Merge branch 'refactoring' into refactoring_sigma0

CMakeLists.txt

@@ -2,8 +2,8 @@ cmake_minimum_required(VERSION 3.9)
 
 # set default build type cache entry (do so before project(...) is called, which would create this cache entry on its own)
 if(NOT CMAKE_BUILD_TYPE)
-	message(STATUS "setting default build type: Release")
-	set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: None(CMAKE_CXX_FLAGS or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.")
+  message(STATUS "setting default build type: Release")
+  set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: None(CMAKE_CXX_FLAGS or CMAKE_C_FLAGS used) Debug Release RelWithDebInfo MinSizeRel.")
 endif()
 
 project(FESOM2.0)
@@ -17,7 +17,9 @@ set(OIFS_COUPLED OFF CACHE BOOL "compile fesom coupled to OpenIFS. (Also needs F
 set(CRAY OFF CACHE BOOL "compile with cray ftn")
 set(USE_ICEPACK OFF CACHE BOOL "compile fesom with the Iceapck modules for sea ice column physics.")
 set(OPENMP_REPRODUCIBLE OFF CACHE BOOL "serialize OpenMP loops that are critical for reproducible results")
-
-#set(VERBOSE OFF CACHE BOOL "toggle debug output")
+set(USE_MULTIO OFF CACHE BOOL "Use MULTIO for IO, either grib or binary for now. This also means path to MULTIO installation has to provided using env MULTIO_INSTALL_PATH='..' and multio configuration yamls must be present to run the model with MULTIO")
+set(OASIS_WITH_YAC OFF CACHE BOOL "Useing a version of OASIS compiled with YAC instead of SCRIP for interpolation?")
+set(ASYNC_ICEBERGS ON CACHE BOOL "compile fesom with or without support for asynchronous iceberg computations")
+set(VERBOSE OFF CACHE BOOL "toggle debug output")
 #add_subdirectory(oasis3-mct/lib/psmile)
 add_subdirectory(src)

cmake/FindMULTIO.cmake

@@ -0,0 +1,50 @@
+# FindMULTIO.cmake
+
+include(FindPackageHandleStandardArgs)
+
+# Use the environment variable as a hint
+set(MULTIO_HINT_PATH $ENV{MULTIO_INSTALL_PATH})
+
+# Try to find the library
+find_library(MULTIO_FAPI_LIBRARY
+    NAMES multio-fapi # Adjust this if the library name is different
+    HINTS ${MULTIO_HINT_PATH}/lib
+)
+
+# Try to find the dependency library
+find_library(MULTIO_API_LIBRARY
+    NAMES multio-api
+    HINTS ${MULTIO_HINT_PATH}/lib
+)
+
+# Try to find the dependency library
+find_library(MULTIO_LIBRARY
+    NAMES multio
+    HINTS ${MULTIO_HINT_PATH}/lib
+)
+
+# Try to find the Fortran module path
+find_path(MULTIO_MODULE_PATH
+    NAMES multio_api.mod # Replace <module_name> with an actual module name you expect to find
+    HINTS ${MULTIO_HINT_PATH}/module ${MULTIO_HINT_PATH}/multio/module
+)
+
+
+# Aggregate the libraries for easier linking
+set(MULTIO_LIBRARIES ${MULTIO_FAPI_LIBRARY} ${MULTIO_API_LIBRARY} ${MULTIO_LIBRARY})
+
+
+# Handle the results
+find_package_handle_standard_args(MULTIO 
+    REQUIRED_VARS MULTIO_LIBRARIES MULTIO_MODULE_PATH
+    FOUND_VAR MULTIO_FOUND
+)
+
+# If found, set the MULTIO_LIBRARIES and MULTIO_INCLUDE_DIRS variables for easy use
+if(MULTIO_FOUND)
+    set(MULTIO_INCLUDE_DIRS ${MULTIO_MODULE_PATH})
+endif()
+
+# Mark variables as advanced
+mark_as_advanced(MULTIO_LIBRARY MULTIO_MODULE_PATH)
+

cmake/FindOASISYAC.cmake

@@ -0,0 +1,19 @@
+find_path(OASIS_Fortran_INCLUDE_DIRECTORIES mod_oasis.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile)
+find_library(OASIS_Fortran_LIBRARIES psmile HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile)
+
+find_path(MCT_Fortran_INCLUDE_DIRECTORIES mct_mod.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct)
+find_library(MCT_Fortran_LIBRARIES mct HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct)
+
+find_path(MPEU_Fortran_INCLUDE_DIRECTORIES m_mpout.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct)
+find_library(MPEU_Fortran_LIBRARIES mpeu HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/mct)
+
+find_path(SCRIP_Fortran_INCLUDE_DIRECTORIES remap_bicubic_reduced.mod HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/scrip)
+find_library(SCRIP_Fortran_LIBRARIES scrip HINTS ${TOPLEVEL_DIR}/../oasis/build/lib/psmile/scrip)
+
+find_path(YAC_Fortran_INCLUDE_DIRECTORIES mo_yac_utils.mod HINTS ${TOPLEVEL_DIR}/../oasis/lib/yac/include)
+find_library(YACUTILS_Fortran_LIBRARIES yac_utils HINTS ${TOPLEVEL_DIR}/../oasis/lib/yac/lib)
+find_library(YACCORE_Fortran_LIBRARIES yac_core HINTS ${TOPLEVEL_DIR}/../oasis/lib/yac/lib)
+
+find_path(YAXT_Fortran_INCLUDE_DIRECTORIES yaxt.mod HINTS ${TOPLEVEL_DIR}/../oasis/lib/yaxt/include)
+find_library(YAXT_Fortran_LIBRARIES yaxt HINTS ${TOPLEVEL_DIR}/../oasis/lib/yaxt/lib)
+find_library(YAXTC_Fortran_LIBRARIES yaxt_c HINTS ${TOPLEVEL_DIR}/../oasis/lib/yaxt/lib)

