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:1.2

Use-cases

There are a few problems with XML, DCD, and other dump files that the GSD schema hoomd solves.

  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

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.

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/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/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/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/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.