diff --git a/.github/workflows/conda_pip.yml b/.github/workflows/conda_pip.yml index 8599938..b62ef39 100644 --- a/.github/workflows/conda_pip.yml +++ b/.github/workflows/conda_pip.yml @@ -40,6 +40,8 @@ jobs: - name: "Install Python dependencies" run: "pip install 'black'" + - run: "black --version" + - name: "Run linters" run: "black --diff ./" @@ -61,11 +63,14 @@ jobs: SCHISM_ENV: "SCHISM_ENV" DELFT3D_ENV: "DELFT3D_ENV" PYPOSEIDON_ENV: "PYPOSEIDON_ENV" + PYPOS_TEL_ENV: "PYPOS_TEL_ENV" # SCHISM_LOCK: locks/conda-${{ matrix.os }}-schism_${{ matrix.mpi }}.lock DELFT3D_LOCK: locks/conda-${{ matrix.os }}-delft3d_${{ matrix.mpi }}.lock PYPOSEIDON_LOCK: locks/conda-${{ matrix.os }}-binary-p${{ matrix.python }}.lock + PYPOS_TEL_LOCK: locks/conda-${{ matrix.os }}-binary-telemac-${{ matrix.mpi }}-p${{ matrix.python }}.lock REQUIREMENTS_CI: locks/requirements-ci.txt + REQUIREMENTS_CI_TEL: locks/requirements-ci-telemac.txt REQUIREMENTS_VIZ: locks/requirements-viz.txt defaults: @@ -92,6 +97,7 @@ jobs: channel_priority: strict channels: - gbrey + - tomsail - conda-forge EOF - run: cat ~/.condarc @@ -123,6 +129,16 @@ jobs: ${{ matrix.os }}-${{ matrix.python }}-${{ env.PYPOSEIDON_ENV }}-${{ hashFiles( env.PYPOSEIDON_LOCK )}} ${{ matrix.os }}-${{ matrix.python }}-${{ env.PYPOSEIDON_ENV }}- + - name: "Cache ${{ env.PYPOS_TEL_ENV }}" + uses: actions/cache@v3 + id: cache-PYPOS_TEL_ENV + with: + path: ~/micromamba/envs/${{ env.PYPOS_TEL_ENV }} + key: ${{ matrix.os }}-${{ matrix.python }}-${{ env.PYPOS_TEL_ENV }}-${{ hashFiles( env.PYPOS_TEL_LOCK )}}-${{ hashFiles( env.REQUIREMENTS_CI_TEL )}} + restore-keys: | + ${{ matrix.os }}-${{ matrix.python }}-${{ env.PYPOS_TEL_ENV }}-${{ hashFiles( env.PYPOS_TEL_LOCK )}} + ${{ matrix.os }}-${{ matrix.python }}-${{ env.PYPOS_TEL_ENV }}- + - name: Cache tests/data/ uses: actions/cache@v3 env: @@ -144,11 +160,9 @@ jobs: if: steps.cache-PYPOSEIDON_ENV.outputs.cache-hit != 'true' run: micromamba create --yes --name ${PYPOSEIDON_ENV} -f ${PYPOSEIDON_LOCK} - - name: "Check schism version" - run: | - eval "$(micromamba shell hook)" - micromamba activate "${SCHISM_ENV}" - schism -v + - name: "Create ${{ env.PYPOS_TEL_ENV }}" + if: steps.cache-PYPOS_TEL_ENV.outputs.cache-hit != 'true' + run: micromamba create --yes --name ${PYPOS_TEL_ENV} -f ${PYPOS_TEL_LOCK} - name: "Install python dependencies" run: | @@ -158,6 +172,14 @@ jobs: python -mpip install -r "${REQUIREMENTS_CI}" python -mpip install ./ + - name: "Install python dependencies for pyposeidon + telemac" + run: | + eval "$(micromamba shell hook)" + micromamba activate "${PYPOS_TEL_ENV}" + python -mpip install -U pip + python -mpip install -r "${REQUIREMENTS_CI_TEL}" + python -mpip install ./ + - name: "Run tests: Basic" run: | eval "$(micromamba shell hook)" @@ -178,14 +200,18 @@ jobs: run: | eval "$(micromamba shell hook)" micromamba activate "${SCHISM_ENV}" - # micromamba activate --stack "${DELFT3D_ENV}" micromamba activate --stack "${PYPOSEIDON_ENV}" make test_schism - name: "Run tests: Delft" run: | eval "$(micromamba shell hook)" - # micromamba activate "${SCHISM_ENV}" - micromamba activate --stack "${DELFT3D_ENV}" + micromamba activate "${DELFT3D_ENV}" micromamba activate --stack "${PYPOSEIDON_ENV}" make test_delft + + - name: "Run tests: TELEMAC" + run: | + eval "$(micromamba shell hook)" + micromamba activate "${PYPOS_TEL_ENV}" + make test_telemac diff --git a/Makefile b/Makefile index 14b5c79..c3603ad 100644 --- a/Makefile +++ b/Makefile @@ -6,10 +6,10 @@ init: poetry install -E viz --with dev --with docs --with test test: - pytest -vl --durations=10 -m 'not (schism or delft or viz or slow)' -n auto + pytest -vl --durations=10 -m 'not (schism or delft or telemac or viz or slow)' -n auto test_fail: - pytest -vl --lf --runschism --rundelft --runviz + pytest -vl --lf --runschism --rundelft --runtelemac --runviz test_viz: pytest -vl --durations=10 --runviz -m viz @@ -20,8 +20,11 @@ test_schism: test_delft: pytest -vl --durations=10 --rundelft -m delft +test_telemac: + pytest -vl --durations=10 --runtelemac -m telemac + test_full: - pytest -vl --durations=20 --runschism --rundelft --runviz + pytest -vl --durations=20 --runschism --rundelft --runtelemac --runviz conda_lock: ./scripts/generate_envs.sh @@ -32,6 +35,7 @@ poetry_lock: poetry export --without-hashes -f requirements.txt -o locks/requirements.txt poetry export --without-hashes -f requirements.txt --extras viz -o locks/requirements-viz.txt poetry export --without-hashes -f requirements.txt --with dev --with test -o locks/requirements-ci.txt + poetry export --without-hashes -f requirements.txt --with dev --with test --with telemac -o locks/requirements-ci-telemac.txt poetry export --without-hashes -f requirements.txt --extras viz --with dev --with docs --with test -o locks/requirements-full.txt lock: \ diff --git a/Tutorial/TELEMAC.ipynb b/Tutorial/TELEMAC.ipynb new file mode 100644 index 0000000..bd8a06b --- /dev/null +++ b/Tutorial/TELEMAC.ipynb @@ -0,0 +1,724 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "2e3e73eb", + "metadata": { + "tags": [] + }, + "source": [ + "# The Model module" + ] + }, + { + "cell_type": "markdown", + "id": "b55dcdc7", + "metadata": {}, + "source": [ + "The top module handles the main setup of the instance. \n", + "\n", + "\n", + "- Requires:\n", + "\n", + " - The data folder. See [README](README.md) in this folder." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c7dc5c43", + "metadata": {}, + "outputs": [], + "source": [ + "#to use the full width of the browser window\n", + "from IPython.display import display, HTML\n", + "display(HTML(\"\"))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "aca5a378", + "metadata": {}, + "outputs": [], + "source": [ + "# Not neccessarily needed. Just to check version. Must be >= 0.6\n", + "import pyposeidon\n", + "pyposeidon.__version__" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cac5ab42", + "metadata": {}, + "outputs": [], + "source": [ + "import pyposeidon.model as pm" + ] + }, + { + "cell_type": "markdown", + "id": "66071b72", + "metadata": {}, + "source": [ + "### Graphics" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "356b1f61", + "metadata": {}, + "outputs": [], + "source": [ + "import pyposeidon.utils.pplot # initialize matplolib accessor" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "dc0b09e2", + "metadata": {}, + "outputs": [], + "source": [ + "#optional\n", + "#pyposeidon.utils.pplot.__init__(dark_background=True) # set plt style for pplot graphics below" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "f2817124", + "metadata": {}, + "outputs": [], + "source": [ + "import pyposeidon.utils.hplot # initialize pyviz accessor" + ] + }, + { + "cell_type": "markdown", + "id": "6a6d2620", + "metadata": {}, + "source": [ + "- In order to have within the Notebook the executable binaries installed in the conda env of the Kernel we add the corresponding path to the env PATH. This is not needed when we are running from python." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4c745b1b", + "metadata": {}, + "outputs": [], + "source": [ + "#Create a folder to save the output\n", + "import os\n", + "if not os.path.exists('test'):\n", + " os.makedirs('test')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "9fb41bc5", + "metadata": {}, + "outputs": [], + "source": [ + "import numpy\n", + "cpath = numpy.__path__[0].split('/lib/')[0] # get the current kernel path\n", + "\n", + "os.environ['PATH'] += os.pathsep + cpath + '/bin' # add to PATH" + ] + }, + { + "cell_type": "markdown", + "id": "598b91bf", + "metadata": {}, + "source": [ + "## Setup" + ] + }, + { + "cell_type": "markdown", + "id": "93bcdedd", + "metadata": {}, + "source": [ + "The minimum information required is the geometry's extent. In the most simple case that is a lat/lon box that defines the area of interest. Without loss of generality we select below Iceland as a test case. Feel free to modify the coordinates. \n", + "\n", + "In addition, the coastlines need to be provided as internal boundaries. Without loss of generality, natural earth's 'intermediate' resolution (https://www.naturalearthdata.com/downloads/) is used here.\n", + "\n", + "The coastlines can be given as a shapefile or GeoDataFrame." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "15b6d59b", + "metadata": {}, + "outputs": [], + "source": [ + "# use cartopy to get coastlines\n", + "import cartopy.feature as cf\n", + "\n", + "cr='i'\n", + "\n", + "coast = cf.NaturalEarthFeature(\n", + " category='physical',\n", + " name='land',\n", + " scale='{}m'.format({'l':110, 'i':50, 'h':10}[cr]))" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5a2151f9", + "metadata": {}, + "outputs": [], + "source": [ + "import geopandas as gp\n", + "ne_i = gp.GeoDataFrame(geometry = [x for x in coast.geometries()])" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ae446407", + "metadata": {}, + "outputs": [], + "source": [ + "# observations: get SEASET data\n", + "import pandas as pd\n", + "seaset = pd.read_csv(\"https://raw.githubusercontent.com/tomsail/seaset/main/Notebooks/catalog_full.csv\",\n", + " index_col=0)\n", + "seaset.to_csv(\"data/seaset_full.csv\")\n", + "seaset.head()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a0d18560", + "metadata": {}, + "outputs": [], + "source": [ + "#define in a dictionary the properties of the model..\n", + "model={'solver_name':'telemac',\n", + " 'geometry':{'lon_min' : -25,'lon_max' : -12.,'lat_min' : 56.,'lat_max' : 74.},\n", + " 'coastlines':ne_i, # coastlines\n", + "# 'manning':.12, #uniform manning value\n", + "# 'windrot':0.00001, #uniform windrot value\n", + "# 'tag':'schism', # optional tag \n", + " 'mesh_generator' : 'jigsaw', # set mesh generator \n", + " 'start_date':'2017-10-1 0:0:0',\n", + " 'time_frame':'12H',\n", + " 'meteo_source' : ['./data/erai.grib'], #path to meteo files\n", + " 'dem_source' : './data/dem.nc', #path to dem file\n", + "# 'ncores': 4 , # optional number of cores\n", + " 'dt' : 50,\n", + " 'rpath':'./test/telemac/', #location of calc folder\n", + "# 'update':['all'], #set which component should be updated (meteo,dem,model)\n", + " 'monitor':True, # get time series for observation points\n", + " 'obs' : \"data/seaset_full.csv\",\n", + " }" + ] + }, + { + "cell_type": "markdown", + "id": "dbe6859d", + "metadata": {}, + "source": [ + "## Initialize" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a5579622", + "metadata": {}, + "outputs": [], + "source": [ + "#initialize a model\n", + "model['mesh_generator'] = 'jigsaw'\n", + "b = pm.set(**model)" + ] + }, + { + "cell_type": "markdown", + "id": "b798571e", + "metadata": {}, + "source": [ + "## Step by Step process" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "72e0ce36", + "metadata": {}, + "outputs": [], + "source": [ + "b.create()\n", + "b.mesh.Dataset.pplot.mesh()" + ] + }, + { + "cell_type": "markdown", + "id": "934a4e51", + "metadata": {}, + "source": [ + "TPXO tide have been implemented, but have not been tested in pyposeidon.\n", + "\n", + "We will show here a simple case of surge model, without tide forcing at the boundaries" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "287fad5a", + "metadata": {}, + "outputs": [], + "source": [ + "b.mesh.Dataset.type[:] = 'closed' # here for a surge application, we will close all boundaries" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "acdc35fb", + "metadata": {}, + "outputs": [], + "source": [ + "b.output()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c40436e9", + "metadata": {}, + "outputs": [], + "source": [ + "b.save() # saves the json model file" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b088274b", + "metadata": {}, + "outputs": [], + "source": [ + "b.set_obs() # setup station points" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "405739f1", + "metadata": {}, + "outputs": [], + "source": [ + "b.run() # execute" + ] + }, + { + "cell_type": "markdown", + "id": "4bb8672d", + "metadata": {}, + "source": [ + "## ... or simply in one step\n" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a8957dd6", + "metadata": {}, + "outputs": [], + "source": [ + "#initialize a model\n", + "b = pm.set(**model)\n", + "b.execute()" + ] + }, + { + "cell_type": "markdown", + "id": "4fd6fac9", + "metadata": {}, + "source": [ + "The various datasets incorporated in the model can be accessed independently as attributes, namely :" + ] + }, + { + "cell_type": "markdown", + "id": "7c966830", + "metadata": {}, + "source": [ + "- Meteo" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3adcd3b0", + "metadata": {}, + "outputs": [], + "source": [ + "#plt.figure() # xarray uses existing ax if any. You might need to create a new figure to do it separately.\n", + "b.meteo.Dataset.msl[2,:,:].plot()" + ] + }, + { + "cell_type": "markdown", + "id": "fda43cb1", + "metadata": {}, + "source": [ + "- Mesh" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e0cb7609", + "metadata": {}, + "outputs": [], + "source": [ + "b.mesh.Dataset.hplot.mesh() " + ] + }, + { + "cell_type": "markdown", + "id": "4245edff", + "metadata": {}, + "source": [ + "- Dem" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "ce61dd43", + "metadata": {}, + "outputs": [], + "source": [ + "b.dem.Dataset.elevation.plot()" + ] + }, + { + "cell_type": "markdown", + "id": "6301c07c", + "metadata": {}, + "source": [ + "- Coastlines" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "e7f11425", + "metadata": {}, + "outputs": [], + "source": [ + "b.coastlines.plot()" + ] + }, + { + "cell_type": "markdown", + "id": "a5c6208f", + "metadata": {}, + "source": [ + "- Boundaries" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "7ffdcae7", + "metadata": {}, + "outputs": [], + "source": [ + "b.mesh.boundary.show()" + ] + }, + { + "cell_type": "markdown", + "id": "3e936652", + "metadata": {}, + "source": [ + "## Output" + ] + }, + { + "cell_type": "markdown", + "id": "0642af80", + "metadata": {}, + "source": [ + "The output of the simulations could be in separate files (due to MPI) or specific folders. pyposeidon can incorporate the resulting Datasets with " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "edee32bb", + "metadata": {}, + "outputs": [], + "source": [ + "b.results(remove_zarr=False) # integrate output" + ] + }, + { + "cell_type": "markdown", + "id": "f614eb62", + "metadata": {}, + "source": [ + "using [xarray-selafin](https://github.com/seareport/xarray-selafin/) directly on the selafin files: " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "35a2c144", + "metadata": {}, + "outputs": [], + "source": [ + "import xarray as xr\n", + "out = xr.open_dataset(b.rpath + '/results_2D.slf', engine = 'selafin', lazy_loading = False)\n", + "out" + ] + }, + { + "cell_type": "markdown", + "id": "52dfbe98", + "metadata": {}, + "source": [ + "Or using xarray on the generated results: " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "5ed5d149", + "metadata": {}, + "outputs": [], + "source": [ + "! tar -xvf test/telemac/outputs/out_2D.zarr.tar" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "10a1de6a", + "metadata": {}, + "outputs": [], + "source": [ + "out = xr.open_dataset('out_2D.zarr')\n", + "out" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b4256c07", + "metadata": {}, + "outputs": [], + "source": [ + "out.pplot.mesh(x='longitude', y = 'latitude', e='face_nodes')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "88bd5215", + "metadata": {}, + "outputs": [], + "source": [ + "it = 2\n", + "u, v = out.u.isel(time = it).values, out.v.isel(time = it).values\n", + "out.pplot.quiver(x='longitude', y = 'latitude', it = 2, u=u, v=v, scale=.5, title='hvel', color='k')" + ] + }, + { + "cell_type": "markdown", + "id": "fc1eeecd", + "metadata": {}, + "source": [ + "### with hvplot" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a0cf4968", + "metadata": {}, + "outputs": [], + "source": [ + "out.hplot.contourf(var='depth')#,tiles=True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3084498c", + "metadata": {}, + "outputs": [], + "source": [ + "out.hplot.mesh(width=800, height=400,tiles=True)" + ] + }, + { + "cell_type": "markdown", + "id": "dab51e7b", + "metadata": {}, + "source": [ + "### Animate" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "494c484d", + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np \n", + "v = out.pplot.frames(x='longitude', \n", + " y = 'latitude', \n", + " e='face_nodes',\n", + " var='elev',\n", + " title='SSH', \n", + " vmin = -.5, \n", + " vmax =.5) # change to hplot for holoviews\n", + "v" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "37ad3906", + "metadata": {}, + "outputs": [], + "source": [ + "v.save('test/elev.mp4')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "b06c0fd4", + "metadata": {}, + "outputs": [], + "source": [ + "u, v = out.u.values, out.v.values\n", + "out.pplot.qframes(x='longitude', \n", + " y = 'latitude', \n", + " e='face_nodes',\n", + " u=u,v=v,title='Vel',scale=.5)#, color='w')" + ] + }, + { + "cell_type": "markdown", + "id": "9741c129", + "metadata": {}, + "source": [ + "## Read Model" + ] + }, + { + "cell_type": "markdown", + "id": "dcb38bee", + "metadata": {}, + "source": [ + "If a model is created by `pyposeidon` then there is a `json` file that describes the model. Such a file can be read into `pyposeidon` with " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c5c0555f", + "metadata": {}, + "outputs": [], + "source": [ + "a = pyposeidon.model.read('test/telemac/telemac2d_model.json')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "80e32da8", + "metadata": {}, + "outputs": [], + "source": [ + "a.execute()" + ] + }, + { + "cell_type": "markdown", + "id": "12ec7eeb", + "metadata": {}, + "source": [ + "However, there might be a model created by other means. `pyposeidon` does its best to incorporate such model with" + ] + }, + { + "cell_type": "markdown", + "id": "aacd277e", + "metadata": {}, + "source": [ + "TELEMAC Works up until here \n", + "\n", + "`read_folder()` class function is yet to be implemented" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "39a6005e", + "metadata": {}, + "outputs": [], + "source": [ + "c = pm.set(solver_name='telemac', rfolder = './test/telemac/', load_geo=True, load_meteo=True)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "3f5254c4", + "metadata": {}, + "outputs": [], + "source": [ + "c.mesh.Dataset" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "c2b4eaac", + "metadata": {}, + "outputs": [], + "source": [ + "c.meteo.Dataset" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.13" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/dependencies/telemac_mpich.yml b/dependencies/telemac_mpich.yml new file mode 100644 index 0000000..b3214a3 --- /dev/null +++ b/dependencies/telemac_mpich.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - tomsail +dependencies: + - opentelemac=main*=mpich* diff --git a/dependencies/telemac_openmpi.yml b/dependencies/telemac_openmpi.yml new file mode 100644 index 0000000..467520b --- /dev/null +++ b/dependencies/telemac_openmpi.