From e59cba5a5dbf78b160f02e40eea9e7002e9d66de Mon Sep 17 00:00:00 2001 From: liamhuber Date: Mon, 8 May 2023 11:21:50 -0700 Subject: [PATCH] Clean up at the end of the example --- notebooks/example.ipynb | 330 +++++++++++++++++++++++++--------------- 1 file changed, 205 insertions(+), 125 deletions(-) diff --git a/notebooks/example.ipynb b/notebooks/example.ipynb index e5e4455..5edaf24 100644 --- a/notebooks/example.ipynb +++ b/notebooks/example.ipynb @@ -78,6 +78,8 @@ " atomistics.UserInput,\n", " atomistics.PyironObject,\n", " atomistics.PhysicalProperty,\n", + " atomistics.Energy,\n", + " atomistics.Force,\n", " atomistics.ChemicalElement,\n", " atomistics.MaterialProperty,\n", " atomistics.BulkModulus,\n", @@ -131,7 +133,9 @@ "data": { "text/plain": [ "[atomistics.project,\n", + " atomistics.userinput1,\n", " atomistics.project_input_name,\n", + " atomistics.atomisticsproject1,\n", " atomistics.project_output_atomistics_project,\n", " atomistics.bulk_structure,\n", " atomistics.generic1,\n", @@ -144,32 +148,48 @@ " atomistics.structure2,\n", " atomistics.surface_structure_output_structure,\n", " atomistics.lammps,\n", + " atomistics.atomisticsproject2,\n", + " atomistics.lammps_input_project,\n", " atomistics.structure3,\n", " atomistics.lammps_input_structure,\n", " atomistics.lammps1,\n", " atomistics.lammps_output_job,\n", " atomistics.vasp,\n", + " atomistics.atomisticsproject3,\n", + " atomistics.vasp_input_project,\n", " atomistics.generic3,\n", " atomistics.vasp_input_structure,\n", " atomistics.vasp1,\n", " atomistics.vasp_output_job,\n", - " atomistics.murnaghan,\n", - " atomistics.atomisticsproject1,\n", - " atomistics.murnaghan_input_project,\n", + " atomistics.atomistic_taker,\n", " atomistics.atomisticsjob1,\n", " atomistics.structure4,\n", + " atomistics.atomistic_taker_job,\n", + " atomistics.energy1,\n", + " atomistics.atomistic_taker_output_energy_pot,\n", + " atomistics.force1,\n", + " atomistics.atomistic_taker_output_forces,\n", + " atomistics.murnaghan,\n", + " atomistics.atomisticsproject4,\n", + " atomistics.murnaghan_input_project,\n", + " atomistics.atomisticsjob2,\n", + " atomistics.structure5,\n", " atomistics.murnaghan_input_job,\n", " atomistics.bulkmodulus1,\n", " atomistics.murnaghan_output_bulk_modulus,\n", " atomistics.bprime1,\n", " atomistics.murnaghan_output_b_prime,\n", " atomistics.surface_energy,\n", - " atomistics.atomisticsjob2,\n", - " atomistics.bulk1,\n", - " atomistics.surface_energy_input_bulk_job,\n", - " atomistics.atomisticsjob3,\n", - " atomistics.hassurface1,\n", - " atomistics.surface_energy_input_slab_job,\n", + " atomistics.structure6,\n", + " atomistics.surface_energy_input_bulk_structure,\n", + " atomistics.energy2,\n", + " atomistics.structure7,\n", + " atomistics.surface_energy_input_bulk_energy,\n", + " atomistics.structure8,\n", + " atomistics.surface_energy_input_slab_structure,\n", + " atomistics.energy3,\n", + " atomistics.structure9,\n", + " atomistics.surface_energy_input_slab_energy,\n", " atomistics.surfaceenergy1,\n", " atomistics.surface_energy_output_surface_energy]" ] @@ -200,11 +220,11 @@ { "data": { "text/plain": [ - "[atomistics.PyironOntoThing,\n", - " atomistics.IO,\n", - " owl.Thing,\n", + "[atomistics.IO,\n", " atomistics.Input,\n", + " owl.Thing,\n", " atomistics.Parameter,\n", + " atomistics.PyironOntoThing,\n", " atomistics.WorkflowThing]" ] }, @@ -226,14 +246,14 @@ { "data": { "text/plain": [ - "[atomistics.Dimensional,\n", - " atomistics.PyironObject,\n", - " atomistics.Generic,\n", - " atomistics.PyironOntoThing,\n", + "[atomistics.ThreeD,\n", + " atomistics.Dimensional,\n", " owl.Thing,\n", - " atomistics.Structure,\n", " atomistics.Parameter,\n", - " atomistics.ThreeD]" + " atomistics.Structure,\n", + " atomistics.Generic,\n", + " atomistics.PyironObject,\n", + " atomistics.PyironOntoThing]" ] }, "execution_count": 6, @@ -262,7 +282,9 @@ { "data": { "text/plain": [ - "([atomistics.vasp_input_structure], None, [atomistics.vasp_input_structure])" + "([atomistics.vasp_input_project, atomistics.vasp_input_structure],\n", + " None,\n", + " [atomistics.vasp_input_project, atomistics.vasp_input_structure])" ] }, "execution_count": 7, @@ -314,10 +336,10 @@ "output_type": "stream", "text": [ "some_code atomistics.vasp\n", - "first_input atomistics.vasp_input_structure\n", - "appears_elsewhere [atomistics.vasp_input_structure]\n", - "can_come_from [atomistics.bulk_structure_output_structure, atomistics.surface_structure_output_structure]\n", - "which_is_produced_by atomistics.bulk_structure\n" + "first_input atomistics.vasp_input_project\n", + "appears_elsewhere [atomistics.vasp_input_project]\n", + "can_come_from [atomistics.project_output_atomistics_project]\n", + "which_is_produced_by atomistics.project\n" ] } ], @@ -357,11 +379,14 @@ "output_type": "stream", "text": [ "lammps\n", + "\tlammps_input_project\n", + "\t\tproject_output_atomistics_project\n", + "\t\t\tproject\n", "\tlammps_input_structure\n", - "\t\tbulk_structure_output_structure\n", - "\t\t\tbulk_structure\n", "\t\tsurface_structure_output_structure\n", - "\t\t\tsurface_structure\n" + "\t\t\tsurface_structure\n", + "\t\tbulk_structure_output_structure\n", + "\t\t\tbulk_structure\n" ] } ], @@ -395,14 +420,22 @@ "\tmurnaghan_output_bulk_modulus\n", "\t\tmurnaghan\n", "\t\t\tmurnaghan_input_project\n", + "\t\t\t\tproject_output_atomistics_project\n", + "\t\t\t\t\tproject\n", "\t\t\tmurnaghan_input_job\n", "\t\t\t\tlammps_output_job\n", "\t\t\t\t\tlammps\n", + "\t\t\t\t\t\tlammps_input_project\n", + "\t\t\t\t\t\t\tproject_output_atomistics_project\n", + "\t\t\t\t\t\t\t\tproject\n", "\t\t\t\t\t\tlammps_input_structure\n", "\t\t\t\t\t\t\tbulk_structure_output_structure\n", "\t\t\t\t\t\t\t\tbulk_structure\n", "\t\t\t\tvasp_output_job\n", "\t\t\t\t\tvasp\n", + "\t\t\t\t\t\tvasp_input_project\n", + "\t\t\t\t\t\t\tproject_output_atomistics_project\n", + "\t\t\t\t\t\t\t\tproject\n", "\t\t\t\t\t\tvasp_input_structure\n", "\t\t\t\t\t\t\tbulk_structure_output_structure\n", "\t\t\t\t\t\t\t\tbulk_structure\n" @@ -440,7 +473,7 @@ { "data": { "text/plain": [ - "(,\n", + "(,\n", " [atomistics.murnaghan_output_b_prime])" ] }, @@ -462,7 +495,7 @@ { "data": { "text/plain": [ - "(, [atomistics.murnaghan])" + "(, [atomistics.murnaghan])" ] }, "execution_count": 14, @@ -483,7 +516,7 @@ { "data": { "text/plain": [ - "(,\n", + "(,\n", " [atomistics.murnaghan_input_project, atomistics.murnaghan_input_job])" ] }, @@ -513,7 +546,7 @@ { "data": { "text/plain": [ - "(,\n", + "(,\n", " [atomistics.lammps_output_job, atomistics.vasp_output_job])" ] }, @@ -535,7 +568,7 @@ { "data": { "text/plain": [ - "(, [atomistics.vasp])" + "(, [atomistics.vasp])" ] }, "execution_count": 17, @@ -556,8 +589,8 @@ { "data": { "text/plain": [ - "(,\n", - " [atomistics.vasp_input_structure])" + "(,\n", + " [atomistics.vasp_input_project, atomistics.vasp_input_structure])" ] }, "execution_count": 18, @@ -578,8 +611,8 @@ { "data": { "text/plain": [ - "(,\n", - " [atomistics.bulk_structure_output_structure])" + "(,\n", + " [atomistics.project_output_atomistics_project])" ] }, "execution_count": 19, @@ -600,8 +633,7 @@ { "data": { "text/plain": [ - "(,\n", - " [atomistics.bulk_structure])" + "(, [atomistics.project])" ] }, "execution_count": 20, @@ -622,7 +654,7 @@ { "data": { "text/plain": [ - "(, [])" + "(, [])" ] }, "execution_count": 21, @@ -650,9 +682,9 @@ "\t\t\tmurnaghan_input_job\n", "\t\t\t\tvasp_output_job\n", "\t\t\t\t\tvasp\n", - "\t\t\t\t\t\tvasp_input_structure\n", - "\t\t\t\t\t\t\tbulk_structure_output_structure\n", - "\t\t\t\t\t\t\t\tbulk_structure\n" + "\t\t\t\t\t\tvasp_input_project\n", + "\t\t\t\t\t\t\tproject_output_atomistics_project\n", + "\t\t\t\t\t\t\t\tproject\n" ] } ], @@ -687,10 +719,30 @@ "id": "81d4f04a-1ed3-43a0-8a82-dbfbe4c14cf3", "metadata": {}, "outputs": [ + { + "data": { + "text/html": [ + "
\n"
+      ],
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "data": {
+      "text/html": [
+       "
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+      ],
+      "text/plain": []
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "9d50b39700fd41dea0bb1fde6541ea8f",
+       "model_id": "739f6ba574ba447ba0351e5d7c533857",
        "version_major": 2,
        "version_minor": 0
       },
@@ -735,12 +787,12 @@
     {
      "data": {
       "application/vnd.jupyter.widget-view+json": {
-       "model_id": "5c1e6945cff444a9a22997878c89695f",
+       "model_id": "441b49b5f43e4d4fbb3657a519c1443e",
        "version_major": 2,
        "version_minor": 0
       },
       "text/plain": [
-       "  0%|          | 0/2 [00:00\n",
        "    \n",
        "      1\n",
-       "      Ag10Cu98\n",
-       "      133.054571\n",
+       "      Ag9Cu99\n",
+       "      134.392608\n",
        "      GPa\n",
        "      Lammps\n",
        "    \n",
        "    \n",
        "      2\n",
-       "      Ag21Cu87\n",
-       "      108.145058\n",
+       "      Ag24Cu84\n",
+       "      NaN\n",
        "      GPa\n",
        "      Lammps\n",
        "    \n",
@@ -938,14 +1003,14 @@
        "    \n",
        "      4\n",
        "      Cu99Ni9\n",
-       "      145.898783\n",
+       "      145.901172\n",
        "      GPa\n",
        "      Lammps\n",
        "    \n",
        "    \n",
        "      5\n",
-       "      Cu85Ni23\n",
-       "      151.789724\n",
+       "      Cu83Ni25\n",
+       "      152.635624\n",
        "      GPa\n",
        "      Lammps\n",
        "    \n",
