Commit c5094e69 authored by Antoine Berchet's avatar Antoine Berchet
Browse files

Merge branch 'LSCE' into 'master'

Lsce

See merge request !3
parents c5340be7 9c9645aa
Pipeline #38 failed with stage
*.pyc *.pyc
*.bin *.bin
*.o *.o
*.e*
*.o*
*.mod *.mod
.idea .idea
pyCIF.egg-info pyCIF.egg-info
config_files
...@@ -13,6 +13,7 @@ pages: ...@@ -13,6 +13,7 @@ pages:
stage: deploy stage: deploy
script: script:
- apk --no-cache add py2-pip python-dev - apk --no-cache add py2-pip python-dev
- apk --no-cache add graphviz
- pip install sphinx - pip install sphinx
- pip install sphinxcontrib-plantuml - pip install sphinxcontrib-plantuml
- pip install sphinx-rtd-theme - pip install sphinx-rtd-theme
......
#QSUB -s /bin/tcsh #QSUB -s /bin/tcsh
#PBS -q xlongp #PBS -q xlongp
#PBS -l nodes=1:ppn=8 #PBS -l nodes=1:ppn=6
#cd ~/PYVAR/pyvar/trunk #cd ~/PYVAR/pyvar/trunk
cd ~/CIF cd ~/CIF
#python -m pyvar examples/config_variational.yml #python -m pycif config_files/config_inv_gcp_inca_m1qn3.yml
python -m pycif examples/config_inv_gcp_inca.yml python -m pycif examples/config_lmdz_adjtltest.yml
##################### #####################
# PYVAR config file # #####################
# PYVAR config file #
##################### #####################
# Define here all parameters for PYVAR following Yaml syntax # Define here all parameters for PYVAR following Yaml syntax
...@@ -22,22 +23,23 @@ ...@@ -22,22 +23,23 @@
# Verbose level # Verbose level
# 1 = Basic information # 1 = Basic information
# 2 = Debugging # 2 = Debugging
verbose : 2 verbose : 1
# Log file (to be saved in $wordkir) # Log file (to be saved in $wordkir)
logfile: pyvar.logtest logfile: pyvar.logtest
# Execution directory # Execution directory
#workdir : /home/satellites13/msaunois/PYVAR_FWD/GCP_2018/run_00_18_testadtl/ #workdir : /home/satellites13/msaunois/INVERSION/GCP_2018/run_00_18_inca_base_network/
workdir : /home/satellites13/aberchet/msaunois/ #workdir : /home/satellites13/aberchet/msaunois/
workdir : /home/chimereges/aberchet/test_sat/
# Initial date # Initial date
# Use the following compatible format for the date: # Use the following compatible format for the date:
# YYYY-mm-dd or YYYY-mm-dd HH:mm # YYYY-mm-dd or YYYY-mm-dd HH:mm
datei : 2000-01-01 datei : 2010-01-01
# End date (same as for the initial date) # End date (same as for the initial date)
datef : 2001-01-01 datef : 2010-02-01
##################################################################### #####################################################################
##################################################################### #####################################################################
...@@ -46,7 +48,17 @@ datef : 2001-01-01 ...@@ -46,7 +48,17 @@ datef : 2001-01-01
##################################################################### #####################################################################
# To-Do for initializing PYVAR # To-Do for initializing PYVAR
# Can be commented if running PYVAR directly # Can be commented if running PYVAR directly
#todo_init: [measurements] #todo_init: [model]
#####################################################################
#####################################################################
#####################################################################
#####################################################################
platform:
plugin:
name: LSCE
version: obelix
##################################################################### #####################################################################
##################################################################### #####################################################################
