fix GNUmakefiles (#1927)

* fix GNUmakefiles

* update docs

Docs/sphinx_doc/RegressionTests.rst

@@ -247,9 +247,9 @@ Test Location: `Tests/test_files/ScalarAdvectionUniformU`_
 
 .. _`Tests/test_files/ScalarAdvectionUniformU`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/ScalarAdvectionUniformU
 
-Problem Location: `Exec/RegTests/ScalarAdvDiff`_
+Problem Location: `Exec/DryRegTests/ScalarAdvDiff`_
 
-.. _`Exec/RegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/ScalarAdvDiff
+.. _`Exec/DryRegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/ScalarAdvDiff
 
 .. |a2| image:: figures/tests/scalar_advec_uniform_u_start.png
         :width: 200
@@ -275,9 +275,9 @@ Test Location: `Tests/test_files/ScalarAdvectionShearedU`_
 
 .. _`Tests/test_files/ScalarAdvectionShearedU`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/ScalarAdvectionShearedU
 
-Problem Location: `Exec/RegTests/ScalarAdvDiff`_
+Problem Location: `Exec/DryRegTests/ScalarAdvDiff`_
 
-.. _`Exec/RegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/ScalarAdvDiff
+.. _`Exec/DryRegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/ScalarAdvDiff
 
 .. |a3| image:: figures/tests/scalar_advec_sheared_u_start.png
         :width: 200
@@ -304,9 +304,9 @@ Test Location: `Tests/test_files/ScalarDiffusionGaussian`_
 
 .. _`Tests/test_files/ScalarDiffusionGaussian`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/ScalarDiffusionGaussian
 
-Problem Location: `Exec/RegTests/ScalarAdvDiff`_
+Problem Location: `Exec/DryRegTests/ScalarAdvDiff`_
 
-.. _`Exec/RegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/ScalarAdvDiff
+.. _`Exec/DryRegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/ScalarAdvDiff
 
 .. |a5| image:: figures/tests/scalar_diff_start.png
         :width: 300
@@ -332,9 +332,9 @@ Test Location: `Tests/test_files/ScalarDiffusionSine`_
 
 .. _`Tests/test_files/ScalarDiffusionSine`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/ScalarDiffusionSine
 
-Problem Location: `Exec/RegTests/ScalarAdvDiff`_
+Problem Location: `Exec/DryRegTests/ScalarAdvDiff`_
 
-.. _`Exec/RegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/ScalarAdvDiff
+.. _`Exec/DryRegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/ScalarAdvDiff
 
 .. |a6| image:: figures/tests/scalar_diff_sine_start.png
         :width: 300
@@ -361,9 +361,9 @@ Test Location (for 2nd order): `Tests/test_files/ScalarAdvDiff_order2`_
 
 .. _`Tests/test_files/ScalarAdvDiff_order2`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/ScalarAdvDiff_order2
 
-Problem Location: `Exec/RegTests/ScalarAdvDiff`_
+Problem Location: `Exec/DryRegTests/ScalarAdvDiff`_
 
-.. _`Exec/RegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/ScalarAdvDiff
+.. _`Exec/DryRegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/ScalarAdvDiff
 
 .. |a7| image:: figures/tests/scalar_advec_diff_start.png
         :width: 300
@@ -391,9 +391,9 @@ Test Location: `Tests/test_files/RayleighDamping`_
 
 .. _`Tests/test_files/RayleighDamping`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/RayleighDamping
 
-Problem Location: `Exec/RegTests/ScalarAdvDiff`_
+Problem Location: `Exec/DryRegTests/ScalarAdvDiff`_
 
-.. _`Exec/RegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/ScalarAdvDiff
+.. _`Exec/DryRegTests/ScalarAdvDiff`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/ScalarAdvDiff
 
 
 Isentropic Vortex: Stationary
@@ -404,9 +404,9 @@ Test Location: `Tests/test_files/IsentropicVortexStationary`_
 
 .. _`Tests/test_files/IsentropicVortexStationary`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/IsentropicVortexStationary
 
-Problem Location: `Exec/RegTests/IsentropicVortex`_
+Problem Location: `Exec/DryRegTests/IsentropicVortex`_
 
-.. _`Exec/RegTests/IsentropicVortex`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/IsentropicVortex
+.. _`Exec/DryRegTests/IsentropicVortex`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/IsentropicVortex
 
