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GETM setup Elbe 2D Warner
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ElbeXtreme
GETM setup Elbe 2D Warner
Commits
df0fdbc7
Commit
df0fdbc7
authored
4 months ago
by
Xiangyu Li
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Merge branch 'main' of helmholtz:dam-elbextreme/getm-setup-elbe-2d into main
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environment.yaml
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-327
42 additions, 327 deletions
environment.yaml
fabm.mspec.yaml
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fabm.mspec.yaml
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327 deletions
environment.yaml
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327
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df0fdbc7
...
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@@ -4,332 +4,47 @@
name
:
elbextreme
channels
:
-
conda-forge
-
defaults
dependencies
:
-
_r-mutex=1.0.1=anacondar_1
-
archspec=0.2.3=pyhd8ed1ab_0
-
aws-c-auth=0.7.22=h8a62e84_10
-
aws-c-cal=0.7.1=h94d0942_1
-
aws-c-common=0.9.23=h99b78c6_0
-
aws-c-compression=0.2.18=h94d0942_7
-
aws-c-event-stream=0.4.2=hb74cd8f_15
-
aws-c-http=0.8.2=had1507a_6
-
aws-c-io=0.14.10=hcdb10ff_1
-
aws-c-mqtt=0.10.4=h856d8ab_8
-
aws-c-s3=0.6.0=ha9fd6de_2
-
aws-c-sdkutils=0.1.16=h94d0942_3
-
aws-checksums=0.1.18=h94d0942_7
-
aws-crt-cpp=0.27.3=h9d3339c_2
-
aws-sdk-cpp=1.11.329=he6360a2_9
-
azure-core-cpp=1.13.0=hd01fc5c_0
-
azure-identity-cpp=1.8.0=h13ea094_2
-
azure-storage-blobs-cpp=12.12.0=hfde595f_0
-
azure-storage-common-cpp=12.7.0=hcf3b6fd_1
-
blosc=1.21.6=h5499902_0
-
boltons=24.0.0=pyhd8ed1ab_0
-
brotli-python=1.1.0=py312h9f69965_1
-
bwidget=1.9.14=hce30654_1
-
bzip2=1.0.8=h99b78c6_7
-
c-ares=1.33.0=h99b78c6_0
-
ca-certificates=2024.7.4=hf0a4a13_0
-
cairo=1.18.0=hb4a6bf7_3
-
cctools=986=h4c9edd9_3
-
cctools_osx-arm64=986=hf2da8af_3
-
certifi=2024.7.4=pyhd8ed1ab_0
-
cffi=1.17.0=py312h80c9ed6_0
-
cfitsio=4.4.1=h793ed5c_0
-
cftime=1.6.4=py312hbebd99a_0
-
charset-normalizer=3.3.2=pyhd8ed1ab_0
-
clang=18.1.8=default_h675cc0c_2
-
clang-18=18.1.8=default_h5c12605_2
-
clang_impl_osx-arm64=18.1.8=h2ae9ea5_19
-
clang_osx-arm64=18.1.8=h54d7cd3_19
-
clangxx=18.1.8=default_h675cc0c_2
-
clangxx_impl_osx-arm64=18.1.8=h555f467_19
-
clangxx_osx-arm64=18.1.8=h54d7cd3_19
-
cmake=3.30.2=had79d8f_0
-
colorama=0.4.6=pyhd8ed1ab_0
-
compiler-rt=18.1.8=h28df8ea_0
-
compiler-rt_osx-arm64=18.1.8=h56c4e69_0
