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Symmetry operation specifications in Jones faithful notation (defined by PCRE) #464

Merged
merged 110 commits into from
Dec 19, 2023
Merged

Symmetry operation specifications in Jones faithful notation (defined by PCRE) #464

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aad366e
Patching the Java source and target versions to '1.7' so that OPTIMADE
Oct 21, 2022
5b01bb1
Starting grammar of symmetry operators.
Oct 21, 2022
96d8872
Merge github.com:Materials-Consortia/OPTIMADE into develop
sauliusg Jun 5, 2023
5771aa2
Describing symmetry operation syntax using PCRE.
sauliusg Jun 6, 2023
712484a
Simplifying a comment.
sauliusg Jun 6, 2023
76ec076
Rearranging the symop PCRE code to be consistent with other definitions.
sauliusg Jun 6, 2023
101843f
Correcting a header.
sauliusg Jun 6, 2023
9df28e9
Correcting the PCRE language designator.
sauliusg Jun 6, 2023
21d8fa5
Correcting the second faulty PCRE language designator.
sauliusg Jun 6, 2023
7ad872c
Correcting PCRE syntax for symops.
sauliusg Jun 6, 2023
9a75f6a
Adding a test for the symmetry operator PCER.
sauliusg Jun 6, 2023
5601d3b
Switching back to the default RE delimiters.
sauliusg Jun 6, 2023
65f15b2
Adding another test for symop strings, to get those strings that do not
sauliusg Jun 6, 2023
54a41c7
Contracting all duplicated symop regexps into Perl variables to ensure
sauliusg Jun 6, 2023
2627864
Describing the 'space_group_symmetry_operation_xyz' property.
Jun 18, 2023
9a8ec03
Checking and correcting spelling.
Jun 18, 2023
8022a25
Merge github.com:Materials-Consortia/OPTIMADE into develop
Jun 18, 2023
9be9e64
The currently installed hooks have a very unclear error message, but
Jun 18, 2023
79e6388
Crosss-referencing the appendix.
Jun 18, 2023
160acd9
Removing extra space.
Jun 18, 2023
0dc89fb
Removing another significant space.
Jun 18, 2023
1342f5d
Giving all designators for the 'C 2' group.
Jun 18, 2023
256df5f
Adding the :val: typesetting marks.
Jun 18, 2023
50dff96
Fixing spelling.
Jun 18, 2023
8efee4c
Adding an article.
Jun 18, 2023
ad3bcc9
Adding comma in the bibliography entry.
Jun 18, 2023
cf8215f
Changing quote characters.
Jun 18, 2023
655dd4a
Adding an ISBN link to the cited book.
Jun 18, 2023
034a4b6
Removing extra comma.
Jun 18, 2023
22b2a0d
Correcting the '-z' typesetting.
Jun 18, 2023
891e645
Changing the description of the general position coordinates.
Jun 18, 2023
aeea992
Correcting th esymmetry operator description.
Jun 18, 2023
1edd738
Correcting a word (s/code/core/).
Jun 18, 2023
0247682
Typesetting a property name as in other places.
Jun 18, 2023
1458f9b
Corrected wording in the 'symop' string descriptions.
Jun 18, 2023
33677d1
Explaining the REs for symmetry operation strings.
Jun 18, 2023
b3041ef
Changing a file example designator from :file: to :code:.
Jun 18, 2023
e33eafd
Adding tests for those symmetry operation strings that are used as ex…
Jun 18, 2023
88bd87b
Correcting comments in the symop test cases.
Jun 18, 2023
7a88ff6
Spelling fix, thanks to Antanas.
sauliusg Jun 19, 2023
d657f6d
Changed the wording at the suggestion of Antanas V.
sauliusg Jun 19, 2023
8ee6879
Fixing the B&C 1972 reference.
sauliusg Jun 19, 2023
778b54b
Adding spaces to the bibliography reference.
sauliusg Jun 19, 2023
c4cbeae
Adding description of the Hermann-Mauguin symbol property.
sauliusg Jun 19, 2023
c777905
Adding reference to the ITC Vol. A, Table 4.3.2.1.
sauliusg Jun 21, 2023
e10e3cb
Fixing the underline.
Jun 22, 2023
3e2bd43
Adding spacing for more readability.
Jun 22, 2023
3a53786
Adding full citations of the Hall symbol papers and the IUCr ITC vols A
Jun 22, 2023
d233718
Adding two more Hall symbol examples from the COD entries 1001841 and
Jun 22, 2023
985de34
Describing extended H-M symbols. Commenting examples of the extended H-M
Jun 22, 2023
58e7630
Adding component 'symbol_' to the space group symbol property names.
