From 5ac8a39616b56620aec1070ded3606ff05637782 Mon Sep 17 00:00:00 2001 From: Jake Faulkner Date: Mon, 31 Aug 2026 20:29:52 +1200 Subject: [PATCH] Generate SW4 input files from a realisation `create-sw4-input` renders the SW4 input file for a realisation: the grid, the refinement stack, the source, the stations, and whatever commands the `sw4` section carries. The requested domain becomes the grid's *interior*. The grid is padded laterally by one supergrid width on each side, so the sponge sits outside the region anyone asked to simulate rather than eating into it. `adjust_for_topography` handles the interaction between topography and the refinement stack. Topography lifts the top of the grid above z=0, which thins the first layer; SW4 requires every grid in the stack to hold at least `nz_min` cells, so any layer left too thin is pushed down until it does. The topography surface participates in that count as a boundary but is not itself returned as a refinement -- the caller gets back the real layers plus the depth used. Commands come from the realisation rather than being hard-coded, so a run can add or override any SW4 command without a code change. Output commands that take a time window are merged with the simulation duration on the way out. `test_bottom_refinement_holds_the_sponge` asserts against the shipped v26.7.1Hz configuration rather than a synthetic one: the invariant that matters is that the bottom refinement of a *real* domain is thick enough to hold the bottom sponge, at every depth we support. Requires nzcvm (for `nzcvm.formats.sfile`, used to read the model's lateral footprint), which in turn forces `requires-python >= 3.13`. nzcvm is currently a git dependency and this cannot merge until it is released. Co-Authored-By: Claude Opus 5 --- pyproject.toml | 5 +- tests/test_sw4_template.py | 178 ++++++++ uv.lock | 717 +++++++++++++++++-------------- workflow/scripts/sw4_template.py | 445 +++++++++++++++++++ 4 files changed, 1011 insertions(+), 334 deletions(-) create mode 100644 tests/test_sw4_template.py create mode 100644 workflow/scripts/sw4_template.py diff --git a/pyproject.toml b/pyproject.toml index d5bd1055..013bf13c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,7 +7,7 @@ name = "workflow" authors = [{ name = "QuakeCoRE" }] description = "Next generation workflow powered by cylc." readme = "README.md" -requires-python = ">=3.12" +requires-python = ">=3.13" dynamic = ["version"] dependencies = [ # UCGMSim Dependencies @@ -38,6 +38,7 @@ dependencies = [ "parse>=1.21.0", "rich>=14.3.2", "dask>=2026.6.0", + "nzcvm", ] [project.optional-dependencies] @@ -70,6 +71,7 @@ generate-rupture-propagation = "workflow.scripts.generate_rupture_propagation:ap copy-domain-parameters = "workflow.scripts.copy_velocity_model_parameters:app" srf-to-hdf5 = "workflow.scripts.srf_to_hdf5:app" create-e3d-par = "workflow.scripts.create_e3d_par:app" +create-sw4-input = "workflow.scripts.sw4_template:app" generate-stoch = "workflow.scripts.generate_stoch:app" merge-ts = "workflow.scripts.merge_ts:app" hf-sim = "workflow.scripts.hf_sim:app" @@ -174,4 +176,5 @@ exclude = [ # don't report on objects that match any of these regex ] [tool.uv.sources] +nzcvm = { git = "https://github.com/lispandfound/nzcvm" } im-calculation = { git = "https://github.com/ucgmsim/im_calculation", branch = "no_parallel" } diff --git a/tests/test_sw4_template.py b/tests/test_sw4_template.py new file mode 100644 index 00000000..14a97c51 --- /dev/null +++ b/tests/test_sw4_template.py @@ -0,0 +1,178 @@ +"""Tests for `workflow.scripts.sw4_template`. + +The interesting behaviour here is geometric: the requested domain has to end up +as the *interior* of the SW4 grid, and the bottom refinement has to stay thick +enough to hold the bottom sponge. Both are invariants rather than values, so +they are tested as invariants. +""" + +from pathlib import Path + +import h5py +import numpy as np +import pytest +from nzcvm.formats import sfile + +from velocity_modelling.bounding_box import BoundingBox +from workflow import defaults, sw4 +from workflow.realisations import Refinement, Refinements, SW4Parameters +from workflow.scripts import sw4_template + +SPONGE_KM = 12.0 +"""The v26_7_1Hz sponge width, in kilometres.""" + + +@pytest.fixture +def domain() -> BoundingBox: + """A rotated 100 x 80 km domain, so the padding cannot be axis-aligned. + + Returns + ------- + BoundingBox + The domain. + """ + return BoundingBox.from_centroid_bearing_extents( + centroid=np.array([-43.5, 172.5]), + bearing=35.0, + extent_x=100.0, + extent_y=80.0, + ) + + +def test_padding_grows_each_axis_by_two_sponges(domain: BoundingBox) -> None: + """One sponge per face, so an axis grows by exactly two sponge widths.""" + padded = domain.pad(pad_x=(SPONGE_KM, SPONGE_KM), pad_y=(SPONGE_KM, SPONGE_KM)) + + assert padded.extent_x == pytest.approx(domain.extent_x + 2 * SPONGE_KM) + assert padded.extent_y == pytest.approx(domain.extent_y + 2 * SPONGE_KM) + + +def test_padding_preserves_orientation(domain: BoundingBox) -> None: + """A rotated box must stay rotated the same way. + + `BoundingBox.pad` pads along the box's own axes and then re-normalises the + corner order in `__init__`. If the re-normalisation picked a different + bottom-left corner the roles of `extent_x` and `extent_y` would swap and the + SW4 grid would be transposed relative to the velocity model. + """ + padded = domain.pad(pad_x=(SPONGE_KM, SPONGE_KM), pad_y=(SPONGE_KM, SPONGE_KM)) + + assert padded.bearing == pytest.approx(domain.bearing) + assert padded.great_circle_bearing == pytest.approx( + domain.great_circle_bearing, abs=1e-3 + ) + # Symmetric padding keeps the centroid, which is what makes the velocity + # model and the SW4 grid concentric. + assert padded.origin == pytest.approx(domain.origin, abs=1e-6) + + +def test_padded_grid_strictly_contains_the_requested_domain( + domain: BoundingBox, +) -> None: + """The requested domain becomes the interior, not a slice of the sponge.""" + padded = domain.pad(pad_x=(SPONGE_KM, SPONGE_KM), pad_y=(SPONGE_KM, SPONGE_KM)) + + assert padded.polygon.contains_properly(domain.polygon) + # Every edge of the original is a full sponge width inside the padded box. + assert domain.polygon.exterior.distance(padded.polygon.exterior) == pytest.approx( + SPONGE_KM * 1000.0, rel=1e-6 + ) + + +@pytest.mark.parametrize("depth_km", [10.0, 30.0, 60.0, 120.0, 350.0]) +def test_bottom_refinement_holds_the_sponge(depth_km: float) -> None: + """SW4's `check_supergrid_thickness` requires `nz[0] >` the sponge thickness. + + Only grid 0 carries a bottom taper, so the requirement is on the bottom + refinement alone. `adjust_for_topography` runs first and can move the + bottoms around, so the invariant is checked after it, exactly as + `generate_sw4_input` orders the two. + """ + version = defaults.DefaultsVersion.v26_7_1Hz + theoretical = Refinements.read_from_defaults(version) + sw4_params = SW4Parameters.read_from_defaults(version) + + refinements = theoretical.refinements_for_depth(depth_km) + refinements, _ = sw4_template.adjust_for_topography( + refinements, topography_zmax=1500.0, nzmin=sw4_params.nz_min + ) + refinements = sorted(refinements, key=lambda r: r.bottom) + + coarsest = refinements[-1].resolution + assert coarsest == sw4.coarsest_resolution(theoretical, depth_km) + + supergrid_width = sw4.supergrid_width(sw4_params, coarsest) + thickness_before = refinements[-1].bottom - ( + refinements[-2].bottom if len(refinements) > 1 else 0.0 + ) + refinements[-1].bottom += supergrid_width + thickness = thickness_before + supergrid_width + + # Strictly greater: the sponge must be *contained* in the layer, so there has + # to be at least one cell of the layer that is not sponge. + assert thickness > supergrid_width + assert thickness / coarsest > supergrid_width / coarsest + + +def