FIX: Canonicalize coordination number sorting in DAT reader

[jorgepazsoldanpalma]

(This summary added from the comments in the PR)

Previously PyCalphad would alphabetically express the quadruplets and because of this if the coordination numbers of a binary quadruplet in the database were not expressed in alphabetic order in the database parameters, then the coordination numbers would be incorrectly ordered. Sometimes this would trigger a calculation of coordination number, instead of a lookup. A fix has been added to the cs_dat parser to canonically sort coordination numbers when DAT files are read.

The test makes sure that the order in which the species are entered in the DAT file does not affect the calculated energy. In this specific test the Ni is entered before the K species.

[codecov]

Codecov Report

Merging #416 (54305ec) into develop (f8e3951) will increase coverage by 0.19%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #416      +/-   ##
===========================================
+ Coverage    90.67%   90.86%   +0.19%     
===========================================
  Files           45       45              
  Lines         6335     6469     +134     
===========================================
+ Hits          5744     5878     +134     
  Misses         591      591              

Impacted Files	Coverage Δ
pycalphad/models/model_mqmqa.py	88.42% <ø> (ø)
pycalphad/io/cs_dat.py	81.28% <100.00%> (+0.15%)	⬆️
pycalphad/tests/test_energy.py	98.88% <100.00%> (+0.03%)	⬆️
pycalphad/codegen/sympydiff_utils.py	98.21% <0.00%> (-1.79%)	⬇️
pycalphad/tests/test_utils.py	100.00% <0.00%> (ø)
pycalphad/tests/test_database.py	100.00% <0.00%> (ø)
pycalphad/tests/test_calculate.py	100.00% <0.00%> (ø)
pycalphad/model.py	91.84% <0.00%> (+0.16%)	⬆️
pycalphad/io/tdb.py	89.70% <0.00%> (+0.35%)	⬆️
pycalphad/io/database.py	87.24% <0.00%> (+0.44%)	⬆️
... and 1 more

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[jorgepazsoldanpalma]

Yup

…

On Wed, May 18, 2022 at 6:40 PM Brandon Bocklund ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In pycalphad/tests/test_energy.py <#416 (comment)>: > + + F = v.Species('F-1.0',constituents={'F':1.0}, charge=-1) + K = v.Species('K+1.0',constituents={'K':1.0}, charge=1) + NI = v.Species('NI+2.0',constituents={'NI':1.0}, charge=2) + mod = ModelMQMQA(dbf, ["K", "NI", "F"], "LIQUID2") + + assert K in mod.cations + assert NI in mod.cations + assert F in mod.anions + + subs_dict={mod._X_ijkl(NI,NI,F,F):0.36820754040431064, + mod._X_ijkl(K,NI,F,F):0.52716983838275622, + mod._X_ijkl(K,K,F,F):0.10462262121293306, + v.T: 1600} + + check_energy(mod, subs_dict, -3.35720E+05, mode="sympy") # Thermochimica energy @jorgepazsoldanpalma <https://github.com/jorgepazsoldanpalma> just to confirm, this energy is from Thermochimica, right? — Reply to this email directly, view it on GitHub <#416 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPINJNKJTYMAMSN42DFQZDVKVWVBANCNFSM5WJ2OEAA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[bocklund]

Thanks for the test and the fix, @jorgepazsoldanpalma! And congratulations on your first PR to PyCalphad!

[jorgepazsoldanpalma]

My pleasure!

…

On Thu, May 19, 2022 at 12:36 PM Brandon Bocklund ***@***.***> wrote: Thanks for the test and the fix, @jorgepazsoldanpalma <https://github.com/jorgepazsoldanpalma>! And congratulations on your first PR to PyCalphad! — Reply to this email directly, view it on GitHub <#416 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPINJNDD7CQLOCSZB3CPU3VKZU2JANCNFSM5WJ2OEAA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[jorgepazsoldanpalma]

yup

…

On Wed, May 18, 2022 at 6:40 PM Brandon Bocklund ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In pycalphad/tests/test_energy.py <#416 (comment)>: > + + F = v.Species('F-1.0',constituents={'F':1.0}, charge=-1) + K = v.Species('K+1.0',constituents={'K':1.0}, charge=1) + NI = v.Species('NI+2.0',constituents={'NI':1.0}, charge=2) + mod = ModelMQMQA(dbf, ["K", "NI", "F"], "LIQUID2") + + assert K in mod.cations + assert NI in mod.cations + assert F in mod.anions + + subs_dict={mod._X_ijkl(NI,NI,F,F):0.36820754040431064, + mod._X_ijkl(K,NI,F,F):0.52716983838275622, + mod._X_ijkl(K,K,F,F):0.10462262121293306, + v.T: 1600} + + check_energy(mod, subs_dict, -3.35720E+05, mode="sympy") # Thermochimica energy @jorgepazsoldanpalma <https://github.com/jorgepazsoldanpalma> just to confirm, this energy is from Thermochimica, right? — Reply to this email directly, view it on GitHub <#416 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFPINJNKJTYMAMSN42DFQZDVKVWVBANCNFSM5WJ2OEAA> . You are receiving this because you were mentioned.Message ID: ***@***.***>