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SageMD2 (code description)

SageMD2 code is a user-friendly software package for research, engineering, and educational needs in atomic scale materials design. SageMD2 can be used in various operating systems, such as: Linux, FreeBSD, SGI IRIX, HP-UX, IBM AIX, SUN Solaris, DEC/Compaq Tru64 UNIX, and MS-Windows. SageMD2 main window is shown in Figure.

Figure. SageMD2 main window

The SageMD2 code includes a graphic user interface (GUI) for solid state and molecular materials design at the atomic scale, a large set of computational modules for molecular dynamics, and databases of empirical force field potentials and crystal structures, as well as interfaces for various commercial quantum mechanical (QM) codes. SageMD2 code can be used to model properties of materials at constant temperature and/or constant pressure, to study behavior of a crystal lattice under expansion or compression, to calculate Radial Distribution Functions (RDF) and Mean-Square Deviations (MSD) to derive atomic diffusion coefficients. The software allows using different boundary conditions namely: periodic boundary conditions, free surfaces, and movable walls. In addition, the charge equilibrium (QEq) approach for interatomic energy calculation which takes into account the atomic charge distribution has been incorporated into SageMD2 code for modeling the properties of materials with covalent chemical bonds.


SageMD2 basics

  • Microcanonical (NVE), canonical (NVT), constant pressure (NPT), and constant stress (NST) molecular dynamics simulations;
  • Pair and non-pair interatomic potentials incorporated in SageMD2 code as follows: Morse modified Morse, Buckingham, Embedded Atom Method (EAM), QEq, Stillinger-Weber, Tersoff B, Tersoff C, Maruyama models, etc.;
  • Long range electrostatics are treated using the well-known direct Coulomb and Ewald summation techniques;
  • Charge equilibration is treated using the QEq approach;
  • Shock wave simulation;
  • Various boundary conditions: Periodic boundaries, free surfaces, and movable walls;
  • Ab initio calculations using quantum chemistry codes;
  • One or more selected fragments of simulation material can be specified in the computation cell during MD simulation. For these selected fragments, it is possible to calculate local characteristics of the material;
  • Code can be used to simulate the properties of materials changing for different effects upon the material externally, such as temperature, pressure and shock-wave loading effects;
  • Editing the atom types and positions is a capability which helps easily create crystalline defects and calculate their properties;
  • Also, the code package offers sufficient capabilities for computing the collision dynamics of complex polyatomic molecules;
  • Cleaving surface of the specified crystal structure;
  • Constructing symmetrical tilt and twist grain boundaries;
  • Constructing bi-crystal slabs.

SageMD2 GUI Capabilities

  • Opening of several atomic or molecular structures at a time in different code windows;
  • Viewing of the structures in different projections;
  • Rotating models and shifting them by moving the mouse;
  • Building lattices using the easy-to-use lattice builder;
  • Displaying and labeling lattice axes;
  • Selecting atoms by mouse click, including options for atom selection by means of box, sphere, cylinder, and atom type and for changing atom types of the selected atoms;
  • Customizing atom color and size, as well as the background color;
  • Calculating and displaying bonds between atoms;
  • Calculating distance and angles between atoms;
  • Examining orthogonal or perspective views of models;
  • Zooming models;
  • Exporting models to car, xtl, fdf, cif, pdb and xyz formats;
  • Copying of any part of the SageMD2 screen to the clipboard as a bitmap image;
  • Displaying temperature versus time graphs and the structure changes during MD simulation;
  • Displaying RDF, MSD, temperature, energy, and stress graphs after the MD simulation;
  • Copying RDF, MSD, temperature, energy, and stress graphs to MS Excel and MS Word.

The Applications

Multiple industrial applications, such as:

  1. Microelectronics industry:
    • Materials at extreme conditions (explosives, high pressure, stress, etc.);
    • Coating industry;
    • Inorganic materials for different applications (alloys, complex materials with new mechanical, thermal and electric properties, etc.)
    • Bioorganic and bioinorganic materials;
    • Polymers for the different applications;
    • Chemical discovery and development;
    • Life science modeling and simulation;
    • Nanotechnology: materials and process design, etc.
  2. Education: undergraduate and graduate curriculum, basic and materials science, engineering, physics and chemistry, molecular biology, etc.
  3. Research: process, materials and device design at the atomic scale.



The SageMD2 graphic user interface has been developed using FOX library fox-toolkit. The computing modules are written in Fortran 90. The graphics is implemented with Open GL library which allows using the tools of advanced 3D graphic accelerators to quickly create and edit atomic structures.

SageMD2 consists of three main modules:

  • input and processing of initial data;
  • numerical solution of the equations of motion;
  • processing of the calculation results.

There is a suitable interface provided in SageMD2 for running the quantum chemistry codes for computations of interatomic and intermolecular force fields.






Simulation results

  Control panel 







Set potential

Ewald summation

Shock wave

Cleaving surface




Display parameters

Choose color

Display graph