| 修訂 | ab7f90a5debcd862c7a5f4e232d3361d7dfdfce1 (tree) |
|---|---|
| 時間 | 2018-12-29 17:54:24 |
| 作者 |  mitsuaki1987 <kawamitsuaki@gmai...> |
| Commiter | mitsuaki1987 |
Report samle
sample/report/.gitignore (diff)
sample/report/band.pdf (diff) sample/report/pdos.pdf (diff) sample/report/report.bib (diff)
sample/report/report.tex (diff)
sample/report/tmp.pp_K001_B002.png (diff)
sample/report/tmp.pp_K001_B003.png (diff) sample/report/tmp.pp_K001_B004.pdf (diff)
sample/report/tmp.pp_K001_B004.png (diff)
sample/report/vfermi.png (diff)
tool/cif2qe.py (diff)
tool/pdos.sh (diff)| @@ -0,0 +1,5 @@ | ||
| 1 | +report.aux | |
| 2 | +report.bbl | |
| 3 | +report.blg | |
| 4 | +report.log | |
| 5 | +report.pdf |
| @@ -0,0 +1,222 @@ | ||
| 1 | +% | |
| 2 | +% Quantum ESPRESSO | |
| 3 | +% | |
| 4 | +@article{0953-8984-29-46-465901, | |
| 5 | + author={P Giannozzi and O Andreussi and T Brumme and O Bunau and M Buongiorno Nardelli and M Calandra and R Car and C Cavazzoni and D | |
| 6 | +Ceresoli and M Cococcioni and N Colonna and I Carnimeo and A Dal Corso and S de Gironcoli and P Delugas and R A DiStasio Jr and A | |
| 7 | +Ferretti and A Floris and G Fratesi and G Fugallo and R Gebauer and U Gerstmann and F Giustino and T Gorni and J Jia and M Kawamura and H-Y | |
| 8 | +Ko and A Kokalj and E K\"u\c{c}\"ukbenli and M Lazzeri and M Marsili and N Marzari and F Mauri and N L Nguyen and H-V Nguyen and A | |
| 9 | +Otero-de-la-Roza and L Paulatto and S Ponc\'e and D Rocca and R Sabatini and B Santra and M Schlipf and A P Seitsonen and A Smogunov and I | |
| 10 | +Timrov and T Thonhauser and P Umari and N Vast and X Wu and S Baroni}, | |
| 11 | + title={Advanced capabilities for materials modelling with Q uantum ESPRESSO}, | |
| 12 | + journal={Journal of Physics: Condensed Matter}, | |
| 13 | + volume={29}, | |
| 14 | + number={46}, | |
| 15 | + pages={465901}, | |
| 16 | + url={http://stacks.iop.org/0953-8984/29/i=46/a=465901}, | |
| 17 | + year={2017}, | |
| 18 | +} | |
| 19 | +% | |
| 20 | +% VESTA | |
| 21 | +% | |
| 22 | +@article{Momma:db5098, | |
| 23 | +author = "Momma, Koichi and Izumi, Fujio", | |
| 24 | +title = "{{\it VESTA3} for three-dimensional visualization of crystal, volumetric and morphology data}", | |
| 25 | +journal = "Journal of Applied Crystallography", | |
| 26 | +year = "2011", | |
| 27 | +volume = "44", | |
| 28 | +number = "6", | |
| 29 | +pages = "1272--1276", | |
| 30 | +month = "Dec", | |
| 31 | +doi = {10.1107/S0021889811038970}, | |
| 32 | +url = {https://doi.org/10.1107/S0021889811038970}, | |
| 33 | +keywords = {VESTA 3, data visualization, electronic state calculations, Voronoi tessellation, computer programs}, | |
| 34 | +} | |
| 35 | +% | |
| 36 | +% FermiSurfer | |
| 37 | +% | |
| 38 | +@article{fermisurfer, | |
| 39 | + title={FermiSurfer: Expressive Fermi-surface viewer}, | |
| 40 | + author={Kawamura, Mitsuaki}, | |
