X-ray Absorption Near Edge Structure (XANES)

For the source code, see xas.

Visualizing the WorkGraph Builder

from workgraph_collections.ase.espresso.xas import xas_workgraph
from aiida import load_profile
load_profile()

task = xas_workgraph.task()
task.to_html()

Visualizing the WorkGraph

from workgraph_collections.ase.espresso.xas import xas_workgraph
from aiida import load_profile
load_profile()

wg = xas_workgraph()
wg.to_html()

Example: Silicon XANES

Prepare the inputs and submit the workflow

from ase.io import read
from aiida import load_profile
from workgraph_collections.ase.espresso.xas import xas_workgraph
from ase.build import bulk

load_profile()

atoms = bulk('Si')


metadata = {
    "options": {
        'prepend_text' : """eval "$(conda shell.posix hook)"
        conda activate aiida
        export OMP_NUM_THREADS=1
        """,
    }
}

input_data = {
        "CONTROL": {
            "calculation": "scf",
        },
        "SYSTEM": {
            "ecutwfc": 40,
            "ecutrho": 320,
            "occupations": "fixed",
        },
    }
kpts = (4, 4, 4)
# pseudo_dir = "/home/xing/data/ase/espresso_pseudo"
pseudo_dir = "/home/wang_x3/datas/pseudos/xas"
# Pseudos from https://github.com/PNOGillespie/Core_Level_Spectra_Pseudos
pseudopotentials = {"Si": "Si.pbe-van_gipaw.UPF"}
core_hole_pseudos = {
    "Si": "Si.star1s-pbe-van_gipaw.UPF",
}
#
metadata = {
    "options": {
        'prepend_text' : """eval "$(conda shell.posix hook)"
        conda activate aiida
        export OMP_NUM_THREADS=1
        """,
    }
}
inputs = {
    "pw": {
        "computer": "localhost",
        "metadata": metadata,
        "input_data": input_data,
        "kpts": kpts,
        "pseudopotentials": pseudopotentials,
        "pseudo_dir": pseudo_dir,
    },
    "xspectra": {
        "computer": "localhost",
        "metadata": metadata,
        "kpts": kpts,
        "input_data": {
            "INPUT_XSPECTRA":{
                "calculation": "xanes_dipole",
                "prefix": "pwscf",
                "xonly_plot": False,
                "xniter": 2000,
                "xcheck_conv": 10,
                "xerror": 0.001},
            "PLOT":{
                "xgamma": 0.5,
                "xnepoint": 2000,
                "xemin": -10,
                "xemax": 30,
                "terminator": True,
                "cut_occ_states": True,
                },
            "CUT_OCC":{
                "cut_desmooth": 0.1,
            }
        },
    }
}
# ===============================================================================
wg = xas_workgraph(
    atoms=atoms,
    commands={"pw": "mpirun -np 4 pw.x",
              "xspectra": "mpirun -np 4 xspectra.x"},
    element_list=["Si"],
    inputs=inputs,
    eps_vectors=[[1., 0., 0.]],
    core_hole_pseudos=core_hole_pseudos,
    core_hole_treatment="FULL",
    metadata=metadata,
    is_molecule=False,
)
wg.name = "ASE-espresso-XAS-Si"
# wg.run()
wg.submit(wait=True, timeout=300)

06/13/2024 02:59:52 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: Continue workgraph.

update_nested_dict:  AttributeDict({'_awaitable_actions': [], 'new_data': {}, 'input_nodes': {}, 'max_number_awaitables': 1000000, '_count': 0}) sequence []
Continue workgraph.

