From f7762bb13cb53a9692eb868f4a45479395667c9f Mon Sep 17 00:00:00 2001 From: Maarten Pronk <8655030+evetion@users.noreply.github.com> Date: Fri, 17 May 2024 20:27:16 +0200 Subject: [PATCH] Offline coupling with Delwaq (#1137) Fixes #649 This PR adds a folder `coupling/delwaq` for offline coupling with Delwaq, with a more extensive description provided in `README.md` in the same folder. A test is provided in `test.py`, that is also run on Teamcity on Windows, using the weekly DIMR releases. The `basic` testmodel (the only with built-in substance concentration values) is used for this. In order to speed-up the CI one can now do `pixi run ribasim-core-testmodels basic` to only run the `basic` model (but any or multiple model names can be used). --------- Co-authored-by: Martijn Visser Co-authored-by: Jingru Feng --- coupling/delwaq/.gitignore | 5 + coupling/delwaq/README.md | 47 + coupling/delwaq/generate.py | 379 + coupling/delwaq/parse.py | 52 + coupling/delwaq/reference/dimr_config.xml | 18 + coupling/delwaq/template/B5_bounddata.inc.j2 | 32 + coupling/delwaq/template/delwaq.atr.j2 | 16 + coupling/delwaq/template/delwaq.inp.j2 | 182 + coupling/delwaq/test.py | 22 + coupling/delwaq/util.py | 169 + docs/_quarto.yml | 1 + docs/core/index.qmd | 7 +- docs/core/usage.qmd | 52 + pixi.lock | 12047 ++++++++--------- pixi.toml | 11 +- python/ribasim/ribasim/model.py | 2 +- utils/testmodelrun.jl | 8 + 17 files changed, 6919 insertions(+), 6131 deletions(-) create mode 100644 coupling/delwaq/.gitignore create mode 100644 coupling/delwaq/README.md create mode 100644 coupling/delwaq/generate.py create mode 100644 coupling/delwaq/parse.py create mode 100644 coupling/delwaq/reference/dimr_config.xml create mode 100644 coupling/delwaq/template/B5_bounddata.inc.j2 create mode 100644 coupling/delwaq/template/delwaq.atr.j2 create mode 100644 coupling/delwaq/template/delwaq.inp.j2 create mode 100644 coupling/delwaq/test.py create mode 100644 coupling/delwaq/util.py diff --git a/coupling/delwaq/.gitignore b/coupling/delwaq/.gitignore new file mode 100644 index 000000000..2f6df2647 --- /dev/null +++ b/coupling/delwaq/.gitignore @@ -0,0 +1,5 @@ +model +*.map +*.nc +*.pdf +*.out diff --git a/coupling/delwaq/README.md b/coupling/delwaq/README.md new file mode 100644 index 000000000..c21bc9c46 --- /dev/null +++ b/coupling/delwaq/README.md @@ -0,0 +1,47 @@ +# Ribasim Delwaq coupling +This folder contains scripts to setup a Delwaq model from a Ribasim model, and to update the Ribasim model with the Delwaq output. + +## Steps +Setup a Ribasim model with substances and concentrations and run it. For example, we can run the basic testmodel with some default concentrations using the Ribasim CLI: + +```bash +ribasim generated_testmodels/basic/ribasim.toml +``` + +Afterwards we can use the Ribasim model and the generated output to setup a Delwaq model using Python from this folder. + +```python +from pathlib import Path + +from generate import generate +from parse import parse +from util import run_delwaq + +toml_path = Path("generated_testmodels/basic/ribasim.toml") + +graph, substances = generate(toml_path) +run_delwaq() +model = parse(toml_path, graph, substances) +``` + +The resulting Ribasim model will have an updated `model.basin.concentration_external` table with the Delwaq output. +We also store the same table in the `basin_concentration_external.arrow` file in the results folder, which can be +referred to using the Ribasim config file. + +## Running Delwaq +If you have access to a DIMR release, you can find the Delwaq executables in the `bin` folder. You can run a model directly with the `run_dimr.bat` script, and providing the path to the generated `.inp` file to it. In `util.py` we provide a `run_delwaq` (as used above) that does this for you, if you set the `D3D_HOME` environment variable to the path of the unzipped DIMR release, using the generated `model/ribasim.inp` configuration file. + +### Running Delwaq with Docker +Alternative to running Delwaq with a DIMR release, you can also run the Delwaq model in a Docker container if you are a Deltares employee. +First install WSL and install docker in WSL, then create a CLI secret and log into the Deltares containers. To install docker in WSL and create a CLI secret for the following steps, follow this guide https://publicwiki.deltares.nl/display/Delft3DContainers/. + +Log into Deltares containers in docker: +```bash +docker login containers.deltares.nl # use your deltares email + token +``` + +You can now run the Delwaq model from this directory. +```bash +docker run --mount type=bind,source="$(pwd)/model",target=/mnt/myModel \ + --workdir /mnt/myModel containers.deltares.nl/delft3d/delft3dfm run_dimr.sh +``` diff --git a/coupling/delwaq/generate.py b/coupling/delwaq/generate.py new file mode 100644 index 000000000..6ea139bf2 --- /dev/null +++ b/coupling/delwaq/generate.py @@ -0,0 +1,379 @@ +"""Setup a Delwaq model from a