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - tomsail +dependencies: + - opentelemac=main*=openmpi* diff --git a/environments/binary-telemac-mpich-p3.10.yml b/environments/binary-telemac-mpich-p3.10.yml new file mode 100644 index 0000000..97a0900 --- /dev/null +++ b/environments/binary-telemac-mpich-p3.10.yml @@ -0,0 +1,16 @@ +channels: + - conda-forge + - gbrey + - tomsail +dependencies: + - compilers + - eccodes + - ffmpeg + - gdal + - geos + - gmsh>=4.9.3 + - jigsaw>=0.9.12 + - opentelemac=main*=mpich* + - pip + - proj + - python=3.10 diff --git a/environments/binary-telemac-mpich-p3.11.yml b/environments/binary-telemac-mpich-p3.11.yml new file mode 100644 index 0000000..36b91ae --- /dev/null +++ b/environments/binary-telemac-mpich-p3.11.yml @@ -0,0 +1,16 @@ +channels: + - conda-forge + - gbrey + - tomsail +dependencies: + - compilers + - eccodes + - ffmpeg + - gdal + - geos + - gmsh>=4.9.3 + - jigsaw>=0.9.12 + - opentelemac=main*=mpich* + - pip + - proj + - python=3.11 diff --git a/environments/binary-telemac-mpich-p3.9.yml b/environments/binary-telemac-mpich-p3.9.yml new file mode 100644 index 0000000..f1af5ab --- /dev/null +++ b/environments/binary-telemac-mpich-p3.9.yml @@ -0,0 +1,16 @@ +channels: + - conda-forge + - gbrey + - tomsail +dependencies: + - compilers + - eccodes + - ffmpeg + - gdal + - geos + - gmsh>=4.9.3 + - jigsaw>=0.9.12 + - opentelemac=main*=mpich* + - pip + - proj + - python=3.9 diff --git a/environments/binary-telemac-openmpi-p3.10.yml b/environments/binary-telemac-openmpi-p3.10.yml new file mode 100644 index 0000000..4014660 --- /dev/null +++ b/environments/binary-telemac-openmpi-p3.10.yml @@ -0,0 +1,16 @@ +channels: + - conda-forge + - gbrey + - tomsail +dependencies: + - compilers + - eccodes + - ffmpeg + - gdal + - geos + - gmsh>=4.9.3 + - jigsaw>=0.9.12 + - opentelemac=main*=openmpi* + - pip + - proj + - python=3.10 diff --git a/environments/binary-telemac-openmpi-p3.11.yml b/environments/binary-telemac-openmpi-p3.11.yml new file mode 100644 index 0000000..7c04431 --- /dev/null +++ b/environments/binary-telemac-openmpi-p3.11.yml @@ -0,0 +1,16 @@ +channels: + - conda-forge + - gbrey + - tomsail +dependencies: + - compilers + - eccodes + - ffmpeg + - gdal + - geos + - gmsh>=4.9.3 + - jigsaw>=0.9.12 + - opentelemac=main*=openmpi* + - pip + - proj + - python=3.11 diff --git a/environments/binary-telemac-openmpi-p3.9.yml b/environments/binary-telemac-openmpi-p3.9.yml new file mode 100644 index 0000000..81b2bce --- /dev/null +++ b/environments/binary-telemac-openmpi-p3.9.yml @@ -0,0 +1,16 @@ +channels: + - conda-forge + - gbrey + - tomsail +dependencies: + - compilers + - eccodes + - ffmpeg + - gdal + - geos + - gmsh>=4.9.3 + - jigsaw>=0.9.12 + - opentelemac=main*=openmpi* + - pip + - proj + - python=3.9 diff --git a/locks/binary-p3.10.yml b/locks/binary-p3.10.yml index 2c56268..e874f7d 100644 --- a/locks/binary-p3.10.yml +++ b/locks/binary-p3.10.yml @@ -601,7 +601,6 @@ package: harfbuzz: '>=9.0.0,<10.0a0' lame: '>=3.100,<3.101.0a0' libass: '>=0.17.1,<0.17.2.0a0' - libgcc-ng: '>=12' libiconv: '>=1.17,<2.0a0' libopenvino: '>=2024.2.0,<2024.2.1.0a0' libopenvino-auto-batch-plugin: '>=2024.2.0,<2024.2.1.0a0' @@ -1225,66 +1224,27 @@ package: category: main optional: false - name: gettext - version: 0.22.5 + version: 0.21.1 manager: conda platform: linux-64 dependencies: - gettext-tools: 0.22.5 - libasprintf: 0.22.5 - libasprintf-devel: 0.22.5 libgcc-ng: '>=12' - libgettextpo: 0.22.5 - libgettextpo-devel: 0.22.5 - libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/gettext-0.22.5-h59595ed_2.conda + url: https://conda.anaconda.org/conda-forge/linux-64/gettext-0.21.1-h27087fc_0.tar.bz2 hash: - md5: 219ba82e95d7614cf7140d2a4afc0926 - sha256: 386181254ddd2aed1fccdfc217da5b6545f6df4e9979ad8e08f5e91e22eaf7dc + md5: 14947d8770185e5153fdd04d4673ed37 + sha256: 4fcfedc44e4c9a053f0416f9fc6ab6ed50644fca3a761126dbd00d09db1f546a category: main optional: false - name: gettext - version: 0.22.5 - manager: conda - platform: osx-64 - dependencies: - gettext-tools: 0.22.5 - libasprintf: 0.22.5 - libasprintf-devel: 0.22.5 - libcxx: '>=16' - libgettextpo: 0.22.5 - libgettextpo-devel: 0.22.5 - libiconv: '>=1.17,<2.0a0' - libintl: 0.22.5 - libintl-devel: 0.22.5 - url: https://conda.anaconda.org/conda-forge/osx-64/gettext-0.22.5-h5ff76d1_2.conda - hash: - md5: c09b3dcf2adc5a2a32d11ab90289b8fa - sha256: ba9a4680b018a4ca517ec20beb25b09c97e293ecd16b931075e689db10291712 - category: main - optional: false -- name: gettext-tools - version: 0.22.5 - manager: conda - platform: linux-64 - dependencies: - libgcc-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/gettext-tools-0.22.5-h59595ed_2.conda - hash: - md5: 985f2f453fb72408d6b6f1be0f324033 - sha256: 67d7b1d6fe4f1c516df2000640ec7dcfebf3ff6ea0785f0276870e730c403d33 - category: main - optional: false -- name: gettext-tools - version: 0.22.5 + version: 0.21.1 manager: conda platform: osx-64 dependencies: libiconv: '>=1.17,<2.0a0' - libintl: 0.22.5 - url: https://conda.anaconda.org/conda-forge/osx-64/gettext-tools-0.22.5-h5ff76d1_2.conda + url: https://conda.anaconda.org/conda-forge/osx-64/gettext-0.21.1-h8a4c099_0.tar.bz2 hash: - md5: 37e1cb0efeff4d4623a6357e37e0105d - sha256: 4db71a66340d068c57e16c574c356db6df54ac0147b5b26d3313093f7854ee6d + md5: 1e3aff29ce703d421c43f371ad676cc5 + sha256: 915d3cd2d777b9b3fc2e87a25901b8e4a6aa1b2b33cf2ba54e9e9ed4f6b67d94 category: main optional: false - name: gfortran @@ -1526,12 +1486,12 @@ package: manager: conda platform: linux-64 dependencies: - libgcc-ng: '>=12' - libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda + libgcc-ng: '>=7.5.0' + libstdcxx-ng: '>=7.5.0' + url: https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h58526e2_1001.tar.bz2 hash: - md5: f87c7b7c2cb45f323ffbce941c78ab7c - sha256: 0595b009f20f8f60f13a6398e7cdcbd2acea5f986633adcf85f5a2283c992add + md5: 8c54672728e8ec6aa6db90cf2806d220 + sha256: 65da967f3101b737b08222de6a6a14e20e480e7d523a5d1e19ace7b960b5d6b1 category: main optional: false - name: graphite2 @@ -1539,11 +1499,11 @@ package: manager: conda platform: osx-64 dependencies: - libcxx: '>=16' - url: https://conda.anaconda.org/conda-forge/osx-64/graphite2-1.3.13-h73e2aa4_1003.conda + libcxx: '>=10.0.1' + url: https://conda.anaconda.org/conda-forge/osx-64/graphite2-1.3.13-h2e338ed_1001.tar.bz2 hash: - md5: fc7124f86e1d359fc5d878accd9e814c - sha256: b71db966e47cd83b16bfcc2099b8fa87c07286f24a0742078fede4c84314f91a + md5: 5f6e7f98caddd0fc2d345b207531814c + sha256: 1dba68533e6888c5e2a7e37119a77d6f388fb82721c530ba3bd28d541828e59b category: main optional: false - name: gxx @@ -1760,7 +1720,6 @@ package: platform: linux-64 dependencies: freeglut: '>=3.2.2,<4.0a0' - libgcc-ng: '>=12' libglu: '>=9.0.0,<10.0a0' libjpeg-turbo: '>=3.0.0,<4.0a0' url: https://conda.anaconda.org/conda-forge/linux-64/jasper-4.2.4-h536e39c_0.conda @@ -2052,28 +2011,28 @@ package: category: main optional: false - name: libaec - version: 1.1.3 + version: 1.1.2 manager: conda platform: linux-64 dependencies: libgcc-ng: '>=12' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.2-h59595ed_1.conda hash: - md5: 5e97e271911b8b2001a8b71860c32faa - sha256: 2ef420a655528bca9d269086cf33b7e90d2f54ad941b437fb1ed5eca87cee017 + md5: 127b0be54c1c90760d7fe02ea7a56426 + sha256: fdde15e74dc099ab1083823ec0f615958e53d9a8fae10405af977de251668bea category: main optional: false - name: libaec - version: 1.1.3 + version: 1.1.2 manager: conda platform: osx-64 dependencies: - libcxx: '>=16' - url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.3-h73e2aa4_0.conda + libcxx: '>=15.0.7' + url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.2-he965462_1.conda hash: - md5: 66d3c1f6dd4636216b4fca7a748d50eb - sha256: dae5921339c5d89f4bf58a95fd4e9c76270dbf7f6a94f3c5081b574905fcccf8 + md5: faa179050abc6af1385e0fe9dd074f91 + sha256: 1b0a0b9b67e8f155ebdc7205a7421c7aff4850a740fc9f88b3fa23282c98ed72 category: main optional: false - name: libarchive @@ -2117,55 +2076,6 @@ package: sha256: 9e46db25e976630e6738b351d76d9b79047ae232638b82f9f45eba774caaef8a category: main optional: false -- name: libasprintf - 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category: main - optional: false -- name: libasprintf-devel - version: 0.22.5 - manager: conda - platform: osx-64 - dependencies: - libasprintf: 0.22.5 - url: https://conda.anaconda.org/conda-forge/osx-64/libasprintf-devel-0.22.5-h5ff76d1_2.conda - hash: - md5: c7182eda3bc727384e2f98f4d680fa7d - sha256: 39fa757378b49993142013c1f69dd56248cc3703c2f04c5bcf4cc4acdc644ae3 - category: main - optional: false - name: libass version: 0.17.1 manager: conda @@ -2209,11 +2119,11 @@ package: manager: conda platform: linux-64 dependencies: - libopenblas: '>=0.3.27,<1.0a0' - url: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-22_linux64_openblas.conda + libopenblas: '>=0.3.26,<1.0a0' + url: https://conda.anaconda.org/conda-forge/linux-64/libblas-3.9.0-21_linux64_openblas.conda hash: - md5: 1a2a0cd3153464fee6646f3dd6dad9b8 - sha256: 082b8ac20d43a7bbcdc28b3b1cd40e4df3a8b5daf0a2d23d68953a44d2d12c1b + md5: 0ac9f44fc096772b0aa092119b00c3ca + sha256: ebd5c91f029f779fb88a1fcbd1e499559a9c258e3674ff58a2fbb4e375ae56d9 category: main optional: false - name: libblas @@ -2221,11 +2131,11 @@ package: manager: conda platform: osx-64 dependencies: - libopenblas: '>=0.3.27,<1.0a0' - url: https://conda.anaconda.org/conda-forge/osx-64/libblas-3.9.0-22_osx64_openblas.conda + libopenblas: '>=0.3.26,<1.0a0' + url: https://conda.anaconda.org/conda-forge/osx-64/libblas-3.9.0-21_osx64_openblas.conda hash: - md5: b80966a8c8dd0b531f8e65f709d732e8 - sha256: d72060239f904b3a81d2329efcf84dc62c2dfd66dbc4efc8dcae1afdf8f02b59 + md5: 23286066c595986aa0df6452a8416c08 + sha256: 5381eab20f4793996cf22e58461ea8a3a4dff1442bb45663b5920f2d26288688 category: main optional: false - name: libcblas @@ -2234,10 +2144,10 @@ package: platform: linux-64 dependencies: libblas: 3.9.0 - url: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-22_linux64_openblas.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libcblas-3.9.0-21_linux64_openblas.conda hash: - md5: 4b31699e0ec5de64d5896e580389c9a1 - sha256: da1b2faa017663c8f5555c1c5518e96ac4cd8e0be2a673c1c9e2cb8507c8fe46 + md5: 4a3816d06451c4946e2db26b86472cb6 + sha256: 467bbfbfe1a1aeb8b1f9f6485eedd8ed1b6318941bf3702da72336ccf4dc25a6 category: main optional: false - name: libcblas @@ -2246,10 +2156,10 @@ package: platform: osx-64 dependencies: libblas: 3.9.0 - url: https://conda.anaconda.org/conda-forge/osx-64/libcblas-3.9.0-22_osx64_openblas.conda + url: https://conda.anaconda.org/conda-forge/osx-64/libcblas-3.9.0-21_osx64_openblas.conda hash: - md5: b9fef82772330f61b2b0201c72d2c29b - sha256: 6a2ba9198e2320c3e22fe3d121310cf8a8ac663e94100c5693b34523fcb3cc04 + md5: 7a1b54774bad723e8ba01ca48eb301b5 + sha256: e2b1455612d4cfb3ac3170f0c538516ebd0b113780ac6603338245354e1b2f02 category: main optional: false - name: libclang-cpp16 @@ -2314,26 +2224,26 @@ package: category: main optional: false - name: libdeflate - version: '1.20' + version: '1.19' manager: conda platform: linux-64 dependencies: libgcc-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.20-hd590300_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.19-hd590300_0.conda hash: - md5: 8e88f9389f1165d7c0936fe40d9a9a79 - sha256: f8e0f25c382b1d0b87a9b03887a34dbd91485453f1ea991fef726dba57373612 + md5: 1635570038840ee3f9c71d22aa5b8b6d + sha256: 985ad27aa0ba7aad82afa88a8ede6a1aacb0aaca950d710f15d85360451e72fd category: main optional: false - name: libdeflate - version: '1.20' + version: '1.19' manager: conda platform: osx-64 dependencies: {} - url: https://conda.anaconda.org/conda-forge/osx-64/libdeflate-1.20-h49d49c5_0.conda + url: https://conda.anaconda.org/conda-forge/osx-64/libdeflate-1.19-ha4e1b8e_0.conda hash: - md5: d46104f6a896a0bc6a1d37b88b2edf5c - sha256: 8c2087952db55c4118dd2e29381176a54606da47033fd61ebb1b0f4391fcd28d + md5: 6a45f543c2beb40023df5ee7e3cedfbd + sha256: d0f789120fedd0881b129aba9993ec5dcf0ecca67a71ea20c74394e41adcb503 category: main optional: false - name: libdrm @@ -2525,8 +2435,8 @@ package: libarchive: '>=3.7.4,<3.8.0a0' libcurl: '>=8.8.0,<9.0a0' libcxx: '>=16' - libdeflate: '>=1.20,<1.21.0a0' - libexpat: '>=2.6.2,<3.0a0' + libdeflate: '>=1.19,<1.20.0a0' + libexpat: '>=2.6.1,<3.0a0' libiconv: '>=1.17,<2.0a0' libjpeg-turbo: '>=3.0.0,<4.0a0' libkml: '>=1.3.0,<1.4.0a0' @@ -2802,31 +2712,6 @@ package: sha256: 54430e45dffa8cbe3cbf12a3f4376947e7e2d50c67db90a90e91c3350510823e category: main optional: false -- name: libintl - 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name: x264 @@ -5181,7 +5066,7 @@ package: category: main optional: false - name: xorg-libx11 - version: 1.8.9 + version: 1.8.7 manager: conda platform: linux-64 dependencies: @@ -5197,7 +5082,7 @@ package: category: main optional: false - name: xorg-libx11 - version: 1.8.9 + version: 1.8.7 manager: conda platform: osx-64 dependencies: diff --git a/locks/binary-p3.9.yml b/locks/binary-p3.9.yml index fc149eb..aa62a0d 100644 --- a/locks/binary-p3.9.yml +++ b/locks/binary-p3.9.yml @@ -601,7 +601,6 @@ package: harfbuzz: '>=9.0.0,<10.0a0' lame: '>=3.100,<3.101.0a0' libass: '>=0.17.1,<0.17.2.0a0' - libgcc-ng: '>=12' libiconv: '>=1.17,<2.0a0' libopenvino: '>=2024.2.0,<2024.2.1.0a0' libopenvino-auto-batch-plugin: '>=2024.2.0,<2024.2.1.0a0' @@ -1225,66 +1224,27 @@ package: category: main optional: false - name: gettext - version: 0.22.5 + version: 0.21.1 manager: conda platform: linux-64 dependencies: - gettext-tools: 0.22.5 - libasprintf: 0.22.5 - libasprintf-devel: 0.22.5 libgcc-ng: '>=12' - libgettextpo: 0.22.5 - 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url: https://conda.anaconda.org/conda-forge/osx-64/libtiff-4.6.0-h129831d_3.conda + url: https://conda.anaconda.org/conda-forge/osx-64/libtiff-4.6.0-h684deea_2.conda hash: - md5: 568593071d2e6cea7b5fc1f75bfa10ca - sha256: f9b35c5ec1aea9a2cc20e9275a0bb8f056482faa8c5a62feb243ed780755ea30 + md5: 2ca10a325063e000ad6d2a5900061e0d + sha256: 1ef5bd7295f4316b111f70ad21356fb9f0de50b85a341cac9e3a61ac6487fdf1 category: main optional: false - name: libunistring @@ -4133,11 +4018,11 @@ package: manager: conda platform: osx-64 dependencies: - gmp: '>=6.3.0,<7.0a0' - url: https://conda.anaconda.org/conda-forge/osx-64/mpfr-4.2.1-h4f6b447_1.conda + gmp: '>=6.2.1,<7.0a0' + url: https://conda.anaconda.org/conda-forge/osx-64/mpfr-4.2.1-h0c69b56_0.conda hash: - md5: b90df08f0deb2f58631447c1462c92a7 - sha256: 002209e7d1f21cdd04de17050ab2050de4347e5bf04210ce6a636cbabf43e1d0 + md5: d545aecded064848432bc994075dfccf + sha256: e7c93a5399661b0528981c6fd53e8614eee3f9ba97f92e8167c092c4a5d9368c category: main optional: false - 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DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV binary-telemac-mpich-p3.10.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile binary-telemac-mpich-p3.10.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f ../environments/binary-telemac-mpich-p3.10.yml --lockfile binary-telemac-mpich-p3.10.yml +version: 1 +metadata: + content_hash: + linux-64: 080812959e7a80d4bc7c5e532c369c75322a1875d1437f1b2ea3ba1e138302c7 + channels: + - url: conda-forge + used_env_vars: [] + - url: gbrey + used_env_vars: [] + - url: tomsail + used_env_vars: [] + platforms: + - linux-64 + sources: + - ../environments/binary-telemac-mpich-p3.10.yml 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optional: false diff --git a/locks/binary-telemac-mpich-p3.11.yml b/locks/binary-telemac-mpich-p3.11.yml new file mode 100644 index 0000000..b8acce7 --- /dev/null +++ b/locks/binary-telemac-mpich-p3.11.yml @@ -0,0 +1,4565 @@ +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV binary-telemac-mpich-p3.11.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile binary-telemac-mpich-p3.11.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f ../environments/binary-telemac-mpich-p3.11.yml --lockfile binary-telemac-mpich-p3.11.yml +version: 1 +metadata: + content_hash: + linux-64: f473efcedd6e22a16154cb5740fb21afaec2a8536bdad8247fe375a2e1a5af0c + channels: + - url: conda-forge + used_env_vars: [] + - url: gbrey + used_env_vars: [] + - url: tomsail + used_env_vars: [] + platforms: + - linux-64 + sources: + - ../environments/binary-telemac-mpich-p3.11.yml 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DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV binary-telemac-openmpi-p3.10.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile binary-telemac-openmpi-p3.10.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f ../environments/binary-telemac-openmpi-p3.10.yml --lockfile binary-telemac-openmpi-p3.10.yml +version: 1 +metadata: + content_hash: + linux-64: 0ede2a903d0e663faa7b47a9ad32ce50c4d0638b93c3a9b9a6734fa8e7ac78e5 + channels: + - url: conda-forge + used_env_vars: [] + - url: gbrey + used_env_vars: [] + - url: tomsail + used_env_vars: [] + platforms: + - linux-64 + sources: + - 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optional: false diff --git a/locks/binary-telemac-openmpi-p3.11.yml b/locks/binary-telemac-openmpi-p3.11.yml new file mode 100644 index 0000000..64ad86e --- /dev/null +++ b/locks/binary-telemac-openmpi-p3.11.yml @@ -0,0 +1,4567 @@ +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV binary-telemac-openmpi-p3.11.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile binary-telemac-openmpi-p3.11.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f ../environments/binary-telemac-openmpi-p3.11.yml --lockfile binary-telemac-openmpi-p3.11.yml +version: 1 +metadata: + content_hash: + linux-64: 22ba93cf398a1a83842de7e3903bd201f257560a559f30ee7f835eb12ec27cff + channels: + - url: conda-forge + used_env_vars: [] + - url: gbrey + used_env_vars: [] + - url: tomsail + used_env_vars: [] + platforms: + - linux-64 + sources: + - 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Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV binary-telemac-openmpi-p3.9.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile binary-telemac-openmpi-p3.9.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f ../environments/binary-telemac-openmpi-p3.9.yml --lockfile binary-telemac-openmpi-p3.9.yml +version: 1 +metadata: + content_hash: + linux-64: 30011127cde2eec967e481e3b08cf2e0604bb450223c148d14130533c1c2edfc + channels: + - url: conda-forge + used_env_vars: [] + - url: gbrey + used_env_vars: [] + - url: tomsail + used_env_vars: [] + platforms: + - linux-64 + sources: + - 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fdde15e74dc099ab1083823ec0f615958e53d9a8fae10405af977de251668bea category: main optional: false - name: libaec - version: 1.1.3 + version: 1.1.2 manager: conda platform: osx-64 dependencies: - libcxx: '>=16' - url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.3-h73e2aa4_0.conda + libcxx: '>=15.0.7' + url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.2-he965462_1.conda hash: - md5: 66d3c1f6dd4636216b4fca7a748d50eb - sha256: dae5921339c5d89f4bf58a95fd4e9c76270dbf7f6a94f3c5081b574905fcccf8 + md5: faa179050abc6af1385e0fe9dd074f91 + sha256: 1b0a0b9b67e8f155ebdc7205a7421c7aff4850a740fc9f88b3fa23282c98ed72 category: main optional: false - name: libcurl diff --git a/locks/delft3d_openmpi.yml b/locks/delft3d_openmpi.yml index c2b2831..6082a26 100644 --- a/locks/delft3d_openmpi.yml +++ b/locks/delft3d_openmpi.yml @@ -356,28 +356,28 @@ package: category: main optional: false - name: libaec - version: 1.1.3 + version: 1.1.2 manager: conda platform: linux-64 dependencies: libgcc-ng: '>=12' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.2-h59595ed_1.conda hash: - md5: 5e97e271911b8b2001a8b71860c32faa - sha256: 2ef420a655528bca9d269086cf33b7e90d2f54ad941b437fb1ed5eca87cee017 + md5: 127b0be54c1c90760d7fe02ea7a56426 + sha256: fdde15e74dc099ab1083823ec0f615958e53d9a8fae10405af977de251668bea category: main optional: false - name: libaec - version: 1.1.3 + version: 1.1.2 manager: conda platform: osx-64 dependencies: - libcxx: '>=16' - url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.3-h73e2aa4_0.conda + libcxx: '>=15.0.7' + url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.2-he965462_1.conda hash: - md5: 66d3c1f6dd4636216b4fca7a748d50eb - sha256: dae5921339c5d89f4bf58a95fd4e9c76270dbf7f6a94f3c5081b574905fcccf8 + md5: faa179050abc6af1385e0fe9dd074f91 + sha256: 1b0a0b9b67e8f155ebdc7205a7421c7aff4850a740fc9f88b3fa23282c98ed72 category: main optional: false - name: libcurl diff --git a/locks/requirements-ci-telemac.txt b/locks/requirements-ci-telemac.txt new file mode 100644 index 0000000..dea048b --- /dev/null +++ b/locks/requirements-ci-telemac.txt @@ -0,0 +1,113 @@ +affine==2.4.0 ; python_version >= "3.9" and python_version < "4" +annotated-types==0.6.0 ; python_version >= "3.9" and python_version < "4.0" +anyio==4.3.0 ; python_version >= "3.9" and python_version < "4.0" +asciitree==0.3.3 ; python_version >= "3.9" and python_version < "4" +attrs==23.2.0 ; python_version >= "3.9" and python_version < "4" +beautifulsoup4==4.12.3 ; python_version >= "3.9" and python_version < "4" +black==24.3.0 ; python_version >= "3.9" and python_version < "4" +bump2version==1.0.1 ; python_version >= "3.9" and python_version < "4" +cartopy==0.22.0 ; python_version >= "3.9" and python_version < "4" +catalogue==2.0.10 ; python_version >= "3.9" and python_version < "4" +certifi==2024.2.2 ; python_version >= "3.9" and python_version < "4" +cffi==1.16.0 ; python_version >= "3.9" and python_version < "4" +cfgrib==0.9.11.0 ; python_version >= "3.9" and python_version < "4" +cftime==1.6.3 ; python_version >= "3.9" and python_version < "4" +charset-normalizer==3.3.2 ; python_version >= "3.9" and python_version < "4" +click-plugins==1.1.1 ; python_version >= "3.9" and python_version < "4" +click==8.1.7 ; python_version >= "3.9" and python_version < "4" +cligj==0.7.2 ; python_version >= "3.9" and python_version < "4" +cloudpickle==3.0.0 ; python_version >= "3.9" and python_version < "4" +colorama==0.4.6 ; python_version >= "3.9" and python_version < "4" and (sys_platform == "win32" or platform_system == "Windows") +colorlog==6.8.2 ; python_version >= "3.9" and python_version < "4" +configobj==5.0.8 ; python_version >= "3.9" and python_version < "4" +contourpy==1.2.1 ; python_version >= "3.9" and python_version < "4" +coverage[toml]==7.4.4 ; python_version >= "3.9" and python_version < "4" +cycler==0.12.1 ; python_version >= "3.9" and python_version < "4" +dask==2024.4.1 ; python_version >= "3.9" and python_version < "4" +dataretrieval==1.0.6 ; python_version >= "3.9" and python_version < "4.0" +deprecated==1.2.14 ; python_version >= "3.9" and python_version < "4.0" +docopt==0.6.2 ; python_version >= "3.9" and python_version < "4" +donfig==0.8.1.post0 ; python_version >= "3.9" and python_version < "4" +eccodes==1.7.0 ; python_version >= "3.9" and python_version < "4" +erddapy==2.2.0 ; python_version >= "3.9" and python_version < "4.0" +exceptiongroup==1.2.0 ; python_version >= "3.9" and python_version < "3.11" +execnet==2.1.1 ; python_version >= "3.9" and python_version < "4" +f90nml==1.4.4 ; python_version >= "3.9" and python_version < "4" +fasteners==0.19 ; python_version >= "3.9" and python_version < "4" and sys_platform != "emscripten" +findlibs==0.0.5 ; python_version >= "3.9" and python_version < "4" +fiona==1.9.6 ; python_version >= "3.9" and python_version < "4" +fonttools==4.51.0 ; python_version >= "3.9" and python_version < "4" +fsspec==2024.3.1 ; python_version >= "3.9" and python_version < "4" +geopandas==0.14.3 ; python_version >= "3.9" and python_version < "4" +gmsh==4.12.2 ; python_version >= "3.9" and python_version < "4" +h11==0.14.0 ; python_version >= "3.9" and python_version < "4.0" +html5lib==1.1 ; python_version >= "3.9" and python_version < "4.0" +httpcore==1.0.5 ; python_version >= "3.9" and python_version < "4.0" +httpx==0.27.0 ; python_version >= "3.9" and python_version < "4.0" +idna==3.6 ; python_version >= "3.9" and python_version < "4" +importlib-metadata==7.1.0 ; python_version >= "3.9" and python_version < "3.12" +importlib-resources==6.4.0 ; python_version >= "3.9" and python_version < "4.0" +iniconfig==2.0.0 ; python_version >= "3.9" and python_version < "4" +jinja2==3.1.3 ; python_version >= "3.9" and python_version < "4" +joblib==1.4.0 ; python_version >= "3.9" and python_version < "4" +kiwisolver==1.4.5 ; python_version >= "3.9" and python_version < "4" +limits==3.10.1 ; python_version >= "3.9" and python_version < "4.0" +llvmlite==0.42.0 ; python_version >= "3.9" and python_version < "4" +locket==1.0.0 ; python_version >= "3.9" and python_version < "4" +lxml==5.2.1 ; python_version >= "3.9" and python_version < "4.0" +markupsafe==2.1.5 ; python_version >= "3.9" and python_version < "4" +matplotlib==3.8.4 ; python_version >= "3.9" and python_version < "4" +mpi4py==3.1.5 ; python_version >= "3.9" and python_version < "4" +mypy-extensions==1.0.0 ; python_version >= "3.9" and python_version < "4" +netcdf4==1.6.5 ; python_version >= "3.9" and python_version < "4" +numcodecs==0.12.1 ; python_version >= "3.9" and python_version < "4" +numpy==1.26.4 ; python_version >= "3.9" and python_version < "4" +packaging==24.0 ; python_version >= "3.9" and python_version < "4" +pandas==2.2.1 ; python_version >= "3.9" and python_version < "4" +partd==1.4.1 ; python_version >= "3.9" and python_version < "4" +pathspec==0.12.1 ; python_version >= "3.9" and python_version < "4" +pillow==10.3.0 ; python_version >= "3.9" and python_version < "4" +platformdirs==4.2.0 ; python_version >= "3.9" and python_version < "4" +pluggy==1.4.0 ; python_version >= "3.9" and python_version < "4" +psutil==5.9.8 ; python_version >= "3.9" and python_version < "4" +pycparser==2.22 ; python_version >= "3.9" and python_version < "4" +pydantic-core==2.16.3 ; python_version >= "3.9" and python_version < "4.0" +pydantic==2.6.4 ; python_version >= "3.9" and python_version < "4.0" +pydap==3.4.1 ; python_version >= "3.9" and python_version < "4" +pykdtree==1.3.11 ; python_version >= "3.9" and python_version < "4" +pyogrio==0.7.2 ; python_version >= "3.9" and python_version < "4" +pyparsing==3.1.2 ; python_version >= "3.9" and python_version < "4" +pyproj==3.6.1 ; python_version >= "3.9" and python_version < "4" +pyresample==1.28.2 ; python_version >= "3.9" and python_version < "4" +pyshp==2.3.1 ; python_version >= "3.9" and python_version < "4" +pytest-cov==5.0.0 ; python_version >= "3.9" and python_version < "4" +pytest-xdist==3.5.0 ; python_version >= "3.9" and python_version < "4" +pytest==8.1.1 ; python_version >= "3.9" and python_version < "4" +python-dateutil==2.9.0.post0 ; python_version >= "3.9" and python_version < "4" +pytz==2024.1 ; python_version >= "3.9" and python_version < "4" +pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "4" +rasterio==1.3.9 ; python_version >= "3.9" and python_version < "4" +requests==2.31.0 ; python_version >= "3.9" and python_version < "4" +rioxarray==0.15.0 ; python_version >= "3.9" and python_version < "4" +scipy==1.13.0 ; python_version >= "3.9" and python_version < "4" +searvey==0.3.11 ; python_version >= "3.9" and python_version < "4.0" +setuptools==69.2.0 ; python_version >= "3.9" and python_version < "4" +shapely==2.0.3 ; python_version >= "3.9" and python_version < "4" +six==1.16.0 ; python_version >= "3.9" and python_version < "4" +sniffio==1.3.1 ; python_version >= "3.9" and python_version < "4.0" +snuggs==1.4.7 ; python_version >= "3.9" and python_version < "4" +soupsieve==2.5 ; python_version >= "3.9" and python_version < "4" +srsly==2.4.8 ; python_version >= "3.9" and python_version < "4" +tomli==2.0.1 ; python_version >= "3.9" and python_full_version <= "3.11.0a6" +toolz==0.12.1 ; python_version >= "3.9" and python_version < "4" +tqdm==4.66.2 ; python_version >= "3.9" and python_version < "4" +typing-extensions==4.11.0 ; python_version >= "3.9" and python_version < "4.0" +tzdata==2024.1 ; python_version >= "3.9" and python_version < "4" +urllib3==2.2.1 ; python_version >= "3.9" and python_version < "4" +webencodings==0.5.1 ; python_version >= "3.9" and python_version < "4.0" +webob==1.8.7 ; python_version >= "3.9" and python_version < "4" +wrapt==1.16.0 ; python_version >= "3.9" and python_version < "4.0" +xarray-selafin==0.1.4 ; python_version >= "3.9" and python_version < "4" +xarray==2024.3.0 ; python_version >= "3.9" and python_version < "4" +zarr==2.17.2 ; python_version >= "3.9" and python_version < "4" +zipp==3.18.1 ; python_version >= "3.9" and python_version < "3.12" diff --git a/locks/schism_mpich.yml b/locks/schism_mpich.yml index 6fe0f68..2899ec2 100644 --- a/locks/schism_mpich.yml +++ b/locks/schism_mpich.yml @@ -307,28 +307,28 @@ package: category: main optional: false - name: libaec - version: 1.1.3 + version: 1.1.2 manager: conda platform: linux-64 dependencies: libgcc-ng: '>=12' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.2-h59595ed_1.conda hash: - md5: 5e97e271911b8b2001a8b71860c32faa - sha256: 2ef420a655528bca9d269086cf33b7e90d2f54ad941b437fb1ed5eca87cee017 + md5: 127b0be54c1c90760d7fe02ea7a56426 + sha256: fdde15e74dc099ab1083823ec0f615958e53d9a8fae10405af977de251668bea category: main optional: false - name: libaec - version: 1.1.3 + version: 1.1.2 manager: conda platform: osx-64 dependencies: - libcxx: '>=16' - url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.3-h73e2aa4_0.conda + libcxx: '>=15.0.7' + url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.2-he965462_1.conda hash: - md5: 66d3c1f6dd4636216b4fca7a748d50eb - sha256: dae5921339c5d89f4bf58a95fd4e9c76270dbf7f6a94f3c5081b574905fcccf8 + md5: faa179050abc6af1385e0fe9dd074f91 + sha256: 1b0a0b9b67e8f155ebdc7205a7421c7aff4850a740fc9f88b3fa23282c98ed72 category: main optional: false - name: libcurl diff --git a/locks/schism_openmpi.yml b/locks/schism_openmpi.yml index 7b6d6f7..3154c51 100644 --- a/locks/schism_openmpi.yml +++ b/locks/schism_openmpi.yml @@ -307,28 +307,28 @@ package: category: main optional: false - name: libaec - version: 1.1.3 + version: 1.1.2 manager: conda platform: linux-64 dependencies: libgcc-ng: '>=12' libstdcxx-ng: '>=12' - url: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.3-h59595ed_0.conda + url: https://conda.anaconda.org/conda-forge/linux-64/libaec-1.1.2-h59595ed_1.conda hash: - md5: 5e97e271911b8b2001a8b71860c32faa - sha256: 2ef420a655528bca9d269086cf33b7e90d2f54ad941b437fb1ed5eca87cee017 + md5: 127b0be54c1c90760d7fe02ea7a56426 + sha256: fdde15e74dc099ab1083823ec0f615958e53d9a8fae10405af977de251668bea category: main optional: false - name: libaec - version: 1.1.3 + version: 1.1.2 manager: conda platform: osx-64 dependencies: - libcxx: '>=16' - url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.3-h73e2aa4_0.conda + libcxx: '>=15.0.7' + url: https://conda.anaconda.org/conda-forge/osx-64/libaec-1.1.2-he965462_1.conda hash: - md5: 66d3c1f6dd4636216b4fca7a748d50eb - sha256: dae5921339c5d89f4bf58a95fd4e9c76270dbf7f6a94f3c5081b574905fcccf8 + md5: faa179050abc6af1385e0fe9dd074f91 + sha256: 1b0a0b9b67e8f155ebdc7205a7421c7aff4850a740fc9f88b3fa23282c98ed72 category: main optional: false - name: libcurl diff --git a/locks/telemac_mpich.yml b/locks/telemac_mpich.yml new file mode 100644 index 0000000..4a74220 --- /dev/null +++ b/locks/telemac_mpich.yml @@ -0,0 +1,2602 @@ +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV telemac_mpich.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile telemac_mpich.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f ../dependencies/telemac_mpich.yml --lockfile telemac_mpich.yml +version: 1 +metadata: + content_hash: + linux-64: 06cb4200f68255a20c8a8d844846f3c5f32fb2fbf5a8aee7257c4e4e70fe4e82 + channels: + - url: conda-forge + used_env_vars: [] + - url: tomsail + used_env_vars: [] + platforms: + - linux-64 + sources: + - ../dependencies/telemac_mpich.yml +package: +- name: _libgcc_mutex + version: '0.1' + manager: conda + platform: linux-64 + dependencies: {} + url: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 + hash: + md5: d7c89558ba9fa0495403155b64376d81 + sha256: fe51de6107f9edc7aa4f786a70f4a883943bc9d39b3bb7307c04c41410990726 + category: main + optional: false +- name: _openmp_mutex + version: '4.5' + manager: conda + platform: linux-64 + dependencies: + _libgcc_mutex: '0.1' + libgomp: '>=7.5.0' + url: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 + hash: + md5: 73aaf86a425cc6e73fcf236a5a46396d + sha256: fbe2c5e56a653bebb982eda4876a9178aedfc2b545f25d0ce9c4c0b508253d22 + category: main + optional: false +- name: aed2-otm + version: 1.2.0 + manager: conda + platform: linux-64 + dependencies: {} + url: https://conda.anaconda.org/tomsail/linux-64/aed2-otm-1.2.0-1.tar.bz2 + hash: + md5: a47c08cbf17c8b639a33c4926738bcb3 + sha256: 8c8b2e30984b954c09e73d5fb7d2b1e78f787e0b3928094c65f0b7dce99e6c64 + category: main + optional: false +- name: alsa-lib + 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diff --git a/locks/telemac_openmpi.yml b/locks/telemac_openmpi.yml new file mode 100644 index 0000000..cc7c52d --- /dev/null +++ b/locks/telemac_openmpi.yml @@ -0,0 +1,2604 @@ +# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). DO NOT EDIT! +# +# A "lock file" contains a concrete list of package versions (with checksums) to be installed. Unlike +# e.g. `conda env create`, the resulting environment will not change as new package versions become +# available, unless you explicitly update the lock file. +# +# Install this environment as "YOURENV" with: +# conda-lock install -n YOURENV telemac_openmpi.yml +# To update a single package to the latest version compatible with the version constraints in the source: +# conda-lock lock --lockfile telemac_openmpi.yml --update PACKAGE +# To re-solve the entire environment, e.g. after changing a version constraint in the source file: +# conda-lock -f ../dependencies/telemac_openmpi.yml --lockfile telemac_openmpi.yml +version: 1 +metadata: + content_hash: + linux-64: 86c2d37ac783825da40951d94e119ec4b65f073b9e478df8b813e132d0a834c3 + channels: + - url: conda-forge + used_env_vars: [] + - url: tomsail + used_env_vars: [] + platforms: + - linux-64 + sources: + - ../dependencies/telemac_openmpi.yml +package: +- name: _libgcc_mutex + version: '0.1' + manager: conda + platform: linux-64 + 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version = "2024.6.0" @@ -5989,4 +6040,4 @@ viz = ["geoviews", "holoviews", "hvplot", "ipykernel", "itkwidgets", "matplotlib [metadata] lock-version = "2.0" python-versions = ">=3.9, <4" -content-hash = "38d4082978f66a07caeea2a453769bdf945b44756efeacce68699148488fe17d" +content-hash = "3b82313d68e68c02a7b42b03ee5678adaec056d90fb8bfc773ecc1858c069f9e" diff --git a/pyposeidon/dem.py b/pyposeidon/dem.py index 1273e8b..95ee934 100644 --- a/pyposeidon/dem.py +++ b/pyposeidon/dem.py @@ -88,7 +88,6 @@ def __init__(self, dem_source: str, **kwargs): self.adjust(coastline, **kwargs) def adjust(self, coastline, **kwargs): - tiles = kwargs.get("tiles", False) if tiles: diff --git a/pyposeidon/dem_tools.py b/pyposeidon/dem_tools.py index 138164a..404375d 100644 --- a/pyposeidon/dem_tools.py +++ b/pyposeidon/dem_tools.py @@ -67,9 +67,9 @@ def get_tiles(data, **kwargs): return perms -def fix_dem(dem, coastline, dbuffer=0.0, **kwargs): +def fix_dem(dem, coastline, buffer=0.0, **kwargs): - perms = get_tiles(dem, **kwargs) + perms = get_tiles(dem) i = 0 check = True @@ -78,7 +78,6 @@ def fix_dem(dem, coastline, dbuffer=0.0, **kwargs): os.makedirs("./fixtmp/") for (i1, i2), (j1, j2) in tqdm(perms, total=len(perms)): - lon1 = dem.longitude.data[i1:i2][0] lon2 = dem.longitude.data[i1:i2][-1] lat1 = dem.latitude.data[j1:j2][0] diff --git a/pyposeidon/misc/telemac2d.cas b/pyposeidon/misc/telemac2d.cas new file mode 100755 index 0000000..3e5bcf6 --- /dev/null +++ b/pyposeidon/misc/telemac2d.cas @@ -0,0 +1,187 @@ +/-------------------------------------------------------------------/ +/ TELEMAC-2D - MED MESH 5KM - TIDES USING TPXO , WINDS AND / +/ GRAVITY FORCE / +/-------------------------------------------------------------------/ +/ +/---------------------------------------------- +/ COMPUTER INFORMATIONS +/---------------------------------------------- +/ +GEOMETRY FILE = '{{geo_file}}' +BOUNDARY CONDITIONS FILE = '{{cli_file}}' +RESULTS FILE = '{{out_2D_file}}' +BINARY ATMOSPHERIC DATA FILE = +'{{inp_wind_file}}' +{% if monitor %}TIME SERIES FILE 1 = '{{out_1D_file}}' +TIME SERIES COORDINATES FILE 1 = '{{station_coords}}'{% endif %} +/CHECKING THE MESH = YES +/PARALLEL PROCESSORS = {{ ncsize }} +{% if fortran %}FORTRAN FILE = 'user_fortran' +{% endif %} +/ +/---------------------------------------------- +/ GENERAL INFORMATIONS - OUTPUTS +/---------------------------------------------- +/ +TITLE = '{{title}}' +VARIABLES FOR GRAPHIC PRINTOUTS = U,V,S / L,H,P +GRAPHIC PRINTOUT PERIOD = {{tstep_graph}} +LISTING PRINTOUT PERIOD = {{tstep_list}} +TIME STEP = {{tstep}} +DURATION = {{duration}} +ORIGINAL DATE OF TIME = {{datestart}} +ORIGINAL HOUR OF TIME = {{timestart}} +MASS-BALANCE = {{ 'YES' if mass_balance else 'NO' }} +/Determines whether a check of the mass-balance over the domain is made or not +/ +/---------------------------------------------- +/ INITIAL CONDITIONS +/---------------------------------------------- +/ +COMPUTATION CONTINUED = {{ 'YES' if computation_continued else 'NO' }} /Determines whether the computation under way is independent result or is following an earlier result +{% if computation_continued %}PREVIOUS COMPUTATION FILE = {{ previous_computation_file }} +PREVIOUS COMPUTATION FILE FORMAT = 'SERAFIND' +{% else %} +INITIAL CONDITIONS = '{{initial_conditions}}' /ZERO ELEVATION, +/ /CONSTANT ELEVATION, +/ /INITIAL ELEVATION, +/ /ZERO DEPTH, +/ /CONSTANT DEPTH (together with INITIAL DEPTH), +/ /SPECIAL, +/ /TPXO SATELLITE ALTIMETRY{% endif %} +/ +/--------------------------------------------------------------------- +/ CREATE RESTART CONDITIONS +/--------------------------------------------------------------------- +{% if hotstart %}RESTART MODE = YES +RESTART FILE = {{ restart_file }} +/RECORD NUMBER IN RESTART FILE = {{ restart_tstep }} +RESTART FILE FORMAT = 'SERAFIND' {% endif %} +/ +/--------------------------------------------------------------------- +/ SPATIAL CONDITIONS - COORDINATE SYSTEM +/--------------------------------------------------------------------- +SPHERICAL COORDINATES = {{ 'YES' if spherical_coords else 'NO' }} +SPATIAL PROJECTION TYPE = {{spatial_proj}} /1=CARTESIAN, NOT GEOREFERENCED + /2=MERCATOR + /3=LATITUDE LONGITUDE +/ 'Option 2 or 3 mandatory for spherical coordinates / Option 3: latitude and longitude in degrees!' +RESULT FILE IN LONGITUDE-LATITUDE = {{ 'YES' if result_ll else 'NO' }} +LATITUDE OF ORIGIN POINT = {{lon_orig}} +LONGITUDE OF ORIGIN POINT = {{lat_orig}} +GEOGRAPHIC SYSTEM = {{geo_sys}} /0="DEFINED BY USER" +/ /1="WGS84 LONGITUDE/LATITUDE IN REAL DEGREES" +/ /2="WGS84 NORTHERN UTM" +/ /3="WGS84 SOUTHERN UTM" +/ /4="LAMBERT" +/ /5="MERCATOR FOR TELEMAC" +ZONE NUMBER IN GEOGRAPHIC SYSTEM = {{zone_no}} +/ +/---------------------------------------------- +/ PHYSICAL PARAMETERS +/---------------------------------------------- +/ +LAW OF BOTTOM FRICTION = {{friction_law}} +FRICTION COEFFICIENT = {{friction_coef}} +DENSITY EFFECTS = {{ 'YES' if density_effects else 'NO' }} +CORIOLIS = {{ 'YES' if coriolis else 'NO' }} +/ALWAYS DEFAULT WHEN TAKING SPHERICAL COORDINATES +WATER DENSITY = {{water_density}} +TURBULENCE MODEL = {{turb_model}} /'1="CONSTANT VISCOSITY"'; +/ /'2="ELDER"'; +/ /'3="K-EPSILON MODEL"'; +/ /'4="SMAGORINSKI"'; +/ /'5="MIXING LENGTH"'; +/ /'6="SPALART-ALLMARAS"' +VELOCITY DIFFUSIVITY = {{velocity_diffusivity}} / Sets the value of the coefficient of global (dynamic+turbulent) viscosity, +/ this value may have a significant effect both on the shapes and sizes of recirculation zones +BOTTOM SMOOTHINGS = {{no_smoothings}} /Number of smoothings on bottom topography. +/ Each smoothing is mass conservative. To be used when interpolation of bathymetry on the mesh gives very rough results +/ +/---------------------------------------------- +/ WIND +/---------------------------------------------- +/ +{% if wind %}WIND = YES /Determines whether the wind effects are to be taken into account or not +AIR PRESSURE = {{ 'YES' if pressure else 'NO' }} +OPTION FOR WIND = {{wind_type}} /'1="constant in time and space"'; +/ /'2="variable in time given by formated file"'; +/ /'3="variable in time and space given by formated file"' +/COEFFICIENT OF WIND INFLUENCE = {{wind_coef}} /Sets the value of the wind driving coefficient +THRESHOLD DEPTH FOR WIND = {{depth_threshold_wind}} {% endif %} +/ +/---------------------------------------------- +/ TSUNAMI +/---------------------------------------------- +{% if tsunami %}OPTION FOR TSUNAMI GENERATION = YES +PHYSICAL CHARACTERISTICS OF THE TSUNAMI = +{{tsunami_fault}} {% endif %} +/ +/--------------------------------------------------------------------- +/ NUMERICAL PARAMETERS +/--------------------------------------------------------------------- +/ +ADVECTION OF U AND V = {{ 'YES' if adv_u_v else 'NO' }} +DIFFUSION OF VELOCITY = {{ 'YES' if diff_velocity else 'NO' }} +PRECONDITIONING = {{preconditioning}} +MATRIX STORAGE = {{matrix_storage}} +/ +INFORMATION ABOUT SOLVER = {{ 'YES' if info_solver else 'NO' }} +SOLVER = {{solver}} +SOLVER OPTION = {{solver_option}} +/ +TYPE OF ADVECTION = {{type_advection}} /Advection schemes for every variable +SUPG OPTION = {{supg_option}} /Upwindinding schemes for every variable +PROPAGATION = {{ 'YES' if propagation else 'NO' }} /Determines whether the propagation step is taken into account +SOLVER ACCURACY = {{solver_accuracy}} /Required accuracy for solving the propagation step +MATRIX-VECTOR PRODUCT = {{matrix_vector_product}} +MASS-LUMPING ON H = {{mass_lumping}} /more stable, artificially smoothed +DISCRETIZATIONS IN SPACE = {{discretizations_space}} /(1)U,V (2)H (3)T (4)K,EPSILON +FREE SURFACE GRADIENT COMPATIBILITY = {{surface_gradient_compatibility}} +INITIAL GUESS FOR U = {{initial_guess_u}} +INITIAL GUESS FOR H = {{initial_guess_h}} +/ +IMPLICITATION FOR DEPTH = {{implicitation_depth}} +IMPLICITATION FOR VELOCITY = {{implicitation_velocity}} +/ +/--------------------------------------------------------------------- +/ TIDES +/--------------------------------------------------------------------- +/ +TIDE GENERATING FORCE = {{ 'YES' if tide_generating_force else 'NO' }} +{% if tide %} +OPTION FOR TIDAL BOUNDARY CONDITIONS = {{ tidal_boundary_conditions|repeat_value(N_bc) }} +OPTION FOR LIQUID BOUNDARIES = {{ liquid_boundaries|repeat_value(N_bc) }} +TIDAL DATA BASE = {{ tidal_database|repeat_value(N_bc) }} +BINARY DATABASE 1 FOR TIDE = '{{db1_tide}}' +BINARY DATABASE 2 FOR TIDE = '{{db2_tide}}' +MINOR CONSTITUENTS INFERENCE = {{ 'YES' if minor_constituents_inference else 'NO' }} +{% endif %} +/ +/--------------------------------------------------------------------- +/ TIDAL FLATS +/--------------------------------------------------------------------- +/ +TIDAL FLATS = {{ 'YES' if tidal_flats else 'NO' }} +OPTION FOR THE TREATMENT OF TIDAL FLATS = {{tidal_flats_option}} +TREATMENT OF NEGATIVE DEPTHS = {{negative_depths_treatment}} +OPTION FOR THE DIFFUSION OF VELOCITIES = {{diffusion_velocities_option}} +CONTINUITY CORRECTION = {{ 'YES' if continuity_correction else 'NO' }} +{% if friction_law_boundaries > 0 %} +LAW OF FRICTION ON LATERAL BOUNDARIES = {{friction_law_boundaries}} +ROUGHNESS COEFFICIENT OF BOUNDARIES = {{friction_coef_boundaries}}{% endif %} +/ +/---------------------------------------------- +/ TRACERS +/---------------------------------------------- +{% if tracer %} +TYPE OF ADVECTION = 14;5;14 +/ +NUMBER OF TRACERS = {{no_tracers}} +/NAMES OF TRACERS = 'TRACER 1'; 'TRACER 2' +/ +INITIAL VALUES OF TRACERS = 0.; 0. +PRESCRIBED TRACERS VALUES = 0.0;0.0 ; 0.0;0.0 +/ +DIFFUSION OF TRACERS = True +COEFFICIENT FOR DIFFUSION OF TRACERS = 1.;1.