Merge branch 'main' into refactoring_addDVDsergeyandknut

config/namelist.config.toy_dbgyre

@@ -0,0 +1,79 @@
+! This is the namelist file for model general configuration
+
+&modelname
+runid='fesom'
+/
+
+&timestep
+step_per_day=45 !96 !96 !72 !72 !45 !72 !96
+run_length=1 !62 !62 !62 !28
+run_length_unit='d' ! y, m, d, s
+/
+
+&clockinit              ! the model starts at
+timenew=0.0
+daynew=1
+yearnew=1900
+/
+
+&paths
+MeshPath=''
+ResultPath='../results_tmp/'
+/
+
+&restart_log
+restart_length=1           ! --> do netcdf restart ( only required for d,h,s cases, y, m take 1)
+restart_length_unit='y'     !output period: y, d, h, s, off
+raw_restart_length=1        ! --> do core dump restart
+raw_restart_length_unit='off' ! e.g. y, d, h, s, off
+bin_restart_length=1        ! --> do derived type binary restart 
+bin_restart_length_unit='off' ! e.g. y, d, h, s, off
+logfile_outfreq=72     !in logfile info. output frequency, # steps
+/
+
+&ale_def
+which_ALE='linfs'       ! 'linfs','zlevel', 'zstar'
+use_partial_cell=.false.
+/
+
+&geometry
+cartesian=.false.
+fplane=.false.
+cyclic_length=90       ![degree]
+rotated_grid=.false.     !option only valid for coupled model case now
+force_rotation=.false.
+alphaEuler=0          ![degree] Euler angles, convention:
+betaEuler=0           ![degree] first around z, then around new x,
+gammaEuler=0         ![degree] then around new z.
+/
+
+&calendar
+include_fleapyear=.false.
+/
+
+&run_config
+use_ice=.false.                  ! ocean+ice
+use_cavity=.false.              !
+use_cavity_partial_cell=.false. 
+use_floatice = .false.
+use_sw_pene=.true.
+flag_debug=.false.
+flag_warn_cflz=.false.
+toy_ocean=.true.
+which_toy="dbgyre"
+flag_debug=.false.
+/
+
+&machine
+n_levels=1
+n_part=24
+/
+
+&icebergs
+use_icesheet_coupling=.false.
+ib_num=1
+use_icebergs=.false.
+steps_per_ib_step=8
+ib_async_mode=0
+/
+

config/namelist.dyn.toy_dbgyre

@@ -0,0 +1,25 @@
+&dynamics_visc
+visc_gamma0  = 0.005 ! [m/s],   backgroung viscosity= gamma0*len, it should be as small a s possible (keep it < 0.01 m/s).
+visc_gamma1  = 0.3   ! [nodim], for computation of the flow aware viscosity
+visc_gamma2  = 0.20 ! [s/m],   is only used in easy backscatter option
+visc_easybsreturn= 0.0
+
+opt_visc     = 5    
+check_opt_visc=.false.  ! check if optvisc=5 is valid based on ratio resol/rossbyR
+! 5=Kinematic (easy) Backscatter
+! 6=Biharmonic flow aware (viscosity depends on velocity Laplacian)
+! 7=Biharmonic flow aware (viscosity depends on velocity differences)
+! 8=Dynamic Backscatter
+
+use_ivertvisc= .true.  
+/
+
+&dynamics_general
+momadv_opt   = 2       ! option for momentum advection in moment only =2
+use_freeslip = .false. ! Switch on free slip
+use_wsplit   = .false. ! Switch for implicite/explicte splitting of vert. velocity
+wsplit_maxcfl= 1.0     ! maximum allowed CFL criteria in vertical (0.5 < w_max_cfl < 1.) 
+                       ! in older FESOM it used to be w_exp_max=1.e-3
+ldiag_KE=.false.       ! activates energy diagnostics
+AB_order=2
+/

config/namelist.io

@@ -9,6 +9,7 @@ ldiag_dMOC       =.false.
 ldiag_DVD        =.false.
 ldiag_forc       =.false.
 ldiag_extflds    =.false.
+ldiag_destinE    =.false. ! enables computation of heatcontent. (hc300m, hc700m, hc) in io_list
 ldiag_trflx      =.false.
 ldiag_uvw_sqr    =.false.
 ldiag_trgrd_xyz  =.false.
@@ -56,4 +57,5 @@ io_list =  'sst       ',1, 'm', 4,
            'bolus_w   ',1, 'y', 4,
            'fw        ',1, 'm', 4,
            'fh        ',1, 'm', 4,
-/
+           'otracers  ',1, 'y', 4,
+/

