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:

Every frame of GSD output is viable to restart a simulation
Support varying numbers of particles, bonds, etc…
Support varying attributes (type, mass, etc…)
Support orientation, angular momentum, and other fields.
Binary format on disk
High performance file read and write
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/*.

Added 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.

Added 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.

Added in version 1.1.

pairs/group¶

Type:: uint32
Size:: Nx2
Default:: 0,0
Units:: number

Store the particle tags in each special pair interaction.

Added 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.

Added 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.

Added 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.

Added 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.

Added in version 1.2.

state/hpmc/integrate/a¶

Type:: double
Size:: 1x1
Units:: number

a is the size of the maximum rotation move.

Added in version 1.2.

state/hpmc/sphere/radius¶

Type:: float
Size:: NTx1
Units:: length

Sphere radius for each particle type.

Added in version 1.2.

state/hpmc/sphere/orientable¶

Type:

uint8

Size:

NTx1

Units:

boolean

Orientable flag for each particle type.

Added 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.

Added 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.

Added 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.

Added in version 1.2.

state/hpmc/convex_polyhedron/N¶

Type:: uint32
Size:: NTx1
Units:: number

Number of vertices defined for each type.

Added 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…

Added in version 1.2.

state/hpmc/convex_spheropolyhedron/N¶

Type:: uint32
Size:: NTx1
Units:: number

Number of vertices defined for each type.

Added 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…

Added in version 1.2.

state/hpmc/convex_spheropolyhedron/sweep_radius¶

Type:: float
Size:: NTx1
Units:: length

Sweep radius for each type.

Added in version 1.2.

state/hpmc/convex_polygon/N¶

Type:: uint32
Size:: NTx1
Units:: number

Number of vertices defined for each type.

Added 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…

Added in version 1.2.

state/hpmc/convex_spheropolygon/N¶

Type:: uint32
Size:: NTx1
Units:: number

Number of vertices defined for each type.

Added 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…

Added in version 1.2.

state/hpmc/convex_spheropolygon/sweep_radius¶

Type:: float
Size:: NTx1
Units:: length

Sweep radius for each type.

Added in version 1.2.

state/hpmc/simple_polygon/N¶

Type:: uint32
Size:: NTx1
Units:: number

Number of vertices defined for each type.

Added 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…

Added in version 1.2.