-
conda=24.7.1=py312h81bd7bf_0
-
conda-libmamba-solver=24.7.0=pyhd8ed1ab_0
-
conda-package-handling=2.3.0=pyh7900ff3_0
-
conda-package-streaming=0.10.0=pyhd8ed1ab_0
-
curl=8.9.1=hbf5303f_0
-
distro=1.9.0=pyhd8ed1ab_0
-
expat=2.6.2=hebf3989_0
-
fmt=10.2.1=h2ffa867_0
-
font-ttf-dejavu-sans-mono=2.37=hab24e00_0
-
font-ttf-inconsolata=3.000=h77eed37_0
-
font-ttf-source-code-pro=2.038=h77eed37_0
-
font-ttf-ubuntu=0.83=h77eed37_2
-
fontconfig=2.14.2=h82840c6_0
-
fonts-conda-ecosystem=1=0
-
fonts-conda-forge=1=0
-
freetype=2.12.1=hadb7bae_2
-
freexl=2.0.0=hfbad9fb_0
-
fribidi=1.0.10=h27ca646_0
-
frozendict=2.4.4=py312h7e5086c_0
-
geos=3.12.2=h00cdb27_1
-
geotiff=1.7.3=h7e5fb84_2
-
gfortran=12.3.0=h1ca8e4b_1
-
gfortran_impl_osx-arm64=12.3.0=h53ed385_3
-
gfortran_osx-arm64=12.3.0=h57527a5_1
-
giflib=5.2.2=h93a5062_0
-
gmp=6.3.0=h7bae524_2
-
graphite2=1.3.13=hebf3989_1003
-
gsl=2.7=h6e638da_0
-
h2=4.1.0=pyhd8ed1ab_0
-
harfbuzz=9.0.0=h997cde5_1
-
hdf4=4.2.15=h2ee6834_7
-
hdf5=1.14.3=mpi_mpich_hb65fe4a_5
-
hpack=4.0.0=pyh9f0ad1d_0
-
hyperframe=6.0.1=pyhd8ed1ab_0
-
icu=75.1=hfee45f7_0
-
idna=3.7=pyhd8ed1ab_0
-
isl=0.26=imath32_h347afa1_101
-
json-c=0.17=he54c16a_1
-
jsonpatch=1.33=pyhd8ed1ab_0
-
jsonpointer=3.0.0=py312h81bd7bf_0
-
kealib=1.5.3=h848a2d4_1
-
krb5=1.21.3=h237132a_0
-
lcms2=2.16=ha0e7c42_0
-
ld64=711=h4c6efb1_3
-
ld64_osx-arm64=711=h5ecc89c_3
-
lerc=4.0.0=h9a09cb3_0
-
libabseil=20240116.2=cxx17_h00cdb27_1
-
libaec=1.1.3=hebf3989_0
-
libarchive=3.7.4=h83d404f_0
-
libasprintf=0.22.5=h8414b35_3
-
libblas=3.9.0=23_osxarm64_openblas
-
libcblas=3.9.0=23_osxarm64_openblas
-
libclang-cpp18.1=18.1.8=default_h5c12605_2
-
libcrc32c=1.1.2=hbdafb3b_0
-
libcurl=8.9.1=hfd8ffcc_0
-
libcxx=18.1.8=h5a72898_4
-
libdeflate=1.21=h99b78c6_0
-
libedit=3.1.20191231=hc8eb9b7_2
-
libev=4.33=h93a5062_2
-
libexpat=2.6.2=hebf3989_0
-
libffi=3.4.2=h3422bc3_5
-
libgdal=3.9.2=hce30654_0
-
libgdal-core=3.9.2=h6decb56_0
-
libgdal-fits=3.9.2=h7a7a030_0
-
libgdal-grib=3.9.2=hdd4b840_0
-
libgdal-hdf4=3.9.2=h94124bd_0
-
libgdal-hdf5=3.9.2=hf90b89a_0
-
libgdal-jp2openjpeg=3.9.2=h54bcb16_0
-
libgdal-kea=3.9.2=hacb1b3e_0
-
libgdal-netcdf=3.9.2=h1723b65_0
-
libgdal-pdf=3.9.2=h7ee6820_0
-
libgdal-pg=3.9.2=h7d28298_0
-
libgdal-postgisraster=3.9.2=h7d28298_0
-
libgdal-tiledb=3.9.2=h6fe8b47_0
-
libgdal-xls=3.9.2=hb39617b_0
-
libgettextpo=0.22.5=h8414b35_3
-
libgfortran=5.0.0=13_2_0_hd922786_3
-
libgfortran-devel_osx-arm64=12.3.0=hc62be1c_3
-
libgfortran5=13.2.0=hf226fd6_3
-
