Update to OPS-LT v5.0.2.1

COMPILING.md

@@ -0,0 +1,137 @@
+# Compiling OPS
+
+This is a short manual on how to compile the OPS model on a Linux machine.
+
+## Dependencies
+
+The following dependencies are required:
+
+* Intel `ifort` Fortran compiler (RIVM uses version 2021.3.0 downloaded from [Intel oneAPI HPC](https://www.intel.com/content/www/us/en/developer/tools/oneapi/hpc-toolkit-download.html))
+* CMake (RIVM uses version 3.18.2 downloaded from [cmake](https://cmake.org/download/))
+* math77 library (RIVM uses Release 6 downloaded from [netlib](https://netlib.org/math/))
+* pFUnit (RIVM uses [commit 594a6e2](https://github.com/Goddard-Fortran-Ecosystem/pFUnit/commit/594a6e2d26df70d45ead4392da65cdec69a0b869))
+
+First, download and install/compile the above dependencies before proceeding.
+
+## Compiling
+
+After the dependencies are installed, OPS can be compiled using CMake. The OPS model is split into two parts (a library and an executable) that should be compiled separately.
+
+### Specifying environment variables
+
+The following environment variables need to be specified:
+
+The build type. Choose from `Debug` or `Release`. The `Debug` version turns off optimizations and turns on tracebacks, warnings and debugging information.
+Use the `Debug` version during development. The `Release` version results in an optimized executable, which should typically be used.
+The specific compiler flags can be found in the `./ops_lib/CMakeLists.txt` and `./ops_lt/CMakeLists.txt` files. 
+
+```bash
+export CMAKE_BUILD_TYPE="Release" 
+```
+
+The location of the Math77 and pFUnit libraries. Example paths should be changed to the appropriate location on your system.
+
+```bash
+export MATHLIB_DIR="/home/user/MATH77/"
+export PFUNIT_DIR="/home/user/pfunit/src/build/"
+```
+
+### Compiling the OPS library
+
+First, change to the `ops_lib` folder and set its path as our `CMAKE_TOPDIR`:
+
+```bash
+cd ops_lib
+export CMAKE_TOPDIR=`realpath .`
+```
+
+Create a `build` directory for cmake and change into it:
+```bash
+mkdir build
+cd build
+```
+
+Next, we can compile the OPS library using CMake. First, we need to generate the necessary CMake files as follows:
+
+```bash
+cmake -DCMAKE_BUILD_TYPE="${CMAKE_BUILD_TYPE}" \
+      -DBIN_DIR="${CMAKE_TOPDIR}/bin" -DSRC_DIR="${CMAKE_TOPDIR}/src" \
+      -DMOD_DIR="${CMAKE_TOPDIR}/build/mod" \
+      -DTST_DIR="${CMAKE_TOPDIR}/tst" \
+      -DMOD_TST_DIR="${CMAKE_TOPDIR}/build/mod_tst" \
+      -DCOV_DIR="${CMAKE_TOPDIR}/build/codecov" \
+      -DMATHLIB_DIR="${MATHLIB_DIR}" \
+      -DPFUNIT_DIR="${PFUNIT_DIR}" "${CMAKE_TOPDIR}"
+```
+
+Then, we can build the library:
+
+```bash
+cmake --build .
+```
+
+In the final step, the library is installed into the `../bin` folder:
+
+```bash
+cmake --install .
+```
+
+Now, it is ready to be used by the main OPS executable. First, store the path of the `bin` folder:
+
+```bash
+export OPSLIB_DIR="${CMAKE_TOPDIR}/bin/"
+```
+
+Optionally, the unit tests can be run with:
+
+```bash
+cd ..
+./bin/tst.exe
+```
+
+### Compiling the OPS executable
+
+Then, change to the `ops_lt` folder and set its path as our `CMAKE_TOPDIR`:
+
+```bash
+cd "${CMAKE_TOPDIR}/../ops_lt"
+export CMAKE_TOPDIR=`realpath .`
+```
+
+Create a `build` directory for cmake and change into it:
+```bash
+mkdir build
+cd build
+```
+
+Next, we can compile the final OPS executable using CMake. First, we need to generate the necessary CMake files as follows:
+
+```bash
+cmake -DCMAKE_BUILD_TYPE="${CMAKE_BUILD_TYPE}" \
+      -DBIN_DIR="${CMAKE_TOPDIR}/bin" -DSRC_DIR="${CMAKE_TOPDIR}/src" \
+      -DMOD_DIR="${CMAKE_TOPDIR}/build/mod" \
+      -DTST_DIR="${CMAKE_TOPDIR}/tst" \
+      -DMOD_TST_DIR="${CMAKE_TOPDIR}/build/mod_tst" \
+      -DCOV_DIR="${CMAKE_TOPDIR}/build/codecov" \
+      -DOPSLIB_DIR="${OPSLIB_DIR}" -DMATHLIB_DIR="${MATHLIB_DIR}" \
+      -DPFUNIT_DIR="${PFUNIT_DIR}" "${CMAKE_TOPDIR}"
+```
+
+Then, we can build the executable:
+
+```bash
+cmake --build .
+```
+
+In the final step, the executable is installed into the `../bin` folder:
+
+```bash
+cmake --install .
+```
+
+Optionally, the unit tests can be run with:
+
+```bash
+cd ..
+./bin/tst.exe
+```

