Category:Electronic Scale

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== Overview ==
+
= Overview =
  
 
First principles methods based on Density Functional Theory ([http://en.wikipedia.org/wiki/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.<br />
 
First principles methods based on Density Functional Theory ([http://en.wikipedia.org/wiki/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.<br />
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See also: [[First_Principles|Data and models pertaining to the ICME Phase Equilibria task]].
 
See also: [[First_Principles|Data and models pertaining to the ICME Phase Equilibria task]].
  
== Material Models ==
+
= 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, SIESTA, and Poseidon. Some pre and post processing codes, and visualization codes are necessary to work in conjunction with material models.
 +
 
 +
 
 +
= Material Models =
 
* [[Code:_VASP|VASP ]]<ref> G. Kresse and J. Hafner, "Ab initio molecular dynamics for liquid metals" Phys. Rev. B, 47:558, 1993</ref><ref> 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 </ref><ref> 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 </ref><ref> 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. </ref> is a pay-package to use and can be bought from http://cms.mpi.univie.ac.at/vasp/  
 
* [[Code:_VASP|VASP ]]<ref> G. Kresse and J. Hafner, "Ab initio molecular dynamics for liquid metals" Phys. Rev. B, 47:558, 1993</ref><ref> 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 </ref><ref> 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 </ref><ref> 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. </ref> is a pay-package to use and can be bought from http://cms.mpi.univie.ac.at/vasp/  
 
* [[Code:_SIESTA|SIESTA]]<ref>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)</ref><ref>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)</ref> is an open source package to perform ''ab initio'' calculation and can be downloaded from http://www.icmab.es/siesta/
 
* [[Code:_SIESTA|SIESTA]]<ref>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)</ref><ref>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)</ref> is an open source package to perform ''ab initio'' calculation and can be downloaded from http://www.icmab.es/siesta/
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* [[Code: Edmol|Edmol]]
 
* [[Code: Edmol|Edmol]]
  
=== Preprocessing & Postprocessing Codes ===
+
== Preprocessing & Postprocessing Codes ==
  
==== PreProcessor: Crystal Structures Generator ====
+
=== PreProcessor: Crystal Structures Generator ===
  
 
<font color="red">Note: This page is under a continuous developing stage.</font>
 
<font color="red">Note: This page is under a continuous developing stage.</font>
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<font color="green">A very basic sample program [[csg.py| csg.py]] to generate the bcc, fcc and hcp crystal structure with orthogonal basis are given .</font>
 
<font color="green">A very basic sample program [[csg.py| csg.py]] to generate the bcc, fcc and hcp crystal structure with orthogonal basis are given .</font>
  
==== Postprocessing Codes ====
+
=== Postprocessing Codes ===
===== Description =====
+
==== Description ====
 
Here is a small collection of VASP related scripts that are routinely used.
 
Here is a small collection of VASP related scripts that are routinely used.
 
* [[Cleanvaspfiles| Cleanvaspfiles:]] Remove all the output files generated by running VASP.
 
* [[Cleanvaspfiles| Cleanvaspfiles:]] Remove all the output files generated by running VASP.
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* [[Media:VASP.pos2pdb.txt‎|pos2pdb.py]]  (to use this script change the extension from .txt to .py)
 
* [[Media:VASP.pos2pdb.txt‎|pos2pdb.py]]  (to use this script change the extension from .txt to .py)
  
=====Curve Fitting=====
+
====Curve Fitting====
 
[[Evfit]] is a code used to fit Energy-Volume (E-V) curves of crystals. The FORTRAN source code is provided [[Evfit|here]] and can be compiled with standard FORTRAN compilers.
 
[[Evfit]] is a code used to fit Energy-Volume (E-V) curves of crystals. The FORTRAN source code is provided [[Evfit|here]] and can be compiled with standard FORTRAN compilers.
  
==== Visualization ====
+
=== Visualization ===
  
 
This subsection shows links to visualization packages used at the atomistic scale at CAVS.
 
This subsection shows links to visualization packages used at the atomistic scale at CAVS.
  
=====Free software=====
+
====Free software====
 
* [http://ovito.org/ OVITO ] (The Open Visualization Tool) is a scientific visualization and analysis software for atomistic simulation data.
 
