A Collection of Visualization Software
This post collects the visualization software that I found useful. The recommended installation method, mainly for Linux and WSL, is documented.
Note for WSL
The accelerated GPU rendering with Nvidia graphic card can be launched for specific software, if CPU rendering is not explicitly recommended in the corresponding note. Check Nvidia Graphic Card for WSL2 for implementation details.
VESTA
Best free crystal visualization tool on Windows — it sets the standard. A not comprehensive summary of features includes:
- Atomic structure visualization
- 3D isosurface plot
- 2D cross-section contour plot
- 1D line profile plot
- Crystal morphology plot
- Miller plane calculation and plot
- Vector plot on atoms
- Geometry format conversion
- Structure generation and modification with space symmetry
- A lot more features available in the manual
Ubuntu WSL
It is distributed as click-and-run, since it is (as far as I know) not open-source. Download the binary, check the gtk version (according to the requirements on download page), and install extra dependencies:
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$ apt list --installed | grep 'gtk'
$ sudo apt install libwebkit2gtk-4.0-37
Note
- AI diagnose identified a compatibility issue of Mesa D3D12 with WSL apps base on legacy OpenGL lib. This means that rendering with GPU would be extremely slow, so CPU rendering is suggested.
VMD 2.0.0
Widely used for molecular dynamics. Periodic boundary is also supported.
Some features compared to VESTA:
- Tcl scripting available, to control the rendering of multiple systems.
- Contour plot on 3D isosurfaces, for molecular electrostatic potential (MEP) analysis, non-covalent interaction (NCI) index, etc.
- Animation rendering
WSL
Download binary version and unzip the tarball. cd to the unzipped directory and use the following commands:
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$ sed -i "s|/usr/local|$(pwd)|g" configure
$ ./configure
$ cd src/ | make install
Note
- Similar to VESTA, VMD is also based on legacy OpenGL libs and CPU rendering is recommended.
- AI diagnose identified an issue with the graphic user interface. Prepend
env VMDTITLE=off VMDNOOPTIX=1to the command launching VMD.
Jmol
Similar to VESTA, without in symmetry and lattice.
Some features:
- ‘click-and-run’, better supported than VESTA
- Vibration analysis, including vectors and animation
WSL
Download the binary version and run the script ‘jmol.sh’.
Avogadro 2
A modern visualization tool for non-periodic molecules, with moderate support for crystals. Some features that stand out compared to VESTA:
- Templates for metallic center, ligands, and functional groups
- Easy manipulation of atom coordinates, bond types etc, good for adsorption modelling
- Interface to non-periodic DFT and MD codes
- Interface to [OpenBabel]{https://openbabel.org/index.html} for initial geometry relaxation and conformer search, based on classical force field
WSL
Download the AppImage version, then run:
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$ chmod 'ugo+x' Avogadro2-x86_64.AppImage
XCrySDen 1.6.2
A visualization tool for crystals, good for specific tasks when needed. However, it is not well-updated and might cause conflicts in package dependence.
Some features compared to VESTA:
- More intuitive 2D cross-section contour plot, which includes both the heat map and the atomic structure (it is also possible to do that in VESTA, but needs to check the manual)
- Fermi surface visualization in reciprocal space (i.e. 3D isosurface for band structure)
- 1st Brillouin zone and k path visualization
- Animation rendering
- Interface to CRYSTAL, Quantum Espresso, and Wien2k
Ubuntu WSL
Download the WSL shared version and install the following packages:
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$ sudo apt install tk libglu1-mesa libtogl2 libxmu6 libgfortran4 libfftw3-bin \
openbabel imagemagick
Notes
- The ‘fftw3-3’ package in official tutorial is deprecated and can lead to conflicts in dependence. The new ‘fftw3-bin’ package is used.
- Similar to VESTA, XCrySDen is also based on legacy OpenGL libs. CPU rendering is suggested.
Cygwin
Download the Cygwin shared version and install the packages specified in the tutorial via installer. To setup Xming forwarding, check Cygwin as an Alternative Linux Environment on Windows.
Source code compilation
In Ubuntu, install development packages following the second command below:
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$ sudo apt install tk libglu1-mesa libtogl2 libxmu6 libgfortran4 libfftw3-bin \
openbabel imagemagick
$ sudo apt install libx11-dev libxmu-dev tcl8.6-dev tk8.6-dev mesa-common-dev \
libglu1-mesa-dev libtogl-dev libfftw3-dev
$ cd <source code directory>
$ cp system/Make.sys-shared Make.sys
In ‘Make.sys’, insert -fcommon before -pedantic -Wall for CPPFLAGS to address a new default of GCC compiler that may cause error in compilation.
Comment the variable declaration in ‘C/xcBz.c:1400’, as it conflicts with the latest header file:
/* double fabs(); */
Then run serial compilation make -j1 all.
GDIS
Similar to XCrySDen, good for specific tasks but not up-to-date. Features compared to VESTA:
- Better slab modelling for molecular crystals, which generates wrinkled surfaces to preserve the integrity of molecules intersecting with the Miller plane
- Interface to GULP, allowing calculations for crystals based on classical force field (symmetry in lammps sucks)
- Interface to VASP
Ubuntu WSL Compilation
Install the following packages and download the GitHub repository:
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$ sudo apt install libgtk2.0-bin libgtk2.0-common libgtk2.0-0t64 libgtk2.0-dev \
libgtkglext1 libgtkglext1-dev
$ git clone https://github.com/arohl/gdis.git
In ‘src/makefile.linux’, insert the -std=gnu17 flag as the first flag for CFLAGS. Then run ./install and follow the instructions. Use chmod 'ugo+x' gdis to add permissions.
Cygwin Compilation
Install gtk+2 and gtkglext packages with Cygwin installer. Then follow the same procedures as the previous section.