Merge branch 'MFlowCode:master' into io

Author: wilfonba

.gitignore

@@ -28,6 +28,7 @@ __pycache__
 
 docs/*/initial*
 docs/*/result*
+docs/documentation/*-example.png
 docs/documentation/examples.md
 
 examples/*batch/*/

CMakeLists.txt

@@ -65,7 +65,18 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
     endif()
 elseif ((CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_Fortran_COMPILER_ID STREQUAL "PGI"))
     if (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 21.7)
-        message(FATAL_ERROR "${__err_msg}ERROR: NVHPC v21.7 or newer is required to build MFC.")
+        message(FATAL_ERROR "${__err_msg}ERROR: When using NVHPC, v21.7 or newer is required to build MFC.")
+    endif()
+    if (MAKE_BUILD_TYPE STREQUAL "Debug")
+        if (MFC_OpenACC)
+            if (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 23.0)
+                message(FATAL_ERROR "${__err_msg}ERROR: When using NVHPC, v23.0 or newer is required to build MFC with Debug and GPU options.")
+            endif()
+        else()
+            if (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 23.8)
+                message(FATAL_ERROR "${__err_msg}ERROR: Debug is not working with NVHPC 23.X and older and CPU options at present.")
+            endif()
+        endif()
     endif()
 elseif (CMAKE_Fortran_COMPILER_ID STREQUAL "AppleClang" OR CMAKE_C_COMPILER_ID STREQUAL "AppleClang")
     message(FATAL_ERROR "${__err_msg}ERROR: MFC does not support the Apple Clang compilers. Please consult the documentation.")
@@ -145,7 +156,7 @@ elseif ((CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_Fortran_COMPILER_
     endif()
 
     if (CMAKE_BUILD_TYPE STREQUAL "Debug")
-        add_compile_options(-C -g -traceback -Mchkptr -Mchkstk -Minform=inform -Mbounds)
+        add_compile_options(-C -g -O0 -traceback -Mchkptr -Mchkstk -Minform=inform -Mbounds)
     endif()
 endif()
 
@@ -229,6 +240,8 @@ macro(HANDLE_SOURCES target useCommon)
     set(${target}_DIR "${CMAKE_SOURCE_DIR}/src/${target}")
     set(common_DIR    "${CMAKE_SOURCE_DIR}/src/common")
 
+    string(TOUPPER ${target} ${target}_UPPER)
+
     # Gather src/[<target>,common]/*.f90
     file(GLOB ${target}_F90s CONFIGURE_DEPENDS "${${target}_DIR}/*.f90")
     set(${target}_SRCs ${${target}_F90s})
@@ -245,9 +258,9 @@ macro(HANDLE_SOURCES target useCommon)
     endif()
 
     # Locate src/[<target>,common]/include/*.fpp
-    if (EXISTS "${${target}_DIR}/include")
-        file(GLOB ${target}_incs CONFIGURE_DEPENDS "${${target}_DIR}/include/*.fpp")
-    endif()
+    file(GLOB ${target}_incs CONFIGURE_DEPENDS "${${target}_DIR}/include/*.fpp"
+                                               "${CMAKE_CURRENT_BINARY_DIR}/include/*.fpp")
+
     if (${useCommon})
         file(GLOB common_incs CONFIGURE_DEPENDS "${common_DIR}/include/*.fpp")
         list(APPEND ${target}_incs ${common_incs})
@@ -261,11 +274,14 @@ macro(HANDLE_SOURCES target useCommon)
         add_custom_command(
             OUTPUT   ${f90}
             COMMAND  ${FYPP_EXE} -m re
-                                 -I "${common_DIR}"
-                                 -I "${common_DIR}/include"
+                                 -I "${CMAKE_CURRENT_BINARY_DIR}/include"
                                  -I "${${target}_DIR}/include"
+                                 -I "${common_DIR}/include"
+                                 -I "${common_DIR}"
                                  -D MFC_${CMAKE_Fortran_COMPILER_ID}
+                                 -D MFC_${${target}_UPPER}
                                  -D MFC_COMPILER="${CMAKE_Fortran_COMPILER_ID}"
+                                 -D MFC_CASE_OPTIMIZATION=False
                                  --line-numbering
                                  --no-folding
                                  "${fpp}" "${f90}"
@@ -317,10 +333,10 @@ function(MFC_SETUP_TARGET)
             "${CMAKE_SOURCE_DIR}/src/${ARGS_TARGET}/include")
     endif()
 
