Merge pull request #3 from nanotech-empa/release/1.4.0

Release/1.4.0
nanotech-empa · Mar 13, 2021 · ee1389f · ee1389f
2 parents 2204933 + 7a522dc
commit ee1389f
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Showing 5 changed files with 99 additions and 14 deletions.
diff --git a/afm/submit_afm.ipynb b/afm/submit_afm.ipynb
@@ -15,7 +15,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "from aiida_cp2k.calculations import Cp2kCalculation\n",
     "\n",
     "from aiida.orm import ArrayData\n",
@@ -67,6 +66,9 @@
     "        \n",
     "        #slab_analyzed = find_mol.analyze_slab(atoms)\n",
     "        viewer_widget.setup(atoms)\n",
+    "        \n",
+    "        if structure.creator is not None:\n",
+    "            text_calc_description.value = structure.creator.description\n",
     "\n",
     "    \n",
     "struct_browser = StructureBrowserWidget()\n",
@@ -264,6 +266,25 @@
     "    return paramdata"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Submission"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Description for the calculation (try to read from the structure creator)\n",
+    "\n",
+    "text_calc_description = ipw.Text(description='Description:', layout={'width': '45%'})\n",
+    "display(text_calc_description)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -299,7 +320,7 @@
     "        except:\n",
     "            wfn_file_path = \"\"\n",
     "        if wfn_file_path == \"\":\n",
-    "            print(\"Didn't find any accessible .wfn file.\")\n",
+    "            print(\"Info: didn't find any accessible .wfn file.\")\n",
     "            \n",
     "        node = submit(\n",
     "            AfmWorkChain,\n",
@@ -311,7 +332,8 @@
     "            afm_pp_code=drop_pp.value,\n",
     "            afm_pp_params=afm_pp_params,\n",
     "            afm_2pp_code=drop_2pp.value,\n",
-    "            afm_2pp_params=afm_2pp_params\n",
+    "            afm_2pp_params=afm_2pp_params,\n",
+    "            metadata={'description': text_calc_description.value}\n",
     "        )\n",
     "                \n",
     "        # set calculation version; also used to determine post-processing\n",

diff --git a/metadata.json b/metadata.json
@@ -1,7 +1,7 @@
 {
     "description": "App to run scanning probe microscopy simulations.",
     "title": "Empa nanotech@surfaces Laboratory - Scanning Probe Microscopy",
-    "version": "1.3",
+    "version": "1.4.0",
     "logo": "miscellaneous/logos/empa.png",
     "authors": "nanotech@surfaces laboratory, Empa",
     "state": "stable"

diff --git a/orb/submit_orb.ipynb b/orb/submit_orb.ipynb
@@ -15,7 +15,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "\n",
     "from aiida_cp2k.calculations import Cp2kCalculation\n",
     "\n",
     "from aiida.orm import Code, Computer\n",
@@ -74,7 +73,10 @@
     "        viewer_widget.setup(atoms, slab_analyzed)\n",
     "        \n",
     "        #cell_text.value = \" \".join([str(c) for c in np.diag(atoms.cell)])\n",
-    "\n",
+    "    \n",
+    "        if structure.creator is not None:\n",
+    "            text_calc_description.value = structure.creator.description\n",
+    "            \n",
     "    \n",
     "struct_browser = StructureBrowserWidget()\n",
     "struct_browser.results.observe(on_struct_change, names='value')\n",
@@ -283,6 +285,25 @@
     "display(n_homo_inttext, n_lumo_inttext, heights_text, isovals_text, fwhms_text, extrap_plane_floattext)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Submission"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Description for the calculation (try to read from the structure creator)\n",
+    "\n",
+    "text_calc_description = ipw.Text(description='Description:', layout={'width': '45%'})\n",
+    "display(text_calc_description)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -366,7 +387,8 @@
     "            wfn_file_path=Str(wfn_file_path),\n",
     "            dft_params=dft_params,\n",
     "            stm_code=stm_code,\n",
-    "            stm_params=stm_params\n",
+    "            stm_params=stm_params,\n",
+    "            metadata={'description': text_calc_description.value}\n",
     "        )\n",
     "        \n",
     "        # set calculation version; also used to determine post-processing\n",

