Changeset 2813 for trunk/LMDZ.MARS

Timestamp:

Nov 8, 2022, 3:32:12 PM (2 years ago)

Author:

romain.vande

Message:

DYNAMICO MARS
Update startarchive2icosa repertory for new version of Dynamico
RV

Location:

trunk/LMDZ.MARS

Files:

• README (modified) (1 diff)
• util/startarchive2icosa/README (modified) (2 diffs)
• util/startarchive2icosa/callphys.def_no_start (added)
• util/startarchive2icosa/compile (modified) (2 diffs)
• util/startarchive2icosa/icosa_finalize.bash (modified) (3 diffs)
• util/startarchive2icosa/run_icosa.def_no_start (added)
• util/startarchive2icosa/traceur.def_no_start (added)

trunk/LMDZ.MARS/README

@@ -3757 +3757 @@
 Bug fix in jthermcalc_e107 (wrong indexes used in some computations involving
 NO2 and H2).
+
+== 08/11/2022 == RV
+Update startarchive2icosa repertory for new version of Dynamico

trunk/LMDZ.MARS/util/startarchive2icosa/README

@@ -6 +6 @@
 Run a dynamico simulation (with startphy_file=false for example) with the desired resolution to get
 start.nc and startfi.nc. These files will be used as reference (rename as *_ref.nc) in the script.
+You can use the files named *_no_start to have an example of callphys etc to run without startfiles
 
 Job_mpi is the file you need to run start_archive2icosa on Occigen
@@ -18 +19 @@
 --------------
 1) input file start_archive.nc needs some minor adaptations:
-- variable "nivsigs" needs be renamed "sigs" (XIOS requires CF-compliant files)
+- variable "nivsigs" needs be renamed "sigs" (XIOS requires CF-compliant files) (RV: No neeeded anymore)
 ncrename -vnivsigs,sigs start_archive.nc
 - input file start_archive.nc need be converted to NetCDF4 format
-nccopy -k 'netCDF-4' start_archive.nc start_archive_nc4.nc
+nccopy -k 4 start_archive.nc start_archive_nc4.nc
 2) script "compile" can be used to compile main tool start_archive2icosa.f90
    as well as rearrange_startphy.f90

trunk/LMDZ.MARS/util/startarchive2icosa/compile

@@ -1 +1 @@
 #!/usr/bin/bash
 
-source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.env
-source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.path
+source ../../../../../trunk_Dynamico/trunk/XIOS/arch.env
+source ../../../../../trunk_Dynamico/trunk/XIOS/arch.path
 
 mpif90 -g -traceback start_archive2icosa.f90 \
 $NETCDF_INCDIR $NETCDF_LIBDIR $NETCDF_LIB \
 $HDF5_INCDIR $HDF5_LIBDIR $HDF5_LIB \
--I /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/inc \
--L /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/lib -lxios -lstdc++ \
+-I ../../../../../trunk_Dynamico/trunk/XIOS/inc \
+-L ../../../../../trunk_Dynamico/trunk/XIOS/lib -lxios -lstdc++ \
 -o start_archive2icosa
 
@@ -14 +14 @@
 $NETCDF_INCDIR $NETCDF_LIBDIR $NETCDF_LIB \
 $HDF5_INCDIR $HDF5_LIBDIR $HDF5_LIB \
--I /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/inc \
--L /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/lib -lxios -lstdc++ \
+-I ../../../../../trunk_Dynamico/trunk/XIOS/inc \
+-L ../../../../../trunk_Dynamico/trunk/XIOS/lib -lxios -lstdc++ \
 -o rearrange_startphy
 

trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash

@@ -7 +7 @@
 # load nco module
 module purge
-source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.env
-module load nco/4.7.9-gcc-4.8.5-hdf5-1.8.18-openmpi-2.0.4
+source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.env #You have to adapt to your own path
+#module load nco/4.7.9-gcc-4.8.5-hdf5-1.8.18-openmpi-2.0.4 #Example of version of the module needed
+module load nco
 
 #conversion to netcdf 3 in order to rename and add variables, not properly done with netcdf4 files
@@ -24 +25 @@
 #Temporay soildepth array from Dynamico restartfi
 ncks -A -v soildepth \
-         ../../mars_dynamico_update_basic/startfi_0.nc startphy_nc3.nc
+         ../../mars_dynamico_update_basic/startfi_0.nc startphy_nc3.nc #You have to adapt to your own path
 
-nccopy -k 'netCDF-4' startphy_nc3.nc startfi.nc
+nccopy -k 4 startphy_nc3.nc startfi.nc
 
 #Temporary Time variable from start2archive; should be added with xios
-ncks -A -v Time \
-         start_archive_nc4.nc startfi.nc
+#ncks -A -v Time \
+#         start_archive_nc4.nc startfi.nc
+ncks -O -x -v time_counter startfi.nc startfi.nc_tmp
+ncks -A -v Time start.nc startfi.nc_tmp
+cp startfi.nc_tmp startfi.nc
 
 rearrange_startphy > rearrange_startphy.out 2>&1
@@ -47 +51 @@
      start_icosa_ref.nc start_icosa.nc
 
+# In the current version of Dynamico, the variable q for tracer is needed but unused.
+# To create this unused variable simply run this short python code
+
+#import numpy as np
+#import netCDF4 as nc
+
+#fn = 'start_icosa.nc'
+#ds = nc.Dataset(fn, 'a', format='NETCDF4')
+#nq = ds.createDimension('nq', 7)
+
+#q = ds.createVariable('q', 'f8', ('nq','lev', 'cell_mesh',))
+#nqq = ds.createVariable('nq', 'f8', ('nq',))
+#q[:,:,:]=0.
+#q.online_operation = "once"
+#q.coordinates = "lat lon"
+#ds.close()
+
 # cleanup
 rm -rf startphy_icosa_nc3.nc startphy_nc3.nc