hoomd¶
Overview
Define box dimensions. 

A mutable collection of operations which act on a 

Define a simulation. 

Selfcontained copy of the simulation 

The state of a 
Details
HOOMDblue python package.
hoomd
is the top level HOOMDblue Python package. It consists of the common
code shared among all types of HOOMDblue simulations. The core data structures
used to construct a simulation include:
See the table of contents or the modules section for a full list of classes, methods, and variables in the API.
hoomd
also contains subpackages that implement specific types of simulations:
hoomd.hpmc
 Hard particle Monte Carlo.hoomd.md
 Molecular dynamics.
See also
Tutorial: Introducing HOOMDblue
Signal handling
On import, hoomd
installs a SIGTERM
signal handler that calls sys.exit
so that open gsd files have a chance to flush write buffers
(hoomd.write.GSD.flush
) when a user’s process is terminated. Use
signal.signal
to adjust this behavior as needed.
 class hoomd.Box(Lx, Ly, Lz=0, xy=0, xz=0, yz=0)¶
Define box dimensions.
 Parameters:
Lx (float) – box extent in the x direction \([\mathrm{length}]\).
Ly (float) – box extent in the y direction \([\mathrm{length}]\).
Lz (float) – box extent in the z direction \([\mathrm{length}]\).
xy (float) – tilt factor xy \([\mathrm{dimensionless}]\).
xz (float) – tilt factor xz \([\mathrm{dimensionless}]\).
yz (float) – tilt factor yz \([\mathrm{dimensionless}]\).
Particles in a simulation exist in a triclinic box with periodic boundary conditions. A triclinic box is defined by six values: the extents \(L_x\), \(L_y\) and \(L_z\) of the box in the three directions, and three tilt factors \(xy\), \(xz\) and \(yz\).
The parameter matrix is defined in terms of the lattice vectors \(\vec a_1\), \(\vec a_2\) and \(\vec a_3\):
\[\left( \vec a_1, \vec a_2, \vec a_3 \right)\]The first lattice vector \(\vec a_1\) is parallel to the unit vector \(\vec e_x = (1,0,0)\). The tilt factor \(xy\) indicates how the second lattice vector \(\vec a_2\) is tilted with respect to the first one. Similarly, \(xz\) and \(yz\) indicate the tilt of the third lattice vector \(\vec a_3\) with respect to the first and second lattice vector.
The full cell parameter matrix is:
\[\begin{split}\left(\begin{array}{ccc} L_x & xy L_y & xz L_z \\ 0 & L_y & yz L_z \\ 0 & 0 & L_z \\ \end{array}\right)\end{split}\]The tilt factors \(xy\), \(xz\) and \(yz\) are dimensionless. The relationships between the tilt factors and the box angles \(\alpha\), \(\beta\) and \(\gamma\) are as follows:
\[\begin{split}\cos\gamma &= \cos(\angle\vec a_1, \vec a_2) &=& \frac{xy}{\sqrt{1+xy^2}}\\ \cos\beta &= \cos(\angle\vec a_1, \vec a_3) &=& \frac{xz}{\sqrt{1+xz^2+yz^2}}\\ \cos\alpha &= \cos(\angle\vec a_2, \vec a_3) &=& \frac{xy \cdot xz + yz}{\sqrt{1+xy^2} \sqrt{1+xz^2+yz^2}}\end{split}\]Given an arbitrarily oriented lattice with box vectors \(\vec v_1, \vec v_2, \vec v_3\), the parameters for the rotated box can be found as follows:
\[\begin{split}L_x &= v_1\\ a_{2x} &= \frac{\vec v_1 \cdot \vec v_2}{v_1}\\ L_y &= \sqrt{v_2^2  a_{2x}^2}\\ xy &= \frac{a_{2x}}{L_y}\\ L_z &= \vec v_3 \cdot \frac{\vec v_1 \times \vec v_2}{\left \vec v_1 \times \vec v_2 \right}\\ a_{3x} &= \frac{\vec v_1 \cdot \vec v_3}{v_1}\\ xz &= \frac{a_{3x}}{L_z}\\ yz &= \frac{\vec v_2 \cdot \vec v_3  a_{2x}a_{3x}}{L_y L_z}\end{split}\]Box images
HOOMDblue always stores particle positions \(\vec{r}\) inside the primary box image which includes the origin at the center. The primary box image include the left, bottom, and back face while excluding the right, top, and front face. In cubic boxes, this implies that the particle coordinates in the primary box image are in the interval \(\left[ \frac{L}{2},\frac{L}{2} \right)\).
Unless otherwise noted in the documentation, operations apply the minimum image convention when computing pairwise interactions between particles:
\[\vec{r}_{ij} = \mathrm{minimum\_image}(\vec{r}_j  \vec{r}_i)\]When running simulations with a fixed box size, use the particle images \(\vec{n}\) to compute the unwrapped coordinates:
\[\vec{r}_\mathrm{unwrapped} = \vec{r} + n_x \vec{a}_1 + n_y \vec{a}_2 + n_z \vec{a}_3\]Two dimensional systems
Set
Lz == 0
to make the box 2D. 2D boxes ignorexz
andyz
. Changing the box dimensionality from 2D to 3D (or from 3D to 2D) during a simulation will result in undefined behavior.In 2D boxes, volume is in units of \([\mathrm{length}]^2\).
Factory Methods
Box
has factory methods to enable easier creation of boxes:cube
,square
,from_matrix
,from_basis_vectors
, andfrom_box
. See each method’s documentation for more details.Example:
box = hoomd.Box(Lx=10, Ly=20, Lz=30, xy=0.5, xz=0.2, yz=0.1)
 property L¶
The box lengths,
[Lx, Ly, Lz]
\([\mathrm{length}]\).Can be set with a float which sets all lengths, or a length 3 vector.
