├── LICENSE ├── Part_1-Structures_Molecules ├── POSCAR ├── files │ ├── BiFeO3.cif │ ├── PbTiO3.cif │ └── SrYCoO.cif ├── graphics │ ├── chatgpt.png │ ├── inheritance.png │ ├── matsci_discourse.png │ ├── pmg_tests.png │ ├── python_file_api.png │ ├── site_diagram.png │ ├── struct_mol.png │ ├── structure_mod.png │ └── title.png ├── my_POSCAR ├── output.cif ├── output.xyz └── pymatgen_pt1_structures_molecules.ipynb ├── Part_2-Pymatgen_and_VASP ├── INCAR ├── KPOINTS ├── POSCAR ├── POTCAR ├── files │ ├── LICENSE │ ├── README.md │ ├── Si_HSE_band_structure_line │ │ ├── CONTCAR │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OUTCAR │ │ ├── POSCAR │ │ ├── POTCAR.spec │ │ └── vasprun.xml │ ├── Si_HSE_band_structure_uniform │ │ └── vasprun.xml │ ├── Si_HSE_relax_output │ │ ├── CONTCAR │ │ ├── INCAR │ │ ├── OUTCAR │ │ ├── POSCAR │ │ ├── POTCAR.spec │ │ └── vasprun.xml │ ├── Si_optics │ │ ├── CONTCAR │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OUTCAR │ │ ├── POSCAR │ │ ├── POTCAR.spec │ │ └── vasprun.xml │ └── Si_relax_output │ │ ├── CHGCAR │ │ ├── CONTCAR │ │ ├── DOSCAR │ │ ├── EIGENVAL │ │ ├── IBZKPT │ │ ├── INCAR │ │ ├── KPOINTS │ │ ├── OSZICAR │ │ ├── OUTCAR │ │ ├── PCDAT │ │ ├── POSCAR │ │ ├── POTCAR │ │ ├── PROCAR │ │ ├── REPORT │ │ ├── WAVECAR │ │ ├── XDATCAR │ │ ├── vasp.out │ │ ├── vaspout.h5 │ │ └── vasprun.xml ├── graphics │ ├── input_from_previous.png │ ├── input_methods.png │ ├── title.png │ ├── vasp_output.png │ ├── vis_automation.png │ └── vis_hierarchy.png └── pymatgen_pt2_vasp_io.ipynb ├── Part_3-Materials_Project_API ├── graphics │ ├── ElasticityRester.png │ ├── MPRester.png │ ├── SummaryRester.png │ ├── TaskRester.png │ ├── api_comparison.png │ ├── nested_search.png │ ├── subresters.png │ └── title.png └── pymatgen_pt3_materials_project_api.ipynb ├── Part_4-Transformations_Symmetry ├── graphics │ └── title.png ├── pymatgen_pt4_transformations_symmetry.ipynb └── structures │ ├── CsCl.json │ ├── LiFePO4.json │ └── Si.json ├── Part_5-Five_Features ├── bandstructure.json ├── files │ ├── KPOINTS │ └── vasprun.xml ├── graphics │ ├── cost_per_kg.png │ ├── cost_per_mol.png │ ├── hhi_production.png │ ├── hhi_reserve.png │ └── title.png ├── pymatgen_pt5_five_features.ipynb ├── structure.json ├── structures │ ├── BaTiO3.cif │ ├── MgAl2O4.cif │ ├── Si_conventional.cif │ ├── Si_reduced.cif │ └── TiPbO3.cif └── supplement │ └── Cost and HHI plots.ipynb └── README.md /LICENSE: -------------------------------------------------------------------------------- 1 | Attribution 4.0 International 2 | Anubhav Jain 3 | Pymatgen tutorials: https://github.com/computron/pymatgen_tutorials 4 | ======================================================================= 5 | 6 | Creative Commons Corporation ("Creative Commons") is not a law firm and 7 | does not provide legal services or legal advice. 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For 393 | the avoidance of doubt, this paragraph does not form part of the 394 | public licenses. 395 | 396 | Creative Commons may be contacted at creativecommons.org. 397 | -------------------------------------------------------------------------------- /Part_1-Structures_Molecules/POSCAR: -------------------------------------------------------------------------------- 1 | Ti6 Sn6 H6 S18 2 | 1.0 3 | 11.6999999999999993 0.0000000000000000 0.0000000000000007 4 | -0.0000000000000009 14.0399999999999991 0.0000000000000009 5 | 0.0000000000000000 0.0000000000000000 3.8999999999999999 6 | Sn Ti S H S 7 | 6 6 12 6 6 8 | direct 9 | 0.0000000000000000 0.0000000000000000 0.0000000000000000 Sn 10 | 0.0000000000000000 0.3333333333333333 0.0000000000000000 Sn 11 | 0.0000000000000000 0.6666666666666666 0.0000000000000000 Sn 12 | 0.5000000000000000 0.0000000000000000 0.0000000000000000 Sn 13 | 0.5000000000000000 0.3333333333333333 0.0000000000000000 Sn 14 | 0.4999999999999999 0.6666666666666666 0.0000000000000000 Sn 15 | 0.2500000000000000 0.1666666666666667 0.5000000000000000 Ti 16 | 0.2500000000000000 0.5000000000000000 0.4999999999999999 Ti 17 | 0.2500000000000000 0.8333333333333333 0.5000000000000001 Ti 18 | 0.7499999999999999 0.1666666666666667 0.5000000000000000 Ti 19 | 0.7499999999999999 0.5000000000000000 0.5000000000000001 Ti 20 | 0.7500000000000000 0.8333333333333333 0.5000000000000000 Ti 21 | 0.2500000000000000 0.1666666666666667 0.0000000000000000 S 22 | 0.2500000000000000 0.5000000000000000 0.0000000000000000 S 23 | 0.2500000000000000 0.8333333333333333 0.0000000000000000 S 24 | 0.7499999999999999 0.1666666666666667 0.0000000000000000 S 25 | 0.7499999999999999 0.5000000000000000 0.0000000000000000 S 26 | 0.7500000000000000 0.8333333333333333 0.0000000000000000 S 27 | 0.0000000000000000 0.1666666666666667 0.5000000000000001 S 28 | 0.0000000000000000 0.5000000000000000 0.5000000000000000 S 29 | 0.0000000000000000 0.8333333333333333 0.5000000000000001 S 30 | 0.5000000000000000 0.1666666666666667 0.5000000000000001 S 31 | 0.5000000000000000 0.5000000000000000 0.5000000000000001 S 32 | 0.4999999999999999 0.8333333333333333 0.5000000000000001 S 33 | 0.1250000000000000 0.0833333333333333 0.2500000000000000 H 34 | 0.1250000000000000 0.4166666666666666 0.2500000000000001 H 35 | 0.1250000000000000 0.7500000000000000 0.2500000000000001 H 36 | 0.6250000000000000 0.0833333333333333 0.2500000000000001 H 37 | 0.6250000000000000 0.4166666666666666 0.2500000000000000 H 38 | 0.6249999999999999 0.7500000000000000 0.2500000000000000 H 39 | 0.2500000000000000 0.0000000000000000 0.5000000000000001 S 40 | 0.2500000000000000 0.3333333333333333 0.5000000000000000 S 41 | 0.2500000000000000 0.6666666666666666 0.5000000000000001 S 42 | 0.7499999999999999 0.0000000000000000 0.5000000000000001 S 43 | 0.7499999999999999 0.3333333333333333 0.5000000000000001 S 44 | 0.7499999999999999 0.6666666666666666 0.5000000000000000 S 45 | -------------------------------------------------------------------------------- /Part_1-Structures_Molecules/files/BiFeO3.cif: -------------------------------------------------------------------------------- 1 | # generated using pymatgen 2 | data_FeBiO3 3 | _symmetry_space_group_name_H-M P4mm 4 | _cell_length_a 3.75141500 5 | _cell_length_b 3.75141500 6 | _cell_length_c 4.87982800 7 | _cell_angle_alpha 90.00000000 8 | _cell_angle_beta 90.00000000 9 | _cell_angle_gamma 90.00000000 10 | _symmetry_Int_Tables_number 99 11 | _chemical_formula_structural FeBiO3 12 | _chemical_formula_sum 'Fe1 Bi1 O3' 13 | _cell_volume 68.67437820 14 | _cell_formula_units_Z 1 15 | loop_ 16 | _symmetry_equiv_pos_site_id 17 | _symmetry_equiv_pos_as_xyz 18 | 1 'x, y, z' 19 | 2 '-y, x, z' 20 | 3 '-x, -y, z' 21 | 4 'y, -x, z' 22 | 5 '-x, y, z' 23 | 6 'y, x, z' 24 | 7 'x, -y, z' 25 | 8 '-y, -x, z' 26 | loop_ 27 | _atom_type_symbol 28 | _atom_type_oxidation_number 29 | Fe3+ 3.0 30 | Bi3+ 3.0 31 | O2- -2.0 32 | loop_ 33 | _atom_site_type_symbol 34 | _atom_site_label 35 | _atom_site_symmetry_multiplicity 36 | _atom_site_fract_x 37 | _atom_site_fract_y 38 | _atom_site_fract_z 39 | _atom_site_occupancy 40 | Fe3+ Fe0 1 0.00000000 0.00000000 0.52383500 1 41 | Bi3+ Bi1 1 0.50000000 0.50000000 0.95129300 1 42 | O2- O2 2 0.00000000 0.50000000 0.66958750 1 43 | O2- O3 1 0.00000000 0.00000000 0.14369550 1 44 | -------------------------------------------------------------------------------- /Part_1-Structures_Molecules/files/PbTiO3.cif: -------------------------------------------------------------------------------- 1 | # generated using pymatgen 2 | data_TiPbO3 3 | _symmetry_space_group_name_H-M P4mm 4 | _cell_length_a 3.87955190 5 | _cell_length_b 3.87955190 6 | _cell_length_c 4.28588762 7 | _cell_angle_alpha 90.00000000 8 | _cell_angle_beta 90.00000000 9 | _cell_angle_gamma 90.00000000 10 | _symmetry_Int_Tables_number 99 11 | _chemical_formula_structural TiPbO3 12 | _chemical_formula_sum 'Ti1 Pb1 O3' 13 | _cell_volume 64.50656432 14 | _cell_formula_units_Z 1 15 | loop_ 16 | _symmetry_equiv_pos_site_id 17 | _symmetry_equiv_pos_as_xyz 18 | 1 'x, y, z' 19 | 2 '-y, x, z' 20 | 3 '-x, -y, z' 21 | 4 'y, -x, z' 22 | 5 '-x, y, z' 23 | 6 'y, x, z' 24 | 7 'x, -y, z' 25 | 8 '-y, -x, z' 26 | loop_ 27 | _atom_type_symbol 28 | _atom_type_oxidation_number 29 | Ti4+ 4.0 30 | Pb2+ 2.0 31 | O2- -2.0 32 | loop_ 33 | _atom_site_type_symbol 34 | _atom_site_label 35 | _atom_site_symmetry_multiplicity 36 | _atom_site_fract_x 37 | _atom_site_fract_y 38 | _atom_site_fract_z 39 | _atom_site_occupancy 40 | Ti4+ Ti0 1 0.50000000 0.50000000 0.58251444 1 41 | Pb2+ Pb1 1 0.00000000 0.00000000 0.12358795 1 42 | O2- O2 2 0.00000000 0.50000000 0.49415765 1 43 | O2- O3 1 0.50000000 0.50000000 0.99578232 1 44 | -------------------------------------------------------------------------------- /Part_1-Structures_Molecules/files/SrYCoO.cif: -------------------------------------------------------------------------------- 1 | #### CIF created by Crystallographica 2 #### 2 | 3 | data_StrontiumYttriumCobaltOxide 4 | 5 | _audit_creation_method 'Crystallographica 2' 6 | _cell_angle_alpha 90 7 | _cell_angle_beta 90 8 | _cell_angle_gamma 90 9 | _cell_formula_units_Z 16 10 | _cell_length_a 7.6239 11 | _cell_length_b 7.6239 12 | _cell_length_c 15.327 13 | _cell_volume 890.864 14 | _cgraph_comments 'Crystal structure of the novel complex cobalt oxide Sr0.7 15 | 16 | Y0.3 Co O2.62 17 | 18 | ' 19 | _cgraph_title 'Strontium Yttrium Cobalt Oxide (0.7/0.3/1/2.62)' 20 | _chemical_formula_sum '(Sr0.7 Y0.3) Co O2.62' 21 | _symmetry_space_group_name_H-M 'I 4/m m m' 22 | _symmetry_space_group_name_Hall '-I 4 2' 23 | 24 | loop_ 25 | _symmetry_equiv_pos_as_xyz 26 | 'x, y, z' 27 | 'x+1/2, y+1/2, z+1/2' 28 | '-x, -y, -z' 29 | '-x+1/2, -y+1/2, -z+1/2' 30 | '-y, x, z' 31 | '-y+1/2, x+1/2, z+1/2' 32 | 'y, -x, -z' 33 | 'y+1/2, -x+1/2, -z+1/2' 34 | '-x, -y, z' 35 | '-x+1/2, -y+1/2, z+1/2' 36 | 'x, y, -z' 37 | 'x+1/2, y+1/2, -z+1/2' 38 | 'y, -x, z' 39 | 'y+1/2, -x+1/2, z+1/2' 40 | '-y, x, -z' 41 | '-y+1/2, x+1/2, -z+1/2' 42 | 'x, -y, -z' 43 | 'x+1/2, -y+1/2, -z+1/2' 44 | '-x, y, z' 45 | '-x+1/2, y+1/2, z+1/2' 46 | '-x, y, -z' 47 | '-x+1/2, y+1/2, -z+1/2' 48 | 'x, -y, z' 49 | 'x+1/2, -y+1/2, z+1/2' 50 | 'y, x, -z' 51 | 'y+1/2, x+1/2, -z+1/2' 52 | '-y, -x, z' 53 | '-y+1/2, -x+1/2, z+1/2' 54 | '-y, -x, -z' 55 | '-y+1/2, -x+1/2, -z+1/2' 56 | 'y, x, z' 57 | 'y+1/2, x+1/2, z+1/2' 58 | 59 | loop_ 60 | _atom_site_label 61 | _atom_site_type_symbol 62 | _atom_site_fract_x 63 | _atom_site_fract_y 64 | _atom_site_fract_z 65 | _atom_site_U_iso_or_equiv 66 | _atom_site_thermal_displace_type 67 | _atom_site_occupancy 68 | Sr1 Sr2+ 0 0 0.8785 0.0146916 Uiso 0.7 69 | Y1 Y3+ 0 0 0.8785 0.0146916 Uiso 0.3 70 | Sr2 Sr2+ 0 0.5 0.867 0.0102588 Uiso 0.7 71 | Y2 Y3+ 0 0.5 0.867 0.0102588 Uiso 0.3 72 | Sr3 Sr2+ 0 0 0.3503 0.00949886 Uiso 0.7 73 | Y3 Y3+ 0 0 0.3503 0.00949886 Uiso 0.3 74 | Co1 Co3+ 0.7483 0.7483 0 0.0135517 Uiso 1 75 | Co2 Co3+ 0.25 0.75 0.25 0.00544601 Uiso 1 76 | O1 O2- 0 0.2494 0.24 0.0100055 Uiso 1 77 | O2 O2- 0.2905 0.2905 0.1176 0.0191244 Uiso 1 78 | O3 O2- 0 0.7241 0 0.0227973 Uiso 1 79 | O4 O2- 0.387 0.5 0 0.00379954 Uiso 0.25 80 | 81 | _eof 82 | 83 | #### End of Crystallographic Information File #### 84 | -------------------------------------------------------------------------------- /Part_1-Structures_Molecules/graphics/chatgpt.