Merge branch 'master' into master

BUILD_CFG/DOMAIN/job_create.slurm → BUILD_CFG/DOMAIN/job_create_template.slurm

@@ -28,4 +28,4 @@ export OMP_NUM_THREADS=1
 # Launch the parallel job
 #   Using 512 MPI processes and 128 MPI processes per node
 #   srun picks up the distribution from the sbatch options
-srun --distribution=block:block --hint=nomultithread --het-group=0 /work/n01/n01/jelt/NEMO-REGION/BUILD_EXE/TOOLS_r8395/TOOLS/DOMAINcfg/BLD/bin/make_domain_cfg.exe
+srun --distribution=block:block --hint=nomultithread --het-group=0 XXX_TDIR_XXX/DOMAINcfg/BLD/bin/make_domain_cfg.exe

BUILD_CFG/DOMAIN/namelist.input_SEVERN

@@ -0,0 +1,34 @@
+&input_output
+    iom_activated = true
+/
+&coarse_grid_files
+    parent_coordinate_file = 'coordinates_AMM15.nc'
+/
+&bathymetry
+/
+&nesting
+    imin = 694
+    imax = 807
+    jmin = 400
+    jmax = 490
+    rho  = 3
+    rhot = 3
+    bathy_update = false
+/
+&vertical_grid
+/
+&partial_cells
+    partial_steps      = .true.
+/
+&nemo_coarse_grid
+/
+&forcing_files
+/
+&interp
+/
+&restart
+/
+&restart_trc
+/
+&restart_ice
+/

BUILD_CFG/DOMAIN/s-sig_DOMAINcfg_namelist_cfg

@@ -16,18 +16,18 @@
 &namcfg        !   parameters of the configuration
 !-----------------------------------------------------------------------
    !
-   ln_e3_dep   = .false.   ! =T : e3=dk[depth] in discret sens.
+   ln_e3_dep   = .true.   ! =T : e3=dk[depth] in discret sens.
    !                       !      ===>>> will become the only possibility in v4.0
    !                       ! =F : e3 analytical derivative of depth function
    !                       !      only there for backward compatibility test with v3.6
    !                       !
    cp_cfg      =  "orca"   !  name of the configuration
-   jp_cfg      =      12   !  resolution of the configuration
-   jpidta      =     684   !  1st lateral dimension ( >= jpi )
-   jpjdta      =     554   !  2nd    "         "    ( >= jpj )
-   jpkdta      =      51   !  number of levels      ( >= jpk )
-   jpiglo      =     684   !  1st dimension of global domain --> i =jpidta
-   jpjglo      =     554   !  2nd    -                  -    --> j  =jpjdta
+   jp_cfg      =     220   !  resolution of the configuration
+   jpidta      =     342   !  1st lateral dimension ( >= jpi )
+   jpjdta      =     273   !  2nd    "         "    ( >= jpj )
+   jpkdta      =      31   !  number of levels      ( >= jpk )
+   jpiglo      =     342   !  1st dimension of global domain --> i =jpidta
+   jpjglo      =     273   !  2nd    -                  -    --> j  =jpjdta
    jpizoom     =       1   !  left bottom (i,j) indices of the zoom
    jpjzoom     =       1   !  in data domain indices
    jperio      =       0   !  lateral cond. type (between 0 and 6)

BUILD_CFG/OPEN_BOUNDARIES/NCML/CMEMS_2005.ncml

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<netcdf title="aggregation example" xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
+  <variable name="vozocrtx"  orgName="uo" />
+  <variable name="vomecrty" orgName="vo" />
+  <variable name="votemper" orgName="thetao" />
+  <variable name="vosaline" orgName="so" />
+  <variable name="sossheig" orgName="zos" /> 
+  <variable name="time_counter" orgName="time">
+    <attribute type="string"  name="units" value= "hours since 1950-01-01 00:00:00" />
+  </variable>
+  <aggregation type="union" >
+     <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
+        <aggregation type="joinExisting" dimName="time" >
+           <scan location="/projectsa/accord/SANH_jenjar/CMEMS_SANH/CMEMS_data/2005/"  regExp=".*download.nc$" />
+        </aggregation>
+     </netcdf>
+     <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2">
+        <aggregation type="joinExisting" dimName="time" >
+           <scan location="/projectsa/accord/SANH_jenjar/CMEMS_SANH/UV_components/2005/"  regExp=".*download_UV.nc$" />
+        </aggregation>
+     </netcdf>
+  </aggregation>
+</netcdf>

BUILD_CFG/OPEN_BOUNDARIES/README.md

@@ -1,2 +1,3 @@
-This directory contains the namelist files to generate the harmonic and time varying open boundary conditions. See wiki note:
+This directory contains the namelist files to generate the harmonic and time varying open boundary conditions. See wiki notes:
 https://github.com/NOC-MSM/SEAsia/wiki/generate_NEMO_obc
+https://github.com/JMMP-Group/SEVERN-SWOT/wiki/3.-Make-tidal-boundary-conditions

