Optimize First-Principles-derived Tight-Binding Models¶
-
workchain
aiida_tbextraction.optimize_fp_tb.
OptimizeFirstPrinciplesTightBinding
Creates a tight-binding model by first running first-principles calculations to get a reference bandstructure and Wannier90 input, and then optimizing the energy window to get an optimized symmetric tight-binding model.
Inputs:
- code_tbmodels, Code, required – Code that runs the TBmodels CLI.
- cost_tol, Float, optional – Tolerance in the ‘cost_value’ for the window optimization.
- fp_run, Namespace – Inputs passed to the
fp_run_workflow
- fp_run_workflow, Str, required – Workflow which executes the first-principles calculations
- initial_window, List, optional – Initial value for the disentanglement energy windows, given as a list
[dis_win_min, dis_froz_min, dis_froz_max, dis_win_max]
. - kpoints, KpointsData, required – k-points on which the bandstructure is evaluated.
- kpoints_mesh, KpointsData, required – K-points mesh used when calculating the Wannier inputs.
- metadata, Namespace
Namespace Ports
- call_link_label, str, optional, non_db – The label to use for the CALL link if the process is called by another process.
- description, str, optional, non_db – Description to set on the process node.
- label, str, optional, non_db – Label to set on the process node.
- store_provenance, bool, optional, non_db – If set to False provenance will not be stored in the database.
- model_evaluation, Namespace – Inputs that will be passed to the
model_evaluation_workflow
. - model_evaluation_workflow, Str, required – AiiDA workflow that will be used to evaluate the tight-binding model.
- slice_reference_bands, List, optional – Indices for the reference bands which should be included in the model evaluation.
- slice_tb_model, List, optional – Indices for slicing (re-ordering) the tight-binding model.
- structure, StructureData, required – Structure of the material for which the tight-binding model should be calculated.
- symmetries, SinglefileData, optional – File containing the symmetries which will be applied to the tight-binding model. The file must be in
symmetry-representation
HDF5 format. - wannier, Namespace
Namespace Ports
- code, Code, required – The Code to use for this job.
- kpoint_path, Dict, optional – Description of the kpoints-path to be used for bands interpolation; it should contain two properties: a list ‘path’ of length-2 tuples with the labels of the endpoints of the path; and a dictionary ‘point_coords’ giving the scaled coordinates for each high-symmetry endpoint
- metadata, Namespace
Namespace Ports
- call_link_label, str, optional, non_db – The label to use for the CALL link if the process is called by another process.
- computer, Computer, optional, non_db – When using a “local” code, set the computer on which the calculation should be run.
- description, str, optional, non_db – Description to set on the process node.
- dry_run, bool, optional, non_db – When set to True will prepare the calculation job for submission but not actually launch it.
- label, str, optional, non_db – Label to set on the process node.
- options, Namespace
Namespace Ports
- account, str, optional, non_db – Set the account to use in for the queue on the remote computer
- append_text, str, optional, non_db – Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
- custom_scheduler_commands, str, optional, non_db – Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the prepend_text is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
- environment_variables, dict, optional, non_db – Set a dictionary of custom environment variables for this calculation
- import_sys_environment, bool, optional, non_db – If set to true, the submission script will load the system environment variables
- input_filename, str, optional, non_db – Filename to which the input for the code that is to be run will be written.
- max_memory_kb, int, optional, non_db – Set the maximum memory (in KiloBytes) to be asked to the scheduler
- max_wallclock_seconds, int, optional, non_db – Set the wallclock in seconds asked to the scheduler
- mpirun_extra_params, (list, tuple), optional, non_db – Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] … exec.x
- output_filename, str, optional, non_db – Filename to which the content of stdout of the code that is to be run will be written.
- parser_name, (str), optional, non_db
- prepend_text, str, optional, non_db – Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
- priority, str, optional, non_db – Set the priority of the job to be queued
- qos, str, optional, non_db – Set the quality of service to use in for the queue on the remote computer
- queue_name, str, optional, non_db – Set the name of the queue on the remote computer
- resources, dict, required, non_db – Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
- scheduler_stderr, str, optional, non_db – Filename to which the content of stderr of the scheduler will be written.
