HOOMD Schema¶

HOOMD-blue supports a wide variety of per particle attributes and properties. Particles, bonds, and types can be dynamically added and removed during simulation runs. The hoomd schema can handle all of these situations in a reasonably space efficient and high performance manner. It is also backwards compatible with previous versions of itself, as we only add new additional data chunks in new versions and do not change the interpretation of the existing data chunks. Any newer reader will initialize new data chunks with default values when they are not present in an older version file.

Schema name

hoomd

Schema version

1.4

Use-cases¶

The GSD schema hoomd provides:

1. Every frame of GSD output is viable for restart from init.read_gsd

2. No need for a separate topology file - everything is in one .gsd file.

3. Support varying numbers of particles, bonds, etc…

4. Support varying attributes (type, mass, etc…)

5. Support orientation, angular momentum, and other fields that DCD cannot.

6. Simple interface for dump - limited number of options that produce valid files

7. Binary format on disk

8. High performance file read and write

9. Support logging computed quantities

Data chunks¶

Each frame the hoomd schema may contain one or more data chunks. The layout and names of the chunks closely match that of the binary snapshot API in HOOMD-blue itself (at least at the time of inception). Data chunks are organized in categories. These categories have no meaning in the hoomd schema specification, and are simply an organizational tool. Some file writers may implement options that act on categories (i.e. write attributes out to every frame, or just frame 0).

Values are well defined for all fields at all frames. When a data chunk is present in frame i, it defines the values for the frame. When it is not present, the data chunk of the same name at frame 0 defines the values for frame i (when N is equal between the frames). If the data chunk is not present in frame 0, or N differs between frames, values are assumed default. Default values allow files sizes to remain small. For example, a simulation with point particles where orientation is always (1,0,0,0) would not write any orientation chunk to the file.

N may be zero. When N is zero, an index entry may be written for a data chunk with no actual data written to the file for that chunk.

Name

Category

Type

Size

Default

Units

Configuration

configuration/step

uint64

1x1

0

number

configuration/dimensions

uint8

1x1

3

number

configuration/box

float

6x1

varies

Particle data

particles/N

attribute

uint32

1x1

0

number

particles/types

attribute

int8

NTxM

[‘A’]

UTF-8

particles/typeid

attribute

uint32

Nx1

0

number

particles/type_shapes

attribute

int8

NTxM

UTF-8

particles/mass

attribute

float

Nx1

1.0

mass

particles/charge

attribute

float

Nx1

0.0

charge

particles/diameter

attribute

float

Nx1

1.0

length

particles/body

attribute

int32

Nx1

-1

number

particles/moment_inertia

attribute

float

Nx3

0,0,0

mass * length^2

particles/position

property

float

Nx3

0,0,0

length

particles/orientation

property

float

Nx4

1,0,0,0

unit quaternion

particles/velocity

momentum

float

Nx3

0,0,0

length/time

particles/angmom

momentum

float

Nx4

0,0,0,0

quaternion

particles/image

momentum

int32

Nx3

0,0,0

number

Bond data

bonds/N

topology

uint32

1x1

0

number

bonds/types

topology

int8

NTxM

UTF-8

bonds/typeid

topology

uint32

Nx1

0

number

bonds/group

topology

uint32

Nx2

0,0

number

Angle data

angles/N

topology

uint32

1x1

0

number

angles/types

topology

int8

NTxM

UTF-8

angles/typeid

topology

uint32

Nx1

0

number

angles/group

topology

uint32

Nx3

0,0,0

number

Dihedral data

dihedrals/N

topology

uint32

1x1

0

number

dihedrals/types

topology

int8

NTxM

UTF-8

dihedrals/typeid

topology

uint32

Nx1

0

number

dihedrals/group

topology

uint32

Nx4

0,0,0,0

number

Improper data

impropers/N

topology

uint32

1x1

0

number

impropers/types

topology

int8

NTxM

UTF-8

impropers/typeid

topology

uint32

Nx1

0

number

impropers/group

topology

uint32

Nx4

0,0,0,0

number

Constraint data

constraints/N

topology

uint32

1x1

0

number

constraints/value

topology

float

Nx1

0

length

constraints/group

topology

uint32

Nx2

0,0

number

Special pairs data

pairs/N

topology

uint32

1x1

0

number

pairs/types

topology

int8

NTxM

utf-8

pairs/typeid

topology

uint32

Nx1

0

number

pairs/group

topology

uint32

Nx2

0,0

number

Configuration¶

configuration/step
Type

uint64

Size

1x1

Default

0

Units

number

Simulation time step.

