GEOS-ESM · mathomp4 · Aug 31, 2022 · Jun 6, 2022 · Jun 7, 2022 · Jun 27, 2022
@@ -1,35 +1,25 @@
 version: 2.1
 
+# Anchors to prevent forgetting to update a version
+baselibs_version: &baselibs_version v7.5.0
+bcs_version: &bcs_version v10.22.3
+
 orbs:
-  circleci-tools: geos-esm/circleci-tools@0.11.0
+  ci: geos-esm/circleci-tools@1
 
 workflows:
   build-test:
     jobs:
-      - build-GEOSgcm:
+      # Build GEOSgcm
+      - ci/build:
           name: build-GEOSgcm-on-<< matrix.compiler >>
+          context:
+            - docker-hub-creds
           matrix:
             parameters:
               compiler: [gfortran, ifort]
-          context: 
-            - docker-hub-creds
-
-jobs:
-  build-GEOSgcm:
-    parameters:
-      compiler:
-        type: string
-    executor: circleci-tools/<< parameters.compiler >>
-    working_directory: /root/project
-    steps:
-      - circleci-tools/checkout_fixture
-      - circleci-tools/mepoclone
-      - circleci-tools/mepodevelop
-      - circleci-tools/checkout_if_exists
-      - circleci-tools/cmake:
-          compiler: << parameters.compiler >>
-      - circleci-tools/buildinstall
-      - circleci-tools/compress_artifacts
-      - store_artifacts:
-          path: /logfiles
-
+          baselibs_version: *baselibs_version
+          repo: GEOSgcm
+          checkout_fixture: true
+          mepodevelop: true
+          persist_workspace: false # Needs to be true to run fv3/gcm experiment, costs extra
@@ -20,7 +20,7 @@ ENERGETICS_SFC_PBL = True
 USE_MLD_ITERATION = False
 MASS_WEIGHT_IN_PRESSURE_GRADIENT = True
 
-VERBOSITY = 9
+!VERBOSITY = 9
 DEBUG = True
 FATAL_UNUSED_PARAMS = True
 

@@ -0,0 +1,74 @@
+netcdf MAPL_Tripolar {
+dimensions:
+	string = 255 ;
+        n_center_x = 1440 ;
+        n_center_y = 1080 ;
+        n_corner_x = 1441 ;
+        n_corner_y = 1081 ;
+	n_levels = 75 ;
+
+variables:
+        float lon_centers(n_center_y,n_center_x) ;
+                lon_centers:long_name = "longitude of cell center" ;
+                lon_centers:units = "degrees_E" ;
+        float lat_centers(n_center_y,n_center_x) ;
+                lat_centers:long_name = "latitude cell center" ;
+                lat_centers:units = "degrees_N" ;
+        float lon_corners(n_corner_y,n_corner_x) ;
+                lon_corners:long_name = "longitude of cell corner" ;
+                lon_corners:units = "degrees_E" ;
+        float lat_corners(n_corner_y,n_corner_x) ;
+                lat_corners:long_name = "latitude of cell corner" ;
+                lat_corners:units = "degrees_N" ;
+	float lev(n_levels) ;
+	        lev:long_name = "depth of layer center" ;
+                lev:units = "meters" ;
+	float mask(n_center_y,n_center_x) ;
+	        mask:long_name = "land/sea mask (0=land) on cell center" ;
+                mask:units = "none" ;
+	double htn(n_center_y,n_center_x) ;
+	        htn:long_name = "length of northern edge of T-Cell" ;
