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OpenMX Viewer: A web-based crystalline and molecular graphical user interface program.

Yung-Ting Lee1, Taisuke Ozaki1

  • 1Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8581, Japan.

Journal of Molecular Graphics & Modelling
|March 26, 2019
PubMed
Summary
This summary is machine-generated.

The OpenMX Viewer is a web-based tool for visualizing and analyzing material structures and 3D grid data. It offers easy-to-use features for exploring electron density and molecular orbitals without installations.

Keywords:
HTML5IsosurfaceOpenMXViewerWebGL

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Area of Science:

  • Materials Science
  • Computational Chemistry
  • Data Visualization

Background:

  • Crystalline and molecular structure visualization and analysis are crucial in materials science and computational chemistry.
  • Existing tools often require complex installations and updates, hindering accessibility.

Purpose of the Study:

  • To introduce the OpenMX Viewer, a web-based GUI for visualizing and analyzing material structures and 3D grid data.
  • To provide a user-friendly, installation-free platform for researchers.

Main Methods:

  • Web-based graphical user interface (GUI) development.
  • Implementation of file input (XYZ, CIF, OpenMX) with drag-and-drop functionality.
  • Integration of 3D isosurface techniques (marching cubes, tetrahedra, surface nets) with Affine transformation.
  • Inclusion of analysis tools for Mulliken charges, molecular dynamics, geometry optimization, and band structure.

Main Results:

  • The OpenMX Viewer facilitates quick visualization of crystalline and molecular structures.
  • It enables convenient analysis of static/dynamic structural properties within a web browser.
  • 3D isosurface visualization of electron density and molecular/crystalline orbitals is supported.
  • A dedicated Band Structure Viewer is integrated.

Conclusions:

  • The OpenMX Viewer offers an accessible, installation-free solution for material structure visualization and analysis.
  • Its web-based nature ensures users always access the latest version.
  • It simplifies complex data exploration for researchers in materials science and related fields.