config/namelist.oce.toy_dbgyre

@@ -0,0 +1,28 @@
+! The namelist file for the finite-volume ocean model
+
+&oce_dyn
+state_equation=0       ! 1 - full equation of state, 0 - linear equation of state
+C_d=0.001             ! Bottom drag, nondimensional, use C_d=0.001 for double gyre setup based on Bagaeva et al.(2024)
+A_ver= 1.e-4	       ! Vertical viscosity, m^2/s
+scale_area=5.8e9       ! Visc. and diffus. are for an element with scale_area
+SPP=.false.                 ! Salt Plume Parameterization
+Fer_GM=.false.               ! to swith on/off GM after Ferrari et al. 2010
+K_GM_max     = 2000.0       ! max. GM thickness diffusivity (m2/s)
+K_GM_min     = 2.0          ! max. GM thickness diffusivity (m2/s)
+K_GM_bvref   = 2            ! def of bvref in ferreira scaling 0=srf,1=bot mld,2=mean over mld,3=weighted mean over mld
+K_GM_rampmax = -1.0         ! Resol >K_GM_rampmax[km] GM on
+K_GM_rampmin = -1.0         ! Resol <K_GM_rampmin[km] GM off, in between linear scaled down
+K_GM_resscalorder = 1
+
+scaling_Ferreira   =.false.  ! GM vertical scaling after Ferreira et al.(2005) (as also implemented by Qiang in FESOM 1.4)
+scaling_Rossby     =.false. ! GM is smoothly switched off according to Rossby radius (from 1. in coarse areas to 0. where resolution reaches 2 points/Rossby radius)
+scaling_resolution =.true.  ! GM is spatially scaled with resolution; A value of K_GM corresponds then to a resolution of 100km
+scaling_FESOM14    =.false.  ! special treatment of GM in the NH (as also implemented by Qiang in FESOM 1.4; it is zero within the boundary layer)
+
+Redi  =.false.
+visc_sh_limit=5.0e-3       ! for KPP, max visc due to shear instability
+mix_scheme='PP'           ! vertical mixing scheme: KPP, PP 
+Ricr   = 0.3               ! critical bulk Richardson Number
+concv  = 1.6               ! constant for pure convection (eqn. 23) (Large 1.5-1.6; MOM default 1.8)
+/
+

config/namelist.tra.toy_dbgyre

@@ -0,0 +1,57 @@
+&tracer_listsize
+num_tracers=100 !number of tracers to allocate. shallbe large or equal to the number of streams in &nml_list
+/
+
+&tracer_list
+nml_tracer_list =  
+1  , 'MFCT',       'QR4C',       'FCT ',        1.,          1., 
+2  , 'MFCT',       'QR4C',       'FCT ',        1.,          1., 
+!101, 'UPW1',       'UPW1',       'NON ',        0.,          0.
+/
+
+&tracer_init3d                            ! initial conditions for tracers
+n_ic3d   = 2                              ! number of tracers to initialize
+idlist   = 2, 1                           ! their IDs (0 is temperature, 1 is salinity, etc.). The reading order is defined here!
+filelist = 'phc3.0_winter.nc', 'phc3.0_winter.nc' ! list of files in ClimateDataPath to read (one file per tracer), same order as idlist
+varlist  = 'salt', 'temp'                 ! variables to read from specified files
+t_insitu = .true.                         ! if T is insitu it will be converted to potential after reading it
+/
+
+&tracer_init2d                                      ! initial conditions for 2D tracers (sea ice)
+n_ic2d   = 3                                        ! number of tracers to initialize
+idlist   = 1, 2, 3                                  ! their IDs (0 is a_ice, 1 is m_ice, 3 m_snow). The reading order is defined here!
+filelist = 'a_ice.nc', 'm_ice.nc', 'm_snow.nc' ! list of files in ClimateDataPath to read (one file per tracer), same order as idlist
+varlist  = 'a_ice', 'm_ice', 'm_snow'                 ! variables to read from specified files
+ini_ice_from_file=.false.
+/
+
+&tracer_general
+! bharmonic diffusion for tracers. We recommend to use this option in very high resolution runs (Redi is generally off there).
+smooth_bh_tra =.false.     ! use biharmonic diffusion (filter implementation) for tracers
+gamma0_tra    = 0.0005     ! gammaX_tra are analogous to those in the dynamical part
+gamma1_tra    = 0.0125
+gamma2_tra    = 0.
+i_vert_diff   =.true.
+/
+
+&tracer_phys
+use_momix     = .false.     ! switch on/off  !Monin-Obukhov -> TB04 mixing
+momix_lat     = -50.0      ! latitidinal treshhold for TB04, =90 --> global
+momix_kv      = 0.01       ! PP/KPP, mixing coefficient within MO length
+use_instabmix = .true.     ! enhance convection in case of instable stratification
+instabmix_kv  = 0.1
+use_windmix   = .false.    ! enhance mixing trough wind only for PP mixing (for stability)
+windmix_kv    = 1.e-3
+windmix_nl    = 2
+diff_sh_limit=5.0e-3       ! for KPP, max diff due to shear instability
+Kv0_const=.false.
+double_diffusion=.false.   ! for KPP,dd switch
+K_ver=1.0e-5
+K_hor=10.
+surf_relax_T=0.0
+surf_relax_S=1.929e-06   ! 50m/300days 6.43e-07! m/s 10./(180.*86400.)
+balance_salt_water =.false. ! balance virtual-salt or freshwater flux or not
+clim_relax=0.0	           ! 1/s, geometrical information has to be supplied
+ref_sss_local=.true.
+ref_sss=34.
+/

