Commit 9c9645aa authored by Antoine Berchet's avatar Antoine Berchet
Browse files

Merge branch 'aberchet' into 'master'

Aberchet

See merge request satinv/cif!28
parents a0c924d5 988a00d5
*.pyc
*.bin
*.o
*.e*
*.o*
*.mod
.idea
pyCIF.egg-info
config_files
#QSUB -s /bin/tcsh
#PBS -q xlongp
#PBS -l nodes=1:ppn=8
#PBS -l nodes=1:ppn=6
#cd ~/PYVAR/pyvar/trunk
cd ~/CIF
#python -m pyvar examples/config_variational.yml
python -m pycif examples/config_lmdz_variational.yml
#python -m pycif examples/config_inv_gcp_inca_congrad.yml
#python -m pycif config_files/config_inv_gcp_inca_m1qn3.yml
python -m pycif examples/config_lmdz_adjtltest.yml
#####################
#####################
# PYVAR config file #
#####################
# Define here all parameters for PYVAR following Yaml syntax
# For details on Yaml syntax, please see:
# http://docs.ansible.com/ansible/latest/YAMLSyntax.html
# For non-specified parameters, one can either comment the corresponding line
# or give the value "null"
# Some parameters are switches that need to be activated or not.
# PYVAR expects a boolean True/False
# Yaml accepts the following syntax to be converted to booleans:
# y|Y|yes|Yes|YES|n|N|no|No|NO|true|True|TRUE|false|False|FALSE|on|On|ON|off|Off|OFF
# This offers flexibility, but one should stick to a style for consistency
#####################################################################
#####################################################################
# PYVAR parameters
# Verbose level
# 1 = Basic information
# 2 = Debugging
verbose : 1
# Log file (to be saved in $wordkir)
logfile: pyvar.logtest
# Execution directory
#workdir : /home/satellites13/msaunois/INVERSION/GCP_2018/run_00_18_inca_base_network/
#workdir : /home/satellites13/aberchet/msaunois/
workdir : /home/chimereges/aberchet/test_sat/
# Initial date
# Use the following compatible format for the date:
# YYYY-mm-dd or YYYY-mm-dd HH:mm
datei : 2010-01-01
# End date (same as for the initial date)
datef : 2010-02-01
#####################################################################
#####################################################################
#####################################################################
#####################################################################
# To-Do for initializing PYVAR
# Can be commented if running PYVAR directly
#todo_init: [model]
#####################################################################
#####################################################################
#####################################################################
#####################################################################
platform:
plugin:
name: LSCE
version: obelix
#####################################################################
#####################################################################
#####################################################################
#####################################################################
# 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:
plugin:
name: adj-tl_test
version: std
increments: 0.2
incrmode: cst
testspace: control
reload_results: True
#####################################################################
#####################################################################
#####################################################################
#####################################################################
# Transport model
# Accepts any model registered in pyvar.models
model :
plugin:
name : LMDZ
version : std
# Length of simulation sub-periods (use a Pandas frequency syntax)
periods: 1MS
# Executable
ficexec : /home/users/aberchet/CIF/model_sources/DISPERSION_gch/dispersion.e
# Definition file (includes some parameters for the simulation)
ficdef : /home/users/aberchet/CIF/model_sources/DISPERSION_gch/def/run.def
# Ap, Bp file
fic_vcoord: /home/inversion/msaunois/LMDZ/39L/restartT2029-2006-1_MCFscaled2CH4scaled.nc
# Initial conditions recovered from:
inicond:
dir : /home/inversion/msaunois/LMDZ/39L/
fic : restartT2029-2006-1_MCFscaled2CH4scaled.nc
# Include physics and thermals
# Default is True and False respectively
physic : True
thermals : False
# Convection scheme: One of :
# 'TK' = Tiedke
# 'KE' = 'Kerry Emmanuel'
# 'KE-Therm' = 'Kerry Emmanuel + some thermics'
conv_scheme: TK