Ribasim model and results.""" + +import csv +import shutil +from datetime import timedelta +from pathlib import Path + +import networkx as nx +import numpy as np +import pandas as pd +import ribasim +from jinja2 import Environment, FileSystemLoader +from util import ( + strfdelta, + ugrid, + write_flows, + write_pointer, + write_volumes, +) + +delwaq_dir = Path(__file__).parent + +env = Environment(autoescape=True, loader=FileSystemLoader(delwaq_dir / "template")) + +# Add evaporation edges, so mass balance is correct +# To simulate salt increase due to evaporation, set to False +USE_EVAP = True + + +def generate(toml_path: Path) -> tuple[nx.DiGraph, set[str]]: + """Generate a Delwaq model from a Ribasim model and results.""" + + # Read in model and results + model = ribasim.Model.read(toml_path) + basins = pd.read_feather(toml_path.parent / "results" / "basin.arrow") + flows = pd.read_feather(toml_path.parent / "results" / "flow.arrow") + + output_folder = delwaq_dir / "model" + output_folder.mkdir(exist_ok=True) + + # Setup flow network + G = nx.DiGraph() + for row in model.node_table().df.itertuples(): + if row.node_type not in ribasim.geometry.edge.SPATIALCONTROLNODETYPES: + G.add_node( + row.node_id, + type=row.node_type, + id=row.node_id, + x=row.geometry.x, + y=row.geometry.y, + pos=(row.geometry.x, row.geometry.y), + ) + for row in model.edge.df.itertuples(): + if row.edge_type == "flow": + G.add_edge(row.from_node_id, row.to_node_id, id=[row.Index], duplicate=None) + + # Simplify network, only keeping Basins and Boundaries. + # We find an unwanted node, remove it, + # and merge the flow edges to/from the node. + remove_nodes = [] + for node_id, out in G.succ.items(): + if G.nodes[node_id]["type"] not in [ + "Basin", + "Terminal", + "LevelBoundary", + "FlowBoundary", + "UserDemand", + ]: + inneighbor_ids = G.pred[node_id] + assert len(inneighbor_ids) == 1 + inneighbor_id = list(inneighbor_ids)[0] + remove_nodes.append(node_id) + + for outneighbor_id in out.keys(): + if outneighbor_id in remove_nodes: + print("Not making edge to removed node.") + continue + edge = (inneighbor_id, outneighbor_id) + edge_id = G.get_edge_data(node_id, outneighbor_id)["id"][0] + if G.has_edge(*edge): + data = G.get_edge_data(*edge) + data["id"].append(edge_id) + else: + G.add_edge(*edge, id=[edge_id]) + + for node_id in remove_nodes: + G.remove_node(node_id) + + # Due to the simplification, we can end up with cycles of length 2. + # This happens when a UserDemand is connected to and from a Basin, + # but can also happen in other cases (rivers with a outlet and pump), + # for which we do nothing. We merge these UserDemand cycles edges to + # a single edge, and later merge the flows. + merge_edges = [] + for loop in nx.simple_cycles(G): + if len(loop) == 2: + if ( + G.nodes[loop[0]]["type"] != "UserDemand" + and G.nodes[loop[1]]["type"] != "UserDemand" + ): + print("Found cycle that is not a UserDemand.") + else: + edge_ids = G.edges[*loop]["id"] + G.edges[*reversed(loop)]["id"].extend(edge_ids) + merge_edges.extend(edge_ids) + G.remove_edge(*loop) + + # Relabel the nodes as consecutive integers for Delwaq + # Note that the node["id"] is the original node_id + basin_id = 0 + boundary_id = 0 + node_mapping = {} + for node_id, node in G.nodes.items(): + if node["type"] == "Basin": + basin_id += 1 + node_mapping[node_id] = basin_id + elif node["type"] in [ + "Terminal", + "UserDemand", + "LevelBoundary", + "FlowBoundary", + ]: + boundary_id -= 1 + node_mapping[node_id] = boundary_id + else: + raise Exception("Found unexpected node $node_id in delwaq graph.") + + nx.relabel_nodes(G, node_mapping, copy=False) + + # Add basin boundaries + for node_id, node in list(G.nodes(data=True)): + if node["type"] == "Basin": + boundary_id -= 1 + G.add_node( + boundary_id, + type="Drainage", + id=node["id"], + pos=(node["pos"][0] - 0.2, node["pos"][1] + 0.2), + ) + G.add_edge( + boundary_id, + node_id, + key=edge_id, + id=[-1], + boundary=(node["id"], "drainage"), + ) + + boundary_id -= 1 + G.add_node( + boundary_id, + type="Precipitation", + id=node["id"], + pos=(node["pos"][0] + 0, node["pos"][1] + 0.2), + ) + G.add_edge( + boundary_id, + node_id, + key=edge_id, + id=[-1], + boundary=(node["id"], "precipitation"), + ) + + if USE_EVAP: + boundary_id -= 1 + G.add_node( + boundary_id, + type="Evaporation", + id=node["id"], + pos=(node["pos"][0] + 0.2, node["pos"][1] + 0.2), + ) + G.add_edge( + node_id, + boundary_id, + key=edge_id, + id=[-1], + boundary=(node["id"], "evaporation"), + ) + + # Setup edge mapping + edge_mapping = {} + for i, (a, b, d) in enumerate(G.edges(data=True)): + for edge_id in d["id"]: + edge_mapping[edge_id] = i + + # Plot + # nx.draw( + # G, + # pos={k: v["pos"] for k, v in G.nodes(data=True)}, + # with_labels=True, + # labels={k: v["id"] for k, v in G.nodes(data=True)}, + # ) + + # Setup metadata + if model.solver.saveat == 0 or np.isposinf(model.solver.saveat): + raise