Jun 22, 2023
9349661
Correcting the bibliographic reference section names. Adding reference
Jun 22, 2023
27d2fff
Forbiding space group summetry operations for non-periodic structures.
Jun 22, 2023
095f62c
Using different term to refer to long versions of the H-M symbols.
Jun 22, 2023
1e61b57
Fixing spelling.
Jun 22, 2023
075f46e
Specifying conventions for encoding H-M symbols as computer strings.
Jun 22, 2023
6a542ce
Specifying the designation of the screw axes (subscript indices).
Jun 22, 2023
abfc5b2
Clarifying the minus sign position.
Jun 22, 2023
dd070ff
Checking and fixing the spelling. Removing strings from ~/.words.lst
Jun 22, 2023
be8c17a
Changing the 'check_spelling.sh' script so that it does not mask STDERR
Jun 22, 2023
a8cd0f1
Addng a newly generated '.words.lst' list.
Jun 22, 2023
3f9340b
For now, removing trailing white space from .words.lst.
Jun 22, 2023
b686fb2
Excluding ".words.lst" from the trailing space check.
Jun 22, 2023
5c6f83d
Merge branch 'develop' of github.com:Materials-Consortia/OPTIMADE int…
Jun 22, 2023
0a3dbdc
Makging formulations uniform.
Jun 22, 2023
5495195
Indded, we should consistently use "operations" (thanks A.V.!)
sauliusg Jun 22, 2023
ac6d613
ACK, we should consistenly use "operations" as a term.
sauliusg Jun 22, 2023
ede9df5
Consistently using "operations" as a term.
sauliusg Jun 22, 2023
58f0afd
Grammar fix (thx, A.V.)
sauliusg Jun 22, 2023
8bd50b9
Rewording the text after an A.V. remark. The term "short symbol" is used
Jun 22, 2023
3cc525c
Accepting the spelling fixes (thanks, A.V.)
sauliusg Jun 22, 2023
76a7121
Correcting definitions of the H-M symbols (short and extended).
Jun 22, 2023
74397e3
Merge branch 'develop' of github.com:sauliusg/OPTIMADE into develop
Jun 22, 2023
5bf227e
Probably OK...
sauliusg Jun 22, 2023
18dd8a2
Fixing the description of the extended H-M symbol.
Jun 22, 2023
8d93ad4
Checking and correcting spelling
Jun 22, 2023
f796eb9
Removing the spurious character.
Jun 22, 2023
1b5c213
Correcting the 'space\_group\_symbol\_Hermann_Mauguin...' propery names.
Jun 22, 2023
61583a4
Fixing the 'null' value typesetting.
Jun 22, 2023
9501310
Probablu OK...
sauliusg Jun 22, 2023
d0c8790
Agree, specifying as an example indeed looks nicer :)
sauliusg Jun 22, 2023
aec9fb8
Accepting unification.
sauliusg Jun 22, 2023
dadbc7a
Extend the title underline.
sauliusg Jun 22, 2023
7a33510
Noting that the symmetry operations are a 'set' (in math sense).
sauliusg Jun 22, 2023
5d4eb87
Merge branch 'develop' into develop
ml-evs Jun 22, 2023
08ffe09
Accepting the fix from a native English speaker :).
sauliusg Jun 30, 2023
075f8e6
Changing the wording of the ITC number description.
Jun 30, 2023
96b6f9b
Accepting the comma suggestion.
sauliusg Jun 30, 2023
94a148c
Accepting the comma.
sauliusg Jun 30, 2023
3c405b3
Adding spaces in front of the eample text.
Jun 30, 2023
5b7cc23
Merge branch 'develop' of github.com:sauliusg/OPTIMADE into develop
Jun 30, 2023
8e4c65e
Update optimade.rst
sauliusg Jun 30, 2023
68be043
Apppending spaces to bibliography list
sauliusg Jun 30, 2023
071610c
Indenting all bibliographic references for consistency.
