CHIMERE
/ std
¶
Description¶
This is the plugin to run the CTM CHIMERE. Please see further details on the CTM itself here
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:
Mandatory arguments¶
direxec: (mandatory)
Path to CHIMERE sources and/or executables. For executables,
fwdchimere.e
,tlchimere.e
andachimere.e
should be in${path}/src
,${path}/src_tl
and${path}/src_ad
respective sub-folders.accepted type: <class ‘str’>
nphour_ref: (mandatory)
Number of physical steps per hour. 6 is well tested for regional cases.
accepted type: <class ‘int’>
ichemstep: (mandatory)
Number of chemical refined iterations, i.e., refined time steps relative to physical time steps. Down to 1/4 degree resolution, phys=6 and step=1 is fine; For finer grids (5-10 kms), take at least step=4; For grids of 2-5 kms, try step=6 or more.
accepted type: <class ‘int’>
ideepconv: (mandatory)
Computation of the deep convection.
accepted values:
0: No deep convection
1: Select deep convection automatically according to resolution, deep conv fluxes from Tiedtke
2: Select deep convection automatically according to resolution, deep conv fluxes from meteorological data
nivout: (mandatory)
Number of vertical layers in output files.
accepted type: <class ‘int’>
nlevemis: (mandatory)
Number of levels for emissions. Applies to AEMISSION files.
accepted type: <class ‘int’>
Optional arguments¶
autoflush: (optional): False
Cleans big temporary files when the simulation is done. Triggers the function
flushrun
of the model if availableaccepted type: <class ‘bool’>
dir_sources: (optional):
Path to CHIMERE sources. Overwrites direxec if specified.
accepted type: <class ‘str’>
periods: (optional): 1D
Length of sub-simulations periods. Use Pandas frequency strings
accepted type: <class ‘str’>
ihoursu: (optional): 0
Number of spin-up hours.
accepted type: <class ‘int’>
useemisb: (optional): False
Include biogenic emissions, i.e. the file BEMISSIONS.nc
accepted type: <class ‘bool’>
dumpnctype: (optional): float
Precision for the output NetCDF files. Do not impact the values in mod.txt
accepted values:
double: double precision: needed if precise post-processing of output files
float: float precision: save some disk space
dumpncoutput: (optional): True
Dump outputs into a NetCDF file.
accepted type: <class ‘bool’>
dumpncpar: (optional): False
Dump parameters into a NetCDF file.
accepted type: <class ‘bool’>
usechemistry: (optional): 0
Use chemistry.
accepted values: [0, 1]
useemissions: (optional): 1
Use emisions.
accepted values: [0, 1]
usetransmix: (optional): 1
Use transport and mixing.
accepted values: [0, 1]
usewetdepos: (optional): 0
Use wet deposition.
accepted values: [0, 1]
usedepos: (optional): 0
Use dry deposition.
accepted values: [0, 1]
nsavedepos: (optional): 4
Save deposition in NetCDF file every … hours.
accepted type: <class ‘int’>
nitgs: (optional): 1
Number of Gauss-Seidel iterations in the TWOSTEP solver.
accepted values:
1: for model testing, and when using the adjoint
2: for better accuracy
nitgssu: (optional): 1
Same during spin-up
accepted values:
1: for model testing, and when using the adjoint
2: for better accuracy
useabsclipconc: (optional): 0
Clip small (in absolute value) concentrations when = 1; clip small (including all negative) concentrations when = 0. Warning: the clipping is done in twostep, not only when writing the output writing; thus, clipping must be used with care as it can alter the mass conservationsee CHIMERE doc for more information on the use of clipconc
accepted values: [0, 1]
clipconc: (optional): 1
Clipping concentration (in molecule/cm3)
accepted type: <class ‘float’>
ntyperate: (optional): 50
Max number of reaction types
accepted type: <class ‘int’>
nvegtype: (optional): 16
Number of vegetation types
accepted type: <class ‘int’>
nlduse: (optional): 9
Max number of landuse classes
accepted type: <class ‘int’>
nparammax: (optional): 30
Max number of output parameters
accepted type: <class ‘int’>
hpulse: (optional): 0
Hour of emission pulse. All emissions before this hour from the beginning of the simulations are ignored, and all transport/chemistry computations are skipped.To be used when computing response functions from a given hour
accepted type: <class ‘int’>
auto-recompile: (optional): False
Auto-compile executables before running if executables not available
accepted type: <class ‘bool’>
force-recompile: (optional): False
Force compilation even if executables available
accepted type: <class ‘bool’>
compile-mode: (optional): PROD
Compilation mode
accepted values:
PROD: production mode; all optimizations are activated
DEBUG: check-all and traceback are activated, hence slowing down the execution
compile-clean: (optional): True
Cleaning repositories before compiling; slows the compilation but prevent side-effects from re-compiling.Can be switched of for minor modifications in the code
accepted type: <class ‘bool’>
compile-only: (optional): [‘A’, ‘L’, ‘D’]
Compile only part of the available CHIMERE modes (tangent-linear, forward and adjoint)
accepted type: <class ‘list’>
force-compile-stderr: (optional): False
Force printing stderr from compiling (even when executable correctly generated at compiling
accepted type: <class ‘bool’>
nlevemis_bio: (optional): 1
Number of vertical levels in biogenic emissions (BEMISSIONS.nc)
accepted type: <class ‘int’>
nmdoms: (optional): 1
Number of parallel domains in meridional direction
accepted type: <class ‘int’>
nzdoms: (optional): 1
Number of parallel domains in zonal direction
accepted type: <class ‘int’>
mpirun: (optional): mpirun
path to mpirun
accepted type: <class ‘str’>
ignore_input_dates: (optional): False
Forces CHIMERE to by-pass the checks on the consistency of dates in AEMISSIONS, BEMISSIONS, BOUN_CONCS, INI_COCNS and METEO; useful to use input files from another periodwithout duplicating them only for the dates.
