From da611fbc6dcfdd9fc4ca6ba742a7eeb6850b97fa Mon Sep 17 00:00:00 2001 From: Aron Walsh Date: Thu, 25 Jul 2024 10:07:01 +0100 Subject: [PATCH 01/20] Initial cleanup of oxidation state data files Added comment lines on dataset origins --- paper.bib | 88 +++++++---------- smact/data/{HHIs.txt => hhi.txt} | 0 smact/data/oxidation_states.txt | 4 + smact/data/oxidation_states_SP.txt | 4 + smact/data/oxidation_states_icsd.txt | 4 + smact/data/oxidation_states_pmg.txt | 4 + smact/data/oxidation_states_wiki.txt | 4 + smact/data/oxidationstates.data | 135 --------------------------- smact/data_loader.py | 2 +- 9 files changed, 57 insertions(+), 188 deletions(-) rename smact/data/{HHIs.txt => hhi.txt} (100%) delete mode 100644 smact/data/oxidationstates.data diff --git a/paper.bib b/paper.bib index 25775f63..1217ca54 100644 --- a/paper.bib +++ b/paper.bib @@ -1,21 +1,20 @@ @article{davies_computational_2016, - title = {Computational {Screening} of {All} {Stoichiometric} {Inorganic} {Materials}}, - volume = {1}, - issn = {24519294}, - url = {http://www.cell.com/chem/abstract/S2451-9294(16)30155-3}, - doi = {10.1016/j.chempr.2016.09.010}, - abstract = {Forming a four-component compound from the first 103 elements of the periodic table results in more than 1012 combinations. Such a materials space is intractable to high-throughput experiment or first-principle computation. We introduce a framework to address this problem and quantify how many materials can exist. We apply principles of valency and electronegativity to filter chemically implausible compositions, which reduces the inorganic quaternary space to 1010 combinations. We demonstrate that estimates of band gaps and absolute electron energies can be made simply on the basis of the chemical composition and apply this to the search for new semiconducting materials to support the photoelectrochemical splitting of water. We show the applicability to predicting crystal structure by analogy with known compounds, including exploration of the phase space for ternary combinations that form a perovskite lattice. Computer screening reproduces known perovskite materials and predicts the feasibility of thousands more. Given the simplicity of the approach, large-scale searches can be performed on a single workstation.}, - number = {4}, - journal = {Chem}, - author = {Davies, Daniel W. and Butler, Keith T. and Jackson, Adam J. and Morris, Andrew and Frost, Jarvist M. and Skelton, Jonathan M. and Walsh, Aron}, - year = {2016}, - keywords = {Perovskites, Data, Materials Design, Screening, Water splitting}, - pages = {617--627} +title = {Computational Screening of All Stoichiometric Inorganic Materials}, +volume = {1}, +issn = {24519294}, +url = {http://www.cell.com/chem/abstract/S2451-9294(16)30155-3}, +doi = {10.1016/j.chempr.2016.09.010}, +abstract = {Forming a four-component compound from the first 103 elements of the periodic table results in more than 1012 combinations. Such a materials space is intractable to high-throughput experiment or first-principle computation. We introduce a framework to address this problem and quantify how many materials can exist. We apply principles of valency and electronegativity to filter chemically implausible compositions, which reduces the inorganic quaternary space to 1010 combinations. We demonstrate that estimates of band gaps and absolute electron energies can be made simply on the basis of the chemical composition and apply this to the search for new semiconducting materials to support the photoelectrochemical splitting of water. We show the applicability to predicting crystal structure by analogy with known compounds, including exploration of the phase space for ternary combinations that form a perovskite lattice. Computer screening reproduces known perovskite materials and predicts the feasibility of thousands more. Given the simplicity of the approach, large-scale searches can be performed on a single workstation.}, +number = {4}, +journal = {Chem}, +author = {Davies, Daniel W. and Butler, Keith T. and Jackson, Adam J. and Morris, Andrew and Frost, Jarvist M. and Skelton, Jonathan M. and Walsh, Aron}, +year = {2016}, +pages = {617--627} } @article{pamplin1964, title = "A systematic method of deriving new semiconducting compounds by structural analogy", -journal = "Journal of Physics and Chemistry of Solids", +journal = "J. Phys. Chem. Solids", volume = "25", number = "7", pages = "675 - 684", @@ -29,7 +28,7 @@ @article{pamplin1964 @article{goodman1958, title = "The prediction of semiconducting properties in inorganic compounds", -journal = "Journal of Physics and Chemistry of Solids", +journal = "J. Phys. Chem. Solids", volume = "6", number = "4", pages = "305 - 314", @@ -44,38 +43,28 @@ @article{goodman1958 @article{gaultois2013, author = {Gaultois, Michael W. and Sparks, Taylor D. and Borg, Christopher K. H. and Seshadri, Ram and Bonificio, William D. and Clarke, David R.}, title = {Data-Driven Review of Thermoelectric Materials: Performance and Resource Considerations}, -journal = {Chemistry of Materials}, +journal = {Chem. Mater.}, volume = {25}, number = {15}, pages = {2911-2920}, year = {2013}, doi = {10.1021/cm400893e}, - -URL = { - https://doi.org/10.1021/cm400893e -}, -eprint = { - https://doi.org/10.1021/cm400893e} - +URL = {https://doi.org/10.1021/cm400893e}, +eprint = {https://doi.org/10.1021/cm400893e} } @article{pelatt2011, author = {Pelatt, Brian D. and Ravichandran, Ram and Wager, John F. and Keszler, Douglas A.}, title = {Atomic Solid State Energy Scale}, -journal = {Journal of the American Chemical Society}, +journal = {J. Am. Chem. Soc.}, volume = {133}, number = {42}, pages = {16852-16860}, year = {2011}, doi = {10.1021/ja204670s}, - note ={PMID: 21861503}, - -URL = { - https://doi.org/10.1021/ja204670s -}, -eprint = { - https://doi.org/10.1021/ja204670s -} +note ={PMID: 21861503}, +URL = {https://doi.org/10.1021/ja204670s}, +eprint = {https://doi.org/10.1021/ja204670s} } @Article{davies2018, @@ -86,7 +75,6 @@ @Article{davies2018 volume ="211", issue ="0", pages ="553-568", -publisher ="The Royal Society of Chemistry", doi ="10.1039/C8FD00032H", url ="http://dx.doi.org/10.1039/C8FD00032H", abstract ="The likelihiood of an element to adopt a specific oxidation state in a solid{,} given a certain set of neighbours{,} might often be obvious to a trained chemist. However{,} encoding this information for use in high-throughput searches presents a significant challenge. We carry out a statistical analysis of the occurrence of oxidation states in 16 735 ordered{,} inorganic compounds and show that a large number of cations are only likely to exhibit certain oxidation states in combination with particular anions. We use this data to build a model that ascribes probabilities to the formation of hypothetical compounds{,} given the proposed oxidation states of their constituent species. The model is then used as part of a high-throughput materials design process{,} which significantly narrows down the vast compositional search space for new ternary metal halide compounds. Finally{,} we employ a machine learning analysis of existing compounds to suggest likely structures for a small subset of the candidate compositions. We predict two new compounds{,} MnZnBr4 and YSnF7{,} that are thermodynamically stable according to density functional theory{,} as well as four compounds{,} MnCdBr4{,} MnRu2Br8{,} ScZnF5 and ZnCoBr4{,} which lie within the window of metastability." @@ -100,29 +88,27 @@ @Article{goldschmidt1929 volume ="25", issue ="0", pages ="253-283", -publisher ="The Royal Society of Chemistry", doi ="10.1039/TF9292500253", url ="http://dx.doi.org/10.1039/TF9292500253", abstract =""} @article{nethercot1974, - title = {Prediction of Fermi Energies and Photoelectric Thresholds Based on Electronegativity Concepts}, - author = {Nethercot, Arthur H.}, - journal = {Phys. Rev. Lett.}, - volume = {33}, - issue = {18}, - pages = {1088--1091}, - numpages = {0}, - year = {1974}, - month = {Oct}, - publisher = {American Physical Society}, - doi = {10.1103/PhysRevLett.33.1088}, - url = {https://link.aps.org/doi/10.1103/PhysRevLett.33.1088} +title = {Prediction of Fermi Energies and Photoelectric Thresholds Based on Electronegativity Concepts}, +author = {Nethercot, Arthur H.}, +journal = {Phys. Rev. Lett.