Molecula Numerica

From Physica_Numerica

This page is for Molecula Numerica Version 0.2. The description for 0.1 is here.

Molecula Numerica is a software categorized in Molecular Dynamics Simulator. The software is produced to give priority to the visualization of the atoms/molecules. You can see what happened in the atomic world in a REAL-TIME sense. Of course the actual time scale of the phenomena in atomic world is pretty small, we mean you can see the computation results in REAL-TIME.

The software simulates not only translating motions but also rotational motions of atoms/molecules. Multi-atom molecules are dealt as a rigid body. So the software has a limitation coming from which High frequency vibration of the bonding is neglected. But the time integration is effectively fast by the simple model. To solve the rotational motion the simulator adopts quaternion based rotational equation. As for the scheme for time stepping, a Leap-Frog is adopted.

Contents 1 Overall 1.1 First 1.2 What is Molecula 1.3 What Molecula can do 1.3.1 Initial Condition 1.3.2 Simulation Control 1.3.3 Visualization 1.3.4 Movie (a series of images) Creation 1.3.5 Requirement 1.4 Characteristics 1.4.1 Emsemble 1.4.2 Thermostat 1.4.3 Quaternion-based rotational equation 1.4.4 Multi-Thread 1.4.5 SIMD vectorized 1.5 The others 1.6 Acknowledgement 1.7 Have fun! 2 Download 3 Installation 4 Sample Video 5 Screen Shot 6 Change Log

Overall

First

Molecula is in beta quality (beta 0.2.x) as of July 2008. The software is released with a hope to be useful to the users but still beta quality, please consider it when you use it. As the very first step, you might be intersted in the Installation instruction. If you already installed the software, you might want to see the First Step.

What is Molecula

Molecula Numerica (Molecula) is a Molecular Dynamic Simulator to solve dynamics of the atoms which is governed under the Lennard-Jones / Ions / Coulombic interactions. The multi-atom is treated as a rigid-body. Quaternion based governing equation is adopted for the molecules' rotational motions.

The software is made with a hope to be some helps for young people (incl. kids) to understand physics. So if you have any idea to improve the software please send it to me.

What Molecula can do

Any mixture of atoms can be simulated. As of version 0.2, several type of single atoms (He,Ne,Ar,Kr), ions (Na+,Cl-) and water (SPC/E model) can be available. Any type of two body interactions can be treated internally. As examples, Lennard-Jones/Born-Mayer-Huggins-Tosi-Fumi/Coulombic are implemented so far. Three body or more interactions would be supported in future. The availability would be depend upon the demand.

Initial Condition

Maxwellian and bulk velocity distribution. Location is lattice type, staggered lattice type and two type of random distributor are avaiable. Staggered lattice is like checkered pattern. This is for setting crystal of salt (NaCl). Only very simple funcionts are only available. If you have any idea for the initial condition please tell me!

Simulation Control

You can set the total simulation time. You can start/stop whenever you like. Click "Revert" to reset the simulation to the initial condition. If you use "Random"-wise initial condition, the exact location/velocity of the atoms become different from the previous simulation.

Visualization

Molecula provides you both two and three dimensional view. It shows you the overall 3D view of the particles. In 2D view you can see the temperature of the system and the distribution of the distance between the atoms. To change the line of sight in 3D view, just mouse-drag to rotate and shift-drag to zoom in/out. To move the eyepoint, opt-drag to move.

Movie (a series of images) Creation

Molecula can save images of 3D visual to a series of images. The image is exactly same with the 3DView window. You can set the interval of saving image with preference panel (Preference menu).

Requirement

The software is provided as a Universal Binary for Macintosh. MacOS 10.4 or higher on PPC/Intel is required. MS Windows version is now available. Windows XP is recommended because it is my environment. As for MSW version, you must have "Pthread for Win32". You have to download Pthread for Win32 from http://sourceware.org/pthreads-win32/ GLUT for Win32 is no longer necessary.

Characteristics

Emsemble

NVE and NVT ensemble are available so far.

Thermostat

As for NVT ensemble, three control methods are avaialbe. They are; wall temperature control, temperature scaling, Berendsen control.

Quaternion-based rotational equation

Molecula adopts quaternion-based rotational equation as the rotational motion of molecule. This gives you the robustness of simulating rotational motion.

Multi-Thread

Molecula is multi-thread-ed so you would get the benefit of multi-core processors. Setting too many thread might cause application crush. It would be best to set the number of thread to the same number of CPU cores.

SIMD vectorized

Molecula is vectorized for SIMD architectures. So far only Macintosh (PowerPC and Intel) version has the benefit.

The others

Acknowledgement

The author of the software is grateful to the Open Source Communities for the useful softwares, which are wxWidgets, wxmathplot and Loki, also grateful for Pthread-Win32 which are specific for MS Windows.

Have fun!

The author of the software is ABE Hiroshi. You can reach me at:

habe36 at gmail.com

ABE Hiroshi, from Tokorozawa, JAPAN. 17th July 2008.

Download

Molecula Numerica version 0.2 binaries are avalable from this site.
You can get MacOS X version (Universal Binary)
Also you can get MS Windows version

Installation

Here is an installation instruction of Molecula Numerica.

Sample Video

Screen Shot

Here is a screen shot of MacOS X version.

Change Log

Here is the change log of the software.