# Chemistry
chemistry :
fic_yaml : /home/users/aberchet/CIF/config_files/sacs_chem_scheme_CH4.yml
# Fluxes
emis_species:
CH4:
dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/
fic: sflx_CH4_GCP2018_%Y_LMDZ9696_phy.nc
# Dump outputs into a NetCDF file
dump: False
# Flushing trajq.bin files when not needed anymore
autoflush: False
#####################################################################
#####################################################################
#####################################################################
#####################################################################
# Observation operator
# Used to run the model and translates information from model/measurement
# spaces to control/observation spaces
obsoperator:
plugin:
name: standard
version: std
autorestart: True
#####################################################################
#####################################################################
#####################################################################
#####################################################################
# Arguments to define the state vector
# These are specific to the state vector and inversion method you chose
# Please refer to the documentation to know what to include here
# For the standard LMDZ, include the following:
# - ficlsm: land-sea mask (must be consistent with LMDZ grid)
# - correl: Use correlation or not in B
# - dircorrel: path to pre-computed correlations
# - sigma_land: spatial correlation length for prior errors over land (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):
# - calcstd: calculate global standard deviation
# - hresol: resolution at which fields are scaled
# (choice = bands,regions,pixels;
# if regions, provide a netcdf file ficregion
# 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)
# - glob_err (optional) = uncertainty on global budget
controlvect:
plugin:
name: standard
version: std
components:
# fluxes:
# parameters:
# CH4 :
# plugin:
# name: 'LMDZ'
# version: 'sflx'
# hresol : hpixels
# # type : physical
# # errtype : max
# err : 1
# period : 1MS
# subperiod: 10D
# dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/
# fic: sflx_CH4_GCP2018_%Y_LMDZ9696_phy.nc
# hcorrelations :
# landsea: True
# ficlsm : /home/inversion/LMDZ/DATA_INV/lmdz9696/lsm.lmdz9696.nc
# dump_hcorr : True
# dircorrel : /home/satellites13/aberchet/LMDZ_DATA/CORREL/
# sigma_land: 500
# sigma_sea: 1000
# MCF:
# plugin:
# name: 'LMDZ'
# version: 'sflx'
# hresol : hpixels
# period : 1MS
# subperiod: 10D
# err : 0.01
# hcorrelations :
# landsea: True
# ficlsm : /home/inversion/LMDZ/DATA_INV/lmdz9696/lsm.lmdz9696.nc
# dump_hcorr : True
# dircorrel : /home/satellites13/aberchet/LMDZ_DATA/CORREL/
# 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 :
parameters:
CH4:
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 : 0.05
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 :
plugin :
name : LMDZ
version : std
xmin : -180
xmax : 180
ymin : -90
ymax : 90
nlon : 97
nlat : 96
nlev : 39
type : deg
ficgrid : /home/users/aberchet/PYVAR/msaunois/pyvar/grid_LMDZ96_96.txt
#####################################################################
#####################################################################
#####################################################################
#####################################################################
# How to build your observation vector and observation uncertainties if needed
# Also projects information from the observation to the model space
# - fic_obsvect: observation vector from previous simulations
obsvect:
plugin:
name: standard
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/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
wfunc : False
fic_statlev: /home/users/aberchet/PYVAR/msaunois/pyvar/ReadObs/stations_levels_LMDZ39lev.txt
#####################################################################
#####################################################################
#####################################################################
#####################################################################
# Definition of meteo parameters
# This can be model dependent, please refer to corresponding documentation for details
meteo:
