Use dict keys as strings (#13)

* Use dict keys as strings

* bug fix

* another fix

Author: jan-janssen

jobflow_to_pyiron_base_qe.ipynb

@@ -84,7 +84,12 @@
   {
    "id": "07598344-0f75-433b-8902-bea21a42088c",
    "cell_type": "code",
-   "source": "calculate_qe = job(_calculate_qe, data=[\"energy\", \"volume\", \"structure\"])\ngenerate_structures = job(_generate_structures, data=[\"i\" for i in range(100)])\nplot_energy_volume_curve = job(_plot_energy_volume_curve)\nget_bulk_structure = job(_get_bulk_structure)",
+   "source": [
+    "calculate_qe = job(_calculate_qe, data=[\"energy\", \"volume\", \"structure\"])\n",
+    "generate_structures = job(_generate_structures, data=[f\"s_{i}\" for i in range(100)])\n",
+    "plot_energy_volume_curve = job(_plot_energy_volume_curve)\n",
+    "get_bulk_structure = job(_get_bulk_structure)"
+   ],
    "metadata": {
     "trusted": true
    },
@@ -140,7 +145,21 @@
   {
    "id": "53e979ac-21db-4aa5-ae58-7cfc08dfa87b",
    "cell_type": "code",
-   "source": "job_strain_lst = []\nfor i in range(number_of_strains):\n    calc_strain = calculate_qe(\n        working_directory=\"strain_\" + str(i),\n        input_dict={\n            \"structure\": getattr(structure_lst.output, str(i)),\n            \"pseudopotentials\": pseudopotentials,\n            \"kpts\": (3, 3, 3),\n            \"calculation\": \"scf\",\n            \"smearing\": 0.02,\n        },\n    )\n    job_strain_lst.append(calc_strain)",
+   "source": [
+    "job_strain_lst = []\n",
+    "for i in range(number_of_strains):\n",
+    "    calc_strain = calculate_qe(\n",
+    "        working_directory=\"strain_\" + str(i),\n",
+    "        input_dict={\n",
+    "            \"structure\": getattr(structure_lst.output, f\"s_{i}\"),\n",
+    "            \"pseudopotentials\": pseudopotentials,\n",
+    "            \"kpts\": (3, 3, 3),\n",
+    "            \"calculation\": \"scf\",\n",
+    "            \"smearing\": 0.02,\n",
+    "        },\n",
+    "    )\n",
+    "    job_strain_lst.append(calc_strain)"
+   ],
    "metadata": {
     "trusted": true
    },

quantum_espresso_workflow.py

@@ -58,7 +58,7 @@ def generate_structures(structure, strain_lst):
             structure_strain.cell * strain ** (1 / 3), scale_atoms=True
         )
         structure_lst.append(structure_strain)
-    return {str(i): atoms_to_json_dict(atoms=s) for i, s in enumerate(structure_lst)}
+    return {f"s_{i}": atoms_to_json_dict(atoms=s) for i, s in enumerate(structure_lst)}
 
 
 def plot_energy_volume_curve(volume_lst, energy_lst):
@@ -110,4 +110,4 @@ def atoms_to_json_dict(atoms):
         else:
             json_dict[key] = value
 
-    return json_dict
+    return json_dict

workflow_qe.json

@@ -47,35 +47,35 @@
     {"target": 2, "targetHandle": "structure", "source": 1, "sourceHandle": "structure"},
     {"target": 2, "targetHandle": "strain_lst", "source": 18, "sourceHandle": null},
     {"target": 3, "targetHandle": "working_directory", "source": 19, "sourceHandle": null},
-    {"target": 20, "targetHandle": "structure", "source": 2, "sourceHandle": "0"},
+    {"target": 20, "targetHandle": "structure", "source": 2, "sourceHandle": "s_0"},
     {"target": 20, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
     {"target": 20, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
     {"target": 20, "targetHandle": "calculation", "source": 21, "sourceHandle": null},
     {"target": 20, "targetHandle": "smearing", "source": 17, "sourceHandle": null},
     {"target": 3, "targetHandle": "input_dict", "source": 20, "sourceHandle": null},
     {"target": 4, "targetHandle": "working_directory", "source": 22, "sourceHandle": null},
-    {"target": 23, "targetHandle": "structure", "source": 2, "sourceHandle": "1"},
+    {"target": 23, "targetHandle": "structure", "source": 2, "sourceHandle": "s_1"},
     {"target": 23, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
     {"target": 23, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
     {"target": 23, "targetHandle": "calculation", "source": 21, "sourceHandle": null},
     {"target": 23, "targetHandle": "smearing", "source": 17, "sourceHandle": null},
     {"target": 4, "targetHandle": "input_dict", "source": 23, "sourceHandle": null},
     {"target": 5, "targetHandle": "working_directory", "source": 24, "sourceHandle": null},
-    {"target": 25, "targetHandle": "structure", "source": 2, "sourceHandle": "2"},
+    {"target": 25, "targetHandle": "structure", "source": 2, "sourceHandle": "s_2"},
     {"target": 25, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
     {"target": 25, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
     {"target": 25, "targetHandle": "calculation", "source": 21, "sourceHandle": null},
     {"target": 25, "targetHandle": "smearing", "source": 17, "sourceHandle": null},
     {"target": 5, "targetHandle": "input_dict", "source": 25, "sourceHandle": null},
     {"target": 6, "targetHandle": "working_directory", "source": 26, "sourceHandle": null},
-    {"target": 27, "targetHandle": "structure", "source": 2, "sourceHandle": "3"},
+    {"target": 27, "targetHandle": "structure", "source": 2, "sourceHandle": "s_3"},
     {"target": 27, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
     {"target": 27, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
     {"target": 27, "targetHandle": "calculation", "source": 21, "sourceHandle": null},
     {"target": 27, "targetHandle": "smearing", "source": 17, "sourceHandle": null},
     {"target": 6, "targetHandle": "input_dict", "source": 27, "sourceHandle": null},
     {"target": 7, "targetHandle": "working_directory", "source": 28, "sourceHandle": null},
-    {"target": 29, "targetHandle": "structure", "source": 2, "sourceHandle": "4"},
+    {"target": 29, "targetHandle": "structure", "source": 2, "sourceHandle": "s_4"},
     {"target": 29, "targetHandle": "pseudopotentials", "source": 14, "sourceHandle": null},
     {"target": 29, "targetHandle": "kpts", "source": 15, "sourceHandle": null},
     {"target": 29, "targetHandle": "calculation", "source": 21, "sourceHandle": null},