ops_lib/.gitattributes

@@ -0,0 +1,2 @@
+# Set the default behavior for EOL conversion, in case people don't have core.autocrlf set.
+* text=auto

ops_lib/.gitignore

@@ -0,0 +1,56 @@
+# build directories
+build
+mod
+
+# .F90 files at test directory (are generated by pFUnit)
+tst/*.F90
+
+# Generated sources
+*__genmod.f90
+
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Code coverage files (unit tests)
+*.spi
+*.spl
+*.dyn
+*.200
+*.dpi
+*.dpi.lock
+
+# OPS output files
+*.log
+
+# vim
+*.swp

ops_lib/CMakeLists.txt

@@ -0,0 +1,67 @@
+# CMake project file for OPS-Lib
+cmake_minimum_required (VERSION 3.18)
+project (ops_lib Fortran)
+enable_language (Fortran)
+
+# Add our local modules (.cmake files) to the module path
+# Note: CMAKE_SOURCE_DIR is the top-level directory (where .git is located)
+#       CMAKE_MODULE_PATH specifies a search path for CMake modules to be loaded by include() or find_package()
+SET(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake/")
+
+# Directories should be specified as command line arguments (e.g. -D BLD_DIR=./build)
+# The following should be set:
+# BLD_DIR, BIN_DIR, SRC_DIR, MOD_DIR, TST_DIR, MOD_TST_DIR, COV_DIR
+# NETCDF_DIR, OPSLIB_DIR, MATHLIB_DIR, PFUNIT_DIR.
+
+# make sure that the default build type is DEBUG
+set ( CMAKE_CONFIGURATION_TYPES "Debug" "Release" "Coverage" )
+if (NOT CMAKE_BUILD_TYPE)
+  set (CMAKE_BUILD_TYPE DEBUG CACHE STRING
+      "Choose the type of build, options are: Debug, Release, Coverage."
+      FORCE)
+endif (NOT CMAKE_BUILD_TYPE)
+message (STATUS "CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
+
+# append build type to output files
+set(CMAKE_DEBUG_POSTFIX "_debug")
+set(CMAKE_RELEASE_POSTFIX "_optim")
+set(CMAKE_COVERAGE_POSTFIX "_cov")
+
+# Get name of Fortran compiler (without directory):
+get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
+
+# Compile flags depend on the compiler:
+if (Fortran_COMPILER_NAME MATCHES "ifort.*")
+  # ifort (default/preferred compiler)
+  set (CMAKE_Fortran_FLAGS_RELEASE "-nowarn -DUNIX -fpp -assume byterecl -O2 -extend-source -module ${MOD_DIR}")
+  set (CMAKE_Fortran_FLAGS_DEBUG   "-warn unused -diag-disable8291 -diag-disable7841 -DUNIX -fpp -assume byterecl -check -warn interfaces -debug-parameters all -traceback -O0 -g -extend-source -module ${MOD_DIR}") 
+  set (CMAKE_Fortran_FLAGS_COVERAGE   "${CMAKE_Fortran_FLAGS_DEBUG} -prof-gen=srcpos -prof-dir=${COV_DIR}") 
+else ()
+  message (STATUS "CMAKE_Fortran_COMPILER full path: " ${CMAKE_Fortran_COMPILER})
+  message (STATUS "Fortran compiler: " ${Fortran_COMPILER_NAME})
+  message (STATUS "No optimized Fortran compiler flags are known for compilers other than ifort, we just try -O2...")
+  set (CMAKE_Fortran_FLAGS_RELEASE "-O2")
+  set (CMAKE_Fortran_FLAGS_DEBUG   "-O0 -g")
+  set (CMAKE_Fortran_FLAGS_COVERAGE   "${CMAKE_Fortran_FLAGS_DEBUG} -prof-gen=srcpos -prof-dir=${COV_DIR}") 
+endif (Fortran_COMPILER_NAME MATCHES "ifort.*")
+
+# Rerun CMake if the library paths change
+set_property (DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${CMAKE_SOURCE_DIR}/library_paths_config.txt")
+
+# Double-check required library paths so we can give a clear error message
+if ("${MATHLIB_DIR}" STREQUAL "")
+    message(FATAL_ERROR "MATHLIB_DIR should be set in ${CMAKE_SOURCE_DIR}/library_paths_config.txt")
+endif()
+if ("${PFUNIT_DIR}" STREQUAL "")
+    message(FATAL_ERROR "PFUNIT_DIR should be set in ${CMAKE_SOURCE_DIR}/library_paths_config.txt")
+endif()
+
+# Find math77 library
+find_package (MATH77 REQUIRED)
+
+# OPS lib source files in src, put output files in build/mod directory; then process CMakeLists.txt in src:
+add_subdirectory(${SRC_DIR} ${MOD_DIR})
+
+# OPS lib tst files (.pf) in tst, put output files in build/mod_tst directory; then process CMakeLists.txt in tst:
+add_subdirectory(${TST_DIR} ${MOD_TST_DIR})
+