| 41 | + journal={arXiv preprint arXiv:1811.06177}, | |
| 42 | + year={2018} | |
| 43 | +} | |
| 44 | +% | |
| 45 | +% GGA-PBE functional | |
| 46 | +% | |
| 47 | +@article{PhysRevLett.78.1396, | |
| 48 | + volume = {78}, | |
| 49 | + journal = {Phys. Rev. Lett.}, | |
| 50 | + author = {Perdew, John P. and Burke, Kieron and Ernzerhof, Matthias}, | |
| 51 | + title = {Generalized Gradient Approximation Made Simple [Phys. Rev. Lett. 77, 3865 (1996)]}, | |
| 52 | + year = {1997}, | |
| 53 | + url = {http://link.aps.org/doi/10.1103/PhysRevLett.78.1396}, | |
| 54 | + doi = {10.1103/PhysRevLett.78.1396}, | |
| 55 | + issue = {7}, | |
| 56 | + publisher = {American Physical Society}, | |
| 57 | + pages = {1396} | |
| 58 | +} | |
| 59 | +% | |
| 60 | +% Norm conserving, multiple projectors pseudopotentials (used in SG15) | |
| 61 | +% | |
| 62 | +@article{PhysRevB.88.085117, | |
| 63 | + title = {Optimized norm-conserving Vanderbilt pseudopotentials}, | |
| 64 | + author = {Hamann, D. R.}, | |
| 65 | + journal = {Phys. Rev. B}, | |
| 66 | + volume = {88}, | |
| 67 | + issue = {8}, | |
| 68 | + pages = {085117}, | |
| 69 | + numpages = {10}, | |
| 70 | + year = {2013}, | |
| 71 | + month = {Aug}, | |
| 72 | + publisher = {American Physical Society}, | |
| 73 | + doi = {10.1103/PhysRevB.88.085117}, | |
| 74 | + url = {https://link.aps.org/doi/10.1103/PhysRevB.88.085117} | |
| 75 | +} | |
| 76 | +% | |
| 77 | +% Ultrasoft pseudopotential | |
| 78 | +% | |
| 79 | +@article{PhysRevB.41.7892, | |
| 80 | + title = {Soft self-consistent pseudopotentials in a generalized eigenvalue formalism}, | |
| 81 | + author = {Vanderbilt, David}, | |
| 82 | + journal = {Phys. Rev. B}, | |
| 83 | + volume = {41}, | |
| 84 | + issue = {11}, | |
| 85 | + url = {http://link.aps.org/doi/10.1103/PhysRevB.41.7892}, | |
| 86 | + pages = {7892}, | |
| 87 | + year = {1990}, | |
| 88 | + doi = {10.1103/PhysRevB.41.7892}, | |
| 89 | + publisher = {American Physical Society} | |
| 90 | +} | |
| 91 | +% | |
| 92 | +% Projector augmented wave | |
| 93 | +% | |
| 94 | +@article{PhysRevB.50.17953, | |
| 95 | + title = {Projector augmented-wave method}, | |
| 96 | + author = {Bl\"ochl, P. E.}, | |
| 97 | + journal = {Phys. Rev. B}, | |
| 98 | + volume = {50}, | |
| 99 | + issue = {24}, | |
| 100 | + pages = {17953--17979}, | |
| 101 | + numpages = {0}, | |
| 102 | + year = {1994}, | |
| 103 | + month = {Dec}, | |
| 104 | + publisher = {American Physical Society}, | |
| 105 | + doi = {10.1103/PhysRevB.50.17953}, | |
| 106 | + url = {https://link.aps.org/doi/10.1103/PhysRevB.50.17953} | |
| 107 | +} | |
| 108 | +% | |
| 109 | +% Optimized tetrahedron method | |
| 110 | +% | |
| 111 | +@article{PhysRevB.89.094515, | |
| 112 | + title = {Improved tetrahedron method for the Brillouin-zone integration applicable to response functions}, | |