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/computron/pymatgen_tutorials/81b42a79052ba0108ad7fc68958ef8a22020923a/Part_1-Structures_Molecules/graphics/chatgpt.png -------------------------------------------------------------------------------- /Part_1-Structures_Molecules/graphics/inheritance.png: -------------------------------------------------------------------------------- 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/Part_1-Structures_Molecules/my_POSCAR: -------------------------------------------------------------------------------- 1 | Ti6 Pb6 O18 2 | 1.0 3 | 7.7999999999999998 0.0000000000000000 0.0000000000000005 4 | -0.0000000000000007 11.6999999999999993 0.0000000000000007 5 | 0.0000000000000000 0.0000000000000000 4.2000000000000002 6 | Pb Ti O 7 | 6 6 18 8 | direct 9 | 0.0000000000000000 0.0000000000000000 0.0000000000000000 Pb 10 | 0.0000000000000000 0.3333333333333333 0.0000000000000000 Pb 11 | 0.0000000000000000 0.6666666666666666 0.0000000000000000 Pb 12 | 0.5000000000000000 0.0000000000000000 0.0000000000000000 Pb 13 | 0.5000000000000000 0.3333333333333333 0.0000000000000000 Pb 14 | 0.5000000000000001 0.6666666666666666 0.0000000000000000 Pb 15 | 0.2500000000000000 0.1666666666666667 0.5000000000000000 Ti 16 | 0.2500000000000000 0.5000000000000000 0.5000000000000001 Ti 17 | 0.2500000000000000 0.8333333333333331 0.5000000000000000 Ti 18 | 0.7500000000000000 0.1666666666666667 0.5000000000000001 Ti 19 | 0.7500000000000000 0.5000000000000000 0.5000000000000000 Ti 20 | 0.7500000000000001 0.8333333333333331 0.5000000000000001 Ti 21 | 0.2500000000000000 0.1666666666666667 0.0000000000000000 O 22 | 0.2500000000000000 0.5000000000000000 0.0000000000000000 O 23 | 0.2500000000000000 0.8333333333333331 0.0000000000000000 O 24 | 0.7500000000000000 0.1666666666666667 0.0000000000000000 O 25 | 0.7500000000000000 0.5000000000000000 0.0000000000000000 O 26 | 0.7500000000000001 0.8333333333333331 0.0000000000000000 O 27 | 0.0000000000000000 0.1666666666666667 0.4999999999999999 O 28 | 0.0000000000000000 0.5000000000000000 0.5000000000000000 O 29 | 0.0000000000000000 0.8333333333333331 0.4999999999999999 O 30 | 0.5000000000000000 0.1666666666666667 0.5000000000000000 O 31 | 0.5000000000000000 0.5000000000000000 0.4999999999999999 O 32 | 0.5000000000000001 0.8333333333333331 0.5000000000000000 O 33 | 0.2500000000000000 0.0000000000000000 0.4999999999999999 O 34 | 0.2500000000000001 0.3333333333333333 0.5000000000000000 O 35 | 0.2500000000000001 0.6666666666666666 0.4999999999999999 O 36 | 0.7500000000000000 0.0000000000000000 0.5000000000000000 O 37 | 0.7500000000000000 0.3333333333333333 0.4999999999999999 O 38 | 0.7500000000000001 0.6666666666666666 0.5000000000000000 O 39 | -------------------------------------------------------------------------------- /Part_1-Structures_Molecules/output.cif: -------------------------------------------------------------------------------- 1 | # generated using pymatgen 2 | data_TiSnHS3 3 | _symmetry_space_group_name_H-M 'P 1' 4 | _cell_length_a 11.70000000 5 | _cell_length_b 14.04000000 6 | _cell_length_c 3.90000000 7 | _cell_angle_alpha 90.00000000 8 | _cell_angle_beta 90.00000000 9 | _cell_angle_gamma 90.00000000 10 | _symmetry_Int_Tables_number 1 11 | _chemical_formula_structural TiSnHS3 12 | _chemical_formula_sum 'Ti6 Sn6 H6 S18' 13 | _cell_volume 640.64520000 14 | _cell_formula_units_Z 6 15 | loop_ 16 | _symmetry_equiv_pos_site_id 17 | _symmetry_equiv_pos_as_xyz 18 | 1 'x, y, z' 19 | loop_ 20 | _atom_site_type_symbol 21 | _atom_site_label 22 | _atom_site_symmetry_multiplicity 23 | _atom_site_fract_x 24 | _atom_site_fract_y 25 | _atom_site_fract_z 26 | _atom_site_occupancy 27 | Sn Sn0 1 0.00000000 0.00000000 0.00000000 1.0 28 | Sn Sn1 1 0.00000000 0.33333333 0.00000000 1.0 29 | Sn Sn2 1 0.00000000 0.66666667 0.00000000 1.0 30 | Sn Sn3 1 0.50000000 0.00000000 0.00000000 1.0 31 | Sn Sn4 1 0.50000000 0.33333333 0.00000000 1.0 32 | Sn Sn5 1 0.50000000 0.66666667 0.00000000 1.0 33 | Ti Ti6 1 0.25000000 0.16666667 0.50000000 1 34 | Ti Ti7 1 0.25000000 0.50000000 0.50000000 1 35 | Ti Ti8 1 0.25000000 0.83333333 0.50000000 1 36 | Ti Ti9 1 0.75000000 0.16666667 0.50000000 1 37 | Ti Ti10 1 0.75000000 0.50000000 0.50000000 1 38 | Ti Ti11 1 0.75000000 0.83333333 0.50000000 1 39 | S S12 1 0.25000000 0.16666667 0.00000000 1.0 40 | S S13 1 0.25000000 0.50000000 0.00000000 1.0 41 | S S14 1 0.25000000 0.83333333 0.00000000 1.0 42 | S S15 1 0.75000000 0.16666667 0.00000000 1.0 43 | S S16 1 0.75000000 0.50000000 0.00000000 1.0 44 | S S17 1 0.75000000 0.83333333 0.00000000 1.0 45 | S S18 1 0.00000000 0.16666667 0.50000000 1.0 46 | S S19 1 0.00000000 0.50000000 0.50000000 1.0 47 | S S20 1 0.00000000 0.83333333 0.50000000 1.0 48 | S S21 1 0.50000000 0.16666667 0.50000000 1.0 49 | S S22 1 0.50000000 0.50000000 0.50000000 1.0 50 | S S23 1 0.50000000 0.83333333 0.50000000 1.0 51 | H H24 1 0.12500000 0.08333333 0.25000000 1 52 | H H25 1 0.12500000 0.41666667 0.25000000 1 53 | H H26 1 0.12500000 0.75000000 0.25000000 1 54 | H H27 1 0.62500000 0.08333333 0.25000000 1 55 | H H28 1 0.62500000 0.41666667 0.25000000 1 56 | H H29 1 0.62500000 0.75000000 0.25000000 1 57 | S S30 1 0.25000000 0.00000000 0.50000000 1.0 58 | S S31 1 0.25000000 0.33333333 0.50000000 1.0 59 | S S32 1 0.25000000 0.66666667 0.50000000 1.0 60 | S S33 1 0.75000000 0.00000000 0.50000000 1.0 61 | S S34 1 0.75000000 0.33333333 0.50000000 1.0 62 | S S35 1 0.75000000 0.66666667 0.50000000 1.0 63 | -------------------------------------------------------------------------------- /Part_1-Structures_Molecules/output.xyz: -------------------------------------------------------------------------------- 1 | 10 2 | H6 C3 O1 3 | H 2.047100 0.102900 0.725100 4 | C 1.437600 0.081800 -0.187500 5 | H 1.664300 0.989400 -0.762000 6 | H 1.761600 -0.779600 -0.786000 7 | C -0.037700 -0.003500 0.096800 8 | O -0.479700 -0.044600 1.229400 9 | C -0.929400 -0.034500 -1.115000 10 | H -0.784400 0.870300 -1.719500 11 | H -0.685600 -0.898600 -1.746700 12 | H -1.994800 -0.097900 -0.858700 -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/INCAR: -------------------------------------------------------------------------------- 1 | ALGO = All 2 | EDIFF = 1e-05 3 | ENAUG = 1360.0 4 | ENCUT = 680.0 5 | GGA = Pe 6 | HFSCREEN = 0.2 7 | ISMEAR = -5 8 | ISPIN = 2 9 | LAECHG = True 10 | LASPH = True 11 | LCHARG = True 12 | LELF = True 13 | LHFCALC = True 14 | LMIXTAU = True 15 | LORBIT = 11 16 | LREAL = False 17 | LVTOT = True 18 | LWAVE = False 19 | MAGMOM = 2*0.0 20 | NELM = 200 21 | NSW = 0 22 | PREC = Accurate 23 | PRECFOCK = Fast 24 | SIGMA = 0.05 25 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/KPOINTS: -------------------------------------------------------------------------------- 1 | pymatgen with grid density = 1235 / number of atoms 2 | 0 3 | Gamma 4 | 8 8 8 5 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/POSCAR: -------------------------------------------------------------------------------- 1 | Si2 2 | 1.0 3 | 3.3294085500000001 0.0000000000000000 1.9222347600000000 4 | 1.1098025199999999 3.1389971600000002 1.9222347600000000 5 | 0.0000000000000000 0.0000000000000000 3.8444704999999999 6 | Si 7 | 2 8 | direct 9 | 0.2500000000000000 0.2500000000000000 0.2500000000000000 Si 10 | -0.0000000000000000 -0.0000000000000000 -0.0000000000000000 Si 11 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/LICENSE: -------------------------------------------------------------------------------- 1 | atomate2 Copyright (c) 2015, The Regents of the University of 2 | California, through Lawrence Berkeley National Laboratory (subject 3 | to receipt of any required approvals from the U.S. Dept. of Energy). 4 | All rights reserved. 5 | 6 | Redistribution and use in source and binary forms, with or without 7 | modification, are permitted provided that the following conditions 8 | are met: 9 | 10 | (1) Redistributions of source code must retain the above copyright 11 | notice, this list of conditions and the following disclaimer. 12 | 13 | (2) Redistributions in binary form must reproduce the above 14 | copyright notice, this list of conditions and the following 15 | disclaimer in the documentation and/or other materials provided with 16 | the distribution. 17 | 18 | (3) Neither the name of the University of California, Lawrence 19 | Berkeley National Laboratory, U.S. Dept. of Energy nor the names of 20 | its contributors may be used to endorse or promote products derived 21 | from this software without specific prior written permission. 22 | 23 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS 24 | "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 25 | LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS 26 | FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE 27 | COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, 28 | INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, 29 | BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 30 | LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 31 | CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT 32 | LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN 33 | ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 34 | POSSIBILITY OF SUCH DAMAGE. 35 | 36 | You are under no obligation whatsoever to provide any bug fixes, 37 | patches, or upgrades to the features, functionality or performance 38 | of the source code ("Enhancements") to anyone; however, if you 39 | choose to make your Enhancements available either publicly, or 40 | directly to Lawrence Berkeley National Laboratory or its 41 | contributors, without imposing a separate written license agreement 42 | for such Enhancements, then you hereby grant the following license: 43 | a non-exclusive, royalty-free perpetual license to install, use, 44 | modify, prepare derivative works, incorporate into other computer 45 | software, distribute, and sublicense such enhancements or derivative 46 | works thereof, in binary and source code form. 47 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/README.md: -------------------------------------------------------------------------------- 1 | # Test files for pymatgen tutorial 2 | 3 | Notes: 4 | 5 | 1. Test files are a modified version of those found in the atomate2 repo; hence the atomate2 license is copied here. 6 | 2. Note that some output files are removed for conciseness, these are not always intended to be complete. 7 | 3. Note that POTCAR files in particular are cleaned up due to VASP license terms. 8 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_HSE_band_structure_line/CONTCAR: -------------------------------------------------------------------------------- 1 | Si2 2 | 1.00000000000000 3 | 3.3488980000000002 0.0000000000000000 1.9334870000000000 4 | 1.1162989999999999 3.1573720000000001 1.9334870000000000 5 | 0.0000000000000000 0.0000000000000000 3.8669750000000001 6 | Si 7 | 2 8 | Direct 9 | 0.2500000000000000 0.2500000000000000 0.2500000000000000 10 | 0.0000000000000000 0.0000000000000000 0.0000000000000000 11 | 12 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 13 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 14 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_HSE_band_structure_line/INCAR: -------------------------------------------------------------------------------- 1 | ALGO = All 2 | EDIFF = 1e-05 3 | EDIFFG = -0.02 4 | ENAUG = 1360.0 5 | ENCUT = 680.0 6 | GGA = Pe 7 | HFSCREEN = 0.2 8 | IBRION = 2 9 | ISIF = 3 10 | ISMEAR = 0 11 | ISPIN = 1 12 | LAECHG = True 13 | LASPH = True 14 | LCHARG = False 15 | LELF = True 16 | LHFCALC = True 17 | LMIXTAU = True 18 | LORBIT = 11 19 | LREAL = Auto 20 | LVTOT = True 21 | LWAVE = False 22 | NBANDS = 11 23 | NCORE = 4 24 | NELM = 200 25 | NELMIN = 5 26 | NSW = 0 27 | PREC = Accurate 28 | PRECFOCK = Fast 29 | SIGMA = 0.01 30 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_HSE_band_structure_line/KPOINTS: -------------------------------------------------------------------------------- 1 | Hybrid run along symmetry lines 2 | 180 3 | Reciprocal 4 | 0.0 0.0 0.0 1 5 | 0.16666666666666666 0.0 0.0 8 6 | 0.3333333333333333 0.0 0.0 8 7 | 0.5 0.0 0.0 4 8 | 0.16666666666666666 0.16666666666666666 0.0 6 9 | 0.3333333333333333 0.16666666666666666 0.0 24 10 | 0.5 0.16666666666666666 0.0 24 11 | -0.3333333333333333 0.16666666666666666 0.0 24 12 | -0.16666666666666666 0.16666666666666666 0.0 12 13 | 0.3333333333333333 0.3333333333333333 0.0 6 14 | 0.5 0.3333333333333333 0.0 24 15 | -0.3333333333333333 0.3333333333333333 0.0 12 16 | 0.5 0.5 0.0 3 17 | 0.5 0.3333333333333333 0.16666666666666666 24 18 | -0.3333333333333333 0.3333333333333333 0.16666666666666666 24 19 | -0.3333333333333333 0.5 0.16666666666666666 12 20 | 0.0 0.0 0.0 0 \Gamma 21 | 0.02173913043478261 0.0 0.02173913043478261 0 22 | 0.04347826086956522 0.0 0.04347826086956522 0 23 | 0.06521739130434782 0.0 0.06521739130434782 0 24 | 0.08695652173913045 0.0 0.08695652173913045 0 25 | 0.10869565217391304 0.0 0.10869565217391304 0 26 | 0.13043478260869565 0.0 0.13043478260869565 0 27 | 0.15217391304347827 0.0 0.15217391304347827 0 28 | 0.1739130434782609 0.0 0.1739130434782609 0 29 | 0.1956521739130435 0.0 0.1956521739130435 0 30 | 0.21739130434782608 0.0 0.21739130434782608 0 31 | 0.2391304347826087 0.0 0.2391304347826087 0 32 | 0.2608695652173913 0.0 0.2608695652173913 0 33 | 0.2826086956521739 0.0 0.2826086956521739 0 34 | 0.30434782608695654 0.0 0.30434782608695654 0 35 | 0.32608695652173914 0.0 0.32608695652173914 0 36 | 0.3478260869565218 0.0 0.3478260869565218 0 37 | 0.3695652173913043 0.0 0.3695652173913043 0 38 | 0.391304347826087 0.0 0.391304347826087 0 39 | 0.41304347826086957 0.0 0.41304347826086957 0 40 | 0.43478260869565216 0.0 0.43478260869565216 0 41 | 0.4565217391304348 0.0 0.4565217391304348 0 42 | 0.4782608695652174 0.0 0.4782608695652174 0 43 | 0.5 0.0 0.5 0 X 44 | 0.5 0.0 0.5 0 X 45 | 0.5 0.020833333333333336 0.5208333333333334 0 46 | 0.5 0.04166666666666667 0.5416666666666666 0 47 | 0.5 0.0625 0.5625 0 48 | 0.5 0.08333333333333334 0.5833333333333334 0 49 | 0.5 0.10416666666666667 0.6041666666666666 0 50 | 0.5 0.125 0.625 0 51 | 0.5 0.14583333333333334 0.6458333333333333 0 52 | 0.5 0.16666666666666669 0.6666666666666666 0 53 | 0.5 0.1875 0.6875 0 54 | 0.5 0.20833333333333334 0.7083333333333333 0 55 | 0.5 0.22916666666666669 0.7291666666666666 0 56 | 0.5 0.25 0.75 0 W 57 | 0.5 0.25 0.75 0 W 58 | 0.48611111111111116 0.2638888888888889 0.75 0 59 | 0.4722222222222222 0.2777777777777778 0.75 0 60 | 0.45833333333333337 0.2916666666666667 0.75 0 61 | 0.4444444444444445 0.3055555555555555 0.75 0 62 | 0.4305555555555556 0.3194444444444445 0.75 0 63 | 0.41666666666666674 0.33333333333333337 0.75 0 64 | 0.40277777777777785 0.34722222222222227 0.75 0 65 | 0.38888888888888895 0.3611111111111111 0.75 0 66 | 0.37500000000000006 0.375 0.75 0 K 67 | 0.37500000000000006 0.375 0.75 0 K 68 | 0.36000000000000004 0.36 0.72 0 69 | 0.3450000000000001 0.34500000000000003 0.6900000000000001 0 70 | 0.33000000000000007 0.33 0.66 0 71 | 0.31500000000000006 0.315 0.63 0 72 | 0.30000000000000004 0.3 0.6000000000000001 0 73 | 0.28500000000000003 0.285 0.5700000000000001 0 74 | 0.27 0.27 0.54 0 75 | 0.25500000000000006 0.255 0.51 0 76 | 0.24000000000000005 0.24000000000000005 0.4800000000000001 0 77 | 0.22500000000000003 0.22499999999999998 0.44999999999999996 0 78 | 0.21000000000000005 0.21000000000000002 0.42000000000000004 0 79 | 0.19500000000000003 0.195 0.39 0 80 | 0.18000000000000002 0.18 0.36 0 81 | 0.165 0.16499999999999998 0.32999999999999996 0 82 | 0.15000000000000002 0.15000000000000002 0.30000000000000004 0 83 | 0.135 0.135 0.27 0 84 | 0.12000000000000002 0.11999999999999997 0.24 0 85 | 0.10500000000000002 0.10500000000000002 0.21000000000000002 0 86 | 0.09000000000000001 0.09000000000000001 0.18 0 87 | 0.07500000000000001 0.07499999999999997 0.14999999999999997 0 88 | 0.06000000000000001 0.06000000000000001 0.12000000000000002 0 89 | 0.045000000000000005 0.045000000000000005 0.09 0 90 | 0.030000000000000006 0.030000000000000006 0.06000000000000001 0 91 | 0.015000000000000003 0.015000000000000003 0.030000000000000006 0 92 | 0.0 0.0 0.0 0 \Gamma 93 | 0.0 0.0 0.0 0 \Gamma 94 | 0.025 0.025 0.025 0 95 | 0.05 0.05 0.05 0 96 | 0.07500000000000001 0.075 0.07500000000000001 0 97 | 0.1 0.1 0.1 0 98 | 0.125 0.125 0.125 0 99 | 0.15000000000000002 0.15 0.15000000000000002 0 100 | 0.175 0.175 0.175 0 101 | 0.2 0.2 0.2 0 102 | 0.22500000000000003 0.22500000000000003 0.22500000000000003 0 103 | 0.25 0.25 0.25 0 104 | 0.275 0.275 0.275 0 105 | 0.30000000000000004 0.3 0.30000000000000004 0 106 | 0.325 0.325 0.325 0 107 | 0.35 0.35 0.35 0 108 | 0.375 0.375 0.375 0 109 | 0.4 0.4 0.4 0 110 | 0.42500000000000004 0.425 0.42500000000000004 0 111 | 0.45000000000000007 0.45000000000000007 0.45000000000000007 0 112 | 0.475 0.475 0.475 0 113 | 0.5 0.5 0.5 0 L 114 | 0.5 0.5 0.5 0 L 115 | 0.5083333333333333 0.4833333333333334 0.5083333333333333 0 116 | 0.5166666666666667 0.46666666666666673 0.5166666666666667 0 117 | 0.525 0.44999999999999996 0.525 0 118 | 0.5333333333333333 0.43333333333333335 0.5333333333333333 0 119 | 0.5416666666666667 0.4166666666666667 0.5416666666666667 0 120 | 0.55 0.4 0.55 0 121 | 0.5583333333333333 0.38333333333333336 0.5583333333333333 0 122 | 0.5666666666666667 0.3666666666666667 0.5666666666666667 0 123 | 0.575 0.35 0.575 0 124 | 0.5833333333333334 0.33333333333333337 0.5833333333333334 0 125 | 0.5916666666666667 0.3166666666666667 0.5916666666666667 0 126 | 0.6 0.3 0.6 0 127 | 0.6083333333333334 0.2833333333333333 0.6083333333333334 0 128 | 0.6166666666666667 0.26666666666666666 0.6166666666666667 0 129 | 0.625 0.25 0.625 0 U 130 | 0.625 0.25 0.625 0 U 131 | 0.6111111111111112 0.25 0.6388888888888888 0 132 | 0.5972222222222222 0.25 0.6527777777777777 0 133 | 0.5833333333333334 0.25 0.6666666666666666 0 134 | 0.5694444444444444 0.25 0.6805555555555556 0 135 | 0.5555555555555556 0.25 0.6944444444444444 0 136 | 0.5416666666666666 0.25 0.7083333333333333 0 137 | 0.5277777777777778 0.25 0.7222222222222222 0 138 | 0.513888888888889 0.25 0.736111111111111 0 139 | 0.5 0.25 0.75 0 W 140 | 0.5 0.25 0.75 0 W 141 | 0.5 0.2647058823529412 0.7352941176470589 0 142 | 0.5 0.27941176470588236 0.7205882352941176 0 143 | 0.5 0.29411764705882354 0.7058823529411764 0 144 | 0.5 0.3088235294117647 0.6911764705882353 0 145 | 0.5 0.3235294117647059 0.6764705882352942 0 146 | 0.5 0.3382352941176471 0.6617647058823529 0 147 | 0.5 0.3529411764705882 0.6470588235294118 0 148 | 0.5 0.3676470588235294 0.6323529411764706 0 149 | 0.5 0.3823529411764706 0.6176470588235294 0 150 | 0.5 0.3970588235294118 0.6029411764705882 0 151 | 0.5000000000000001 0.4117647058823529 0.5882352941176471 0 152 | 0.5 0.42647058823529416 0.5735294117647058 0 153 | 0.5 0.4411764705882353 0.5588235294117647 0 154 | 0.5 0.45588235294117646 0.5441176470588236 0 155 | 0.5 0.47058823529411764 0.5294117647058824 0 156 | 0.5 0.48529411764705876 0.5147058823529412 0 157 | 0.5 0.5 0.5 0 L 158 | 0.5 0.5 0.5 0 L 159 | 0.4916666666666667 0.4916666666666667 0.5166666666666666 0 160 | 0.4833333333333334 0.48333333333333334 0.5333333333333333 0 161 | 0.4750000000000001 0.47500000000000003 0.55 0 162 | 0.4666666666666667 0.4666666666666667 0.5666666666666667 0 163 | 0.45833333333333337 0.45833333333333337 0.5833333333333334 0 164 | 0.45000000000000007 0.44999999999999996 0.6000000000000001 0 165 | 0.4416666666666667 0.44166666666666665 0.6166666666666667 0 166 | 0.43333333333333335 0.4333333333333334 0.6333333333333333 0 167 | 0.42500000000000004 0.42500000000000004 0.65 0 168 | 0.4166666666666667 0.41666666666666674 0.6666666666666667 0 169 | 0.40833333333333344 0.4083333333333334 0.6833333333333333 0 170 | 0.4000000000000001 0.39999999999999997 0.7 0 171 | 0.3916666666666667 0.3916666666666667 0.7166666666666668 0 172 | 0.3833333333333334 0.38333333333333336 0.7333333333333334 0 173 | 0.37500000000000006 0.375 0.75 0 K 174 | 0.625 0.25 0.625 0 U 175 | 0.6111111111111112 0.22222222222222224 0.6111111111111112 0 176 | 0.5972222222222222 0.19444444444444445 0.5972222222222222 0 177 | 0.5833333333333334 0.16666666666666669 0.5833333333333334 0 178 | 0.5694444444444444 0.13888888888888892 0.5694444444444444 0 179 | 0.5555555555555556 0.1111111111111111 0.5555555555555556 0 180 | 0.5416666666666666 0.08333333333333334 0.5416666666666666 0 181 | 0.5277777777777778 0.05555555555555555 0.5277777777777778 0 182 | 0.513888888888889 0.02777777777777781 0.513888888888889 0 183 | 0.5 0.0 0.5 0 X 184 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_HSE_band_structure_line/POSCAR: -------------------------------------------------------------------------------- 1 | Si2 2 | 1.0 3 | 3.348898 0.000000 1.933487 4 | 1.116299 3.157372 1.933487 5 | 0.000000 0.000000 3.866975 6 | Si 7 | 2 8 | direct 9 | 0.250000 0.250000 0.250000 Si 10 | 0.000000 0.000000 0.000000 Si 11 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_HSE_band_structure_line/POTCAR.spec: -------------------------------------------------------------------------------- 1 | Si 2 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_HSE_relax_output/CONTCAR: -------------------------------------------------------------------------------- 1 | Si2 2 | 1.00000000000000 3 | 3.3294085465396401 0.0000000032454955 1.9222347577431924 4 | 1.1098025205129833 3.1389971553704812 1.9222347577431931 5 | 0.0000000033599839 0.0000000023758681 3.8444705038470586 6 | Si 7 | 2 8 | Direct 9 | 0.2500000000000000 0.2500000000000000 0.2500000000000000 10 | -0.0000000000000000 -0.0000000000000000 -0.0000000000000000 11 | 12 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 13 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 14 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_HSE_relax_output/INCAR: -------------------------------------------------------------------------------- 1 | ALGO = All 2 | EDIFF = 1e-05 3 | EDIFFG = -0.02 4 | ENAUG = 1360 5 | ENCUT = 680 6 | GGA = Pe 7 | HFSCREEN = 0.2 8 | IBRION = 2 9 | ISIF = 3 10 | ISMEAR = 0 11 | ISPIN = 2 12 | KSPACING = 0.4 13 | LAECHG = True 14 | LASPH = True 15 | LCHARG = True 16 | LELF = True 17 | LHFCALC = True 18 | LMIXTAU = True 19 | LORBIT = 11 20 | LREAL = Auto 21 | LVTOT = True 22 | LWAVE = False 23 | MAGMOM = 2*0.6 24 | NELM = 200 25 | NSW = 99 26 | PREC = Accurate 27 | PRECFOCK = Fast 28 | SIGMA = 0.05 29 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_HSE_relax_output/POSCAR: -------------------------------------------------------------------------------- 1 | Si2 2 | 1.0 3 | 3.348898 0.000000 1.933487 4 | 1.116299 3.157372 1.933487 5 | 0.000000 0.000000 3.866975 6 | Si 7 | 2 8 | direct 9 | 0.250000 0.250000 0.250000 Si 10 | 0.000000 0.000000 0.000000 Si 11 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_HSE_relax_output/POTCAR.spec: -------------------------------------------------------------------------------- 1 | Si 2 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_optics/CONTCAR: -------------------------------------------------------------------------------- 1 | Si2 2 | 1.00000000000000 3 | 3.3488980000000002 0.0000000000000000 1.9334870000000000 4 | 1.1162989999999999 3.1573720000000001 1.9334870000000000 5 | 0.0000000000000000 0.0000000000000000 3.8669750000000001 6 | Si 7 | 2 8 | Direct 9 | 0.2500000000000000 0.2500000000000000 0.2500000000000000 10 | 0.0000000000000000 0.0000000000000000 0.0000000000000000 11 | 12 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 13 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 14 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_optics/INCAR: -------------------------------------------------------------------------------- 1 | ALGO = Normal 2 | EDIFF = 1e-05 3 | EDIFFG = -0.02 4 | ENAUG = 1360.0 5 | ENCUT = 680.0 6 | IBRION = -1 7 | ICHARG = 11 8 | ISIF = 3 9 | ISMEAR = -5 10 | ISPIN = 1 11 | ISYM = 2 12 | LAECHG = True 13 | LASPH = True 14 | LCHARG = False 15 | LELF = True 16 | LMIXTAU = True 17 | LOPTICS = True 18 | LORBIT = 11 19 | LREAL = Auto 20 | LVTOT = True 21 | LWAVE = False 22 | NBANDS = 11 23 | NCORE = 4 24 | NEDOS = 4544 25 | NELM = 200 26 | NSW = 0 27 | PREC = Accurate 28 | SIGMA = 0.2 29 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_optics/KPOINTS: -------------------------------------------------------------------------------- 1 | pymatgen with grid density = 1213 / number of atoms 2 | 0 3 | Gamma 4 | 8 8 8 5 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_optics/POSCAR: -------------------------------------------------------------------------------- 1 | Si2 2 | 1.0 3 | 3.348898 0.000000 1.933487 4 | 1.116299 3.157372 1.933487 5 | 0.000000 0.000000 3.866975 6 | Si 7 | 2 8 | direct 9 | 0.250000 0.250000 0.250000 Si 10 | 0.000000 0.000000 0.000000 Si 11 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_optics/POTCAR.spec: -------------------------------------------------------------------------------- 1 | Si 2 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/CHGCAR: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/computron/pymatgen_tutorials/81b42a79052ba0108ad7fc68958ef8a22020923a/Part_2-Pymatgen_and_VASP/files/Si_relax_output/CHGCAR -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/CONTCAR: -------------------------------------------------------------------------------- 