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Add the initial ML analysis #5

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c4ad675
Add K-nn
bcamino May 4, 2022
5f7dc3e
Add CaMgO2 data
bcamino May 4, 2022
9f10233
Add the neighbours_spatial_dist_all json files
bcamino May 5, 2022
4f4ace9
Prepare for NN
bcamino May 5, 2022
700dfc7
New descriptor
bcamino May 31, 2022
e40238d
Use new crystal_functions sintax for reading files
bcamino Sep 22, 2022
292aec4
Add notebook for calculations
bcamino Sep 22, 2022
7c4b353
Fix descriptor formulation - pymatgen implementation
bcamino Feb 1, 2023
2504c49
Add sp output + initial cell output
bcamino Feb 1, 2023
05bcd2e
Notebook before tidying up
bcamino Feb 2, 2023
db1bb66
Reorganise nb
bcamino Feb 3, 2023
4e67774
Add index
bcamino Feb 3, 2023
76f3f8b
Update fullopt2 function
bcamino Feb 13, 2023
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19,283 changes: 17,646 additions & 1,637 deletions Classification_ML.ipynb
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143 changes: 127 additions & 16 deletions Li2TiS.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -12,20 +12,12 @@
},
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 8,
"id": "1b2ba234",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"<frozen importlib._bootstrap>:228: RuntimeWarning: scipy._lib.messagestream.MessageStream size changed, may indicate binary incompatibility. Expected 56 from C header, got 64 from PyObject\n"
]
}
],
"outputs": [],
"source": [
"from crystal_functions.file_readwrite import Crystal_output, Properties_input, Properties_output, Crystal_input, write_crystal_gui, write_crystal_input\n",
"from crystal_functions.file_readwrite import Crystal_output, Properties_input, Properties_output, Crystal_input, Crystal_gui, write_crystal_gui, write_crystal_input\n",
"from crystal_functions.execute import runcry\n",
"from crystal_functions.convert import cry_gui2pmg, cry_bands2pmg\n",
"\n",
Expand Down Expand Up @@ -54,7 +46,7 @@
},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 6,
"id": "211cf3b2",
"metadata": {},
"outputs": [],
Expand All @@ -69,12 +61,13 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 9,
"id": "1deba385",
"metadata": {},
"outputs": [],
"source": [
"original_structure = cry_gui2pmg('data/LTS_CONFCNT_ONLY.gui')\n",
"original_structure_gui = Crystal_gui().read_cry_gui('data/LTS_CONFCNT_ONLY.gui')\n",
"original_structure = cry_gui2pmg(original_structure_gui)\n",
"new_atom = 'Li'\n",
"structures = []\n",
"ti_atoms = []\n",
Expand All @@ -89,6 +82,124 @@
"li_atoms = (np.array(manual_li)-1).tolist()"
]
},
{
"cell_type": "markdown",
"id": "187aecdb",
"metadata": {},
"source": [
"## TMP: image for descriptor"
]
},
{
"cell_type": "code",
"execution_count": 30,
"id": "c9ee59ed",
"metadata": {},
