(Semi-)Compiled input decks

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "external/kokkos"]
 	path = external/Kokkos
 	url = https://github.com/kokkos/kokkos.git
+[submodule "external/rummy"]
+	path = external/rummy
+	url = https://github.com/lanl/rummy.git

CMakeLists.txt

@@ -404,6 +404,22 @@ set(CMAKE_INSTALL_INCLUDEDIR "${CMAKE_INSTALL_INCLUDEDIR}/parthenon")
 set(DOC_GEN_PATH "${CMAKE_SOURCE_DIR}/doc/sphinx/src/generated" CACHE STRING
   "Path to save generated data for docs.")
 
+find_package(Rummy QUIET)
+
+if (NOT Rummy_FOUND)
+  # If Rummy is not found, instead use the git submodule
+  if (NOT EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/external/rummy/single_include)
+    # Unable to find the header files for Rummy or they don't exist
+    message(STATUS "Downloading Rummy submodule.")
+
+    # Clone the submodule
+    execute_process(COMMAND git submodule update --init --force -- external/rummy WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+  endif()
+
+  add_subdirectory(external/rummy)
+  list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/external/rummy/contrib")
+endif()
+
 add_subdirectory(src)
 add_subdirectory(example)
 add_subdirectory(benchmarks)

example/advection/parthinput.advection

@@ -16,29 +16,29 @@
 # ========================================================================================
 
 <parthenon/job>
-problem_id = advection
+problem_id = "advection"
 
 <parthenon/mesh>
-refinement = adaptive
+refinement = "adaptive"
 numlevel = 3
 
 nx1 = 64
 x1min = -0.5
 x1max = 0.5
-ix1_bc = periodic
-ox1_bc = periodic
+ix1_bc = "periodic"
+ox1_bc = "periodic"
 
 nx2 = 64
 x2min = -0.5
 x2max = 0.5
-ix2_bc = periodic
-ox2_bc = periodic
+ix2_bc = "periodic"
+ox2_bc = "periodic"
 
 nx3 = 1
 x3min = -0.5
 x3max = 0.5
-ix3_bc = periodic
-ox3_bc = periodic
+ix3_bc = "periodic"
+ox3_bc = "periodic"
 
 <parthenon/meshblock>
 nx1 = 16
@@ -48,15 +48,15 @@ nx3 = 1
 <parthenon/time>
 nlim = -1
 tlim = 1.0
-integrator = rk2
+integrator = "rk2"
 ncycle_out_mesh = -10000
 
 <Advection>
 cfl = 0.45
 vx = 1.0
 vy = 1.0
 vz = 1.0
-profile = hard_sphere
+profile = "hard_sphere"
 
 refine_tol = 0.3    # control the package specific refinement tagging function
 derefine_tol = 0.03
@@ -66,28 +66,28 @@ vec_size = 1 # size of each variable
 fill_derived = false # whether to fill one-copy test vars
 
 <parthenon/output1>
-file_type = rst
+file_type = "rst"
 dt = 0.05
 
 <parthenon/output0>
-file_type = hdf5
+file_type = "hdf5"
 dt = 0.05
-variables = advected, advected_1, & # comments are ok
-            one_minus_advected, &
-            one_minus_advected_sq, & # on every (& characters are ok in comments)
-            one_minus_sqrt_one_minus_advected_sq, & # line
-            my_derived_var
+variables = "advected", "advected_1", & # comments are ok
+            "one_minus_advected", &
+            "one_minus_advected_sq", & # on every (& characters are ok in comments)
+            "one_minus_sqrt_one_minus_advected_sq", & # line
+            "my_derived_var"
 
 <parthenon/output3>
-file_type = hst
+file_type = "hst"
 dt = 0.05
 
 <parthenon/output4>
-file_type = hst
+file_type = "hst"
 dt = 0.1
-packages = advection_app
+packages = "advection_app"
 
 <parthenon/output5>
-file_type = ascent
+file_type = "ascent"
 dt = -0.05   # soft disabled by default, as Ascent is an optional dependency
-actions_file = custom_ascent_actions.yaml
+actions_file = "custom_ascent_actions.yaml"

example/boundary_exchange/parthinput.example

@@ -12,10 +12,10 @@
 # ========================================================================================
 
 <parthenon/job>
-problem_id = boundary_exchange
+problem_id = "boundary_exchange"
 
 <parthenon/mesh>
-refinement = static
+refinement = "static"
 numlevel = 1
 # The structure of the mesh is built in main as a forest
 
@@ -29,6 +29,6 @@ nx2 = 4
 nx3 = 1
 
 <parthenon/output0>
-file_type = hdf5
+file_type = "hdf5"
 ghost_zones = true
-variables = morton_num
+variables = "morton_num"

example/calculate_pi/parthinput.example

@@ -16,23 +16,23 @@
 # ========================================================================================
 
 <parthenon/job>
-problem_id = pi_calculator
+problem_id = "pi_calculator"
 
