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Adding to_kinds and get_kinds functionalities.
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*Missing:
            - Give custom threshold and use kind_tags as defined in
              structure.properties.positions.kind_tags.

Questions:
        answered, but worth to leave it here for now: What is then the value of each property associated to each kind? an average? maybe yes.
        This can be then generated in another function which takes the averages. Maybe in the property specific
        to_kind methods. Maybe indeed the average point which is obtained during the space_grid generation.
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@mikibonacci
mikibonacci committed Feb 7, 2024
1 parent bef8984 commit 6a9daeb
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207 changes: 161 additions & 46 deletions aiida_atomistic/data/structure/5_feb.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -43,21 +43,26 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"properties = {\n",
" \"cell\":{\"value\":((1.0,0,0),(0,1,0),(0,0,1))},\n",
" \"pbc\":{\"value\":[True,False,True]},\n",
" \"positions\":{\"value\":[[1,1,1],[2,3,3]]},\n",
" \"symbols\":{\"value\":[\"He\",\"Cu\"]},\n",
" \"positions\":{\n",
" \"value\":[[1,1,1],[2,3,3],[3,4,5],[1,2,3]],\n",
" \"kind_tags\":[\"He1\",\"\",\"\",\"He1\"]\n",
" },\n",
" \"symbols\":{\"value\":[\"He\",\"Cu\",\"He\",\"He\"]},\n",
" \"mass\":{\"value\":[1.551,9,1.5512,2],},\n",
" \"charge\":{\"value\":[1,0,1,0]}\n",
" }"
]
},
{
"cell_type": "code",
"execution_count": 6,
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -66,16 +71,16 @@
},
{
"cell_type": "code",
"execution_count": 7,
"execution_count": 5,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Cell(parent=<StructureData: uuid: aa4ae241-35d6-4788-bfff-d63143c95659 (unstored)>, value=((1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0)), domain='global')"
"Cell(parent=<StructureData: uuid: 109f80df-7dcf-4228-9e15-1088abff849a (unstored)>, value=((1.0, 0.0, 0.0), (0.0, 1.0, 0.0), (0.0, 0.0, 1.0)), domain='global')"
]
},
"execution_count": 7,
"execution_count": 5,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -86,16 +91,16 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 6,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['pbc', 'cell', 'positions', 'symbols', 'custom']"
"['pbc', 'cell', 'positions', 'symbols', 'mass', 'charge', 'custom']"
]
},
"execution_count": 8,
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -106,22 +111,40 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 7,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<StructureData: uuid: aa4ae241-35d6-4788-bfff-d63143c95659 (pk: 13813)>"
"['charge', 'symbols', 'pbc', 'cell', 'positions', 'mass']"
]
},
"execution_count": 9,
"execution_count": 7,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"structure.store()"
"structure.properties.get_defined_properties()"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"#structure.store()"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"#s = orm.load_node(structure.pk)"
]
},
{
Expand All @@ -130,27 +153,16 @@
"metadata": {},
"outputs": [],
"source": [
"s = orm.load_node(structure.pk)"
"#s.properties"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"<aiida_atomistic.data.structure.properties.property_collector.PropertyCollector at 0x7f64bd218970>"
]
},
"execution_count": 11,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"s.properties"
"#s.properties.positions"
]
},
{
Expand All @@ -161,7 +173,7 @@
{
"data": {
"text/plain": [
"Positions(parent=<StructureData: uuid: aa4ae241-35d6-4788-bfff-d63143c95659 (pk: 13813)>, value=[(1.0, 1.0, 1.0), (2.0, 3.0, 3.0)], domain='per-site')"
"['pbc', 'cell', 'positions', 'symbols', 'mass', 'charge', 'custom']"
]
},
