config_test.yml

## IMI configuration file
## Documentation @ https://imi.readthedocs.io/en/latest/getting-started/imi-config-file.html

## General
RunName: "2024_Jan_download"
UseSlurm: true
SafeMode: true
S3Upload: false

## Period of interest
StartDate: 20240101
EndDate: 20240201
SpinupMonths: 1

## Use blended TROPOMI+GOSAT data (true)? Or use operational TROPOMI data (false)?
BlendedTROPOMI: false

## Use observations over water? Set to false to filter out water observations
UseWaterObs: false

## Is this a regional inversion? Set to false for global inversion
isRegional: true

## Select two character region ID (for using pre-cropped meteorological fields)
##   Current options are listed below with ([lat],[lon]) bounds:
##     "AF" : Africa ([-37,40], [-20,53])
##     "AS" : Asia ([-11,55],[60,150])
##     "EU" : Europe ([33,61],[-30,70])
##     "ME" : Middle East ([12,50], [-20,70])
##     "NA" : North America ([10,70],[-140,-40])
##     "OC" : Oceania ([-50,5], [110,180])
##     "RU" : Russia ([41,83], [19,180])
##     "SA" : South America ([-59,16], [-88,-31])
##     ""   : Use for global global simulation or custom regions
##   For example, if the region of interest is in Europe ([33,61],[-30,70]), select "EU".
RegionID: "NA"

## Region of interest
##   These lat/lon bounds are only used if CreateAutomaticRectilinearStateVectorFile: true
##   Otherwise lat/lon bounds are determined from StateVectorFile
LonMin: -121
LonMax: -117
LatMin: 32.5
LatMax: 36

## Kalman filter options
KalmanMode: false
UpdateFreqDays: 7
NudgeFactor: 0.1
MakePeriodsCSV: true
CustomPeriodsCSV: "/path/to/periods.csv"

## State vector
CreateAutomaticRectilinearStateVectorFile: false
nBufferClusters: 8
BufferDeg: 5
LandThreshold: 0.25
OffshoreEmisThreshold: 0
OptimizeBCs: true
OptimizeOH: false

## Point source datasets
## Used for visualizations and state vector clustering
PointSourceDatasets: ["SRON"]

## Clustering Options
ReducedDimensionStateVector: false
DynamicKFClustering: false
ClusteringMethod: "kmeans"
NumberOfElements: 45
ForcedNativeResolutionElements:
  - [31.5, -104]
EmissionRateFilter: 2500
PlumeCountFilter: 50
GroupByCountry: false

## Custom state vector
StateVectorFile: "/projects/befa4441/integrated_methane_inversion/src/custom_statevectors/CA_fullres.nc"
ShapeFile: "/projects/befa4441/integrated_methane_inversion/src/shapefiles/CA/CA/CA_only_imi.shp"

## Inversion
## Notes:
## - PriorError is a relative fraction (e.g. 0.5 = 50%)
## - If lognormal PriorError is the geometric standard deviation (e.g. 2 = factor of 2 uncertainty)
## - PriorErrorOH is a relative fraction (e.g. 0.1 = 10%)
## - PriorErrorBCs is in ppb
## - PriorErrorBufferElements is only used if LognormalErrors is true
LognormalErrors: true
PriorError: [2]
PriorErrorBCs: [10.0]
PriorErrorBufferElements: [0.5]
PriorErrorOH: [0.1]
ObsError: [15]
Gamma: [1.0]
PrecomputedJacobian: false
#ReferenceRunDir: "/scratch/alpine/befa4441/imi/IMI_output/2024_Jan_lognorm"

## Grid
##   Options are 0.125x0.15625 (GEOS-FP only), 0.25x0.3125 (GEOS-FP only),
##   0.5x0.625, 2.0x2.5, or 4.0x5.0
Res: "0.25x0.3125"

## Meteorology
##   Options are GEOSFP or MERRA2
Met: "GEOSFP"

## Setup modules
##   Turn on/off different steps in setting up the inversion
RunSetup: true
SetupTemplateRundir: true
SetupSpinupRun: true
SetupJacobianRuns: true
SetupInversion: true
SetupPosteriorRun: true

## Run modules
##   Turn on/off different steps in performing the inversion
DoHemcoPriorEmis: true
DoSpinup: true
DoJacobian: true
ReDoJacobian: true
DoInversion: true
DoPosterior: true

## IMI preview
##   NOTE: RunSetup must be true to run preview
DoPreview: false
DOFSThreshold: 0

## Resource allocation settings for slurm jobs
RequestedCPUs: 8
RequestedMemory: 20000
InversionCPUs: 32
InversionMemory: 50000
RequestedTime: "0-12:00"
SchedulerPartition: "amilan"