configuration/dimensions
Type

uint8

Size

1x1

Default

3

Units

number

Number of dimensions in the simulation. Must be 2 or 3.

configuration/box
Type

float

Size

6x1

Default

[1,1,1,0,0,0]

Units

varies

Simulation box. Each array element defines a different box property. See the hoomd documentation for a full description on how these box parameters map to a triclinic geometry.

• box[0:3]: $$(l_x, l_y, l_z)$$ the box length in each direction, in length units

• box[3:]: $$(xy, xz, yz)$$ the tilt factors, unitless values

Particle data¶

Within a single frame, the number of particles N and NT are fixed for all chunks. N and NT may vary from one frame to the next. All values are stored in hoomd native units.

Attributes¶

particles/N
Type

uint32

Size

1x1

Default

0

Units

number

Define N, the number of particles, for all data chunks particles/*.

particles/types
Type

int8

Size

NTxM

Default

[‘A’]

Units

UTF-8

Implicitly define NT, the number of particle types, for all data chunks particles/*. M must be large enough to accommodate each type name as a null terminated UTF-8 character string. Row i of the 2D matrix is the type name for particle type i.

particles/typeid
Type

uint32

Size

Nx1

Default

0

Units

number

Store the type id of each particle. All id’s must be less than NT. A particle with type id has a type name matching the corresponding row in particles/types.

particles/type_shapes
Type

int8

Size

NTxM

Default

empty

Units

UTF-8

Store a per-type shape definition for visualization. A dictionary is stored for each of the NT types, corresponding to a shape for visualization of that type. M must be large enough to accommodate the shape definition as a null-terminated UTF-8 JSON-encoded string. See: Shape Visualization for examples.

particles/mass
Type

float (32-bit)

Size

Nx1

Default

1.0

Units

mass

Store the mass of each particle.

particles/charge
Type

float (32-bit)

Size

Nx1

Default

0.0

Units

charge

Store the charge of each particle.

particles/diameter
Type

float (32-bit)

Size

Nx1

Default

1.0

Units

length

Store the diameter of each particle.

particles/body
Type

int32

Size

Nx1

Default

-1

Units

number

Store the composite body associated with each particle. The value -1 indicates no body. The body field may be left out of input files, as hoomd will create the needed constituent particles.

particles/moment_inertia
Type

float (32-bit)

Size

Nx3

Default

0,0,0

Units

mass * length^2

Store the moment_inertia of each particle $$(I_{xx}, I_{yy}, I_{zz})$$. This inertia tensor is diagonal in the body frame of the particle. The default value is for point particles.

Properties¶

particles/position
Type

float (32-bit)

Size

Nx3

Default

0,0,0

Units

length

Store the position of each particle (x, y, z).

All particles in the simulation are referenced by a tag. The position data chunk (and all other per particle data chunks) list particles in tag order. The first particle listed has tag 0, the second has tag 1, …, and the last has tag N-1 where N is the number of particles in the simulation.

All particles must be inside the box:

• $$x > -l_x/2 + (xz-xy \cdot yz) \cdot z + xy \cdot y$$ and $$x < l_x/2 + (xz-xy \cdot yz) \cdot z + xy \cdot y$$

• $$y > -l_y/2 + yz \cdot z$$ and $$y < l_y/2 + yz \cdot z$$

• $$z > -l_z/2$$ and $$z < l_z/2$$

particles/orientation
Type

float (32-bit)

Size

Nx4

Default

1,0,0,0

Units

unit quaternion

Store the orientation of each particle. In scalar + vector notation, this is $$(r, a_x, a_y, a_z)$$, where the quaternion is $$q = r + a_xi + a_yj + a_zk$$. A unit quaternion has the property: $$\sqrt{r^2 + a_x^2 + a_y^2 + a_z^2} = 1$$.

