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Merge Feature/met in master #24

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merged 14 commits into from
Oct 19, 2021
Merged

Merge Feature/met in master #24

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eadaad4
updates for ERA5 forcing: extract and weights files
jpolton Sep 2, 2021
8c7c7cf
start EXP for tides + met
jpolton Sep 2, 2021
9118e4f
mods to inspect hydrolic jump issue
jpolton Sep 2, 2021
91a4e8e
typo: rename to create_LSM.py
jpolton Sep 3, 2021
7557fbe
add mask fix at coastal point (land --> sea)
jpolton Sep 3, 2021
7b72c3c
change LSM edit to a comment
jpolton Sep 3, 2021
cd6943d
Delete RUN_DIRECTORIES/EXP_fullforcing directory
jpolton Sep 8, 2021
200db69
Delete RUN_DIRECTORIES/EXP_eORCAR12 directory
jpolton Sep 8, 2021
1038080
update python2 --> python3: print syntax
jpolton Sep 28, 2021
e086294
Merge branch 'feature/met' of https://github.com/JMMP-Group/SEVERN-SW…
jpolton Sep 28, 2021
3b0434f
added slurm script
mpayopayo Oct 14, 2021
c999534
slurm script for ERA5 weights generation
mpayopayo Oct 18, 2021
6ef048f
Merge branch 'feature/met' of https://github.com/JMMP-Group/SEVERN-SW…
mpayopayo Oct 18, 2021
04f584d
Delete create_weight_ERA5..sh because wrong location
mpayopayo Oct 18, 2021
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47 changes: 47 additions & 0 deletions BUILD_CFG/SURFACE_FORCING/create_LSM.py
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from netCDF4 import Dataset
import numpy as np

coorfile = 'ERA5_MSL_y2013.nc' ## One ERA forcing file generated previously
maskfile = 'my_era5_LSM.nc' ## Land Sea Mask from ncks
outfile = 'ERA5_LSM.nc' ## Output file

#----------------------------------------------------------------------------

## READ SRC BATHYMETRY
#nc_c = Dataset( coorfile, 'r' )
#lon_src = nc_c.variables[ 'lon' ][:]
#lat_src = nc_c.variables[ 'lat' ][:]
#nc_c.close()
#print(coorfile, "loaded", lon_src.shape)

## READ SRC BATHYMETRY
nc_src = Dataset( maskfile, 'r' )
msk_src = nc_src.variables[ 'lsm' ][0,::-1] ## lat to be reverse as it was done in the generation of the forcing files
lat_src = nc_src.variables['latitude'][::-1]
lon_src = nc_src.variables['longitude'][:]
print(maskfile, "loaded", msk_src.shape)
#msk_src[(msk_src==0.)] = -1
#msk_src[(msk_src<1)] = -1
seas = msk_src < 0.5
land = msk_src >= 0.5
msk_src[seas] = -1
msk_src[land] = 1
nlat = msk_src.shape[0]
nlon = msk_src.shape[1]