## Max number of simultaneous Jacobian runs from the job array (-1: no limit)
MaxSimultaneousRuns: -1

## Number of Jacobians tracers to use for each jacobian simulation
##   Specifying a value = 1 will submit a separate jacobian simulation for each
##   state vector element. Specifying a value > 1 will combine state vector
##   elements into a single jacobian simulation.
NumJacobianTracers: 5

##====================================================================
##
## Advanced Settings (optional)
##
##====================================================================

## These settings are intended for advanced users who wish to:
##   a. modify additional GEOS-Chem options, or
##   b. run the IMI on a local cluster.
##   c. do an Observing System Simulation Experiment (OSSE)
## They can be ignored for any standard cloud application of the IMI.


##--------------------------------------------------------------------
## Settings for Observing System Simulation Experiment (OSSE)
##--------------------------------------------------------------------
## If true, the IMI will run on synthetic observations
EnableOSSE: false
## Run the simulation with randomly perturbed emissions to generate synthetic observations
DoOSSE: false
## Perturbation to apply to the prior emissions 
EmisPerturbationOSSE: 0.5
## Noise added to the synthetic observations
ObsErrorOSSE: 15
## Use randomly perturbed scale factor as "true" emissions (true)
CreateAutomaticScaleFactorFileOSSE: true
## Path to a custom scale factor file if CreateAutomaticScaleFactorFileOSSE is false
ScaleFactorFileOSSE: "/path/to/ScaleFactor.nc"

##--------------------------------------------------------------------
## Additional settings for GEOS-Chem simulations
##--------------------------------------------------------------------

## Jacobian settings
## Note PerturbValue is in 1e-8 kg/m2/s. eg specifying 1 means the
## perturbation will be 1e-8 kg/m2/s
## PerturbValueOH is a relative scale factor and PerturbValueBCs is in ppb
PerturbValue: 1.0
PerturbValueOH: 1.1
PerturbValueBCs: 10.0

## Save out hourly diagnostics from GEOS-Chem?
## For use in satellite operators via post-processing -- required for TROPOMI
## inversions
HourlyCH4: true

## IMI validation
## Turn on ObsPack diagnostic in GEOS-Chem?
DoObsPack: false

## Turn on planeflight diagnostic in GEOS-Chem?
## For use in comparing GEOS-Chem against planeflight data. The path
## to those data must be specified in geoschem_config.yml.
PLANEFLIGHT: false

## Turn on old observation operators in GEOS-Chem?
## These will save out text files comparing GEOS-Chem to observations, but have
## to be manually incorporated into the IMI
GOSAT: false
TCCON: false
AIRS: false

##------------------------------------------------------------------
## Settings for running on local cluster
##------------------------------------------------------------------

## Path for IMI runs and output
OutputPath: "/scratch/alpine/befa4441/imi/IMI_output"

## Path to GEOS-Chem input data
DataPath: "/scratch/alpine/befa4441/imi/ExtData"

## Path to TROPOMI Data
DataPathTROPOMI:

## Conda environment file
## See envs/README to create the Conda environment specified below
CondaEnv: "imi_env"
CondaFile: "/projects/befa4441/integrated_methane_inversion/envs/CURC-Alpine/condafile.sh"

## GEOS-Chem environment file (with fortran compiler, netcdf libraries, etc.)
##   NOTE: Copy your own file in the envs/ directory within the IMI
GEOSChemEnv: "/projects/befa4441/integrated_methane_inversion/envs/CURC-Alpine/gcclassic.rocky+gnu12.minimal.env"

## Download initial restart file from AWS S3?
##   NOTE: Must have AWS CLI enabled
RestartDownload: true

## Path to initial GEOS-Chem restart file + prefix
##   ("YYYYMMDD_0000z.nc4" will be appended)

RestartFilePrefix: "/scratch/alpine/befa4441/imi/IMI_inputs/ch4/tropomi-boundary-conditions/v2025-06/GEOSChem.BoundaryConditions."

## Path to GEOS-Chem boundary condition files (for regional simulations)
## BCversion will be appended to the end of this path. ${BCpath}/${BCversion}
BCpath: "/scratch/alpine/befa4441/imi/IMI_inputs/ch4/tropomi-boundary-conditions"
BCversion: "v2025-06"

## Options to download missing GEOS-Chem input data from AWS S3
##   NOTE: Must have AWS CLI enabled
HemcoPriorEmisDryRun: true
SpinupDryrun: true
ProductionDryRun: true
PosteriorDryRun: true
BCdryrun: true