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Fixing .kinetics.py file #4

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Fixing .kinetics.py file #4

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7ebb513
A standalone script convertThermo.py for making Thermo Library files.
rwest May 10, 2013
486fcde
Help constructing SMILES strings when converting thermo files.
rwest May 10, 2013
e3cda31
Read reactions block in thermoconverter.
rwest May 11, 2013
5fb7658
Thermo converter now loads RMG database, ready for species guessing.
rwest May 11, 2013
b67792b
Convert thermo creates RMG core/edge reaction model and imports species.
rwest May 11, 2013
cdce60e
Trying to make the importer tool more object oriented.
rwest May 11, 2013
a0cdaa9
Got chemkin importer working! (I think)
rwest May 13, 2013
2abdaf7
Check the whole edge when running out of things to match
rwest May 13, 2013
7d3336d
Don't check chemkin reactions that are fully identified
rwest May 13, 2013
e9f64b9
Partial prune of reactions not likely to be useful.
rwest May 13, 2013
2a15748
Log the current voting
rwest May 14, 2013
9c4cf6a
Reorganize importer.
rwest May 14, 2013
41b804a
Redo vote reporting.
rwest May 15, 2013
6e45a2b
Draw pictures of species.
rwest May 17, 2013
a1ed3ad
Add a few more known species for the Huyn methylbutanoate test case.
rwest May 17, 2013
b870cca
Report enthalpy difference on match and in voting.
rwest May 17, 2013
e706d2f
When run out of options, ask for more help!
rwest May 17, 2013
364f07e
Save enthalpy discrepancy in matching list file.
rwest May 19, 2013
a139d20
Keep track of which edge reactions need re-checking.
rwest May 19, 2013
65ce32b
Fix problem trying to prune a reaction that's not in the edge.
rwest May 19, 2013
86a7648
Use DFT_QCI_thermo database before comparing thermo estimates.
rwest May 19, 2013
56a4fd5
Refactor the chemkin importer code.
rwest May 22, 2013
5623db3
Refactor vote printing into its own function.
rwest May 22, 2013
1ed9877
Make votes into sets instead of lists
rwest May 22, 2013
8f6d90a
Prune voting: remove reactions that vote for all possible matches!
rwest May 22, 2013
ca980e1
Use unique (pruned) votes when deciding matches.
rwest May 22, 2013
505f807
Prune votes for things with big enthalpy discrepancies.
rwest May 23, 2013
9dd5c25
Use pruned votes to decide if a match is unique.
rwest May 23, 2013
077b865
Tiny tweaks for speed.
rwest May 23, 2013
df73f32
Better help when making manual matches
rwest May 23, 2013
0ce1396
Speed up the reaction comparison function.
rwest May 23, 2013
a996f0c
Only print voting when you need user input.
rwest May 23, 2013
bc6906f
Make an embedded web server to keep track of the job!
rwest May 24, 2013
f96879d
Experiment with web server response.
rwest May 24, 2013
75feacd
Added a view that shows current voting.
rwest May 24, 2013
b0160d2
Can make matches through the web interface
rwest May 24, 2013
ba20905
Use the web front end when run out of things to do.
rwest May 24, 2013
68c1579
Serve on all available network interfaces.
rwest May 24, 2013
379ca01
Add a bunch of known species for the Huynh methyl butanoate case.
rwest May 26, 2013
56193cb
Use more thermo libraries.
rwest May 26, 2013
f0e5763
Re-order the loading of things.
rwest May 26, 2013
c24150b
Added a few more known species for methyl butanoate.
rwest May 28, 2013
f3e3561
Added an ajax-updated progress indicator to the header of each page.
rwest May 28, 2013
8503412
Tweaks to formatting (by PyDev).
rwest May 28, 2013
2462136
Allow you to change port for cherrypy server
rwest May 30, 2013
81239ec
Make progress meter prettier
rwest May 28, 2013
ed531cc
Add Argon to known formulae list
rwest May 30, 2013
d009722
Split loadModel into loadSpecies and loadThermo
rwest May 30, 2013
232e13f
Avoid race condition when you manually match a species that's about t…
rwest May 30, 2013
db4fe53
Load (and update) a known species list.
rwest May 30, 2013
5d986d9
Run CherryPy in a daemon thread, and RMG in the main one.
rwest May 30, 2013
dcea7c9
Stop cherrypy access logging polluting the RMG log and stdout.
rwest May 30, 2013
2454b1b
Moved Farooq test-case into better folder.
rwest May 30, 2013
bf3c76b
Rename convertThermo.py to importChemkin.py (and associated files)
rwest May 30, 2013
f9ddede
Add Helium to known species list.
faribas Jul 29, 2013
ce3a4ef
Added some more small molecules to known species list.
faribas Jul 29, 2013
31af922
Remove C2H2 from known formula list.
