Aten v1.6 (r1511)
Aten v1.6 (r1511)
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Aten v1.6 (r1511)

User Manual

Tristan Youngs

Table of Contents

1. Disclaimer
2. Acknowledgements
3. Getting Started
Using Aten
Compilation From Source
Linux
Installation
Filters
User Filters
The ~/.aten Directory
Referencing Aten
The Command Line
Switch Order
Switches
4. Import / Export
Supported File Formats
Model Formats
Trejactory Formats
Gridded Data Formats
Expression Data Formats
Filters
Filter Contents
Filter Locations
Overriding Existing Filters
Filter Definitions
Filter Options
Trajectory Files
Trajectories in Separate Files
Reading and Writing
Formatted Output
Printing Data
Formatted Input
Specifiers
Extra Specifiers Within Aten
Escaped Characters
Delimited Reading and Writing
Unformatted Reading and Writing
5. The GUI
GUI Overview
Mouse Control
Toolbars
Bonding
Build
Draw Style
Edit
File
Forcefields
Measure
Mouse
Select
Tool Stack
Trajectory
Tool Windows
Atom List Window
Build Window
Cell Definition Window
Cell Transform Window
Command Window
Disordered Builder Window
Forcefield Window
Fragment Library Window
Geometry Window
Glyphs Window
Grids Window
Minimiser Window
Atom Position Window
Select Window
Atom Transform Window
ZMatrix Window
6. Command Language
Command Language Overview
General Input Style
Variables
Arrays
Predefined Constants
Blocks, Scope, and Variable Hiding
Functions
User Defined Functions
Return Values
Arithmetic Expressions and Operators
Variable Types
Overview
Aten Type
Atom Type
BasisPrimitive Type
BasisShell Type
Bond Type
Bound Type
Cell Type
ColourScale Type
ColourScalePoint Type
Eigenvector Type
Element Type
EnergyStore Type
FFAtom Type
FFBound Type
Forcefield Type
Glyph
GlyphData Type
Grid Type
Measurement Type
Model Type
Pattern Type
Prefs Type
Region Type
Site Type
UnitCell Type
Vector Type
Command Reference
Atom Commands
Bond Commands
Building Commands
Cell Commands
Charges Commands
ColourScales Commands
Disordered Commands
Edit Commands
Energy Commands
Flow Commands
Forcefield Commands
Forces Commands
Glyph Commands
Grid Commands
Image Commands
Labeling Commands
Math Commands
Measuring Commands
Messaging Commands
Minimiser Commands
Model Commands
Model Extras Commands
Monte Carlo Commands
Pattern Commands
Read / Write Commands
Script Commands
Selection Commands
Site Commands
String Commands
System Commands
Trajectory Commands
Transform Commands
View Commands
7. Topics of Interest
Colourscales
Glyphs
Patterns
Determination of Patterns
Pattern Granularity
8. Forcefields and Typing
Overview
File Format
Example - SPC Water
Supplied Forcefields
Canongia-Lopes & Padua Ionic Liquids (cldp-il.ff)
Youngs, Kohanoff, & Del Pópolo [dmim]Cl (dmimcl-fm.ff)
Youngs & Hardacre [dmim]Cl (dmimcl-fm2.ff)
Jorgensen at al. OPLS-AA (oplsaa.ff)
Berensen et al.s Simple Point Charge Water (spc.ff)
Berensen et al.s Extended Simple Point Charge Water (spce.ff)
Rappe et al.s Universal Forcefield (testing/uff.ff)
Mayo, Olafson & Goddard II's Generic Forcefield (testing/dreiding.ff)
General Amber Forcefield (testing/gaff.ff)
Liu, Wu & Wang's United-Atom Ionic Liquids Forcefield (lww-il.ff)
Keyword Reference
General Keywords
Block Keywords
Wildcards
Rule-Based Forcefields
Functions
Typing
Language Examples
Description Depth
Type Scores
Reusing Types
NETA Reference
~X (any bond to X)
-X (single bond to X)
=X (double bond to X)
bond
chain
n
nbonds
nh
aromatic
noring
planar
ring
size
Geometries
VDW Functional Forms
Bond Functional Forms
Angle Functional Forms
Torsion Functional Forms
9. Methods
Custom Algorithms
NETA
Augment
Autoellipsoids
Autopolyhedra
Rebond
Literature Methods
10. Enumerations
Basis Shell Types
Bond Types
Bound Types
Cell Types
Colour Schemes
Combination Rules
Drawing Styles
Energy Units
Glyph Types
Grid Styles
Grid Types
Label Types
Output Types
Parse Options
Read Success Integers
Region Shapes
View Objects
ZMapping Types
11. TODO
12. Changelogs
Version 1.1
Version 1.2
Version 1.3
Version 1.4
Version 1.5
Version 1.6
Index

