malada.utils package¶

Submodules¶

malada.utils.cell_transformations module¶

WILL BE DELETED: Transformation matrices for supercell creation.

malada.utils.convergence_guesses module¶

Initial guesses for convergence calculations.

malada.utils.custom_converter module¶

Collection of custom converters.

malada.utils.custom_converter.kelvin_to_eV(temperature_K)¶

Convert a temperature from Kelvin to electron volts.

Parameters: temperature_K (float) – Temperature in Kelvin.
Returns: temperature_Ry – Temperature expressed in electron volts.
Return type: float

malada.utils.custom_converter.kelvin_to_rydberg(temperature_K)¶

Convert a temperature from Kelvin to Rydberg energy units.

Parameters: temperature_K (float) – Temperature in Kelvin.
Returns: temperature_Ry – Temperature expressed in Rydberg.
Return type: float

malada.utils.custom_converter.second_to_rydberg_time(time_s)¶

Convert a time from second to Rydberg unit time.

This is used in e.g. QE.

Parameters: time_s (float) – Time in seconds.
Returns: time_ry – Time in Rydberg unit time.
Return type: float

malada.utils.parameters module¶

Collection of all parameters for the pipeline.

class malada.utils.parameters.Parameters¶

Bases: object

Holds parameters needed for constructing a data acqusition pipeline.

temperature¶

Temperature in K.

Type: float

number_of_atoms¶

Number of atoms in supercell.

Type: int

crystal_structure¶

Crystal structure, this is used for supercell creation because it determines the transformations.

Type: string

element¶

Name of the element for which to generate data.

Type: string

base_folder¶

Base folder to operate in.

Type: string

dft_calculator¶

Name of the DFT calculator, currently only QuantumESPRESSO and VASP are supported.

Type: string

md_calculator¶

Name of the DFT-MD calculator, currently only QuantumESPRESSO and VASP are supported.

Type: string

pseudopotential¶

Dictionary for the pseudopotential. Needs to contain “path” for path to pseudopotential, “name” for name, and “valence_electrons” for number of valence electrons.

Type: dict

run_system¶

Run system used during pipeline, currently only “bash” and “slurm_creator” are supported.

Type: string

dft_slurm¶

Slurm parameters used for DFT calculations

Type: malada.SlurmParameters

md_slurm¶

Slurm parameters used for DFT-MD calculations. Please note that these should not be set here, as they will be overwritten in the pipeline.

Type: malada.SlurmParameters

dft_conv_accuracy_meVperatom¶

Accuracy of the DFT convergence calculations in meV/atom.

Type: float

maximum_cutoff_try¶

Maxmimum number of cutoff convergence iterations. If the optimal cutoff is not found with initial values, calculation of it it is retried maximum_cutoff_try number of times.

Type: int

maximum_kpoint_try¶

Maxmimum number of k-grid convergence iterations. If the optimal k-grid is not found with initial values, calculation of it it is retried maximum_kpoint_try number of times.

Type: int

dft_scf_accuracy_per_atom_Ry¶

Accuracy of all DFT calculation in terms of total energy/per atom.

Type: float

md_at_gamma_point¶

If True, MD simulations will be run at the gamma point.

Type: bool

maximum_number_of_timesteps¶

Maximum number of timesteps for MD calculation.

Type: int

time_step_fs¶

Timestep for MD calculation in fs.

Type: float

md_thermostat_controller¶

Thermostat controller for MD calculation. This is “NRAISE” for QE and “SMASS” for VASP.

Type: float

snapshot_parsing_beginning¶

The snapshot after which snapshot parsing is started. If < 0 automatic detection of this snapshot will be performed (currently not supported)

Type: int

snapshot_parsing_temperature_tolerance_percent¶

Maximum deviation of temperature between snapshot and desired temperature for snapshot to be considered for DFT calculation (in percent)

Type: float

snapshot_parsing_criterion¶

Criterion with which to parse the snapshots, currently only “random” is supported.

Type: string

number_of_snapshots¶

Number of snapshots the pipeline shoudl generate.

Type: int

distance_metric_snapshots¶

Distance metric to determine how alike two atomic snapshots are. Currently only “realspace”, i.e. the realspace distance between atoms is calculated.

Type: string

distance_metric_snapshots_cutoff¶

Minimum distance in terms of distance_metric_snapshots after which after which two snapshots are considered distinct by the algorithm.

Type: float

number_of_bands_factor¶

Determines how many more many more bands then number of electrons will be used. E.g. if =0.05, the overall number of bands will be the number of electrons times 1.05. Has to be scaled with temperature. Default is 0.05, which should be ok up to ~2500K.

Type: float

malada.utils.slurmparams module¶

Parameters to create a slurm run script.

class malada.utils.slurmparams.SlurmParameters¶

Bases: object

Class holding slurm parameters.

scf_executable¶

Executable called for the DFT/MD calculation.

Type: string

module_loading_string¶

String to be executed prior to regular execution. Contains e.g. module loading on HPC infrastructures.

Type: string

execution_time¶

Runtime of job in hours.

Type: int

partition_string¶

String to be written on the top of a batch script containing information about which partition/account to use.

Type: string

mpi_runner¶

MPI executable to be called for MPI jobs. There can be considerable differences in using mpiexec vs. mpirun.

Type: string

tasks_per_node¶

Number of tasks per node.

Type: int

nodes¶

Number of nodes.

Type: int

classmethod from_xml(filename)¶

Create a SlurmParameters object from an xml file.

Parameters: filename (string) – Path to file from which to create the parameters.
Returns: slurm_parameters – The new parameters with values from the file
Return type: SlurmParameters

get_mpirunner_process_params()¶

Get the correct call parameter for the number of processes.

For srun it is “-n”, for mpiexec it is “-np”, etc.

Returns: processparameter – The correct call parameter for this type of MPI runner.
Return type: string

save(filename)¶

Save the parameters to a xml file.

Parameters: filename (string) – Path to file to save parameters to.

malada.utils.vasp_utils module¶

Utilities for setting up VASP calculations.

class malada.utils.vasp_utils.VaspUtils¶

Bases: object

Collection of functions to write to VASP files other then POSCAR.

static write_to_incar(folder, vasp_array)¶

Write a dictionary of VASP input quantities to an INCAR file.

Currently, there is NO sanity checking done here. Meaning that wrong INCAR files can be reated very easily.

Parameters

folder (string) – Path to where to write the INCAR file.
vasp_array (dict) – Dictionary of VASP quantities.

static write_to_kpoints(folder, kgrid)¶

Write a k-grid to VASP KPOINTS file.

Parameters

folder (string) – Path to where to write the INCAR file.
kgrid (tuple) – k-grid to write in form of (kx, ky, kz).

static write_to_potcar_copy(folder, pspstring)¶

Create a file that will copy the POTCAR file to the run folder.

VASP always looks for the POTCAR (PSP) in the current folder. Therefore, before running, we have to copy it.

Parameters

folder (string) – Path tto where to create this script.
pspstring (string) – Path to POTCAR file.

Module contents¶

MALADA utils provides utilities for building data acquistion pipelines.