ops_lib/cmake/FindMATH77.cmake

@@ -0,0 +1,26 @@
+# - Find MATH77 lib. Note that MATH77 has not been built with CMake.
+include(FindPackageHandleStandardArgs)
+
+# Find path for MATH77 library and if lib exists:
+find_path(MATH77_INCLUDE_DIRS NAMES "libmath77_optim.a" PATHS "${MATHLIB_DIR}")
+find_library(MATH77_LIBRARIES math77_optim PATHS "${MATHLIB_DIR}")
+
+#message (" math include dir:  ${MATH77_INCLUDE_DIRS}: ")
+#message (" math lib:          ${MATH77_LIBRARIES}: ")
+
+# Set MATH77_FOUND; DEFAULT_MSG produces a standard error message if not found;
+# report succes (first time only) if found :
+find_package_handle_standard_args(MATH77
+ DEFAULT_MSG
+ MATH77_INCLUDE_DIRS
+ MATH77_LIBRARIES
+)
+
+# Set advanced state (for cmake-gui, so not necessary)
+mark_as_advanced(MATH77_LIBRARIES MATH77_INCLUDE_DIRS)
+
+# Set MATH77_LIBRARIES, MATH77_INCLUDE_DIRS; are used in other cmake scripts:
+# if(MATH77_FOUND)
+#   set(MATH77_LIBRARIES    ${MATH77_LIBRARY})
+#   set(MATH77_INCLUDE_DIRS ${MATH77_INCLUDE_DIR})
+# endif()

ops_lib/src/CMakeLists.txt

@@ -0,0 +1,23 @@
+# build OPS library
+
+# Make a list of .f90 source files:
+file(GLOB SRC_FILES *.f90)
+
+# Define ops library (static) 
+add_library(ops STATIC ${SRC_FILES})
+
+# Link MATH77 lib to ops lib:
+target_link_libraries(ops PUBLIC ${MATH77_LIBRARIES})
+
+# Set include directories to use when compiling target ops
+target_include_directories(ops PUBLIC ${MATH77_INCLUDE_DIRS})
+
+# After compilation, move .a (library archive) to ./bin
+install(TARGETS ops DESTINATION ${BIN_DIR})
+
+# After compilation, move .mod (module files) to ./bin/mod
+# Trailing slash of MOD_DIR important, so that we can choose the name
+# of the target directory
+install(DIRECTORY "${MOD_DIR}/" DESTINATION "${BIN_DIR}/mod"
+        FILES_MATCHING PATTERN "*.mod" # include files matching *.mod
+        PATTERN "CMakeFiles" EXCLUDE) # exclude the CMakeFiles directory

m_commonconst_lib.f90 → ops_lib/src/m_commonconst_lib.f90

@@ -28,7 +28,7 @@ MODULE m_commonconst_lib
 INTEGER*4, PARAMETER                             :: NMETREG     = 6                    ! number of meteo regions
 