-    string(TOUPPER "${ARGS_TARGET}" ARGS_TARGET_UPPER)
+    string(TOUPPER "${ARGS_TARGET}" ${ARGS_TARGET}_UPPER)
     target_compile_definitions(
         ${ARGS_TARGET} PRIVATE MFC_${CMAKE_Fortran_COMPILER_ID}
-                               MFC_${ARGS_TARGET_UPPER}
+                               MFC_${${ARGS_TARGET}_UPPER}
     )
 
     if (MFC_MPI AND ARGS_MPI)
@@ -430,6 +446,19 @@ if (MFC_SYSCHECK)
 endif()
 
 if (MFC_DOCUMENTATION)
+    # Files in docs/examples are used to generate docs/documentation/examples.md
+    file(GLOB_RECURSE examples_DOCs CONFIGURE_DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/examples/*")
+
+    add_custom_command(
+        OUTPUT  "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/examples.md"
+        DEPENDS "${examples_DOCs}"
+        COMMAND "bash" "${CMAKE_CURRENT_SOURCE_DIR}/docs/examples.sh" 
+                       "${CMAKE_CURRENT_SOURCE_DIR}"
+        COMMENT "Generating examples.md"
+    )
+
+    file(GLOB common_DOCs CONFIGURE_DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/*")
+
     # GEN_DOCS: Given a target name (herein <target>), this macro sets up a
     # target, <target>_docs, that generates documentation for <target> using
     # Doxygen. It is then added as a dependency of the documentation target.
@@ -456,13 +485,20 @@ if (MFC_DOCUMENTATION)
             "${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in"
             "${CMAKE_CURRENT_BINARY_DIR}/${target}-Doxyfile" @ONLY)
 
+        set(opt_example_dependency "")
+        if (target STREQUAL "documentation")
+            set(opt_example_dependency "${CMAKE_CURRENT_SOURCE_DIR}/docs/documentation/examples.md")
+        endif()
+
+        file(GLOB_RECURSE ${target}_DOCs CONFIGURE_DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/docs/${target}/*")
+        list(APPEND ${target}_DOCs "${common_DOCs}")
+
         add_custom_command(
             OUTPUT  "${CMAKE_CURRENT_BINARY_DIR}/${target}/html/index.html"
             DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/${target}-Doxyfile"
-                    "${${target}_SRCs}"
-            COMMAND  "bash" "${CMAKE_CURRENT_SOURCE_DIR}/docs/examples.sh" 
-                            "${CMAKE_CURRENT_SOURCE_DIR}" && 
-                    "${DOXYGEN_EXECUTABLE}" "${target}-Doxyfile"
+                    "${opt_example_dependency}"
+                    "${${target}_SRCs}" "${${target}_DOCs}"
+            COMMAND "${DOXYGEN_EXECUTABLE}" "${target}-Doxyfile"
             WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}"
             COMMENT "${target}: Generating documentation"
         )
@@ -487,7 +523,7 @@ if (MFC_DOCUMENTATION)
     ExternalProject_Add(doxygen-awesome-css
         PREFIX            doxygen-awesome-css
         GIT_REPOSITORY    "https://github.com/jothepro/doxygen-awesome-css"
-        GIT_TAG           "df83fbf22cfff76b875c13d324baf584c74e96d0"
+        GIT_TAG           "df88fe4fdd97714fadfd3ef17de0b4401f804052"
         CONFIGURE_COMMAND ""
         BUILD_COMMAND     ""
         INSTALL_COMMAND   ""