Example:
box.L = (15, 30, 60)
 Type:
(3, )
numpy.ndarray
offloat
 property Lx¶
The length of the box in the x dimension \([\mathrm{length}]\).
Example:
box.Lx = 15
 Type:
 property Ly¶
The length of the box in the y dimension \([\mathrm{length}]\).
Example:
box.Ly = 30
 Type:
 property Lz¶
The length of the box in the z dimension \([\mathrm{length}]\).
Example:
box.Lz = 60
 Type:
 __eq__(other)¶
Test if boxes are equal.
 __neq__(other)¶
Test if boxes are not equal.
 __reduce__()¶
Reduce values to picklable format.
 __repr__()¶
Executable representation of the object.
 classmethod cube(L)¶
Create a cube with side lengths
L
. Parameters:
L (float) – The box side length \([\mathrm{length}]\).
 Returns:
The created 3D box.
 Return type:
Example:
box = hoomd.Box.cube(L=13)
 property dimensions¶
The dimensionality of the box.
If
Lz == 0
, the box is treated as 2D, otherwise it is 3D. This property is not settable.Example:
if box.dimensions == 2: pass
 Type:
 classmethod from_basis_vectors(box_matrix)¶
Initialize a Box instance from a box matrix.
 Parameters:
box_matrix ((3, 3)
numpy.ndarray
offloat
) – A 3x3 matrix or list of lists representing a set of lattice basis vectors.
Note
The created box will be rotated with respect to the lattice basis. As a consequence the output of
to_matrix
will not be the same as the input provided to this function. This function also returns a rotation matrix comensurate with this transformation. Using this rotation matrix users can rotate the original points into the new box by applying the rotation to the points.Note
When passing a 2D basis vectors, the third vector should be set to all zeros, while first two vectors should have the last element set to zero.
 Returns:
 A tuple containing:
hoomd.Box: The created box configured according to the given basis vectors.
numpy.ndarray: A 3x3 floatingpoint rotation matrix that can be used to transform the original basis vectors to align with the new box basis vectors.
 Return type:
Example:
points = np.array([[0, 0, 0], [0.5, 0, 0], [0.25, 0.25, 0]]) box, rotation = hoomd.Box.from_basis_vectors( box_matrix = [[ 1, 1, 0], [ 1, 1, 0], [ 0, 0, 1]]) rotated_points = rotation @ points
 classmethod from_box(box)¶
Initialize a Box instance from a boxlike object.
 Parameters:
box (box_like) – A boxlike object.
Note
If all values are provided, a triclinic box will be constructed. If only
Lx, Ly, Lz
are provided, an orthorhombic box will be constructed. If onlyLx, Ly
are provided, a rectangular (2D) box will be constructed. Returns:
The resulting box object.
 Return type:
Example:
box = hoomd.Box.from_box(box=[10, 20, 30, 0.5, 0.2, 0.1])
 classmethod from_matrix(box_matrix)¶
Create a box from an upper triangular matrix.
 Parameters:
box_matrix ((3, 3)
numpy.ndarray
offloat
) –An upper triangular matrix representing a box. The values for
Lx
,Ly
,Lz
,xy
,xz
, andyz
are related to the matrix:\[\begin{split}\begin{bmatrix} L_x & L_y \cdot xy & L_z \cdot xz \\ 0 & L_y & L_z \cdot yz \\ 0 & 0 & L_z \end{bmatrix}\end{split}\] Returns:
The created box.
 Return type:
Example:
box = hoomd.Box.from_matrix( box_matrix = [[10, 12, 14], [0, 8, 16], [0, 0, 18]])
 property is2D¶
Flag whether the box is 2D.
If
Lz == 0
, the box is treated as 2D, otherwise it is 3D. This property is not settable.Example:
if box.is2D: pass
 Type:
 property periodic¶
The periodicity of each dimension.
periodic
is always(True, True, True)
for the box associated with the simulationState
. Some components ofperiodic
may beFalse
in thehoomd.data.LocalSnapshot
box attribute in MPI domain decomposition simulations. This indicates which box directions are communicated with neighboring ranks (False
) and which are not (True
). Type:
(3, )
numpy.ndarray
ofbool
 scale(s)¶
Scale box dimensions.
Scales the box in place by the given scale factors. Tilt factors are not modified.
 Parameters:
s (float or list[float]) – scale factors in each dimension. If a single float is given then scale all dimensions by s; otherwise, s must be a sequence of 3 values used to scale each dimension.
 Returns:
self
Examples:
box.scale(2)
box.scale((1, 2, 4))
 classmethod square(L)¶
Create a square with side lengths
L
. Parameters:
L (float) – The box side length \([\mathrm{length}]\).
 Returns:
The created 2D box.
 Return type:
box = hoomd.Box.square(L=128)
 property tilts¶
The box tilts,
[xy, xz, yz]
.Can be set using one tilt for all axes or three tilts. If the box is 2D
xz
andyz
will automatically be set to zero.Example:
box.tilts = (1.1, 0.8, 0.2)
 Type:
(3, )
numpy.ndarray
offloat
 to_matrix()¶
(3, 3)
numpy.ndarray
float
: The upper triangular matrix that defines the box.[[Lx, Ly * xy, Lz * xz], [0, Ly, Lz * yz], [0, 0, Lz]]
Example:
matrix = box.to_matrix()
 property volume¶
Volume of the box.
\([\mathrm{length}]^{2}\) in 2D and \([\mathrm{length}]^{3}\) in 3D.
When setting volume the aspect ratio of the box is maintained while the lengths are changed.