+		htn:units = "meters" ;
+	double hte(n_center_y,n_center_x) ;
+	        hte:long_name = "length of eastern edge of T-Cell" ;
+		hte:units = "meters" ;
+	double hus(n_center_y,n_center_x) ;
+	        hus:long_name = "length of southern edge of U-Cell" ;
+		hus:units = "meters" ;
+	double huw(n_center_y,n_center_x) ;
+	        huw:long_name = "length of western edge of U-Cell" ;
+		huw:units = "meters" ;
+	double areat(n_center_y,n_center_x) ;
+	        areat:long_name = "area of T-Cell" ;
+		areat:units = "m2" ;
+	double areau(n_center_y,n_center_x) ;
+	        areau:long_name = "area of U-Cell" ;
+		areau:units = "m2" ;
+	float anglet(n_center_y,n_center_x) ;
+	        anglet:long_name = "rotation angle centered on T-Cell" ;
+		anglet:units = "degrees_east" ;
+	float angleu(n_center_y,n_center_x) ;
+	        angleu:long_name = "rotation angle centered on U-Cell" ;
+		angleu:units = "degrees_east" ;
+	float basin(n_center_y,n_center_x) ;
+	        basin:long_name = "basin_masks" ;
+	float atl_mask(n_center_y,n_center_x) ;
+	        atl_mask:long_name = "Atlantic_mask" ;
+	char mom_file(string) ;
+	        mom_file:standard_name = "path_to_ocean_hgrid_file" ;
+	char vgrid_file(string) ;
+	        vgrid_file:standard_name = "path_to_vgrid_file" ;
+	char topo_file(string) ;
+	        topo_file:standard_name = "path_to_ocean_topog_file" ;
+	char basin_file(string) ;
+	        vgrid_file:standard_name = "path_to_basin_codes_file" ;
+
+// global attributes:
+		:author = "Yury Vikhliaev" ;
+
+data:
+	mom_file = "/discover/nobackup/projects/gmao/ssd/aogcm/ocean_bcs/MOM6/1440x1080_newtopo/INPUT/ocean_hgrid.nc" ;
+	vgrid_file = "/discover/nobackup/projects/gmao/ssd/aogcm/ocean_bcs/MOM6/1440x1080_newtopo/INPUT/vgrid.nc" ;
+	topo_file = "/discover/nobackup/projects/gmao/ssd/aogcm/ocean_bcs/MOM6/1440x1080_newtopo/INPUT/ocean_topog.nc" ;
+	basin_file = "/discover/nobackup/projects/gmao/ssd/aogcm/ocean_bcs/MOM6/1440x1080_newtopo/INPUT/basin_codes.nc" ;
+}
@@ -0,0 +1,37 @@
+`mk_MAPL_Tripolar.py` utily creates `MAPL_Tripolar.nc` file from MOM6 mosaic grid. It takes as an argument `MAPL_Tripolar.cdl` file. `MAPL_Tripolar.cdl` file should edited before running `mk_MAPL_Triporal.py`. Metadata section in `MAPL_Tripolar.cdl` defines grid dimentions, variable names, precision and attributes. Example of metadata section:
+
+```
+dimensions:
+	string = 255 ;
+        n_center_x = 1440 ;
+        n_center_y = 1080 ;
+        n_corner_x = 1441 ;
+        n_corner_y = 1081 ;
+	n_levels = 75 ;
+
+variables:
+        float lon_centers(n_center_y,n_center_x) ;
+                lon_centers:long_name = "longitude of cell center" ;
+                lon_centers:units = "degrees_E" ;
+        float lat_centers(n_center_y,n_center_x) ;
+                lat_centers:long_name = "latitude cell center" ;
+                lat_centers:units = "degrees_N" ;
+.................................................................
