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dwinston/nmgc_nanoporous_data.ipynb

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Access raw NMGC nanoporous material data from the Materials Project
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nmgc_nanoporous_data.ipynb
{
"cells": [
{
"cell_type": "code",
"execution_count": 29,
"metadata": {
"collapsed": false
},
"outputs": [],
"source": [
"import requests\n",
"\n",
"url = 'https://www.materialsproject.org/porous/{nmgc_id}/data'\n",
"\n",
"def get_nmgc_data(nmgc_id):\n",
" response = requests.get(url.format(nmgc_id=nmgc_id))\n",
" return response.json()"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"data = get_nmgc_data('NMGC-239531')"
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {
"collapsed": true
},
"outputs": [],
"source": [
"from pymatgen.core import Structure"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"Structure Summary\n",
"Lattice\n",
" abc : 14.564337999999999 17.767748999999998 15.196960000000001\n",
" angles : 90.0 90.0 90.0\n",
" volume : 3932.6009518885794\n",
" A : 14.564337999999999 0.0 8.9180849567000803e-16\n",
" B : 2.8572719600669404e-15 17.767748999999998 1.087960847045179e-15\n",
" C : 0.0 0.0 15.196960000000001\n",
"PeriodicSite: Si (12.4461, 16.4574, 4.8704) [0.8546, 0.9263, 0.3205]\n",
"PeriodicSite: Si (12.4909, 1.6525, 3.9548) [0.8576, 0.0930, 0.2602]\n",
"PeriodicSite: Si (2.1456, 11.7362, 1.6587) [0.1473, 0.6605, 0.1091]\n",
"PeriodicSite: Si (5.2230, 14.8086, 13.9342) [0.3586, 0.8335, 0.9169]\n",
"PeriodicSite: Si (7.9564, 2.8926, 6.3540) [0.5463, 0.1628, 0.4181]\n",
"PeriodicSite: Si (5.1131, 10.5783, 6.4064) [0.3511, 0.5954, 0.4216]\n",
"PeriodicSite: Si (0.3667, 14.9122, 4.1083) [0.0252, 0.8393, 0.2703]\n",
"PeriodicSite: Si (1.2830, 7.9802, 7.3567) [0.0881, 0.4491, 0.4841]\n",
"PeriodicSite: O (10.9233, 16.1024, 4.4877) [0.7500, 0.9063, 0.2953]\n",
"PeriodicSite: O (12.5928, 16.4028, 6.4687) [0.8646, 0.9232, 0.4257]\n",
"PeriodicSite: O (13.3927, 15.3834, 4.1317) [0.9196, 0.8658, 0.2719]\n",
"PeriodicSite: O (12.8557, 0.1409, 4.3227) [0.8827, 0.0079, 0.2844]\n",
"PeriodicSite: O (10.9233, 1.9449, 4.1618) [0.7500, 0.1095, 0.2739]\n",
"PeriodicSite: O (12.9490, 1.9441, 2.4307) [0.8891, 0.1094, 0.1599]\n",
"PeriodicSite: O (13.3374, 2.6544, 4.8718) [0.9158, 0.1494, 0.3206]\n",
"PeriodicSite: O (3.6411, 11.1667, 1.9637) [0.2500, 0.6285, 0.1292]\n",
"PeriodicSite: O (2.2185, 13.3258, 1.6713) [0.1523, 0.7500, 0.1100]\n",
"PeriodicSite: O (1.0975, 11.2258, 2.7661) [0.0754, 0.6318, 0.1820]\n",
"PeriodicSite: O (1.6115, 11.2742, 0.1934) [0.1106, 0.6345, 0.0127]\n",
"PeriodicSite: O (3.6411, 14.6758, 13.9763) [0.2500, 0.8260, 0.9197]\n",
"PeriodicSite: O (5.8331, 13.3258, 13.6709) [0.4005, 0.7500, 0.8996]\n",
"PeriodicSite: O (7.7452, 4.4419, 6.6319) [0.5318, 0.2500, 0.4364]\n",
"PeriodicSite: O (9.0623, 2.2985, 7.3575) [0.6222, 0.1294, 0.4841]\n",
"PeriodicSite: O (6.4949, 2.2059, 6.5441) [0.4459, 0.1242, 0.4306]\n",
"PeriodicSite: O (3.6411, 11.1031, 6.0021) [0.2500, 0.6249, 0.3950]\n",
"PeriodicSite: O (6.1981, 11.0537, 5.3529) [0.4256, 0.6221, 0.3522]\n",
"PeriodicSite: O (5.0313, 8.9511, 6.5008) [0.3455, 0.5038, 0.4278]\n",