Example:
box.volume = 2000
 Type:
 class hoomd.Operations¶
A mutable collection of operations which act on a
Simulation
.An
Operations
class instance contains all the operations acting on a simulation. These operations are classes that perform various actions on ahoomd.Simulation
. Operations can be added and removed at any point from ahoomd.Operations
instance. The class provides the interface defined bycollections.abc.Collection
. Other methods for manipulating instances mimic Python objects where possible, but the class is not simply a mutable list or set.Operations
objects manage multiple independent sequences described below.The types of operations which can be added to an
Operations
object are tuners, updaters, integrators, writers, and computes. AnOperations
instance can have zero or one integrator and any number of tuners, updaters, writers, or computes. To see examples of these types of operations seehoomd.tune
(tuners),hoomd.update
(updaters),hoomd.hpmc.integrate
orhoomd.md.Integrator
(integrators),hoomd.write
(writers), andhoomd.md.compute.ThermodynamicQuantities
(computes).A given instance of an operation class can only be added to a single
Operations
container. Likewise, a single instance cannot be added to the sameOperations
container more than once.All
Operations
instances start with ahoomd.tune.ParticleSorter
instance in theirtuners
attribute. This increases simulation performance. However, users can choose to modify or remove this tuner if desired.Note
An
Operations
object is created by default when a new simulation is created. __contains__(operation)¶
Whether an operation is contained in this container.
 Parameters:
operation – Returns whether this exact operation is contained in the collection.
Example:
operation in simulation.operations
 __getstate__()¶
Get the current state of the operations container for pickling.
 __iadd__(operation)¶
Works the same as
Operations.add
. Parameters:
operation (hoomd.operation.Operation) – A HOOMDblue tuner, updater, integrator, writer, or compute to add to the object.
Example:
simulation.operations += operation
 __isub__(operation)¶
Works the same as
Operations.remove
. Parameters:
operation (hoomd.operation.Operation) – A HOOMDblue integrator, tuner, updater, integrator, analyzer, or compute to remove from the collection.
Example:
simulation.operations = operation
 __iter__()¶
Iterates through all contained operations.
Example:
for operation in simulation.operations: pass
 __len__()¶
Return the number of operations contained in this collection.
Example:
len(simulation.operations)
 add(operation)¶
Add an operation to this container.
Adds the provided operation to the appropriate attribute of the
Operations
instance. Parameters:
operation (hoomd.operation.Operation) – A HOOMDblue tuner, updater, integrator, writer, or compute to add to the collection.
 Raises:
TypeError – If
operation
is not of a valid type.
Note
Since only one integrator can be associated with an
Operations
object at a time, this removes the current integrator when called with an integrator operation. Also, theintegrator
property cannot be set toNone
using this function. Useoperations.integrator = None
explicitly for this.Example:
simulation.operations.add(operation)
 property computes¶
A list of compute operations.
Holds the list of computes associated with this collection. The list can be modified as a standard Python list.
 Type:
list[
hoomd.operation.Compute
]
 property integrator¶
An MD or HPMC integrator object.
Operations
objects have an initialintegrator
property ofNone
. Can be set to MD or HPMC integrators. The property can also be set toNone
.Examples:
simulation.operations.integrator = hoomd.md.Integrator(dt=0.001)
simulation.operations.integrator = None
 property is_tuning_complete¶
Check whether all children have completed tuning.
True
whenis_tuning_complete
isTrue
for all children.Note
In MPI parallel execution,
is_tuning_complete
isTrue
only when all children on all ranks have completed tuning.Example:
while (not simulation.operations.is_tuning_complete): simulation.run(1000)
 Type:
 remove(operation)¶
Remove an operation from the
Operations
object.Remove the item from the collection whose Python object
id
is the same asoperation
. Parameters:
operation (hoomd.operation.Operation) – A HOOMDblue integrator, tuner, updater, integrator, or compute to remove from the container.
 Raises:
ValueError – If
operation
is not found in this container.TypeError – If
operation
is not of a valid type.
Example:
simulation.operations.remove(operation)
 tune_kernel_parameters()¶
Start tuning kernel parameters in all children.
Example:
simulation.operations.tune_kernel_parameters()
 property tuners¶
A list of tuner operations.
Holds the list of tuners associated with this collection. The list can be modified as a standard Python list.
 Type:
list[
hoomd.operation.Tuner
]
 property updaters¶
A list of updater operations.
Holds the list of updaters associated with this collection. The list can be modified as a standard Python list.
 Type:
list[
hoomd.operation.Updater
]
 property writers¶
A list of writer operations.
Holds the list of writers associated with this collection. The list can be modified as a standard Python list.
 Type:
list[
hoomd.operation.Writer
]
 class hoomd.Simulation(device, seed=None)¶
Define a simulation.
 Parameters:
device (hoomd.device.Device) – Device to execute the simulation.
seed (int) – Random number seed.
Simulation
is the central class that defines a simulation, including thestate
of the system, theoperations
that apply to the state during a simulationrun
, and thedevice
to use when executing the simulation.seed
sets the seed for the random number generator used by all operations added to thisSimulation
.Newly initialized
Simulation
objects have no state. Callcreate_state_from_gsd
orcreate_state_from_snapshot
to initialize the simulation’sstate
.Example:
simulation = hoomd.Simulation(device=hoomd.device.CPU(), seed=1)
 __del__()¶
Clean up dangling references to simulation.
 property always_compute_pressure¶
Always compute the virial and pressure (defaults to
False
).By default, HOOMD only computes the virial and pressure on timesteps where it is needed (when
hoomd.write.GSD
writes log data to a file or when using an NPT integrator). Setalways_compute_pressure
to True to make the per particle virial, net virial, and system pressure available to query any time by property or through thehoomd.logging.Logger
interface.Note
Enabling this flag will result in a moderate performance penalty when using MD pair potentials.
Example:
simulation.always_compute_pressure = True
 Type:
 create_state_from_gsd(filename, frame=1, domain_decomposition=(None, None, None))¶
Create the simulation state from a GSD file.
 Parameters:
filename (str) – GSD file to read
frame (int) – Index of the frame to read from the file. Negative values index back from the last frame in the file.
domain_decomposition (tuple) – Choose how to distribute the state across MPI ranks with domain decomposition. Provide a tuple of 3 integers indicating the number of evenly spaced domains in the x, y, and z directions (e.g.
