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Commit df0fdbc7 authored by Xiangyu Li's avatar 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
+ 42
− 327
View file @ df0fdbc7
......@@ -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
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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