"PeriodicSite: O (0.4358, 13.3258, 4.2564) [0.0299, 0.7500, 0.2801]\n",
"PeriodicSite: O (0.0000, 8.8839, 7.5985) [0.0000, 0.5000, 0.5000]"
]
},
"execution_count": 32,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"Structure.from_dict(data)"
]
},
{
"cell_type": "code",
"execution_count": 33,
"metadata": {
"collapsed": false
},
"outputs": [
{
"data": {
"text/plain": [
"{u'about': {u'mpid': u'NMGC-239531',\n",
" u'srcid': u'PCOD-8239531',\n",
" u'submitters': [{u'email': u'mwdeem@rice.edu', u'name': u'Michael Deem'}]},\n",
" u'all_references': u'@article{\\n author = {Pophale, Ramdas and Cheeseman, Phillip A. and Deem, Michael W.},\\n title = {A database of new zeolite-like materials},\\n journal = {Physical Chemistry Chemical Physics},\\n volume = {13},\\n number = {27},\\n pages = {12407-12412},\\n year = {2011}\\n}\\n\\n@misc{ \\n title = {Pore discriptors were computed using Zeo++ http://www.maciejharanczyk.info/Zeopp/} \\n}\\n\\n@article{\\n author = {Simon, C. M. and Kim, J. and Gomez-Gualdron, D.A. and J. S. Camp, Y.G. Chung and Martin, R.L. and Mercado, R. and Deem, M.W. and Gunter, D. and Haranczyk, M. and Sholl, D.S. and Snurr, R.Q. and Smit, B.},\\n title = {The Materials Genome in Action: Finding the Best\\nMaterial for Methane Storage},\\n journal = {submitted},\\n}\\n\\n@article{\\n author = {Haldoupis, E. and Camp, J. S. and Chung, Y. G. and Nazarian, D. and Gunter, D. and Winston, D. and Brafman, M. and Bai, P. and Gomez-Gualdron, D. A. and Kim, J. and Simon, C. M. and Deem, M. W. and Gagliardi, L. and Sholl, D. S. and Smit, B. and Snurr, R. Q. and Truhlar, D. G. and Persson, K. A. and Haranczyk, M. and Siepmann, J. I.},\\n title = {The Nanoporous Materials Explorer: Accelerating materials discovery through a genome approach.},\\n journal = {in preparation},\\n}\\n\\n@article{\\nauthor = {Ong, Shyue Ping and Richards, William Davidson and Jain, Anubhav and Hautier, Geoffroy and Kocher, Michael and Cholia, Shreyas and Gunter, Dan and Chevrier, Vincent L. and Persson, Kristin A. and Ceder, Gerbrand},\\ndoi = {10.1016/j.commatsci.2012.10.028},\\njournal = {Computational Materials Science},\\npages = {314--319},\\ntitle = {Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis},\\nvolume = {68},\\nyear = {2013}\\n}',\n",
" u'all_submitters': [{u'email': u'mwdeem@rice.edu', u'name': u'Michael Deem'},\n",
" {u'email': u'mharanczyk@lbl.gov', u'name': u'Maciej Haranczyk'},\n",
" {u'email': u'Cory.M.Simon@gmail.com', u'name': u'Cory Simon'}],\n",
" u'cif': u'data_PCOD8239531\\n_publ_section_title\\n;\\nStructure prediction by ZEFSAII (Michael W. Deem and Ramdas Pophale) SiO2 \\n PCOD8239531\\nProbable space group: P M M N\\n;\\n_chemical_formula_sum \"Si O2\"\\n_cell_formula_units_Z 64\\n_cell_length_a 14.564338\\n_cell_length_b 17.767749\\n_cell_length_c 15.196960\\n_cell_angle_alpha 90.000000\\n_cell_angle_beta 90.000000\\n_cell_angle_gamma 90.000000\\n_cell_volume 3932.600952\\n_symmetry_space_group_name_H-M \"P M M N\"\\n_symmetry_group_IT_number 59\\n_space_group.IT_coordinate_system_code \\'2\\'\\n_symmetry_cell_setting \\'orthorhombic\\'\\nloop_\\n_space_group_symop_operation_xyz\\nx,y,z\\n1/2-x,1/2-y,z\\n1/2+x,-y,-z\\n-x,1/2+y,-z\\n-x,-y,-z\\n1/2+x,1/2+y,-z\\n1/2-x,y,z\\nx,1/2-y,z\\nloop_\\n_atom_site_type_symbol\\n_atom_site_label\\n_atom_site_fract_x\\n_atom_site_fract_y\\n_atom_site_fract_z\\nSi