Michigan Technological University Digital Commons @ Michigan Tech Dissertations, Master's Theses and Master's Dissertations, Master's Theses and Master's Reports - Open Reports 2014 DENSITY OF AMORPHOUS CARBON BY USING DENSITY FUNCTIONAL THEORY Sorayot Chinkanjanarot Michigan Technological University Follow this and additional works at: https://digitalcommons.mtu.edu/etds Part of the Mechanical Engineering Commons Copyright 2014 Sorayot Chinkanjanarot Recommended Citation Chinkanjanarot, Sorayot, "DENSITY OF AMORPHOUS CARBON BY USING DENSITY FUNCTIONAL THEORY", Master's report, Michigan Technological University, 2014. https://doi.org/10.37099/mtu.dc.etds/809 Follow this and additional works at: https://digitalcommons.mtu.edu/etds Part of the Mechanical Engineering Commons DENSITY OF AMORPHOUS CARBON BY USING DENSITY FUNCTIONAL THEORY By Sorayot Chinkanjanarot A REPORT Submitted in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE In Mechanical Engineering MICHIGAN TECHNOLOGICAL UNIVERISITY 2014 © 2014 Sorayot Chinkanjanarot This report has been approved in partial fulfillment of the requirement for the Degree of MASTER OF SCIENCE in Mechanical Engineering. Department of Mechanical Engineering – Engineering Mechanics Report Advisor: Dr. Gregory M. Odegard Committee Member: Dr. John A. Jaszczak Committee Member: Dr. Gowtham S Department Chair: Dr. William W. Predebon Table of Contents Table of Contents ........................................................................ v List of Figures ........................................................................... vii List of Tables .............................................................................. xi Acknowledgments ..................................................................... xii Abstract ................................................................................... xiii Chapter 1: Introduction .............................................................. 1 Chapter 2: Background ................................................................ 4 2.1 Introduction ............................................................................................................ 4 2.2 Reactive Force Field ...........................................................................................13 2.3 Density Functional Theory (DFT) ..................................................................14 Chapter 3: Molecular Modeling and Position Refinement ........... 16 3.1 Preparation ............................................................................................................16 3.2 Minimization and Position’s Refinement by DFT .....................................21 3.3 Visualization ..........................................................................................................32 Chapter 4: Results and Discussion ............................................ 35 4.1 Density ....................................................................................................................35 4.2 Structure analysis ...............................................................................................36 4.3 Energy analysis....................................................................................................48 Chapter 5: Conclusion ............................................................... 51 Chapter 6: References ............................................................... 54 v Appendix A ................................................................................ 56 A.1 Selection of Energy Cutoff and KPOINTS ................................................. 56 A.2 Calculation of the standard deviation ........................................................ 58 Appendix B: Computer Commands ............................................. 59 B.1 Unix Command ................................................................................................... 59 B.2 Computing Cluster ............................................................................................. 61 Appendix C: Input files of LAMMPS (ReaxFF) ............................ 62 C.1 script.coords ........................................................................................................ 62 C.2 lmp_control .......................................................................................................... 62 C.3 in.ac ........................................................................................................................ 63 vi List of Figures Figure 1 Plot of the percentage sp3 bonding and the density of amorphous carbon, reprinted from P. J Fallon et al. (1993) ......5 Figure 2 Plot of comparison between theoretical RDF and experimental RDF by J. Kakinoki et al. (1960), reprinted from Galli et al. (1990) ..............................................................................7 Figure 3 Plot of S(Q) of TBMD (solid line) compared to experiment (dash line) ..........................................................................8 Figure 4 Plot of RDF of TBMD (solid line) compared to experiment (dash line) of sample I and sample II, respectively ..................9 Figure 5 The overall procedure of this work that has three main parts: preparation, energy minimization and position refinement, and visualization...................................................................... 17 Figure 6 The first model of initial structure of amorphous carbon generated by random placement method ............................. 18 Figure 7 The first model of initial structure of amorphous carbon generated by liquid-quench method .................................... 20 Figure 8 The appearance of OVITO analyzing the first model of amorphous carbon created by the random placement method 33 Figure 9 The rendering process of OVITO analyzing the first model of amorphous carbon structure created by the random placement method ............................................................................ 34 vii Figure 10 Shown the densities of amorphous carbon structures created by the random placement method and the liquid-quench method.......................................................................... 35 Figure 11 The RDF plot of each final model of amorphous carbon created by the random placement method .................................... 36 Figure 12 Shown the bond order of the first final amorphous carbon model created by the random placement method with sp3 bonded atom red, sp2 green and sp blue ............................ 37 Figure 13 shown the bond order of the second final amorphous carbon model created by the random placement method with sp3 bonded atom red and sp2 green ........................................ 38 Figure 15 shown the bond order of the third final amorphous carbon model created by the random placement method with sp3 bonded atom red and sp2 green ........................................ 39 Figure 14 shown the bond order of the forth final amorphous carbon model created by the random placement method with sp3 bonded atom red, sp2 green and sp blue ............................ 39 Figure 16 shown the bond order of the fifth final amorphous carbon model created by the random placement method with sp3 bonded atom red, sp2 green and sp blue ............................ 40 Figure 17 shown the RDF plot of each final model of amorphous carbon created by the liquid-quench method ................................ 41 viii Figure 18 shown the bond order of the first final amorphous carbon model created by the liquid-quench method with sp3 bonded atom red and sp2 green .................................................... 42 Figure 19 shown the bond order of the second final amorphous carbon model created by the liquid-quench method with sp3 bonded atom red, sp2 green and sp blue ........................................ 42 Figure 20 shown the bond order of the third final amorphous carbon model created by the liquid-quench method with sp3 bonded atom red, sp2 green and sp blue ........................................ 43 Figure 21 shown the bond order of the forth final amorphous carbon model created by the liquid-quench method with sp3 bonded atom red, sp2 green and sp blue ........................................ 44 Figure 22 shown the bond order of the fifth final amorphous carbon model created by the liquid-quench method with sp3 bonded atom red, sp2 green and sp blue ........................................ 44 Figure 23 shown the average percentages of each bond order of the final amorphous carbon models by using OVITO ......................... 45 Figure 24 compared the average sp3 percentage of amorphous carbon created by both methods using OVITO and Equation 1 ......... 46 Figure 25 compared average RDF of amorphous carbon structure created by the random placement method and the liquid-quench method .......................................................................... 47 ix Figure 26 shown the ground-state energies of amorphous carbon structure generated by both methods changing by the ionic step .............................................................................. 48 Figure 27 shown the densities of amorphous carbon structure generated by both methods changing by the ionic step ....................... 49 Figure 28 compared the ground energies of amorphous carbon by changing energy cutoff variable ........................................ 56 x List of Tables Table 1 shown all combination of ISIF parameters ...........................................22 Table