...@@ -54,20 +66,42 @@ datef : 2001-01-01 ...@@ -54,20 +66,42 @@ datef : 2001-01-01
##################################################################### #####################################################################
##################################################################### #####################################################################
# Running mode for PYVAR # Running mode for PYVAR
#mode:
# plugin:
# name: 4dvar
# version: std
# minimizer:
# plugin:
# name: M1QN3
# version: std
# simulator:
# plugin:
# name: gausscost
# version: std
# reload_from_previous: True
# maxiter: 20
# epsg: 0.02
# df1: 0.01
# chi_min:
# chi_max:
mode: mode:
module: plugin:
name: adj-tl_test name: adj-tl_test
version: std version: std
increments: 0.2 increments: 0.2
incrmode: cst incrmode: cst
testspace: control testspace: control
reload_results: True
#####################################################################
#####################################################################
##################################################################### #####################################################################
##################################################################### #####################################################################
# Transport model # Transport model
# Accepts any model registered in pyvar.models # Accepts any model registered in pyvar.models
model : model :
module: plugin:
name : LMDZ name : LMDZ
version : std version : std
...@@ -75,146 +109,59 @@ model : ...@@ -75,146 +109,59 @@ model :
periods: 1MS periods: 1MS
# Executable # Executable
ficexec : /home/users/msaunois/newpyvar/model_sources/DISPERSION_gch/dispersion.e ficexec : /home/users/aberchet/CIF/model_sources/DISPERSION_gch/dispersion.e
# Definition file (includes some parameters for the simulation) # Definition file (includes some parameters for the simulation)
ficdef : /home/users/msaunois/newpyvar/model_sources/DISPERSION_gch/def/run.def ficdef : /home/users/aberchet/CIF/model_sources/DISPERSION_gch/def/run.def
# Ap, Bp file # Ap, Bp file
fic_vcoord: /home/inversion/msaunois/LMDZ/39L/restartT2029-2006-1_MCFscaled2CH4scaled.nc fic_vcoord: /home/inversion/msaunois/LMDZ/39L/restartT2029-2006-1_MCFscaled2CH4scaled.nc
# Initial conditions recovered from: # Initial conditions recovered from:
restart: inicond:
dir : /home/inversion/msaunois/LMDZ/39L/ dir : /home/inversion/msaunois/LMDZ/39L/
fic : restartT2029-2006-1_MCFscaled2CH4scaled.nc fic : restartT2029-2006-1_MCFscaled2CH4scaled.nc
# Include physics and thermals # Include physics and thermals
# Default is True and False respectively
physic : True physic : True
thermals : False thermals : False
# Convection scheme: One of :
# 'TK' = Tiedke
# 'KE' = 'Kerry Emmanuel'
# 'KE-Therm' = 'Kerry Emmanuel + some thermics'
conv_scheme: TK
# Chemistry # Chemistry
chemistry : chemistry :
kinetic : fic_yaml : /home/users/aberchet/CIF/config_files/sacs_chem_scheme_CH4.yml
dir : /home/inversion/yyin/CHEMFILES/INCA/
fic : inca.an2008.m%m.nc # Fluxes
prescrconcs : emis_species:
OH :
dir : /home/inversion/yyin/CHEMFILES/INCA/
fic : inca.an2008.m%m.nc
convOH : True
O1D :
dir : /home/inversion/yyin/CHEMFILES/INCA/
fic : inca.an2008.m%m.nc
# Species to be transported in the model
species:
CH4: CH4:
restart_id: 27
dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/ dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/
fic: sflx_CH4_GCP2018_%Y_LMDZ9696_phy.nc fic: sflx_CH4_GCP2018_%Y_LMDZ9696_phy.nc
MCF:
restart_id: 06
dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/
fic: sflx_MCF_scaled_%Y_LMDZ9696_phy.nc
