diff --git a/dependencies/binary.yml b/dependencies/binary.yml index 7f7ce539..a0379c64 100644 --- a/dependencies/binary.yml +++ b/dependencies/binary.yml @@ -1,5 +1,4 @@ channels: - - gbrey - conda-forge dependencies: - compilers diff --git a/dependencies/dev.yml b/dependencies/dev.yml index 72c54d63..01f24d48 100644 --- a/dependencies/dev.yml +++ b/dependencies/dev.yml @@ -2,7 +2,6 @@ channels: - "conda-forge" - - "gbrey" dependencies: - "black<24.0" diff --git a/dependencies/docs.yml b/dependencies/docs.yml index f5fb8885..88a3a3a5 100644 --- a/dependencies/docs.yml +++ b/dependencies/docs.yml @@ -2,7 +2,6 @@ channels: - "conda-forge" - - "gbrey" dependencies: - "mkdocs" diff --git a/dependencies/main.yml b/dependencies/main.yml index 0cb75638..9d976526 100644 --- a/dependencies/main.yml +++ b/dependencies/main.yml @@ -1,7 +1,6 @@ --- channels: - "conda-forge" - - "gbrey" dependencies: - "bottleneck" diff --git a/dependencies/python3.10.yml b/dependencies/python3.10.yml index dffc4b84..d551df24 100644 --- a/dependencies/python3.10.yml +++ b/dependencies/python3.10.yml @@ -1,5 +1,4 @@ channels: - - gbrey - conda-forge dependencies: - python=3.10 diff --git a/dependencies/python3.11.yml b/dependencies/python3.11.yml index df8be7cd..a7a34d40 100644 --- a/dependencies/python3.11.yml +++ b/dependencies/python3.11.yml @@ -1,5 +1,4 @@ channels: - - gbrey - conda-forge dependencies: - python=3.11 diff --git a/dependencies/python3.12.yml b/dependencies/python3.12.yml index 8ef45069..3b21d6a7 100644 --- a/dependencies/python3.12.yml +++ b/dependencies/python3.12.yml @@ -1,5 +1,4 @@ channels: - - gbrey - conda-forge dependencies: - python=3.12 diff --git a/dependencies/python3.9.yml b/dependencies/python3.9.yml index c372b2df..e6fe6679 100644 --- a/dependencies/python3.9.yml +++ b/dependencies/python3.9.yml @@ -1,5 +1,4 @@ channels: - - gbrey - conda-forge dependencies: - python=3.9 diff --git a/dependencies/telemac.yml b/dependencies/telemac.yml new file mode 100644 index 00000000..fb64a988 --- /dev/null +++ b/dependencies/telemac.yml @@ -0,0 +1,4 @@ +channels: + - conda-forge +dependencies: + - opentelemac diff --git a/dependencies/telemac_mpich.yml b/dependencies/telemac_mpich.yml deleted file mode 100644 index b3214a39..00000000 --- a/dependencies/telemac_mpich.yml +++ /dev/null @@ -1,5 +0,0 @@ -channels: - - conda-forge - - tomsail -dependencies: - - opentelemac=main*=mpich* diff --git a/dependencies/telemac_openmpi.yml b/dependencies/telemac_openmpi.yml deleted file mode 100644 index 467520b8..00000000 --- a/dependencies/telemac_openmpi.yml +++ /dev/null @@ -1,5 +0,0 @@ -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 deleted file mode 100644 index 8d069516..00000000 --- a/environments/binary-telemac-mpich-p3.10.yml +++ /dev/null @@ -1,15 +0,0 @@ -channels: - - conda-forge -dependencies: - - compilers - - eccodes - - ffmpeg - - gdal - - geos - - gmsh>=4.9.3 - - jigsaw>=0.9.12 - - opentelemac - - pip - - proj - - python=3.10 - - numpy<2 diff --git a/environments/binary-telemac-mpich-p3.11.yml b/environments/binary-telemac-mpich-p3.11.yml deleted file mode 100644 index 8aff5142..00000000 --- a/environments/binary-telemac-mpich-p3.11.yml +++ /dev/null @@ -1,15 +0,0 @@ -channels: - - conda-forge -dependencies: - - compilers - - eccodes - - ffmpeg - - gdal - - geos - - gmsh>=4.9.3 - - jigsaw>=0.9.12 - - opentelemac - - pip - - proj - - python=3.11 - - numpy<2 diff --git a/environments/binary-telemac-openmpi-p3.10.yml b/environments/binary-telemac-p3.10.yml similarity index 93% rename from environments/binary-telemac-openmpi-p3.10.yml rename to environments/binary-telemac-p3.10.yml index 8d069516..26b3fa35 100644 --- a/environments/binary-telemac-openmpi-p3.10.yml +++ b/environments/binary-telemac-p3.10.yml @@ -12,4 +12,4 @@ dependencies: - pip - proj - python=3.10 - - numpy<2 + diff --git a/environments/binary-telemac-openmpi-p3.11.yml b/environments/binary-telemac-p3.11.yml similarity index 93% rename from