Update sprinkling class msw model #1232
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Fixes #964 # Description Implements from_imod5 classmethod to StructuredDiscretization classmethod. NOTE: I had to modify the default regridding method of "idomain" as the "mode" method appears to have a bug with perfectly aligned structured grids. This bug requires further investigation. Will post an issue if found. # Checklist <!--- Before requesting review, please go through this checklist: --> - [x] Links to correct issue - [ ] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #965 # Description Adds a function to import an npf package from an imod5 project file. Adds tests. # Checklist - [x] Links to correct issue - [ ] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
Fixes #961 # Description implements importing from a imod5 project file for storage and initial conditions. # Checklist - [X] Links to correct issue - [ ] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
…eltares/imod-python into imod5_converter_feature_branch
Fixes #969 # Description implements importing recharge packages from a project file. The recharge can be imported using a planar grid, in which case it assigns the recharge to the uppermost active cell for each column. The recharge can also be imported from a non-planar (so fully 3d) grid in which case it is just regridded to the target grid. # Checklist - [X] Links to correct issue - [ ] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
# Conflicts: # imod/mf6/dis.py # imod/mf6/package.py # imod/tests/test_typing/test_typing_grid.py # imod/typing/grid.py
Fixes #967 # Description implements importing drainage packages from imod5 data. Adds tests. Methods for allocation and conductivity assignment can be specified per package, but it requires knowledge on what the packages are called in the imod5 project file (like "drn-1" and "drn-2"). If not specified, defaults are in place. # Checklist - [X] Links to correct issue - [ ] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
Fixes #1041 # Description Adds a function that imports a simulation from an imod5 project file. It creates a simulation, containing 1 GroundwaterFlowModel, containing the packages for which we support importing currently. This includes the mandatory flow packages like NPF and STO, and some boundary conditions (like DRN and RCH) but not yet CHD or WEL. # Checklist - [X] Links to correct issue - [ ] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
Fixes #1053 # Description On importing wells, the filter top and bottom are now parsed and stored in the project file data structure # Checklist - [X] Links to correct issue - [X] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #968 # Description Imports riverpackages from IMOD5. The infiltration factor (which does not exist in MF6) is accounted for by creating a drainage package. # Checklist <!--- Before requesting review, please go through this checklist: --> - [x] Links to correct issue - [ ] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
Fixes #1052 # Description when importing wells from imod5: If not all wells could be assigned to the modflow6 model (this can be due to inactive cells, or due to constraints of minimum thickness/permeability) then a log message will be generated to document in the log file that not all wells were successfully imported. # Checklist - [X] Links to correct issue - [X] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
Fixes #502 # Description Converts hfb's from imod5 to mf6, but only in the following cases: - the hfb has an assgined layer that is not zero - the hfb is mappable to the LayeredHorizontalFlowBarrierResistance class. It creates a single mf6 hfb package containing all the hfb's that are present in the model domain area. The hfb package is added to the simulation. # Checklist - [X] Links to correct issue - [ ] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
Follow-up on: #1070 # Description For some reason, I erronously merged #1070. This implements my suggestion to concatenate pandas dataframes. # Checklist <!--- Before requesting review, please go through this checklist: --> - [x] Links to correct issue - [ ] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [ ] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: luitjan <[email protected]>
# Conflicts: # docs/api/changelog.rst # imod/mf6/dis.py # imod/mf6/drn.py # imod/mf6/ic.py # imod/mf6/npf.py # imod/mf6/oc.py # imod/mf6/package.py # imod/mf6/rch.py # imod/mf6/riv.py # imod/mf6/sto.py # pixi.lock
# Conflicts: # pixi.lock
Fixes #1083 # Description When importing wells, we now make sure that when the ipf file defines 2 or more wells with the same x, y , filter_top, filter_bottom and id, then the ID of the second well is appended with "_1", and so on for successive findings of a well with the same characteristics (_2, _3 etc). # Checklist - [X] Links to correct issue - [ ] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1064 # Description Imports wells as grid-agnostic well packages, based on filter top and filter bottom, and x/y location as stated in the imod5_dataset object. # Checklist - [X] Links to correct issue - [ ] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