ValueError("Unsupported saveat, must be positive and finite.") + else: + timestep = timedelta(seconds=model.solver.saveat) + + # Write topology to delwaq pointer file + pointer = pd.DataFrame(G.edges(), columns=["from_node_id", "to_node_id"]) + pointer.to_csv(output_folder / "network.csv", index=False) # not needed + write_pointer(output_folder / "ribasim.poi", pointer) + + total_segments = basin_id + total_exchanges = len(pointer) + + # Write attributes template + template = env.get_template("delwaq.atr.j2") + with open(output_folder / "ribasim.atr", mode="w") as f: + f.write( + template.render( + nsegments=total_segments, + ) + ) + + # Generate mesh and write to NetCDF + uds = ugrid(G) + uds.ugrid.to_netcdf(output_folder / "ribasim.nc") + + # Generate area and flows + # File format is int32, float32 based + # Time is internal clock, not real time! + flows.time = (flows.time - flows.time[0]).dt.total_seconds().astype("int32") + basins.time = (basins.time - basins.time[0]).dt.total_seconds().astype("int32") + + # Invert flows for half-edge of cycles so later summing is correct + m = flows.edge_id.isin(merge_edges) + flows.loc[m, "flow_rate"] = flows.loc[m, "flow_rate"] * -1 + + # Map edge_id to the new edge_id and merge any duplicate flows + flows["edge_id"] = flows["edge_id"].map(edge_mapping) + flows.dropna(subset=["edge_id"], inplace=True) + flows["edge_id"] = flows["edge_id"].astype("int32") + nflows = flows.copy() + nflows = flows.groupby(["time", "edge_id"]).sum().reset_index() + nflows.drop( + columns=["from_node_id", "from_node_type", "to_node_id", "to_node_type"], + inplace=True, + ) + + # Add basin boundaries to flows + for edge_id, (a, b, (node_id, boundary_type)) in enumerate( + G.edges(data="boundary", default=(None, None)) + ): + if boundary_type is None: + continue + df = basins[basins.node_id == node_id][["time", boundary_type]].rename( + columns={boundary_type: "flow_rate"} + ) + df["edge_id"] = edge_id + nflows = pd.concat([nflows, df], ignore_index=True) + + # Save flows to Delwaq format + nflows.sort_values(by=["time", "edge_id"], inplace=True) + nflows.to_csv(output_folder / "flows.csv", index=False) # not needed + nflows.drop( + columns=["edge_id"], + inplace=True, + ) + write_flows(output_folder / "ribasim.flo", nflows, timestep) + write_flows( + output_folder / "ribasim.are", nflows, timestep + ) # same as flow, so area becomes 1 + + # Write volumes to Delwaq format + basins.drop(columns=["level"], inplace=True) + volumes = basins[["time", "node_id", "storage"]] + volumes.loc[:, "node_id"] = ( + volumes["node_id"].map(node_mapping).astype(pd.Int32Dtype()) + ) + volumes = volumes.sort_values(by=["time", "node_id"]) + volumes.to_csv(output_folder / "volumes.csv", index=False) # not needed + volumes.drop(columns=["node_id"], inplace=True) + write_volumes(output_folder / "ribasim.vol", volumes, timestep) + write_volumes( + output_folder / "ribasim.vel", volumes, timestep + ) # same as volume, so vel becomes 1 + + # Length file + # Timestep and flattened (2, nsegments) of identical lengths + # for left right, so 0, 1., 1., 3., 3., 4., 4. etc. + # TODO(Maarten) Make use of geometry to calculate lengths + lengths = nflows.copy() + lengths.flow_rate = 1 + lengths.iloc[np.repeat(np.arange(len(lengths)), 2)] + write_flows(output_folder / "ribasim.len", lengths, timestep) + + # Find all boundary substances and concentrations + boundaries = [] + substances = set() + + def make_boundary(id, type): + # Delwaq has a limit of 12 characters for the boundary name + return type[:9] + "_" + str(id) + + assert model.level_boundary.concentration.df is not None + for i, row in model.level_boundary.concentration.df.groupby(["node_id"]): + row = row.drop_duplicates(subset=["substance"]) + bid = make_boundary(row.node_id.iloc[0], "LevelBoundary") + boundaries.append( + { + "name": bid, + "concentrations": row.concentration.to_list(), + "substances": row.substance.to_list(), + } + ) + substances.update(row.substance) + + assert model.flow_boundary.concentration.df is not None + for i, row in model.flow_boundary.concentration.df.groupby("node_id"): + row = row.drop_duplicates(subset=["substance"]) + bid = make_boundary(row.node_id.iloc[0], "FlowBoundary") + boundaries.append( + { + "name": bid, + "concentrations": row.concentration.to_list(), + "substances": row.substance.to_list(), + } + ) + substances.update(row.substance) + + # Write boundary data with substances and concentrations + template = env.get_template("B5_bounddata.inc.j2") + with open(output_folder / "B5_bounddata.inc", mode="w") as f: + f.write( + template.render( + states=[], # no states yet + boundaries=boundaries, + ) + ) + + # Write boundary list, ordered by bid to map the unique boundary names + # to the edges described in the pointer file. + bnd = pointer.copy() + bnd["bid"] = np.minimum(bnd["from_node_id"], bnd["to_node_id"]) + bnd = bnd[bnd["bid"] < 