask[i] & groupbit_s) {
          partnerID = (tagint) ubuf(partner[i]).i;
          if (partnerID == 0) flag = 1;
        }
      }
  
      int flagall;
      MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
      if (flagall) error->all(FLERR,"Core/shell partners were not all found");
    }
  
    // calculate DOF for temperature
  
    dof_compute();
  }
  
  /* ---------------------------------------------------------------------- */
  
  void ComputeTempCS::dof_compute()
  {
    adjust_dof_fix();
    int nper = domain->dimension;
    natoms_temp = group->count(igroup);
    dof = nper * natoms_temp;
    dof -= nper * nshells;
    dof -= extra_dof + fix_dof;
    if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
    else tfactor = 0.0;
  }
  
  /* ---------------------------------------------------------------------- */
  
  double ComputeTempCS::compute_scalar()
  {
    double vthermal[3];
  
    invoked_scalar = update->ntimestep;
  
    vcm_pairs();
  
    // calculate thermal scalar in respect to atom velocities as center-of-mass
    // velocities of its according core/shell pairs
  
    double **v = atom->v;
    int *mask = atom->mask;
    int *type = atom->type;
    double *mass = atom->mass;
    double *rmass = atom->rmass;
    int nlocal = atom->nlocal;
  
    double t = 0.0;
  
    for (int i = 0; i < nlocal; i++){
      if (mask[i] & groupbit) {
        vthermal[0] = v[i][0] - vint[i][0];
        vthermal[1] = v[i][1] - vint[i][1];
        vthermal[2] = v[i][2] - vint[i][2];
        if (rmass)
          t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
                vthermal[2]*vthermal[2]) * rmass[i];
        else
          t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
                vthermal[2]*vthermal[2]) * mass[type[i]];
      }
    }
  
    MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
    if (dynamic) dof_compute();
    if (dof < 0.0 && natoms_temp > 0.0)
      error->all(FLERR,"Temperature compute degrees of freedom < 0");
    scalar *= tfactor;
    return scalar;
  }
  
  /* ---------------------------------------------------------------------- */
  
  void ComputeTempCS::compute_vector()
  {
    invoked_vector = update->ntimestep;
  
    double **v = atom->v;
    int *mask = atom->mask;
    int *type = atom->type;
    double *mass = atom->mass;
    double *rmass = atom->rmass;
    int nlocal = atom->nlocal;
    double massone;
  
    double t[6];
    for (int i = 0; i < 6; i++) t[i] = 0.0;
  
    for (int i = 0; i < nlocal; i++){
      if (mask[i] & groupbit) {
        if (rmass) massone = rmass[i];
        else massone = mass[type[i]];
        t[0] += massone * v[i][0]*v[i][0];
        t[1] += massone * v[i][1]*v[i][1];
        t[2] += massone * v[i][2]*v[i][2];
        t[3] += massone * v[i][0]*v[i][1];
        t[4] += massone * v[i][0]*v[i][2];
        t[5] += massone * v[i][1]*v[i][2];
      }
    }
  
    MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
    for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
  }
  
  /* ---------------------------------------------------------------------- */
  
  void ComputeTempCS::vcm_pairs()
  {
    int i,j;
    double massone,masstwo;
    double vcm[3];
  
    // reallocate vint if necessary
  
    int nlocal = atom->nlocal;
  
    if (atom->nmax > maxatom) {
      memory->destroy(vint);
      maxatom = atom->nmax;
      memory->create(vint,maxatom,3,"temp/cs:vint");
    }
  
    // vcm = COM velocity of each CS pair
    // vint = internal velocity of each C/S atom, used as bias
  
    double **v = atom->v;
    int *mask = atom->mask;
    int *type = atom->type;
    double *mass = atom->mass;
    double *rmass = atom->rmass;
  
    double *partner = fix->vstore;
    tagint partnerID;
  
    for (i = 0; i < nlocal; i++) {
      if ((mask[i] & groupbit) &&
          (mask[i] & groupbit_c || mask[i] & groupbit_s)) {
        if (rmass) massone = rmass[i];
        else massone = mass[type[i]];
        vcm[0] = v[i][0]*massone;
        vcm[1] = v[i][1]*massone;
        vcm[2] = v[i][2]*massone;
  
        partnerID = (tagint) ubuf(partner[i]).i;
        j = atom->map(partnerID);
        if (j == -1) error->one(FLERR,"Core/shell partner atom not found");
  
        if (rmass) masstwo = rmass[j];
        else masstwo = mass[type[j]];
        vcm[0] += v[j][0]*masstwo;
        vcm[1] += v[j][1]*masstwo;
        vcm[2] += v[j][2]*masstwo;
        vcm[0] /= (massone + masstwo);
        vcm[1] /= (massone + masstwo);
        vcm[2] /= (massone + masstwo);
  
        vint[i][0] = v[i][0] - vcm[0];
        vint[i][1] = v[i][1] - vcm[1];
        vint[i][2] = v[i][2] - vcm[2];
      } else vint[i][0] = vint[i][1] = vint[i][2] = 0.0;
    }
  }
  