BUILD_CFG/OPEN_BOUNDARIES/inputs_dst.ncml

@@ -1,9 +1,12 @@
 <ns0:netcdf xmlns:ns0="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2" title="NEMO aggregation">
   <ns0:aggregation type="union">
-    <ns0:netcdf location="file:domain_cfg.nc">
+    <ns0:netcdf location="file:../DOMAIN/domain_cfg.nc">
     <ns0:variable name="mbathy" orgName="bottom_level" />
     <ns0:variable name="e3u" orgName="e3u_0" />
     <ns0:variable name="e3v" orgName="e3v_0" />
+    <ns0:variable name="e3t" orgName="e3t_0" />
+    <ns0:variable name="e3w" orgName="e3w_0" />
     </ns0:netcdf>
   </ns0:aggregation>
 </ns0:netcdf>
+

BUILD_CFG/OPEN_BOUNDARIES/inputs_src_zgr.ncml

@@ -0,0 +1,8 @@
+<ns0:netcdf xmlns:ns0="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2" title="NEMO aggregation">
+  <ns0:aggregation type="union">
+    <ns0:netcdf location="file:./CMEMS_subdomain_coordinates.nc">
+    <ns0:variable name="gdept_0" orgName="depth" />
+
+    </ns0:netcdf>
+  </ns0:aggregation>
+</ns0:netcdf>

BUILD_CFG/OPEN_BOUNDARIES/namelist_FES14.bdy

@@ -1,4 +1,4 @@
-!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 !! NEMO/OPA  : namelist for BDY generation tool
 !!            
 !!             User inputs for generating open boundary conditions
@@ -7,125 +7,152 @@
 !!            
 !!             More info here.....
 !!            
-!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
+!!>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
 
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
 !   vertical coordinate
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
    ln_zco      = .false.   !  z-coordinate - full    steps   (T/F)  
    ln_zps      = .true.    !  z-coordinate - partial steps   (T/F)
    ln_sco      = .false.   !  s- or hybrid z-s-coordinate    (T/F)
    rn_hmin     =   -10     !  min depth of the ocean (>0) or 
                            !  min number of ocean level (<0)
 
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
 !   s-coordinate or hybrid z-s-coordinate
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
    rn_sbot_min =   10.     !  minimum depth of s-bottom surface (>0) (m)
-   rn_sbot_max = 6000.     !  maximum depth of s-bottom surface 
+   rn_sbot_max = 7000.     !  maximum depth of s-bottom surface 
                            !  (= ocean depth) (>0) (m)
-   ln_s_sigma  = .true.   !  hybrid s-sigma coordinates
-   rn_hc       =  39.0    !  critical depth with s-sigma
+   ln_s_sigma  = .false.   !  hybrid s-sigma coordinates
+   rn_hc       =  150.0    !  critical depth with s-sigma
 
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
 !  grid information 
-!-----------------------------------------------------------------------
-   sn_src_hgr = './mesh_hgr_src_N06.nc'   !  parent /grid/
-   sn_src_zgr = './mesh_zgr_src_N06_renamed.nc'   !  parent
-   sn_dst_hgr = './domain_cfg.nc'
-   sn_dst_zgr = './inputs_dst.ncml' ! rename output variables
-   sn_src_msk = './mask_src_N06.nc'       ! parent
-   sn_bathy   = './bathy_meter.nc'        ! child 
+!------------------------------------------------------------------------------
+  sn_src_hgr = '/projectsa/accord/SANH_jenjar/CMEMS_SANH/TEST_pynemo3/CMEMS_subdomain_coordinates.nc'   !  parent /grid/
+   sn_src_zgr = '/projectsa/accord/SANH_jenjar/CMEMS_SANH/TEST_pynemo3/inputs_src_zgr.ncml'   !  parent
+   sn_dst_hgr = '../DOMAIN/domain_cfg.nc'  ! child
+   sn_dst_zgr = 'inputs_dst.ncml' ! rename output variables
+   sn_src_msk = '/projectsa/accord/SANH_jenjar/CMEMS_SANH/TEST_pynemo3/CMEMS_subdomain_mask.nc'       ! parent
+   sn_bathy   = '../DOMAIN/bathy_meter.nc'        ! child
 