1 | Si2 2 | 1.000000000000000 3 | 3.3496744307422048 0.0000000000000000 1.9339351614767313 4 | 1.1165581435807350 3.1581045923790994 1.9339351614767313 5 | 0.0000000000000000 0.0000000000000000 3.8678703229534626 6 | Si 7 | 2 8 | Direct 9 | 0.8750000000000000 0.8750000000000000 0.8750000000000000 10 | 0.1250000000000000 0.1250000000000000 0.1250000000000000 11 | 12 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 13 | 0.00000000E+00 0.00000000E+00 0.00000000E+00 14 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/EIGENVAL: -------------------------------------------------------------------------------- 1 | 2 2 99 2 2 | 0.2045837E+02 0.3867871E-09 0.3867872E-09 0.3867870E-09 0.5000000E-15 3 | 1.0000000000000000E-004 4 | CAR 5 | unknown system 6 | 8 20 16 7 | 8 | 0.1262379E-14 0.1262379E-14 0.1262379E-14 0.2915452E-02 9 | 1 -6.199117 -6.199118 1.000000 1.000000 10 | 2 5.611395 5.611391 1.000000 1.000000 11 | 3 5.611395 5.611391 1.000000 1.000000 12 | 4 5.611398 5.611394 1.000000 1.000000 13 | 5 8.166998 8.166996 0.000000 0.000000 14 | 6 8.167005 8.167003 0.000000 0.000000 15 | 7 8.167007 8.167005 0.000000 0.000000 16 | 8 8.737713 8.737720 0.000000 0.000000 17 | 9 13.318890 13.318889 0.000000 0.000000 18 | 10 13.318891 13.318890 0.000000 0.000000 19 | 11 13.489555 13.489557 0.000000 0.000000 20 | 12 16.791097 16.791097 0.000000 0.000000 21 | 13 16.791100 16.791100 0.000000 0.000000 22 | 14 16.791101 16.791101 0.000000 0.000000 23 | 15 20.886068 20.886062 0.000000 0.000000 24 | 16 28.459607 28.460368 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19.923380 0.000000 0.000000 363 | 13 20.774538 20.774538 0.000000 0.000000 364 | 14 21.891120 21.891119 0.000000 0.000000 365 | 15 23.013776 23.013665 0.000000 0.000000 366 | 16 23.850068 23.853608 0.000000 0.000000 367 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/IBZKPT: -------------------------------------------------------------------------------- 1 | Automatically generated mesh 2 | 20 3 | Reciprocal lattice 4 | 0.00000000000000 0.00000000000000 0.00000000000000 1 5 | 0.14285714285715 0.00000000000000 0.00000000000000 8 6 | 0.28571428571429 0.00000000000000 0.00000000000000 8 7 | 0.42857142857143 0.00000000000000 0.00000000000000 8 8 | 0.14285714285715 0.14285714285715 0.00000000000000 6 9 | 0.28571428571429 0.14285714285715 0.00000000000000 24 10 | 0.42857142857143 0.14285714285715 0.00000000000000 24 11 | -0.42857142857143 0.14285714285715 0.00000000000000 24 12 | -0.28571428571428 0.14285714285715 0.00000000000000 24 13 | -0.14285714285714 0.14285714285715 0.00000000000000 12 14 | 0.28571428571429 0.28571428571429 0.00000000000000 6 15 | 0.42857142857143 0.28571428571429 0.00000000000000 24 16 | -0.42857142857143 0.28571428571429 0.00000000000000 24 17 | -0.28571428571428 0.28571428571429 0.00000000000000 12 18 | 0.42857142857143 0.42857142857143 0.00000000000000 6 19 | -0.42857142857143 0.42857142857143 0.00000000000000 12 20 | 0.42857142857143 0.28571428571429 0.14285714285715 24 21 | -0.42857142857143 0.28571428571429 0.14285714285715 48 22 | -0.42857142857143 0.42857142857143 0.14285714285715 24 23 | -0.28571428571428 0.42857142857143 0.14285714285715 24 24 | Tetrahedra 25 | 58 0.00048590864917 26 | 48 2 3 6 10 27 | 48 6 9 10 17 28 | 24 9 9 10 17 29 | 48 3 6 9 10 30 | 48 9 14 17 18 31 | 48 8 9 14 18 32 | 24 9 9 14 17 33 | 48 8 13 18 18 34 | 48 7 8 13 18 35 | 48 8 13 14 18 36 | 48 7 12 17 18 37 | 48 6 7 12 17 38 | 48 7 12 13 18 39 | 24 6 6 11 17 40 | 24 5 6 6 11 41 | 48 6 11 12 17 42 | 24 5 6 6 10 43 | 48 2 5 6 10 44 | 48 6 7 9 17 45 | 48 3 6 7 9 46 | 48 12 17 18 19 47 | 24 17 18 18 19 48 | 24 14 17 18 18 49 | 48 7 9 17 18 50 | 48 18 19 20 20 51 | 24 18 18 20 20 52 | 48 13 18 18 20 53 | 24 18 18 19 20 54 | 24 14 18 18 20 55 | 48 13 14 18 20 56 | 48 13 18 19 20 57 | 48 12 13 18 19 58 | 24 12 12 17 19 59 | 24 11 12 12 17 60 | 24 6 6 10 17 61 | 48 12 13 16 19 62 | 24 16 19 19 20 63 | 12 19 19 20 20 64 | 24 19 20 20 20 65 | 48 13 16 19 20 66 | 6 20 20 20 20 67 | 48 7 8 8 18 68 | 48 7 8 9 18 69 | 24 13 13 16 20 70 | 24 8 8 18 18 71 | 24 2 2 5 10 72 | 48 3 4 7 9 73 | 48 4 7 8 9 74 | 24 13 13 14 20 75 | 24 12 12 15 19 76 | 24 11 12 12 15 77 | 48 12 15 16 19 78 | 48 4 7 8 8 79 | 12 16 16 19 19 80 | 24 15 16 16 19 81 | 24 4 4 8 8 82 | 12 15 15 16 16 83 | 24 1 2 2 5 84 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/INCAR: -------------------------------------------------------------------------------- 1 | ALGO = Fast 2 | EDIFF = 0.0001 3 | ENCUT = 520.0 4 | IBRION = 2 5 | ISIF = 3 6 | ISMEAR = -5 7 | ISPIN = 2 8 | LASPH = True 9 | LORBIT = 11 10 | LREAL = Auto 11 | LWAVE = False 12 | MAGMOM = 2*-0.0 13 | NELM = 100 14 | NSW = 99 15 | PREC = Accurate 16 | SIGMA = 0.05 17 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/KPOINTS: -------------------------------------------------------------------------------- 1 | pymatgen with grid density = 776 / number of atoms 2 | 0 3 | Gamma 4 | 7 7 7 5 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/OSZICAR: -------------------------------------------------------------------------------- 1 | N E dE d eps ncg rms rms(c) 2 | DAV: 1 -0.133097315926E+01 -0.13310E+01 -0.33109E+03 1280 0.403E+02 3 | DAV: 2 -0.109517951747E+02 -0.96208E+01 -0.96036E+01 1888 0.372E+01 4 | DAV: 3 -0.110107039148E+02 -0.58909E-01 -0.58909E-01 1440 0.368E+00 5 | DAV: 4 -0.110108565494E+02 -0.15263E-03 -0.15263E-03 2384 0.201E-01 6 | DAV: 5 -0.110108565559E+02 -0.65514E-08 -0.65514E-08 1456 0.122E-03 0.475E+00 7 | RMM: 6 -0.108940848399E+02 0.11677E+00 -0.25517E-02 1280 0.560E-01 0.290E+00 8 | RMM: 7 -0.108399729817E+02 0.54112E-01 -0.60522E-02 1280 0.939E-01 0.180E-01 9 | RMM: 8 -0.108412694186E+02 -0.12964E-02 -0.29961E-03 1280 0.265E-01 0.740E-02 10 | RMM: 9 -0.108414229340E+02 -0.15352E-03 -0.36837E-04 1278 0.946E-02 0.734E-02 11 | RMM: 10 -0.108414565603E+02 -0.33626E-04 -0.74815E-05 1020 0.452E-02 12 | 1 F= -.10841457E+02 E0= -.10841457E+02 d E =-.108415E+02 mag= -0.0000 13 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/PCDAT: -------------------------------------------------------------------------------- 1 | 1 2 1 0 0.2045837E+02 0.1000000E-03 2 | CAR 3 | unknown system 4 | 0 0 0 5 | 1 1 6 | 256 256 256 7 | 256 8 | 0.1000000E-09 9 | 0.3906250E-11 10 | 1 11 | 0.5000000E-15 0.3867871E-09 0.3867872E-09 0.3867870E-09 12 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/POSCAR: -------------------------------------------------------------------------------- 1 | Si2 2 | 1.0 3 | 3.3496744307422048 0.0000000000000000 1.9339351614767313 4 | 1.1165581435807350 3.1581045923790994 1.9339351614767313 5 | 0.0000000000000000 0.0000000000000000 3.8678703229534626 6 | Si 7 | 2 8 | direct 9 | 0.8750000000000000 0.8750000000000000 0.8750000000000000 Si 10 | 0.1250000000000000 0.1250000000000000 0.1250000000000000 Si 11 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/REPORT: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/computron/pymatgen_tutorials/81b42a79052ba0108ad7fc68958ef8a22020923a/Part_2-Pymatgen_and_VASP/files/Si_relax_output/REPORT -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/WAVECAR: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/computron/pymatgen_tutorials/81b42a79052ba0108ad7fc68958ef8a22020923a/Part_2-Pymatgen_and_VASP/files/Si_relax_output/WAVECAR -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/XDATCAR: -------------------------------------------------------------------------------- 1 | unknown system 2 | 1 3 | 3.349674 0.000000 1.933935 4 | 1.116558 3.158105 1.933935 5 | 0.000000 0.000000 3.867870 6 | Si 7 | 2 8 | Direct configuration= 1 9 | 0.87500000 0.87500000 0.87500000 10 | 0.12500000 0.12500000 0.12500000 11 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/vasp.out: -------------------------------------------------------------------------------- 1 | ---------------------------------------------------- 2 | OOO PPPP EEEEE N N M M PPPP 3 | O O P P E NN N MM MM P P 4 | O O PPPP EEEEE N N N M M M PPPP -- VERSION 5 | O O P E N NN M M P 6 | OOO P EEEEE N N M M P 7 | ---------------------------------------------------- 8 | running 16 mpi-ranks, with 4 threads/rank 9 | distrk: each k-point on 16 cores, 1 groups 10 | distr: one band on 1 cores, 16 groups 11 | vasp.6.3.2 27Jun22 (build Jun 30 2023 15:13:53) complex 12 | POSCAR found type information on POSCAR Si 13 | POSCAR found : 1 types and 2 ions 14 | Reading from existing POTCAR 15 | scaLAPACK will be used 16 | Reading from existing POTCAR 17 | ----------------------------------------------------------------------------- 18 | | | 19 | | ----> ADVICE to this user running VASP <---- | 20 | | | 21 | | You have a (more or less) 'small supercell' and for smaller cells | 22 | | it is recommended to use the reciprocal-space projection scheme! | 23 | | The real-space optimization is not efficient for small cells and it | 24 | | is also less accurate ... | 25 | | Therefore, set LREAL=.FALSE. in the INCAR file. | 26 | | | 27 | ----------------------------------------------------------------------------- 28 | 29 | LDA part: xc-table for Pade appr. of Perdew 30 | POSCAR, INCAR and KPOINTS ok, starting setup 31 | FFT: planning ... GRIDC 32 | FFT: planning ... GRID_SOFT 33 | FFT: planning ... GRID 34 | WAVECAR not read 35 | WARNING: random wavefunctions but no delay for mixing, default for NELMDL 36 | entering main loop 37 | N E dE d eps ncg rms rms(c) 38 | DAV: 1 -0.133097315926E+01 -0.13310E+01 -0.33109E+03 1280 0.403E+02 39 | DAV: 2 -0.109517951747E+02 -0.96208E+01 -0.96036E+01 1888 0.372E+01 40 | DAV: 3 -0.110107039148E+02 -0.58909E-01 -0.58909E-01 1440 0.368E+00 41 | DAV: 4 -0.110108565494E+02 -0.15263E-03 -0.15263E-03 2384 0.201E-01 42 | DAV: 5 -0.110108565559E+02 -0.65514E-08 -0.65514E-08 1456 0.122E-03 0.475E+00 43 | RMM: 6 -0.108940848399E+02 0.11677E+00 -0.25517E-02 1280 0.560E-01 0.290E+00 44 | RMM: 7 -0.108399729817E+02 0.54112E-01 -0.60522E-02 1280 0.939E-01 0.180E-01 45 | RMM: 8 -0.108412694186E+02 -0.12964E-02 -0.29961E-03 1280 0.265E-01 0.740E-02 46 | RMM: 9 -0.108414229340E+02 -0.15352E-03 -0.36837E-04 1278 0.946E-02 0.734E-02 47 | RMM: 10 -0.108414565603E+02 -0.33626E-04 -0.74815E-05 1020 0.452E-02 48 | 1 F= -.10841457E+02 E0= -.10841457E+02 d E =-.108415E+02 mag= -0.0000 49 | curvature: 0.00 expect dE= 0.000E+00 dE for cont linesearch 0.000E+00 50 | trial: gam= 0.00000 g(F)= 0.255E-43 g(S)= 0.503E-05 ort = 0.000E+00 (trialstep = 0.100E+01) 51 | search vector abs. value= 0.503E-05 52 | reached required accuracy - stopping structural energy minimisation 53 | PROFILE, used timers: 371 54 | -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/files/Si_relax_output/vaspout.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/computron/pymatgen_tutorials/81b42a79052ba0108ad7fc68958ef8a22020923a/Part_2-Pymatgen_and_VASP/files/Si_relax_output/vaspout.h5 -------------------------------------------------------------------------------- /Part_2-Pymatgen_and_VASP/graphics/input_from_previous.png: -------------------------------------------------------------------------------- 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/Part_3-Materials_Project_API/graphics/title.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/computron/pymatgen_tutorials/81b42a79052ba0108ad7fc68958ef8a22020923a/Part_3-Materials_Project_API/graphics/title.png -------------------------------------------------------------------------------- /Part_3-Materials_Project_API/pymatgen_pt3_materials_project_api.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [ 3 | { 4 | "cell_type": "code", 5 | "execution_count": null, 6 | "id": "1f0879d7", 7 | "metadata": { 8 | "slideshow": { 9 | "slide_type": "skip" 10 | } 11 | }, 12 | "outputs": [], 13 | "source": [ 14 | "import warnings\n", 15 | "warnings.filterwarnings('ignore')" 16 | ] 17 | }, 18 | { 19 | "cell_type": "markdown", 20 | "id": "f8a58e40", 21 | "metadata": { 22 | "slideshow": { 23 | "slide_type": "skip" 24 | } 25 | }, 26 | "source": [ 27 | "# About this notebook\n", 28 | "\n", 29 | "* Author: Anubhav Jain\n", 30 | "* Github repo: https://github.com/computron/pymatgen_tutorials\n", 31 | "* YouTube video: https://youtu.be/e4hSkv1Ghbk\n", 32 | "\n", 33 | "## Important update!