@@ -956,11 +1021,11 @@
       "text/plain": [
        "  Chemical Formula  atomistics.BulkModulus unit  Engine\n",
        "0            Cu108              141.949581  GPa  Lammps\n",
-       "1         Ag10Cu98              133.054571  GPa  Lammps\n",
-       "2         Ag21Cu87              108.145058  GPa  Lammps\n",
+       "1          Ag9Cu99              134.392608  GPa  Lammps\n",
+       "2         Ag24Cu84                     NaN  GPa  Lammps\n",
        "3            Cu108              141.949581  GPa  Lammps\n",
-       "4          Cu99Ni9              145.898783  GPa  Lammps\n",
-       "5         Cu85Ni23              151.789724  GPa  Lammps"
+       "4          Cu99Ni9              145.901172  GPa  Lammps\n",
+       "5         Cu83Ni25              152.635624  GPa  Lammps"
       ]
      },
      "execution_count": 28,
@@ -1023,15 +1088,15 @@
        "    \n",
        "    \n",
        "      1\n",
-       "      Ag10Cu98\n",
-       "      6.431123\n",
+       "      Ag9Cu99\n",
+       "      6.157580\n",
        "      None\n",
        "      Lammps\n",
        "    \n",
        "    \n",
        "      2\n",
-       "      Ag21Cu87\n",
-       "      10.219065\n",
+       "      Ag24Cu84\n",
+       "      NaN\n",
        "      None\n",
        "      Lammps\n",
        "    \n",
@@ -1045,14 +1110,14 @@
        "    \n",
        "      4\n",
        "      Cu99Ni9\n",
-       "      4.310008\n",
+       "      4.309860\n",
        "      None\n",
        "      Lammps\n",
        "    \n",
        "    \n",
        "      5\n",
-       "      Cu85Ni23\n",
-       "      4.136946\n",
+       "      Cu83Ni25\n",
+       "      4.112948\n",
        "      None\n",
        "      Lammps\n",
        "    \n",
@@ -1063,11 +1128,11 @@
       "text/plain": [
        "  Chemical Formula  atomistics.BPrime  unit  Engine\n",
        "0            Cu108           4.393195  None  Lammps\n",
-       "1         Ag10Cu98           6.431123  None  Lammps\n",
-       "2         Ag21Cu87          10.219065  None  Lammps\n",
+       "1          Ag9Cu99           6.157580  None  Lammps\n",
+       "2         Ag24Cu84                NaN  None  Lammps\n",
        "3            Cu108           4.393195  None  Lammps\n",
-       "4          Cu99Ni9           4.310008  None  Lammps\n",
-       "5         Cu85Ni23           4.136946  None  Lammps"
+       "4          Cu99Ni9           4.309860  None  Lammps\n",
+       "5         Cu83Ni25           4.112948  None  Lammps"
       ]
      },
      "execution_count": 29,
@@ -1092,10 +1157,33 @@
    "execution_count": 30,
    "id": "3aea218a-9c08-449e-83c6-dbfc9799ed88",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/var/folders/ff/j3764z6n37386m647kqygyzw0000gp/T/ipykernel_94195/3270375829.py:1: DeprecationWarning: pyiron_base.project.generic.remove_jobs_silently is deprecated: Use pr.remove_jobs(silently=True) rather than pr.remove_jobs_silently()..\n",
+      "  pr.remove_jobs_silently(recursive=True)\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "e6589d0f80274bd3878895b811c6a071",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "  0%|          | 0/48 [00:00