Skip to content

User/mjh/tools #66

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
adcroft merged 11 commits into from
Oct 6, 2014
Merged

User/mjh/tools #66

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
11 commits
Select commit Hold shift + click to select a range
97e199b
Reference latest version of MIDAS
MJHarrison-GFDL Oct 2, 2014
6360f31
Fix Makefile.
MJHarrison-GFDL Oct 2, 2014
a662c8d
Changed version of nco to 4.3.1 from 4.0.3
adcroft Oct 2, 2014
1845194
Updated MIDAS version in tools/python/025gridGeneration
MJHarrison-GFDL Oct 2, 2014
49b57fa
More fixes to work with MIDAS
adcroft Oct 3, 2014
db58684
Updated rules for calculating md5sums
adcroft Oct 3, 2014
3ffa85b
Added basin_codes.nc to list of required targets
adcroft Oct 3, 2014
88c710b
New version of MIDAS
MJHarrison-GFDL Oct 3, 2014
c46fbc3
Altered interpWOA05 to use local grid/topog files
adcroft Oct 5, 2014
40f3f07
Latest version of MIDAS added meta-data to WOA05
adcroft Oct 5, 2014
e81b3ff
Added rule for WOA05_ptemp_salt_annual.nc
adcroft Oct 5, 2014
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion tools/python/025gridGeneration/MIDAS
Open in desktop
Submodule MIDAS updated 2 files
+3 −3 Makefile_GFDL
+32 −21 midas/rectgrid.py
38 changes: 26 additions & 12 deletions tools/python/025gridGeneration/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,12 +9,20 @@
# make supergrid.nc
# make interpolated_topog.nc

# nco module version
NCO = nco/4.3.1

SHELL=tcsh

all: md5sums.txt ocean_hgrid.nc ocean_topog.nc
all: input forcing obs
md5sum -c md5sums.txt

input: ocean_hgrid.nc ocean_topog.nc basin_codes.nc

forcing: salt_restore.nc seawifs_1998-2006_smoothed_2X.nc tidal_amplitude.nc

obs: WOA05_ptemp_salt_monthly.nc WOA05_ptemp_salt_annual.nc

# Grids
supergrid.nc: mercator_supergrid.nc ncap_supergrid.nc antarctic_spherical_supergrid.nc scap_supergrid.nc local
unlimit stacksize; setenv PYTHONPATH ./local/lib/python; python merge_grids.py
Expand Down Expand Up @@ -43,36 +51,39 @@ scap_topog_gebco.nc so_topog_gebco.nc: mercator_supergrid.nc ncap_supergrid.nc a

# Sets char tile='tile1'
ocean_hgrid.nc: supergrid.nc
module load nco; ncks -h -d ny,80, -d nyp,80, supergrid.nc ocean_hgrid.nc
module load $(NCO); ncks -h -d ny,80, -d nyp,80, supergrid.nc ocean_hgrid.nc
./changeChar.py ocean_hgrid.nc tile tile1

topog.nc: edit_topog.nc
topog.nc: edit_topog.nc interpolated_topog.nc
./ice9.py edit_topog.nc --output topog.nc

ocean_topog.nc: topog.nc
module load nco; ncks -h -d ny,40, topog.nc ocean_topog.nc
module load nco;ncap -h -s 'jEdit=jEdit-40' --overwrite ocean_topog.nc ocean_topog.nc
module load $(NCO); ncks -h -d ny,40, topog.nc ocean_topog.nc
module load $(NCO);ncap -h -s 'jEdit=jEdit-40' --overwrite ocean_topog.nc ocean_topog.nc
./addDimension.py ocean_topog.nc ntiles 1
# Removes rows 1-40
# Adjusts jEdit values
# Adds back the dimension "ntiles"

basin_codes.nc: ocean_topog.nc
unlimit stacksize; setenv PYTHONPATH ./local/lib/python; python make_basin_mask.py
module load nco; ncatted -h -a flag_meanings,basin,c,c,'1:Southern Ocean, 2:Atlantic Ocean, 3:Pacific Ocean, 4:Arctic Ocean, 5:Indian Ocean, 6:Mediterranean Sea, 7:Black Sea, 8:Hudson Bay, 9:Baltic Sea, 10:Red Sea, 11:Persian Gulf' basin_codes.nc
module load nco; ncatted -h -a flag_values,basin,c,c,'1,2,3,4,5,6,7,8,9,10,11' basin_codes.nc
module load $(NCO); ncatted -h -a flag_meanings,basin,c,c,'1:Southern Ocean, 2:Atlantic Ocean, 3:Pacific Ocean, 4:Arctic Ocean, 5:Indian Ocean, 6:Mediterranean Sea, 7:Black Sea, 8:Hudson Bay, 9:Baltic Sea, 10:Red Sea, 11:Persian Gulf' basin_codes.nc
module load $(NCO); ncatted -h -a flag_values,basin,c,c,'1,2,3,4,5,6,7,8,9,10,11' basin_codes.nc

WOA05_ptemp_salt_annual.nc: WOA05_ptemp_salt_monthly.nc
module load $(NCO); ncra -h -O $< $@

