matador.workflows.castep package¶

The workflows.castep submodule contains any workflows that rely on CASTEP-specific implementation, for example electronic spectropscopy or phonons.

matador.workflows.castep.castep_full_phonon(computer, calc_doc, seed, **kwargs)[source]¶

Perform a “full” phonon calculation on a system, i.e. first perform a relaxation in a standardised unit cell, then compute the dynamical matrix, then finally interpolate that dynamical matrix into dispersion curves and DOS. This function is a wrapper for the CastepPhononWorkflow class.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

Returns:

True if Workflow completed successfully, or False otherwise.

Return type:

bool

matador.workflows.castep.castep_full_spectral(computer, calc_doc, seed, **kwargs)[source]¶

Perform a “full” spectral calculation on a system, i.e. first perform an SCF then interpolate to different kpoint paths/grids to form DOS and dispersions. Optionally use OptaDOS for post-processing of DOS.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

Returns:

True if Workflow completed successfully, or False otherwise.

Return type:

bool

matador.workflows.castep.castep_elastic(computer, calc_doc, seed, **kwargs)[source]¶

Perform a calculation of the elastic tensor on a system. Currently only calculation of the bulk modulus is implemented.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

Returns:

True if Workflow completed successfully, or False otherwise.

Return type:

bool

matador.workflows.castep.castep_full_magres(computer, calc_doc, seed, final_elec_energy_tol=1e-11, **kwargs)[source]¶

Perform a “full” magres calculation on a system, i.e. first perform a relaxation, then do a high quality SCF and compute NMR properties in the same step.

This function is a wrapper for the CastepMagresWorkflow class.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

Returns:

True if Workflow completed successfully, or False otherwise.

Return type:

bool

Submodules¶

matador.workflows.castep.common module¶

This submodule implements some common workflow steps for use in more complicated workflows.

matador.workflows.castep.common.castep_prerelax(computer, calc_doc, seed, write_checkpoint='all', required_keys=None, forbidden_keys=None)[source]¶

Run a self-consistent (i.e. restarted) geometry optimisation. Optionally write a check file containing the final structure and density.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

Keyword Arguments:

write_checkpoint (bool or str) – keyword to pass to CASTEP’s write_checkpoint parameter. If True (False), CASTEP parameter set to ALL (NONE).
required_keys (list of str) – list of keys required in calc doc to perform the calculation.
forbidden_keys (list of str) – list of keys to scrub from calc doc to perform the calculation.

Returns:

whether or not the relaxation was successful.

Return type:

bool

matador.workflows.castep.common.castep_scf(computer, calc_doc, seed, elec_energy_tol=None, write_checkpoint='ALL', required_keys=None, forbidden_keys=None)[source]¶

Run a singleshot SCF calculation.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

Keyword Arguments:

elec_energy_tol (float or str) – keyword to pass to elec_energy_tol.
write_checkpoint (bool or str) – keyword to pass to CASTEP’s write_checkpoint parameter. If True (False), CASTEP parameter set to ALL (NONE).
required_keys (list of str) – list of keys required in calc doc to perform the calculation.
forbidden_keys (list of str) – list of keys to scrub from calc doc to perform the calculation.

Returns:

whether or not the SCF was successful.

Return type:

bool

matador.workflows.castep.elastic module¶

This module implements the CastepElasticWorkflow, which performs elastic tensor calculations with CASTEP. So far, only bulk modulus calculations (i.e. varying volume from equilibrium) have been implemented.

matador.workflows.castep.elastic.castep_elastic(computer, calc_doc, seed, **kwargs)[source]¶

Perform a calculation of the elastic tensor on a system. Currently only calculation of the bulk modulus is implemented.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

Returns:

True if Workflow completed successfully, or False otherwise.

Return type:

bool

class matador.workflows.castep.elastic.CastepElasticWorkflow(computer, calc_doc, seed, **workflow_kwargs)[source]¶

Bases: Workflow

Perform a “full” spectral calculation on a system, i.e. first perform an SCF then interpolate to different kpoint paths/grids to form DOS and dispersions. Optionally use OptaDOS for post-processing of DOS.

computer¶

the object that calls CASTEP.

Type:: ComputeTask

calc_doc¶

the interim dictionary of structural and calculation parameters.

Type:: dict

seed¶

the root seed for the calculation.

Type:: str

volume_rescale¶

a list of floats containing the amounts by which to rescale volumes when performing bulk modulus calculation.

Type:: list

success¶

the status of the Workflow: only set to True after post-processing method completes.

