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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.
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SageMD2 basics
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Microcanonical (NVE),
canonical (NVT), constant pressure (NPT), and constant stress (NST) molecular
dynamics simulations;
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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.;
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Long range
electrostatics are treated using the well-known direct Coulomb and Ewald summation techniques;
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Charge equilibration is
treated using the QEq approach;
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Shock wave simulation;
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Various boundary
conditions: Periodic boundaries, free surfaces, and movable walls;
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Ab initio calculations
using quantum chemistry codes;
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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;
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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;
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Editing the atom types
and positions is a capability which helps easily create crystalline defects and calculate their properties;
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Also, the code package
offers sufficient capabilities for computing the collision dynamics of complex
polyatomic molecules;
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Cleaving surface of
the specified crystal structure;
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Constructing symmetrical tilt and twist grain boundaries;
- Constructing bi-crystal slabs.
SageMD2 GUI Capabilities
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Opening of several atomic or molecular structures at a time in different code
windows;
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Viewing of the
structures in different projections;
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Rotating models and
shifting them by moving the mouse;
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Building lattices using
the easy-to-use lattice builder;
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Displaying and labeling
lattice axes;
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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;
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Customizing atom color
and size, as well as the background color;
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Calculating and
displaying bonds between atoms;
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Calculating distance and
angles between atoms;
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Examining orthogonal or
perspective views of models;
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Zooming models;
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Exporting models to car,
xtl, fdf, cif, pdb and xyz formats;
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Copying of any part of
the SageMD2 screen to the clipboard as a bitmap image;
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Displaying temperature
versus time graphs and the structure changes during MD simulation;
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Displaying RDF, MSD,
temperature, energy, and stress graphs after the MD simulation;
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Copying RDF, MSD,
temperature, energy, and stress graphs to MS Excel and MS Word.
The Applications
Multiple industrial
applications, such as:
- Microelectronics
industry:
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Materials at extreme
conditions (explosives, high pressure, stress, etc.);
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Coating industry;
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Inorganic materials for
different applications (alloys, complex materials with new mechanical, thermal
and electric properties, etc.)
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Bioorganic and
bioinorganic materials;
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Polymers for the different
applications;
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Chemical discovery and
development;
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Life science modeling
and simulation;
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Nanotechnology:
materials and process design, etc.
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Education: undergraduate
and graduate curriculum, basic and materials science, engineering, physics and
chemistry, molecular biology, etc.
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Research: process,
materials and device design at the atomic scale.
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Arhiticture
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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.
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