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 |
.. seealso::
`hoomd.State` for a full description of how HOOMD interprets this
data.
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
Each frame the hoomd schema may contain one or more data chunks. The layout
and names of the chunksmatch that of the binary snapshot 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 | |||||
| :chunk:`configuration/step` | uint64 | 1x1 | 0 | number | |
| :chunk:`configuration/dimensions` | uint8 | 1x1 | 3 | number | |
| :chunk:`configuration/box` | float | 6x1 | varies | ||
| Particle data | |||||
| :chunk:`particles/N` | attribute | uint32 | 1x1 | 0 | number |
| :chunk:`particles/types` | attribute | int8 | NTxM | ['A'] | UTF-8 |
| :chunk:`particles/typeid` | attribute | uint32 | Nx1 | 0 | number |
| :chunk:`particles/type_shapes` | attribute | int8 | NTxM | UTF-8 | |
| :chunk:`particles/mass` | attribute | float | Nx1 | 1.0 | mass |
| :chunk:`particles/charge` | attribute | float | Nx1 | 0.0 | charge |
| :chunk:`particles/diameter` | attribute | float | Nx1 | 1.0 | length |
| :chunk:`particles/body` | attribute | int32 | Nx1 | -1 | number |
| :chunk:`particles/moment_inertia` | attribute | float | Nx3 | 0,0,0 | mass * length^2 |
| :chunk:`particles/position` | property | float | Nx3 | 0,0,0 | length |
| :chunk:`particles/orientation` | property | float | Nx4 | 1,0,0,0 | unit quaternion |
| :chunk:`particles/velocity` | momentum | float | Nx3 | 0,0,0 | length/time |
| :chunk:`particles/angmom` | momentum | float | Nx4 | 0,0,0,0 | quaternion |
| :chunk:`particles/image` | momentum | int32 | Nx3 | 0,0,0 | number |
| Bond data | |||||
| :chunk:`bonds/N` | topology | uint32 | 1x1 | 0 | number |
| :chunk:`bonds/types` | topology | int8 | NTxM | UTF-8 | |
| :chunk:`bonds/typeid` | topology | uint32 | Nx1 | 0 | number |
| :chunk:`bonds/group` | topology | uint32 | Nx2 | 0,0 | number |
| Angle data | |||||
| :chunk:`angles/N` | topology | uint32 | 1x1 | 0 | number |
| :chunk:`angles/types` | topology | int8 | NTxM | UTF-8 | |
| :chunk:`angles/typeid` | topology | uint32 | Nx1 | 0 | number |
| :chunk:`angles/group` | topology | uint32 | Nx3 | 0,0,0 | number |
| Dihedral data | |||||
| :chunk:`dihedrals/N` | topology | uint32 | 1x1 | 0 | number |
| :chunk:`dihedrals/types` | topology | int8 | NTxM | UTF-8 | |
| :chunk:`dihedrals/typeid` | topology | uint32 | Nx1 | 0 | number |
| :chunk:`dihedrals/group` | topology | uint32 | Nx4 | 0,0,0,0 | number |
| Improper data | |||||
| :chunk:`impropers/N` | topology | uint32 | 1x1 | 0 | number |
| :chunk:`impropers/types` | topology | int8 | NTxM | UTF-8 | |
| :chunk:`impropers/typeid` | topology | uint32 | Nx1 | 0 | number |
| :chunk:`impropers/group` | topology | uint32 | Nx4 | 0,0,0,0 | number |
| Constraint data | |||||
| :chunk:`constraints/N` | topology | uint32 | 1x1 | 0 | number |
| :chunk:`constraints/value` | topology | float | Nx1 | 0 | length |
| :chunk:`constraints/group` | topology | uint32 | Nx2 | 0,0 | number |
| Special pairs data | |||||
| :chunk:`pairs/N` | topology | uint32 | 1x1 | 0 | number |
| :chunk:`pairs/types` | topology | int8 | NTxM | utf-8 | |
| :chunk:`pairs/typeid` | topology | uint32 | Nx1 | 0 | number |
| :chunk:`pairs/group` | topology | uint32 | Nx2 | 0,0 | number |
.. chunk:: configuration/step
:Type: uint64
:Size: 1x1
:Default: 0
:Units: number
Simulation time step.
.. chunk:: 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.Snapshot`, the object will try to intelligently default to a
dimension. When setting a box with :math:`L_z = 0`, ``dimensions`` will default to
2 otherwise 3. Explicit setting of this value by users always takes precedence.