{% endif %} \ No newline at end of file diff --git a/pyposeidon/misc/telemac2d.json b/pyposeidon/misc/telemac2d.json new file mode 100644 index 0000000..9168b5d --- /dev/null +++ b/pyposeidon/misc/telemac2d.json @@ -0,0 +1,88 @@ +{"params": + { + "geo_file": "geo.slf", + "cli_file": "geo.cli", + "out_2D_file": "results_2D.slf", + "out_1D_file": "results_1D.slf", + "station_coords": "station.in", + "monitor": false, + "inp_wind_file": "input_wind.slf", + "hotstart": true, + "restart_file": "restart_2D.slf", + "restart_tstep": -1, + "fortran": false, + "title": "TELEMAC 2D Model", + "ncsize": 1, + "tstep_graph": 12, + "tstep_list": 6, + "tstep": 300, + "duration": "None", + "datestart": "None", + "timestart": "None", + "mass_balance": true, + "no_tracers": 1, + "computation_continued": false, + "previous_computation_file": "placeholder.slf", + "initial_conditions": "ZERO ELEVATION", + "spherical_coords": true, + "spatial_proj": 3, + "result_ll": true, + "lon_orig": 0, + "lat_orig": 0, + "geo_sys": 5, + "zone_no": 33, + "friction_law": 2, + "friction_coef": 40, + "friction_law_boundaries": 0, + "friction_coef_boundaries": 40, + "density_effects": false, + "coriolis": true, + "water_density": 1025, + "turb_model": 1, + "velocity_diffusivity": 1.0, + "no_smoothings": 0, + "wind": true, + "pressure": true, + "wind_type": 3, + "wind_coef": 3.4E-6, + "depth_threshold_wind": 1, + "tsunami": false, + "tsunami_fault": "100.;210000.;75000.;13.6;13.;36.;13.;0.;0.;3.", + "adv_u_v": true, + "diff_velocity": true, + "preconditioning": 2, + "matrix_storage": 3, + "info_solver": true, + "solver": 7, + "solver_option": 3, + "type_advection": "13;13", + "supg_option": "0;0", + "propagation": true, + "solver_accuracy": "1.E-5", + "matrix_vector_product": 1, + "mass_lumping": 1, + "discretizations_space": "11;11", + "surface_gradient_compatibility": 0.5, + "initial_guess_u": 2, + "initial_guess_h": 2, + "implicitation_depth": 0.55, + "implicitation_velocity": 0.55, + "tide_generating_force": false, + "tidal_boundary_conditions": 1, + "liquid_boundaries": 2, + "tidal_database": 2, + "db1_tide": "TPXO/h_LOCAL", + "db2_tide": "TPXO/uv_LOCAL", + "minor_constituents_inference": true, + "tidal_flats": true, + "tidal_flats_option": 1, + "negative_depths_treatment": 2, + "diffusion_velocities_option": 1, + "continuity_correction": true, + "tracer": false, + "source_x": -266565, + "source_y": 232753, + "source_flow": 1, + "tracer_values": 1000000 + } +} \ No newline at end of file diff --git a/pyposeidon/misc/telemac3d.cas b/pyposeidon/misc/telemac3d.cas new file mode 100755 index 0000000..fd9777b --- /dev/null +++ b/pyposeidon/misc/telemac3d.cas @@ -0,0 +1,99 @@ +/---------------------------------------------- +/ COMPUTER INFORMATIONS +/---------------------------------------------- +/ +FORTRAN FILE = '{{ fortran_file }}' +GEOMETRY FILE = '{{ geo_file }}' +BOUNDARY CONDITIONS FILE = '{{ cli_file }}' +3D RESULT FILE = '{{ out_3D_file }}' +2D RESULT FILE = '{{ out_2D_file }}' +FORMATTED DATA FILE 1 = '{{ formatted_data_file_1 }}' +DEBUGGER={{ debugger }} +{% if fortran %}FORTRAN FILE = 'user_fortran' +{% endif %} +/ +/---------------------------------------------- +/ GENERAL INFORMATIONS - OUTPUTS +/---------------------------------------------- +/ +TITLE = '{{ title }}' +VARIABLES FOR 3D GRAPHIC PRINTOUTS : '{{ variables_3d_graphics }}' +VARIABLES FOR 2D GRAPHIC PRINTOUTS : '{{ variables_2d_graphics }}' +GRAPHIC PRINTOUT PERIOD = {{ graphic_printout_period }} +LISTING PRINTOUT PERIOD = {{ listing_printout_period }} +TIME STEP = {{ time_step }} +NUMBER OF TIME STEPS = {{ number_of_time_steps }} +CHECKING THE MESH = {{ checking_mesh }} +{% if nonlinearities %}NUMBER OF SUB ITERATIONS FOR NON LINEARITIES : {{no_subiter}} {% endif %} +/ +/----------------------------------------------------------------------/ +/ INITIAL CONDITIONS +/----------------------------------------------------------------------/ +ORIGINAL DATE OF TIME = {{ original_date_of_time }} +ORIGINAL HOUR OF TIME = {{ original_hour_of_time }} +/NUMBER OF DROGUES = {{ number_of_drogues }} +/PRINTOUT PERIOD FOR DROGUES = {{ printout_period_drogues }} +/DROGUES FILE = '{{ drogues_file }}' +MASS-BALANCE = {{ mass_balance }} +/ +/---------------------------------------------- +/ PHYSICAL PARAMETERS +/---------------------------------------------- +/ +LAW OF BOTTOM FRICTION = {{ law_of_bottom_friction }} +FRICTION COEFFICIENT FOR THE BOTTOM = {{ friction_coefficient_bottom }} +/TIDE GENERATING FORCE = {{ tide_generating_force }} +/FRICTION COEFFICIENT FOR THE BOTTOM = {{ friction_coefficient_bottom_2 }} +CORIOLIS = {{ coriolis }} +INITIAL CONDITIONS = '{{ initial_conditions }}' +/ +/--------------------------------------------------------------------- +/ SPATIAL CONDITIONS - COORDINATE SYSTEM +/--------------------------------------------------------------------- +SPHERICAL COORDINATES = {{ spherical_coordinates }} +SPATIAL PROJECTION TYPE = {{ spatial_projection_type }} +GEOGRAPHIC SYSTEM = {{ geographic_system }} +RESULT FILE IN LONGITUDE-LATITUDE = {{ result_file_in_longitude_latitude }} +/------------------------------------------------------ +/ NUMERICAL PARAMETERS +/---------------------------------------------- +/ +SCHEME FOR ADVECTION OF DEPTH = {{ scheme_for_advection_of_depth }} +/SCHEME FOR ADVECTION OF VELOCITIES = {{ scheme_for_advection_of_velocities }} +ACCURACY FOR PROPAGATION = {{ accuracy_for_propagation }} +ACCURACY FOR DIFFUSION OF VELOCITIES = {{ accuracy_for_diffusion_of_velocities }} +ACCURACY FOR PPE = {{ accuracy_for_ppe }} +/ +MAXIMUM NUMBER OF ITERATIONS FOR ADVECTION SCHEMES = {{ max_iterations_advection_schemes }} +MAXIMUM NUMBER OF ITERATIONS FOR PROPAGATION = {{ max_iterations_propagation }} +MAXIMUM NUMBER OF ITERATIONS FOR DIFFUSION OF VELOCITIES = {{ max_iterations_diffusion_velocities }} +MAXIMUM NUMBER OF ITERATIONS FOR PPE = {{ max_iterations_ppe }} +MAXIMUM NUMBER OF ITERATIONS FOR DIFFUSION OF K-EPSILON = {{ max_iterations_diffusion_k_epsilon }} +/ +SOLVER FOR PPE = {{ solver_for_ppe }} +SOLVER FOR PROPAGATION = {{ solver_for_propagation }} +OPTION OF SOLVER FOR PROPAGATION = {{ option_solver_for_propagation }} +IMPLICITATION FOR DEPTH = {{ implicitation_for_depth }} +IMPLICITATION FOR VELOCITIES = {{ implicitation_for_velocities }} +COEFFICIENT FOR HORIZONTAL DIFFUSION OF VELOCITIES = {{ coefficient_horizontal_diffusion_velocities }} +COEFFICIENT FOR VERTICAL DIFFUSION OF VELOCITIES = {{ coefficient_vertical_diffusion_velocities }} +FREE SURFACE GRADIENT COMPATIBILITY = {{ free_surface_gradient_compatibility }} +/ +/---------------------------------------------------------------------- +/ VERTICAL DESCRIPTION (LAYERS, MESH, ETC...) +/---------------------------------------------------------------------- +/ +MESH TRANSFORMATION = {{ mesh_transformation }} +NUMBER OF HORIZONTAL LEVELS = {{ number_of_horizontal_levels }} +NUMBER OF BOTTOM SMOOTHINGS = {{ number_of_bottom_smoothings }} +/ +/---------------------------------------------- +/ DRY-WET ELEMENTS +/---------------------------------------------- +/ +/TIDAL FLATS = {{ tidal_flats }} +/MINIMAL VALUE FOR DEPTH = {{ minimal_value_for_depth }} +/TREATMENT OF NEGATIVE DEPTHS = {{ treatment_of_negative_depths }} +/TREATMENT ON TIDAL FLATS FOR VELOCITIES = {{ treatment_on_tidal_flats_for_velocities }} +/OPTION FOR THE TREATMENT OF TIDAL FLATS = {{ option_for_treatment_of_tidal_flats }} +/ \ No newline at end of file diff --git a/pyposeidon/misc/telemac3d.json b/pyposeidon/misc/telemac3d.json new file mode 100644 index 0000000..b919fc2 --- /dev/null +++ b/pyposeidon/misc/telemac3d.json @@ -0,0 +1,63 @@ +{ + "fortran_file": "user_fortran", + "geo_file": "Global_10km_100km.slf", + "cli_file": "Global_10km_100km_t.cli", + "out_3D_file": "res.3d.slf", + "out_2D_file": "res.2d.slf", + "formatted_data_file_1": "tsunamis.txt", + "fortran": false, + "debugger": 0, + "title": "TELEMAC 3D MODEL", + "variables_3d_graphics": "Z,U,V,W", + "variables_2d_graphics": "U,V,H,S", + "graphic_printout_period": 10, + "listing_printout_period": 10, + "time_step": 60, + "number_of_time_steps": 2000, + "checking_mesh": false, + "nonlinearities": false, + "no_subiter": 20, + "original_date_of_time": "2011;3;11", + "original_hour_of_time": "05;46;0", + "number_of_drogues": 2, + "printout_period_drogues": 60, + "drogues_file": "drogues.dat", + "mass_balance": true, + "law_of_bottom_friction": 5, + "friction_coefficient_bottom": 0.01, + "tide_generating_force": true, + "law_of_bottom_friction_2": 3, + "friction_coefficient_bottom_2": 60.0, + "mesh_transformation": 1, + "coriolis": true, + "initial_conditions": "SPECIAL", + "spherical_coordinates": true, + "spatial_projection_type": 3, + "geographic_system": 1, + "result_file_in_longitude_latitude": true, + "scheme_for_advection_of_depth": 5, + "scheme_for_advection_of_velocities": 14, + "accuracy_for_propagation": 1.0E-3, + "accuracy_for_diffusion_of_velocities": 1.0E-3, + "accuracy_for_ppe": 1.0E-3, + "max_iterations_advection_schemes": 200, + "max_iterations_propagation": 300, + "max_iterations_diffusion_velocities": 200, + "max_iterations_ppe": 200, + "max_iterations_diffusion_k_epsilon": 200, + "solver_for_ppe": 6, + "solver_for_propagation": 7, + "option_solver_for_propagation": 4, + "implicitation_for_depth": 0.6, + "implicitation_for_velocities": 0.6, + "coefficient_horizontal_diffusion_velocities": 1.0, + "coefficient_vertical_diffusion_velocities": 1.0, + "free_surface_gradient_compatibility": 0.5, + "number_of_horizontal_levels": 2, + "number_of_bottom_smoothings": 1, + "tidal_flats": true, + "minimal_value_for_depth": -10.0, + "treatment_of_negative_depths": 2, + "treatment_on_tidal_flats_for_velocities": 0, + "option_for_treatment_of_tidal_flats": 1 +} diff --git a/pyposeidon/misc/tomawac.cas b/pyposeidon/misc/tomawac.cas new file mode 100755 index 0000000..e374596 --- /dev/null +++ b/pyposeidon/misc/tomawac.cas @@ -0,0 +1,87 @@ +/ TOMAWAC INPUT FILE DEFINITIONS +/******************************************************************** +GEOMETRY FILE : '{{geo_file}}' +BOUNDARY CONDITIONS FILE : '{{cli_file}}' +BINARY WINDS FILE : '{{inp_wind_file}}' +WINDS FILE FORMAT : {{wind_file_format}} +{% if hotstart %}GLOBAL RESULT FILE = {{ restart_file }} +{% endif %} +{% if fortran %}FORTRAN FILE = 'user_fortran' +{% endif %} +/------------------------------------------------------------------/ +2D RESULTS FILE : '{{out_2D_file}}' +2D RESULTS FILE FORMAT : 'SERAFIN' +{% if monitor %}TIME SERIES FILE = '{{out_1D_file}}' +TIME SERIES COORDINATES FILE = '{{station_coords}}'{% endif %} +/------------------------------------------------------------------/ +/ COMPUTATION_ENVIRONMENT +/------------------------------------------------------------------/ +TITLE : '{{title}}' +PERIOD FOR LISTING PRINTOUTS : {{tstep_list}} +PERIOD FOR GRAPHIC PRINTOUTS : {{tstep_graph}} +VARIABLES FOR 2D GRAPHIC PRINTOUTS : HM0;DMOY;TMOY;TPD;SPD;TPR8 + +/------------------------------------------------------------------/ +/ GENERAL_PARAMETERS +/------------------------------------------------------------------/ +NAMES OF VARIABLES : 'PATM UI '; +'TAIR DEGREES '; +'WINDX M/S '; +'WINDY M/S ' +NUMBER OF TIME STEP : {{nb_tsteps}} +TIME STEP : {{tstep}} +DATE OF COMPUTATION BEGINNING : {{datestart}} + +/***** DISCRETISATION ***** +NUMBER OF DIRECTIONS : {{num_directions}} +MINIMAL FREQUENCY : {{min_frequency}} +FREQUENTIAL RATIO : {{freq_ratio}} +NUMBER OF FREQUENCIES : {{num_frequencies}} + +CONSIDERATION OF A STATIONARY CURRENT : {{stationary_current}} +CONSIDERATION OF A WIND : {{consider_wind}} +STATIONARY WIND : {{stationary_wind}} +CONSIDERATION OF TIDE : {{consider_tide}} +MINIMUM WATER DEPTH : {{min_water_depth}} +SPHERICAL COORDINATES : {{spherical_coordinates}} +INFINITE DEPTH : {{infinite_depth}} +/ +/------------------------------------------------------------------/ +/ SOURCES/SINKS CONDITIONS +/------------------------------------------------------------------/ +BAJ MODELING : {{baj_modeling}} +CONSIDERATION OF SOURCE TERMS : {{consider_source_terms}} +WIND GENERATION : {{wind_generation}} +WIND GENERATION COEFFICIENT : {{wind_gen_coef}} +AIR DENSITY : {{air_density}} +WATER DENSITY : {{water_density}} +WIND DRAG COEFFICIENT : {{wind_drag_coef}} +VON KARMAN CONSTANT : {{von_karman_const}} +SHIFT GROWING CURVE DUE TO WIND : {{shift_growing_curve}} +LINEAR WAVE GROWTH : {{linear_wave_growth}} +WHITE CAPPING DISSIPATION : {{whitecap_diss}} +WHITE CAPPING DISSIPATION COEFFICIENT : {{whitecap_diss_coef}} +WHITE CAPPING WEIGHTING COEFFICIENT : {{whitecap_diss_wgt}} +BOTTOM FRICTION DISSIPATION : {{bottom_friction_diss}} +BOTTOM FRICTION COEFFICIENT : {{bottom_friction_coef}} +STANDARD CONFIGURATION PARAMETER : {{standard_config_param}} +NUMBER OF ITERATIONS FOR THE SOURCE TERMS : {{source_terms_iterations}} +DISSIPATION BY STRONG CURRENT : {{dissipation_strong_current}} +DEPTH-INDUCED BREAKING DISSIPATION : {{depth_induced_breaking_diss}} +NUMBER OF BREAKING TIME STEPS : {{breaking_time_steps}} +MAXIMUM VALUE OF THE RATIO HM0 ON D : {{max_ratio_hm0_d}} +WAVE GROWTH LIMITER : {{wave_growth_limiter}} +TRIAD INTERACTIONS : {{triad_interactions}} +NON-LINEAR TRANSFERS BETWEEN FREQUENCIES : {{nonlinear_transfers_freq}} +/VEGETATION TAKEN INTO ACCOUNT : {{vegetation_account}} +/------------------------------------------------------------------/ +/ BOUNDARY_CONDITIONS +/------------------------------------------------------------------/ +/ +/------------------------------------------------------------------/ +/ INITIAL_CONDITIONS +/------------------------------------------------------------------/ +/ +{% if computation_continued %} +PREVIOUS COMPUTATION FILE = {{ previous_computation_file }} +{% endif %} \ No newline at end of file diff --git a/pyposeidon/misc/tomawac.json b/pyposeidon/misc/tomawac.json new file mode 100644 index 0000000..052feb7 --- /dev/null +++ b/pyposeidon/misc/tomawac.json @@ -0,0 +1,58 @@ +{"params": + { + "geo_file": "geo.slf", + "cli_file": "geo.cli", + "inp_wind_file": "input_wind.slf", + "wind_file_format": 3, + "out_2D_file": "results_2D.slf", + "out_1D_file": "results_1D.slf", + "station_coords": "station.in", + "computation_continued": false, + "previous_computation_file": "placeholder.slf", + "fortran": false, + "hotstart": true, + "restart_file": "restart_2D.slf", + "title": "TOMAWAC Model Simulation", + "tstep_list": 3600, + "tstep_graph": 3600, + "nb_tsteps": 100, + "tstep": 60, + "datestart": "YYYY/MM/DD", + "num_directions": 24, + "min_frequency": 0.03, + "freq_ratio": 1.1, + "num_frequencies": 31, + "stationary_current": "NO", + "consider_wind": "YES", + "stationary_wind": "NO", + "consider_tide": "NO", + "min_water_depth": 0.1, + "spherical_coordinates": "YES", + "infinite_depth": "NO", + "baj_modeling": 0, + "consider_source_terms": "YES", + "wind_generation": 1, + "wind_gen_coef": 1.2, + "air_density": 1.225, + "water_density": 1026.0, + "wind_drag_coef": 0.0012875, + "von_karman_const": 0.41, + "shift_growing_curve": 0.011, + "linear_wave_growth": 1, + "whitecap_diss": 1, + "whitecap_diss_coef": 0.04, + "whitecap_diss_wgt": 1.0, + "bottom_friction_diss": 1, + "bottom_friction_coef": 0.038, + "standard_config_param": 0.25, + "source_terms_iterations": 1, + "dissipation_strong_current": 0, + "depth_induced_breaking_diss": 1, + "breaking_time_steps": 1, + "max_ratio_hm0_d": 1.0, + "wave_growth_limiter": 1, + "triad_interactions": 0, + "nonlinear_transfers_freq": 1, + "vegetation_account": "NO" + } +} diff --git a/pyposeidon/telemac.py b/pyposeidon/telemac.py new file mode 100644 index 0000000..1cd86a2 --- /dev/null +++ b/pyposeidon/telemac.py @@ -0,0 +1,1488 @@ +""" +TELEMAC model of pyposeidon. It controls the creation, execution & output of a complete simulation based on SCHISM. + +""" + +# Copyright 2018 European Union +# This file is part of pyposeidon. +# Licensed under the EUPL, Version 1.2 or – as soon they will be approved by the European Commission - subsequent versions of the EUPL (the "Licence"). +# Unless required by applicable law or agreed to in writing, software distributed under the Licence is distributed on an "AS IS" basis, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the Licence for the specific language governing permissions and limitations under the Licence. + +import os +import datetime +import numpy as np +import sys +import json +import pandas as pd +import glob +import xarray as xr +import geopandas as gp +import shapely +import jinja2 +from searvey import ioc +import shutil +import typing as T +from scipy.spatial import Delaunay +import dask.array as da + +# local modules +import pyposeidon +import pyposeidon.mesh as pmesh +import pyposeidon.meteo as pmeteo +import pyposeidon.dem as pdem +from pyposeidon.paths import DATA_PATH +from pyposeidon.utils.get_value import get_value +from pyposeidon.utils.converter import myconverter +from pyposeidon.utils.cpoint import closest_n_points +from pyposeidon.utils import data +from pyposeidon.utils.norm import normalize_column_names +from pyposeidon.utils.norm import normalize_varnames +from pyposeidon.utils.obs import get_obs_data +from pyposeidon.utils.post import export_xarray +from pyposeidon.utils.post import remove +from pyposeidon.utils.cast import copy_files + +# telemac (needs telemac stack on conda) +from telapy.api.t2d import Telemac2d +from telapy.api.t3d import Telemac3d +from telapy.api.art import Artemis +from telapy.api.wac import Tomawac +from execution.telemac_cas import TelemacCas +from data_manip.formats.selafin import Selafin +from data_manip.extraction.telemac_file import TelemacFile +from pretel.extract_contour import detecting_boundaries +from pretel.generate_atm import generate_atm +from pretel.extract_contour import sorting_boundaries +from utils.progressbar import ProgressBar +from utils.geometry import get_weights +from utils.geometry import interp +from pretel.manip_telfile import spherical2longlat +from pretel.manip_telfile import longlat2spherical +from xarray_selafin.xarray_backend import SelafinAccessor +from mpi4py import MPI + +import numpy as np + +import logging + +from . import tools + +# Types +ResultTypes = T.Literal["1D", "2D", "3D"] + +logger = logging.getLogger(__name__) + + +TELEMAC_NAME = "telemac" + + +def divisors(n): + result = set() + for i in