RunOpenMMSimulation¶

class propertyestimator.protocols.simulation.RunOpenMMSimulation(protocol_id)[source]¶

Performs a molecular dynamics simulation in a given ensemble using an OpenMM backend.

__init__(protocol_id)[source]¶: Initialize self. See help(type(self)) for accurate signature.

Methods

`__init__`(protocol_id)	Initialize self.
`apply_replicator`(replicator, template_values)	Applies a ProtocolReplicator to this protocol.
`can_merge`(other)	Determines whether this protocol can be merged with another.
`execute`(directory, available_resources)	Execute the protocol.
`get_attribute_type`(reference_path)	Returns the type of one of the protocol input/output attributes.
`get_value`(reference_path)	Returns the value of one of this protocols inputs / outputs.
`get_value_references`(input_path)	Returns a dictionary of references to the protocols which one of this protocols inputs (specified by input_path) takes its value from.
`merge`(other)	Merges another BaseProtocol with this one.
`replace_protocol`(old_id, new_id)	Finds each input which came from a given protocol
`set_uuid`(value)	Store the uuid of the calculation this protocol belongs to
`set_value`(reference_path, value)	Sets the value of one of this protocols inputs.

Attributes

`allow_gpu_platforms`	If true, OpenMM will be allowed to run using a GPU if available, otherwise it will be constrained to only using CPUs.
`allow_merging`	If true, this protocol is allowed to merge with other identical protocols.
`dependencies`	A list of pointers to the protocols which this protocol takes input from.
`enable_pbc`	If true, periodic boundary conditions will be enabled.
`ensemble`	The thermodynamic ensemble to simulate in.
`high_precision`	If true, OpenMM will be run using a platform with high precision settings.
`id`	The unique id of this protocol.
`input_coordinate_file`	The file path to the starting coordinates.
`output_coordinate_file`	The file path to the coordinates of the final system configuration.
`output_frequency`	The frequency with which to write to the output statistics and trajectory files.
`save_rolling_statistics`	If True, the statisitics file will be written to every output_frequency number of steps, rather than just once at the end of the simulation.
`schema`	A serializable schema for this object.
`statistics_file_path`	The file path to the statistics sampled during the simulation.
`steps`	The number of timesteps to evolve the system by.
`system_path`	A path to the XML system object which defines the forces present in the system.
`thermodynamic_state`	The thermodynamic conditions to simulate under
`thermostat_friction`	The thermostat friction coefficient.
`timestep`	The timestep to evolve the system by at each step.
`trajectory_file_path`	The file path to the trajectory sampled during the simulation.

steps¶: The number of timesteps to evolve the system by.

thermostat_friction¶: The thermostat friction coefficient.

timestep¶: The timestep to evolve the system by at each step.

output_frequency¶: The frequency with which to write to the output statistics and trajectory files.

ensemble¶: The thermodynamic ensemble to simulate in.

thermodynamic_state¶: The thermodynamic conditions to simulate under

input_coordinate_file¶: The file path to the starting coordinates.

system_path¶: A path to the XML system object which defines the forces present in the system.

enable_pbc¶: If true, periodic boundary conditions will be enabled.

save_rolling_statistics¶

If True, the statisitics file will be written to every output_frequency number of steps, rather than just once at the end of the simulation.

Notes

In future when either saving the statistics to file has been optimised, or an option for the frequency to save to the file has been added, this option will be removed.

allow_gpu_platforms¶: If true, OpenMM will be allowed to run using a GPU if available, otherwise it will be constrained to only using CPUs.

high_precision¶: If true, OpenMM will be run using a platform with high precision settings. This will be the Reference platform when only a CPU is available, or double precision mode when a GPU is available.

output_coordinate_file¶: The file path to the coordinates of the final system configuration.

trajectory_file_path¶: The file path to the trajectory sampled during the simulation.

statistics_file_path¶: The file path to the statistics sampled during the simulation.

execute(directory, available_resources)[source]¶

Execute the protocol.

Protocols may be chained together by passing the output of previous protocols as input to the current one.