.. chunk:: 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]``: :math:`(l_x, l_y, l_z)` the box length in each direction, in length units
* ``box[3:]``: :math:`(xy, xz, yz)` the tilt factors, dimensionless values
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.
.. chunk:: particles/N
:Type: uint32
:Size: 1x1
:Default: 0
:Units: number
Define *N*, the number of particles, for all data chunks ``particles/*``.
.. chunk:: 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*.
.. chunk:: 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
:chunk:`particles/types`.
.. chunk:: 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: :ref:`shapes` for
examples.
.. chunk:: particles/mass
:Type: float (32-bit)
:Size: Nx1
:Default: 1.0
:Units: mass
Store the mass of each particle.
.. chunk:: particles/charge
:Type: float (32-bit)
:Size: Nx1
:Default: 0.0
:Units: charge
Store the charge of each particle.
.. chunk:: particles/diameter
:Type: float (32-bit)
:Size: Nx1
:Default: 1.0
:Units: length
Store the diameter of each particle.
.. chunk:: 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.
.. chunk:: particles/moment_inertia
:Type: float (32-bit)
:Size: Nx3
:Default: 0,0,0
:Units: mass * length^2
Store the moment_inertia of each particle :math:`(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.
.. chunk:: 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:
* :math:`-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`
* :math:`-l_y/2 + yz \cdot z \le y < l_y/2 + yz \cdot z`
* :math:`-l_z/2 \le z < l_z/2`
Where :math:`l_x`, :math:`l_y`, :math:`l_z`, :math:`xy`, :math:`xz`, and :math:`yz` are the
simulation box parameters (:chunk:`configuration/box`).
.. chunk:: 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
:math:`(r, a_x, a_y, a_z)`,
where the quaternion is :math:`q = r + a_xi + a_yj + a_zk`. A unit
quaternion has the property: :math:`\sqrt{r^2 + a_x^2 + a_y^2 + a_z^2} = 1`.
.. chunk:: particles/velocity
:Type: float (32-bit)
:Size: Nx3
:Default: 0,0,0
:Units: length/time
Store the velocity of each particle :math:`(v_x, v_y, v_z)`.
.. chunk:: 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.
.. chunk:: particles/image
:Type: int32
:Size: Nx3
:Default: 0,0,0
:Units: number
Store the number of times each particle has wrapped around the box
:math:`(i_x, i_y, i_z)`. In constant volume simulations, the unwrapped
position in the particle's full trajectory is
* :math:`x_u = x + i_x \cdot l_x + xy \cdot i_y \cdot l_y + xz \cdot i_z \cdot l_z`
* :math:`y_u = y + i_y \cdot l_y + yz \cdot i_z \cdot l_z`
* :math:`z_u = z + i_z \cdot l_z`
.. chunk:: bonds/N
:Type: uint32
:Size: 1x1
:Default: 0
:Units: number
Define *N*, the number of bonds, for all data chunks ``bonds/*``.
.. chunk:: 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.
.. chunk:: 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
:chunk:`bonds/types`.
.. chunk:: bonds/group
:Type: uint32
:Size: Nx2
:Default: 0,0
:Units: number
Store the particle tags in each bond.
.. chunk:: angles/N
:Type: uint32
:Size: 1x1
:Default: 0
:Units: number
Define *N*, the number of angles, for all data chunks ``angles/*``.
.. chunk:: 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.
.. chunk:: 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
:chunk:`angles/types`.
.. chunk:: angles/group
:Type: uint32
:Size: Nx3
:Default: 0,0,0
:Units: number
Store the particle tags in each angle.
.. chunk:: dihedrals/N
:Type: uint32
:Size: 1x1
:Default: 0
:Units: number
Define *N*, the number of dihedrals, for all data chunks ``dihedrals/*``.
.. chunk:: 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.
.. chunk:: 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
:chunk:`dihedrals/types`.
.. chunk:: dihedrals/group
:Type: uint32
:Size: Nx4
:Default: 0,0,0,0
:Units: number
Store the particle tags in each dihedral.
.. chunk:: impropers/N
:Type: uint32
:Size: 1x1
:Default: 0
:Units: number
Define *N*, the number of impropers, for all data chunks ``impropers/*``.
.. chunk:: 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.
.. chunk:: 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
:chunk:`impropers/types`.