test_adjust_for_topography_leaves_resolutions_alone() -> None: + """The coarsest resolution can be read before or after adjustment. + + `generate_sw4_input` reads the sponge width from the adjusted refinements + while `create-nzvm-input` reads it from the theoretical ones. That only + agrees because adjustment moves bottoms, never resolutions. + """ + refinements = [ + Refinement(resolution=100.0, bottom=5000.0), + Refinement(resolution=200.0, bottom=25000.0), + Refinement(resolution=400.0, bottom=40000.0), + ] + adjusted, _ = sw4_template.adjust_for_topography( + refinements, topography_zmax=1500.0, nzmin=12 + ) + + assert [r.resolution for r in adjusted] == [100.0, 200.0, 400.0] + + +def write_sfile(path: Path, shape: tuple[int, int], resolution: float) -> None: + """Write a minimal sfile carrying only what the footprint reader needs. + + Parameters + ---------- + path : Path + Where to write the file. + shape : tuple[int, int] + The (north, east) gridpoint counts of the coarsest grid. + resolution : float + The coarsest grid's horizontal spacing, in metres. + """ + with h5py.File(path, "w") as f: + material = f.create_group(sfile.MATERIAL_GROUP) + # A finer grid over the same footprint, to check the reader picks the + # coarsest and still gets the same answer. + for index, factor in enumerate((2, 1)): + grid = material.create_group(f"grid_{index}") + grid.attrs[sfile.HORIZONTAL_ATTR] = resolution / factor + grid.attrs[sfile.NUMBER_OF_COMPONENTS_ATTR] = np.int32(1) + grid.create_dataset( + "Cs", + data=np.zeros( + ( + (shape[0] - 1) * factor + 1, + (shape[1] - 1) * factor + 1, + 3, + ), + dtype=np.float32, + ), + ) + + +def test_lateral_footprint_from_velocity_model(tmp_path: Path) -> None: + """The footprint is `(n - 1) * h`, read off the coarsest grid.""" + path = tmp_path / "model.sfile" + write_sfile(path, shape=(319, 269), resolution=400.0) + + with h5py.File(path, "r") as f: + extent_x, extent_y = sw4_template.lateral_footprint_from_velocity_model(f) + + assert extent_x == pytest.approx(318 * 400.0) + assert extent_y == pytest.approx(268 * 400.0) diff --git a/uv.lock b/uv.lock index 2a43ba87..c0762b94 100644 --- a/uv.lock +++ b/uv.lock @@ -1,19 +1,25 @@ version = 1 revision = 3 -requires-python = ">=3.12" +requires-python = 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"cycle", "cycleInterval"}) +"""Parameter keys that determine when an `imagehdf5` command fires. If none of +these are set, SW4 never emits the image, so we default to the simulation end time.""" + +SW4_TEMPLATE = string.Template(""" +${fileio} + +${grid} + +${time} + +${rupturehdf5} +${refinements} + +${other_commands} + +${sfile} +${rechdf5} +""") + + +def azimuth_from_velocity_model(velocity_model: h5py.File) -> float: + """ + Extract the azimuth value from a velocity model HDF5 file. + + Parameters + ---------- + velocity_model : h5py.File + HDF5 file object containing velocity model attributes. + + Returns + ------- + float + The azimuth value stored in the file's attribute. + """ + _, _, azimuth = velocity_model.attrs[sfile.ORIGIN_AZIM_ATTR] + return float(azimuth) + + +def topography_height_from_velocity_model( + velocity_model: h5py.File, +) -> tuple[float, float]: + """ + Extract the minimum topography height from a velocity model HDF5 file. + + Parameters + ---------- + velocity_model : h5py.File + HDF5 file object containing velocity model attributes. + + Returns + ------- + float + The minimum depth (topography height) stored in the file's attribute. + """ + global_min, zmax = velocity_model.attrs[sfile.MIN_MAX_DEPTH_ATTR] + return -float(global_min), float(zmax) + + +def lateral_footprint_from_velocity_model( + velocity_model: h5py.File, +) -> tuple[float, float]: + """Measure the lateral footprint of a velocity model sfile, in metres. + + An sfile does not record its own lateral extent, so it is recovered from the + shape of a material grid and that grid's