## Edit the LSM as required
# E.g. FIX AN COASTAL POINT TO MAKE IT OCEAN.
# msk_src[20,19] = -1

## NETCDF OUTPUT
ncout = Dataset( outfile, 'w', format='NETCDF3_CLASSIC' )
ncout.createDimension( 'nlat', nlat )
ncout.createDimension( 'nlon', nlon )
lon = ncout.createVariable( 'lon', 'f4', ('nlat', 'nlon',), zlib='True' )
lat = ncout.createVariable( 'lat', 'f4', ('nlat', 'nlon',), zlib='True' )
lon[:] = np.broadcast_to(lon_src.reshape(1,nlon), (nlat,nlon))
lat[:] = np.broadcast_to(lat_src.reshape(nlat,1), (nlat,nlon))
bout = ncout.createVariable( "LSM", 'f4', ('nlat','nlon',), zlib='True', fill_value=-999. )
bout[:] = msk_src
ncout.close()
62 changes: 31 additions & 31 deletions BUILD_CFG/SURFACE_FORCING/namelist_reshape_bicubic_atmos
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Expand Up @@ -12,18 +12,18 @@
nemo_lat: name of latitude variable in the coordinates.nc
/
&grid_inputs
input_file = '/work/n01/n01/acc/DFS/DFS5.2/1960/drowned_precip_DFS5.2_y1960.nc'
nemo_file = 'coordinates.nc'
input_file = './ERA5_MSL_y2013.nc'
nemo_file = './coordinates.nc'
datagrid_file = 'remap_data_grid_atmos.nc'
nemogrid_file = 'remap_nemo_grid_atmos.nc'
method = 'regular'
input_lon = 'lon0'
input_lat = 'lat0'
nemo_lon = 'glamt'
nemo_lat = 'gphit'
nemo_mask = 'none'
nemo_mask_value = 0
input_mask = 'none'
method = 'regular'
input_lon = 'lon'
input_lat = 'lat'
nemo_lon = 'glamt'
nemo_lat = 'gphit'
nemo_mask = 'none'
nemo_mask_value = 0
input_mask = 'none'
input_mask_value = 0
/
&comments
Expand All @@ -45,38 +45,38 @@
- output_opt may be supplied and set to either 'scrip' or 'ncar-csm'
/
&remap_inputs
num_maps = 1
grid1_file = 'remap_data_grid_atmos.nc'
grid2_file = 'remap_nemo_grid_atmos.nc'
interp_file1 = 'data_nemo_bicubic_atmos.nc'
interp_file2 = 'nemo_data_bicubic_atmos.nc'
map1_name = 'atmos to nemo bicubic Mapping'
map2_name = 'nemo to atmos bicubic Mapping'
map_method = 'bicubic'
num_maps = 1
grid1_file = 'remap_data_grid_atmos.nc'
grid2_file = 'remap_nemo_grid_atmos.nc'
interp_file1 = 'data_nemo_bicubic_atmos.nc'
interp_file2 = 'nemo_data_bicubic_atmos.nc'
map1_name = 'atmos to nemo bicubic Mapping'
map2_name = 'nemo to atmos bicubic Mapping'
map_method = 'bicubic'
normalize_opt = 'frac'
output_opt = 'scrip'
output_opt = 'scrip'
restrict_type = 'latitude'
num_srch_bins = 90
luse_grid1_area = .false.
luse_grid2_area = .false.
/
&interp_inputs
input_file = "nothing.nc"
interp_file = "data_nemo_bicubic_atmos.nc"
input_name = "nothing"
input_start = 1,1
input_file = "nothing.nc"
interp_file = "data_nemo_bicubic_atmos.nc"
input_name = "nothing"
input_start = 1,1
input_stride = 1,1
input_stop = 0,0
input_stop = 0,0
/

&interp_outputs
output_file = "nothing.nc"
output_mode = "create"
output_dims = 'x', 'y'
output_file = "nothing.nc"
output_mode = "create"
output_dims = 'x', 'y'
output_scaling = "topo|1.0"
output_name = 'topo'
output_lon = 'x'
output_lat = 'y'
output_name = 'topo'
output_lon = 'x'
output_lat = 'y'
/

