Bugfix: remove rho2 diagnostic from MOM_input accidentally carried ov…

…er from my project. Turn off tides. Ensure that toolpath can be either string or path object

demos/premade_run_directories/common_files/MOM_input

@@ -104,7 +104,7 @@ OBC_COMPUTED_STRAIN = True      !   [Boolean] default = False
 OBC_ZERO_BIHARMONIC = True      !   [Boolean] default = False
                                 ! If true, zeros the Laplacian of flow on open boundaries in the biharmonic
                                 ! viscosity term.
-OBC_TIDE_N_CONSTITUENTS = 1     ! default = 0
+OBC_TIDE_N_CONSTITUENTS = 0     ! default = 0
                                 ! Number of tidal constituents being added to the open boundary.
 OBC_SEGMENT_001 = "J=0,I=0:N,FLATHER,ORLANSKI,NUDGED,ORLANSKI_TAN,NUDGED_TAN" !
                                 ! Documentation needs to be dynamic?????
@@ -263,20 +263,20 @@ VELOCITY_CONFIG = "file"        ! default = "zero"
                                 !     USER - call a user modified routine.
 VELOCITY_FILE = "forcing/init_vel.nc" !
                                 ! The name of the velocity initial condition file.
-OBC_SEGMENT_001_DATA = "U=file:forcing/forcing_obc_segment_001.nc(u),V=file:forcing/forcing_obc_segment_001.nc(v),SSH=file:forcing/forcing_obc_segment_001.nc(eta),TEMP=file:forcing/forcing_obc_segment_001.nc(temp),SALT=file:forcing/forcing_obc_segment_001.nc(salt),Uamp=file:forcing/tu_001.nc(uamp),Uphase=file:forcing/tu_001.nc(uphase),Vamp=file:forcing/tu_001.nc(vamp),Vphase=file:forcing/tu_001.nc(vphase),SSHamp=file:forcing/tz_001.nc(zamp),SSHphase=file:forcing/tz_001.nc(zphase)" !
+OBC_SEGMENT_001_DATA = "U=file:forcing/forcing_obc_segment_001.nc(u),V=file:forcing/forcing_obc_segment_001.nc(v),SSH=file:forcing/forcing_obc_segment_001.nc(eta),TEMP=file:forcing/forcing_obc_segment_001.nc(temp),SALT=file:forcing/forcing_obc_segment_001.nc(salt)" !
                                 ! OBC segment docs
-OBC_SEGMENT_002_DATA = "U=file:forcing/forcing_obc_segment_002.nc(u),V=file:forcing/forcing_obc_segment_002.nc(v),SSH=file:forcing/forcing_obc_segment_002.nc(eta),TEMP=file:forcing/forcing_obc_segment_002.nc(temp),SALT=file:forcing/forcing_obc_segment_002.nc(salt),Uamp=file:forcing/tu_002.nc(uamp),Uphase=file:forcing/tu_002.nc(uphase),Vamp=file:forcing/tu_002.nc(vamp),Vphase=file:forcing/tu_002.nc(vphase),SSHamp=file:forcing/tz_002.nc(zamp),SSHphase=file:forcing/tz_002.nc(zphase)" !
+OBC_SEGMENT_002_DATA = "U=file:forcing/forcing_obc_segment_002.nc(u),V=file:forcing/forcing_obc_segment_002.nc(v),SSH=file:forcing/forcing_obc_segment_002.nc(eta),TEMP=file:forcing/forcing_obc_segment_002.nc(temp),SALT=file:forcing/forcing_obc_segment_002.nc(salt)" !
                                 ! OBC segment docs
-OBC_SEGMENT_003_DATA = "U=file:forcing/forcing_obc_segment_003.nc(u),V=file:forcing/forcing_obc_segment_003.nc(v),SSH=file:forcing/forcing_obc_segment_003.nc(eta),TEMP=file:forcing/forcing_obc_segment_003.nc(temp),SALT=file:forcing/forcing_obc_segment_003.nc(salt),Uamp=file:forcing/tu_003.nc(uamp),Uphase=file:forcing/tu_003.nc(uphase),Vamp=file:forcing/tu_003.nc(vamp),Vphase=file:forcing/tu_003.nc(vphase),SSHamp=file:forcing/tz_003.nc(zamp),SSHphase=file:forcing/tz_003.nc(zphase)" !
+OBC_SEGMENT_003_DATA = "U=file:forcing/forcing_obc_segment_003.nc(u),V=file:forcing/forcing_obc_segment_003.nc(v),SSH=file:forcing/forcing_obc_segment_003.nc(eta),TEMP=file:forcing/forcing_obc_segment_003.nc(temp),SALT=file:forcing/forcing_obc_segment_003.nc(salt)" !
                                 ! OBC segment docs
-OBC_SEGMENT_004_DATA = "U=file:forcing/forcing_obc_segment_004.nc(u),V=file:forcing/forcing_obc_segment_004.nc(v),SSH=file:forcing/forcing_obc_segment_004.nc(eta),TEMP=file:forcing/forcing_obc_segment_004.nc(temp),SALT=file:forcing/forcing_obc_segment_004.nc(salt),Uamp=file:forcing/tu_004.nc(uamp),Uphase=file:forcing/tu_004.nc(uphase),Vamp=file:forcing/tu_004.nc(vamp),Vphase=file:forcing/tu_004.nc(vphase),SSHamp=file:forcing/tz_004.nc(zamp),SSHphase=file:forcing/tz_004.nc(zphase)" !
+OBC_SEGMENT_004_DATA = "U=file:forcing/forcing_obc_segment_004.nc(u),V=file:forcing/forcing_obc_segment_004.nc(v),SSH=file:forcing/forcing_obc_segment_004.nc(eta),TEMP=file:forcing/forcing_obc_segment_004.nc(temp),SALT=file:forcing/forcing_obc_segment_004.nc(salt)" !
                                 ! OBC segment docs
 