libglib=2.80.3=h59d46d9_2
-
libgoogle-cloud=2.26.0=hfe08963_0
-
libgoogle-cloud-storage=2.26.0=h1466eeb_0
-
libgrpc=1.62.2=h9c18a4f_0
-
libiconv=1.17=h0d3ecfb_2
-
libintl=0.22.5=h8414b35_3
-
libjpeg-turbo=3.0.0=hb547adb_1
-
libkml=1.3.0=h00ed6cc_1020
-
liblapack=3.9.0=23_osxarm64_openblas
-
libllvm18=18.1.8=h5090b49_2
-
libmamba=1.5.8=h90c426b_0
-
libmambapy=1.5.8=py312h344e357_0
-
libnetcdf=4.9.2=mpi_mpich_hf75f9b5_14
-
libnghttp2=1.58.0=ha4dd798_1
-
libopenblas=0.3.27=openmp_h517c56d_1
-
libpnetcdf=1.13.0=mpi_mpich_h0f1c85a_101
-
libpng=1.6.43=h091b4b1_0
-
libpq=16.4=h7afe498_0
-
libprotobuf=4.25.3=hbfab5d5_0
-
libre2-11=2023.09.01=h7b2c953_2
-
librttopo=1.1.0=h31fb324_16
-
libsolv=0.7.30=h6c9b7f8_0
-
libspatialite=5.1.0=hf7a34df_9
-
libsqlite=3.46.0=hfb93653_0
-
libssh2=1.11.0=h7a5bd25_0
-
libtiff=4.6.0=hf8409c0_4
-
libudunits2=2.2.28=h5f3f34b_3
-
libuv=1.48.0=h93a5062_0
-
libwebp-base=1.4.0=h93a5062_0
-
libxml2=2.12.7=h01dff8b_4
-
libzip=1.10.1=ha0bc3c6_3
-
libzlib=1.3.1=hfb2fe0b_1
-
llvm-openmp=18.1.8=hde57baf_1
-
llvm-tools=18.1.8=h5090b49_2
-
llvm-tools-18=18.1.8=h5090b49_2
-
lz4-c=1.9.4=hb7217d7_0
-
lzo=2.10=h93a5062_1001
-
make=4.3=he57ea6c_1
-
mamba=1.5.8=py312h14bc7db_0
-
menuinst=2.1.2=py312h81bd7bf_0
-
minizip=4.0.7=h27ee973_0
-
mosh=1.4.0=pl5321h54a41c2_8
-
mpc=1.3.1=h91ba8db_0
-
mpfr=4.2.1=h1cfca0a_2
-
mpi=1.0=mpich
-
mpich=4.2.2=h9ee2227_101
-
ncurses=6.5=hb89a1cb_0
-
netcdf-fortran=4.6.1=mpi_mpich_hf3c9fff_4
-
netcdf4=1.7.1=nompi_py312hec02768_101
-
nspr=4.35=hb7217d7_0
-
nss=3.103=hc42bcbf_0
-
numpy=2.1.0=py312hb544834_0
-
openjpeg=2.5.2=h9f1df11_0
-
openssl=3.3.1=h8359307_3
-
packaging=24.1=pyhd8ed1ab_0
-
pango=1.54.0=h9ee27a3_2
-
parallelio=2.6.3=mpi_mpich_h24e929f_100
-
pcre2=10.44=h297a79d_2
-
perl=5.32.1=7_h4614cfb_perl5
-
pip=24.2=pyhd8ed1ab_0
-
pixman=0.43.4=hebf3989_0
-
platformdirs=4.2.2=pyhd8ed1ab_0
-
pluggy=1.5.0=pyhd8ed1ab_0
-
poppler=24.08.0=h9787579_0
-
poppler-data=0.4.12=hd8ed1ab_0
-
postgresql=16.4=h2cc7dc1_0
-
proj=9.4.1=hfb94cee_1
-
pybind11-abi=4=hd8ed1ab_3
-
pycosat=0.6.6=py312h02f2b3b_0
-
pycparser=2.22=pyhd8ed1ab_0
-
pysocks=1.7.1=pyha2e5f31_6
-
python=3.12.5=h30c5eda_0_cpython
-
python_abi=3.12=5_cp312
-
pyyaml=6.0.2=py312h7e5086c_0
-
r=4.3=r43hd8ed1ab_1008
-
r-assertthat=0.2.1=r43hc72bb7e_5
-
r-base=4.3.3=h11bd7ca_14
-
r-boot=1.3_30=r43hc72bb7e_2
-
r-brio=1.1.5=r43h07cda29_1
-
r-callr=3.7.6=r43hc72bb7e_1
-
r-class=7.3_22=r43h07cda29_2
-
r-classint=0.4_10=r43h7807725_1
-
r-cli=3.6.3=r43hd76f289_1