&comments
Expand All @@ -86,6 +86,6 @@
/
&shape_inputs
interp_file = 'data_nemo_bicubic_atmos.nc'
output_file = 'weights_bicubic_atmos.nc'
output_file = 'weights_era5_SEVERN_bicubic.nc'
ew_wrap = -1
/
62 changes: 31 additions & 31 deletions BUILD_CFG/SURFACE_FORCING/namelist_reshape_bilin_atmos
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Original file line number Diff line number Diff line change
Expand Up @@ -12,18 +12,18 @@
nemo_lat: name of latitude variable in the coordinates.nc
/
&grid_inputs
input_file = '/work/n01/n01/acc/DFS/DFS5.2/1960/drowned_precip_DFS5.2_y1960.nc'
nemo_file = 'coordinates.nc'
input_file = './ERA5_MSL_y2013.nc'
nemo_file = './coordinates.nc'
datagrid_file = 'remap_data_grid_atmos.nc'
nemogrid_file = 'remap_nemo_grid_atmos.nc'
method = 'regular'
input_lon = 'lon0'
input_lat = 'lat0'
nemo_lon = 'glamt'
nemo_lat = 'gphit'
nemo_mask = 'none'
nemo_mask_value = 0
input_mask = 'none'
method = 'regular'
input_lon = 'lon'
input_lat = 'lat'
nemo_lon = 'glamt'
nemo_lat = 'gphit'
nemo_mask = 'none'
nemo_mask_value = 0
input_mask = 'none'
input_mask_value = 0
/
&comments
Expand All @@ -45,38 +45,38 @@
- output_opt may be supplied and set to either 'scrip' or 'ncar-csm'
/
&remap_inputs
num_maps = 1
grid1_file = 'remap_data_grid_atmos.nc'
grid2_file = 'remap_nemo_grid_atmos.nc'
interp_file1 = 'data_nemo_bilin_atmos.nc'
interp_file2 = 'nemo_data_bilin_atmos.nc'
map1_name = 'atmos to nemo bilin Mapping'
map2_name = 'nemo to atmos bilin Mapping'
map_method = 'bilinear'
num_maps = 1
grid1_file = 'remap_data_grid_atmos.nc'
grid2_file = 'remap_nemo_grid_atmos.nc'
interp_file1 = 'data_nemo_bilin_atmos.nc'
interp_file2 = 'nemo_data_bilin_atmos.nc'
map1_name = 'atmos to nemo bilin Mapping'
map2_name = 'nemo to atmos bilin Mapping'
map_method = 'bilinear'
normalize_opt = 'frac'
output_opt = 'scrip'
output_opt = 'scrip'
restrict_type = 'latitude'
num_srch_bins = 90
luse_grid1_area = .false.
luse_grid2_area = .false.
/
&interp_inputs
input_file = "nothing.nc"
interp_file = "data_nemo_bilin_atmos.nc"
input_name = "nothing"
input_start = 1,1
input_file = "nothing.nc"
interp_file = "data_nemo_bilin_atmos.nc"
input_name = "nothing"
input_start = 1,1
input_stride = 1,1
input_stop = 0,0
input_stop = 0,0
/

&interp_outputs
output_file = "nothing.nc"
output_mode = "create"
output_dims = 'x', 'y'
output_file = "nothing.nc"
output_mode = "create"
output_dims = 'x', 'y'
output_scaling = "topo|1.0"
output_name = 'topo'
output_lon = 'x'
output_lat = 'y'
output_name = 'topo'
output_lon = 'x'
output_lat = 'y'
/

&comments
Expand All @@ -86,6 +86,6 @@
/
&shape_inputs
interp_file = 'data_nemo_bilin_atmos.nc'
output_file = 'weights_bilinear_atmos.nc'
output_file = 'weights_era5_SEVERN_bilin.nc'
ew_wrap = -1
/
35 changes: 35 additions & 0 deletions RUN_DIRECTORIES/EXP_barotropicTide_ERA5/context_nemo.xml
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<!--
==============================================================================================
NEMO context
==============================================================================================
-->
<context id="nemo">
<!-- $id$ -->
<!-- Fields definition -->
<field_definition src="./field_def_nemo-oce.xml"/> <!-- NEMO ocean dynamics -->

<!-- Files definition -->
<file_definition src="./file_def_nemo-oce.xml"/> <!-- NEMO ocean dynamics -->
<!--
============================================================================================================
= grid definition = = DO NOT CHANGE =
============================================================================================================
-->

<axis_definition>
<axis id="deptht" long_name="Vertical T levels" unit="m" positive="down" />
<axis id="depthu" long_name="Vertical U levels" unit="m" positive="down" />
<axis id="depthv" long_name="Vertical V levels" unit="m" positive="down" />
<axis id="depthw" long_name="Vertical W levels" unit="m" positive="down" />
<axis id="nfloat" long_name="Float number" unit="-" />
<axis id="icbcla" long_name="Iceberg class" unit="1" />
<axis id="ncatice" long_name="Ice category" unit="1" />
<axis id="iax_20C" long_name="20 degC isotherm" unit="degC" />
<axis id="iax_28C" long_name="28 degC isotherm" unit="degC" />
</axis_definition>

<domain_definition src="./domain_def_nemo.xml"/>

<grid_definition src="./grid_def_nemo.xml"/>

</context>
79 changes: 79 additions & 0 deletions RUN_DIRECTORIES/EXP_barotropicTide_ERA5/file_def_nemo-oce.xml
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<?xml version="1.0"?>

