TM5/std TM5/std

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

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:

model:
  plugin:
    name: TM5
    version: std
    type: model

    # Mandatory arguments
    direxec: XXXXX  # str
    auto_recompile: XXXXX  # bool
    make_clean: XXXXX  # bool
    fc: XXXXX  # str
    linker: XXXXX  # str

    # Optional arguments
    autoflush: XXXXX  # bool
    tracer: XXXXX  # str
    nlay: XXXXX  # int
    levs: XXXXX  # str
    eclevs: XXXXX  # str
    projs: XXXXX  # list
    make_options: XXXXX  # str
    makedeps_dir: XXXXX  # str
    fflags_gfortran: XXXXX  # str
    ldflags_gfortran: XXXXX  # str
    fflags_ifort: XXXXX  # str
    ldflags_ifort: XXXXX  # str
    meteo_macros: XXXXX  # list
    model_macros: XXXXX  # list
    mdf_macros: XXXXX  # list
    optim_emis_type: XXXXX  # int
    TCCON_FTS_list: XXXXX  # str