Add Jupiter CRM (#103)

add jupiter_crm to test case
chengcli · Oct 31, 2023 · e2ae7e7 · e2ae7e7
1 parent 146332f
commit e2ae7e7
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Showing 40 changed files with 685 additions and 368 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -77,6 +77,14 @@ endif()
 
 ## 6. set up unit tests and examples
 message(STATUS "6. Set up unit tests")
+
+# load all macros
+FILE(GLOB _macro_files "${CMAKE_SOURCE_DIR}/cmake/macros/*.cmake")
+FOREACH(_file ${_macro_files})
+  MESSAGE(STATUS "Include ${_file}")
+  INCLUDE(${_file})
+ENDFOREACH()
+
 add_subdirectory(examples)
 add_subdirectory(tests)
 

diff --git a/cmake/sedimentation.cmake → cmake/jupiter_crm.cmake b/cmake/sedimentation.cmake → cmake/jupiter_crm.cmake
@@ -1,4 +1,4 @@
-# configure file for test sedimentation
+# configure file for test jupiter crm
 
 macro(SET_IF_EMPTY _variable)
   if("${${_variable}}" STREQUAL "")
@@ -10,8 +10,8 @@ endmacro()
 set_if_empty(NUMBER_GHOST_CELLS 3)
 
 # canoe configure
-set(NVAPOR 2)
-set(NCLOUD 4)
+set(NVAPOR 1)
+set(NCLOUD 2)
 set(NPHASE_LEGACY 3)
 set(NETCDF ON)
 set(PNETCDF ON)

diff --git a/cmake/macros/macro_setup_problem.cmake b/cmake/macros/macro_setup_problem.cmake
@@ -0,0 +1,23 @@
+# A small macro used for setting up the build of a problem.
+#
+# Usage: setup_problem(name)
+
+string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
+string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
+
+macro(setup_problem namel)
+  add_executable(${namel}.${buildl} ${namel}.cpp
+                                    ${CMAKE_BINARY_DIR}/main_${TASK}.cpp)
+
+  set_target_properties(
+    ${namel}.${buildl}
+    PROPERTIES RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
+               COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}})
+
+  target_link_libraries(${namel}.${buildl} ${CANOE_LIBRARY_${buildu}})
+
+  target_include_directories(
+    ${namel}.${buildl}
+    PRIVATE ${CMAKE_BINARY_DIR} ${CANOE_INCLUDE_DIR} ${EIGEN3_INCLUDE_DIR}
+            ${MPI_CXX_INCLUDE_PATH} ${NETCDF_INCLUDES} ${PNETCDF_INCLUDE_DIR})
+endmacro()
diff --git a/cmake/macros/macro_setup_test.cmake b/cmake/macros/macro_setup_test.cmake
@@ -0,0 +1,31 @@
+# A small macro used for setting up the build of a test.
+#
+# Usage: setup_test(name)
+
+macro(setup_test namel)
+  string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
+  string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
+
+  add_executable(${namel}.${buildl} ${namel}.cpp globals.cpp)
+
+  set_target_properties(${namel}.${buildl}
+                        PROPERTIES COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}})
+
+  target_include_directories(
+    ${namel}.${buildl}
+    PRIVATE $<$<BOOL:${PVFMM}>:${PVFMM_SOURCE_DIR}/SCTL/include>
+            ${CMAKE_BINARY_DIR}
+            ${CANOE_INCLUDE_DIR}
+            ${EIGEN3_INCLUDE_DIR}
+            ${MPI_CXX_INCLUDE_PATH}
+            ${NETCDF_INCLUDES}
+            ${PNETCDF_INCLUDE_DIR}
+            ${OpenMP_CXX_INCLUDE_DIR}
+            ${FFTW_INCLUDE_DIRS})
+
+  target_link_libraries(
+    ${namel}.${buildl} gtest_main $<$<BOOL:${PVFMM}>:pvfmmStatic>
+    ${CANOE_LIBRARY_${buildu}})
+
+  add_test(NAME ${namel}.${buildl} COMMAND ${namel}.${buildl})
+endmacro()
diff --git a/examples/2019-Li-snap/CMakeLists.txt b/examples/2019-Li-snap/CMakeLists.txt
@@ -1,56 +1,20 @@
-string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
-string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
+# ============================================
+# Examples published in Li et al. (2019), ApJS
+# ============================================
 
