ichor.core.files.dl_poly package

Submodules

ichor.core.files.dl_poly.dl_poly_config module

class DlPolyConfig(system_name: str, trajectory: Trajectory, path: Path | str = PosixPath('CONFIG'), cell_size: float = 50.0, comment_line='Frame :         1\n')

Bases: WriteFile

Write out a DLPoly CONFIG file. The name of the file needs to be CONFIG, so DL POLY knows to use it.

Parameters:

• system_name – the name of the chemical system

• trajectory – a Trajectory instance containing the geometries that are going to be written to the CONFIG file. Each timestep in the trajectory is an Atoms instance.

• path – The path to the CONFIG file, defaults to Path(‘CONFIG’)

• cell_size – The size of the box, float

• line (comment) –

  The very first line in the CONFIG file. Must be below 72 characters

  Note

  ALL of the timesteps in the Trajectory will be written to one CONFIG file. Each timestep groups geometries which should be represented by a GP model. For example, if each timestep is only one molecule, then it means it is a monomer model and the labels of the atoms in the CONFIG will show that. If each timestep is two molecules, it means it is a dimer model, so then the labels in the CONFIG file will make sure that two molecules which should be represented by one GP model have the correct atom labeling in the CONFIG file.

path: Path | str

ichor.core.files.dl_poly.dl_poly_control module

class DlPolyControl(system_name: str, path: Path = PosixPath('CONTROL'), ensemble: str = 'nvt', thermostat: str = 'hoover', thermostat_settings: list = [0.04], temperature: int = 1, timestep=0.001, steps=500, scale=100, cutoff=8.0, rvwd=8.0, dump=1000, trajectory_i=0, trajectory_j=1, trajectory_k=0, print_every=1, stats_every=1, job_time=10000000, close_time=20000)

Bases: WriteFile

Write out a DLPoly CONTROL file. The name of the file needs to be CONTROL, so DL POLY knows to use it. The default Control file is made to be used for geometry optimizations at very low temperatures. Settings must be changed to write out a file for water box simulations for example.

path: Path | str

ichor.core.files.dl_poly.dl_poly_fflux module

class DlPolyFFLUX(path: Path | str = PosixPath('FFLUX'))

Bases: ReadFile

READS the FFLUX file from FFLUX.

Parameters:

path – Path to FFLUX file

Variables:

• df – A pandas dataframe storing all the data in the FFLUX file.

• sum_iqa_energy – The total energies array of shape ntimesteps

• vdw_energy – The Van der Waals energies of each timestep. Only computed if there are multiple molecules. Otherwise they will be 0.0

• electrostatic_energy – The electrostatic energies of each timestep. Only computed if there are multiple molecules. Otherwise they will be 0.0

classmethod check_path(path: Path) → bool

Checks the suffix of the given path matches the filetype associated with class that subclasses from File :param path: A Path object to check :return: True if the Path object has the same suffix as the class filetype, False otherwise

property delta_between_timesteps: List[float]

Calculates the delta energy (in kJ mol-1) between each pairs of timesteps. Useful for checking convergence of energy when doing optimizations.

Returns:

List containing the first index (timestep) where the threshold is met as well as the list of differences for all timesteps

property delta_between_timesteps_kj_mol: List[float]

Calculates the delta energy (in kJ mol-1) between each pairs of timesteps. Useful for checking convergence of energy when doing optimizations.

Returns:

List containing the first index (timestep) where the threshold is met as well as the list of differences for all timesteps

property electrostatic_energy

first_index_where_delta_less_than(delta=0.0001) → int

Returns first index where the energy between timesteps is below delta (in kJ mol-1)

Parameters:

delta – The threshold when geometry is converged, defaults to 1e-4 kJ mol-1

property kinetic_energy

property ntimesteps

path: Path | str

plot_abs_differences(until_converged_energy=True)

property sum_iqa_energy

property total_energy

property total_energy_kj_mol

property vdw_energy

ichor.core.files.dl_poly.dl_poly_field module

class ConnectedAtom(atom: Atom, parent: ConnectedAtoms)

Bases: Atom

set_angle(other: Atom)

set_bond(other: Atom)

set_dihedral(other: Atom)

class ConnectedAtoms(atoms)

Bases: Atoms

angle_names() → List[str]

property angles

bond_names() → List[str]

property bonds

dihedral_names() → List[str]

property dihedrals

names()

Return a list of atom names that are held in the instance of Atoms.

class DlPolyField(system_name: str, atoms: Atoms, path: Path | str = PosixPath('FIELD'), nummols=1)

