Unverified Commit f286155d authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1306 from stanmoore1/kk_angle_cosine 

Add Kokkos version of angle/cosine
parents f04d97e6 54b9a133

doc/src/Commands_bond.txt

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@@ -61,7 +61,7 @@ OPT. 
"charmm (iko)"_angle_charmm.html,

"class2 (ko)"_angle_class2.html,

"class2/p6"_angle_class2.html,

"cosine (o)"_angle_cosine.html,

"cosine (ko)"_angle_cosine.html,

"cosine/buck6d"_angle_cosine_buck6d.html,

"cosine/delta (o)"_angle_cosine_delta.html,

"cosine/periodic (o)"_angle_cosine_periodic.html,

doc/src/angle_cosine.txt

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@@ -8,6 +8,7 @@ 


angle_style cosine command :h3

angle_style cosine/omp command :h3

angle_style cosine/kk command :h3



[Syntax:]

src/KOKKOS/Install.sh

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@@ -49,6 +49,8 @@ action angle_charmm_kokkos.cpp angle_charmm.cpp 
action angle_charmm_kokkos.h angle_charmm.h

action angle_class2_kokkos.cpp angle_class2.cpp 

action angle_class2_kokkos.h angle_class2.h

action angle_cosine_kokkos.cpp angle_cosine.cpp 

action angle_cosine_kokkos.h angle_cosine.h

action angle_harmonic_kokkos.cpp angle_harmonic.cpp 

action angle_harmonic_kokkos.h angle_harmonic.h 

action atom_kokkos.cpp

src/KOKKOS/angle_cosine_kokkos.cpp

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

   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: Stan Moore (SNL)

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



#include <cmath>

#include <cstdlib>

#include "angle_cosine_kokkos.h"

#include "atom_kokkos.h"

#include "neighbor_kokkos.h"

#include "domain.h"

#include "comm.h"

#include "force.h"

#include "math_const.h"

#include "memory_kokkos.h"

#include "error.h"

#include "atom_masks.h"



using namespace LAMMPS_NS;

using namespace MathConst;



#define SMALL 0.001



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



template<class DeviceType>

AngleCosineKokkos<DeviceType>::AngleCosineKokkos(LAMMPS *lmp) : AngleCosine(lmp)

{

  atomKK = (AtomKokkos *) atom;

  neighborKK = (NeighborKokkos *) neighbor;

  execution_space = ExecutionSpaceFromDevice<DeviceType>::space;

  datamask_read = X_MASK | F_MASK | ENERGY_MASK | VIRIAL_MASK;

  datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;

}



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



template<class DeviceType>

AngleCosineKokkos<DeviceType>::~AngleCosineKokkos()

{

  if (!copymode) {

    memoryKK->destroy_kokkos(k_eatom,eatom);

    memoryKK->destroy_kokkos(k_vatom,vatom);

  }

}



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



template<class DeviceType>

void AngleCosineKokkos<DeviceType>::compute(int eflag_in, int vflag_in)

{

  eflag = eflag_in;

  vflag = vflag_in;



  if (eflag || vflag) ev_setup(eflag,vflag,0);

  else evflag = 0;



  // reallocate per-atom arrays if necessary



  if (eflag_atom) {

    memoryKK->destroy_kokkos(k_eatom,eatom);

    memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"angle:eatom");

    d_eatom = k_eatom.template view<DeviceType>();

  }

  if (vflag_atom) {

    memoryKK->destroy_kokkos(k_vatom,vatom);

    memoryKK->create_kokkos(k_vatom,vatom,maxvatom,6,"angle:vatom");

    d_vatom = k_vatom.template view<DeviceType>();

  }



  //atomKK->sync(execution_space,datamask_read);

  k_k.template sync<DeviceType>();

  //  if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);

  //  else atomKK->modified(execution_space,F_MASK);



  x = atomKK->k_x.template view<DeviceType>();

  f = atomKK->k_f.template view<DeviceType>();

  neighborKK->k_anglelist.template sync<DeviceType>();

  anglelist = neighborKK->k_anglelist.template view<DeviceType>();

  int nanglelist = neighborKK->nanglelist;

  nlocal = atom->nlocal;

  newton_bond = force->newton_bond;



  copymode = 1;



  // loop over neighbors of my atoms



  EV_FLOAT ev;



  if (evflag) {

    if (newton_bond) {

      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleCosineCompute<1,1> >(0,nanglelist),*this,ev);

