BaseSimulation

class propertyestimator.protocols.simulation.BaseSimulation(protocol_id)[source]

A base class for protocols which will perform a molecular simulation in a given ensemble and at a specified state.

__init__(protocol_id)

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.

from_json(file_path)

Create this object from a JSON file.

from_schema(schema)

Initializes a protocol from it’s schema definition.

get_attributes([attribute_type])

Returns all attributes of a specific attribute_type.

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.

json([file_path, format])

Creates a JSON representation of this class.

merge(other)

Merges another Protocol with this one.

parse_json(string_contents[, encoding])

Parses a typed json string into the corresponding class structure.

replace_protocol(old_id, new_id)

Finds each input which came from a given protocol

set_uuid(value)

Prepend a unique identifier to this protocols id.

set_value(reference_path, value)

Sets the value of one of this protocols inputs.

validate([attribute_type])

Validate the values of the attributes.

Attributes

allow_gpu_platforms

Input - If true, the simulation will be performed using a GPU if available, otherwise it will be constrained to only using CPUs.

allow_merging

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

checkpoint_frequency

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

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

ensemble

Input - The thermodynamic ensemble to simulate in.

high_precision

Input - If true, the simulation will be run using double precision.

id

The unique id of this protocol.

input_coordinate_file

Input - The file path to the starting coordinates.

output_coordinate_file

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

output_frequency

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

outputs

A dictionary of the outputs of this property.

required_inputs

The inputs which must be set on this protocol.

schema

A serializable schema for this object.

statistics_file_path

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

steps_per_iteration

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

system_path

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

thermodynamic_state

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

Input - The thermostat friction coefficient.

timestep

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

total_number_of_iterations

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

trajectory_file_path

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

steps_per_iteration

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

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

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

Type

int

checkpoint_frequency

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. When two protocols are merged, the largest value of this attribute from either protocol is retained. The default value of this attribute is 10. This attribute is optional.

Type

int

timestep

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

Type

Quantity

thermodynamic_state

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

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

Type

Ensemble

thermostat_friction

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

Type

Quantity

input_coordinate_file

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

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

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

Type

bool

allow_gpu_platforms

Input - If true, the simulation will be performed 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

Input - If true, the simulation will be run using double precision. The default value of this attribute is False.

Type

bool

output_coordinate_file

Output - The file path to the coordinates of the final system configuration. The default value of this attribute is not set and must be set by the user..

Type

str

trajectory_file_path

Output - The file path to the trajectory sampled during the simulation. The default value of this attribute is not set and must be set by the user..

Type

str

statistics_file_path

Output - The file path to the statistics sampled during the simulation. The default value of this attribute is not set and must be set by the user..

Type

str

allow_merging

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 (Protocol) – 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

execute(directory='', available_resources=None)

Execute the protocol.

Parameters
  • directory (str) – The directory to store output data in.

  • available_resources (ComputeResources) – The resources available to execute on. If None, the protocol will be executed on a single CPU.

classmethod from_json(file_path)

Create this object from a JSON file.

Parameters

file_path (str) – The path to load the JSON from.

Returns

The parsed class.

Return type

cls

classmethod from_schema(schema)

Initializes a protocol from it’s schema definition.

Parameters

schema (ProtocolSchema) – The schema to initialize the protocol using.

Returns

The initialized protocol.

Return type

cls

classmethod get_attributes(attribute_type=None)

Returns all attributes of a specific attribute_type.

Parameters

attribute_type (type of Attribute, optional) – The type of attribute to search for.

Returns

The names of the attributes of the specified type.

Return type

list of str

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

id

The unique id of this protocol. The default value of this attribute is not set and must be set by the user..

Type

str

json(file_path=None, format=False)

Creates a JSON representation of this class.

Parameters
  • file_path (str, optional) – The (optional) file path to save the JSON file to.

  • format (bool) – Whether to format the JSON or not.

Returns

The JSON representation of this class.

Return type

str

merge(other)

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

Parameters

other (Protocol) – 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]

property outputs

A dictionary of the outputs of this property.

Type

dict of ProtocolPath and Any

classmethod parse_json(string_contents, encoding='utf8')

Parses a typed json string into the corresponding class structure.

Parameters
  • string_contents (str or bytes) – The typed json string.

  • encoding (str) – The encoding of the string_contents.

Returns

The parsed class.

Return type

Any

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 required_inputs

The inputs which must be set on this protocol.

Type

list of ProtocolPath

property schema

A serializable schema for this object.

Type

ProtocolSchema

set_uuid(value)

Prepend a unique identifier to this protocols id. If the id already has a prepended uuid, it will be overwritten by this value.

Parameters

value (str) – The uuid to prepend.

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.

validate(attribute_type=None)

Validate the values of the attributes. If attribute_type is set, only attributes of that type will be validated.

Parameters

attribute_type (type of Attribute, optional) – The type of attribute to validate.

Raises

ValueError or AssertionError