Jun 30, 2023
1c898c6
Update optimade.rst
sauliusg Jul 3, 2023
6dd707d
Update optimade.rst
sauliusg Jul 3, 2023
9bc0abc
Correcting English grammar as discussed with M.E. (2023-07-04 07:14 e…
Sep 28, 2023
6c7aff0
Merge branch 'develop' of github.com:sauliusg/OPTIMADE into develop
Sep 28, 2023
9f51105
Update optimade.rst
sauliusg Sep 28, 2023
6488f0b
Update optimade.rst
sauliusg Sep 28, 2023
746de3e
Rephrasing requirements for symmetry operations so that thei do not d…
Sep 28, 2023
75e468f
Accepting grammar fixes.
sauliusg Sep 28, 2023
31694cc
Clarifying application of symmetry operations.
sauliusg Nov 3, 2023
1b1e3c0
Changing a word.
sauliusg Nov 3, 2023
f76a13f
Changing the wording: "and" -> "or".
sauliusg Nov 3, 2023
4756819
I am not sure that this is definite, but lets assume it is since "to …
sauliusg Nov 3, 2023
da58d94
Update optimade.rst
sauliusg Dec 19, 2023
8faa070
Update optimade.rst
sauliusg Dec 19, 2023
1d10e07
Apply suggestions from code review
sauliusg Dec 19, 2023
00d524c
Merge branch 'develop' into develop
sauliusg Dec 19, 2023
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3 changes: 2 additions & 1 deletion .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,8 @@ repos:
(?x)^(
tests/inputs/various-whitespace.filter|
tests/inputs/fuzzystring-leading-trailing-spaces.filter|
units/definitions.units
units/definitions.units|
.words.lst
)$

- repo: https://github.com/Lucas-C/pre-commit-hooks
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75 changes: 41 additions & 34 deletions .words.lst
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Original file line number Diff line number Diff line change
@@ -1,69 +1,75 @@
personal_ws-1.1 en 205
personal_ws-1.1 en 216
ABNF
ACM
Aa
Acta
Ao
BaCa
BadLuck
Bb
BibTeX
CCaO
CECAM
CIF
CSV
CaCO
ClNa
ClosingBrace
CommonMark
ConstantFirstComparison
Cryst
Cracknell
Crystallographica
DOI
Dordrecht
EBNF
EREs
Edsger
EqualityOperator
EscapedChar
ExpressionClause
ExpressionPhrase
FuzzyStringOpRhs
Grammatica
Hermann
IANA
IEEE
ITC
IUCr
IUPAC's
IdentifierFirstComparison
IdentifierZipAddon
Kluwer
KnownOpRhs
LD
Lausanne
LengthComparison
LengthOpRhs
LowercaseLetter
Mauguin
NaCl
NaN
NaO
Namespace
OPTIMADE
OpenAPI
OpeningBrace
OperatorComparison
OrderedConstant
OrderedValue
POSCAR
POSIX
PredicateComparison
PropertyFirstComparison
PropertyZipAddon
Punctuator
Queryable
REs
RST
RelativeComparisonOperator
SPDX
Schmit
SetOpRhs
SetZipOpRhs
Shmueli
SiGe
SiO
Springer
Substring
Theo
URI
UTC
UUID
UnescapedChar
UnicodeHighChar
UnorderedConstant
Unversioned
UppercaseLetter
ValueEqRhs
ValueList
Expand All @@ -82,7 +88,6 @@ api
atime
backend
backends
bandgap
bd
booktitle
boolean
Expand All @@ -91,35 +96,36 @@ calc
cartesian
checksums
cif
conformant
coreCIF
cr
crossref
css
csv
ctime
deNOx
dec
denox
dep
dependentRequired
describedby
designator
dimensionality
discoverability
discoverable
doi
downloadable
eb
ebnf
edf
enum
exclusiveMaximum
exclusiveMinimum
exmpl
ferroelectric
fieldname
firstname
hdf
hermann
howpublished
href
html
http
hydrogens
hydroperoxide
Expand All @@ -133,26 +139,22 @@ jsonc
jsonlines
kvak
lastname
libc
lst
lt
maintainer's
mauguin
maxItems
maxLength
maxProperties
md
metadata
minItems
minLength
minProperties
mistyped
mtime
multi
multipleOf
namespace
namespaces
nattached
nbsp
nd
nelements
nl
nonperiodic
Expand All @@ -162,49 +164,54 @@ occupancies
ok
optimade
organisation
overbar
overbars
oxygens
param
pcre
perovskites
piezoelectic
pre
prepended
prepending
prescreen
prev
qudt
queryable
rc
regex
renormalize
sectnum
sha
sortable
spacegroup
structs
subfield
subfields
substring
substrings
supercell
symop
symops
testdb
timestamp
timestamps
th
typesetted
ucum
undelying
uniqueItems
unrequested
unversioned
uri
uris
url
urls
uuid
vMAJOR
versioning
vnd
vt
whitespace
workflow
xml
xy
xyz
yacc
yb
zeo
zeolites
ångström
ångström
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