Momenta¶

particles/velocity
Type

float (32-bit)

Size

Nx3

Default

0,0,0

Units

length/time

Store the velocity of each particle $$(v_x, v_y, v_z)$$.

particles/angmom
Type

float (32-bit)

Size

Nx4

Default

0,0,0,0

Units

quaternion

Store the angular momentum of each particle as a quaternion. See the HOOMD documentation for information on how to convert to a vector representation.

particles/image
Type

int32

Size

Nx3

Default

0,0,0

Units

number

Store the number of times each particle has wrapped around the box $$(i_x, i_y, i_z)$$. In constant volume simulations, the unwrapped position in the particle’s full trajectory is

• $$x_u = x + i_x \cdot l_x + xy \cdot i_y \cdot l_y + xz \cdot i_z \cdot l_z$$

• $$y_u = y + i_y \cdot l_y + yz \cdot i_z * l_z$$

• $$z_u = z + i_z \cdot l_z$$

Topology¶

bonds/N
Type

uint32

Size

1x1

Default

0

Units

number

Define N, the number of bonds, for all data chunks bonds/*.

bonds/types
Type

int8

Size

NTxM

Default

empty

Units

UTF-8

Implicitly define NT, the number of bond types, for all data chunks bonds/*. M must be large enough to accommodate each type name as a null terminated UTF-8 character string. Row i of the 2D matrix is the type name for bond type i. By default, there are 0 bond types.

bonds/typeid
Type

uint32

Size

Nx1

Default

0

Units

number

Store the type id of each bond. All id’s must be less than NT. A bond with type id has a type name matching the corresponding row in bonds/types.

bonds/group
Type

uint32

Size

Nx2

Default

0,0

Units

number

Store the particle tags in each bond.

angles/N
Type

uint32

Size

1x1

Default

0

Units

number

Define N, the number of angles, for all data chunks angles/*.

angles/types
Type

int8

Size

NTxM

Default

empty

Units

UTF-8

Implicitly define NT, the number of angle types, for all data chunks angles/*. M must be large enough to accommodate each type name as a null terminated UTF-8 character string. Row i of the 2D matrix is the type name for angle type i. By default, there are 0 angle types.

angles/typeid
Type

uint32

Size

Nx1

Default

0

Units

number

Store the type id of each angle. All id’s must be less than NT. A angle with type id has a type name matching the corresponding row in angles/types.

angles/group
Type

uint32

Size

Nx2

Default

0,0

Units

number

Store the particle tags in each angle.

dihedrals/N
Type

uint32

Size

1x1

Default

0

Units

number

Define N, the number of dihedrals, for all data chunks dihedrals/*.

dihedrals/types
Type

int8

Size

NTxM

Default

empty

Units

UTF-8

Implicitly define NT, the number of dihedral types, for all data chunks dihedrals/*. M must be large enough to accommodate each type name as a null terminated UTF-8 character string. Row i of the 2D matrix is the type name for dihedral type i. By default, there are 0 dihedral types.

dihedrals/typeid
Type

uint32

Size

Nx1

Default

0

Units

number

Store the type id of each dihedral. All id’s must be less than NT. A dihedral with type id has a type name matching the corresponding row in dihedrals/types.

dihedrals/group
Type

uint32

Size

Nx2

Default

0,0

Units

number

Store the particle tags in each dihedral.

impropers/N
Type

uint32

Size

1x1

Default

0

Units

number

Define N, the number of impropers, for all data chunks impropers/*.

impropers/types
Type

int8

Size

NTxM

Default

empty

Units

UTF-8

Implicitly define NT, the number of improper types, for all data chunks impropers/*. M must be large enough to accommodate each type name as a null terminated UTF-8 character string. Row i of the 2D matrix is the type name for improper type i. By default, there are 0 improper types.

impropers/typeid
Type

uint32

Size

Nx1

Default

0

Units

number

Store the type id of each improper. All id’s must be less than NT. A improper with type id has a type name matching the corresponding row in impropers/types.

impropers/group
Type

uint32

Size

Nx2

Default

0,0

Units

number

Store the particle tags in each improper.

constraints/N
Type

uint32

Size

1x1

Default

0

Units

number

Define N, the number of constraints, for all data chunks constraints/*.

constraints/value
Type

float

Size

Nx1

Default

0

Units

length

Store the distance of each constraint. Each constraint defines a fixed distance between two particles.

constraints/group
Type

uint32

Size

Nx2

Default

0,0

Units

number

Store the particle tags in each constraint.

pairs/N
Type

uint32

Size

1x1

Default

0

Units

number

Define N, the number of special pair interactions, for all data chunks pairs/*.

