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General
Introduction
Release 2019
Set up
Mouse
Running Remotely
OpenGL3.2+, fallback mode
Font issues
ADFjobs Queues
Quantum ESPRESSO
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
Keyboard Shortcuts
ADFinput
ADFview
ADFmovie
ADFlevels
ADFtail (Logfile)
ADFoutput
ADFspectra
BANDstructure
ADFdos
ADFjobs
Input
Input: options
Normal Options
Expert Options
Units
Input: buttons
Searching
The “>” details buttons
Using the ”?” info buttons
Searching
Panel search details
Key search details
Documentation search details
Molecule search details
Crystals and Slabs
Periodicity
Building crystals
Build slabs
Crystal menu
Generate Super Cell...
Map Atoms To (-0.5..0.5)
Map Atoms To (0..1)
Set (0.5, 0.5, 0.5)
Builder (packmol)
Building molecules
Bonding mode
Atom Details: Connectors (valency) and Lone Pairs, Atom mass
Pre-optimization
Geometry adjustments
Sliders
Edit box
Centroids
Move an atom (possibly perpendicular to the screen)
Rotate or translate the selection
Coordinates
Z-Matrix
Set Center Of Mass
Set Origin
Symmetry
Rotate 90
Align
Mirror
Update coordinates via ADFmovie
Bonds
Importing and exporting your molecule
Importing your molecule
Copy/Paste between GUI modules, XYZ coordinates, SMILES or InChI strings
Exporting your molecule
Regions
Proteins (from PDB or mol2 files)
Presets and Defaults
Using a preset
Color Code
Make your own presets
Multiple presets are used
Input options remarks
Empty fields
Spin and Occupation
User Input
ADFjobs
Jobs
Job list: per folder or global
Job status (including WARNING and ERROR info)
Selecting Jobs
Running a job: .run and .job
Job files
Local files
Remote files
Clean Up
Archive jobs
Import / Export jobs
Find job 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
Series of jobs depending on each other
ADFview
Visualization methods
Spinor: spin magnetization density
Fields
Steric Interaction
Properties
Comparing data from several molecules
Temporary Files
Calculating Fields
ADFmovie
Geometries
Scalar Atomic Properties
Atomic Vectors
Graphs
Trajectory Analysis
KFbrowser
Non-expert mode
Expert mode
Conformers
Fukui Function
Minimum Energy Crossing Point
Quantum ESPRESSO
Input
Running
Visualization of results
Scripting support
ADFtrain
General
Overview
File handling
Open
Add
Save
Tables
Header menus: sort and filter
Search
Selection
Training set
Systems
Training set
Mouse interaction
Editing
Show
Warnings and errors
Reference data
Generating reference jobs
Running reference jobs
Importing results from reference jobs
Force field
Type: lgDispersion, ACKS2 or eReaxFF
Force field parameters
Adding records
Editing parameters and optimization details
Mouse interaction
ADFcrs: COSMO-RS
Menu Commands
File menu
Compounds menu
Method menu
Properties menu
Solvent Optimizations menu
Analysis menu
Graph menu
Help Menu
GUI Environment Variables
Required Citations
General References
External programs and Libraries
GUI
Documentation
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GUI
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Index
Index