-!-----------------------------------------------------------------------
+
+!------------------------------------------------------------------------------
 !  I/O 
-!-----------------------------------------------------------------------
-   sn_src_dir = 'ORCA0083_N06_1960.ncml'       ! src_files/'
-   sn_dst_dir = '/projectsa/accord/SEAsia/INPUTS/TIDES/'
-   sn_fn      = 'SEAsia'                 ! prefix for output files
-   nn_fv      = -1e20                     !  set fill value for output files
-   nn_src_time_adj = 0					  ! src time adjustment
-   sn_dst_metainfo = 'metadata info: jelt'
+!------------------------------------------------------------------------------
+   sn_src_dir      = './NCML/CMEMS_2005.ncml' ! src_files/'
+   sn_dst_dir      = './OUTPUT'
+   sn_ncml_out     = './output_NCML'
+   sn_model_prefix = 'NEMO'
+
+   sn_fn      = 'SEVERN_FES14'             ! prefix for output files
+   nn_fv      = -1e20                 !  set fill value for output files
+   nn_src_time_adj = 0                ! src time adjustment
+   sn_dst_metainfo = 'CMEMS example'
+
+!------------------------------------------------------------------------------
+!  CMEMS Data Source Configuration
+!------------------------------------------------------------------------------
+   ln_download_cmems        = .false.
+   sn_cmems_dir             = '/projectsa/accord/SANH_jenjar/CMEMS_SANH/CMEMS_data' ! where to download CMEMS input files (static and variable)
+   ln_download_static       = .false.
+   ln_subset_static         = .false.
+   nn_num_retry             = 4 ! how many times to retry CMEMS download after non critical errors?
+!------------------------------------------------------------------------------
+!  CMEMS MOTU Configuration (for Boundary Data)
+!------------------------------------------------------------------------------
+   sn_motu_server           = 'http://nrt.cmems-du.eu/motu-web/Motu'
+ !  sn_cmems_config_template = '/Users/thopri/Projects/PyNEMO/pynemo/config/motu_config_template.ini'
+ !  sn_cmems_config          = '/Users/thopri/Projects/PyNEMO/pynemo/config/motu_config.ini'
+   sn_cmems_model           = 'GLOBAL_ANALYSIS_FORECAST_PHY_001_024-TDS'
+   sn_cmems_product         = 'global-analysis-forecast-phy-001-024'
+   sn_dl_prefix             = 'subset'
+!------------------------------------------------------------------------------
+!  CMEMS FTP Configuration (for Static Files)
+!------------------------------------------------------------------------------
+   sn_ftp_server            = 'nrt.cmems-du.eu'
+   sn_static_dir            = '/Core/GLOBAL_ANALYSIS_FORECAST_PHY_001_024/global-analysis-forecast-phy-001-024-statics'
+   sn_static_filenames      = 'GLO-MFC_001_024_coordinates.nc GLO-MFC_001_024_mask_bathy.nc GLO-MFC_001_024_mdt.nc'
+   sn_cdo_loc               = '/opt/local/bin/cdo' ! location of cdo executable can be found by running "where cdo"
+!------------------------------------------------------------------------------
+!  CMEMS Extent Configuration
+!------------------------------------------------------------------------------
+   nn_latitude_min          = 40
+   nn_latitude_max          = 66
+   nn_longitude_min         = -22
+   nn_longitude_max         = 16
+   nn_depth_min             = 0.493
+   nn_depth_max             = 5727.918000000001
 
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
 !  unstructured open boundaries                         
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
     ln_coords_file = .true.               !  =T : produce bdy coordinates files
-    cn_coords_file = 'coordinates.bdy.nc' !  name of bdy coordinates files (if ln_coords_file=.TRUE.)
-    ln_mask_file   = .false.              !  =T : read mask from file
-    cn_mask_file   = './bdy_mask.nc'                   !  name of mask file (if ln_mask_file=.TRUE.)
-    ln_dyn2d       = .false.               !  boundary conditions for barotropic fields
-    ln_dyn3d       = .false.               !  boundary conditions for baroclinic velocities
+    cn_coords_file = 'coordinates.bdy.nc' !  name of bdy coordinates files 
+                                          !  (if ln_coords_file=.TRUE.)
+    ln_mask_file   = .true.              !  =T : read mask from file
+    cn_mask_file   = '../DOMAIN/bdy_mask.nc'            !  name of mask file
+                                          !  (if ln_mask_file=.TRUE.)
+    ln_dyn2d       = .false.              !  boundary conditions for
+                                          !  barotropic fields
+    ln_dyn3d       = .false.              !  boundary conditions for
+                                          !  baroclinic velocities
     ln_tra         = .false.               !  boundary conditions for T and S
-    ln_ice         = .false.               !  ice boundary condition   
-    nn_rimwidth    = 1                    !  width of the relaxation zone
+    ln_ice         = .false.              !  ice boundary condition   
+    nn_rimwidth    = 9                    !  width of the relaxation zone
 
