Unverified Commit 7bd32152 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
Browse files

Merge pull request #1894 from stanmoore1/kk_snap_chunk 

Make Kokkos pair SNAP chunksize variable user-settable
parents ba560bc9 49b07a23

doc/src/compute_sna_atom.rst

+0 −2
Original line number Diff line number Diff line
@@ -46,8 +46,6 @@ Syntax 
          *0* = do not generate quadratic terms

          *1* = generate quadratic terms







Examples

""""""""

doc/src/pair_snap.rst

+14 −2
Original line number Diff line number Diff line
@@ -139,7 +139,7 @@ The SNAP parameter file can contain blank and comment lines (start 
with #) anywhere. Each non-blank non-comment line must contain one

keyword/value pair. The required keywords are *rcutfac* and

*twojmax*\ . Optional keywords are *rfac0*\ , *rmin0*\ ,

*switchflag*\ , and *bzeroflag*\ .

*switchflag*\ , *bzeroflag*\, and *chunksize*\.



The default values for these keywords are
@@ -148,8 +148,20 @@ The default values for these keywords are 
* *switchflag* = 0

* *bzeroflag* = 1

* *quadraticflag* = 1

* *chunksize* = 2000



The keyword *chunksize* is only applicable when using the

pair style *snap* with the KOKKOS package and is ignored otherwise. 

This keyword controls

the number of atoms in each pass used to compute the bispectrum

components and is used to avoid running out of memory. For example

if there are 4000 atoms in the simulation and the *chunksize*

is set to 2000, the bispectrum calculation will be broken up

into two passes.



Detailed definitions for all the other keywords 

are given on the :doc:`compute sna/atom <compute_sna_atom>` doc page. 



Detailed definitions for all the keywords are given on the :doc:`compute sna/atom <compute_sna_atom>` doc page.

If *quadraticflag* is set to 1, then the SNAP energy expression includes the quadratic term,

0.5\*B\^t.alpha.B, where alpha is a symmetric *K* by *K* matrix.

The SNAP element file should contain *K*\ (\ *K*\ +1)/2 additional coefficients

src/KOKKOS/pair_snap_kokkos.h

+1 −1
Original line number Diff line number Diff line
@@ -122,7 +122,7 @@ protected: 
  t_dbvec dbvec;

  SNAKokkos<DeviceType> snaKK;



  int inum,max_neighs,chunk_offset;

  int inum,max_neighs,chunk_size,chunk_offset;



  int eflag,vflag;

src/KOKKOS/pair_snap_kokkos_impl.h

+16 −13
Original line number Diff line number Diff line
@@ -198,7 +198,7 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in) 
    d_ninside = Kokkos::View<int*, DeviceType>("PairSNAPKokkos:ninside",inum);

  }



  int chunk_size = MIN(2000,inum);

  chunk_size = MIN(chunksize,inum); // "chunksize" variable is set by user

  chunk_offset = 0;



  snaKK.grow_rij(chunk_size,max_neighs);
@@ -221,7 +221,7 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in) 
    Kokkos::parallel_for("PreUi",policy_preui,*this);



    //ComputeUi

    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi> policy_ui(((inum+team_size-1)/team_size)*max_neighs,team_size,vector_length);

    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi> policy_ui(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);

    Kokkos::parallel_for("ComputeUi",policy_ui,*this);



    //Ulisttot transpose
@@ -253,11 +253,11 @@ void PairSNAPKokkos<DeviceType>::compute(int eflag_in, int vflag_in) 
    Kokkos::parallel_for("ComputeYi",policy_yi,*this);



    //ComputeDuidrj

    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrj> policy_duidrj(((inum+team_size-1)/team_size)*max_neighs,team_size,vector_length);

    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrj> policy_duidrj(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);

    Kokkos::parallel_for("ComputeDuidrj",policy_duidrj,*this);



    //ComputeDeidrj

    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrj> policy_deidrj(((inum+team_size-1)/team_size)*max_neighs,team_size,vector_length);

    typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrj> policy_deidrj(((chunk_size+team_size-1)/team_size)*max_neighs,team_size,vector_length);

    Kokkos::parallel_for("ComputeDeidrj",policy_deidrj,*this);



    //ComputeForce
@@ -514,11 +514,12 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeUi,const typename 
  SNAKokkos<DeviceType> my_sna = snaKK;



  // Extract the atom number

  int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size()));

  if (ii >= inum) return;

  int ii = team.team_rank() + team.team_size() * (team.league_rank() %

           ((chunk_size+team.team_size()-1)/team.team_size()));

  if (ii >= chunk_size) return;



  // Extract the neighbor number

  const int jj = team.league_rank() / ((inum+team.team_size()-1)/team.team_size());

  const int jj = team.league_rank() / ((chunk_size+team.team_size()-1)/team.team_size());

  const int ninside = d_ninside(ii);

  if (jj >= ninside) return;
@@ -560,11 +561,12 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeDuidrj,const type 
  SNAKokkos<DeviceType> my_sna = snaKK;



  // Extract the atom number

  int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size()));

  if (ii >= inum) return;

  int ii = team.team_rank() + team.team_size() * (team.league_rank() %

           ((chunk_size+team.team_size()-1)/team.team_size()));

  if (ii >= chunk_size) return;



  // Extract the neighbor number

  const int jj = team.league_rank() / ((inum+team.team_size()-1)/team.team_size());

  const int jj = team.league_rank() / ((chunk_size+team.team_size()-1)/team.team_size());

  const int ninside = d_ninside(ii);

  if (jj >= ninside) return;
@@ -577,11 +579,12 @@ void PairSNAPKokkos<DeviceType>::operator() (TagPairSNAPComputeDeidrj,const type 
  SNAKokkos<DeviceType> my_sna = snaKK;



  // Extract the atom number

  int ii = team.team_rank() + team.team_size() * (team.league_rank() % ((inum+team.team_size()-1)/team.team_size()));

  if (ii >= inum) return;

  int ii = team.team_rank() + team.team_size() * (team.league_rank() %

           ((chunk_size+team.team_size()-1)/team.team_size()));

  if (ii >= chunk_size) return;



  // Extract the neighbor number

  const int jj = team.league_rank() / ((inum+team.team_size()-1)/team.team_size());

  const int jj = team.league_rank() / ((chunk_size+team.team_size()-1)/team.team_size());

  const int ninside = d_ninside(ii);

  if (jj >= ninside) return;

src/SNAP/pair_snap.cpp

+3 −0
Original line number Diff line number Diff line
@@ -635,6 +635,7 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) 
  switchflag = 1;

  bzeroflag = 1;

  quadraticflag = 0;

  chunksize = 2000;



  // open SNAP parameter file on proc 0
@@ -698,6 +699,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename) 
      bzeroflag = atoi(keyval);

    else if (strcmp(keywd,"quadraticflag") == 0)

      quadraticflag = atoi(keyval);

    else if (strcmp(keywd,"chunksize") == 0)

      chunksize = atoi(keyval);

    else

      error->all(FLERR,"Incorrect SNAP parameter file");

  }

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