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[, path_replacements])

Determines whether this protocol can be merged with another.

execute(directory, available_resources)

Execute the protocol.

get_class_attribute(reference_path)

Returns one of this protocols, or any of its children’s, attributes directly (rather than its value).

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

Protocol Input - If true, OpenMM will be allowed to run using a GPU if available, otherwise it will be constrained to only using CPUs.

allow_merging

Protocol Input - Defines whether this protocols is allowed to merge with other protocols.

checkpoint_frequency

Protocol Input - The frequency (in multiples of output_frequency) with which to write to a checkpoint file, e.g.

dependencies

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

enable_pbc

Protocol Input - If true, periodic boundary conditions will be enabled.

ensemble

Protocol Input - The thermodynamic ensemble to simulate in.

high_precision

Protocol Input - If true, OpenMM will be run using a platform with high precision settings.

id

The unique id of this protocol.

input_coordinate_file

Protocol Input - The file path to the starting coordinates.

output_coordinate_file

Protocol Output - The file path to the coordinates of the final system configuration.

output_frequency

Protocol Input - The frequency (in number of steps) with which to write to the output statistics and trajectory files.

schema

A serializable schema for this object.

statistics_file_path

Protocol Output - The file path to the statistics sampled during the simulation.

steps_per_iteration

Protocol Input - The number of steps to propogate the system by at each iteration.

system_path

Protocol Input - A path to the XML system object which defines the forces present in the system.

thermodynamic_state

Protocol Input - The thermodynamic conditions to simulate under The default value of this attribute is not set and must be set by the user..

thermostat_friction

Protocol Input - The thermostat friction coefficient.

timestep

Protocol Input - The timestep to evolve the system by at each step.

total_number_of_iterations

Protocol Input - The number of times to propogate the system forward by the steps_per_iteration number of steps.

trajectory_file_path

Protocol Output - The file path to the trajectory sampled during the simulation.

steps_per_iteration

Protocol Input - The number of steps to propogate the system by at each iteration. The total number of steps performed by this protocol will be total_number_of_iterations * steps_per_iteration. The default value of this attribute is 1000000.

Type

int

total_number_of_iterations

Protocol Input - The number of times to propogate the system forward by the steps_per_iteration number of steps. The total number of steps performed by this protocol will be total_number_of_iterations * steps_per_iteration. The default value of this attribute is 1.

Type

int

output_frequency

Protocol Input - The frequency (in number of steps) with which to write to the output statistics and trajectory files. The default value of this attribute is 3000. When two protocols are merged, the largest value of this attribute from either protocol is retained.

Type

int

checkpoint_frequency

Protocol Input - The frequency (in multiples of output_frequency) with which to write to a checkpoint file, e.g. if output_frequency=100 and checkpoint_frequency==2, a checkpoint file would be saved every 200 steps. The default value of this attribute is 10. When two protocols are merged, the largest value of this attribute from either protocol is retained. This input is optional.

Type

int

timestep

Protocol Input - The timestep to evolve the system by at each step. The default value of this attribute is 2.0 femtosecond. When two protocols are merged, the largest value of this attribute from either protocol is retained.

Type

Quantity

thermodynamic_state

Protocol Input - The thermodynamic conditions to simulate under The default value of this attribute is not set and must be set by the user..

Type

ThermodynamicState

ensemble

Protocol Input - The thermodynamic ensemble to simulate in. The default value of this attribute is Ensemble.NPT.

Type

Ensemble

thermostat_friction

Protocol Input - The thermostat friction coefficient. The default value of this attribute is 1.0 / picosecond. When two protocols are merged, the largest value of this attribute from either protocol is retained.

Type

Quantity

input_coordinate_file

Protocol Input - The file path to the starting coordinates. The default value of this attribute is not set and must be set by the user..

Type

str

system_path

Protocol Input - A path to the XML system object which defines the forces present in the system. The default value of this attribute is not set and must be set by the user..

Type

str

enable_pbc

Protocol Input - If true, periodic boundary conditions will be enabled. The default value of this attribute is True.

Type

bool

allow_gpu_platforms

Protocol Input - If true, OpenMM will be allowed to run using a GPU if available, otherwise it will be constrained to only using CPUs. The default value of this attribute is True.

Type

bool

high_precision

Protocol Input - 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. The default value of this attribute is False.

Type

bool

output_coordinate_file

Protocol Output - The file path to the coordinates of the final system configuration.

Type

str

trajectory_file_path

Protocol Output - The file path to the trajectory sampled during the simulation.

Type

str

statistics_file_path

Protocol Output - The file path to the statistics sampled during the simulation.

Type

str

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

Protocol Input - Defines whether this protocols is allowed to merge with other protocols. The default value of this attribute is True.

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, path_replacements=None)

Determines whether this protocol can be merged with another.

Parameters
  • other (BaseProtocol) – The protocol to compare against.

  • path_replacements (list of tuple of str, optional) – Replacements to make in any value reference protocol paths before comparing for equality.

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_class_attribute(reference_path)

Returns one of this protocols, or any of its children’s, attributes directly (rather than its value).

Parameters

reference_path (ProtocolPath) – The path pointing to the attribute to return.

Returns

The class attribute.

Return type

object

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.