transition_sampling.engines.cp2k package¶

Submodules¶

transition_sampling.engines.cp2k.CP2K_engine module¶

Engine implementation of CP2K

class transition_sampling.engines.cp2k.CP2K_engine.CP2KEngine(inputs, working_dir=None, **kwargs)¶

Bases: transition_sampling.engines.abstract_engine.AbstractEngine

Engine implementation of CP2K.

Relevant docstrings for overridden methods can be found in the base class.

Parameters

inputs (dict) –

In addition to the inputs required by AbstractEngine, CP2KEngine also requires

cp2k_inputsstr
The path to the CP2K inputs file to use for the simulations. This file will not be modified

cp2k_inputs¶

The inputs associated with this engine. Used to do low level manipulation of the inputs.

Type: CP2KInputsHandler

property atoms: Sequence[str]¶

Get the atoms held by the engine.

Get a sequence of the string representations of the atoms in use by this engine. String representations are the same as the periodic table.

Return type: Sequence[str]
Returns: An ordered sequence of atoms in the engine.

property box_size: tuple¶

Get the box size of the engine in A.

Return type: tuple[float]
Returns: Box size (x, y, z) the engine is set to in A

flip_velocity()¶

Flip the velocities currently held by multiplying by -1

Return type: None

get_engine_str()¶

Get the string representation of this engine.

This string is what defines the engine name in the inputs dictionary.

Return type: str
Returns: String of the engine’s representation

set_delta_t(value)¶

Set the time offset of this engine. Set the value of the time offset of frame to save in femtoseconds. If this isn’t a multiple of the engine’s time step, the closest frame will be taken.

Parameters: value (float) – Time offset in femtoseconds
Return type: None

set_positions(positions)¶

Set the positions of atoms in the engine.

Positions are ordered for n atoms, in shape (n, 3). Rows represent atoms and columns represent (x, y, z) dimensions.

Parameters: positions (np.ndarray with shape (n, 3)) – The positions for atoms to be set to.
Raises: ValueError – If the array does not match the required specifications
Return type: None

set_velocities(velocities)¶

Set the velocities of atoms in the engine.

Velocities are ordered for n atoms, in shape (n, 3). Rows represent atoms and columns represent (x, y, z) dimensions.

Parameters: velocities (np.ndarray with shape (n, 3)) – The velocities for atoms to be set to.
Raises: ValueError – If the array does not match the required specifications
Return type: None

validate_inputs(inputs)¶

Validate the given inputs for the specific engine.

Given a dictionary input, validate that it represents a well-formed input with all requirements for this engine

Parameters

inputs – dict of engine-specific inputs

Returns

(True, “”) if the inputs passed validation. Otherwise,
(False, “<Relevant Error Message>”)

transition_sampling.engines.cp2k.CP2K_inputs module¶

class transition_sampling.engines.cp2k.CP2K_inputs.CP2KInputsHandler(cp2k_inputs_file, logger=None)¶

Bases: object

Handles manipulating the raw CP2K Inputs data structure.

This class parses a CP2K inputs file into a memory, then supplies methods for altering it. The original file is not modified. Once the in-memory inputs have been changed, the current state can be written out into an equivalent CP2K inputs file.

Parameters: cp2k_inputs_file (str) – The cp2k inputs file that serves as a template for this class

cp2k_dict¶

The in-memory data structure representing the current inputs

Type: dict

property atoms: list¶

Get the atoms in this input

Gets the name of the atoms in the inputs as represented by CP2K.

Return type: list[str]
Returns: An ordered sequence of atoms in the inputs.

property box_size: list¶

Get the box_size of the input in A.

Return type: list[float]
Returns: Box size [x, y, z] of the input is set to in A

flip_velocity()¶

Modify state by multiplying every velocity component by -1

Return type: None

read_timestep()¶

Gets the time per frame in femtoseconds

Return type: float
Returns: How many femtoseconds each frame is given

set_plumed_file(plumed_file_path)¶

Set the plumed input file to the passed path

Parameters: plumed_file_path (str) – The full path of the plumed input file
Return type: None

set_positions(positions)¶

Set the positions of atoms in the inputs.

Positions are ordered for n atoms, in shape (n, 3). Rows represent atoms and columns represent (x, y, z) dimensions.

Parameters: positions (np.ndarray with shape (n, 3)) – The positions for atoms to be set to.
Return type: None

set_project_name(projname)¶

Set the CP2K project name of the inputs

Parameters: projname (str) – The project name to be set
Return type: None

set_traj_print_file(file_path)¶

Set the file the traj will be printed to. Appended with -pos-1.xyz

Note that cp2k automatically appends -pos-1.xyz to this filename.

Parameters: file_path (str) – The path the trajectory will be printed to
Return type: None

set_traj_print_freq(step)¶

Set how often the trajectory should be printed

Parameters: step (int) – The number of MD steps between each print. Must be an integer and must be greater than 0
Raises: ValueError – if step is not an integer or greater than 0
Return type: None

set_velocities(velocities)¶

Set the velocities of atoms in the inputs.

Velocities are ordered for n atoms, in shape (n, 3). Rows represent atoms and columns represent (x, y, z) dimensions.

Parameters: velocities (np.ndarray with shape (n, 3)) – The positions for atoms to be set to.
Return type: None

property temp: float¶

Get the temperature of the input.

Return type: float
Returns: Temperature the input is set to in Kelvin

write_cp2k_inputs(filename)¶

Write the current state of the inputs to the passed file name.

Creates the standard cp2k input format. Overwrites anything present.

Parameters: filename (str) – The file to write the input to
Return type: None

transition_sampling.engines.cp2k.CP2K_outputs module¶

class transition_sampling.engines.cp2k.CP2K_outputs.CP2KOutputHandler(name, working_dir)¶

Bases: object

check_warnings()¶

Check the output file for any warnings.

Returns a list of warnings. The list is empty if there are none.

Return type: Sequence
Returns: A list of warnings from this output file

copy_out_file(new_location)¶

Copy the output file to a new location

Parameters: new_location (str) – The full path of the location to copy to
Return type: None

get_out_file()¶

Get the full name of the output file

Return type: str
Returns: Full path of output file

read_frames_2_3()¶

Read the second (first t!=0) and third frames from the trajectory

Return type

ndarray

Returns

Array of the xyz coordinates in the second and third frame. Has the
shape (2, n_atoms, 3).

Raises

EOFError – If EOF was reached before the end of the third frame

transition_sampling.engines.cp2k package¶

Submodules¶

transition_sampling.engines.cp2k.CP2K_engine module¶

transition_sampling.engines.cp2k.CP2K_inputs module¶

transition_sampling.engines.cp2k.CP2K_outputs module¶

Module contents¶