New in version 1.1.

pairs/types
Type

int8

Size

NTxM

Default

empty

Units

UTF-8

Implicitly define NT, the number of special pair types, for all data chunks pairs/*. M must be large enough to accommodate each type name as a null terminated UTF-8 character string. Row i of the 2D matrix is the type name for particle type i. By default, there are 0 special pair types.

New in version 1.1.

pairs/typeid
Type

uint32

Size

Nx1

Default

0

Units

number

Store the type id of each special pair interaction. All id’s must be less than NT. A pair with type id has a type name matching the corresponding row in pairs/types.

New in version 1.1.

pairs/group
Type

uint32

Size

Nx2

Default

0,0

Units

number

Store the particle tags in each special pair interaction.

New in version 1.1.

State data¶

HOOMD stores auxiliary state information in state/* data chunks. Auxiliary state encompasses internal state to any integrator, updater, or other class that is not part of the particle system state but is also not a fixed parameter. For example, the internal degrees of freedom in integrator. Auxiliary state is useful when restarting simulations.

HOOMD only stores state in GSD files when requested explicitly by the user. Only a few of the documented state data chunks will be present in any GSD file and not all state chunks are valid. Thus, state data chunks do not have default values. If a chunk is not present in the file, that state does not have a well-defined value.

Name

Type

Size

Units

HPMC integrator state

state/hpmc/integrate/d

double

1x1

length

state/hpmc/integrate/a

double

1x1

number

state/hpmc/sphere/radius

float

NTx1

length

state/hpmc/sphere/orientable

uint8

NTx1

boolean

state/hpmc/ellipsoid/a

float

NTx1

length

state/hpmc/ellipsoid/b

float

NTx1

length

state/hpmc/ellipsoid/c

float

NTx1

length

state/hpmc/convex_polyhedron/N

uint32

NTx1

number

state/hpmc/convex_polyhedron/vertices

float

sum(N)x3

length

state/hpmc/convex_spheropolyhedron/N

uint32

NTx1

number

state/hpmc/convex_spheropolyhedron/vertices

float

sum(N)x3

length

state/hpmc/convex_spheropolyhedron/sweep_radius

float

NTx1

length

state/hpmc/convex_polygon/N

uint32

NTx1

number

state/hpmc/convex_polygon/vertices

float

sum(N)x2

length

state/hpmc/convex_spheropolygon/N

uint32

NTx1

number

state/hpmc/convex_spheropolygon/vertices

float

sum(N)x2

length

state/hpmc/convex_spheropolygon/sweep_radius

float

NTx1

length

state/hpmc/simple_polygon/N

uint32

NTx1

number

state/hpmc/simple_polygon/vertices

float

sum(N)x2

length

HPMC integrator state¶

NT is the number of particle types.

state/hpmc/integrate/d
Type

double

Size

1x1

Units

length

d is the maximum trial move displacement.

New in version 1.2.

state/hpmc/integrate/a
Type

double

Size

1x1

Units

number

a is the size of the maximum rotation move.

New in version 1.2.

state/hpmc/sphere/radius
Type

float

Size

NTx1

Units

length

Sphere radius for each particle type.

New in version 1.2.

state/hpmc/sphere/orientable
Type

uint8

Size

NTx1

Units

boolean

Orientable flag for each particle type.

New in version 1.3.

state/hpmc/ellipsoid/a
Type

float

Size

NTx1

Units

length

Size of the first ellipsoid semi-axis for each particle type.

New in version 1.2.

state/hpmc/ellipsoid/b
Type

float

Size

NTx1

Units

length

Size of the second ellipsoid semi-axis for each particle type.

New in version 1.2.

state/hpmc/ellipsoid/c
Type

float

Size

NTx1

Units

length

Size of the third ellipsoid semi-axis for each particle type.

