Interactive graphical analysis with VMD
prepare the preconfigured VMD session for UseCase1
ssh hydra.rzg.mpg.de
mkdir -p $HOME/Desktop
cp /u/mjr/public/NOMAD-VIZ/UseCase1_VMD.desktop $HOME/Desktop
### connect to pRVS
establish a TurboVNC connection to the MPCDF remote visualization service [[as described here|MPCDF-RVS]]
### launch the preconfigured VMD session for UseCase1
double click on the Desktop launcher named NOMAD-VIZ_UseCase1_VMD
or start VMD manually on the commandline:
~>module load vmd ~>vglrun vmd -e /u/mjr/public/NOMAD-VIZ/UseCase1_VMD.vmd
(the -e ... option manually loads the preconfigured session for UseCase1 on the commandline)
### Instructions for working with the GUI
(_assessment of UseCase1 is work in progress_)

* predefine some default view and enable comprehensive analysis work
flows for the user (Fig 1).
- save and load views.
- use different graphic representations - points, bonds, `VDW'
- atoms as spheres
* basic user interaction:
* start, pause, continue time evolution
- load different molecules and switch between them
- no default "player" functionality like in VisIt or ParaView
* rotate, transfer, zoom in or out, change the number of shown unit
cells (_works_)
* determine species type and atom number by clicking the sphere
representing that atom
- different types of analysis (Figs 2,3,4) but from the menu and not by simply clicking on the atom. The window is not
interactive.
* change the iso-value for the density, colour scale for the
volumetric data (_not yet identified_)
* calculate the density integral within a 3D box selection (_not yet identified_)
* display distances, angles, and dihedral angles by selecting atoms (_not yet identified_)
* interactively replicate the unit cell (_not yet identified_)


