My ROMS output .NC file does not contain all the variables required, can I still use Parcels?

[Xyx105]

Hi,

I am currently trying to use OceanParcels to model particle movemtn within the Irish Sea with the output from a ROMS model. I have been trying ti use the code found in #620 but I am finding it tricky to replicate as the output .NC files I am working with do not have all the required/same variables.

Below is the details of the first timestep/ first netcdf file in the collection. I have been able to create Cs_r using another program but I am still missing crucial variables used in #620:

Dimensions:
x = 398
y = 357
y_2 = 358
s_rho = 40
ocean_time = 1 (UNLIMITED)
Variables:
lon_rho
Size: 398x357
Dimensions: x,y
Datatype: double
Attributes:
standard_name = 'longitude'
long_name = 'longitude'
units = 'degrees_east'
_CoordinateAxisType = 'Lon'
lat_rho
Size: 398x357
Dimensions: x,y
Datatype: double
Attributes:
standard_name = 'latitude'
long_name = 'latitude'
units = 'degrees_north'
_CoordinateAxisType = 'Lat'
lon_u
Size: 398x358
Dimensions: x,y_2
Datatype: double
Attributes:
standard_name = 'longitude'
long_name = 'longitude'
units = 'degrees_east'
_CoordinateAxisType = 'Lon'
lat_u
Size: 398x358
Dimensions: x,y_2
Datatype: double
Attributes:
standard_name = 'latitude'
long_name = 'latitude'
units = 'degrees_north'
_CoordinateAxisType = 'Lat'
lon_v
Size: 398x358
Dimensions: x,y_2
Datatype: double
Attributes:
standard_name = 'longitude'
long_name = 'longitude'
units = 'degrees_east'
_CoordinateAxisType = 'Lon'
lat_v
Size: 398x358
Dimensions: x,y_2
Datatype: double
Attributes:
standard_name = 'latitude'
long_name = 'latitude'
units = 'degrees_north'
_CoordinateAxisType = 'Lat'
s_rho
Size: 40x1
Dimensions: s_rho
Datatype: double
Attributes:
long_name = 'S-coordinate at RHO-points'
positive = 'up'
axis = 'Z'
ocean_time
Size: 1x1
Dimensions: ocean_time
Datatype: double
Attributes:
standard_name = 'time'
long_name = 'time since initialization'
units = 'seconds since 1968-5-23 00:00:00'
calendar = 'standard'
axis = 'T'
h
Size: 398x357
Dimensions: x,y
Datatype: double
Attributes:
long_name = 'bathymetry at RHO-points'
units = 'meter'
coordinates = 'lat_rho lon_rho'
grid = 'grid'
location = 'face'
field = 'bath, scalar'
angle
Size: 398x357
Dimensions: x,y
Datatype: double
Attributes:
long_name = 'angle between XI-axis and EAST'
units = 'radians'
coordinates = 'lat_rho lon_rho'
grid = 'grid'
location = 'face'
field = 'angle, scalar'
mask_rho
Size: 398x357
Dimensions: x,y
Datatype: double
Attributes:
long_name = 'mask on RHO-points'
coordinates = 'lat_rho lon_rho'
flag_values = [0 1]
flag_meanings = 'land water'
grid = 'grid'
location = 'face'
zeta
Size: 398x357x1
Dimensions: x,y,ocean_time
Datatype: single
Attributes:
long_name = 'free-surface'
units = 'meter'
coordinates = 'lat_rho lon_rho'
_FillValue = 9.999999933815813e+36
missing_value = 9.999999933815813e+36
time = 'ocean_time'
grid = 'grid'
location = 'face'
field = 'free-surface, scalar, series'
mask_u
Size: 398x358
Dimensions: x,y_2
Datatype: double
Attributes:
long_name = 'mask on U-points'
coordinates = 'lat_u lon_u'
flag_values = [0 1]
flag_meanings = 'land water'
grid = 'grid'
location = 'edge1'
ubar
Size: 398x358x1
Dimensions: x,y_2,ocean_time
Datatype: single
Attributes:
long_name = 'vertically integrated u-momentum component'
units = 'meter second-1'
coordinates = 'lat_u lon_u'
_FillValue = 9.999999933815813e+36
missing_value = 9.999999933815813e+36
time = 'ocean_time'
grid = 'grid'
location = 'edge1'
field = 'ubar-velocity, scalar, series'
u
Size: 398x358x40x1
Dimensions: x,y_2,s_rho,ocean_time
Datatype: single
Attributes:
long_name = 'u-momentum component'
units = 'meter second-1'
coordinates = 'lat_u lon_u'
_FillValue = 9.999999933815813e+36
missing_value = 9.999999933815813e+36
time = 'ocean_time'
grid = 'grid'
location = 'edge1'
field = 'u-velocity, scalar, series'
mask_v
Size: 398x358
Dimensions: x,y_2
Datatype: double
Attributes:
long_name = 'mask on V-points'
coordinates = 'lat_v lon_v'
flag_values = [0 1]
flag_meanings = 'land water'
grid = 'grid'
location = 'edge2'
vbar
Size: 398x358x1
Dimensions: x,y_2,ocean_time
Datatype: single
Attributes:
long_name = 'vertically integrated v-momentum component'
units = 'meter second-1'
coordinates = 'lat_v lon_v'
_FillValue = 9.999999933815813e+36
missing_value = 9.999999933815813e+36
time = 'ocean_time'
grid = 'grid'
location = 'edge2'
field = 'vbar-velocity, scalar, series'
v
Size: 398x358x40x1
Dimensions: x,y_2,s_rho,ocean_time
Datatype: single
Attributes:
long_name = 'v-momentum component'
units = 'meter second-1'
coordinates = 'lat_v lon_v'
_FillValue = 9.999999933815813e+36
missing_value = 9.999999933815813e+36
time = 'ocean_time'
grid = 'grid'
location = 'edge2'
field = 'v-velocity, scalar, series'

How would I go about using OceanParcles with a library of netcdf files structured this way?

[erikvansebille]

Thanks for reporting this, @Xyx105. I don't use ROMS myself, so can't help you. But perhaps someone else in this discussion forum could?

[JamiePringle]

I would strongly suggest posting this to the ROMS forum at https://www.myroms.org/forum/index.php . If you are using one of the ROMS forks, you may have to did a little harder.

But as you point you, you can re-create Cs_r from the grid stretching parameters.

Jamie