}, +volume = {33}, +issue = {18}, +pages = {1088--1091}, +numpages = {0}, +year = {1974}, +month = {Oct}, +doi = {10.1103/PhysRevLett.33.1088}, +url = {https://link.aps.org/doi/10.1103/PhysRevLett.33.1088} } @article{ward2018, title = "Matminer: An open source toolkit for materials data mining", -journal = "Computational Materials Science", +journal = "Comp. Mater. Sci.", volume = "152", pages = "60 - 69", year = "2018", @@ -130,13 +116,12 @@ @article{ward2018 doi = "https://doi.org/10.1016/j.commatsci.2018.05.018", url = "http://www.sciencedirect.com/science/article/pii/S0927025618303252", author = "Logan Ward and Alexander Dunn and Alireza Faghaninia and Nils E.R. Zimmermann and Saurabh Bajaj and Qi Wang and Joseph Montoya and Jiming Chen and Kyle Bystrom and Maxwell Dylla and Kyle Chard and Mark Asta and Kristin A. Persson and G. Jeffrey Snyder and Ian Foster and Anubhav Jain", -keywords = "Data mining, Open source software, Machine learning, Materials informatics", abstract = "As materials data sets grow in size and scope, the role of data mining and statistical learning methods to analyze these materials data sets and build predictive models is becoming more important. This manuscript introduces matminer, an open-source, Python-based software platform to facilitate data-driven methods of analyzing and predicting materials properties. Matminer provides modules for retrieving large data sets from external databases such as the Materials Project, Citrination, Materials Data Facility, and Materials Platform for Data Science. It also provides implementations for an extensive library of feature extraction routines developed by the materials community, with 47 featurization classes that can generate thousands of individual descriptors and combine them into mathematical functions. Finally, matminer provides a visualization module for producing interactive, shareable plots. These functions are designed in a way that integrates closely with machine learning and data analysis packages already developed and in use by the Python data science community. We explain the structure and logic of matminer, provide a description of its various modules, and showcase several examples of how matminer can be used to collect data, reproduce data mining studies reported in the literature, and test new methodologies." } @article{ong2013, title = "Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis", -journal = "Computational Materials Science", +journal = "Comp. Mater. Sci.", volume = "68", pages = "314 - 319", year = "2013", @@ -144,7 +129,6 @@ @article{ong2013 doi = "https://doi.org/10.1016/j.commatsci.2012.10.028", url = "http://www.sciencedirect.com/science/article/pii/S0927025612006295", author = "Shyue Ping Ong and William Davidson Richards and Anubhav Jain and Geoffroy Hautier and Michael Kocher and Shreyas Cholia and Dan Gunter and Vincent L. Chevrier and Kristin A. Persson and Gerbrand Ceder", -keywords = "Materials, Project, Design, Thermodynamics, High-throughput", abstract = "We present the Python Materials Genomics (pymatgen) library, a robust, open-source Python library for materials analysis. A key enabler in high-throughput computational materials science efforts is a robust set of software tools to perform initial setup for the calculations (e.g., generation of structures and necessary input files) and post-calculation analysis to derive useful material properties from raw calculated data. The pymatgen library aims to meet these needs by (1) defining core Python objects for materials data representation, (2) providing a well-tested set of structure and thermodynamic analyses relevant to many applications, and (3) establishing an open platform for researchers to collaboratively develop sophisticated analyses of materials data obtained both from first principles calculations and experiments. The pymatgen library also provides convenient tools to obtain useful materials data via the Materials Project’s REpresentational State Transfer (REST) Application Programming Interface (API). As an example, using pymatgen’s interface to the Materials Project’s RESTful API and phasediagram package, we demonstrate how the phase and electrochemical stability of a recently synthesized material, Li4SnS4, can be analyzed using a minimum of computing resources. We find that Li4SnS4 is a stable phase in the Li–Sn–S phase diagram (consistent with the fact that it can be synthesized), but the narrow range of lithium chemical potentials for which it is predicted to be stable would suggest that it is not intrinsically stable against typical electrodes used in lithium-ion batteries." } @@ -170,7 +154,7 @@ @Article{oboyle2011 and Vandermeersch, Tim and Hutchison, Geoffrey R.", title="Open Babel: An open chemical toolbox", -journal="Journal of Cheminformatics", +journal="J. Cheminf.", year="2011", month="Oct", day="07", @@ -191,11 +175,11 @@ @article{ase-paper Peterson and Carsten Rostgaard and Jakob Schiøtz and Ole Schütt and Mikkel Strange and Kristian S Thygesen and Tejs Vegge and Lasse Vilhelmsen and Michael Walter and Zhenhua Zeng and Karsten W Jacobsen}, title={The atomic simulation environment—a Python library for working with atoms}, - journal={Journal of Physics: Condensed Matter}, + journal={J. Condens. Matter Phys.}, volume={29}, number={27}, pages={273002}, url={http://stacks.iop.org/0953-8984/29/i=27/a=273002}, year={2017}, abstract={The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.} -} +} \ No newline at end of file diff --git a/smact/data/HHIs.txt b/smact/data/hhi.txt similarity index 100% rename from smact/data/HHIs.txt rename to smact/data/hhi.txt diff --git a/smact/data/oxidation_states.txt b/smact/data/oxidation_states.txt index 122f9ee0..4ff8add3 100644 --- a/smact/data/oxidation_states.txt +++ b/smact/data/oxidation_states.txt @@ -1,3 +1,7 @@ +# +# Oxidation state set +# Source: Original SMACT set manually compiled (2014) +# H -1 +1 He Li +1 diff --git a/smact/data/oxidation_states_SP.txt b/smact/data/oxidation_states_SP.txt index 697bd41c..4713e62d 100644 --- a/smact/data/oxidation_states_SP.txt +++ b/smact/data/oxidation_states_SP.txt @@ -1,3 +1,7 @@ +# +# Oxidation state set +# Source: Pymatgen structure predictor (2017) +# H 1 He Li 1 diff --git a/smact/data/oxidation_states_icsd.txt b/smact/data/oxidation_states_icsd.txt index f7fcca86..b575d52e 100644 --- a/smact/data/oxidation_states_icsd.txt +++ b/smact/data/oxidation_states_icsd.txt @@ -1,3 +1,7 @@ +# +# Oxidation state set +# Source: ICSD (2016) +# H -1 1 He Li 1 diff --git a/smact/data/oxidation_states_pmg.txt b/smact/data/oxidation_states_pmg.txt index ee82221b..36a42f71 100644 --- a/smact/data/oxidation_states_pmg.txt +++ b/smact/data/oxidation_states_pmg.txt @@ -1,3 +1,7 @@ +# +# Oxidation state set +# Source: Pymatgen (2017) +# H -1 1 He Li 1 diff --git a/smact/data/oxidation_states_wiki.txt b/smact/data/oxidation_states_wiki.txt index 1da2e152..615cee37 100644 --- a/smact/data/oxidation_states_wiki.txt +++ b/smact/data/oxidation_states_wiki.txt @@ -1,3 +1,7 @@ +# +# Oxidation state set +# Source: Wikipedia (2022) +# H -1 1 He Li 0 1 diff --git a/smact/data/oxidationstates.data b/smact/data/oxidationstates.data deleted file mode 100644 index ff0180d9..00000000 --- a/smact/data/oxidationstates.data +++ /dev/null @@ -1,135 +0,0 @@ -H-1 -1 -He 0 -Li1 1 -Be2 2 -B3 3 -C-4 -4 -C-3 -3 -C-2 -2 -C-1 -1 -C1 1 -C2 2 -C3 3 -N-3 -3 -N3 3 -N5 5 -O-2 -2 -F-1 -1 -Ne 0 -Na1 1 -Mg2 2 -Al3 3 -Si-4 -4 -Si4 4 -P-3 -3 -P3 3 -P5 5 -S-2 -2 -S2 2 -S4 4 -S6 6 -Cl-1 -1 -Ar 0 -K1 1 -Ca2 2 -Sc3 3 -Ti4 4 -V5 5 -Cr3 3 -Cr6 6 -Mn2 2 -Mn4 4 -Mn7 7 -Fe2 2 -Fe3 3 -Fe6 6 -Co2 2 -Co3 3 -Ni2 2 -Cu2 2 -Zn2 2 -Ga3 3 -Ge-4 -4 -Ge2 2 -Ge4 4 -As-3 -3 -As3 3 -As5 5 -Se-2 -2 -Se2 2 -Se4 4 -Se6 6 -Br-1 -1 -Kr 0 -Rb1 1 -Sr2 2 -Y3 3 -Zr4 4 -Nb5 5 -Mo4 4 -Mo6 6 -Tc4 4 -Tc7 7 -Ru3 3 -Ru4 4 -Rh3 3 -Pd2 2 -Pd4 4 -Ag1 1 -Cd2 2 -In3 3 -Sn-4 -4 -Sn2 2 -Sn4 4 -Sb-3 -3 -Sb3 3 -Sb5 5 -Te-2 -2 -Te2 2 -Te4 4 -Te6 6 -I-1 -1 -Cs1 1 -Ba2 2 -La3 3 -Ce3 3 -Ce4 4 -Pr3 3 -Nd3 3 -Pm3 3 -Sm3 3 -Eu2 2 -Eu3 3 -Gd3 3 -Tb3 3 -Dy3 3 -Ho3 3 -Er3 3 -Tm3 3 -Yb3 3 -Lu3 3 -Hf4 4 -Ta5 5 -W4 4 -W6 6 -Re4 4 -Os4 4 -Ir3 3 -Ir4 4 -Pt2 2 -Pt3 3 -Pt4 4 -Au3 3 -Hg1 1 -Hg2 2 -Tl1 1 -Tl3 3 -Pb-4 -4 -Pb2 2 -Bi-3 -3 -Bi3 3 -Po-2 -2 -Po2 2 -Po4 4 -At-1 -1 -At1 1 diff --git a/smact/data_loader.py b/smact/data_loader.py index 79e0dd8a..ac27bd24 100644 --- a/smact/data_loader.py +++ b/smact/data_loader.py @@ -346,7 +346,7 @@ def lookup_element_hhis(symbol): if _element_hhis is None: _element_hhis = {} - with open(os.path.join(data_directory, "HHIs.txt")) as file: + with open(os.path.join(data_directory, "hhi.txt")) as file: for line in file: line = line.strip() From b3c544fc42b6b4de9c6a937c62f0c89f99c798c7 Mon Sep 17 00:00:00 2001 From: Aron Walsh Date: Thu, 25 Jul 2024 10:25:14 +0100 Subject: [PATCH 02/20] ICSD (2024) oxidation states Populated from ICSD API - raw count json - raw oxidation state list - filtered list with > 5 entries per oxidation state --- .../data/oxidation_states_icsd24_counts.json | 1 + .../data/oxidation_states_icsd24_filtered.txt | 112 ++++++++++++++++++ smact/data/oxidation_states_icsd24_raw.txt | 112 ++++++++++++++++++ 3 files changed, 225 insertions(+) create mode 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\ No newline at end of file diff --git a/smact/data/oxidation_states_icsd24_filtered.txt b/smact/data/oxidation_states_icsd24_filtered.txt new file mode 100644 index 00000000..96dbd31f --- /dev/null +++ b/smact/data/oxidation_states_icsd24_filtered.txt @@ -0,0 +1,112 @@ +# +# Oxidation state set +# Source: ICSD (2024), filtered for > 5 reports +# +H -1 1 +He +Li 1 +Be 2 +B -3 -2 -1 1 2 3 +C -4 -3 -2 -1 1 2 3 4 +N -5 -4 -3 -2 -1 1 2 3 4 5 +O -2 -1 +F -1 +Ne +Na 1 +Mg 2 +Al 3 +Si -4 -3 -2 -1 2 3 4 +P -3 -2 -1 1 2 3 4 5 +S -2 -1 1 2 3 4 5 6 +Cl -1 1 3 +Ar +K 1 +Ca 2 +Sc 1 2 3 +Ti 2 3 4 +V 1 2 3 4 5 +Cr 1 2 3 4 5 6 +Mn -1 1 2 3 4 5 6 7 +Fe 1 2 3 4 5 6 +Co -1 1 2 3 4 +Ni 1 2 3 4 +Cu 1 2 3 +Zn 2 3 +Ga -3 1 2 3 4 +Ge -4 -3 -2 -1 2 3 4 +As -3 -2 -1 1 2 3 4 5 +Se -2 -1 1 2 4 6 +Br -1 1 3 5 7 +Kr 2 +Rb 1 +Sr 2 4 +Y 1 2 3 4 +Zr 1 2 3 4 +Nb 1 2 3 5 6 +Mo -1 1 2 3 5 6 +Tc 1 2 3 4 5 7 +Ru 1 2 3 4 5 6 7 +Rh -1 1 2 3 4 5 +Pd 1 2 3 4 +Ag 1 2 3 +Cd 2 +In -3 -1 1 2 3 +Sn -4 -2 -1 2 3 4 +Sb -3 -2 -1 2 3 4 5 +Te -3 -2 -1 1 2 4 5 6 +I -1 1 3 5 7 +Xe 2 4 6 8 +Cs 1 +Ba 2 +La 1 2 3 4 +Ce 2 3 4 +Pr 2 3 4 +Nd 2 3 4 +Pm +Sm 2 3 +Eu 2 3 4 +Gd 2 3 4 +Tb 2 3 4 +Dy 2 3 4 +Ho 2 3 +Er 2 3 4 +Tm 2 3 +Yb 2 3 +Lu 2 3 +Hf 2 3 4 +Ta 1 2 3 4 5 +W 2 3 4 5 6 +Re 1 2 3 4 +Os 1 2 3 4 5 6 7 8 +Ir 1 2 3 4 5 6 +Pt 2 3 4 5 +Au -1 1 2 5 +Hg 2 +Tl -1 1 2 3 +Pb -4 -1 2 3 4 +Bi -2 -1 1 2 3 4 5 +Po 4 +At +Rn +Fr +Ra +Ac 3 +Th 2 3 4 +Pa 4 5 +U 2 3 4 5 6 +Np 2 3 4 5 6 7 +Pu +Am +Cm +Bk +Cf +Es +Fm +Md +No +Lr +Rf +Db +Sg +Bh +Hs \ No newline at end of file diff --git a/smact/data/oxidation_states_icsd24_raw.txt b/smact/data/oxidation_states_icsd24_raw.txt new file mode 100644 index 00000000..57d21803 --- /dev/null +++ b/smact/data/oxidation_states_icsd24_raw.txt @@ -0,0 +1,112 @@ +# +# Oxidation state set +# Source: ICSD (2024) +# +H -1 1 2 3 +He +Li 1 +Be 2 +B -5 -3 -2 -1 1 2 3 +C -4 -3 -2 -1 1 2 3 4 +N -5 -4 -3 -2 -1 1 2 3 4 5 +O -3 -2 -1 1 2 +F -1 1 2 +Ne +Na -1 1 +Mg 2 3 +Al -3 1 2 3 +Si -4 -3 -2 -1 1 2 3 4 +P -4 -3 -2 -1 1 2 3 4 5 6 +S -3 -2 -1 1 2 3 4 5 6 +Cl -4 -1 1 2 3 4 +Ar +K 1 +Ca -1 1 2 +Sc 1 2 3 5 6 +Ti 1 2 3 4 5 6 +V 1 2 3 4 5 6 +Cr 1 2 3 4 5 6 +Mn -1 1 2 3 4 5 6 7 +Fe -4 -2 -1 1 2 3 4 5 6 +Co -1 1 2 3 4 5 +Ni -2 1 2 3 4 +Cu 1 2 3 4 +Zn 1 2 3 4 +Ga -4 -3 -2 -1 1 2 3 4 +Ge -4 -3 -2 -1 1 2 3 4 5 +As -5 -3 -2 -1 1 2 3 4 5 +Se -2 -1 1 2 3 4 5 6 8 +Br -1 1 3 4 5 7 +Kr 2 +Rb -1 1 2 +Sr -2 2 4 +Y 1 2 3 4 +Zr 1 2 3 4 6 +Nb 1 2 3 5 6 +Mo -1 1 2 3 5 6 7 +Tc 1 2 3 4 5 6 7 +Ru -4 -3 -2 -1 1 2 3 4 5 6 7 8 +Rh -1 1 2 3 4 5 6 +Pd 1 2 3 4 +Ag 1 2 3 4 +Cd 1 2 +In -3 -2 -1 1 2 3 4 +Sn -4 -3 -2 -1 1 2 3 4 +Sb -3 -2 -1 1 2 3 4 5 6 +Te -3 -2 -1 1 2 3 4 5 6 +I -2 -1 1 3 5 7 +Xe 2 3 4 6 8 +Cs 1 +Ba 1 2 +La 1 2 3 4 +Ce -1 1 2 3 4 +Pr 1 2 3 4 +Nd 1 2 3 4 5 +Pm 3 +Sm 1 2 3 4 +Eu 1 2 3 4 5 6 +Gd 1 2 3 4 +Tb 1 2 3 4 5 +Dy 2 3 4 5 6 +Ho 2 3 4 5 6 +Er 2 3 4 5 6 +Tm 2 3 4 +Yb 2 3 4 +Lu 2 3 4 +Hf 1 2 3 4 +Ta 1 2 3 4 5 6 7 +W 1 2 3 4 5 6 7 +Re -1 1 2 3 4 +Os 1 2 3 4 5 6 7 8 +Ir -1 1 2 3 4 5 6 +Pt -2 1 2 3 4 5 6 +Au -1 1 2 4 5 +Hg 2 4 +Tl -2 -1 1 2 3 5 +Pb -4 -1 1 2 3 4 +Bi -2 -1 1 2 3 4 5 +Po -2 2 4 +At +Rn +Fr +Ra 2 +Ac 3 +Th 2 3 4 5 6 +Pa 2 3 4 5 +U -3 1 2 3 4 5 6 +Np -1 2 3 4 5 6 7 +Pu 5 +Am 1 +Cm 2 +Bk 2 +Cf +Es +Fm +Md +No +Lr +Rf +Db +Sg +Bh +Hs \ No newline at end of file From fbd1be30126d67f600c909150eca82991025abf2 Mon Sep 17 00:00:00 2001 From: Aron Walsh Date: Sat, 27 Jul 2024 14:39:40 +0100 Subject: [PATCH 03/20] Create oxidation_states_icsd24_common.txt Add set that lists the oxidation state with the most results for each element --- smact/data/oxidation_states_icsd24_common.txt | 112 ++++++++++++++++++ 1 file changed, 112 insertions(+) create mode 100644 smact/data/oxidation_states_icsd24_common.txt diff --git a/smact/data/oxidation_states_icsd24_common.txt b/smact/data/oxidation_states_icsd24_common.txt new file mode 100644 index 00000000..ae0a8c6e --- /dev/null +++ b/smact/data/oxidation_states_icsd24_common.txt @@ -0,0 +1,112 @@ +# +# Oxidation state set +# Source: ICSD (2024), most common non-zero values +# +H 1 +He +Li 1 +Be 2 +B 3 +C 4 +N -3 +O -2 +F -1 +Ne +Na 1 +Mg 2 +Al 3 +Si 4 +P 5 +S -2 +Cl -1 +Ar +K 1 +Ca 2 +Sc 3 +Ti 4 +V 5 +Cr 3 +Mn 2 +Fe 3 +Co 2 +Ni 2 +Cu 2 +Zn 2 +Ga 3 +Ge 4 +As 5 +Se -2 +Br -1 +Kr 2 +Rb 1 +Sr 2 +Y 3 +Zr 4 +Nb 5 +Mo 6 +Tc 7 +Ru 5 +Rh 3 +Pd 2 +Ag 1 +Cd 2 +In 3 +Sn 4 +Sb 3 +Te -2 +I -1 +Xe 6 +Cs 1 +Ba 2 +La 3 +Ce 3 +Pr 3 +Nd 3 +Pm 3 +Sm 3 +Eu 3 +Gd 3 +Tb 3 +Dy 3 +Ho 3 +Er 3 +Tm 3 +Yb 3 +Lu 3 +Hf 4 +Ta 5 +W 6 +Re 3 +Os 5 +Ir 4 +Pt 4 +Au 1 +Hg 2 +Tl 1 +Pb 2 +Bi 3 +Po 4 +At +Rn +Fr +Ra 2 +Ac 3 +Th 4 +Pa 5 +U 6 +Np 6 +Pu 5 +Am 1 +Cm 2 +Bk 2 +Cf +Es +Fm +Md +No +Lr +Rf +Db +Sg +Bh +Hs \ No newline at end of file From ba132de3e38598a90fc5176549582b0285b09311 Mon Sep 17 00:00:00 2001 From: Aron Walsh Date: Sun, 28 Jul 2024 11:35:08 +0100 Subject: [PATCH 04/20] Update oxidation_states_icsd24_counts.json Final list up to Lr --- smact/data/oxidation_states_icsd24_counts.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/smact/data/oxidation_states_icsd24_counts.json b/smact/data/oxidation_states_icsd24_counts.json index 651666e9..1ae6b7a9 100644 --- a/smact/data/oxidation_states_icsd24_counts.json +++ b/smact/data/oxidation_states_icsd24_counts.json @@ -1 +1 @@ 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\ No newline at end of file From 0be9b0b3de6e324a85842d31285f489f87f03ef7 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Thu, 15 Aug 2024 14:02:05 +0100 Subject: [PATCH 05/20] Make the filtered 2024 icsd oxidation states available through data_loader --- smact/data_loader.py | 56 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/smact/data_loader.py b/smact/data_loader.py index ac27bd24..e664e999 100644 --- a/smact/data_loader.py +++ b/smact/data_loader.py @@ -322,6 +322,62 @@ def lookup_element_oxidation_states_custom(symbol, filepath, copy=True): return None +_el_ox_states_icsd24 = None + + +def lookup_element_oxidation_states_icsd24(symbol, copy=True): + """ + Retrieve a list of known oxidation states for an element. + The oxidation states list used contains only those found + in the 2024 version of the ICSD (and has >=5 reports). + + Args: + symbol (str) : the atomic symbol of the element to look up. + copy (Optional(bool)): if True (default), return a copy of the + oxidation-state list, rather than a reference to the cached + data -- only use copy=False in performance-sensitive code + and where the list will not be modified! + + Returns: + list: List of known oxidation states for the element. + + Returns None if oxidation states for the Element were not + found in the external data. + """ + + global _el_ox_states_icsd24 + + if _el_ox_states_icsd24 is None: + _el_ox_states_icsd24 = {} + + for items in _get_data_rows( + os.path.join(data_directory, "oxidation_states_icsd24_filtered.txt") + ): + _el_ox_states_icsd24[items[0]] = [ + int(oxidationState) for oxidationState in items[1:] + ] + + if symbol in _el_ox_states_icsd24: + if copy: + # _el_ox_states_icsd24 stores lists -> if copy is set, make an implicit + # deep copy. The elements of the lists are integers, which are + # "value types" in Python. + + return [ + oxidationState + for oxidationState in _el_ox_states_icsd24[symbol] + ] + else: + return _el_ox_states_icsd24[symbol] + else: + if _print_warnings: + print( + "WARNING: Oxidation states for element {} " + "not found.".format(symbol) + ) + return None + + # Loader and cache for the element HHI scores. _element_hhis = None From e062c1cfc1547505902a00249e8b65bc5e4e3c06 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Thu, 15 Aug 2024 14:03:18 +0100 Subject: [PATCH 06/20] Make oxidation_states_icsd24 available through the Element class --- smact/__init__.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/smact/__init__.py b/smact/__init__.py index e19dc51b..f60eab94 100644 --- a/smact/__init__.py +++ b/smact/__init__.py @@ -3,13 +3,12 @@ A collection of fast screening tools from elemental data """ - import itertools import warnings from math import gcd from operator import mul as multiply from os import path -from typing import Iterable, List, Optional, Sequence, Tuple, Union +from typing import Iterable, List, Optional, Tuple, Union import pandas as pd @@ -55,12 +54,14 @@ class Element: Element.oxidation_states_sp (list) : List of oxdation states recognised by the Pymatgen Structure Predictor - Element.oxidation_states_icsd (list) : List of oxidation states that appear in the ICSD + Element.oxidation_states_icsd (list) : List of oxidation states that appear in the 2016 version of the ICSD Element.oxidation_states_wiki (list): List of oxidation states that appear wikipedia (https://en.wikipedia.org/wiki/Template:List_of_oxidation_states_of_the_elements) Data retrieved: 2022-09-22 Element.oxidation_states_custom (list | None ): List of oxidation states that appear in the custom data file supplied (if any) + Element.oxidation_states_icsd24 (list): List of oxidation states that appear in the 2024 version of the ICSD + Element.coord_envs (list): The allowed coordination enviroments for the ion Element.covalent_radius (float) : Covalent radius of the element @@ -169,6 +170,10 @@ def __init__( "oxidation_states_wiki", data_loader.lookup_element_oxidation_states_wiki(symbol), ), + ( + "oxidation_states_icsd24", + data_loader.lookup_element_oxidation_states_icsd24(symbol), + ), ("dipol", dataset["dipol"]), ("pauling_eneg", dataset["el_neg"]), ("SSE", sse), From 1e668fc9cef40f46465dffbbf0cfb07d7cd382c4 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Thu, 15 Aug 2024 16:19:06 +0100 Subject: [PATCH 07/20] Add oxidation states utility functions --- smact/utils/oxidation.py | 94 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 smact/utils/oxidation.py diff --git a/smact/utils/oxidation.py b/smact/utils/oxidation.py new file mode 100644 index 00000000..b795e905 --- /dev/null +++ b/smact/utils/oxidation.py @@ -0,0 +1,94 @@ +"""Utility functions for handling oxidation states.""" +import json +import os +from os import path + +import pandas as pd + +# get correct path for datafiles when called from another directory +from smact import data_directory, data_loader, ordered_elements + + +class ICSD24OxStatesFilter: + """Class to handle filtering the ICSD 24 oxidation states list.""" + + def __init__(self): + self.ox_states_df = pd.read_json( + path.join(data_directory, "oxidation_states_icsd24_counts.json") + ) + + def filter(self, threshold: int, include_zero: bool = False): + """Filter the ICSD 24 oxidation states list by a threshold. + + Args: + threshold (int): The threshold for filtering the oxidation states list. + include_zero (bool): Include oxidation state of zero in the filtered list. Default is False. + + Returns: + pd.DataFrame: The filtered oxidation states list as a DataFrame. + """ + if not include_zero: + filtered_df = self.ox_states_df[ + self.ox_states_df["oxidation_state"] != 0 + ].reset_index(drop=True) + else: + filtered_df = self.ox_states_df + summary_df = ( + filtered_df[(filtered_df["results_count"] > 0)] + .groupby("element") + .apply(self._filter_oxidation_states, threshold) + .reset_index() + ) + summary_df.columns = ["element", "oxidation_state"] + return summary_df + + def write( + self, + filename: str | os.PathLike, + threshold: int, + include_zero: bool = False, + comment: str = None, + ): + """Write the filtered ICSD 24 oxidation states list to a SMACT-compatible oxidation states txt file. + + Args: + filename (str | os.PathLike): The filename to write the filtered oxidation states list to. + threshold (int): The threshold for filtering the oxidation states list. + include_zero (bool): Include oxidation state of zero in the filtered list. Default is False. + comment (str): A comment to include in the txt file. Default is None. + """ + filtered_df = self.filter(threshold, include_zero) + # Convert the DataFrame to the require format + summary_dict = filtered_df.set_index("element")[ + "oxidation_state" + ].to_dict() + all_elements = ordered_elements(1, 103) + final_summary = [] + + for element in all_elements: + oxidation_states = summary_dict.get(element, "") + + if oxidation_states: + final_summary.append(f"{element} {oxidation_states}".strip()) + else: + final_summary.append(element) + + # Write the filtered oxidation states list to a txt file + if not filename.endswith(".txt"): + filename += ".txt" + with open(filename, "w") as f: + f.write( + f"#\n# Oxidation state set\n# Source: ICSD (2024), filtered for > {threshold} reports\n#\n" + ) + if comment: + f.write(f"# {comment}\n") + for line in final_summary: + f.write(line + "\n") + + def _filter_oxidation_states( + self, group: pd.DataFrame.groupby, threshold: int + ): + """Filter the oxidation states list by a threshold.""" + filtered_states = group[group["results_count"] > threshold] + + return " ".join(map(str, sorted(filtered_states["oxidation_state"]))) From ec8120e11c32c94be81e1c8774215fc877b8be8a Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Thu, 15 Aug 2024 18:03:54 +0100 Subject: [PATCH 08/20] Add test files --- ...test_icsd_oxidation_states_filter_1000.txt | 109 +++++++++++++++++ ...dation_states_filter_1000_w_0_ox_state.txt | 111 ++++++++++++++++++ 2 files changed, 220 insertions(+) create mode 100644 smact/tests/files/test_icsd_oxidation_states_filter_1000.txt create mode 100644 smact/tests/files/test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt diff --git a/smact/tests/files/test_icsd_oxidation_states_filter_1000.txt b/smact/tests/files/test_icsd_oxidation_states_filter_1000.txt new file mode 100644 index 00000000..1daa1ab9 --- /dev/null +++ b/smact/tests/files/test_icsd_oxidation_states_filter_1000.txt @@ -0,0 +1,109 @@ +# +# Oxidation state set +# Source: ICSD (2024), filtered for > 1000 reports +# +# Testing writing of ICSD 24 oxidation states list. +# +H -1 1 +He +Li 1 +Be +B 3 +C -2 2 3 4 +N -3 5 +O -2 +F -1 +Ne +Na 1 +Mg 2 +Al 3 +Si 4 +P -3 5 +S -2 6 +Cl -1 +Ar +K 1 +Ca 2 +Sc 3 +Ti 4 +V 4 5 +Cr 3 +Mn 2 3 4 +Fe 2 3 +Co 2 3 +Ni 2 +Cu 1 2 +Zn 2 +Ga 3 +Ge 4 +As -3 3 5 +Se -2 4 +Br -1 +Kr +Rb 1 +Sr 2 +Y 3 +Zr 4 +Nb 5 +Mo 6 +Tc +Ru +Rh +Pd +Ag 1 +Cd 2 +In 3 +Sn 2 4 +Sb 3 5 +Te -2 4 +I -1 +Xe +Cs 1 +Ba 2 +La 3 +Ce 3 4 +Pr 3 +Nd 3 +Pm +Sm 3 +Eu 3 +Gd 3 +Tb 3 +Dy 3 +Ho 3 +Er 3 +Tm +Yb 3 +Lu +Hf +Ta 5 +W 6 +Re +Os +Ir +Pt +Au +Hg 2 +Tl 1 +Pb 2 +Bi 3 +Po +At +Rn +Fr +Ra +Ac +Th +Pa +U 6 +Np +Pu +Am +Cm +Bk +Cf +Es +Fm +Md +No +Lr diff --git a/smact/tests/files/test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt b/smact/tests/files/test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt new file mode 100644 index 00000000..ba6ea2b0 --- /dev/null +++ b/smact/tests/files/test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt @@ -0,0 +1,111 @@ +# +# Oxidation state set +# Source: ICSD (2024), filtered for > 1000 reports +# +# Testing writing of ICSD 24 oxidation states list. +# +# Includes oxidation state 0 +# +H -1 0 1 +He +Li 0 1 +Be +B 0 3 +C -2 0 2 3 4 +N -3 0 5 +O -2 0 +F -1 +Ne +Na 1 +Mg 0 2 +Al 0 3 +Si 0 4 +P -3 0 5 +S -2 0 6 +Cl -1 +Ar +K 1 +Ca 0 2 +Sc 0 3 +Ti 0 4 +V 0 4 5 +Cr 0 3 +Mn 0 2 3 4 +Fe 0 2 3 +Co 0 2 3 +Ni 0 2 +Cu 0 1 2 +Zn 0 2 +Ga 0 3 +Ge 0 4 +As -3 3 5 +Se -2 0 4 +Br -1 +Kr +Rb 1 +Sr 0 2 +Y 0 3 +Zr 0 4 +Nb 0 5 +Mo 0 6 +Tc +Ru 0 +Rh 0 +Pd 0 +Ag 1 +Cd 0 2 +In 0 3 +Sn 0 2 4 +Sb 0 3 5 +Te -2 0 4 +I -1 +Xe +Cs 1 +Ba 0 2 +La 0 3 +Ce 0 3 4 +Pr 0 3 +Nd 0 3 +Pm +Sm 0 3 +Eu 0 3 +Gd 0 3 +Tb 0 3 +Dy 0 3 +Ho 0 3 +Er 0 3 +Tm 0 +Yb 0 3 +Lu +Hf 0 +Ta 0 5 +W 6 +Re +Os +Ir +Pt 0 +Au 0 +Hg 2 +Tl 1 +Pb 2 +Bi 3 +Po +At +Rn +Fr +Ra +Ac +Th +Pa +U 0 6 +Np +Pu +Am +Cm +Bk +Cf +Es +Fm +Md +No +Lr From 387585410031dd99f16eb75daa48de69ca0fe361 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Thu, 15 Aug 2024 18:06:20 +0100 Subject: [PATCH 09/20] Update ICSD24OxStatesFilter --- smact/utils/oxidation.py | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/smact/utils/oxidation.py b/smact/utils/oxidation.py index b795e905..0018ce7e 100644 --- a/smact/utils/oxidation.py +++ b/smact/utils/oxidation.py @@ -1,18 +1,23 @@ """Utility functions for handling oxidation states.""" -import json import os from os import path import pandas as pd -# get correct path for datafiles when called from another directory -from smact import data_directory, data_loader, ordered_elements +from smact import data_directory, ordered_elements class ICSD24OxStatesFilter: - """Class to handle filtering the ICSD 24 oxidation states list.""" + """Class to handle filtering the ICSD 24 oxidation states list. + + The ICSD 24 oxidation states list is a list of oxidation states for each element in the ICSD 24 database. + + Attributes: + ox_states_df (pd.DataFrame): The ICSD 24 oxidation states list as a DataFrame. + """ def __init__(self): + """Initialise the ICSD 24 oxidation states list.""" self.ox_states_df = pd.read_json( path.join(data_directory, "oxidation_states_icsd24_counts.json") ) @@ -36,7 +41,9 @@ def filter(self, threshold: int, include_zero: bool = False): summary_df = ( filtered_df[(filtered_df["results_count"] > 0)] .groupby("element") - .apply(self._filter_oxidation_states, threshold) + .apply( + self._filter_oxidation_states, threshold, include_groups=False + ) .reset_index() ) summary_df.columns = ["element", "oxidation_state"] @@ -81,7 +88,9 @@ def write( f"#\n# Oxidation state set\n# Source: ICSD (2024), filtered for > {threshold} reports\n#\n" ) if comment: - f.write(f"# {comment}\n") + f.write(f"# {comment}\n#\n") + if include_zero: + f.write("# Includes oxidation state 0\n#\n") for line in final_summary: f.write(line + "\n") From bf7514554eee5f85e867214ed73911a4289c9a81 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Thu, 15 Aug 2024 18:06:37 +0100 Subject: [PATCH 10/20] Add tests for utils/oxidation --- smact/tests/test_utils.py | 48 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 smact/tests/test_utils.py diff --git a/smact/tests/test_utils.py b/smact/tests/test_utils.py new file mode 100644 index 00000000..b7612495 --- /dev/null +++ b/smact/tests/test_utils.py @@ -0,0 +1,48 @@ +import os +import unittest +from smact.utils.oxidation import ICSD24OxStatesFilter +import pandas as pd +files_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "files") +TEST_ICSD_OX_STATES = os.path.join(files_dir, "test_icsd_oxidation_states_filter_1000.txt") +TEST_ICSD_OX_STATES_W_ZERO = os.path.join(files_dir, "test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt") + +class OxidationStatesTest(unittest.TestCase): + def setUp(self): + self.ox_filter = ICSD24OxStatesFilter() + with open(TEST_ICSD_OX_STATES, "r") as f: + self.test_ox_states = f.read() + with open(TEST_ICSD_OX_STATES_W_ZERO, "r") as f: + self.test_ox_states_w_zero = f.read() + + + def test_oxidation_states_filter(self): + self.assertIsInstance(self.ox_filter.ox_states_df, pd.DataFrame) + threshold = 10 + filtered_df = self.ox_filter.filter(threshold) + + self.assertIsInstance(filtered_df, pd.DataFrame) + self.assertEqual(filtered_df.columns.tolist(), ["element", "oxidation_state"]) + #self.assertEqual(filtered_df.loc[""]) + + def test_oxidation_states_write(self): + ox_filter = ICSD24OxStatesFilter() + threshold = 1000 + filename = "test_ox_states" + filename_w_zero = "test_ox_states_w_zero" + comment = "Testing writing of ICSD 24 oxidation states list." + ox_filter.write(filename, threshold, comment=comment) + ox_filter.write(filename_w_zero, threshold, include_zero=True, comment=comment) + self.assertTrue(os.path.exists(f"{filename}.txt")) + assert ( + [line for line in open(f"{filename}.txt")] + == + [line for line in open(TEST_ICSD_OX_STATES)] + ) + self.assertTrue(os.path.exists(f"{filename}_w_zero.txt")) + assert ( + [line for line in open(f"{filename}_w_zero.txt")] + == + [line for line in open(TEST_ICSD_OX_STATES_W_ZERO)] + ) + + \ No newline at end of file From ef94fcb9defa317158edccaacf6024ceab273e54 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Wed, 21 Aug 2024 11:30:22 +0100 Subject: [PATCH 11/20] Run pre-commit --- smact/tests/test_utils.py | 49 +++++++++++++++++++++------------------ 1 file changed, 27 insertions(+), 22 deletions(-) diff --git a/smact/tests/test_utils.py b/smact/tests/test_utils.py index b7612495..03dee942 100644 --- a/smact/tests/test_utils.py +++ b/smact/tests/test_utils.py @@ -1,28 +1,37 @@ import os import unittest -from smact.utils.oxidation import ICSD24OxStatesFilter + import pandas as pd + +from