diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/.gitignore b/2022_05_Trieste/Fri.AM.2.BoltzWann/.gitignore new file mode 100644 index 0000000..2247701 --- /dev/null +++ b/2022_05_Trieste/Fri.AM.2.BoltzWann/.gitignore @@ -0,0 +1,18 @@ +out/ +scf.out +nscf.out +Si.nnkp +Si.wout +pw2wan.out +Si.amn +Si.chk +Si.eig +Si.mmn +Si.wpout +Si_boltzdos.dat +Si_elcond.dat +Si_kappa.dat +Si_seebeck.dat +Si_sigmas.dat +Si_tdf.dat +Si_seebeck_xx_500K.dat diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.nscf b/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.nscf new file mode 100644 index 0000000..f67d113 --- /dev/null +++ b/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.nscf @@ -0,0 +1,93 @@ +Silicon + &control + calculation = 'nscf' + prefix = 'si' + pseudo_dir = '/media/ictpuser/AiiDA/codes/wannier90/pseudo/' + outdir = 'out/' + iprint = 2 + verbosity = 'high' +/ + &system + ibrav = 2 + celldm(1) = 10.2 + nat = 2 + ntyp = 1 + ecutwfc = 25.0 + nbnd = 12 +/ + &electrons + conv_thr = 1.0d-12 + diagonalization = 'cg' + diago_full_acc = .true. +/ +ATOMIC_SPECIES + Si 28 Si.pbe-n-van.UPF +ATOMIC_POSITIONS {crystal} +Si -0.25 0.75 -0.25 +Si 0.00 0.00 0.00 +K_POINTS {crystal} +64 + 0.00000000 0.00000000 0.00000000 1.562500e-02 + 0.00000000 0.00000000 0.25000000 1.562500e-02 + 0.00000000 0.00000000 0.50000000 1.562500e-02 + 0.00000000 0.00000000 0.75000000 1.562500e-02 + 0.00000000 0.25000000 0.00000000 1.562500e-02 + 0.00000000 0.25000000 0.25000000 1.562500e-02 + 0.00000000 0.25000000 0.50000000 1.562500e-02 + 0.00000000 0.25000000 0.75000000 1.562500e-02 + 0.00000000 0.50000000 0.00000000 1.562500e-02 + 0.00000000 0.50000000 0.25000000 1.562500e-02 + 0.00000000 0.50000000 0.50000000 1.562500e-02 + 0.00000000 0.50000000 0.75000000 1.562500e-02 + 0.00000000 0.75000000 0.00000000 1.562500e-02 + 0.00000000 0.75000000 0.25000000 1.562500e-02 + 0.00000000 0.75000000 0.50000000 1.562500e-02 + 0.00000000 0.75000000 0.75000000 1.562500e-02 + 0.25000000 0.00000000 0.00000000 1.562500e-02 + 0.25000000 0.00000000 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0.75000000 0.50000000 0.75000000 1.562500e-02 + 0.75000000 0.75000000 0.00000000 1.562500e-02 + 0.75000000 0.75000000 0.25000000 1.562500e-02 + 0.75000000 0.75000000 0.50000000 1.562500e-02 + 0.75000000 0.75000000 0.75000000 1.562500e-02 diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.pw2wan b/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.pw2wan new file mode 100644 index 0000000..1be8b0c --- /dev/null +++ b/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.pw2wan @@ -0,0 +1,9 @@ +&inputpp + outdir = 'out/' + prefix = 'si' + seedname = 'Si' + spin_component = 'none' + write_mmn = .true. + write_amn = .true. + write_unk = .false. +/ diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.scf b/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.scf new file mode 100644 index 0000000..0ceb161 --- /dev/null +++ b/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.scf @@ -0,0 +1,28 @@ +Silicon + &control + calculation = 'scf' + restart_mode = 'from_scratch' + prefix = 'si' + tprnfor = .true. + pseudo_dir = '/media/ictpuser/AiiDA/codes/wannier90/pseudo/' + outdir = 'out/' + iprint = 2 +/ + &system + ibrav = 2 + celldm(1) = 10.2 + nat = 2 + ntyp = 1 + ecutwfc = 25.0 +/ + &electrons + conv_thr = 1.0d-12 + diagonalization = 'cg' +/ +ATOMIC_SPECIES + Si 28 Si.pbe-n-van.UPF +ATOMIC_POSITIONS {crystal} +Si -0.25 0.75 -0.25 +Si 0.00 0.00 0.00 +K_POINTS {automatic} +10 10 10 0 0 0 diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.win b/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.win new file mode 100644 