inogs · plazzari · Aug 25, 2025 · Oct 14, 2025 · Nov 10, 2025 · Nov 10, 2025
diff --git a/GeneralCmake.cmake b/GeneralCmake.cmake
@@ -9,7 +9,9 @@ enable_language(Fortran C)
 set (NETCDF_F90 "YES")
 find_package(MPI REQUIRED)
 find_package(NetCDF REQUIRED)
-find_package(BFM REQUIRED)
+#find_package(BFM REQUIRED)
+#find_package(FABM REQUIRED)
+#find_package(YAML REQUIRED)
 find_package(BIOPTIMOD_3STREAM REQUIRED)
 find_package(OASIM_ATM)
 
@@ -52,7 +54,9 @@ else ()
 endif ()
 
 #include
-include_directories(${BFM_INCLUDES})
+#include_directories(${BFM_INCLUDES})
+#include_directories(${FABM_INCLUDES})
+#include_directories(${YAML_INCLUDES})
 include_directories(${BIOPTIMOD_3STREAM_INCLUDES})
 include_directories(${OASIM_ATM_INCLUDES})
 include_directories(${NETCDF_INCLUDES_C})
@@ -68,4 +72,4 @@ endforeach()
 #building
 add_library( ogstm_lib ${FORTRAN_SOURCES})
 add_executable (ogstm.xx application/ogstm_main_caller.f90)
-target_link_libraries( ogstm.xx ogstm_lib ${NETCDFF_LIBRARIES_F90} ${BFM_LIBRARIES} ${BIOPTIMOD_3STREAM_LIBRARIES}  ${OASIM_ATM_LIBRARIES}   )
+target_link_libraries( ogstm.xx ogstm_lib ${NETCDFF_LIBRARIES_F90} ${BFM_LIBRARIES}  ${FABM_LIBRARIES} ${BIOPTIMOD_3STREAM_LIBRARIES}  ${OASIM_ATM_LIBRARIES} )
diff --git a/cmake/FindFABM.cmake b/cmake/FindFABM.cmake
@@ -0,0 +1,23 @@
+# - Find FABM
+# Find FABM package 
+
+
+ find_library( FABM_LIBRARIES NAMES fabm libfabm HINTS $ENV{FABM_LIBRARY} )
+ message(STATUS "FABM library =  ${FABM_LIBRARIES}  ")
+ if (NOT "$ENV{FABM_LIBRARY}" STREQUAL "")
+	 set(EnvironmentVariableName "$ENV{FABM_LIBRARY}" CACHE INTERNAL "Copied from environment variable")
+endif()
+
+message("EnvironmentVariableName = ${EnvironmentVariableName}")
+ if (FABM_LIBRARIES)
+    find_path (FABM_INCLUDES NAMES fabm.h HINTS $ENV{FABM_INCLUDE} NO_DEFAULT_PATH)
+    add_definitions(-Dkey_trc_fabm -Dkey_INCLUDE_FABM_PELCO2)
+    message(STATUS "FABM include =  ${FABM_INCLUDES}  ")
+    set (FABM_has_interfaces "YES")
+ else (FABM_LIBRARIES)
+    set (FABM_has_interfaces "NO")
+ endif (FABM_LIBRARIES)
+
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (FABM DEFAULT_MSG FABM_has_interfaces)
+mark_as_advanced (FABM_LIBRARIES FABM_INCLUDES)
diff --git a/cmake/FindYAML.cmake b/cmake/FindYAML.cmake
@@ -0,0 +1,13 @@
+# - Find FABM
+# Find FABM package 
+
+
+message("EnvironmentVariableName = ${EnvironmentVariableName}")
+find_path (YAML_INCLUDES NAMES yaml.mod  yaml_settings.mod  yaml_types.mod HINTS $ENV{YAML_INCLUDE} NO_DEFAULT_PATH)
+add_definitions(-Dkey_yaml )
+message(STATUS "YAML include =  ${YAML_INCLUDES}  ")
+set (FABM_has_interfaces "YES")
+
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (YAML DEFAULT_MSG FABM_has_interfaces)
+mark_as_advanced (YAML_INCLUDES)
diff --git a/compilers/machine_modules/leonardo.intel b/compilers/machine_modules/leonardo.intel
@@ -0,0 +1,15 @@
+module load intel-oneapi-compilers/2023.2.1
