Table of Contents
GUI Manual
Table of Contents
Introduction
Set up
Mouse
Running Remotely
ADFjobs Queues
MOPAC
SCM menu
Background processes (with no interface)
scmd: communication between GUI modules
scmjobd: monitor running jobs
Viewing your molecule
Molecule style: Balls and Sticks, Sticks, or Wireframe
Camera position: view direction
3D
Fly to selection
Reset View
Mouse Interaction
Rotate, Translate and Zoom
Selecting
Input: ADFinput, BANDinput, ReaxFFinput, ...
ADF, BAND, DFTB, MM, Mopac, Open Babel, QMMM, QUILD, ReaxFF, UFF
Keyboard shortcuts
Searching
The "..." details buttons
Using the "i" info buttons
Crystals and Slabs
Periodicity
Building crystals
Build slabs
Builder (packmol)
Building molecules
Bonding mode
Atom Details: Connectors (valency) and Lone Pairs, Atom mass
Pre-optimization
Geometry adjustments
Sliders
Edit box
Move an atom (possibly perpendicular to the screen)
Rotate or translate the selection
Coordinates
Z-Matrix
Set Origin
Symmetry
Align
Update coordinates via ADFmovie
Bonds
Importing your molecule
Importing from file: .adf, .t21, .xyz, .mol, .mol2, .pdb, .runkf, .band, .cif, .dmol, .rkf, .rxi, .rxkf ...
Copy/Paste between GUI modules, XYZ coordinates or SMILES
Regions
Proteins (from PDB or mol2 files)
Presets and Defaults
Color Code
Make your own presets
Input options remarks
Empty fields
Spin and Occupation
User Input
Basis sets, model Hamiltonians, properties, analysis
Atoms, Basis sets
Model Hamiltonians
Structure and Reactivity
Spectroscopic properties
Analysis
Accuracy and Efficiency
ADFjobs
Job List
Job status (including WARNING and ERROR info)
Selecting Jobs
Running a job: .run and .job
Job files
Local files
Remote files
Test Job
Queues
Interactive Queue
Sequential Queue
Setting up your own Queues
Dynamic queues
Example Queue configurations for SGE and PBS
Tools: set up many jobs and collect data from many jobs
Prepare: set up many jobs at once
Report: collect data from many jobs
ADFview
Visualization methods
Spinor: spin magnetization density
Fields
Properties
Comparing data from several molecules
Temporary Files
ADFcrs: COSMO-RS
Menu Commands
GUI Environment Variables
