Unverified Commit 09bed0c0 authored by Steve Plimpton's avatar Steve Plimpton Committed by GitHub
Browse files

Merge pull request #747 from stanmoore1/kk_reax_hist 

Fix broken charge history in fix qeq/reax/kk
parents 1b51efd6 7d07baa8

src/KOKKOS/atom_vec_hybrid_kokkos.cpp

+5 −0
Original line number Diff line number Diff line
@@ -255,6 +255,7 @@ int AtomVecHybridKokkos::pack_comm_kokkos(const int &n, const DAT::tdual_int_2d 
                     const int &pbc_flag, const int pbc[])

{

  error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");

  return 0;

}

void AtomVecHybridKokkos::unpack_comm_kokkos(const int &n, const int &nfirst,

                        const DAT::tdual_xfloat_2d &buf)
@@ -266,12 +267,14 @@ int AtomVecHybridKokkos::pack_comm_self(const int &n, const DAT::tdual_int_2d &l 
                   const int &pbc_flag, const int pbc[])

{

  error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");

  return 0;

}

int AtomVecHybridKokkos::pack_border_kokkos(int n, DAT::tdual_int_2d k_sendlist,

                       DAT::tdual_xfloat_2d buf,int iswap,

                       int pbc_flag, int *pbc, ExecutionSpace space)

{

  error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");

  return 0;

}

void AtomVecHybridKokkos::unpack_border_kokkos(const int &n, const int &nfirst,

                          const DAT::tdual_xfloat_2d &buf,
@@ -286,12 +289,14 @@ int AtomVecHybridKokkos::pack_exchange_kokkos(const int &nsend,DAT::tdual_xfloat 
                         X_FLOAT lo, X_FLOAT hi)

{

  error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");

  return 0;

}

int AtomVecHybridKokkos::unpack_exchange_kokkos(DAT::tdual_xfloat_2d &k_buf, int nrecv,

                           int nlocal, int dim, X_FLOAT lo, X_FLOAT hi,

                           ExecutionSpace space)

{

  error->all(FLERR,"AtomVecHybridKokkos doesn't yet support threaded comm");

  return 0;

}



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

src/KOKKOS/fix_qeq_reax_kokkos.cpp

+97 −40
Original line number Diff line number Diff line
@@ -64,6 +64,10 @@ FixQEqReaxKokkos(LAMMPS *lmp, int narg, char **arg) : 
  nmax = nmax = m_cap = 0;

  allocated_flag = 0;

  nprev = 4;



  memory->destroy(s_hist);

  memory->destroy(t_hist);

  grow_arrays(atom->nmax);

}



/* ---------------------------------------------------------------------- */
@@ -72,6 +76,9 @@ template<class DeviceType> 
FixQEqReaxKokkos<DeviceType>::~FixQEqReaxKokkos()

{

  if (copymode) return;



  memoryKK->destroy_kokkos(k_s_hist,s_hist);

  memoryKK->destroy_kokkos(k_t_hist,t_hist);

}



/* ---------------------------------------------------------------------- */
@@ -157,25 +164,11 @@ void FixQEqReaxKokkos<DeviceType>::init_shielding_k() 
template<class DeviceType>

void FixQEqReaxKokkos<DeviceType>::init_hist()

{

  int i,j;



  k_s_hist = DAT::tdual_ffloat_2d("qeq/kk:s_hist",atom->nmax,nprev);

  d_s_hist = k_s_hist.template view<DeviceType>();

  h_s_hist = k_s_hist.h_view;

  k_t_hist = DAT::tdual_ffloat_2d("qeq/kk:t_hist",atom->nmax,nprev);

  d_t_hist = k_t_hist.template view<DeviceType>();

  h_t_hist = k_t_hist.h_view;



  for( i = 0; i < atom->nmax; i++ )

    for( j = 0; j < nprev; j++ )

      k_s_hist.h_view(i,j) = k_t_hist.h_view(i,j) = 0.0;



  k_s_hist.template modify<LMPHostType>();

  k_s_hist.template sync<DeviceType>();



  k_t_hist.template modify<LMPHostType>();

  k_t_hist.template sync<DeviceType>();

  Kokkos::deep_copy(d_s_hist,0.0);

  Kokkos::deep_copy(d_t_hist,0.0);



  k_s_hist.template modify<DeviceType>();

  k_t_hist.template modify<DeviceType>();

