Xcroco question

croco tools (pre/post-processing)
1

Hi,

I am currently trying to use Xcroco from croco_pytools-v2.0.1 and I encountered an issue regarding a missing variable.
Since I am using the default outputs from CROCO, I selected croco_native as the model in xcroco.ini. However, when I tried to run tuto_xcroco.ipynb, I received an error stating that the variable Cs_r does not exist. The error appears in gridop.py, and I assume directly modifying the template might lead to further issues, so I am looking for recommended workarounds or best practices.
Looking at the model.py, I see that the croco_native template does not define Cs_r (unlike croco_xios, which has “Cs_rho”: “Cs_r” in rename_vars). I tried different approaches to resolve the problem, but the error persists.
What is the best strategy to overcomes this issue for CROCO ouputs containing Cs_rho?

Thank you in advance.

2

Hi @Jellyfish,

It seems that the variable Cs_r is either missing from your file or has a different name.

This may occur if you have a former version of CROCO with a different naming convention, or if you did not write Cs_r in both history and grid files.

In case of a wrong naming convention the best practice is to edit model.py :

  • add a new model with a name ex: “old_croco_native” like if name == "old_croco_native":
  • copy the dictionary for naming convention that’s closest to your model here “croco_native”
self.rename_vars = {
                # surface wind stress
                "sustr": "xtau_sfc_u",  # x-wind stress component
                ...
  • add a line for misnamed variable “Cs_rho_wrong_name”: “Cs_r”

This is actually the way to deal with any naming convention issue. model.py is just a tool to rename CROCO variables to a standard naming convention.

In case where you do not have access to Cs_rho, you’ll have to recompute it somehow offline, and add it “manually” to croco xarray.dataset and it should be fine.

I hope this helps,
Best,
Jeremy

3

Hello !

Out of curiosity : Can you put a ncdump -h of your croco file here ?

If Cs_r is not at all in the file, it should be (I believe) computed automatically by the get_cs function within xcroco.

Enzo

4

Hi Jeremy,

Thanks for the advice.
I’m going to test it out to see if it works.