Fixes #966 # Description Imports chd packages present in imod5_data. These packages are imported one by one. If none are present, then a chd package is created at all locations where ibound == -1. In that case the starting head of the simulation is assigned as the chd value for each cell with ibound == -1. # Checklist - [X] Links to correct issue - [ ] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #598 # Description There was some confusion (also by me) about the use of the ``LayeredHorizontalFlowBarrier`` classes, so @HendrikKok explained me they were intended for single layers. I therefore changed the following to clarify: - Rename to ``SingleLayerHorizontalFlowBarrier`` classes - Throw ``ValidationError`` if multiple layers are added to dataset - Added missing test for SingleLayerHorizontalFlowBarrier class This means multiple SingleLayerHorizontalFlowBarrier need to be added to GroundwaterFlowModel object, whereas MODFLOW 6 only accepts one single HFB. So these have to be merged together. I think the best opportunity for this is to merge the low level ``Mf6HorizontalFlowBarrier`` objects. # Checklist - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1122, should be merged after #1121 (so duplication in changeset) # Description Adds ``from_imod5_data`` method to ``LayeredWell`` object. # Checklist - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [x] **If feature added**: Added/extended example
Fixes #1120 # Description this PR contains fixes made to be able to import a version of the LHM that is steady state. **Probably not all these changes should be merged. The review should reveal what to keep and what not.** Changes: -sto package can be absent in the imod5 project file. If that is the case, now a default sto package is made which imposes steady state. -rch package can now be absent in the project file. Then no recharge is present in the simulation. - allocation option and distribution option for river imports were hard coded to different defaults . The old defaults gave an error, which could be a new issue in itself. -also for GHB a new default was set, because the old one gave an error. This could be a new issue in itself. # Checklist - [X] Links to correct issue - [ ] Update changelog, if changes affect users - [X] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [X] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Joeri van Engelen <[email protected]>
Fixes #1139 # Description Loading project files turned out to be a time-sink for project file imports- especially when loading prj-file data with transient arrays such as chd-levels per timestep. These arrays were loaded in a function called "apply_factor_and_addition" which accounted for the fact that the user can specify a factor to multiply each array and a constant to add to it. These 2 (factor and addition) can be different for every timestep. Now they are applied at an earlier stage, when loading the ipf data. No new tests were added, because the tests in test_import_prj.py already test the application of factors and additions. (this PR is for improving performance and not changing behavior) # Checklist <!--- Before requesting review, please go through this checklist: --> - [x] Links to correct issue - [ ] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [ ] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1116 # Description - ``open_projectfile_data`` now groups wells by ipf name - ``GridAgnosticWell.from_imod5_data`` now validates associated IPFs whether they meet our requirements - ``GridAgnosticWell.from_imod5_data`` deactivates unassociated IPFs if not present in certain timestep anymore - Remove imod.formats.prj.convert_to_disv - Adds lots of test cases to test the well import from projectfiles # Checklist - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1132 # Description This PR adds the following: - Increase performance for writing the HFB files, by using new xugrid create_snap_to_grid_dataframe. - Fixes error when multiple barriers in a single dataset would be snapped to same edge. These lines are now aggregated. - Add some basic infrastructure for user acceptance test for writing LHM, the path to the LHM projectfile should be set in a .env as LHM_PRJ. This can later be extended to TeamCity. This reduces the time spent writing the HFB packages from 34 minutes to 12.5 minutes on my local machine. I've profiled the causes of the remaining bottlenecks to writing. I'll post a follow-up issue for that. # Checklist - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1158 # Description Fix remaining HFB bottlenecks. This reduces writing the HFB package from the LHM from 12.5 minutes to 2 minutes. - Cache results ``xu.Ugrid2d.from_structured``, as this is a costly operation - Use ``and`` instead of ``&`` operator in the ``scalar_None`` function, to enable shortcutting. - Remove ``mask_all_packages`` function in ``from_imod5_data``, call in tests. - Create separate pixi task for slow unittests, where just in time compilation is enabled. ``pixi run unittests`` still runs all unittests, by starting two pixi tasks ``unittests_njit`` & ``unittests_jit``. # Checklist - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1166 and somewhat fixes #1163 # Description - Moves ``pd.to_datetime`` logic to separate place, use ``errors="coerce"`` setting, which