+module load netcdf-fortran/4.6.1--intel-oneapi-mpi--2021.12.1--oneapi--2024.1.0
+module load gsl/2.7.1--oneapi--2023.2.0
+
+export CC=icx
+export NETCDF_CFLAGS=$(nc-config --cflags)
+export NETCDF_CLIBS=$(nc-config --libs)
+export NETCDF_LIB=$(nc-config --libdir)
+export NETCDF_INC=$(nc-config --includedir)
+
+export FC=ifort
+export NETCDF_FFLAGS=$(nf-config --fflags)
+export NETCDF_FLIBS=$(nf-config --flibs)
+export NETCDFF_LIB=$(nf-config --prefix)/lib
+export NETCDFF_INC=$(nf-config --includedir)
diff --git a/compilers/x86_64.LINUX.intel.dbg.inc b/compilers/x86_64.LINUX.intel.dbg.inc
@@ -7,8 +7,8 @@
         MPILIB= -L $(MPI_LIB)/lib -lmpi_f90
 # F Flags
         FFLAGS_DBG=  -O0 -g -traceback -fp-stack-check -check bounds -fpe0
-	FFLAGS= $(FFLAGS_DBG)  -I$(NETCDF_INC)  -I$(OPENMPI_HOME)/include -I$(BFM_INC) -extend_source
-	LDFLAGS= -L $(NETCDF_LIB) -lnetcdff -lnetcdf -L$(BFM_LIB) -lbfm 
+	FFLAGS= $(FFLAGS_DBG)  -I$(NETCDF_INC)  -I$(OPENMPI_HOME)/include -I$(BFM_INC) -I$(FABM_INC) -extend_source
+	LDFLAGS= -L $(NETCDF_LIB) -lnetcdff -lnetcdf -L$(BFM_LIB) -lbfm  -L$(FABM_LIB) -lfabm
 # C Flags
         CFLAGS_DBG=
         CFLAGS=  ${CFLAGS_DBG} -I$(NETCDF_INC) -I$(OPENMPI_HOME)/include
diff --git a/compilers/x86_64.LINUX.intel.inc b/compilers/x86_64.LINUX.intel.inc
@@ -7,8 +7,8 @@
 # F Flags
     MPILIB= -L $(MPI_LIB)/lib -lmpi_f90    
     FFLAGS_OPT= -fno-math-errno -unroll=3 -opt-subscript-in-range -align all  -cpp -heap-arrays
-    FFLAGS= $(FFLAGS_OPT)  -I$(NETCDF_INC)  -I$(OPENMPI_HOME)/include -I$(BFM_INC) -extend_source
-    LDFLAGS= -L $(NETCDF_LIB) -lnetcdff -lnetcdf -L $(BFM_LIB) -lbfm
+    FFLAGS= $(FFLAGS_OPT)  -I$(NETCDF_INC)  -I$(OPENMPI_HOME)/include -I$(BFM_INC) -I$(FABM_INC) -extend_source
+    LDFLAGS= -L $(NETCDF_LIB) -lnetcdff -lnetcdf -L $(BFM_LIB) -lbfm -L $(FABM_LIB) -lfabm
 # C Flags
     CFLAGS_DBG=
     CFLAGS=  ${CFLAGS_DBG} -I$(NETCDF_INC) -I$(OPENMPI_HOME)/include
diff --git a/src/BC/closed.f90 b/src/BC/closed.f90
@@ -15,8 +15,8 @@ module closed_mod
         ! TO DO: review names
         character(len=3) :: m_name ! ex: 'gib'
         integer :: m_n_vars ! BC_mem.f90:94
-        character(len=20), allocatable, dimension(:) :: m_var_names ! domrea.f90:161-167
-        character(len=20), allocatable, dimension(:) :: m_var_names_data ! bc_gib.f90:113
+        character(len=200), allocatable, dimension(:) :: m_var_names ! domrea.f90:161-167
+        character(len=200), allocatable, dimension(:) :: m_var_names_data ! bc_gib.f90:113
         integer(4), allocatable, dimension(:) :: m_var_names_idx ! tra_matrix_gib
         double precision, allocatable, dimension(:, :, :) :: m_buffer ! replaces m_aux, now it is a 3D matrix
         integer(4) :: m_size ! BC_mem.f90:21
@@ -146,7 +146,7 @@ subroutine init_members(self, bc_name, namelist_file)
         character(len=7), intent(in) :: namelist_file
 
