TM5/std TM5/std

TM5/std TM5/std#

Description#

Plugin for the TM5 global chemistry-transport model.

TM5 (Two-way nested Tracer Model 5) is an offline global atmospheric chemistry and transport model developed at KNMI and IMAU (Utrecht University). It uses pre-computed meteorological fields (typically ECMWF ERA5) to transport chemical species and supports a two-way nested zoom capability for high-resolution regional studies.

The plugin interfaces TM5 as the forward transport model for tracer inversions within CIF, supporting forward, tangent-linear, and adjoint operator evaluation.

Official resources#

Key references#

  • Krol et al. (2005) — TM5 model description: The two-way nested global chemistry-transport zoom model TM5: algorithm and applications, Atmos. Chem. Phys., 5, 417–432, doi:10.5194/acp-5-417-2005.

See also TM5 — Tracer Model, version 5.

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 : str, mandatory

Path to executable and/or sources

auto_recompile : bool, mandatory

Recompile sources

make_clean : bool, mandatory

When compiling, do a ‘make clean’ first.

fc : str, mandatory

Fortran compiler

linker : str, mandatory

Linker

Optional arguments#

autoflush : bool, optional, default False

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

ensrf_restart_file : str, optional

Use in EnSRF mode to point at relevant restart file

ensrf_datei : str, optional

New start date to use in EnSRF

ensrf_same_restart : bool, optional

Use in EnSRF mode to check if same restart

tracer : str, optional, default “CH4”

The tracer to be used in the inverse modelling.

nlay : int, optional, default 25

Number of layers in TM5 vertical grid.

levs : str, optional, default “tropo25a”

Number of layers in TM5 vertical grid.

eclevs : str, optional, default “ml137”

Number of layers in ECMWF vertical grid.

projs : list, optional, default [‘base/src/’, ‘proj/levels/ml137/tropo25a/src/’, ‘proj/levels/ml137/src/’, ‘proj/tracer/CH4/src/’]

Copy these projects from the source dir before compilation. Note that the variable tm5_dir must be defined in the yaml config file.

make_options : str, optional, default “-j4”

Options to pass to make, such as ‘-j n’ to have make run parallel threads.

makedeps_dir : str, optional, default “”

The path to Makefile_makedeps, a makefile that automatically generates a list of dependencies.

fflags_gfortran : str, optional, default “-fdefault-real-8 -fdefault-double-8 -ffree-line-length-0 -g1 -O3 -fbacktrace -fcheck=array-temps -fcheck=bounds -fcheck=do -fcheck=pointer -fcheck=recursion -fallow-argument-mismatch -I/usr/local/gfortran/include “

Compiler flags for gfortran. Note that openmp only works for ifort, but that ifort is not yet supported for compiling TM5 in CIF.

ldflags_gfortran : str, optional, default “-Wl,-rpath=/usr/local/gfortran/lib -Wl,-rpath=/usr/local/gfortran/include -L/usr/local/gfortran/lib -l:libmfhdf.a -l:libdf.a -ljpeg -lz -lsz -L/usr/local/gfortran/lib -lhdf5_hl -lhdf5hl_fortran -lhdf5 -lhdf5_fortran -L/usr/local/gfortran/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5hl_fortran -lhdf5_fortran -lhdf5 -lz -lm -lsz -L/usr/local/gfortran/lib -llapack -lblas “

Linker flags for gfortran.

fflags_ifort : str, optional, default “-traceback -warn errors -warn declarations -qopenmp -r8 -O3 -I/hpc/sw/netcdf-fortran-4.4.2-intel-seq/include -I/hpc/sw/hdf-4.2.9-intel-seq/include -I/hpc/sw/szip-2.1-intel/include -mkl=sequential “

Compiler flags for ifort. Note that compiling TM5 with ifort is not yet supported in CIF.

ldflags_ifort : str, optional, default “-qopenmp -L/hpc/sw/netcdf-fortran-4.4.2-intel-seq/lib -lnetcdff -Wl,-rpath -Wl,/hpc/sw/netcdf-fortran-4.4.2-intel-seq/lib -L/hpc/sw/netcdf-4.3.1.1-intel-seq/lib -lnetcdf -Wl,-rpath -Wl,/hpc/sw/netcdf-4.3.1.1-intel-seq/lib -L/hpc/sw/hdf-4.2.9-intel-seq/lib -lmfhdf -ldf -L/hpc/sw/szip-2.1-intel/lib -lsz -ljpeg -lz -L/opt/intel/composer_xe_2015.0.090/mkl/lib/intel64 -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lpthread -lm -ldl -Wl,-rpath -Wl,/opt/intel/composer_xe_2015.0.090/mkl/lib/intel64 “

Linker flags for ifort.

meteo_macros : list, optional, default [‘with_tmm_tm5’]

Meteo macro’s (my.tmm.define in tmvar-tm5-build.rc)

model_macros : list, optional, default [‘slopes’, ‘with_budgets’, ‘without_wet_deposition’, ‘without_photolysis’, ‘without_dry_deposition’, ‘with_convdiff’, ‘with_lapack’]

Model macro’s. When compiling with ifort, use with_mkl, else with_lapack.

mdf_macros : list, optional, default [‘with_hdf4’, ‘with_netcdf4’]

Datafile macro’s

optim_emis_type : int, optional, default 3

Type of variable to be optimized for emissions

TCCON_FTS_list : str, optional

path to a station list for TCCON sites; this may disappear in the future

Requirements#

The current plugin requires the present plugins to run properly:

Requirement name

Requirement type

Explicit definition

Any valid

Default name

Default version

domain

Domain

False

False

dummy

std

chemistry

Chemistry

False

False

TM5

SINK-TIPP

flux

DataStream

True

False

TM5

std

meteo

DataStream

True

False

TM5

std

inicond

DataStream

True

False

TM5

ic

YAML template#

Please find below a template for a YAML configuration:

 1model:
 2  plugin:
 3    name: TM5
 4    version: std
 5    type: model
 6
 7  # Mandatory arguments
 8  direxec: XXXXX  # str
 9  auto_recompile: XXXXX  # bool
10  make_clean: XXXXX  # bool
11  fc: XXXXX  # str
12  linker: XXXXX  # str
13
14  # Optional arguments
15  autoflush: XXXXX  # bool
16  ensrf_restart_file: XXXXX  # str
17  ensrf_datei: XXXXX  # str
18  ensrf_same_restart: XXXXX  # bool
19  tracer: XXXXX  # str
20  nlay: XXXXX  # int
21  levs: XXXXX  # str
22  eclevs: XXXXX  # str
23  projs: XXXXX  # list
24  make_options: XXXXX  # str
25  makedeps_dir: XXXXX  # str
26  fflags_gfortran: XXXXX  # str
27  ldflags_gfortran: XXXXX  # str
28  fflags_ifort: XXXXX  # str
29  ldflags_ifort: XXXXX  # str
30  meteo_macros: XXXXX  # list
31  model_macros: XXXXX  # list
32  mdf_macros: XXXXX  # list
33  optim_emis_type: XXXXX  # int
34  TCCON_FTS_list: XXXXX  # str

See also

API reference (functions & code)