Aug 2, 2013
979fc3f
Quick change to fix known file reading.
Aug 6, 2013
f60fc7d
Tweak debugging messages for reading thermo files
Aug 6, 2013
5f83ebc
Save chemkin file and RMG_dictionary of processed (core) identified m…
Aug 6, 2013
e4f9d54
Added methanol to unique small molecules list
Aug 6, 2013
e050c4a
Made an unidentifiedreaction.html view.
Aug 6, 2013
0e8f0fd
Added [C] to known small molecules
Aug 7, 2013
1139e2f
Add several libraries to importChemkin to assist with
Aug 7, 2013
9a98a12
Made a new tentative.html view for tentative matches.
rwest Aug 7, 2013
65f1522
Fix tentative match list.
rwest Aug 8, 2013
828e117
Fix for if inert species is last in model.
rwest Aug 8, 2013
4a9cc3a
Tweak html for index and header.
rwest Aug 8, 2013
a140679
Add Helium as an identified specie into the RMG model.
faribas Aug 8, 2013
d586403
Tidy up the comments added to the output thermo file.
rwest Aug 8, 2013
0cb6a0b
Allow "singlet[CH2]" and "triplet[CH2]" in known species SMILES file.
rwest Aug 8, 2013
1364817
Re-order the reactionLibraries and add USC-Mech-ii thermo library.
rwest Aug 8, 2013
b52dc4b
Added new views to allow tentative matches to be proposed and edited!
rwest Aug 9, 2013
2112e70
Tweaks to the web interface of the chemkin importer.
rwest Aug 9, 2013
09bda05
Tweak the javascript alert for more input.
rwest Aug 9, 2013
f93395e
Write a RMG dictionary file for the original chemkin file.
Aug 9, 2013
52d7e98
Remove H atoms from the new RMG_Dictionary
rwest Aug 9, 2013
2518afa
Case typo in Glarborg/highP library name.
rwest Aug 9, 2013
d8265ba
Made a new 'species.html' view to list all the species.
rwest Aug 13, 2013
09f6523
Save the .thermo.py file continuously instead of at the end.
rwest Aug 13, 2013
6fee469
A view to download the (incomplete) thermo library
rwest Aug 13, 2013
ee5f0e0
Added special case for singletC=[C]
rwest Aug 14, 2013
7f01981
Cope with duplicate species in an imported chemkin file.
rwest Aug 14, 2013
1e5f565
Bug fix in header of generated thermo.py file
rwest Aug 14, 2013
84c99bc
Attempt to get chemkinimporter running QM and PDep
rwest Aug 30, 2013
5473bc3
Changes for python 2.6
rwest Sep 26, 2013
efb49ca
Fix typo in previous commit
Sep 26, 2013
9f2da39
Handle the case where the known species file is
Sep 26, 2013
b672ecf
Fix a bug where it wouldn't update the tentative
Sep 26, 2013
8341d9a
Fixed some more bugs related to tentative matches.
Sep 26, 2013
5b4a9be
Add irreversible reaction sign to non-green list
Sep 26, 2013
9d83193
Added thermo source tooltips to enthalpy discrepancies.
rwest Sep 27, 2013
f92725e
By default, don't have PDep when importing Chemkin files.
rwest Sep 28, 2013
c57a0c0
Can now clear tentative matches.
rwest Sep 28, 2013
a4a718b
Put already known things in core ordered smallest first.
rwest Sep 28, 2013
f4312a8
Style formatting of code, by PyDev.
rwest Sep 28, 2013
c2ff8f8
Enthalpy comparison is now done at 298K
rwest Sep 28, 2013
88e0085
Trying to get extrapolation to 298K working
rwest Sep 28, 2013
68300c1
Do thermo comparison at lowest common valid temperature or 298.15K
rwest Sep 28, 2013
a69174c
Fix some bugs in the code for making a tentative match
Oct 2, 2013
0480bc6
Add functionality for finding identical species in
Oct 2, 2013
9bf3603
Try to fix unicode problems in reading "source" files.
rwest Oct 3, 2013
3bac019
Keep track of thermo matches and show in thermomatches.html view
rwest Oct 3, 2013
08cc7d7
Look in sister directories for other (incomplete) thermo libraries.
rwest Oct 3, 2013
03b5967
Fix a bug in confirming thermo matches, but introduce another.