 ! === module MOM_diag_mediator ===
-NUM_DIAG_COORDS = 2             ! default = 1
+NUM_DIAG_COORDS = 1             ! default = 1
                                 ! The number of diagnostic vertical coordinates to use. For each coordinate, an
                                 ! entry in DIAG_COORDS must be provided.
-DIAG_COORDS = "z Z ZSTAR", "rho2 RHO2 RHO" !
+DIAG_COORDS = "z Z ZSTAR" !
                                 ! A list of string tuples associating diag_table modules to a coordinate
                                 ! definition used for diagnostics. Each string is of the form
                                 ! "MODULE_SUFFIX,PARAMETER_SUFFIX,COORDINATE_NAME".
@@ -294,20 +294,6 @@ DIAG_COORD_DEF_Z = "FILE:vcoord.nc,interfaces=zi" ! default = "WOA09"
                                 !                the filename and two variable names, separated
                                 !                by a comma or space, for sigma-2 and dz. e.g.
                                 !                HYBRID:vgrid.nc,sigma2,dz
-DIAG_COORD_DEF_RHO2 = "FILE:diag_rho2.nc,interfaces=rho2" ! default = "WOA09"
-                                ! Determines how to specify the coordinate resolution. Valid options are:
-                                !  PARAM       - use the vector-parameter DIAG_COORD_RES_RHO2
-                                !  UNIFORM[:N] - uniformly distributed
-                                !  FILE:string - read from a file. The string specifies
-                                !                the filename and variable name, separated
-                                !                by a comma or space, e.g. FILE:lev.nc,dz
-                                !                or FILE:lev.nc,interfaces=zw
-                                !  WOA09[:N]   - the WOA09 vertical grid (approximately)
-                                !  FNC1:string - FNC1:dz_min,H_total,power,precision
-                                !  HYBRID:string - read from a file. The string specifies
-                                !                the filename and two variable names, separated
-                                !                by a comma or space, for sigma-2 and dz. e.g.
-                                !                HYBRID:vgrid.nc,sigma2,dz
 
