Ranking phase fields by likelihood with ICSD patterns
Andrij Vasylenko 13.08.2020
Install: >>> pip install . Usage: >>> python ranking_phase_fields.py <input_file>
Supported methods for pattern detection are based on PyOD library
Models:
'AE' : AutoEncoder 'VAE' : Variational AE 'ABOD' : Angle-based outlier detection 'FeatureBagging' : FeatureBagging 'HBOS' : Histogram-Based Outlier Score 'IForest' : Isolation Forest 'KNN' : K-Nearest Neighbours 'LOF' : Local Outlier Factor 'OCSVM' : OCSupport Vector Machine 'PCA' : Principle Component Analysis 'SOS' : SOS(), 'COF' : Connectivity-based OF(), 'CBLOF' : Clustering-Based LOF 'SOD' : SOD(), 'LOCI' : LOCI(), 'MCD' : MCD()
Read more about these methods https://www.pyod.readthedocs.io
[1] Zhao, Y., Nasrullah, Z. and Li, Z., PyOD: A Python Toolbox for Scalable Outlier Detection. Journal of machine learning research 20(96), pp.1-7 (2019).
Supported elemental features:
TABLES/AtomicVolume.table TABLES/AtomicWeight.table TABLES/BCCbandgap.table TABLES/BCCefflatcnt.table TABLES/BCCenergy_pa.table TABLES/BCCenergydiff.table TABLES/BCCfermi.table TABLES/BCCmagmom.table TABLES/BCCvolume_pa.table TABLES/BCCvolume_padiff.table TABLES/BoilingT.table TABLES/Column.table TABLES/CovalentRadius.table TABLES/Density.table TABLES/Electronegativity.table TABLES/FirstIonizationEnergy.table TABLES/GSbandgap.table TABLES/GSefflatcnt.table TABLES/GSenergy_pa.table TABLES/GSestBCClatcnt.table TABLES/GSestFCClatcnt.table TABLES/GSmagmom.table TABLES/GSvolume_pa.table TABLES/ICSDVolume.table TABLES/MeltingT.table TABLES/MendeleevNumber.table TABLES/MiracleRadius.table TABLES/NUnfilled.table TABLES/NValance.table TABLES/NdUnfilled.table TABLES/NdValence.table TABLES/NfUnfilled.table TABLES/NfValence.table TABLES/NpUnfilled.table TABLES/NpValence.table TABLES/NsUnfilled.table TABLES/NsValence.table TABLES/Number.table TABLES/Pettifor.table TABLES/Polarizability.table TABLES/Row.table
[2] Jha, D., Ward, L., Paul, A. et al. ElemNet: Deep Learning the Chemistry of Materials From Only Elemental Composition. Sci Rep 8, 17593 (2018). https://doi.org/10.1038/s41598-018-35934-y [3] Glawe, H., Sanna, A., Gross, E. K. U., Marques, M. A. L., The optimal one dimensional periodic table: a modified Pettifor chemical scale from data mining. N. J. Phys. 18, 093011 (2016). https://doi.org/10.1088/1367-2630/18/9/093011
Parameters of the input file (default values are in rpp.input file)
- icsd_file : (default: icsd2017) ICSD excerpt. A text file, a list of ICSD .cif files
- with specified oxidation states for each element.
- phase_fields : (default: quaternary) binary, ternary, quaternary - are supported.
- Type of phase fields to investigate.
- cations_train : (default: all) list of elements constituting a phase field in ICSD.
- Elements in the first positions (cations), e.g. elements for M and M' in MM'AA' phase fields.
- anions_train : (default: S,O,Cl,Br,F,N,Te,P,Se,As,I) list of elements constituting a phase field in ICSD.
- Elements in the last positions (anions) e.g. elements for A and A' in MM'AA' phase fields.
- nanions_train : (default: 2) Number of anions (elements with negative oxidation states as specified in icsd_file)
- in the training set. Supported values: 0, 1, 2. If 0 - oxidation states are not taken into account.
- cation1_test : (default: Li) list of elements for the first position (e.g. M in MM'AA' phase fields)
- in the phase fields to explore (no reported associated compositions in ICSD).
- cation2_test : (default: all) list of elements for the second position (e.g. M' in MM'AA' phase fields)
- in the phase fields to explore (no reported associated compositions in ICSD). Ignored for binary and ternary (type MAA') phase fields.
- anion1_test : (default: S,O,Cl,Br,I,F,N) list of elements for the 3rd position (e.g. A in MM'AA' phase fields)
- in the phase fields to explore (no reported associated compositions in ICSD). Stands for a 3rd cation in ternary (type MM'M") and quaternary (type MM'M"A) phase fields.
- anion2_test : (default: S,O,Cl,Br,I,F,N) list of elements for the 4th position (e.g. A' in MM'AA' phase fields)
- in the phase fields to explore (no reported associated compositions in ICSD). Ignored for ternary (type MM'A) phase fields.
method : (default: VAE) See all supported models above. average_runs : (default: 1) Number of runs to average the scores over. Makes sense for not neural network based (AE, VAE)
methods.
features : (default: See rpp.input). See all supported features above.