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GeigerJ2GeigerJ2
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Found bug in WorkGraph. Continue now with task order.
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6 files changed

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‎.gitignore‎

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@@ -189,4 +189,13 @@ workflow_qe_pyiron_base.json
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mini/
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.bak/
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workgraph_qe.json
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aiida-qe-construct.json
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aiida_to_jobflow_qe.html
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aiida_to_pyiron_base_qe.html
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evcurve.png
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strain_0/
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strain_1/
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strain_2/
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strain_3/
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strain_4/
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‎aiida_to_jobflow_qe.ipynb‎

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"cells": [
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{
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"cell_type": "code",
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"execution_count": 5,
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"execution_count": 1,
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"metadata": {},
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"outputs": [],
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"outputs": [
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{
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"name": "stderr",
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"output_type": "stream",
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"text": [
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"/home/geiger_j/.aiida_venvs/adis/lib/python3.10/site-packages/paramiko/pkey.py:82: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from this module in 48.0.0.\n",
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" \"cipher\": algorithms.TripleDES,\n",
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"/home/geiger_j/.aiida_venvs/adis/lib/python3.10/site-packages/paramiko/transport.py:253: CryptographyDeprecationWarning: TripleDES has been moved to cryptography.hazmat.decrepit.ciphers.algorithms.TripleDES and will be removed from this module in 48.0.0.\n",
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" \"class\": algorithms.TripleDES,\n"
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]
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}
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],
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"source": [
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"from python_workflow_definition.aiida import write_workflow_json, construct_wg_qe\n",
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"from python_workflow_definition.jobflow import load_workflow_json\n",
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"execution_count": 2,
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"metadata": {},
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"outputs": [
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{
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" "
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"text/plain": [
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"<IPython.lib.display.IFrame at 0x7f649f7e6770>"
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"<IPython.lib.display.IFrame at 0x7fef4c99d390>"
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},
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"execution_count": 6,
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"execution_count": 2,
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"metadata": {},
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"execution_count": 3,
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},
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{
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"cell_type": "code",
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"execution_count": 8,
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"ename": "KeyError",
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"evalue": "0",
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"output_type": "error",
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"traceback": [
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"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
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"\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
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"Cell \u001b[0;32mIn[8], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m flow \u001b[38;5;241m=\u001b[39m \u001b[43mload_workflow_json\u001b[49m\u001b[43m(\u001b[49m\u001b[43mfile_name\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mworkflow_json_filename\u001b[49m\u001b[43m)\u001b[49m\n",
