Add more support to the Grackle interface

[hsinhaoHHuang]

Goals

1. Expand the functionality of GAMER to use GRACKLE.
2. Resolve the issue that GAMER's temperature in the output assumes a fixed mean molecular weight

Changes

User-end

• Add new runtime options to store the derived fields calculated by Grackle in the snapshots.

  • OPT__OUTPUT_GRACKLE_TEMP: output the temperature calculated by Grackle
  • OPT__OUTPUT_GRACKLE_MU: output the mean molecular weight calculated by Grackle
  • OPT__OUTPUT_GRACKLE_TCOOL: output the cooling time calculated by Grackle

• Add more options mapping to Grackle's parameters

  • GRACKLE_USE_V_HEATING_RATE: map to Grackle’s use_volumetric_heating_rate here, and users can create their function and link it to Grackle_vHeatingRate_User_Ptr in their test problem.
  • GRACKLE_USE_S_HEATING_RATE: map to Grackle’s use_specific_heating_rate here, and users can create their function and link it to Grackle_sHeatingRate_User_Ptr in their test problem.
  • GRACKLE_HYDROGEN_MFRAC: map to Grackle's HydrogenFractionByMass here.

• Add a new testing-purposes option to allow Grackle to evolve while the fluid is frozen.

  • OPT__UNFREEZE_GRACKLE: work with OPT__FREEZE_FLUID

• Add a new grid refinement option to flag when the cooling length is not resolved.

  • OPT__FLAG_COOLING_LEN: the refinement criteria of "cooling length/cell size" is set in Input__Flag_CoolingLen

• Add a new time-step criterion from Grackle's cooling time.

  • DT__GRACKLE_COOLING: the time-step is restricted by a factor of the minimum of cooling time

• Add a new test problem to test the Grackle-related functionality and see the Grackle's temperature and chemical species evolution in a controlled setup.

  • Hydro/GrackleTest

• Update the Grackle-related parameters in the wiki.

Internally

• Add new Grackle interface function Grackle_Calculate().
  • It will call the same Grackle_Prepare() to prepare the input arrays, so it can set up Grackle’s parameters consistently as CPU_GrackleSolver().
  • It will call the Grackle’s API functions for the calculation of derived fields:
    • calculate_temperature()
    • calculate_gamma()
    • calculate_cooling_time()
  • Usage:
    • It can be called for outputting data (total and part).
    • It can be called for refinement criteria.
    • It can be called for deciding the time-steps.
  • Currently, it can only calculate the array in the units of "patch group" at a time.

Validation

1. DefaultTestMode = 1 in the new test problem GrackleTest
   The x-axis corresponds to a range of density from 1.0e-29 g/cm^3 to 1.0e-21 g/cm^3, while the y-axis corresponds to a range of T/mu from 1.0 K to 1.0e8 K. We can check the Grackle-calculated derived fields of different phases at once.

   • Cooling Rate
     
   • 1 / Cooling Time
     
   • Cooling Length
     
   • Mean Molecular Weight
     

2. DefaultTestMode = 2 in the new test problem GrackleTest
   A uniform gas of density 1.0e-24 g/cm^3 and T/mu 1.0e4 K.

   • Time-step is based on the cooling time
     dt = 1.40e-02 = 1/17.85 * 0.25
     
   • Time evolution of the temperature and chemical composition
     
   • Temperature calculated by Grackle
     

3. DefaultTestMode = 3 in the new test problem GrackleTest
   A uniform gas of density 1.0e-24 g/cm^3 and T/mu 1.0e4 K initially, with user-provided heating and cooling as a function of spatial coordinates through GRACKLE_USE_V_HEATING_RATE.

   • Cooling rate
     The given central heating rate is 1.0e-24 erg cm^-3 s^-1 n_H^-1 and central cooling rate is 1.6e-20 erg cm^-3 s^-1 n_H^-2
     
     
   • Cooling Length
     
   • Cooling Length / dh
     The criteria are set as 8 cells per cooling length.
     
   • Time evolution of the temperature
     The evolution can match the analytical expectation.
     
   • Temperature calculated by Grackle, after 10 Myr