| 113 | + author = {Kawamura, Mitsuaki and Gohda, Yoshihiro and Tsuneyuki, Shinji}, | |
| 114 | + journal = {Phys. Rev. B}, | |
| 115 | + volume = {89}, | |
| 116 | + issue = {9}, | |
| 117 | + pages = {094515}, | |
| 118 | + numpages = {8}, | |
| 119 | + year = {2014}, | |
| 120 | + month = {Mar}, | |
| 121 | + publisher = {American Physical Society}, | |
| 122 | + doi = {10.1103/PhysRevB.89.094515}, | |
| 123 | + url = {https://link.aps.org/doi/10.1103/PhysRevB.89.094515} | |
| 124 | +} | |
| 125 | +% | |
| 126 | +% Standard Solid State Pseudopotentials (SSSP) | |
| 127 | +% | |
| 128 | +@Article{Prandini2018, | |
| 129 | +author={Prandini, Gianluca | |
| 130 | +and Marrazzo, Antimo | |
| 131 | +and Castelli, Ivano E. | |
| 132 | +and Mounet, Nicolas | |
| 133 | +and Marzari, Nicola}, | |
| 134 | +title={Precision and efficiency in solid-state pseudopotential calculations}, | |
| 135 | +journal={npj Computational Materials}, | |
| 136 | +year={2018}, | |
| 137 | +volume={4}, | |
| 138 | +number={1}, | |
| 139 | +pages={72}, | |
| 140 | +issn={2057-3960}, | |
| 141 | +doi={10.1038/s41524-018-0127-2}, | |
| 142 | +url={https://doi.org/10.1038/s41524-018-0127-2} | |
| 143 | +} | |
| 144 | +% | |
| 145 | +% Optimized norm-conserving pseudopotentials (SG15 library) | |
| 146 | +% | |
| 147 | +@article{SCHLIPF201536, | |
| 148 | +title = "Optimization algorithm for the generation of ONCV pseudopotentials", | |
| 149 | +journal = "Computer Physics Communications", | |
| 150 | +volume = "196", | |
| 151 | +pages = "36 - 44", | |
| 152 | +year = "2015", | |
| 153 | +issn = "0010-4655", | |
| 154 | +doi = "https://doi.org/10.1016/j.cpc.2015.05.011", | |
| 155 | +url = "http://www.sciencedirect.com/science/article/pii/S0010465515001897", | |
| 156 | +author = "Martin Schlipf and Fran\c{c}ois Gygi", | |
| 157 | +} | |
| 158 | +% | |
| 159 | +% Garrity-Bennett-Rabe-Vanderbilt (GBRV) Pseudopotential Library | |
| 160 | +% | |
| 161 | +@article{GARRITY2014446, | |
| 162 | +title = "Pseudopotentials for high-throughput DFT calculations", | |
| 163 | +journal = "Computational Materials Science", | |
| 164 | +volume = "81", | |
| 165 | +pages = "446 - 452", | |
| 166 | +year = "2014", | |
| 167 | +issn = "0927-0256", | |
| 168 | +doi = "https://doi.org/10.1016/j.commatsci.2013.08.053", | |
| 169 | +url = "http://www.sciencedirect.com/science/article/pii/S0927025613005077", | |
| 170 | +author = "Kevin F. Garrity and Joseph W. Bennett and Karin M. Rabe and David Vanderbilt", | |
| 171 | +} | |
| 172 | +% | |
| 173 | +% PS Library v 0.3.1 | |
| 174 | +% | |
| 175 | +@article{kucukbenli2014projector, | |
| 176 | + title={Projector augmented-wave and all-electron calculations across the periodic table: a comparison of structural and energetic properties}, | |
| 177 | + author={Kucukbenli, E and Monni, M and Adetunji, BI and Ge, X and Adebayo, GA and Marzari, N and De Gironcoli, S and Corso, A Dal}, | |