Si1 0.854558 0.926250 0.320482\\nSi Si2 0.857636 0.093006 0.260239\\nSi Si3 0.147316 0.660536 0.109145\\nSi Si4 0.358614 0.833456 0.916904\\nSi Si5 0.546296 0.162801 0.418110\\nSi Si6 0.351068 0.595366 0.421555\\nSi Si7 0.025180 0.839283 0.270338\\nSi Si8 0.088091 0.449138 0.484087\\nO O1 0.750000 0.906272 0.295302\\nO O2 0.864635 0.923176 0.425655\\nO O3 0.919554 0.865802 0.271877\\nO O4 0.882685 0.007928 0.284443\\nO O5 0.750000 0.109462 0.273857\\nO O6 0.889088 0.109416 0.159944\\nO O7 0.915754 0.149393 0.320578\\nO O8 0.250000 0.628481 0.129219\\nO O9 0.152321 0.750000 0.109976\\nO O10 0.075358 0.631807 0.182015\\nO O11 0.110647 0.634533 0.012729\\nO O12 0.250000 0.825979 0.919675\\nO O13 0.400506 0.750000 0.899581\\nO O14 0.531794 0.250000 0.436394\\nO O15 0.622224 0.129363 0.484146\\nO O16 0.445946 0.124153 0.430620\\nO O17 0.250000 0.624902 0.394951\\nO O18 0.425569 0.622119 0.352235\\nO O19 0.345453 0.503782 0.427768\\nO O20 0.029922 0.750000 0.280085\\nO O21 0.000000 0.500000 0.500000\\n#\\n# Coordination Sequence:\\n#\\n# PCOD8239531 Si02\\n# 8\\n# 8 8 8 8 8 8 8 8\\n# 4 11 21 35 50 64 90 132 171 198 235 283\\n# 4 10 18 29 46 69 96 126 158 195 240 288\\n# 4 8 15 29 48 69 96 126 150 181 234 295\\n# 4 8 14 26 45 69 96 124 151 181 228 291\\n# 4 11 20 29 45 70 99 124 156 199 238 275\\n# 4 11 20 31 49 70 94 125 157 193 238 286\\n# 4 11 21 33 48 70 96 123 160 205 242 279\\n# 4 10 18 34 48 62 91 132 162 188 229 286\\n#\\n# _framework density 16.274215999999999\\n#\\n# number of rings (size 3 to 8) (size 9 to 14) (size 15 to 20)\\n# 0.000 2.000 5.000 2.625 0.000 3.000 \\n# 0.000 0.625 0.000 1.125 0.000 0.000 \\n# 0.000 1.000 0.000 7.750 0.000 0.000 \\n#\\n# Total GULP energy -793308.486246 kJ/mol\\n# GULP energy per Si atom -12395.445098 kJ/mol\\n# Density = 1.623718 g / cm^3\\n# Si number density = 16.274216 Si / 1000 Ang^3\\n#\\n#\\n#\\n#\\n# Static dielectric constant tensor:\\n# x y z\\n# x 3.111140 0.000000 0.000000 \\n# y 0.000000 3.134430 0.000000 \\n# z 0.000000 0.000000 3.351000 \\n# \\n# \\n# High freq. dielectric constant tensor:\\n# x y z\\n# x 1.604340 0.000000 0.000000 \\n# y 0.000000 1.608480 0.000000 \\n# z 0.000000 0.000000 1.622040 \\n# \\n# From -- ./inp_files/23442.got.cif\\n# From: 2010.03.12/outbox.cif.g09.slc.cpg/sg59_12_cif.got.tgz:23442.got - 2010.04.16 16:29:54.\\n',\n",
" u'elements': u'O-Si',\n",
" u'formula': u'O21Si8',\n",
" u'id': u'NMGC-239531',\n",
" u'lattice': {u'a': 14.564338,\n",
" u'alpha': 90.0,\n",
" u'b': 17.767749,\n",
" u'beta': 90.0,\n",
" u'c': 15.19696,\n",
" u'gamma': 90.0,\n",
" u'matrix': [[14.564338, 0.0, 8.91808495670008e-16],\n",
" [2.8572719600669404e-15, 17.767749, 1.087960847045179e-15],\n",
" [0.0, 0.0, 15.19696]],\n",
" u'volume': 3932.6009518885794},\n",
" u'name': u'PCOD-8239531',\n",
" u'props': {u'ASA': {u'precision': 2,\n",
" u'title': u'Accessible Surface Area',\n",
" u'units': u'm2/cm3',\n",
" u'value': 0.0},\n",
" u'LCD': {u'precision': 2,\n",
" u'title': u'Largest Cavity Diameter',\n",
" u'units': u'A',\n",
" u'value': 8.02808},\n",
" u'PLD': {u'precision': 2,\n",
" u'title': u'Pore Limiting Diameter',\n",