WOA05_ptemp_salt_monthly.nc: ocean_hgrid.nc ocean_topog.nc /archive/gold/datasets/obs/WOA05_pottemp_salt.nc interpWOA05.py local
unlimit stacksize; setenv PYTHONPATH ./local/lib/python; python interpWOA05.py
module load nco; ncatted -h -a modulo,TIME,c,c,' ' WOA05_ptemp_salt_monthly.nc
module load $(NCO); ncatted -h -a modulo,TIME,c,c,' ' WOA05_ptemp_salt_monthly.nc

salt_restore.nc: ocean_hgrid.nc ocean_topog.nc /archive/gold/datasets/obs/WOA05_pottemp_salt.nc interpSaltRestore.py local
unlimit stacksize; setenv PYTHONPATH ./local/lib/python; python interpSaltRestore.py
module load nco; ncatted -h -a modulo,TIME,c,c,' ' salt_restore.nc
module load $(NCO); ncatted -h -a modulo,TIME,c,c,' ' salt_restore.nc

seawifs_1998-2006_smoothed_2X.nc: ocean_hgrid.nc ocean_topog.nc /archive/gold/datasets/global/siena_201204/INPUT/seawifs_1998-2006_GOLD_smoothed_2X.nc interpCHL.py local
unlimit stacksize; setenv PYTHONPATH ./local/lib/python; python interpCHL.py
module load nco; ncatted -h -a modulo,TIME,c,c,' ' seawifs_1998-2006_smoothed_2X.nc
module load $(NCO); ncatted -h -a modulo,TIME,c,c,' ' seawifs_1998-2006_smoothed_2X.nc

tidal_amplitude.nc: DATA interpTides.py local
unlimit stacksize; setenv PYTHONPATH ./local/lib/python; python interpTides.py
Expand All @@ -89,14 +100,14 @@ MIDAS:

local: MIDAS
-rm -rf MIDAS/build/*
module load python netcdf/4.2 intel_compilers; setenv INSTALL_DIR `pwd`/local ; cd MIDAS;make -f Makefile_GFDL;cd ..;touch local
module load python netcdf/4.2 intel_compilers; if (! -f local) mkdir local;cd MIDAS;make -f Makefile_GFDL INSTALL_PATH=../local;cd ..;touch local



bedmap2.nc GEBCO_08_v1.nc IBCAO_V3_500m_RR.grd:
cp /archive/gold/datasets/topography/$@ .

md5sums.txt: ocean_hgrid.nc antarctic_spherical_supergrid.nc mercator_supergrid.nc ncap_supergrid.nc scap_supergrid.nc supergrid.nc interpolated_topog.nc mercator_topog_gebco.nc ncap_topog_gebco.nc ncap_topog.nc scap_topog_bedmap2.nc scap_topog_gebco.nc so_topog_bedmap2.nc so_topog_gebco.nc ocean_topog.nc basin_codes.nc salt_restore.nc seawifs_1998-2006_smoothed_2X.nc tidal_amplitude.nc
md5sums.txt: ocean_hgrid.nc antarctic_spherical_supergrid.nc mercator_supergrid.nc ncap_supergrid.nc scap_supergrid.nc supergrid.nc interpolated_topog.nc mercator_topog_gebco.nc ncap_topog_gebco.nc ncap_topog.nc scap_topog_bedmap2.nc scap_topog_gebco.nc so_topog_bedmap2.nc so_topog_gebco.nc ocean_topog.nc basin_codes.nc salt_restore.nc seawifs_1998-2006_smoothed_2X.nc tidal_amplitude.nc WOA05_ptemp_salt_monthly.nc WOA05_ptemp_salt_annual.nc
echo Grids > $@
md5sum *supergrid.nc ocean_hgrid.nc >> $@
echo >> $@
Expand All @@ -106,3 +117,6 @@ md5sums.txt: ocean_hgrid.nc antarctic_spherical_supergrid.nc mercator_supergrid.
echo >> $@
echo Data >> $@
md5sum salt_restore.nc seawifs_1998-2006_smoothed_2X.nc tidal_amplitude.nc >> $@
echo >> $@
echo Obs >> $@
md5sum WOA05_ptemp_salt_{monthly,annual}.nc >> $@
13 changes: 8 additions & 5 deletions tools/python/025gridGeneration/interpTides.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,15 +1,18 @@
#!/usr/bin/env python

from midas import *
from midas.rectgrid import *
import netCDF4 as nc
import numpy as np

f=nc.Dataset('DATA/grid_tpxo7_atlas.nc')

lon_u=f.variables['lon_u'][:].T
lat_u=f.variables['lat_u'][:].T
lon_v=f.variables['lon_v'][:].T
lat_v=f.variables['lat_v'][:].T

grid_u=rectgrid(lon=lon_u,lat=lat_u,cyclic=True)
grid_v=rectgrid(lon=lon_v,lat=lat_v,cyclic=True)
grid_u=quadmesh(lon=lon_u,lat=lat_u,cyclic=True)
grid_v=quadmesh(lon=lon_v,lat=lat_v,cyclic=True)