"outputs": [],
"source": [
"import copy\n",
"[0.0, 2.54275, 3.595992, 4.404172, 5.0855, 5.685762, 6.22844, 7.62825]\n"
]
},
{
"cell_type": "code",
"execution_count": 70,
"id": "a79730e3",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Structure Summary\n",
"Lattice\n",
" abc : 10.787974607172563 10.787974607172563 10.787974607172563\n",
" angles : 59.99999999999999 59.99999999999999 59.99999999999999\n",
" volume : 887.7787567405314\n",
" A : 0.0 7.62825 7.62825\n",
" B : 7.62825 0.0 7.62825\n",
" C : 7.62825 7.62825 0.0\n",
"PeriodicSite: Li (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]\n",
"PeriodicSite: Li (2.5428, 2.5427, 0.0000) [-0.0000, 0.0000, 0.3333]\n",
"PeriodicSite: Ti (-2.5428, -2.5427, -0.0000) [0.0000, -0.0000, -0.3333]\n",
"PeriodicSite: Li (2.5427, 0.0000, 2.5427) [-0.0000, 0.3333, 0.0000]\n",
"PeriodicSite: Li (5.0855, 2.5427, 2.5427) [-0.0000, 0.3333, 0.3333]\n",
"PeriodicSite: Li (-0.0000, -2.5428, 2.5427) [-0.0000, 0.3333, -0.3333]\n",
"PeriodicSite: Li (-2.5427, -0.0000, -2.5427) [0.0000, -0.3333, -0.0000]\n",
"PeriodicSite: Ti (0.0000, 2.5428, -2.5427) [0.0000, -0.3333, 0.3333]\n",
"PeriodicSite: Li (-5.0855, -2.5427, -2.5427) [0.0000, -0.3333, -0.3333]\n",
"PeriodicSite: Li (0.0000, 2.5427, 2.5427) [0.3333, -0.0000, 0.0000]\n",
"PeriodicSite: Li (2.5428, 5.0855, 2.5427) [0.3333, 0.0000, 0.3333]\n",
"PeriodicSite: Li (-2.5428, -0.0000, 2.5427) [0.3333, -0.0000, -0.3333]\n",
"PeriodicSite: Ti (2.5427, 2.5427, 5.0855) [0.3333, 0.3333, 0.0000]\n",
"PeriodicSite: Li (5.0855, 5.0855, 5.0855) [0.3333, 0.3333, 0.3333]\n",
"PeriodicSite: Li (-0.0000, -0.0000, 5.0855) [0.3333, 0.3333, -0.3333]\n",
"PeriodicSite: Ti (-2.5427, 2.5427, -0.0000) [0.3333, -0.3333, -0.0000]\n",
"PeriodicSite: Ti (0.0000, 5.0855, -0.0000) [0.3333, -0.3333, 0.3333]\n",
"PeriodicSite: Ti (-5.0855, -0.0000, -0.0000) [0.3333, -0.3333, -0.3333]\n",
"PeriodicSite: Li (-0.0000, -2.5427, -2.5427) [-0.3333, 0.0000, -0.0000]\n",
"PeriodicSite: Li (2.5428, 0.0000, -2.5427) [-0.3333, 0.0000, 0.3333]\n",
"PeriodicSite: Li (2.5427, -2.5427, 0.0000) [-0.3333, 0.3333, 0.0000]\n",
"PeriodicSite: Ti (5.0855, 0.0000, 0.0000) [-0.3333, 0.3333, 0.3333]\n",
"PeriodicSite: Ti (-0.0000, -5.0855, 0.0000) [-0.3333, 0.3333, -0.3333]\n",
"PeriodicSite: Li (-2.5427, -2.5427, -5.0855) [-0.3333, -0.3333, -0.0000]\n",
"PeriodicSite: Ti (0.0000, 0.0000, -5.0855) [-0.3333, -0.3333, 0.3333]\n",
"PeriodicSite: Li (-5.0855, -5.0855, -5.0855) [-0.3333, -0.3333, -0.3333]\n",
"PeriodicSite: S (2.5427, 2.5427, 2.5427) [0.1667, 0.1667, 0.1667]\n",
"PeriodicSite: S (-2.5428, -2.5427, 2.5427) [0.1667, 0.1667, -0.5000]\n",
"PeriodicSite: S (-0.0000, -0.0000, 2.5427) [0.1667, 0.1667, -0.1667]\n",
"PeriodicSite: S (-2.5427, 2.5427, -2.5427) [0.1667, -0.5000, 0.1667]\n",