rwest Oct 3, 2013
26a855d
Fix the clearing and confirming of thermomatches.
rwest Oct 4, 2013
51a35da
Added a 'clear thermo match' link/view.
rwest Oct 4, 2013
f7f9be2
Good/bad thermo matches (based on names) coloured in green/red.
rwest Oct 4, 2013
8acf589
Count of thermomatches shown on index page
rwest Oct 4, 2013
263e9d8
Fix for Python 2.6 on Pharos
rwest Oct 4, 2013
e44eadc
Don't put thermo matches in tentative match list.
rwest Oct 4, 2013
1103b6d
Keep waiting for web front end.
rwest Oct 4, 2013
aaf7fa7
Draw pictures of thermo matches
rwest Oct 4, 2013
bb7629a
Hopefully finally fix the wait-for-web-front-end loop.
rwest Oct 4, 2013
24f4bca
Added a new function for enlarging the model. Currently
Oct 4, 2013
8313729
Rewrite the enlarge code to now only react species
Oct 4, 2013
d1ab7f4
Don't try to match species that don't react.
rwest Oct 7, 2013
52527f0
Don't use USC-Mech-ii when matching thermo
rwest Oct 7, 2013
f9dbca8
Better image titles
rwest Oct 7, 2013
f327ad0
Show thermo matches on voting and tentative pages.
rwest Oct 7, 2013
53f28f5
Allow singlet[CH]O and triplet[CH]O pseudo-SMILES strings.
rwest Oct 7, 2013
4c5d566
Don't load the thermo library of the model you're trying to import.
rwest Oct 7, 2013
c8ab3d3
Speed up the speciesReactAccordingToChemkin method.
rwest Oct 7, 2013
41fd9b7
Fix stupid typo
rwest Oct 7, 2013
9893053
Pester with a javascript Alert() less frequently
rwest Oct 15, 2013
da18a13
Fix the javascript ajax refresh thing.
rwest Oct 15, 2013
201eb8b
Fix bug in themomatching where it would not react
Oct 17, 2013
7b1bda0
Remove unnecessary code in thermomatching.
Oct 17, 2013
92be107
Moved USC_Mech_ii to examples folder and removed other examples.
rwest Nov 27, 2013
2de870b
Delete a bunch of known things from the USC Mech example.
rwest Nov 27, 2013
446885a
Search all of RMG-models if running inside a subdirectory.
rwest Nov 27, 2013
6f8aa32
Fix path to QMfiles (and clean up after the error)
rwest Nov 28, 2013
7cb01fb
Added command line option --noqm to avoid QM thermo calcs.
rwest Nov 28, 2013
7a11d2d
Save small molecule matches to the SMILES.txt file
rwest Dec 4, 2013
d87fd6c
Make the path if it doesn't exist for the QM files.
Dec 9, 2013
e545a93
Don't match small species more than once.
Dec 9, 2013
dd05767
Don't trust thermo libraries used for thermo matching
Dec 9, 2013
0c7ac92
Added a warning for very large thermo differences
Dec 9, 2013
48955e2
Output a kinetics library along with the thermo
Dec 12, 2013
693d125
Fix a bug which causes the reverse reaction to be stored.
Dec 15, 2013
69e3c27
Move saveReactionToKineticsFile to its own method
rwest Dec 17, 2013
59020b7
Comment out kinetics library generation for now.
Dec 17, 2013
6ce5d17
Don't alert when need a match - just change the window title (which h…
rwest May 19, 2014
96a7258
Actually check against loaded thermo libraries
rwest May 19, 2014
b6d5c11
A new view to see what thermo libraries have been loaded.
rwest May 19, 2014
94168df
Revert "Comment out kinetics library generation for now."
Asilvi May 20, 2014
60a23ad
Don't crash if you can't save the .kinetics.py file
Asilvi May 20, 2014
45656a2
Added 'THERM' as a string in initialization of thermo.txt file.
