{ "cells": [ { "cell_type": "markdown", "id": "22d177dc-6cfb-4de2-9509-f1eb45e10cf2", "metadata": {}, "source": [ "# X-ray Absorption Near Edge Structure (XANES)\n", "For the source code, see [xas](https://workgraph-collections.readthedocs.io/en/latest/ase/espresso/module.html#workgraph_collections.ase.espresso.xas.xas_workgraph).\n", "\n", "\n", "## Visualizing the WorkGraph Builder\n" ] }, { "cell_type": "code", "execution_count": 1, "id": "6be40ba7", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " " ], "text/plain": [ "" ] }, "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from workgraph_collections.ase.espresso.xas import xas_workgraph\n", "from aiida import load_profile\n", "load_profile()\n", "\n", "task = xas_workgraph.TaskCls()\n", "task.to_html()" ] }, { "cell_type": "markdown", "id": "9e6360d8", "metadata": {}, "source": [ "## Visualizing the WorkGraph" ] }, { "cell_type": "code", "execution_count": 1, "id": "01bedd69", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", " \n", " " ], "text/plain": [ "" ] }, "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from workgraph_collections.ase.espresso.xas import xas_workgraph\n", "from aiida import load_profile\n", "load_profile()\n", "\n", "wg = xas_workgraph()\n", "wg.to_html()" ] }, { "cell_type": "markdown", "id": "efa095d0", "metadata": {}, "source": [ "## Example: Silicon XANES\n", "\n", "### Prepare the inputs and submit the workflow\n" ] }, { "cell_type": "code", "execution_count": 1, "id": "8ee799d2-0b5b-4609-957f-6b3f2cd451f0", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 02:59:52 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: Continue workgraph.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "update_nested_dict: AttributeDict({'_awaitable_actions': [], 'new_data': {}, 'input_nodes': {}, 'max_number_awaitables': 1000000, '_count': 0}) sequence []\n", "Continue workgraph.\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "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\n", "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\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "------------------------------------------------------------\n", "executor: \n", "args: []\n", "kwargs: {'atoms': , 'min_cell_length': , 'element_list': , 'marker': , 'is_molecule': , 'metadata': {'options': {'prepend_text': 'eval \"$(conda shell.posix hook)\"\\n conda activate aiida\\n export OMP_NUM_THREADS=1\\n '}}}\n", "var_kwargs: None\n", "node type: Python.\n", "node: marked_atoms RUNNING\n", "node: run_all_xspectra_prod CREATED\n", "is workgraph finished: False\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "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`\n", "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.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "on awaitable finished: marked_atoms\n", "update node state: marked_atoms\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 03:00:03 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: Continue workgraph.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Continue workgraph.\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "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\n", "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\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "------------------------------------------------------------\n", "executor: \n", "args: []\n", "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': }\n", "var_kwargs: None\n", "node type: graph_builder.\n", "WorkGraph process created, PK: 21497\n", "submit workgraph: \n", "node: marked_atoms FINISHED\n", "node: run_all_xspectra_prod RUNNING\n", "is workgraph finished: False\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 03:00:08 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: Continue workgraph.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "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]}}\n", "update_nested_dict: AttributeDict({'_awaitable_actions': [], 'new_data': {}, 'input_nodes': {}, 'max_number_awaitables': 1000000, '_count': 0, 'marked_atoms': }) sequence []\n", "Continue workgraph.\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "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\n", "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\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "------------------------------------------------------------\n", "executor: \n", "args: [, ]\n", "kwargs: {'kpts': , 'command': , 'input_data': , 'pseudo_dir': , 'computer': 'localhost', 'metadata': {'options': {'prepend_text': 'eval \"$(conda shell.posix hook)\"\\n conda activate aiida\\n export OMP_NUM_THREADS=1\\n '}}, 'atoms': , 'pseudopotentials': }\n", "var_kwargs: None\n", "node type: Python.