JDFTXInfile Comparison Methods
#4416
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…arameters for JDFTx, unwritten `is_comparable_to` method for `JDFTXInfile`
…s format option for `MultiformatTag`s
…e set as a list with elements of different format options, changing `JDFTXStructure.get_str` to build a dictionary representation of each ion instead of a list (not sure how it was even working before)
…ity handler, and now `_is_equal_to` to the abstractmethod to be implemented which compares two non-list values
…e objects, along convenience arguments to filter which tags to pay attention to. Not sure if `is_comparable_to` is implementable in a way generalizable enough to be useful.
…y in implementations
… `JDFTXInfile.from_structure`
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Summary
Major changes:
feature 1: Convenience methods for comparing
JDFTXInfileobjects--
JDFTXInfile.is_comparable_to--- Returns True if at least one tag is found different
--- Optional arguments
exclude_tags,exclude_tag_categories,ensure_include_tagsto ignore certain tags in the comparison----
exclude_tag_categoriesdefaults to["export", "restart", "structure"]as"export"and"restart"are very rarely pertinent to comparability,"structure"as subtags of this category are generally the one thing being intentionally changed in comparisons (ie different local minima or a slab with/without an adsorbate)--
JDFTXInfile.get_filtered_differing_tags--- What is used in
JDFTXInfile.is_comparable_toto get filtered differing tags betweenJDFTXInfileobjects--- Convenient as a "verbose" alternative to
JDFTXInfile.is_comparable_to--
AbstractTag.is_equal_toandAbstractTag._is_equal_to--- Used in tag comparison for finding differing tags
---
AbstractTag._is_equal_tois an abstract method that must be implemented for eachAbstractTaginheritorfeature 2: Default
JDFTXInfileobjectpymatgen.io.jdftx.inputs.ref_infile-- Initialized from reading default JDFTx settings from
pymatgen.io.jdftx.jdftxinfile_default_inputs.default_inputs: dict-- Used in
JDFTXInfile.get_differing_tags_fromfor tags inselfmissing fromotherthat are identical to the default settingfix 1: Re-ordered contents of
JDFTXInfileto follow the order: magic methods -> class methods / transformation methods -> validation methods -> properties -> private methodsfix 2: Checking for
'selective_dynamics'insite_propertiesfor aStructurepassed inJDFTXInfile.from_structure(used ifselective_dynamicsargument left asNone)Todos
TagContainers to their default values-- The current implementation of comparison for tags to default values only works if the tag as written exactly matches the full default value - at the very least the missing subtags of a partially filled
TagContainerneeds to be filled with the default values before comparing to the full default value-- Some subtags also change depending on the other subtags present for a particular tag (ie convergence threshold depending on algorithm specified for
'fluid-minimize', so an improved mapping for dynamic default values needs to be implemented