}



/* ---------------------------------------------------------------------- */
@@ -235,6 +228,8 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag) 
  Kokkos::parallel_scan(inum,computeH_functor);



  // init_matvec

  k_s_hist.template sync<DeviceType>();

  k_t_hist.template sync<DeviceType>();

  FixQEqReaxKokkosMatVecFunctor<DeviceType> matvec_functor(this);

  Kokkos::parallel_for(inum,matvec_functor);
@@ -262,6 +257,8 @@ void FixQEqReaxKokkos<DeviceType>::pre_force(int vflag) 


  // calculate_Q();

  calculate_q();

  k_s_hist.template modify<DeviceType>();

  k_t_hist.template modify<DeviceType>();



  copymode = 0;
@@ -334,14 +331,6 @@ void FixQEqReaxKokkos<DeviceType>::allocate_array() 
    k_d = DAT::tdual_ffloat_1d("qeq/kk:h_d",nmax);

    d_d = k_d.template view<DeviceType>();

    h_d = k_d.h_view;



    k_s_hist = DAT::tdual_ffloat_2d("qeq/kk:s_hist",nmax,nprev);

    d_s_hist = k_s_hist.template view<DeviceType>();

    h_s_hist = k_s_hist.h_view;



    k_t_hist = DAT::tdual_ffloat_2d("qeq/kk:t_hist",nmax,nprev);

    d_t_hist = k_t_hist.template view<DeviceType>();

    h_t_hist = k_t_hist.h_view;

  }



  // init_storage
@@ -369,8 +358,6 @@ void FixQEqReaxKokkos<DeviceType>::zero_item(int ii) const 
    d_o[i] = 0.0;

    d_r[i] = 0.0;

    d_d[i] = 0.0;

    //for( int j = 0; j < nprev; j++ )

      //d_s_hist(i,j) = d_t_hist(i,j) = 0.0;

  }



}
@@ -405,19 +392,19 @@ void FixQEqReaxKokkos<DeviceType>::compute_h_item(int ii, int &m_fill, const boo 
      const X_FLOAT delz = x(j,2) - ztmp;



      if (neighflag != FULL) {

        // skip half of the interactions

        const tagint jtag = tag(j);

        flag = 0;

        if (j < nlocal) flag = 1;

        else if (itag < jtag) flag = 1;

        else if (itag == jtag) {

          if (delz > SMALL) flag = 1;

          else if (fabs(delz) < SMALL) {

            if (dely > SMALL) flag = 1;

            else if (fabs(dely) < SMALL && delx > SMALL)

              flag = 1;

        if (j >= nlocal) {

          if (itag > jtag) {

            if ((itag+jtag) % 2 == 0) continue;

          } else if (itag < jtag) {

            if ((itag+jtag) % 2 == 1) continue;

          } else {

            if (x(j,2) < ztmp) continue;

            if (x(j,2) == ztmp && x(j,1)  < ytmp) continue;

            if (x(j,2) == ztmp && x(j,1) == ytmp && x(j,0) < xtmp) continue;

          }

        }

        if (!flag) continue;

      }



      const F_FLOAT rsq = delx*delx + dely*dely + delz*delz;
@@ -462,7 +449,7 @@ double FixQEqReaxKokkos<DeviceType>::calculate_H_k(const F_FLOAT &r, const F_FLO 


template<class DeviceType>

KOKKOS_INLINE_FUNCTION

void FixQEqReaxKokkos<DeviceType>::mat_vec_item(int ii) const

void FixQEqReaxKokkos<DeviceType>::matvec_item(int ii) const

{

  const int i = d_ilist[ii];

  const int itype = type(i);
@@ -1183,7 +1170,77 @@ double FixQEqReaxKokkos<DeviceType>::memory_usage() 
  return bytes;

}



/* ---------------------------------------------------------------------- */\

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

   allocate fictitious charge arrays

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



template<class DeviceType>

void FixQEqReaxKokkos<DeviceType>::grow_arrays(int nmax)

{

  k_s_hist.template sync<LMPHostType>(); // force reallocation on host

  k_t_hist.template sync<LMPHostType>();



  memoryKK->grow_kokkos(k_s_hist,s_hist,nmax,nprev,"qeq:s_hist");

  memoryKK->grow_kokkos(k_t_hist,t_hist,nmax,nprev,"qeq:t_hist");



  d_s_hist = k_s_hist.template view<DeviceType>();

  d_t_hist = k_t_hist.template view<DeviceType>();



  k_s_hist.template modify<LMPHostType>();

  k_t_hist.template modify<LMPHostType>();