# Species are read in the file start.nc as qXX with XX the id of the species
restart_ids: [27, 06, 28, 33]
# Dump outputs into a NetCDF file # Dump outputs into a NetCDF file
dump: False dump: False
# Flushing trajq.bin files when not needed anymore
autoflush: False
##################################################################### #####################################################################
##################################################################### #####################################################################
##################################################################### #####################################################################
##################################################################### #####################################################################
# Observation operator # Observation operator
# Used to run the model and translates information from model/measurement # Used to run the model and translates information from model/measurement
# spaces to control/observation spaces # spaces to control/observation spaces
obsoperator: obsoperator:
module: plugin:
name: standard name: standard
version: std version: std
##################################################################### autorestart: True
#####################################################################
#####################################################################
#####################################################################
# Measurements to account for
# Main keys are:
# - infos: infos on tracers to include in the simulation
# - fic_monitor: standard txt file including all observations
measurements :
# File where to save data, if does not exist. Reads from there if exists
fic_monitor : /home/satellites13/msaunois/PYVAR_FWD/GCP_2018/run_00_18_inca/obsoperator/fwd_0000/monitor_selec.nc
dump_type : nc
species :
# List of tracers to include in the monitor file
# For each tracer observations, please specify:
# - provider = list of observation providers
# - format = list of format types
# - dir_obs = directory where to find observation files
# - err_obs (optional) = uncertainty on observations
# - depos (optional) = surface deposition file
# - rescale (optional) = true to change observation scale if necessary
# - na_values (optional) = invalid values to exclude. Default is -999
# - default_unit (optional) = basic unit for reporting the tracer
# everything is then converted to ppm
# - dump (optional) = dump to a monitor file. Default is True
# For tracer fluxes, please specify:
# - dir_flx: directory where reference fluxes are already computed
# - fic_flx: file format to recover fluxes from
CH4 :
dailyPM :
provider : WDCGG
format : std
dir_obs : /home/isomet/msaunois/GCP_2018/Inputs/Obs/CH4/WDCGG_type/*.cn.*
rescale : true
na_values : -999
default_unit : ppb
default_duration: 5
dump : True
err_obs : 0.05
flask :
provider : WDCGG
format : std
dir_obs : /home/isomet/msaunois/GCP_2018/Inputs/Obs/CH4/WDCGG_type/*.fl.*
rescale : true
na_values : -999
default_unit : ppb
default_duration: 1
dump : True
err_obs : 0.05
MCF :
daily_noaa :
provider : WDCGG
format : std
dir_obs : /home/inversion/msaunois/DATA_OBS/MCF/ch3ccl3_20180425_ready/*.aircore.*.cn.*
na_values : -999
err_na_values : -999
default_unit : ppt
default_duration : 24
dump : True
err_obs : 0.1
daily_agage :
provider : WDCGG
format : std
dir_obs : /home/inversion/msaunois/DATA_OBS/MCF/ch3ccl3_20180425_ready/*dmagage.*.cn.*
na_values : 0.
err_na_values : 0.
default_unit : ppt
default_duration : 24
dump : True
err_obs : 0.1
flask :
provider : WDCGG
format : std
dir_obs : /home/inversion/msaunois/DATA_OBS/MCF/ch3ccl3_20180425_ready/*.fl.*
na_values : -999
err_na_values : 0.
