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# Summary
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Electron density is central to electronic structure calculations, providing a
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detailed depiction of electron distribution in materials or molecules. In
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various methodologies, particularly Density Functional Theory, electron density
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is crucial for deriving properties such as energy, potential, and forces. It
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reveals the complexities of chemical bonding and reactivity, crucial for
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predicting and understanding the characteristics of materials and molecules,
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especially in terms of electron redistribution during bond formation or rupture.
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The electron density is a scalar field, which means that it is a function that
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assigns a scalar value to each point in space. In the case of the electron
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density, this scalar value represents the probability density of finding an
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electron at that point in space. Specialized visualization tools and techniques
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are often required to effectively visualize scalar fields such as the electron
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density. These tools may include contour plots, isosurface rendering, or volume
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rendering, among others. Visualizing the electron density is essential for
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gaining insights into the electronic properties and behavior of materials and
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molecules.
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`Den2Obj` is a C++-based command-line tool designed to construct isosurfaces of
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an electron density scalar field. It can parse CHGCAR and PARCHG files of VASP
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as well as Gaussian Cube files. `Den2Obj` also supports converting these into
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native `.d2o` files which offer a significant compression in size with respect
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to these former files. The resulting isosurfaces can be stored in
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Stereolitography (`.stl`), Polygon File Format (`.ply`) and Wavefront (`.obj`)
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files, allowing for facile post-processing in various other programs.
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Electron density plays a foundational role in electronic structure calculations.
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It offers a detailed spatial representation of the distribution of electrons in
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molecules and materials. In computational methodologies, most notably Density
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Functional Theory (DFT), electron density serves as a central quantity from
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which key properties such as total energy, electrostatic potential, and atomic
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forces are derived. The analysis of electron density provides significant
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insights into chemical bonding, reactivity, and electron redistribution,
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especially during bond formation and dissociation. This capability enables the
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prediction and interpretation of the properties of materials and molecular
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systems.
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Electron density is mathematically represented as a scalar field. It assigns a
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scalar value, corresponding to the probability density of finding an electron,
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to each point in three-dimensional space. Due to the complexity and high
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dimensionality of such data, specialized visualization techniques are necessary
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for meaningful interpretation. Common methods include contour plotting,
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isosurface generation, and volumetric rendering. These techniques facilitate the
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exploration of electronic behavior and structural characteristics.
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This utility, `Den2Obj`, is a C++ based command line program developed to
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generate isosurfaces from electron density scalar fields. It supports input
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formats that are commonly used in electronic structure calculations, including
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CHGCAR and PARCHG files produced by VASP, as well as Gaussian Cube files.
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`Den2Obj` is capable of converting these formats into a native `.d2o` file
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format, which achieves substantial reductions in file size through efficient
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compression. The resulting isosurfaces can be exported in several widely
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supported geometry file formats, including STL (Stereolithography), PLY (Polygon
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File Format), and OBJ (Wavefront). These output formats enable convenient
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integration with a broad range of visualization and post-processing software
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tools.
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# Statement of need
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Isosurfaces play a pivotal role in both scientific research and engineering
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applications, offering a powerful tool for visualizing complex data sets and
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understanding intricate phenomena. These surfaces represent points in a field
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where a specific value, known as the isovalue, is constant. Due to its
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importance, there exist many programs that readily support isosurface
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generation, such as `Open Data Explorer`[@OpenDX], `Matlab`[@MATLAB],
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`ParaView`[@ParaView], and `Vesta`[@momma:2011]. These tools are mainly
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designed for interactive use and utilize a graphical user interface of some
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sort.
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In contrast, `Den2Obj` is a C++-based command-line tool that performs isosurface
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construction from `VASP`[@hafner:2008]`CHGCAR` or `PARCHG` and and Gaussian
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[@gaussian] Cube files. The resulting isosurfaces can be stored as
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Stereolitography (`.stl`), Polygon File Format (`.ply`) or Wavefront (`.obj`)
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files. The isosurfaces can be constructed using the marching cubes
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[@lorensen:1987] or the marching tetrahedra [@burke:1994] algorithms by means of
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the command-line arguments. Both these algorithms are implemented using OpenMP
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parallelization making optimal use of modern multi-core CPUs. When rendering
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wavefunctions rather than electron densities, it is convenient to build two
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separate isosurfaces corresponding to the different signs of the lobes. `Den2Obj`
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readily accomodates this via a single command-line argument.
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# picture with benzene orbital
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## Isosurface Visualization with `Den2Obj`
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Isosurfaces play a central role in scientific research and engineering
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applications by providing an effective means of visualizing complex scalar
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fields and understanding intricate physical phenomena. An isosurface represents
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a set of points in a field where a scalar quantity, known as the *isovalue*,
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remains constant. Due to their importance, many software packages support
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isosurface generation, including `Open Data Explorer`[@OpenDX], `MATLAB`
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[@MATLAB], `ParaView`[@ParaView], and `VESTA`[@momma:2011]. These tools are
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primarily designed for interactive use and typically rely on graphical user
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interfaces.
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In contrast, `Den2Obj` is a C++-based command line tool developed for automated
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isosurface extraction from electron density and wavefunction data. It supports
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input formats commonly produced by `VASP`[@hafner:2008], such as `CHGCAR` and
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`PARCHG`, as well as Gaussian [@gaussian] Cube files. The resulting isosurfaces
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can be exported in widely used 3D geometry formats, including Stereolithography
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(`.stl`), Polygon File Format (`.ply`), and Wavefront (`.obj`).
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Isosurface generation in `Den2Obj` is carried out using either the marching
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cubes algorithm [@lorensen:1987] or the marching tetrahedra algorithm
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[@burke:1994], both of which can be selected via command line arguments. These
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algorithms are implemented with OpenMP parallelization to leverage the
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performance of modern multi-core CPUs. When visualizing wavefunctions rather
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than electron densities, it is often useful to generate separate isosurfaces for
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positive and negative lobes. `Den2Obj` accommodates this by enabling dual
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isosurface generation through a single command line argument.
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An illustrative example is presented in \autoref{fig:canonical_mo}, which
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displays the canonical molecular orbitals of the benzene molecule. These
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orbitals were computed using the PyQInt program.[@PyQInt] Isosurfaces were
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generated via the marching cubes algorithm as implemented in Den2Obj, producing
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.ply files that were subsequently imported into Blender[@Blender], along with
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the atomic coordinates of benzene, for rendering.
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For efficient research data management purposes, `Den2Obj` is also able to
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convert `CHGCAR` and `PARCHG` files to its own custom `d2o` format, which is a
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providing a comprehensive and nuanced understanding of the scalar field. In a
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way, volumetric rendering lies in between isosurfaces and contour plots in terms
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of visualizing a scalar field. An example for the molecular orbitals of benzene
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is provided in \autoref{fig:volumetric_rendering}.
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is provided in \autoref{fig:volumetric_rendering}. For demonstration and testing
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purposes, also a scalar field generator functionality is included that can
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create a number of relevant scalar fields to test the algorithms on.
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For demonstration and testing purposes, also a scalar field generator
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functionality is included that can create a number of relevant scalar fields to
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test the algorithms on. An example is provided in
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\autoref{fig:isosurface_examples}.
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`Den2Obj` requires a relatively small set of dependencies, being Eigen3
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