(8,4,2)
). Provide a tuple of 3 lists of floats to set the fraction of the simulation box to include in each domain. The sum of each list of floats must be 1.0 (e.g.([0.25, 0.75], [0.2, 0.8], [1.0])
).
When
timestep
isNone
before calling,create_state_from_gsd
setstimestep
to the value in the selected GSD frame in the file.Note
Set any or all of the
domain_decomposition
tuple elements toNone
andcreate_state_from_gsd
will select a value that minimizes the surface area between the domains (e.g.(2,None,None)
). The domains are spaced evenly along each automatically selected direction. The default value of(None, None, None)
will automatically select the number of domains in all directions.Example:
simulation.create_state_from_gsd(filename=gsd_filename)
 create_state_from_snapshot(snapshot, domain_decomposition=(None, None, None))¶
Create the simulation state from a
Snapshot
. Parameters:
snapshot (Snapshot or gsd.hoomd.Frame) – Snapshot to initialize the state from. A
gsd.hoomd.Frame
will first be converted to ahoomd.Snapshot
.domain_decomposition (tuple) – Choose how to distribute the state across MPI ranks with domain decomposition. Provide a tuple of 3 integers indicating the number of evenly spaced domains in the x, y, and z directions (e.g.
(8,4,2)
). Provide a tuple of 3 lists of floats to set the fraction of the simulation box to include in each domain. The sum of each list of floats must be 1.0 (e.g.([0.25, 0.75], [0.2, 0.8], [1.0])
).
When
timestep
isNone
before calling,create_state_from_snapshot
setstimestep
to 0.Note
Set any or all of the
domain_decomposition
tuple elements toNone
andcreate_state_from_snapshot
will select a value that minimizes the surface area between the domains (e.g.(2,None,None)
). The domains are spaced evenly along each automatically selected direction. The default value of(None, None, None)
will automatically select the number of domains in all directions.Example:
simulation.create_state_from_snapshot(snapshot=snapshot)
 property device¶
Device used to execute the simulation.
 Type:
 property final_timestep¶
run
will end at this timestep.final_timestep
is the timestep on which the currently executingrun
will complete.Example:
logger.add(obj=simulation, quantities=['final_timestep'])
(
Loggable
: category=”scalar”) Type:
 property initial_timestep¶
run
started at this timestep.initial_timestep
is the timestep on which the currently executingrun
started.Example:
logger.add(obj=simulation, quantities=['initial_timestep'])
(
Loggable
: category=”scalar”) Type:
 property operations¶
The operations that apply to the state.
The operations apply to the state during the simulation run when scheduled.
See also
 Type:
 run(steps, write_at_start=False)¶
Advance the simulation a number of steps.
 Parameters:
Note
Initialize the simulation’s state before calling
run
.Simulation
applies itsoperations
to the state during each time step in the order: tuners, updaters, integrator, then writers following the logic in this pseudocode:if write_at_start: for writer in operations.writers: if writer.trigger(timestep): writer.write(timestep) end_step = timestep + steps while timestep < end_step: for tuner in operations.tuners: if tuner.trigger(timestep): tuner.tune(timestep) for updater in operations.updaters: if updater.trigger(timestep): updater.update(timestep) if operations.integrator is not None: operations.integrator(timestep) timestep += 1 for writer in operations.writers: if writer.trigger(timestep): writer.write(timestep)
This order of operations ensures that writers (such as
hoomd.write.GSD
) capture the final output of the last step of the run loop. For example, a writer with a triggerhoomd.trigger.Periodic(period=100, phase=0)
active during arun(500)
would write on steps 100, 200, 300, 400, and 500. Setwrite_at_start=True
on the first call torun
to also obtain output at step 0.Warning
Using
write_at_start=True
in subsequent calls torun
will result in duplicate output frames.Example:
simulation.run(1_000)
 property seed¶
Random number seed.
Seeds are in the range [0, 65535]. When set,
seed
will take only the lowest 16 bits of the given value.HOOMDblue uses a deterministic counter based pseudorandom number generator. Any time a random value is needed, HOOMDblue computes it as a function of the user provided seed
seed
(16 bits), the currenttimestep
(lower 40 bits), particle identifiers, MPI ranks, and other unique identifying values as needed to sample uncorrelated values:random_value = f(seed, timestep, ...)
Example:
simulation.seed = 2
(
Loggable
: category=”scalar”) Type:
 property state¶
The current simulation state.
 Type:
 property timestep¶
The current simulation time step.
timestep
is read only after creating the simulation state.Note
Methods like
create_state_from_gsd
will set the initial timestep from the input. Settimestep
before creating the simulation state to override values fromcreate_
methods:sim.timestep = 5000 sim.create_state_from_gsd('gsd_at_step_10000000.gsd') assert sim.timestep == 5000
(
Loggable
: category=”scalar”) Type:
 property tps¶
The average number of time steps per second.
tps
is the number of steps executed divided by the elapsed walltime in seconds. It is updated during therun
loop and remains fixed afterrun
completes.Warning
The elapsed walltime and timestep are reset at the beginning of each call to
run
. Thus,tps
will provide noisy estimates of performance at the start and stable long term averages after many timesteps.Tip
Use the total elapsed wall time and timestep to average the timesteps executed per second at desired intervals.
Example:
logger.add(obj=simulation, quantities=['tps'])
(
Loggable
: category=”scalar”) Type:
 property walltime¶
The walltime spent during the last call to
run
.walltime
is the number seconds that the last call torun
took to complete. It is updated during therun
loop and remains fixed afterrun
completes.See also
Example:
logger.add(obj=simulation, quantities=['walltime'])
(
Loggable
: category=”scalar”) Type:
 class hoomd.Snapshot(communicator=None)¶
Selfcontained copy of the simulation
State
. Parameters:
communicator (Communicator) – MPI communicator to be used when accessing the snapshot.