Best regards

5

Hi,

This is the output from the ncdump:
netcdf croco_his_Y2019M12 {
dimensions:
xi_rho = 902 ;
xi_u = 901 ;
eta_rho = 902 ;
eta_v = 901 ;
s_rho = 60 ;
s_w = 61 ;
time = UNLIMITED ; // (2 currently)
auxil = 4 ;
variables:
char spherical ;
spherical:long_name = “grid type logical switch” ;
spherical:option_T = “spherical” ;
spherical:option_F = “cartesian” ;
float xl ;
xl:long_name = “domain length in the XI-direction” ;
xl:units = “meter” ;
float el ;
el:long_name = “domain length in the ETA-direction” ;
el:units = “meter” ;
float xi_rho(xi_rho) ;
xi_rho:long_name = “x-dimension of the grid” ;
xi_rho:standard_name = “x_grid_index” ;
xi_rho:axis = “X” ;
xi_rho:c_grid_dynamic_range = “2:901” ;
float xi_u(xi_u) ;
xi_u:long_name = “x-dimension of the grid at u location” ;
xi_u:standard_name = “x_grid_index_at_u_location” ;
xi_u:axis = “X” ;
xi_u:c_grid_axis_shift = 0.5f ;
xi_u:c_grid_dynamic_range = “2:900” ;
float eta_rho(eta_rho) ;
eta_rho:long_name = “y-dimension of the grid” ;
eta_rho:standard_name = “y_grid_index” ;
eta_rho:axis = “Y” ;
eta_rho:c_grid_dynamic_range = “2:901” ;
float eta_v(eta_v) ;
eta_v:long_name = “y-dimension of the grid at v location” ;
eta_v:standard_name = “x_grid_index_at_v_location” ;
eta_v:axis = “Y” ;
eta_v:c_grid_axis_shift = 0.5f ;
eta_v:c_grid_dynamic_range = “2:900” ;
float Vtransform ;
Vtransform:long_name = “vertical terrain-following transformation equatio” ;
float s_rho(s_rho) ;
s_rho:long_name = “S-coordinate at RHO-points” ;
s_rho:axis = “Z” ;
s_rho:positive = “up” ;
s_rho:standard_name = “ocean_s_coordinate_g2” ;
s_rho:Vtransform = “2” ;
s_rho:formula_terms = “s: s_rho C: Cs_rho eta: zeta depth: h depth_c: hc” ;
float s_w(s_w) ;
s_w:long_name = “S-coordinate at W-points” ;
s_w:axis = “Z” ;
s_w:positive = “up” ;
s_w:c_grid_axis_shift = -0.5f ;
s_w:standard_name = “ocean_s_coordinate_g2_at_w_location” ;
s_w:Vtransform = “2” ;
s_w:formula_terms = “s: s_w C: Cs_w eta: zeta depth: h depth_c: hc” ;
float Cs_rho(s_rho) ;
Cs_rho:long_name = “S-coordinate stretching curves at RHO-points” ;
float Cs_w(s_w) ;
Cs_w:long_name = “S-coordinate stretching curves at W-points” ;
float hc ;
hc:long_name = “S-coordinate parameter, critical depth” ;
hc:units = “meter” ;
float h(eta_rho, xi_rho) ;
h:long_name = “bathymetry at RHO-points” ;
h:units = “meter” ;
h:field = “bath, scalar” ;
h:standard_name = “model_sea_floor_depth_below_geoid” ;
h:coordinates = “lat_rho lon_rho” ;
float f(eta_rho, xi_rho) ;
f:long_name = “Coriolis parameter at RHO-points” ;
f:units = “second-1” ;
f:field = “coriolis, scalar” ;
f:standard_name = “coriolis_parameter” ;
f:coordinates = “lat_rho lon_rho” ;
float pm(eta_rho, xi_rho) ;
pm:long_name = “curvilinear coordinates metric in X” ;
pm:units = “meter-1” ;
pm:field = “pm, scalar” ;
pm:coordinates = “lat_rho lon_rho” ;
pm:standard_name = “inverse_of_cell_x_size” ;
float pn(eta_rho, xi_rho) ;
pn:long_name = “curvilinear coordinates metric in ET” ;
pn:units = “meter-1” ;
pn:field = “pn, scalar” ;
pn:coordinates = “lat_rho lon_rho” ;
pn:standard_name = “inverse_of_cell_y_size” ;
float lon_rho(eta_rho, xi_rho) ;
lon_rho:long_name = “longitude of RHO-points” ;
lon_rho:units = “degree_east” ;
lon_rho:field = “lon_rho, scalar” ;
lon_rho:standard_name = “longitude” ;
float lat_rho(eta_rho, xi_rho) ;
lat_rho:long_name = “latitude of RHO-points” ;
