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Merged
superstar54 merged 2 commits into from
Sep 4, 2025
Merged

Update to WorkGraph stable release #30

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7335daf
Update to WorkGraph stable release
superstar54 Jul 15, 2025
95e506a
Use spec
superstar54 Aug 18, 2025
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -158,3 +158,6 @@ cython_debug/
# and can be added to the global gitignore or merged into this file. For a more nuclear
# option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/


.vscode/
184 changes: 81 additions & 103 deletions docs/source/ase/espresso/atomization_energy.ipynb
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Expand Up @@ -24,13 +24,16 @@
"- $E_{\\text{atom}}$ is the energy of an isolated atom.\n",
"- $E_{\\text{molecule}}$ is the energy of the molecule.\n",
"\n",
"## Visualizing the WorkGraph Builder\n"
"## Example: Atomization energy of a molecule N2\n",
"\n",
"### Prepare the inputs and submit the workflow\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 1,
"id": "1a8ebc0d",
"execution_count": 4,
"id": "8ee799d2-0b5b-4609-957f-6b3f2cd451f0",
"metadata": {},
"outputs": [
{
Expand All @@ -40,160 +43,140 @@
" <iframe\n",
" width=\"100%\"\n",
" height=\"600px\"\n",
" src=\"html/atomization_energy0.html\"\n",
" src=\"html/AtomizationEnergy.html\"\n",
" frameborder=\"0\"\n",
" allowfullscreen\n",
" \n",
" ></iframe>\n",
" "
],
"text/plain": [
"<IPython.lib.display.IFrame at 0x7890d71b9810>"
"<IPython.lib.display.IFrame at 0x71c0483c9c10>"
]
},
"execution_count": 1,
"execution_count": 4,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from workgraph_collections.ase.espresso.atomization_energy import atomization_energy\n",
"from ase.build import molecule\n",
"from ase import Atoms\n",
"from aiida import load_profile\n",
"from workgraph_collections.ase.espresso.atomization_energy import AtomizationEnergy\n",
"from aiida_pythonjob.config import config\n",
"# allow pickle\n",
"config[\"allow_pickle\"] = True\n",
"load_profile()\n",
"\n",
"# create input structure\n",
"n_atom = Atoms(\"N\", pbc=True)\n",
"n_atom.center(vacuum=5.0)\n",
"n2_molecule = molecule(\"N2\", pbc=True)\n",
"n2_molecule.center(vacuum=5.0)\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",
"pseudopotentials = {\"N\": \"N.pbe-n-rrkjus_psl.1.0.0.UPF\"}\n",
"pseudo_dir = \"/home/xing/data/ase/espresso_pseudo\"\n",
"# pseudo_dir = \"/home/wang_x3/datas/pseudos/psl\"\n",
"input_data = {\n",
" \"system\": {\"ecutwfc\": 30, \"ecutrho\": 240,\n",
" \"occupations\": \"smearing\",\n",
" \"degauss\": 0.01,\n",
" \"smearing\": \"cold\",},\n",
"}\n",
"#------------------------- Set the inputs -------------------------\n",
"wg = AtomizationEnergy.build_graph(atom=n_atom,\n",
" molecule=n2_molecule,\n",
" pseudopotentials=pseudopotentials,\n",
" input_data=input_data,\n",
" pseudo_dir=pseudo_dir,\n",
" computer=\"localhost\",\n",
" metadata=metadata)\n",
"\n",
"task = atomization_energy.TaskCls()\n",
"task.to_html()"
"wg.to_html()"
]
},
{
"cell_type": "markdown",
"id": "9e6360d8",
"id": "dd873a97",
"metadata": {},
"source": [
"## Visualizing the WorkGraph"
"Run the workflow"
]
},
{
"cell_type": "code",
"execution_count": 2,
"id": "01bedd69",
"id": "c48c10af",
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
" <iframe\n",
" width=\"100%\"\n",
" height=\"600px\"\n",
" src=\"html/Atomization energy.html\"\n",
" frameborder=\"0\"\n",
" allowfullscreen\n",
" \n",
" ></iframe>\n",
" "
],
"text/plain": [
"<IPython.lib.display.IFrame at 0x7890d70670d0>"
]
},
"execution_count": 2,
"metadata": {},
"output_type": "execute_result"
"name": "stderr",
"output_type": "stream",
"text": [
"09/04/2025 07:22:58 AM <581732> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [180058|WorkGraphEngine|continue_workgraph]: tasks ready to run: pw_calculator,pw_calculator1\n",
"REPORT:aiida.orm.nodes.process.workflow.workchain.WorkChainNode:[180058|WorkGraphEngine|continue_workgraph]: tasks ready to run: pw_calculator,pw_calculator1\n",
"09/04/2025 07:23:01 AM <581732> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [180058|WorkGraphEngine|on_wait]: Process status: Waiting for child processes: 180062, 180075\n",
"REPORT:aiida.orm.nodes.process.workflow.workchain.WorkChainNode:[180058|WorkGraphEngine|on_wait]: Process status: Waiting for child processes: 180062, 180075\n",
"09/04/2025 07:23:04 AM <581732> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [180058|WorkGraphEngine|update_task_state]: Task: pw_calculator, type: PYTHONJOB, finished.\n",
"REPORT:aiida.orm.nodes.process.workflow.workchain.WorkChainNode:[180058|WorkGraphEngine|update_task_state]: Task: pw_calculator, type: PYTHONJOB, finished.\n",
"09/04/2025 07:23:04 AM <581732> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [180058|WorkGraphEngine|update_task_state]: Task: pw_calculator1, type: PYTHONJOB, finished.\n",