  /* ----------------------------------------------------------------------
     remove velocity bias from atom I to leave thermal velocity
     thermal velocity in this case is COM velocity of C/S pair
  ------------------------------------------------------------------------- */
  
  void ComputeTempCS::remove_bias(int i, double *v)
  {
    v[0] -= vint[i][0];
    v[1] -= vint[i][1];
    v[2] -= vint[i][2];
  }
  
  /* ----------------------------------------------------------------------
     remove velocity bias from all atoms to leave thermal velocity
     thermal velocity in this case is COM velocity of C/S pair
  ------------------------------------------------------------------------- */
  
  void ComputeTempCS::remove_bias_all()
  {
    double **v = atom->v;
    int *mask = atom->mask;
    int nlocal = atom->nlocal;
  
    for (int i = 0; i < nlocal; i++)
      if (mask[i] & groupbit) {
        v[i][0] -= vint[i][0];
        v[i][1] -= vint[i][1];
        v[i][2] -= vint[i][2];
      }
  }
  
  /* ----------------------------------------------------------------------
     reset thermal velocity of all atoms to be consistent with bias
     called from velocity command after it creates thermal velocities
     this resets each atom's velocity to COM velocity of C/S pair
  ------------------------------------------------------------------------- */
  
  void ComputeTempCS::reapply_bias_all()
  {
    double **v = atom->v;
    int *mask = atom->mask;
    int nlocal = atom->nlocal;
  
    // recalculate current COM velocities
  
    vcm_pairs();
  
    // zero vint after using ti so that Velocity call to restore_bias_all()
    // will not further alter the velocities within a C/S pair
  
    for (int i = 0; i < nlocal; i++)
      if (mask[i] & groupbit) {
        v[i][0] -= vint[i][0];
        v[i][1] -= vint[i][1];
        v[i][2] -= vint[i][2];
        vint[i][0] = 0.0;
        vint[i][1] = 0.0;
        vint[i][2] = 0.0;
      }
  }
  
  /* ----------------------------------------------------------------------
     add back in velocity bias to atom I removed by remove_bias()
     assume remove_bias() was previously called
  ------------------------------------------------------------------------- */
  
  void ComputeTempCS::restore_bias(int i, double *v)
  {
    v[0] += vint[i][0];
    v[1] += vint[i][1];
    v[2] += vint[i][2];
  }
  
  /* ----------------------------------------------------------------------
     add back in velocity bias to all atoms removed by remove_bias_all()
     assume remove_bias_all() was previously called
  ------------------------------------------------------------------------- */
  
  void ComputeTempCS::restore_bias_all()
  {
    double **v = atom->v;
    int *mask = atom->mask;
    int nlocal = atom->nlocal;
  
    for (int i = 0; i < nlocal; i++)
      if (mask[i] & groupbit) {
        v[i][0] += vint[i][0];
        v[i][1] += vint[i][1];
        v[i][2] += vint[i][2];
      }
  }
  
  /* ---------------------------------------------------------------------- */
  
  int ComputeTempCS::pack_reverse_comm(int n, int first, double *buf)
  {
    int i,m,last;
  
    double *partner = fix->vstore;
  
    m = 0;
    last = first + n;
    for (i = first; i < last; i++) buf[m++] = partner[i];
    return m;
  }
  
  /* ---------------------------------------------------------------------- */
  
  void ComputeTempCS::unpack_reverse_comm(int n, int *list, double *buf)
  {
    int i,j,m;
  
    double *partner = fix->vstore;
    tagint partnerID;
  
    m = 0;
    for (i = 0; i < n; i++) {
      j = list[i];
      partnerID = (tagint) ubuf(buf[m++]).i;
      if (partnerID) partner[j] = ubuf(partnerID).d;
    }
  }
  
  /* ----------------------------------------------------------------------
     memory usage of local data
  ------------------------------------------------------------------------- */
  
  double ComputeTempCS::memory_usage()
  {
    double bytes = (bigint) maxatom * 3 * sizeof(double);
    return bytes;
  }
  