06/13/2024 02:59:53 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: nodes ready to run: marked_atoms
06/13/2024 02:59:53 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|run_nodes]: Run node: marked_atoms, type: PYTHONJOB

------------------------------------------------------------
executor:  <function get_non_equivalent_site at 0x7f0c943b4700>
args:  []
kwargs:  {'atoms': <AtomsData: uuid: 0c34a1e7-1918-4f04-a0de-05afb6440643 (pk: 21474) : Atoms(symbols='Si2', pbc=True, cell=[[0.0, 2.715, 2.715], [2.715, 0.0, 2.715], [2.715, 2.715, 0.0]])>, 'min_cell_length': <Float: uuid: 126f806e-136c-44a1-9f91-1914a9f29381 (pk: 21475) value: 4.0>, 'element_list': <List: uuid: 658af454-4a35-4ec9-ac86-44860870ad64 (pk: 21476) value: ['Si']>, 'marker': <Str: uuid: e96ed2e7-6c41-4607-b073-865ca5283838 (pk: 21477) value: X>, 'is_molecule': <Bool: uuid: 5f373e55-a6ce-470a-8a81-c57a10cae4a0 (pk: 21478) value: False>, 'metadata': {'options': {'prepend_text': 'eval "$(conda shell.posix hook)"\n        conda activate aiida\n        export OMP_NUM_THREADS=1\n        '}}}
var_kwargs:  None
node  type: Python.
node:  marked_atoms RUNNING
node:  run_all_xspectra_prod CREATED
is workgraph finished:  False

06/13/2024 02:59:56 PM <2852041> aiida.execmanager: [WARNING] failed to load Node<44ef551d-cc85-4132-8ad3-5db1e5a90eaa> specified in the `local_copy_list`
06/13/2024 03:00:02 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|set_node_result]: Node: marked_atoms finished.

on awaitable finished:  marked_atoms
update node state:  marked_atoms

06/13/2024 03:00:03 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: Continue workgraph.

Continue workgraph.

06/13/2024 03:00:03 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: nodes ready to run: run_all_xspectra_prod
06/13/2024 03:00:03 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|run_nodes]: Run node: run_all_xspectra_prod, type: graph_builder

------------------------------------------------------------
executor:  <function run_all_xspectra_prod at 0x7f0c943c6d40>
args:  [<GeneralData: uuid: 5f26038a-fe91-4b00-aa90-a99024b7ffa4 (pk: 21487) : {'supercell': {'atoms': Atoms(symbols='Si2', pbc=True, cell=[[0.0, 2.715, 2.715], [2.715, 0.0, 2.715], [2.715, 2.715, 0.0]])}, 'Si_0': {'symbol': 'Si', 'atoms': Atoms(symbols='XSi15', pbc=True, cell=[[0.0, 5.43, 5.43], [5.43, 0.0, 5.43], [5.43, 5.43, 0.0]]), 'indices': [0, 1]}}>]
kwargs:  {'commands': {'pw': 'mpirun -np 4 pw.x', 'xspectra': 'mpirun -np 4 xspectra.x'}, 'inputs': {'pw': {'computer': 'localhost', 'input_data': {'CONTROL': {'calculation': 'scf'}, 'SYSTEM': {'ecutrho': 320, 'ecutwfc': 40, 'occupations': 'fixed'}}, 'kpts': (4, 4, 4), 'metadata': {'options': {'prepend_text': 'eval "$(conda shell.posix hook)"\n        conda activate aiida\n        export OMP_NUM_THREADS=1\n        '}}, 'pseudo_dir': '/home/wang_x3/datas/pseudos/xas', 'pseudopotentials': {'Si': 'Si.pbe-van_gipaw.UPF'}}, 'xspectra': {'computer': 'localhost', 'input_data': {'CUT_OCC': {'cut_desmooth': 0.1}, 'INPUT_XSPECTRA': {'calculation': 'xanes_dipole', 'prefix': 'pwscf', 'xcheck_conv': 10, 'xerror': 0.001, 'xniter': 2000, 'xonly_plot': False}, 'PLOT': {'cut_occ_states': True, 'terminator': True, 'xemax': 30, 'xemin': -10, 'xgamma': 0.5, 'xnepoint': 2000}}, 'kpts': (4, 4, 4), 'metadata': {'options': {'prepend_text': 'eval "$(conda shell.posix hook)"\n        conda activate aiida\n        export OMP_NUM_THREADS=1\n        '}}}}, 'eps_vectors': [[1.0, 0.0, 0.0]], 'core_hole_pseudos': {'Si': 'Si.star1s-pbe-van_gipaw.UPF'}, 'core_hole_treatment': 'FULL', 'marked_atoms': <GeneralData: uuid: 5f26038a-fe91-4b00-aa90-a99024b7ffa4 (pk: 21487) : {'supercell': {'atoms': Atoms(symbols='Si2', pbc=True, cell=[[0.0, 2.715, 2.715], [2.715, 0.0, 2.715], [2.715, 2.715, 0.0]])}, 'Si_0': {'symbol': 'Si', 'atoms': Atoms(symbols='XSi15', pbc=True, cell=[[0.0, 5.43, 5.43], [5.43, 0.0, 5.43], [5.43, 5.43, 0.0]]), 'indices': [0, 1]}}>}
var_kwargs:  None
node  type: graph_builder.
WorkGraph process created, PK: 21497
submit workgraph:
node:  marked_atoms FINISHED
node:  run_all_xspectra_prod RUNNING
is workgraph finished:  False