diff --git a/pdos/submit_pdos.ipynb b/pdos/submit_pdos.ipynb
@@ -60,6 +60,11 @@
     "    guess_molecule()\n",
     "    update_view()\n",
     "    \n",
+    "    structure = struct_browser.results.value\n",
+    "    if structure:\n",
+    "         if structure.creator is not None:\n",
+    "            text_calc_description.value = structure.creator.description\n",
+    "    \n",
     "    \n",
     "struct_browser = StructureBrowserWidget()\n",
     "struct_browser.results.observe(on_struct_change, names='value')\n",
@@ -347,6 +352,25 @@
     "display(num_homo_inttext, num_lumo_inttext, emin_floattext, emax_floattext)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Submission"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Description for the calculation (try to read from the structure creator)\n",
+    "\n",
+    "text_calc_description = ipw.Text(description='Description:', layout={'width': '45%'})\n",
+    "display(text_calc_description)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -398,7 +422,7 @@
     "        except:\n",
     "            wfn_file_path = \"\"\n",
     "        if wfn_file_path == \"\":\n",
-    "            print(\"Didn't find any accessible .wfn file.\")\n",
+    "            print(\"Info: didn't find any accessible .wfn file.\")\n",
     "        \n",
     "        mol_structure = StructureData(ase=get_mol_ase())\n",
     "        mol_structure.description = \"mol from slab PK%d\" %  struct.pk\n",
@@ -416,7 +440,8 @@
     "            wfn_file_path=Str(wfn_file_path),\n",
     "            elpa_switch=Bool(elpa_check.value),\n",
     "            overlap_code=overlap_code,\n",
-    "            overlap_params=overlap_params\n",
+    "            overlap_params=overlap_params,\n",
+    "            metadata={'description': text_calc_description.value}\n",
     "        )\n",
     "                \n",
     "        # set calculation version; also used to determine post-processing\n",

diff --git a/stm/submit_stm.ipynb b/stm/submit_stm.ipynb
@@ -69,14 +69,29 @@
     "        viewer_widget.setup(atoms, slab_analyzed)\n",
     "        \n",
     "        #cell_text.value = \" \".join([str(c) for c in np.diag(atoms.cell)])\n",
+    "        \n",
+    "        if structure.creator is not None:\n",
+    "            text_calc_description.value = structure.creator.description\n",
     "\n",
     "    \n",
     "struct_browser = StructureBrowserWidget()\n",
     "struct_browser.results.observe(on_struct_change, names='value')\n",
     "\n",
     "viewer_widget = ViewerDetails()\n",
     "\n",
-    "display(ipw.VBox([struct_browser, viewer_widget]))\n"
+    "display(ipw.VBox([struct_browser, viewer_widget]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Description for the calculation (try to read from the structure creator)\n",
+    "\n",
+    "text_calc_description = ipw.Text(description='Description:', layout={'width': '45%'})\n",
+    "display(text_calc_description)"
    ]
   },
   {
@@ -97,8 +112,8 @@
     "def on_computer_change(c):\n",
     "    global cp2k_codes, stm_codes\n",
     "    if computer_drop.selected_computer is not None:\n",
-    "        cp2k_codes = common.comp_plugin_codes(computer_drop.selected_computer.name, 'cp2k')\n",
-    "        stm_codes = common.comp_plugin_codes(computer_drop.selected_computer.name, 'spm.stm')\n",
+    "        cp2k_codes = common.comp_plugin_codes(computer_drop.selected_computer.label, 'cp2k')\n",
+    "        stm_codes = common.comp_plugin_codes(computer_drop.selected_computer.label, 'spm.stm')\n",
     "\n",
     "        drop_cp2k.options = [c.label for c in cp2k_codes]\n",
     "        drop_stm.options = [c.label for c in stm_codes]\n",
@@ -305,7 +320,7 @@
     "        except:\n",
     "            wfn_file_path = \"\"\n",
     "        if wfn_file_path == \"\":\n",
-    "            print(\"Didn't find any accessible .wfn file.\")\n",
+    "            print(\"Info: didn't find any accessible .wfn file.\")\n",
     "            \n",
     "        node = submit(\n",
     "            STMWorkChain,\n",
@@ -314,7 +329,8 @@
     "            wfn_file_path=Str(wfn_file_path),\n",
     "            dft_params=dft_params,\n",
     "            stm_code=stm_code,\n",
-    "            stm_params=stm_params\n",
+    "            stm_params=stm_params,\n",
+    "            metadata={'description': text_calc_description.value}\n",
     "        )\n",
     "        \n",
     "        # set calculation version; also used to determine post-processing\n",