Yaml arguments

The following arguments are used to configure the plugin. pyCIF will return an exception at the initialization if mandatory arguments are not specified, or if any argument does not fit accepted values or type:

Optional arguments

autoflush: (optional): False

Cleans big temporary files when the simulation is done. Triggers the function flushrun of the model if available

accepted type: bool

read_background: (optional): False

Read sensitivity to the background according to FLEXPART

accepted type: bool

read_surface_sensitivity: (optional): True

Read sensitivity to the surface fluxes according to FLEXPART

accepted type: bool

footprint_type: (optional): FLEXPART

Type of footprints to read

accepted values:

  • FLEXPART: Footprints generated by FLEXPART

  • STILT: Footprints generated by STILT

period: (optional): 1MS

Length of periods along which FLEXPART simulations are split

accepted type: str

subperiod: (optional):

Complementary to period if inputs should be at a better resolution than period

accepted type: str

numscale: (optional): 1000000000000.0

Scaling factor to convert from footprint native resolution to`ppm / (ng/m2/s)`

accepted type: float

coeff: (optional): 0.001

Conversion coefficient to convert from native output unit to ppb/ppt/ppm, etc. A coefficient of 1 returns ppm; 1e-3 returns ppb, etc.

accepted type: float

mmair: (optional): 28.97

Molar mass of dry air

accepted type: float

footprint_dir_format: (optional): %Y%m

Structure for the footprints per stations. The format can use date formatting

accepted type: str

footprint_stat_subdir_format: (optional): {stat}

Structure for the footprints split by stations

accepted type: str

footprint_date_format: (optional): %Y%m%d%H%M%S

Date format for converting observation dates to footprint data

accepted type: str

file_nest_format: (optional):

Format of the footprint file names.


It is possible to dynamically include the name of the station in file_nest_format (but also in footprint_date_format and footprint_dir_format.

To do so, simply include the string {stat} in the variable.

For instance, if file_nest_format is footprint_{stat}_%Y%m.nc, it will be replaced by footprint_PAL_201001.nc for the station PAL for the month of January 2010.

Similarly, the network column can be used with {network}.

accepted type: str

file_glob_format: (optional):

Same as file_nest_format for footprints outside the regional domain.

accepted type: str

file_ini_format: (optional):

Same as file_nest_format for the initial condition sensitivity files.

accepted type: str

run_dir_nest: (optional):

Directory where footprints for the nested domain are stored. In the case of a non-nested domain, this argument is used for the overall domain.


The expected structure of the footprint folder is:


├── station_ID#1 │ └── footprint_dir_format │ └── file_nest_format └── station_ID#1

└── footprint_dir_format

└── file_nest_format

accepted type: str

run_dir_glob: (optional):

Same as run_dir_nest for the outer domain.


For non-nested domains, run_dir_glob is used by default to read footprints. It is possible to force reading the inside domain with force_read_nest

accepted type: str

run_dir_bg: (optional):

Same as run_dir_nest for reading the influence of the background.

accepted type: str

release_shift: (optional): 0H

Releases start X time before observation starts. Accepts pandas date syntax

accepted type: str

footprint_format: (optional): bin

Format of FLEXPART output files ‘grid_time’

accepted values:

  • bin: standard FLEXPART outputs

  • nc: netCDF adaptation of FLEXPART outputs

force_read_nest: (optional): False

Use it to force using the nested format even when simulations where nested, but the CIF uses them as non-nested. It has no impact for nested simulations, but for non-nested, if the original FLEXPART simulation was nested and force_read_nest is False, the CIF will use the outer domain by default, which may lead to shape issues

accepted type: bool

dump_debug: (optional): False

Dumps intermediate datastores (contributions from nested fluxes, global fluxes and initial conditions) in the model sub-directory

accepted type: bool

backward_trajdays: (optional):

Duration of backward trajectories. If not specified, automatically inferred from the domain information.


This argument should be explicitly specified only with STILT

accepted type: str

ref_header_ID: (optional)

Name of the station to be used to initialize the header for the model footprints. If not specified, The first station of the observation files will be used.

accepted type: str

nthreads: (optional): 1

Number of threads to read in parallel grid files. There is a balance to find between to few threads which do not optimize anything and too many threads that overload I/O.

accepted type: int

flexversion: (optional): 10.4

Version of FLEXPART used to generate footprints

accepted type: float

exp_decay: (optional)

Apply an exponential decay of the emitted species from fluxes to observation data.

accepted structure:

halflife: (mandatory)

The half time of the exponential decay to apply

accepted type: str

inverse_decay: (optional): False

Applies a exponential convergence toward an asymptote

accepted type: bool

station_name_dict: (optional)

Information to translate station IDs from CIF to footprint file names.

accepted structure:

dict_file: (mandatory)

Path to the file to use as dictionary

accepted type: str

separator: (optional): ;

Separator to use to parse the parse dict_file

accepted type: str

CIF_stations_id: (optional): CIF_stations_id

Column name to use as CIF station names

accepted type: str

footprint_stations_id: (optional): footprint_stations_id

Column name to use in footprint station name

accepted type: str

reload_footprints: (optional): False

Keeps in memory previous footprint in case other observation have the same release.

accepted type: bool


The current plugin requires the present plugins to run properly:

Requirement name

Requirement type

Explicit definition

Any valid

Default name

Default version













Yaml template

Please find below a template for a Yaml configuration:

 2  plugin:
 3    name: FLEXPART
 4    version: std
 5    type: model
 7  # Optional arguments
 8  autoflush: XXXXX  # bool
 9  read_background: XXXXX  # bool
10  read_surface_sensitivity: XXXXX  # bool
11  footprint_type: XXXXX  # FLEXPART|STILT
12  period: XXXXX  # str
13  subperiod: XXXXX  # str
14  numscale: XXXXX  # float
15  coeff: XXXXX  # float
16  mmair: XXXXX  # float
17  footprint_dir_format: XXXXX  # str
18  footprint_stat_subdir_format: XXXXX  # str
19  footprint_date_format: XXXXX  # str
20  file_nest_format: XXXXX  # str
21  file_glob_format: XXXXX  # str
22  file_ini_format: XXXXX  # str
23  run_dir_nest: XXXXX  # str
24  run_dir_glob: XXXXX  # str
25  run_dir_bg: XXXXX  # str
26  release_shift: XXXXX  # str
27  footprint_format: XXXXX  # bin|nc
28  force_read_nest: XXXXX  # bool
29  dump_debug: XXXXX  # bool
30  backward_trajdays: XXXXX  # str
31  ref_header_ID: XXXXX  # str
32  nthreads: XXXXX  # int
33  flexversion: XXXXX  # float
34  exp_decay:
35    halflife: XXXXX  # str
36    inverse_decay: XXXXX  # bool
37  station_name_dict:
38    dict_file: XXXXX  # str
39    separator: XXXXX  # str
40    CIF_stations_id: XXXXX  # str
41    footprint_stations_id: XXXXX  # str
42  reload_footprints: XXXXX  # bool