| 178 | + journal={arXiv preprint arXiv:1404.3015}, | |
| 179 | + year={2014} | |
| 180 | +} | |
| 181 | +% | |
| 182 | +% PS Library v 1.0.0 | |
| 183 | +% | |
| 184 | +@article{DALCORSO2014337, | |
| 185 | +title = "Pseudopotentials periodic table: From H to Pu", | |
| 186 | +journal = "Computational Materials Science", | |
| 187 | +volume = "95", | |
| 188 | +pages = "337 - 350", | |
| 189 | +year = "2014", | |
| 190 | +issn = "0927-0256", | |
| 191 | +doi = "https://doi.org/10.1016/j.commatsci.2014.07.043", | |
| 192 | +url = "http://www.sciencedirect.com/science/article/pii/S0927025614005187", | |
| 193 | +author = "Andrea Dal Corso", | |
| 194 | +} | |
| 195 | +% | |
| 196 | +% Pseudo Dojo | |
| 197 | +% | |
| 198 | +@article{VANSETTEN201839, | |
| 199 | +title = "The PseudoDojo: Training and grading a 85 element optimized norm-conserving pseudopotential table", | |
| 200 | +journal = "Computer Physics Communications", | |
| 201 | +volume = "226", | |
| 202 | +pages = "39 - 54", | |
| 203 | +year = "2018", | |
| 204 | +issn = "0010-4655", | |
| 205 | +doi = "https://doi.org/10.1016/j.cpc.2018.01.012", | |
| 206 | +url = "http://www.sciencedirect.com/science/article/pii/S0010465518300250", | |
| 207 | +author = "M.J. van Setten and M. Giantomassi and E. Bousquet and M.J. Verstraete and D.R. Hamann and X. Gonze and G.-M. Rignanese", | |
| 208 | +} | |
| 209 | +% | |
| 210 | +% Wentzcovitch Rare-Earce pseudopotential library | |
| 211 | +% | |
| 212 | +@article{TOPSAKAL2014263, | |
| 213 | +title = "Accurate projected augmented wave (PAW) datasets for rare-earth elements (RE=La--Lu)", | |
| 214 | +journal = "Computational Materials Science", | |
| 215 | +volume = "95", | |
| 216 | +pages = "263 - 270", | |
| 217 | +year = "2014", | |
| 218 | +issn = "0927-0256", | |
| 219 | +doi = "https://doi.org/10.1016/j.commatsci.2014.07.030", | |
| 220 | +url = "http://www.sciencedirect.com/science/article/pii/S0927025614005059", | |
| 221 | +author = "M. Topsakal and R.M. Wentzcovitch", | |
| 222 | +} | |
| \ No newline at end of file |
| @@ -0,0 +1,81 @@ | ||
| 1 | +\documentclass[twocolumn,11pt]{article} | |
| 2 | +\usepackage[pdftex]{graphicx} | |
| 3 | +\usepackage{amsmath} | |
| 4 | +\begin{document} | |
| 5 | +\title{Electronic structure of MgB$_2$} | |
| 6 | +\author{Mitsuaki Kawamura} | |
| 7 | +\maketitle | |
| 8 | + | |
| 9 | + | |
| 10 | +\section{Numerical condition} | |
| 11 | + | |
| 12 | +The first-principles calculation based on density functional theory are performed | |
| 13 | +by using the Quantum ESPRESSO program package \cite{0953-8984-29-46-465901}, | |
| 14 | +which employs plane waves and psudopotentials to describe the Kohn--Sham orbitals and the crystalline potential, respectively. | |
| 15 | +The plane-wave cutoff for a wave function is set to 35 Ry. | |
