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pwdft: Commit

Source code and sample for Educational-PWDFT


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Revisionab7f90a5debcd862c7a5f4e232d3361d7dfdfce1 (tree)
Zeit2018-12-29 17:54:24
Autormitsuaki1987 <kawamitsuaki@gmai...>
Commitermitsuaki1987

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--- /dev/null
+++ b/sample/report/.gitignore
@@ -0,0 +1,5 @@
1+report.aux
2+report.bbl
3+report.blg
4+report.log
5+report.pdf
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--- /dev/null
+++ b/sample/report/report.bib
@@ -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
--- /dev/null
+++ b/sample/report/report.tex
@@ -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}
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--- a/tool/cif2qe.py
+++ b/tool/cif2qe.py
@@ -141,13 +141,12 @@ if __name__ == '__main__':
141141 #
142142 # nscf.in : Dense k grid
143143 #
144- with open("nscf.in", 'w') as f:
144+ with open("dense.in", 'w') as f:
145145 print("&CONTROL", file=f)
146146 print(" calculation = \'nscf\'", file=f)
147147 write_middle(f, nat, ntyp, ecutwfc, ecutrho, psdir)
148148 print(" occupations = \'tetrahedra_opt\'", file=f)
149149 print(" nbnd = %d" % nbnd, file=f)
150- print(" la2f = .true.", file=f)
151150 print("/", file=f)
152151 print("&ELECTRONS", file=f)
153152 print("/", file=f)
@@ -155,9 +154,9 @@ if __name__ == '__main__':
155154 print("K_POINTS automatic", file=f)
156155 print(" %d %d %d 0 0 0" % (nk[0]*2, nk[1]*2, nk[2]*2), file=f)
157156 #
158- # band.in : Plot band
157+ # nonscf.in : Plot band
159158 #
160- with open("band.in", 'w') as f:
159+ with open("nonscf.in", 'w') as f:
161160 print("&CONTROL", file=f)
162161 print(" calculation = \'bands\'", file=f)
163162 write_middle(f, nat, ntyp, ecutwfc, ecutrho, psdir)
@@ -184,7 +183,7 @@ if __name__ == '__main__':
184183 #
185184 # proj.in : Read by projwfc.x
186185 #
187- with open("proj.in", 'w') as f:
186+ with open("pdos.in", 'w') as f:
188187 print("&PROJWFC", file=f)
189188 print(" emin = ", file=f)
190189 print(" emax = ", file=f)
--- /dev/null
+++ b/tool/pdos.sh
@@ -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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