# Category:Electronic Scale

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* [https://www.youtube.com/watch?v=VmgeYN681t8&t=5s Generating an Energy-Volume Curve] | * [https://www.youtube.com/watch?v=VmgeYN681t8&t=5s Generating an Energy-Volume Curve] | ||

* [[Structure Optimation]] | * [[Structure Optimation]] | ||

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+ | **[[vc-relax]] | ||

+ | * [[Supercell]] | ||

== Preprocessing & Postprocessing Codes == | == Preprocessing & Postprocessing Codes == |

## Revision as of 12:35, 19 April 2019

## Contents |

# 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.

See also: Data and models pertaining to the ICME Phase Equilibria task.

Finally, to garner more information about the information bridges between length scales go to the MSU Education page.

# 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 Code, SIESTA Code, or Quantum Espresso Code. Some pre and post processing codes, and visualization codes are necessary to work in conjunction with material models.

## VASP

- Intro to VASP Video Tutorial
- VASP Tutorial
- How to calculate basic calculations to get the Lattice parameter, Cohesive energy, and Bulk modulus for Aluminum
- How to calculate vacancy formation energy calculation for Aluminum
- How to calculate interstitial formation energy for Aluminum
- How to calculate surface formation energy for Aluminum
- How to calculate surface Adsorption energy for Aluminum
- How to calculate generalized stacking fault energy curve on (111) glide plane, along [1-10] glide direction for Aluminum
- How to calculate basic calculations to get the Lattice parameter for Pur Manganese-bismuth

## SIESTA

## Quantum Espresso

## 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/.

- Basic crystal structure generator for body centered cubic system
- Basic crystal structure generator for face centered cubic system
- Basic crystal structure generator for hexagonal closed packed system

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.

- VASP_poview
- rasmol_colors
- pos2pdb.py (to use this script change the extension from .txt to .py)

**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

- VASP
^{[2]}^{[3]}^{[4]}^{[5]}is a pay-package to use and can be bought from http://cms.mpi.univie.ac.at/vasp/ - SIESTA
^{[6]}^{[7]}is an open source package to perform*ab initio*calculation and can be downloaded from http://www.icmab.es/siesta/ - Abinit
^{[8]}^{[9]}^{[10]}- 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. - Exciting - is a full-potential all-electron density-functional-theory package implementing the families of linearized augmented planewave methods. It can be applied to all kinds of materials, irrespective of the atomic species involved, and also allows for exploring the physics of core electrons.
- Jacapo
- DFTB - The Density Functional based Tight binding method is based on a second-order expansion of the Kohn-Sham total energy in Density-Functional Theory (DFT) with respect to charge density fluctuations.
- Turbomole -
- FHI-aims - is an accurate all-electron, full-potential electronic structure code package for computational materials science.
- Fleur - a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, based on density-functional theory. The FLAPW-Method (Full Potential Linearized Augmented Plane Wave Method) is an all-electron method which within density functional theory is universally applicable to all atoms of the periodic table and to systems with compact as well as open structures

# DFT Research

## Biomaterials

- ICME overview for Paddlefish Rostrum
- ICME Overview of Mechanical Properties of the Lipid Bilayer during Traumatic Brain Injury
- ICME Overview for Alligator Gar Fish Scale
- Multiscale Model of Brain Gray Matter
- ICME Overview for Bio-Inspired Energy Dissipation System

## Ceramics

- ICME overview of shear thickening fluids in body armor
- ICME Overview of Tetragonal Zirconia Polycrystals (TZP)
- ICME overview of shape memory effect on Bismuth Ferrite ceramic

## Geomaterial

## Metals

### Aluminum

- Structure of AlSb(001) and GaSb(001) surfaces under extreme Sb-rich conditions
^{[11]} - Modified embedded-atom method interatomic potentials for the Mg-Al alloy system
^{[12]} - ICME Analysis for Al 2219-T87 in Friction Stir Welding
- A Multi-Length Scale Approach to Capturing the Effects of Shear Deformation for a Ductile Crystalline Material