| 16 | +We employ the GGA-PBE functional \cite{PhysRevLett.78.1396}. | |
| 17 | +The ultrasoft pseudopotential \cite{PhysRevB.41.7892} \footnote{b\_pbe\_v1.4.uspp.F.UPF} | |
| 18 | +and the dataset of projector-augmented wave \cite{PhysRevB.50.17953} \footnote{Mg.pbe-n-kjpaw\_psl.0.3.0.UPF} | |
| 19 | +used in this study are obtained in Standard Solid State Pseudopotentials \cite{Prandini2018}. | |
| 20 | +They are originary included in the New Soft-Accurate NLCC pseudopotential library \cite{GARRITY2014446} | |
| 21 | +and Pslibrary 0.3.1 \cite{kucukbenli2014projector}. | |
| 22 | +We set the ${\boldsymbol k}$-point grids of Brillouin-zone integrations with the optimized tetrahedron method \cite{PhysRevB.89.094515} | |
| 23 | +for the charge density and the partial density of states to 12$\times$12$\times$9 and 24$\times$24$\times$18, respectively. | |
| 24 | + | |
| 25 | +\section{Result} | |
| 26 | + | |
| 27 | +\begin{figure}[!tb] | |
| 28 | + \begin{center} | |
| 29 | + \includegraphics[width=8cm]{band.pdf} | |
| 30 | + \caption{\label{fig_band} | |
| 31 | + Band structure of MgB$_2$. | |
| 32 | + } | |
| 33 | + \end{center} | |
| 34 | +\end{figure} | |
| 35 | +% | |
| 36 | +Figure \ref{fig_band} shows the band structure of MgB$_2$. | |
| 37 | +% | |
| 38 | +\begin{figure}[!tb] | |
| 39 | + \begin{center} | |
| 40 | + \includegraphics[width=5cm]{vfermi.png} | |
| 41 | + \caption{\label{fig_fs} | |
| 42 | + The fermi surface of MgB$_2$. | |
| 43 | + Color scale indicates the absolute value of the Fermi velocity | |
| 44 | + (red and blue mean the maximum and minimum of that velocity). | |
| 45 | + We use FermiSurfer \cite{fermisurfer} | |
| 46 | + } | |
| 47 | + \end{center} | |
| 48 | +\end{figure} | |
| 49 | +% | |
| 50 | +This material has cylindirical Fermi surfaces at the center of the Brillouin zone and | |
| 51 | +three dimensional Fermi surfaces at the edge of the Brillouin zone (See Fig. \ref{fig_fs}) | |
| 52 | +% | |
| 53 | +\begin{figure}[!tb] | |
| 54 | + \begin{center} | |
| 55 | + \includegraphics[width=8cm]{pdos.pdf} | |
| 56 | + \caption{\label{fig_pdos} | |
| 57 | + Partial density of states of MgB$_2$. | |
| 58 | + Mgenta, green, blue lines indicate | |
| 59 | + the total, Mg-, and B-projected density of states, respectively. | |
| 60 | + } | |
| 61 | + \end{center} | |
| 62 | +\end{figure} | |
| 63 | +% | |
| 64 | +Partial density of states is shown in Fig. \ref{fig_pdos} | |
| 65 | +% | |
| 66 | +\begin{figure}[!tb] | |
| 67 | + \begin{center} | |
| 68 | + \includegraphics[width=2.7cm]{{tmp.pp_K001_B002}.png}\includegraphics[width=2.7cm]{{tmp.pp_K001_B003}.png}\includegraphics[width=2.7cm]{{tmp.pp_K001_B004}.png} | |
| 69 | + \caption{\label{fig_orb} | |
| 70 | + The Kohn--Sham orbitals of (left) second, (center) third, | |
| 71 | + and (right) forth band at $\Gamma$ points, respectively. | |
