crystal_motifs

• Tools for characterizing and comparing different sub-structure motifs between periodic crystal structures
• Scripts to classify DFT optimized inorganic and organic materials as 3D perovskites according to their octahedral network connectivities
• Handles multiple inorganic A and B-sites, and constructs organic A-sites from periodic structures

dependencies

• pymatgen version 2022.0.5 or greater (for pymatgen nearest neighbors finder compatibility)
• scipy (convex hull construction)
• networkx (graph generation)
• pubchempy (querying organic molecules)
• openbabel (smile string representations of organics)

pubchempy and openbabel used to identify molecular perovskite sites, see MAPbI3 test.

classify structures as 3D perovksites on HPC resources

Example execution: classify_submitter.py -s classify_3D.py -d {DIRECTORY_NAME} -w {FILENAME.json} -o {FILENAME} -n 1 -t 1 -cu

• -s: classification script to run. classify_3D.py classifies structures in parallel on the total number of cores available based on the -n argument.
• -d: directory with structures, typically a directory tree of VASP optimized structures with corresponding VASP runfiles.
• -w: .json file where the perovskite/non-perovskite classification is written.
• -o: file to write the standard output of classify_3D.py,
• -n: number of supercomputing nodes used to classify structures in parallel.
• -t: wall time. For Eagle supercomputing cluster, wall time = 1 submits to the debug queue.
• -cu: check unconverged, tag that determines whether unconverged VASP runs should be included with the classification (acts as True/False).

Note: The script classify_3D.py currently only checks for files named "CONTCAR" to perform the classification on.
Note: The classification dictionary keys are also each structures' reduced formula. If there are multiple structures in the same subdirectory with the same reduced formula, these can be overwritten.

example classification file

{"CsGeI3": {"assignment_1": {"is_3d_perovskite": true, "A": ["Cs+"], "B": ["Ge2+"], "X": ["I-"]}, "assignment_2": {"is_3d_perovskite": false, "A": ["Ge2+"], "B": ["Cs+"], "X": ["I-"]}},
"CsPbBr3": {"assignment_1": {"is_3d_perovskite": true, "A": ["Cs+"], "B": ["Pb2+"], "X": ["Br-"]}, "assignment_2": {"is_3d_perovskite": false, "A": ["Pb2+"], "B": ["Cs+"], "X": ["Br-"]}},
"CsPbI3": {"assignment_1": {"is_3d_perovskite": true, "A": ["Cs+"], "B": ["Pb2+"], "X": ["I-"]}, "assignment_2": {"is_3d_perovskite": false, "A": ["Pb2+"], "B": ["Cs+"], "X": ["I-"]}},
"RbPbI3": {"assignment_1": {"is_3d_perovskite": true, "A": ["Rb+"], "B": ["Pb2+"], "X": ["I-"]}, "assignment_2": {"is_3d_perovskite": false, "A": ["Pb2+"], "B": ["Rb+"], "X": ["I-"]}},
"CsSnBr3": {"assignment_1": {"is_3d_perovskite": true, "A": ["Cs+"], "B": ["Sn2+"], "X": ["Br-"]}, "assignment_2": {"is_3d_perovskite": false, "A": ["Sn2+"], "B": ["Cs+"], "X": ["Br-"]}},
"CsSnI3": {"assignment_1": {"is_3d_perovskite": true, "A": ["Cs+"], "B": ["Sn2+"], "X": ["I-"]}, "assignment_2": {"is_3d_perovskite": false, "A": ["Sn2+"], "B": ["Cs+"], "X": ["I-"]}}}

example output file

Running analysis...
CsPbI3: Not all Cs+ B-site nodes are octahedrons
CsPbBr3: Not all Cs+ B-site nodes are octahedrons
CsSnBr3: Not all Cs+ B-site nodes are octahedrons
RbPbI3: Not all Rb+ B-site nodes are octahedrons
CsSnI3: Not all Cs+ B-site nodes are octahedrons
CsGeI3: Not all Cs+ B-site nodes are octahedrons
{'CsGeI3': {'assignment_1': {'is_3d_perovskite': True, 'A': ['Cs+'], 'B': ['Ge2+'], 'X': ['I-']}, 'assignment_2': {'is_3d_perovskite': False, 'A': ['Ge2+'], 'B': ['Cs+'], 'X': ['I-']}}, 'CsPbBr3': {'assignment_1': {'is_3d_perovskite': True, 'A': ['Cs+'], 'B': ['Pb2+'], 'X': ['Br-']}, 'assignment_2': {'is_3d_perovskite': False, 'A': ['Pb2+'], 'B': ['Cs+'], 'X': ['Br-']}}, 'CsPbI3': {'assignment_1': {'is_3d_perovskite': True, 'A': ['Cs+'], 'B': ['Pb2+'], 'X': ['I-']}, 'assignment_2': {'is_3d_perovskite': False, 'A': ['Pb2+'], 'B': ['Cs+'], 'X': ['I-']}}, 'RbPbI3': {'assignment_1': {'is_3d_perovskite': True, 'A': ['Rb+'], 'B': ['Pb2+'], 'X': ['I-']}, 'assignment_2': {'is_3d_perovskite': False, 'A': ['Pb2+'], 'B': ['Rb+'], 'X': ['I-']}}, 'CsSnBr3': {'assignment_1': {'is_3d_perovskite': True, 'A': ['Cs+'], 'B': ['Sn2+'], 'X': ['Br-']}, 'assignment_2': {'is_3d_perovskite': False, 'A': ['Sn2+'], 'B': ['Cs+'], 'X': ['Br-']}}, 'CsSnI3': {'assignment_1': {'is_3d_perovskite': True, 'A': ['Cs+'], 'B': ['Sn2+'], 'X': ['I-']}, 'assignment_2': {'is_3d_perovskite': False, 'A': ['Sn2+'], 'B': ['Cs+'], 'X': ['I-']}}}
Writing data...
Elapsed time: 19.94055724143982
Process time: 5.400594236