environments/binary-telemac-openmpi-p3.11.yml rename to environments/binary-telemac-p3.11.yml index 8aff5142..2afc0846 100644 --- a/environments/binary-telemac-openmpi-p3.11.yml +++ b/environments/binary-telemac-p3.11.yml @@ -12,4 +12,4 @@ dependencies: - pip - proj - python=3.11 - - numpy<2 + diff --git a/environments/binary-telemac-openmpi-p3.9.yml b/environments/binary-telemac-p3.12.yml similarity index 85% rename from environments/binary-telemac-openmpi-p3.9.yml rename to environments/binary-telemac-p3.12.yml index 197080b5..ebfc3cf8 100644 --- a/environments/binary-telemac-openmpi-p3.9.yml +++ b/environments/binary-telemac-p3.12.yml @@ -11,5 +11,5 @@ dependencies: - opentelemac - pip - proj - - python=3.9 - - numpy<2 + - python=3.12 + diff --git a/environments/binary-telemac-mpich-p3.9.yml b/environments/binary-telemac-p3.9.yml similarity index 93% rename from environments/binary-telemac-mpich-p3.9.yml rename to environments/binary-telemac-p3.9.yml index 197080b5..924deb49 100644 --- a/environments/binary-telemac-mpich-p3.9.yml +++ b/environments/binary-telemac-p3.9.yml @@ -12,4 +12,4 @@ dependencies: - pip - proj - python=3.9 - - numpy<2 + diff --git a/locks/binary-telemac-mpich-p3.10.yml b/locks/binary-telemac-mpich-p3.10.yml deleted file mode 100644 index aff38ad8..00000000 --- a/locks/binary-telemac-mpich-p3.10.yml +++ /dev/null @@ -1,4579 +0,0 @@ -# This lock file was generated by conda-lock (https://github.com/conda/conda-lock). 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+https://conda.anaconda.org/conda-forge/linux-64/ffmpeg-7.1.0-gpl_heed6883_705.conda#77806f0330381aed7f104a1b67af7cea +https://conda.anaconda.org/conda-forge/linux-64/gdal-3.10.0-py39he7fce3f_6.conda#f3fd69e389bbc4a9da4d48c8f82ea72f +https://conda.anaconda.org/conda-forge/linux-64/mpi4py-4.0.1-py39h86f8d4e_0.conda#c7374dc1175bd9f66cf304b20a12bcd7 +https://conda.anaconda.org/conda-forge/linux-64/mesalib-24.3.1-h0b126fc_0.conda#12d32a61fb1163e4584731956592cf79 +https://conda.anaconda.org/conda-forge/linux-64/opentelemac-v9.0.0-py39h1a44d1d_0.conda#d1bf4f810facfba457af5bf86c26aef9 +https://conda.anaconda.org/conda-forge/noarch/wslink-2.2.1-pyhd8ed1ab_1.conda#af249fc92d1344913ff6c811f5b9096b +https://conda.anaconda.org/conda-forge/linux-64/vtk-base-9.3.1-osmesa_py39h39dfad7_109.conda#f304c08f5ed303f35c171fb134ef0425 +https://conda.anaconda.org/conda-forge/linux-64/vtk-io-ffmpeg-9.3.1-osmesa_py39hd1cd433_109.conda#eb1f5967bb282edc91149dbd93e9ae07 +https://conda.anaconda.org/conda-forge/linux-64/vtk-9.3.1-osmesa_py39h838d114_109.conda#2ad73c2ea8e78e9a7d3f7b8039993911 +https://conda.anaconda.org/conda-forge/linux-64/occt-7.8.1-all_h4c4714a_203.conda#43aed13aae8e2d25f232e98cb636e139 +https://conda.anaconda.org/conda-forge/linux-64/gmsh-4.13.1-hccb25f3_1.conda#2b0a79df0047cd897b4cb10e49697637 diff --git a/pyposeidon/misc/telemac2d.cas b/pyposeidon/misc/telemac2d.cas index 3e5bcf65..b4e04bc1 100755 --- a/pyposeidon/misc/telemac2d.cas +++ b/pyposeidon/misc/telemac2d.cas @@ -38,7 +38,6 @@ MASS-BALANCE = {{ 'YES' if mass_balance else 'NO' }} / 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 %} @@ -53,8 +52,7 @@ INITIAL CONDITIONS = '{{initial_conditions}}' /ZERO ELEVATION, /--------------------------------------------------------------------- / CREATE RESTART CONDITIONS /--------------------------------------------------------------------- -{% if hotstart %}RESTART MODE = YES -RESTART FILE = {{ restart_file }} +{% if hotstart %}RESTART FILE = {{ restart_file }} /RECORD NUMBER IN RESTART FILE = {{ restart_tstep }} RESTART FILE FORMAT = 'SERAFIND' {% endif %} / diff --git a/pyposeidon/telemac.py b/pyposeidon/telemac.py index 8733574f..a97739f8 100644 --- a/pyposeidon/telemac.py +++ b/pyposeidon/telemac.py @@ -56,8 +56,9 @@ from utils.progressbar import ProgressBar from pretel.manip_telfile import spherical2longlat from pretel.manip_telfile import longlat2spherical -from pretel.extract_contour import detecting_boundaries -from pretel.extract_contour import