Address BWO review comments

parthenon-hpc-lab · Sep 10, 2024 · 4e41e6d · 4e41e6d
1 parent 043a028
commit 4e41e6d
Show file tree

Hide file tree

Showing 7 changed files with 16 additions and 17 deletions.
diff --git a/docs/input.md b/docs/input.md
@@ -72,24 +72,24 @@ conserved to primitive conversion if both are defined.
 Diffusive processes in AthenaPK can be configured in the `<diffusion>` block of the input file.
 ```
 <diffusion>
-integrator = unsplit       # alternatively: rkl2
-#rkl2_max_dt_ratio = 100.0 # limits the ratio between the parabolic and hyperbolic timesteps
-#cfl = 1.0                 # Additional safety factor applied to diffusive timestep constraint. Default to hyperbolic cfl.
+integrator = unsplit       # alternatively: rkl2 (for rkl2 integrator (operator split integrator)
+#rkl2_max_dt_ratio = 100.0 # limits the ratio between the parabolic and hyperbolic timesteps (only used for RKL2 operator split integrator)
+#cfl = 1.0                 # Additional safety factor applied in the caluclation of the diffusive timestep (used in both unsplit and RKL2 integration schemes). Defaults to hyperbolic cfl.
 
 conduction = anisotropic               # none (disabled), or isotropic, or anisotropic
 conduction_coeff = fixed               # alternative: spitzer
-thermal_diff_coeff_code = 0.01         # fixed coefficent in code units
+thermal_diff_coeff_code = 0.01         # fixed coefficent in code units (code_length^2/code_time)
 #spitzer_cond_in_erg_by_s_K_cm = 4.6e7 # spitzer coefficient in cgs units (requires definition of a unit system)
 #conduction_sat_phi = 0.3              # fudge factor to account for uncertainties in saturated fluxes
 
 
 viscosity = none            # none (disabled) or isotropic
 viscosity_coeff = fixed
-mom_diff_coeff_code = 0.25  # fixed coefficent in code units
+mom_diff_coeff_code = 0.25  # fixed coefficent of the kinetmatic viscosity in code units (code_length^2/code_time)
 
 resistivity = none          # none (disabled) or ohmic
 resistivity_coeff = fixed
-ohm_diff_coeff_code = 0.25  # fixed coefficent in code units
+ohm_diff_coeff_code = 0.25  # fixed coefficent of the magnetic (ohmic) diffusivity code units (code_length^2/code_time)
 ```
 (An)isotropic thermal conduction (with fixed or Spitzer coefficient), and isotropic viscosity and
 resistivity with fixed coefficient are currently implemented.
@@ -199,23 +199,23 @@ Default value corresponds to the typical value used in literature and goes back
 #### Viscosity/Momentum diffusion
 
 Only isotropic viscosity with a (spatially and temporally) fixed coefficient in code units
-is currently implemented.
+(`code_length`^2/`code_time`) is currently implemented.
 To enable set (in the `<diffusion>` block)
 ```
 viscosity = isotropic
 viscosity_coeff = fixed
-mom_diff_coeff_code = 0.25  # fixed coefficent in code units
+mom_diff_coeff_code = 0.25  # fixed coefficent of the kinetmatic viscosity in code units (code_length^2/code_time)
 ```
 
 #### Resistivity/Ohmic diffusion
 
 Only resistivity with a (spatially and temporally) fixed coefficient in code units
-is currently implemented.
+(`code_length`^2/`code_time`)is currently implemented.
 To enable set (in the `<diffusion>` block)
 ```
 resistivity = ohmic
 resistivity_coeff = fixed
-ohm_diff_coeff_code = 0.25  # fixed coefficent in code units
+ohm_diff_coeff_code = 0.25  # fixed coefficent of the magnetic (ohmic) diffusivity code units (code_length^2/code_time)
 ```
 
 

diff --git a/inputs/diffusion.in b/inputs/diffusion.in
@@ -1,5 +1,5 @@
 # AthenaPK - a performance portable block structured AMR MHD code
-# Copyright (c) 2021-2023, Athena Parthenon Collaboration. All rights reserved.
+# Copyright (c) 2021-2024, Athena Parthenon Collaboration. All rights reserved.
 # Licensed under the BSD 3-Clause License (the "LICENSE");
 
 <comment>

diff --git a/src/hydro/diffusion/resistivity.cpp b/src/hydro/diffusion/resistivity.cpp
@@ -1,6 +1,6 @@
 //========================================================================================
 // AthenaPK - a performance portable block structured AMR astrophysical MHD code.
-// Copyright (c) 2023, Athena-Parthenon Collaboration. All rights reserved.
+// Copyright (c) 2024, Athena-Parthenon Collaboration. All rights reserved.
 // Licensed under the 3-clause BSD License, see LICENSE file for details
 //========================================================================================
 //! \file resistivity.cpp
@@ -49,7 +49,6 @@ Real EstimateResistivityTimestep(MeshData<Real> *md) {
     fac = 1.0 / 6.0;
   }
 
-  const auto gm1 = hydro_pkg->Param<Real>("AdiabaticIndex");
   const auto &ohm_diff = hydro_pkg->Param<OhmicDiffusivity>("ohm_diff");
 
   if (ohm_diff.GetType() == Resistivity::ohmic &&

diff --git a/src/hydro/diffusion/viscosity.cpp b/src/hydro/diffusion/viscosity.cpp
@@ -1,6 +1,6 @@
 //========================================================================================
 // AthenaPK - a performance portable block structured AMR astrophysical MHD code.
-// Copyright (c) 2021-2023, Athena-Parthenon Collaboration. All rights reserved.
+// Copyright (c) 2021-2024, Athena-Parthenon Collaboration. All rights reserved.
 // Licensed under the 3-clause BSD License, see LICENSE file for details
 //========================================================================================
 // AthenaXXX astrophysical plasma code

diff --git a/src/pgen/diffusion.cpp b/src/pgen/diffusion.cpp
@@ -1,6 +1,6 @@
 
 // AthenaPK - a performance portable block structured AMR MHD code
-// Copyright (c) 2021-2023, Athena Parthenon Collaboration. All rights reserved.
+// Copyright (c) 2021-2024, Athena Parthenon Collaboration. All rights reserved.
 // Licensed under the 3-Clause License (the "LICENSE")
 
 // Parthenon headers

diff --git a/tst/regression/test_suites/diffusion/diffusion.py b/tst/regression/test_suites/diffusion/diffusion.py
@@ -1,6 +1,6 @@
 # ========================================================================================
 # AthenaPK - a performance portable block structured AMR MHD code
-# Copyright (c) 2023, Athena Parthenon Collaboration. All rights reserved.
+# Copyright (c) 2023-2024, Athena Parthenon Collaboration. All rights reserved.
 # Licensed under the 3-clause BSD License, see LICENSE file for details
 # ========================================================================================
 

diff --git a/tst/regression/test_suites/diffusion_linwave3d/diffusion_linwave3d.py b/tst/regression/test_suites/diffusion_linwave3d/diffusion_linwave3d.py
@@ -1,6 +1,6 @@
 # ========================================================================================
 # AthenaPK - a performance portable block structured AMR MHD code
-# Copyright (c) 2023, Athena Parthenon Collaboration. All rights reserved.
+# Copyright (c) 2023-2024, Athena Parthenon Collaboration. All rights reserved.
 # Licensed under the 3-clause BSD License, see LICENSE file for details
 # ========================================================================================