smact.utils.oxidation import ICSD24OxStatesFilter + files_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "files") -TEST_ICSD_OX_STATES = os.path.join(files_dir, "test_icsd_oxidation_states_filter_1000.txt") -TEST_ICSD_OX_STATES_W_ZERO = os.path.join(files_dir, "test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt") +TEST_ICSD_OX_STATES = os.path.join( + files_dir, "test_icsd_oxidation_states_filter_1000.txt" +) +TEST_ICSD_OX_STATES_W_ZERO = os.path.join( + files_dir, "test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt" +) + class OxidationStatesTest(unittest.TestCase): def setUp(self): self.ox_filter = ICSD24OxStatesFilter() - with open(TEST_ICSD_OX_STATES, "r") as f: + with open(TEST_ICSD_OX_STATES) as f: self.test_ox_states = f.read() - with open(TEST_ICSD_OX_STATES_W_ZERO, "r") as f: + with open(TEST_ICSD_OX_STATES_W_ZERO) as f: self.test_ox_states_w_zero = f.read() - def test_oxidation_states_filter(self): self.assertIsInstance(self.ox_filter.ox_states_df, pd.DataFrame) threshold = 10 filtered_df = self.ox_filter.filter(threshold) - + self.assertIsInstance(filtered_df, pd.DataFrame) - self.assertEqual(filtered_df.columns.tolist(), ["element", "oxidation_state"]) - #self.assertEqual(filtered_df.loc[""]) + self.assertEqual( + filtered_df.columns.tolist(), ["element", "oxidation_state"] + ) + # self.assertEqual(filtered_df.loc[""]) def test_oxidation_states_write(self): ox_filter = ICSD24OxStatesFilter() @@ -31,18 +40,14 @@ def test_oxidation_states_write(self): filename_w_zero = "test_ox_states_w_zero" comment = "Testing writing of ICSD 24 oxidation states list." ox_filter.write(filename, threshold, comment=comment) - ox_filter.write(filename_w_zero, threshold, include_zero=True, comment=comment) - self.assertTrue(os.path.exists(f"{filename}.txt")) - assert ( - [line for line in open(f"{filename}.txt")] - == - [line for line in open(TEST_ICSD_OX_STATES)] + ox_filter.write( + filename_w_zero, threshold, include_zero=True, comment=comment ) + self.assertTrue(os.path.exists(f"{filename}.txt")) + assert [line for line in open(f"{filename}.txt")] == [ + line for line in open(TEST_ICSD_OX_STATES) + ] self.assertTrue(os.path.exists(f"{filename}_w_zero.txt")) - assert ( - [line for line in open(f"{filename}_w_zero.txt")] - == - [line for line in open(TEST_ICSD_OX_STATES_W_ZERO)] - ) - - \ No newline at end of file + assert [line for line in open(f"{filename}_w_zero.txt")] == [ + line for line in open(TEST_ICSD_OX_STATES_W_ZERO) + ] From 88e83aceb961131f311e308c74fec1ca864d1024 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Wed, 21 Aug 2024 11:30:37 +0100 Subject: [PATCH 12/20] Update filter --- smact/utils/oxidation.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/smact/utils/oxidation.py b/smact/utils/oxidation.py index 0018ce7e..707f7ffd 100644 --- a/smact/utils/oxidation.py +++ b/smact/utils/oxidation.py @@ -4,7 +4,7 @@ import pandas as pd -from smact import data_directory, ordered_elements +from smact import Element, data_directory, ordered_elements class ICSD24OxStatesFilter: @@ -47,6 +47,15 @@ def filter(self, threshold: int, include_zero: bool = False): .reset_index() ) summary_df.columns = ["element", "oxidation_state"] + # Sort the elements by atomic number + summary_df["atomic_number"] = summary_df["element"].apply( + lambda x: Element(x).number + ) + summary_df = ( + summary_df.sort_values("atomic_number") + .drop(columns="atomic_number") + .reset_index(drop=True) + ) return summary_df def write( From e580d58c27ff8443015da3b727646860f34f2be2 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Wed, 21 Aug 2024 13:59:19 +0100 Subject: [PATCH 13/20] Add method for creating species lists --- smact/utils/oxidation.py | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/smact/utils/oxidation.py b/smact/utils/oxidation.py index 707f7ffd..e4368b9f 100644 --- a/smact/utils/oxidation.py +++ b/smact/utils/oxidation.py @@ -5,6 +5,7 @@ import pandas as pd from smact import Element, data_directory, ordered_elements +from smact.structure_prediction.utilities import unparse_spec class ICSD24OxStatesFilter: @@ -58,6 +59,38 @@ def filter(self, threshold: int, include_zero: bool = False): ) return summary_df + def get_species_list( + self, + threshold: int, + include_zero: bool = False, + include_one_oxidation_state: bool = False, + ): + """Get the filtered ICSD 24 oxidation states list as a list of species. + + Args: + threshold (int): The threshold for filtering the oxidation states list. + include_zero (bool): Include oxidation state of zero in the filtered list. Default is False. + include_one_oxidation_state (bool): Include oxidation states +1 and -1 in the filtered list or include as + and - signs. Default is False. + + Returns: + list: The filtered oxidation states list as a list of species. + """ + filtered_df = self.filter(threshold, include_zero) + species_list = [] + for _, row in filtered_df.iterrows(): + ox_states = row["oxidation_state"].split(" ") + for ox_state in ox_states: + try: + species_list.append( + unparse_spec( + (row["element"], int(ox_state)), + include_one=include_one_oxidation_state, + ) + ) + except ValueError: + continue + return species_list + def write( self, filename: str | os.PathLike, From c1642ab12e49f2f8e94464e9d630a1e36ca5ebb9 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Wed, 21 Aug 2024 14:00:10 +0100 Subject: [PATCH 14/20] Add option to format species as 'X1+' or 'X+' --- smact/structure_prediction/utilities.py | 16 ++++++++++------ 1 file changed, 10 insertions(+), 6 deletions(-) diff --git a/smact/structure_prediction/utilities.py b/smact/structure_prediction/utilities.py index 6c265d79..92e650f7 100644 --- a/smact/structure_prediction/utilities.py +++ b/smact/structure_prediction/utilities.py @@ -1,9 +1,9 @@ """Miscellaneous tools for data parsing.""" import re -from typing import Dict, Optional, Tuple, Union +from typing import Tuple -import pymatgen +from pymatgen.core.structure import Structure from . import logger @@ -36,13 +36,14 @@ def parse_spec(species: str) -> Tuple[str, int]: return ele, charge -def unparse_spec(species: Tuple[str, int]) -> str: +def unparse_spec(species: Tuple[str, int], include_one: bool = True) -> str: """Unparse a species into a string representation. The analogue of :func:`parse_spec`. Args: - A tuple of (element, signed_charge). + species (tuple[str,int]): A tuple of (element, signed_charge). + include_one (bool): If True, include charge of 1 in the output if charge is 1 or -1. Returns: String of {element}{absolute_charge}{sign}. @@ -54,7 +55,10 @@ def unparse_spec(species: Tuple[str, int]) -> str: 'O2-' """ - return f"{species[0]}{abs(species[1])}{get_sign(species[1])}" + if include_one or abs(species[1]) != 1: + return f"{species[0]}{abs(species[1])}{get_sign(species[1])}" + else: + return f"{species[0]}{get_sign(species[1])}" def get_sign(charge: int) -> str: @@ -77,7 +81,7 @@ def get_sign(charge: int) -> str: def convert_next_gen_mprest_data( doc, -) -> Dict[str, Union[pymatgen.core.Structure, Optional[str]]]: +) -> dict[str, Structure | str | None]: """Converts the `MPDataDoc` object returned by a next-gen MP query to a dictionary Args: From 49e7568187167893359c4e419e858248d0108d23 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Wed, 21 Aug 2024 14:01:51 +0100 Subject: [PATCH 15/20] Add test for oxidation filter --- smact/tests/test_utils.py | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/smact/tests/test_utils.py b/smact/tests/test_utils.py index 03dee942..9465f40a 100644 --- a/smact/tests/test_utils.py +++ b/smact/tests/test_utils.py @@ -2,6 +2,7 @@ import unittest import pandas as pd +import pytest from smact.utils.oxidation import ICSD24OxStatesFilter @@ -34,13 +35,12 @@ def test_oxidation_states_filter(self): # self.assertEqual(filtered_df.loc[""]) def test_oxidation_states_write(self): - ox_filter = ICSD24OxStatesFilter() threshold = 1000 filename = "test_ox_states" filename_w_zero = "test_ox_states_w_zero" comment = "Testing writing of ICSD 24 oxidation states list." - ox_filter.write(filename, threshold, comment=comment) - ox_filter.write( + self.ox_filter.write(filename, threshold, comment=comment) + self.ox_filter.write( filename_w_zero, threshold, include_zero=True, comment=comment ) self.assertTrue(os.path.exists(f"{filename}.txt")) @@ -51,3 +51,12 @@ def test_oxidation_states_write(self): assert [line for line in open(f"{filename}_w_zero.txt")] == [ line for line in open(TEST_ICSD_OX_STATES_W_ZERO) ] + # Clean up + os.remove(f"{filename}.txt") + os.remove(f"{filename}_w_zero.txt") + + def test_oxidation_states_filter_species_list(self): + for threshold, length in [(0, 460), (5, 337), (50, 214)]: + species_list = self.ox_filter.get_species_list(threshold) + self.assertIsInstance(species_list, list) + self.assertEqual(len(species_list), length) From 41d7bbb45e416ee56cc14e5978a21203e06a4984 Mon Sep 17 00:00:00 2001 From: Aron Walsh Date: Sat, 24 Aug 2024 12:03:52 +0100 Subject: [PATCH 16/20] Fixed ICSD24 List Regenerated ICSD24 dataset on oxidation states. API had returned 0 values for some species, whilst the web version showed results. Overcome by restarting the session for each search. "oxidation_states_icsd24_filtered" is recommended as the default --- smact/data/oxidation_states_icsd24_common.txt | 23 +++++-------- .../data/oxidation_states_icsd24_counts.json | 2 +- .../data/oxidation_states_icsd24_filtered.txt | 31 ++++++++--------- smact/data/oxidation_states_icsd24_raw.txt | 33 ++++++++----------- 