sorting_boundaries +from pretel.extract_contour import extract_boundaries +from pretel.extract_contour import sort_contours +from pretel.extract_contour import signed_area from collections import defaultdict from xarray_selafin.xarray_backend import SelafinAccessor from mpi4py import MPI @@ -393,41 +394,104 @@ def format_value(value, width, precision=3, is_float=False): return f"{value:{2}}" -def extract_contour(ds: xr.Dataset, tel_path: str): +def get_first_point(ds, bnd_points): """ - Generic function for extraction of contour from a mesh + Determine the southwest points among points given trough their indexes + @param ds (xr.Dataset) dataset files - @param tel_path (str) str to the geo file - @returns (list) List of polygons + @param bnd_points (numpy array of shape (number of points)) contains indexes + of points + @return first_bnd_pt_index (integer) index of the southwest point """ - vertices = np.vstack((ds.node_x, ds.node_y)).T - tel = TelemacFile(tel_path) + x_plus_y = ds.node_x[bnd_points] + ds.node_y[bnd_points] - # Extract boundary edges and nodes - connectivity_bnd_elt, bnd_points = detecting_boundaries(ds.face_nodes.values, len(vertices)) + southwest_bnd_pts_index = bnd_points[ + np.where(x_plus_y == x_plus_y.min())[0] + ] - domains = [] - boundaries_ordered, bnd_idx_left, bnd_elt_left = sorting_boundaries(tel, bnd_points, connectivity_bnd_elt) - domains.extend(boundaries_ordered) + if southwest_bnd_pts_index.shape[0] == 1: + first_bnd_pt_index = southwest_bnd_pts_index[0] + else: + first_bnd_pt_index = southwest_bnd_pts_index[ + np.where( + ds.node_x[southwest_bnd_pts_index] + == ds.node_x[southwest_bnd_pts_index].min() + )[0][0] + ] - 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) - domains.extend(boundaries_ordered) + return first_bnd_pt_index - domains_bnd = [] - domains_idx = [] - for bnd in domains: - coord_bnd = [] - for x, y in zip(tel.meshx[bnd], tel.meshy[bnd]): - coord_bnd.append((x, y)) - domains_bnd.append(coord_bnd) - domains_idx.append(bnd) - return domains_bnd, domains_idx +def extract_contour(ds: xr.Dataset): + """ + Generic function for extraction of contour from a mesh + @param ds (xr.Dataset) dataset files + @returns (list) List of polygons + """ + vertices = np.vstack((ds.node_x, ds.node_y)).T + # Extract boundary edges and nodes + boundary_edges = extract_boundaries(ds.face_nodes.values) + boundary_nodes = set(np.unique(np.hstack(boundary_edges))) + + # Create a list of the neighbours of each node for quick search + node_neighbours = defaultdict(set) + for edge in boundary_edges: + node_neighbours[edge[0]].add(edge[1]) + node_neighbours[edge[1]].add(edge[0]) + + # Group boundary nodes coordinates into contours + contours = [] + contours_idx = [] + while len(boundary_nodes) > 0: + next_vertex = get_first_point(ds, np.array(list(boundary_nodes))) + boundary_nodes.remove(next_vertex) + contour_idx = [next_vertex] + contour = [vertices[next_vertex].tolist()] + while True: + neighbours = node_neighbours[next_vertex].intersection( + boundary_nodes + ) + if len(neighbours) == 0: + break + next_vertex = neighbours.pop() + boundary_nodes.remove(next_vertex) + contour.append(vertices[next_vertex].tolist()) + contour_idx.append(next_vertex) + + # Ensure the contour is closed and append it to the list of contours + contour.append(contour[0]) + contour_idx.append(contour_idx[0]) + contours.append(contour) + contours_idx.append(contour_idx) + + # Build the list of domains while ensuring proper contours orientation + sorted_contours = sort_contours(contours) + domains = [] + domains_idx = [] + for outer, inners in sorted_contours.items(): + contour = contours[outer] + contour_idx = contours_idx[outer] + area = signed_area(contour) + if area < 0: + contour = contour[::-1] + contour_idx = contour_idx[::-1] + domains.append(contour) + domains_idx.append(contour_idx) + if len(inners) > 0: + for i in inners: + contour = contours[i] + contour_idx = contours_idx[i] + area = signed_area(contour) + if