    } else {

      Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagAngleCosineCompute<0,1> >(0,nanglelist),*this,ev);

    }

  } else {

    if (newton_bond) {

      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleCosineCompute<1,0> >(0,nanglelist),*this);

    } else {

      Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagAngleCosineCompute<0,0> >(0,nanglelist),*this);

    }

  }



  if (eflag_global) energy += ev.evdwl;

  if (vflag_global) {

    virial[0] += ev.v[0];

    virial[1] += ev.v[1];

    virial[2] += ev.v[2];

    virial[3] += ev.v[3];

    virial[4] += ev.v[4];

    virial[5] += ev.v[5];

  }



  if (eflag_atom) {

    k_eatom.template modify<DeviceType>();

    k_eatom.template sync<LMPHostType>();

  }



  if (vflag_atom) {

    k_vatom.template modify<DeviceType>();

    k_vatom.template sync<LMPHostType>();

  }



  copymode = 0;

}



template<class DeviceType>

template<int NEWTON_BOND, int EVFLAG>

KOKKOS_INLINE_FUNCTION

void AngleCosineKokkos<DeviceType>::operator()(TagAngleCosineCompute<NEWTON_BOND,EVFLAG>, const int &n, EV_FLOAT& ev) const {



  // The f array is atomic

  Kokkos::View<F_FLOAT*[3], typename DAT::t_f_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > a_f = f;



  const int i1 = anglelist(n,0);

  const int i2 = anglelist(n,1);

  const int i3 = anglelist(n,2);

  const int type = anglelist(n,3);



  // 1st bond



  const F_FLOAT delx1 = x(i1,0) - x(i2,0);

  const F_FLOAT dely1 = x(i1,1) - x(i2,1);

  const F_FLOAT delz1 = x(i1,2) - x(i2,2);



  const F_FLOAT rsq1 = delx1*delx1 + dely1*dely1 + delz1*delz1;

  const F_FLOAT r1 = sqrt(rsq1);



  // 2nd bond



  const F_FLOAT delx2 = x(i3,0) - x(i2,0);

  const F_FLOAT dely2 = x(i3,1) - x(i2,1);

  const F_FLOAT delz2 = x(i3,2) - x(i2,2);



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

  const F_FLOAT r2 = sqrt(rsq2);



  // c = cosine of angle



  F_FLOAT 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



  F_FLOAT eangle = 0.0;

  if (eflag) eangle = d_k[type]*(1.0+c);



  const F_FLOAT a = d_k[type];

  const F_FLOAT a11 = a*c / rsq1;

  const F_FLOAT a12 = -a / (r1*r2);

  const F_FLOAT a22 = a*c / rsq2;



  F_FLOAT f1[3],f3[3];

  f1[0] = a11*delx1 + a12*delx2;

  f1[1] = a11*dely1 + a12*dely2;

  f1[2] = a11*delz1 + a12*delz2;

  f3[0] = a22*delx2 + a12*delx1;

  f3[1] = a22*dely2 + a12*dely1;

  f3[2] = a22*delz2 + a12*delz1;



  // apply force to each of 3 atoms



  if (NEWTON_BOND || i1 < nlocal) {

    a_f(i1,0) += f1[0];

    a_f(i1,1) += f1[1];

    a_f(i1,2) += f1[2];

  }



  if (NEWTON_BOND || i2 < nlocal) {

    a_f(i2,0) -= f1[0] + f3[0];

    a_f(i2,1) -= f1[1] + f3[1];

    a_f(i2,2) -= f1[2] + f3[2];

  }



  if (NEWTON_BOND || i3 < nlocal) {

    a_f(i3,0) += f3[0];

    a_f(i3,1) += f3[1];

    a_f(i3,2) += f3[2];

  }



  if (EVFLAG) ev_tally(ev,i1,i2,i3,eangle,f1,f3,

                       delx1,dely1,delz1,delx2,dely2,delz2);

}



template<class DeviceType>

template<int NEWTON_BOND, int EVFLAG>

KOKKOS_INLINE_FUNCTION

void AngleCosineKokkos<DeviceType>::operator()(TagAngleCosineCompute<NEWTON_BOND,EVFLAG>, const int &n) const {

  EV_FLOAT ev;

  this->template operator()<NEWTON_BOND,EVFLAG>(TagAngleCosineCompute<NEWTON_BOND,EVFLAG>(), n, ev);

}



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



template<class DeviceType>

void AngleCosineKokkos<DeviceType>::allocate()

