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paper.md

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# Summary
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DAMASK, the Düsseldorf Advanced Material Simulation Kit, is a modular multi-physics crystal plasticity simulation package distributed as free and open-source software under the GNU Affero General Public License (AGPL) [@roters2019damask].
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To facilitate easy pre- and post- processing of DAMASK simulations and simplify the creation of custom workflows for Integrated Computational Materials Engineering (ICME), an accompanying Python library has been developed.
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To facilitate easy pre- and post-processing of DAMASK simulations and simplify the creation of custom workflows for Integrated Computational Materials Engineering (ICME), an accompanying Python library has been developed.
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This library, which is also AGPL-licensed, is introduced here.
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# Statement of need
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The DAMASK Python library is a package called `damask` and contains functionality for pre-processing tasks, such as the generation and modification of microstructures, load cases, material definition, or numerical parameters, as well as functionality for post-processing that enables analysis and visualization of DAMASK results.
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A particular focus is laid on finite-strain continuum mechanics and crystallography.
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The routines for conversion between the different kinds of orientation representations, such as Euler angles, rotation matrices, unit quaternions, or axis-angle pairs, are based on a consistent set of conventions [@rowenhorst2015consistent].
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The provided routines and data tructures interoperate seamlessly with other libraries from the Python ecosystem, such as `NumPy` [@harris2020array], `pandas` [@mckinney-proc-scipy-2010], `Matplotlib` [@hunter2007matplotlib], `SciPy` [@2020SciPy-NMeth], `VTK`/`PyVista` [@ahrens200536] [@Sullivan_PyVista_3D_plotting_2019], `PyYAML`, `h5py` [@collette_python_hdf5_2014] [@FolkEtAl2011], and `orix` [@johnstone2020density] to facilitate the definition of custom ICME workflows.
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The provided routines and data structures interoperate seamlessly with other libraries from the Python ecosystem, such as `NumPy` [@harris2020array], `pandas` [@mckinney-proc-scipy-2010], `Matplotlib` [@hunter2007matplotlib], `SciPy` [@2020SciPy-NMeth], `VTK`/`PyVista` [@ahrens200536] [@Sullivan_PyVista_3D_plotting_2019], `PyYAML`, `h5py` [@collette_python_hdf5_2014] [@FolkEtAl2011], and `orix` [@johnstone2020density] to facilitate the definition of custom ICME workflows.
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Apart from its DAMASK-specific processing capabilities, many routines of the library can be used in other material science and continuum mechanics applications.
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## Pre-Processing
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The main goal of the pre-processing tools is to provide users with the possibility to incorporate data from various sources into their simulation setup.
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The main goal of the pre-processing tools is to enable users to incorporate data from various sources into their simulation setup.
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For example, the users can integrate domain-specific software such as `Neper` [@quey2011large], `DREAM.3D` [@groeber2014dream], and `Gmsh` [@geuzaine2009gmsh] to define microstructures and employ the provided Python routines to convert them into DAMASK-compatible input files.
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Similarly, the materialpoint configuration and load case definition are internally represented as particular Python classes that simplify the creation, modification, and export to YAML files.
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In addition to the three mandatory input files, i.e., geometry definition, material configuration, and the load case description, the creation and modification of an optional YAML file to fine-tune numerical parameters is also supported.
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The post-processing tools are centered around the HDF5 output file resulting from a DAMASK simulation.
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This flexible file format is called DADF5, short for "DAMASK HDF5" [@DiehlEtAl2017b], which allows data storage according to the FAIR principles [@WilkinsonEtAl2016].
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All data in DADF5 is enriched with metadata such as the date of creation, a human-understandable description, and the physical unit to ensure that the data is findable by humans and computers.
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All data in DADF5 is enriched with metadata, such as the date of creation, a human-understandable description, and the physical unit, to ensure that the data is findable by humans and computers.
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The `Result` class provides custom views on the hierarchical data layout of the DADF5 file for easy accesibility.
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Moreover, it provides routines the computation of derived quantities that are stored alongside with automatically created metadata in the output file.
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Moreover, it provides routines for the computation of derived quantities that are stored alongside with automatically created metadata in the output file.
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The data can be further processed within Python or exported to various file formats for analysis using third-party tools such as `DREAM.3D`, `ParaView`, or `MTEX` [@BachmannEtAl2010].
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This, together with the fact that the complete simulation setup is stored in the DADF5 file, makes it possible to re-use and re-evaluate the data.
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