 ! CONSTANTS (dimensions of distributions, building effect table)
-INTEGER*4, PARAMETER                             :: MAXDISTR    = 9999                 ! maximal number of distributions (for particle size or emission variation)    
+INTEGER*4, PARAMETER                             :: MAXDISTR    = 999999               ! maximal number of distributions (for particle size or emission variation)    
 INTEGER*4, PARAMETER                             :: ncolBuildingEffectTable = 5        ! 1st column corresponds to distance from building. 2-5 correspond to different building types
 ! 
 ! CONSTANTS - miscellaneous

m_commonfile.f90 → ops_lib/src/m_commonfile.f90

@@ -86,17 +86,19 @@ MODULE m_commonfile
 CHARACTER*512                                    :: lufile                     ! name of file with land use data
 CHARACTER*512                                    :: z0eurnam                   ! name of file with z0 values for Europe
 
-CHARACTER*24                                     :: map_so2(5)                 ! name of file with background map SO2 (for 4 years)
-CHARACTER*24                                     :: map_nox(5)                 ! name of file with background map NOx (for 4 years)
-CHARACTER*24                                     :: map_nh3(5)                 ! name of file with background map NH3 (for 4 years)
+CHARACTER*24                                     :: dir_chem_meteo(2)          ! names of directories with chemical maps for actual (1) or prognosis (2) meteo
+CHARACTER*24                                     :: map_so2(6)                 ! name of file with background map SO2 (for reference years)
+CHARACTER*24                                     :: map_nox(6)                 ! name of file with background map NOx (for reference years)
+CHARACTER*24                                     :: map_nh3(6)                 ! name of file with background map NH3 (for reference years)
 CHARACTER*128                                    :: map_mass_prec              ! filename with MASS_PREC averaged column mass precursor pre chemistry step, used for vchem
 CHARACTER*128                                    :: map_mass_conv_dtfac        ! filename with MASS_CONV_DTFAC = (100/dt) * averaged column mass converted in chemistry step, used for vchem
 CHARACTER*128                                    :: map_no3_distr              ! filename with distribution factors for different secondary species NO3
                                                                                ! HNO3/NO3_total, NO3_C/NO3_total, NO3_F/NO3_total
 
-DATA map_so2  / 'bgso2c1984.ops', 'bgso2c1994.ops', 'bgso2c2005.ops', 'bgso2c2012.ops','bgso2c2020.ops' /
-DATA map_nox  / 'bgnoxc1984.ops', 'bgnoxc1994.ops', 'bgnoxc2005.ops', 'bgnoxc2012.ops','bgnoxc2020.ops' /
-DATA map_nh3  / 'bgnh3c1984.ops', 'bgnh3c1994.ops', 'bgnh3c2005.ops', 'bgnh3c2012.ops','bgnh3c2020.ops' /
+DATA dir_chem_meteo  / 'Chem_meteo_actual', 'Chem_meteo_prognosis' / 
+DATA map_so2  / 'bgso2c1984.ops', 'bgso2c1994.ops', 'bgso2c2005.ops', 'bgso2c2012.ops','bgso2c2018.ops','bgso2cyyyy.ops' /  ! yyyy = year (for years in the future
+DATA map_nox  / 'bgnoxc1984.ops', 'bgnoxc1994.ops', 'bgnoxc2005.ops', 'bgnoxc2012.ops','bgnoxc2018.ops','bgnoxcyyyy.ops' /
+DATA map_nh3  / 'bgnh3c1984.ops', 'bgnh3c1994.ops', 'bgnh3c2005.ops', 'bgnh3c2012.ops','bgnh3c2018.ops','bgnh3cyyyy.ops' /
 DATA map_mass_prec       / 'xxx_mass_prec_yyyy.ops'       /   ! xxx = name primary species (SO2, NOx, NH3), yyyy = year (e.g. 2019)
 DATA map_mass_conv_dtfac / 'xxx_mass_conv_dtfac_yyyy.ops' /
 DATA map_no3_distr       / 'no3_distr_yyyy.ops' /

m_depac.f90 → ops_lib/src/m_depac.f90

@@ -1634,8 +1634,7 @@ subroutine rc_temp_water(day_of_year,tk)
 !        = 286.1842 + 8.3445*sin(2*pi*(day_of_year - 113.5116*365/360)/365) =
 !        = 286.1842 + 8.3445*sin(2*pi*(day_of_year - 115.1)/365)
 
-tk = 286.2 + 8.3*sin(day_of_year -113.5)  
-! tk = 286.2 + 8.34*sin(2*pi*(day_of_year - 115.1)/365)
+tk = 286.2 + 8.34*sin(2*pi*(day_of_year - 115.1)/365)
 
 end subroutine rc_temp_water