Basics of CHEEREIO
About CHEEREIO
Installing CHEEREIO
Overview of CHEEREIO’s capabilities
Debugging CHEEREIO
Using the ensemble
Configuring your simulation
The structure of the ensemble directory
Running the ensemble
The assimilation toolkit
Guide to CHEEREIO core files
The CHEEREIO LETKF implementation
Observations
Existing observation operators
Postprocessing
The postprocessing workflow
CHEEREIO
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Index
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Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
A
ACTIVATE_OBSPACK
command line option
actual_observations and simulated_observations movies
command line option
addData() (ObsData method)
additional_init_perturbation_from_emis
command line option
agg_to_monthly()
built-in function
albedo_nir
command line option
albedo_swir
command line option
altitude
command line option
AMPLIFY_ENSEMBLE_SPREAD_FOR_FIRST_ASSIM_PERIOD
command line option
animation_fps_concentrations
command line option
animation_fps_scalingfactor
command line option
AnimationEnv
command line option
apply_avker()
built-in function
apply_filters()
built-in function
APPROXIMATE_VARON_RERUN
command line option
assim_minus_obs and ctrl_minus_obs plots
command line option
ASSIM_PATH
command line option
ASSIM_START_DATE
command line option
ASSIM_TIME
command line option
ASSIMILATE_OBS
command line option
AV_TO_GC_GRID
command line option
averageByGC()
built-in function
AveragePriorAndPosterior
command line option
AverageScaleFactorPosteriorWithPrior
command line option
B
BC_FILES
command line option
bigY.pkl
command line option
bigy_arrays_for_plotting.pkl
command line option
blended_albedo
command line option
built-in function
agg_to_monthly()
apply_avker()
apply_filters()
averageByGC()
clearEdgesFilterByQAAndFlatten()
combineHemcoDiag()
combineHemcoDiagControl()
combineScaleFactors()
GC_to_sat_levels()
getGCCols()
globDirs()
globSubDir()
globSubDirLevelEdge()
make_filter_fxn()
makeBigYArrays()
makeDatasetForDirectory()
makeDatasetForEnsemble()
makeYEachAssimPeriod()
nearest_loc()
plotEmissions()
plotMap()
plotScaleFactor()
plotSurfaceCell()
plotSurfaceMean()
prep_obspack()
produceSuperObservationFunction()
read_omi()
read_tropomi()
read_tropomi_acmg()
read_tropomi_gosat_corrected()
super_obs()
tsPlot()
tsPlotSatCompare()
tsPlotTotalEmissions()
BURN_IN_END
command line option
C
CH4 extension
command line option
CH4_HEMCO_ROOT
command line option
chemgrid
command line option
clearEdgesFilterByQAAndFlatten()
built-in function
column_AK
command line option
combined_HEMCO_diagnostics.nc file
command line option
combineHemcoDiag()
built-in function
combineHemcoDiagControl()
built-in function
combineScaleFactors()
built-in function
command line option
ACTIVATE_OBSPACK
actual_observations and simulated_observations movies
additional_init_perturbation_from_emis
albedo_nir
albedo_swir
altitude
AMPLIFY_ENSEMBLE_SPREAD_FOR_FIRST_ASSIM_PERIOD
animation_fps_concentrations
animation_fps_scalingfactor
AnimationEnv
APPROXIMATE_VARON_RERUN
assim_minus_obs and ctrl_minus_obs plots
ASSIM_PATH
ASSIM_START_DATE
ASSIM_TIME
ASSIMILATE_OBS
AV_TO_GC_GRID
AveragePriorAndPosterior
AverageScaleFactorPosteriorWithPrior
BC_FILES
bigY.pkl
bigy_arrays_for_plotting.pkl
blended_albedo
BURN_IN_END
CH4 extension
CH4_HEMCO_ROOT
chemgrid
column_AK
combined_HEMCO_diagnostics.nc file
CondaEnv
constant
CONTROL_END
control_HEMCO_diagnostics.nc file
CONTROL_START
CONTROL_VECTOR_CONC
CONTROL_VECTOR_EMIS
controlvar_pp.nc file
ControlWallTime
corrDistances
correlatedInitialScalings
correlatedInitialScalings equals False
correlatedInitialScalings equals True
CUSTOM_CH4_OH_ENTRY
DATA_PATH
default
DIFFERENT_RUN_IN_PLACE_FOR_BURN_IN
DO_BURN_IN
DO_CONTROL_RUN
DO_CONTROL_WITHIN_ENSEMBLE_RUNS
DO_ENS_SPINUP
DO_RUN_IN_PLACE
DO_SPINUP
DO_VARON_RERUN
DOFS_filter
Emissions timeseries
END_DATE
ENS_SPINUP_END
ENS_SPINUP_FROM_BC_RESTART
ENS_SPINUP_START
