KratosHDF5Application

v10.1.0

KRATOS Multiphysics ("Kratos") is a framework for building parallel, multi-disciplinary simulation software, aiming at modularity, extensibility, and high performance. Kratos is written in C++, and counts with an extensive Python interface. For more information about how to use this package see README

Latest version published 4 days ago

License: BSD-2-Clause

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84 / 100

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popularity
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maintenance
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Popularity

Small

GitHub Stars: 1.04K
Forks: 245
Contributors: 150

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Based on project statistics from the GitHub repository for the PyPI package KratosHDF5Application, we found that it has been starred 1,036 times.

Security

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Security and license risk for latest version

Release Date: Nov 19, 2024
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Indirect Vulnerabilities: 0
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License Risk: 0
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License

BSD-2-Clause

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Maintenance

Healthy

Commit Frequency

Open Issues: 336
Open PR: 244
Last Release: 4 days ago
Last Commit: 15 days ago

Further analysis of the maintenance status of KratosHDF5Application based on released PyPI versions cadence, the repository activity, and other data points determined that its maintenance is Healthy.

We found that KratosHDF5Application demonstrates a positive version release cadence with at least one new version released in the past 3 months.

As a healthy sign for on-going project maintenance, we found that the GitHub repository had at least 1 pull request or issue interacted with by the community.

Community

Active

Readme: Yes
Contributing.md: Yes
Code of Conduct: Yes
Contributors: 150
Funding: No

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Package

Python Versions Compatibility: >=3.8

Age: 2 years
Latest Release: 4 days ago
Dependencies: 0 Direct
Versions: 16
Maintainers: 1
Wheels: Windows

Readme

HDF5Application

The HDF5Application enables the serialization of a model part with or without MPI using the HDF5 library. The model part is stored in and HDF5 file, which can be used for:

Viewing a model part with HDFVIEW
Scientific visualization with tools supporting XDMF. Tools, which are known to work, include ParaView 5.4 and VisIt.
Checkpointing (under development).
Re-partitioning (not supported yet).

HDF5Application

Installing HDF5 (minimum version 1.8)

The HDF5 C libraries are used with the HDF5Application. If Kratos is configured with MPI then the parallel HDF5 library must be installed. Otherwise, the serial HDF5 library is used.

Serial HDF5 Library

Ubuntu

    sudo apt-get install libhdf5-dev

Parallel HDF5 Library

Ubuntu

    sudo apt-get install libhdf5-openmpi-dev

Build Instructions

Install serial or parallel HDF5 library
Configure Kratos to build the HDF5Application (following the standard instructions)
- For GNU/Linux:
```
add_app ${KRATOS_APP_DIR}/HDF5Application
```
- For Windows:
```
CALL :add_app %KRATOS_APP_DIR%\HDF5Application;
```
Build Kratos

Installing h5py

This package is needed to use some of the python-files, e.g. xdmf_utils.py

    sudo apt-get install python-h5py / python3-h5py

Note

The minimum version for the GCC compiler is 4.9. This is because earlier version don't fully support regular expressions.

Kratos processes

There are few available HDF5 processes which can be integrated into work flow via ProjectParameters.json file.

Initialization from hdf5 process

This process can be used to initialize a given model part using existing HDF5 files. Illustrated example reads in VELOCITY and PRESSURE variables from "hdf5_output/example_initialization_file.h5" file to nodal historical data value container, and nodal, elemental and condition non-historical data value containers. This process also can read FLAGS from HDF5 file and populate model part accordingly.

For the list_of_variables in either nodal_data_value_settings, element_data_value_settings, condition_data_value_settings one can specify ALL_VARIABLES_FROM_FILE which will read all the variables available in the input hdf5 file and will populate the model part accordingly. This ALL_VARIABLES_FROM_FILE should be used alone (There can be only this entry in the list if it is used).

            {
                "kratos_module": "KratosMultiphysics.HDF5Application",
                "python_module": "initialization_from_hdf5_process",
                "Parameters": {
                    "model_part_name": "MainModelPart",
                    "file_settings": {
                        "file_name": "hdf5_output/example_initialization_file.h5",
                        "echo_level": 1
                    },
                    "nodal_solution_step_data_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_data_value_settings": {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "element_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "condition_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_flag_value_settings": {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "element_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "condition_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    }
                }
            }

Single mesh temporal input process

This process is used to initialize model part variables at each time step from hdf5 files. You can specify the list of hdf5 files to read from by changing the "file_name" with tags <time> as shown in following example. If no <time> tag is present in "file_name", then same file will be read at each time step and the variables specified will be initialized. In this process, mesh is only read from the initial time step file. Results for each container will be read from time series h5 files.


            {
                "kratos_module": "KratosMultiphysics.HDF5Application",
                "python_module": "single_mesh_temporal_input_process",
                "Parameters": {
                    "model_part_name": "MainModelPart",
                    "file_settings": {
                        "file_name": "hdf5_output/-<time>.h5",
                        "time_format": "0.4f",
                        "echo_level": 1
                    },
                    "nodal_solution_step_data_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_data_value_settings": {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "element_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "condition_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_flag_value_settings": {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "element_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "condition_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    }
                }
            }

Single mesh temporal output process

This process can be used to output data from model parts to HDF5. This will write mesh only in the first time step h5 file. Rest of the time series h5 files will contain only results for each nodal/element/condition containers.