\n", 34 | "\n", 35 | "Pymatgen has decided to part ways with using mp-api as of 4/16/2025. This notebook has been updated to use mp-api directly instead of through pymatgen. More information in the v2025.4.16 update here: https://pymatgen.org/CHANGES.html" 36 | ] 37 | }, 38 | { 39 | "cell_type": "markdown", 40 | "id": "25c9b0b5", 41 | "metadata": { 42 | "slideshow": { 43 | "slide_type": "slide" 44 | } 45 | }, 46 | "source": [ 47 | "![alt text](graphics/title.png \"Learn Pymatgen Part 3: Getting Data with the Materials Project API\")" 48 | ] 49 | }, 50 | { 51 | "cell_type": "markdown", 52 | "id": "c81f40fb", 53 | "metadata": { 54 | "slideshow": { 55 | "slide_type": "slide" 56 | } 57 | }, 58 | "source": [ 59 | "# What is the Materials Project API?\n", 60 | "\n", 61 | "* The Materials Project (https://www.materialsproject.org) is a **free** web site / database / design tool that contains high quality simulated properties of various materials via density functional theory calculations.\n", 62 | "* The API allows users to download the various data sets via computer programs such as ``pymatgen``.\n", 63 | " * Note: the API is written in a RESTful manner which means that the API is not tied to any one programming language or software library.\n", 64 | "* Common uses of the data are to:\n", 65 | " * find materials with specific properties\n", 66 | " * help support a scientific analysis with theoretical data\n", 67 | " * use the data to train a machine learning model\n", 68 | "\n", 69 | " \n", 70 | "\n", 71 | "\n", 72 | " " 73 | ] 74 | }, 75 | { 76 | "cell_type": "markdown", 77 | "id": "6f8f77ca", 78 | "metadata": { 79 | "slideshow": { 80 | "slide_type": "slide" 81 | } 82 | }, 83 | "source": [ 84 | "# What data is available through the Materials Project API?\n", 85 | "* At the time of this tutorial (August 2024), the data set contains:\n", 86 | " * >150,000 materials structures\n", 87 | " * >170,000 molecules structures\n", 88 | " * >70,000 electronic band structures / density of states\n", 89 | " * >50,000 x-ray absorption spectra\n", 90 | " * >10,000 elastic tensors\n", 91 | " * >7,000 dielectric tensors\n", 92 | " * >3,000 piezoelectric tensors\n", 93 | " * >1,500 phonon band structures / phonon DOS\n", 94 | " * (among other properties ...)" 95 | ] 96 | }, 97 | { 98 | "cell_type": "markdown", 99 | "id": "03158896", 100 | "metadata": { 101 | "slideshow": { 102 | "slide_type": "slide" 103 | } 104 | }, 105 | "source": [ 106 | "# Optional note #1: New API vs legacy API\n", 107 | "\n", 108 | "* As of the time of this tutorial (August 2024), there are currently **two** APIs for the Materials Project.\n", 109 | "* The new API allows you to access the most recent data sets, offers more features, and will be more future-proof to learn.\n", 110 | "* This tutorial will only cover the **new** API. It will **not** cover the legacy API.\n", 111 | "\n", 112 | "![alt text](graphics/api_comparison.png \"Comparison of old and new Materials Project API\")\n", 113 | "\n", 114 | "\n", 115 | "\n" 116 | ] 117 | }, 118 | { 119 | "cell_type": "markdown", 120 | "id": "7e06bcf7", 121 | "metadata": { 122 | "slideshow": { 123 | "slide_type": "slide" 124 | } 125 | }, 126 | "source": [ 127 | "# Optional note #2: pymatgen's MPRester and the new API\n", 128 | "\n", 129 | "\n", 130 | "* There has been a bit of a messy history between the Materials Project API being accessed through pymatgen or through a dedicated library called ``mp-api``.\n", 131 | "* As of 4/16/2025, pymatgen no longer supports ``mp-api`` use. See changelog: https://pymatgen.org/CHANGES.html\n", 132 | "* This tutorial has therefore been updated to import and use ``mp-api`` directly without involving pymatgen. pymatgen maintains its own built-in functionality for querying the Materials Project API, but this is not covered in this tutorial." 133 | ] 134 | }, 135 | { 136 | "cell_type": "markdown", 137 | "id": "74d7f1eb", 138 | "metadata": { 139 | "slideshow": { 140 | "slide_type": "slide" 141 | } 142 | }, 143 | "source": [ 144 | "# Required set up: Getting and setting your API Key\n", 145 | "\n", 146 | "* You can get your API key at: https://next-gen.materialsproject.org/api" 147 | ] 148 | }, 149 | { 150 | "cell_type": "markdown", 151 | "id": "94f90763", 152 | "metadata": { 153 | "slideshow": { 154 | "slide_type": "slide" 155 | } 156 | }, 157 | "source": [ 158 | "# Required set up: installing the ``mp-api`` library\n", 159 | "\n", 160 | "* **To use the new API, you should install the ``mp-api`` library by running the following command**:\n", 161 | " * ``pip install mp-api``\n", 162 | "* If you do not install ``mp-api``, pymatgen still offers built-in functionality for using the Materials Project API. However, that will not be covered in this tutorial.\n" 163 | ] 164 | }, 165 | { 166 | "cell_type": "markdown", 167 | "id": "b8b46edd", 168 | "metadata": { 169 | "slideshow": { 170 | "slide_type": "slide" 171 | } 172 | }, 173 | "source": [ 174 | "# Importing MPRester\n", 175 | "\n", 176 | "* If your set up is correct, you should be able to import ``MPRester`` and the type of object you get should be ``mp_api.client.mprester.MPRester``.\n", 177 | "* Note that when creating the ``MPRester`` object, you either need to supply your API key or configure your API key using the pymatgen configuration file (better for hiding your key from others)\n", 178 | " * Briefly, you can run the following command to enter your API key into your configuration file: ``pmg config --add PMG_MAPI_KEY ``\n", 179 | " * Full instructions on configuring your API key: https://pymatgen.org/usage.html" 180 | ] 181 | }, 182 | { 183 | "cell_type": "code", 184 | "execution_count": null, 185 | "id": "f7f6f8d0", 186 | "metadata": { 187 | "slideshow": { 188 | "slide_type": "fragment" 189 | } 190 | }, 191 | "outputs": [], 192 | "source": [ 193 | "from mp_api.client import MPRester\n", 194 | "mpr = MPRester() # use this line if you set up the configuration file\n", 195 | "# mpr = MPRester(\"YOUR_API_KEY\") # use this line to enter your API key manually\n", 196 | "\n", 197 | "print(type(mpr)) # should be 'mp_api.client.mprester.MPRester'" 198 | ] 199 | }, 200 | { 201 | "cell_type": "markdown", 202 | "id": "10614e73", 203 | "metadata": { 204 | "slideshow": { 205 | "slide_type": "slide" 206 | } 207 | }, 208 | "source": [ 209 | "# Retrieving data using MPRester: built-in convenience functions\n", 210 | "\n", 211 | "* MPRester contains many convenience functions for getting many common types of data such as crystal structures\n", 212 | "* To use these functions, you typically need to know the Materials Project ID (``material_id``) of the material you want data for\n", 213 | "* You can get the ``material_id`` by browsing the Materials Project web site (www.materialsproject.org) or by performing a search via the API.\n", 214 | "* We'll demonstrate API searches later, for now we will use some known ``material_id`` values to get data." 215 | ] 216 | }, 217 | { 218 | "cell_type": "code", 219 | "execution_count": null, 220 | "id": "1ad2c1ac", 221 | "metadata": { 222 | "slideshow": { 223 | "slide_type": "fragment" 224 | } 225 | }, 226 | "outputs": [], 227 | "source": [ 228 | "# Retrieve the crystal structure for a specific material by its Materials Project ID\n", 229 | "\n", 230 | "material_id = \"mp-2534\" # Example material ID for GaAs\n", 231 | "\n", 232 | "# Fetch structure for the material\n", 233 | "structure = mpr.get_structure_by_material_id(material_id)\n", 234 | "\n", 235 | "# Print fetched data\n", 236 | "print(f\"--Structure:--\\n {structure}\")" 237 | ] 238 | }, 239 | { 240 | "cell_type": "code", 241 | "execution_count": null, 242 | "id": "8485def5", 243 | "metadata": { 244 | "slideshow": { 245 | "slide_type": "fragment" 246 | } 247 | }, 248 | "outputs": [], 249 | "source": [ 250 | "# Retrieve the electronic band structure and DOS by the Materials Project ID \n", 251 | "bs = mpr.get_bandstructure_by_material_id(\"mp-2534\") # mp-2534 is GaAs\n", 252 | "dos = mpr.get_dos_by_material_id(\"mp-2534\")\n", 253 | "\n", 254 | "# Plot using pymatgen\n", 255 | "from pymatgen.electronic_structure.plotter import BSDOSPlotter\n", 256 | "bsp = BSDOSPlotter()\n", 257 | "ax_bs, ax_dos = bsp.get_plot(bs, dos)" 258 | ] 259 | }, 260 | { 261 | "cell_type": "code", 262 | "execution_count": null, 263 | "id": "f71f29b1", 264 | "metadata": { 265 | "slideshow": { 266 | "slide_type": "fragment" 267 | } 268 | }, 269 | "outputs": [], 270 | "source": [ 271 | "# Retrieve the phonon band structure by Materials Project ID\n", 272 | "pbs = mpr.get_phonon_bandstructure_by_material_id(\"mp-406\") # mp-406 is CdTe\n", 273 | "\n", 274 | "# Plot using pymatgen\n", 275 | "from pymatgen.phonon.plotter import PhononBSPlotter\n", 276 | "plotter = PhononBSPlotter(pbs)\n", 277 | "plt = plotter.get_plot()" 278 | ] 279 | }, 280 | { 281 | "cell_type": "code", 282 | "execution_count": null, 283 | "id": "d72b1cab", 284 | "metadata": { 285 | "slideshow": { 286 | "slide_type": "fragment" 287 | } 288 | }, 289 | "outputs": [], 290 | "source": [ 291 | "# Get the Wulff shape of a material (currently available for selected elements only)\n", 292 | "ws = mpr.get_wulff_shape(\"mp-135\") # mp-135 is Li\n", 293 | "ws.get_plot()" 294 | ] 295 | }, 296 | { 297 | "cell_type": "markdown", 298 | "id": "c4db3764", 299 | "metadata": { 300 | "slideshow": { 301 | "slide_type": "slide" 302 | } 303 | }, 304 | "source": [ 305 | "# Using Sub-Resters for Additional Functionality\n", 306 | "\n", 307 | "* The built-in convenience functions of ``MPRester`` are just a small fraction of the functionality available through the Materials Project REST API\n", 308 | "* To access other functions and data as well as to search for materials, you need to use one of the many \"Sub-Resters\" of MPRester\n", 309 | "* Each \"Sub-Rester\" helps retrieve a particular type of data from the Materials Project using one of the REST API endpoints\n", 310 | " * The API endpoints are listed here: https://next-gen.materialsproject.org/api#accessing-data\n", 311 | " * These API endpoints correspond to the ``suffix`` parameter of the Sub-Rester\n", 312 | "* Sub-Resters helps parallelize development, maintenance, and testing of the code across these various endpoints\n", 313 | " * This greatly helps development and maintenance of the REST API and also helps with data transfer efficiency\n", 314 | " * However, it can make usage more difficult for users because you need to find the appropriate Sub-Rester, and you may need to combine information from multiple Sub-Resters to accomplish your goal\n", 315 | "\n", 316 | "![alt text](graphics/subresters.png \"SubResters and API interaction\")" 317 | ] 318 | }, 319 | { 320 | "cell_type": "markdown", 321 | "id": "f2478322", 322 | "metadata": { 323 | "slideshow": { 324 | "slide_type": "slide" 325 | } 326 | }, 327 | "source": [ 328 | "# Example 1: Summary Sub-Rester\n", 329 | "\n", 330 | "* One of the most common Sub-Resters you may want to use is the ``SummaryRester``\n", 331 | "* The ``SummaryRester`` is the closest you get to a \"one-stop-shop\" when searching for materials data. It allows you to search over a variety of different fields and retrieve many kinds of information about a material.