-
r-cluster=2.1.6=r43h7807725_1
-
r-cmocean=0.3_1=r43h142f84f_0
-
r-codetools=0.2_20=r43hc72bb7e_1
-
r-colorspace=2.1_1=r43h07cda29_0
-
r-cpp11=0.4.7=r43hc72bb7e_1
-
r-crayon=1.5.3=r43hc72bb7e_1
-
r-dbi=1.2.3=r43hc72bb7e_1
-
r-desc=1.4.3=r43hc72bb7e_1
-
r-diffobj=0.3.5=r43h07cda29_3
-
r-digest=0.6.37=r43hd76f289_0
-
r-e1071=1.7_14=r43hd76f289_1
-
r-ellipsis=0.3.2=r43h07cda29_3
-
r-evaluate=0.24.0=r43hc72bb7e_1
-
r-fansi=1.0.6=r43h07cda29_1
-
r-farver=2.1.2=r43hd76f289_1
-
r-foreign=0.8_87=r43h07cda29_1
-
r-fs=1.6.4=r43hd76f289_1
-
r-generics=0.1.3=r43hc72bb7e_3
-
r-glue=1.7.0=r43h07cda29_1
-
r-gsw=1.2_0=r43hf400cd2_0
-
r-jsonlite=1.8.8=r43h07cda29_1
-
r-kernsmooth=2.23_24=r43h30ed03b_1
-
r-labeling=0.4.3=r43hc72bb7e_1
-
r-latex2exp=0.9.6=r43hc72bb7e_2
-
r-lattice=0.22_6=r43h07cda29_1
-
r-lifecycle=1.0.4=r43hc72bb7e_1
-
r-lubridate=1.9.3=r43h07cda29_1
-
r-magrittr=2.0.3=r43h07cda29_3
-
r-mass=7.3_60.0.1=r43h07cda29_1
-
r-matrix=1.6_5=r43hded8dfa_1
-
r-mgcv=1.9_1=r43h83b88f1_1
-
r-munsell=0.5.1=r43hc72bb7e_1
-
r-ncdf4=1.23=r43h140e699_0
-
r-nlme=3.1_165=r43h7807725_1
-
r-nnet=7.3_19=r43h07cda29_2
-
r-oce=1.8_3=r43h97112e6_0
-
r-pacman=0.5.1=r43hc72bb7e_3
-
r-pillar=1.9.0=r43hc72bb7e_2
-
r-pkgbuild=1.4.4=r43hc72bb7e_1
-
r-pkgconfig=2.0.3=r43hc72bb7e_4
-
r-pkgload=1.4.0=r43hc72bb7e_0
-
r-praise=1.0.0=r43hc72bb7e_1008
-
r-prettyunits=1.2.0=r43hc72bb7e_1
-
r-processx=3.8.4=r43h07cda29_1
-
r-proxy=0.4_27=r43h07cda29_3
-
r-ps=1.7.7=r43h07cda29_0
-
r-r6=2.5.1=r43hc72bb7e_3
-
r-rcolorbrewer=1.1_3=r43h785f33e_3
-
r-rcpp=1.0.13=r43hd76f289_0
-
r-recommended=4.3=r43hd8ed1ab_1007
-
r-rematch2=2.1.2=r43hc72bb7e_4
-
r-remotes=2.5.0=r43hc72bb7e_1
-
r-rlang=1.1.4=r43hd76f289_1
-
r-rpart=4.1.23=r43h07cda29_1
-
r-rprojroot=2.0.4=r43hc72bb7e_1
-
r-s2=1.1.7=r43h860579f_0
-
r-scales=1.3.0=r43hc72bb7e_1
-
r-sf=1.0_16=r43he0f40e3_8
-
r-spatial=7.3_17=r43h07cda29_1
-
r-stringi=1.8.4=r43h428a9ab_3
-
r-stringr=1.5.1=r43h785f33e_1
-
r-survival=3.7_0=r43h07cda29_1
-
r-teachingdemos=2.13=r43hc72bb7e_1
-
r-testthat=3.2.1.1=r43hd76f289_1
-
r-tibble=3.2.1=r43h07cda29_3
-
r-timechange=0.3.0=r43hd76f289_1
-
r-units=0.8_5=r43hd76f289_1
-
r-utf8=1.2.4=r43h07cda29_1
-
r-vctrs=0.6.5=r43hd76f289_1
-
r-viridislite=0.4.2=r43hc72bb7e_2
-
r-waldo=0.5.2=r43hc72bb7e_1
-
r-withr=3.0.1=r43hc72bb7e_0
-
r-wk=0.9.2=r43hd76f289_1
-
re2=2023.09.01=h4cba328_2
-
readline=8.2=h92ec313_1
-
reproc=14.2.4.post0=h93a5062_1
-
reproc-cpp=14.2.4.post0=h965bd2d_1
-
requests=2.32.3=pyhd8ed1ab_0