range(1, int(n**0.5) + 1): + if n % i == 0: + result.add(i) + result.add(n // i) + return sorted(result) + + +def calculate_time_step_hourly_multiple(resolution, min_water_depth=0.1, courant_number=50): + """ + Calculate the maximum allowable time step for a shallow water equation model + based on the CFL condition, rounded to the closest divisor of an hour. + + :param resolution: Spatial resolution (Δx) in meters + :param min_water_depth: Minimum water depth (h_min) in meters. Default is 1 meter. + :param courant_number: Courant number (C), typically less than 1 for explicit schemes. Can be higher for implicit schemes. + :return: Maximum allowable time step (Δt) in seconds, rounded to the closest divisor of an hour. + """ + resolution *= 111.389 # degrees to meters conversion factor + raw_time_step = courant_number * resolution / (9.81 * min_water_depth) ** 0.5 + # Get all divisors of an hour (3600 seconds) + hour_divisors = divisors(3600) + # Find the closest divisor of an hour to the raw time step + closest_divisor = min(hour_divisors, key=lambda x: abs(x - raw_time_step)) + return closest_divisor + + +# Helper functions +def df_to_gpd(df, x: str = "longitude", y: str = "latitude"): + gpdf = gp.GeoDataFrame( + df, + geometry=gp.points_from_xy( + df[x], + df[y], + ), + crs="EPSG:4326", + ) + return gpdf + + +def xy_to_ll(x, y): + gpdf = gp.GeoDataFrame(geometry=gp.points_from_xy(x, y), crs="EPSG:3857").to_crs("EPSG:4326") + return gpdf.geometry.x, gpdf.geometry.y + + +def is_ccw(tris, meshx, meshy): + x1, x2, x3 = meshx[tris].T + y1, y2, y3 = meshy[tris].T + return (y3 - y1) * (x2 - x1) > (y2 - y1) * (x3 - x1) + + +def flip(tris): + return np.column_stack((tris[:, 2], tris[:, 1], tris[:, 0])) + + +def is_overlapping(tris, meshx): + PIR = 180 + x1, x2, x3 = meshx[tris].T + return np.logical_or(abs(x2 - x1) > PIR, abs(x3 - x1) > PIR, abs(x3 - x3) > PIR) + + +def get_det_mask(tris, meshx, meshy): + t12 = meshx[tris[:, 1]] - meshx[tris[:, 0]] + t13 = meshx[tris[:, 2]] - meshx[tris[:, 0]] + t22 = meshy[tris[:, 1]] - meshy[tris[:, 0]] + t23 = meshy[tris[:, 2]] - meshy[tris[:, 0]] + return t12 * t23 - t22 * t13 > 0 + + +def contains_pole(x, y): + return np.any(y == 90, axis=0) + + +def flip_triangles(x, y, ikle2, corrections): + # Assuming slf.meshx, slf.meshy, and slf.ikle2 are NumPy arrays + ikle2 = np.array(ikle2) + # Ensure all triangles are CCW + ccw_mask = is_ccw(ikle2, x, y) + ikle2[~ccw_mask] = flip(ikle2[~ccw_mask]) + + # triangles accross the dateline + m_ = is_overlapping(ikle2, x) + ikle2[m_] = flip(ikle2[m_]) + + # manual additional corrections + if corrections is not None: + for rev in corrections["reverse"]: + ikle2[rev : rev + 1] = flip(ikle2[rev : rev + 1]) + + # Check for negative determinant + detmask = ~get_det_mask(ikle2, x, y) + logger.debug(f"reversed {detmask.sum()} triangles") + logger.debug("[TEMPORARY FIX]: REMOVE THE POLE TRIANGLES") + return ikle2 + + +def remove_pole_triangles(x, y, ikle2, corrections): + # Assuming slf.meshx, slf.meshy, and slf.ikle2 are NumPy arrays + ikle2 = np.array(ikle2) + pole_mask = contains_pole(x[ikle2].T, y[ikle2].T) + # manual additional corrections + if corrections is not None: + for rem in corrections["remove"]: + pole_mask[rem] = True + + logger.debug(f"pole triangles: {np.where(pole_mask)[0]}") + logger.debug("[TEMPORARY FIX]: REMOVE THE POLE TRIANGLES") + return ikle2[~pole_mask, :] + + +def write_netcdf(ds, outpath): + fileOut = os.path.splitext(outpath)[0] + ".nc" + ds.to_netcdf(fileOut) + + +def extract_t_elev_2D( + ds: xr.Dataset, x: float, y: float, var: str = "elev", xstr: str = "longitude", ystr: str = "latitude" +): + lons, lats = ds[xstr].values, ds[ystr].values + indx, _ = closest_n_points(np.array([x, y]).T, 1, np.array([lons, lats]).T) + ds_ = ds.isel(node=indx[0]) + elev_ = ds_[var].values + t_ = [pd.Timestamp(ti) for ti in ds_.time.values] + return pd.Series(elev_, index=t_), float(ds_[xstr]), float(ds_[ystr]) + + +# Function to subset ERA data based on the mesh extent +def subset_era_from_mesh( + era: xr.Dataset, + mesh: xr.Dataset, + input360: bool, + gtype: str, +) -> xr.Dataset: + """ + Selects a subset of ERA data that overlaps with the provided mesh's geographical extent. + + :param era: The ERA dataset from which to select a subset. + :param mesh: The mesh dataset defining the geographical extent for the subset selection. + :param input360: A flag indicating whether the longitude should be adjusted to a 0-360 range. + :return: A subset of the ERA dataset that falls within the mesh's geographical extent. + """ + xmin, xmax, ymin, ymax = mesh.x.min(), mesh.x.max(), mesh.y.min(), mesh.y.max() + if input360: + xmin, xmax = np.mod(xmin + 360, 360), np.mod(xmax + 360, 360) + if xmax <= xmin: + xmin, xmax = 0, 360 + if gtype == "grid": + era_chunk = era.sel(longitude=slice(xmin, xmax), latitude=slice(ymax, ymin)) + else: # for 01280 grid + mask_lon = (era.longitude >= xmin) & (era.longitude <= xmax) + mask_lat = (era.latitude >= ymin) & (era.latitude <= ymax) + mask = mask_lon & mask_lat + indices = np.where(mask)[0] + era_chunk = era.isel(values=indices) + return era_chunk + + +# Function to write meteorological data onto a mesh +def write_meteo_on_mesh( + era_ds: xr.Dataset, + mesh: xr.Dataset, + file_out: str, + n_time_chunk: int, + n_node_chunk: int, + input360: bool = True, + gtype: str = "grid", + ttype: str = "time", +) -> None: + """ + Writes meteorological data from an ERA dataset onto a mesh and saves the result as a zarr file. + + :param era_ds: The ERA dataset with the meteorological data. + :param mesh: The mesh dataset representing the spatial domain. + :param file_out: The path to the output zarr file. + :param n_time_chunk: The size of the time chunks for processing. + :param n_node_chunk: The size of the node chunks for processing. + :param input360: A flag indicating whether the longitude should be adjusted to a 0-360 range. + """ + # Create the temporary dummy zarr file + if os.path.exists(file_out): + shutil.rmtree(file_out) + x, y, tri = mesh.x.values, mesh.y.values, mesh.attrs["ikle2"] - 1 + nnodes = len(x) + ntimes = len(era_ds.time) + zero = da.zeros((ntimes, nnodes), chunks=(n_time_chunk, n_node_chunk)) + + # Define coordinates and data variables for the output dataset + coords = { + "time": era_ds.time, + "node": np.arange(nnodes), + "lon": ("node", x), + "lat": ("node", y), + "triface_nodes": (("face_nodes", "three"), tri), + } + data_vars = {} + for varin in era_ds.data_vars: + data_vars[varin] = (("time", "node"), zero) + xr.Dataset(data_vars=data_vars, coords=coords).to_zarr(file_out, compute=False) + + # in the case of "tstps" + if ttype == "step": + t0 = pd.Timestamp(era_ds.time.values) + seconds = era_ds.step.values / 1e9 + era_ds.time = pd.to_datetime(t0 + pd.Timedelta(seconds=seconds)) + + # Iterate over nodes in chunks and write data to zarr file + for ins in range(0, nnodes, n_node_chunk): + end_node = min(ins + n_node_chunk, nnodes) + node_chunk = np.arange(ins, end_node) + mesh_chunk = mesh.isel(node=slice(ins, end_node)) + era_chunk = subset_era_from_mesh(era_ds, mesh_chunk, input360=input360, gtype=gtype) + + # drop needless coords + main_coords = [c for c in era_chunk.coords] + main_dims = [d for d in era_chunk.dims] + + # Get weights for interpolation + if gtype == "grid": + nx1d = len(era_chunk.longitude) + ny1d = len(era_chunk.latitude) + xx = np.tile(era_chunk.longitude, ny1d).reshape(ny1d, nx1d).T.ravel() + yy = np.tile(era_chunk.latitude, nx1d) + else: # for O1280 grids + main_dims.extend(["longitude", "latitude"]) + xx = era_chunk.longitude.compute() + yy = era_chunk.latitude.compute() + + drop_coords = set(main_coords) - set(main_dims) + era_chunk = era_chunk.drop_vars(drop_coords) + + if input360: + xx[xx > 180] -= 360 + in_xy = np.vstack((xx, yy)).T + out_xy = np.vstack((mesh_chunk.x, mesh_chunk.y)).T + + logger.debug("computing weigths for interpolation..") + vert, wgts, u_x, g_x = get_weights(in_xy, out_xy) # Assuming get_weights is defined elsewhere + + # Interpolate and write data for each variable and time chunk + for var_name in era_chunk.data_vars: + for it_chunk in range(0, ntimes, n_time_chunk): + t_end = min(it_chunk + n_time_chunk, ntimes) + time_chunk = era_chunk.time[it_chunk:t_end] + data_chunk = da.zeros((len(time_chunk), len(node_chunk)), chunks=(n_time_chunk, n_node_chunk)) + for it, t_ in enumerate(time_chunk): + tmp = np.ravel(np.transpose(era_chunk.isel(time=it_chunk + it)[var_name].values)) + data_chunk[it, :] = interp(tmp, vert, wgts, u_x, g_x) # Assuming interp is defined elsewhere + coords = {"time": time_chunk, "node": node_chunk} + ds = xr.Dataset({var_name: (("time", "node"), data_chunk)}, coords=coords) + region = {"time": slice(it_chunk, t_end), "node": slice(ins, end_node)} + ds.to_zarr(file_out, mode="a", region=region) + + +def write_meteo_selafin(outpath, input_atm_zarr): + xatm = xr.open_dataset(input_atm_zarr, engine="zarr") + t0 = pd.Timestamp(xatm.time.values[0]) + # Define a mapping from the original variable names to the new ones + var_map = { + "u10": ("WINDX", "M/S"), + "v10": ("WINDY", "M/S"), + "msl": ("PATM", "PASCAL"), + "tmp": ("TAIR", "DEGREES C"), + } + var_attrs = {} + for var in xatm.data_vars: + if var in var_map: + # Attributes for the variable + var_attrs[var] = (var_map[var][0], var_map[var][1]) + # Add global attributes after concatenation + xatm.attrs["date_start"] = [t0.year, t0.month, t0.day, t0.hour, t0.minute, t0.second] + xatm.attrs["ikle2"] = xatm.triface_nodes.values + 1 + xatm.attrs["variables"] = {var: attrs for var, attrs in var_attrs.items()} + xatm = xatm.rename({"lon": "x", "lat": "y"}) + xatm = xatm.drop_vars(["triface_nodes"]) + xatm.selafin.write(outpath) + remove(input_atm_zarr) + + +def get_boundary_settings(boundary_type, glo_node, bnd_node): + settings = { + "lihbor": 5 if boundary_type == "open" else 2, + "liubor": 6 if boundary_type == "open" else 2, + "livbor": 6 if boundary_type == "open" else 2, + "hbor": 0.0, + "ubor": 0.0, + "vbor": 0.0, + "aubor": 0.0, + "litbor": 5 if boundary_type == "open" else 2, + "tbor": 0.0, + "atbor": 0.0, + "btbor": 0.0, + "nbor": glo_node + 1, + "k": bnd_node + 1, + } + return settings + + +def format_value(value, width, precision=3, is_float=False): + if is_float: + return f"{value:{5}.{precision}f}" + else: + return f"{value:{2}}" + + +def detect_boundary_points_optimized(connectivity_table, npoints): + # Building adjacency list from connectivity table + adjacency_list = {i: [] for i in range(npoints)} + for row in connectivity_table: + for i in range(3): + adjacency_list[row[i]].extend(row[np.arange(3) != i]) + + buf = [] + connectivity_bnd_elt = [] + + pbar = ProgressBar(npoints) + for i in range(npoints): + pbar.update(i) + # Directly accessing the connections for each point + connections = adjacency_list[i] + + uniq, count = np.unique(connections, return_counts=True) + temp = uniq[count == 1].tolist() + buf.extend(temp) + + if temp: + if i in temp: + temp.remove(i) + temp.append(i) + connectivity_bnd_elt.append(temp) + + pbar.finish() + bnd_points = np.unique(buf) + + return np.array(connectivity_bnd_elt), bnd_points + + +def write_cli(inTel, ds, outCli=None, tel_module="telemac2d", global_=True): + """ + (This function is a modification of the existing extract_contour() function + in scripts/python3/pretel/extract_contour.py of the TELEMAC scripts) + + Generic function for extraction of contour from a mesh (with our without + boundary file) + + @param inTel (str) Path to the mesh file + @param ds (xr.Dataset) xarray Dataset of the mesh file (used to extract the boundary types) + @param outCli (str) Path to the output contour file + + @returns (list) List of polygons + """ + # TELEMAC script PART + domains = [] + tel = TelemacFile(inTel) + + connectivity_bnd_elt, bnd_points = detect_boundary_points_optimized(tel.ikle2, tel.npoin2) + + boundaries_ordered, bnd_idx_left, bnd_elt_left = sorting_boundaries( + tel, bnd_points, connectivity_bnd_elt, global_=global_ + ) + domains.append(boundaries_ordered) + + i = 1 + while bnd_elt_left.size != 0: + i += 1 + + boundaries_ordered, bnd_idx_left, bnd_elt_left = sorting_boundaries( + tel, bnd_idx_left, bnd_elt_left, global_=global_ + ) + domains.append(boundaries_ordered) + + # custom pyposeidon part + if outCli is None: + outCli = os.path.splitext(inTel)[0] + ".cli" + node_to_type = dict(zip(ds.node.values, ds.type.values)) # mapping from node to type + domains_bnd = [] + lines = [] + bnd_node = 0 + for domain in domains: + poly_bnd = [] + for bnd in domain: + coord_bnd = [] + for i, glo_node in enumerate(bnd[:-1]): # not taking the last node (not repeating) + x, y = tel.meshx[glo_node], tel.meshy[glo_node] + coord_bnd.append((x, y)) + # Determine boundary type for the current node + boundary_type = node_to_type.get(glo_node, "Unknown") + if boundary_type == "open": + # Get previous and next node indices in a circular manner + prev_node = bnd[i - 1] if i > 0 else bnd[-2] # -2 to skip the repeated last node + next_node = bnd[i + 1] if i < len(bnd) - 2 else bnd[0] # Wrapping around to the first node + # Get boundary types for previous and next nodes + prev_boundary_type = node_to_type.get(prev_node, "Unknown") + next_boundary_type = node_to_type.get(next_node, "Unknown") + # If both adjacent nodes are not 'open', then bnd is closed + if prev_boundary_type != "open" and next_boundary_type != "open": + boundary_type = "Unknown" + boundary_settings = get_boundary_settings(boundary_type, glo_node, bnd_node) + + keys_order = [ + "lihbor", + "liubor", + "livbor", + "hbor", + "ubor", + "vbor", + "aubor", + "litbor", + "tbor", + "atbor", + "btbor", + "nbor", + "k", + ] + if tel_module == "telemac2d": + line = " ".join(str(boundary_settings[key]) for key in keys_order) + lines.append(line) + bnd_node += 1 + poly_bnd.append((coord_bnd, bnd)) + domains_bnd.append(poly_bnd) + + # Writing to file + with open(outCli, "w") as f: + for line in lines: + formatted_line = " ".join( + format_value(value, 3, is_float=isinstance(value, float)) for value in line.split() + ) + f.write(f"{formatted_line}\n") + + return domains_bnd + + +def write_cas(outpath, tel_module, params): + # Load the Jinja2 template + env = jinja2.Environment(loader=jinja2.FileSystemLoader(os.path.join(DATA_PATH))) + + # Define the custom filter for tidal bounds + def repeat_value(value, count): + return ";".join([str(value)] * count) + + env.filters["repeat_value"] = repeat_value + template = env.get_template(tel_module + ".cas") + ouput = template.render(params) + with open(os.path.join(outpath, tel_module + ".cas"), "w") as f: + f.write(ouput) + + +class Telemac: + def __init__(self, **kwargs): + """ + Create a TELEMAC model: + by default : TELEMAC2D is used. + + Args: + rfolder str: the TELEMAC module to use. Can be one of the following: telemac3d, telemac2d, artemis, tomawac + + + """ + tel_module = kwargs.get("module", "telemac2d") + if tel_module not in ["telemac3d", "telemac2d", "artemis", "tomawac"]: + raise ValueError("module must be one of the following: telemac3d, telemac2d, artemis, tomawac") + + rfolder = kwargs.get("rfolder", None) + if rfolder: + self.read_folder(**kwargs) + + self.geometry = kwargs.get("geometry", None) + + if self.geometry: + if isinstance(self.geometry, dict): + self.lon_min = self.geometry["lon_min"] + self.lon_max = self.geometry["lon_max"] + self.lat_min = self.geometry["lat_min"] + self.lat_max = self.geometry["lat_max"] + elif self.geometry == "global": + logger.warning("geometry is 'global'") + elif isinstance(self.geometry, str): + try: + geo = gp.GeoDataFrame.from_file(self.geometry) + except: + logger.error("geometry argument not a valid geopandas file") + sys.exit(1) + + ( + self.lon_min, + self.lat_min, + self.lon_max, + self.lat_max, + ) = geo.total_bounds + else: + logger.warning("no geometry given") + + # coastlines + coastlines = kwargs.get("coastlines", None) + + if coastlines is not None: + try: + coast = gp.GeoDataFrame.from_file(coastlines) + except: + coast = gp.GeoDataFrame(coastlines) + + self.coastlines = coast + + if not hasattr(self, "start_date"): + start_date = kwargs.get("start_date", None) + self.start_date = pd.to_datetime(start_date) + + if not hasattr(self, "end_date"): + if "time_frame" in kwargs: + time_frame = kwargs.get("time_frame", None) + self.end_date = self.start_date + pd.to_timedelta(time_frame) + elif "end_date" in kwargs: + end_date = kwargs.get("end_date", None) + self.end_date = pd.to_datetime(end_date) + self.time_frame = self.end_date - self.start_date + + # if it is the first computation, set origin time (important for restart) + if not hasattr(self, "rdate"): + self.rdate = get_value(self, kwargs, "rdate", self.start_date) + + if not hasattr(self, "end_date"): + # --------------------------------------------------------------------- + logger.warning("model not set properly, No end_date\n") + # --------------------------------------------------------------------- + + # dt is in parameters + params = kwargs.get("parameters", None) + if params is not None: + self.tstep = params.get("dt", None) + else: + self.tstep = None + + self.module = tel_module + self.tide = kwargs.get("tide", False) + tpxo_ = kwargs.get("tpxo_source", None) + if tpxo_ is not None: + self.tide = True + + self.atm = kwargs.get("atm", True) + self.monitor = kwargs.get("monitor", False) + + self.solver_name = TELEMAC_NAME + # restart + restart = get_value(self, kwargs, "hotstart", None) + if restart: + self.restart = pd.to_datetime(restart) + else: + self.restart = None + + # specific to meteo grib files + self.gtype = get_value(self, kwargs, "meteo_gtype", "grid") + self.ttype = get_value(self, kwargs, "meteo_ttype", "time") + self.ncsize = get_value(self, kwargs, "ncsize", 1) + # convert -180/180 to 0-360 + self.input360 = get_value(self, kwargs, "meteo_input360", False) + self.meteo = get_value(self, kwargs, "meteo_source", None) + + # custom user fortran + self.fortran = get_value(self, kwargs, "fortran", None) + + for attr, value in kwargs.items(): + if not hasattr(self, attr): + setattr(self, attr, value) + + setattr(self, "misc", {}) + + # ============================================================================================ + # CONFIG + # ============================================================================================ + def config(self, config_file=None, output=False, **kwargs): + dic = get_value(self, kwargs, "parameters", None) + # param_file = get_value(self,kwargs,'config_file',None) + path = get_value(self, kwargs, "rpath", "./telemac/") + + if config_file: + # --------------------------------------------------------------------- + logger.info("reading parameter file {}\n".format(config_file)) + # --------------------------------------------------------------------- + else: + # --------------------------------------------------------------------- + logger.info("using default " + self.module + " json config file ...