| 72 | + We use VESTA \cite{Momma:db5098} for displaying this figure. | |
| 73 | + } | |
| 74 | + \end{center} | |
| 75 | +\end{figure} | |
| 76 | +% | |
| 77 | +Figure \ref{fig_orb} shows the Kohn--Sham orbitals at $\Gamma$ point. | |
| 78 | + | |
| 79 | +\bibliographystyle{unsrt} | |
| 80 | +\bibliography{report} | |
| 81 | +\end{document} |
| @@ -141,13 +141,12 @@ if __name__ == '__main__': | ||
| 141 | 141 | # |
| 142 | 142 | # nscf.in : Dense k grid |
| 143 | 143 | # |
| 144 | - with open("nscf.in", 'w') as f: | |
| 144 | + with open("dense.in", 'w') as f: | |
| 145 | 145 | print("&CONTROL", file=f) |
| 146 | 146 | print(" calculation = \'nscf\'", file=f) |
| 147 | 147 | write_middle(f, nat, ntyp, ecutwfc, ecutrho, psdir) |
| 148 | 148 | print(" occupations = \'tetrahedra_opt\'", file=f) |
| 149 | 149 | print(" nbnd = %d" % nbnd, file=f) |
| 150 | - print(" la2f = .true.", file=f) | |
| 151 | 150 | print("/", file=f) |
| 152 | 151 | print("&ELECTRONS", file=f) |
| 153 | 152 | print("/", file=f) |
| @@ -155,9 +154,9 @@ if __name__ == '__main__': | ||
| 155 | 154 | print("K_POINTS automatic", file=f) |
| 156 | 155 | print(" %d %d %d 0 0 0" % (nk[0]*2, nk[1]*2, nk[2]*2), file=f) |
| 157 | 156 | # |
| 158 | - # band.in : Plot band | |
| 157 | + # nonscf.in : Plot band | |
| 159 | 158 | # |
| 160 | - with open("band.in", 'w') as f: | |
| 159 | + with open("nonscf.in", 'w') as f: | |
| 161 | 160 | print("&CONTROL", file=f) |
| 162 | 161 | print(" calculation = \'bands\'", file=f) |
| 163 | 162 | write_middle(f, nat, ntyp, ecutwfc, ecutrho, psdir) |
| @@ -184,7 +183,7 @@ if __name__ == '__main__': | ||
| 184 | 183 | # |
| 185 | 184 | # proj.in : Read by projwfc.x |
| 186 | 185 | # |
| 187 | - with open("proj.in", 'w') as f: | |
| 186 | + with open("pdos.in", 'w') as f: | |
| 188 | 187 | print("&PROJWFC", file=f) |
| 189 | 188 | print(" emin = ", file=f) |
| 190 | 189 | print(" emax = ", file=f) |
| @@ -0,0 +1,25 @@ | ||
| 1 | +#!/bin/bash | |
| 2 | + | |
| 3 | +cat > pdos.gp <<EOF | |
| 4 | +set terminal pdf color enhanced \ | |
| 5 | +dashed dl 0.5 size 8.0cm, 6.0cm | |
| 6 | +set output "pdos.pdf" | |
| 7 | + | |
| 8 | +set border lw 2 | |
| 9 | + | |
| 10 | +set ytics scale 3.0, -0.5 font 'Cmr10,18' | |
| 11 | +set xtics scale 3.0, -0.5 font 'Cmr10,18' | |
| 12 | + | |
| 13 | +set yzeroaxis | |
| 14 | + | |
| 15 | +set ylabel "Partial DOS [eV^{-1}]" offset 0.0, 0.0 font 'Cmr10,18' | |
| 16 | +set xlabel "Energy from {/Cmmi10 \042}_F [eV]" offset 0.0, 0.0 font 'Cmr10,18' | |
| 17 | +set key left top font 'Cmr10,18 | |
| 18 | +plot [][0:] \\ | |
| 19 | +EOF | |
| 20 | + | |
| 21 | +for i in ${@: 2:$#-2} | |
| 22 | +do | |
| 23 | + echo "\"$i\" u (\$1-$1):2 w l tit \"$i\", \\" >> pdos.gp | |
| 24 | +done | |
| 25 | +echo "\"${@: $#}\" u (\$1-$1):2 w l tit \"${@: $#}\"" >> pdos.gp |
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