         integer :: n_vars
-        character(len=20), allocatable, dimension(:) :: vars
+        character(len=200), allocatable, dimension(:) :: vars
         integer(4), allocatable, dimension(:) :: var_names_idx
         double precision :: alpha
         double precision :: reduction_value_t

diff --git a/src/BC/hard_open.f90 b/src/BC/hard_open.f90
@@ -13,8 +13,8 @@ module hard_open_mod
 
         character(len=3) :: m_name ! ex: 'ope'
         integer :: m_n_vars
-        character(len=20), allocatable, dimension(:) :: m_var_names
-        character(len=20), allocatable, dimension(:) :: m_var_names_data
+        character(len=200), allocatable, dimension(:) :: m_var_names
+        character(len=200), allocatable, dimension(:) :: m_var_names_data
         integer(4), allocatable, dimension(:) :: m_var_names_idx
         integer :: m_n_missing_vars
         integer(4), allocatable, dimension(:) :: m_missing_var_names_idx
@@ -228,7 +228,7 @@ subroutine init_members(self, bc_name, namelist_file, n_tracers)
         integer, intent(in) :: n_tracers
 
         integer :: n_vars
-        character(len=20), allocatable, dimension(:) :: vars
+        character(len=200), allocatable, dimension(:) :: vars
         integer(4) :: geometry
         double precision :: damping_coeff
         integer, parameter :: file_unit = 101 ! 100 for data files, 101 for boundary namelist files
@@ -544,7 +544,7 @@ subroutine apply_dirichlet(self)
              ! 2nd loop: provided variables on neighbors
                 do j = 1, self%m_size
 
-                    idx_i = self%m_neighbors(1, i)
+                    idx_i = self%m_neighbors(1, j)
                     idx_j = self%m_neighbors(2, j)
                     idx_k = self%m_neighbors(3, j)
 

diff --git a/src/BC/nudging.f90 b/src/BC/nudging.f90
@@ -23,8 +23,8 @@ module nudging_mod
         class(bc), pointer :: m_bc_no_nudging => null()
         character(len=11) :: m_data_file ! 11 chars in order to handle names like 'bounmask.nc'
         integer :: m_n_nudging_vars
-        character(len=20), allocatable, dimension(:) :: m_nudging_vars
-        character(len=20), allocatable, dimension(:) :: m_nudging_vars_rst
+        character(len=200), allocatable, dimension(:) :: m_nudging_vars
+        character(len=200), allocatable, dimension(:) :: m_nudging_vars_rst
         integer(4), allocatable, dimension(:) :: m_nudging_vars_idx ! tra_matrix_gib
         double precision, allocatable, dimension(:, :, :, :) :: m_rst ! resto
         double precision, allocatable, dimension(:) :: m_rst_corr ! restocorr
@@ -79,7 +79,7 @@ subroutine init_members(self, bc_no_nudging, namelist_file, n_tracers)
 
         integer :: n_vars
         character(len=11) :: data_file ! 11 chars in order to handle names like 'bounmask.nc'
-        character(len=20), allocatable, dimension(:) :: vars
+        character(len=200), allocatable, dimension(:) :: vars
         double precision, allocatable, dimension(:) :: rst_corr
         integer, parameter :: file_unit = 101 ! 100 for data files, 101 for boundary namelist files
 