docs/documentation/case.md

@@ -509,18 +509,24 @@ Implementation of the parameterse into the model follow [Ando (2010)](references
 | Parameter           | Type    | Description |
 | ---:                | :----:  | :--- |
 | `perturb_flow`      | Logical | Perturb the initlal velocity field by random noise |
+| `perturb_flow_fluid`       | Integer | Fluid density whose flow is to be perturbed |
+| `perturb_flow_mag`       | Real | Set the magnitude of flow perturbations |
 | `perturb_sph`       | Logical | Perturb the initial partial density by random noise |
-| `perturb_sph_fluid` | Integer | Fluid component whose partial density to be perturbed |
+| `perturb_sph_fluid` | Integer | Fluid component whose partial density is to be perturbed |
 | `vel_profile`       | Logical | Set the mean streamwise velocity to hyperbolic tangent profile |
 | `instability_wave`  | Logical | Perturb the initial velocity field by instability waves |
 
 The table lists velocity field parameters. The parameters are optionally used to define initial velocity profiles and perturbations.
 
 - `perturb_flow` activates the perturbation of initial velocity by random noise.
 
-- `perturb_sph` activates the perturbation of intial partial density by random noise. 
+- `perturb_flow_fluid` specifies the fluid component whose flow is to be perturbed.
 
-- `perturb_sph_fluid` specifies the fluid component whose the partial density to be perturbed.
+- `perturb_flow` activates the perturbation of initial velocity by random noise.
+
+- `perturb_sph` activates the perturbation of initial partial density by random noise. 
+
+- `perturb_sph_fluid` specifies the fluid component whose partial density is to be perturbed.
 
 - `vel_profile` activates setting the mean streamwise velocity to hyperbolic tangent profile. This option works only for 2D and 3D cases.
 

docs/examples.sh

@@ -7,19 +7,15 @@ rm "$examples_md" || true
 
 echo -e "# Example Cases\n" > "$examples_md"
 
-for casedir in $(find "$1/examples/" -maxdepth 1 -type d); do
-    casename="$(basename $casedir)"
-
-    if [ "$casename" == "examples" ]; then
-        continue
-    fi
+for casedir in $(find "$1/examples/" -mindepth 1 -maxdepth 1 -type d); do
+    casename="$(basename "$casedir")"
 
     if [ -f "$casedir/README.md" ]; then
-        sed -e "s/\.png/-$casename\.png/g" "$casedir/README.md" | sed 's/^#/##/g' >> "$examples_md"
-        echo "" >> "$examples_md"
+        sed -e "s/\.png/-$casename-example\.png/g" "$casedir/README.md" | sed 's/^#/##/g' >> "$examples_md"
+        echo '' >> "$examples_md"
 
-        for png in $(find "$casedir" -maxdepth 1 -name "*.png"); do
-            cp "$png" "$1/docs/documentation/$(basename $png | sed s/\.png//g)-$casename.png"
+        for png in $(find "$casedir" -maxdepth 1 -name '*.png'); do
+            cp "$png" "$1/docs/documentation/$(basename "$png" | sed s/\.png//g)-$casename-example.png"
         done
     fi
 done

src/pre_process/include/case.fpp

@@ -1,7 +1,4 @@
-! This file was generated by MFC. It is only used when analytical patches are
-! present in the input file. It is used to define the analytical patches with
-! expressions that are evaluated at runtime from the input file.
+! By default, no analytical patches are defined.
 