\n", 332 | "\n", 333 | "![alt text](graphics/SummaryRester.png \"Diagram of the SummaryRester\")" 334 | ] 335 | }, 336 | { 337 | "cell_type": "code", 338 | "execution_count": null, 339 | "id": "423edbd7", 340 | "metadata": { 341 | "slideshow": { 342 | "slide_type": "fragment" 343 | } 344 | }, 345 | "outputs": [], 346 | "source": [ 347 | "summary_subrester = mpr.materials.summary # Sub-Resters are usually attributes of MPRester\n", 348 | "\n", 349 | "results = summary_subrester.search(elements=[\"Si\", \"O\"], # Si & O are required, but other elements also allowed\n", 350 | " exclude_elements=[\"Ca\"], # no Calcium allowed\n", 351 | " num_elements=3, # 3 unique elements, i.e., ternaries\n", 352 | " band_gap=(0.5, 1.0)) # band gap from 0.5 - 1.0 eV\n", 353 | "\n", 354 | "print(f\"The number of returned materials is: {len(results)}\")\n", 355 | "print(\"--First material (SummaryDoc)--\")\n", 356 | "print(results[0]) # This is a SummaryDoc object for this Rester" 357 | ] 358 | }, 359 | { 360 | "cell_type": "code", 361 | "execution_count": null, 362 | "id": "9bcba364", 363 | "metadata": { 364 | "slideshow": { 365 | "slide_type": "fragment" 366 | } 367 | }, 368 | "outputs": [], 369 | "source": [ 370 | "# Accessing attributes of the SummaryDoc document\n", 371 | "print(f\"--Structure:--\\n {results[0].structure}\")\n", 372 | "print(f\"Band gap: {results[0].band_gap}\")" 373 | ] 374 | }, 375 | { 376 | "cell_type": "code", 377 | "execution_count": null, 378 | "id": "4e027842", 379 | "metadata": { 380 | "scrolled": true, 381 | "slideshow": { 382 | "slide_type": "slide" 383 | } 384 | }, 385 | "outputs": [], 386 | "source": [ 387 | "# Being data-efficient by restricting 'fields'\n", 388 | "\n", 389 | "# This will result in faster queries and less data transfer\n", 390 | "results = mpr.materials.summary.search(elements=[\"Si\", \"O\"], \n", 391 | " num_elements=3,\n", 392 | " exclude_elements=[\"Ca\"], # no Calcium allowed\n", 393 | " band_gap=(0.5, 1.0),\n", 394 | " fields=[\"material_id\", # We will just retrieve the data in these fields\n", 395 | " \"band_gap\", \n", 396 | " \"symmetry\",\n", 397 | " \"composition\",\n", 398 | " \"origins\"])\n", 399 | "print(results[0])" 400 | ] 401 | }, 402 | { 403 | "cell_type": "code", 404 | "execution_count": null, 405 | "id": "a8932c5a", 406 | "metadata": { 407 | "slideshow": { 408 | "slide_type": "slide" 409 | } 410 | }, 411 | "outputs": [], 412 | "source": [ 413 | "# Getting the individual calculations associated with certain properties - these are called \"Tasks\"\n", 414 | "# Note that this is not complete, so to get the origins of other properties you may need to use the Sub-Rester for that property\n", 415 | "print(results[0].origins)" 416 | ] 417 | }, 418 | { 419 | "cell_type": "markdown", 420 | "id": "703966f8", 421 | "metadata": { 422 | "slideshow": { 423 | "slide_type": "slide" 424 | } 425 | }, 426 | "source": [ 427 | "# Sub-Rester Example 2: Task\n", 428 | "\n", 429 | "* Recall that a single material may have many calculations (Tasks) associated with it, and the overall data from a material is combination of data taken from several Tasks.\n", 430 | "* The ``TaskRester`` allows you to look up the details of an individual calculation, including input parameters and outputs\n", 431 | "* It also has a convenience function to get the trajectory of a calculation (all steps in a structure relaxation)\n", 432 | "\n", 433 | "\n", 434 | "![alt text](graphics/TaskRester.png \"Diagram of the TaskRester\")" 435 | ] 436 | }, 437 | { 438 | "cell_type": "code", 439 | "execution_count": null, 440 | "id": "f942fced", 441 | "metadata": { 442 | "slideshow": { 443 | "slide_type": "fragment" 444 | } 445 | }, 446 | "outputs": [], 447 | "source": [ 448 | "results = mpr.materials.tasks.search(task_ids=[\"mp-1792681\"]) # this is a \"static\" calculation\n", 449 | "\n", 450 | "print(\"--input.incar--\")\n", 451 | "print(results[0].input.parameters)\n", 452 | "print(\"--output.structure--\")\n", 453 | "print(results[0].output.structure)\n", 454 | "print(\"--output.forces--\")\n", 455 | "print(results[0].output.forces)\n", 456 | "print(\"--output.energy--\")\n", 457 | "print(results[0].output.energy)\n", 458 | "\n", 459 | "# note: more information is in the 'calcs_reversed' key, but not demo'ed here\n", 460 | "print(\"--input--\")\n", 461 | "print(results[0].calcs_reversed[0].input)\n", 462 | "print(\"--output--\")\n", 463 | "print(results[0].calcs_reversed[0].output)" 464 | ] 465 | }, 466 | { 467 | "cell_type": "code", 468 | "execution_count": null, 469 | "id": "0b929494", 470 | "metadata": { 471 | "slideshow": { 472 | "slide_type": "fragment" 473 | } 474 | }, 475 | "outputs": [], 476 | "source": [ 477 | "traj = mpr.materials.tasks.get_trajectory(\"mp-19017\") # example of a custom function in a SubRester\n", 478 | "print(traj[0]) # the entire relaxation trajectory as pymatgen.core.trajectory.Trajectory.as_dict()" 479 | ] 480 | }, 481 | { 482 | "cell_type": "markdown", 483 | "id": "40941662", 484 | "metadata": { 485 | "slideshow": { 486 | "slide_type": "slide" 487 | } 488 | }, 489 | "source": [ 490 | "# Sub-Rester Example 3: Elasticity\n", 491 | "\n", 492 | "* Many materials properties have their own Sub-Rester associated with them, which allows you to search on those properties\n", 493 | "* For example, to access the full elastic tensor and derived quantities such as sound velocity estimated from the elastic constants, one would use the ``ElasticityRester``\n", 494 | "\n", 495 | "![alt text](graphics/ElasticityRester.png \"Diagram of the ElasticityRester\")\n", 496 | "\n" 497 | ] 498 | }, 499 | { 500 | "cell_type": "code", 501 | "execution_count": null, 502 | "id": "d0543d5b", 503 | "metadata": { 504 | "slideshow": { 505 | "slide_type": "fragment" 506 | } 507 | }, 508 | "outputs": [], 509 | "source": [ 510 | "elasticity = mpr.elasticity.search(\"mp-2534\")[0] # mp-2534 is GaAs\n", 511 | "print(elasticity)" 512 | ] 513 | }, 514 | { 515 | "cell_type": "code", 516 | "execution_count": null, 517 | "id": "7c48b603", 518 | "metadata": {}, 519 | "outputs": [], 520 | "source": [ 521 | "print(f\"--elastic tensor--\\n: {elasticity.elastic_tensor}\")\n", 522 | "print(f\"--elastic-constant-derived sound velocity--\\n {elasticity.sound_velocity}\")\n", 523 | "\n", 524 | "# Note that one needs context for the data\n", 525 | "# Below is NOT the thermal conductivity of crystalline GaAs but rather the glassy limit\n", 526 | "print(f\"--elastic-constant-derived glassy limit of thermal conductivity--\\n {elasticity.thermal_conductivity}\")" 527 | ] 528 | }, 529 | { 530 | "cell_type": "markdown", 531 | "id": "3ed555ca", 532 | "metadata": { 533 | "slideshow": { 534 | "slide_type": "slide" 535 | } 536 | }, 537 | "source": [ 538 | "# Advanced searches: using multiple Resters\n", 539 | "\n", 540 | "* Sometimes, you are not able to perform the query or get the data you want using a single Sub-Rester\n", 541 | "* In this example, we want to search using both band gap and the total static dielectric constant, and get detailed data on both properties\n", 542 | "* In that case, you need to merge information from multiple Sub-Resters\n", 543 | "* A procedure for doing this is demonstrated next\n", 544 | "![alt text](graphics/nested_search.png \"Nesting search using multiple Resters\")" 545 | ] 546 | }, 547 | { 548 | "cell_type": "code", 549 | "execution_count": null, 550 | "id": "3bf6df8a", 551 | "metadata": { 552 | "slideshow": { 553 | "slide_type": "fragment" 554 | } 555 | }, 556 | "outputs": [], 557 | "source": [ 558 | "from emmet.core.summary import HasProps\n", 559 | "\n", 560 | "# Use SummaryRester for part 1 of search\n", 561 | "search_1 = mpr.materials.summary.search(has_props=[HasProps.dielectric], \n", 562 | " band_gap=[1.5, 3], \n", 563 | " elements=[\"O\"], \n", 564 | " fields=[\"material_id\", \"band_gap\"])\n", 565 | "search_1_data_dict = {x.material_id: x for x in search_1}\n", 566 | "search_1_mpids = search_1_data_dict.keys()\n", 567 | "\n", 568 | "# Use DielectricRester for part 2 of search\n", 569 | "search_2 = mpr.materials.dielectric.search(material_ids=search_1_mpids, \n", 570 | " e_total=[5, 10], \n", 571 | " fields=[\"material_id\", \"e_total\", \n", 572 | " \"e_ionic\", \"e_electronic\", \n", 573 | " \"composition\"])\n", 574 | "search_2_data_dict = {x.material_id: x for x in search_2}\n", 575 | "search_2_mpids = search_2_data_dict.keys()\n", 576 | "\n", 577 | "# (repeat the above steps for other steps to filter the data as needed)" 578 | ] 579 | }, 580 | { 581 | "cell_type": "code", 582 | "execution_count": null, 583 | "id": "45c53708", 584 | "metadata": { 585 | "slideshow": { 586 | "slide_type": "fragment" 587 | } 588 | }, 589 | "outputs": [], 590 | "source": [ 591 | "# Now merge the data\n", 592 | "from collections import namedtuple\n", 593 | "MaterialsData = namedtuple(\"MaterialsData\", [\"summary_data\", \"dielectric_data\"]) # container for the data\n", 594 | "\n", 595 | "all_data = []\n", 596 | "for mpid in search_2_mpids: # only the mpids matching both criteria\n", 597 | " all_data.append(MaterialsData(summary_data=search_1_data_dict[mpid], \n", 598 | " dielectric_data=search_2_data_dict[mpid]))\n", 599 | "\n", 600 | "# Note that if you want the band_gap, you need to get it from summary_data.\n", 601 | "# But if you want the e_total, you need to get it from dielectric_data!\n", 602 | "print(f\"Number of results: {len(all_data)}\")\n", 603 | "print(\"----First result properties----\")\n", 604 | "print(f\"--band gap--\\n {all_data[0].summary_data.band_gap}\")\n", 605 | "print(f\"--static dielectric constant--\\n{all_data[0].dielectric_data.e_total}\")\n", 606 | "print(f\"--all summary data retrieved--\\n{all_data[0].summary_data}\")\n", 607 | "print(f\"--all dielectric data retrieved--\\n{all_data[0].dielectric_data}\")\n" 608 | ] 609 | }, 610 | { 611 | "cell_type": "markdown", 612 | "id": "ef523a6f", 613 | "metadata": { 614 | "slideshow": { 615 | "slide_type": "slide" 616 | } 617 | }, 618 | "source": [ 619 | "# Being faster and more data-efficient with Materials Project\n", 620 | "\n", 621 | "Knowing how to be data-efficient when using the REST API is good for several reasons. It is helpful for you because it results in much faster results and lower data/memory usage on your side when conducting analyses. It is also much better for the Materials Project because it avoids unnecessary data transfer costs. There are several things you can do to make your queries faster and more data-efficient:\n", 622 | "\n", 623 | "* As already covered, restrict the data returned to the specific fields of interest, to the extent possible:\n", 624 | "```\n", 625 | "with MPRester(\"your_api_key_here\") as mpr:\n", 626 | " docs = mpr.materials.summary.search(fields=[\"material_id\", \"volume\", \"elements\"])\n", 627 | "\n", 628 | "```\n", 629 | "\n", 630 | "* If you are just exploring / testing queries and don't want to wait for thousands of results to be retrieved, use ``num_chunks=1`` and ``chunk_size=10`` parameters when calling ``search()`` to limit to 10 example results. This works for all searches with all Resters and avoids unnecessary calls:\n", 631 | "```\n", 632 | "with MPRester(\"your_api_key_here\") as mpr:\n", 633 | " mpr.summary.search(band_gap=[0,10], num_chunks=1, chunk_size=10)\n", 634 | "```\n", 635 | "\n", 636 | "* If you need to get data for many materials, pass the ``materials_ids`` as a list. This minimizes the number of calls to the API (i.e., don't call ``search()`` thousands of times!):\n", 637 | "```\n", 638 | "with MPRester(\"your_api_key_here\") as mpr:\n", 639 | " docs = mpr.materials.summary.search(material_ids=[\"mp-149\", \"mp-13\", \"mp-22526\"])\n", 640 | "```\n", 641 | "\n", 642 | "* For more tips, see https://docs.materialsproject.org/downloading-data/using-the-api/tips-for-large-downloads" 643 | ] 644 | }, 645 | { 646 | "cell_type": "markdown", 647 | "id": "4169588f", 648 | "metadata": { 649 | "slideshow": { 650 | "slide_type": "slide" 651 | } 652 | }, 653 | "source": [ 654 | "# More information\n", 655 | "\n", 656 | "More information about the Materials Project API can be found in the official docs: https://docs.materialsproject.org/downloading-data/how-do-i-download-the-materials-project-database" 657 | ] 658 | } 659 | ], 660 | "metadata": { 661 | "celltoolbar": "Slideshow", 662 | "kernelspec": { 663 | "display_name": "Python 3 (ipykernel)", 664 | "language": "python", 665 | "name": "python3" 666 | }, 667 | "language_info": { 668 | "codemirror_mode": { 669 | "name": "ipython", 670 | "version": 3 671 | }, 672 | "file_extension": ".py", 673 | "mimetype": "text/x-python", 674 | "name": "python", 675 | "nbconvert_exporter": "python", 676 | "pygments_lexer": "ipython3", 677 | "version": "3.11.4" 678 | } 679 | }, 680 | "nbformat": 4, 681 | "nbformat_minor": 5 682 | } 683 | -------------------------------------------------------------------------------- /Part_4-Transformations_Symmetry/graphics/title.