" u'units': u'A',\n",
" u'value': 3.274},\n",
" u'crystal_density': {u'precision': 2,\n",
" u'title': u'Crystal Density',\n",
" u'units': u'g/cm3',\n",
" u'value': 1.62371},\n",
" u'dtype': u'sim',\n",
" u'method': u'zeo++',\n",
" u'ref': u'@misc{ \\n title = {Pore discriptors were computed using Zeo++ http://www.maciejharanczyk.info/Zeopp/} \\n}',\n",
" u'submitters': [{u'email': u'mharanczyk@lbl.gov',\n",
" u'name': u'Maciej Haranczyk'}],\n",
" u'void_fraction': {u'precision': 2,\n",
" u'title': u'Void Fraction',\n",
" u'units': u'',\n",
" u'value': 0.12404000000000001}},\n",
" u'sites': [{u'abc': [0.854557999999999, 0.92625, 0.320482],\n",
" u'label': u'Si',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'Si', u'occu': 1}],\n",
" u'xyz': [12.446071552604002, 16.457377511249998, 4.870352134720002]},\n",
" {u'abc': [0.857636, 0.093005999999999, 0.260239],\n",
" u'label': u'Si',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'Si', u'occu': 1}],\n",
" u'xyz': [12.490900584968, 1.652507263494, 3.954841673440001]},\n",
" {u'abc': [0.147316, 0.660536, 0.109144999999999],\n",
" u'label': u'Si',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'Si', u'occu': 1}],\n",
" u'xyz': [2.145560016808002, 11.736237853463999, 1.658672199200001]},\n",
" {u'abc': [0.358614, 0.833456, 0.916903999999999],\n",
" u'label': u'Si',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'Si', u'occu': 1}],\n",
" u'xyz': [5.222975507532002, 14.808637010543999, 13.934153411840002]},\n",
" {u'abc': [0.546296, 0.162801, 0.41811000000000004],\n",
" u'label': u'Si',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'Si', u'occu': 1}],\n",
" u'xyz': [7.9564395920479996, 2.8926073049489993, 6.354000945600001]},\n",
" {u'abc': [0.351068, 0.595366, 0.421554999999999],\n",
" u'label': u'Si',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'Si', u'occu': 1}],\n",
" u'xyz': [5.113073012984001, 10.578313651133998, 6.406354472800001]},\n",
" {u'abc': [0.02518, 0.839283, 0.270337999999999],\n",
" u'label': u'Si',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'Si', u'occu': 1}],\n",
" u'xyz': [0.36673003084000205, 14.912169683966999, 4.108315772480001]},\n",
" {u'abc': [0.088091, 0.449138, 0.484087],\n",
" u'label': u'Si',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'Si', u'occu': 1}],\n",
" u'xyz': [1.282987098758001, 7.980171250361999, 7.356650775520001]},\n",
" {u'abc': [0.75, 0.906272, 0.295302],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [10.923253500000001, 16.102413421728, 4.487692681920002]},\n",
" {u'abc': [0.864634999999999, 0.923176, 0.425655],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [12.592836386630001, 16.402759450824, 6.468662008800002]},\n",
" {u'abc': [0.919554, 0.865802, 0.271877],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [13.392695265252001, 15.383352619697998, 4.131703893920002]},\n",
" {u'abc': [0.882684999999999, 0.007928, 0.284443],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [12.855722687530001, 0.14086271407199902, 4.322668893280001]},\n",
" {u'abc': [0.75, 0.109461999999999, 0.273856999999999],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [10.9232535, 1.9448933410379992, 4.161793874720002]},\n",