{

  AngleCosine::allocate();



  int n = atom->nangletypes;

  k_k = typename ArrayTypes<DeviceType>::tdual_ffloat_1d("AngleCosine::k",n+1);

  d_k = k_k.template view<DeviceType>();

}



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

   set coeffs for one or more types

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



template<class DeviceType>

void AngleCosineKokkos<DeviceType>::coeff(int narg, char **arg)

{

  AngleCosine::coeff(narg, arg);



  int n = atom->nangletypes;

  for (int i = 1; i <= n; i++)

    k_k.h_view[i] = k[i];



  k_k.template modify<LMPHostType>();

}



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

   proc 0 reads coeffs from restart file, bcasts them

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



template<class DeviceType>

void AngleCosineKokkos<DeviceType>::read_restart(FILE *fp)

{

  AngleCosine::read_restart(fp);



  int n = atom->nangletypes;

  for (int i = 1; i <= n; i++)

    k_k.h_view[i] = k[i];



  k_k.template modify<LMPHostType>();

}



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

   tally energy and virial into global and per-atom accumulators

   virial = r1F1 + r2F2 + r3F3 = (r1-r2) F1 + (r3-r2) F3 = del1*f1 + del2*f3

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



template<class DeviceType>

//template<int NEWTON_BOND>

KOKKOS_INLINE_FUNCTION

void AngleCosineKokkos<DeviceType>::ev_tally(EV_FLOAT &ev, const int i, const int j, const int k,

                     F_FLOAT &eangle, F_FLOAT *f1, F_FLOAT *f3,

                     const F_FLOAT &delx1, const F_FLOAT &dely1, const F_FLOAT &delz1,

                     const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const

{

  E_FLOAT eanglethird;

  F_FLOAT v[6];



  // The eatom and vatom arrays are atomic

  Kokkos::View<E_FLOAT*, typename DAT::t_efloat_1d::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_eatom = k_eatom.template view<DeviceType>();

  Kokkos::View<F_FLOAT*[6], typename DAT::t_virial_array::array_layout,DeviceType,Kokkos::MemoryTraits<Kokkos::Atomic|Kokkos::Unmanaged> > v_vatom = k_vatom.template view<DeviceType>();



  if (eflag_either) {

    if (eflag_global) {

      if (newton_bond) ev.evdwl += eangle;

      else {

        eanglethird = THIRD*eangle;



        if (i < nlocal) ev.evdwl += eanglethird;

        if (j < nlocal) ev.evdwl += eanglethird;

        if (k < nlocal) ev.evdwl += eanglethird;

      }

    }

    if (eflag_atom) {

      eanglethird = THIRD*eangle;



      if (newton_bond || i < nlocal) v_eatom[i] += eanglethird;

      if (newton_bond || j < nlocal) v_eatom[j] += eanglethird;

      if (newton_bond || k < nlocal) v_eatom[k] += eanglethird;

    }

  }



  if (vflag_either) {

    v[0] = delx1*f1[0] + delx2*f3[0];

    v[1] = dely1*f1[1] + dely2*f3[1];

    v[2] = delz1*f1[2] + delz2*f3[2];

    v[3] = delx1*f1[1] + delx2*f3[1];

    v[4] = delx1*f1[2] + delx2*f3[2];

    v[5] = dely1*f1[2] + dely2*f3[2];



    if (vflag_global) {

      if (newton_bond) {

        ev.v[0] += v[0];

        ev.v[1] += v[1];

        ev.v[2] += v[2];

        ev.v[3] += v[3];

        ev.v[4] += v[4];

        ev.v[5] += v[5];

      } else {

        if (i < nlocal) {

          ev.v[0] += THIRD*v[0];

          ev.v[1] += THIRD*v[1];

          ev.v[2] += THIRD*v[2];

          ev.v[3] += THIRD*v[3];

          ev.v[4] += THIRD*v[4];

          ev.v[5] += THIRD*v[5];

        }

        if (j < nlocal) {

          ev.v[0] += THIRD*v[0];

          ev.v[1] += THIRD*v[1];

          ev.v[2] += THIRD*v[2];

          ev.v[3] += THIRD*v[3];

          ev.v[4] += THIRD*v[4];

          ev.v[5] += THIRD*v[5];

        }

        if (k < nlocal) {

          ev.v[0] += THIRD*v[0];



          ev.v[1] += THIRD*v[1];

          ev.v[2] += THIRD*v[2];

          ev.v[3] += THIRD*v[3];

          ev.v[4] += THIRD*v[4];

          ev.v[5] += THIRD*v[5];