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/computron/pymatgen_tutorials/81b42a79052ba0108ad7fc68958ef8a22020923a/Part_4-Transformations_Symmetry/graphics/title.png -------------------------------------------------------------------------------- /Part_4-Transformations_Symmetry/structures/CsCl.json: 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-------------------------------------------------------------------------------- https://raw.githubusercontent.com/computron/pymatgen_tutorials/81b42a79052ba0108ad7fc68958ef8a22020923a/Part_5-Five_Features/graphics/title.png -------------------------------------------------------------------------------- /Part_5-Five_Features/structure.json: -------------------------------------------------------------------------------- 1 | {"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[8.08039119, 0.0, 4.947812603345986e-16], [-4.947812603345986e-16, 8.08039119, 4.947812603345986e-16], [0.0, 0.0, 8.08039119]], "pbc": [true, true, true], "a": 8.08039119, "b": 8.08039119, "c": 8.08039119, "alpha": 90.0, "beta": 90.0, "gamma": 90.0, "volume": 527.5907338699459}, "properties": {}, "sites": [{"species": [{"element": "Mg", "oxidation_state": 2.0, "spin": null, "occu": 1.0}], "abc": [0.0, 0.0, 0.0], "properties": {}, "label": "Mg0", "xyz": [0.0, 0.0, 0.0]}, {"species": [{"element": "Mg", "oxidation_state": 2.0, "spin": null, "occu": 1.0}], "abc": [0.25, 0.25, 0.25], "properties": {}, "label": "Mg0", "xyz": [2.0200977975, 2.0200977975, 2.0200977975000005]}, {"species": [{"element": "Mg", "oxidation_state": 2.0, "spin": null, "occu": 1.0}], "abc": [0.0, 0.5, 0.5], "properties": {}, "label": "Mg0", "xyz": [-2.473906301672993e-16, 4.040195595, 4.040195595]}, {"species": [{"element": "Mg", "oxidation_state": 2.0, "spin": null, "occu": 1.0}], "abc": [0.75, 0.25, 0.75], "properties": {}, "label": "Mg0", "xyz": [6.0602933925, 2.0200977975, 6.060293392500001]}, {"species": [{"element": "Mg", "oxidation_state": 2.0, "spin": null, "occu": 1.0}], "abc": [0.25, 0.75, 0.75], "properties": {}, "label": "Mg0", "xyz": [2.0200977974999996, 6.0602933925, 6.060293392500001]}, {"species": [{"element": "Mg", "oxidation_state": 2.0, "spin": null, "occu": 1.0}], "abc": [0.75, 0.75, 0.25], "properties": {}, "label": "Mg0", "xyz": [6.0602933925, 6.0602933925, 2.020097797500001]}, {"species": [{"element": "Mg", "oxidation_state": 2.0, "spin": null, "occu": 1.0}], "abc": [0.5, 0.0, 0.5], "properties": {}, "label": "Mg0", "xyz": [4.040195595, 0.0, 4.040195595]}, {"species": [{"element": "Mg", "oxidation_state": 2.0, "spin": null, "occu": 1.0}], "abc": [0.5, 0.5, 0.0], "properties": {}, "label": "Mg0", "xyz": [4.040195595, 4.040195595, 4.947812603345986e-16]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.125, 0.125, 0.625], "properties": {}, "label": "Al1", "xyz": [1.01004889875, 1.01004889875, 5.05024449375]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.125, 0.375, 0.875], "properties": {}, "label": "Al1", "xyz": [1.0100488987499998, 3.03014669625, 7.07034229125]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.875, 0.375, 0.125], "properties": {}, "label": "Al1", "xyz": [7.07034229125, 3.03014669625, 1.0100488987500007]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.875, 0.125, 0.375], "properties": {}, "label": "Al1", "xyz": [7.07034229125, 1.01004889875, 3.0301466962500005]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.125, 0.875, 0.375], "properties": {}, "label": "Al1", "xyz": [1.0100488987499996, 7.07034229125, 3.0301466962500005]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.125, 0.625, 0.125], "properties": {}, "label": "Al1", "xyz": [1.0100488987499998, 5.05024449375, 1.0100488987500005]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.875, 0.625, 0.875], "properties": {}, "label": "Al1", "xyz": [7.07034229125, 5.05024449375, 7.070342291250001]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.875, 0.875, 0.625], "properties": {}, "label": "Al1", "xyz": [7.07034229125, 7.07034229125, 5.050244493750001]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.625, 0.125, 0.125], "properties": {}, "label": "Al1", "xyz": [5.05024449375, 1.01004889875, 1.0100488987500005]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.375, 0.875, 0.125], "properties": {}, "label": "Al1", "xyz": [3.0301466962499997, 7.07034229125, 1.0100488987500007]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.375, 0.125, 0.875], "properties": {}, "label": "Al1", "xyz": [3.03014669625, 1.01004889875, 7.07034229125]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.625, 0.875, 0.875], "properties": {}, "label": "Al1", "xyz": [5.05024449375, 7.07034229125, 7.070342291250001]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.375, 0.625, 0.375], "properties": {}, "label": "Al1", "xyz": [3.0301466962499997, 5.05024449375, 3.0301466962500005]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.375, 0.375, 0.625], "properties": {}, "label": "Al1", "xyz": [3.03014669625, 3.03014669625, 5.05024449375]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.625, 0.375, 0.375], "properties": {}, "label": "Al1", "xyz": [5.05024449375, 3.03014669625, 3.0301466962500005]}, {"species": [{"element": "Al", "oxidation_state": 3.0, "spin": null, "occu": 1.0}], "abc": [0.625, 0.625, 0.625], "properties": {}, "label": "Al1", "xyz": [5.05024449375, 5.05024449375, 5.050244493750001]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.11127934, 0.11127934, 0.38872066], "properties": {}, "label": "O2", "xyz": [0.8991805985650146, 0.8991805985650146, 3.1410149964349854]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.13872066, 0.36127934, 0.6387206599999999], "properties": {}, "label": "O2", "xyz": [1.120917198934985, 2.919278396065015, 5.1611127939349855]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.8887206599999999, 0.38872066, 0.8887206599999999], "properties": {}, "label": "O2", "xyz": [7.1812105914349855, 3.1410149964349854, 7.181210591434986]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.8612793400000001, 0.13872066, 0.13872065999999994], "properties": {}, "label": "O2", "xyz": [6.959473991065015, 1.1209171989349853, 1.1209171989349853]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.11127934, 0.8887206599999999, 0.6112793400000001], "properties": {}, "label": "O2", "xyz": [0.8991805985650142, 7.1812105914349855, 4.939376193565016]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.13872066, 0.6387206599999999, 0.36127934], "properties": {}, "label": "O2", "xyz": [1.120917198934985, 5.1611127939349855, 2.9192783960650153]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.8887206599999999, 0.6112793400000001, 0.11127934], "properties": {}, "label": "O2", "xyz": [7.1812105914349855, 4.939376193565015, 0.8991805985650154]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.8612793400000001, 0.8612793400000001, 0.8612793400000001], "properties": {}, "label": "O2", "xyz": [6.959473991065015, 6.959473991065015, 6.959473991065016]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.38872066, 0.11127934, 0.11127934], "properties": {}, "label": "O2", "xyz": [3.1410149964349854, 0.8991805985650146, 0.8991805985650149]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.6387206599999999, 0.13872066, 0.36127934], "properties": {}, "label": "O2", "xyz": [5.1611127939349855, 1.1209171989349853, 2.9192783960650153]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.8887206599999999, 0.8887206599999999, 0.38872066], "properties": {}, "label": "O2", "xyz": [7.1812105914349855, 7.1812105914349855, 3.1410149964349863]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.13872065999999994, 0.8612793400000001, 0.13872066], "properties": {}, "label": "O2", "xyz": [1.1209171989349844, 6.959473991065015, 1.1209171989349858]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.6112793400000001, 0.11127934, 0.8887206599999999], "properties": {}, "label": "O2", "xyz": [4.939376193565015, 0.8991805985650146, 7.1812105914349855]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.36127934, 0.13872066, 0.6387206599999999], "properties": {}, "label": "O2", "xyz": [2.919278396065015, 1.1209171989349853, 5.1611127939349855]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.11127934, 0.38872066, 0.11127934], "properties": {}, "label": "O2", "xyz": [0.8991805985650144, 3.1410149964349854, 0.8991805985650149]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.36127934, 0.6387206599999999, 0.13872066], "properties": {}, "label": "O2", "xyz": [2.9192783960650144, 5.1611127939349855, 1.1209171989349858]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.38872066, 0.8887206599999999, 0.8887206599999999], "properties": {}, "label": "O2", "xyz": [3.141014996434985, 7.1812105914349855, 7.181210591434986]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.13872066, 0.13872065999999994, 0.8612793400000001], "properties": {}, "label": "O2", "xyz": [1.1209171989349853, 1.1209171989349849, 6.959473991065015]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.6387206599999999, 0.36127934, 0.13872066], "properties": {}, "label": "O2", "xyz": [5.1611127939349855, 2.919278396065015, 1.1209171989349858]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.36127934, 0.8612793400000001, 0.36127934], "properties": {}, "label": "O2", "xyz": [2.9192783960650144, 6.959473991065015, 2.9192783960650153]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.11127934, 0.6112793400000001, 0.8887206599999999], "properties": {}, "label": "O2", "xyz": [0.8991805985650143, 4.939376193565015, 7.1812105914349855]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.38872066, 0.38872066, 0.38872066], "properties": {}, "label": "O2", "xyz": [3.1410149964349854, 3.1410149964349854, 3.141014996434986]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.36127934, 0.36127934, 0.8612793400000001], "properties": {}, "label": "O2", "xyz": [2.919278396065015, 2.919278396065015, 6.959473991065015]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.8887206599999999, 0.11127934, 0.6112793400000001], "properties": {}, "label": "O2", "xyz": [7.1812105914349855, 0.8991805985650146, 4.939376193565016]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.8612793400000001, 0.36127934, 0.36127934], "properties": {}, "label": "O2", "xyz": [6.959473991065015, 2.919278396065015, 2.9192783960650153]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.6112793400000001, 0.8887206599999999, 0.11127934], "properties": {}, "label": "O2", "xyz": [4.939376193565015, 7.1812105914349855, 0.8991805985650154]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.6112793400000001, 0.6112793400000001, 0.38872066], "properties": {}, "label": "O2", "xyz": [4.939376193565015, 4.939376193565015, 3.141014996434986]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.6387206599999999, 0.8612793400000001, 0.6387206599999999], "properties": {}, "label": "O2", "xyz": [5.1611127939349855, 6.959473991065015, 5.161112793934986]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.6112793400000001, 0.38872066, 0.6112793400000001], "properties": {}, "label": "O2", "xyz": [4.939376193565015, 3.1410149964349854, 4.939376193565016]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.8612793400000001, 0.6387206599999999, 0.6387206599999999], "properties": {}, "label": "O2", "xyz": [6.959473991065015, 5.1611127939349855, 5.161112793934986]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.6387206599999999, 0.6387206599999999, 0.8612793400000001], "properties": {}, "label": "O2", "xyz": [5.1611127939349855, 5.1611127939349855, 6.959473991065016]}, {"species": [{"element": "O", "oxidation_state": -2, "spin": null, "occu": 1.0}], "abc": [0.38872066, 0.6112793400000001, 0.6112793400000001], "properties": {}, "label": "O2", "xyz": [3.141014996434985, 4.939376193565015, 4.939376193565016]}], "@version": null} -------------------------------------------------------------------------------- /Part_5-Five_Features/structures/BaTiO3.cif: -------------------------------------------------------------------------------- 1 | # generated using pymatgen 2 | data_BaTiO3 3 | _symmetry_space_group_name_H-M P4mm 4 | _cell_length_a 3.99037921 5 | _cell_length_b 3.99037921 6 | _cell_length_c 4.10265539 7 | _cell_angle_alpha 90.00000000 8 | _cell_angle_beta 90.00000000 9 | _cell_angle_gamma 90.00000000 10 | _symmetry_Int_Tables_number 