EnsCtrlSpinupMemory
EnsSpinupWallTime
EXTRA_OBSDATA_FIELDS_TO_REGRID_AND_PLOT
EXTRA_OBSDATA_FIELDS_TO_SAVE_TO_BIG_Y
extra_plot_field_units
filter_obs_poleward_of_n_degrees
GAMMA_FOR_BURN_IN
gc_obspack_path
GC_VERSION
HEMCO diagnostic map plots (various time slices)
hemco_diags_to_process
HISTORY_collections_to_customize
HISTORY_dur
HISTORY_freq
HistoryLevelEdgeDiagsToSave
HistoryObsPackToSave
HistorySpeciesConcToSave
HistoryStateMetToSave
HistoryXXXXXToSave
implements_initialReadDate
InflateScalingsToXOfPreviousStandardDeviation
INFLATION_FACTOR
init_std_dev
LEVS
LOCALIZATION_RADIUS_km
lognormalErrors
Mask60NScaleFactor
Mask60SScaleFactor
MaskCoastsGT25pctOcean
MaskOceanScaleFactor
MaximumScaleFactorRelativeChangePerAssimilationPeriod
MaximumScalingFactorAllowed
MAXNUMOBS
MaxPar
Mean observation and observation counts plots (weighted_mean_obs
Memory
met_name
methane_profile_apriori
min_emis_std_value_to_plot
min_emis_value_to_plot
MIN_OBS_ERROR
MinimumScalingFactorAllowed
MINNUMOBS
module_name
MY_PATH
nEnsemble
NEST
number_of_windows_to_rerun
NumCores
NumCtrlCores
OBS_ERROR
OBS_ERROR_SELF_CORRELATION
OBS_ERROR_TYPE
OBS_TYPE
Observation counts movies (total_aggregated_observation_count and total_raw_observation_counts)
Observation ts compare plots
OBSERVATION_UNITS
OBSERVED_SPECIES
OBSERVERS_TO_PLOT_AS_POINTS
obspack_gc_input_file
obspack_id
OMI_dirs
OMI_NO2 extension
OMI_NO2_filter_cloud_radiance_frac
OMI_NO2_filter_surface_albedo
OMI_NO2_filter_sza
OMI_NO2_FILTERS
omit_diff_cells_with_fewer_than_n_observations
OTHER_OBS_ERROR_PARAMETERS
Partition
platform
POSTPROCESS_END_DATE
POSTPROCESS_START_DATE
preprocess_raw_obspack_files
pressure
PriorWeightinPriorPosteriorAverage
PriorWeightinSFAverage
qa_value
raw_obspack_path
REGION
REGULARIZING_FACTOR_GAMMA
RES
RESTART_FILE
rip_burnin_update_time
rip_update_time
RUN_NAME
SaveArea
SaveDOFS
SaveLevelEdgeDiags
SaveStateMet
Scalefactor .nc files
Scalefactor map movies
Scalefactor map plots (various time slices)
scalefactor_plot_freq
sim_extra_option
sim_name
SIMPLE_SCALE_AT_END_OF_BURN_IN_PERIOD
SIMPLE_SCALE_FOR_FIRST_ASSIM_PERIOD
site_code
smooth_localization_with_gaspari_cohn
species_to_approximate_for_rerun
SpeciesConc map movies
speedyCorrelationApprox
SPINUP_END
SPINUP_HISTORY_dur
SPINUP_HISTORY_freq
SPINUP_START
SpinupWallTime
SPREAD_AMPLIFICATION_FACTOR
sqrt
START_DATE
STATE_VECTOR_CONC
STATE_VECTOR_CONC_REPRESENTATION
SUPER_OBSERVATION_FUNCTION
Surface mean timeseries
total_obs_count)
translator_name
TROPOMI_CH4 extension
TROPOMI_CH4_filter_blended_albedo
TROPOMI_CH4_filter_roughness
TROPOMI_CH4_filter_swir_albedo_high
TROPOMI_CH4_filter_swir_albedo_low
TROPOMI_CH4_filter_swir_aot
TROPOMI_CH4_filter_winter_lat
TROPOMI_CH4_FILTERS
TROPOMI_CO extension
TROPOMI_CO_filter_blended_albedo
TROPOMI_CO_filter_roughness
TROPOMI_CO_filter_swir_albedo_high
TROPOMI_CO_filter_swir_albedo_low
TROPOMI_CO_filter_swir_aot
TROPOMI_CO_filter_winter_lat
TROPOMI_CO_FILTERS
TROPOMI_dirs
USE_CHEEREIO_TEMPLATE_CH4_HEMCO_Config
USE_CUSTOM_CH4_OH_ENTRY
USE_DIFFERENT_GAMMA_FOR_BURN_IN
useLogScaleForEmissionsMaps
utc_conv
verbose
WallTime
WHICH_TROPOMI_PRODUCT
,
[1]
XXXXXXXX_dirs
CondaEnv
command line option
constant
command line option
CONTROL_END
command line option
control_HEMCO_diagnostics.nc file
command line option
CONTROL_START
command line option
CONTROL_VECTOR_CONC
command line option
CONTROL_VECTOR_EMIS
command line option
controlvar_pp.nc file
command line option
ControlWallTime
command line option
corrDistances
command line option
correlatedInitialScalings
command line option
correlatedInitialScalings equals False
command line option
correlatedInitialScalings equals True
command line option
CUSTOM_CH4_OH_ENTRY
command line option
D
DATA_PATH
command line option
default
command line option
DIFFERENT_RUN_IN_PLACE_FOR_BURN_IN
command line option
DO_BURN_IN
command line option
DO_CONTROL_RUN
command line option
DO_CONTROL_WITHIN_ENSEMBLE_RUNS
