# Category:Electronic Scale

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# Overview

First principles methods based on Density Functional Theory (DFT) are widely used for electronic structure calculations in material science. They can be used to determine material properties without any experimental data input. They can be used to simulate systems ranging from tens of atoms to hundreds of atoms. Material properties determined by them are useful in constructing semi-empirical interatomic potentials which can handle millions of atoms. All the codes listed below have their own user manuals. For detailed instructions they should be referred.

In quantum mechanics, a particle is characterized by a wave function that contains the information about the spatial state of the particle at time t and position r. The time evolution of the wave function is governed by the Schrodinger equations. Many methods have been developed for molecular calculations. Due to the computational expense, however, the routine application of such methods to realistic models of systems of interest is not practical and not likely to become so, despite rapid advances in computer technology. The direct solution of the Schrodinger equation is not currently feasible for systems of interest in condense matter science- this is a major motivation for the development and use of density function theory (DFT).

Density function theory is an extremely successful method for the description of ground-state properties of metals, semiconductors, and insulators. The success of DFT not only encompasses standard bulk materials but also complex materials such as proteins and biological materials.[1] In the context of bridging the DFT calculation to the higher atomic scale simulations, it is important to get a few material properties in order to develop a successful semiempirical potential for something like the embedded atom method (EAM) or modified embedded atom method (MEAM) potentials such that the potentials can reproduce several materials or mechanical properties as accurately as possible.

# Tutorials

Electronics principle is currently the lowest length scale to start your research. This would require you to familiarize yourself with at least one software that incorporates DFT in the material model such as VASP, and SIESTA. Some pre and post processing codes, and visualization codes are necessary to work in conjunction with material models.

## Preprocessing & Postprocessing Codes

### PreProcessor: Crystal Structures Generator

This subsection includes atomic positions of various crystal systems used as input for the codes. For more details on a particular structure and various other crystallographic structures, please check http://cst-www.nrl.navy.mil/lattice/.

A very basic sample program csg.py to generate the bcc, fcc and hcp crystal structure with orthogonal basis are given .

### Postprocessing Codes

Here is a small collection of VASP related scripts that are routinely used.

• Cleanvaspfiles: Remove all the output files generated by running VASP.
• d2c.py: Converts vasp's CONTCAR file into a cartesian coordinate file named POSCAR.new.
• relax_total: calculates energy difference between starting and final configuration.

calling “VASP_posview POSCAR” will convert the POSCAR to a pdb file and open with rasmol. VASP_posview, rasmol, rasmol_colors, and pos2pdb.py are used in conjunction to quickly visualize a atomic file in VASP POSCAR format.

Curve Fitting

• Evfit is a code used to fit Energy-Volume (E-V) curves of crystals. The FORTRAN source code is provided here and can be compiled with standard FORTRAN compilers.

## Visualization

This subsection shows links to visualization packages used at the atomistic scale at CAVS.

#### Free software

• OVITO (The Open Visualization Tool) is a scientific visualization and analysis software for atomistic simulation data.
• RasMol is Molecular Visualization Freeware for proteins, dna and macromolecules.
• XCrysDen visualizes Crystalline Structures and Densities
• OpenDX is open source visualization software package based on IBM's Visualization Data Explorer.
• Raster3D is a set of tools for generating high quality raster images of proteins or other molecules.
• VMD is Visual Molecular Dynamics, molecular graphics software for MacOS X, Unix, and Windows.
• AtomEye is an atomistic configuration viewer.
• Geomview is an interactive 3D viewing program for Unix.

#### Commercial software

• Ensight is a visualization tool available in HPCC.

# Material Models

refs with no name must have contentCite error: Invalid `<ref>` tag; refs with no name must have contentCite error: Invalid `<ref>` tag; refs with no name must have content - ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis.

# References

1. M.F. Horstemeyer, Integrated Computational Materials Engineering (ICME) For Metals: Using Multiscale Modeling to Invigorate Engineering Design with Science. Hoboken, N.J:WILEY-TMS, 2013
2. G. Kresse and J. Hafner, "Ab initio molecular dynamics for liquid metals" Phys. Rev. B, 47:558, 1993
3. G. Kresse and J. Hafner, "Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium" Phys. Rev. B, 49:14251, 1994
4. G. Kresse and J. Furthmüller, "Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set" Comput. Mat. Sci., 6:15, 1996
5. G. Kresse and J. Furthmüller, "Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set" Phys. Rev. B, 54:11169, 1996.
6. José M. Soler, Emilio Artacho, Julian D. Gale, Alberto García, Javier Junquera, Pablo Ordejón and Daniel Sánchez-Portal, "The Siesta method for ab initio order-N materials simulation" J. Phys.: Condens. Matter 14, 2745-2779 (2002)
7. E. Artacho, E. Anglada, O. Dieguez, J. D. Gale, A. García, J. Junquera, R. M. Martin, P. Ordejón, J. M. Pruneda, D. Sánchez-Portal and J. M. Soler,"The Siesta method; developments and applicability" J. Phys.: Condens. Matter 20, 064208 (2008)
8. Jeff Houze, Sungho Kim, Seong-Gon Kim, "Structure of AlSb(001) and GaSb(001) surfaces under extreme Sb-rich conditions" Phys. Rev. B 76, 205303 (2007)
9. B. Jelinek, J. Houze, Sungho Kim, M. F. Horstemeyer, M. I. Baskes, and Seong-Gon Kim, "Modified embedded-atom method interatomic potentials for the Mg-Al alloy system" Phys. Rev. B 75, 054106 (2007)
10. Jeff Houze, Sungho Kim, Seong-Gon Kim, "Structure of AlSb(001) and GaSb(001) surfaces under extreme Sb-rich conditions" Phys. Rev. B 76, 205303 (2007)
11. J. Houze, Sungho Kim, Seong-Gon Kim, Seong-Jin Park, Randall M. German, and M. F. Horstemeyer, "The effect of Fe atoms on the adsorption of a W atom on W(100) surface" JOURNAL OF APPLIED PHYSICS 103, 106103 (2008)
12. B. Jelinek, J. Houze, Sungho Kim, M. F. Horstemeyer, M. I. Baskes, and Seong-Gon Kim, "Modified embedded-atom method interatomic potentials for the Mg-Al alloy system" Phys. Rev. B 75, 054106 (2007)
13. Amitava Moitra, Kiran N. Solanki, and M.F. Horstemeyer, "The location of atomic hydrogen in NiTi alloy: A first principles study" Computational Materials Science Volume 50, Issue 3, January 2011, Pages 820-823
14. Amitava Moitra, Kiran N. Solanki, and M.F. Horstemeyer, "The location of atomic hydrogen in NiTi alloy: A first principles study" Computational Materials Science Volume 50, Issue 3, January 2011, Pages 820-823
15. J. Houze, Sungho Kim, Seong-Gon Kim, Seong-Jin Park, Randall M. German, and M. F. Horstemeyer, "The effect of Fe atoms on the adsorption of a W atom on W(100) surface" JOURNAL OF APPLIED PHYSICS 103, 106103 (2008)
16. Sungho Kim, Seong-Gon Kim and S. C. Erwin, "Structure of the hydrogen double vacancy on Pd(111)" Phys. Rev. B 76, 214109 (2007)

## Subcategories

This category has only the following subcategory.

## Pages in category "Electronic Scale"

The following 48 pages are in this category, out of 48 total.