index 0000000..1a3a1a8 --- /dev/null +++ b/2022_05_Trieste/Fri.AM.2.BoltzWann/Si.win @@ -0,0 +1,125 @@ +!!! -- Begin of BoltzWann input -- !!! +boltzwann = true +boltz_calc_also_dos = true +boltz_dos_energy_step = 0.01 +smr_type = gauss +boltz_dos_adpt_smr = false +boltz_dos_smr_fixed_en_width = 0.03 +kmesh = 40 +boltz_mu_min = 5. +boltz_mu_max = 8. +boltz_mu_step = 0.01 +boltz_temp_min = 300. +boltz_temp_max = 300. +boltz_temp_step = 50 +boltz_relax_time = 10. +!! Next variable is commented because 2 is its default value +!num_elec_per_state = 2 +!!! --- End of BoltzWann input --- !!! + +#restart = plot +#bands_plot = true +#bands_plot_format = xmgr + +num_bands = 12 +num_wann = 8 +dis_win_max = 17.d0 +dis_froz_max = 6.4d0 +dis_num_iter = 120 +dis_mix_ratio = 1.d0 + +num_iter = 500 +num_print_cycles = 50 + +begin unit_cell_cart +bohr +-5.1000 0.0000 5.1000 + 0.0000 5.1000 5.1000 +-5.1000 5.1000 0.0000 +end unit_cell_cart + +begin atoms_frac +Si 0.00 0.00 0.00 +Si -0.25 0.75 -0.25 +End atoms_frac + +begin projections +Si : sp3 +end projections + +begin kpoint_path +L 0.50000 0.50000 0.5000 G 0.00000 0.00000 0.0000 +G 0.00000 0.00000 0.0000 X 0.50000 0.00000 0.5000 +X 0.50000 -0.50000 0.0000 K 0.37500 -0.37500 0.0000 +K 0.37500 -0.37500 0.0000 G 0.00000 0.00000 0.0000 +end kpoint_path + + +mp_grid = 4 4 4 + +begin kpoints + 0.00000000 0.00000000 0.00000000 + 0.00000000 0.00000000 0.25000000 + 0.00000000 0.00000000 0.50000000 + 0.00000000 0.00000000 0.75000000 + 0.00000000 0.25000000 0.00000000 + 0.00000000 0.25000000 0.25000000 + 0.00000000 0.25000000 0.50000000 + 0.00000000 0.25000000 0.75000000 + 0.00000000 0.50000000 0.00000000 + 0.00000000 0.50000000 0.25000000 + 0.00000000 0.50000000 0.50000000 + 0.00000000 0.50000000 0.75000000 + 0.00000000 0.75000000 0.00000000 + 0.00000000 0.75000000 0.25000000 + 0.00000000 0.75000000 0.50000000 + 0.00000000 0.75000000 0.75000000 + 0.25000000 0.00000000 0.00000000 + 0.25000000 0.00000000 0.25000000 + 0.25000000 0.00000000 0.50000000 + 0.25000000 0.00000000 0.75000000 + 0.25000000 0.25000000 0.00000000 + 0.25000000 0.25000000 0.25000000 + 0.25000000 0.25000000 0.50000000 + 0.25000000 0.25000000 0.75000000 + 0.25000000 0.50000000 0.00000000 + 0.25000000 0.50000000 0.25000000 + 0.25000000 0.50000000 0.50000000 + 0.25000000 0.50000000 0.75000000 + 0.25000000 0.75000000 0.00000000 + 0.25000000 0.75000000 0.25000000 + 0.25000000 0.75000000 0.50000000 + 0.25000000 0.75000000 0.75000000 + 0.50000000 0.00000000 0.00000000 + 0.50000000 0.00000000 0.25000000 + 0.50000000 0.00000000 0.50000000 + 0.50000000 0.00000000 0.75000000 + 0.50000000 0.25000000 0.00000000 + 0.50000000 0.25000000 0.25000000 + 0.50000000 0.25000000 0.50000000 + 0.50000000 0.25000000 0.75000000 + 0.50000000 0.50000000 0.00000000 + 0.50000000 0.50000000 0.25000000 + 0.50000000 0.50000000 0.50000000 + 0.50000000 0.50000000 0.75000000 + 0.50000000 0.75000000 0.00000000 + 0.50000000 0.75000000 0.25000000 + 0.50000000 0.75000000 0.50000000 + 0.50000000 0.75000000 0.75000000 + 0.75000000 0.00000000 0.00000000 + 0.75000000 0.00000000 0.25000000 + 0.75000000 0.00000000 0.50000000 + 0.75000000 0.00000000 0.75000000 + 0.75000000 0.25000000 0.00000000 + 0.75000000 0.25000000 0.25000000 + 0.75000000 0.25000000 0.50000000 + 0.75000000 0.25000000 0.75000000 + 0.75000000 0.50000000 0.00000000 + 0.75000000 0.50000000 0.25000000 + 0.75000000 0.50000000 0.50000000 + 0.75000000 0.50000000 0.75000000 + 0.75000000 0.75000000 0.00000000 + 0.75000000 0.75000000 0.25000000 + 0.75000000 0.75000000 0.50000000 + 0.75000000 0.75000000 0.75000000 +end kpoints diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/.gitignore