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"File \u001b[0;32m~/aiida_projects/adis/git-repos/python-workflow-definition/python_workflow_definition/src/python_workflow_definition/jobflow.py:188\u001b[0m, in \u001b[0;36mload_workflow_json\u001b[0;34m(file_name)\u001b[0m\n\u001b[1;32m 186\u001b[0m input_dict \u001b[38;5;241m=\u001b[39m _get_input_dict(nodes_dict\u001b[38;5;241m=\u001b[39mnodes_new_dict)\n\u001b[1;32m 187\u001b[0m new_total_dict \u001b[38;5;241m=\u001b[39m _resort_total_lst(total_dict\u001b[38;5;241m=\u001b[39mtotal_dict, nodes_dict\u001b[38;5;241m=\u001b[39mnodes_new_dict)\n\u001b[0;32m--> 188\u001b[0m task_lst \u001b[38;5;241m=\u001b[39m \u001b[43m_get_workflow\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 189\u001b[0m \u001b[43m \u001b[49m\u001b[43mnodes_dict\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnodes_new_dict\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 190\u001b[0m \u001b[43m \u001b[49m\u001b[43minput_dict\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43minput_dict\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 191\u001b[0m \u001b[43m \u001b[49m\u001b[43mtotal_dict\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnew_total_dict\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 192\u001b[0m \u001b[43m \u001b[49m\u001b[43msource_handles_dict\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43msource_handles_dict\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 193\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 194\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m Flow(task_lst)\n",
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"File \u001b[0;32m~/aiida_projects/adis/git-repos/python-workflow-definition/python_workflow_definition/src/python_workflow_definition/jobflow.py:141\u001b[0m, in \u001b[0;36m_get_workflow\u001b[0;34m(nodes_dict, input_dict, total_dict, source_handles_dict)\u001b[0m\n\u001b[1;32m 139\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 140\u001b[0m fn \u001b[38;5;241m=\u001b[39m job(method\u001b[38;5;241m=\u001b[39mv)\n\u001b[0;32m--> 141\u001b[0m kwargs \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m 142\u001b[0m kw: input_dict[vw[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msource\u001b[39m\u001b[38;5;124m'\u001b[39m]] \u001b[38;5;28;01mif\u001b[39;00m vw[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msource\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;129;01min\u001b[39;00m input_dict \u001b[38;5;28;01melse\u001b[39;00m get_attr_helper(\n\u001b[1;32m 143\u001b[0m obj\u001b[38;5;241m=\u001b[39mmemory_dict[vw[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msource\u001b[39m\u001b[38;5;124m'\u001b[39m]], source_handle\u001b[38;5;241m=\u001b[39mvw[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msourceHandle\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[1;32m 144\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m kw, vw \u001b[38;5;129;01min\u001b[39;00m total_dict[k]\u001b[38;5;241m.\u001b[39mitems()\n\u001b[1;32m 145\u001b[0m }\n\u001b[1;32m 146\u001b[0m memory_dict[k] \u001b[38;5;241m=\u001b[39m fn(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 147\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mlist\u001b[39m(memory_dict\u001b[38;5;241m.\u001b[39mvalues())\n",
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"File \u001b[0;32m~/aiida_projects/adis/git-repos/python-workflow-definition/python_workflow_definition/src/python_workflow_definition/jobflow.py:143\u001b[0m, in \u001b[0;36m<dictcomp>\u001b[0;34m(.0)\u001b[0m\n\u001b[1;32m 139\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 140\u001b[0m fn \u001b[38;5;241m=\u001b[39m job(method\u001b[38;5;241m=\u001b[39mv)\n\u001b[1;32m 141\u001b[0m kwargs \u001b[38;5;241m=\u001b[39m {\n\u001b[1;32m 142\u001b[0m kw: input_dict[vw[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msource\u001b[39m\u001b[38;5;124m'\u001b[39m]] \u001b[38;5;28;01mif\u001b[39;00m vw[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msource\u001b[39m\u001b[38;5;124m'\u001b[39m] \u001b[38;5;129;01min\u001b[39;00m input_dict \u001b[38;5;28;01melse\u001b[39;00m get_attr_helper(\n\u001b[0;32m--> 143\u001b[0m obj\u001b[38;5;241m=\u001b[39m\u001b[43mmemory_dict\u001b[49m\u001b[43m[\u001b[49m\u001b[43mvw\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msource\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m]\u001b[49m, source_handle\u001b[38;5;241m=\u001b[39mvw[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124msourceHandle\u001b[39m\u001b[38;5;124m'\u001b[39m])\n\u001b[1;32m 144\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m kw, vw \u001b[38;5;129;01min\u001b[39;00m total_dict[k]\u001b[38;5;241m.\u001b[39mitems()\n\u001b[1;32m 145\u001b[0m }\n\u001b[1;32m 146\u001b[0m memory_dict[k] \u001b[38;5;241m=\u001b[39m fn(\u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n\u001b[1;32m 147\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mlist\u001b[39m(memory_dict\u001b[38;5;241m.\u001b[39mvalues())\n",
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"\u001b[0;31mKeyError\u001b[0m: 0"
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]
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}
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],
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"outputs": [],
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"source": [
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"\n",
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"flow = load_workflow_json(file_name=workflow_json_filename)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 5,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"2025-03-15 11:21:45,872 INFO Started executing jobs locally\n",
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"2025-03-15 11:21:46,028 INFO Starting job - add_x_and_y (31bed0f7-49cd-4e63-9a53-8c9679e74dd2)\n",
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"2025-03-15 11:21:46,030 INFO Finished job - add_x_and_y (31bed0f7-49cd-4e63-9a53-8c9679e74dd2)\n",
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"2025-03-15 11:21:46,031 INFO Starting job - add_x_and_y_and_z (7d74164e-3d5b-40d0-b72b-4fc5434a98e1)\n",