-macro(setup_problem namel)
-  set_target_properties(
-      ${namel}.${buildl}
-      PROPERTIES
-      RUNTIME_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/bin"
-      COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}}
-      )
+# 1. Compile straka, robert and bryan
+setup_problem(straka)
+setup_problem(robert)
+setup_problem(bryan)
 
-  target_link_libraries(${namel}.${buildl}
-      ${CANOE_LIBRARY_${buildu}}
-      )
-
-  target_include_directories(${namel}.${buildl}
-      PRIVATE
-      ${CMAKE_BINARY_DIR}
-      ${CANOE_INCLUDE_DIR}
-      ${EIGEN3_INCLUDE_DIR}
-      ${MPI_CXX_INCLUDE_PATH}
-      ${NETCDF_INCLUDES}
-      ${PNETCDF_INCLUDE_DIR}
-      )
-endmacro()
-
-# 1. Compile straka and robert
-foreach(namel straka robert)
-  add_executable(${namel}.${buildl} ${namel}.cpp
-    ${CMAKE_BINARY_DIR}/main_${TASK}.cpp)
-  setup_problem(${namel})
-endforeach()
-
-# 2. Compile bryan
-if (${NVAPOR} EQUAL 1 AND ${NCLOUD} EQUAL 1 AND ${NPHASE_LEGACY} EQUAL 2)
-  set(namel bryan)
-
-  add_executable(${namel}.${buildl} ${namel}_pgen.cpp ${namel}_mods.cpp
-    ${CMAKE_BINARY_DIR}/main_${TASK}.cpp)
-
-  setup_problem(${namel})
-endif()
-
-# 3. Compile sedimentation
+# 2. Compile sedimentation
 if (${NVAPOR} EQUAL 2 AND ${NCLOUD} EQUAL 4 AND ${NPHASE_LEGACY} EQUAL 3)
-  set(namel sedimentation)
-
-  add_executable(${namel}.${buildl} ${namel}.cpp ../giants_enroll_vapor_functions.cpp
-    ${CMAKE_BINARY_DIR}/main_${TASK}.cpp)
-
-  setup_problem(${namel})
+  setup_problem(sedimentation)
 endif()
 
+# 3. Compile jupiter crm
+setup_problem(jupiter_crm)
+
 # 4. Copy input files to run directory
 file(GLOB inputs *.inp *.yaml)
 foreach(input ${inputs})

diff --git a/examples/2019-Li-snap/bryan_pgen.cpp → examples/2019-Li-snap/bryan.cpp b/examples/2019-Li-snap/bryan_pgen.cpp → examples/2019-Li-snap/bryan.cpp
@@ -38,6 +38,9 @@
 // snap
 #include <snap/thermodynamics/thermodynamics.hpp>
 
+// special includes
+#include "bryan_vapor_functions.hpp"
+
 int iH2O, iH2Oc;
 Real p0, grav;
 

diff --git a/examples/2019-Li-snap/bryan_mods.cpp → ...es/2019-Li-snap/bryan_vapor_functions.hpp b/examples/2019-Li-snap/bryan_mods.cpp → ...es/2019-Li-snap/bryan_vapor_functions.hpp
@@ -12,17 +12,19 @@ double sat_vapor_p_H2O(double T) {
   return SatVaporPresIdeal(T / tr, pr, betal, gammal);
 }
 
-void Thermodynamics::enrollVaporFunctions() { enrollVaporFunctionH2O(); }
-
 // water svp
-void Thermodynamics::enrollVaporFunctionH2O() {
+void enroll_vapor_Function_H2O(Thermodynamics::SVPFunc1Container &svp_func1) {
   Application::Logger app("snap");
   app->Log("Enrolling H2O vapor pressures");
 
   auto pindex = IndexMap::GetInstance();
   int iH2O = pindex->GetVaporId("H2O");
 