.. chunk:: impropers/group
:Type: uint32
:Size: Nx4
:Default: 0,0,0,0
:Units: number
Store the particle tags in each improper.
.. chunk:: constraints/N
:Type: uint32
:Size: 1x1
:Default: 0
:Units: number
Define *N*, the number of constraints, for all data chunks
``constraints/*``.
.. chunk:: 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.
.. chunk:: constraints/group
:Type: uint32
:Size: Nx2
:Default: 0,0
:Units: number
Store the particle tags in each constraint.
.. chunk:: pairs/N
:Type: uint32
:Size: 1x1
:Default: 0
:Units: number
Define *N*, the number of special pair interactions, for all data chunks
``pairs/*``.
.. versionadded:: 1.1
.. chunk:: 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.
.. versionadded:: 1.1
.. chunk:: 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 :chunk:`pairs/types`.
.. versionadded:: 1.1
.. chunk:: pairs/group
:Type: uint32
:Size: Nx2
:Default: 0,0
:Units: number
Store the particle tags in each special pair interaction.
.. versionadded:: 1.1
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 |
|---|---|---|---|
| :chunk:`log/particles/user_defined` | n/a | NxM | user-defined |
| :chunk:`log/bonds/user_defined` | n/a | NxM | user-defined |
| :chunk:`log/user_defined` | n/a | NxM | user-defined |
.. chunk:: 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.
.. versionadded:: 1.4
.. chunk:: 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.
.. versionadded:: 1.4
.. chunk:: 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.
.. versionadded:: 1.4
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.
NT is the number of particle types.
.. chunk:: state/hpmc/integrate/d
:Type: double
:Size: 1x1
:Units: length
*d* is the maximum trial move displacement.
.. versionadded:: 1.2
.. chunk:: state/hpmc/integrate/a
:Type: double
:Size: 1x1
:Units: number
*a* is the size of the maximum rotation move.
.. versionadded:: 1.2
.. chunk:: state/hpmc/sphere/radius
:Type: float
:Size: NTx1
:Units: length
Sphere radius for each particle type.
.. versionadded:: 1.2
.. chunk:: state/hpmc/sphere/orientable
:Type: uint8
:Size: NTx1
:Units: boolean
Orientable flag for each particle type.
.. versionadded:: 1.3
.. chunk:: state/hpmc/ellipsoid/a
:Type: float
:Size: NTx1
:Units: length
Size of the first ellipsoid semi-axis for each particle type.
.. versionadded:: 1.2
.. chunk:: state/hpmc/ellipsoid/b
:Type: float
:Size: NTx1
:Units: length
Size of the second ellipsoid semi-axis for each particle type.
.. versionadded:: 1.2
.. chunk:: state/hpmc/ellipsoid/c
:Type: float
:Size: NTx1
:Units: length
Size of the third ellipsoid semi-axis for each particle type.
.. versionadded:: 1.2
.. chunk:: state/hpmc/convex_polyhedron/N
:Type: uint32
:Size: NTx1
:Units: number
Number of vertices defined for each type.
.. versionadded:: 1.2
.. chunk:: 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...
.. versionadded:: 1.2
.. chunk:: state/hpmc/convex_spheropolyhedron/N
:Type: uint32
:Size: NTx1
:Units: number
Number of vertices defined for each type.
.. versionadded:: 1.2
.. chunk:: 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...
.. versionadded:: 1.2
.. chunk:: state/hpmc/convex_spheropolyhedron/sweep_radius
:Type: float
:Size: NTx1
:Units: length
Sweep radius for each type.
.. versionadded:: 1.2
.. chunk:: state/hpmc/convex_polygon/N
:Type: uint32
:Size: NTx1
:Units: number
Number of vertices defined for each type.
.. versionadded:: 1.2
.. chunk:: 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...
.. versionadded:: 1.2
.. chunk:: state/hpmc/convex_spheropolygon/N
:Type: uint32
:Size: NTx1
:Units: number
Number of vertices defined for each type.
.. versionadded:: 1.2
.. chunk:: 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...
.. versionadded:: 1.2
.. chunk:: state/hpmc/convex_spheropolygon/sweep_radius
:Type: float
:Size: NTx1
:Units: length
Sweep radius for each type.
.. versionadded:: 1.2
.. chunk:: state/hpmc/simple_polygon/N
:Type: uint32
:Size: NTx1
:Units: number
Number of vertices defined for each type.
.. versionadded:: 1.2
.. chunk:: 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...
.. versionadded:: 1.2