Bases: WriteFile

path: Path | str

ichor.core.files.dl_poly.dl_poly_history module

class DlPolyHistory(path: Path | None = PosixPath('HISTORY'))

Bases: Trajectory

DLPOLY HISTORY File

Inherits from Trajectory as is a list of Atoms Builds on the Trajectory class by adding DLPOLY information provided by the HISTORY file

Warning

Indexing the history as a python list, i.e. history[1000] is not guaranteed to give the 1000th timestep (0-indexed). This is because sometimes there is binary written to the HISTORY file which messes up some geometries. These geometries are excluded from the read in data, so indexing as a list will might return a different timestep.

To make sure that the exact timestep is returned (useful when you also want to get data from FFLUX or IQA_ENERGIES/IQA_FORCES file, then ensure that you check the ntimestep attribute of a timestep). This will be correct, even if some geoemtries are missing.

To get a list of missing timesteps, use the self.removed_timesteps attribute of the DlPolyHistory class.

classmethod check_path(path: Path) → bool

Checks the suffix of the given path matches the filetype associated with class that subclasses from File :param path: A Path object to check :return: True if the Path object has the same suffix as the class filetype, False otherwise

path: Path | str

write_final_geometry_to_xyz(xyz_path: Path)

write_to_trajectory(path: str = 'TRAJECTORY.xyz')

Writes a trajectory .xyz file from the DL POLY HISTORY file.

class DlpolyPeriodicBoundary(value)

Bases: Enum

An enumeration.

Cubic = 1

HexagonalPrism = 7

NoBoundary = 0

Orthorhombic = 2

Parallelepiped = 3

RhombicDodecahedral = 5

TruncatedOctahedral = 4

XYParallelogram = 6

class DlpolyTimestep

Bases: Atoms

class DlpolyTimestepAtom(ty: str, x: float, y: float, z: float, index: int | None = None, parent: Atoms | None = None, units: AtomicDistance = AtomicDistance.Angstroms, velocity=None, force=None)

Bases: Atom

property force

property velocity

class DlpolyTrajectoryKey(value)

Bases: Enum

An enumeration.

Coordinate = 0

CoordinateVelocity = 1

CoordinateVelocityForce = 2

exception ForceNotDefined

Bases: Exception

exception VelocityNotDefined

Bases: Exception

ichor.core.files.dl_poly.dl_poly_iqa_energies module

class DlPolyIQAEnergies(path: Path | str = PosixPath('IQA_ENERGIES'))

Bases: ReadFile

READS the IQA_ENERGIES file from FFLUX.

Parameters:

path – Path to IQA_ENERGIES file

Variables:

• natoms – Number of atoms in system

• energies – Array of shape ntimesteps x natoms for read energies

classmethod check_path(path: Path) → bool

Checks the suffix of the given path matches the filetype associated with class that subclasses from File :param path: A Path object to check :return: True if the Path object has the same suffix as the class filetype, False otherwise

path: Path | str

ichor.core.files.dl_poly.dl_poly_iqa_forces module

class DlPolyIQAForces(path: Path | str = PosixPath('IQA_FORCES'))

Bases: ReadFile

READS the IQA_FORCES file from FFLUX.

Parameters:

path – Path to IQA_FORCES file

Variables:

• forces – The forces array of shape ntimesteps x natoms x 3. Initialized as FileContents prior to file reading.

• natoms – Number of atoms in each timestep

check_forces_less_than_value(value=0.001) → ndarray

Checks what timesteps have all forces less than value. The GP models will revert back to prior mean when far away from training data, so that the forces on atoms will be 0.

We can check for that because if the forces are consistently less than the value then either the simulation has crashed or a minimum is reached

Parameters:

value – Value for which all forces need to be less than

Returns:

np.ndarray containing timestep indices for which condition is true If len(array) is 0, then the condition is not met for any timestep. Could be useful to check if a geometry is optimized or simulation crashed.

classmethod check_path(path: Path) → bool

Checks the suffix of the given path matches the filetype associated with class that subclasses from File :param path: A Path object to check :return: True if the Path object has the same suffix as the class filetype, False otherwise

path: Path | str

ichor.core.files.dl_poly.fflux_directory module

class FFLUXDirectory(path: Path | str)

Bases: AnnotatedDirectory

READS a FFLUX Directory containing FFLUX, IQA_ENERGIES, IQA_FORCEs and HISTORY file

