Can I submit issues and or PR here?

With the most recent changes on the develop branch, I get an error when trying to run PCR-GLOBWB with dynamicFloodPlain set to False (I'm using the Rhine-Meuse config file in grpc4bmi-examples repository). The error I get when running the deterministic_runner.py script is the following,

Traceback (most recent call last):
...
AttributeError: 'Routing' object has no attribute 'channelStorageCapacity'

As far as I can tell, the fix is simply to wrap the flood-plain specific code in something like: if self.floodPlain - at least that seems to work for my case. I will send a pull request with my fixes to see what you all think.

When I try to run the following code: python deterministic_runner.py <ini_configuration_file (with absolute file path)>, python seems unable to detect the pcraster module.

I have tried to install pcraster inside the model folder using the following code:
conda install -c conda-forge pcraster

However the issue persists. I would request a help to resolve it.

Description
Feature to use preFactors for tuning/adjusting model parameters.

Problem
There are some developments related to this feature. We should finalize this and make this feature formal.

Implementation
I suggest to merge from the development created in https://github.com/edwinkost/PCR-GLOBWB_model/blob/uly_2024/config/ulysses/version_2023-12-31/setup_6arcmin_ulysses_2LCs_version_2023-12-31_finalize_global_clean.ini

Downsides
None.

Face trouble when trying to open .map file. Which software should I use to edit the import data?
It's extremely difficult to reproduce customized local simulation.

It would be good to make a separate "develop" branch (see also https://stackoverflow.com/a/39586780). This branch will accumulate enhancements/features developed for PCR-GLOBWB. The development branch can then be used for testing and added to the master branch when appropriate. Hotfixes will be added directly to the master branch.

Description
Include GLOBGM (the MODFLOW groundwater model of PCR-GLOBWB) as a module.

Problem
Although it is known that PCR-GLOBWB can include a MODFLOW groundwater model (e.g. since Sutanudjaja et al. 2011 to Verkaik et al., 2014), we have not really formalized this feature yet in https://github.com/UU-Hydro/PCR-GLOBWB_model.

Implementation
Edwin will try to merge the latest developments in the respect of GLOBGM, more specifically from https://github.com/UU-Hydro/GLOBGM and https://github.com/edwinkost/PCR-GLOBWB_GM-GLOB (e.g. https://github.com/edwinkost/PCR-GLOBWB_GM-GLOB/tree/modularizing)

Downsides
None, I guess.

See https://peps.python.org/pep-0008/#imports

isort does this automatically for you. It can be set-up as a pre-commit hook so you will never have to think about it again.

The model code is littered with modules that are imported by not used. This slows down the parsing of the code and adds dependencies that are not needed.

A static analyzer like pyright can be used to detect these. I recommend to at least configure a pre-commit hook to detect them before code gets committed.

This issue will list and track the progress made for PCR-GLOBWB 3. This is a general overview. For each specific item, a separate issue will be made that contains more details.

Enhancements

• #45
• PCR-GLOBWB supporting modules refactoring
• PCR-GLOBWB core modules refactoring
• PCR-GLOBWB continuous integration

Features

• Flexible landcover type support
• Flexible soil layers support
• Flexible input file read frequency
• Temporal input/output file naming (e.g. per year or per month)
• Zarr file format support
• Endothermic lake water balance
• Demand-driven reservoir operations
• Units switch from [m] to [kg m-2]
• Non-linear baseflow
• Lateral snow movement

Currently, the frequency at which input parameters are read from file is hard coded in the model. For example the yearly land-surface inputs:

        # - assumption: annual resolution
        if self.noAnnualChangesInLandCoverParameter == False and self.dynamicIrrigationArea == False and \
          (currTimeStep.timeStepPCR == 1 or currTimeStep.doy == 1):
            msg = 'Read land cover fractions based on the given netcdf file.'```

It would be better for this frequency to be derived from the files themselves, meaning that if a monthly file is given, data is read monthly. Moreover, if the final timestep of the input file is reached, the input data of the final timestep is re-read every year. This is not needed.

Would like to see that the input-file string can contain formatting patterns that match the time of the current model timestep. This is especially useful for meteorological forcing inputs that often come in yearly NetCDF files.

A simple key-based format would be sufficient, and would also allow for user-customized formatting options (such as the number of digits). As an example:
netcdf_file_name = self.preFileNC.format(year = currTimeStep.year, month = currTimeStep.month, day = currTimeStep.day, hour = currTimeStep.hour, second = currTimeStep.second, milisecond = currTimeStep.milisecond)

Description
Make the output files that are available on https://geo.data.uu.nl/research-pcrglobwb/pcr-globwb_gmd_paper_sutanudjaja_et_al_2018/ COMPLETETLY OPEN (without having for requesting access to E.H.Sutanudjaja).