Type:: bool

Initialise the Workflow object from a matador.compute.ComputeTask, calculation parameters and the seed name.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be running the computation.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

preprocess()[source]¶: Decide which parts of the Workflow need to be performed, and set the appropriate CASTEP parameters.

postprocess()[source]¶: Fit some equations of state, then save a plot and a datafile.

matador.workflows.castep.elastic.castep_rescaled_volume_scf(computer, calc_doc, seed, rescale=1)[source]¶

Run a singleshot SCF calculation.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

Keyword Arguments:

rescale (float) – amount to rescale volume by.

matador.workflows.castep.elastic.castep_elastic_prerelax(computer, calc_doc, seed)[source]¶

Run a geometry optimisation before re-scaling volumes SCF-style calculation.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.magres module¶

This module implements the CastepMagresWorkflow class, which performs magres calculations with CASTEP in multiple steps (only when necessary):

Try to pre-relax structure (skipped if check file is already present).

Perform an SCF with lower electronic tolerances.

Calculate NMR properties, e.g. shielding and EFG.

matador.workflows.castep.magres.castep_full_magres(computer, calc_doc, seed, final_elec_energy_tol=1e-11, **kwargs)[source]¶

Perform a “full” magres calculation on a system, i.e. first perform a relaxation, then do a high quality SCF and compute NMR properties in the same step.

This function is a wrapper for the CastepMagresWorkflow class.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

Returns:

True if Workflow completed successfully, or False otherwise.

Return type:

bool

class matador.workflows.castep.magres.CastepMagresWorkflow(computer, calc_doc, seed, **workflow_kwargs)[source]¶

Bases: Workflow

Perform a “full” magres calculation on a system, i.e. first perform a relaxation in a standardised unit cell, then do a high quality SCF, then compute NMR properties.

computer¶

the object that calls CASTEP.

Type:: ComputeTask

calc_doc¶

the interim dictionary of structural and calculation parameters.

Type:: dict

seed¶

the root seed for the calculation.

Type:: str

success¶

the status of the Workflow: only set to True after post-processing method completes.

Type:: bool

final_elec_energy_tol¶

the electronic energy tolerance to use in the high-quality SCF calculation.

Type:: float

Initialise the Workflow object from a matador.compute.ComputeTask, calculation parameters and the seed name.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be running the computation.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

preprocess()[source]¶: Decide which parts of the Workflow need to be performed, and set the appropriate CASTEP parameters.

matador.workflows.castep.magres.castep_magres_scf(computer, calc_doc, seed, elec_energy_tol=1e-11)[source]¶

Run a singleshot SCF calculation with a high elec_energy_tol.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

Returns:

whether or not the SCF was successful.

Return type:

bool

matador.workflows.castep.magres.castep_magres(computer, calc_doc, seed, elec_energy_tol=1e-11)[source]¶

Runs a NMR properties calculation on top of a completed SCF calculation.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.phonons module¶

This module implements the CastepPhononWorkflow class, which performs phonon calculations with CASTEP in multiple steps (only when necessary):

Try to pre-relax structure (skipped if check file
is already present).

Calculate dynamical matrix.

If phonon_fine_kpoint_mp_spacing keyword is found, interpolate dynamical matrix to form phonon DOS.

If phonon_fine_kpoint_path_spacing key word is found, interpolate dynamical matrix to form phonon dispersion on the path given by seekpath.

If task=thermodynamics, perform a CASTEP thermodynamics calculation for the temperature-dependence of the free energy.

matador.workflows.castep.phonons.castep_full_phonon(computer, calc_doc, seed, **kwargs)[source]¶

Perform a “full” phonon calculation on a system, i.e. first perform a relaxation in a standardised unit cell, then compute the dynamical matrix, then finally interpolate that dynamical matrix into dispersion curves and DOS. This function is a wrapper for the CastepPhononWorkflow class.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

Returns:

True if Workflow completed successfully, or False otherwise.

Return type:

bool

class matador.workflows.castep.phonons.CastepPhononWorkflow(computer, calc_doc, seed, **workflow_kwargs)[source]¶

Bases: Workflow

Perform a “full” phonon calculation on a system, i.e. first perform a relaxation in a standardised unit cell, then compute the dynamical matrix, then finally interpolate that dynamical matrix into dispersion curves and DOS.

computer¶

the object that calls CASTEP.

Type:: ComputeTask

calc_doc¶

the interim dictionary of structural and calculation parameters.

Type:: dict

seed¶

the root seed for the calculation.

Type:: str

success¶

the status of the Workflow: only set to True after post-processing method completes.

