adding the Kinds property.

Issue: recursion if call get_kinds from the Kinds validator.
aiidateam · Feb 23, 2024 · 1af101e · 1af101e
1 parent b05dfce
commit 1af101e
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diff --git a/docs/source/user_guide/structuredata/user_guide_SData.ipynb b/docs/source/user_guide/structuredata/user_guide_SData.ipynb
@@ -107,7 +107,7 @@
      "output_type": "stream",
      "text": [
       "The whole list of currently supported properties is: \n",
-      "['cell', 'symbols', 'pbc', 'charge', 'positions', 'mass', 'custom']\n"
+      "['symbols', 'cell', 'mass', 'charge', 'positions', 'kinds', 'custom', 'pbc']\n"
      ]
     }
    ],
@@ -130,7 +130,7 @@
     {
      "data": {
       "text/plain": [
-       "<StructureData: uuid: 04631aff-7725-43e3-b4d0-9a307d3af3a2 (unstored)>"
+       "<StructureData: uuid: 2b7cd70e-8a33-4666-8043-d80df3e373b3 (unstored)>"
       ]
      },
      "execution_count": 4,
@@ -160,7 +160,7 @@
      "output_type": "stream",
      "text": [
       "The cell property class: \n",
-      "parent=<StructureData: uuid: 04631aff-7725-43e3-b4d0-9a307d3af3a2 (unstored)> value=[[3.5, 0.0, 0.0], [0.0, 3.5, 0.0], [0.0, 0.0, 3.5]] domain='global'\n",
+      "parent=<StructureData: uuid: 2b7cd70e-8a33-4666-8043-d80df3e373b3 (unstored)> value=[[3.5, 0.0, 0.0], [0.0, 3.5, 0.0], [0.0, 0.0, 3.5]] domain='global'\n",
       "\n",
       "The cell property value: \n",
       "[[3.5, 0.0, 0.0], [0.0, 3.5, 0.0], [0.0, 0.0, 3.5]]\n",
@@ -187,7 +187,7 @@
      "output_type": "stream",
      "text": [
       "The positions property class: \n",
-      "parent=<StructureData: uuid: 04631aff-7725-43e3-b4d0-9a307d3af3a2 (unstored)> domain='intra-site' value=[[0.0, 0.0, 0.0], [1.5, 1.5, 1.5]]\n",
+      "parent=<StructureData: uuid: 2b7cd70e-8a33-4666-8043-d80df3e373b3 (unstored)> domain='intra-site' value=[[0.0, 0.0, 0.0], [1.5, 1.5, 1.5]]\n",
       "\n",
       "The positions property value: \n",
       "[[0.0, 0.0, 0.0], [1.5, 1.5, 1.5]]\n",
@@ -214,7 +214,7 @@
      "output_type": "stream",
      "text": [
       "Stored properties are: \n",
-      "['cell', 'pbc', 'symbols', 'positions']\n"
+      "['symbols', 'cell', 'mass', 'positions', 'pbc']\n"
      ]
     }
    ],
@@ -259,7 +259,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
@@ -270,7 +270,7 @@
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mNotImplementedError\u001b[0m                       Traceback (most recent call last)",
       "Cell \u001b[0;32mIn[9], line 1\u001b[0m\n\u001b[0;32m----> 1\u001b[0m \u001b[43mstructure\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mproperties\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcell\u001b[49m \u001b[38;5;241m=\u001b[39m [[\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m2\u001b[39m,\u001b[38;5;241m3\u001b[39m],[\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m2\u001b[39m,\u001b[38;5;241m3\u001b[39m],[\u001b[38;5;241m1\u001b[39m,\u001b[38;5;241m2\u001b[39m,\u001b[38;5;241m3\u001b[39m]]\n",
-      "File \u001b[0;32m~/Envs/aiida-muonic/codes/aiida-atomistic/src/aiida_atomistic/data/structure/properties/property_utils.py:112\u001b[0m, in \u001b[0;36mPropertyMixinMetaclass.__new__.<locals>.<lambda>\u001b[0;34m(self, pname, pvalue)\u001b[0m\n\u001b[1;32m    106\u001b[0m         func_get \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mlambda\u001b[39;00m \u001b[38;5;28mself\u001b[39m, type_hint\u001b[38;5;241m=\u001b[39mtype_hint, attr\u001b[38;5;241m=\u001b[39mattr: \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_template_property(type_hint\u001b[38;5;241m=\u001b[39mtype_hint, attr\u001b[38;5;241m=\u001b[39mattr)\n\u001b[1;32m    108\u001b[0m         \u001b[38;5;66;03m# We do not allow to set any property after the creation of the instance: \u001b[39;00m\n\u001b[1;32m    109\u001b[0m         \u001b[38;5;66;03m#===> WE CAN DEACTIVATE THE METHOD, using the `allow_no_calls_decorator`.\u001b[39;00m\n\u001b[1;32m    110\u001b[0m         \u001b[38;5;66;03m# Here below, we leave it there for now, in case it is needed in the future.\u001b[39;00m\n\u001b[1;32m    111\u001b[0m         \u001b[38;5;66;03m#func_set = lambda self, type_hint=type_hint, attr=attr: self._template_property(type_hint=type_hint, attr=attr)\u001b[39;00m\n\u001b[0;32m--> 112\u001b[0m         func_set \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mlambda\u001b[39;00m \u001b[38;5;28mself\u001b[39m, pname\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, pvalue\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m: \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_set_property\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpname\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpvalue\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    113\u001b[0m         \u001b[38;5;28msetattr\u001b[39m(\u001b[38;5;28mcls\u001b[39m, attr, \u001b[38;5;28mproperty\u001b[39m(fget\u001b[38;5;241m=\u001b[39mfunc_get,fset\u001b[38;5;241m=\u001b[39mfunc_set))\n\u001b[1;32m    115\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mcls\u001b[39m\n",
