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434 lines (343 loc) · 21.6 KB
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================================================================================
Node: tb2j_wannier_spinor
Function Mapping: tbj2.nodes.wannier_spinor.tb2j_wannier_spinor
Description: Run ``wann2J.py --spinor`` for non-collinear / SOC Wannier90 Hamiltonians.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | tbj2.models.wannier_input.WannierSpinorInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : TB2J exchange-parameter output files
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: vasp_wannier_minimal
Function Mapping: vasp.nodes.vasp_wannier_minimal.vasp_wannier_minimal
Description: Run a minimal VASP (``LWANNIER90``) step, then Wannier90 on its interface files.
Both steps share the node workdir so ``wannier90*.mmn`` / ``.amn`` / ``.eig``
from ``vasp_run`` are visible to ``wannier90_run``.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | vasp.models.vasp_wannier_minimal.VaspWannierMinimalInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : Pipeline files from VASP and Wannier90
info_files | List[simstack.models.files.FileStack] | : Diagnostic files from both steps
efermi | simstack.models.base_types.FloatData | : Fermi energy from VASP when present
Called Nodes (Children):
- vasp.nodes.run_vasp.vasp_run
- vasp.nodes.run_wannier90.wannier90_run
--------------------------------------------------------------------------------
================================================================================
Node: tb2j_rotate
Function Mapping: tbj2.nodes.rotate.tb2j_rotate
Description: Run ``TB2J_rotate.py`` to generate rotated crystal structures.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | tbj2.models.rotate_input.TB2JRotateInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : Rotated ``atoms_*`` structure files
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: tb2j_siesta
Function Mapping: tbj2.nodes.siesta.tb2j_siesta
Description: Run ``siesta2J.py`` on Siesta Hamiltonian / overlap output.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | tbj2.models.siesta_input.SiestaInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : TB2J exchange-parameter output files
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: wannier90_run
Function Mapping: vasp.nodes.run_wannier90.wannier90_run
Description: Optionally write ``{seed}.win``, then run ``program.wannier90`` for each channel.
Binary / launcher come from ``config.toml``
(``[<resource>.program.wannier90] run_command``); each seedname is appended
as the Wannier90 seed argument. After a successful VASP ``LWANNIER90`` run,
``.mmn`` / ``.amn`` / ``.eig`` must be present. Produces ``*_hr.dat`` and
``*_centres.xyz`` for TB2J.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | vasp.models.wannier90_input.Wannier90RunInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : Wannier90 ``*_hr.dat`` / ``*_centres.xyz`` (and related) outputs
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: async_adder
Function Mapping: simstack.methods.multiple_executor.async_adder
Description: WARNING: Missing description
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
arg | simstack.models.base_types.BinaryOperationInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
result | simstack.models.base_types.FloatData | None
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: multiple_executor
Function Mapping: simstack.methods.multiple_executor.multiple_executor
Description: WARNING: Missing description
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
executor | simstack.methods.multiple_executor.MultipleExecutorInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
result | simstack.methods.multiple_executor.MultipleExecutorOutput | None
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: multiple_executor_adder
Function Mapping: simstack.methods.multiple_executor.multiple_executor_adder
Description: WARNING: Missing description
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
arg1 | simstack.models.base_types.BinaryOperationInput | None
arg2 | simstack.models.base_types.BinaryOperationInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
result | simstack.models.base_types.BinaryOperationInput | None
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: archive_upload
Function Mapping: simstack.methods.upload_helpers.archive_upload
Description: Asynchronously processes a file upload, extracts files from supported archive formats
(.zip, .tar, .tar.gz), and returns a list of extracted files wrapped in FileStack
instances. If the file is not an archive, it is added as-is to the output.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
file_upload | simstack.models.files.FileStack | The uploaded file to be processed.
**kwargs: Additional keyword arguments.
Result Mappings:
(none)
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: file_list_upload_all
Function Mapping: simstack.methods.upload_helpers.file_list_upload_all
Description: WARNING: Missing description
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
file_stack | simstack.models.files.FileStack | None
Result Mappings:
(none)
Called Nodes (Children):
- simstack.methods.upload_helpers.archive_upload
- simstack.methods.upload_helpers.file_list_upload_test
--------------------------------------------------------------------------------
================================================================================
Node: file_list_upload_test
Function Mapping: simstack.methods.upload_helpers.file_list_upload_test
Description: WARNING: Missing description
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
file_list | simstack.models.file_list.FileListModel | None
Result Mappings:
(none)
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: archive_file
Function Mapping: simstack.methods.archive_files.archive_file
Description: WARNING: Missing description
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
file_stack | simstack.models.files.FileStack | None
Result Mappings:
(none)
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: archive_files
Function Mapping: simstack.methods.archive_files.archive_files
Description: WARNING: Missing description
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
file_list | simstack.models.file_list.FileList | None
Result Mappings:
(none)
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: archive_node
Function Mapping: simstack.methods.archive_files.archive_node
Description: Archives FileStacks matching the criteria in archive_config and deletes local instances upon success.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
archive_config | simstack.methods.archive_files.ArchiveConfig | Configuration for the archive process.