"PeriodicSite: S (-7.6283, -2.5427, -2.5427) [0.1667, -0.5000, -0.5000]\n",
"PeriodicSite: S (-5.0855, -0.0000, -2.5427) [0.1667, -0.5000, -0.1667]\n",
"PeriodicSite: S (0.0000, 2.5427, -0.0000) [0.1667, -0.1667, 0.1667]\n",
"PeriodicSite: S (-5.0855, -2.5427, -0.0000) [0.1667, -0.1667, -0.5000]\n",
"PeriodicSite: S (-2.5427, -0.0000, -0.0000) [0.1667, -0.1667, -0.1667]\n",
"PeriodicSite: S (2.5427, -2.5427, -2.5427) [-0.5000, 0.1667, 0.1667]\n",
"PeriodicSite: S (-2.5428, -7.6282, -2.5427) [-0.5000, 0.1667, -0.5000]\n",
"PeriodicSite: S (-0.0000, -5.0855, -2.5427) [-0.5000, 0.1667, -0.1667]\n",
"PeriodicSite: S (-2.5427, -2.5427, -7.6283) [-0.5000, -0.5000, 0.1667]\n",
"PeriodicSite: S (-7.6283, -7.6283, -7.6283) [-0.5000, -0.5000, -0.5000]\n",
"PeriodicSite: S (-5.0855, -5.0855, -7.6283) [-0.5000, -0.5000, -0.1667]\n",
"PeriodicSite: S (0.0000, -2.5427, -5.0855) [-0.5000, -0.1667, 0.1667]\n",
"PeriodicSite: S (-5.0855, -7.6283, -5.0855) [-0.5000, -0.1667, -0.5000]\n",
"PeriodicSite: S (-2.5427, -5.0855, -5.0855) [-0.5000, -0.1667, -0.1667]\n",
"PeriodicSite: S (2.5427, 0.0000, 0.0000) [-0.1667, 0.1667, 0.1667]\n",
"PeriodicSite: S (-2.5428, -5.0855, 0.0000) [-0.1667, 0.1667, -0.5000]\n",
"PeriodicSite: S (-0.0000, -2.5427, 0.0000) [-0.1667, 0.1667, -0.1667]\n",
"PeriodicSite: S (-2.5427, 0.0000, -5.0855) [-0.1667, -0.5000, 0.1667]\n",
"PeriodicSite: S (-7.6283, -5.0855, -5.0855) [-0.1667, -0.5000, -0.5000]\n",
"PeriodicSite: S (-5.0855, -2.5427, -5.0855) [-0.1667, -0.5000, -0.1667]\n",
"PeriodicSite: S (0.0000, 0.0000, -2.5427) [-0.1667, -0.1667, 0.1667]\n",
"PeriodicSite: S (-5.0855, -5.0855, -2.5427) [-0.1667, -0.1667, -0.5000]\n",
"PeriodicSite: S (-2.5427, -2.5427, -2.5427) [-0.1667, -0.1667, -0.1667]"
]
},
"execution_count": 70,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"structure = copy.deepcopy(structures[0])\n",
"structure.distance_matrix[30] > 5.2 \n",
"#sites = np.where((structure.distance_matrix[30] > 5.2) + (structure.distance_matrix[30] < 3. ))[0]\n",
"\n",
"sites = np.where(structure.distance_matrix[30] > 7)[0]\n",
"\n",
"structure.remove_sites(sites)\n",
"structure"
]
},
{
"cell_type": "code",
"execution_count": 71,
"id": "b42c3132",
"metadata": {},
"outputs": [],
"source": [
"from pymatgen.io.cif import CifWriter\n",
"CifWriter(structure).write_file('1_shell.cif')"
]
},
{
"cell_type": "markdown",
"id": "81aef12c",
Expand All @@ -99,7 +210,7 @@
},
{
"cell_type": "code",
"execution_count": 31,
"execution_count": 10,
"id": "c34475ef",
"metadata": {},
"outputs": [
Expand All @@ -109,7 +220,7 @@
"<Popen: returncode: None args: ['/Users/brunocamino/miniconda3/envs/test_env...>"
]
},
"execution_count": 31,
"execution_count": 10,
"metadata": {},
"output_type": "execute_result"
},
Expand Down
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