See
State
andgsd.hoomd.Frame
for detailed documentation on the components ofSnapshot
.Note
Snapshot
is ducktype compatible withgsd.hoomd.Frame
except that arrays inSnapshot
are not assignable. You can edit their contents: e.g.snapshot.particles.typeid[:] == 0
.Warning
Data is only present on the root rank:
if snapshot.communicator.rank == 0: pos = snapshot.particles.position[0]
Example:
snapshot = hoomd.Snapshot()
 communicator¶
MPI communicator.
 Type:
 property angles¶
Angles.
 angles.typeid¶
Angle type id.
 Type:
(N,)
numpy.ndarray
ofuint32
 angles.group¶
Tags of the particles in the angle.
 Type:
(N, 3)
numpy.ndarray
ofuint32
Note
Set
N
to change the size of the arrays.Example:
if snapshot.communicator.rank == 0: snapshot.angles.N = 1 snapshot.angles.group[:] = [[0, 1, 2]] snapshot.angles.types = ['ABB'] snapshot.angles.typeid[:] = [0]
 property bonds¶
Bonds.
 bonds.typeid¶
Bond type id.
 Type:
(N,)
numpy.ndarray
ofuint32
 bonds.group¶
Tags of the particles in the bond.
 Type:
(N, 2)
numpy.ndarray
ofuint32
Note
Set
N
to change the size of the arrays.Example:
if snapshot.communicator.rank == 0: snapshot.bonds.N = 2 snapshot.bonds.group[:] = [[0, 1], [2, 3]] snapshot.bonds.types = ['AB'] snapshot.bonds.typeid[:] = [0, 0]
 property configuration¶
Snapshot box configuration.
 box¶
Simulation box parameters
[Lx, Ly, Lz, xy, xz, yz]
.
Note
box
accepts any values thatBox.from_box
allows when setting.See also
Example:
snapshot.configuration.box = [10, 20, 30, 0.1, 0.2, 0.3]
 property constraints¶
Constraints.
 constraints.value¶
Constraint length.
 Type:
(N, )
numpy.ndarray
offloat
 constraints.group¶
Tags of the particles in the constraint.
 Type:
(N, 2)
numpy.ndarray
ofuint32
Note
Set
N
to change the size of the arrays.Example:
if snapshot.communicator.rank == 0: snapshot.constraints.N = 2 snapshot.constraints.group[:] = [[0, 1], [2, 3]] snapshot.constraints.value[:] = [1, 1]
 property dihedrals¶
Dihedrals.
 dihedrals.typeid¶
Dihedral type id.
 Type:
(N,)
numpy.ndarray
ofuint32
 dihedrals.group¶
Tags of the particles in the dihedral.
 Type:
(N, 4)
numpy.ndarray
ofuint32
Note
Set
N
to change the size of the arrays.Example:
if snapshot.communicator.rank == 0: snapshot.dihedrals.N = 1 snapshot.dihedrals.group[:] = [[0, 1, 2, 3]] snapshot.dihedrals.types = ['ABBA'] snapshot.dihedrals.typeid[:] = [0]
 classmethod from_gsd_frame(gsd_snap, communicator)¶
Constructs a
hoomd.Snapshot
from agsd.hoomd.Frame
object. Parameters:
gsd_snap (gsd.hoomd.Frame) – The gsd frame to convert to a
hoomd.Snapshot
.communicator (hoomd.communicator.Communicator) – The MPI communicator to use for the snapshot. This prevents the snapshot from being stored on every rank.
Tip
Use
Simulation.create_state_from_gsd
to efficiently initialize the system state from a GSD file.Note
from_gsd_frame
only accesses thegsd_snap
argument on rank 0. In MPI simulations, avoid duplicating memory and file reads by reading GSD files only on rank 0 and passinggsd_snap=None
on other ranks.
 classmethod from_gsd_snapshot(gsd_snap, communicator)¶
Constructs a
hoomd.Snapshot
from agsd.hoomd.Snapshot
object.Deprecated since version 4.0.0: Use
from_gsd_frame
.
 property impropers¶
Impropers.
 impropers.typeid¶
Improper type id.
 Type:
(N,)
numpy.ndarray
ofuint32
 impropers.group¶
Tags of the particles in the improper.
 Type:
(N, 4)
numpy.ndarray
ofuint32
Note
Set
N
to change the size of the arrays.if snapshot.communicator.rank == 0: snapshot.impropers.N = 1 snapshot.impropers.group[:] = [[0, 1, 2, 3]] snapshot.impropers.types = ['ABBA'] snapshot.impropers.typeid[:] = [0]
 property mpcd¶
MPCD data.
 mpcd.position¶
Particle position \([\mathrm{length}]\).
 Type:
(N, 3)
numpy.ndarray
offloat
 mpcd.velocity¶
Particle velocity \([\mathrm{velocity}]\).
 Type:
(N, 3)
numpy.ndarray
offloat
 mpcd.typeid¶
Particle type id.
 Type:
(N, )
numpy.ndarray
ofuint32
Note
Set
N
to change the size of the arrays.Note
This attribute is only available when HOOMDblue is built with the MPCD component.
 property pairs¶
Special pairs.
 pairs.typeid¶
Special pair type id.
 Type:
(N,)
numpy.ndarray
ofuint32
 pairs.group¶
Tags of the particles in the special pair.
 Type:
(N, 2)
numpy.ndarray
ofuint32
Note
Set
N
to change the size of the arrays.Example:
if snapshot.communicator.rank == 0: snapshot.pairs.N = 2 snapshot.pairs.group[:] = [[0, 1], [2, 3]] snapshot.pairs.types = ['AB'] snapshot.pairs.typeid[:] = [0, 0]
 property particles¶
Particles.
 particles.position¶
Particle position \([\mathrm{length}]\).