4 files changed, 37 insertions(+), 52 deletions(-) diff --git a/smact/data/oxidation_states_icsd24_common.txt b/smact/data/oxidation_states_icsd24_common.txt index ae0a8c6e..4c2f9097 100644 --- a/smact/data/oxidation_states_icsd24_common.txt +++ b/smact/data/oxidation_states_icsd24_common.txt @@ -1,6 +1,6 @@ # # Oxidation state set -# Source: ICSD (2024), most common non-zero values +# Source: ICSD (2024, V2), most common non-zero values # H 1 He @@ -45,7 +45,7 @@ Zr 4 Nb 5 Mo 6 Tc 7 -Ru 5 +Ru 4 Rh 3 Pd 2 Ag 1 @@ -76,7 +76,7 @@ Lu 3 Hf 4 Ta 5 W 6 -Re 3 +Re 7 Os 5 Ir 4 Pt 4 @@ -95,18 +95,13 @@ Th 4 Pa 5 U 6 Np 6 -Pu 5 -Am 1 -Cm 2 -Bk 2 -Cf -Es +Pu 3 +Am 3 +Cm 3 +Bk 3 +Cf 3 +Es 3 Fm Md No Lr -Rf -Db -Sg -Bh -Hs \ No newline at end of file diff --git a/smact/data/oxidation_states_icsd24_counts.json b/smact/data/oxidation_states_icsd24_counts.json index 1ae6b7a9..3ecb480d 100644 --- a/smact/data/oxidation_states_icsd24_counts.json +++ b/smact/data/oxidation_states_icsd24_counts.json @@ -1 +1 @@ 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\ No newline at end of file diff --git a/smact/data/oxidation_states_icsd24_filtered.txt b/smact/data/oxidation_states_icsd24_filtered.txt index 96dbd31f..0c6e6ff3 100644 --- a/smact/data/oxidation_states_icsd24_filtered.txt +++ b/smact/data/oxidation_states_icsd24_filtered.txt @@ -1,6 +1,6 @@ # # Oxidation state set -# Source: ICSD (2024), filtered for > 5 reports +# Source: ICSD (2024, V2), filtered for > 5 reports # H -1 1 He @@ -18,7 +18,7 @@ Al 3 Si -4 -3 -2 -1 2 3 4 P -3 -2 -1 1 2 3 4 5 S -2 -1 1 2 3 4 5 6 -Cl -1 1 3 +Cl -1 1 3 5 7 Ar K 1 Ca 2 @@ -42,8 +42,8 @@ Rb 1 Sr 2 4 Y 1 2 3 4 Zr 1 2 3 4 -Nb 1 2 3 5 6 -Mo -1 1 2 3 5 6 +Nb 1 2 3 4 5 6 +Mo -1 1 2 3 4 5 6 Tc 1 2 3 4 5 7 Ru 1 2 3 4 5 6 7 Rh -1 1 2 3 4 5 @@ -76,15 +76,15 @@ Lu 2 3 Hf 2 3 4 Ta 1 2 3 4 5 W 2 3 4 5 6 -Re 1 2 3 4 +Re 1 2 3 4 5 6 7 Os 1 2 3 4 5 6 7 8 Ir 1 2 3 4 5 6 Pt 2 3 4 5 -Au -1 1 2 5 -Hg 2 +Au -1 1 2 3 5 +Hg 1 2 Tl -1 1 2 3 Pb -4 -1 2 3 4 -Bi -2 -1 1 2 3 4 5 +Bi -3 -2 -1 1 2 3 4 5 Po 4 At Rn @@ -95,18 +95,13 @@ Th 2 3 4 Pa 4 5 U 2 3 4 5 6 Np 2 3 4 5 6 7 -Pu -Am -Cm -Bk -Cf +Pu 2 3 4 6 7 +Am 2 3 4 +Cm 3 +Bk 3 +Cf 3 Es Fm Md No Lr -Rf -Db -Sg -Bh -Hs \ No newline at end of file diff --git a/smact/data/oxidation_states_icsd24_raw.txt b/smact/data/oxidation_states_icsd24_raw.txt index 57d21803..bd9bddad 100644 --- a/smact/data/oxidation_states_icsd24_raw.txt +++ b/smact/data/oxidation_states_icsd24_raw.txt @@ -1,6 +1,6 @@ # # Oxidation state set -# Source: ICSD (2024) +# Source: ICSD (2024, V2) # H -1 1 2 3 He @@ -18,7 +18,7 @@ Al -3 1 2 3 Si -4 -3 -2 -1 1 2 3 4 P -4 -3 -2 -1 1 2 3 4 5 6 S -3 -2 -1 1 2 3 4 5 6 -Cl -4 -1 1 2 3 4 +Cl -4 -1 1 2 3 4 5 7 Ar K 1 Ca -1 1 2 @@ -42,8 +42,8 @@ Rb -1 1 2 Sr -2 2 4 Y 1 2 3 4 Zr 1 2 3 4 6 -Nb 1 2 3 5 6 -Mo -1 1 2 3 5 6 7 +Nb 1 2 3 4 5 6 +Mo -1 1 2 3 4 5 6 7 Tc 1 2 3 4 5 6 7 Ru -4 -3 -2 -1 1 2 3 4 5 6 7 8 Rh -1 1 2 3 4 5 6 @@ -76,15 +76,15 @@ Lu 2 3 4 Hf 1 2 3 4 Ta 1 2 3 4 5 6 7 W 1 2 3 4 5 6 7 -Re -1 1 2 3 4 +Re -1 1 2 3 4 5 6 7 Os 1 2 3 4 5 6 7 8 Ir -1 1 2 3 4 5 6 Pt -2 1 2 3 4 5 6 -Au -1 1 2 4 5 -Hg 2 4 +Au -1 1 2 3 4 5 +Hg 1 2 4 Tl -2 -1 1 2 3 5 Pb -4 -1 1 2 3 4 -Bi -2 -1 1 2 3 4 5 +Bi -3 -2 -1 1 2 3 4 5 Po -2 2 4 At Rn @@ -95,18 +95,13 @@ Th 2 3 4 5 6 Pa 2 3 4 5 U -3 1 2 3 4 5 6 Np -1 2 3 4 5 6 7 -Pu 5 -Am 1 -Cm 2 -Bk 2 -Cf -Es +Pu 2 3 4 5 6 7 +Am 1 2 3 4 5 6 +Cm 2 3 4 +Bk 2 3 4 +Cf 2 3 4 5 6 +Es 3 Fm Md No Lr -Rf -Db -Sg -Bh -Hs \ No newline at end of file From 13e6eb906c311d00bdcb4d990063ad0fcf25a0f2 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Fri, 30 Aug 2024 10:52:18 +0100 Subject: [PATCH 17/20] Add function for getting a dataframe of species occurrences --- smact/utils/oxidation.py | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/smact/utils/oxidation.py b/smact/utils/oxidation.py index e4368b9f..e2ed26c0 100644 --- a/smact/utils/oxidation.py +++ b/smact/utils/oxidation.py @@ -91,6 +91,36 @@ def get_species_list( continue return species_list + def get_species_occurrences_df( + self, + include_one_oxidation_state: bool = False, + ): + """Get the ICSD 24 oxidation states list as a dataframe of species with their occurrences. + + Args: + include_one_oxidation_state (bool): Include oxidation states +1 and -1 in the species or include as + and - signs. Default is False. + Returns: + dataframe: The species list as a dataframe of species with their occurrences. + """ + + species_occurrences_df = self.ox_states_df[ + (self.ox_states_df.results_count > 0) + & (self.ox_states_df.oxidation_state != 0) + ].reset_index(drop=True) + species_occurrences_df["species"] = species_occurrences_df.apply( + lambda x: unparse_spec( + (x["element"], x["oxidation_state"]), + include_one=include_one_oxidation_state, + ), + axis=1, + ) + species_occurrences_df = species_occurrences_df[ + ["species", "results_count"] + ] + return species_occurrences_df.sort_values( + "results_count", ascending=False + ).reset_index(drop=True) + def write( self, filename: str | os.PathLike, From b8982beb3224b8a7e88541ea91d2d03f53fa76d3 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Fri, 30 Aug 2024 10:52:34 +0100 Subject: [PATCH 18/20] Update tests and add test for getting occurences --- smact/tests/test_utils.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/smact/tests/test_utils.py b/smact/tests/test_utils.py index 9465f40a..1264005f 100644 --- a/smact/tests/test_utils.py +++ b/smact/tests/test_utils.py @@ -56,7 +56,20 @@ def test_oxidation_states_write(self): os.remove(f"{filename}_w_zero.txt") def test_oxidation_states_filter_species_list(self): - for threshold, length in [(0, 460), (5, 337), (50, 214)]: + for threshold, length in [(0, 490), (5, 358), (50, 227)]: species_list = self.ox_filter.get_species_list(threshold) self.assertIsInstance(species_list, list) self.assertEqual(len(species_list), length) + + def test_oxidation_states_filter_species_occurrences(self): + species_occurrences_df = self.ox_filter.get_species_occurrences_df() + self.assertIsInstance(species_occurrences_df, pd.DataFrame) + self.assertEqual( + species_occurrences_df.columns.tolist(), + ["species", "results_count"], + ) + self.assertEqual(species_occurrences_df.shape, (490, 2)) + self.assertEqual(species_occurrences_df.iloc[0]["species"], "O2-") + self.assertEqual( + species_occurrences_df.iloc[0]["results_count"], 116910 + ) From 9125edb6d9087270eb7e9fecfe778d0dff2e855f Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Fri, 30 Aug 2024 10:53:18 +0100 Subject: [PATCH 19/20] Update test files --- .../files/test_icsd_oxidation_states_filter_1000.txt | 4 ++-- ...csd_oxidation_states_filter_1000_w_0_ox_state.txt | 12 ++++++------ 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/smact/tests/files/test_icsd_oxidation_states_filter_1000.txt b/smact/tests/files/test_icsd_oxidation_states_filter_1000.txt index 1daa1ab9..57ebddab 100644 --- a/smact/tests/files/test_icsd_oxidation_states_filter_1000.txt +++ b/smact/tests/files/test_icsd_oxidation_states_filter_1000.txt @@ -7,7 +7,7 @@ H -1 1 He Li 1 -Be +Be 2 B 3 C -2 2 3 4 N -3 5 @@ -26,7 +26,7 @@ K 1 Ca 2 Sc 3 Ti 4 -V 4 5 +V 3 4 5 Cr 3 Mn 2 3 4 Fe 2 3 diff --git a/smact/tests/files/test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt b/smact/tests/files/test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt index ba6ea2b0..9f9dde80 100644 --- a/smact/tests/files/test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt +++ b/smact/tests/files/test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt @@ -9,7 +9,7 @@ H -1 0 1 He Li 0 1 -Be +Be 2 B 0 3 C -2 0 2 3 4 N -3 0 5 @@ -28,7 +28,7 @@ K 1 Ca 0 2 Sc 0 3 Ti 0 4 -V 0 4 5 +V 0 3 4 5 Cr 0 3 Mn 0 2 3 4 Fe 0 2 3 @@ -38,7 +38,7 @@ Cu 0 1 2 Zn 0 2 Ga 0 3 Ge 0 4 -As -3 3 5 +As -3 0 3 5 Se -2 0 4 Br -1 Kr @@ -52,7 +52,7 @@ Tc Ru 0 Rh 0 Pd 0 -Ag 1 +Ag 0 1 Cd 0 2 In 0 3 Sn 0 2 4 @@ -82,13 +82,13 @@ Ta 0 5 W 6 Re Os -Ir +Ir 0 Pt 0 Au 0 Hg 2 Tl 1 Pb 2 -Bi 3 +Bi 0 3 Po At Rn From 3c7328500d8847677222551fd2d935e14c6594d4 Mon Sep 17 00:00:00 2001 From: Anthony Onwuli Date: Wed, 20 Nov 2024 00:12:31 +0000 Subject: [PATCH 20/20] Run pre-commit --- paper.bib | 2 +- smact/__init__.py | 4 +- .../data/oxidation_states_icsd24_counts.json | 1857 ++++++++++++++++- smact/data_loader.py | 19 +- smact/structure_prediction/utilities.py | 6 +- smact/tests/test_utils.py | 35 +- smact/utils/oxidation.py | 53 +- 7 files changed, 1891 insertions(+), 85 deletions(-) diff --git a/paper.bib b/paper.bib index 1217ca54..925ab639 100644 --- a/paper.bib +++ b/paper.bib @@ -182,4 +182,4 @@ @article{ase-paper url={http://stacks.iop.org/0953-8984/29/i=27/a=273002}, year={2017}, abstract={The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple ‘for-loop’ construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.