06/13/2024 03:00:08 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: Continue workgraph.

update_nested_dict:  AttributeDict({'_awaitable_actions': [], 'new_data': {}, 'input_nodes': {}, 'max_number_awaitables': 1000000, '_count': 0}) marked_atoms uuid: 5f26038a-fe91-4b00-aa90-a99024b7ffa4 (pk: 21487) : {'supercell': {'atoms': Atoms(symbols='Si2', pbc=True, cell=[[0.0, 2.715, 2.715], [2.715, 0.0, 2.715], [2.715, 2.715, 0.0]])}, 'Si_0': {'symbol': 'Si', 'atoms': Atoms(symbols='XSi15', pbc=True, cell=[[0.0, 5.43, 5.43], [5.43, 0.0, 5.43], [5.43, 5.43, 0.0]]), 'indices': [0, 1]}}
update_nested_dict:  AttributeDict({'_awaitable_actions': [], 'new_data': {}, 'input_nodes': {}, 'max_number_awaitables': 1000000, '_count': 0, 'marked_atoms': <GeneralData: uuid: 5f26038a-fe91-4b00-aa90-a99024b7ffa4 (pk: 21487) : {'supercell': {'atoms': Atoms(symbols='Si2', pbc=True, cell=[[0.0, 2.715, 2.715], [2.715, 0.0, 2.715], [2.715, 2.715, 0.0]])}, 'Si_0': {'symbol': 'Si', 'atoms': Atoms(symbols='XSi15', pbc=True, cell=[[0.0, 5.43, 5.43], [5.43, 0.0, 5.43], [5.43, 5.43, 0.0]]), 'indices': [0, 1]}}>}) sequence []
Continue workgraph.

06/13/2024 03:00:08 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: nodes ready to run: scf
06/13/2024 03:00:08 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|run_nodes]: Run node: scf, type: PYTHONJOB

------------------------------------------------------------
executor:  <function pw_calculator at 0x7f0c9421fd00>
args:  [<AtomsData: uuid: cfeab8d1-7be0-41d4-8841-bd9ca1d95420 (pk: 21488) : Atoms(symbols='XSi15', pbc=True, cell=[[0.0, 5.43, 5.43], [5.43, 0.0, 5.43], [5.43, 5.43, 0.0]])>, <Dict: uuid: d3e3551b-4760-4377-b50d-9f99053165d6 (pk: 21489)>]
kwargs:  {'kpts': <GeneralData: uuid: 6e15620e-85cb-47a4-879a-5e76d9243cd4 (pk: 21490) : (4, 4, 4)>, 'command': <Str: uuid: 8b211bd9-0ee3-4462-8955-fe6069a3dc49 (pk: 21491) value: mpirun -np 4 pw.x>, 'input_data': <Dict: uuid: bf18f728-9f3b-418f-85a7-b3c16a481cff (pk: 21492)>, 'pseudo_dir': <Str: uuid: 489994f5-3941-4cfc-8cad-6fbee374d9d8 (pk: 21493) value: /home/wang_x3/datas/pseudos/xas>, 'computer': 'localhost', 'metadata': {'options': {'prepend_text': 'eval "$(conda shell.posix hook)"\n        conda activate aiida\n        export OMP_NUM_THREADS=1\n        '}}, 'atoms': <AtomsData: uuid: cfeab8d1-7be0-41d4-8841-bd9ca1d95420 (pk: 21488) : Atoms(symbols='XSi15', pbc=True, cell=[[0.0, 5.43, 5.43], [5.43, 0.0, 5.43], [5.43, 5.43, 0.0]])>, 'pseudopotentials': <Dict: uuid: d3e3551b-4760-4377-b50d-9f99053165d6 (pk: 21489)>}
var_kwargs:  None
node  type: Python.
node:  scf RUNNING
node:  xspectra_Si_0_0 CREATED
is workgraph finished:  False