+	double areat(n_center_y,n_center_x) ;
+	        areat:long_name = "area of T-Cell" ;
+		areat:units = "m2" ;
+	double areau(n_center_y,n_center_x) ;
+	        areau:long_name = "area of U-Cell" ;
+		areau:units = "m2" ;
+```
+
+Data section contains path to input files. Example of data section
+
+```
+data:
+	mom_file = "/discover/nobackup/projects/gmao/ssd/aogcm/ocean_bcs/MOM6/1440x1080_newtopo/INPUT/ocean_hgrid.nc" ;
+	vgrid_file = "/discover/nobackup/projects/gmao/ssd/aogcm/ocean_bcs/MOM6/1440x1080_newtopo/INPUT/vgrid.nc" ;
+	topo_file = "/discover/nobackup/projects/gmao/ssd/aogcm/ocean_bcs/MOM6/1440x1080_newtopo/INPUT/ocean_topog.nc" ;
+	basin_file = "/discover/nobackup/projects/gmao/ssd/aogcm/ocean_bcs/MOM6/1440x1080_newtopo/INPUT/basin_codes.nc" ;
+```
+
@@ -0,0 +1,77 @@
+#!/usr/bin/env python3 
+
+'''
+To use this script load appropriate python and ncl modules, edit top of MAPL_Tripolar.cdl file,
+then run it as:
+
+./mk_MAPL_Tripolar.py MAPL_Tripolar.cdl
+
+'''
+
+import os, sys
+import numpy as np
+import netCDF4 as nc
+
+mapl_file='MAPL_Tripolar.nc'
+cdl_file=sys.argv[1]
+os.system(f'ncgen -o {mapl_file} {cdl_file}')
+
+with nc.Dataset(mapl_file) as ff:
+    mom_file=ff['mom_file'][:].data.tobytes().decode().replace('\x00','')
+    vgrid_file=ff['vgrid_file'][:].data.tobytes().decode().replace('\x00','')
+    topo_file=ff['topo_file'][:].data.tobytes().decode().replace('\x00','')
+    basin_file=ff['basin_file'][:].data.tobytes().decode().replace('\x00','')
+
+with nc.Dataset(mom_file) as ff:
+    # Grid dimension: (jm,im) 
+    xx=ff['x'][:]              # (2*jm+1, 2*im+1)
+    yy=ff['y'][:]              # (2*jm+1, 2*im+1)
+    dx=ff['dx'][:]             # (2*jm+1, 2*im)
+    dy=ff['dy'][:]             # (2*jm, 2*im+1)
+    angle_dx=ff['angle_dx'][:] # (2*jm+1, 2*im+1)
+    area=ff['area'][:]         # (2*jm, 2*im)
+
+with nc.Dataset(vgrid_file) as ff:
+    dz=ff['dz'][:]
+
+with nc.Dataset(topo_file) as ff:
+    mask=ff['wet'][:]
+
+with nc.Dataset(basin_file) as ff:
+    basin=ff['basin'][:]
+    atl_mask=np.where(basin==2.0, 1.0, 0.0)
+
+with nc.Dataset(mapl_file, mode='r+') as ff:
+    ff['lon_centers'][:]=xx[1::2,1::2]
+    ff['lat_centers'][:]=yy[1::2,1::2]
+    ff['lon_corners'][:]=xx[0::2,0::2]
+    ff['lat_corners'][:]=yy[0::2,0::2]
+    ff['lev'][:]=np.cumsum(dz)-0.5*dz
+    ff['mask'][:]=mask[:]
+
+    ff['htn'][:]=dx[2::2,0::2]+dx[2::2,1::2]
+    ff['hte'][:]=dy[0::2,2::2]+dy[1::2,2::2]
+
+    ff['huw'][0:-1,:]=dy[1:-1:2,1::2]+dy[2::2,1::2]
+    ff['huw'][-1,:]=dy[-1,1::2]+dy[-1,-1:1:-2]
+
+    ff['hus'][:,0:-1]=dx[1::2,1:-1:2]+dx[1::2,2::2]
+    ff['hus'][:,-1]=dx[1::2,-1]+dx[1::2,0]
+
+    ff['areat'][:]=area[0::2,0::2]+area[1::2,0::2]+area[1::2,1::2]+area[0::2,1::2]
+
+    ll=ul=ur=lr=np.zeros(ff['areau'].shape)
+    ll=area[1::2,1::2]; # lower left corner
+    ul[0:-1,:]=area[2::2,1::2]; ul[-1,:]=area[-1,-1::-2] # upper left corner