lat_rho:units = “degree_north” ;
lat_rho:field = “lat_rho, scalar” ;
lat_rho:standard_name = “latitude” ;
float lon_u(eta_rho, xi_u) ;
lon_u:long_name = “longitude of U-points” ;
lon_u:units = “degree_east” ;
lon_u:field = “lon_u, scalar” ;
lon_u:standard_name = “longitude_at_u_location” ;
float lat_u(eta_rho, xi_u) ;
lat_u:long_name = “latitude of U-points” ;
lat_u:units = “degree_north” ;
lat_u:field = “lat_u, scalar” ;
lat_u:standard_name = “latitude_at_u_location” ;
float lon_v(eta_v, xi_rho) ;
lon_v:long_name = “longitude of V-points” ;
lon_v:units = “degree_east” ;
lon_v:field = “lon_v, scalar” ;
lon_v:standard_name = “longitude_at_v_location” ;
float lat_v(eta_v, xi_rho) ;
lat_v:long_name = “latitude of V-points” ;
lat_v:units = “degree_north” ;
lat_v:field = “lat_v, scalar” ;
lat_v:standard_name = “latitude_at_v_location” ;
float angle(eta_rho, xi_rho) ;
angle:long_name = “angle between XI-axis and EAST” ;
angle:units = “radians” ;
angle:field = “angle, scalar” ;
angle:coordinates = “lat_rho lon_rho” ;
float mask_rho(eta_rho, xi_rho) ;
mask_rho:long_name = “mask on RHO-points” ;
mask_rho:option_0 = “land” ;
mask_rho:option_1 = “water” ;
mask_rho:standard_name = “land_binary_mask” ;
mask_rho:coordinates = “lat_rho lon_rho” ;
int time_step(time, auxil) ;
time_step:long_name = “time step and record numbers from initialization” ;
double scrum_time(time) ;
scrum_time:long_name = “time since initialization” ;
scrum_time:units = “second” ;
scrum_time:field = “time, scalar, series” ;
scrum_time:standard_name = “time” ;
scrum_time:axis = “T” ;
double time(time) ;
time:long_name = “time since initialization” ;
time:units = “second” ;
time:field = “time, scalar, series” ;
time:standard_name = “time” ;
time:axis = “T” ;
float zeta(time, eta_rho, xi_rho) ;
zeta:long_name = “free-surface” ;
zeta:units = “meter” ;
zeta:field = “free-surface, scalar, series” ;
zeta:standard_name = “sea_surface_height” ;
zeta:coordinates = “lat_rho lon_rho” ;
float ubar(time, eta_rho, xi_u) ;
ubar:long_name = “vertically integrated u-momentum component” ;
ubar:units = “meter second-1” ;
ubar:field = “ubar-velocity, scalar, series” ;
ubar:standard_name = “barotropic_sea_water_x_velocity_at_u_location” ;
ubar:coordinates = “lat_u lon_u” ;
float vbar(time, eta_v, xi_rho) ;
vbar:long_name = “vertically integrated v-momentum component” ;
vbar:units = “meter second-1” ;
vbar:field = “vbar-velocity, scalar, series” ;
vbar:standard_name = “barotropic_sea_water_y_velocity_at_v_location” ;
vbar:coordinates = “lat_v lon_v” ;
float u(time, s_rho, eta_rho, xi_u) ;
u:long_name = “u-momentum component” ;
u:units = “meter second-1” ;
u:field = “u-velocity, scalar, series” ;
u:standard_name = “sea_water_x_velocity_at_u_location” ;
u:coordinates = “lat_u lon_u” ;
float v(time, s_rho, eta_v, xi_rho) ;
v:long_name = “v-momentum component” ;
v:units = “meter second-1” ;
v:field = “v-velocity, scalar, series” ;
v:standard_name = “sea_water_y_velocity_at_v_location” ;
v:coordinates = “lat_v lon_v” ;
float temp(time, s_rho, eta_rho, xi_rho) ;
temp:long_name = “potential temperature” ;
temp:units = “Celsius” ;
temp:field = “temperature, scalar, series” ;
temp:standard_name = “sea_water_potential_temperature” ;
temp:coordinates = “lat_rho lon_rho” ;
float salt(time, s_rho, eta_rho, xi_rho) ;
salt:long_name = “salinity” ;
salt:units = “PSU” ;
salt:field = “salinity, scalar, series” ;
