GitLab

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:
 

(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_)

![vmd_screenshot1](vmd_screenshot-1.png "Fig 1")

* 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_)


![vmd_screenshot1](vmd_screenshot-2.png "Fig 2")

![vmd_screenshot1](vmd_screenshot-3.png "Fig 3")

![vmd_screenshot1](vmd_screenshot-4.png "Fig 4")