Nano-Hive 1.2.0 Beta1 reviewDownload
Nano-Hive is a modular simulator used for modeling the physical world at a nanometer scale. The intended purpose of the simulator
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:
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.
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