config/namelist.transit

@@ -1,11 +1,16 @@
 ! The namelist file for transient tracers
 
 &transit_param
+l_r14c  = .false.
+l_r39ar = .false.
+l_f11   = .false.
+l_f12   = .false.
+l_sf6   = .false.
 anthro_transit=.false.
 paleo_transit=.false.
 length_transit=1                ! 166 for anthro_transit=.true.
 ti_start_transit=1              ! 1 for D14C, 80 for CFC-12
-ifile_transit='/work/ollie/mbutzin/fesom2/input/trace_gases/Table_CO2_isoC_CFC12_SF6.txt'
+ifile_transit='/work/ab0246/a270108/fesom2_recom_config/input-for-awiesm/Table_CO2_isoC_CFCs1112_SF6.txt'
 r14c_a  = 1.0000  ! atm. 14C/C ratio, global mean
 r39ar_a = 1.0000	! atm. 39Ar/Ar ratio, global mean
 xarg_a  = 9.34e-3	! atm. Argon concn. (mole fraction), global mean

docs/conf.py

@@ -33,11 +33,8 @@
 extensions = [
     "sphinx.ext.mathjax",
     "sphinxcontrib.bibtex",
-    "sphinxfortran.fortran_domain",
-    "sphinxfortran.fortran_autodoc",
 ]
 bibtex_bibfiles = ["mybib_fesom2.bib"]
-fortran_src = ["../src/"]
 
 numfig = True
 # Add any paths that contain templates here, relative to this directory.

docs/getting_started/getting_started.rst

@@ -57,13 +57,12 @@ Change to the `fesom2` folder and execute:
 ::
 
     cd fesom2
-    git checkout refactoring
 
-As a good practice, if one wants to make modifications to the source code or any of the files, it is advisable to create a branch from refactoring:
+As a good practice, if one wants to make modifications to the source code or any of the files, it is advisable to create a branch from main:
 
 ::
 
-    git checkout -b <my branch> refactoring
+    git checkout -b <my branch> main
 
 After confirming that the right FESOM2 branch is being used, compile the model with:
 
@@ -460,20 +459,23 @@ The best way to run the model locally is to use Docker container. You obviously
 
 - Get the image::
     
-    docker pull koldunovn/fesom2_test:refactoring2
+    docker pull ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master
+    # if you use Mac Silicon (M1 M2 etc) use:
+    docker pull --platform linux/amd64 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master
 
 - Go to the folder with your version of fesom2 folder (NOT inside fesom2 folder, one up, the one you run ``git clone https://github.com/FESOM/fesom2.git`` in).
 - Run::
 
-    docker run -it -v "$(pwd)"/fesom2:/fesom/fesom2 koldunovn/fesom2_test:refactoring2 /bin/bash
+    docker run -it -v "$(pwd)"/fesom2:/fesom/fesom2 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master /bin/bash
+    # if you use Mac Silicon (M1 M2 etc) use:
+    docker run --platform linux/amd64 -it -v "$(pwd)"/fesom2:/fesom/fesom2 ghcr.io/fesom/fesom2_docker:fesom2_test_refactoring-master /bin/bash
 
 - This should get you inside the container. You now can edit the files in your fesom2 folder (on host system), but run compule and run the model inside the container.
 - When inside the container, to compile do:
 
   ::
 
     cd fesom2
-    git checkout refactoring
     bash -l configure.sh ubuntu
 
 - To prepare the run (this will do the test with pi mesh)::

docs/requirements.txt

@@ -1,3 +1,3 @@
-sphinx==4.1.2
-sphinxcontrib-bibtex==2.3.0
+sphinx>=5.0
+sphinxcontrib-bibtex>=2.5
 sphinx_rtd_theme

env.sh

@@ -89,6 +89,8 @@ elif [[ $LOGINHOST =~ \.bullx$ ]]; then
    STRATEGY="atosecmwf"
 elif [[ $LOGINHOST =~ uan[0-9][0-9] ]]; then
    STRATEGY="lumi"
+elif [[ $LOGINHOST =~ nesh-login[1-3] ]]; then
+   STRATEGY="nesh"
 elif [[ -d $DIR/env/$LOGINHOST ]]; then # check if directory with LOGINHOST exists in env
 STRATEGY=$LOGINHOST
 else