For the list_of_variables in nodal_solution_step_data_settings, one can specify ALL_VARIABLES_FROM_VARIABLES_LIST as the only item (Then this list should only have that entry) so it will write all the variables in the corresponding model's solution step variable list.

            {
                "kratos_module": "KratosMultiphysics.HDF5Application",
                "python_module": "single_mesh_temporal_output_process",
                "Parameters": {
                    "model_part_name": "MainModelPart",
                    "file_settings": {
                        "file_name": "hdf5_output/-<time>.h5",
                        "time_format": "0.4f",
                        "max_files_to_keep": "unlimited",
                        "echo_level": 1
                    },
                    "output_time_settings": {
                        "step_frequency": 1,
                        "time_frequency": 1.0
                    },
                    "nodal_solution_step_data_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_data_value_settings": {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "element_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "element_gauss_point_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "condition_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "condition_gauss_point_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_flag_value_settings": {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "element_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "condition_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    }
                }
            }

Multiple mesh temporal output process

This process is used to output model part variable data to HDF5 with mesh written for each time step. This is useful in the case if required to write down deformed mesh in each time step.

            {
                "kratos_module": "KratosMultiphysics.HDF5Application",
                "python_module": "multiple_mesh_temporal_output_process",
                "Parameters": {
                    "model_part_name": "MainModelPart",
                    "file_settings": {
                        "file_name": "hdf5_output/-<time>.h5",
                        "time_format": "0.4f",
                        "max_files_to_keep": "unlimited",
                        "echo_level": 1
                    },
                    "output_time_settings": {
                        "step_frequency": 1,
                        "time_frequency": 1.0
                    },
                    "model_part_output_settings": {
                        "prefix": "/ModelData"
                    },
                    "nodal_solution_step_data_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_data_value_settings": {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "element_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "element_gauss_point_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "condition_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "condition_gauss_point_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_flag_value_settings": {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "element_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "condition_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    }
                }
            }

Single mesh xdmf output process for Paraview

This process outputs model part variable data for each time step, additionally it writes down the XDMF file after each time step which is required to visualize HDF5 data in paraview. This process requires h5py to be installed in the python version (which is compiled with Kratos Multiphysics)

            {
                "kratos_module": "KratosMultiphysics.HDF5Application",
                "python_module": "single_mesh_xdmf_output_process",
                "Parameters": {
                    "model_part_name": "MainModelPart",
                    "file_settings": {
                        "file_name": "hdf5_output/-<time>.h5",
                        "time_format": "0.4f",
                        "max_files_to_keep": "unlimited",
                        "echo_level": 1
                    },
                    "output_time_settings": {
                        "step_frequency": 1,
                        "time_frequency": 1.0
                    },
                    "model_part_output_settings": {
                        "prefix": "/ModelData"
                    },
                    "nodal_solution_step_data_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_data_value_settings": {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "element_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "condition_data_value_settings" : {
                        "list_of_variables": [
                            "VELOCITY",
                            "PRESSURE"
                        ]
                    },
                    "nodal_flag_value_settings": {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "element_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    },
                    "condition_flag_value_settings" : {
                        "list_of_variables": [
                            "SLIP"
                        ]
                    }
                }
            }

User defined I/O process

Users can build their own I/O processes by using components of HDF5 application. Following is such example. This example writes model part, and DISPLACEMENT values for each time step at finalize_solution_step

            {
                "kratos_module": "KratosMultiphysics.HDF5Application",
                "python_module": "user_defined_io_process",
                "Parameters": {
                    "model_part_name": "MainModelPart",
                    "process_step": "finalize_solution_step",
                    "controller_settings": {
                        "controller_type": "temporal_controller",
                        "time_frequency": 0.5
                    },
                    "io_settings": {
                        "file_name": "results/-<time>.h5"
                    },
                    "list_of_operations": [
                        {
                            "operation_type": "model_part_output"
                        },
                        {
                            "operation_type": "nodal_solution_step_data_output",
                            "list_of_variables": ["DISPLACEMENT"]
                        }
                    ]
                }
            }

FAQs

What is KratosHDF5Application?

KRATOS Multiphysics ("Kratos") is a framework for building parallel, multi-disciplinary simulation software, aiming at ... Visit Snyk Advisor to see a full health score report for KratosHDF5Application, including popularity, security, maintenance & community analysis.

Is KratosHDF5Application popular?

The python package KratosHDF5Application receives a total of 644 weekly downloads. As such, KratosHDF5Application popularity was classified as small. Visit the popularity section on Snyk Advisor to see the full health analysis.

Is KratosHDF5Application well maintained?

We found that KratosHDF5Application demonstrated a healthy version release cadence and project activity. It has a community of 150 open source contributors collaborating on the project. See the full package health analysis to learn more about the package maintenance status.

Is KratosHDF5Application safe to use?

The python package KratosHDF5Application was scanned for known vulnerabilities and missing license, and no issues were found. Thus the package was deemed as safe to use. See the full health analysis review.

Last updated on 22 November-2024, at 19:38 (UTC).

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Readme

HDF5Application

Installing HDF5 (minimum version 1.8)

Serial HDF5 Library

Ubuntu

Parallel HDF5 Library

Ubuntu

Build Instructions

Installing h5py

Note

Kratos processes

Initialization from hdf5 process

Single mesh temporal input process

Single mesh temporal output process

Multiple mesh temporal output process

Single mesh xdmf output process for Paraview

User defined I/O process

FAQs

What is KratosHDF5Application?

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