New in version 1.2.

state/hpmc/convex_polyhedron/N
Type

uint32

Size

NTx1

Units

number

Number of vertices defined for each type.

New in version 1.2.

state/hpmc/convex_polyhedron/vertices
Type

float

Size

sum(N)x3

Units

length

Position of the vertices in the shape for all types. The shape for type 0 is the first N[0] vertices, the shape for type 1 is the next N[1] vertices, and so on…

New in version 1.2.

state/hpmc/convex_spheropolyhedron/N
Type

uint32

Size

NTx1

Units

number

Number of vertices defined for each type.

New in version 1.2.

state/hpmc/convex_spheropolyhedron/vertices
Type

float

Size

sum(N)x3

Units

length

Position of the vertices in the shape for all types. The shape for type 0 is the first N[0] vertices, the shape for type 1 is the next N[1] vertices, and so on…

New in version 1.2.

state/hpmc/convex_spheropolyhedron/sweep_radius
Type

float

Size

NTx1

Units

length

New in version 1.2.

state/hpmc/convex_polygon/N
Type

uint32

Size

NTx1

Units

number

Number of vertices defined for each type.

New in version 1.2.

state/hpmc/convex_polygon/vertices
Type

float

Size

sum(N)x2

Units

length

Position of the vertices in the shape for all types. The shape for type 0 is the first N[0] vertices, the shape for type 1 is the next N[1] vertices, and so on…

New in version 1.2.

state/hpmc/convex_spheropolygon/N
Type

uint32

Size

NTx1

Units

number

Number of vertices defined for each type.

New in version 1.2.

state/hpmc/convex_spheropolygon/vertices
Type

float

Size

sum(N)x2

Units

length

Position of the vertices in the shape for all types. The shape for type 0 is the first N[0] vertices, the shape for type 1 is the next N[1] vertices, and so on…

New in version 1.2.

state/hpmc/convex_spheropolygon/sweep_radius
Type

float

Size

NTx1

Units

length

New in version 1.2.

state/hpmc/simple_polygon/N
Type

uint32

Size

NTx1

Units

number

Number of vertices defined for each type.

New in version 1.2.

state/hpmc/simple_polygon/vertices
Type

float

Size

sum(N)x2

Units

length

Position of the vertices in the shape for all types. The shape for type 0 is the first N[0] vertices, the shape for type 1 is the next N[1] vertices, and so on…

New in version 1.2.

Logged data¶

Users may store logged data in log/* data chunks. Logged data encompasses values computed at simulation time that are too expensive or cumbersome to re-compute in post processing. This specification does not define specific chunk names or define logged data. Users may select any valid name for logged data chunks as appropriate for their workflow.

For any named logged data chunks present in any frame frame the file: If a chunk is not present in a given frame i != 0, the implementation should provide the quantity as read from frame 0 for that frame. GSD files that include a logged data chunk only in some frames i != 0 and not in frame 0 are invalid.

By convention, per-particle and per-bond logged data should have a chunk name starting with log/particles/ and log/bonds, respectively. Scalar, vector, and string values may be stored under a different prefix starting with log/. This specification may recognize additional conventions in later versions without invalidating existing files.

Name

Type

Size

Units

log/particles/user_defined

n/a

NxM

user-defined

log/bonds/user_defined

n/a

NxM

user-defined

log/user_defined

n/a

NxM

user-defined

log/particles/user_defined
Type

user-defined

Size

NxM

Units

user-defined

This chunk is a place holder for any number of user defined per-particle quantities. N is the number of particles in this frame. M, the data type, the units, and the chunk name (after the prefix log/particles/) are user-defined.

New in version 1.4.

log/bonds/user_defined
Type

user-defined

Size

NxM

Units

user-defined

This chunk is a place holder for any number of user defined per-bond quantities. N is the number of bonds in this frame. M, the data type, the units, and the chunk name (after the prefix log/bonds/) are user-defined.

New in version 1.4.

log/user_defined
Type

user-defined

Size

NxM

Units

user-defined

This chunk is a place holder for any number of user defined quantities. N, M, the data type, the units, and the chunk name (after the prefix log/) are user-defined.

New in version 1.4.