-
Notifications
You must be signed in to change notification settings - Fork 227
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Non-cat changes to master from cat branch, 2 #1542
Commits on Feb 6, 2019
-
Snapshots (PNGs and CSVs) now track moles not mole fractions.
Unsure if this has consequences on flux diagrams or sensitivity analyses, etc. but I think it's a helpful start towards making more sense of simulation outputs, especially for two-phase heterogeneous systems.
Configuration menu - View commit details
-
Copy full SHA for a7f9d5e - Browse repository at this point
Copy the full SHA a7f9d5eView commit details -
Configuration menu - View commit details
-
Copy full SHA for a18692e - Browse repository at this point
Copy the full SHA a18692eView commit details -
A combination of commits with these messages: replaced part of the adjlist in the test that I accidentally deleted added in a quadruple bond to orders Added in quadruple bond type in converter added in more instances of quadruple bonds Adding Cq to R and R!H atom types added in todos to add unit tests for quadruple bonded elements
Configuration menu - View commit details
-
Copy full SHA for 61c9488 - Browse repository at this point
Copy the full SHA 61c9488View commit details -
Updates since AtomType.getFeatures() now includes quadruple bonds
It's unfortunate how fragile this code is, using integer indexing. Had to change getFeatures to include Benzene in its corrcect spot,
Configuration menu - View commit details
-
Copy full SHA for 765ea4a - Browse repository at this point
Copy the full SHA 765ea4aView commit details -
changed H bonds to 0.1 in the definitions
A combination of several commits, with these messages: changed the remove H bonds to remove anything close to 0.1 Hydrogen-bonds now have order 0.1 This way of doing things is a bit fragile, and not very satisfying. But I think this fixes at least a couple of places where this change needs to be made. Detect 0.1 bond orders (for H bonds) more robustly. Now passes last unit test. (It was something like 0.1000000000000149)
Configuration menu - View commit details
-
Copy full SHA for 996cb34 - Browse repository at this point
Copy the full SHA 996cb34View commit details -
Configuration menu - View commit details
-
Copy full SHA for 4d4c6fa - Browse repository at this point
Copy the full SHA 4d4c6faView commit details -
Adding van der Waals bonds (which have order 0)
Reaction recipes can make Van der Waals bonds (with order 0) Remove 'vdW' from bond types accepted (should be 0). This is a hold-over from when bond types were strings not floating point numbers.
Configuration menu - View commit details
-
Copy full SHA for 173051f - Browse repository at this point
Copy the full SHA 173051fView commit details -
Configuration menu - View commit details
-
Copy full SHA for f419f8a - Browse repository at this point
Copy the full SHA f419f8aView commit details -
More helpful error logging when failing to load reaction library.
Might not make a difference if you could see the logging.info call two lines earlier, but when running unit tests (databaseTest) that is not necessarily the case.
Configuration menu - View commit details
-
Copy full SHA for 7ff2527 - Browse repository at this point
Copy the full SHA 7ff2527View commit details