HOOMD Schema¶
HOOMDblue 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 
Usecases¶
There are a few problems with XML, DCD, and other dump files that the GSD schema hoomd
solves.
 Every frame of GSD output is viable for restart from
init.read_gsd
 No need for a separate topology file  everything is in one
.gsd
file.  Support varying numbers of particles, bonds, etc…
 Support varying attributes (type, mass, etc…)
 Support orientation, angular momentum, and other fields that DCD cannot.
 Simple interface for dump  limited number of options that produce valid files
 Binary format on disk
 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 HOOMDblue 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’]  UTF8 
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  UTF8  
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  UTF8  
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  UTF8  
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  UTF8  
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  utf8  
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: UTF8 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 UTF8 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 (32bit) Size: Nx1 Default: 1.0 Units: mass Store the mass of each particle.

particles/charge
¶ Type: float (32bit) Size: Nx1 Default: 0.0 Units: charge Store the charge of each particle.

particles/diameter
¶ Type: float (32bit) 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 (32bit) 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 (32bit) 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 N1 where N is the number of particles in the simulation.
All particles must be inside the box:
 \(x > l_x/2 + (xzxy \cdot yz) \cdot z + xy \cdot y\) and \(x < l_x/2 + (xzxy \cdot yz) \cdot z + xy \cdot y\)
 \(y > l_y/2 + yz \cdot z\) and \(y < l_y/2 + yz \cdot z\)
 \(z > l_z/2\) and \(z < l_z/2\)

particles/orientation
¶ Type: float (32bit) 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 (32bit) 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 (32bit) 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: UTF8 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 UTF8 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: UTF8 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 UTF8 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: UTF8 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 UTF8 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: UTF8 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 UTF8 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: UTF8 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 UTF8 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 welldefined 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 semiaxis for each particle type.
New in version 1.2.

state/hpmc/ellipsoid/b
¶ Type: float Size: NTx1 Units: length Size of the second ellipsoid semiaxis for each particle type.
New in version 1.2.

state/hpmc/ellipsoid/c
¶ Type: float Size: NTx1 Units: length Size of the third ellipsoid semiaxis 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.