 Isentropic Vortex: Advecting
 ----------------------------
@@ -416,9 +416,9 @@ Test Location: `Tests/test_files/IsentropicVortexAdvecting`_
 
 .. _`Tests/test_files/IsentropicVortexAdvecting`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/IsentropicVortexAdvecting
 
-Problem Location: `Exec/RegTests/IsentropicVortex`_
+Problem Location: `Exec/DryRegTests/IsentropicVortex`_
 
-.. _`Exec/RegTests/IsentropicVortex`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/IsentropicVortex
+.. _`Exec/DryRegTests/IsentropicVortex`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/IsentropicVortex
 
 Taylor Green Vortex: Advection
 ------------------------------------------------
@@ -428,9 +428,9 @@ Test Location: `Tests/test_files/TaylorGreenAdvecting`_
 
 .. _`Tests/test_files/TaylorGreenAdvecting`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/TaylorGreenAdvecting
 
-Problem Location: `Exec/RegTests/TaylorGreenVortex`_
+Problem Location: `Exec/DryRegTests/TaylorGreenVortex`_
 
-.. _`Exec/RegTests/TaylorGreenVortex`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/TaylorGreenVortex
+.. _`Exec/DryRegTests/TaylorGreenVortex`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/TaylorGreenVortex
 
 Taylor Green Vortex: Advection and Diffusion
 ------------------------------------------------
@@ -440,9 +440,9 @@ Test Location: `Tests/test_files/TaylorGreenAdvectingDiffusing`_
 
 .. _`Tests/test_files/TaylorGreenAdvectingDiffusing`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/TaylorGreenAdvectingDiffusing
 
-Problem Location: `Exec/RegTests/TaylorGreenVortex`_
+Problem Location: `Exec/DryRegTests/TaylorGreenVortex`_
 
-.. _`Exec/RegTests/TaylorGreenVortex`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/TaylorGreenVortex
+.. _`Exec/DryRegTests/TaylorGreenVortex`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/TaylorGreenVortex
 
 .. |a8| image:: figures/tests/TGV_start.png
         :width: 300
@@ -472,9 +472,9 @@ Test Location: `Tests/test_files/CouetteFlow_x`_
 
 .. _`Tests/test_files/CouetteFlow`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/CouetteFlow_x
 
-Problem Location: `Exec/RegTests/CouetteFlow_x`_
+Problem Location: `Exec/DryRegTests/CouetteFlow_x`_
 
-.. _`Exec/RegTests/Couette_Poiseuille`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/Couette_Poiseuille
+.. _`Exec/DryRegTests/Couette_Poiseuille`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/Couette_Poiseuille
 
 Couette Flow (y-direction)
 ---------------------------
@@ -488,9 +488,9 @@ Test Location: `Tests/test_files/CouetteFlow_y`_
 
 .. _`Tests/test_files/CouetteFlow`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/CouetteFlow_y
 
-Problem Location: `Exec/RegTests/CouetteFlow_y`_
+Problem Location: `Exec/DryRegTests/CouetteFlow_y`_
 
-.. _`Exec/RegTests/Couette_Poiseuille`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/Couette_Poiseuille
+.. _`Exec/DryRegTests/Couette_Poiseuille`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/Couette_Poiseuille
 
 Poiseuille Flow (x-direction)
 -----------------------------
@@ -504,9 +504,9 @@ Test Location: `Tests/test_files/PoiseuilleFlow_x`_
 
 .. _`Tests/test_files/PoiseuilleFlow_x`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/PoiseuilleFlow_x
 
-Problem Location: `Exec/RegTests/PoiseuilleFlow_x`_
+Problem Location: `Exec/DryRegTests/PoiseuilleFlow_x`_
 
-.. _`Exec/RegTests/Couette_Poiseuille`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/Couette_Poiseuille
+.. _`Exec/DryRegTests/Couette_Poiseuille`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/Couette_Poiseuille
 
 Poiseuille Flow (y-direction)
 -----------------------------
@@ -520,9 +520,9 @@ Test Location: `Tests/test_files/PoiseuilleFlow_y`_
 
 .. _`Tests/test_files/PoiseuilleFlow_y`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/PoiseuilleFlow_y
 
-Problem Location: `Exec/RegTests/PoiseuilleFlow_y`_
+Problem Location: `Exec/DryRegTests/PoiseuilleFlow_y`_
 