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"2025-03-15 11:21:46,033 INFO Finished job - add_x_and_y_and_z (7d74164e-3d5b-40d0-b72b-4fc5434a98e1)\n",
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"2025-03-15 11:21:46,033 INFO Finished executing jobs locally\n"
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"2025-03-17 13:03:08,254 INFO Started executing jobs locally\n",
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"2025-03-17 13:03:08,350 INFO Starting job - get_bulk_structure (2752a57d-0f42-46d2-b030-a2061311d315)\n",
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"2025-03-17 13:03:08,506 INFO Finished job - get_bulk_structure (2752a57d-0f42-46d2-b030-a2061311d315)\n",
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"2025-03-17 13:03:08,507 INFO Starting job - get_dict (798cca09-0626-4cf6-8236-c5c6f5340458)\n",
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"> \u001b[0;32m/home/geiger_j/.aiida_venvs/adis/lib/python3.10/site-packages/jobflow/core/reference.py\u001b[0m(189)\u001b[0;36mresolve\u001b[0;34m()\u001b[0m\n",
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"\u001b[0;32m 188 \u001b[0;31m \u001b[0mdata\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mattr\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0m\u001b[0;32m--> 189 \u001b[0;31m \u001b[0;32mif\u001b[0m \u001b[0mattr_type\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;34m\"i\"\u001b[0m \u001b[0;32mor\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdict\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0m\u001b[0;32m 190 \u001b[0;31m \u001b[0;32melse\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mattr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
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"\u001b[0m\n",
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"--KeyboardInterrupt--\n",
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"\n",
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"KeyboardInterrupt: Interrupted by user\n",
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"2025-03-17 13:04:08,108 INFO get_dict failed with exception:\n",
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"Traceback (most recent call last):\n",
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" File \"/home/geiger_j/.aiida_venvs/adis/lib/python3.10/site-packages/jobflow/managers/local.py\", line 117, in _run_job\n",
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" response = job.run(store=store)\n",
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" File \"/home/geiger_j/.aiida_venvs/adis/lib/python3.10/site-packages/jobflow/core/job.py\", line 593, in run\n",
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" self.resolve_args(store=store)\n",
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" File \"/home/geiger_j/.aiida_venvs/adis/lib/python3.10/site-packages/jobflow/core/job.py\", line 709, in resolve_args\n",
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" resolved_kwargs = find_and_resolve_references(\n",
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" File \"/home/geiger_j/.aiida_venvs/adis/lib/python3.10/site-packages/jobflow/core/reference.py\", line 474, in find_and_resolve_references\n",
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" resolved_references = resolve_references(\n",
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" File \"/home/geiger_j/.aiida_venvs/adis/lib/python3.10/site-packages/jobflow/core/reference.py\", line 362, in resolve_references\n",
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" resolved_references[ref] = ref.resolve(\n",
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" File \"/home/geiger_j/.aiida_venvs/adis/lib/python3.10/site-packages/jobflow/core/reference.py\", line 188, in resolve\n",
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" data[attr]\n",
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"KeyError: 'result'\n",
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"\n",
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"2025-03-17 13:04:08,109 INFO Finished executing jobs locally\n"
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]
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{
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"data": {
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"text/plain": [
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"{'31bed0f7-49cd-4e63-9a53-8c9679e74dd2': {1: Response(output={'x': 1, 'y': 2, 'z': 3}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/geiger_j/aiida_projects/adis/git-repos/python-workflow-definition'))},\n",
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" '7d74164e-3d5b-40d0-b72b-4fc5434a98e1': {1: Response(output=6, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/geiger_j/aiida_projects/adis/git-repos/python-workflow-definition'))}}"
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"{'2752a57d-0f42-46d2-b030-a2061311d315': {1: Response(output={'numbers': [13, 13, 13, 13], 'positions': [[0.0, 0.0, 0.0], [0.0, 2.025, 2.025], [2.025, 0.0, 2.025], [2.025, 2.025, 0.0]], 'cell': [[4.05, 0.0, 0.0], [0.0, 4.05, 0.0], [0.0, 0.0, 4.05]], 'pbc': [True, True, True]}, detour=None, addition=None, replace=None, stored_data=None, stop_children=False, stop_jobflow=False, job_dir=PosixPath('/home/geiger_j/aiida_projects/adis/git-repos/python-workflow-definition'))}}"
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},
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"execution_count": 6,
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"execution_count": 5,
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"metadata": {},
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"output_type": "execute_result"
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}

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