+      "File \u001b[0;32m~/Envs/aiida-muonic/codes/aiida-atomistic/src/aiida_atomistic/data/structure/properties/property_utils.py:113\u001b[0m, in \u001b[0;36mPropertyMixinMetaclass.__new__.<locals>.<lambda>\u001b[0;34m(self, pname, pvalue)\u001b[0m\n\u001b[1;32m    107\u001b[0m         func_get \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mlambda\u001b[39;00m \u001b[38;5;28mself\u001b[39m, type_hint\u001b[38;5;241m=\u001b[39mtype_hint, attr\u001b[38;5;241m=\u001b[39mattr: \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_template_property(type_hint\u001b[38;5;241m=\u001b[39mtype_hint, attr\u001b[38;5;241m=\u001b[39mattr)\n\u001b[1;32m    109\u001b[0m         \u001b[38;5;66;03m# We do not allow to set any property after the creation of the instance: \u001b[39;00m\n\u001b[1;32m    110\u001b[0m         \u001b[38;5;66;03m#===> WE CAN DEACTIVATE THE METHOD, using the `allow_no_calls_decorator`.\u001b[39;00m\n\u001b[1;32m    111\u001b[0m         \u001b[38;5;66;03m# Here below, we leave it there for now, in case it is needed in the future.\u001b[39;00m\n\u001b[1;32m    112\u001b[0m         \u001b[38;5;66;03m#func_set = lambda self, type_hint=type_hint, attr=attr: self._template_property(type_hint=type_hint, attr=attr)\u001b[39;00m\n\u001b[0;32m--> 113\u001b[0m         func_set \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mlambda\u001b[39;00m \u001b[38;5;28mself\u001b[39m, pname\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m, pvalue\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mNone\u001b[39;00m: \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_set_property\u001b[49m\u001b[43m(\u001b[49m\u001b[43mpname\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpvalue\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m    114\u001b[0m         \u001b[38;5;28msetattr\u001b[39m(\u001b[38;5;28mcls\u001b[39m, attr, \u001b[38;5;28mproperty\u001b[39m(fget\u001b[38;5;241m=\u001b[39mfunc_get,fset\u001b[38;5;241m=\u001b[39mfunc_set))\n\u001b[1;32m    116\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mcls\u001b[39m\n",
       "File \u001b[0;32m~/Envs/aiida-muonic/codes/aiida-atomistic/src/aiida_atomistic/data/structure/properties/property_utils.py:38\u001b[0m, in \u001b[0;36mallow_no_calls_decorator.<locals>.wrapper\u001b[0;34m(*args, **kwargs)\u001b[0m\n\u001b[1;32m     35\u001b[0m \u001b[38;5;28mlocals\u001b[39m \u001b[38;5;241m=\u001b[39m frame\u001b[38;5;241m.\u001b[39mf_back\u001b[38;5;241m.\u001b[39mf_locals\n\u001b[1;32m     37\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlocals\u001b[39m\u001b[38;5;241m.\u001b[39mget(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mself\u001b[39m\u001b[38;5;124m'\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;129;01mis\u001b[39;00m args[\u001b[38;5;241m0\u001b[39m]:\n\u001b[0;32m---> 38\u001b[0m     \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mNotImplementedError\u001b[39;00m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mAfter the initialization, `properties` and its attributes are read-only!\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m     39\u001b[0m     \u001b[38;5;28mprint\u001b[39m(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mCalled from this class!\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m     40\u001b[0m     func(\u001b[38;5;241m*\u001b[39margs, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkwargs)\n",
       "\u001b[0;31mNotImplementedError\u001b[0m: After the initialization, `properties` and its attributes are read-only!"
      ]
@@ -304,7 +304,8 @@
        "{'cell': {'value': [[3.5, 0.0, 0.0], [0.0, 3.5, 0.0], [0.0, 0.0, 3.5]]},\n",
        " 'pbc': {'value': [True, True, True]},\n",
        " 'positions': {'value': [[0.0, 0.0, 0.0], [1.5, 1.5, 1.5]]},\n",
-       " 'symbols': {'value': ['Li', 'Li']}}"
+       " 'symbols': {'value': ['Li', 'Li']},\n",
+       " 'mass': {'value': [6.941, 6.941]}}"
       ]
      },
      "execution_count": 9,
@@ -323,6 +324,20 @@
     "Here below and example where we want to change the dimensionality of the structure: we elongate the cell along Z and we fix the pbc property consistently."