\n") + # --------------------------------------------------------------------- + + config_file = os.path.join(DATA_PATH, self.module + ".json") + + # Load the parameters from the JSON file + with open(config_file, "r") as json_file: + config = json.load(json_file) + params = config["params"] + + res_min = get_value(self, kwargs, "resolution_min", 0.5) + # update key values + if self.start_date is not None: + if "telemac" in self.module: + params["datestart"] = self.start_date.strftime("%Y;%m;%d") + params["timestart"] = self.start_date.strftime("%H;%M;%S") + elif "tomawac" in self.module: + params["datestart"] = self.start_date.strftime("%Y%m%d%H%M") + else: + logger.info(f"self.start_date not set for {self.module} yet\n") + + if hasattr(self, "time_frame"): + duration = pd.to_timedelta(self.time_frame).total_seconds() + else: + self.time_frame = self.end_date - self.start_date + duration = self.time_frame.total_seconds() + + params["duration"] = duration + + # export grid data every hour + if self.tstep: + tstep = self.tstep + else: + tstep = calculate_time_step_hourly_multiple(res_min) + params["tstep"] = tstep + params["nb_tsteps"] = int(duration / tstep) + params["tstep_graph"] = int(3600 / tstep) + params["tstep_list"] = int(3600 / tstep) + params["ncsize"] = self.ncsize + + # tide + if self.tide: + params["tide"] = True + params["initial_conditions"] = "TPXO SATELLITE ALTIMETRY" + + # hotstart + if self.restart is not None: + hotout = int((self.restart - self.rdate).total_seconds() / (params["tstep"] * params["tstep_graph"])) + params["hotstart"] = True + params["restart_tstep"] = hotout + + if self.monitor: + params["monitor"] = True + + # custom fortran file + if self.fortran: + params["fortran"] = True + if os.path.isfile(self.fortran): + file = os.path.split(self.fortran)[1] + os.makedirs(os.path.join(path, "user_fortran"), exist_ok=True) + shutil.copy(self.fortran, os.path.join(path, "user_fortran", file)) + elif os.path.isdir(self.fortran): + files_to_copy = [os.path.basename(x) for x in glob.glob(f"{self.fortran}/*.f*")] + files_to_copy += [os.path.basename(x) for x in glob.glob(f"{self.fortran}/*.F*")] + dest_name = os.path.join(path, "user_fortran") + copy_files(dest_name, self.fortran, files_to_copy) + else: + raise ValueError(f"Couldn't find valid FORTRAN files in {self.fortran}") + logger.info(f"Copied FORTRAN files to {path}") + + # update + if dic: + for key in dic.keys(): + params[key] = dic[key] + if "params" in kwargs.keys(): + for key in kwargs["params"].keys(): + params[key] = kwargs["params"][key] + + self.params = params + + if output: + # save params + # --------------------------------------------------------------------- + logger.info("output " + self.module + " CAS file ...\n") + # --------------------------------------------------------------------- + write_cas(path, self.module, params) + + # ============================================================================================ + # METEO + # ============================================================================================ + def force(self, **kwargs): + meteo_source = get_value(self, kwargs, "meteo_source", None) + + kwargs.update({"meteo_source": meteo_source}) + + flag = get_value(self, kwargs, "update", ["all"]) + + z = {**self.__dict__, **kwargs} # merge self and possible kwargs + + # check if files exist + if flag: + if ("meteo" in flag) | ("all" in flag): + self.meteo = pmeteo.Meteo(**z) + else: + logger.info("skipping meteo ..\n") + else: + self.meteo = pmeteo.Meteo(**z) + + def to_force(self, geo, outpath): + # # WRITE METEO FILE + logger.info("saving meteo file.. ") + # define file names + atm_zarr = os.path.join(outpath, "atm.zarr") + geo_mesh = xr.open_dataset(geo, engine="selafin") + meteoFile = os.path.join(outpath, "input_wind.slf") + # temp zarr file + write_meteo_on_mesh( + self.meteo.Dataset, + geo_mesh, + atm_zarr, + 50, + len(geo_mesh.x), + gtype=self.gtype, + ttype=self.ttype, + input360=self.input360, + ) + # zarr to selafin + write_meteo_selafin(meteoFile, atm_zarr) + + # ============================================================================================ + # TPXO + # ============================================================================================ + def tpxo(self, tpxo_suffix="tpxo9_atlas_30_v4", **kwargs): + tpxo_source = get_value(self, kwargs, "tpxo_source", None) + path = get_value(self, kwargs, "rpath", "./telemac") + + lat_min = np.round(self.lat_min - 1 if self.lat_min > -89 else self.lat_min, 2) + lat_max = np.round(self.lat_max + 1 if self.lat_max < 89 else self.lat_max, 2) + lon_min = np.round(self.lon_min - 1, 2) + lon_max = np.round(self.lon_max + 1, 2) + + if lon_min < 0 and lon_max < 0: + lon_min += 360 + lon_max += 360 + + if tpxo_source is None: + # --------------------------------------------------------------------- + logger.error("model not set properly: define tpxo_source\n") + raise ValueError("model not set properly: define tpxo_source") + # --------------------------------------------------------------------- + os.makedirs(os.path.join(path, "TPXO"), exist_ok=True) + + logger.info("extracting tides..\n") + # + lines = [] + lines.append(f"{path}/TPXO/input_sources !") + lines.append(f"{path}/TPXO/Model_Local ! Local area Model name") + lines.append(f"{lat_min} {lat_max} ! Lat limits (degrees N)") + lines.append(f"{lon_min} {lon_max} ! Lon limits (degrees E, range -180 +360)") + with open(f"{path}/TPXO/setup.local", "w") as file: + file.write("\n".join(lines)) + + # input sources + lines = [] + lines.append(f"{tpxo_source}/h_*_{tpxo_suffix}") + lines.append(f"{tpxo_source}/u_*_{tpxo_suffix}") + lines.append(f"{tpxo_source}/grid_{tpxo_suffix}") + with open(f"{path}/TPXO/input_sources", "w") as file: + file.write("\n".join(lines)) + + # output files + lines = [] + lines.append(f"{path}/TPXO/h_LOCAL") + lines.append(f"{path}/TPXO/uv_LOCAL") + lines.append(f"{path}/TPXO/grid_LOCAL") + with open(f"{path}/TPXO/Model_Local", "w") as file: + file.write("\n".join(lines)) + + os.system(f"cp {DATA_PATH}/extract_local_model {path}/TPXO/extract_local_model") + os.system(f"{path}/TPXO/extract_local_model<{path}/TPXO/setup.local") + + # ============================================================================================ + # DEM + # ============================================================================================ + def bath(self, **kwargs): + # z = self.__dict__.copy() + + if self.mesh.Dataset is not None: + kwargs["grid_x"] = self.mesh.Dataset.SCHISM_hgrid_node_x.values + kwargs["grid_y"] = self.mesh.Dataset.SCHISM_hgrid_node_y.values + + dpath = get_value(self, kwargs, "dem_source", None) + + kwargs.update({"dem_source": dpath}) + + flag = get_value(self, kwargs, "update", ["all"]) + # check if files exist + if flag: + if ("dem" in flag) | ("all" in flag): + kwargs.update( + { + "lon_min": self.lon_min, + "lat_min": self.lat_min, + "lon_max": self.lon_max, + "lat_max": self.lat_max, + } + ) + self.dem.Dataset = pdem.dem_on_mesh(self.dem.Dataset, **kwargs) + + if kwargs.get("adjust_dem", True): + coastline = kwargs.get("coastlines", None) + if coastline is None: + logger.warning("coastlines not present, aborting adjusting dem\n") + elif "adjusted" in self.dem.Dataset.data_vars.keys(): + logger.info("Dem already adjusted\n") + elif "fval" in self.dem.Dataset.data_vars.keys(): + logger.info("Dem already adjusted\n") + else: + self.dem.adjust(coastline, **kwargs) + try: + self.get_depth_from_dem() + except AttributeError as e: + logger.info("Keeping bathymetry in hgrid.gr3 due to {}\n".format(e)) + else: + logger.info("dem from mesh file\n") + + def get_depth_from_dem(self): + try: + logger.info("Dem already adjusted\n") + bat = -self.dem.Dataset.fval.values.astype(float) # minus for hydro run + if np.isinf(bat).sum() != 0: + raise Exception("Bathymetry contains Infs") + if np.isnan(bat).sum() != 0: + raise Exception("Bathymetry contains NaNs") + + except: + bat = -self.dem.Dataset.ival.values.astype(float) # minus for hydro run + + self.mesh.Dataset.depth.loc[: bat.size] = bat + logger.info("updating bathymetry ..\n") + + @staticmethod + def mesh_to_slf( + x, y, z, tri, outpath, tag="telemac2d", chezy=None, manning=0.027, friction_type="chezy", **kwargs + ): + # + ds = xr.Dataset( + { + "B": (("time", "node"), z[np.newaxis, :]), + # Add other variables as needed + }, + coords={ + "x": ("node", x), + "y": ("node", y), + "time": [pd.Timestamp.now()], + }, + ) + ds.attrs["ikle2"] = tri + 1 + # bottom friction only in the case of TELEMAC2D + if tag == "telemac2d": + if chezy: + c = np.ones(len(z)) * chezy + else: + if friction_type == "chezy": + c = (abs(z) ** (1 / 6)) / manning + else: + print("only Chezy implemented so far! ") + sys.exit() + ds["W"] = xr.Variable(dims=["node"], data=c) + logger.info("Manning file created..\n") + ds.selafin.write(outpath) + + def to_slf(self, outpath, global_=True, flip_=True, friction_type="chezy", **kwargs): + corrections = get_value(self, kwargs, "mesh_corrections", {"reverse": [], "remove": []}) + + X = self.mesh.Dataset.SCHISM_hgrid_node_x.data + Y = self.mesh.Dataset.SCHISM_hgrid_node_y.data + # depth + Z = -self.mesh.Dataset.depth.data + nan_mask = np.isnan(Z) + inf_mask = np.isinf(Z) + if np.any(nan_mask) or np.any(inf_mask): + Z[nan_mask] = 0 + Z[inf_mask] = 0 + logger.info("Z contains . Cleaning needed.") + # connectivity + IKLE2 = self.mesh.Dataset.SCHISM_hgrid_face_nodes.data + remove(outpath) + + if global_: + # suppress the pole triangles (for now) + IKLE2 = remove_pole_triangles(X, Y, IKLE2, corrections) + if flip_: + # adjust triangles orientation on the dateline + IKLE2 = flip_triangles(X, Y, IKLE2, corrections) + + if IKLE2.shape != self.mesh.Dataset.SCHISM_hgrid_face_nodes.data.shape: + reassign_ikle = True + else: + if not np.array_equal(IKLE2, self.mesh.Dataset.SCHISM_hgrid_face_nodes.data): + reassign_ikle = True + else: + reassign_ikle = False + + if reassign_ikle: + self.mesh.Dataset["SCHISM_hgrid_face_nodes"] = xr.Variable( + ("nSCHISM_hgrid_face", "nMaxSCHISM_hgrid_face_nodes"), + IKLE2, + ) + + # write mesh + chezy = get_value(self, kwargs, "chezy", None) + manning = get_value(self, kwargs, "manning", 0.027) + self.mesh_to_slf(X, Y, Z, IKLE2, outpath, self.module, chezy, manning, friction_type) + + # ============================================================================================ + # EXECUTION + # ============================================================================================ + def create(self, **kwargs): + if not kwargs: + kwargs = self.__dict__.copy() + + # Set background dem as scale for mesh generation + dpath = get_value(self, kwargs, "dem_source", None) + if dpath: + self.dem = pdem.Dem(**kwargs) + # kwargs.update({"dem_source": self.dem.Dataset}) + else: + logger.info("no dem available\n") + + # Mesh + self.mesh = pmesh.set(type="tri2d", **kwargs) + + # set lat/lon from file + if self.mesh.Dataset is not None: + kwargs.update({"lon_min": self.mesh.Dataset.SCHISM_hgrid_node_x.values.min()}) + kwargs.update({"lon_max": self.mesh.Dataset.SCHISM_hgrid_node_x.values.max()}) + kwargs.update({"lat_min": self.mesh.Dataset.SCHISM_hgrid_node_y.values.min()}) + kwargs.update({"lat_max": self.mesh.Dataset.SCHISM_hgrid_node_y.values.max()}) + + self.lon_min = self.mesh.Dataset.SCHISM_hgrid_node_x.values.min() + self.lon_max = self.mesh.Dataset.SCHISM_hgrid_node_x.values.max() + self.lat_min = self.mesh.Dataset.SCHISM_hgrid_node_y.values.min() + self.lat_max = self.mesh.Dataset.SCHISM_hgrid_node_y.values.max() + + # get bathymetry + if len(self.mesh.Dataset.depth) == len(self.mesh.Dataset.SCHISM_hgrid_node_y): + if np.all(self.mesh.Dataset.depth == 0): + logger.info("bathy is set to 0, interpolating dem on mesh") + self.bath(**kwargs) + logger.info("found bathy in mesh file\n") + elif self.mesh.Dataset is not None: + self.bath(**kwargs) + else: + raise ValueError("No bathymetry found") + + # get meteo + if self.atm: + self.force(**kwargs) + + # get tide + if self.tide: + self.tpxo(**kwargs) + + self.config(**kwargs) + + def output(self, **kwargs): + path = get_value(self, kwargs, "rpath", "./telemac/") + global_ = get_value(self, kwargs, "global", True) + chezy = self.params.get("chezy", None) + flip_ = get_value(self, kwargs, "flip", True) + + if not os.path.exists(path): + os.makedirs(path) + + # Mesh related files + if self.mesh.Dataset is not None: + try: + self.get_depth_from_dem() + except AttributeError as e: + logger.info("Keeping bathymetry from hgrid.gr3 ..\n") + + logger.info("saving geometry file.. ") + geo = os.path.join(path, "geo.slf") + self.to_slf(geo, global_=global_, flip_=flip_, chezy=chezy) + self.mesh.to_file(filename=os.path.join(path, "hgrid.gr3")) + write_netcdf(self.mesh.Dataset, geo) + + # WRITE METEO FILE + logger.info("saving meteo file.. ") + meteoFile = os.path.join(path, "input_wind.slf") + atm_zarr = os.path.join(path, "atm.zarr") + geo_mesh = xr.open_dataset(geo, engine="selafin") + if isinstance(self.meteo, list): + self.meteo = pmeteo.Meteo(self.meteo_source) + else: + pass + + if self.meteo: + write_meteo_on_mesh( + self.meteo.Dataset, + geo_mesh, + atm_zarr, + 50, + len(geo_mesh.x), + gtype=self.gtype, + ttype=self.ttype, + input360=self.input360, + ) + write_meteo_selafin(meteoFile, atm_zarr) + + # WRITE BOUNDARY FILE + logger.info("saving boundary file.. ") + domain = write_cli(geo, self.mesh.Dataset, global_=global_) + self.params["N_bc"] = len(domain[0]) + + # WRITE CAS FILE + logger.info("saving CAS file.. ") + write_cas(path, self.module, self.params) + + # --------------------------------------------------------------------- + logger.info("output done\n") + # --------------------------------------------------------------------- + + def run(self, api=True, **kwargs): + calc_dir = get_value(self, kwargs, "rpath", "./telemac/") + cpu = get_value(self, kwargs, "cpu", os.cpu_count()) + cwd = os.getcwd() + + # --------------------------------------------------------------------- + logger.info("executing model\n") + # --------------------------------------------------------------------- + comm = MPI.COMM_WORLD + + cas_file = self.module + ".cas" + os.chdir(calc_dir) + if not tools.is_mpirun_installed(): + logger.warning("mpirun is not installed, ending.. \n") + return + + if self.fortran: + user_fortran = 'user_fortran' + else: + user_fortran = None + + if api: + if self.module == "telemac2d": + # Creation of the instance Telemac2d + study = Telemac2d(cas_file, user_fortran=user_fortran, comm=comm, stdout=0, recompile=True) + elif self.module == "telemac3d": + study = Telemac3d(cas_file, user_fortran=user_fortran, comm=comm, stdout=0, recompile=True) + elif self.module == "tomawac": + study = Tomawac(cas_file, user_fortran=user_fortran, comm=comm, stdout=0, recompile=True) + else: + raise ValueError("this module", self.module, "is not implemented yet!") + + # Testing construction of variable list + _ = study.variables + + study.set_case() + if self.module == "tomawac": + study.set("MODEL.RESULTFILE", "results_2D.slf") + # Initalization + study.init_state_default() + ntimesteps = study.get("MODEL.NTIMESTEPS") + pbar = ProgressBar(ntimesteps) + for it in range(ntimesteps): + study.run_one_time_step() + pbar.update(it) + + # Ending the run + study.finalize() + pbar.finish() + else: + logger.info("no api mode, running telemac manually.. \n") + os.system(f"{self.module}.py {cas_file} --ncsize {cpu} -s") + # + os.chdir(cwd) + + def save(self, **kwargs): + path = get_value(self, kwargs, "rpath", "./telemac/") + + lista = [key for key, value in self.__dict__.items() if key not in ["meteo", "dem", "mesh"]] + dic = {k: self.__dict__.get(k, None) for k in lista} + + mesh = self.__dict__.get("mesh", None) + if isinstance(mesh, str): + dic.update({"mesh": mesh}) + else: + dic.update({"mesh": mesh.__class__.__name__}) + + dem = self.__dict__.get("dem", None) + if isinstance(dem, str): + dic.update({"dem": dem}) + elif isinstance(dem, pdem.Dem): + dic.update({"dem_attrs": dem.Dataset.elevation.attrs}) + + meteo = self.__dict__.get("meteo", None) + if isinstance(meteo, str): + dic.update({"meteo": meteo}) + elif isinstance(meteo, pmeteo.Meteo): + try: + dic.update({"meteo": [meteo.Dataset.attrs]}) + except: + dic.update({"meteo": [x.attrs for x in meteo.Dataset]}) + + coastlines = self.__dict__.get("coastlines", None) + if coastlines is not None: + # Save the path to the serialized coastlines - #130 + coastlines_database = os.path.join(path, "coastlines.json") + coastlines.to_file(coastlines_database) + dic.update({"coastlines": coastlines_database}) + else: + dic.update({"coastlines": None}) + + dic["version"] = pyposeidon.__version__ + + for attr, value in dic.items(): + if isinstance(value, datetime.datetime): + dic[attr] = value.isoformat() + if isinstance(value, pd.Timedelta): + dic[attr] = value.isoformat() + if isinstance(value, pd.DataFrame): + dic[attr] = value.to_dict() + if isinstance(value, gp.GeoDataFrame): + dic[attr] = value.to_json() + + filename = os.path.join(path, f"{self.module}_model.json") + json.dump(dic, open(filename, "w"), indent=4, default=myconverter) + + def execute(self, **kwargs): + self.create(**kwargs) + self.output(**kwargs) + if self.monitor: + self.set_obs() + self.save(**kwargs) + self.run(**kwargs) + + def read_folder(self, rfolder, **kwargs): + self.rpath = rfolder + geo = glob.glob(os.path.join(rfolder, "geo.slf")) + cli = glob.glob(os.path.join(rfolder, "/geo.cli")) + mfiles = glob.glob(os.path.join(rfolder, "/input_wind.slf")) + + mykeys = ["start_year", "start_month", "start_day"] + sdate = [self.params["opt"][x] for x in mykeys] # extract date info from param.nml + sd = "-".join(str(item) for item in sdate) # join in str + sd = pd.to_datetime(sd) # convert to datestamp + + sh = [self.params["opt"][x] for x in ["start_hour", "utc_start"]] # get time attrs + sd = sd + pd.to_timedelta("{}H".format(sh[0] + sh[1])) # complete start_date + + ed = sd + pd.to_timedelta("{}D".format(self.params["core"]["rnday"])) # compute end date based on rnday + + self.start_date = sd # set attrs + self.end_date = ed + + load_mesh = get_value(self, kwargs, "load_mesh", False) + + if load_mesh: + try: + self.mesh = pmesh.set(type="tri2d", mesh_file=hfile) + except: + logger.warning("loading mesh failed") + pass + else: + logger.warning("no mesh loaded") + + load_meteo = get_value(self, kwargs, "load_meteo", False) + + # meteo + if load_meteo is True: + try: + pm = [] + for key, val in mfiles.items(): + msource = xr.open_mfdataset(val) + pm.append(msource) + if len(pm) == 1: + pm = pm[0] + self.meteo = pmeteo.Meteo(meteo_source=pm) + + except: + pm = [] + for key, val in mfiles.items(): + ma = [] + + for ifile in mfiles: + g = xr.open_dataset(ifile) + ts = "-".join(g.time.attrs["base_date"].astype(str)[:3]) + time_r = pd.to_datetime(ts) + try: + times = time_r + pd.to_timedelta(g.time.values, unit="D").round("H") + g = g.assign_coords({"time": times}) + ma.append(g) + except: + logger.warning("loading meteo failed") + break + if ma: + msource = xr.merge(ma) + pm.append(msource) + + if len(pm) == 1: + pm = pm[0] + + self.meteo = pmeteo.Meteo(meteo_source=pm) + + else: + logger.warning("no meteo loaded") + + def hotstart(self, t=None, **kwargs): + filename2d = get_value(self, kwargs, "filename2d", "out_2D.zarr") + ppath = get_value(self, kwargs, "ppath", self.rpath) + out2d = os.path.join(ppath, "outputs", filename2d) + ds = xr.open_dataset(out2d) + t_ = ds.time.values + it = np.where(t_ == t)[0] + xdat = ds.isel(time=it) + hfile = f"hotstart_{t.strftime('%Y%m%d.