VASP plugins for VMD

Atomic configurations

Atomic configurations using Van der Waals (VDW) drawing method. VASP plugins read atomic geometries from xml, POSCAR and CONTCAR file. Practically, you can read them from charge density files (e.g. CHGCAR). VASP plugins read the atom species from POTCAR file, if the file exists. If not, through the title line of POSCAR, CONTCAR and charge density files, one can provide the atom species. (e.g. Cu C O H : CH3OH/Cu(100)) VASP plugins use this information to assign atom type and name. If you fail to feed this information, all atoms will be identical and assigned to mysterious atom "X".



Dioxymethylene on Cu(110) Mono-layer alloy: Cu3Pd/Ru(0001) substrate
Methoxy on Cu(110)

Select VASP file: File>New Molecule
  1. Select corresponding file type (POSCAR)
  2. Browse and select VASP file
  3. Press "Load" button

Define atom properties: Graphics>Representations
  1. Select molecule
  2. Select each atom using "name <Atom> <return>" command
  3. Select Van der Waals (VDW) for drawing method
  4. Color method, ColorID is recommanded
  5. Select material property, opaque for solid surface and transparent for transparent surface. Transparent will be properly described after Tachyon or POV-Ray render process, not in OpenGL.
  6. Scale Van der Waals radius for each atom
  7. Adjust sphere resolution. It demands much OpenGL performance, but you render using POV-Ray then leave it low quality. POV-Ray enhances the resolution during render process. OpenGL and POV-Ray renders are independent.

Set multiplication: Graphics>Representations
  1. Multiplicate selected atoms in unit cell vector directions
  2. Set number of multiplicated images

Set material: Graphics>Materials
  1. Select material type
  2. In POV-Ray, one tenth of this value is used for finish command. Roughness is only valid for POV-Ray render, in OpenGL this value does not affect to rendering.

Aduust color: Graphics>Colors
  1. Change background color
  2. Adjust color definition

File render: File>Render
  1. Select render method, POV-Ray is recommanded (Default: snapshot)
  2. Set output file name (Default: plot.***)
  3. Press "Start Rendering" button
Tip: Keep in mind that VMD is originally designed to visualize the classical MD simulations. Thus, CPK drawings predict poorly the bonds in the most of crystal calculations. Then, try to use 10-20 % smaller scaling factor compared to the DFT calculations. The overal system wil be compressed by the change of the scaling factor, but it will show the same atomic structure.

  1. Atomic configurations
  2. Movie of molecular dynamics calculations
  3. Isosurfaces of charge density
  4. Customize VMD startup configuration
  5. Periodic charge densities
  6. Create movie embedded pdf file
  7. Save coordinates in POSCAR format
  8. Back to VASP plugins page

Photo_

Dr. Sung Sakong

Ulm University
Institute of Theoretical Chemistry
Albert-Einstein-Allee 11
89069 Ulm, Germany

Room: 025/339
Tel.: +49-731-5022812
Email: sung.sakong _at_ uni-ulm.de
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