List of Figures

5.1. Atom List Window
5.2. Build Window
5.3. Cell Definition Window
5.4. Cell Transform Window, Replicate Panel
5.5. Cell Transform Window, Scale Panel
5.6. Command Window, Prompt Panel
5.7. Command Window, Scripts Panel
5.8. Command Window, Command Index Panel
5.9. Disordered Builder Window
5.10. Forcefield Window
5.11. Fragment Library Window
5.12. Geometry Window
5.13. Glyphs Window
5.14. Grids Window - Data / Cutoff Page
5.15. Grids Window - Origin / Axes Page
5.16. Grids Window - Style Page
5.17. Grids Window - Shift Page
5.18. Grids Window - Orbitals Page
5.19. Minimiser Window
5.20. Atom Position Window, Centre Panel
5.21. Atom Position Window, Flip Panel
5.22. Atom Position Window, Translate Panel
5.23. Atom Position Window, Shift Panel
5.24. Atom Position Window, Reposition Panel
5.25. Select Window
5.26. Atom Transform Window, Rotate Panel
5.27. Atom Transform Window, Matrix Transform Panel
5.28. Atom Transform Window, Matrix Convert Panel
5.29. ZMatrix Window
7.1. Pattern Example, System 1
7.2. Pattern Example, System 2
7.3. Pattern Example, System 3
7.4. Pattern Example, System 4
8.1. Water
8.2. 3-hydroxypropanoic acid
8.3. N,N,2,5-tetramethylpyridin-4-amine

List of Tables

4.1. Supported Model Formats
4.2. Supported Trajectory Formats
4.3. Supported Grid Data Formats
4.4. Supported Expression Data Formats
4.5. Filter properties
4.6. Filter types
4.7. Option Types
4.8. Layout Commands
4.9. Formatted output commands
4.10. Formatted input commands
4.11. Extra read/write specifiers
4.12. Escaped characters in format strings
4.13. Delimited read/write commands
5.1. Mouse Button Actions
5.2. Bonding Toolbar Icons
5.3. Build Toolbar Icons
5.4. Draw Style Toolbar Icons
5.5. Edit Toolbar Icons
5.6. File Toolbar Icons
5.7. Forcefield Toolbar Icons
5.8. Mouse Toolbar Icons
5.9. Mouse Toolbar Icons
5.10. Select Toolbar Icons
5.11. Tool Window Toolbar Icons
5.12. Trajectory Toolbar Icons
5.13.
5.14.
5.15.
5.16.
5.17.
5.18.
5.19.
5.20.
5.21.
6.1. Built-in Constants
6.2. Aten Type Members
6.3. Bond Type Functions
6.4. Atom Type Members
6.5. Atom Type Functions
6.6. BasisPrimitive Type Members
6.7. BasisPrimitive Type Functions
6.8. BasisShell Type Members
6.9. BasisShell Type Functions
6.10. Bond Type Members
6.11. Bond Type Functions
6.12. Bound Type Members
6.13. Bound Type Functions
6.14. Cell Type Members
6.15. ColourScale Type Members
6.16. ColourScale Type Functions
6.17. ColourScalePoint Type Members
6.18. Eigenvector Type Members
6.19. Element Type Members
6.20. EnergyStore Type Members
6.21. FFAtom Type Members
6.22. FFAtom Type Functions
6.23. FFBound Type Members
6.24. FFBound Type Functions
6.25. Forcefield Type Members
6.26. Forcefield Type Functions
6.27. Glyph Type Members
6.28. Glyph Type Functions
6.29. GlyphData Type Members
6.30. Grid Type Members
6.31. Measurement Type Members
6.32. Model Type Members
6.33. Model Type Functions
6.34. Pattern Type Members
6.35. Prefs Type Members
6.36. Region Type Members
6.37. Site Type Members
6.38. UnitCell Type Members
6.39. Vector Type Members
6.40. Test Operators
6.41. Autopolyhedra options
6.42. Newglyph options
6.43. Bitmap image formats
7.1. Glyph type data
7.2. Pattern Examples
8.1. Allowable FF Rule Functions
8.2. NETA keyword '~X' examples
8.3. NETA keyword '~X' examples
8.4. NETA keyword '-X' examples
8.5. NETA keyword '=X' examples
8.6. NETA keyword 'bond' examples
8.7. NETA keyword 'chain' examples
8.8. NETA keyword 'n' examples
8.9. NETA keyword 'nbonds' examples
8.10. NETA keyword 'nh' examples
8.11. NETA keyword 'aromatic' examples
8.12. NETA keyword 'noring' examples
8.13. NETA keyword 'planar' examples
8.14. NETA keyword 'ring' examples
8.15. NETA keyword 'size' examples
8.16. NETA geometry keywords
8.17. VDW Functional Forms
8.18. Bond Functional Forms
8.19. Angle Functional Forms
8.20. Torsion Functional Forms
9.1. Literature Methods
10.1. Basis shell type keywords
10.2. Bond type keywords
10.3. Bound type keywords
10.4. Cell type keywords
10.5. Colour scheme keywords
10.6. Combination Rules
10.7. Draw style keywords
10.8. Energy unit keywords
10.9. Glyph type keywords
10.10. Grid style keywords
10.11. Grid type keywords
10.12. Label type keywords
10.13. Output type keywords
10.14. Parse option keywords
10.15. Read/write return values
10.16. Region Shapes
10.17. View object keywords
10.18. Map type keywords
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   Chapter 1. Disclaimer