06/13/2024 03:00:12 PM <2852041> aiida.execmanager: [WARNING] failed to load Node<d1f12f2e-d656-433d-8082-e962b619dd81> specified in the `local_copy_list`

on awaitable finished:  scf
update node state:  scf
item:  results scf_results.Si_0 uuid: 4bdd46af-3fc7-4afc-af1c-e03b8f6fe6c8 (pk: 21508)
update_nested_dict:  AttributeDict({'_awaitable_actions': [21504], 'new_data': {}, 'input_nodes': {}, 'max_number_awaitables': 1000000, '_count': 0, 'marked_atoms': <GeneralData: uuid: 5f26038a-fe91-4b00-aa90-a99024b7ffa4 (pk: 21487) : {'supercell': {'atoms': Atoms(symbols='Si2', pbc=True, cell=[[0.0, 2.715, 2.715], [2.715, 0.0, 2.715], [2.715, 2.715, 0.0]])}, 'Si_0': {'symbol': 'Si', 'atoms': Atoms(symbols='XSi15', pbc=True, cell=[[0.0, 5.43, 5.43], [5.43, 0.0, 5.43], [5.43, 5.43, 0.0]]), 'indices': [0, 1]}}>, 'sequence': [], 'nodes': {'scf': {'action': 'NONE', 'ctrl_inputs': [{'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'link_limit': 1000, 'links': [], 'name': 'entry', 'node_uuid': 'd9ad4c92-2984-11ef-971e-58112291ee1a', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'type': 'INPUT', 'uuid': 'd9adf3c2-2984-11ef-971e-58112291ee1a'}, {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'link_limit': 1000, 'links': [], 'name': 'ctrl', 'node_uuid': 'd9ad4c92-2984-11ef-971e-58112291ee1a', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'type': 'INPUT', 'uuid': 'd9adf494-2984-11ef-971e-58112291ee1a'}], 'ctrl_outputs': [{'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'link_limit': 1, 'links': [], 'name': 'exit', 'node_uuid': 'd9ad4c92-2984-11ef-971e-58112291ee1a', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'type': 'OUTPUT', 'uuid': 'd9adf55c-2984-11ef-971e-58112291ee1a'}, {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'link_limit': 1000, 'links': [], 'name': 'ctrl', 'node_uuid': 'd9ad4c92-2984-11ef-971e-58112291ee1a', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'type': 'OUTPUT', 'uuid': 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'function_name': 'pw_calculator', 'function_source_code': 'def pw_calculator(\n    atoms: Atoms,\n    pseudopotentials: dict,\n    kpts: list = None,\n    kspacing: float = None,\n    command: str = "pw.x",\n    input_data: dict = None,\n    pseudo_dir: str = "./pseudopotentials",\n    calculation: str = None,\n) -> dict:\n    """Run a Quantum Espresso calculation on the given atoms object."""\n    from ase.io.espresso import Namelist\n    from ase_quantumespresso.espresso import Espresso, EspressoProfile\n\n    input_data = {} if input_data is None else input_data\n\n    profile = EspressoProfile(command=command, pseudo_dir=pseudo_dir)\n\n    input_data = Namelist(input_data)\n    input_data.to_nested(binary="pw")\n    # set the calculation type\n    if calculation:\n        input_data.setdefault("CONTROL", {})\n        input_data["CONTROL"]["calculation"] = calculation\n\n    # Set the output directory\n    input_data.setdefault("CONTROL", {})\n    input_data["CONTROL"]["outdir"] = "out"\n\n    calc = Espresso(\n        profile=profile,\n        pseudopotentials=pseudopotentials,\n        input_data=input_data,\n        kpts=kpts,\n        kspacing=kspacing,\n    )\n\n    atoms.calc = calc\n\n    atoms.get_potential_energy()\n    results = atoms.calc.results\n    new_atoms = results.pop("atoms")\n    # we only update the position and cell of the atoms object\n    atoms.positions = new_atoms.positions\n    atoms.cell = new_atoms.cell\n    # Set atoms.calc to None to avoid pickling error\n    atoms.calc = None\n    return {"atoms": atoms, "results": results}\n', 'import_statements': 'from ase.atoms import