 ! === module MOM_lateral_mixing_coeffs ===
 
@@ -345,7 +331,7 @@ KHTH_MAX_CFL = 0.1              !   [nondimensional] default = 0.8
 ! === module MOM_porous_barriers ===
 
 ! === module MOM_dynamics_split_RK2 ===
-TIDES = True                    !   [Boolean] default = False
+TIDES = False                    !   [Boolean] default = False
                                 ! If true, apply tidal momentum forcing.
 ! === module MOM_continuity ===
 

demos/premade_run_directories/era5_surface/data_table

@@ -1,9 +1,9 @@
-"ATM", "p_surf", "sp", "./INPUT/forcing/sp_ERA5", "bilinear", 1.0
-"ATM", "p_bot",  "sp", "./INPUT/forcing/sp_ERA5", "bilinear", 1.0
-"ATM", "t_bot",  "t2m", "./INPUT/forcing/2t_ERA5", "bilinear", 1.0
-"ATM", "sphum_bot", "q", "./INPUT/forcing/q_ERA5", "bilinear", 1.0
-"ATM", "u_bot", "u10", "./INPUT/forcing/10u_ERA5", "bicubic", 1.0
-"ATM", "v_bot", "v10", "./INPUT/forcing/10v_ERA5", "bicubic", 1.0
+"ATM", "p_surf", "sp", "./INPUT/forcing/sp_ERA5.nc", "bilinear", 1.0
+"ATM", "p_bot",  "sp", "./INPUT/forcing/sp_ERA5.nc", "bilinear", 1.0
+"ATM", "t_bot",  "t2m", "./INPUT/forcing/2t_ERA5.nc", "bilinear", 1.0
+"ATM", "sphum_bot", "q", "./INPUT/forcing/q_ERA5.nc", "bilinear", 1.0
+"ATM", "u_bot", "u10", "./INPUT/forcing/10u_ERA5.nc", "bicubic", 1.0
+"ATM", "v_bot", "v10", "./INPUT/forcing/10v_ERA5.nc", "bicubic", 1.0
 "ATM", "z_bot", "", "", "bilinear", 10.0
 "ATM", "gust", "", "", "bilinear", 1.0e-4
 "ICE", "lw_flux_dn", "", "", "bilinear", 1.0

regional_mom6/regional_mom6.py

@@ -495,7 +495,7 @@ def __init__(
         self.vlayers = vlayers
         self.dz_ratio = dz_ratio
         self.depth = depth
-        self.toolpath = toolpath
+        self.toolpath = Path(toolpath)
         self.hgrid = self._make_hgrid(gridtype)
         self.vgrid = self._make_vgrid()
         self.gridtype = gridtype
@@ -1197,7 +1197,7 @@ def FRE_tools(self, layout):
         print(
             "MAKE SOLO MOSAIC",
             subprocess.run(
-                self.toolpath
+                str(self.toolpath)
                 + "make_solo_mosaic/make_solo_mosaic --num_tiles 1 --dir . --mosaic_name ocean_mosaic --tile_file hgrid.nc",
                 shell=True,
                 cwd=self.mom_input_dir,
@@ -1208,7 +1208,7 @@ def FRE_tools(self, layout):
         print(
             "QUICK MOSAIC",
             subprocess.run(
-                self.toolpath
+                str(self.toolpath)
                 + "make_quick_mosaic/make_quick_mosaic --input_mosaic ocean_mosaic.nc --mosaic_name grid_spec --ocean_topog topog.nc",
                 shell=True,
                 cwd=self.mom_input_dir,
@@ -1219,7 +1219,7 @@ def FRE_tools(self, layout):
         print(
             "CHECK MASK",
             subprocess.run(
-                self.toolpath
+                str(self.toolpath)
                 + f"check_mask/check_mask --grid_file ocean_mosaic.nc --ocean_topog topog.nc --layout {layout[0]},{layout[1]} --halo 4",
                 shell=True,
                 cwd=self.mom_input_dir,