-.. _`Exec/RegTests/Couette_Poiseuille`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/Couette_Poiseuille
+.. _`Exec/DryRegTests/Couette_Poiseuille`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/Couette_Poiseuille
 
 Nonlinear Density Current
 ---------------------------
@@ -534,9 +534,9 @@ Test Location: `Tests/test_files/DensityCurrent`_
 
 .. _`Tests/test_files/DensityCurrent`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/DensityCurrent
 
-Problem Location: `Exec/RegTests/DensityCurrent`_
+Problem Location: `Exec/DryRegTests/DensityCurrent`_
 
-.. _`Exec/DensityCurrent`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/DensityCurrent
+.. _`Exec/DensityCurrent`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/DensityCurrent
 
 Ekman Spiral
 ---------------------------
@@ -548,6 +548,6 @@ Test Location: `Tests/test_files/EkmanSpiral`_
 
 .. _`Tests/test_files/EkmanSpiral`: https://github.com/erf-model/ERF/tree/development/Tests/test_files/EkmanSpiral
 
-Problem Location: `Exec/RegTests/EkmanSpiral`_
+Problem Location: `Exec/DryRegTests/EkmanSpiral`_
 
-.. _`Exec/RegTests/EkmanSpiral`: https://github.com/erf-model/ERF/tree/development/Exec/RegTests/EkmanSpiral
+.. _`Exec/DryRegTests/EkmanSpiral`: https://github.com/erf-model/ERF/tree/development/Exec/DryRegTests/EkmanSpiral

Docs/sphinx_doc/building.rst

@@ -33,10 +33,10 @@ ERF uses the paradigm that different executables are built in different subdirec
 using gmake (see below), the user/developer should build in the directory of the selected problem.  When using
 cmake (see below), separate executables are built for all of the problem directories listed in ``Exec/CMakeLists.txt``.
 The problem directories within ``Exec`` are sorted into 1) science-relevant setups, such as ``ABL`` for modeling the atmospheric
-boundary layer or ``DensityCurrent`` for running the standard density current test case, etc, 2) regression tests in
-``Exec/RegTests`` that are used for testing specific known aspects of the code functionality, such as boundary conditions or
-Rayleigh damping, and 3) tests for features under development in ``Exec/DevTests``, such as moving terrain.  There is a
-README in each problem directory that describes the purpose/role of that problem.
+boundary layer or ``DensityCurrent`` for running the standard density current test case, etc, 2) dry and moist regression tests in
+``Exec/DryRegTests`` and ``Exec/MoistRegTests`` respectively, that are used for testing specific known aspects of the code functionality,
+such as boundary conditions or Rayleigh damping, and 3) tests for features under development in ``Exec/DevTests``, such as moving terrain.
+There is a README in each problem directory that describes the purpose/role of that problem.
 
