Chapter 3. Quick Start Tutorial

To get started using NanoHive-1, we'll simulate the following carbon nanotube.

Note

To run this simulation, you'll need these plugins installed: RC_Traverser, AIREBO, MeasurementSetToFile, and NetCDF_DataSet. They are all part of the standard set of plugins installed with NanoHive-1.

The files for this simulation are in the examples/nanotube-5x5 directory:

NanoHive-1/examples/nanotube-5x5
  cnt55-sim.xml                 <-- simulation specification file
  cnt55.nml                     <-- nanotube description file
  simflow.tcl                   <-- simulation workflow file

Windows users will find this directory where they installed NanoHive-1 (there's also a shortcut to it called "Examples Folder" in the NanoHive-1 program group.) Unix users installed this directory when they ran the install-examples script.

Here are the highlights of our simulation as described in the simulation specification file:

500 iterations will be run with 5x10^-16 seconds of (simulation) timelapse between each iteration.
The simulation thermometer will be set to 300 Kelvin (about room temperature)
The AIREBO physical interaction plugin will be used to calculate the interactions between the nanotube's carbon atoms. AIREBO is a molecular dynamics plugin specially for hydrocarbon systems.
The MeasurementSetToFile simulation results plugin will be used to output simulation measurements such as total energy and ideal temperature to results.txt, a tab-separated data file.
The NetCDF_DataSet simulation results plugin will be used to output results in a format that HiveKeeper can use to show a visualization of the simulation.

Start NanoHive-1

Windows - Click the NanoHive-1 icon in the NanoHive-1 program group, or double-click the NanoHive-1 icon on your desktop.
Unix - Run NanoHive (no hyphen) from the command line.

You should see something like the following, but if there is a problem, see the Troubleshooting section.

  NanoHive-1 (TM) Version 1.2.0 Copyright (C) 2004,2005 NanoHive-1, LLC
  NanoHive-1 comes with ABSOLUTELY NO WARRANTY; for details run 'NanoHive -l'
  This is free software, and you are welcome to redistribute it under certain
  conditions; run 'NanoHive -l' for details.

  Loading configuration file: C:\Program Files\NanoHive-1\conf\configs.txt
  Logging to C:\Program Files\NanoHive-1/log/NanoHive-1.log
  ConsoleCommand Version 1.2.0 started. (Press Enter to begin interactive mode.)
  SocketsControl Version 1.2.0 started.

Run the simulation

Hit the Enter key, then enter the following command at the > command prompt to load the simulation. The -f option indicates the simulation specification file, and the -n option indicates a name for the simulation.
- Windows
```
  > load simulation -f "C:\Program Files\NanoHive-1\examples\nanotube-5x5\cnt55-sim.xml" -n cnt55
```
  Note
  In Windows XP, you can drag and drop the .xml file into the command window after typing the "load simulation -f " part and it will fill in the path and filename for you. A shortcut to the NanoHive-1\examples folder has been added to the NanoHive-1 program group for your convenience.
- Unix - assuming you're in the directory where you ran the install-examples script:
```
  > load simulation -f NanoHive-1/examples/nanotube-5x5/cnt55-sim.xml -n cnt55
```
Run the simulation: run cnt55
The command line will notify you when the simulation is done, or you can see the status of the simulation by entering: status cnt55
Enter help to get a command summary.

After the simulation has finished, there will be two additional files in the nanotube-5x5 directory: cnt55-out.nml is the nanoML description of the nanotube after simulation, and results.txt contains simulation measurements. Here is a sampling of those results:

  Iteration  Timestamp (s)  Ideal Temperature (K)  Total Energy (J)
   0          5e-016         0                      0
   20         1.1e-014       328.05646239868577    -3.5509475437549161e-016
   40         2.1e-014       302.22761057089201    -3.5547835267918064e-016
   60         3.1e-014       326.58338061380152    -3.548842822784157e-016
   80         4.1e-014       317.93140467153665    -3.5513028886709029e-016
   100        5.1e-014       327.61161242370457    -3.540485866467119e-016
   120        6.1e-014       335.63659585646531    -3.5387027654503099e-016
   140        7.1e-014       327.79441462546794    -3.5319209001085585e-016
   160        8.1e-014       326.42341023714528    -3.5396366087355515e-016
   180        9.1e-014       321.66359530328941    -3.5426654655060054e-016
   200        1e-013         316.84105488524222    -3.5497281413934345e-016

We see the ideal temperature near 300 K (our thermometer setting), and the total energy of the system stays relatively the same as it should, with Conservation of Energy.

Even Quicker Start With HiveKeeper

If you chose to install the HiveKeeper application, follow these steps to perform the simulation.

- Windows - Click the HiveKeeper icon in the NanoHive-1 program group, or double-click the HiveKeeper icon on your desktop.
- Unix - Execute HiveKeeper from the command-line.
If NanoHive-1 isn't already running from the above exercise, click the Start Instance button to start NanoHive-1.

Once connection is established with the NanoHive-1 instance, choose File | Open Simulation... from the menu bar and open, in Windows:

  NetCDF result files directory:
    C:\Program Files\NanoHive-1\examples\nanotube-5x5\results
  Simulation specification file:
    C:\Program Files\NanoHive-1\examples\nanotube-5x5\cnt55-sim.xml

or in Unix:

  NetCDF result files directory:
    ~/NanoHive-1/examples/nanotube-5x5/results
  Simulation specification file:
    ~/NanoHive-1/examples/nanotube-5x5/cnt55-sim.xml

In the new window that opens, click the Start button to run the simulation. Once the simulation has started you can click the Play button to start playing the visualization as the simulation is progressing.
For a complete description of the visualization controls choose Help | Contents... from the visualization window menu bar. You can use the mouse in the visualization display to rotate, pan, and zoom the nanotube.
- Left mouse button + drag: rotate the scene
- Right mouse button + drag: pan/move the scene
- Control key + left mouse button + drag: zoom in (mouse down) and out (mouse up)

This is a relatively tame simulation of an already stable molecule - for a more dynamic system, try the POVRayVideo plugin's Example Usage: Hydrogen Abstraction Video where you'll simulate hydrogen abstraction from a diamond seed, then create an MPEG video of the results.


4. Plugin Distributions		Chapter 4. Using NanoHive-1

Documentation