salt:standard_name = “sea_water_salinity” ;
salt:coordinates = “lat_rho lon_rho” ;
float w(time, s_rho, eta_rho, xi_rho) ;
w:long_name = “vertical momentum component” ;
w:units = “meter second-1” ;
w:field = “w-velocity, scalar, series” ;
w:standard_name = “upward_sea_water_velocity” ;
w:coordinates = “lat_rho lon_rho” ;
float bostr(time, eta_rho, xi_rho) ;
bostr:long_name = “Kinematic bottom stress” ;
bostr:units = “N/m2” ;
bostr:coordinates = “lat_rho lon_rho” ;
float wstr(time, eta_rho, xi_rho) ;
wstr:long_name = “Kinematic wind stress” ;
wstr:units = “N/m2” ;
wstr:standard_name = “magnitude_of_surface_downward_stress” ;
wstr:coordinates = “lat_rho lon_rho” ;
float sustr(time, eta_rho, xi_u) ;
sustr:long_name = “Kinematic u wind stress component” ;
sustr:units = “N/m2” ;
sustr:standard_name = “surface_downward_eastward_stress” ;
sustr:coordinates = “lat_u lon_u” ;
float svstr(time, eta_v, xi_rho) ;
svstr:long_name = “Kinematic v wind stress component” ;
svstr:units = “N/m2” ;
svstr:standard_name = “surface_downward_northward_stress” ;
svstr:coordinates = “lat_v lon_v” ;
float AKt(time, s_w, eta_rho, xi_rho) ;
AKt:long_name = “temperature vertical diffusion coefficient” ;
AKt:units = “meter2 second-1” ;
AKt:field = “AKt, scalar, series” ;
AKt:standard_name = “ocean_vertical_heat_diffusivity_at_w_location” ;
AKt:coordinates = “lat_rho lon_rho” ;
float hbl(time, eta_rho, xi_rho) ;
hbl:long_name = “depth of planetary boundary layer” ;
hbl:units = “meter” ;
hbl:field = “hbl, scalar, series” ;
hbl:standard_name = “ocean_mixed_layer_thickness_defined_by_mixing_scheme” ;
hbl:coordinates = “lat_rho lon_rho” ;
float hbbl(time, eta_rho, xi_rho) ;
hbbl:long_name = “depth of bottom boundary layer” ;
hbbl:units = “meter” ;
hbbl:field = “hbbl, scalar, series” ;
hbbl:coordinates = “lat_rho lon_rho” ;
float shflux(time, eta_rho, xi_rho) ;
shflux:long_name = “surface net heat flux” ;
shflux:units = “Watts meter-2” ;
shflux:coordinates = “lat_rho lon_rho” ;
float swflux(time, eta_rho, xi_rho) ;
swflux:long_name = “surface freshwater flux (E-P)” ;
swflux:units = “centimeter day-1” ;
swflux:coordinates = “lat_rho lon_rho” ;
float radsw(time, eta_rho, xi_rho) ;
radsw:long_name = “Short-wave surface radiation” ;
radsw:units = “Watts meter-2” ;
radsw:coordinates = “lat_rho lon_rho” ;
float shflx_rlw(time, eta_rho, xi_rho) ;
shflx_rlw:long_name = “Long-wave surface radiation” ;
shflx_rlw:units = “Watts meter-2” ;
shflx_rlw:coordinates = “lat_rho lon_rho” ;
float shflx_lat(time, eta_rho, xi_rho) ;
shflx_lat:long_name = “Latent surface heat flux” ;
shflx_lat:units = “Watts meter-2” ;
shflx_lat:coordinates = “lat_rho lon_rho” ;
float shflx_sen(time, eta_rho, xi_rho) ;
shflx_sen:long_name = “Sensible surface heat flux” ;
shflx_sen:units = “Watts meter-2” ;
shflx_sen:coordinates = “lat_rho lon_rho” ;
It doesn’t have the Cs_r, but the Cs_rho.

6

Then I believe you can do as Jeremy said and add to the “croco_native” dict in model.py the line :
"Cs_rho": "Cs_r", # S-coordinates at mass points

7

I have the encountered the same error and resolved it by modifying
“Cs_rho”: “Cs_r”, # S-coordinates at mass points
in the gridop.py

8

Since i applied the "Cs_rho": "Cs_r", # S-coordinates at mass points everything is working fine.
I didn´t need to change anything in gridop.py yet.

9

Hi,
Where in gridop.py you applied that change?