0] + bnd.sort_values(by="bid", ascending=False, inplace=True) + bnd["node_type"] = [G.nodes(data="type")[bid] for bid in bnd["bid"]] + bnd["node_id"] = [G.nodes(data="id")[bid] for bid in bnd["bid"]] + bnd["fid"] = list(map(make_boundary, bnd["node_id"], bnd["node_type"])) + bnd["comment"] = "" + bnd = bnd[["fid", "comment", "node_type"]] + bnd.to_csv( + output_folder / "ribasim_bndlist.inc", + index=False, + header=False, + sep=" ", + quotechar="'", + quoting=csv.QUOTE_ALL, + ) + + # Setup DIMR configuration for running Delwaq via DIMR + dimrc = delwaq_dir / "reference/dimr_config.xml" + shutil.copy(dimrc, output_folder / "dimr_config.xml") + + # Write main Delwaq input file + template = env.get_template("delwaq.inp.j2") + with open(output_folder / "delwaq.inp", mode="w") as f: + f.write( + template.render( + startime=model.starttime, + endtime=model.endtime - timestep, + timestep=strfdelta(timestep), + nsegments=total_segments, + nexchanges=total_exchanges, + substances=substances, + ) + ) + + # Return the graph with original edges and the substances + # so we can parse the results back to the original model + return G, substances + + +if __name__ == "__main__": + # Generate a Delwaq model from the default Ribasim model + repo_dir = delwaq_dir.parents[1] + toml_path = repo_dir / "generated_testmodels/basic/ribasim.toml" + graph, substances = generate(toml_path) diff --git a/coupling/delwaq/parse.py b/coupling/delwaq/parse.py new file mode 100644 index 000000000..9bb6616aa --- /dev/null +++ b/coupling/delwaq/parse.py @@ -0,0 +1,52 @@ +"""Read a Delwaq model generated from a Ribasim model and inject the results back to Ribasim.""" + +from pathlib import Path + +import pandas as pd +import ribasim +import xarray as xr +import xugrid as xu + +delwaq_dir = Path(__file__).parent +repo_dir = delwaq_dir.parents[1] +output_folder = delwaq_dir / "model" + + +def parse(toml_path: Path, graph, substances) -> ribasim.Model: + model = ribasim.Model.read(toml_path) + + # Output of Delwaq + ds = xr.open_dataset(output_folder / "delwaq_map.nc") + ug = xu.UgridDataset(ds) + + mapping = dict(graph.nodes(data="id")) + # Continuity is a (default) tracer representing the mass balance + substances.add("Continuity") + + dfs = [] + for substance in substances: + df = ug[f"ribasim_{substance}"].to_dataframe().reset_index() + df.rename( + columns={ + "ribasim_nNodes": "node_id", + "nTimesDlwq": "time", + f"ribasim_{substance}": "concentration", + }, + inplace=True, + ) + df["substance"] = substance + df.drop(columns=["ribasim_node_x", "ribasim_node_y"], inplace=True) + # Map the node_id (logical index) to the original node_id + # TODO Check if this is correct + df.node_id += 1 + df.node_id = df.node_id.map(mapping) + + dfs.append(df) + + df = pd.concat(dfs).reset_index(drop=True) + df.sort_values(["time", "node_id"], inplace=True) + + model.basin.concentration_external = df + df.to_feather(toml_path.parent / "results" / "basin_concentration_external.arrow") + + return model diff --git a/coupling/delwaq/reference/dimr_config.xml b/coupling/delwaq/reference/dimr_config.xml new file mode 100644 index 000000000..a4d3ede3a --- /dev/null +++ b/coupling/delwaq/reference/dimr_config.xml @@ -0,0 +1,18 @@ + + + + 1.1 + Deltares, Coupling team + 2016-01-20T07:56:32+01:00 + + + + + + + delwaq + . + + delwaq.inp + + diff --git a/coupling/delwaq/template/B5_bounddata.inc.j2 b/coupling/delwaq/template/B5_bounddata.inc.j2 new file mode 100644 index 000000000..c9fd273ea --- /dev/null +++ b/coupling/delwaq/template/B5_bounddata.inc.j2 @@ -0,0 +1,32 @@ +ITEM 'LevelBoundary' +CONCENTRATIONS 'Continuity' 'LevelBoundary' +DATA 1 1 + +ITEM 'Terminal' +CONCENTRATIONS 'Continuity' +DATA 1 + +ITEM 'FlowBoundary' +CONCENTRATIONS 'Continuity' 'FlowBoundary' +DATA 1 1 + +ITEM 'Drainage' +CONCENTRATIONS 'Continuity' 'Drainage' +DATA 1 1 + +ITEM 'Precipitation' +CONCENTRATIONS 'Continuity' 'Precipitation' +DATA 1 1 + +{% for boundary in boundaries -%} +ITEM '{{ boundary.name }}' +CONCENTRATIONS {{ boundary.substances|join(' ')}} +DATA {{ boundary.concentrations|join(' ')}} + +{% endfor -%} +{% for state in states -%} +ITEM '{{ state.name }}' +CONCENTRATIONS {{ state.substances|join(' ')}} +DATA {{ state.concentrations|join(' ')}} + +{% endfor -%} diff --git a/coupling/delwaq/template/delwaq.atr.j2 b/coupling/delwaq/template/delwaq.atr.j2 new file mode 100644 index 000000000..dd6a370b1 --- /dev/null +++ b/coupling/delwaq/template/delwaq.atr.j2 @@ -0,0 +1,16 @@ + ; DELWAQ_COMPLETE_ATTRIBUTES + 2 ; two blocks with input + 1 ; number of attributes, they are : + 1 ; '1' is active '0' is not + 1 ; data follows in this file + 1 ; all data is given without defaults + ; layer: 1 +{{ nsegments }}*1 + 1 ; number of attributes, they are : + 2 ; '1' has surface '3' has bottom + ; '0' has both '2' has none + 1 ; data follows in this file + 1 ; all data is given without defaults + ; layer: 1 +{{ nsegments }}*0 + 0 ; no time dependent attributes diff --git a/coupling/delwaq/template/delwaq.inp.j2 b/coupling/delwaq/template/delwaq.inp.j2 new file mode 100644 index 000000000..d18230a30 --- /dev/null +++ b/coupling/delwaq/template/delwaq.inp.j2 @@ -0,0 +1,182 @@ +1000 80 ';' +;DELWAQ_VERSION_4.910 ; Delwaq version number +;PRINT_OUTPUT_OPTION_9 ; Debug level + +; TEMPLATE FILE FOR WATER QUALITY CALCULATION +; First input block +'Water quality calculation' +' ' +' ' +'T0: {{startime.strftime("%Y.