b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/.gitignore new file mode 100644 index 0000000..d790b0e --- /dev/null +++ b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/.gitignore @@ -0,0 +1,9 @@ +.vscode +main.aux +main.bcf +main.log +main.out +main.pdf +main.run.xml +main.blg +main.bbl diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/fig/dos.pdf b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/fig/dos.pdf new file mode 100644 index 0000000..00e1d1b Binary files /dev/null and b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/fig/dos.pdf differ diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/fig/seebeck.pdf b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/fig/seebeck.pdf new file mode 100644 index 0000000..1a5438f Binary files /dev/null and b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/fig/seebeck.pdf differ diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/main.bib b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/main.bib new file mode 100644 index 0000000..211d0b1 --- /dev/null +++ b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/main.bib @@ -0,0 +1,32 @@ +@article{Pizzi2014, + author = {Pizzi, Giovanni and Volja, Dmitri and Kozinsky, Boris and Fornari, Marco and Marzari, Nicola}, + date = {2014-01}, + doi = {10.1016/j.cpc.2013.09.015}, + issn = {0010-4655}, + journaltitle = {Comput. Phys. Commun.}, + keywords = {Maximally-localized Wannier functions, Wannier90, Band interpolation, Band velocities, Thermoelectric properties}, + number = {1}, + pages = {422--429}, + shorttitle = {{BoltzWann}}, + title = {{BoltzWann}: {A} code for the evaluation of thermoelectric and electronic transport properties with a maximally-localized {Wannier} functions basis}, + url = {http://www.sciencedirect.com/science/article/pii/S0010465513003160}, + urldate = {2021-02-03}, + volume = {185} +} + +@article{Pizzi2014a, + author = {Pizzi, Giovanni and Volja, Dmitri and Kozinsky, Boris and Fornari, Marco and Marzari, Nicola}, + date = {2014-08}, + doi = {10.1016/j.cpc.2014.05.004}, + issn = {0010-4655}, + journaltitle = {Comput. Phys. Commun.}, + keywords = {Maximally-localized Wannier functions, Wannier90, Band interpolation, Band velocities, Thermoelectric properties}, + number = {8}, + pages = {2311--2312}, + shorttitle = {An updated version of {BoltzWann}}, + title = {An updated version of {BoltzWann}: {A} code for the evaluation of thermoelectric and electronic transport properties with a maximally-localized {Wannier} functions basis}, + url = {http://www.sciencedirect.com/science/article/pii/S0010465514001581}, + urldate = {2021-02-03}, + volume = {185} +} + diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/main.tex b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/main.tex new file mode 100644 index 0000000..6e76ec7 --- /dev/null +++ b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/main.tex @@ -0,0 +1,211 @@ +\documentclass[11pt,a4paper]{article} + +\usepackage[a4paper,margin=1in,footskip=0.25in]{geometry} +\usepackage{amsmath} +\usepackage{amssymb} +\usepackage{graphicx} +\usepackage{dcolumn} +\usepackage{bm} +\usepackage{cprotect} +\usepackage{spverbatim} + +\usepackage{siunitx} + +\usepackage[caption=false]{subfig} +\usepackage{printlen} +\usepackage{xspace} + +\usepackage{fancyhdr} +\pagestyle{fancy} +\fancyhf{} +\rhead{Wannier 2022 Summer School} +\lhead{Giovanni Pizzi, Junfeng Qiao} +\cfoot{\thepage} + +\usepackage{tabularx} +\usepackage{dcolumn} +\usepackage{booktabs} +\usepackage[inline]{enumitem} + +\usepackage[cache=false]{minted}% + +\usepackage{hyperref} +\usepackage[capitalize]{cleveref} + +\usepackage[backend=biber,style=phys]{biblatex} +\addbibresource{main.bib} + +\begin{document} + +\definecolor{LightGray}{gray}{0.9} +\setminted{ + bgcolor=LightGray, } + +\title{Hands-on:\\ + \textbf{Thermoelectric and electronic transport properties with Wannier90+BoltzWann}} + +\author{Giovanni Pizzi} +\author{Junfeng Qiao} + +\date{\today} +\maketitle + +\newcommand{\wan}{\texttt{Wannier90}\xspace} +\newcommand{\boltzwan}{\texttt{BoltzWann}\xspace} +\newcommand{\pwx}{\texttt{pw.x}\xspace} +\newcommand{\ptowx}{\textnormal{\texttt{pw2wannier90.x}}\xspace} +\newcommand{\wanx}{\textnormal{\texttt{wannier90.x}}\xspace} +\newcommand{\postwanx}{\textnormal{\texttt{postw90.x}}\xspace} + +\section{Outline} + +\begin{itemize} + \item Obtain MLWFs for the valence and low-lying conduction states of silicon. + \item Calculate the electrical conductivity, the Seebeck coefficient and the thermal + conductivity in the constant relaxation time approximation using the \boltzwan + module\cite{Pizzi2014,Pizzi2014a}. +\end{itemize} + +\section{Input files \& executables} +\begin{itemize} + \item{Directory: \texttt{wannier-tutorials/2022\_05\_Trieste/Fri.AM.2.BoltzWann/}} + \item{Input Files} + \begin{itemize} + \item \texttt{Si.scf}: The \pwx input file for ground state + calculation + \item \texttt{Si.nscf}: The \pwx input file to obtain Bloch + states on a uniform grid + \item \texttt{Si.pw2wan}: Input file for \ptowx + \item \texttt{Si.win}: The \wanx and \postwanx input file + \end{itemize} + \item Executables: + \begin{itemize} + \item \pwx, \ptowx, \wanx, and \postwanx + \item Available in \texttt{/media/ictpuser/AiiDA/bin/} + \end{itemize} +\end{itemize} + +\section{Steps} +We will first run the standard Wannierization of silicon, then run the +\postwanx with \boltzwan related parameters added to the input file. +\begin{enumerate} + \item Run \pwx to obtain the ground state of silicon + \begin{minted}{bash} +pw.x < Si.scf > scf.out +\end{minted} + + \item Run \pwx to obtain the Bloch states on a uniform k-point grid. + \begin{minted}{bash} +pw.x < Si.nscf > nscf.out + \end{minted} + + \item Run \wanx to generate a list of the required overlaps (written into the + \texttt{Si.nnkp} file). + \begin{minted}{bash} +wannier90.x -pp Si + \end{minted} + + \item Run \ptowx to compute the overlap between Bloch states and the projections for + the starting guess (written in the \texttt{Si.mmn} and \texttt{Si.amn} files). + \begin{minted}{bash} +pw2wannier90.x < Si.pw2wan > pw2wan.out + \end{minted} + + \item Run \wanx to compute the MLWFs. + \begin{minted}{bash} +wannier90.x Si +\end{minted} + + Inspect the output file \texttt{Si.wout} and check if the convergence was + reached both in the disentanglement and in the Wannierization steps. You may + also want to plot the Wannier functions and the interpolated band structure. + + \item Run \postwanx to calculate the transport coefficients. + \begin{minted}{bash} +# serial execution +postw90.x Si +# or parallel execution with, e.g. 4 MPI processes +mpirun -np 4 postw90.x Si +\end{minted} +\end{enumerate} + +\section{Analysis} +\begin{itemize} +\item Inspect the output file \texttt{Si.wpout}. It summarizes the main details of +the calculation (more details can be obtained by setting a larger value of the +\texttt{iprint} flag). Check if no warnings are issued. Note that if no special +flags are passed to \boltzwan, it assumes that the ab-initio calculation did +not include magnetization effects, and thus it sets to 2 the number of +electrons per state. + +\item Note also that the value of the relaxation time $\tau$ = \SI{10}{fs} in the +example is set only as a representative