 Type:
(N, 3)
numpy.ndarray
offloat
 particles.orientation¶
Particle orientation.
 Type:
(N, 4)
numpy.ndarray
offloat
 particles.typeid¶
Particle type id.
 Type:
(N, )
numpy.ndarray
ofuint32
 particles.mass¶
Particle mass \([\mathrm{mass}]\).
 Type:
(N, )
numpy.ndarray
offloat
 particles.charge¶
Particle charge \([\mathrm{charge}]\).
 Type:
(N, )
numpy.ndarray
offloat
 particles.diameter¶
Particle diameter \([\mathrm{length}]\).
 Type:
(N, )
numpy.ndarray
offloat
 particles.body¶
Particle body.
 Type:
(N, )
numpy.ndarray
ofint32
 particles.moment_inertia¶
Particle moment of inertia \([\mathrm{mass} \cdot \mathrm{length}^2]\).
 Type:
(N, 3)
numpy.ndarray
offloat
 particles.velocity¶
Particle velocity \([\mathrm{velocity}]\).
 Type:
(N, 3)
numpy.ndarray
offloat
 particles.angmom¶
Particle angular momentum \([\mathrm{mass} \cdot \mathrm{velocity} \cdot \mathrm{length}]\).
 Type:
(N, 4)
numpy.ndarray
offloat
 particles.image¶
Particle image.
 Type:
(N, 3)
numpy.ndarray
ofint32
Note
Set
N
to change the size of the arrays.Example:
if snapshot.communicator.rank == 0: snapshot.particles.N = 4 snapshot.particles.position[:] = [[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1]] snapshot.particles.types = ['A', 'B'] snapshot.particles.typeid[:] = [0, 1, 1, 0]
 replicate(nx, ny, nz=1)¶
Replicate the snapshot along the periodic box directions.
 Parameters:
Performs the same operation as
State.replicate
on aSnapshot
. Returns:
self
Example:
snapshot.replicate(nx=2, ny=2, nz=2)
 wrap()¶
Wrap particles into the snapshot box.
 Returns:
self
Example:
snapshot.wrap()
 class hoomd.State(simulation, snapshot, domain_decomposition)¶
The state of a
Simulation
object.Note
This object cannot be directly instantiated. Use
Simulation.create_state_from_gsd
andSimulation.create_state_from_snapshot
to instantiate aState
object as part of a simulation.Overview
State
stores the data that describes the thermodynamic microstate of aSimulation
object. This data consists of the box, particles, bonds, angles, dihedrals, impropers, special pairs, and constraints.Box
The simulation
box
describes the space that contains the particles as aBox
object.Particles
The state contains
N_particles
particles. Each particle has a position, orientation, type id, body, mass, moment of inertia, charge, diameter, velocity, angular momentum, image, and tag:\(\vec{r}\): position \([\mathrm{length}]\)  X,Y,Z cartesian coordinates defining the position of the particle in the box.
\(\mathbf{q}\): orientation \([\mathrm{dimensionless}]\)  Unit quaternion defining the rotation from the particle’s local reference frame to the box reference frame. The four components are in the order \(s\), \(a_x\), \(a_y\), \(a_z\) for the in complex notation \(s + a_x i + a_y j + a_z k\).
particle_typeid
: type id \([\mathrm{dimensionless}]\)  An integer in the interval[0,len(particle_types)
) that identifies the particle’s type.particle_types
maps type ids to names with:name = particle_types[particle_typeid]
.particle_body
: body id \([\mathrm{dimensionless}]\)  An integer that identifies the particle’s rigid body. A value of1
indicates that this particle does not belong to a body. A positive value indicates that the particle belongs to the bodyparticle_body
. This particle is the central particle of a body when the body id is equal to the tag \(\mathrm{particle\_body} = \mathrm{particle\_tag}\). (used byhoomd.md.constrain.Rigid
)\(m\): mass \([\mathrm{mass}]\)  The particle’s mass.
\(I\): moment of inertia \([\mathrm{mass} \cdot \mathrm{length}^2]\)  \(I_{xx}\), \(I_{yy}\), \(I_{zz}\) elements of the diagonal moment of inertia tensor in the particle’s local reference frame. The offdiagonal elements are 0.
\(q\): charge \([\mathrm{charge}]\)  The particle’s charge.
\(d\): diameter \([\mathrm{length}]\)  Deprecated in v3.0.0. HOOMDblue reads and writes particle diameters, but does not use them in any computations.
\(\vec{v}\): velocity \([\mathrm{velocity}]\)  X,Y,Z components of the particle’s velocity in the box’s reference frame.
\(\mathbf{P_S}\): angular momentum \([\mathrm{mass} \cdot \mathrm{velocity} \cdot \mathrm{length}]\)  Quaternion defining the particle’s angular momentum (see note).
\(\vec{n}\) : image \([\mathrm{dimensionless}]\)  Integers x,y,z that record how many times the particle has crossed each of the periodic box boundaries.
particle_tag
: tag \([\mathrm{dimensionless}]\)  An integer that uniquely identifies a given particle. The particles are stored in tag order when writing and initializing to/from a GSD file or snapshot: \(\mathrm{particle\_tag}_i = i\). When accessing data in local snapshots, particles may be in any order.