%m.%d %H:%M:%S")}} (scu= 1s)' + +; Hard coded Substances for mass balance check: +; number of active and inactive substances +{{substances|length+5}} 0 + ; active substances +1 'Continuity' +2 'Basin' +3 'LevelBoundary' +4 'FlowBoundary' +5 'Terminal' +{% for substance in substances -%} +{{5+loop.index}} '{{substance}}' +{% endfor -%} + ; passive substances + +#1; + +;############################################################################### +; Second input block +1 'DDHHMMSS' 'DDHHMMSS' ; system clock +; Integration options: +15.70 ; integration option, no balance keywords yet + +; Simulation start, stop and timestep: + {{ startime.strftime("%Y/%m/%d-%H:%M:%S") }} ; start time + {{ endtime.strftime("%Y/%m/%d-%H:%M:%S") }} ; stop time + 0 ; timestep constant +; dddhhmmss + {{ timestep }} ; timestep + 1 ; Monitoring areas in this file +; Todo: Monitoring areas +0 + 2 ; No monitoring cross areas +; Output timesteps. Equal to Ribasim timestep: +; output control (see DELWAQ-manual) +; yyyy/mm/dd-hh:mm:ss yyyy/mm/dd-hh:mm:ss dddhhmmss + {{ startime.strftime("%Y/%m/%d-%H:%M:%S") }} {{ endtime.strftime("%Y/%m/%d-%H:%M:%S") }} {{ timestep }} ; start, stop and step for balance output + {{ startime.strftime("%Y/%m/%d-%H:%M:%S") }} {{ endtime.strftime("%Y/%m/%d-%H:%M:%S") }} {{ timestep }} ; start, stop and step for map output + {{ startime.strftime("%Y/%m/%d-%H:%M:%S") }} {{ endtime.strftime("%Y/%m/%d-%H:%M:%S") }} {{ timestep }} ; start, stop and step for his output + + +#2; +;############################################################################### +; Third input block +; Ribasim Ugrid file: +UGRID 'ribasim.nc' ; Reference to the waqgeom file for UGRID NetCDF output + +; nr of segments +{{ nsegments }} ; nr of segments + + 2 ; Structure matrix not used + +INCLUDE 'ribasim.atr' ; From UI: attributes file + +; Volume file +-2 ; volumes will be interpolated from a binary file +'ribasim.vol' ; From UI: volumes-file + +#3; +;############################################################################### +; Fourth input block +; nr of exchanges in three directions. Only first is used, followed by two zeros. +{{ nexchanges }} 0 0 ; nr of exchanges + 0 ; Number of dispersion arrays (this is different when spatial dispersion is implemented) + 0 ; Number of velocity arrays + 1 ; Input format of the pointers. + +; Pointer file +0 ; pointers from binary file. +'ribasim.poi' ; From Ribasim + 1 ; Dispersions in this file + 1.0 1.0 1.0 ; Scale factors for 3 directions + +; Default dispersion: +1 0.0 1E-07 ; constant dispersion + +; Area file +-2 ; areas will be interpolated from a binary file +'ribasim.are' ; From Ribasim + +; Flow file +-2 ; flows from binary file +'ribasim.flo' ; From Ribasim + +0 ; Vary in space +; Length file +1 1 1 1 ; Lengths from binary file + +#4; +;############################################################################### +; Fifth input block, water quality calculation + +; Boundary list +;'NodeID' 'Comment field' 'Boundary name used for data grouping' +INCLUDE 'ribasim_bndlist.inc' ; From UI: Boundary segments + +0 ; No Tatcher-Harleman time lags +; Boundary data: +INCLUDE 'B5_bounddata.inc' ; From UI: Boundary data + + +#5; +;############################################################################### +; Sixth input block, Dry Waste Loads block + +0; Number of loads + +#6; +;############################################################################### +; Seventh input block + +CONSTANTS 'ONLY_ACTIVE' DATA 0 ; Only active processes + +;INCLUDE 'includes_deltashell/B7_processes.inc' ; From UI: Processes +;INCLUDE 'includes_deltashell/B7_constants.inc' ; From UI: Constants +;INCLUDE 'includes_deltashell/B7_functions.inc' ; From UI: Functions +;INCLUDE 'includes_deltashell/B7_parameters.inc' ; From UI: Parameters +;INCLUDE 'includes_deltashell/B7_dispersion.inc' ; FROM UI: Spatial dispersion +;INCLUDE 'includes_deltashell/B7_vdiffusion.inc' ; FROM UI: Vertical diffusion + +;INCLUDE 'includes_deltashell/B7_segfunctions.inc' ; FROM UI: SEG_FUNCTION blocks +;INCLUDE 'includes_deltashell/B7_numerical_options.inc' ; FROM UI: numerical options + +#7 +;############################################################################### +; Eighth input block + +;INCLUDE 'includes_deltashell/B8_initials.inc' ; From UI: Initials + +; Hard coded initials for mass balance check. +MASS/M2 ; The bed substances are specified in mass/m2 +INITIALS +'Continuity' +'Basin' +'LevelBoundary' +'FlowBoundary' +'Terminal' +{% for