Atoms\nfrom builtins import dict, str, float, list\nfrom typing import Optional', 'is_pickle': True, 'type': 'function'}, 'hash': '', 'inner_id': 1, 'inputs': [{'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'link_limit': 1, 'links': [], 'name': 'atoms', 'node_uuid': 'd9ad4c92-2984-11ef-971e-58112291ee1a', 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pw_calculator(\n    atoms: Atoms,\n    pseudopotentials: dict,\n    kpts: list = None,\n    kspacing: float = None,\n    command: str = "pw.x",\n    input_data: dict = None,\n    pseudo_dir: str = "./pseudopotentials",\n    calculation: str = None,\n) -> dict:\n    """Run a Quantum Espresso calculation on the given atoms object."""\n    from ase.io.espresso import Namelist\n    from ase_quantumespresso.espresso import Espresso, EspressoProfile\n\n    input_data = {} if input_data is None else input_data\n\n    profile = EspressoProfile(command=command, pseudo_dir=pseudo_dir)\n\n    input_data = Namelist(input_data)\n    input_data.to_nested(binary="pw")\n    # set the calculation type\n    if calculation:\n        input_data.setdefault("CONTROL", {})\n        input_data["CONTROL"]["calculation"] = calculation\n\n    # Set the output directory\n    input_data.setdefault("CONTROL", {})\n    input_data["CONTROL"]["outdir"] = "out"\n\n    calc = Espresso(\n        profile=profile,\n        pseudopotentials=pseudopotentials,\n        input_data=input_data,\n        kpts=kpts,\n        kspacing=kspacing,\n    )\n\n    atoms.calc = calc\n\n    atoms.get_potential_energy()\n    results = atoms.calc.results\n    new_atoms = results.pop("atoms")\n    # we only update the position and cell of the atoms object\n    atoms.positions = new_atoms.positions\n    atoms.cell = new_atoms.cell\n    # Set atoms.calc to None to avoid pickling error\n    atoms.calc = None\n    return {"atoms": atoms, "results": results}\n\x94\x8c\x11import_statements\x94\x8ccfrom ase.atoms import Atoms\nfrom builtins import dict, str, float, list\nfrom typing import 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pw_calculator(\n    atoms: Atoms,\n    pseudopotentials: dict,\n    kpts: list = None,\n    kspacing: float = None,\n    command: str = "pw.x",\n    input_data: dict = None,\n    pseudo_dir: str = "./pseudopotentials",\n    calculation: str = None,\n) -> dict:\n    """Run a Quantum Espresso calculation on the given atoms object."""\n    from ase.io.espresso import Namelist\n    from ase_quantumespresso.espresso import Espresso, EspressoProfile\n\n    input_data = {} if input_data is None else input_data\n\n    profile = EspressoProfile(command=command, pseudo_dir=pseudo_dir)\n\n    input_data = Namelist(input_data)\n    input_data.to_nested(binary="pw")\n    # set the calculation type\n    if calculation:\n        input_data.setdefault("CONTROL", {})\n        input_data["CONTROL"]["calculation"] = calculation\n\n    # Set the output directory\n    input_data.setdefault("CONTROL", {})\n    input_data["CONTROL"]["outdir"] = "out"\n\n    calc = Espresso(\n        profile=profile,\n        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'to_context': [['results', 'xspectra_results.Si_0.prod_0']], 'uuid': 'd9b1af4e-2984-11ef-971e-58112291ee1a', 'version': 'node_graph@0.0.1', 'wait': [], 'results': None}}, 'state': 'CREATED', 'uuid': 'd9a95d76-2984-11ef-971e-58112291ee1a', 'version': 'node_graph@0.0.1', 'workgraph_type': 'NORMAL'}, 'msgs': [], '_execution_count': 0, 'scf': <CalcJobNode: uuid: 147222bd-bcfd-46d3-a21f-02ccde2206ac (pk: 21504) (aiida.calculations:workgraph.python)>}) scf_results.Si_0 uuid: 4bdd46af-3fc7-4afc-af1c-e03b8f6fe6c8 (pk: 21508)