}



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

   copy values within fictitious charge arrays

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



template<class DeviceType>

void FixQEqReaxKokkos<DeviceType>::copy_arrays(int i, int j, int delflag)

{

  k_s_hist.template sync<LMPHostType>();

  k_t_hist.template sync<LMPHostType>();



  for (int m = 0; m < nprev; m++) {

    s_hist[j][m] = s_hist[i][m];

    t_hist[j][m] = t_hist[i][m];

  }



  k_s_hist.template modify<LMPHostType>();

  k_t_hist.template modify<LMPHostType>();

}



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

   pack values in local atom-based array for exchange with another proc

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



template<class DeviceType>

int FixQEqReaxKokkos<DeviceType>::pack_exchange(int i, double *buf)

{

  k_s_hist.template sync<LMPHostType>();

  k_t_hist.template sync<LMPHostType>();



  for (int m = 0; m < nprev; m++) buf[m] = s_hist[i][m];

  for (int m = 0; m < nprev; m++) buf[nprev+m] = t_hist[i][m];

  return nprev*2;

}



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

   unpack values in local atom-based array from exchange with another proc

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



template<class DeviceType>

int FixQEqReaxKokkos<DeviceType>::unpack_exchange(int nlocal, double *buf)

{

  for (int m = 0; m < nprev; m++) s_hist[nlocal][m] = buf[m];

  for (int m = 0; m < nprev; m++) t_hist[nlocal][m] = buf[nprev+m];



  k_s_hist.template modify<LMPHostType>();

  k_t_hist.template modify<LMPHostType>();



  return nprev*2;

}



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



namespace LAMMPS_NS {

template class FixQEqReaxKokkos<LMPDeviceType>;

src/KOKKOS/fix_qeq_reax_kokkos.h

+7 −3
Original line number Diff line number Diff line
@@ -57,7 +57,7 @@ class FixQEqReaxKokkos : public FixQEqReax { 
  void compute_h_item(int, int &, const bool &) const;



  KOKKOS_INLINE_FUNCTION

  void mat_vec_item(int) const;

  void matvec_item(int) const;



  KOKKOS_INLINE_FUNCTION

  void sparse12_item(int) const;
@@ -145,7 +145,7 @@ class FixQEqReaxKokkos : public FixQEqReax { 
  void unpack_reverse_comm(int, int *, double *);

  double memory_usage();



 protected:

 private:

  int inum;

  int allocated_flag;
@@ -210,6 +210,10 @@ class FixQEqReaxKokkos : public FixQEqReax { 
  typename AT::t_int_2d d_sendlist;

  typename AT::t_xfloat_1d_um v_buf;



  void grow_arrays(int);

  void copy_arrays(int, int, int);

  int pack_exchange(int, double *);

  int unpack_exchange(int, double *);

};



template <class DeviceType>
@@ -235,7 +239,7 @@ struct FixQEqReaxKokkosMatVecFunctor { 
  };

  KOKKOS_INLINE_FUNCTION

  void operator()(const int ii) const {

    c.mat_vec_item(ii);

    c.matvec_item(ii);

  }

};

src/USER-REAXC/fix_qeq_reax.h

+9 −9
Original line number Diff line number Diff line
@@ -122,15 +122,15 @@ class FixQEqReax : public Fix { 
  //int GMRES(double*,double*);

  virtual void sparse_matvec(sparse_matrix*,double*,double*);



  int pack_forward_comm(int, int *, double *, int, int *);

  void unpack_forward_comm(int, int, double *);

  int pack_reverse_comm(int, int, double *);

  void unpack_reverse_comm(int, int *, double *);

  double memory_usage();

  void grow_arrays(int);

  void copy_arrays(int, int, int);

  int pack_exchange(int, double *);

  int unpack_exchange(int, double *);

  virtual int pack_forward_comm(int, int *, double *, int, int *);

  virtual void unpack_forward_comm(int, int, double *);

  virtual int pack_reverse_comm(int, int, double *);

  virtual void unpack_reverse_comm(int, int *, double *);

  virtual double memory_usage();

  virtual void grow_arrays(int);

  virtual void copy_arrays(int, int, int);

  virtual int pack_exchange(int, double *);

  virtual int unpack_exchange(int, double *);



  virtual double parallel_norm( double*, int );

  virtual double parallel_dot( double*, double*, int );

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