-  svp_func1_[iH2O][0] = [](AirParcel const &qfrac, int, int) {
+  svp_func1[iH2O][0] = [](AirParcel const &qfrac, int, int) {
     return sat_vapor_p_H2O(qfrac.w[IDN]);
   };
 }
+
+void Thermodynamics::enrollVaporFunctions() {
+  enroll_vapor_Function_H2O(svp_func1_);
+}
diff --git a/examples/2019-Li-snap/jupiter2d.inp b/examples/2019-Li-snap/jupiter2d.inp
@@ -0,0 +1,99 @@
+<comment>
+problem     = test jupiter
+
+<job>
+problem_id  = jupiter2d     # problem ID: basename of output filenames
+
+<output0>
+file_type   = rst
+dt          = 10.E5
+
+<output1>
+file_type   = hst           # History data dump
+dt          = 2.E4          # time increment between outputs
+
+<output2>
+file_type   = netcdf        # Netcdf format output
+variable    = prim          # variables to be output
+dt          = 1.E4          # time increment between outputs
+
+<output3>
+file_type   = netcdf        # Netcdf format output
+variable    = uov           # diagnostic variables
+dt          = 1.E4          # time increment
+
+<time>
+cfl_number  = 0.9
+nlim        = -1            # cycle limit
+tlim        = 2.E5
+xorder      = 5             # horizontal reconstruction order
+integrator  = rk3           # integration method
+
+<mesh>
+nx1         = 80          # Number of zones in X1-direction
+x1min       = -320.E3     # minimum value of X1
+x1max       = 40.E3       # maximum value of X1
+ix1_bc      = reflecting  # Inner-X1 boundary condition flag
+ox1_bc      = reflecting  # Outer-X1 boundary condition flag
+
+nx2         = 320         # Number of zones in X2-direction
+x2min       = 0.          # minimum value of X2
+x2max       = 3200.E3     # maximum value of X2
+ix2_bc      = periodic    # Inner-X2 boundary condition flag
+ox2_bc      = periodic    # Outer-X2 boundary condition flag
+
+nx3         = 1           # Number of zones in X3-direction
+x3min       = -0.5        # minimum value of X3
+x3max       = 0.5         # maximum value of X3
+ix3_bc      = periodic    # Inner-X3 boundary condition flag
+ox3_bc      = periodic    # Outer-X3 boundary condition flag
+
+<meshblock>
+nx1         = 80
+nx2         = 40
+nx3         = 1
+
+<hydro>
+gamma       = 1.42
+grav_acc1   = -24.79
+implicit_flag = 1
+
+#<species>
+#vapor = H2O, NH3
+#cloud = H2O(c), NH3(c), H2O(p), NH3(p)
+
+<species>
+vapor = H2O
+cloud = H2O(c), H2O(p)
+
+<chemistry>
+microphysics_config = water_ammonia.yaml
+
+<thermodynamics>
+Rd          = 3777.   # mu = 2.3175 g/mol
+eps1        = 8.18    8.18    8.18
+beta1       = 0.      24.845  24.845
+rcp1        = 0.15    0.33    0.33
+Ttriple1    = 273.16
+Ptriple1    = 611.7
+
+eps2        = 7.72    7.72    7.72
+rcp2        = 0.078   0.16    0.16
+beta2       = 0.      23.67   23.67
+Ttriple2    = 195.4
+Ptriple2    = 6060.
+
+sa.relax    = 1.0
+sa.max_iter = 4
+sa.ftol     = 1.e-2
+
+<problem>
+qH2O.ppmv   = 25000.
+qNH3.ppmv   = 320.
+
+P0          = 1.E5
+T0          = 169.
+Tmin        = 110.
+hrate       = -100.
+prad        = 2.e5
+init_Ttol   = 2.