" {u'abc': [0.889088, 0.109416, 0.159944],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [12.948978143744, 1.9440760245839992, 2.430662570240001]},\n",
" {u'abc': [0.915754, 0.149393, 0.320578],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [13.337350780851999, 2.654377326357, 4.871811042880001]},\n",
" {u'abc': [0.25, 0.628481, 0.129219],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [3.641084500000001, 11.166692659268998, 1.9637359742400011]},\n",
" {u'abc': [0.152320999999999, 0.75, 0.109975999999999],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [2.218454528498002, 13.32581175, 1.6713008729600012]},\n",
" {u'abc': [0.075358, 0.631807, 0.182014999999999],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [1.097539383004001, 11.225788192443, 2.7660746744000013]},\n",
" {u'abc': [0.110647, 0.634533, 0.012728999999999002],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [1.611500306686001, 11.274223076217, 0.19344210384000002]},\n",
" {u'abc': [0.25, 0.825978999999999, 0.919674999999999],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [3.641084500000002, 14.675787551270998, 13.976264188000004]},\n",
" {u'abc': [0.400506, 0.75, 0.899581],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [5.8331047550280015, 13.32581175, 13.670896473760003]},\n",
" {u'abc': [0.531794, 0.25, 0.436394],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [7.7452275623719995, 4.44193725, 6.631862162240001]},\n",
" {u'abc': [0.622224, 0.129363, 0.484145999999999],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [9.062280647711999, 2.298489313887, 7.357547396160002]},\n",
" {u'abc': [0.445945999999999, 0.124153, 0.43062000000000006],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [6.494908273748, 2.205919341596999, 6.544114915200001]},\n",
" {u'abc': [0.25, 0.624902, 0.394951],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [3.641084500000001, 11.103101885597999, 6.002054548960001]},\n",
" {u'abc': [0.425569, 0.622119, 0.352234999999999],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
" u'xyz': [6.198130758322001, 11.053654240131, 5.352901205600001]},\n",
" {u'abc': [0.345453, 0.503782, 0.427768],\n",
" u'label': u'O',\n",
" u'properties': {},\n",
" u'species': [{u'element': u'O', u'occu': 1}],\n",
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" u'submitters': [{u'email': u'Cory.M.Simon@gmail.com',\n",
" u'name': u'Cory Simon'}]}],\n",
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" u'precision': 2,\n",
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" u'value': [100.2,\n",
" 587.6,\n",
" 1022.8,\n",
" 1552.0,\n",
" 2648.1000000000004,\n",
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" 3797.8,\n",
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" u'submitters': [{u'email': u'Cory.M.Simon@gmail.com',\n",
" u'name': u'Cory Simon'}],\n",
" u'temper': {u'precision': 2,\n",
" u'title': u'Temperature',\n",
" u'units': u'Kelvin',\n",
" u'value': 298.0}}],\n",
" u'name': u'CH4',\n",
" u'sorbate_class': [{u'name': u'alkanes', u'title': u'Alkanes'},\n",
" {u'name': u'CH4', u'title': u'Methane'}],\n",
" u'title': u'methane'}]}"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"data"
]
}
],
"metadata": {
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