area > 0: + contour = contour[::-1] + contour_idx = contour_idx[::-1] + domains.append(contour) + domains_idx.append(contour_idx) + + + return domains, domains_idx def export_cli(ds: xr.Dataset, tel_path: str, outCli: str, tel_module: str = "telemac2d"): """ @@ -456,7 +520,7 @@ def export_cli(ds: xr.Dataset, tel_path: str, outCli: str, tel_module: str = "te domains_bnd = [] lines = [] bnd_node = 0 - contours, contours_idx = extract_contour(ds, tel_path) + contours, contours_idx = extract_contour(ds) for bnd in contours_idx: poly_bnd = [] coord_bnd = [] diff --git a/scripts/generate_envs.sh b/scripts/generate_envs.sh index 2d9a944a..14a23bfa 100755 --- a/scripts/generate_envs.sh +++ b/scripts/generate_envs.sh @@ -10,12 +10,10 @@ set -xeuo pipefail ./scripts/merge_environment_yaml.py ./dependencies/python3.12.yml ./dependencies/binary.yml | sed '/^$/d' > ./environments/binary-p3.12.yml # Binary + Telemac -./scripts/merge_environment_yaml.py ./dependencies/python3.9.yml ./dependencies/binary.yml ./dependencies/telemac_mpich.yml > ./environments/binary-telemac-mpich-p3.9.yml -./scripts/merge_environment_yaml.py ./dependencies/python3.10.yml ./dependencies/binary.yml ./dependencies/telemac_mpich.yml > ./environments/binary-telemac-mpich-p3.10.yml -./scripts/merge_environment_yaml.py ./dependencies/python3.11.yml ./dependencies/binary.yml ./dependencies/telemac_mpich.yml > ./environments/binary-telemac-mpich-p3.11.yml -./scripts/merge_environment_yaml.py ./dependencies/python3.9.yml ./dependencies/binary.yml ./dependencies/telemac_openmpi.yml > ./environments/binary-telemac-openmpi-p3.9.yml -./scripts/merge_environment_yaml.py ./dependencies/python3.10.yml ./dependencies/binary.yml ./dependencies/telemac_openmpi.yml > ./environments/binary-telemac-openmpi-p3.10.yml -./scripts/merge_environment_yaml.py ./dependencies/python3.11.yml ./dependencies/binary.yml ./dependencies/telemac_openmpi.yml > ./environments/binary-telemac-openmpi-p3.11.yml +./scripts/merge_environment_yaml.py ./dependencies/python3.9.yml ./dependencies/binary.yml ./dependencies/telemac.yml > ./environments/binary-telemac-p3.9.yml +./scripts/merge_environment_yaml.py ./dependencies/python3.10.yml ./dependencies/binary.yml ./dependencies/telemac.yml > ./environments/binary-telemac-p3.10.yml +./scripts/merge_environment_yaml.py ./dependencies/python3.11.yml ./dependencies/binary.yml ./dependencies/telemac.yml > ./environments/binary-telemac-p3.11.yml +./scripts/merge_environment_yaml.py ./dependencies/python3.12.yml ./dependencies/binary.yml ./dependencies/telemac.yml > ./environments/binary-telemac-p3.12.yml # Base ./scripts/merge_environment_yaml.py ./dependencies/python3.9.yml ./dependencies/binary.yml ./dependencies/main.yml | sed '/^$/d' > ./environments/base-p3.9.yml diff --git a/scripts/generate_locks.sh b/scripts/generate_locks.sh index 44fe9f8f..ce81a748 100755 --- a/scripts/generate_locks.sh +++ b/scripts/generate_locks.sh @@ -34,18 +34,14 @@ 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-p3.12.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 +conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-p3.9.yml --lockfile locks/binary-telemac-p3.9.yml +conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-p3.10.yml --lockfile locks/binary-telemac-p3.10.yml +conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-p3.11.yml --lockfile locks/binary-telemac-p3.11.yml +conda-lock lock --mamba --check-input-hash -p linux-64 -f environments/binary-telemac-p3.12.yml --lockfile locks/binary-telemac-p3.12.yml +conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-p3.9.lock locks/binary-telemac-p3.9.yml +conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-p3.10.lock locks/binary-telemac-p3.10.yml +conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-p3.11.lock locks/binary-telemac-p3.11.yml +conda-lock render -p linux-64 --filename-template locks/conda-ubuntu-latest-binary-telemac-p3.12.lock locks/binary-telemac-p3.12.yml # Pyposeidon-Base