%H')}.nc" + logger.info("saving hotstart file\n") + xdat.to_netcdf(os.path.join(ppath, f"outputs/{hfile}")) + + @staticmethod + def set_attrs(ds): + lat_coord_standard_name = "latitude" + lon_coord_standard_name = "longitude" + x_units = "degrees_east" + y_units = "degrees_north" + + # set Attrs + ds.longitude.attrs = { + "long_name": "node x-coordinate", + "standard_name": lon_coord_standard_name, + "units": x_units, + "mesh": "TELEMAC_Selafin", + } + + ds.latitude.attrs = { + "long_name": "node y-coordinate", + "standard_name": lat_coord_standard_name, + "units": y_units, + "mesh": "TELEMAC_Selafin", + } + + if "depth" in ds.variables: + ds.depth.attrs = { + "long_name": "Bathymetry", + "units": "meters", + "positive": "down", + "mesh": "TELEMAC_Selafin", + "location": "node", + } + + ds.time.attrs = { + "long_name": "Time", + "base_date": pd.Timestamp(*ds.attrs["date_start"]).strftime("%Y-%m-%d %H:%M:%S"), + "standard_name": "time", + } + + # Dataset Attrs + ds.attrs = { + "Conventions": "CF-1.0, UGRID-1.0", + "title": "TELEMAC Model output", + "source": "TELEMAC model output version vV8P4", + "references": "https://gitlab.pam-retd.fr/otm/telemac-mascaret", + "history": "created by pyposeidon", + "comment": "TELEMAC Model output", + "type": "TELEMAC Model output", + } + return ds + + @staticmethod + def slf_to_xarray(file: str, res_type: ResultTypes = "2D"): + """ + Open a Selafin file and convert it to an xarray dataset. + + Args: + file (str): Path to the Selafin file. + type (str, optional): Type of the Selafin file. Defaults to "2D". + + Returns: + xr.Dataset: The xarray dataset. + """ + assert res_type in ("1D", "2D", "3D") + ds = xr.open_dataset(file, engine="selafin") + dic = {} + varsn = normalize_varnames(ds.variables) + for var, varn in zip(ds.variables, varsn): + dic.update({var: varn}) + ds = ds.rename(dic) + ds["triface_nodes"] = xr.Variable(("triface", "three"), np.array(ds.attrs["ikle2"]) - 1) + if res_type == "1D": + # bug in TELEMAC coord: CONVERT BACK FROM MERCATOR (NOT FIXED YET) + x2, y2 = spherical2longlat(ds.longitude.values, ds.latitude.values, 0, 0) + ds["lon"] = xr.Variable(("node"), x2) + ds["lat"] = xr.Variable(("node"), y2) + return ds + + def results(self, **kwargs): + path = get_value(self, kwargs, "rpath", "./telemac/") + filename = get_value(self, kwargs, "filename", "stations.zarr") + filename2d = get_value(self, kwargs, "filename2d", "out_2D.zarr") + remove_zarr = get_value(self, kwargs, "remove_zarr", True) + chunk = get_value(self, kwargs, "chunk", None) + + logger.info("get combined 2D netcdf files \n") + # check for new IO output + res = os.path.join(path, "results_2D.slf") + xc = self.slf_to_xarray(res) + xc = self.set_attrs(xc) + + os.makedirs(os.path.join(path, "outputs"), exist_ok=True) + out2d = os.path.join(path, "outputs", filename2d) + remove(out2d) + export_xarray(xc, out2d, chunk=chunk, remove_dir=remove_zarr) + + if self.monitor: + logger.info("export observations file\n") + # idx = stations["gindex"] # not need for now + + res_1D = os.path.join(path, "results_1D.slf") + xc = self.slf_to_xarray(res_1D, res_type="1D") + xc = self.set_attrs(xc) + + out_obs = os.path.join(path, "outputs", filename) + remove(out_obs) + export_xarray(xc, out_obs, chunk=chunk, remove_dir=remove_zarr) + logger.info("done with output results files 1D/2D\n") + + def set_obs(self, **kwargs): + path = get_value(self, kwargs, "rpath", "./telemac/") + nspool_sta = get_value(self, kwargs, "nspool_sta", 1) + tg_database = get_value(self, kwargs, "obs", None) + max_dist = get_value(self, kwargs, "max_dist", np.inf) + id_str = get_value(self, kwargs, "id_str", "ioc_code") + offset = get_value(self, kwargs, "offset", 0) + + if tg_database: + logger.info("get stations from {}\n".format(tg_database)) + tg = pd.read_csv(tg_database, index_col=0).reset_index(drop=True) + else: + logger.info("get stations using searvey\n") + geometry = get_value(self, kwargs, "geometry", None) + if geometry == "global": + tg = ioc.get_ioc_stations() + else: + geo_box = shapely.geometry.box(self.lon_min, self.lat_min, self.lon_max, self.lat_max) + tg = ioc.get_ioc_stations(region=geo_box) + tg = tg.reset_index(drop=True) + ### save in compatible to searvey format + tg["country"] = tg.country.values.astype("str") # fix an issue with searvey see #43 therein + logger.info("save station DataFrame \n") + tg_database = os.path.join(path, "stations.json") + tg.to_file(tg_database) + ##### normalize to be used inside pyposeidon + tgn = normalize_column_names(tg.copy()) + + ##### make sure lat/lon are floats + tgn = tgn.astype({"latitude": float, "longitude": float, "location": str}) + ## FOR TIDE GAUGE MONITORING + + logger.info("set in-situ measurements locations \n") + + if self.mesh == "tri2d": + self.mesh = pmesh.set(type="tri2d", mesh_file=self.mesh_file) + + if not self.mesh.Dataset: + logger.warning("no mesh available skipping \n") + return + + gpoints = np.array( + list( + zip( + self.mesh.Dataset.SCHISM_hgrid_node_x.values, + self.mesh.Dataset.SCHISM_hgrid_node_y.values, + ) + ) + ) + + coords = np.array([tgn.longitude.values, tgn.latitude.values]).T + cp, mask = closest_n_points(coords, 1, gpoints, max_dist) + mesh_index = cp + stations = gpoints[cp] + + if len(stations) == 0: + logger.warning("no observations available\n") + + stations = pd.DataFrame(stations, columns=["lon", "lat"]) + stations["z"] = 0 + stations.index += 1 + stations["gindex"] = mesh_index + stations["unique_id"] = stations.index + stations[id_str] = tgn[id_str].values[mask] + stations["longitude"] = stations.lon.values[mask] + stations["latitude"] = stations.lat.values[mask] + # convert to MERCATOR coordinates + # dirty fix (this needs to be fixed in TELEMAC directly) + x, y = longlat2spherical(stations["longitude"], stations["latitude"],0,0) + stations["x"] = x + stations["y"] = y + + self.stations_mesh_id = stations + + logger.info("write out stations.csv file \n") + tgn[mask].to_csv(os.path.join(path, "stations.csv"), index=False) + + logger.info("write out stations.in file \n") + # output to file + with open(os.path.join(path, "station.in"), "w") as f: + f.write(f"1 {stations.shape[0]}\n") # 1st line: number of periods and number of points + f.write( + f"{0 + offset} {int(self.params['duration']) + offset} {self.params['tstep']}\n" + ) # 2nd line: period 1: start time, end time and interval (in seconds) + stations.loc[:, ["x", "y", "unique_id", id_str]].to_csv( + f, header=None, sep=" ", index=False + ) # 3rd-10th line: output points; x coordinate, y coordinate, station number, and station name + + def get_output_data(self, **kwargs): + dic = self.__dict__ + + dic.update(kwargs) + + self.data = data.get_output(**dic) + + def get_station_obs_data(self, **kwargs): + self.station_obs_data = get_obs_data(self.obs, self.start_date, self.end_date) + + def open_thalassa(self, **kwargs): + # open a Thalassa instance to visualize the output + return diff --git a/pyposeidon/tools.py b/pyposeidon/tools.py index 095ed61..7801ab1 100644 --- a/pyposeidon/tools.py +++ b/pyposeidon/tools.py @@ -191,6 +191,10 @@ def get_solver(solver_name: str): from .d3d import d3d solver = d3d + elif solver_name == "telemac": + from .telemac import Telemac + + solver = Telemac else: raise ValueError(f"Unknown solver_name: {solver_name}") return solver diff --git a/pyposeidon/utils/cast.py b/pyposeidon/utils/cast.py index d5f2252..2b5b2f8 100644 --- a/pyposeidon/utils/cast.py +++ b/pyposeidon/utils/cast.py @@ -35,6 +35,8 @@ def set(solver_name: str, **kwargs): instance = D3DCast(**kwargs) elif solver_name == "schism": instance = SchismCast(**kwargs) + elif solver_name == "telemac": + instance = TelemacCast(**kwargs) else: raise ValueError(f"Don't know how to handle solver: {solver_name}") return instance @@ -62,6 +64,24 @@ def symlink_files(rpath: str, ppath: str, filenames: list[str]) -> None: logger.debug("symlinked src -> dst: %s -> %s", src, dst) +def copy_or_symlink(inresfile, outresfile, copy): + if copy: + logger.info("Copying: %s -> %s", inresfile, outresfile) + copy2(inresfile, outresfile) + else: + logger.info("Symlinking`: %s -> %s", inresfile, outresfile) + try: + os.symlink(inresfile, outresfile) + except OSError as e: + if e.errno == errno.EEXIST: + logger.warning("Restart link present\n") + logger.warning("overwriting\n") + os.remove(outresfile) + os.symlink(inresfile, outresfile) + else: + raise e + + class D3DCast: def __init__(self, **kwargs): for attr, value in kwargs.items(): @@ -387,21 +407,8 @@ def run(self, **kwargs): else: logger.info("Hotstart file already existing. Skipping creation.\n") - if copy: - logger.info("Copying: %s -> %s", inresfile, outresfile) - copy2(inresfile, outresfile) - else: - logger.info("Symlinking`: %s -> %s", inresfile, outresfile) - try: - os.symlink(inresfile, outresfile) - except OSError as e: - if e.errno == errno.EEXIST: - logger.warning("Restart link present\n") - logger.warning("overwriting\n") - os.remove(outresfile) - os.symlink(inresfile, outresfile) - else: - raise e + copy_or_symlink(inresfile, outresfile, copy) + # get new meteo logger.info("process meteo\n") @@ -474,3 +481,141 @@ def run(self, **kwargs): logger.info("done for date : %s", self.sdate.strftime("%Y%m%d.%H")) os.chdir(pwd) + + +class TelemacCast: + model_files = [ + "TPXO/grid_LOCAL", + "TPXO/uv_LOCAL", + "TPXO/h_LOCAL", + "geo.slf", + "geo.cli", + "station.in", + ] + + def __init__(self, **kwargs): + for attr, value in kwargs.items(): + setattr(self, attr, value) + + def run(self, **kwargs): + if isinstance(self.model, str): + self.model = pyposeidon.model.read(self.model) + + for attr, value in self.model.__dict__.items(): + if not hasattr(self, attr): + setattr(self, attr, value) + + execute = get_value(self, kwargs, "execute", True) + + copy = get_value(self, kwargs, "copy", False) + + pwd = os.getcwd() + + self.origin = self.model.rpath + ppath = self.ppath + + ppath = os.path.realpath(ppath) + + if not os.path.exists(self.origin): + sys.stdout.write(f"Initial folder not present {self.origin}\n") + sys.exit(1) + + # create the new folder/run path + rpath = os.path.realpath(self.cpath) + if not os.path.exists(rpath): + os.makedirs(rpath) + + model_definition_filename = f"{self.tag}_model.json" + copy2(os.path.join(ppath, model_definition_filename), rpath) # copy the info file + + # load model + with open(os.path.join(rpath, model_definition_filename), "rb") as f: + data = json.load(f) + data = pd.json_normalize(data, max_level=0) + info = data.to_dict(orient="records")[0] + + try: + args = info.keys() & kwargs.keys() # modify dic with kwargs + for attr in list(args): + if isinstance(info[attr], dict): + info[attr].update(kwargs[attr]) + else: + info[attr] = kwargs[attr] + setattr(self, attr, info[attr]) + except Exception as e: + logger.exception("problem with kwargs integration\n") + raise e + + # add optional additional kwargs + for attr in kwargs.keys(): + if attr not in info.keys(): + info[attr] = kwargs[attr] + + info["config_file"] = os.path.join(ppath, self.tag + "_model.json") + + self.time_origin = pd.Timestamp(info["rdate"]) + + # update the properties + info["params"]["rdate"] = self.sdate + info["params"]["start_date"] = self.sdate + info["start_date"] = self.sdate + info["params"]["time_frame"] = self.end_date - self.sdate + info["params"]["end_date"] = self.end_date + if info["tag"] == "telemac2d": + info["params"]["datestart"] = self.time_origin.strftime("%Y;%m;%d") + info["params"]["timestart"] = self.time_origin.strftime("%H;%M;%S") + elif info["tag"] == "tomawac": + info["params"]["datestart"] = self.time_origin.strftime("%Y%m%d%H%M") + + info["params"]["duration"] = pd.to_timedelta(info["params"]["time_frame"]).total_seconds() + info["rpath"] = rpath + + m = pm.set(**info) + m.rpath = rpath + # copy/link necessary files + if copy: + logger.debug("Copy model files") + copy_files(rpath=rpath, ppath=ppath, filenames=self.model_files) + else: + logger.debug("Symlink model files") + symlink_files(rpath=rpath, ppath=ppath, filenames=self.model_files) + + logger.debug(".. done") + + # create restart file + logger.debug("copy restart file") + # link restart file - TELEMAC + inresfile = os.path.join(ppath, f"restart_2D.slf") + outresfile = os.path.join(rpath, "prev_2D.slf") + copy_or_symlink(inresfile, outresfile, True) + # need True for telemac: symlink does not work + + # get new meteo + logger.info("process meteo\n") + if "meteo" in self.__dict__: + info["meteo_source"] = self.meteo + m.force(**info) + geo = os.path.join(rpath, "geo.slf") + m.to_force(geo, rpath) + + # complete information for initial hotstart conditions + info["params"]["computation_continued"] = True + info["params"]["initial_guess_u"] = 2 + info["params"]["initial_guess_h"] = 2 + info["params"]["previous_computation_file"] = "prev_2D.slf" + m.config(output=True, **info) # save new CAS file + + m.config_file = os.path.join(rpath, info["tag"] + "_model.json") + + if m.monitor: + offset = (self.sdate - self.start).total_seconds() + m.set_obs(offset=offset) + m.save() + + if execute: + m.run() + + logger.info("done for date : %s", self.sdate.strftime("%Y%m%d.%H")) + + os.chdir(pwd) + return m diff --git a/pyposeidon/utils/cpoint.py b/pyposeidon/utils/cpoint.py index 7273539..754fac7 100644 --- a/pyposeidon/utils/cpoint.py +++ b/pyposeidon/utils/cpoint.py @@ -6,6 +6,8 @@ import pandas as pd import sklearn.neighbors from scipy.spatial.distance import cdist +from scipy.spatial import cKDTree +import numpy as np def closest_node(node, nodes): diff --git a/pyposeidon/utils/data.py b/pyposeidon/utils/data.py index 810f262..2542323 100644 --- a/pyposeidon/utils/data.py +++ b/pyposeidon/utils/data.py @@ -15,11 +15,9 @@ from pyposeidon.mesh import r2d import pyposeidon.model as pm from pyposeidon.tools import flat_list -from pyposeidon.utils.get_value import get_value -import datetime +from pyposeidon.utils.cpoint import closest_n_points import xarray as xr import glob -import sys import logging import json @@ -33,12 +31,25 @@ def get_output(solver_name: str, **kwargs): solver_class = SchismResults elif solver_name == "d3d": solver_class = D3DResults + elif solver_name == "telemac": + solver_class = TelemacResults else: raise ValueError(f"Unknown solver_name: {solver_name}") instance = solver_class(**kwargs) return instance +def extract_t_elev_2D( + ds: xr.Dataset, x: float, y: float, var: str = "elev", xstr: str = "longitude", ystr: str = "latitude" +): + lons, lats = ds[xstr].values, ds[ystr].values + indx, _ = closest_n_points(np.array([x, y]).T, 1, np.array([lons, lats]).T) + ds_ = ds.isel(node=indx[0]) + elev_ = ds_[var].values + t_ = [pd.Timestamp(ti) for ti in ds_.time.values] + return pd.Series(elev_, index=t_), float(ds_[xstr]), float(ds_[ystr]) + + class D3DResults: def __init__(self, **kwargs): rpath = kwargs.get("rpath", "./d3d/") @@ -205,3 +216,109 @@ def __init__(self, **kwargs): else: self.Dataset = [xr.open_mfdataset(x, combine="by_coords", data_vars="minimal") for x in datai] + + +class TelemacResults: + def __init__(self, **kwargs): + """ + this class has been copied on the Schism class above + although there are a few subtilities that TELEMAC introduced : + 1. there are 1D AND 2D results, they need to be addressed separately + 2. selafin are readable directly in xarray, so we can skip the conversion step + """ + rpath = kwargs.get("rpath", "./telemac/") + res_type = kwargs.get("result_type", "2D") + convert = kwargs.get("convert_results", True) + extract_TS = kwargs.get("extract_TS", False) + station_id_str = kwargs.get("id_str", "ioc_code") + + if res_type not in ["1D", "2D"]: + raise ValueError("results_type needs to be '1D' or '2D'!") + if res_type == "1D": + out_default = "stations.zarr" + else: + out_default = "out_2D.zarr" + + folders = kwargs.get("folders", None) + + if folders: + self.folders = folders + else: + self.folders = [rpath] + + datai = [] + + tag = kwargs.get("tag", "telemac2d") + + misc = kwargs.get("misc", {}) + + for folder in self.folders: + logger.info(" Combining output for folder {}\n".format(folder)) + + with open(folder + "/" + tag + "_model.json", "r") as f: + data = json.load(f) + data = pd.json_normalize(data, max_level=0) + info = data.to_dict(orient="records")[0] + + p = pm.set(**info) + p.misc = misc + + # read from output file + if convert: + xdat = glob.glob(folder + "/outputs/" + out_default) + var, model_xstr, model_ystr = "elev", "longitude", "latitude" + + if len(xdat) > 0: + datai.append(xdat) # append to list + + else: # run merge output + p.results( + filename="stations.zarr", + filename2d="out_2D.zarr", + remove_zarr=False, # remove zarr files after tarballing + ) + + self.misc = p.misc + xdat = glob.glob(folder + "/outputs/" + out_default) + datai.append(xdat) # append to list + else: # read from selafin file + xdat = glob.glob(folder + f"/results_{res_type}.slf") + datai.append(xdat) # append to list + var, model_xstr, model_ystr = "S", "x", "y" + + if not any(datai): + logger.warning("no output files found") + self.Dataset = None + else: + merge = kwargs.get("merge", True) + + if merge: + datai = flat_list(datai) + self.Dataset = xr.open_mfdataset(datai, data_vars="minimal") + else: + self.Dataset = [xr.open_mfdataset(x, data_vars="minimal") for x in datai] + + # export parquet time series + if extract_TS: + if "stations_mesh_id" in p.__dict__: + if isinstance(p.stations_mesh_id, dict): + stations = pd.DataFrame(p.stations_mesh_id) + elif isinstance(p.stations_mesh_id, pd.DataFrame): + stations = p.stations_mesh_id + else: + raise ValueError("stations_mesh_id format not supported") + elif "stations.csv" in os.listdir(rpath): + stations = pd.read_csv(os.path.join(rpath, "stations.csv")) + elif "obs" in self.__dict__: + p.set_obs() + stations = p.stations_mesh_id + else: + raise ValueError("no stations file info found") + + logger.info("extracting parquet files from TELEMAC Selafin output \n") + for i_s, id_ in enumerate(stations[station_id_str]): + s = stations[stations[station_id_str] == id_] + mod, mlon, mlat = extract_t_elev_2D( + self.Dataset, s.longitude.values[0], s.latitude.values[0], var, model_xstr, model_ystr + ) + mod.to_frame().to_parquet(f"{rpath}{id_}.parquet") diff --git a/pyposeidon/utils/global_bgmesh.py b/pyposeidon/utils/global_bgmesh.py index e3bfa14..678e7e6 100644 --- a/pyposeidon/utils/global_bgmesh.py +++ b/pyposeidon/utils/global_bgmesh.py @@ -135,7 +135,6 @@ def fillv(dem, perms, m, **kwargs): gbuffer = kwargs.get("gbuffer", 5) for (i1, i2), (j1, j2) in tqdm(perms, total=len(perms)): - lon1 = dem.longitude.data[i1:i2][0] lon2 = dem.longitude.data[i1:i2][-1] lat1 = dem.latitude.data[j1:j2][0] @@ -155,44 +154,27 @@ def fillv(dem, perms, m, **kwargs): bm = m.isel(nSCHISM_hgrid_node=indices_of_nodes_in_bbox) ids = np.argwhere(np.isnan(bm.depth.values)).flatten() - xw, yw = bm.x.data[ids], bm.y.data[ids] - - var = kwargs.get("var", "adjusted") - logger.info(f"using '{var}' variable data") - - if var not in dem.data_vars: - var = "elevation" - logger.info(f"variable {var} not present switching to 'elevation' data") - - function = kwargs.get("function", "nearest") - logger.info(f"using {function} resample function") - - # Define points with positive bathymetry - x, y = np.meshgrid(de.longitude, de.latitude) - - # fill the nan, if present, with values in order to compute values there if needed. - # de[var].data[np.isnan(de[var].values)] = 9999.0 + grid_x, grid_y = bm.x.data, bm.y.data - orig = pyresample.geometry.SwathDefinition(lons=x, lats=y) # original bathymetry points - targ = pyresample.geometry.SwathDefinition(lons=xw, lats=yw) # wet points + bd = resample(de, grid_x, grid_y, var="adjusted", wet=True, flag=0, function="gauss") - mdem = de[var].values.astype(float) + m["depth"].loc[dict(nSCHISM_hgrid_node=indices_of_nodes_in_bbox)] = -bd - if function == "nearest": - bw = pyresample.kd_tree.resample_nearest(orig, mdem, targ, radius_of_influence=100000, fill_value=np.nan) - elif function == "gauss": - bw = pyresample.kd_tree.resample_gauss( - orig, mdem, targ, radius_of_influence=500000, neighbours=10, sigmas=250000, fill_value=np.nan - ) +def dem_on_mesh(mesh, dem): - m["depth"].loc[dict(nSCHISM_hgrid_node=indices_of_nodes_in_bbox[ids])] = bw + ilats = dem.elevation.chunk("auto").chunks[0] + ilons = dem.elevation.chunk("auto").chunks[1] + if len(ilons) == 1: + ilons = (int(ilons[0] / 2), int(ilons[0] / 2)) -def dem_on_mesh(mesh, dem, **kwargs): + idx = [sum(ilons[:i]) for i in range(len(ilons) + 1)] + jdx = [sum(ilats[:i]) for i in range(len(ilats) + 1)] - logger.info("resample dem on mesh") + blon = list(zip(idx[:-1], idx[1:])) + blat = list(zip(jdx[:-1], jdx[1:])) - perms = get_tiles(dem, **kwargs) + perms = [(x, y) for x in blon for y in blat] fillv(dem, perms, mesh, **kwargs) diff --git a/pyposeidon/utils/norm.py b/pyposeidon/utils/norm.py index 5267ca0..5f84daa 100644 --- a/pyposeidon/utils/norm.py +++ b/pyposeidon/utils/norm.py @@ -2,8 +2,61 @@ import pandas as pd # to be used for name normalization -LONGITUDE_NAMES = {"longitude", "lon", "x", "Lon", "LONGITUDE", "LON", "X"} -LATITUDE_NAMES = {"latitude", "lat", "y", "Lat", "LATITUDE", "LAT", "Y"} +LONGITUDE_NAMES = {"longitude", "lon", "x", "Lon", "LONGITUDE", "LON", "X", "SCHISM_hgrid_node_x"} +LATITUDE_NAMES = {"latitude", "lat", "y", "Lat", "LATITUDE", "LAT", "Y", "SCHISM_hgrid_node_y"} +LOCATION_NAMES = {"location", "loc", "LOCATION", "Station_Name", "Station", "ioc_code", "provider_id"} + +TEL_MAP_LONG = { + "VELOCITY U ": "u-current-velocity", + "VELOCITY V ": "v-current-velocity", + "FREE SURFACE ": "free-surface", + "WAVE HEIGHT HM0 ": "significant-wave-height", + "MEAN DIRECTION ": "mean-direction", + "MEAN PERIOD TM01": "mean-period-tm01", + "MEAN PERIOD TM02": "mean-period-tm02", + "MEAN PERIOD TMOY": "mean-period-tmoy", + "PEAK PERIOD TPR8": "peak-period-tpr8", + "PEAK PERIOD TPD ": "peak-period-tpd", + "WIND VELOCITY U ": "10m-u-component-of-wind", + "WIND VELOCITY V ": "10m-v-component-of-wind", + "SURFACE PRESSURE": "mean-sea-level-pressure", + "AIR TEMPERATURE ": "air-temperature", +} +TEL_MAP_SHORT = { + "VELOCITY U ": "u", + "VELOCITY V ": "v", + "FREE SURFACE ": "elev", + "WAVE HEIGHT HM0 ": "hm0", + "MEAN DIRECTION ": "dir", + "MEAN PERIOD TM01": "tm01", + "MEAN PERIOD TM02": "tm02", + "MEAN PERIOD TMOY": "tmoy", + "PEAK PERIOD TPR8": "tp", + "PEAK PERIOD TPD ": "tp", + "WIND VELOCITY U ": "u10", + "WIND VELOCITY V ": "v10", + "SURFACE