+    lr[:,0:-1]=area[1::2,2::2]; lr[:,-1]=area[1::2,0] # lower right corner
+    ur[0:-1,0:-1]=area[2::2,2::2]
+    ur[0:-1,-1]=area[2::2,0]
+    ur[-1,0:-1]=area[-1,-2:1:-2]
+    ur[-1,-1]=area[-1,0] # upper right corner
+    ff['areau'][:]=ll+ul+ur+lr
+
+    ff['angleu'][:]=angle_dx[2::2,2::2]
+    ff['anglet'][:]=angle_dx[1::2,1::2]
+
+    ff['basin'][:]=basin[:]
+    ff['atl_mask'][:]=atl_mask[:]
@@ -25,6 +25,9 @@ list( APPEND MOM6_SRCS
    src/ALE/coord_slight.F90
    src/ALE/coord_zlike.F90
    src/ALE/MOM_ALE.F90
+   src/ALE/MOM_hybgen_regrid.F90
+   src/ALE/MOM_hybgen_remap.F90
+   src/ALE/MOM_hybgen_unmix.F90
    src/ALE/MOM_regridding.F90
    src/ALE/MOM_remapping.F90
    src/ALE/P1M_functions.F90
@@ -40,6 +43,7 @@ list( APPEND MOM6_SRCS
    src/ALE/regrid_solvers.F90
    src/core/MOM_barotropic.F90
    src/core/MOM_boundary_update.F90
+   src/core/MOM_check_scaling.F90
    src/core/MOM_checksum_packages.F90
    src/core/MOM_continuity.F90
    src/core/MOM_continuity_PPM.F90
@@ -57,6 +61,7 @@ list( APPEND MOM6_SRCS
    src/core/MOM_PressureForce.F90
    src/core/MOM_PressureForce_FV.F90
    src/core/MOM_PressureForce_Montgomery.F90
+   src/core/MOM_stoch_eos.F90
    src/core/MOM_transcribe_grid.F90
    src/core/MOM_unit_tests.F90
    src/core/MOM_variables.F90
@@ -88,6 +93,7 @@ list( APPEND MOM6_SRCS
 #  src/equation_of_state/TEOS10/gsw_gibbs.f90
 #  src/equation_of_state/TEOS10/gsw_gibbs_ice.f90
 #  src/equation_of_state/TEOS10/gsw_gibbs_pt0_pt0.f90
+#  src/equation_of_state/TEOS10/gsw_mod_error_functions.f90
 #  src/equation_of_state/TEOS10/gsw_mod_freezing_poly_coefficients.f90
 #  src/equation_of_state/TEOS10/gsw_mod_gibbs_ice_coefficients.f90
 #  src/equation_of_state/TEOS10/gsw_mod_kinds.f90
@@ -134,8 +140,11 @@ list( APPEND MOM6_SRCS
    src/framework/MOM_restart.F90
    src/framework/MOM_safe_alloc.F90
    src/framework/MOM_string_functions.F90
+   src/framework/MOM_unique_scales.F90
    src/framework/MOM_unit_scaling.F90
    src/framework/MOM_write_cputime.F90
+   src/framework/posix.F90
+   src/framework/posix.h
    src/ice_shelf/MOM_ice_shelf_diag_mediator.F90
    src/ice_shelf/MOM_ice_shelf_dynamics.F90
    src/ice_shelf/MOM_ice_shelf.F90
@@ -202,6 +211,7 @@ list( APPEND MOM6_SRCS
    src/tracer/MOM_tracer_flow_control.F90
    src/tracer/MOM_tracer_hor_diff.F90
    src/tracer/MOM_tracer_registry.F90
+   src/tracer/MOM_tracer_types.F90
    src/tracer/MOM_tracer_Z_init.F90
    src/tracer/nw2_tracers.F90
    src/tracer/oil_tracer.F90
@@ -484,7 +494,11 @@ list( APPEND MOM6_SRCS
    config_src/external/drifters/MOM_particles.F90
    config_src/external/drifters/MOM_particles_types.F90
    # stochastic physics
+   config_src/external/stochastic_physics/get_stochy_pattern.F90
    config_src/external/stochastic_physics/stochastic_physics.F90
+   # database comms
+   config_src/external/database_comms/database_client_interface.F90
+   config_src/external/database_comms/MOM_database_comms.F90
 )