-
rhash=1.4.4=hb547adb_0
-
ruamel.yaml=0.18.6=py312he37b823_0
-
ruamel.yaml.clib=0.2.8=py312he37b823_0
-
setuptools=72.1.0=pyhd8ed1ab_0
-
sigtool=0.1.3=h44b9a77_0
-
six=1.16.0=pyh6c4a22f_0
-
snappy=1.2.1=hd02b534_0
-
spdlog=1.14.1=h9c441cc_0
-
sqlite=3.46.0=h5838104_0
-
tapi=1100.0.11=he4954df_0
-
tiledb=2.25.0=h5123ab7_3
-
tk=8.6.13=h5083fa2_1
-
tktable=2.10=h1e387b8_6
-
tornado=6.4.1=py312h7e5086c_0
-
tqdm=4.66.5=pyhd8ed1ab_0
-
truststore=0.8.0=pyhd8ed1ab_0
-
tzcode=2024a=h93a5062_0
-
tzdata=2024a=h0c530f3_0
-
uriparser=0.9.8=h00cdb27_0
-
urllib3=2.2.2=pyhd8ed1ab_1
-
wheel=0.44.0=pyhd8ed1ab_0
-
xerces-c=3.2.5=h0a46525_1
-
xmlstore=0.9.14=pyhd8ed1ab_0
-
xz=5.2.6=h57fd34a_0
-
yaml=0.2.5=h3422bc3_2
-
yaml-cpp=0.8.0=h13dd4ca_0
-
zlib=1.3.1=hfb2fe0b_1
-
zstandard=0.23.0=py312h721a963_0
-
zstd=1.5.6=hb46c0d2_0
-
cmake
-
fontconfig
-
geos
-
geotiff
-
gfortran
-
hdf5
-
libnetcdf
-
mpich
-
netcdf-fortran
-
netcdf4
-
numpy
-
pip
-
python=3.12
-
pyyaml
-
r-base
-
r-cluster
# - r-cmocean # seems not available in conda-forge channel
-
r-colorspace
-
r-latex2exp
-
r-matrix
-
r-ncdf4
-
r-pacman
-
r-pillar
-
r-rcolorbrewer
-
r-sf
-
r-spatial
-
r-stringi
-
r-stringr
-
r-teachingdemos
-
sqlite
-
xerces-c
-
xmlstore
-
yaml-cpp
-
fonttools
-
kiwisolver
-
matplotlib
-
pillow
-
pyparsing
-
python-dateutil
-
xmlplot
-
pip
:
-
contourpy==1.2.1
-
cycler==0.12.1
-
editscenario==0.11.7
-
fonttools==4.53.1
-
gotmgui==0.1.2
-
kiwisolver==1.4.5
-
matplotlib==3.9.2
-
pillow==10.4.0
-
pyparsing==3.1.2
-
python-dateutil==2.9.0.post0
-
xmlplot==0.9.29
\ No newline at end of file
-
editscenario
-
gotmgui
\ No newline at end of file
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fabm.mspec.yaml
0 → 100644
+
97
−
0
View file @
df0fdbc7
instances
:
nut
:
long_name
:
nutrient
model
:
examples/npzd/nut
initialization
:
c
:
5.5
# concentration (mmol m-3)
det
:
long_name
:
detritus
model
:
examples/npzd/det
parameters
:
w_d
:
-0.1
# vertical velocity (<0 for sinking) (m d-1), default = -5.0
kc
:
0.03
# specific light extinction (m2 mmol-1), default = 0.03
rdn
:
0.003
# remineralization rate (d-1), default = 0.003
initialization
:
c
:
5.5
# concentration (mmol m-3)
coupling
:
mineralisation_target
:
nut/c
# sink for remineralized matter (mmol m-3)
phy
:
long_name
:
phytoplankton2
model
:
mspec/phy
parameters
:
m0
:
0.0225
# background concentration (mmol m-3), default = 0.0225
rmn
:
0.01
# excretion rate (d-1), default = 0.01
rmd
:
0.02
# mortality (d-1), default = 0.02
rmax