plugin:
name: LMDZ
version: mass-fluxes
dirmeteo: /home/satellites1/fcheval/LMDZ5/
#####################################################################
#####################################################################
##################
# Parameters below are not yet included in PYVAR
#
#
## surface geopotential file
#ficgeopot : null
#
## first guess path of the file if wanted
#prevanal: null
## LMDz precomputed (1) or not (0)
#precalc : 0
## perturb predefined prior/concentrations
#perturbdir : null
## seed for random number generation
#seed : 3
## diagnostics (0=none; 1=1D(time); 2=2D(lev,time); 3=4D(lat,lon,lev,time) )
#diag : 0
#
#
#
#
#
......@@ -39,7 +39,7 @@ workdir : /home/chimereges/aberchet/GCP_adjtl/
datei : 2000-01-01
# End date (same as for the initial date)
datef : 2000-02-01
datef : 2000-03-01
#####################################################################
#####################################################################
......@@ -155,82 +155,82 @@ obsoperator:
# Main keys are:
# - infos: infos on tracers to include in the simulation
# - fic_monitor: standard txt file including all observations
measurements :
plugin:
name: standard
version: std
# File where to save data, if does not exist. Reads from there if exists
fic_monitor : /home/satellites13/aberchet/LMDZ_DATA/monit/monitor_allobs.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
#measurements :
# plugin:
# name: standard
# version: std
#
# # File where to save data, if does not exist. Reads from there if exists
# fic_monitor : /home/satellites13/aberchet/LMDZ_DATA/monit/monitor_allobs.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
#####################################################################
#####################################################################
......@@ -260,27 +260,27 @@ controlvect:
name: standard
version: std
components:
fluxes:
parameters:
CH4 :
plugin:
name: 'LMDZ'
version: 'sflx'
hresol : hpixels
# type : physical
# errtype : max
err : 1
period : 1MS
subperiod: 10D
dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/
fic: sflx_CH4_GCP2018_%Y_LMDZ9696_phy.nc
hcorrelations :
landsea: True
ficlsm : /home/inversion/LMDZ/DATA_INV/lmdz9696/lsm.lmdz9696.nc
dump_hcorr : True
dircorrel : /home/satellites13/aberchet/LMDZ_DATA/CORREL/
sigma_land: 500
sigma_sea: 1000
# fluxes:
# parameters:
# CH4 :
# plugin:
# name: 'LMDZ'
# version: 'sflx'
# hresol : hpixels
# # type : physical
# # errtype : max
# err : 1
# period : 1MS
# subperiod: 10D
# dir: /home/inversion/msaunois/FLUXES/CH4/PYVAR/
# fic: sflx_CH4_GCP2018_%Y_LMDZ9696_phy.nc
# hcorrelations :
# landsea: True
# ficlsm : /home/inversion/LMDZ/DATA_INV/lmdz9696/lsm.lmdz9696.nc
# dump_hcorr : True
# dircorrel : /home/satellites13/aberchet/LMDZ_DATA/CORREL/
# sigma_land: 500
# sigma_sea: 1000
## MCF:
## plugin:
## name: 'LMDZ'
......@@ -361,7 +361,7 @@ obsvect:
name: standard
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/aberchet/LMDZ_DATA/monit/monitor_pycif_test.nc
fic_obsvect : /home/satellites13/aberchet/LMDZ_DATA/monit/monitor_allobs.nc
dump: True
wfunc : False
fic_statlev: /home/users/aberchet/PYVAR/msaunois/pyvar/ReadObs/stations_levels_LMDZ39lev.txt
......
......@@ -31,7 +31,7 @@ logfile: pyvar.logtest
# Execution directory
#workdir : /home/satellites13/msaunois/INVERSION/GCP_2018/run_00_18_inca_base_network/
#workdir : /home/satellites13/aberchet/msaunois/
workdir : /home/chimereges/aberchet/GCP_m1qn3_obs/
workdir : /home/chimereges/aberchet/GCP_congrad_obs/
# Initial date
# Use the following compatible format for the date:
......@@ -39,7 +39,7 @@ workdir : /home/chimereges/aberchet/GCP_m1qn3_obs/
datei : 2000-01-01
# End date (same as for the initial date)
datef : 2000-03-01
datef : 2018-03-01
#####################################################################
#####################################################################
......@@ -72,7 +72,7 @@ mode:
version: std
minimizer:
plugin:
name: M1QN3
name: congrad
version: std
simulator:
plugin:
......@@ -118,7 +118,7 @@ model :
fic_vcoord: /home/inversion/msaunois/LMDZ/39L/restartT2029-2006-1_MCFscaled2CH4scaled.nc
# Initial conditions recovered from:
restart:
inicond:
dir : /home/inversion/msaunois/LMDZ/39L/
fic : restartT2029-2006-1_MCFscaled2CH4scaled.nc
......