config/namelist.config

@@ -65,3 +65,11 @@ flag_debug=.false.
 n_levels=2
 n_part= 12, 36          ! 432 number of partitions on each hierarchy level
 /
+
+&icebergs
+use_icesheet_coupling=.false.
+ib_num=1
+use_icebergs=.false.
+steps_per_ib_step=8
+ib_async_mode=0
+/

config/namelist.config.toy_soufflet

@@ -1,3 +1,4 @@
+
 ! This is the namelist file for model general configuration
 
 &modelname
@@ -6,26 +7,30 @@ runid='fesom'
 
 &timestep
 step_per_day=72 !96 !96 !72 !72 !45 !72 !96
-run_length= 10 !62 !62 !62 !28
-run_length_unit='y'		! y, m, d, s
+run_length=10 !62 !62 !62 !28
+run_length_unit='d' ! y, m, d, s
 /
 
 &clockinit              ! the model starts at
 timenew=0.0
 daynew=1
-yearnew=1948
+yearnew=1958
 /
 
 &paths
-MeshPath='/work/ollie/sjuricke/Soufflet_20/'
-ClimateDataPath='/work/ollie/dsidoren/input/hydrography/phc3.0/'
-ResultPath='/home/ollie/dsidoren/test_visc/'
+MeshPath='/albedo/home/pscholz/fesom2/test/meshes/soufflet/'
+ClimateDataPath='/albedo/work/projects/p_fesom/FROM-OLLIE/FESOM2/hydrography/phc3.0/'
+ResultPath='../result_tmp/'
 /
 
 &restart_log
-restart_length=1        !only required for d,h,s cases,  y, m take 1
-restart_length_unit='y' !output period: y,  d, h, s 
-logfile_outfreq=960     !in logfile info. output frequency, # steps
+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
@@ -34,10 +39,10 @@ use_partial_cell=.false.
 /
 
 &geometry
-cartesian=.false.
+cartesian=.true.
 fplane=.false.
 cyclic_length=4.5       ![degree]
-rotated_grid=.false.    !option only valid for coupled model case now
+rotated_grid=.false.     !option only valid for coupled model case now
 force_rotation=.false.
 alphaEuler=50.          ![degree] Euler angles, convention:
 betaEuler=15.           ![degree] first around z, then around new x,
@@ -49,15 +54,22 @@ include_fleapyear=.false.
 /
 
 &run_config
-use_ice=.false.         ! ocean+ice
+use_ice=.false.                  ! ocean+ice
+use_cavity=.false.              !
+use_cavity_partial_cell=.false. 
 use_floatice = .false.
 use_sw_pene=.false.
+flag_debug=.false.
+flag_warn_cflz=.false.
 toy_ocean=.true.
 which_toy="soufflet"
-flag_debug=.true.
+flag_debug=.false.
+
 /
 
 &machine
-n_levels=2
-n_part= 12, 36          ! 432 number of partitions on each hierarchy level
+!PS n_levels=2
+!PS n_part= 70, 128          ! 432 number of partitions on each hierarchy level
+n_levels=1
+n_part= 128 !6096          ! 432 number of partitions on each hierarchy level
 /

config/namelist.cvmix

@@ -26,7 +26,9 @@ idemix_mu0         = 0.33333333 ! dissipation parameter (dimensionless)
 idemix_sforcusage  = 0.2
 idemix_n_hor_iwe_prop_iter = 5  ! iterations for contribution from horiz. wave propagation
 idemix_surforc_file = '/work/ollie/clidyn/forcing/IDEMIX/fourier_smooth_2005_cfsr_inert_rgrid.nc'
+idemix_surforc_vname= 'var706'
 idemix_botforc_file = '/work/ollie/clidyn/forcing/IDEMIX/tidal_energy_gx1v6_20090205_rgrid.nc'
+idemix_botforc_vname= 'wave_dissipation'
 /
 
 ! namelist for PP

config/namelist.dyn

@@ -21,5 +21,6 @@ use_wsplit   = .false. ! Switch for implicite/explicte splitting of vert. veloci
 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.forcing