Asilvi May 29, 2014
98a2fe8
Check for missing thermo and give better error message.
rwest Jun 6, 2014
b98885c
Better handling and checking of console arguments
rwest Jun 6, 2014
e51247e
rmgpy/qm/mopac.py: Wait for 1 sec for the buffer to write to disc.
keceli Oct 4, 2013
5bce60a
Better error message if it can't save a reaction for some strange rea…
rwest Jun 12, 2014
3bd736d
Don't insert a blank line in the SMILES.txt every time.
rwest Jun 12, 2014
0f35dd8
Save the kinetics file (and prune the unmatched reactions) at the start.
rwest Jun 12, 2014
e276625
Can now quit when exhausted instead of waiting for input from web fro…
rwest Jun 12, 2014
9d9ed1c
Tidy up importer example and add instructions.
rwest Jul 11, 2014
c758023
Stop using getUsername() which is slow, deprecated, and about to vanish.
rwest Oct 23, 2014
65c231f
Display reaction family in voting reactions view.
rwest Oct 23, 2014
ba7814e
Don't make species that can't possibly match the chemkin file.
rwest Oct 23, 2014
56c2920
When importing models, say in the log file which reaction family gene…
rwest Dec 5, 2014
8f77258
Add view and link to see the original chemkin file.
rwest Dec 12, 2014
ec9dc04
Create a username, stored with a cookie.
rwest Dec 12, 2014
3e7df85
Save who identified (confirmed) what.
rwest Dec 12, 2014
9098788
Report how many things still need to be processed on index page.
rwest Dec 12, 2014
b6b5e86
Tweak the spacing of the "Home" link
rwest Dec 12, 2014
b7fbdd9
Report how many votes for a tentative match.
rwest Dec 12, 2014
2d02662
Track who proposed a tentative match if manually entered.
rwest Dec 12, 2014
14691c4
Avoid line-wrap on reactions.
rwest Dec 12, 2014
2538602
Tentative matches now have link to check votes from species.html view
rwest Dec 12, 2014
66bc919
Another white-space: nowrap style on the voting reactions.
rwest Dec 13, 2014
3a30b59
A Voting Reactions Table view at votes2.html
rwest Dec 13, 2014
fdcd9a9
Fix bug when matching duplicate species and things with no votes.
rwest Dec 16, 2014
bbfd3bd
Make table view default for voting reactions links.
rwest Dec 16, 2014
8cc46a2
Links to jump within the voting2.html page
rwest Dec 16, 2014
5fdb4ee
Allow you to block proposed matches.
rwest Dec 17, 2014
2e7d94e
Generate resonance isomers when loading blocked match list.
rwest Dec 17, 2014
d64d2bb
Cope with empty SMILES-BLOCKED files
rwest Jan 10, 2015
a2e2acc
limitEnlarge now checks for A+A->products self-reactions.
rwest Jan 10, 2015
5e6dd6f
Added some docstrings, tweaked some log messages.
rwest Jan 11, 2015
4a6b81b
Defer saving of matched reactions, until after matched species are pr…
rwest Jan 11, 2015
2011dfb
Trying a new type of kinetics.py output file.
rwest Jan 11, 2015
c4dff92
Faffing around trying to stop it segfaulting!
rwest Jan 11, 2015
13bda42
Stop segfault due to None atomtype on Argon
rwest Jan 11, 2015
b0acb8c
Make the new kinetics output more terse
rwest Jan 11, 2015
f5c716b
Make name cookie last a month not a week
rwest Feb 27, 2015
84e0b85
Sort table view matches by enthalpy discrepancy as well as number of …
rwest Feb 27, 2015
cf758e9
Show source of enthalpy estimate in table view.
rwest Feb 27, 2015
a815ce4
Revert to long-form .kinetics.py files
rwest Feb 27, 2015
6d2ef28
Sort the table view enthalpies the correct way around!
rwest Feb 27, 2015
c0ccfde
Generate resonance isomers when loading known species
rwest Feb 27, 2015
452ebd2
Improving code formatting.
rwest Apr 5, 2015
b99a2d7
Log what duplicate definition is
rwest May 21, 2015
ad9c5fd
Tell MOPAC to use PM3 when generating thermo
Jun 20, 2015
f1e37cc
Quietly skip duplicates when loading other thermo libraries
rwest Jun 21, 2015
27fd483
Initialize database properly for kinetics estimates.
rwest Jun 23, 2015
f9880f0
Avoid problem of calculating QM thermo for same species twice.
rwest Jun 23, 2015
a8334c1
Say which port it's waiting on
rwest Jun 24, 2015
1b49ad4
Remove the deprecated event log
rwest Jun 24, 2015
222108c
Improve error message for bad valency InvalidAdjacencyListError
rwest Jun 24, 2015
c3bf1f1
Failing unit test for fused aromatics valency checker
rwest Jun 24, 2015
943791c
Don't save aromatic adjacency lists to thermo file.
rwest Jun 24, 2015
9aa0b7a
Fix bug when avoiding thermo comparison error.
rwest Jun 24, 2015
80dfb77
Store longDesc as unicode
rwest Jun 24, 2015
fb4cdf5
Try to reduce errors on exit
rwest Jun 26, 2015
ddb812c
Log a broken thermo line if it errors while reading.
