libantioch/antioch — pull request #93 by SylvainPlessis (2014-12-05 18:25:48+00:00)
Title: Opt transport

### Common part
This is one PR of a bunch of PRs to finalize parsing, thermodynamics and transport. There will be several PRs, the only thing missing now is the merging with *master*, which will come once the setup of the PRs is made. To make things as clear as I can, all the PRs will have a common section showing the graph with a star to mark the current PR.
```
xml_parser <-- input_parsing_format <-- ascii_parser <-- species_parsing <-- \
\
NASA polynomials <-- UnifiedThermo <---------------------------------------------- thermo_parsing <--
\ \
transport_new <------------------------ transport_thermo <--------------------------------------------- transport_thermo_parser
```
So here is the parser/thermo/transport bunch of PR. There are also two more PRs, the ```opt_transport``` and the ```almost_Exact```.
The ```opt_transport``` merges ```transport_thermo_parser``` with ```conditions_reac```, which enables to pass a ```KineticsConditions``` object instead of temperature, which translates into computing once and for all the ```TempCache``` object instead of locally where it's needed.
```almost_Exact``` takes in the ```kin_reset```.

### This PR

This one adapts the ```KineticsConditions``` to the transport, so changes are mostly on the calling method.
Note that only the high level object ```WilkeEvaluator``` can perform the backwards compatibility with the former version, i.e. passing only the temperature. For details on how it is done, see the Conditions reac PR (#74).

This object can be generalized to contains also references or pointers to density, molar/mass composition. I haven't done it for two reasons: it would be a change of API with no backward compatibility (short of overloading), it is the temperature that requires special treatment (such a pimp…).

This PR makes the transport more efficient by computing the temperature cache only once, it doesn't affect the kinetics, as the cache is required for the thermo anyway (or you have solely non reversible reactions, in that case we're sorry it computes the cache and you don't need it).