06/13/2024 03:00:39 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|set_node_result]: Node: scf finished.
06/13/2024 03:00:40 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: Continue workgraph.

Continue workgraph.

06/13/2024 03:00:41 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: nodes ready to run: xspectra_Si_0_0
06/13/2024 03:00:41 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|run_nodes]: Run node: xspectra_Si_0_0, type: PYTHONJOB

------------------------------------------------------------
executor:  <function xspectra_calculator at 0x7f0c944bb130>
args:  []
kwargs:  {'command': <Str: uuid: 43180c54-0735-4b4a-bc44-75b846338666 (pk: 21494) value: mpirun -np 4 xspectra.x>, 'input_data': <Dict: uuid: bc41ed57-9c9d-40dd-9e3a-9743202b12ec (pk: 21495)>, 'kpts': <GeneralData: uuid: f4495a84-dc88-45b4-a72b-d5dcf85241da (pk: 21496) : (4, 4, 4)>, 'computer': 'localhost', 'metadata': {'options': {'prepend_text': 'eval "$(conda shell.posix hook)"\n        conda activate aiida\n        export OMP_NUM_THREADS=1\n        '}}, 'parent_folder': <RemoteData: uuid: 16927499-f8ce-4aba-8536-93239f39340c (pk: 21505)>, 'parent_folder_name': 'out', 'parent_output_folder': 'out'}
var_kwargs:  None
node  type: Python.
node:  scf FINISHED
node:  xspectra_Si_0_0 RUNNING
is workgraph finished:  False

06/13/2024 03:00:44 PM <2852041> aiida.execmanager: [WARNING] failed to load Node<f422d878-c9c4-485f-a793-29cea00b9657> specified in the `local_copy_list`
06/13/2024 03:00:51 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|set_node_result]: Node: xspectra_Si_0_0 finished.