"REPORT:aiida.orm.nodes.process.workflow.workchain.WorkChainNode:[180058|WorkGraphEngine|update_task_state]: Task: pw_calculator1, type: PYTHONJOB, finished.\n",
"09/04/2025 07:23:06 AM <581732> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [180058|WorkGraphEngine|continue_workgraph]: tasks ready to run: calc_atomization_energy\n",
"REPORT:aiida.orm.nodes.process.workflow.workchain.WorkChainNode:[180058|WorkGraphEngine|continue_workgraph]: tasks ready to run: calc_atomization_energy\n",
"INFO:aiida_pythonjob.decorator:Executing process function, current stack status: 47 frames of 3000\n",
"09/04/2025 07:23:07 AM <581732> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [180058|WorkGraphEngine|update_task_state]: Task: calc_atomization_energy, type: PYFUNCTION, finished.\n",
"REPORT:aiida.orm.nodes.process.workflow.workchain.WorkChainNode:[180058|WorkGraphEngine|update_task_state]: Task: calc_atomization_energy, type: PYFUNCTION, finished.\n",
"09/04/2025 07:23:07 AM <581732> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [180058|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n",
"REPORT:aiida.orm.nodes.process.workflow.workchain.WorkChainNode:[180058|WorkGraphEngine|continue_workgraph]: tasks ready to run: \n",
"09/04/2025 07:23:07 AM <581732> aiida.orm.nodes.process.workflow.workchain.WorkChainNode: [REPORT] [180058|WorkGraphEngine|finalize]: Finalize workgraph.\n",
"REPORT:aiida.orm.nodes.process.workflow.workchain.WorkChainNode:[180058|WorkGraphEngine|finalize]: Finalize workgraph.\n"
]
}
],
"source": [
"from workgraph_collections.ase.espresso.atomization_energy import atomization_energy\n",
"\n",
"wg = atomization_energy()\n",
"wg.to_html()"
"wg.run()\n"
]
},
{
"cell_type": "markdown",
"id": "efa095d0",
"id": "2e7efd9d",
"metadata": {},
"source": [
"## Example: Atomization energy of a molecule N2\n",
"\n",
"### Prepare the inputs and submit the workflow\n"
"Print out the result"
]
},
{
"cell_type": "code",
"execution_count": 3,
"id": "8ee799d2-0b5b-4609-957f-6b3f2cd451f0",
"id": "72481d10",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"WorkGraph process created, PK: 16469\n",
"Energy of a N atom: -269.881\n",
"Energy of an un-relaxed N2 molecule: -556.008\n",
"Atomization energy: 16.246 eV\n"
"Atomization energy: 16.262 eV\n"
]
}
],
"source": [
"from ase.build import molecule\n",
"from ase import Atoms\n",
"from aiida import load_profile\n",
"from workgraph_collections.ase.espresso.atomization_energy import atomization_energy\n",
"\n",
"load_profile()\n",
"\n",
"# create input structure\n",
"n_atom = Atoms(\"N\", pbc=True)\n",
"n_atom.center(vacuum=5.0)\n",
"n2_molecule = molecule(\"N2\", pbc=True)\n",
"n2_molecule.center(vacuum=5.0)\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",
"pseudopotentials = {\"N\": \"N.pbe-n-rrkjus_psl.1.0.0.UPF\"}\n",
"# pseudo_dir = \"/home/xing/data/ase/espresso_pseudo\"\n",
"pseudo_dir = \"/home/wang_x3/datas/pseudos/psl\"\n",
"input_data = {\n",
" \"system\": {\"ecutwfc\": 30, \"ecutrho\": 240,\n",
" \"occupations\": \"smearing\",\n",
" \"degauss\": 0.01,\n",
" \"smearing\": \"cold\",},\n",
"}\n",
"#------------------------- Set the inputs -------------------------\n",
"wg = atomization_energy()\n",
"wg.tasks[\"scf_atom\"].set({\"atoms\": n_atom,\n",
" \"pseudopotentials\": pseudopotentials,\n",
" \"pseudo_dir\": pseudo_dir,\n",
" \"input_data\": input_data,\n",
" \"computer\": \"localhost\",\n",
" \"metadata\": metadata})\n",
"wg.tasks[\"scf_mol\"].set({\"atoms\": n2_molecule,\n",
" \"pseudopotentials\": pseudopotentials,\n",
" \"pseudo_dir\": pseudo_dir,\n",
" \"input_data\": input_data,\n",
" \"computer\": \"localhost\",\n",
" \"metadata\": metadata})\n",
"wg.tasks[\"calc_atomization_energy\"].set({\"molecule\": n2_molecule, \"computer\": \"localhost\"})\n",
"#------------------------- Submit the calculation -------------------\n",
"# wg.run()\n",
"wg.submit(wait=True, timeout=200)\n",
"#------------------------- Print the output -------------------------\n",
"print('Energy of a N atom: {:0.3f}'.format(wg.tasks['scf_atom'].outputs[\"results\"].value.value['energy']))\n",
"print('Energy of an un-relaxed N2 molecule: {:0.3f}'.format(wg.tasks['scf_mol'].outputs[\"results\"].value.value['energy']))\n",
"print('Atomization energy: {:0.3f} eV'.format(wg.tasks['calc_atomization_energy'].outputs[\"result\"].value.value))\n",
"\n"
"print('Atomization energy: {:0.3f} eV'.format(wg.outputs.atomization_energy.value.value))"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3 (ipykernel)",
"display_name": "aiida",
"language": "python",
"name": "python3"
},
Expand All @@ -208,11 +191,6 @@
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.0"
},
"vscode": {
"interpreter": {
"hash": "2f450c1ff08798c4974437dd057310afef0de414c25d1fd960ad375311c3f6ff"
}
}
},
"nbformat": 4,
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