99 11 | _chemical_formula_structural BaTiO3 12 | _chemical_formula_sum 'Ba1 Ti1 O3' 13 | _cell_volume 65.32709969 14 | _cell_formula_units_Z 1 15 | loop_ 16 | _symmetry_equiv_pos_site_id 17 | _symmetry_equiv_pos_as_xyz 18 | 1 'x, y, z' 19 | 2 '-y, x, z' 20 | 3 '-x, -y, z' 21 | 4 'y, -x, z' 22 | 5 '-x, y, z' 23 | 6 'y, x, z' 24 | 7 'x, -y, z' 25 | 8 '-y, -x, z' 26 | loop_ 27 | _atom_type_symbol 28 | _atom_type_oxidation_number 29 | Ba2+ 2.0 30 | Ti4+ 4.0 31 | O2- -2.0 32 | loop_ 33 | _atom_site_type_symbol 34 | _atom_site_label 35 | _atom_site_symmetry_multiplicity 36 | _atom_site_fract_x 37 | _atom_site_fract_y 38 | _atom_site_fract_z 39 | _atom_site_occupancy 40 | Ba2+ Ba0 1 0.50000000 0.50000000 0.58254146 1 41 | Ti4+ Ti1 1 0.00000000 0.00000000 0.10004270 1 42 | O2- O2 2 0.00000000 0.50000000 0.06422054 1 43 | O2- O3 1 0.00000000 0.00000000 0.54897175 1 44 | -------------------------------------------------------------------------------- /Part_5-Five_Features/structures/MgAl2O4.cif: -------------------------------------------------------------------------------- 1 | # generated using pymatgen 2 | data_MgAl2O4 3 | _symmetry_space_group_name_H-M Fd-3m 4 | _cell_length_a 8.08039119 5 | _cell_length_b 8.08039119 6 | _cell_length_c 8.08039119 7 | _cell_angle_alpha 90.00000000 8 | _cell_angle_beta 90.00000000 9 | _cell_angle_gamma 90.00000000 10 | _symmetry_Int_Tables_number 227 11 | _chemical_formula_structural MgAl2O4 12 | _chemical_formula_sum 'Mg8 Al16 O32' 13 | _cell_volume 527.59073364 14 | _cell_formula_units_Z 8 15 | loop_ 16 | _symmetry_equiv_pos_site_id 17 | _symmetry_equiv_pos_as_xyz 18 | 1 'x, y, z' 19 | 2 '-y+1/4, x+1/4, z+1/4' 20 | 3 '-x, -y+1/2, z+1/2' 21 | 4 'y+3/4, -x+1/4, z+3/4' 22 | 5 'x, -y, -z' 23 | 6 '-y+1/4, -x+3/4, -z+3/4' 24 | 7 '-x, y+1/2, -z+1/2' 25 | 8 'y+3/4, x+3/4, -z+1/4' 26 | 9 'z, x, y' 27 | 10 'z+1/4, -y+1/4, x+1/4' 28 | 11 'z+1/2, -x, -y+1/2' 29 | 12 'z+3/4, y+3/4, -x+1/4' 30 | 13 '-z, x, -y' 31 | 14 '-z+3/4, -y+1/4, -x+3/4' 32 | 15 '-z+1/2, -x, y+1/2' 33 | 16 '-z+1/4, y+3/4, x+3/4' 34 | 17 'y, z, x' 35 | 18 'x+1/4, z+1/4, -y+1/4' 36 | 19 '-y+1/2, z+1/2, -x' 37 | 20 '-x+1/4, z+3/4, y+3/4' 38 | 21 '-y, -z, x' 39 | 22 '-x+3/4, -z+3/4, -y+1/4' 40 | 23 'y+1/2, -z+1/2, -x' 41 | 24 'x+3/4, -z+1/4, y+3/4' 42 | 25 '-x+1/4, -y+1/4, -z+1/4' 43 | 26 'y, -x, -z' 44 | 27 'x+1/4, y+3/4, -z+3/4' 45 | 28 '-y+1/2, x, -z+1/2' 46 | 29 '-x+1/4, y+1/4, z+1/4' 47 | 30 'y, x+1/2, z+1/2' 48 | 31 'x+1/4, -y+3/4, z+3/4' 49 | 32 '-y+1/2, -x+1/2, z' 50 | 33 '-z+1/4, -x+1/4, -y+1/4' 51 | 34 '-z, y, -x' 52 | 35 '-z+3/4, x+1/4, y+3/4' 53 | 36 '-z+1/2, -y+1/2, x' 54 | 37 'z+1/4, -x+1/4, y+1/4' 55 | 38 'z+1/2, y, x+1/2' 56 | 39 'z+3/4, x+1/4, -y+3/4' 57 | 40 'z, -y+1/2, -x+1/2' 58 | 41 '-y+1/4, -z+1/4, -x+1/4' 59 | 42 '-x, -z, y' 60 | 43 'y+3/4, -z+3/4, x+1/4' 61 | 44 'x, -z+1/2, -y+1/2' 62 | 45 'y+1/4, z+1/4, -x+1/4' 63 | 46 'x+1/2, z+1/2, y' 64 | 47 '-y+3/4, z+3/4, x+1/4' 65 | 48 '-x+1/2, z, -y+1/2' 66 | 49 'x+1/2, y+1/2, z' 67 | 50 '-y+3/4, x+3/4, z+1/4' 68 | 51 '-x+1/2, -y, z+1/2' 69 | 52 'y+1/4, -x+3/4, z+3/4' 70 | 53 'x+1/2, -y+1/2, -z' 71 | 54 '-y+3/4, -x+1/4, -z+3/4' 72 | 55 '-x+1/2, y, -z+1/2' 73 | 56 'y+1/4, x+1/4, -z+1/4' 74 | 57 'z+1/2, x+1/2, y' 75 | 58 'z+3/4, -y+3/4, x+1/4' 76 | 59 'z, -x+1/2, -y+1/2' 77 | 60 'z+1/4, y+1/4, -x+1/4' 78 | 61 '-z+1/2, x+1/2, -y' 79 | 62 '-z+1/4, -y+3/4, -x+3/4' 80 | 63 '-z, -x+1/2, y+1/2' 81 | 64 '-z+3/4, y+1/4, x+3/4' 82 | 65 'y+1/2, z+1/2, x' 83 | 66 'x+3/4, z+3/4, -y+1/4' 84 | 67 '-y, z, -x' 85 | 68 '-x+3/4, z+1/4, y+3/4' 86 | 69 '-y+1/2, -z+1/2, x' 87 | 70 '-x+1/4, -z+1/4, -y+1/4' 88 | 71 'y, -z, -x' 89 | 72 'x+1/4, -z+3/4, y+3/4' 90 | 73 '-x+3/4, -y+3/4, -z+1/4' 91 | 74 'y+1/2, -x+1/2, -z' 92 | 75 'x+3/4, y+1/4, -z+3/4' 93 | 76 '-y, x+1/2, -z+1/2' 94 | 77 '-x+3/4, y+3/4, z+1/4' 95 | 78 'y+1/2, x, z+1/2' 96 | 79 'x+3/4, -y+1/4, z+3/4' 97 | 80 '-y, -x, z' 98 | 81 '-z+3/4, -x+3/4, -y+1/4' 99 | 82 '-z+1/2, y+1/2, -x' 100 | 83 '-z+1/4, x+3/4, y+3/4' 101 | 84 '-z, -y, x' 102 | 85 'z+3/4, -x+3/4, y+1/4' 103 | 86 'z, y+1/2, x+1/2' 104 | 87 'z+1/4, x+3/4, -y+3/4' 105 | 88 'z+1/2, -y, -x+1/2' 106 | 89 '-y+3/4, -z+3/4, -x+1/4' 107 | 90 '-x+1/2, -z+1/2, y' 108 | 91 'y+1/4, -z+1/4, x+1/4' 109 | 92 'x+1/2, -z, -y+1/2' 110 | 93 'y+3/4, z+3/4, -x+1/4' 111 | 94 'x, z, y' 112 | 95 '-y+1/4, z+1/4, x+1/4' 113 | 96 '-x, z+1/2, -y+1/2' 114 | 97 'x+1/2, y, z+1/2' 115 | 98 '-y+3/4, x+1/4, z+3/4' 116 | 99 '-x+1/2, -y+1/2, z' 117 | 100 'y+1/4, -x+1/4, z+1/4' 118 | 101 'x+1/2, -y, -z+1/2' 119 | 102 '-y+3/4, -x+3/4, -z+1/4' 120 | 103 '-x+1/2, y+1/2, -z' 121 | 104 'y+1/4, x+3/4, -z+3/4' 122 | 105 'z+1/2, x, y+1/2' 123 | 106 'z+3/4, -y+1/4, x+3/4' 124 | 107 'z, -x, -y' 125 | 108 'z+1/4, y+3/4, -x+3/4' 126 | 109 '-z+1/2, x, -y+1/2' 127 | 110 '-z+1/4, -y+1/4, -x+1/4' 128 | 111 '-z, -x, y' 129 | 112 '-z+3/4, y+3/4, x+1/4' 130 | 113 'y+1/2, z, x+1/2' 131 | 114 'x+3/4, z+1/4, -y+3/4' 132 | 115 '-y, z+1/2, -x+1/2' 133 | 116 '-x+3/4, z+3/4, y+1/4' 134 | 117 '-y+1/2, -z, x+1/2' 135 | 118 '-x+1/4, -z+3/4, -y+3/4' 136 | 119 'y, -z+1/2, -x+1/2' 137 | 120 'x+1/4, -z+1/4, y+1/4' 138 | 121 '-x+3/4, -y+1/4, -z+3/4' 139 | 122 'y+1/2, -x, -z+1/2' 140 | 123 'x+3/4, y+3/4, -z+1/4' 141 | 124 '-y, x, -z' 142 | 125 '-x+3/4, y+1/4, z+3/4' 143 | 126 'y+1/2, x+1/2, z' 144 | 127 'x+3/4, -y+3/4, z+1/4' 145 | 128 '-y, -x+1/2, z+1/2' 146 | 129 '-z+3/4, -x+1/4, -y+3/4' 147 | 130 '-z+1/2, y, -x+1/2' 148 | 131 '-z+1/4, x+1/4, y+1/4' 149 | 132 '-z, -y+1/2, x+1/2' 150 | 133 'z+3/4, -x+1/4, y+3/4' 151 | 134 'z, y, x' 152 | 135 'z+1/4, x+1/4, -y+1/4' 153 | 136 'z+1/2, -y+1/2, -x' 154 | 137 '-y+3/4, -z+1/4, -x+3/4' 155 | 138 '-x+1/2, -z, y+1/2' 156 | 139 'y+1/4, -z+3/4, x+3/4' 157 | 140 'x+1/2, -z+1/2, -y' 158 | 141 'y+3/4, z+1/4, -x+3/4' 159 | 142 'x, z+1/2, y+1/2' 160 | 143 '-y+1/4, z+3/4, x+3/4' 161 | 144 '-x, z, -y' 162 | 145 'x, y+1/2, z+1/2' 163 | 146 '-y+1/4, x+3/4, z+3/4' 164 | 147 '-x, -y, z' 165 | 148 'y+3/4, -x+3/4, z+1/4' 166 | 149 'x, -y+1/2, -z+1/2' 167 | 150 '-y+1/4, -x+1/4, -z+1/4' 168 | 151 '-x, y, -z' 169 | 152 'y+3/4, x+1/4, -z+3/4' 170 | 153 'z, x+1/2, y+1/2' 171 | 154 'z+1/4, -y+3/4, x+3/4' 172 | 155 'z+1/2, -x+1/2, -y' 173 | 156 'z+3/4, y+1/4, -x+3/4' 174 | 157 '-z, x+1/2, -y+1/2' 175 | 158 '-z+3/4, -y+3/4, -x+1/4' 176 | 159 '-z+1/2, -x+1/2, y' 177 | 160 '-z+1/4, y+1/4, x+1/4' 178 | 161 'y, z+1/2, x+1/2' 179 | 162 'x+1/4, z+3/4, -y+3/4' 180 | 163 '-y+1/2, z, -x+1/2' 181 | 164 '-x+1/4, z+1/4, y+1/4' 182 | 165 '-y, -z+1/2, x+1/2' 183 | 166 '-x+3/4, -z+1/4, -y+3/4' 184 | 167 'y+1/2, -z, -x+1/2' 185 | 168 'x+3/4, -z+3/4, y+1/4' 186 | 169 '-x+1/4, -y+3/4, -z+3/4' 187 | 170 'y, -x+1/2, -z+1/2' 188 | 171 'x+1/4, y+1/4, -z+1/4' 189 | 172 '-y+1/2, x+1/2, -z' 190 | 173 '-x+1/4, y+3/4, z+3/4' 191 | 174 'y, x, z' 192 | 175 'x+1/4, -y+1/4, z+1/4' 193 | 176 '-y+1/2, -x, z+1/2' 194 | 177 '-z+1/4, -x+3/4, -y+3/4' 195 | 178 '-z, y+1/2, -x+1/2' 196 | 179 '-z+3/4, x+3/4, y+1/4' 197 | 180 '-z+1/2, -y, x+1/2' 198 | 181 'z+1/4, -x+3/4, y+3/4' 199 | 182 'z+1/2, y+1/2, x' 200 | 183 'z+3/4, x+3/4, -y+1/4' 201 | 184 'z, -y, -x' 202 | 185 '-y+1/4, -z+3/4, -x+3/4' 203 | 186 '-x, -z+1/2, y+1/2' 204 | 187 'y+3/4, -z+1/4, x+3/4' 205 | 188 'x, -z, -y' 206 | 189 'y+1/4, z+3/4, -x+3/4' 207 | 190 'x+1/2, z, y+1/2' 208 | 191 '-y+3/4, z+1/4, x+3/4' 209 | 192 '-x+1/2, z+1/2, -y' 210 | loop_ 211 | _atom_type_symbol 212 | _atom_type_oxidation_number 213 | Mg2+ 2.0 214 | Al3+ 3.0 215 | O2- -2.0 216 | loop_ 217 | _atom_site_type_symbol 218 | _atom_site_label 219 | _atom_site_symmetry_multiplicity 220 | _atom_site_fract_x 221 | _atom_site_fract_y 222 | _atom_site_fract_z 223 | _atom_site_occupancy 224 | Mg2+ Mg0 8 0.00000000 0.00000000 0.00000000 1 225 | Al3+ Al1 16 0.12500000 0.12500000 0.62500000 1 226 | O2- O2 32 0.11127934 0.11127934 0.38872066 1 227 | -------------------------------------------------------------------------------- /Part_5-Five_Features/structures/Si_conventional.cif: -------------------------------------------------------------------------------- 1 | # generated using pymatgen 2 | data_Si 3 | _symmetry_space_group_name_H-M 'P 1' 4 | _cell_length_a 5.43086099 5 | _cell_length_b 5.43086099 6 | _cell_length_c 5.43086099 7 | _cell_angle_alpha 90.00000000 8 | _cell_angle_beta 90.00000000 9 | _cell_angle_gamma 90.00000000 10 | _symmetry_Int_Tables_number 1 11 | _chemical_formula_structural Si 12 | _chemical_formula_sum Si8 13 | _cell_volume 160.17917810 14 | _cell_formula_units_Z 8 15 | loop_ 16 | _symmetry_equiv_pos_site_id 17 | _symmetry_equiv_pos_as_xyz 18 | 1 'x, y, z' 19 | loop_ 20 | _atom_site_type_symbol 21 | _atom_site_label 22 | _atom_site_symmetry_multiplicity 23 | _atom_site_fract_x 24 | _atom_site_fract_y 25 | _atom_site_fract_z 26 | _atom_site_occupancy 27 | Si Si0 1 0.00000000 0.00000000 0.00000000 1.0 28 | Si Si1 1 0.75000000 0.75000000 0.25000000 1.0 29 | Si Si2 1 0.00000000 0.50000000 0.50000000 1.0 30 | Si Si3 1 0.75000000 0.25000000 0.75000000 1.0 31 | Si Si4 1 0.50000000 0.00000000 0.50000000 1.0 32 | Si Si5 1 0.25000000 0.75000000 0.75000000 1.0 33 | Si Si6 1 0.50000000 0.50000000 0.00000000 1.0 34 | Si Si7 1 0.25000000 0.25000000 0.25000000 1.0 35 | -------------------------------------------------------------------------------- /Part_5-Five_Features/structures/Si_reduced.cif: -------------------------------------------------------------------------------- 1 | # generated using pymatgen 2 | data_Si 3 | _symmetry_space_group_name_H-M 'P 1' 4 | _cell_length_a 3.84019793 5 | _cell_length_b 3.84019899 6 | _cell_length_c 3.84019793 7 | _cell_angle_alpha 119.99999086 8 | _cell_angle_beta 90.00000000 9 | _cell_angle_gamma 60.00000914 10 | _symmetry_Int_Tables_number 1 11 | _chemical_formula_structural Si 12 | _chemical_formula_sum Si2 13 | _cell_volume 40.04479464 14 | _cell_formula_units_Z 2 15 | loop_ 16 | _symmetry_equiv_pos_site_id 17 | _symmetry_equiv_pos_as_xyz 18 | 1 'x, y, z' 19 | loop_ 20 | _atom_site_type_symbol 21 | _atom_site_label 22 | _atom_site_symmetry_multiplicity 23 | _atom_site_fract_x 24 | _atom_site_fract_y 25 | _atom_site_fract_z 26 | _atom_site_occupancy 27 | Si Si0 1 0.00000000 0.00000000 0.00000000 1 28 | Si Si1 1 0.75000000 0.50000000 0.75000000 1 29 | -------------------------------------------------------------------------------- /Part_5-Five_Features/structures/TiPbO3.cif: -------------------------------------------------------------------------------- 1 | # generated using pymatgen 2 | data_TiPbO3 3 | _symmetry_space_group_name_H-M P4mm 4 | _cell_length_a 3.87955190 5 | _cell_length_b 3.87955190 6 | _cell_length_c 4.28588762 7 | _cell_angle_alpha 90.00000000 8 | _cell_angle_beta 90.00000000 9 | _cell_angle_gamma 90.00000000 10 | _symmetry_Int_Tables_number 99 11 | _chemical_formula_structural TiPbO3 12 | _chemical_formula_sum 'Ti1 Pb1 O3' 13 | _cell_volume 64.50656432 14 | _cell_formula_units_Z 1 15 | loop_ 16 | _symmetry_equiv_pos_site_id 17 | _symmetry_equiv_pos_as_xyz 18 | 1 'x, y, z' 19 | 2 '-y, x, z' 20 | 3 '-x, -y, z' 21 | 4 'y, -x, z' 22 | 5 '-x, y, z' 23 | 6 'y, x, z' 24 | 7 'x, -y, z' 25 | 8 '-y, -x, z' 26 | loop_ 27 | _atom_type_symbol 28 | _atom_type_oxidation_number 29 | Ti4+ 4.0 30 | Pb2+ 2.0 31 | O2- -2.0 32 | loop_ 33 | _atom_site_type_symbol 34 | _atom_site_label 35 | _atom_site_symmetry_multiplicity 36 | _atom_site_fract_x 37 | _atom_site_fract_y 38 | _atom_site_fract_z 39 | _atom_site_occupancy 40 | Ti4+ Ti0 1 0.50000000 0.50000000 0.58251444 1 41 | Pb2+ Pb1 1 0.00000000 0.00000000 0.12358795 1 42 | O2- O2 2 0.00000000 0.50000000 0.49415765 1 43 | O2- O3 1 0.50000000 0.50000000 0.99578232 1 44 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # pymatgen_tutorials 2 | Tutorials for using the pymatgen library 3 | 4 | # Video tutorials: 5 | 6 | * Part 1 (Structures & Molecules): https://youtu.be/b0tieiedGdg 7 | * Part 2 (VASP inputs & outputs): https://youtu.be/Uz6Fm78z2xM 8 | * Part 3 (Getting data from the Materials Project API): https://youtu.be/e4hSkv1Ghbk 9 | * Part 4 (Structure transformations, symmetry analysis, & local environments): https://youtu.be/2-L6lax1DFU 10 | * Part 5 (5 Features You Should Know): https://youtu.be/R6ez_jgzPto 11 | --------------------------------------------------------------------------------