Parameters

directory (str) – The directory to store output data in.
available_resources (ComputeResources) – The resources available to execute on.

Returns

The output of the execution.

Return type

Dict[str, Any]

allow_merging¶

If true, this protocol is allowed to merge with other identical protocols.

Type: bool

apply_replicator(replicator, template_values, template_index=-1, template_value=None, update_input_references=False)¶

Applies a ProtocolReplicator to this protocol. This method should clone any protocols whose id contains the id of the replicator (in the format $(replicator.id)).

Parameters

replicator (ProtocolReplicator) – The replicator to apply.
template_values (list of Any) –
A list of the values which will be inserted into the newly replicated protocols.

This parameter is mutually exclusive with template_index and template_value
template_index (int, optional) –
A specific value which should be used for any protocols flagged as to be replicated by the replicator. This option is mainly used when replicating children of an already replicated protocol.

This parameter is mutually exclusive with template_values and must be set along with a template_value.
template_value (Any, optional) –
A specific index which should be used for any protocols flagged as to be replicated by the replicator. This option is mainly used when replicating children of an already replicated protocol.

This parameter is mutually exclusive with template_values and must be set along with a template_index.
update_input_references (bool) –
If true, any protocols which take their input from a protocol which was flagged for replication will be updated to take input from the actually replicated protocol. This should only be set to true if this protocol is not nested within a workflow or a protocol group.

This option cannot be used when a specific template_index or template_value is providied.

Returns

A dictionary of references to all of the protocols which have been replicated, with keys of original protocol ids. Each value is comprised of a list of the replicated protocol ids, and their index into the template_values array.

Return type

dict of ProtocolPath and list of tuple of ProtocolPath and int

can_merge(other)¶

Determines whether this protocol can be merged with another.

Parameters: other (BaseProtocol) – The protocol to compare against.
Returns: True if the two protocols are safe to merge.
Return type: bool

property dependencies¶

A list of pointers to the protocols which this protocol takes input from.

Type: list of ProtocolPath

get_attribute_type(reference_path)¶

Returns the type of one of the protocol input/output attributes.

Parameters: reference_path (ProtocolPath) – The path pointing to the value whose type to return.
Returns: The type of the attribute.
Return type: type

get_value(reference_path)¶

Returns the value of one of this protocols inputs / outputs.

Parameters: reference_path (ProtocolPath) – The path pointing to the value to return.
Returns: The value of the input / output
Return type: Any

get_value_references(input_path)¶

Returns a dictionary of references to the protocols which one of this protocols inputs (specified by input_path) takes its value from.

Notes

Currently this method only functions correctly for an input value which is either currently a ProtocolPath, or a list / dict which contains at least one ProtocolPath.

Parameters: input_path (propertyestimator.workflow.utils.ProtocolPath) – The input value to check.
Returns: A dictionary of the protocol paths that the input targeted by input_path depends upon.
Return type: dict of ProtocolPath and ProtocolPath

property id¶

The unique id of this protocol.

Type: str

merge(other)¶

Merges another BaseProtocol with this one. The id of this protocol will remain unchanged.

It is assumed that can_merge has already returned that these protocols are compatible to be merged together.

Parameters: other (BaseProtocol) – The protocol to merge into this one.
Returns: A map between any original protocol ids and their new merged values.
Return type: Dict[str, str]

replace_protocol(old_id, new_id)¶

Finds each input which came from a given protocol: and redirects it to instead take input from a new one.

Notes

This method is mainly intended to be used only when merging multiple protocols into one.

Parameters

old_id (str) – The id of the old input protocol.
new_id (str) – The id of the new input protocol.

property schema¶

A serializable schema for this object.

Type: ProtocolSchema

set_uuid(value)¶

Store the uuid of the calculation this protocol belongs to

Parameters: value (str) – The uuid of the parent calculation.

set_value(reference_path, value)¶

Sets the value of one of this protocols inputs.

Parameters

reference_path (ProtocolPath) – The path pointing to the value to return.
value (Any) – The value to set.