diff --git a/src/BC/rivers.f90 b/src/BC/rivers.f90
@@ -19,8 +19,8 @@ module rivers_mod
         ! TO DO: review names
         character(len=3) :: m_name ! ex: 'riv'
         integer :: m_n_vars ! BC_mem.f90:95
-        character(len=20), allocatable, dimension(:) :: m_var_names
-        character(len=20), allocatable, dimension(:) :: m_var_names_data ! bc_tin.f90:116
+        character(len=200), allocatable, dimension(:) :: m_var_names
+        character(len=200), allocatable, dimension(:) :: m_var_names_data ! bc_tin.f90:116
         integer(4), allocatable, dimension(:) :: m_var_names_idx ! tra_matrix_riv
         double precision, allocatable, dimension(:, :) :: m_buffer ! replaces m_aux, now it is a 2D matrix
         integer(4) :: m_size
@@ -139,7 +139,7 @@ subroutine init_members(self, bc_name, namelist_file)
         character(len=7), intent(in) :: namelist_file
 
         integer :: n_vars
-        character(len=20), allocatable, dimension(:) :: vars
+        character(len=200), allocatable, dimension(:) :: vars
         integer, parameter :: file_unit = 101 ! 100 for data files, 101 for boundary namelist files
         integer :: i
         namelist /vars_dimension/ n_vars

diff --git a/src/BC/sponge.f90 b/src/BC/sponge.f90
@@ -18,8 +18,8 @@ module sponge_mod
         ! TO DO: review names
         character(len=3) :: m_name ! ex: 'gib'
         integer :: m_n_vars ! BC_mem.f90:94
-        character(len=20), allocatable, dimension(:) :: m_var_names ! domrea.f90:161-167
-        character(len=20), allocatable, dimension(:) :: m_var_names_data ! bc_gib.f90:113
+        character(len=200), allocatable, dimension(:) :: m_var_names ! domrea.f90:161-167
+        character(len=200), allocatable, dimension(:) :: m_var_names_data ! bc_gib.f90:113
         integer(4), allocatable, dimension(:) :: m_var_names_idx ! tra_matrix_gib
         double precision, allocatable, dimension(:, :, :) :: m_buffer ! replaces m_aux, now it is a 3D matrix
         integer(4) :: m_size ! BC_mem.f90:21
@@ -149,7 +149,7 @@ subroutine init_members(self, bc_name, namelist_file)
         character(len=7), intent(in) :: namelist_file
 
         integer :: n_vars
-        character(len=20), allocatable, dimension(:) :: vars
+        character(len=200), allocatable, dimension(:) :: vars
         double precision :: alpha
         double precision :: reduction_value_t
         double precision :: length

diff --git a/src/BIO-OPTICS/OPT_mem.f90 b/src/BIO-OPTICS/OPT_mem.f90
@@ -12,7 +12,7 @@ MODULE OPT_mem
 
        public
 
-
+      LOGICAL :: oasim_bioptimod=.FALSE., oasim_fabm=.FALSE.
       INTEGER, allocatable :: itabe(:),imaske(:,:) 
       double precision, allocatable :: zpar(:,:),xEPS_ogstm(:,:)
       double precision, allocatable :: zpar0m(:),zpar100(:) 
@@ -34,19 +34,27 @@ MODULE OPT_mem
       double precision, allocatable :: asympIO(:,:,:,:)
       double precision, allocatable :: ssalbIO(:,:,:,:)
 