horizontal spacing. Every grid in an + sfile covers the same footprint, so any of them would do; the coarsest is + used because it is the smallest array to describe. + + The sfile format requires the outermost axis to be due north, which is SW4's + `x`, so the returned pair is in SW4's axis convention and not the workflow's. + + Parameters + ---------- + velocity_model : h5py.File + HDF5 file object containing a velocity model sfile. + + Returns + ------- + tuple[float, float] + The extents of the model along SW4's `x` (north) and `y` (east) axes, in + metres. + """ + material = velocity_model[sfile.MATERIAL_GROUP] + grid_name = max( + material, key=lambda name: material[name].attrs[sfile.HORIZONTAL_ATTR] + ) + grid = material[grid_name] + resolution = float(grid.attrs[sfile.HORIZONTAL_ATTR]) + # Every material component of a grid has the same shape, so the first one is + # representative. + nx, ny = next(iter(grid.values())).shape[:2] + return (nx - 1) * resolution, (ny - 1) * resolution + + +def build_sw4_commands( + sw4_params: SW4Parameters, + x: float, + y: float, + z: float, + dx: float, + azimuth: float, + lon: float, + lat: float, + velocity_model_name: str, + velocity_model_directory: Path, + topography_zmax: float, + simulation_time: float, +) -> tuple[SW4Command, list[SW4Command]]: + """Resolve SW4Parameters.commands, layering in runtime-computed values. + + Parameters + ---------- + sw4_params : SW4Parameters + The SW4 parameters read from the realisation (or defaults). + x, y, z : float + Simulation domain extents (metres). + dx : float + Grid spacing of the bottom refinement layer (metres). + azimuth : float + Grid azimuth, taken from the velocity model. + lon, lat : float + Grid origin coordinates. + velocity_model_name : str + Filename of the velocity model sfile. + velocity_model_directory : Path + Directory containing the velocity model sfile. + topography_zmax : float + Computed maximum topography depth. + simulation_time : float + Simulation duration (seconds), used as the default image output time. + + Returns + ------- + tuple[SW4Command, list[SW4Command]] + The resolved `grid` command, and every other resolved command. + + Raises + ------ + ValueError + If `sw4_params.commands` has no `grid` command. + """ + commands = sw4_params.commands + grid = find_command(commands, "grid") + if grid is None: + raise ValueError("SW4 configuration is missing a required 'grid' command") + topography = find_command(commands, "topography") + + grid_command = None + other_commands = [] + for command in commands: + if command is grid: + grid_command = command.merged( + x=x, y=y, z=z, h=dx, az=azimuth, lon=lon, lat=lat + ) + elif topography is not None and command is topography: + other_commands.append( + command.merged( + input="sfile", + zmax=topography_zmax, + file=f"{velocity_model_directory}/{velocity_model_name}", + ) + ) + elif command.name == "imagehdf5" and not ( + IMAGE_TIME_KEYS & command.parameters.keys() + ): + other_commands.append(command.merged(time=simulation_time)) + else: + other_commands.append(command) + + return grid_command, other_commands + + +def adjust_for_topography( + refinements: list[Refinement], topography_zmax: float, nzmin: int = 12 +) -> tuple[list[Refinement], float]: + """Deepen refinement layers so each holds at least `nzmin` cells. + + Topography raises the top of the grid above z=0, which eats into the + first refinement layer. SW4 needs every grid in the stack to be at + least `nzmin` cells deep, so any layer left too thin is pushed down + until it is. The topography surface is inserted as a boundary for the + purpose of that count, but is not returned as a refinement. + + Parameters + ---------- + refinements : list of Refinement + The refinement layers, resolved for the domain depth. + topography_zmax : float + Depth of the lowest point of the topography (metres, positive + down). + nzmin : int, optional + Minimum number of cells in any layer. + + Returns + ------- + tuple + The adjusted refinements, and the topography depth used. + """ + # Ensure no side effects + refinements = copy.deepcopy(refinements) + # By shallow copying the refinements before modifying them this view into the refinements will only have the updated refinements, and not the topography and bottom. + real_refinements = refinements.copy() + topography_resolution = min( + ( + refinement + for refinement in refinements + if refinement.bottom > topography_zmax + ), + key=lambda r: r.bottom, + ).resolution + topography = Refinement(bottom=topography_zmax, resolution=topography_resolution) + refinements.append(topography) + refinements.sort(key=lambda r: r.bottom) + + for above, below in itertools.pairwise(refinements): + thickness = below.bottom - above.bottom + nz = thickness // below.resolution + cells_needed = nzmin - nz + if cells_needed > 0: + below.bottom += cells_needed * below.resolution + + topography_zmax = topography.bottom + + return real_refinements, topography_zmax + + +@cli.from_docstring(app) +def generate_sw4_input( + realisation_ffp: Path, + station_path: Path, + srf_path: Path, + velocity_model: Path, + work_directory: Path, + output_path: Path, +) -> None: + """Generate SW4 template for realisation + + Parameters + ---------- + realisation_ffp : Path + Path to realisation file. + station_path : Path + Path to station file. + srf_path : Path + Path to srf file. + velocity_model : Path + Path to velocity model file. + work_directory : Path + Path to work directory. + output_path : Path + Path to output SW4 file. + """ + metadata = RealisationMetadata.read_from_realisation(realisation_ffp) + domain_parameters = DomainParameters.read_from_realisation(realisation_ffp) + theoretical_refinements = Refinements.read_from_realisation_or_defaults( + realisation_ffp, metadata.defaults_version + ) + sw4_params = SW4Parameters.read_from_realisation_or_defaults( + realisation_ffp, metadata.defaults_version + ) + velocity_model_parameters = ( + VelocityModelParameters.read_from_realisation_or_defaults( + realisation_ffp, metadata.defaults_version + ) + ) + logger = log_utils.get_logger(__name__) + + with h5py.File(velocity_model, "r") as f: + # Azimuth must be the same as the velocity model inside SW4 + azimuth = azimuth_from_velocity_model(f) + topography_height, sfile_zmax = topography_height_from_velocity_model(f) + sfile_x, sfile_y = lateral_footprint_from_velocity_model(f) + + # HACK: SW4 User Guide (Chapter 5) suggests + # z_max >= -e_min + 3 (e_max - e_min) where e_min, e_max are the minimum + # and maximum topography level of the velocity model we will assume that the + # minimum elevation is zero (i.e. every simulation contains ocean, and there + # is no ocean bathymetry). + topography_zmax = 3 * topography_height + + depth = domain_parameters.depth + time = domain_parameters.duration + refinements = theoretical_refinements.refinements_for_depth(depth) + + refinements, topography_zmax = adjust_for_topography( + refinements, topography_zmax, nzmin=sw4_params.nz_min + ) + refinements = sorted(refinements, key=lambda r: r.bottom) + # The sponge width is a single scalar in SW4, measured on the coarsest grid, + # and it applies to every face of every grid. + coarsest_resolution = refinements[-1].resolution + supergrid_width = sw4.supergrid_width(sw4_params, coarsest_resolution) + + # Gate B: the last gate before an SW4 run. This catches hand-edited + # realisations and those produced by `copy-domain-parameters` or + # `import-realisation`, which never go through `generate-domain`. + sw4.check_fault_buffer( + velocity_model_parameters.fault_buffer, sw4_params, coarsest_resolution + ) + + # Per the SW4 User Guide, the supergrid sponge (30 gridpoints by default) at the bottom of the domain + # must be contained in the bottom refinement. + refinements[-1].bottom += supergrid_width + depth += supergrid_width / 1000.0 + + # The sponge is carved out of the grid, not out of the requested domain, so + # the SW4 grid is the requested domain padded by one sponge width per lateral + # face. Without this the lateral sponges eat into the region the domain was + # sized to cover and a source can end up inside the absorbing layer. + # `BoundingBox.pad` works in kilometres and pads along the box's own rotated + # axes, so no trigonometry is needed here. The velocity model is padded by at + # least as much in `create-nzvm-input`, so SW4 never queries outside the sfile. + supergrid_width_km = supergrid_width / 1000.0 + padded_domain = domain_parameters.domain.pad( + pad_x=(supergrid_width_km, supergrid_width_km), + pad_y=(supergrid_width_km, supergrid_width_km), + ) + x = padded_domain.extent_x * 1000.0 + y = padded_domain.extent_y * 1000.0 + + # In SW4 the domain should always begin from the bottom-left (which is corners[0] by construction) + lat, lon = padded_domain.corners[0] + + # NOTE: In SW4 x = north, but in the workflow y = north. + sw4.check_lateral_gridpoints(y, x, sw4_params, coarsest_resolution) + + if refinements[-1].bottom > sfile_zmax: + raise ValueError("Bottom of domain exceeds velocity model bounds") + + # The sfile and the SW4 grid are padded symmetrically about the same + # centroid with the same azimuth, so comparing extents is a containment + # check. + if y > sfile_x or x > sfile_y: + raise ValueError( + f"The SW4 grid ({y / 1000.0:.3f} x {x / 1000.0:.3f} km, " + "north x east, including its supergrid padding) is not contained in " + f"the velocity model ({sfile_x / 1000.0:.3f} x " + f"{sfile_y / 1000.0:.3f} km). Regenerate the velocity model with " + "`create-nzvm-input`, which pads the model to cover the padded SW4 " + "grid." + ) + + logger.info( + "SW4 supergrid geometry", + supergrid_width_m=supergrid_width, + absorbed_period_normal_incidence_s=sw4.absorbed_period( + sw4_params, + coarsest_resolution, + # NOTE: `s_wave_velocity` is in m/s, `absorbed_period` wants km/s. + velocity_model_parameters.s_wave_velocity / 1000.0, + ), + absorbed_period_60_degrees_s=sw4.absorbed_period( + sw4_params, + coarsest_resolution, + # NOTE: `s_wave_velocity` is in m/s, `absorbed_period` wants km/s. + velocity_model_parameters.s_wave_velocity / 1000.0, + incidence_degrees=60.0, + ), + fault_buffer_km=velocity_model_parameters.fault_buffer, + ) + + refinements_str = "\n".join( + SW4Command("refinement", {"zmax": f"{refinement.bottom:.1f}"}).render() + for refinement in refinements[ + :-1 + ] # Last refinement layer is implicitly the bottom of the domain + ) + dx = refinements[-1].resolution + + velocity_model_directory = velocity_model.parent + velocity_model_name = velocity_model.name + + grid_command, other_commands = build_sw4_commands( + sw4_params, + # NOTE: In SW4 x = north, but in the workflow y = north. + x=y, + y=x, + z=depth * 1000.0, + dx=dx, + azimuth=azimuth, + lon=lon, + lat=lat, + velocity_model_name=velocity_model_name, + velocity_model_directory=velocity_model_directory, + topography_zmax=topography_zmax, + simulation_time=time, + ) + + low_frequency_output = work_directory / "out.h5" + output_path.write_text( + SW4_TEMPLATE.substitute( + fileio=SW4Command( + "fileio", + { + "path": work_directory, + "verbose": sw4_params.verbose, + "printcycle": sw4_params.printcycle, + }, + ).render(), + grid=grid_command.render(), + time=SW4Command("time", {"t": time}).render(), + rupturehdf5=SW4Command("rupturehdf5", {"file": srf_path}).render(), + refinements=refinements_str, + other_commands="\n".join(command.render() for command in other_commands), + sfile=SW4Command( + "sfile", + { + "filename": velocity_model_name, + "directory": velocity_model_directory, + }, + ).render(), + rechdf5=SW4Command( + "rechdf5", + { + "infile": station_path, + "outfile": low_frequency_output.relative_to(work_directory), + }, + ).render(), + ) + )