substance in substances -%} +'{{substance}}' +{% endfor -%} +DEFAULTS +1 +0 +0 +0 +0 +{% for substance in substances -%} +0 +{% endfor -%} +#8 +;############################################################################### +; Ninth input block + 1 ; Conditions follow in this file + 1 ; Default monitor-file + 0 ; No grid-file +; INCLUDE 'includes_deltashell/B9_Hisvar.inc' ; From UI: History-file +2 ; perform default output and extra parameters listed below +0 ; number of parameters listed + +; INCLUDE 'includes_deltashell/B9_Mapvar.inc' ; From UI: Map-file +2 ; perform default output and extra parameters listed below +1 ; number of parameters listed +'Volume' + ; Binary/Nefis and History/Map + 1 ; Switch on binary History file + 1 ; Switch on binary Map file + 1 ; Switch off Nefis History file + 1 ; Switch off Nefis Map file +#9 +;############################################################################### +; Tenth input block +#10 diff --git a/coupling/delwaq/test.py b/coupling/delwaq/test.py new file mode 100644 index 000000000..247c6b564 --- /dev/null +++ b/coupling/delwaq/test.py @@ -0,0 +1,22 @@ +from pathlib import Path + +from generate import generate +from parse import parse +from util import run_delwaq + +delwaq_dir = Path(__file__).parent + + +def test_offline_delwaq_coupling(): + repo_dir = delwaq_dir.parents[1] + toml_path = repo_dir / "generated_testmodels/basic/ribasim.toml" + + graph, substances = generate(toml_path) + run_delwaq() + model = parse(toml_path, graph, substances) + + df = model.basin.concentration_external.df + assert df is not None + assert df.shape[0] > 0 + assert df.node_id.nunique() == 4 + assert sorted(df.substance.unique()) == ["Cl", "Continuity", "Tracer"] diff --git a/coupling/delwaq/util.py b/coupling/delwaq/util.py new file mode 100644 index 000000000..906a3aebd --- /dev/null +++ b/coupling/delwaq/util.py @@ -0,0 +1,169 @@ +"""Utilities to write Delwaq (binary) input files.""" + +import os +import platform +import struct +import subprocess +from datetime import timedelta +from pathlib import Path + +import numpy as np +import pandas as pd +from ribasim.utils import MissingOptionalModule + +try: + import xugrid +except ImportError: + xugrid = MissingOptionalModule("xugrid") + + +def strfdelta(tdelta) -> str: + # dddhhmmss format + days = tdelta.days + hours, rem = divmod(tdelta.seconds, 3600) + minutes, seconds = divmod(rem, 60) + return f"{days:03d}{hours:02d}{minutes:02d}{seconds:02d}" + + +def write_pointer(fn: Path | str, data: pd.DataFrame) -> None: + """Write pointer file for Delwaq. + + The format is a matrix of int32 of edges + with 4 columns: from_node_id, to_node_id, 0, 0 + + This saves as column major order for Fortran compatibility. + + Data is a DataFrame with columns from_node_id, to_node_id. + """ + with open(fn, "wb") as f: + for a, b in data.to_numpy(): + f.write(struct.pack("<4i", a, b, 0, 0)) + + +def write_lengths(fn: Path | str, data: np.ndarray[np.float32]) -> None: + """Write lengths file for Delwaq. + + The format is an int defining time/edges (?) + Followed by a matrix of float32 of 2, n_edges + Defining the length of the half-edges. + + This saves as column major order for Fortran compatibility. + + Data is an array of float32. + """ + with open(fn, "wb") as f: + f.write(struct.pack(" None: + """Write volumes file for Delwaq. + + The format is an int defining the time + followed by the volume for each node + The order should be the same as the nodes in the mesh. + + This saves as column major order for Fortran compatibility. + + Data is a DataFrame with columns time, storage + """ + with open(fn, "wb") as f: + for time, group in data.groupby("time"): + f.write(struct.pack(" None: + """Write flows file for Delwaq. + + The format is an int defining the time + followed by the flow for each edge + The order should be the same as the nodes in the pointer. + + This saves as column major order for Fortran compatibility. + + Data is a DataFrame with columns time, flow + """ + with open(fn, "wb") as f: + for time, group in data.groupby("time"): + f.write(struct.pack(" xugrid.UgridDataset: + # TODO Deduplicate with ribasim.Model.to_xugrid + edge_df = pd.DataFrame(G.edges(), columns=["from_node_id", "to_node_id"]) + node_df = pd.DataFrame(G.nodes(), columns=["node_id"]) + node_df["x"] = [i[1] for i in G.nodes(data="x")] + node_df["y"] = [i[1] for i in G.nodes(data="y")] + node_df = node_df[node_df.node_id > 0] + edge_df = edge_df[ + edge_df.from_node_id.isin(node_df.node_id) + & edge_df.to_node_id.isin(node_df.node_id) + ] + + node_id = node_df.node_id.to_numpy() + edge_id = edge_df.index.to_numpy() + from_node_id = edge_df.from_node_id.to_numpy() + to_node_id = edge_df.to_node_id.to_numpy() + + # from node_id to the node_dim index + node_lookup = pd.Series( + index=node_id, + data=node_id.argsort().astype(np.int32), + name="node_index", + ) + + grid = xugrid.Ugrid1d( + node_x=node_df.x, + node_y=node_df.y, + fill_value=-1, + edge_node_connectivity=np.column_stack( + ( + node_lookup[from_node_id], + node_lookup[to_node_id], + ) + ), + name="ribasim", + ) + + edge_dim = grid.edge_dimension + node_dim = grid.node_dimension + + uds = xugrid.UgridDataset(None, grid) + uds = uds.assign_coords(node_id=(node_dim, node_id)) + uds = uds.assign_coords(edge_id=(edge_dim, edge_id)) + uds = uds.assign_coords(from_node_id=(edge_dim, from_node_id)) + uds = uds.assign_coords(to_node_id=(edge_dim, to_node_id)) + + return uds + + +def run_delwaq() -> None: + d3d_home = os.environ.get("D3D_HOME") + if d3d_home is None: + raise ValueError("D3D_HOME is not set.") + else: + d3d_home = Path(d3d_home) + binfolder = (d3d_home / "bin").absolute() + folder = Path(__file__).parent + inp_path = folder / "model" / "delwaq.inp" + system = platform.system() + if system == "Windows": + # run_delwaq.bat prepends working directory to the inp file + subprocess.run( + [binfolder / "run_delwaq.bat", "delwaq.inp"], + cwd=(folder / "model").absolute(), + ) + elif system == "Linux": + subprocess.run([binfolder / "run_delwaq.sh", inp_path.absolute()]) + else: + raise OSError(f"No support for running Delwaq automatically on {system}.") diff --git a/docs/_quarto.yml b/docs/_quarto.yml index b360503d7..6339555ed 100644 --- a/docs/_quarto.yml +++ b/docs/_quarto.yml @@ -32,6 +32,7 @@ website: - core/equations.qmd - core/allocation.qmd - core/numerics.qmd + - core/coupling.qmd - title: "Python tooling" contents: - python/index.qmd diff --git a/docs/core/index.qmd b/docs/core/index.qmd index 86df98110..3fed095e8 100644 --- a/docs/core/index.qmd +++ b/docs/core/index.qmd @@ -11,7 +11,7 @@ The theory is described on the [equations](equations.qmd) page, and more in-dept The core is implemented in the [Julia programming language](https://julialang.org/), and can be found in the [Ribasim repository](https://github.com/Deltares/Ribasim) under the `core/` folder. For developers we also advise to read the -[developer documentation](../contribute/core.qmd). +[developer documentation](../contribute/core.qmd). Information on coupling can be found [here](coupling.qmd). An overview of all components is given on the [home page](../index.qmd#sec-components) @@ -119,8 +119,3 @@ end allocation_subNetwork->>user_demand: allocated user_demand->>basin: abstracted ``` - -# Coupling - -Ribasim can also be coupled to other kernels with the help of iMOD Coupler. -The corresponding documentation can be found within the [iMOD Suite Documentation](https://deltares.github.io/iMOD-Documentation/coupler.html). diff --git a/docs/core/usage.qmd b/docs/core/usage.qmd index a54d48a6d..0f71eff94 100644 --- a/docs/core/usage.qmd +++ b/docs/core/usage.qmd @@ -356,6 +356,38 @@ Water levels beyond the last `basin_level` are linearly extrapolated. Note that the interpolation to subgrid water level is not constrained by any water balance within Ribasim. Generally, to create physically meaningful subgrid water levels, the subgrid table must be parametrized properly such that the spatially integrated water volume of the subgrid elements agrees with the total storage volume of the basin. +## Basin / concentration {#sec-basin-conc} +This table defines the concentration(s) of (a) substance(s) for the inflow boundaries of a Basin node. + +column | type | unit | restriction +------------- | -------- | --------------- | ----------- +node_id | Int32 | - | sorted +time | DateTime | - | sorted per node_id +substance | String | | can correspond to known Delwaq substances +drainage | Float64 | $g m^{-3}$ | (optional) +precipitation | Float64 | $g m^{-3}$ | (optional) + +## Basin / concentrationstate {#sec-basin-conc-state} +This table defines the concentration(s) of (a) substance(s) in the basin at the start of the simulation. + +column | type | unit | restriction +-------------- | -------- | ------------ | ----------- +node_id | Int32 | - | sorted +time | DateTime | - | sorted per node_id +substance | String | - | can correspond to known Delwaq substances +concentration | Float64 | $g m^{-3}$ | + +## Basin / concentrationexternal +This table is used for (external) concentrations, that can be used for Control lookups. + +column | type | unit | restriction +-------------- | -------- | ------------ | ----------- +node_id | Int32 | - | sorted +time | DateTime | - | sorted per node_id +substance | String | - | can correspond to known Delwaq substances +concentration | Float64 | $g m^{-3}$ | + + # FractionalFlow {#sec-fractional-flow} Lets a fraction (in [0,1]) of the incoming flow trough. @@ -557,6 +589,16 @@ node_id | Int32 | - | sorted time | DateTime | - | sorted per node_id level | Float64 | $m$ | - +## LevelBoundary / concentration {#sec-level-boundary-conc} +This table defines the concentration(s) of (a) substance(s) for the flow from the LevelBoundary. + +column | type | unit | restriction +-------------- | -------- | ------------ | ----------- +node_id | Int32 | - | sorted +time | DateTime | - | sorted per node_id +substance | String | - | can correspond to known Delwaq substances +concentration | Float64 | $g m^{-3}$ | + # FlowBoundary {#sec-flow-boundary} Pump water to a destination node. @@ -588,6 +630,16 @@ node_id | Int32 | - | sorted time | DateTime | - | sorted per node_id flow_rate | Float64 | $m^3 s^{-1}$ | non-negative +## FlowBoundary / concentration {#sec-flow-boundary-conc} +This table defines the concentration(s) of (a) substance(s) for the flow from the FlowBoundary. + +column | type | unit | restriction +-------------- | -------- | ------------ | ----------- +node_id | Int32 | - | sorted +time | DateTime | - | sorted per node_id +substance | String | - | can correspond to known Delwaq substances +concentration | Float64 | $g m^{-3}$ | + # LinearResistance {#sec-linear-resistance} Flow proportional to the level difference between the connected basins. diff --git a/pixi.lock b/pixi.lock index 5cc507ac5..ba4fa19dd 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,19 +11,19 @@ environments: - 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libgcc-ng >=12 + - libstdcxx-ng >=12 - libzlib >=1.2.13,<1.3.0a0 license: BSD-3-Clause license_family: BSD - size: 499383 - timestamp: 1693151312586 + size: 554846 + timestamp: 1714722996770 - kind: conda name: zstd - version: 1.5.5 - build: hfc55251_0 - subdir: linux-64 - url: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.5-hfc55251_0.conda - sha256: 607cbeb1a533be98ba96cf5cdf0ddbb101c78019f1fda063261871dad6248609 - md5: 04b88013080254850d6c01ed54810589 + version: 1.5.6 + build: hb46c0d2_0 + subdir: osx-arm64 + url: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.6-hb46c0d2_0.conda + sha256: 2d4fd1ff7ee79cd954ca8e81abf11d9d49954dd1fef80f27289e2402ae9c2e09 + md5: d96942c06c3e84bfcc5efb038724a7fd depends: - - libgcc-ng >=12 - - libstdcxx-ng >=12 + - __osx >=11.0 - libzlib >=1.2.13,<1.3.0a0 license: BSD-3-Clause license_family: BSD - size: 545199 - timestamp: 1693151163452 + size: 405089 + timestamp: 1714723101397 diff --git a/pixi.toml b/pixi.toml index 7ca1a8741..cc99cb819 100644 --- a/pixi.toml +++ b/pixi.toml @@ -22,11 +22,7 @@ test-ribasim-api = "pytest --basetemp=python/ribasim_api/tests/temp --junitxml=r # Installation install-julia = "juliaup add 1.10.3 && juliaup default 1.10.3" install-pre-commit = "pre-commit install" -install-ci = { depends_on = [ - "install-julia", - "update-registry-julia", - -] } +install-ci = { depends_on = ["install-julia", "update-registry-julia"] } install = { depends_on = [ "install-ci", "install-qgis-plugins", @@ -49,7 +45,7 @@ build-julia-docs = { cmd = "julia --project docs/make.jl", depends_on = [ ], outputs = [ "docs/build", ] } -quartodoc-build = { cmd = "quartodoc build && rm objects.json", cwd="docs", inputs = [ +quartodoc-build = { cmd = "quartodoc build && rm objects.json", cwd = "docs", inputs = [ "docs/_quarto.yml", "python/ribasim", ], outputs = [ @@ -98,6 +94,7 @@ generate-testmodels = { cmd = "python utils/generate-testmodels.py", inputs = [ "generated_testmodels", ] } tests = { depends_on = ["lint", "test-ribasim-python", "test-ribasim-core"] } +delwaq = { cmd = "pytest coupling/delwaq/test.py" } # Codegen codegen = { cmd = "julia --project utils/gen_python.jl && ruff format python/ribasim/ribasim/schemas.py", depends_on = [ "initialize-julia", @@ -153,6 +150,7 @@ github-release = "python utils/github-release.py" [dependencies] geopandas = "*" hatchling = "*" +jinja2 = "*" matplotlib = "*" netCDF4 = "*" numpy = "*" @@ -173,6 +171,7 @@ tomli-w = "*" xmipy = "*" xugrid = "*" xarray = "*" +networkx = ">=3.3" [pypi-dependencies] ribasim = { path = "python/ribasim", editable = true } diff --git a/python/ribasim/ribasim/model.py b/python/ribasim/ribasim/model.py index f47cda53d..c7b1454ef 100644 --- a/python/ribasim/ribasim/model.py +++ b/python/ribasim/ribasim/model.py @@ -204,7 +204,7 @@ def _apply_crs_function(self, function_name: str, crs: str) -> None: def node_table(self) -> NodeTable: """Compute the full NodeTable from all node types.""" - df_chunks = [node.node.df.set_crs(self.crs) for node in self._nodes()] # type: ignore + df_chunks = [node.node.df.set_crs(self.crs) for node in self._nodes()] # type:ignore df = pd.concat(df_chunks, ignore_index=True) node_table = NodeTable(df=df) node_table.sort() diff --git a/utils/testmodelrun.jl b/utils/testmodelrun.jl index 6cefde49e..4d0aacb69 100644 --- a/utils/testmodelrun.jl +++ b/utils/testmodelrun.jl @@ -2,8 +2,16 @@ import Ribasim include("utils.jl") +""" +Run all testmodels in parallel and check if they pass. + +A selection can be made by passing the name(s) of the individual testmodel(s) as (an) argument(s). +""" function main(ARGS) toml_paths = get_testmodels() + if length(ARGS) > 0 + toml_paths = filter(x -> basename(dirname(x)) in ARGS, toml_paths) + end n_model = length(toml_paths) n_pass = 0 n_fail = 0