 #:def analytical()
-
 #:enddef

src/pre_process/m_check_patches.fpp

@@ -302,6 +302,7 @@ contains
 
     end subroutine s_check_2D_TaylorGreen_vortex_patch_geometry! --------------
 
+
     !>  This subroutine verifies that the geometric parameters of
         !!      the analytical patch have consistently been inputted by
         !!      the user.

src/pre_process/m_checker.f90

@@ -543,11 +543,15 @@ subroutine s_check_inputs()
             call s_mpi_abort('Unsupported choice for the value of '// &
                 'num_patches. Exiting ...')
             ! Constraints on perturbing the initial condition
-        elseif ((perturb_flow .and. perturb_flow_fluid == dflt_int) &
+        elseif ((perturb_flow &
+                .and. &
+                (perturb_flow_fluid == dflt_int .or. perturb_flow_mag == dflt_real)) &
                 .or. &
-                ((perturb_flow .neqv. .true.) .and. (perturb_flow_fluid /= dflt_int))) then
+                ((perturb_flow .neqv. .true.) &
+                .and. &
+                (perturb_flow_fluid /= dflt_int .or. perturb_flow_mag /= dflt_real))) then
             call s_mpi_abort('Unsupported choice of the combination of '// &
-                'values for perturb_flow and perturb_flow_fluid. '// &
+                'values for perturb_flow, perturb_flow_fluid, and perturb_flow_mag. '// &
                 'Exiting ...')
         elseif ((perturb_flow_fluid > num_fluids) &
                 .or. &

src/pre_process/m_global_parameters.fpp

@@ -104,6 +104,7 @@ module m_global_parameters
     ! Perturb density of surrounding air so as to break symmetry of grid
     logical :: perturb_flow
     integer :: perturb_flow_fluid   !< Fluid to be perturbed with perturb_flow flag
+    real(kind(0d0)) :: perturb_flow_mag   !< Magnitude of perturbation with perturb_flow flag
     logical :: perturb_sph
     integer :: perturb_sph_fluid    !< Fluid to be perturbed with perturb_sph flag
     real(kind(0d0)), dimension(num_fluids_max) :: fluid_rho
@@ -256,6 +257,7 @@ contains
         instability_wave = .false.
         perturb_flow = .false.
         perturb_flow_fluid = dflt_int
+        perturb_flow_mag = dflt_real
         perturb_sph = .false.
         perturb_sph_fluid = dflt_int
         fluid_rho = dflt_real

src/pre_process/m_initial_condition.fpp

@@ -324,7 +324,7 @@ contains
 !                            q_prim_vf(perturb_flow_fluid)%sf(i,j,k) = q_prim_vf(perturb_flow_fluid)%sf(i,j,k) + rand_real
                     ! Perturb velocity
                     call random_number(rand_real)
-                    rand_real = rand_real*1.d-2
+                    rand_real = rand_real*perturb_flow_mag
                     q_prim_vf(mom_idx%beg)%sf(i, j, k) = (1.d0 + rand_real)*q_prim_vf(mom_idx%beg)%sf(i, j, k)
                     q_prim_vf(mom_idx%end)%sf(i, j, k) = rand_real*q_prim_vf(mom_idx%beg)%sf(i, j, k)
                     if (bubbles) then

src/pre_process/m_mpi_proxy.fpp

@@ -65,8 +65,8 @@ contains
             & 'y_domain%end', 'z_domain%beg', 'z_domain%end', 'a_x', 'a_y',    &
             & 'a_z', 'x_a', 'x_b', 'y_a', 'y_b', 'z_a', 'z_b', 'bc_x%beg',     &
             & 'bc_x%end', 'bc_y%beg', 'bc_y%end', 'bc_z%beg', 'bc_z%end',      &
-            & 'pref', 'rhoref', 'poly_sigma', 'R0ref', 'Web', 'Ca', 'Re_inv',  &
-            & 'sigR', 'sigV', 'rhoRV' ]
+            & 'perturb_flow_mag', 'pref', 'rhoref', 'poly_sigma', 'R0ref',     &
+            & 'Web', 'Ca', 'Re_inv', 'sigR', 'sigV', 'rhoRV' ]
             call MPI_BCAST(${VAR}$, 1, MPI_DOUBLE_PRECISION, 0, MPI_COMM_WORLD, ierr)
         #:endfor