default_unit : ppt
default_duration: 1
dump : True
err_obs : 0.1
##################################################################### #####################################################################
##################################################################### #####################################################################
...@@ -232,69 +179,93 @@ measurements : ...@@ -232,69 +179,93 @@ measurements :
# - sigma_sea: spatial correlation length for prior errors over ocean (km) # - sigma_sea: spatial correlation length for prior errors over ocean (km)
# - tracers: list of tracers to put in the state vector (with definition arguments): # - tracers: list of tracers to put in the state vector (with definition arguments):
# - calcstd: calculate global standard deviation # - calcstd: calculate global standard deviation
# - resol: resolution at which fields are scaled # - hresol: resolution at which fields are scaled
# (choice = bands,regions,pixels; # (choice = bands,regions,pixels;
# if regions, provide a netcdf file ficregion # if regions, provide a netcdf file ficregion
# if bands, define a list of latitudes as band limits (n+1 for n bands) # if bands, define a list of latitudes as band limits (n+1 for n bands)
# - periodflux: period of variation for increments within a month (days) # - periodflux: period of variation for increments within a month (days)
# - glob_err (optional) = uncertainty on global budget # - glob_err (optional) = uncertainty on global budget
controlvect: controlvect:
module: plugin:
name: standard name: standard
version: std version: std
components: components:
fluxes: # fluxes:
CH4 : # parameters:
resol : hpixels # CH4 :
type : physical # plugin:
errtype : max # name: 'LMDZ'
err : 1 # version: 'sflx'
period : 8 # hresol : hpixels
dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/ # # type : physical
fic: sflx_CH4_GCP2018_%Y_LMDZ9696_phy.nc # # errtype : max
hcorrelations : # err : 1
ficlsm : /home/inversion/LMDZ/DATA_INV/lmdz9696/lsm.lmdz9696.nc # period : 1MS
dump_hcorr : True # subperiod: 10D
dircorrel : /home/inversion/LMDZ/DATA_INV/lmdz9696/CORREL/ # dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/
sigma_land: 500 # fic: sflx_CH4_GCP2018_%Y_LMDZ9696_phy.nc
sigma_sea: 1000 # hcorrelations :
MCF: # landsea: True
resol : hpixels # ficlsm : /home/inversion/LMDZ/DATA_INV/lmdz9696/lsm.lmdz9696.nc
period : 8 # dump_hcorr : True
err : 0.01 # dircorrel : /home/satellites13/aberchet/LMDZ_DATA/CORREL/
hcorrelations : # sigma_land: 500
ficlsm : /home/inversion/LMDZ/DATA_INV/lmdz9696/lsm.lmdz9696.nc # sigma_sea: 1000
dump_hcorr : True # MCF:
dircorrel : /home/inversion/LMDZ/DATA_INV/lmdz9696/CORREL/ # plugin:
sigma_land: 500 # name: 'LMDZ'
sigma_sea: 1000 # version: 'sflx'
dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/ # hresol : hpixels
fic: sflx_MCF_scaled_%Y_LMDZ9696_phy.nc # period : 1MS
prescrconcs : # subperiod: 10D
OH: # err : 0.01
resol : bands # hcorrelations :
period : 8 # landsea: True
bands_lat : [-90, -45, 0, 45, 90] # ficlsm : /home/inversion/LMDZ/DATA_INV/lmdz9696/lsm.lmdz9696.nc
bands_lon : [-180, 180] # dump_hcorr : True
err : 0.1 # dircorrel : /home/satellites13/aberchet/LMDZ_DATA/CORREL/
calcstd : False # sigma_land: 500
# sigma_sea: 1000
# dir: /home/inversion/msaunois/FLUXES/MCF/
# fic: sflx_MCF_scaled_%Y_LMDZ9696_phy.nc
# prescrconcs :
# parameters:
# OH:
# hresol : bands
# period : 1MS
# subperiod: 8D
# bands_lat : [-90, -45, 0, 45, 90]
# bands_lon : [-180, 180]
# err : 0.1
# calcstd : False
inicond : inicond :
CH4: parameters:
resol : global CH4:
err : 0.05 hresol : bands
MCF: bands_lat : [-90.1, -60, -30, 0, 30, 60, 90.1]
resol : global bands_lon : [-180.1, -150, -120, -90, -60, -30,
err : 0.1 0, 30, 60, 90, 120, 150, 180.1]
err : 0.05
calcstd : False
# MCF:
# hresol : bands
# bands_lat : [-90.1, -60, -30, 0, 30, 60, 90.1]
# bands_lon : [-180.1, -150, -120, -90, -60, -30,
# 0, 30, 60, 90, 120, 150, 180.1]
# err : 0.1
# calcstd : False
#hresol : global
#err : 0.1
##################################################################### #####################################################################