on awaitable finished:  xspectra_Si_0_0
update node state:  xspectra_Si_0_0
item:  results xspectra_results.Si_0.prod_0 uuid: 6603776c-a900-43c5-8510-ebd9dc5aec6f (pk: 21518) : None
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'function_name': 'pw_calculator', 'function_source_code': 'def pw_calculator(\n    atoms: Atoms,\n    pseudopotentials: dict,\n    kpts: list = None,\n    kspacing: float = None,\n    command: str = "pw.x",\n    input_data: dict = None,\n    pseudo_dir: str = "./pseudopotentials",\n    calculation: str = None,\n) -> dict:\n    """Run a Quantum Espresso calculation on the given atoms object."""\n    from ase.io.espresso import Namelist\n    from ase_quantumespresso.espresso import Espresso, EspressoProfile\n\n    input_data = {} if input_data is None else input_data\n\n    profile = EspressoProfile(command=command, pseudo_dir=pseudo_dir)\n\n    input_data = Namelist(input_data)\n    input_data.to_nested(binary="pw")\n    # set the calculation type\n    if calculation:\n        input_data.setdefault("CONTROL", {})\n        input_data["CONTROL"]["calculation"] = calculation\n\n    # Set the output directory\n    input_data.setdefault("CONTROL", {})\n    input_data["CONTROL"]["outdir"] = 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pw_calculator(\n    atoms: Atoms,\n    pseudopotentials: dict,\n    kpts: list = None,\n    kspacing: float = None,\n    command: str = "pw.x",\n    input_data: dict = None,\n    pseudo_dir: str = "./pseudopotentials",\n    calculation: str = None,\n) -> dict:\n    """Run a Quantum Espresso calculation on the given atoms object."""\n    from ase.io.espresso import Namelist\n    from ase_quantumespresso.espresso import Espresso, EspressoProfile\n\n    input_data = {} if input_data is None else input_data\n\n    profile = EspressoProfile(command=command, pseudo_dir=pseudo_dir)\n\n    input_data = Namelist(input_data)\n    input_data.to_nested(binary="pw")\n    # set the calculation type\n    if calculation:\n        input_data.setdefault("CONTROL", {})\n        input_data["CONTROL"]["calculation"] = calculation\n\n    # Set the output directory\n    input_data.setdefault("CONTROL", {})\n    input_data["CONTROL"]["outdir"] = "out"\n\n    calc = Espresso(\n        profile=profile,\n        pseudopotentials=pseudopotentials,\n        input_data=input_data,\n        kpts=kpts,\n        kspacing=kspacing,\n    )\n\n    atoms.calc = calc\n\n    atoms.get_potential_energy()\n    results = atoms.calc.results\n    new_atoms = results.pop("atoms")\n    # we only update the position and cell of the atoms object\n    atoms.positions = new_atoms.positions\n    atoms.cell = new_atoms.cell\n    # Set atoms.calc to None to avoid pickling error\n    atoms.calc = None\n    return {"atoms": atoms, "results": results}\n\x94\x8c\x11import_statements\x94\x8ccfrom ase.atoms import Atoms\nfrom builtins import dict, str, float, list\nfrom typing import 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pw_calculator(\n    atoms: Atoms,\n    pseudopotentials: dict,\n    kpts: list = None,\n    kspacing: float = None,\n    command: str = "pw.x",\n    input_data: dict = None,\n    pseudo_dir: str = "./pseudopotentials",\n    calculation: str = None,\n) -> dict:\n    """Run a Quantum Espresso calculation on the given atoms object."""\n    from ase.io.espresso import Namelist\n    from ase_quantumespresso.espresso import Espresso, EspressoProfile\n\n    input_data = {} if input_data is None else input_data\n\n    profile = EspressoProfile(command=command, pseudo_dir=pseudo_dir)\n\n    input_data = Namelist(input_data)\n    input_data.to_nested(binary="pw")\n    # set the calculation type\n    if calculation:\n        input_data.setdefault("CONTROL", {})\n        input_data["CONTROL"]["calculation"] = calculation\n\n    # Set the output directory\n    input_data.setdefault("CONTROL", {})\n    input_data["CONTROL"]["outdir"] = "out"\n\n    calc = Espresso(\n        profile=profile,\n        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'value': None}, 'metadata.description': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.description', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.dry_run': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.dry_run', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.label': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.label', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': {}}, 'name': 'metadata.options', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': {}}, 'metadata.options.account': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.account', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.additional_retrieve_list': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.additional_retrieve_list', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.append_text': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.append_text', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.custom_scheduler_commands': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.custom_scheduler_commands', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.environment_variables': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.environment_variables', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.environment_variables_double_quotes': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.environment_variables_double_quotes', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.import_sys_environment': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.import_sys_environment', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.input_filename': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.input_filename', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.max_memory_kb': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.max_memory_kb', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.max_wallclock_seconds': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.max_wallclock_seconds', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.mpirun_extra_params': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.mpirun_extra_params', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.output_filename': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.output_filename', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.parser_name': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.parser_name', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.prepend_text': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.prepend_text', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.priority': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.priority', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.qos': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.qos', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.queue_name': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.queue_name', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.rerunnable': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.rerunnable', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.resources': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.resources', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.scheduler_stderr': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.scheduler_stderr', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.scheduler_stdout': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.scheduler_stdout', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.stash': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': {}}, 'name': 'metadata.options.stash', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': {}}, 'metadata.options.stash.source_list': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.stash.source_list', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.stash.stash_mode': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.stash.stash_mode', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.stash.target_base': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.stash.target_base', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.submit_script_filename': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.submit_script_filename', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.options.withmpi': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.options.withmpi', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'metadata.store_provenance': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'metadata.store_provenance', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'monitors': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': {}}, 'name': 'monitors', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': {}}, 'output_name_list': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'output_name_list', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'parent_folder': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'parent_folder', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'parent_folder_name': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'parent_folder_name', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': 'out'}, 'parent_output_folder': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'parent_output_folder', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': 'out'}, 'prepend_text': {'deserialize': {'name': 'deserialize_json', 'path': 'node_graph.serializer'}, 'identifier': 'String', 'metadata': {'default': None}, 'name': 'prepend_text', 'serialize': {'name': 'serialize_json', 'path': 'node_graph.serializer'}, 'value': None}, 'remote_folder': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': 'remote_folder', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 'upload_files': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': {}}, 'name': 'upload_files', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': {}}}, 'state': 'FINISHED', 'to_context': [['results', 'xspectra_results.Si_0.prod_0']], 'uuid': 'd9b1af4e-2984-11ef-971e-58112291ee1a', 'version': 'node_graph@0.0.1', 'wait': [], 'results': <NodeLinksManager: Manager for outgoing CREATE links for node pk=21515>}}, 'state': 'CREATED', 'uuid': 'd9a95d76-2984-11ef-971e-58112291ee1a', 'version': 'node_graph@0.0.1', 'workgraph_type': 'NORMAL'}, 'msgs': [], '_execution_count': 0, 'scf': <CalcJobNode: uuid: 147222bd-bcfd-46d3-a21f-02ccde2206ac (pk: 21504) (aiida.calculations:workgraph.python)>, 'scf_results': {'Si_0': <Dict: uuid: 4bdd46af-3fc7-4afc-af1c-e03b8f6fe6c8 (pk: 21508)>}, 'xspectra_Si_0_0': <CalcJobNode: uuid: f9c563c4-f6a4-4a8e-9a62-b79ff8685aac (pk: 21515) (aiida.calculations:workgraph.python)>}) xspectra_results.Si_0.prod_0 uuid: 6603776c-a900-43c5-8510-ebd9dc5aec6f (pk: 21518) : None