 GNU Make
 ~~~~~~~~
@@ -70,7 +70,7 @@ or if using tcsh,
 
    setenv AMREX_HOME /path/to/external/amrex
 
-#. ``cd`` to the desired build directory, e.g.  ``ERF/Exec/RegTests/IsentropicVortex/``
+#. ``cd`` to the desired build directory, e.g.  ``ERF/Exec/DryRegTests/IsentropicVortex/``
 
 #. Edit the ``GNUmakefile``; options include
 
@@ -130,7 +130,7 @@ or if using tcsh,
 
    The name of the resulting executable (generated by the GNUmake system) encodes several of the build characteristics, including dimensionality of the problem, compiler name, and whether MPI and/or OpenMP were linked with the executable.
    Thus, several different build configurations may coexist simultaneously in a problem folder.
-   For example, the default build in ``ERF/Exec/RegTests/IsentropicVortex`` will look
+   For example, the default build in ``ERF/Exec/DryRegTests/IsentropicVortex`` will look
    like ``ERF3d.gnu.MPI.ex``, indicating that this is a 3-d version of the code, made with
    ``COMP=gnu``, and ``USE_MPI=TRUE``.
 

Docs/sphinx_doc/testing.rst

@@ -52,10 +52,11 @@ Adding Tests
 
 Developers are encouraged to add tests to ERF and in this section we describe how the tests are organized in the
 CTest framework. The locations (relative to the ERF code base) of the tests are in ``Tests``. To add a test, first
-create a problem directory with a name in ``Exec/RegTests/<prob_name>`` (for problems to be used
-as regression tests) or ``Exec/DevTests/<prob_name>`` (for problems testing features under development),
+create a problem directory with a name in ``Exec/DryRegTests/<prob_name>`` or
+``Exec/MoistRegTests/<prob_name>`` (for problems to be used as regression tests)
+or ``Exec/DevTests/<prob_name>`` (for problems testing features under development),
 depending on which type of test is being added.  Prepare a suitable input file.
-As an example, the ``TaylorGreenVortex`` problem with input file ``Exec/RegTests/TaylorGreenVortex/inputs_ex``
+As an example, the ``TaylorGreenVortex`` problem with input file ``Exec/DryRegTests/TaylorGreenVortex/inputs_ex``
 solves a simple advection-diffusion problem. The corresponding regression tests are driven by the input files
 ``Tests/test_files/TaylorGreenAdvecting/TaylorGreenAdvecting.i`` and
 ``Tests/test_files/TaylorGreenAdvectingDiffusing/TaylorGreenAdvectingDiffusing.i``.

Exec/DryRegTests/Couette_Poiseuille/GNUmakefile

@@ -29,5 +29,5 @@ Bpack := ./Make.package
 Blocs := .
 
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/Couette_Poiseuille
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/Couette_Poiseuille
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/DensityCurrent/GNUmakefile

@@ -30,5 +30,5 @@ USE_POISSON_SOLVE = TRUE
 Bpack := ./Make.package
 Blocs := .
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/DensityCurrent
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/DensityCurrent
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/EkmanSpiral/GNUmakefile

@@ -32,5 +32,5 @@ Bpack := ./Make.package
 Blocs := .
 
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/EkmanSpiral
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/EkmanSpiral
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/IsentropicVortex/GNUmakefile

@@ -29,5 +29,5 @@ Bpack := ./Make.package
 Blocs := .
 
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/IsentropicVortex
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/IsentropicVortex
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/ParticlesOverWoA/GNUmakefile

@@ -31,5 +31,5 @@ Bpack := ./Make.package
 Blocs := .
 
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/ParticlesOverWoA
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/ParticlesOverWoA
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/ScalarAdvDiff/GNUmakefile

@@ -29,5 +29,5 @@ Bpack := ./Make.package
 Blocs := .
 
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/ScalarAdvDiff
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/ScalarAdvDiff
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/StokesSecondProblem/GNUmakefile

@@ -29,5 +29,5 @@ USE_TERRAIN_VELOCITY = TRUE
 Bpack := ./Make.package
 Blocs := .
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/StokesSecondProblem
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/StokesSecondProblem
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/TaylorGreenVortex/GNUmakefile

@@ -29,5 +29,5 @@ Bpack := ./Make.package
 Blocs := .
 
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/TaylorGreenVortex
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/TaylorGreenVortex
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/Terrain2d_Cylinder/GNUmakefile

@@ -28,5 +28,5 @@ USE_ASSERTION = TRUE
 Bpack := ./Make.package
 Blocs := .
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/Terrain2d_Cylinder
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/Terrain2d_Cylinder
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/Terrain3d_Hemisphere/GNUmakefile

@@ -28,5 +28,5 @@ USE_ASSERTION = TRUE
 Bpack := ./Make.package
 Blocs := .
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/Terrain3d_Hemisphere
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/Terrain3d_Hemisphere
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/TurbulentInflow/GNUmakefile

@@ -31,5 +31,5 @@ USE_POISSON_SOLVE = FALSE
 Bpack := ./Make.package
 Blocs := .
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/TurbulentInflow
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/TurbulentInflow
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/WPS_Test/GNUmakefile

@@ -32,5 +32,5 @@ Bpack := ./Make.package
 Blocs := .
 
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/WPS_Test
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/WPS_Test
 include $(ERF_HOME)/Exec/Make.ERF

Exec/DryRegTests/WitchOfAgnesi/GNUmakefile

@@ -29,5 +29,5 @@ Bpack := ./Make.package
 Blocs := .
 
 ERF_HOME := ../../..
-ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/RegTests/WitchOfAgnesi
+ERF_PROBLEM_DIR = $(ERF_HOME)/Exec/DryRegTests/WitchOfAgnesi
 include $(ERF_HOME)/Exec/Make.ERF