##################################################################### #####################################################################
##################################################################### #####################################################################
##################################################################### #####################################################################
# Domain definition # Domain definition
domain : domain :
module : plugin :
name : LMDZ name : LMDZ
version : std version : std
xmin : -180 xmin : -180
...@@ -309,16 +280,20 @@ domain : ...@@ -309,16 +280,20 @@ domain :
##################################################################### #####################################################################
##################################################################### #####################################################################
##################################################################### #####################################################################
##################################################################### #####################################################################
# How to build your observation vector and observation uncertainties if needed # How to build your observation vector and observation uncertainties if needed
# Also projects information from the observation to the model space # Also projects information from the observation to the model space
# - fic_obsvect: observation vector from previous simulations # - fic_obsvect: observation vector from previous simulations
obsvect: obsvect:
module: plugin:
name: standard name: standard
version: std version: std
#fic_obsvect : /home/satellites13/msaunois/PYVAR_FWD/GCP_2018/run_00_18_inca/obsoperator/fwd_0000/monitor_selec1.nc #fic_obsvect : /home/satellites13/msaunois/PYVAR_FWD/GCP_2018/run_00_18_inca/obsoperator/fwd_0000/monitor_selec1.nc
# fic_obsvect : /home/satellites13/aberchet/LMDZ_DATA/monit/monitor_pycif_test.nc
fic_obsvect : /home/chimereges/aberchet/satellites/monitor_201001.nc
dir_satellites : /home/chimereges/aberchet/satellites/
dump: True dump: True
wfunc : False wfunc : False
fic_statlev: /home/users/aberchet/PYVAR/msaunois/pyvar/ReadObs/stations_levels_LMDZ39lev.txt fic_statlev: /home/users/aberchet/PYVAR/msaunois/pyvar/ReadObs/stations_levels_LMDZ39lev.txt
...@@ -331,32 +306,33 @@ obsvect: ...@@ -331,32 +306,33 @@ obsvect:
# Definition of meteo parameters # Definition of meteo parameters
# This can be model dependent, please refer to corresponding documentation for details # This can be model dependent, please refer to corresponding documentation for details
meteo: meteo:
dirmeteo: /home/comdata1/PYVARLMDZ_files_96x96x39/MASS_FLUXES/TD/ plugin:
name: LMDZ
version: mass-fluxes
dirmeteo: /home/satellites1/fcheval/LMDZ5/
##################################################################### #####################################################################
##################################################################### #####################################################################
################## ##################
# Parameters below are not yet included in PYVAR # Parameters below are not yet included in PYVAR
#
#
# surface geopotential file ## surface geopotential file
ficgeopot : null #ficgeopot : null
#
# first guess path of the file if wanted ## first guess path of the file if wanted
prevanal: null #prevanal: null
# LMDz precomputed (1) or not (0) ## LMDz precomputed (1) or not (0)
precalc : 0 #precalc : 0
# perturb predefined prior/concentrations ## perturb predefined prior/concentrations
perturbdir : null #perturbdir : null
# seed for random number generation ## seed for random number generation
seed : 3 #seed : 3
# diagnostics (0=none; 1=1D(time); 2=2D(lev,time); 3=4D(lat,lon,lev,time) ) ## diagnostics (0=none; 1=1D(time); 2=2D(lev,time); 3=4D(lat,lon,lev,time) )
diag : 0 #diag : 0
#
#
#
#
#
...@@ -35,7 +35,7 @@ extensions = ['sphinx.ext.autodoc', ...@@ -35,7 +35,7 @@ extensions = ['sphinx.ext.autodoc',
'sphinx.ext.coverage', 'sphinx.ext.coverage',
'sphinx.ext.mathjax', 'sphinx.ext.mathjax',
'sphinx.ext.viewcode', 'sphinx.ext.viewcode',
'sphinxcontrib.plantuml'] 'sphinx.ext.graphviz']