Problem
Make the output files that are available on https://geo.data.uu.nl/research-pcrglobwb/pcr-globwb_gmd_paper_sutanudjaja_et_al_2018/ COMPLETETLY OPEN (without having for requesting access to E.H.Sutanudjaja).

Implementation

• Work with the Yoda team.
• Rearrange the files, and push them to the vault.
• Create a readme.
• Publish.

Downsides
None

Guidelines for refactoring PCR-GLOBWB.

Planning

• Create design diagrams before refactoring
  • Should include classes and their purpose
  • Should include interactions between classes through (public) function calls
• Create a GitHub issue for the specific refactor (see the contributing document)

Structure

• Modules and classes should be designed to be closed for modification but open for extension
• Modules and classes should be independent (i.e. avoid interactions between classes)
• Avoid methods not in a class (i.e. static methods)
• Class methods should be small, with a maximum of two to three indentations, and have a specific purpose
• Class variables are allocated during __init__()
• Avoid class variable modification in deeper sub-functions

Styling

• Code styling mainly follows the Python PEP8 specifications
  • Classes use TitleCase whereas properties/methods (and others) use snake_case
  • A leading underscore is used for private properties/methods
  • Avoid try-except block. If necessary, specify the exception expected
  • Prefer with block instead of calling 'close()'
  • Annotate all functions with the expected types (type-hinting)
  • Place (independent) classes and functions in separate files
• Before publishing a refactor, format your code using isort (for imports) and black (for code).
  • Consider using a git pre-commit hook to do so automatically

Especially long higher-resolution simulations, storing all timesteps (for a single variable) into a single output file results in very large output files. It would be nice if an output frequency could be specified under the reportingOptions in the configuration file. For example:

[reportingOptions]
formatNetCDF = NETCDF4
frequency = year
zlib = True

We need something like this: https://github.com/mobxjs/mobx/issues/new/choose

Hi, I am Bart, RSE at the eScience Center. I am currently working on getting the newest versions of PCR-GLOB to work with eWaterCycle.

For this I have created a Docker container which packages this model with grpc4bmi. You can view that here (as a text file): Dockerfile.txt.

Things seem to mostly work, until I am trying to initialize the model. Note that I am using version 2.4.0, with the setup_30min.ini config file.

After 25 seconds of initialization (and network activity indicating that files are downloaded using opendap), the model fails with the following error:

    No such file or directory: '/home/bart/ewatercycle/output/pcrglobwb_20231206_095919/global_30min/initialConditions/non-natural/consistent_run_201903XX/1999/interceptStor_forest_1999-12-31.nc'"

Which is strange, because the global_30min/... part is supposed to come from the input directory, and not the output directory right?

The global options on the ini are as following:

outputDir = /home/bart/ewatercycle/output/pcrglobwb_20231206_095919
cloneMap = /home/bart/ewatercycle/parameter-sets/pcrglobwb_rhinemeuse_30min/cloneMaps/RhineMeuse30min.map
inputDir = https://opendap.4tu.nl/thredds/dodsC/data2/pcrglobwb/version_2019_11_beta/pcrglobwb2_input/

When regridding a course resolution (netCDF) array, a factor is applied and the array is uniformly downscaled based on this factor. However, for cases where the fine resolution bounds to not match up with the coarse resolution bounds, this will not work. Rather the regridded coarse resolution array will be too large.

At minimum, the model should stop running and give a clear error when this may occur. Better would be to incorporate regridding for unaligned grids.

I hope to read the map file of the 5arcmin model, and I tried to install the Pcraster, but I don’t know how to open and convert this file format (to asc or nc, etc.) . I would be very grateful if you could give me some information about it.

Dear author,
I found that the channelStorage of each grid cell is directly contributed by the total runoff. Does this mean that the presence of a river in each grid cell is not important? Because I did not see any code identifying whether there is a river in the grid cell.
I think that means the routing module doesn't include slope routing concentration calculations，is it reasonable？

The model code is littered with useless white space. Editors that are configured to show white space, like mine, make it hard to read the code. See also the first item here: https://peps.python.org/pep-0008/#other-recommendations

Suggestion: use a pre-commit hook to prevent spurious space to end up in the repository. Something like Black will automatically remove the all useless white space.

When running long high-resolution PCR-GLOBWB simulations, it is often the case the the simulation time exceeds the time allowed by the slurm manager on external servers. Or, it may be that there is some other error that causes (longer) simulations to stop. It would be nice if we could continue previously unfinished runs, using the same output directory.

Currently, PCR-GLOBWB appends its outputs to the output NetCDFs per timestep and stores its states to the state pcraster maps per year. An argument should be added to the PCR-GLOBWB runner (e.g. --continue), where the model does not clean up the output directory. Rather it checks:

1. If the output files already exist
2. If the state files already exist
3. The latest available state file

And than continues the previous run from the latest available state file, appending to the output files when necessary.