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# 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

See also

`hoomd.State` for a full description of how HOOMD interprets this data.

## Use-cases

The GSD schema `hoomd` provides:

1. Every frame of GSD output is viable to restart a simulation

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

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

4. Support orientation, angular momentum, and other fields.

5. Binary format on disk

6. High performance file read and write

7. Support logging computed quantities

## Data chunks

Each frame the `hoomd` schema may contain one or more data chunks. The layout and names of the chunksmatch that of the binary frame API in HOOMD-blue itself. 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 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.

  Note

  When using `gsd.hoomd.Frame`, the object will try to intelligently default to a dimension. When setting a box with \(L_z = 0\), `dimensions` will default to 2 otherwise 3. Explicit setting of this value by users always takes precedence.

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, dimensionless 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:

  - \(-l_x/2 + (xz-xy \cdot yz) \cdot z + xy \cdot y \le x < l_x/2 + (xz-xy \cdot yz) \cdot z + xy \cdot y\)

  - \(-l_y/2 + yz \cdot z \le y < l_y/2 + yz \cdot z\)

  - \(-l_z/2 \le z < l_z/2\)

  Where \(l_x\), \(l_y\), \(l_z\), \(xy\), \(xz\), and \(yz\) are the simulation box parameters (`configuration/box`).

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

  - \(x_u = x + i_x \cdot l_x + xy \cdot i_y \cdot l_y + xz \cdot i_z \cdot l_z\)

  - \(y_u = y + i_y \cdot l_y + yz \cdot i_z \cdot l_z\)

  - \(z_u = z + i_z \cdot l_z\)

## 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:

    Nx3

  Default:

    0,0,0

  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:

    Nx4

  Default:

    0,0,0,0

  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:

    Nx4

  Default:

    0,0,0,0

  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.

## 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.

## 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.

Note

HOOMD-blue >= v3.0.0 do not write state data.

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

  Sweep radius for each type.

  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

  Sweep radius for each type.

  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.