**kwargs: Additional arguments.
Result Mappings:
(none)
Called Nodes (Children):
- simstack.methods.archive_files.archive_files
--------------------------------------------------------------------------------
================================================================================
Node: tb2j_wannier_collinear
Function Mapping: tbj2.nodes.wannier_collinear.tb2j_wannier_collinear
Description: Run ``wann2J.py`` for collinear (up/down) Wannier90 Hamiltonians.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | tbj2.models.wannier_input.WannierCollinearInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : TB2J exchange-parameter output files
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: get_file
Function Mapping: simstack.methods.get_file.get_file
Description: Retrieves a file from a given source and saves it to the specified target path.
This function is responsible for handling the retrieval of files from a
FileStack source and storing them to a local resource's target location.
It will update the FileStack
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
file_getter_args | simstack.models.files.FileGetterArgs | The arguments for the file retrieval operation.
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
result | simstack.models.files.FileStack | FileStack: The modified FileStack with the local resource.
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: switch_git
Function Mapping: simstack.methods.switch_git.switch_git
Description: WARNING: Missing description
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
branch | simstack.models.base_types.StringData | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
result | builtins.bool | None
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: vasp_wannier_tb2j
Function Mapping: master.nodes.vasp_wannier_tb2j.vasp_wannier_tb2j
Description: Run the collinear or spinor magnetism pipeline end-to-end.
1. ``vasp_run`` (expects ``LWANNIER90`` / interface files)
2. ``wannier90_run``
3. ``vasp_stage_wannier_for_tb2j`` (sets ``efermi`` as ``FloatData``)
4. ``tb2j_wannier_collinear`` or ``tb2j_wannier_spinor``
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | master.models.workflow_input.VaspWannierTB2JInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : Aggregated files from VASP, Wannier90, and TB2J steps
efermi | simstack.models.base_types.FloatData | : Fermi energy (eV) used for TB2J
Called Nodes (Children):
- tbj2.nodes.wannier_collinear.tb2j_wannier_collinear
- tbj2.nodes.wannier_spinor.tb2j_wannier_spinor
- vasp.nodes.run_vasp.vasp_run
- vasp.nodes.run_wannier90.wannier90_run
- vasp.nodes.stage_tb2j.vasp_stage_wannier_for_tb2j
--------------------------------------------------------------------------------
================================================================================
Node: tb2j_merge
Function Mapping: tbj2.nodes.merge.tb2j_merge
Description: Run ``TB2J_merge.py`` on rotated TB2J result directories.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | tbj2.models.merge_input.TB2JMergeInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : Merged TB2J exchange-parameter output files
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: vasp_run
Function Mapping: vasp.nodes.run_vasp.vasp_run
Description: Write INCAR/KPOINTS/POSCAR/POTCAR in cwd, then run ``program.vasp``.
Binary and launcher come from ``config.toml``
(``[<resource>.program.vasp] run_command``). MPI size is taken from the
Slurm allocation on ``kwargs["parent_parameters"]`` (do not pass a local
``mpi_prefix``). Parses ``E-fermi`` from OUTCAR onto ``node_runner.efermi``.
Pipeline outputs (Wannier90 interface files) go to ``files`` with
``in_memory=False`` and ``secure_source=True``. Inputs and diagnostic
VASP outputs go to ``info_files`` only.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | vasp.models.vasp_input.VaspJobInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : Wannier90 interface files for downstream nodes
info_files | List[simstack.models.files.FileStack] | : Inputs and diagnostic VASP outputs
efermi | simstack.models.base_types.FloatData | : Fermi energy from OUTCAR (eV), when parseable
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------
================================================================================
Node: vasp_stage_wannier_for_tb2j
Function Mapping: vasp.nodes.stage_tb2j.vasp_stage_wannier_for_tb2j
Description: Confirm TB2J-ready Wannier files exist and expose ``efermi`` for wann2J.
Collinear: ``prefix_up`` / ``prefix_down``. Spinor: ``prefix_spinor``.
Hand off to ``tbj2.tb2j_wannier_collinear`` / ``tbj2_wannier_spinor``.
Input Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
opts | vasp.models.wannier90_input.StageWannierForTB2JInput | None
Result Mappings:
Arg Name | Model | Field
---------------------+----------------------------------------------------+---------------------
files | List[simstack.models.files.FileStack] | : Staged Wannier90 Hamiltonian / centres files for TB2J
efermi | simstack.models.base_types.FloatData | : Fermi energy (eV) for wann2J
Called Nodes (Children):
(none)
--------------------------------------------------------------------------------