md.data#

Overview

ForceLocalAccess

Access HOOMD-Blue force data buffers on the CPU.

ForceLocalAccessGPU

Access HOOMD-Blue force data buffers on the GPU.

NeighborListLocalAccess

Access HOOMD-Blue neighbor list data buffers on the CPU.

NeighborListLocalAccessGPU

Access HOOMD-Blue neighbor list data buffers on the GPU.

Details

Force data local access.

ForceLocalAccess, ForceLocalAccessGPU, and related classes provide direct access to the data buffers managed by hoomd.md.force.Force. This means that MPI rank locality must be considered in accessing the arrays in a multi-rank simulation.

See also

hoomd.md.force.Force

hoomd.md.force.Custom

class hoomd.md.data.ForceLocalAccess(force_obj, state)#

Access HOOMD-Blue force data buffers on the CPU.

force#

Local force data. \([\mathrm{force}]\)

Type:

(N_particles, 3) hoomd.data.array of float

potential_energy#

Local potential energy data. \([\mathrm{energy}]\)

Type:

(N_particles,) hoomd.data.array of float

torque#

Local torque data. \([\mathrm{force} \cdot \mathrm{length}]\)

Type:

(N_particles, 3) hoomd.data.array of float

virial#

Local virial data. \([\mathrm{energy}]\)

Type:

(N_particles, 6) hoomd.data.array of float

class hoomd.md.data.ForceLocalAccessGPU(*args, **kwargs)#

Access HOOMD-Blue force data buffers on the GPU.

force#

Local force data. \([\mathrm{force}]\)

Type:

(N_particles, 3) hoomd.data.array of float

potential_energy#

Local potential energy data. \([\mathrm{energy}]\)

Type:

(N_particles,) hoomd.data.array of float

torque#

Local torque data. \([\mathrm{force} \cdot \mathrm{length}]\)

Type:

(N_particles, 3) hoomd.data.array of float

virial#

Local virial data. \([\mathrm{energy}]\)

Type:

(N_particles, 6) hoomd.data.array of float

class hoomd.md.data.NeighborListLocalAccess(nlist_obj, state)#

Access HOOMD-Blue neighbor list data buffers on the CPU.

The internal NeighborList implementation of HOOMD is comprised of essentially three array buffers. The buffers are:

  • nlist: Ragged array of neighbor data.

  • head_list: Indexes for particles to read from the neighbor list.

  • n_neigh: Number of neighbors for each particle.

The neighbor indices of particle \(i\) are stored in the slice nlist[head_list[i]:head_list[i]+n_neigh[i]]. The result of access outside of these bounds is undefined. The half_nlist property is used to query whether the neighbor list stores a single copy for each pair (True), or two copies for each pair (False). Under MPI, pairs that cross domains are stored twice, once in each domain rank.

head_list#

Local head list.

Type:

(N_particles,) hoomd.data.array of unsigned long

n_neigh#

Number of neighbors.

Type:

(N_particles,) hoomd.data.array of unsigned int

nlist#

Raw neighbor list data.

Type:

(…) hoomd.data.array of unsigned int

half_nlist#

Convenience property to check if the storage mode is ‘half’.

Type:

bool

class hoomd.md.data.NeighborListLocalAccessGPU(*args, **kwargs)#

Access HOOMD-Blue neighbor list data buffers on the GPU.

The internal NeighborList implementation of HOOMD is comprised of essentially three array buffers. The buffers are:

  • nlist: Ragged array of neighbor data.

  • head_list: Indexes for particles to read from the neighbor list.

  • n_neigh: Number of neighbors for each particle.

The neighbor indices of particle \(i\) are stored in the slice nlist[head_list[i]:head_list[i]+n_neigh[i]]. The result of access outside of these bounds is undefined. The half_nlist property is used to query whether the neighbor list stores a single copy for each pair (True), or two copies for each pair (False). Under MPI, pairs that cross domains are stored twice, once in each domain rank.

head_list#

Local head list.

Type:

(N_particles,) hoomd.data.array of unsigned long

n_neigh#

Number of neighbors.

Type:

(N_particles,) hoomd.data.array of unsigned int

nlist#

Raw neighbor list data.

Type:

(…) hoomd.data.array of unsigned int

half_nlist#

Convenience property to check if the storage mode is ‘half’.

Type:

bool

Modules