} -} \ No newline at end of file +} diff --git a/smact/__init__.py b/smact/__init__.py index fa662484..7a8d22f8 100644 --- a/smact/__init__.py +++ b/smact/__init__.py @@ -4,7 +4,6 @@ A collection of fast screening tools from elemental data """ - from __future__ import annotations import itertools @@ -12,7 +11,6 @@ from math import gcd from operator import mul as multiply from os import path - from typing import TYPE_CHECKING import pandas as pd @@ -74,7 +72,7 @@ class Element: Element.oxidation_states_icsd24 (list): List of oxidation states that appear in the 2024 version of the ICSD - Element.coord_envs (list): The allowed coordination enviroments for the ion + Element.coord_envs (list): The allowed coordination environments for the ion Element.covalent_radius (float) : Covalent radius of the element diff --git a/smact/data/oxidation_states_icsd24_counts.json b/smact/data/oxidation_states_icsd24_counts.json index 3ecb480d..38f21786 100644 --- a/smact/data/oxidation_states_icsd24_counts.json +++ b/smact/data/oxidation_states_icsd24_counts.json @@ -1 +1,1856 @@ 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"results_count": 0 }, + { "element": "Cm", "oxidation_state": -1, "results_count": 0 }, + { "element": "Cm", "oxidation_state": 0, "results_count": 39 }, + { "element": "Cm", "oxidation_state": 1, "results_count": 0 }, + { "element": "Cm", "oxidation_state": 2, "results_count": 1 }, + { "element": "Cm", "oxidation_state": 3, "results_count": 33 }, + { "element": "Cm", "oxidation_state": 4, "results_count": 5 }, + { "element": "Cm", "oxidation_state": 5, "results_count": 0 }, + { "element": "Cm", "oxidation_state": 6, "results_count": 0 }, + { "element": "Cm", "oxidation_state": 7, "results_count": 0 }, + { "element": "Cm", "oxidation_state": 8, "results_count": 0 }, + { "element": "Bk", "oxidation_state": -9, "results_count": 0 }, + { "element": "Bk", "oxidation_state": -8, "results_count": 0 }, + { "element": "Bk", "oxidation_state": -7, "results_count": 0 }, + { "element": "Bk", "oxidation_state": -6, "results_count": 0 }, + { "element": "Bk", "oxidation_state": -5, "results_count": 0 }, + { "element": "Bk", "oxidation_state": -4, "results_count": 0 }, + { "element": "Bk", "oxidation_state": -3, "results_count": 0 }, + { "element": "Bk", "oxidation_state": -2, "results_count": 0 }, + { "element": "Bk", "oxidation_state": -1, "results_count": 0 }, + { "element": "Bk", "oxidation_state": 0, "results_count": 16 }, + { "element": "Bk", "oxidation_state": 1, "results_count": 0 }, + { "element": "Bk", "oxidation_state": 2, "results_count": 1 }, + { "element": "Bk", "oxidation_state": 3, "results_count": 10 }, + { "element": "Bk", "oxidation_state": 4, "results_count": 4 }, + { "element": "Bk", "oxidation_state": 5, "results_count": 0 }, + { "element": "Bk", "oxidation_state": 6, "results_count": 0 }, + { "element": "Bk", "oxidation_state": 7, "results_count": 0 }, + { "element": "Bk", "oxidation_state": 8, "results_count": 0 }, + { "element": "Cf", "oxidation_state": -9, "results_count": 0 }, + { "element": "Cf", "oxidation_state": -8, "results_count": 0 }, + { "element": "Cf", "oxidation_state": -7, "results_count": 0 }, + { "element": "Cf", "oxidation_state": -6, "results_count": 0 }, + { "element": "Cf", "oxidation_state": -5, "results_count": 0 }, + { "element": "Cf", "oxidation_state": -4, "results_count": 0 }, + { "element": "Cf", "oxidation_state": -3, "results_count": 0 }, + { "element": "Cf", "oxidation_state": -2, "results_count": 0 }, + { "element": "Cf", "oxidation_state": -1, "results_count": 0 }, + { "element": "Cf", "oxidation_state": 0, "results_count": 12 }, + { "element": "Cf", "oxidation_state": 1, "results_count": 0 }, + { "element": "Cf", "oxidation_state": 2, "results_count": 1 }, + { "element": "Cf", "oxidation_state": 3, "results_count": 17 }, + { "element": "Cf", "oxidation_state": 4, "results_count": 1 }, + { "element": "Cf", "oxidation_state": 5, "results_count": 1 }, + { "element": "Cf", "oxidation_state": 6, "results_count": 1 }, + { "element": "Cf", "oxidation_state": 7, "results_count": 0 }, + { "element": "Cf", "oxidation_state": 8, "results_count": 0 }, + { "element": "Es", "oxidation_state": -9, "results_count": 0 }, + { "element": "Es", "oxidation_state": -8, "results_count": 0 }, + { "element": "Es", "oxidation_state": -7, "results_count": 0 }, + { "element": "Es", "oxidation_state": -6, "results_count": 0 }, + { "element": "Es", "oxidation_state": -5, "results_count": 0 }, + { "element": "Es", "oxidation_state": -4, "results_count": 0 }, + { "element": "Es", "oxidation_state": -3, "results_count": 0 }, + { "element": "Es", "oxidation_state": -2, "results_count": 0 }, + { "element": "Es", "oxidation_state": -1, "results_count": 0 }, + { "element": "Es", "oxidation_state": 0, "results_count": 0 }, + { "element": "Es", "oxidation_state": 1, "results_count": 0 }, + { "element": "Es", "oxidation_state": 2, "results_count": 0 }, + { "element": "Es", "oxidation_state": 3, "results_count": 3 }, + { "element": "Es", "oxidation_state": 4, "results_count": 0 }, + { "element": "Es", "oxidation_state": 5, "results_count": 0 }, + { "element": "Es", "oxidation_state": 6, "results_count": 0 }, + { "element": "Es", "oxidation_state": 7, "results_count": 0 }, + { "element": "Es", "oxidation_state": 8, "results_count": 0 }, + { "element": "Fm", "oxidation_state": -9, "results_count": 0 }, + { "element": "Fm", "oxidation_state": -8, "results_count": 0 }, + { "element": "Fm", "oxidation_state": -7, "results_count": 0 }, + { "element": "Fm", "oxidation_state": -6, "results_count": 0 }, + { "element": "Fm", "oxidation_state": -5, "results_count": 0 }, + { "element": "Fm", "oxidation_state": -4, "results_count": 0 }, + { "element": "Fm", "oxidation_state": -3, "results_count": 0 }, + { "element": "Fm", "oxidation_state": -2, "results_count": 0 }, + { "element": "Fm", "oxidation_state": -1, "results_count": 0 }, + { "element": "Fm", "oxidation_state": 0, "results_count": 0 }, + { "element": "Fm", "oxidation_state": 1, "results_count": 0 }, + { "element": "Fm", "oxidation_state": 2, "results_count": 0 }, + { "element": "Fm", "oxidation_state": 3, "results_count": 0 }, + { "element": "Fm", "oxidation_state": 4, "results_count": 0 }, + { "element": "Fm", "oxidation_state": 5, "results_count": 0 }, + { "element": "Fm", "oxidation_state": 6, "results_count": 0 }, + { "element": "Fm", "oxidation_state": 7, "results_count": 0 }, + { "element": "Fm", "oxidation_state": 8, "results_count": 0 }, + { "element": "Md", "oxidation_state": -9, "results_count": 0 }, + { "element": "Md", "oxidation_state": -8, "results_count": 0 }, + { "element": "Md", "oxidation_state": -7, "results_count": 0 }, + { "element": "Md", "oxidation_state": -6, "results_count": 0 }, + { "element": "Md", "oxidation_state": -5, "results_count": 0 }, + { "element": "Md", "oxidation_state": -4, "results_count": 0 }, + { "element": "Md", "oxidation_state": -3, "results_count": 0 }, + { "element": "Md", "oxidation_state": -2, "results_count": 0 }, + { "element": "Md", "oxidation_state": -1, "results_count": 0 }, + { "element": "Md", "oxidation_state": 0, "results_count": 0 }, + { "element": "Md", "oxidation_state": 1, "results_count": 0 }, + { "element": "Md", "oxidation_state": 2, "results_count": 0 }, + { "element": "Md", "oxidation_state": 3, "results_count": 0 }, + { "element": "Md", "oxidation_state": 4, "results_count": 0 }, + { "element": "Md", "oxidation_state": 5, "results_count": 0 }, + { "element": "Md", "oxidation_state": 6, "results_count": 0 }, + { "element": "Md", "oxidation_state": 7, "results_count": 0 }, + { "element": "Md", "oxidation_state": 8, "results_count": 0 }, + { "element": "No", "oxidation_state": -9, "results_count": 0 }, + { "element": "No", "oxidation_state": -8, "results_count": 0 }, + { "element": "No", "oxidation_state": -7, "results_count": 0 }, + { "element": "No", "oxidation_state": -6, "results_count": 0 }, + { "element": "No", "oxidation_state": -5, "results_count": 0 }, + { "element": "No", "oxidation_state": -4, "results_count": 0 }, + { "element": "No", "oxidation_state": -3, "results_count": 0 }, + { "element": "No", "oxidation_state": -2, "results_count": 0 }, + { "element": "No", "oxidation_state": -1, "results_count": 0 }, + { "element": "No", "oxidation_state": 0, "results_count": 0 }, + { "element": "No", "oxidation_state": 1, "results_count": 0 }, + { "element": "No", "oxidation_state": 2, "results_count": 0 }, + { "element": "No", "oxidation_state": 3, "results_count": 0 }, + { "element": "No", "oxidation_state": 4, "results_count": 0 }, + { "element": "No", "oxidation_state": 5, "results_count": 0 }, + { "element": "No", "oxidation_state": 6, "results_count": 0 }, + { "element": "No", "oxidation_state": 7, "results_count": 0 }, + { "element": "No", "oxidation_state": 8, "results_count": 0 }, + { "element": "Lr", "oxidation_state": -9, "results_count": 0 }, + { "element": "Lr", "oxidation_state": -8, "results_count": 0 }, + { "element": "Lr", "oxidation_state": -7, "results_count": 0 }, + { "element": "Lr", "oxidation_state": -6, "results_count": 0 }, + { "element": "Lr", "oxidation_state": -5, "results_count": 0 }, + { "element": "Lr", "oxidation_state": -4, "results_count": 0 }, + { "element": "Lr", "oxidation_state": -3, "results_count": 0 }, + { "element": "Lr", "oxidation_state": -2, "results_count": 0 }, + { "element": "Lr", "oxidation_state": -1, "results_count": 0 }, + { "element": "Lr", "oxidation_state": 0, "results_count": 0 }, + { "element": "Lr", "oxidation_state": 1, "results_count": 0 }, + { "element": "Lr", "oxidation_state": 2, "results_count": 0 }, + { "element": "Lr", "oxidation_state": 3, "results_count": 0 }, + { "element": "Lr", "oxidation_state": 4, "results_count": 0 }, + { "element": "Lr", "oxidation_state": 5, "results_count": 0 }, + { "element": "Lr", "oxidation_state": 6, "results_count": 0 }, + { "element": "Lr", "oxidation_state": 7, "results_count": 0 }, + { "element": "Lr", "oxidation_state": 8, "results_count": 0 } +] diff --git a/smact/data_loader.py b/smact/data_loader.py index 81c633f5..f69e4c94 100644 --- a/smact/data_loader.py +++ b/smact/data_loader.py @@ -320,18 +320,13 @@ def