Support for TChem in PartMC (gas phase)

[jcurtis2]

Coupling PartMC and TChem gas phase chemistry:

• Add TChem library and dependencies to PartMC Makefile
• Pass configuration data from PartMC to TChem
  • Mechanism and species files: Chemfile
  • Time integration and numerical solver tolerances information (new yaml file required)
• Create gas_data%names from TChem data kmcd.
• Mapping between PartMC env_state to TChem state vector
• Mapping between PartMC gas_state%mix_rat and TChem state vector
• Construct time stepper to do a single delta t time step

Test cases:

• Simplified gas mechanism (Chapman cycle)
  • Compare against PartMC-TChem saved output where we know it worked
• Compare PartMC-TChem against plain TChem.
  • Add simple CB05CL_AE5 test case from TChem.

Other:

• Dockerfile to build and test PartMC-TChem (currently checks out TChem branch with driver code)
• Test on GPU
• Change to system_clock in order to accurately measure the wall clock time for a TChem run.

Other things to investigate:

• PartMC-TChem compared to PartMC-CAMP
  • Compare against CAMP with tight tolerances.
  • Compare against version of CAMP without clipping.