Note
HOOMD stores angular momentum as a quaternion because that is the form used when integrating the equations of motion (see Kamberaj 2005). The angular momentum quaternion \(\mathbf{P_S}\) is defined with respect to the orientation quaternion of the particle \(\mathbf{q}\) and the vector angular momentum of the particle, lifted into pure imaginary quaternion form \(\mathbf{S}^{(4)}\) as:
\[\mathbf{P_S} = 2 \mathbf{q} \times \mathbf{S}^{(4)}\]. Following this, the angular momentum vector \(\vec{S}\) in the particle’s local reference frame is:
\[\vec{S} = \frac{1}{2}im(\mathbf{q}^* \times \mathbf{P_S})\]Bonded groups
The state contains
N_bonds
bonds,N_angles
angles,N_dihedrals
dihedrals,N_impropers
impropers, andN_special_pairs
special pairs. Each of these data structures is similar, differing in the number of particles in the group and what operations use them. Bonds, angles, dihedrals, and impropers contain 2, 3, 4, and 4 particles per group respectively. Bonds specify the toplogy used when computing energies and forces inmd.bond
, angles define the same formd.angle
, dihedrals formd.dihedral
and impropers formd.improper
. These collectively implement bonding potentials used in molecular dynamics force fields. Like bonds, special pairs define connections between two particles, but special pairs are intended to adjust the 14 pairwise interactions in some molecular dynamics force fields: seemd.special_pair
. Each bonded group is defined by a type id, the group members, and a tag.bond_typeid
: type id \([\mathrm{dimensionless}]\)  An integer in the interval[0,len(bond_types))
that identifies the bond’s type.bond_types
maps type ids to names with:name = bond_types[bond_typeid]
. Similarly,angle_types
lists the angle types,dihedral_types
lists the dihedral types,improper_types
lists the improper types, andspecial_pair_types
lists the special pair types.bond_group
: A list of integers in the interval \([0, \max(\mathrm{particle\_tag})]\) that defines the tags of the particles in the bond (2), angle inangle_group
(3), dihedral indihedral_group
(4), improper inimproper_group
(4), or special pair inpair_group
(2).bond_tag
: tag \([\mathrm{dimensionless}]\)  An integer that uniquely identifies a given bond. The bonds are in tag order when writing and initializing to/from a GSD file or snapshot \(\mathrm{bond\_tag}_i = i\). When accessing data in local snapshots, bonds may be in any order. The same applies to angles withangle_tag
, dihedrals withdihedral_tag
, impropers withimproper_tag
, and special pairs withpair_tag
.
Constraints
The state contains
N_constraints
distance constraints between particles. These constraints are used byhoomd.md.constrain.Distance
. Each distance constraint consists of a distance value and the group members.constraint_group
: A list of 2 integers in the interval \([0, \max(\mathrm{particle\_tag})]\) that identifies the tags of the particles in the constraint.\(d\): constraint value \([\mathrm{length}]\)  The distance between particles in the constraint.
MPI domain decomposition
When running in serial or on 1 MPI rank, the entire simulation state is stored in that process. When using more than 1 MPI rank, HOOMDblue employs a domain decomposition approach to split the simulation box an integer number of times in the x, y, and z directions (
domain_decomposition
). Each MPI rank stores and operates on the particles local to that rank. Local particles are those contained within the region defined by the split planes (domain_decomposition_split_fractions
). Each MPI rank communicates with its neighbors to obtain the properties of particles near the boundary between ranks (ghost particles) so that it can compute interactions across the boundary.Accessing Data
Two complementary APIs provide access to the state data: local snapshots that access data directly available on the local MPI rank (including the local and ghost particles) and global snapshots that collect the entire state on rank 0. See
State.cpu_local_snapshot
,State.gpu_local_snapshot
,get_snapshot
, andset_snapshot
for information about these data access patterns.See also
To write the simulation to disk, use
write.GSD
. property N_angles¶
The number of angles in the simulation state.
Example:
N_angles = simulation.state.N_angles
 Type:
 property N_bonds¶
The number of bonds in the simulation state.
Example:
N_bonds = simulation.state.N_bonds
 Type:
 property N_constraints¶
The number of constraints in the simulation state.
Example:
N_constraints = simulation.state.N_constraints
 Type:
 property N_dihedrals¶
The number of dihedrals in the simulation state.
Example:
N_dihedrals = simulation.state.N_dihedrals
 Type:
 property N_impropers¶
The number of impropers in the simulation state.
Example:
N_impropers = simulation.state.N_impropers
 Type:
 property N_particles¶
The number of particles in the simulation state.
Example:
N_particles = simulation.state.N_particles
 Type:
 property angle_types¶
List of all angle types in the simulation state.
Example:
angle_types = simulation.state.angle_types
 property bond_types¶
List of all bond types in the simulation state.
Example:
bond_types = simulation.state.bond_types
 property box¶
A copy of the current simulation box.
Example:
box = simulation.state.box
 Type:
 property cpu_local_snapshot¶
Expose simulation data on the CPU.
Provides access directly to the system state’s particle, bond, angle, dihedral, improper, constaint, and pair data through a context manager. Data in
State.cpu_local_snapshot
is MPI rank local, and thehoomd.data.LocalSnapshot
object is only usable within a context manager (i.e.with sim.state.cpu_local_snapshot as data:
). Attempts to assess data outside the context manager will result in errors. The local snapshot interface is similar to that ofSnapshot
.The
hoomd.data.LocalSnapshot
data access is mediated throughhoomd.data.array.HOOMDArray
objects. This lets us ensure memory safety when directly accessing HOOMDblue’s data. The interface provides zerocopy access (zerocopy is guaranteed on CPU, access may be zerocopy if running on GPU).Changing the data in the buffers exposed by the local snapshot will change the data across the HOOMDblue simulation. For a trivial example, this example would set all particle zaxis positions to 0.
with simulation.state.cpu_local_snapshot as local_snapshot: local_snapshot.particles.position[:, 2] = 0
Note
The state’s box and the number of particles, bonds, angles, dihedrals, impropers, constaints, and pairs cannot change within the context manager.
Note
Getting a local snapshot object is order \(O(1)\) and setting a single value is of order \(O(1)\).
 Type:
 property dihedral_types¶
List of all dihedral types in the simulation state.
Example:
angle_types = simulation.state.angle_types
 property domain_decomposition¶
Number of domains in the x, y, and z directions.
 property domain_decomposition_split_fractions¶
Box fractions of the domain split planes in the x, y, and z directions.
 get_snapshot()¶
Make a copy of the simulation current state.