lookup_element_oxidation_states_icsd24(symbol, copy=True): Returns None if oxidation states for the Element were not found in the external data. """ - global _el_ox_states_icsd24 if _el_ox_states_icsd24 is None: _el_ox_states_icsd24 = {} - for items in _get_data_rows( - os.path.join(data_directory, "oxidation_states_icsd24_filtered.txt") - ): - _el_ox_states_icsd24[items[0]] = [ - int(oxidationState) for oxidationState in items[1:] - ] + for items in _get_data_rows(os.path.join(data_directory, "oxidation_states_icsd24_filtered.txt")): + _el_ox_states_icsd24[items[0]] = [int(oxidationState) for oxidationState in items[1:]] if symbol in _el_ox_states_icsd24: if copy: @@ -339,18 +334,12 @@ def lookup_element_oxidation_states_icsd24(symbol, copy=True): # deep copy. The elements of the lists are integers, which are # "value types" in Python. - return [ - oxidationState - for oxidationState in _el_ox_states_icsd24[symbol] - ] + return list(_el_ox_states_icsd24[symbol]) else: return _el_ox_states_icsd24[symbol] else: if _print_warnings: - print( - "WARNING: Oxidation states for element {} " - "not found.".format(symbol) - ) + print(f"WARNING: Oxidation states for element {symbol} " "not found.") return None diff --git a/smact/structure_prediction/utilities.py b/smact/structure_prediction/utilities.py index 46949fee..006cb611 100644 --- a/smact/structure_prediction/utilities.py +++ b/smact/structure_prediction/utilities.py @@ -1,8 +1,5 @@ """Miscellaneous tools for data parsing.""" - - -from pymatgen.core.structure import Structure from __future__ import annotations import re @@ -11,7 +8,7 @@ from . import logger if TYPE_CHECKING: - import pymatgen + from pymatgen.core.structure import Structure def parse_spec(species: str) -> tuple[str, int]: @@ -53,7 +50,6 @@ def unparse_spec(species: tuple[str, int], include_one: bool = True) -> str: The analogue of :func:`parse_spec`. Args: - species (tuple[str,int]): A tuple of (element, signed_charge). include_one (bool): If True, include charge of 1 in the output if charge is 1 or -1. diff --git a/smact/tests/test_utils.py b/smact/tests/test_utils.py index 70e83a91..c54a9081 100644 --- a/smact/tests/test_utils.py +++ b/smact/tests/test_utils.py @@ -1,15 +1,16 @@ - from __future__ import annotations import os import unittest +import pandas as pd from pymatgen.core import Composition from smact import Element from smact.screening import smact_filter from smact.utils.composition import comp_maker, formula_maker, parse_formula from smact.utils.crystal_space import generate_composition_with_smact +from smact.utils.oxidation import ICSD24OxStatesFilter class TestComposition(unittest.TestCase): @@ -94,15 +95,10 @@ def test_convert_formula(self): def test_download_compounds_with_mp_api(self): pass -from smact.utils.oxidation import ICSD24OxStatesFilter files_dir = os.path.join(os.path.dirname(os.path.realpath(__file__)), "files") -TEST_ICSD_OX_STATES = os.path.join( - files_dir, "test_icsd_oxidation_states_filter_1000.txt" -) -TEST_ICSD_OX_STATES_W_ZERO = os.path.join( - files_dir, "test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt" -) +TEST_ICSD_OX_STATES = os.path.join(files_dir, "test_icsd_oxidation_states_filter_1000.txt") +TEST_ICSD_OX_STATES_W_ZERO = os.path.join(files_dir, "test_icsd_oxidation_states_filter_1000_w_0_ox_state.txt") class OxidationStatesTest(unittest.TestCase): @@ -119,9 +115,7 @@ def test_oxidation_states_filter(self): filtered_df = self.ox_filter.filter(threshold) self.assertIsInstance(filtered_df, pd.DataFrame) - self.assertEqual( - filtered_df.columns.tolist(), ["element", "oxidation_state"] - ) + self.assertEqual(filtered_df.columns.tolist(), ["element", "oxidation_state"]) # self.assertEqual(filtered_df.loc[""]) def test_oxidation_states_write(self): @@ -130,17 +124,14 @@ def test_oxidation_states_write(self): filename_w_zero = "test_ox_states_w_zero" comment = "Testing writing of ICSD 24 oxidation states list." self.ox_filter.write(filename, threshold, comment=comment) - self.ox_filter.write( - filename_w_zero, threshold, include_zero=True, comment=comment - ) + self.ox_filter.write(filename_w_zero, threshold, include_zero=True, comment=comment) self.assertTrue(os.path.exists(f"{filename}.txt")) - assert [line for line in open(f"{filename}.txt")] == [ - line for line in open(TEST_ICSD_OX_STATES) - ] + with open(f"{filename}.txt") as f: + self.assertEqual(f.read(), self.test_ox_states) + self.assertTrue(os.path.exists(f"{filename}_w_zero.txt")) - assert [line for line in open(f"{filename}_w_zero.txt")] == [ - line for line in open(TEST_ICSD_OX_STATES_W_ZERO) - ] + with open(f"{filename}_w_zero.txt") as f: + self.assertEqual(f.read(), self.test_ox_states_w_zero) # Clean up os.remove(f"{filename}.txt") os.remove(f"{filename}_w_zero.txt") @@ -160,6 +151,4 @@ def test_oxidation_states_filter_species_occurrences(self): ) self.assertEqual(species_occurrences_df.shape, (490, 2)) self.assertEqual(species_occurrences_df.iloc[0]["species"], "O2-") - self.assertEqual( - species_occurrences_df.iloc[0]["results_count"], 116910 - ) + self.assertEqual(species_occurrences_df.iloc[0]["results_count"], 116910) diff --git a/smact/utils/oxidation.py b/smact/utils/oxidation.py index e2ed26c0..09d28588 100644 --- a/smact/utils/oxidation.py +++ b/smact/utils/oxidation.py @@ -1,4 +1,7 @@ """Utility functions for handling oxidation states.""" + +from __future__ import annotations + import os from os import path @@ -19,9 +22,7 @@ class ICSD24OxStatesFilter: def __init__(self): """Initialise the ICSD 24 oxidation states list.""" - self.ox_states_df = pd.read_json( - path.join(data_directory, "oxidation_states_icsd24_counts.json") - ) + self.ox_states_df = pd.read_json(path.join(data_directory, "oxidation_states_icsd24_counts.json")) def filter(self, threshold: int, include_zero: bool = False): """Filter the ICSD 24 oxidation states list by a threshold. @@ -34,30 +35,19 @@ def filter(self, threshold: int, include_zero: bool = False): pd.DataFrame: The filtered oxidation states list as a DataFrame. """ if not include_zero: - filtered_df = self.ox_states_df[ - self.ox_states_df["oxidation_state"] != 0 - ].reset_index(drop=True) + filtered_df = self.ox_states_df[self.ox_states_df["oxidation_state"] != 0].reset_index(drop=True) else: filtered_df = self.ox_states_df summary_df = ( filtered_df[(filtered_df["results_count"] > 0)] .groupby("element") - .apply( - self._filter_oxidation_states, threshold, include_groups=False - ) + .apply(self._filter_oxidation_states, threshold, include_groups=False) .reset_index() ) summary_df.columns = ["element", "oxidation_state"] # Sort the elements by atomic number - summary_df["atomic_number"] = summary_df["element"].apply( - lambda x: Element(x).number - ) - summary_df = ( - summary_df.sort_values("atomic_number") - .drop(columns="atomic_number") - .reset_index(drop=True) - ) - return summary_df + summary_df["atomic_number"] = summary_df["element"].apply(lambda x: Element(x).number) + return summary_df.sort_values("atomic_number").drop(columns="atomic_number").reset_index(drop=True) def get_species_list( self, @@ -99,13 +89,12 @@ def get_species_occurrences_df( Args: include_one_oxidation_state (bool): Include oxidation states +1 and -1 in the species or include as + and - signs. Default is False. + Returns: dataframe: The species list as a dataframe of species with their occurrences. """ - species_occurrences_df = self.ox_states_df[ - (self.ox_states_df.results_count > 0) - & (self.ox_states_df.oxidation_state != 0) + (self.ox_states_df.results_count > 0) & (self.ox_states_df.oxidation_state != 0) ].reset_index(drop=True) species_occurrences_df["species"] = species_occurrences_df.apply( lambda x: unparse_spec( @@ -114,19 +103,15 @@ def get_species_occurrences_df( ), axis=1, ) - species_occurrences_df = species_occurrences_df[ - ["species", "results_count"] - ] - return species_occurrences_df.sort_values( - "results_count", ascending=False - ).reset_index(drop=True) + species_occurrences_df = species_occurrences_df[["species", "results_count"]] + return species_occurrences_df.sort_values("results_count", ascending=False).reset_index(drop=True) def write( self, filename: str | os.PathLike, threshold: int, include_zero: bool = False, - comment: str = None, + comment: str | None = None, ): """Write the filtered ICSD 24 oxidation states list to a SMACT-compatible oxidation states txt file. @@ -138,9 +123,7 @@ def write( """ filtered_df = self.filter(threshold, include_zero) # Convert the DataFrame to the require format - summary_dict = filtered_df.set_index("element")[ - "oxidation_state" - ].to_dict() + summary_dict = filtered_df.set_index("element")["oxidation_state"].to_dict() all_elements = ordered_elements(1, 103) final_summary = [] @@ -156,9 +139,7 @@ def write( if not filename.endswith(".txt"): filename += ".txt" with open(filename, "w") as f: - f.write( - f"#\n# Oxidation state set\n# Source: ICSD (2024), filtered for > {threshold} reports\n#\n" - ) + f.write(f"#\n# Oxidation state set\n# Source: ICSD (2024), filtered for > {threshold} reports\n#\n") if comment: f.write(f"# {comment}\n#\n") if include_zero: @@ -166,9 +147,7 @@ def write( for line in final_summary: f.write(line + "\n") - def _filter_oxidation_states( - self, group: pd.DataFrame.groupby, threshold: int - ): + def _filter_oxidation_states(self, group: pd.DataFrame.groupby, threshold: int): """Filter the oxidation states list by a threshold.""" filtered_states = group[group["results_count"] > threshold]