Su=state(grid=grid_u)
Sv=state(grid=grid_v)
Expand Down Expand Up @@ -82,7 +85,7 @@
Su.add_field_from_array(ua,'ua',var_dict=vdict_u)
Sv.add_field_from_array(va,'va',var_dict=vdict_v)

grid=rectgrid(lon=lon_v,lat=lat_u,cyclic=True)
grid=quadmesh(lon=lon_v,lat=lat_u,cyclic=True)
grid.wet=np.ones((grid.jm,grid.im))

S=Su.horiz_interp('ua',target=grid,src_modulo=True,method='bilinear')
Expand All @@ -100,7 +103,7 @@
S.add_field_from_array(umod,'umod',var_dict=vdict)

sgrid=supergrid(file='ocean_hgrid.nc',cyclic_x=True,tripolar_n=True)
output_grid = rectgrid(supergrid=sgrid,cyclic=True)
output_grid = quadmesh(supergrid=sgrid,cyclic=True)
output_grid.D=nc.Dataset('ocean_topog.nc').variables['depth'][:]
output_grid.wet = np.zeros(output_grid.D.shape)
output_grid.wet[output_grid.D>0.]=1.
Expand Down
12 changes: 5 additions & 7 deletions tools/python/025gridGeneration/interpWOA05.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,14 +4,14 @@
import netCDF4 as nc
import numpy as np

sgrid=supergrid(file='/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_hgrid.nc',cyclic_x=True,tripolar_n=True)
sgrid=supergrid(file='ocean_hgrid.nc',cyclic_x=True,tripolar_n=True)
grid=quadmesh(supergrid=sgrid)
grid.lath=grid.y_T[:,grid.im/4]
grid.latq=grid.y_T_bounds[:,grid.im/4]
grid.D=nc.Dataset('/archive/gold/datasets/OM4_025/mosaic.v20140610.unpacked/ocean_topog.nc').variables['depth'][:]
grid.D=nc.Dataset('ocean_topog.nc').variables['depth'][:]
grid.wet=np.zeros(grid.D.shape)
grid.wet[grid.D>0.]=1
S=state(grid=grid)
S=state(grid=grid)

dz=nc.Dataset('../../../examples/ocean_SIS/OM4_025/INPUT/vgrid_75_2m.nc').variables['dz'][:]
nk = dz.shape[0]
Expand All @@ -30,12 +30,11 @@
O.rename_field('SALT','salt')
OM=O.horiz_interp('salt',target=S.grid,method='bilinear')
OM=O.horiz_interp('ptemp',target=S.grid,method='bilinear',PrevState=OM)
OM.adjust_thickness('ptemp')
OM.adjust_thickness('salt')
OM.adjust_thickness('ptemp')
OM.adjust_thickness('salt')
OM.fill_interior('salt',smooth=True,num_pass=10000)
OM.fill_interior('ptemp',smooth=True,num_pass=10000)


OM.remap_ALE(fields=['ptemp','salt'],z_bounds=zb,zbax_data=-zi,method='ppm_h4',bndy_extrapolation=False)
OM.rename_field('ptemp_remap','ptemp')
OM.rename_field('salt_remap','salt')
Expand All @@ -46,4 +45,3 @@
OM.write_nc('WOA05_ptemp_salt_monthly.nc',['ptemp','salt'],append=False,write_interface_positions=True)
else:
OM.write_nc('WOA05_ptemp_salt_monthly.nc',['ptemp','salt'],append=True,write_interface_positions=True)

9 changes: 5 additions & 4 deletions tools/python/025gridGeneration/make_basin_mask.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
#!/usr/bin/env python

from midas import *
from midas.rectgrid import *
from midas.rectgrid_gen import *
import netCDF4
import numpy

Expand Down Expand Up @@ -168,9 +169,9 @@ def southOf(x, y, xy0, xy1):
else: print 'All points assigned a basin code'

sgrid=supergrid(file='ocean_hgrid.nc',cyclic_x=True,tripolar_n=True)
grid=rectgrid(supergrid=sgrid)
grid.D=nc.Dataset('ocean_topog.nc').variables['depth'][:]
grid.wet=np.zeros(grid.D.shape)
grid=quadmesh(supergrid=sgrid)
grid.D=netCDF4.Dataset('ocean_topog.nc').variables['depth'][:]
grid.wet=numpy.zeros(grid.D.shape)
grid.wet[grid.D>0.]=1.0
grid.lath=grid.y_T[:,grid.im/4] # should not be needed
grid.latq=grid.y_T_bounds[:,grid.im/4+1] # ditto
Expand Down
4 changes: 4 additions & 0 deletions tools/python/025gridGeneration/md5sums.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,3 +24,7 @@ Data
7d2993615f5225ae43659a1b39b12423 salt_restore.nc
f07acf60f16f3addf77b906c45349626 seawifs_1998-2006_smoothed_2X.nc
27b75fed981c011654a3512bcc094100 tidal_amplitude.nc

Obs
8a5b6c0ed1207725060ea71c0053f95f WOA05_ptemp_salt_monthly.nc
c18f42259b7e2454723692ce66c9271a WOA05_ptemp_salt_annual.nc