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
 !  unstructured open boundaries tidal parameters                        
-!-----------------------------------------------------------------------
-    ln_tide        = .true.               !  =T : produce bdy tidal conditions
-!FES
-        clname(1) ='2N2'
-        clname(2)='EPS2'
-        clname(3)='J1'
-        clname(4)='K1'
-        clname(5)='K2'
-        clname(6)='L2'
-        clname(7)='LA2'
-        clname(8)='M2'
-        clname(9)='M3'
-        clname(10)='M4'
-        clname(11)='M6'
-        clname(12)='M8'
-        clname(13)='MF'
-        clname(14)='MKS2'
-        clname(15)='MM'
-        clname(16)='MN4'
-        clname(17)='MS4'
-        clname(18)='MSF'
-        clname(19)='MSQM'
-        clname(20)='MTM'
-        clname(21)='MU2'
-        clname(22)='N2'
-        clname(23)='N4'
-        clname(24)='NU2'
-        clname(25)='O1'
-        clname(26)='P1'
-        clname(27)='Q1'
-        clname(28)='R2'
-        clname(29)='S1'
-        clname(30)='S2'
-        clname(31)='S4'
-        clname(32)='SA'
-        clname(33)='SSA'
-        clname(34)='T2'
-    ln_trans       = .false.
-    sn_tide_h     = '' # Hardwired with FES14 path
-    sn_tide_u     = '' # Hardwired with FES14 path
-
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
+    ln_tide        = .true.              !  =T : produce bdy tidal conditions
+    sn_tide_model  = 'fes'                !  Name of tidal model (fes|tpxo)
+    clname(1)      = 'M2'                 !  constituent name
+    clname(2)      = 'S2'
+    !clname(3)      = 'N2'
+    !clname(4)      = 'O1'
+    !clname(5)      = 'K1'
+    !clname(6)      = 'K2'
+    !clname(7)      = 'L2'
+    !clname(8)      = 'NU2'
+    !clname(9)      = 'M4'
+    !clname(10)     = 'MS4'
+    !clname(11)     = 'Q1'
+    !clname(12)     = 'P1'
+    !clname(13)     = 'S1'
+    !clname(14)     = '2N2'
+    !clname(15)     = 'MU2'
+    ln_trans       = .false.                !  interpolate transport rather than velocities
+    ln_tide_checker = .false.                ! run tide checker on PyNEMO tide output
+    sn_ref_model    = 'fes'                 ! which model to check output against (FES only)
+!------------------------------------------------------------------------------
 !  Time information
-!-----------------------------------------------------------------------
-    nn_year_000     = 1960        !  year start
-    nn_year_end     = 1960          !  year end
-    nn_month_000    = 1          !  month start (default = 1 is years>1)
-    nn_month_end    = 12         !  month end (default = 12 is years>1)
+!------------------------------------------------------------------------------
+    nn_year_000     = 2005        !  year start
+    nn_year_end     = 2005        !  year end
+    nn_month_000    = 01          !  month start (default = 1 is years>1)
+    nn_month_end    = 04       !  month end (default = 12 is years>1)
     sn_dst_calendar = 'gregorian' !  output calendar format
-    nn_base_year    = 1900        !  base year for time counter in output data
-    sn_tide_grid    = '' # Hard wired for FES14 paths #/work/jelt/tpxo7.2/grid_tpxo7.2.nc'
-    nn_src_time_adj = 0  != -3168000 - 86400 ! N01: fix to align model time stamp
-!-----------------------------------------------------------------------
+    nn_base_year    = 1960        !  base year for time counter
+    ! TPXO file locations
+	sn_tide_grid   = '/work/jelt/tpxo7.2/grid_tpxo7.2.nc'
+	sn_tide_h      = '/work/jelt/tpxo7.2/h_tpxo7.2.nc'
+	sn_tide_u      = '/work/jelt/tpxo7.2/u_tpxo7.2.nc'
+	! location of FES data
+	sn_tide_fes      = './FES2014/'
+
+!------------------------------------------------------------------------------
 !  Additional parameters
-!-----------------------------------------------------------------------
+!------------------------------------------------------------------------------
     nn_wei  = 1                   !  smoothing filter weights 
     rn_r0   = 0.041666666         !  decorrelation distance use in gauss
                                   !  smoothing onto dst points. Need to 
                                   !  make this a funct. of dlon
-    sn_history  = 'bdy files produced by jelt from ORCA0083-N01'
+    sn_history  = 'Tide-only test case'
                                   !  history for netcdf file
     ln_nemo3p4  = .true.          !  else presume v3.2 or v3.3
     nn_alpha    = 0               !  Euler rotation angle
     nn_beta     = 0               !  Euler rotation angle
     nn_gamma    = 0               !  Euler rotation angle
-    rn_mask_max_depth = 300.0	  !  Maximum depth to be ignored for the mask
-    rn_mask_shelfbreak_dist = 60    !  Distance from the shelf break
+	rn_mask_max_depth = 100.0     !  Maximum depth to be ignored for the mask
+	rn_mask_shelfbreak_dist = 20000.0 !  Distance from the shelf break