turns datetimes beyond the year 2261 to ``pd.NaT``. These seem to be consequently ignored in the ``resample_timeseries``. - Truncate well names to max 16 characters - Support wells defined in "steady-state" entry in the projectfile. - Add test cases for this. # Checklist - [x] Links to correct issue - [ ] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1164 # Description This implements the following cleanup utilities for the robin boundary conditions, namely the DRN, GHB, and RIV. - Cleanup helper functions, which are part of the public API (so that people could also use them outside MODFLOW 6) - Cleanup methods to the River, GeneralHeadBoundary, Drain package for convenience. These call the corresponding helper function. Save the user the hassle of manually finding the right arguments to clean up grids. - Add a utility method: Call function on grids, which separates grid variables from settings, calls a function on them, and then merges these dicts again. - Converted the fixtures in ``test_mf6_riv`` to regular functions, as they were used as such anyway. Without this, RivDisCases could not be used outside the ``test_mf6_riv`` module, now it can be imported. # Checklist <!--- Before requesting review, please go through this checklist: --> - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1176 # Description - Assign wells with point filters (filters with a zero length) to layers. Before, these would be removed in the compute_overlap method. - Add test case for wells with a point filter - Set validation so that screen_top can equal screen_bottom - Rename vague variable name "df" to "df_factor" # Checklist <!--- Before requesting review, please go through this checklist: --> - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example --------- Co-authored-by: Sunny Titus <[email protected]>
Fixes #1187 # Description Adds cleanup utility for wells, as well as a method on the ``Well`` object. ``LayeredWell`` doesn't have ``cleanup`` method yet, as cleaning up almost purely focuses on adjusting filter screen levels for now. The function as well as the method are a bit more involved than the other cleanup utilities, because we are dealing here with a comparison of point data and grids. # Checklist - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1216 # Description iMOD5 interprets recharge rate in mm/d, whereas MODFLOW6 is unit consistent, and thus uses m/d. This PR adds a conversion function to do that. I updated the tests to also test if this conversion is done. # Checklist - [x] Links to correct issue - [ ] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1210 # Description This PR modifies the allocation and conductance distribution methods somewhat, to allow boundary conditions to be allocated to the first model layer when located above model top. This is similar to how iMOD5 does these things. # Checklist - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1209 # Description - Add setting to ``to_mf6_pkg``: ``error_on_well_removal``, which throws an error if wells are removed entirely during well assignment. - Separated code to collect filtered well ids in separate method. This method is now also called to collect ids of errors being removed in error message. - Added attribute ``_is_from_imod5`` to Modflow6Simulation to keep track if the simulation is loaded from iMOD5 data or not. Based on this, some validation settings might be set to be a bit more permissive. (Or call some extra cleanup?) - ``is_from_imod5`` property to WriteContext to keep track of the same thing within the writing context. # Checklist - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [x] Unit tests were added - [ ] **If feature added**: Added/extended example
Fixes #1222 # Description - Add a ``ValidationContext`` dataclass - Add a ``_validation_context`` attribute to ``Modflow6Simulation``; this replaces the ``_is_from_imod5`` attribute. - The ``ValidationContext`` contains an attribute for strict well checks, turned on by default. This is set to False when calling ``from_imod5`` or for split simulations. - Adds a ``_to_mf6_pkg`` method in a similar design as proposed in #1223, this to preserve public API. - Refactor ``WriteContext``, to make it a dataclass again. I had to ignore type annotation for ``write_directory``, otherwise MyPy would throw errors. The whole property shebang presumably started with MyPy throwing errors. Reverting it back to a dataclass reduces the lines of code considerably, which makes it more maintainable. - Use jit for examples run, this speeds them up considerably. The examples ran into a TimeOut on TeamCity, and this reduces the change of that happening again. # Checklist <!--- Before requesting review, please go through this checklist: --> - [x] Links to correct issue - [x] Update changelog, if changes affect users - [x] PR title starts with ``Issue #nr``, e.g. ``Issue #737`` - [ ] Unit tests were added - [ ] **If feature added**: Added/extended example
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HendrikKok
changed the base branch from
master
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imod5_converter_feature_branch
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Fixes #
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Issue #nr, e.g.Issue #737