env/juwels/shell

@@ -1,44 +1,20 @@
-##########
-module --force purge 
-module use /gpfs/software/juwels/otherstages   
-module load Stages/2020
-module load Intel/2020.2.254-GCC-9.3.0
-module load ParaStationMPI/5.4.7-1
-module load CMake/3.18.0
-module load imkl/2020.2.254
-module load netCDF-Fortran/4.5.3
-module load netCDF/4.7.4
-module load Perl/5.32.0
-module load netCDF
+#!/usr/bin/bash
+# ENVIRONMENT used in new_test15_compute_20000101-20000101.run
+# Use this file to source the environment in your
+# preprocessing or postprocessing scripts
 
-export LC_ALL=en_US.UTF-8
-export TMPDIR=/tmp
-export FC=mpifort
-export F77=mpifort
-export MPIFC=mpifort
-export FCFLAGS=-free
-export CC=mpicc
-export CXX=mpic++
-
-export NETCDF_Fortran_INCLUDE_DIRECTORIES=$EBROOTNETCDFMINFORTRAN/include
-export NETCDF_Fortran_LIBRARIES=$EBROOTNETCDFMINFORTRAN/lib
-
-#module use /gpfs/software/juwels/otherstages
-#module load Stages/2019a                
-#module load StdEnv
-## For intel MPI
-##module load Intel/2019.3.199-GCC-8.3.0  IntelMPI/2018.5.288 imkl/2019.3.199
-##export FC=mpiifort CC=mpiicc CXX=mpiicpc
-
-## For ParaStation MPI 
-#module load  Intel/2019.3.199-GCC-8.3.0 ParaStationMPI/5.4 imkl/2019.5.281
-#export FC=mpifort CC=mpicc CXX=mpicxx
-
-#module load netCDF/4.6.3 
-#module load netCDF-Fortran/4.4.5 
-#module load CMake
-#export NETCDF_DIR=$EBROOTNETCDF
-#export NETCDFF_DIR=$EBROOTNETCDFMINFORTRAN
-#export NETCDF_Fortran_INCLUDE_DIRECTORIES=${NETCDFF_DIR}/include/
-#export NETCDF_C_INCLUDE_DIRECTORIES=${NETCDF_DIR}/include/
-#export NETCDF_CXX_INCLUDE_DIRECTORIES=${NETCDFCXX_DIR}/include/
+module --force purge
+module use $OTHERSTAGES
+module --force purge
+module load Stages/2023
+module load GCC/11.3.0
+module load OpenMPI/4.1.4
+module load CMake/3.26.3
+module load Python/3.10.4
+module load imkl/2022.1.0
+module load Perl/5.34.1
+module load git
+module load CDO
+module unload ecCodes
+module load libaec FFTW imkl cURL netCDF netCDF-Fortran
+module list

env/nesh/shell

@@ -0,0 +1,15 @@
+# Inspired by environment for albedo
+module load oneapi2023-env/2023.2.0
+
+module load cmake/3.27.4
+module load oneapi/2023.2.0
+module load oneapi-mkl/2023.1.0
+module load oneapi-mpi/2021.10.0
+module load netcdf-c/4.9.2-with-oneapi-mpi-2021.10.0
+module load netcdf-fortran/4.6.0-with-oneapi-mpi-2021.10.0
+export FC=mpiifort CC=mpiicc CXX=mpiicpc
+
+
+# haven't set any environment variables. hopefully fine by now
+export I_MPI_PMI=pmi2
+export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi2.so

mesh_part/CMakeLists.txt

@@ -1,6 +1,9 @@
 cmake_minimum_required(VERSION 3.4)
 
 project(fesom_ini C Fortran)
+find_package(MPI REQUIRED)
+
+
 
 # get our source files
 set(src_home ${CMAKE_CURRENT_LIST_DIR}/../src)
@@ -26,5 +29,5 @@ elseif(${CMAKE_Fortran_COMPILER_ID} STREQUAL  GNU )
       target_compile_options(${PROJECT_NAME} PRIVATE -fallow-argument-mismatch) # gfortran v10 is strict about erroneous API calls: "Rank mismatch between actual argument at (1) and actual argument at (2) (scalar and rank-1)"
    endif()
 endif()
-target_link_libraries(${PROJECT_NAME} ${PROJECT_NAME}_C)
+target_link_libraries(${PROJECT_NAME} ${PROJECT_NAME}_C MPI::MPI_Fortran)
 set_target_properties(${PROJECT_NAME} PROPERTIES LINKER_LANGUAGE Fortran)