 <parthenon/mesh>
-refinement = adaptive
+refinement = "adaptive"
 numlevel = 5
 
 nx1 = 64
 x1min = -2.0
 x1max = 2.0
-ix1_bc = outflow
-ox1_bc = outflow
+ix1_bc = "outflow"
+ox1_bc = "outflow"
 
 nx2 = 64
 x2min = -2.0
 x2max = 2.0
-ix2_bc = outflow
-ox2_bc = outflow
+ix2_bc = "outflow"
+ox2_bc = "outflow"
 
 nx3 = 1
 x3min = -0.5
@@ -48,8 +48,8 @@ nx2 = 8
 nx3 = 1
 
 <parthenon/refinement0>
-field = in_or_out               # the name of the variable we want to refine on
-method = derivative_order_1     # selects the first derivative method
+field = "in_or_out"               # the name of the variable we want to refine on
+method = "derivative_order_1"     # selects the first derivative method
 refine_tol = 0.5                # tag for refinement if |(dfield/dx)/field| > refine_tol
 derefine_tol = 0.05             # tag for derefinement if |(dfield/dx)/field| < derefine_tol
 max_level = 2                   # if set, limits refinement level from this criteria to no greater than max_level
@@ -59,5 +59,5 @@ radius = 1.5
 use_sparse = 0 # Set to 1 to use sparse variables
 
 <parthenon/output0>
-file_type = hdf5
-variables = in_or_out
+file_type = "hdf5"
+variables = "in_or_out"

example/diffusion/parthinput.diffusion

@@ -16,29 +16,29 @@
 # ========================================================================================
 
 <parthenon/job>
-problem_id = diffusion
+problem_id = "diffusion"
 
 <parthenon/mesh>
-refinement = static
+refinement = "static"
 multigrid = true 
 
 nx1 = 64
 x1min = -1.0
 x1max = 1.0
-ix1_bc = outflow 
-ox1_bc = outflow
+ix1_bc = "outflow" 
+ox1_bc = "outflow"
 
 nx2 = 64
 x2min = -1.0
 x2max = 1.0
-ix2_bc = outflow
-ox2_bc = outflow
+ix2_bc = "outflow"
+ox2_bc = "outflow"
 
 nx3 = 1
 x3min = 0.0
 x3max = 1.0
-ix3_bc = periodic
-ox3_bc = periodic
+ix3_bc = "periodic"
+ox3_bc = "periodic"
 
 <parthenon/meshblock>
 nx1 = 32
@@ -48,25 +48,25 @@ nx3 = 1
 <parthenon/time>
 nlim = -1
 tlim = 0.02
-integrator = rk1
+integrator = "rk1"
 #ncycle_out_mesh = -10000
 
 <parthenon/output0>
-file_type = hdf5
+file_type = "hdf5"
 dt = 0.0001
-variables = diffusion.u
+variables = "diffusion.u"
 ghost_zones = false
 
 <parthenon/static_refinement0> 
 x1min = -0.15
-x1max = +0.15
+x1max = 0.15
 x2min = -0.15
-x2max = +0.15
+x2max = 0.15
 level = 3
 
 <diffusion>
 #solver = BiCGSTAB # or MG
-solver = MG
+solver = "MG"
 flux_correct = true
 diagonal_alpha = 1.0
 cfl = 10.0
@@ -82,5 +82,5 @@ precondition = true
 max_iterations = 20
 residual_tolerance = 1.e-9
 print_per_step = true
-smoother = SRJ2
+smoother = "SRJ2"
 do_FAS = true

example/fine_advection/parthinput.advection

@@ -12,29 +12,29 @@
 # ========================================================================================
 
 <parthenon/job>
-problem_id = advection
+problem_id = "advection"
 
 <parthenon/mesh>
-refinement = adaptive
+refinement = "adaptive"
 numlevel = 3
 
 nx1 = 64
 x1min = -0.5
 x1max = 0.5
-ix1_bc = periodic
-ox1_bc = periodic
+ix1_bc = "periodic"
+ox1_bc = "periodic"
 
 nx2 = 64
 x2min = -0.5
 x2max = 0.5
-ix2_bc = periodic
-ox2_bc = periodic
+ix2_bc = "periodic"
+ox2_bc = "periodic"
 
 nx3 = 1
 x3min = -0.5
 x3max = 0.5
-ix3_bc = periodic
-ox3_bc = periodic
+ix3_bc = "periodic"
+ox3_bc = "periodic"
 
 <parthenon/meshblock>
 nx1 = 16
@@ -44,15 +44,15 @@ nx3 = 1
 <parthenon/time>
 nlim = -1
 tlim = 1.0
-integrator = rk2
+integrator = "rk2"
 ncycle_out_mesh = -10000
 
 <Advection>
 cfl = 0.45
 vx = 1.0
 vy = 1.0
 vz = 1.0
-profile = hard_sphere
+profile = "hard_sphere"
 
 refine_tol = 0.3    # control the package specific refinement tagging function
 derefine_tol = 0.03
@@ -65,10 +65,10 @@ do_fine_advection = true
 do_CT_advection = true
 
 <parthenon/output1>
-file_type = rst
+file_type = "rst"
 dt = 0.05
 
 <parthenon/output0>
-file_type = hdf5
+file_type = "hdf5"
 dt = 0.05
-variables = advection.scalar, advection.scalar_fine_restricted
+variables = "advection.scalar", "advection.scalar_fine_restricted"