- scheduler_stdout, str, optional, non_db – Filename to which the content of stdout of the scheduler will be written.
- seedname, (str), optional, non_db
- withmpi, bool, optional, non_db
- store_provenance, bool, optional, non_db – If set to False provenance will not be stored in the database.
- projections, (OrbitalData, Dict, List), optional – Starting projections for the Wannierisation procedure
- settings, Dict, optional –
Additional settings to manage the Wannier90 calculation.
It can contain the following keys:
General options:
- random_projections: Enables using random projections if
or not enough projections are defined.
- postproc_setup: Use Wannier90 in ‘postproc_setup’ mode.
This affects which input and output files are expected.
File handling options:
- additional_remote_symlink_list: List of custom files to
link on the remote.
- additional_remote_copy_list: List of custom files to
copy from a source on the remote.
- additional_local_copy_list: List of custom files to copy
from a local source.
- additional_retrieve_list: List of additional filenames
to be retrieved.
- exclude_retrieve_list: List of filename patterns to
exclude from retrieving. Does not affect files listed in additional_retrieve_list.
- wannier_parameters, Dict, optional – Parameters of the Wannier calculation. This output needs to be set if the parameters are modified by the workchain in any way.
- wannier_projections, (OrbitalData, List), optional – Projections used in the Wannier90 calculation, given either as
OrbitalData
, or a list of strings corresponding to the lines in thewannier90.win
projections input block. - window_tol, Float, optional – Tolerance in energy windows for the window optimization.
Outputs:
- window, List, required
Outline:
fp_run(Runs the first-principles calculation workflow.) run_window_search(Runs the workflow which creates the optimized tight-binding model.) finalize(Add the outputs of the window_search sub-workflow.)
-
workchain
aiida_tbextraction.optimize_strained_fp_tb.
OptimizeStrainedFirstPrinciplesTightBinding
Workflow to optimize a DFT-based tight-binding model for different strain values.
Inputs:
- code_tbmodels, Code, required – Code that runs the TBmodels CLI.
- cost_tol, Float, optional – Tolerance in the ‘cost_value’ for the window optimization.
- fp_run, Namespace – Inputs passed to the
fp_run_workflow
- fp_run_workflow, Str, required – Workflow which executes the first-principles calculations
- initial_window, List, optional – Initial value for the disentanglement energy windows, given as a list
[dis_win_min, dis_froz_min, dis_froz_max, dis_win_max]
. - kpoints, KpointsData, required – k-points on which the bandstructure is evaluated.
- kpoints_mesh, KpointsData, required – K-points mesh used when calculating the Wannier inputs.
- metadata, Namespace
Namespace Ports
- call_link_label, str, optional, non_db – The label to use for the CALL link if the process is called by another process.
- description, str, optional, non_db – Description to set on the process node.
- label, str, optional, non_db – Label to set on the process node.
- store_provenance, bool, optional, non_db – If set to False provenance will not be stored in the database.
- model_evaluation, Namespace – Inputs that will be passed to the
model_evaluation_workflow
. - model_evaluation_workflow, Str, required – AiiDA workflow that will be used to evaluate the tight-binding model.
- slice_reference_bands, List, optional – Indices for the reference bands which should be included in the model evaluation.
- slice_tb_model, List, optional – Indices for slicing (re-ordering) the tight-binding model.
- strain_kind, Str, required
- strain_parameters, Str, required
- strain_strengths, List, required
- structure, StructureData, required
- symmetries, SinglefileData, required
- symmetry_repr_code, Code, required
- wannier, Namespace
Namespace Ports
- code, Code, required – The Code to use for this job.
- kpoint_path, Dict, optional – Description of the kpoints-path to be used for bands interpolation; it should contain two properties: a list ‘path’ of length-2 tuples with the labels of the endpoints of the path; and a dictionary ‘point_coords’ giving the scaled coordinates for each high-symmetry endpoint
- metadata, Namespace
Namespace Ports
- call_link_label, str, optional, non_db – The label to use for the CALL link if the process is called by another process.