rwest Jun 26, 2015
c40e11e
Deal with specific third body colliders for pressure dependent reactions
Jul 21, 2015
0246e36
Improve formatting of code (no actual change)
rwest Jul 26, 2015
14d15df
More whitespace and comment changes to improve readability
rwest Jul 26, 2015
1524830
Show SMILES of all resonance isomers in All Species view.
rwest Jul 26, 2015
d1be70a
Print all families that vote for a species in votes tables.
rwest Jul 27, 2015
9f8c7ff
Fix missing </td> in malformed HTML in votes table view
rwest Jul 27, 2015
b7ab33d
Show SMILES of all resonance isomers in votes table view.
rwest Jul 27, 2015
52c087d
Add thermo matches to voting table view even if no voting reactions.
rwest Jul 27, 2015
cdae4b1
Add link to check votes from thermo match view.
rwest Jul 27, 2015
2086e34
Catch KeyError when looking for reactions for thermoMatch species
Jul 28, 2015
aa24c23
Don't run QM calculations if missing InChI support
rwest Jul 29, 2015
c2451dd
Allow thermo matches to be confirmed from votes table view.
rwest Jul 29, 2015
257169e
Fixing QM file store and scratch paths.
rwest Aug 11, 2015
5c783b8
Exception handling when trying to add species to core.
rwest Aug 11, 2015
e8af597
Made a saveJavaKineticsLibrary() method.
rwest Aug 12, 2015
03fd1e6
Store a ThermoLibrary, updated with matched species.
rwest Aug 12, 2015
296678f
Added a saveJavaThermoLibrary() method.
rwest Aug 12, 2015
ce1aca4
Update the Java thermo and kinetics library files when exhausted.
rwest Aug 12, 2015
4f8fb8f
Save the unusable reactions in the java kinetics library.
rwest Aug 12, 2015
4629e0e
Show user-proposed matches in table view.
rwest Aug 12, 2015
5511631
Skip check_partial_charge on fused benezene atom types.
rwest Aug 13, 2015
3d6c5fe
Refactor makeOrEmptyDirectory out of library saving methods.
rwest Aug 14, 2015
fd244c3
Make and update a kineticsLibrary.
rwest Aug 14, 2015
0ecad92
Save -Py and -Java libraries at the same time.
rwest Aug 14, 2015
5ea43c5
Remove missing import warnings from eclipse
rwest Aug 14, 2015
a2373dd
Minor tweaks.
rwest Aug 14, 2015
b6288f1
Save kinetics extra info file
rwest Aug 14, 2015
f13b5f0
Load sibling thermo libraries from new locations.
rwest Aug 14, 2015
afab2b0
Small bug fix in logging
rwest Aug 14, 2015
2802c30
Remove *labels from kinetics library dictionaries.
rwest Aug 15, 2015
6e94e91
Don't modify the list you're iterating through!!
rwest Aug 15, 2015
1fbe483
Get mechanism name from its path.
rwest Aug 15, 2015
7d970cb
Catch and avoid another "Unable to calculate degeneracy" error.
rwest Aug 15, 2015
4800e16
fixup! Get mechanism name from its path.
rwest Aug 15, 2015
78844b3
Use RMG_MAKE_INFO_FILES environment variable to make .kinetics.py files
rwest Aug 16, 2015
3b17fb2
Fix writing of `kinetics.py` file
Aug 19, 2015
f115857
Replace `dot` in `.kinetics.py` file with underscore
Aug 19, 2015
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Add a few more known species for the Huyn methylbutanoate test case.
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@rwest
rwest committed Aug 18, 2015
commit a1ed3ad56269677004c29063e20c6da91a01afc5
8 changes: 7 additions & 1 deletion convertThermo.py
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Original file line number Diff line number Diff line change
Expand Up @@ -453,7 +453,13 @@ def identifySmallMolecules(self):
}
identified_labels = []
known_labels = {
'mb': 'CCCC(=O)OC'
'mb': 'CCCC(=O)OC',
'mb3d': 'C=CCC(=O)OC',
'c2h5coch3': 'CCC(=O)C',
'c3h4-a': 'C=C=C',
'mb4j': '[CH2]CCC(=O)OC',
'mb3j': 'C[CH]CC(=O)OC',
'mbmj': 'CCCC(=O)O[CH2]',
}
# use speciesList if it is not None or empty, else the formulaDict keys.
for species_label in [s.label for s in self.speciesList or []] or self.formulaDict.keys():
Expand Down