"execution_count": 12,
Expand All @@ -170,7 +182,7 @@
}
],
"source": [
"s.properties.positions"
"list(structure.properties.get_valid_properties())"
]
},
{
Expand All @@ -181,7 +193,7 @@
{
"data": {
"text/plain": [
"['pbc', 'cell', 'positions', 'symbols', 'custom']"
"4"
]
},
"execution_count": 13,
Expand All @@ -190,7 +202,7 @@
}
],
"source": [
"list(s.properties.get_valid_properties())"
"len(structure.properties.positions.value)"
]
},
{
Expand All @@ -201,7 +213,7 @@
{
"data": {
"text/plain": [
"2"
"Symbols(parent=<StructureData: uuid: 109f80df-7dcf-4228-9e15-1088abff849a (unstored)>, value=['He', 'Cu', 'He', 'He'], domain='per-site')"
]
},
"execution_count": 14,
Expand All @@ -210,7 +222,7 @@
}
],
"source": [
"len(s.properties.positions.value)"
"structure.properties.symbols "
]
},
{
Expand All @@ -221,7 +233,13 @@
{
"data": {
"text/plain": [
"Symbols(parent=<StructureData: uuid: aa4ae241-35d6-4788-bfff-d63143c95659 (pk: 13813)>, value=['He', 'Cu'], domain='per-site')"
"{'cell': {'value': ((1.0, 0, 0), (0, 1, 0), (0, 0, 1))},\n",
" 'pbc': {'value': [True, False, True]},\n",
" 'positions': {'value': [[1, 1, 1], [2, 3, 3], [3, 4, 5], [1, 2, 3]],\n",
" 'kind_tags': ['He1', '', '', 'He1']},\n",
" 'symbols': {'value': ['He', 'Cu', 'He', 'He']},\n",
" 'mass': {'value': [1.551, 9, 1.5512, 2]},\n",
" 'charge': {'value': [1, 0, 1, 0]}}"
]
},
"execution_count": 15,
Expand All @@ -230,7 +248,7 @@
}
],
"source": [
"s.properties.symbols "
"structure.base.attributes.get('_property_attributes')"
]
},
{
Expand All @@ -241,10 +259,13 @@
{
"data": {
"text/plain": [
"{'pbc': {'value': [True, False, True]},\n",
" 'cell': {'value': [[1.0, 0, 0], [0, 1, 0], [0, 0, 1]]},\n",
" 'symbols': {'value': ['He', 'Cu']},\n",
" 'positions': {'value': [[1, 1, 1], [2, 3, 3]]}}"
"{'cell': {'value': ((1.0, 0, 0), (0, 1, 0), (0, 0, 1))},\n",
" 'pbc': {'value': [True, False, True]},\n",
" 'positions': {'value': [[1, 1, 1], [2, 3, 3], [3, 4, 5], [1, 2, 3]],\n",
" 'kind_tags': ['He1', '', '', 'He1']},\n",
" 'symbols': {'value': ['He', 'Cu', 'He', 'He']},\n",
" 'mass': {'value': [1.551, 9, 1.5512, 2]},\n",
" 'charge': {'value': [1, 0, 1, 0]}}"
]
},
"execution_count": 16,
Expand All @@ -253,7 +274,7 @@
}
],
"source": [
"s.base.attributes.get('_property_attributes')"
"structure.to_dict()"
]
},
{
Expand All @@ -264,10 +285,7 @@
{
"data": {
"text/plain": [
"{'pbc': {'value': [True, False, True]},\n",
" 'cell': {'value': [[1.0, 0, 0], [0, 1, 0], [0, 0, 1]]},\n",
" 'symbols': {'value': ['He', 'Cu']},\n",
" 'positions': {'value': [[1, 1, 1], [2, 3, 3]]}}"
"[1.551, 9.0, 1.5512, 2.0]"
]
},
"execution_count": 17,
Expand All @@ -276,7 +294,104 @@
}
],
"source": [
"s.to_dict()"
"structure.properties.mass.value"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"0.001"
]
},
"execution_count": 18,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"structure.properties.mass.default_kind_threshold"
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"(array([ 0, 74, 0, 4]),\n",
" [1.601, 9.001000000000007, 1.601, 2.0010000000000003])"
]
},
"execution_count": 19,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"structure.properties.mass.to_kinds(thr = 0.1, kind_names=False)"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"['He', 'Cu', 'He', 'He']"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"structure.properties.symbols.value"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"He\n",
"Cu\n",
"He\n",
"He\n"
]
},
{
"data": {
"text/plain": [
"([2, 1, 2, 3],\n",
" ['He2', 'Cu1', 'He2', 'He3'],\n",
" {'charge': [1.1250000000000002, 0.225, 1.1250000000000002, 0.225],\n",
" 'mass': [1.5514999999999999,\n",
" 9.000499999999178,\n",
" 1.5514999999999999,\n",
" 2.0004999999999504]})"
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"get_kinds(structure)"
]
},
{
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