The AtomSim program, which has been in development since 2008, enables the user to study the behaviour of crystalline and polycrystalline substances at various dimensional scales (multi-scale analysis). The core of the program is an atomic network based on the self-organizing network principle. Self-organizing networks are special neural networks which learn “without supervision”. The atomic network can be employed for describing, displaying and simulating crystalline substances under stress.

About the program

AtomSim - Atomové sítě is a software tool for modelling crystal lattices of metals including basic lattice defects. It does not track the dynamics of the system but it considers optimal mean positions of atoms in the crystal lattice. The program output consists of files that describe their mean atomic positions, their bonds, the elastic response of the entire atomic system at the boundary of the scene, as well as some other variables. Elastic bonds within crystal lattices of metals (FCC and BCC) are described using the Lennard-Jones potential.

Format of .xml input file

‹AtomicNetwork name="Project 1" ›
‹Box x="50" y="50" z="50" /›
‹BorderVelocity type="press" dir="x" stepLength="0.2" stepCount="3" /›
‹Crystal matrix="BCC" a="1.0" lje="1.0" ljd="0.866" ›
‹Seed x="5" y="5" z="5" /›
‹Alpha x="1" y="0" z="0" /›
‹Beta x="0" y="1" z="0" /›
‹Gama x="0" y="0" z="1" /›
‹Vacancy ratio="0.0005" /›
‹Substitution ratio="0.01" a="2.0" lje="1.5" ljd="1.732" /›


- definition of scene dimensions [x, y, z]


- definition of scene boundary movement
- [type="press|pull"] stress type: tension, compression
- [dir="x|y|z"] stress axis
- [stepLength] distance by which the scene boundary is displaced in each step
- [stepCount] number of steps in scene boundary displacement


- definition of fundamental parameters of the crystal lattice
- [matrix="BCC|FCC"] crystal lattice type
- [a] lattice parameter
- [lje] the E parameter of the Lennard-Jones potential
- [ljd] the D parameter of the Lennard-Jones potential


- position of the base atom of the crystal lattice (nucleus) which dictates the positions of the other atoms, depending on orientation ‹Alpha›, ‹Beta›, ‹Gama›


- crystal lattice orientation


- [ratio] definition of the relative proportion of vacancies in the system


- [ratio] definition of the relative proportion of substitutions in the system
- [a] lattice parameter for substitution
- [lje] the E parameter of the Lennard-Jones potential for substitution
- [ljd] the D parameter of the Lennard-Jones potential for substitution

Output format

*.mol2 file – a standard file type for molecular dynamics simulations, containing essential information about every atom of the scene and about the bonds. Various visualization-based molecular dynamics simulation tools can open this type of file, such as VMD, VESTA or Xcrysden.


AtomSim has been designed for Ubuntu Linux platform 11.04 64bit with the CUDA Tollkit 4.1.28.

First, the following packages must be installed:
build-essential – the fundamental developer package for a linux platform, containing c++ compilers, linkers and the essential C++ libraries.
qt4-dev-tools - this package contains QT support libraries.

The packages are installed using the command sudo apt-get install build-essential qt4-dev-tools

The following instructions are required for installing and running AtomSim:
1) Download AtomicNetwork.tar.gz
2) tar xvzf AtomicNetwork.tar.gz
3) cd AtomicNetwork
4) qmake
5) cd out
6) AtomicNetwork -cubin ../cubin/gener_f.cubin -xml ../prj.xml

Parameters for launching the program:
-listcuda - listing the devices that support CUDA
-cubin - the full path, including the name of the file, to the compiled CUDA kernel
-xml - the full path, including the name of the file, to the file with input project definitions

Example launch instruction: "AtomicNetwork -cubin ../cubin/gener_f.cubin -xml ../prj.xml"

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