Parameters:

path – Path to FFLUX Directory

contents = {'fflux_file': <class 'ichor.core.files.dl_poly.dl_poly_fflux.DlPolyFFLUX'>, 'history_file': <class 'ichor.core.files.dl_poly.dl_poly_history.DlPolyHistory'>, 'iqa_energies_file': <class 'ichor.core.files.dl_poly.dl_poly_iqa_energies.DlPolyIQAEnergies'>, 'iqa_forces_file': <class 'ichor.core.files.dl_poly.dl_poly_iqa_forces.DlPolyIQAForces'>}

property coordinates: ndarray

Returns coordinates as array of shape ntimesteps x natoms x 3

property iqa_energies: ndarray

Returns individual atom iqa enegy array of shape ntimesteps x natoms

property iqa_forces: ndarray

Returns iqa forces array of shape ntimesteps x natoms x 3

property natoms: int

Returns number of atoms

path: Path | str

property total_iqa_energies: ndarray

Returns total energy array of shape ntimesteps

Module contents

class DlPolyConfig(system_name: str, trajectory: Trajectory, path: Path | str = PosixPath('CONFIG'), cell_size: float = 50.0, comment_line='Frame :         1\n')

Bases: WriteFile

Write out a DLPoly CONFIG file. The name of the file needs to be CONFIG, so DL POLY knows to use it.

Parameters:

• system_name – the name of the chemical system

• trajectory – a Trajectory instance containing the geometries that are going to be written to the CONFIG file. Each timestep in the trajectory is an Atoms instance.

• path – The path to the CONFIG file, defaults to Path(‘CONFIG’)

• cell_size – The size of the box, float

• line (comment) –

  The very first line in the CONFIG file. Must be below 72 characters

  Note

  ALL of the timesteps in the Trajectory will be written to one CONFIG file. Each timestep groups geometries which should be represented by a GP model. For example, if each timestep is only one molecule, then it means it is a monomer model and the labels of the atoms in the CONFIG will show that. If each timestep is two molecules, it means it is a dimer model, so then the labels in the CONFIG file will make sure that two molecules which should be represented by one GP model have the correct atom labeling in the CONFIG file.

path: Path | str

class DlPolyControl(system_name: str, path: Path = PosixPath('CONTROL'), ensemble: str = 'nvt', thermostat: str = 'hoover', thermostat_settings: list = [0.04], temperature: int = 1, timestep=0.001, steps=500, scale=100, cutoff=8.0, rvwd=8.0, dump=1000, trajectory_i=0, trajectory_j=1, trajectory_k=0, print_every=1, stats_every=1, job_time=10000000, close_time=20000)

Bases: WriteFile

Write out a DLPoly CONTROL file. The name of the file needs to be CONTROL, so DL POLY knows to use it. The default Control file is made to be used for geometry optimizations at very low temperatures. Settings must be changed to write out a file for water box simulations for example.

path: Path | str

class DlPolyFFLUX(path: Path | str = PosixPath('FFLUX'))

Bases: ReadFile

READS the FFLUX file from FFLUX.

Parameters:

path – Path to FFLUX file

Variables:

• df – A pandas dataframe storing all the data in the FFLUX file.

• sum_iqa_energy – The total energies array of shape ntimesteps

• vdw_energy – The Van der Waals energies of each timestep. Only computed if there are multiple molecules. Otherwise they will be 0.0

• electrostatic_energy – The electrostatic energies of each timestep. Only computed if there are multiple molecules. Otherwise they will be 0.0

classmethod check_path(path: Path) → bool

Checks the suffix of the given path matches the filetype associated with class that subclasses from File :param path: A Path object to check :return: True if the Path object has the same suffix as the class filetype, False otherwise

property delta_between_timesteps: List[float]

Calculates the delta energy (in kJ mol-1) between each pairs of timesteps. Useful for checking convergence of energy when doing optimizations.

Returns:

List containing the first index (timestep) where the threshold is met as well as the list of differences for all timesteps

property delta_between_timesteps_kj_mol: List[float]

Calculates the delta energy (in kJ mol-1) between each pairs of timesteps. Useful for checking convergence of energy when doing optimizations.

