Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/KOKKOS/neigh_bond_kokkos.h
688b1f1efc46efficient_neuronet

Last Change
Raw File

neigh_bond_kokkos.h
View Options

/* -*- 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.
------------------------------------------------------------------------- */
#ifndef LMP_NEIGH_BOND_KOKKOS_H
#define LMP_NEIGH_BOND_KOKKOS_H
#include "neighbor.h"
#include "kokkos_type.h"
#include "domain_kokkos.h"
#include "pointers.h"
namespace LAMMPS_NS {
struct TagNeighBondBondAll{};
struct TagNeighBondBondPartial{};
struct TagNeighBondBondCheck{};
struct TagNeighBondAngleAll{};
struct TagNeighBondAnglePartial{};
struct TagNeighBondAngleCheck{};
struct TagNeighBondDihedralAll{};
struct TagNeighBondDihedralPartial{};
struct TagNeighBondDihedralCheck{};
struct TagNeighBondImproperAll{};
struct TagNeighBondImproperPartial{};
template<class DeviceType>
class NeighBondKokkos : protected Pointers {
public:
typedef ArrayTypes<DeviceType> AT;
typedef int value_type;
NeighBondKokkos(class LAMMPS *);
~NeighBondKokkos() {}
void init_topology_kk();
void build_topology_kk();
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondBondAll, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondBondPartial, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondBondCheck, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondAngleAll, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondAnglePartial, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondAngleCheck, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondDihedralAll, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondDihedralPartial, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondDihedralCheck, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondImproperAll, const int&, int&) const;
KOKKOS_INLINE_FUNCTION
void operator()(TagNeighBondImproperPartial, const int&, int&) const;
DAT::tdual_int_2d k_bondlist;
DAT::tdual_int_2d k_anglelist;
DAT::tdual_int_2d k_dihedrallist;
DAT::tdual_int_2d k_improperlist;
// KOKKOS host/device flag and data masks
ExecutionSpace execution_space;
unsigned int datamask_read,datamask_modify;
int maxbond,maxangle,maxdihedral,maximproper; // size of bond lists
int me,nprocs;
private:
DAT::tdual_int_1d k_map_array;
typename AT::t_int_1d_randomread map_array;
DAT::tdual_int_1d k_sametag;
typename AT::t_int_1d_randomread sametag;
typename AT::t_int_2d v_bondlist;
typename AT::t_int_2d v_anglelist;
typename AT::t_int_2d v_dihedrallist;
typename AT::t_int_2d v_improperlist;
typename AT::t_int_2d list;
typename AT::t_x_array_randomread x;
typename AT::t_tagint_1d_randomread tag;
typename AT::t_int_1d num_bond;
typename AT::t_int_2d bond_type;
typename AT::t_tagint_2d bond_atom;
typename AT::t_int_1d num_angle;
typename AT::t_int_2d angle_type;
typename AT::t_tagint_2d angle_atom1,angle_atom2,angle_atom3;
typename AT::t_int_1d num_dihedral;
typename AT::t_int_2d dihedral_type;
typename AT::t_tagint_2d dihedral_atom1,dihedral_atom2,
dihedral_atom3,dihedral_atom4;
typename AT::t_int_1d num_improper;
typename AT::t_int_2d improper_type;
typename AT::t_tagint_2d improper_atom1,improper_atom2,
improper_atom3,improper_atom4;
DAT::tdual_int_scalar k_nlist;
typename AT::t_int_scalar d_nlist;
HAT::t_int_scalar h_nlist;
DAT::tdual_int_scalar k_fail_flag;
typename AT::t_int_scalar d_fail_flag;
HAT::t_int_scalar h_fail_flag;
KOKKOS_INLINE_FUNCTION
int closest_image(const int, int) const;
KOKKOS_INLINE_FUNCTION
void minimum_image(X_FLOAT &dx, X_FLOAT &dy, X_FLOAT &dz) const;
void update_domain_variables();
// topology build functions
typedef void (NeighBondKokkos::*BondPtr)(); // ptrs to topology build functions
BondPtr bond_build_kk; // ptr to bond list functions
void bond_all(); // bond list with all bonds
void bond_template(); // bond list with templated bonds
void bond_partial(); // exclude certain bonds
void bond_check();
BondPtr angle_build_kk; // ptr to angle list functions
void angle_all(); // angle list with all angles
void angle_template(); // angle list with templated bonds
void angle_partial(); // exclude certain angles
void angle_check();
BondPtr dihedral_build_kk; // ptr to dihedral list functions
void dihedral_all(); // dihedral list with all dihedrals
void dihedral_template(); // dihedral list with templated bonds
void dihedral_partial(); // exclude certain dihedrals
void dihedral_check(int, typename AT::t_int_2d list);
BondPtr improper_build_kk; // ptr to improper list functions
void improper_all(); // improper list with all impropers
void improper_template(); // improper list with templated bonds
void improper_partial(); // exclude certain impropers
int nlocal,newton_bond,lostbond,nmissing;
int triclinic;
int xperiodic,yperiodic,zperiodic;
X_FLOAT xprd_half,yprd_half,zprd_half;
X_FLOAT xprd,yprd,zprd;
X_FLOAT xy,xz,yz;
};
}
#endif
/* ERROR/WARNING messages:
E: Must use atom map style array with Kokkos
See the atom_modify map command.
E: Bond atoms missing on proc %d at step %ld
The 2nd atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
W: Bond atoms missing at step %ld
The 2nd atom needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
E: Cannot (yet) use molecular templates with Kokkos
Self-explanatory.
E: Bond extent > half of periodic box length
This error was detected by the neigh_modify check yes setting. It is
an error because the bond atoms are so far apart it is ambiguous how
it should be defined.
E: Angle atoms missing on proc %d at step %ld
One or more of 3 atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
W: Angle atoms missing at step %ld
One or more of 3 atoms needed to compute a particular angle are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the angle has blown apart and an atom is
too far away.
E: Angle extent > half of periodic box length
This error was detected by the neigh_modify check yes setting. It is
an error because the angle atoms are so far apart it is ambiguous how
it should be defined.
E: Dihedral atoms missing on proc %d at step %ld
One or more of 4 atoms needed to compute a particular dihedral are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the dihedral has blown apart and an atom is
too far away.
W: Dihedral atoms missing at step %ld
One or more of 4 atoms needed to compute a particular dihedral are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the dihedral has blown apart and an atom is
too far away.
E: Dihedral/improper extent > half of periodic box length
This error was detected by the neigh_modify check yes setting. It is
an error because the dihedral atoms are so far apart it is ambiguous
how it should be defined.
E: Improper atoms missing on proc %d at step %ld
One or more of 4 atoms needed to compute a particular improper are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the improper has blown apart and an atom is
too far away.
W: Improper atoms missing at step %ld
One or more of 4 atoms needed to compute a particular improper are
missing on this processor. Typically this is because the pairwise
cutoff is set too short or the improper has blown apart and an atom is
too far away.
*/
c4science · Help