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)
    • 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

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

1. Install serial or parallel HDF5 library

2. 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;
   

3. 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.

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": "single_mesh_temporal_input_process",
                "Parameters": {
                    "model_part_name": "MainModelPart",
                    "file_settings": {
                        "file_name": "hdf5_output/<model_part_name>-<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/<model_part_name>-<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.

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": "multiple_mesh_temporal_output_process",
                "Parameters": {
                    "model_part_name": "MainModelPart",
                    "file_settings": {
                        "file_name": "hdf5_output/<model_part_name>-<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)

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_xdmf_output_process",
                "Parameters": {
                    "model_part_name": "MainModelPart",
                    "file_settings": {
                        "file_name": "hdf5_output/<model_part_name>-<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/<model_part_name>-<time>.h5"
                    },
                    "list_of_operations": [
                        {
                            "operation_type": "model_part_output"
                        },
                        {
                            "operation_type": "nodal_solution_step_data_output",
                            "list_of_variables": ["DISPLACEMENT"]
                        }
                    ]
                }
            }