- computer, Computer, optional, non_db – When using a “local” code, set the computer on which the calculation should be run.
- description, str, optional, non_db – Description to set on the process node.
- dry_run, bool, optional, non_db – When set to True will prepare the calculation job for submission but not actually launch it.
- label, str, optional, non_db – Label to set on the process node.
- options, Namespace
Namespace Ports
- account, str, optional, non_db – Set the account to use in for the queue on the remote computer
- append_text, str, optional, non_db – Set the calculation-specific append text, which is going to be appended in the scheduler-job script, just after the code execution
- custom_scheduler_commands, str, optional, non_db – Set a (possibly multiline) string with the commands that the user wants to manually set for the scheduler. The difference of this option with respect to the prepend_text is the position in the scheduler submission file where such text is inserted: with this option, the string is inserted before any non-scheduler command
- environment_variables, dict, optional, non_db – Set a dictionary of custom environment variables for this calculation
- import_sys_environment, bool, optional, non_db – If set to true, the submission script will load the system environment variables
- input_filename, str, optional, non_db – Filename to which the input for the code that is to be run will be written.
- max_memory_kb, int, optional, non_db – Set the maximum memory (in KiloBytes) to be asked to the scheduler
- max_wallclock_seconds, int, optional, non_db – Set the wallclock in seconds asked to the scheduler
- mpirun_extra_params, (list, tuple), optional, non_db – Set the extra params to pass to the mpirun (or equivalent) command after the one provided in computer.mpirun_command. Example: mpirun -np 8 extra_params[0] extra_params[1] … exec.x
- output_filename, str, optional, non_db – Filename to which the content of stdout of the code that is to be run will be written.
- parser_name, (str), optional, non_db
- prepend_text, str, optional, non_db – Set the calculation-specific prepend text, which is going to be prepended in the scheduler-job script, just before the code execution
- priority, str, optional, non_db – Set the priority of the job to be queued
- qos, str, optional, non_db – Set the quality of service to use in for the queue on the remote computer
- queue_name, str, optional, non_db – Set the name of the queue on the remote computer
- resources, dict, required, non_db – Set the dictionary of resources to be used by the scheduler plugin, like the number of nodes, cpus etc. This dictionary is scheduler-plugin dependent. Look at the documentation of the scheduler for more details.
- scheduler_stderr, str, optional, non_db – Filename to which the content of stderr of the scheduler will be written.
- scheduler_stdout, str, optional, non_db – Filename to which the content of stdout of the scheduler will be written.
- seedname, (str), optional, non_db
- withmpi, bool, optional, non_db
- store_provenance, bool, optional, non_db – If set to False provenance will not be stored in the database.
- projections, (OrbitalData, Dict, List), optional – Starting projections for the Wannierisation procedure
- settings, Dict, optional –
Additional settings to manage the Wannier90 calculation.
It can contain the following keys:
General options:
- random_projections: Enables using random projections if
or not enough projections are defined.
- postproc_setup: Use Wannier90 in ‘postproc_setup’ mode.
This affects which input and output files are expected.
File handling options:
- additional_remote_symlink_list: List of custom files to
link on the remote.
- additional_remote_copy_list: List of custom files to
copy from a source on the remote.
- additional_local_copy_list: List of custom files to copy
from a local source.
- additional_retrieve_list: List of additional filenames
to be retrieved.
- exclude_retrieve_list: List of filename patterns to
exclude from retrieving. Does not affect files listed in additional_retrieve_list.
- wannier_parameters, Dict, optional – Parameters of the Wannier calculation. This output needs to be set if the parameters are modified by the workchain in any way.
- wannier_projections, (OrbitalData, List), optional – Projections used in the Wannier90 calculation, given either as
OrbitalData
, or a list of strings corresponding to the lines in thewannier90.win
projections input block. - window_tol, Float, optional – Tolerance in energy windows for the window optimization.
Outputs:
None defined.
Outline:
run_strain(Apply strain to the initial structure to get the strained structures.) run_optimize_dft_tb(Run the tight-binding optimization for each strained structure.) finalize(Retrieve and output results.)