\n", "node: scf RUNNING\n", "node: xspectra_Si_0_0 CREATED\n", "is workgraph finished: False\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 03:00:12 PM <2852041> aiida.execmanager: [WARNING] failed to load Node specified in the `local_copy_list`\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "on awaitable finished: scf\n", "update node state: scf\n", "item: results scf_results.Si_0 uuid: 4bdd46af-3fc7-4afc-af1c-e03b8f6fe6c8 (pk: 21508)\n", "update_nested_dict: AttributeDict({'_awaitable_actions': [21504], 'new_data': {}, 'input_nodes': {}, 'max_number_awaitables': 1000000, '_count': 0, 'marked_atoms': , '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'}, 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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', 'serialize': {'name': 'serialize_pickle', 'path': 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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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'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'link_limit': 1, 'links': [], 'name': 'remote_stash', 'node_uuid': 'd9ad4c92-2984-11ef-971e-58112291ee1a', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'type': 'OUTPUT', 'uuid': 'd9adf1d8-2984-11ef-971e-58112291ee1a'}, {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'link_limit': 1, 'links': [], 'name': 'retrieved', 'node_uuid': 'd9ad4c92-2984-11ef-971e-58112291ee1a', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'type': 'OUTPUT', 'uuid': 'd9adf2b4-2984-11ef-971e-58112291ee1a'}], 'position': [30, 30], 'process': , 'properties': {'_wait': {'deserialize': {'name': 'deserialize_pickle', 'path': 'node_graph.serializer'}, 'identifier': 'General', 'metadata': {'default': None}, 'name': '_wait', 'serialize': {'name': 'serialize_pickle', 'path': 'node_graph.serializer'}, 'value': None}, 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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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'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': 'CREATED', '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': }) scf_results.Si_0 uuid: 4bdd46af-3fc7-4afc-af1c-e03b8f6fe6c8 (pk: 21508)\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 03:00:39 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|set_node_result]: Node: scf finished.\n", "06/13/2024 03:00:40 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: Continue workgraph.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Continue workgraph.\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "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\n", "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\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "------------------------------------------------------------\n", "executor: \n", "args: []\n", "kwargs: {'command': , 'input_data': , 'kpts': , 'computer': 'localhost', 'metadata': {'options': {'prepend_text': 'eval \"$(conda shell.posix hook)\"\\n conda activate aiida\\n export OMP_NUM_THREADS=1\\n '}}, 'parent_folder': , 'parent_folder_name': 'out', 'parent_output_folder': 'out'}\n", "var_kwargs: None\n", "node type: Python.\n", "node: scf FINISHED\n", "node: xspectra_Si_0_0 RUNNING\n", "is workgraph finished: False\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 03:00:44 PM <2852041> aiida.execmanager: [WARNING] failed to load Node specified in the `local_copy_list`\n", "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.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "on awaitable finished: xspectra_Si_0_0\n", "update node state: xspectra_Si_0_0\n", "item: results xspectra_results.Si_0.prod_0 uuid: 6603776c-a900-43c5-8510-ebd9dc5aec6f (pk: 21518) : None\n", "update_nested_dict: AttributeDict({'_awaitable_actions': [21504, 21515], 'new_data': {}, 'input_nodes': {}, 'max_number_awaitables': 1000000, '_count': 0, 'marked_atoms': , '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': 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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 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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'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': }}, 'state': 'CREATED', 'uuid': 'd9a95d76-2984-11ef-971e-58112291ee1a', 'version': 'node_graph@0.0.1', 'workgraph_type': 'NORMAL'}, 'msgs': [], '_execution_count': 0, 'scf': , 'scf_results': {'Si_0': }, 'xspectra_Si_0_0': }) xspectra_results.Si_0.prod_0 uuid: 6603776c-a900-43c5-8510-ebd9dc5aec6f (pk: 21518) : None\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 03:00:53 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: Continue workgraph.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Continue workgraph.