liquidlib.api package

Submodules

liquidlib.api.atom_selector module

Classes for atom selection

class liquidlib.api.atom_selector.AtomSelector

Bases: object

Base class for atom selection

select(input_parameters, trajectory, **kwargs)

class liquidlib.api.atom_selector.SelectByAtomId

Bases: liquidlib.api.atom_selector.AtomSelector

select(input_parameters, trajectory, **kwargs)

class liquidlib.api.atom_selector.SelectByZDepth

Bases: liquidlib.api.atom_selector.AtomSelector

select(input_parameters, trajectory, **kwargs)

liquidlib.api.input_parser module

Parse input parameters from the input file

class liquidlib.api.input_parser.InputParser

Bases: object

Utility class to parse the input file

static parse(input_file)

Parse the input file to retrieve input parameters

Parameters:input_file – an input file defining the computation parameters Returns:a dictionary of input parameters

liquidlib.api.input_validator module

Validate input parameters for the calculation

class liquidlib.api.input_validator.DecoratorOfInputValidator

Bases: liquidlib.api.input_validator.InputValidator

Abstract base decorator of input validators

class liquidlib.api.input_validator.GenericInputValidator

Bases: liquidlib.api.input_validator.InputValidator

Concrete class to check generic parameters for each calculation

validate(input_parameters)

Validate generic parameters

class liquidlib.api.input_validator.InputValidator

Bases: abc.ABC

Abstract base class for validating input parameters

validate(input_parameters)

Abstract method to validate input parameters

Parameters:input_parameters – a dictionary of input parameters Returns:a boolean value indicating success (true) or failure (false)

class liquidlib.api.input_validator.KSpaceDecorator(input_validator)

Bases: liquidlib.api.input_validator.DecoratorOfInputValidator

Decorator to validate parameters for reciprocal-space quantity

validate(input_parameters)

class liquidlib.api.input_validator.KSpaceTDomainValidator

Bases: liquidlib.api.input_validator.InputValidator

Validate parameters for the quantity in reciprocal-space and time-domain

validate(input_parameters)

class liquidlib.api.input_validator.KSpaceValidator

Bases: liquidlib.api.input_validator.InputValidator

Validate parameters for reciprocal-space quantity

validate(input_parameters)

class liquidlib.api.input_validator.RSpaceDecorator(input_validator)

Bases: liquidlib.api.input_validator.DecoratorOfInputValidator

Decorator to validate parameters for real-space quantity

validate(input_parameters)

class liquidlib.api.input_validator.RSpaceTDomainValidator

Bases: liquidlib.api.input_validator.InputValidator

Validate parameters for the quantity in real-space and time-domain

validate(input_parameters)

class liquidlib.api.input_validator.RSpaceValidator

Bases: liquidlib.api.input_validator.InputValidator

Validate parameters for real-space quantity

validate(input_parameters)

class liquidlib.api.input_validator.TDomainDecorator(input_validator)

Bases: liquidlib.api.input_validator.DecoratorOfInputValidator

Decorator to validate parameters for time-domain quantity

validate(input_parameters)

class liquidlib.api.input_validator.TDomainValidator

Bases: liquidlib.api.input_validator.InputValidator

Validate parameters for time-domain quantity

validate(input_parameters)

liquidlib.api.kvector_generator module

Classes for k-vectors generation

class liquidlib.api.kvector_generator.KvectorGenerator

Bases: object

Base class of strategy to generate k-vector

generate(kvalue, max_kvec_num=100, **kwargs)

Abstract method to generate k-vectors

This method needs to be implemented in the derived class

class liquidlib.api.kvector_generator.PermutationKevectorGenerator

Bases: liquidlib.api.kvector_generator.KvectorGenerator

generate(kvalue, max_kvec_num=100, **kwargs)

class liquidlib.api.kvector_generator.RecursionKvectorGenerator

Bases: liquidlib.api.kvector_generator.KvectorGenerator

generate(kvalue, max_kvec_num=100, **kwargs)

liquidlib.api.output_writer module

Write the output to file

class liquidlib.api.output_writer.OutputWriter

Bases: object

Utility class to write the output to file

static write1D(filename, x, fx, header=None)

Write 1D data to a file

Parameters:

• filename – name of output file
• x – a list of variable values
• fx – a list of results, forming pairs of (x, fx)
• header – header to print in the top of output file

static write2D(filename, x, y, fxy, header=None)

Write 2D data to a file

Parameters:

• filename – name of output file
• x – a list of values of the 1st variable, which would be printed in a single column in the output file
• y – a list of values of the end variable, which would be printed in a column aligned with the columns of fxy
• fx – a list of results, forming pairs of (y, fx1y, fx2y, …)
• header – header to print in the top of output file

liquidlib.api.quantity module

Quantity: Base class for the quantities computed in liquidlib

class liquidlib.api.quantity.Quantity(input_file='quantity.in')

Bases: abc.ABC

Abstract base class for quantities computed in liquidlib

atom_selector

execute()

Executes all the procedures for calculation

input_validator

trajectory_factory

liquidlib.api.trajectory module

Classes of trajectory

class liquidlib.api.trajectory.LammpsTrajectory

Bases: liquidlib.api.trajectory.Trajectory

read(input_parameters)

Read .lammpstrj file

class liquidlib.api.trajectory.PdbTrajectory

Bases: liquidlib.api.trajectory.Trajectory

read(input_parameters)

Read .pdb file

class liquidlib.api.trajectory.Trajectory

Bases: abc.ABC

Abstract base class of trajectory

compute_velocities()

Compute velocities from the coordinates

read(input_parameters)

Read trajectory from the trajectory file

Parameters:input_parameters – Returns:

unwrap_coordinates()

Unwrap the coordinates (periodic boundary condition removed)

wrap_coordinates()

Wrap the coordinates (reinforce the periodic boundary condition)

class liquidlib.api.trajectory.TrrTrajectory

Bases: liquidlib.api.trajectory.Trajectory

read(input_parameters)

Read .trr file

class liquidlib.api.trajectory.XtcTrajectory

Bases: liquidlib.api.trajectory.Trajectory

read(input_parameters)

Read .xtc file

class liquidlib.api.trajectory.XyzTrajectory

Bases: liquidlib.api.trajectory.Trajectory

read(input_parameters)

Read .xyz file

liquidlib.api.trajectory_factory module

A simple factory to create trajectory

class liquidlib.api.trajectory_factory.DemoTrajectoryFactory

Bases: liquidlib.api.trajectory_factory.TrajectoryFactory

A demo class to extend TrajectoryFactory

prepare_trajectory(trajectory_file_name)

class liquidlib.api.trajectory_factory.TrajectoryFactory

Bases: object

A simple factory to prepare trajectory

create_trajectory(trajectory_file_name)

Returns a specific trajectory type based on the file type

Parameters:trajectory_file_name – file name of the trajectory file

Module contents