### Antimony

### Copper

- ICME analysis of modeling copper during penetration
- Multiscale modeling of armor fragmentation due to the impact of an explosively formed projectile
- Multi-Scale Modeling of Copper Electrochemical Catalyst

### Iron

- The effect of Fe atoms on the absorption of a W atom on W(100) surface
^{[14]} - Modeling a projectile penetrating a steel plate
- Multiscale Modeling of Pressure Vessel Failure
- Multiscale Modeling of a Magnetostrictive Sound Detector
- ICME approach to develop 3rd Generation of Advanced High Strength Steel

### Magnesium

- Modified embedded-atom method interatomic potentials for the Mg-Al alloy system
^{[15]} - ICME Overview for Wrought Magnesium Alloys
- ICME Overview of the Chemo-mechanical Effects on Magnesium Alloys
- First principles calculations of doped MnBi compounds

### Nickel

- The location of atomic hydrogen in NiTi alloy: A first principles study
^{[16]} - ICME overview of Turbine Blade Cracking
- Multiscale Modeling of a Magnetostrictive Sound Detector

### Titanium

- The location of atomic hydrogen in NiTi alloy: A first principles study
^{[17]} - Coherent Multiscale Hierarchical Modeling Scheme (CMHM) for Hierarchically Structured Titanium-Boron Based Armor System

### Tungsten

### Palladium

## Polymers

- ICME Overview for Polycarbonate
- ICME overview of Polymeric Composite Overwrap Pressure Vessel (COPV)
- Multiscale Modeling of the Fracture Behavior in Semicrystaline Polymers
- ICME overview of shear thickening fluids in body armor
- ICME Overview of Polymer Solar Cell Active Layer

## Python Based Testing of Atomistic Potentials

# References

- ↑ 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
- ↑ G. Kresse and J. Hafner, "Ab initio molecular dynamics for liquid metals" Phys. Rev. B, 47:558, 1993
- ↑ 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
- ↑ 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
- ↑ 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.
- ↑ 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)
- ↑ 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)
- ↑ X. Gonze, B. Amadon, P.M. Anglade, J.-M. Beuken, F. Bottin, P. Boulanger, F. Bruneval, D. Caliste, R. Caracas, M. Cote, T. Deutsch, L. Genovese, Ph. Ghosez, M. Giantomassi, S. Goedecker, D. Hamann, P. Hermet, F. Jollet, G. Jomard, S. Leroux, M. Mancini, S. Mazevet, M.J.T. Oliveira, G. Onida, Y. Pouillon, T. Rangel, G.-M. Rignanese, D. Sangalli, R. Shaltaf, M. Torrent, M.J. Verstraete, G. Zérah, J.W. Zwanziger. Computer Physics Communications 180, 2582-2615 (2009). "ABINIT : first-principles approach to material and nanosystem properties"
- ↑ X. Gonze, G.-M. Rignanese, M. Verstraete, J.-M. Beuken, Y. Pouillon, R. Caracas, F. Jollet, M. Torrent, G. Zerah, M. Mikami, Ph. Ghosez, M. Veithen, J.-Y. Raty, V. Olevano, F. Bruneval, L. Reining, R. Godby, G. Onida, D.R. Hamann, and D.C. Allan. Zeit. Kristallogr. 220, 558-562 (2005). "A brief introduction to the ABINIT software package."
- ↑ X. Gonze, J.-M. Beuken, R. Caracas, F. Detraux, M. Fuchs, G.-M. Rignanese, L. Sindic, M. Verstraete, G. Zerah, F. Jollet, M. Torrent, A. Roy, M. Mikami, Ph. Ghosez, J.-Y. Raty, D.C. Allan. Computational Materials Science 25, 478-492 (2002). "First-principles computation of material properties : the ABINIT software project."
- ↑ 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)
- ↑ 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)
- ↑ 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)
- ↑ 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)
- ↑ 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)
- ↑ 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
- ↑ 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
- ↑ 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)
- ↑ Sungho Kim, Seong-Gon Kim and S. C. Erwin, "Structure of the hydrogen double vacancy on Pd(111)" Phys. Rev. B 76, 214109 (2007)

## Pages in category "Electronic Scale"

The following 47 pages are in this category, out of 47 total.