\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 03:00:53 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|continue_workgraph]: nodes ready to run: \n", "06/13/2024 03:00:53 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21497|WorkGraphEngine|finalize]: Finalize\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "node: scf FINISHED\n", "node: xspectra_Si_0_0 FINISHED\n", "is workgraph finished: True\n", "group outputs: [['context.scf_results', 'scf'], ['context.xspectra_results', 'xspectra']]\n", "output: ['context.scf_results', 'scf']\n", "update_nested_dict: {} scf {'Si_0': }\n", "output: ['context.xspectra_results', 'xspectra']\n", "update_nested_dict: {'scf': {'Si_0': }} xspectra {'Si_0': {'prod_0': }}\n", "Finalize workgraph run_all_xspectra_prod\n", "\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "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.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "on awaitable finished: run_all_xspectra_prod\n", "update node state: run_all_xspectra_prod\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 03:00:55 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: Continue workgraph.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Continue workgraph.\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "06/13/2024 03:00:55 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|continue_workgraph]: nodes ready to run: \n", "06/13/2024 03:00:55 PM <2852041> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [21479|WorkGraphEngine|finalize]: Finalize\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "node: marked_atoms FINISHED\n", "node: run_all_xspectra_prod FINISHED\n", "is workgraph finished: True\n", "group outputs: []\n", "Finalize workgraph ASE-espresso-XAS-Si\n", "\n" ] }, { "data": { "text/plain": [ "{'group_outputs': {},\n", " 'new_data': {},\n", " 'execution_count': }" ] }, "execution_count": 1, "metadata": {}, "output_type": "execute_result" } ], "source": [ "from ase.io import read\n", "from aiida import load_profile\n", "from workgraph_collections.ase.espresso.xas import xas_workgraph\n", "from ase.build import bulk\n", "\n", "load_profile()\n", "\n", "atoms = bulk('Si')\n", "\n", "\n", "metadata = {\n", " \"options\": {\n", " 'prepend_text' : \"\"\"eval \"$(conda shell.posix hook)\"\n", " conda activate aiida\n", " export OMP_NUM_THREADS=1\n", " \"\"\",\n", " }\n", "}\n", "\n", "input_data = {\n", " \"CONTROL\": {\n", " \"calculation\": \"scf\",\n", " },\n", " \"SYSTEM\": {\n", " \"ecutwfc\": 40,\n", " \"ecutrho\": 320,\n", " \"occupations\": \"fixed\",\n", " },\n", " }\n", "kpts = (4, 4, 4)\n", "# pseudo_dir = \"/home/xing/data/ase/espresso_pseudo\"\n", "pseudo_dir = \"/home/wang_x3/datas/pseudos/xas\"\n", "# Pseudos from https://github.com/PNOGillespie/Core_Level_Spectra_Pseudos\n", "pseudopotentials = {\"Si\": \"Si.pbe-van_gipaw.UPF\"}\n", "core_hole_pseudos = {\n", " \"Si\": \"Si.star1s-pbe-van_gipaw.UPF\",\n", "}\n", "#\n", "metadata = {\n", " \"options\": {\n", " 'prepend_text' : \"\"\"eval \"$(conda shell.posix hook)\"\n", " conda activate aiida\n", " export OMP_NUM_THREADS=1\n", " \"\"\",\n", " }\n", "}\n", "inputs = {\n", " \"pw\": {\n", " \"computer\": \"localhost\",\n", " \"metadata\": metadata,\n", " \"input_data\": input_data,\n", " \"kpts\": kpts,\n", " \"pseudopotentials\": pseudopotentials,\n", " \"pseudo_dir\": pseudo_dir,\n", " },\n", " \"xspectra\": {\n", " \"computer\": \"localhost\",\n", " \"metadata\": metadata,\n", " \"kpts\": kpts,\n", " \"input_data\": {\n", " \"INPUT_XSPECTRA\":{\n", " \"calculation\": \"xanes_dipole\",\n", " \"prefix\": \"pwscf\",\n", " \"xonly_plot\": False,\n", " \"xniter\": 2000,\n", " \"xcheck_conv\": 10,\n", " \"xerror\": 0.001},\n", " \"PLOT\":{\n", " \"xgamma\": 0.5,\n", " \"xnepoint\": 2000,\n", " \"xemin\": -10,\n", " \"xemax\": 30,\n", " \"terminator\": True,\n", " \"cut_occ_states\": True,\n", " },\n", " \"CUT_OCC\":{\n", " \"cut_desmooth\": 0.1,\n", " }\n", " },\n", " }\n", "}\n", "# ===============================================================================\n", "wg = xas_workgraph(\n", " atoms=atoms,\n", " commands={\"pw\": \"mpirun -np 4 pw.x\",\n", " \"xspectra\": \"mpirun -np 4 xspectra.x\"},\n", " element_list=[\"Si\"],\n", " inputs=inputs,\n", " eps_vectors=[[1., 0., 0.]],\n", " core_hole_pseudos=core_hole_pseudos,\n", " core_hole_treatment=\"FULL\",\n", " metadata=metadata,\n", " is_molecule=False,\n", ")\n", "wg.name = \"ASE-espresso-XAS-Si\"\n", "# wg.run()\n", "wg.submit(wait=True, timeout=300)" ] }, { "cell_type": "markdown", "id": "a533e6c8", "metadata": {}, "source": [ "## Print the results\n" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.10.0" }, "vscode": { "interpreter": { "hash": "2f450c1ff08798c4974437dd057310afef0de414c25d1fd960ad375311c3f6ff" } } }, "nbformat": 4, "nbformat_minor": 5 }