value; note also that only the +electrical and thermal conductivity depend on $\tau$, while the Seebeck +coefficient is independent of $\tau$. + +\item Using your favorite plotting program, plot the \texttt{Si\_boltzdos.dat} file +to inspect the DOS, e.g. with \texttt{gnuplot}, see \cref{fig:dos}. +\begin{minted}{gnuplot} +set xlabel 'E (eV)' +set ylabel 'DOS (ang^{-3})' +plot 'Si_boltzdos.dat' w l +\end{minted} +\begin{figure}[htb] + \centering + \includegraphics[width=.7\textwidth]{fig/dos.pdf} + \caption{DOS of silicon using \boltzwan module.} + \label{fig:dos} +\end{figure} + +\item Using your favorite plotting program, plot columns 1 and 3 of the +\texttt{Si\_seebeck.dat} file to inspect the $S_{xx}$ component of the Seebeck +coefficient as a function of the chemical potential $\mu$, at $T$ = +\SI{300}{K}. For example, with \texttt{gnuplot}, see \cref{fig:seebeck}. +\begin{minted}{gnuplot} +set xlabel 'E (eV)' +set ylabel 'DOS (S_{xx} (V/K))' +plot 'Si_seebeck.dat' u 1:3 w l +\end{minted} +\begin{figure}[htb] + \centering + \includegraphics[width=.7\textwidth]{fig/seebeck.pdf} + \caption{$S_{xx}$ of silicon using \boltzwan module.} + \label{fig:seebeck} +\end{figure} +\end{itemize} + +\subsection{Further ideas} + +\begin{itemize} + \item Change the interpolation to a $60\times 60\times 60$ mesh and run again + \postwanx to check if the results for the transport properties are converged. + + \item Change the \texttt{Si.win} input file so that it calculates the transport + coefficients for temperatures from \SIrange{300}{700}{K}, with steps of + \SI{200}{K}. Rerun \postwanx and verify that the increase in execution time is + neglibile (in fact, most of the time is spent to interpolate the band structure + on the $k$ mesh). + + Plot the Seebeck coefficient for the three temperatures $T$ = \SI{300}{K}, $T$ + = \SI{500}{K} and $T$ = \SI{700}{K}. To do this, you have to filter the + \texttt{Si\_seebeck.dat} to select only those lines where the second column is + equal to the required temperature. A possible script to select the $S_{xx}$ + component of the Seebeck coefficient for $T$ = \SI{500}{K} using the + \texttt{awk/gawk} command line program is the following: + \begin{minted}{bash} +awk '{if ($2 == 500) {print $1, $3;}}' < Si_seebeck.dat \ + > Si_seebeck_xx_500K.dat +\end{minted} + Then, you can plot columns 1 and 2 of the output file + \verb#Si_seebeck_xx_500K.dat#. + \item Try to calculate the Seebeck coefficient as a function of the temperature, for + a $n-$doped sample with, e.g., $n$ = \SI{1e18}{cm^{-3}}. Note that to this aim, + you need to calculate consistently the value $\mu(T)$ of the chemical potential + as a function of the temperature, so as to reproduce the given value of $n$. + Then, you have to write a small program/script to interpolate the output of + \boltzwan, that you should have run on a suitable grid of $(\mu,T)$ points. +\end{itemize} + +\printbibliography + +\end{document} diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/makefile b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/makefile new file mode 100644 index 0000000..0cffa91 --- /dev/null +++ b/2022_05_Trieste/Fri.AM.2.BoltzWann/latex/makefile @@ -0,0 +1,7 @@ +all: main.tex main.bib + lualatex -shell-escape main.tex + biber main + lualatex -shell-escape main.tex + +clean: + rm main.aux main.bcf main.log main.out main.pdf main.run.xml main.blg main.bbl diff --git a/2022_05_Trieste/Fri.AM.2.BoltzWann/tutorial.pdf b/2022_05_Trieste/Fri.AM.2.BoltzWann/tutorial.pdf new file mode 100644 index 0000000..43dfadc Binary files /dev/null and b/2022_05_Trieste/Fri.AM.2.BoltzWann/tutorial.pdf differ