Nano-Hive 1.2.0 Beta1

Nano-Hive is a modular simulator used for modeling the physical world at a nanometer scale.

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GPL (GNU General Public License) 
2.9/5 18
Nano-Hive, LLC.
ROOT \ Science and Engineering \ Visualization
Nano-Hive is a modular simulator used for modeling the physical world at a nanometer scale.

The intended purpose of the simulator is to act as a tool for the study, experimentation, and development of nanotech entities.

Nano-Hive is a GPL/LGPL licensed open-source development - you can download and use it for free.

Nano-Hive can be run stand-alone, or easily integrated to support other applications such as CAD tools.


· Common C++ 1.3.6 or higher
· Log for C++ 0.3.0 or higher
· Xerces C++ XML Parser 2.3.0 or higher
· TCL 8.0 or higher
· Open Babel 1.100.2 or higher

Here are some key features of "Nano Hive":

· Designed for scalability across distributed and parallel computing networks from the ground up.
· Highly flexible plugin architecture utilizing plugins for the
· Physical interactions between atomic and molecular entities
· Traversal of atomic and molecular entities in time and space for the calculation of interactions - allows for multiresolution, hybrid meso-scale/molecular dynamics/quantum mechanics simulations
· Distribution of work units to compute network nodes
· Management of entity data in dynamic and static storage
· Management and presentation of simulation results - both realtime and post-simulation
· Import and export of entity data from, and to, the various data formats
· Control of the simulator
· Atoms and molecules in the simulation space can be powered or simply forced to follow predetermined paths by the simulator - useful for activating motors, modelling dynamic phenomena, or moving molecular tools in to, and out of, molecular work areas, for example. Activators include linear forces, torques, and hard-pathing of atoms and molecules.
· The workflow of each simulation is scriptable for maximum flexibility and customization. With scripting the user can control
· Loading of input data
· Application of pathing instructions to molecular "handles"
· How many times to repeat a simulation and how to change each repitition - useful for exploring multiple nanosystem alternatives and adjustments in a single simulator run
· Ordering and parallelization of physical interaction calculations
· Intermediate and final output of simulation results
· Intermediate and final output of nanosystem state
· The default scripting language is TCL. Other scripting languages may be added depending on demand.

What's New in 1.1.2 Release:

· The main feature of this beta release is that Nano-Hive is now fully distributable across computing networks (DC). Note that this release is not the @home-style DC client - that client, based on the BOINC platform, will be made available early 2006 - this release is mainly for dedicated DC networks. Other features of this release include:
New plugins.
· SocketsPIC_Control - This Distributed PIC Control plugin controls slave Nano-Hive instances via sockets, and transfers work units to/from them via FTP, or NFS.
· AIREBO - This Physical Interaction plugin employs the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential is an extension of the REBO potential (used by the REBO_MBM plugin) that adds non-bonded intermolecular interactions, and four-body torsional interaction.
· nanorexMMP_ImportExport - This Data Import/Export plugin handles nanoENGINEER-1's MMP file format. Along with this, the mmpShaft atom set type was introduced, allowing nE-1 users to easily specify atom sets for use with Nano-Hive.
· Added linear force and rotary force activators to the pathing system. These new activators provide a more realistic way to activate molecular machines than the original constant velocity pathing mechanism (which still has great value and still exists.)
· Added the BoxedSet simulation specification atom set descriptor for use in pathing atoms and molecules. With this descriptor, the user can simply specify two opposite points of a box and all the atoms inside become an atom set.
· Switched threading, sockets, and mutexes from the Common C++ library to the Netscape Portable Runtime (NSPR) library, and added a homegrown StringTokenizer class.
· Alpha 4 of the HiveKeeper Graphical User Interface for Nano-Hive is included with this release. The new capabilities of this alpha version include:
· Support for multiple local and remote Nano-Hive (N-H) instances
· A simulation summary tab for each N-H instance
· A Physical Interaction Calculator (PIC), ie, N-H slave instances summary tab for each DC network
· A visualization recenter macro, vdW representation, and variable playback speed for the simulation visualization frame

What's New in 1.2.0 Beta1 Release:

· This release makes Nano-Hive fully distributable across computing networks (DC).
· Other features include SocketsPIC_Control (controls slave Nano-Hive instances via sockets); AIREBO (employs the Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential); the addition of linear force and rotary force activators to the pathing system; and the BoxedSet simulation specification atom set descriptor for use in pathing atoms and molecules.

Last updated on February 14th, 2006

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