06/13/2024 03:00:53 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: Continue workgraph.

Continue workgraph.

06/13/2024 03:00:53 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: nodes ready to run:
06/13/2024 03:00:53 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|finalize]: Finalize

node:  scf FINISHED
node:  xspectra_Si_0_0 FINISHED
is workgraph finished:  True
group outputs:  [['context.scf_results', 'scf'], ['context.xspectra_results', 'xspectra']]
output:  ['context.scf_results', 'scf']
update_nested_dict:  {} scf {'Si_0': <Dict: uuid: 4bdd46af-3fc7-4afc-af1c-e03b8f6fe6c8 (pk: 21508)>}
output:  ['context.xspectra_results', 'xspectra']
update_nested_dict:  {'scf': {'Si_0': <Dict: uuid: 4bdd46af-3fc7-4afc-af1c-e03b8f6fe6c8 (pk: 21508)>}} xspectra {'Si_0': {'prod_0': <GeneralData: uuid: 6603776c-a900-43c5-8510-ebd9dc5aec6f (pk: 21518) : None>}}
Finalize workgraph run_all_xspectra_prod

06/13/2024 03:00:54 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|set_node_result]: Node: run_all_xspectra_prod finished.

on awaitable finished:  run_all_xspectra_prod
update node state:  run_all_xspectra_prod

06/13/2024 03:00:55 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: Continue workgraph.

Continue workgraph.

06/13/2024 03:00:55 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: nodes ready to run:
06/13/2024 03:00:55 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|finalize]: Finalize

node:  marked_atoms FINISHED
node:  run_all_xspectra_prod FINISHED
is workgraph finished:  True
group outputs:  []
Finalize workgraph ASE-espresso-XAS-Si

{'group_outputs': {},
 'new_data': {},
 'execution_count': <Int: uuid: 6cfd6675-c8f1-4316-a9d0-27542f0609ad (pk: 21520) value: 0>}

Print the results