Require newer version of RDKit and add rdkit channel
Alphabetize dependencies
Remove libgcc and libgfortran (they are included implicitly)
Remove scoop

RDKit now generates different SMILES strings for some molecules

Update environment files, including RDKit and Cantera versions

The 1.014 factor represents the relationship between the harmonic
frequencies scaling factor and the zero point energy scaling factor,
see https://pubs.acs.org/doi/10.1021/ct100326h Section 3.1.3.

Previously we used E0 for the electronic energy, and E0_withZPE for the
corrected energy.
The updated terminology is E0 = e_electronic + ZPE
(E0 includes the ZPE)

- Corrected scaling factors which were for ZPE instead of freq
- Organized the references
- Removed commented out levels
- Added some more levels (one of which calculated by Duminda, as noted)

Scaling zpe

v2.4.0 release changes

Merge stable branch into master

Reaction Mechanism Simulator YAML File Generation

Previously, NASA.as_dict would throw an error if attributes like
Tmin, Tmax, E0 were unset. These variables, however, are optional,
so Arkane should not crash if they are unset.

This commit fixes the as_dict method to not throw an error
for optional attributes

This commit adds two test methods for NASA.as_dict and
two tests to load species from nasa polynomials in Arkane.

squash! Add tests to load species from NASA polynomials

…as_dict

Bugfix nasa as dict

…a_dependencies

Fix Travis builds by adding in missing miniconda dependencies

Modified the Arkane ScanLog documentation

Make new encorr package which handles all energy corrections. Store all
correction parameters in a dedicated data file. Handle bond additivity
corrections in its own module, so that new types of bond additivity
corrections can easily be implemented in the future.

Instead of correcting the electronic energy using explicitly defined bond
types, Anantharaman and Melius (JPCA, 2005) only use three fitted
parameters per atom type to correct the energy. Implement the framework
for this type of correction in the encorr package.

bondCorrectionType can be set to 'p' to use conventional bond additivity
corrections or to 'm' to use the newly implemented Melius-type corrections.

…rrections

Refactor energy corrections in Arkane and implement new bond additivity correction type

Calculated using Truhlar's method

Added two frequency scaling factors to Arkane

Should work no matter how many objects or dictionaries or lists are nested in each other. Most objects that inherits from RMGObject should work by default without  having to overwrite the make_object method

…_dictionary

Recursive as dictionary

Otherwise when trying to make a sample molecule
with an F groupAtom, it fails (and crashes
with a segfault)

This list should cover all elements used in atomTypes.

Fluorine fixes

…xamples

Fix frequencyScaleFactor in Arkane examples

Motivation:
- processNewReactions requires a newSpecies argument which was not
being properly identified after multiprocessing changes in #1459

Background:
- The newSpecies argument is retained from early RMG when reactions
were generated right after adding a new species to the core.
- Hence, newSpecies referred to the newly added core species which
was used to generate the new reactions.
- The overall model generation algorithm has since changed, so
identifying newSpecies is not as straightforward.
- The multiprocessing PR changed newSpecies to be any core species,
missing the original purpose of identifying the species from which
the reaction was generated.

Changes:
- Use the species tuples created during reaction generation to
keep track of which species were used to generate the reaction
- Update unit tests which are affected by the changes in return values
from react and react_all

Also rename the spc_tuples arg in the react method to spc_fam_tuples
to reflect updated usage.

Sort alphabetically and also remove relative imports

This reverts commit d59da68.

Lesson to be learned: If a unit test fails, make sure you
understand why before changing the correct answer...

With tests for pdep network generation

Fix pressure dependent network generation in RMG jobs

For now only tests the element_count_from_conformer() method, should be
expanded.

THe Species.props['element_counts'] is only used in Arkane. renamed
elementCounts to element_counts to be consistent with prior changes

…t_from_conf

Element count from conformer

Silence numpy warnings and use new default behavior

From numpy documentation:

Changed in version 1.14.0: If not set, a FutureWarning is given.
The previous default of -1 will use the machine precision as rcond
parameter, the new default will use the machine precision times max(M, N).
To silence the warning and use the new default, use rcond=None,
to keep using the old behavior, use rcond=-1.

…_multi

Support reversing PDepArrhenius objects containing MultiArrhenius rates