Returns:

List containing the first index (timestep) where the threshold is met as well as the list of differences for all timesteps

property electrostatic_energy

first_index_where_delta_less_than(delta=0.0001) → int

Returns first index where the energy between timesteps is below delta (in kJ mol-1)

Parameters:

delta – The threshold when geometry is converged, defaults to 1e-4 kJ mol-1

property kinetic_energy

property ntimesteps

path: Path | str

plot_abs_differences(until_converged_energy=True)

property sum_iqa_energy

property total_energy

property total_energy_kj_mol

property vdw_energy

class DlPolyField(system_name: str, atoms: Atoms, path: Path | str = PosixPath('FIELD'), nummols=1)

Bases: WriteFile

path: Path | str

class DlPolyHistory(path: Path | None = PosixPath('HISTORY'))

Bases: Trajectory

DLPOLY HISTORY File

Inherits from Trajectory as is a list of Atoms Builds on the Trajectory class by adding DLPOLY information provided by the HISTORY file

Warning

Indexing the history as a python list, i.e. history[1000] is not guaranteed to give the 1000th timestep (0-indexed). This is because sometimes there is binary written to the HISTORY file which messes up some geometries. These geometries are excluded from the read in data, so indexing as a list will might return a different timestep.

To make sure that the exact timestep is returned (useful when you also want to get data from FFLUX or IQA_ENERGIES/IQA_FORCES file, then ensure that you check the ntimestep attribute of a timestep). This will be correct, even if some geoemtries are missing.

To get a list of missing timesteps, use the self.removed_timesteps attribute of the DlPolyHistory class.

classmethod check_path(path: Path) → bool

Checks the suffix of the given path matches the filetype associated with class that subclasses from File :param path: A Path object to check :return: True if the Path object has the same suffix as the class filetype, False otherwise

path: Path | str

write_final_geometry_to_xyz(xyz_path: Path)

write_to_trajectory(path: str = 'TRAJECTORY.xyz')

Writes a trajectory .xyz file from the DL POLY HISTORY file.

class DlPolyIQAEnergies(path: Path | str = PosixPath('IQA_ENERGIES'))

Bases: ReadFile

READS the IQA_ENERGIES file from FFLUX.

Parameters:

path – Path to IQA_ENERGIES file

Variables:

• natoms – Number of atoms in system

• energies – Array of shape ntimesteps x natoms for read energies

classmethod check_path(path: Path) → bool

Checks the suffix of the given path matches the filetype associated with class that subclasses from File :param path: A Path object to check :return: True if the Path object has the same suffix as the class filetype, False otherwise

path: Path | str

class DlPolyIQAForces(path: Path | str = PosixPath('IQA_FORCES'))

Bases: ReadFile

READS the IQA_FORCES file from FFLUX.

Parameters:

path – Path to IQA_FORCES file

Variables:

• forces – The forces array of shape ntimesteps x natoms x 3. Initialized as FileContents prior to file reading.

• natoms – Number of atoms in each timestep

check_forces_less_than_value(value=0.001) → ndarray

Checks what timesteps have all forces less than value. The GP models will revert back to prior mean when far away from training data, so that the forces on atoms will be 0.

We can check for that because if the forces are consistently less than the value then either the simulation has crashed or a minimum is reached

Parameters:

value – Value for which all forces need to be less than

Returns:

np.ndarray containing timestep indices for which condition is true If len(array) is 0, then the condition is not met for any timestep. Could be useful to check if a geometry is optimized or simulation crashed.

classmethod check_path(path: Path) → bool

Checks the suffix of the given path matches the filetype associated with class that subclasses from File :param path: A Path object to check :return: True if the Path object has the same suffix as the class filetype, False otherwise

path: Path | str

class FFLUXDirectory(path: Path | str)

Bases: AnnotatedDirectory

READS a FFLUX Directory containing FFLUX, IQA_ENERGIES, IQA_FORCEs and HISTORY file

Parameters:

path – Path to FFLUX Directory

contents = {'fflux_file': <class 'ichor.core.files.dl_poly.dl_poly_fflux.DlPolyFFLUX'>, 'history_file': <class 'ichor.core.files.dl_poly.dl_poly_history.DlPolyHistory'>, 'iqa_energies_file': <class 'ichor.core.files.dl_poly.dl_poly_iqa_energies.DlPolyIQAEnergies'>, 'iqa_forces_file': <class 'ichor.core.files.dl_poly.dl_poly_iqa_forces.DlPolyIQAForces'>}

property coordinates: ndarray

Returns coordinates as array of shape ntimesteps x natoms x 3

property iqa_energies: ndarray

Returns individual atom iqa enegy array of shape ntimesteps x natoms

property iqa_forces: ndarray

Returns iqa forces array of shape ntimesteps x natoms x 3

property natoms: int

Returns number of atoms

path: Path | str

property total_iqa_energies: ndarray

Returns total energy array of shape ntimesteps