-      double precision, allocatable :: sp(:,:)
-      double precision, allocatable :: msl(:,:)
-      double precision, allocatable :: t2m(:,:)
-      double precision, allocatable :: d2m(:,:)
-      double precision, allocatable :: tcc(:,:)
-      double precision, allocatable :: w10(:,:)
-      double precision, allocatable :: tclw(:,:)
-      double precision, allocatable :: tco3(:,:)
-      double precision, allocatable :: cdrem(:,:)
-      double precision, allocatable :: cldtcm(:,:)
-      double precision, allocatable :: taua(:,:,:)
-      double precision, allocatable :: asymp(:,:,:)
-      double precision, allocatable :: ssalb(:,:,:)
+      double precision, allocatable,target :: sp(:,:)
+      double precision, allocatable,target :: msl(:,:)
+      double precision, allocatable,target :: t2m(:,:)
+      double precision, allocatable,target :: d2m(:,:)
+      double precision, allocatable,target :: tcc(:,:)
+      double precision, allocatable,target :: w10(:,:)
+      double precision, allocatable,target :: tclw(:,:)
+      double precision, allocatable,target :: tco3(:,:)
+      double precision, allocatable,target :: cdrem(:,:)
+      double precision, allocatable,target :: cldtcm(:,:)
+      double precision, allocatable,target :: taua(:,:,:)
+      double precision, allocatable,target :: asymp(:,:,:)
+      double precision, allocatable,target :: ssalb(:,:,:)
+!     FABM optical model variables
+      double precision, target :: yearday
+      double precision, allocatable, target :: surface_downwelling_shortwave_flux(:,:)
+      double precision, allocatable, target :: atmosphere_mass_content_of_water_vapor(:,:)
+      double precision, allocatable, target :: visibility_in_air(:,:)
+      double precision, allocatable, target :: aerosol_air_mass_type(:,:)
+      double precision, allocatable, target :: surface_specific_humidity(:,:)
+
 ! ############
       real, allocatable :: zkef_f (:,:)
       CHARACTER(LEN=7), allocatable,dimension(:) :: Ednm, Esnm, Eunm
@@ -63,11 +71,17 @@ MODULE OPT_mem
       integer, parameter            :: nlt=33                     
       integer                       :: lam(33)
       double precision              :: WtoQ(33)
+! Wavelength strings with 4-digit zero padding      
+      CHARACTER(LEN=4), parameter   :: lam_strings(33) = (/ &
+           '0250', '0325', '0350', '0375', '0400', '0425', '0450', '0475', '0500', '0525', &
+           '0550', '0575', '0600', '0625', '0650', '0675', '0700', '0725', '0775', '0850', &
+           '0950', '1050', '1150', '1250', '1350', '1450', '1550', '1650', '1750', '1900', &
+           '2200', '2900', '3700'   /)
 ! Radiative transfer model parameter OASIM Native coordinates
       double precision              :: Ed_0m_COARSE(33,12,18,48), Es_0m_COARSE(33,12,18,48) ! lon, lat, day period, wave length
       double precision              :: OASIM_lon(18,48), OASIM_lat(18,48)  
 ! Radiative transfer model parameter OGSTM coordinates    
-      double precision,allocatable  :: Ed_0m(:,:,:), Es_0m(:,:,:) ! wav, lat, lon
+      double precision,target,allocatable  :: Ed_0m(:,:,:), Es_0m(:,:,:) ! wav, lat, lon
 