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## The `get_kinds()` method\n",
+    "\n",
+    "It is possible to get a list of kinds using the `get_kinds` method. \n",
+    "This will generate the corresponding predicted kinds for all the properties (the \"intra-site\" ones) \n",
+    "and then generate the list of global different kinds. \n",
+    "The default threshold used for each property can be found under the attribute ``\n",
+    "\n",
+    "This method should be used in the plugins which requires a kind-based definition of properties, e.g. the aiida-quantumespresso one."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 10,
@@ -348,31 +363,17 @@
     "print(f\"The cell property value: \\n{new_structure.properties.cell.value}\\n\")"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## The `get_kinds()` method\n",
-    "\n",
-    "It is possible to get a list of kinds using the `get_kinds` method. \n",
-    "This will generate the corresponding predicted kinds for all the properties (the \"intra-site\" ones) \n",
-    "and then generate the list of global different kinds. \n",
-    "The default threshold used for each property can be found under the attribute ``\n",
-    "\n",
-    "This method should be used in the plugins which requires a kind-based definition of properties, e.g. the aiida-quantumespresso one."
-   ]
-  },
   {
    "cell_type": "code",
-   "execution_count": 29,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "['Li0', 'Li1']\n",
-      "{'charge': [1.0, 0.0], 'mass': [6.941, 6.941]}\n"
+      "{'mass': {'value': [6.941, 6.941]}, 'charge': {'value': [1.0, 0.0]}}\n"
      ]
     }
    ],
@@ -416,7 +417,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 30,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [
     {
@@ -425,7 +426,7 @@
        "0.1"
       ]
      },
-     "execution_count": 30,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -436,20 +437,20 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "['Li0', 'Li1']\n",
-      "{'charge': [1.0, 0.0], 'mass': [6.941, 6.941]}\n"
+      "['Li0', 'Li0']\n",
+      "{'mass': {'value': [6.941, 6.941]}, 'charge': {'value': [0.0, 0.0]}}\n"
      ]
     }
    ],
    "source": [
-    "kinds, kinds_values = structure.get_kinds(custom_thr={\"charge\":0.6})\n",
+    "kinds, kinds_values = structure.get_kinds(custom_thr={\"charge\":2})\n",
     "\n",
     "print(kinds)\n",
     "print(kinds_values)"
@@ -468,15 +469,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
+   "execution_count": 14,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "['Li1', 'Li2', 'Cu1', 'Cu1']\n",
-      "{'charge': [1.0, 0.0], 'mass': [6.941, 6.941]}\n"
+      "{'mass': {'value': [6.941, 6.941]}, 'charge': {'value': [1.0, 0.0]}}\n"
      ]
     }
    ],
@@ -496,15 +497,15 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 34,
+   "execution_count": 15,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "['Li0', 'Li0']\n",
-      "{'mass': [6.941, 6.941]}\n"
+      "{'mass': {'value': [6.941, 6.941]}}\n"
      ]
     }
    ],
@@ -514,6 +515,118 @@
     "print(kinds)\n",
     "print(kinds_values)"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "It is possible to combine the `to_dict` and the `get_kinds` methods, in such a way to have a ready-to-use dictionary with also the kinds, automatically generated:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'cell': {'value': [[3.5, 0.0, 0.0], [0.0, 3.5, 0.0], [0.0, 0.0, 3.5]]},\n",
+       " 'pbc': {'value': [True, True, True]},\n",
+       " 'positions': {'value': [[0.0, 0.0, 0.0], [1.5, 1.5, 1.5]]},\n",
+       " 'symbols': {'value': ['Li', 'Li']},\n",
+       " 'mass': {'value': [6.941, 6.941]},\n",
+       " 'charge': {'value': [0.0, 0.0]},\n",
+       " 'kinds': {'value': ['Li0', 'Li0']}}"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "new_properties = structure.to_dict(generate_kinds= True, kinds_exclude=['mass'],kinds_thresholds={\"charge\":1.5})\n",
+    "new_properties"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 20,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "structure_with_kinds = StructureData(properties=new_properties)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 22,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Kinds(parent=<StructureData: uuid: 89aa0c75-d80f-4c9f-bfce-d7079852ead0 (unstored)>, domain='intra-site', value=['Li0', 'Li0'])"
+      ]
+     },
+     "execution_count": 22,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "structure_with_kinds.properties.kinds"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 23,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "<StructureData: uuid: 89aa0c75-d80f-4c9f-bfce-d7079852ead0 (pk: 13824)>"
+      ]
+     },
+     "execution_count": 23,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "structure_with_kinds.store()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "loaded_structure_kinds = orm.load_node(structure_with_kinds.pk)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 26,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "Kinds(parent=<StructureData: uuid: 89aa0c75-d80f-4c9f-bfce-d7079852ead0 (pk: 13824)>, domain='intra-site', value=['Li0', 'Li0'])"
+      ]
+     },
+     "execution_count": 26,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "loaded_structure_kinds.properties.kinds"
+   ]
   }
  ],
  "metadata": {