command line option
DO_ENS_SPINUP
command line option
DO_RUN_IN_PLACE
command line option
DO_SPINUP
command line option
DO_VARON_RERUN
command line option
DOFS_filter
command line option
E
Emissions timeseries
command line option
END_DATE
command line option
ENS_SPINUP_END
command line option
ENS_SPINUP_FROM_BC_RESTART
command line option
ENS_SPINUP_START
command line option
EnsCtrlSpinupMemory
command line option
EnsSpinupWallTime
command line option
EXTRA_OBSDATA_FIELDS_TO_REGRID_AND_PLOT
command line option
EXTRA_OBSDATA_FIELDS_TO_SAVE_TO_BIG_Y
command line option
extra_plot_field_units
command line option
F
filter_obs_poleward_of_n_degrees
command line option
G
GAMMA_FOR_BURN_IN
command line option
gc_obspack_path
command line option
GC_to_sat_levels()
built-in function
GC_VERSION
command line option
gcCompare() (Observation_Translator method)
getCols() (ObsData method)
getDataByKey() (ObsData method)
getGCCol() (ObsData method)
getGCCols()
built-in function
getLatLon() (ObsData method)
getObsCol() (ObsData method)
getObservations() (Observation_Translator method)
getObsTime() (ObsData method)
globDirs()
built-in function
globSubDir()
built-in function
globSubDirLevelEdge()
built-in function
H
HEMCO diagnostic map plots (various time slices)
command line option
hemco_diags_to_process
command line option
HISTORY_collections_to_customize
command line option
HISTORY_dur
command line option
HISTORY_freq
command line option
HistoryLevelEdgeDiagsToSave
command line option
HistoryObsPackToSave
command line option
HistorySpeciesConcToSave
command line option
HistoryStateMetToSave
command line option
HistoryXXXXXToSave
command line option
I
implements_initialReadDate
command line option
InflateScalingsToXOfPreviousStandardDeviation
command line option
INFLATION_FACTOR
command line option
init_std_dev
command line option
initialReadDate() (Observation_Translator method)
L
LEVS
command line option
LOCALIZATION_RADIUS_km
command line option
lognormalErrors
command line option
M
make_filter_fxn()
built-in function
makeBigYArrays()
built-in function
makeDatasetForDirectory()
built-in function
makeDatasetForEnsemble()
built-in function
makeYEachAssimPeriod()
built-in function
Mask60NScaleFactor
command line option
Mask60SScaleFactor
command line option
MaskCoastsGT25pctOcean
command line option
MaskOceanScaleFactor
command line option
MaximumScaleFactorRelativeChangePerAssimilationPeriod
command line option
MaximumScalingFactorAllowed
command line option
MAXNUMOBS
command line option
MaxPar
command line option
Mean observation and observation counts plots (weighted_mean_obs
command line option
Memory
command line option
met_name
command line option
methane_profile_apriori
command line option
min_emis_std_value_to_plot
command line option
min_emis_value_to_plot
command line option
MIN_OBS_ERROR
command line option
MinimumScalingFactorAllowed
command line option
MINNUMOBS
command line option
module_name
command line option
MY_PATH
command line option
N
nearest_loc()
built-in function
nEnsemble
command line option
NEST
command line option
number_of_windows_to_rerun
command line option
NumCores
command line option
NumCtrlCores
command line option
O
OBS_ERROR
command line option
OBS_ERROR_SELF_CORRELATION
command line option
OBS_ERROR_TYPE
command line option
OBS_TYPE
command line option
ObsData (built-in class)
Observation counts movies (total_aggregated_observation_count and total_raw_observation_counts)
command line option
Observation ts compare plots
command line option
Observation_Translator (built-in class)
OBSERVATION_UNITS
command line option
OBSERVED_SPECIES
command line option
OBSERVERS_TO_PLOT_AS_POINTS
command line option
obspack_gc_input_file
command line option
obspack_id
command line option
OMI_dirs
command line option
OMI_NO2 extension
command line option
OMI_NO2_filter_cloud_radiance_frac
command line option
OMI_NO2_filter_surface_albedo
command line option