* [http://ovito.org/ OVITO ] (The Open Visualization Tool) is a scientific visualization and analysis software for atomistic simulation data.
 
* [http://rasmol.org/ RasMol] is Molecular Visualization Freeware for proteins, dna and macromolecules.
 
* [http://rasmol.org/ RasMol] is Molecular Visualization Freeware for proteins, dna and macromolecules.
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* [http://www.geomview.org/ Geomview] is an interactive 3D viewing program for Unix.
 
* [http://www.geomview.org/ Geomview] is an interactive 3D viewing program for Unix.
  
=====Commercial software=====
+
====Commercial software====
 
* [http://www.ensight.com Ensight ] is a visualization tool available in HPCC.
 
* [http://www.ensight.com Ensight ] is a visualization tool available in HPCC.
  
== Aluminum Example Simulations ==
+
= Aluminum Example Simulations =
  
 
This subsection includes required atomic structures and related scripts to investigate various properties. All the simulation examples are for VASP users.
 
This subsection includes required atomic structures and related scripts to investigate various properties. All the simulation examples are for VASP users.
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* [[Al_P6-DFT | Generalized stacking fault energy curve on (111) glide plane, along [1-10] glide direction for Aluminum]]
 
* [[Al_P6-DFT | Generalized stacking fault energy curve on (111) glide plane, along [1-10] glide direction for Aluminum]]
  
== ICME course material ==
+
= ICME course material =
 
* Material related to electronic scale calculations can be found [[ICME 2012 HW1|here]]
 
* Material related to electronic scale calculations can be found [[ICME 2012 HW1|here]]
  
== DFT Research==
+
= DFT Research=
 
<font color="red"> The page is under a continuously developing stage. Please do not forget to cite our contributions wherever suit.</font>
 
<font color="red"> The page is under a continuously developing stage. Please do not forget to cite our contributions wherever suit.</font>
  
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* [[The location of atomic hydrogen in NiTi alloy: A first principles study]]<ref> Amitava Moitra, Kiran N. Solanki, and M.F. Horstemeyer, "The location of atomic hydrogen in NiTi alloy: A first principles study" Computational Materials Science
 
* [[The location of atomic hydrogen in NiTi alloy: A first principles study]]<ref> 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 </ref>
 
Volume 50, Issue 3, January 2011, Pages 820-823 </ref>
== Python Based Testing of Atomistic Potentials==  
+
= Python Based Testing of Atomistic Potentials=
 
* [[Media:Bohumir_NIST2011_ASE.pdf‎‎|The universal interface for testing atomistic potentials]]
 
* [[Media:Bohumir_NIST2011_ASE.pdf‎‎|The universal interface for testing atomistic potentials]]
  
 
* [[Media:Bohumir_CCP2011_LAMMPS_ASE.pdf|Routines for basic tests of atomistic potentials with universal interface]]
 
* [[Media:Bohumir_CCP2011_LAMMPS_ASE.pdf|Routines for basic tests of atomistic potentials with universal interface]]
  
== References==
+
= References=
 
<references/>
 
<references/>
  

Revision as of 09:43, 14 March 2016

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.

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, SIESTA, and Poseidon. Some pre and post processing codes, and visualization codes are necessary to work in conjunction with material models.


Material Models

Preprocessing & Postprocessing Codes

PreProcessor: Crystal Structures Generator

Note: This page is under a continuous developing stage.

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

Description

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.

Aluminum Example Simulations

This subsection includes required atomic structures and related scripts to investigate various properties. All the simulation examples are for VASP users.

ICME course material

  • Material related to electronic scale calculations can be found here

DFT Research

The page is under a continuously developing stage. Please do not forget to cite our contributions wherever suit.

Python Based Testing of Atomistic Potentials

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. 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)
  9. 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)
  10. 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)
  11. Sungho Kim, Seong-Gon Kim and S. C. Erwin, "Structure of the hydrogen double vacancy on Pd(111)" Phys. Rev. B 76, 214109 (2007)
  12. 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

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.

A

B

C

C cont.

E

F

G

I

M

M cont.

O

P

R

S

T

V

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