State.get_snapshot
makes a copy of the simulation state and makes it available in a single object.set_snapshot
resets the internal state to that in the given snapshot. Use these methods to implement techniques like hybrid MD/MC or umbrella sampling where entire system configurations need to be reset to a previous one after a rejected move.Note
Data across all MPI ranks and from GPUs is gathered on the root MPI rank’s memory. When accessing data in MPI simulations, use a
if snapshot.communicator.rank == 0:
conditional to access data arrays only on the root rank.Note
State.get_snapshot
is an order \(O(N_{particles} + N_{bonds} + \ldots)\) operation.See also
 Returns:
The current simulation state
 Return type:
Example:
snapshot = simulation.state.get_snapshot()
 property gpu_local_snapshot¶
Expose simulation data on the GPU.
Provides access directly to the system state’s particle, bond, angle, dihedral, improper, constaint, and pair data through a context manager. Data in
State.gpu_local_snapshot
is GPU local, and thehoomd.data.LocalSnapshotGPU
object is only usable within a context manager (i.e.with sim.state.gpu_local_snapshot as data:
). Attempts to assess data outside the context manager will result in errors. The local snapshot interface is similar to that ofSnapshot
.The
hoomd.data.LocalSnapshotGPU
data access is mediated throughhoomd.data.array.HOOMDGPUArray
objects. This helps us maintain memory safety when directly accessing HOOMDblue’s data. The interface provides zerocopy access on the GPU (assuming data was last accessed on the GPU).Changing the data in the buffers exposed by the local snapshot will change the data across the HOOMDblue simulation. For a trivial example, this example would set all particle zaxis positions to 0.
with simulation.state.gpu_local_snapshot as local_snapshot: local_snapshot.particles.position[:, 2] = 0
Warning
This property is only available when running on a GPU (or multiple GPUs).
Note
The state’s box and the number of particles, bonds, angles, dihedrals, impropers, constaints, and pairs cannot change within the context manager.
Note
Getting a local snapshot object is order \(O(1)\) and setting a single value is of order \(O(1)\).
 property improper_types¶
List of all improper types in the simulation state.
Example:
improper_types = simulation.state.improper_types
 property particle_types¶
List of all particle types in the simulation state.
Example:
particle_types = simulation.state.particle_types
 replicate(nx, ny, nz=1)¶
Replicate the state of the system along the periodic box directions.
 Parameters:
replicate
makes the system statenx * ny * nz
times larger. In each of the new periodic box images, it places a copy of the initial state with the particle positions offset to locate them in the image and the bond, angle, dihedral, improper, and pair group tags offset to apply to the copied particles. All other particle properties (mass, typeid, velocity, charge, …) are copied to the new particles without change.After placing the particles,
replicate
expands the simulation box by a factor ofnx
,ny
, andnz
in the direction of the first, second, and third box lattice vectors respectively and adjusts the particle positions to center them in the new box.Example:
simulation.state.replicate(nx=2, ny=2, nz=2)
 set_box(box)¶
Set a new simulation box.
 Parameters:
box (hoomd.box.box_like) – New simulation box.
Note
All particles must be inside the new box.
set_box
does not change any particle properties.See also
Example:
simulation.state.set_box(box)
 set_snapshot(snapshot)¶
Restore the state of the simulation from a snapshot.
Also calls
update_group_dof
to count the number of degrees in the system with the new state. Parameters:
snapshot (Snapshot) – Snapshot of the system from
get_snapshot
Warning
set_snapshot
can only make limited changes to the simulation state. While it can change the number of particles/bonds/etc… or their properties, it cannot change the number or names of the particle/bond/etc.. types.Note
set_snapshot
is an order \(O(N_{particles} + N_{bonds} + \ldots)\) operation and is very expensive when the simulation device is a GPU.Example:
simulation.state.set_snapshot(snapshot)
 property special_pair_types¶
List of all special pair types in the simulation state.
Example:
special_pair_types = simulation.state.special_pair_types
 thermalize_particle_momenta(filter, kT)¶
Assign random values to particle momenta.
 Parameters:
filter (hoomd.filter.filter_like) – Particles to modify
kT (float) – Thermal energy to set \([\mathrm{energy}]\)
thermalize_particle_momenta
assigns the selected particle’s velocities and angular momentum to random values drawn from a Gaussian distribution consistent with the given thermal energy kT.Velocity
thermalize_particle_momenta
assigns random velocities to the x and y components of each particle’s velocity. When the simulation box is 3D, it also assigns a random velocity to the z component. When the simulation box is 2D, it sets the z component to 0. Finally, sets the center of mass velocity of the selected particles to 0.Angular momentum
thermalize_particle_momenta
assigns random angular momenta to each rotational degree of freedom that has a nonzero moment of intertia. Each particle can have 0, 1, 2, or 3 rotational degrees of freedom as determine by its moment of inertia.Example:
simulation.state.thermalize_particle_momenta( filter=hoomd.filter.All(), kT=1.5)
 property types¶
dictionary of all types in the state.
Combines the data from
particle_types
,bond_types
,angle_types
,dihedral_types
,improper_types
, andspecial_pair_types
into a dictionary with keys matching the property names.
 update_group_dof()¶
Schedule an update to the number of degrees of freedom in each group.
update_group_dof
requests thatSimulation
update the degrees of freedom provided to each group by the Integrator.Simulation
will perform this update at the start ofSimulation.run
or at the start of the next timestep during an ongoing call toSimulation.run
.This method is called automatically when:
An Integrator is assigned to the
Simulation
’s operations.The
hoomd.md.Integrator.integrate_rotational_dof
parameter is set.set_snapshot
is called.On timesteps where a
hoomd.update.FilterUpdater
triggers.
Call
update_group_dof
manually to force an update, such as when you modify particle moments of inertia withcpu_local_snapshot
.Example:
box = simulation.state.update_group_dof()
Modules