Bug in checkpoint function with Alquimia

[levuvietphong]

There is a minor bug in the checkpoint function of ats when running alquimia with subgrid. The issue arises due to an invalid key generated by splitKey(), which incorrectly includes a reaction from the Pflotran file.

Running the code attached produced the following error:

libc++abi: terminating due to uncaught exception of type Errors::Message: Keys::splitKey() called with invalid argument "transport_coupler_next.cell.1.0e+00 DOM1  + 1.0e+00 O2(aq)  -> 1.0e+00 HCO3- + 1.0 H+ aq kin rate cnst"

It seems that the splitKey() function does not correctly extract the name and tag, leading to an invalid key that includes the reaction from the Pflotran file:

# DOM aerobic respiration
MICROBIAL_REACTION
  REACTION 1.0e+00 DOM1  + 1.0e+00 O2(aq)  -> 1.0e+00 HCO3- + 1.0 H+ 
  RATE_CONSTANT      0
  MONOD
    SPECIES_NAME        O2(aq)
    HALF_SATURATION_CONSTANT 0
    THRESHOLD_CONCENTRATION 1.1e-20
  /
/

Removing checkpoint tag from the xml input avoids this bug, as no checkpoint files are written. Setting single file checkpoint = true fixes the issue in serial runs, but does not resolve in parallel runs.

checkpoint_bugs_example.zip