:
1.0225
# maximum growth rate (d-1)
vmax
:
.95
# maximum uptake rate (d-1)
#clight: 0.02
#alpha: 1.3
initialization
:
c
:
0.1
# concentration (mmol m-3)
q
:
0.5
coupling
:
excretion_target
:
nut/c
# sink for excreted matter (mmol m-3)
mortality_target
:
det/c
# sink for dead matter (mmol m-3)
uptake_target
:
nut/c
# nutrient source (mmol m-3)
mixo
:
use
:
true
long_name
:
mixotroph
model
:
mspec/mspec
parameters
:
m0
:
0.00225
# background concentration (mmol m-3), default = 0.0225
rmn
:
0.01
# excretion rate (d-1), default = 0.01
rmd
:
0.02
# mortality (d-1), default = 0.02
rmax
:
.5
# maximum growth rate (d-1)
ha
:
1.
ia
:
true
# instantaneous acclimation (switch)
vmax
:
.8
rr
:
.10
alpha
:
1.6
clight
:
0.01
tau
:
0.7
initialization
:
c
:
0.01
# concentration (mmol m-3)
f
:
0.5
q
:
0.5
coupling
:
grazing_target
:
phy/c
# prey source (mmol m-3)
grazing_target_nutrient
:
phy/q
# prey nutrient content
excretion_target
:
nut/c
# sink for excreted matter (mmol m-3)
mortality_target
:
det/c
# sink for dead matter (mxmol m-3)
uptake_target
:
nut/c
# nutrient source (mmol m-3)
zoo
:
use
:
true
long_name
:
zooplankton
model
:
mspec/zoo
parameters
:
m0
:
0.0225
# background concentration (mmol m-3), default = 0.0225
rmax
:
0.5
# maximum specific grazing rate (d-1), default = 0.5
iv
:
.01
# Ivlev grazing constant (m3 mmol-1), default = 1.1
rmn
:
0.01
# excretion rate (d-1), default = 0.01
rmd
:
0.21
# mortality (d-1), default = 0.02
initialization
:
c
:
1e-2
# concentration (mmol m-3)
q
:
0.5
coupling
:
grazing_target
:
phy/c
# prey source (mmol m-3)
grazing_target_nutrient
:
phy/q
# prey nutrient content
excretion_target
:
nut/c
# sink for excreted matter (mmol m-3)
mortality_target
:
det/c
# sink for dead matter (mmol m-3)
zoo2
:
use
:
true
long_name
:
zooplankton2
model
:
mspec/zoo
parameters
:
m0
:
0.0225
# background concentration (mmol m-3), default = 0.0225
rmax
:
1.5
# maximum specific grazing rate (d-1), default = 0.5
iv
:
1.1
# Ivlev grazing constant (m3 mmol-1), default = 1.1
rmn
:
0.01
# excretion rate (d-1), default = 0.01
rmd
:
0.21
# mortality (d-1), default = 0.02
initialization
:
c
:
1e-2
# concentration (mmol m-3)
q
:
0.5
coupling
:
grazing_target
:
mixo/c
# prey source (mmol m-3)
grazing_target_nutrient
:
mixo/q
# prey nutrient content
excretion_target
:
nut/c
# sink for excreted matter (mmol m-3)
mortality_target
:
det/c
# sink for dead matter (mmol m-3)
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