OMI_NO2_filter_sza
command line option
OMI_NO2_FILTERS
command line option
omit_diff_cells_with_fewer_than_n_observations
command line option
OTHER_OBS_ERROR_PARAMETERS
command line option
P
Partition
command line option
platform
command line option
plotEmissions()
built-in function
plotMap()
built-in function
plotScaleFactor()
built-in function
plotSurfaceCell()
built-in function
plotSurfaceMean()
built-in function
POSTPROCESS_END_DATE
command line option
POSTPROCESS_START_DATE
command line option
prep_obspack()
built-in function
preprocess_raw_obspack_files
command line option
pressure
command line option
PriorWeightinPriorPosteriorAverage
command line option
PriorWeightinSFAverage
command line option
produceSuperObservationFunction()
built-in function
Q
qa_value
command line option
R
raw_obspack_path
command line option
read_omi()
built-in function
read_tropomi()
built-in function
read_tropomi_acmg()
built-in function
read_tropomi_gosat_corrected()
built-in function
REGION
command line option
REGULARIZING_FACTOR_GAMMA
command line option
RES
command line option
RESTART_FILE
command line option
rip_burnin_update_time
command line option
rip_update_time
command line option
RUN_NAME
command line option
S
SaveArea
command line option
SaveDOFS
command line option
SaveLevelEdgeDiags
command line option
SaveStateMet
command line option
Scalefactor .nc files
command line option
Scalefactor map movies
command line option
Scalefactor map plots (various time slices)
command line option
scalefactor_plot_freq
command line option
setGCCol() (ObsData method)
setObsCol() (ObsData method)
sim_extra_option
command line option
sim_name
command line option
SIMPLE_SCALE_AT_END_OF_BURN_IN_PERIOD
command line option
SIMPLE_SCALE_FOR_FIRST_ASSIM_PERIOD
command line option
site_code
command line option
smooth_localization_with_gaspari_cohn
command line option
species_to_approximate_for_rerun
command line option
SpeciesConc map movies
command line option
speedyCorrelationApprox
command line option
SPINUP_END
command line option
SPINUP_HISTORY_dur
command line option
SPINUP_HISTORY_freq
command line option
SPINUP_START
command line option
SpinupWallTime
command line option
SPREAD_AMPLIFICATION_FACTOR
command line option
sqrt
command line option
START_DATE
command line option
STATE_VECTOR_CONC
command line option
STATE_VECTOR_CONC_REPRESENTATION
command line option
super_obs()
built-in function
SUPER_OBSERVATION_FUNCTION
command line option
Surface mean timeseries
command line option
T
total_obs_count)
command line option
translator_name
command line option
TROPOMI_CH4 extension
command line option
TROPOMI_CH4_filter_blended_albedo
command line option
TROPOMI_CH4_filter_roughness
command line option
TROPOMI_CH4_filter_swir_albedo_high
command line option
TROPOMI_CH4_filter_swir_albedo_low
command line option
TROPOMI_CH4_filter_swir_aot
command line option
TROPOMI_CH4_filter_winter_lat
command line option
TROPOMI_CH4_FILTERS
command line option
TROPOMI_CO extension
command line option
TROPOMI_CO_filter_blended_albedo
command line option
TROPOMI_CO_filter_roughness
command line option
TROPOMI_CO_filter_swir_albedo_high
command line option
TROPOMI_CO_filter_swir_albedo_low
command line option
TROPOMI_CO_filter_swir_aot
command line option
TROPOMI_CO_filter_winter_lat
command line option
TROPOMI_CO_FILTERS
command line option
TROPOMI_dirs
command line option
tsPlot()
built-in function
tsPlotSatCompare()
built-in function
tsPlotTotalEmissions()
built-in function
U
USE_CHEEREIO_TEMPLATE_CH4_HEMCO_Config
command line option
USE_CUSTOM_CH4_OH_ENTRY
command line option
USE_DIFFERENT_GAMMA_FOR_BURN_IN
command line option
useLogScaleForEmissionsMaps
command line option
utc_conv
command line option
V
verbose
command line option
W
WallTime
command line option
WHICH_TROPOMI_PRODUCT
command line option
,
[1]
X
XXXXXXXX_dirs
command line option
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