       INTEGER                       :: day_RTcheck
 ! in-water model
@@ -155,7 +169,10 @@ subroutine myalloc_OPT()
 !       kef     = huge(kef(1,1))
 !       allocate(kextIO(jpj,jpi,2))
 !       kextIO  = huge(kextIO(1,1,1))
-
+#ifdef key_trc_bfm
+      oasim_bioptimod=.TRUE.
+      write(numout,*) 'OASIM optical model will be used'
+#endif
        allocate(sp (jpj,jpi))     ;   sp =huge(sp(1,1))
        allocate(msl(jpj,jpi))     ;   msl=huge(sp(1,1))
        allocate(t2m(jpj,jpi))     ;   t2m=huge(sp(1,1))
@@ -169,6 +186,22 @@ subroutine myalloc_OPT()
        allocate(taua(33,jpj,jpi)) ;  taua=huge(sp(1,1))
        allocate(asymp(33,jpj,jpi)); asymp=huge(sp(1,1))
        allocate(ssalb(33,jpj,jpi)); ssalb=huge(sp(1,1))
+!     FABM optical model variables
+      allocate(surface_downwelling_shortwave_flux(jpj,jpi))
+      surface_downwelling_shortwave_flux=huge(surface_downwelling_shortwave_flux(1,1))
+
+      allocate(atmosphere_mass_content_of_water_vapor(jpj,jpi))
+      atmosphere_mass_content_of_water_vapor=huge(atmosphere_mass_content_of_water_vapor(1,1))
+
+      allocate(visibility_in_air(jpj,jpi))
+      visibility_in_air=huge(visibility_in_air(1,1))
+
+      allocate(aerosol_air_mass_type(jpj,jpi))
+      aerosol_air_mass_type=huge(surface_specific_humidity(1,1))
+
+      allocate(surface_specific_humidity(jpj,jpi))
+      surface_specific_humidity=huge(surface_specific_humidity(1,1))
+
 
        allocate(spIO (jpj,jpi,2))     ; spIO   =huge(sp(1,1))
        allocate(mslIO(jpj,jpi,2))     ; mslIO  =huge(sp(1,1))
@@ -207,7 +240,7 @@ subroutine myalloc_OPT()
        allocate(ea(jpj,jpi,3))
        ea     =huge(ea(1,1,1))
 
-       call lidata()
+       call lidata_ogstm()
 
        allocate(Edaux(nlt))
        allocate(Esaux(nlt))

diff --git a/src/BIO-OPTICS/lidata.F90 → src/BIO-OPTICS/lidata_ogstm.F90 b/src/BIO-OPTICS/lidata.F90 → src/BIO-OPTICS/lidata_ogstm.F90
@@ -1,5 +1,4 @@
-      subroutine lidata()
-!     subroutine lidata(lam,aw,bw,ac,bc)
+      subroutine lidata_ogstm()
 
       USE OPT_mem, ONLY: nlt, nchl, lam,aw,bw,ac,ac_ps,bc,bbc,apoc,bpoc,bbpoc,acdom
       USE myalloc, only: lwp,numout

diff --git a/src/BIO-OPTICS/oasim_caller.f90 b/src/BIO-OPTICS/oasim_caller.f90
@@ -2,6 +2,7 @@ subroutine OASIM_CALLER(datestring)
 
 use myalloc
 use OPT_mem
+use BIO_mem
 use TIME_MANAGER
 use mpi
 use oasim, only: calc_unit, oasim_lib
@@ -39,6 +40,8 @@ subroutine OASIM_CALLER(datestring)
 CALL forcings_atm_clim(datestring)
 CALL forcings_atm_aero(datestring)
 
+if (oasim_bioptimod) then
+
 counter=1
 do ji=1,jpi
 do jj=1,jpj
@@ -87,6 +90,7 @@ subroutine OASIM_CALLER(datestring)
 
 call trc3streams(datestring) ! 3-stream radiative model
 
+end if ! oasim_bioptimod
 
 trcoptparttime = MPI_WTIME() - trcoptparttime ! cronometer-stop
 trcopttottime = trcopttottime + trcoptparttime

diff --git a/src/BIO-OPTICS/trc3streams.f90 b/src/BIO-OPTICS/trc3streams.f90
@@ -24,7 +24,7 @@ SUBROUTINE trc3streams(datestring)
       INTEGER :: MODE ! 0-exact, 1-approx
       INTEGER :: year, month, day, ihr
       INTEGER :: it_actual
-      CHARACTER(LEN=20) :: V_POSITION     
+      CHARACTER(LEN=200) :: V_POSITION     
       double precision :: solz(jpj,jpi), rmud(jpj,jpi)
       double precision :: Edz(jpk,nlt),Esz(jpk,nlt),Euz(jpk,nlt)
       double precision, allocatable::  E(:,:,:) !(3,jpk+1,nlt)