<!--
============================================================================================================
= output files definition =
= Define your own files =
= put the variables you want... =
============================================================================================================
-->
<file_definition type="one_file" name="@expname@_@freq@" sync_freq="1d" min_digits="4">
<!--<file_definition type="multiple_file" name="@expname@_@freq@_@startdate@_@enddate@" sync_freq="1d" min_digits="4">-->

<file_group id="1ts" output_freq="1ts" output_level="10" enabled=".TRUE."> <!-- 1 time step files -->
<file id="file1" name_suffix="_t" description="1ts t-grid" enabled=".TRUE.">
<field field_ref="ssh" name="ssh" />
<field field_ref="sst" name="sst" />
</file>
<file id="file2" name_suffix="_u" description="1ts u-grid" enabled=".TRUE.">
<field field_ref="ubar" name="ubar" />
</file>
<file id="file3" name_suffix="_v" description="1ts v-grid" enabled=".TRUE.">
<field field_ref="vbar" name="vbar" />
</file>
</file_group>

<file_group id="3h" output_freq="3h" output_level="10" enabled=".TRUE."/> <!-- 3h files -->
<file_group id="2h" output_freq="2h" output_level="10" enabled=".TRUE."/> <!-- 2h files -->
<!-- <file id="file1" name_suffix="_2h" description="3d u and v output every 2 hours" enabled=".TRUE." >
<field field_ref="uoce_abs_max" name="uoce_abs_max" />
<field field_ref="voce_abs_max" name="voce_abs_max" />
</file>
</file_group>
-->

<file_group id="1h" output_freq="1h" output_level="10" enabled=".TRUE."> <!-- 1h files -->
<file id="file0" name_suffix="_t" description="1h mean t-grid" enabled=".TRUE.">
<field field_ref="ssh" name="ssh" />
</file>
</file_group>

<file_group id="6h" output_freq="6h" output_level="10" enabled=".TRUE."/> <!-- 6h files -->

<file_group id="4h" output_freq="4h" output_level="10" enabled=".TRUE."/>

<file_group id="1d" output_freq="1d" output_level="10" enabled=".TRUE."> <!-- 1d files -->
<!-- <file id="file1" name_suffix="_t" description="daily mean t-grid" split_freq="1mo" split_freq_format="%y%mo%d" enabled=".TRUE."> -->
<!--
<file id="file2" name_suffix="_t" description="daily mean t-grid" enabled=".TRUE.">
<field field_ref="ssh" name="ssh" />
</file>
<file id="file3" name_suffix="_u" description="daily mean u-grid" enabled=".TRUE.">
<field field_ref="ubar" name="ubar" />
</file>
<file id="file4" name_suffix="_v" description="daily mean v-grid" enabled=".TRUE.">
<field field_ref="vbar" name="vbar" />
</file>
-->
</file_group>

<file_group id="25h_mean" output_freq="1d" output_level="10" enabled=".TRUE."/> <!-- 3d files -->

<file_group id="5d" output_freq="5d" output_level="10" enabled=".TRUE."/> <!-- 5d files -->

<file_group id="1m" output_freq="1mo" output_level="10" enabled=".TRUE."/> <!-- real monthly files -->

<file_group id="2m" output_freq="2mo" output_level="10" enabled=".TRUE."/> <!-- real 2m files -->
<file_group id="3m" output_freq="3mo" output_level="10" enabled=".TRUE."/> <!-- real 3m files -->
<file_group id="4m" output_freq="4mo" output_level="10" enabled=".TRUE."/> <!-- real 4m files -->
<file_group id="6m" output_freq="6mo" output_level="10" enabled=".TRUE."/> <!-- real 6m files -->

<file_group id="1y" output_freq="1y" output_level="10" enabled=".TRUE."/> <!-- real yearly files -->
<file_group id="2y" output_freq="2y" output_level="10" enabled=".TRUE."/> <!-- real 2y files -->
<file_group id="5y" output_freq="5y" output_level="10" enabled=".TRUE."/> <!-- real 5y files -->
<file_group id="10y" output_freq="10y" output_level="10" enabled=".TRUE."/> <!-- real 10y files -->


</file_definition>


0 RUN_DIRECTORIES/EXP_eORCAR12/iodef.xml → ...CTORIES/EXP_barotropicTide_ERA5/iodef.xml
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