accepted type: <class ‘bool’>
useRAMonly: (optional): False
Force relying on the RAM only, instead of TMP files, to save forward simulations necessary for the adjoint. This trades I/O burden with TMP files with RAM burden
Warning
This option can use a LOT of RAM. Please test the option on a simple case and compare with a case using TMP files. Depending on your cluster and your test case, choose the fastest one.
accepted type: <class ‘bool’>
force_clean_run: (optional): False
Clean run subdirectory just after running to limit disk space usage
accepted type: <class ‘bool’>
stopORmore: (optional): []
To avoid running simulations for which the simulated concentrations are smaller than a given thresholdfor a set of species; please provide a list of tuples (species,threshold) (species is from ACTIVE_SPECIES and treshold in XXUNITXX
accepted type: <class ‘list’>
Requirements¶
The current plugin requires the present plugins to run properly:
Requirement name |
Requirement type |
Explicit definition |
Any valid |
Default name |
Default version |
---|---|---|---|---|---|
domain |
False |
False |
CHIMERE |
std |
|
chemistry |
False |
False |
CHIMERE |
gasJtab |
|
flux |
True |
False |
CHIMERE |
AEMISSIONS |
|
bioflux |
True |
False |
CHIMERE |
AEMISSIONS |
|
meteo |
True |
False |
CHIMERE |
std |
|
latcond |
True |
False |
CHIMERE |
icbc |
|
topcond |
True |
False |
CHIMERE |
icbc |
|
inicond |
True |
False |
CHIMERE |
icbc |
Yaml template¶
Please find below a template for a Yaml configuration:
1model:
2 plugin:
3 name: CHIMERE
4 version: std
5 type: model
6
7 # Mandatory arguments
8 direxec: XXXXX
9 nphour_ref: XXXXX
10 ichemstep: XXXXX
11 ideepconv: XXXXX
12 nivout: XXXXX
13 nlevemis: XXXXX
14
15 # Optional arguments
16 autoflush: XXXXX
17 dir_sources: XXXXX
18 periods: XXXXX
19 ihoursu: XXXXX
20 useemisb: XXXXX
21 dumpnctype: XXXXX
22 dumpncoutput: XXXXX
23 dumpncpar: XXXXX
24 usechemistry: XXXXX
25 useemissions: XXXXX
26 usetransmix: XXXXX
27 usewetdepos: XXXXX
28 usedepos: XXXXX
29 nsavedepos: XXXXX
30 nitgs: XXXXX
31 nitgssu: XXXXX
32 useabsclipconc: XXXXX
33 clipconc: XXXXX
34 ntyperate: XXXXX
35 nvegtype: XXXXX
36 nlduse: XXXXX
37 nparammax: XXXXX
38 hpulse: XXXXX
39 auto-recompile: XXXXX
40 force-recompile: XXXXX
41 compile-mode: XXXXX
42 compile-clean: XXXXX
43 compile-only: XXXXX
44 force-compile-stderr: XXXXX
45 nlevemis_bio: XXXXX
46 nmdoms: XXXXX
47 nzdoms: XXXXX
48 mpirun: XXXXX
49 ignore_input_dates: XXXXX
50 useRAMonly: XXXXX
51 force_clean_run: XXXXX
52 stopORmore: XXXXX