PRESSURE": "msl", + "AIR TEMPERATURE ": "tair", +} + +TEL_MAP_SHORT2 = { + "x": "longitude", + "y": "latitude", + "U": "u", + "V": "v", + "S": "elev", + "HM0": "hm0", + "DIRM": "dir", + "TM01": "tm01", + "TM02": "tm02", + "TMOY": "tmoy", + "TPR8": "tp", + "TPD": "tp", + "WINDX": "u10", + "WINDY": "v10", + "PATM": "msl", + "TAIR": "tair", +} def normalize_coord_names(dataset: xr.Dataset) -> xr.Dataset: @@ -28,6 +81,12 @@ def normalize_coord_names(dataset: xr.Dataset) -> xr.Dataset: def normalize_column_names(dataframe: pd.DataFrame) -> pd.DataFrame: """Return a dataframe with columns containing "longitude" and "latitude" """ cols = dataframe.columns.tolist() + # location + for location in LOCATION_NAMES: + if location in cols: + break + else: + raise ValueError(f"Couldn't normalize location: {cols}") # longitude for lon_name in LONGITUDE_NAMES: if lon_name in cols: @@ -41,8 +100,20 @@ def normalize_column_names(dataframe: pd.DataFrame) -> pd.DataFrame: else: raise ValueError(f"Couldn't normalize latitude: {cols}") - dic = {lon_name: "longitude", lat_name: "latitude"} + dic = {lon_name: "longitude", lat_name: "latitude", location: "location"} new_cols = [dic.get(n, n) for n in cols] dataframe.columns = new_cols return dataframe + + +def normalize_varnames(varnames, mapping=TEL_MAP_SHORT2, mapping1=TEL_MAP_SHORT): + normalized_names = [] + for v in varnames: + if v in mapping: + normalized_names.append(mapping[v]) + elif v in mapping1: + normalized_names.append(mapping1[v]) + else: + normalized_names.append(v.strip().lower()) + return normalized_names diff --git a/pyposeidon/utils/post.py b/pyposeidon/utils/post.py index 9381aa9..d15e754 100644 --- a/pyposeidon/utils/post.py +++ b/pyposeidon/utils/post.py @@ -6,6 +6,9 @@ import numpy as np from tqdm.auto import tqdm import glob +import numcodecs +import tarfile +import shutil import pyposeidon from pyposeidon.tools import to_geodataframe @@ -51,6 +54,88 @@ def get_encoding(ename): } +def remove(path): + try: + if os.path.isfile(path): + os.remove(path) # Remove a file + elif os.path.isdir(path): + if not os.listdir(path): # Check if the directory is empty + os.rmdir(path) + else: + shutil.rmtree(path) + except OSError as e: + print(f"Error: {e.strerror}") + + +def tar_directory(input_directory, output_filename, compress=False): + """ + Tar a Zarr directory. + + Parameters + ---------- + input_directory : str + The path to the Zarr directory to archive. + output_filename : str + The path and filename for the output archive. + compress : bool, optional + Whether to compress the archive with gzip. Default is True. + """ + mode = "w:gz" if compress else "w" + with tarfile.open(output_filename, mode) as tar: + tar.add(input_directory, arcname=os.path.basename(input_directory)) + + +def export_xarray(ds, filename_out, chunk=None, remove_dir=False): + """ + Export an xarray dataset to netcdf or zarr format. + + Parameters + ---------- + ds : xr.Dataset + The xarray dataset to export. + filename_out : str + The path and filename of the output file. + chunk : dict, optional + The chunk size to use when saving the dataset to zarr format, by default None. + example: chunk = {'nodes': 1000, 'time': 100} + + Returns + ------- + None + + Raises + ------ + ValueError + If the filename does not have a .nc or .zarr extension. + """ + if not filename_out.endswith(".nc") and not filename_out.endswith(".zarr"): + raise ValueError("Invalid filename extension. Must be .nc or .zarr") + if filename_out.endswith(".nc"): + encoding = {} + default_encoding = {"zlib": True, "complevel": 1} + for varname in list(ds.variables): + encoding[varname] = default_encoding + if chunk: + chunksizes = dict(ds[varname].sizes) + for key in chunk: + if key in chunksizes: + chunksizes[key] = chunk[key] + encoding[varname]["chunksizes"] = list(chunksizes.values()) + ds.to_netcdf(filename_out, encoding=encoding) + elif filename_out.endswith(".zarr"): + compressor = numcodecs.Blosc(cname="zstd", clevel=1) + if chunk is not None: + ds = ds.chunk(chunk) + encoding = {} + for varname in list(ds.variables): + encoding.update({varname: {"compressor": compressor}}) + ds.to_zarr(filename_out, encoding=encoding, consolidated=True) + tar_directory(filename_out, filename_out + ".tar") + if remove_dir: + remove(filename_out) + logger.info(f"Removed directory {filename_out}") + + def save_leads(stations, st, start_date, dt, leads, rpath="./skill/"): ## save results in lead chunks diff --git a/pyproject.toml b/pyproject.toml index 97201d1..0e62c4e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -109,6 +109,11 @@ mkdocs = "*" mkdocstrings-python = "*" pymdown-extensions = "*" + +[tool.poetry.group.telemac.dependencies] +mpi4py = "*" +xarray-selafin = "*" + [build-system] requires = ["poetry-core>=1.0.0"] build-backend = "poetry.core.masonry.api" @@ -127,6 +132,7 @@ filterwarnings = [ "ignore:A private pytest class or function was used.:pytest.PytestDeprecationWarning" ] markers = [ + "telemac: mark a test as a Telemac based test. Needs --runtelemac to run", "schism: mark a test as a Schism based test. Needs --runschism to run", "delft: mark a test as a Delft3D based test. Needs --rundelft to run", "slow: mark a test as a slow one. Needs --runslow to run", diff --git a/scripts/generate_envs.sh b/scripts/generate_envs.sh index a8dc06b..2d9a944 100755 --- a/scripts/generate_envs.sh +++ b/scripts/generate_envs.sh @@ -9,12 +9,21 @@ set -xeuo pipefail ./scripts/merge_environment_yaml.py ./dependencies/python3.11.yml ./dependencies/binary.yml | sed '/^$/d' > ./environments/binary-p3.11.yml ./scripts/merge_environment_yaml.py ./dependencies/python3.12.yml ./dependencies/binary.yml | sed '/^$/d' > ./environments/binary-p3.12.yml +# Binary + Telemac +./scripts/merge_environment_yaml.py ./dependencies/python3.9.yml ./dependencies/binary.yml ./dependencies/telemac_mpich.yml > ./environments/binary-telemac-mpich-p3.9.yml +./scripts/merge_environment_yaml.py ./dependencies/python3.10.yml ./dependencies/binary.yml ./dependencies/telemac_mpich.yml > ./environments/binary-telemac-mpich-p3.10.yml +./scripts/merge_environment_yaml.py ./dependencies/python3.11.yml ./dependencies/binary.yml ./dependencies/telemac_mpich.yml > ./environments/binary-telemac-mpich-p3.11.yml +./scripts/merge_environment_yaml.py ./dependencies/python3.9.yml ./dependencies/binary.yml ./dependencies/telemac_openmpi.yml > ./environments/binary-telemac-openmpi-p3.9.yml +./scripts/merge_environment_yaml.py ./dependencies/python3.10.yml ./dependencies/binary.yml ./dependencies/telemac_openmpi.yml > ./environments/binary-telemac-openmpi-p3.10.yml +./scripts/merge_environment_yaml.py ./dependencies/python3.11.yml ./dependencies/binary.yml ./dependencies/telemac_openmpi.yml > ./environments/binary-telemac-openmpi-p3.11.yml + # Base ./scripts/merge_environment_yaml.py ./dependencies/python3.9.yml ./dependencies/binary.yml ./dependencies/main.yml | sed '/^$/d' > ./environments/base-p3.9.yml ./scripts/merge_environment_yaml.py ./dependencies/python3.10.yml ./dependencies/binary.yml ./dependencies/main.yml | sed '/^$/d' > ./environments/base-p3.10.yml ./scripts/merge_environment_yaml.py ./dependencies/python3.11.yml ./dependencies/binary.yml ./dependencies/main.yml | sed '/^$/d' > ./environments/base-p3.11.yml ./scripts/merge_environment_yaml.py ./dependencies/python3.12.yml ./dependencies/binary.yml ./dependencies/main.yml | sed '/^$/d' > ./environments/base-p3.12.yml + # Viz ./scripts/merge_environment_yaml.py ./dependencies/python3.9.yml ./dependencies/binary.yml ./dependencies/main.yml ./dependencies/viz.yml | sed '/^$/d' > ./environments/viz-p3.9.yml ./scripts/merge_environment_yaml.py ./dependencies/python3.10.yml ./dependencies/binary.yml ./dependencies/main.yml ./dependencies/viz.yml | sed '/^$/d' > ./environments/viz-p3.10.yml diff --git a/scripts/generate_locks.sh b/scripts/generate_locks.sh index ad766b2..44fe9f8 100755 --- a/scripts/generate_locks.sh +++ b/scripts/generate_locks.sh @@ -33,6 +33,21 @@ conda-lock render -p osx --filename-template locks/conda-macos-latest-binary-p3. conda-lock render -p osx --filename-template locks/conda-macos-latest-binary-p3.11.lock locks/binary-p3.11.yml conda-lock render -p osx --filename-template locks/conda-macos-latest-binary-p3.12.lock locks/binary-p3.12.yml +# Telemac +# conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-mpich-p3.9.yml --lockfile locks/binary-telemac-mpich-p3.9.yml +conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-mpich-p3.10.yml --lockfile locks/binary-telemac-mpich-p3.10.yml +conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-mpich-p3.11.yml --lockfile locks/binary-telemac-mpich-p3.11.yml +conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-openmpi-p3.9.yml --lockfile locks/binary-telemac-openmpi-p3.9.yml +conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-openmpi-p3.10.yml --lockfile locks/binary-telemac-openmpi-p3.10.yml +conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-openmpi-p3.11.yml --lockfile locks/binary-telemac-openmpi-p3.11.yml +# conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-mpich-p3.9.lock locks/binary-telemac-mpich-p3.9.yml +conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-mpich-p3.10.lock locks/binary-telemac-mpich-p3.10.yml +conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-mpich-p3.11.lock locks/binary-telemac-mpich-p3.11.yml +conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-openmpi-p3.9.lock locks/binary-telemac-openmpi-p3.9.yml +conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-openmpi-p3.10.lock locks/binary-telemac-openmpi-p3.10.yml +conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-openmpi-p3.11.lock locks/binary-telemac-openmpi-p3.11.yml + + # Pyposeidon-Base # Pyposeidon-Viz # Pyposeidon-Full diff --git a/tests/conftest.py b/tests/conftest.py index 671ee8c..d40ab74 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -30,6 +30,7 @@ def move_tests_to_the_end(items): def pytest_addoption(parser): + parser.addoption("--runtelemac", action="store_true", default=False, help="run telemac tests") parser.addoption("--runschism", action="store_true", default=False, help="run schism tests") parser.addoption("--rundelft", action="store_true", default=False, help="run delft tests") parser.addoption("--runslow", action="store_true", default=False, help="run slow tests") @@ -37,11 +38,13 @@ def pytest_addoption(parser): def pytest_collection_modifyitems(config, items): + should_run_telemac = config.getoption("--runtelemac") should_run_schism = config.getoption("--runschism") should_run_delft = config.getoption("--rundelft") should_run_slow = config.getoption("--runslow") should_run_viz = config.getoption("--runviz") + skip_telemac = pytest.mark.skip(reason="need --runtelemac option to run") skip_schism = pytest.mark.skip(reason="need --runshism option to run") skip_delft = pytest.mark.skip(reason="need --rundelft option to run") skip_slow = pytest.mark.skip(reason="need --runslow option to run") @@ -51,6 +54,8 @@ def pytest_collection_modifyitems(config, items): for item in items: if any(mark in item.keywords for mark in run_last_marks): item.add_marker(RUNLAST_MARK) + if "telemac" in item.keywords and not should_run_telemac: + item.add_marker(skip_telemac) if "schism" in item.keywords and not should_run_schism: item.add_marker(skip_schism) if "delft" in item.keywords and not should_run_delft: diff --git a/tests/test_telemac.py b/tests/test_telemac.py new file mode 100644 index 0000000..54e2bf7 --- /dev/null +++ b/tests/test_telemac.py @@ -0,0 +1,116 @@ +import os +import numpy as np +import xarray as xr +import multiprocessing + +# from . import DATA_DIR +import pathlib + +import pyposeidon +import pytest + +from . import DATA_DIR + +try: + import telapy +except ImportError: + pytest.skip(reason="requires telapy", allow_module_level=True) + + +MESH_FILE = (DATA_DIR / "hgrid.gr3").as_posix() +DEM_FILE = (DATA_DIR / "dem.nc").as_posix() + +# define in a dictionary the properties of the model.. +case0 = { + "solver_name": "telemac", + "mesh_file": MESH_FILE, + "start_date": "2017-10-1 0:0:0", + "time_frame": "12H", + "meteo_source": [(DATA_DIR / "erai.grib").as_posix()], # meteo file + "dem_source": DEM_FILE, + "update": ["all"], # update only meteo, keep dem + "parameters": { + "chezy": 30, + "dt": 50, + }, +} + +case1 = { + "solver_name": "telemac", + "mesh_file": MESH_FILE, + "start_date": "2017-10-1 0:0:0", + "end_date": "2017-10-2 0:0:0", # optional instead of time_frame + "dem_source": DEM_FILE, + "meteo_source": [(DATA_DIR / "erai.grib").as_posix()], # meteo file + "update": ["all"], # update only meteo, keep dem + "parameters": { + "chezy": 100, + "dt": 200, + }, +} + + +case2 = { + "solver_name": "telemac", + "mesh_file": MESH_FILE, + "start_date": "2011-1-1 0:0:0", + "time_frame": "12H", + "meteo_source": [(DATA_DIR / "era5.grib").as_posix()], # meteo file + "dem_source": DEM_FILE, + "update": ["all"], # update only meteo, keep dem + "parameters": { + "dt": 200, + }, +} + + +case3 = { + "solver_name": "telemac", + "mesh_file": MESH_FILE, + "module": "tomawac", + "start_date": "2011-1-1 0:0:0", + "time_frame": "12H", + "meteo_source": [(DATA_DIR / "era5.grib").as_posix()], # meteo file + "dem_source": DEM_FILE, + "update": ["all"], # update only meteo, keep dem + "parameters": { + "dt": 1800, + }, +} + + +@pytest.mark.telemac +@pytest.mark.parametrize("case", [case0, case1, case2, case3]) +def test_telemac(tmpdir, case): + # initialize a model + rpath = str(tmpdir) + "/" + case.update({"rpath": rpath}) # use tmpdir for running the model + + b = pyposeidon.model.set(**case) + b.create() + b.mesh.Dataset.type[:] = "closed" + b.output() + b.save() + b.run() + b.results() + zarr_tar = b.rpath + "/outputs/out_2D.zarr.tar" + assert os.path.exists(zarr_tar) + a = pyposeidon.model.read(rpath + b.module + "_model.json") # read model + a.create() + a.mesh.Dataset.type[:] = "closed" + a.output() + a.save() + a.run() + a.results() + zarr_tar = a.rpath + "/outputs/out_2D.zarr.tar" + res = a.rpath + "/results_2D.slf" + assert os.path.exists(zarr_tar) + ds = xr.open_dataset(res, engine="selafin") + if "WH" in ds.variables: + max_WH = ds.WH.max().values + assert np.isclose(max_WH, 4.13, atol=1e-2) + elif "S" in ds.variables: + max_S = ds.S.max().values + assert max_S < 1 + else: + pass diff --git a/tests/test_telemac_cast.py b/tests/test_telemac_cast.py new file mode 100644 index 0000000..96a172a --- /dev/null +++ b/tests/test_telemac_cast.py @@ -0,0 +1,200 @@ +from copy import deepcopy +import datetime +import filecmp +import os +import xarray as xr + +import numpy as np +import pytest +import pyposeidon +from pyposeidon.utils import cast, data +import pandas as pd + +from . import DATA_DIR + + +MESH_FILE = (DATA_DIR / "hgrid.gr3").as_posix() +DEM_FILE = (DATA_DIR / "dem.nc").as_posix() +METEO_FILES_1 = [(DATA_DIR / name).as_posix() for name in ("uvp_2018100100.grib", "uvp_2018100112.grib")] +METEO_FILES_2 = [ + (DATA_DIR / name).as_posix() + for name in ( + "uvp_2018100100.grib", + "uvp_2018100112.grib", + "uvp_2018100200.grib", + "uvp_2018100212.grib", + ) +] + + +# define in a dictionary the properties of the model.. +test_case = { + "solver_name": "telemac", + "mesh_file": MESH_FILE, + "tag": "telemac2d", + "start_date": "2018-10-1 0:0:0", + "time_frame": "12h", + "dem_source": DEM_FILE, + "meteo_source": METEO_FILES_1, + "meteo_merge": "last", # combine meteo + "meteo_combine_by": "nested", + "meteo_xr_kwargs": {"concat_dim": "step"}, + "update": ["all"], # update only meteo, keep dem + "parameters": { + "dt": 200, + }, +} + +# define in a dictionary the properties of the model.. +check = { + "solver_name": "telemac", + "mesh_file": MESH_FILE, + "tag": "telemac2d", + "start_date": "2018-10-1 0:0:0", + "time_frame": "36h", + "dem_source": DEM_FILE, + "meteo_source": METEO_FILES_2, + "meteo_merge": "last", # combine meteo + "meteo_combine_by": "nested", + "meteo_xr_kwargs": {"concat_dim": "step"}, + "update": ["all"], # update only meteo, keep dem + "parameters": { + "dt": 200, + }, +} + + +@pytest.mark.telemac +@pytest.mark.parametrize( + "copy", + [pytest.param(True, id="copy files"), pytest.param(False, id="symlink files")], +) +def test_telemac_cast(tmpdir, copy): + base_rpath = os.path.join(tmpdir, "telemac") + original_rpath = os.path.join(base_rpath, "20181001.00") + next_rpath = os.path.join(base_rpath, "20181001.12") + + # initialize a model + original_model_info = deepcopy(test_case) + original_model_info.update( + { + "rpath": original_rpath, + }, + ) + original_model = pyposeidon.model.set(**original_model_info) + original_model.create() # constructs all required parts e.g. mesh, dem, meteo, etc. + original_model.mesh.Dataset.type[:] = "closed" + original_model.output() # save to files + original_model.save() # saves the json model reference file + # original_model.set_obs() # setup station points + original_model.run() + + casted = cast.set( + solver_name="telemac", + model=original_model, + ppath=original_model.rpath, # old path + cpath=next_rpath, # new path + meteo=METEO_FILES_1, + sdate=pd.to_datetime("2018-10-01 12:00:00"), + # end_date=end_, # new end date + start=pd.to_datetime("2018-10-01 12:00:00"), # start + copy=copy, + ) + casted.run(execute=False) + + copied_files = [] + if copy: + copied_files.extend(cast.TelemacCast.model_files) + + for filename in copied_files: + original_file = os.path.join(original_model.rpath, filename) + if os.path.exists(original_file): + copied_file = os.path.join(next_rpath, filename) + assert os.path.exists(copied_file) + assert not os.path.islink(copied_file) + assert filecmp.cmp(original_file, copied_file, shallow=False) + + if not copy: + for filename in cast.TelemacCast.model_files: + original_file = os.path.join(original_model.rpath, filename) + if os.path.exists(original_file): + symlinked_file = os.path.join(next_rpath, filename) + assert os.path.exists(symlinked_file) + assert os.path.islink(symlinked_file) + if not os.path.islink(original_file): + assert os.path.realpath(symlinked_file) == original_file + + +@pytest.mark.telemac +def test_telemac_cast_workflow(tmpdir): + # initialize a model + rpath = str(tmpdir) + "/telemac/" + test_case.update({"rpath": rpath + "20181001.00/"}) # use tmpdir for running the model + + b = pyposeidon.model.set(**test_case) + + b.create() + b.mesh.Dataset.type[:] = "closed" + b.output() + b.save() + b.run() + + # creating a time sequence of the runs + start_date = pd.to_datetime("2018-10-1 0:0:0") + end_date = pd.to_datetime("2018-10-2 0:0:0") + date_list = pd.date_range(start_date, end_date, freq="12h") + + # creating a sequence of folder to store the runs. In this case we name them after the date attribute. + # NOTE: the first folder is the first run already performed + rpaths = [rpath + datetime.datetime.strftime(x, "%Y%m%d.%H") + "/" for x in date_list] + + # creating a sequence of folder from which we read the meteo. + meteo = [] + for date in date_list: + end_date = pd.to_datetime(date) + pd.to_timedelta("12h") + end_date = end_date.strftime(format="%Y-%m-%d %H:%M:%S") + dr = pd.date_range(date, end_date, freq="12h") + names = ["uvp_" + datetime.datetime.strftime(x, "%Y%m%d%H") + ".grib" for x in dr] + dur = [(DATA_DIR / name).as_posix() for name in names] + meteo.append(dur) + + # set cast + for l in range(len(rpaths) - 1): + h = cast.set( + solver_name="telemac", + model=b, + ppath=rpaths[l], + cpath=rpaths[l + 1], + meteo=meteo[l + 1], + sdate=date_list[l + 1], + end_date=date_list[l + 1] + pd.to_timedelta("12h"), + start=date_list[l + 1], + ) + + b2 = h.run(execute=False) + b2.run() + + # Run check case - Total duration + check.update({"rpath": rpath + "check/"}) # use tmpdir for running the model + + c = pyposeidon.model.set(**check) + + c.create() + c.mesh.Dataset.type[:] = "closed" + c.output() + c.save() + c.run() + + # COMPARE + ds = xr.open_mfdataset([p + "/results_2D.slf" for p in rpaths]) + ds = ds.drop_duplicates("time", keep="first") # remove duplicate time stamps + ds_check = xr.open_dataset(rpath + "/check/results_2D.slf") + + for var in ["S"]: + flag = False + inode = np.random.randint(len(ds.x)) + mdif = np.abs(ds[var].isel(node=inode).values - ds_check[var].isel(node=inode).values).max() + if mdif < 1.0e-14: + flag = True + + assert flag