        }

      }

    }



    if (vflag_atom) {

      if (newton_bond || i < nlocal) {

        v_vatom(i,0) += THIRD*v[0];

        v_vatom(i,1) += THIRD*v[1];

        v_vatom(i,2) += THIRD*v[2];

        v_vatom(i,3) += THIRD*v[3];

        v_vatom(i,4) += THIRD*v[4];

        v_vatom(i,5) += THIRD*v[5];

      }

      if (newton_bond || j < nlocal) {

        v_vatom(j,0) += THIRD*v[0];

        v_vatom(j,1) += THIRD*v[1];

        v_vatom(j,2) += THIRD*v[2];

        v_vatom(j,3) += THIRD*v[3];

        v_vatom(j,4) += THIRD*v[4];

        v_vatom(j,5) += THIRD*v[5];

      }

      if (newton_bond || k < nlocal) {

        v_vatom(k,0) += THIRD*v[0];

        v_vatom(k,1) += THIRD*v[1];

        v_vatom(k,2) += THIRD*v[2];

        v_vatom(k,3) += THIRD*v[3];

        v_vatom(k,4) += THIRD*v[4];

        v_vatom(k,5) += THIRD*v[5];



      }

    }

  }

}



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



namespace LAMMPS_NS {

template class AngleCosineKokkos<LMPDeviceType>;

#ifdef KOKKOS_HAVE_CUDA

template class AngleCosineKokkos<LMPHostType>;

#endif

}

src/KOKKOS/angle_cosine_kokkos.h

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/* -*- c++ -*- ----------------------------------------------------------

   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.

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



#ifdef ANGLE_CLASS



AngleStyle(cosine/kk,AngleCosineKokkos<LMPDeviceType>)

AngleStyle(cosine/kk/device,AngleCosineKokkos<LMPDeviceType>)

AngleStyle(cosine/kk/host,AngleCosineKokkos<LMPHostType>)



#else



#ifndef LMP_ANGLE_COSINE_KOKKOS_H

#define LMP_ANGLE_COSINE_KOKKOS_H



#include "angle_cosine.h"

#include "kokkos_type.h"



namespace LAMMPS_NS {



template<int NEWTON_BOND, int EVFLAG>

struct TagAngleCosineCompute{};



template<class DeviceType>

class AngleCosineKokkos : public AngleCosine {



 public:

  typedef DeviceType device_type;

  typedef EV_FLOAT value_type;



  AngleCosineKokkos(class LAMMPS *);

  virtual ~AngleCosineKokkos();

  void compute(int, int);

  void coeff(int, char **);

  void read_restart(FILE *);



  template<int NEWTON_BOND, int EVFLAG>

  KOKKOS_INLINE_FUNCTION

  void operator()(TagAngleCosineCompute<NEWTON_BOND,EVFLAG>, const int&, EV_FLOAT&) const;



  template<int NEWTON_BOND, int EVFLAG>

  KOKKOS_INLINE_FUNCTION

  void operator()(TagAngleCosineCompute<NEWTON_BOND,EVFLAG>, const int&) const;



  //template<int NEWTON_BOND>

  KOKKOS_INLINE_FUNCTION

  void ev_tally(EV_FLOAT &ev, const int i, const int j, const int k,

                     F_FLOAT &eangle, F_FLOAT *f1, F_FLOAT *f3,

                     const F_FLOAT &delx1, const F_FLOAT &dely1, const F_FLOAT &delz1,

                     const F_FLOAT &delx2, const F_FLOAT &dely2, const F_FLOAT &delz2) const;



 protected:



  class NeighborKokkos *neighborKK;



  typename ArrayTypes<DeviceType>::t_x_array_randomread x;

  typename ArrayTypes<DeviceType>::t_f_array f;

  typename ArrayTypes<DeviceType>::t_int_2d anglelist;



  typename ArrayTypes<DeviceType>::tdual_efloat_1d k_eatom;

  typename ArrayTypes<DeviceType>::tdual_virial_array k_vatom;

  typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;

  typename ArrayTypes<DeviceType>::t_virial_array d_vatom;



  int nlocal,newton_bond;

  int eflag,vflag;



  typename ArrayTypes<DeviceType>::tdual_ffloat_1d k_k;

  typename ArrayTypes<DeviceType>::t_ffloat_1d d_k;



  void allocate();

};



}



#endif

#endif



/* ERROR/WARNING messages:



*/

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