Type:: bool

Initialise the Workflow object from a matador.compute.ComputeTask, calculation parameters and the seed name.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be running the computation.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

preprocess()[source]¶: Decide which parts of the Workflow need to be performed, and set the appropriate CASTEP parameters.

matador.workflows.castep.phonons.castep_phonon_prerelax(computer, calc_doc, seed)[source]¶

Run a singleshot geometry optimisation before an SCF-style calculation. This is typically used to ensure phonon calculations start successfully. The phonon calculation will then be restarted from the .check file produced here.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.phonons.castep_phonon_dynmat(computer, calc_doc, seed)[source]¶

Runs a singleshot phonon dynmat calculation, with no “fine_method” interpolation.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.phonons.castep_phonon_dos(computer, calc_doc, seed)[source]¶

Runs a DOS interpolation on top of a completed phonon calculation.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.phonons.castep_phonon_dispersion(computer, calc_doc, seed)[source]¶

Runs a dispersion interpolation on top of a completed phonon calculation.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.phonons.castep_phonon_thermodynamics(computer, calc_doc, seed)[source]¶

Runs a “thermodynamics” interpolation on top of a completed phonon calculation, using the phonon_fine_kpoint_mp_grid.

Parameters:

computer (ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.spectral module¶

This module implements the CastepSpectralWorkflow, which performs spectral calculations with CASTEP in multiple steps:

Performs a singlepoint calculation (if check file is not found).
If the spectral_kpoints_mp_spacing keyword is found, interpolate wavefunction to DOS grid. - If an OptaDOS input file (.odi) with the root seedname

is found, run OptaDOS on the resulting density of states.
If spectral_kpoints_path_spacing keyword is present, create a bandstructure on the SeeK-path generated path.

matador.workflows.castep.spectral.castep_full_spectral(computer, calc_doc, seed, **kwargs)[source]¶

Perform a “full” spectral calculation on a system, i.e. first perform an SCF then interpolate to different kpoint paths/grids to form DOS and dispersions. Optionally use OptaDOS for post-processing of DOS.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

Returns:

True if Workflow completed successfully, or False otherwise.

Return type:

bool

class matador.workflows.castep.spectral.CastepSpectralWorkflow(computer, calc_doc, seed, **workflow_kwargs)[source]¶

Bases: Workflow

Perform a “full” spectral calculation on a system, i.e. first perform an SCF then interpolate to different kpoint paths/grids to form DOS and dispersions. Optionally use OptaDOS for post-processing of DOS.

computer¶

the object that calls CASTEP.

Type:: matador.compute.ComputeTask

calc_doc¶

the interim dictionary of structural and calculation parameters.

Type:: dict

seed¶

the root seed for the calculation.

Type:: str

success¶

the status of the Workflow: only set to True after post-processing method completes.

Type:: bool

Initialise the Workflow object from a matador.compute.ComputeTask, calculation parameters and the seed name.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be running the computation.
calc_doc (dict) – dictionary of structure and calculation parameters.
seed (str) – root seed for the calculation.

Raises:

RuntimeError – if any part of the calculation fails.

preprocess()[source]¶: Decide which parts of the Workflow need to be performed, and set the appropriate CASTEP parameters.

matador.workflows.castep.spectral.castep_spectral_scf(computer, calc_doc, seed)[source]¶

Run a singleshot SCF calculation.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.spectral.castep_spectral_dos(computer, calc_doc, seed)[source]¶

Runs a DOS interpolation on top of a completed SCF. If a single .odi file is found, run OptaDOS on the resulting DOS.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.spectral.castep_spectral_dispersion(computer, calc_doc, seed)[source]¶

Runs a dispersion interpolation on top of a completed SCF calculation, optionally running orbitals2bands and OptaDOS projected dispersion.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling CASTEP.
calc_doc (dict) – the structure to run on.
seed (str) – root filename of structure.

matador.workflows.castep.spectral.optados_pdos(computer, _, seed)[source]¶

Run an OptaDOS projected-DOS.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling OptaDOS.
_ – second parameter is required but ignored.
seed (str) – root filename of structure.

matador.workflows.castep.spectral.optados_dos_broadening(computer, _, seed)[source]¶

Run an OptaDOS total DOS broadening.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling OptaDOS.
_ – second parameter is required but ignored.
seed (str) – root filename of structure.

matador.workflows.castep.spectral.optados_pdispersion(computer, _, seed)[source]¶

Runs an OptaDOS projected dispersion calculation.

Parameters:

computer (matador.compute.ComputeTask) – the object that will be calling OptaDOS.
_ – second parameter is required but ignored.
seed (str) – root filename of structure.