Table of Contents
ADF-GUI Reference Manual
Table of Contents
Introduction
The ADF-GUI modules
The SCM (logo) menu
Automatic bug reports
Installation of the ADF-GUI: Dynamic Queues
Environment Variables
Mouse Interaction
Rotate, Translate and Zoom
Selecting
Shared Menus
Pop-up menus
Pop-up menu on atom X
Atom Info: name, charges etc.
Color Atoms By...
Atom Radius From...
Geometric Info
Info Style
Atom Radius
Define X color
Hide all X atoms
Select all X atoms
Pop-up menu in empty space
Atom Info: name, charges etc.
Color Atoms By...
Atom Radius From...
Geometric Info
Info Style
Show bonds to hidden atoms
Hide bonds to hidden atoms
Default atom properties
Select All Atoms
Select All Bonds
View Menu
Reset View
View Direction
Parallel Perspective
Fly to selection
Align screen
Mouse as
Anti-alias
Axes
Molecule Ball &Sticks
Molecule Resolution
Show Atoms
Show Bonds
Show Bond Type
Bond Lines Only
Capped Bonds Only
Bigger, Smaller
Background
ADF-GUI modules
ADFjobs
Introduction
Starting ADFjobs
Use as Launcher
File and Job listing
Job elements
Selecting
Changing directories, open a job, change a job name
Filtering
Job details
Local files
Remote files
Change job name
Queues
Menu commands
File menu
New Directory
Delete Directory
Check For Update
Quit
Edit menu
Job menu
Run
Kill
Transfer To Remote
Transfer From Remote
Delete
Delete Remote
Generate Test Job
Reset
Queue menu
New...
New From Job
Edit...
Delete
Set Default
Restore Queue Configurationt
Status
Queue name
Sort menu
Filter menu
Tools menu
Prepare...
New Report Template...
Edit Report Template...
Delete Report Template...
Build ... Report
Update Last Report
Style menu
ADFinput
Introduction
Starting ADFinput
Menu Commands
File menu
New
Open...
Import Coordinates...
Export Coordinates...
Save
Save As...
Revert...
Save Picture...
Default Picture Format
Picture Resolution
Run
Quit
Edit menu
Undo
Redo
Cut
Copy
Paste
Clear
Group
Ungroup
Set origin
Bond Lengths constrained
Add Bond
Add Hydrogen
Remove Hydrogen
Fuse Atoms
Select All
Select Molecule
Select Connected
Invert Selection
Guess Bonds
Remove Bonds
View menu
Standard View commands
Model menu
Properties menu
Details menu
Help menu
Pop-up menu
Standard pop-up commands
Delete atom(s)
Connectors
Change atom(s) type
Add structure(s)
New Fragment...
Another ... Fragment
Add to ... Fragment
Buttons and Tools
Getting and changing geometry details
Keyboard shortcuts
Preoptimizer: MM, MOPAC or DFTB
MM
DFTB
MOPAC
Presets and Defaults
Use a Preset
Revert to preset values
Color Code
Make your own presets
Defaults
Calculation Tasks
Fragment Analysis
Frequencies
Geometry Optimization
IRC (Intrinsic Reaction Coordinate)
Linear Transit
Properties Only
Single Point
Transition State Search
Structures
Replacing an existing atom
Left-click in empty space
Metal Complexes
Dummy atoms and Multidentate ligands
Your own structures
Symmetry
Molecule Editor Tricks
Selecting
Delete an atom
Delete a bond
Delete the selection
Make a bond
Make a bond, alternative method
Change the bond type
Move an atom (possibly perpendicular to the screen)
Rotate or translate the selection
Run Script
Input options remarks
Empty fields
Coordinates
Spin and Occupation
User Input
Protein QMMM calculations with PDB files
ADFview
Introduction
Starting ADFview
Menu commands
File
New
Open...
Save Picture...
Default Picture Format
Picture Resolution
Export As VRML...
Export Fields As Cube Files
Quit
Add
Isosurface
Isosurface: Colored
Isosurface: Double (+/-)
Cut Plane: Colored
Cut Plane: Contours
Cut Plane: Contours (+/-)
COSMO surface: Colored
Spinor: spin magnetization density
Add Bond
Delete Bond
HOMO-1
HOMO
LUMO
LUMO+1
Fields
Calculated
Interpolated
Grid
Sort by
View
Standard View commands
Show Scene Light
Show All Geometries
Auto Update
Update
Help
Pop-up menus
Standard pop-up commands
Comparing data from several molecules
The current geometry
Comparing different calculations
Temporary Files
ADFspectra
Introduction
Starting ADFspectra
Zooming in or out
Peak width and shape
Scaling peak positions
Axes menu
Horizontal Unit
Flip Horizontal or Vertical
Save Postscript
Export XY values
DOS (density of states)
Vibration (IR spectrum)
Optical spectrum
CD spectrum
Raman
VCD
ADFmovie
Introduction
Starting ADFmovie
Buttons
Input Files
TAPE21 and logfile
ADFmovie files
Geometry Information
Menu Commands
File: Open...
File: Save Geometry...
File: Update Geometry in ADFinput
File: Save Picture...
File: Save Movie Frames...
File: Save Movie...
File: Default Picture Format
File: Picture Resolution
File: Save As PostScript
File: Save As XY
File: Quit
View: Standard Commands
View: Add Graph
View: Delete Graph
View: Graph X Axes
View: Graph Y Axes
View: Loop
View: Converged Geometry Only
View: Displacement Vectors
Pop-up: Standard Commands
ADFlevels
Introduction
Starting ADFlevels
ADFlevels window
Stacks: Molecule, Fragment types, Fragments
Mouse interaction
Zooming and Translating
Selecting
Moving a stack
Menu commands
File: Open...
File: Add...
File: Save Postscript...
File: Quit
Axes: Reset Zoom
Axes: Unit
View: Interactions
View: Occupations
View: Labels
View: Fragments
View: Fragment Types
View: Hide Stacks
Help
Pop-up menus
Background (white space) pop-up
Stack pop-up
Level pop-up
ADFtail
Introduction
Starting ADFtail
ADFtail window
ADFoutput
Introduction
Starting ADFoutput
ADFoutput window
Click on Marked Items
Include Menu
Other Menus
GUIprefs
Preferences
Save and Apply
Display
Colors
Atom Colors
Fields
Pre-Optimizer
ADFjobs
Environment