@@ -23,6 +23,16 @@ ncar_bulk_z_shum=10.0 ! height at which humi forcing is located (CORE, JRA-do: 1
 use_landice_water=.false.
 landice_start_mon=5
 landice_end_mon=10
+fwf_path='./mesh/'
+
+/
+
+&age_tracer
+use_age_tracer=.false.
+use_age_mask=.false.
+age_tracer_path='./mesh/'
+age_start_year=2000
+
 /
 
 &nam_sbc

config/namelist.io

@@ -9,10 +9,11 @@ ldiag_dMOC       =.false.
 ldiag_DVD        =.false.
 ldiag_forc       =.false.
 ldiag_extflds    =.false.
+ldiag_trflx      =.false.
 /
 
 &nml_general
-io_listsize    =100 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list
+io_listsize    =120 !number of streams to allocate. shallbe large or equal to the number of streams in &nml_list
 vec_autorotate =.false.
 /
 
@@ -21,6 +22,7 @@ vec_autorotate =.false.
 ! for 'fer_C', 'bolus_u', 'bolus_v', 'bolus_w', 'fer_K' to work Fer_GM must be .true. otherwise no output
 ! 'otracers' - all other tracers if applicable
 ! for 'dMOC' to work ldiag_dMOC must be .true. otherwise no output
+! for 'utemp', 'vtemp', 'usalt', 'vsalt' output, set ldiag_trflx=.true.
 &nml_list
 io_list =  'sst       ',1, 'm', 4,
            'sss       ',1, 'm', 4,
@@ -48,4 +50,7 @@ io_list =  'sst       ',1, 'm', 4,
            'bolus_u   ',1, 'y', 4,
            'bolus_v   ',1, 'y', 4,
            'bolus_w   ',1, 'y', 4,
+           'icb       ',1, 'm', 4,
+           'fw        ',1, 'm', 4,
+           'fh        ',1, 'm', 4,
 /

config/namelist.oce.toy_soufflet

@@ -3,81 +3,25 @@
 &oce_dyn
 state_equation=0       ! 1 - full equation of state, 0 - linear equation of state
 C_d=0.0025             ! Bottom drag, nondimensional
-gamma0=0.00            ! [m/s],   backgroung viscosity= gamma0*len, it should be as small as possible (keep it < 0.01 m/s).
-gamma1=0.002           ! [nodim], for computation of the flow aware viscosity
-gamma2=0.02            ! [s/m],   is only used in easy backscatter option
-Div_c=.5  	       ! the strength of the modified Leith viscosity, nondimensional, 0.3 -- 1.0
-Leith_c=.5	       ! the strength of the Leith viscosity
-visc_option=5          ! 1=Harmonic Leith parameterization;
-                       ! 2=Laplacian+Leith+biharmonic background
-                       ! 3=Biharmonic Leith parameterization
-                       ! 4=Biharmonic flow aware
-                       ! 5=Easy Backscatter
-                       ! 6=Biharmonic flow aware (viscosity depends on velocity Laplacian)
-                       ! 7=Biharmonic flow aware (viscosity depends on velocity differences)
-easy_bs_return= 1.5     ! coefficient for returned sub-gridscale energy, to be used with visc_option=5 (easy backscatter)
 A_ver= 1.e-4	       ! Vertical viscosity, m^2/s
 scale_area=5.8e9       ! Visc. and diffus. are for an element with scale_area
-mom_adv=2              ! 1=vector CV, p1 vel, 2=sca. CV, 3=vector inv.
-free_slip=.false.      ! Switch on free slip
-i_vert_visc=.true.    
-w_split=.false.
-w_exp_max=1.e-3
 SPP=.false.                 ! Salt Plume Parameterization
-Fer_GM=.false.              ! to swith on/off GM after Ferrari et al. 2010
-K_GM_max     = 3000.0       ! max. GM thickness diffusivity (m2/s)
+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 = 40.0         ! Resol >K_GM_rampmax[km] GM on
-K_GM_rampmin = 30.0         ! Resol <K_GM_rampmin[km] GM off, in between linear scaled down
+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   =.true.  ! GM vertical scaling after Ferreira et al.(2005) (as also implemented by Qiang in FESOM 1.4)
+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    =.true.  ! special treatment of GM in the NH (as also implemented by Qiang in FESOM 1.4; it is zero within the boundary layer)
+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 
+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)
 /
-
-&oce_tra 
-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=0.0             ! 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.
-i_vert_diff=.true.  ! true
-tracer_adv =2       ! 1=MUSCL, 2=MUSCL+FCT
-! Implemented trassers (3d restoring):
-! 301 - Fram strait.
-! 302 - Bering Strait
-! 303 - BSO 
-num_tracers=2       !number of all tracers
-tracer_ID  =0,1     !their IDs (0 and 1 are reserved for temperature and salinity)
-/
-
-&oce_init3d                               ! initial conditions for tracers
-n_ic3d   = 2                              ! number of tracers to initialize
-idlist   = 1, 0                           ! 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
-/

config/namelist.tra

@@ -32,6 +32,7 @@ gamma0_tra    = 0.0005     ! gammaX_tra are analogous to those in the dynamical
 gamma1_tra    = 0.0125
 gamma2_tra    = 0.
 i_vert_diff   =.true.
+AB_order      = 2
 /
 
 &tracer_phys