Documentation

Version 1.2.0 Beta 1
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Table of Contents

1. Introduction
1. Overview
1.1. Complexity
1.2. Computational Intensity
1.3. Software Architecture
2. Applications
3. Feature List and Plan
3.1. NanoHive-1 Version 1.0 - Done
3.2. NanoHive-1 Version 1.1 - Done
3.3. NanoHive-1 Version 1.2 - Currently in Beta
3.4. NanoHive-1 Plugin Build-Out
3.5. NanoHive-1 Nano-Wars
4. Platforms
5. License Information
5.1. NanoHive-1 Core Licensing Options
5.2. NanoHive-1 SourceForge Plugins Licensing
5.3. 3rd Party Libraries and Code
6. Notices
2. Installation
1. Overview
2. Binary Distributions
2.1. MS Windows Installer
3. Source Distributions
3.1. General System Requirements
3.2. MS Windows
3.3. Unix
4. Plugin Distributions
3. Quick Start Tutorial
4. Using NanoHive-1
1. Some Typical Usage Scenarios
1.1. Molecular Relaxation and Stabilization
1.2. Tool Interaction With a Workbase
1.3. Electrostatic Potential Characterization
2. Overview
3. Starting NanoHive-1
3.1. The Configuration File
3.1.1. Logging
3.1.2. Simulation Specification Schema
3.1.3. Command Queue
3.1.4. Entity Manager
3.1.5. Physical Interaction Calculators
4. Creating Simulations
4.1. Simulation Workflow Scripting
4.2. The Simulation Specification
4.3. Pathing
4.3.1. Atom Sets
4.3.2. Pathing Instructions
4.3.3. The Velocity/Anchoring Activator
4.3.4. Linear and Rotary Force Activators
5. Running Simulations
5.1. Viewing and Modifying Parameters
6. Distributed Computing with NanoHive-1
6.1. Configuration
6.1.1. The Master's Configuration File
6.1.2. The Slave Configuration Files
6.2. Simulation Specification and Execution
7. Working with CAD Software
7.1. Nanorex's nanoENGINEER-1
7.1.1. Anchoring Sets of Atoms
7.1.2. Creating Velocity and Linear Force Activators
7.1.3. Creating Rotary Force Activated Atom Sets
8. Troubleshooting
5. Plugin Reference
1. Physical Interaction Plugins
1.1. AIREBO
1.1.1. Configuration
1.1.2. Operation Notes
1.2. BondCalculator
1.3. MPQC_SClib
1.3.1. Common Configuration
1.3.2. What Level of Theory Should I Use?
1.3.3. MPQC_SClib Gradient Dynamics Configuration
1.3.4. Cytosine-Guanine Example
1.3.5. Electostatic Potential (ESP) Plane Configuration
1.3.6. Electrostatic Potential of a 5,5 Carbon Nanotube Example
1.4. REBO_MBM
1.4.1. Configuration
1.4.2. Operation Notes
1.4.3. Mechanosynthesis of Diamond Simulation Example
2. Entity Traversal Plugins
2.1. BasicCellTraverser
2.1.1. Configuration
2.2. RC_Traverser
3. Distributed PIC Control Plugins
3.1. SocketsPIC_Control
3.1.1. Configuration
4. Entity Management Plugins
4.1. RAMEntityManager
5. Simulaton Results Plugins
5.1. MeasurementSetToFile
5.1.1. Configuration
5.2. NetCDF_DataSet
5.2.1. Configuration
5.3. POVRayVideo
5.3.1. Configuration
5.3.2. Include and Macro Files
5.3.3. Example Usage: Hydrogen Abstraction Video
5.3.4. Frequently Asked Questions (FAQ)
6. Data Import/Export Plugins
6.1. nanorexMMP_ImportExport
6.2. nanoML_ImportExport
6.3. OpenBabelImportExport
7. Simulation Control Plugins
7.1. ConsoleCommand
7.1.1. Configuration
7.2. RMI_Control
7.2.1. Configuration
7.2.2. Running the Test Client
7.2.3. Troubleshooting
7.3. SocketsControl
7.3.1. Configuration
7.3.2. Communication
6. NanoHive-1 Software Development
1. Overview
1.1. Application Programmer's Interface (API)
2. Numbers
3. Logging
4. Plugin Development
4.1. Overview
4.2. Plugin Documentation
4.3. Physical Interaction Plugins (PIPs)
4.3.1. PIP Properties
4.3.2. Measurement Sets
4.3.3. PIP Life
4.4. Entity Traversal Plugins
4.5. Distributed PIC Control Plugins
4.6. Entity Management Plugins
4.7. Simulaton Results Plugins
4.8. Data Import/Export Plugins
4.9. Simulation Control Plugins
5. Frequently Asked Questions (FAQ)
A. Release Notes
1. Version 1.2.0 Beta 1 (12/28/06)
1.1. Compatibility With Version 1.1.2
1.2. New Plugin Versions
2. Version 1.1.2 (6/04/05)
2.1. Compatibility With Version 1.1.1
2.2. New Plugin Versions
3. Version 1.1.1 (5/08/05)
3.1. Compatibility With Version 1.1.0
4. Version 1.1.0 (3/30/05)
4.1. Compatibility With Version 1.0.1
4.2. New Plugin Versions
5. Version 1.0.1 (5/10/04)
5.1. Compatibility With Version 1.0.0
5.2. New Plugin Versions
6. Version 1.0.0 (3/31/04)
6.1. Compatibility With All Beta Versions
B. Notes on Nanospace Simulation
1. van Gunstern-Berendsen Thermostat
C. Simulation Specifications Schema
D. GNU General Public License
E. GNU Lesser General Public License
F. Mozilla Public License
G. GD License
H. Apache Software License
I. CCmdLine License
J. MPEG_ENCODE License
K. BSD License

List of Figures

1.1. Software Architecture Overview
4.1. Configuration and Simulation Files Overview
4.2. Force Activator Near-Target-Speed Dampening
4.3. Example NanoHive-1 Distributed Computing Network
4.4. Effects of Cell Size on Distributed Computation

List of Tables

1.1. 3rd Party Libraries and Code Used by NanoHive-1
2.1. NanoHive-1 Configure Script Options
4.1. Logging Output Level Codes
4.2. Simulation Workflow Functions Summary
4.3. Simulation Parameters
4.4. Simulation Parameters
5.1. AIREBO Configuration Parameters
5.2. MPQC_SClib Common Parameters
5.3. MPQC_SClib Comparison of Various Levels of Theory
5.4. MPQC_SClib Gradient Dynamics Parameters
5.5. MPQC_SClib Electrostatic Potential Plane Parameters
5.6. REBO_MBM Configuration Parameters
5.7. BasicCellTraverser Configuration Parameters
5.8. SocketsPIC_Control Configuration Parameters
5.9. MeasurementSetToFile Configuration Parameters
5.10. NetCDF_DataSet Configuration Parameters
5.11. 3rd Party Libraries and Code Used by POVRayVideo
5.12. POVRayVideo Configuration Parameters
5.13. File Formats Handled by OpenBabelImportExport
5.14. ConsoleCommand Plugin Configuration Parameters
5.15. RMI_Control Plugin Configuration Parameters
5.16. SocketsControl Configuration Parameters
6.1. Typedefs for Counting and Measuring
6.2. Logging Output Levels

List of Equations

4.1. Force Activator Near-Target-Speed Dampening Multiplier
5.1. The AIREBO Potential
5.2. Electrostatic Potential
5.3. REBO Potential
B.1. van Gunstern-Berendsen Thermostat
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   Chapter 1. Introduction
Last Modified: 5/17/2006