Looking at simulations across jobs

[gilrrei]

If you want to have a look at the outputs of simulations generated with QUEENS, which are in VTK formats, you can create a PVD file. Here is an example:

import pathlib
import tqdm
import xml.etree.ElementTree as ET
import sys

def create_pvd(file_list, output_path, timestep=None, **additional_datasets):
    # sanity check
    if file_list is None:
        raise ValueError("file_list has to be provided!")

    # create timesteps
    if timestep is None:
        timestep = list(range(len(file_list)))

    # update data
    additional_datasets["timestep"] = timestep
    additional_datasets["file"] = file_list

    # create the tree
    tree = create_xml(**additional_datasets)

    # export to a pvd file
    tree.write(output_path, xml_declaration=True, encoding="utf-8")


def create_xml(**xml_dataset_dict):
    pvd = ET.Element(
        "VTKFile",
        type="Collection",
        version="0.1",
        byte_order="LittleEndian",
        compressor="vtkZLibDataCompressor",
    )
    collection = ET.SubElement(pvd, "Collection")

    # get DataSet field names
    keys = xml_dataset_dict.keys()

    # add each entry
    for value_i in zip(*xml_dataset_dict.values(), strict=True):
        kwargs = dict(zip(keys, [str(value_ij) for value_ij in value_i]))
        ET.SubElement(collection, "DataSet", **kwargs)

    # create tree
    tree = ET.ElementTree(pvd)

    # use indents, makes it easier for humans to read
    ET.indent(tree, space="\t", level=0)
    return tree


def create_pvd_from_samples():
    filename = sys.argv[1]

    experiment_dir = pathlib.Path(".")
    experiment_name = experiment_dir.resolve().name

    files = []
    job_ids = []

    for d in tqdm.tqdm(sorted(experiment_dir.glob("*"))):
        if d.is_dir():
            if (d / filename).is_file():
                job_ids.append(int(d.name))
                files.append(str(d / filename))

    create_pvd(
        files,
        experiment_dir / f"{experiment_name}_{filename.split('.')[0]}.pvd",
        job_ids,
    )

if __name__ == "__main__":
     create_pvd_from_samples()

Now you can call the script with python <the_script> <vtk_file_name> in the experiment dir and generate PVD files to open in paraview. The job id provided by QUEENS is set as timestep. Here an output example, showing the last timestep of the simulation with the job id 1028:

NOTE: not all vtk files can be used in a PVD file. For example PVD files consisting of PVD files do not work. Still it is cool to look at the outputs.

[sbrandstaeter]

Super cool idea. Thanks for sharing!