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    Metnum Ex1

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    This document provides instructions for running atomic calculations using the Quantum ESPRESSO software distribution. It describes how to install the necessary software, run self-consistent atomic calculations, calculate atomic energies for different atoms and functionals, and plot the resulting Kohn-Sham orbitals. Key steps include compiling the atomic code, specifying input parameters like the atom type and electronic configuration in a namelist, and using gnuplot to visualize the orbital wavefunctions from the output file. Comparisons can be made to literature data on atomic energies and properties like ionization energies.

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    Metnum Ex1

    Uploaded by

    baig79
    60 views3 pages
    This document provides instructions for running atomic calculations using the Quantum ESPRESSO software distribution. It describes how to install the necessary software, run self-consistent atomic calculations, calculate atomic energies for different atoms and functionals, and plot the resulting Kohn-Sham orbitals. Key steps include compiling the atomic code, specifying input parameters like the atom type and electronic configuration in a namelist, and using gnuplot to visualize the orbital wavefunctions from the output file. Comparisons can be made to literature data on atomic energies and properties like ionization energies.

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    This document provides instructions for running atomic calculations using the Quantum ESPRESSO software distribution. It describes how to install the necessary software, run self-consistent atomic calculations, calculate atomic energies for different atoms and functionals, and plot the resulting Kohn-Sham orbitals. Key steps include compiling the atomic code, specifying input parameters like the atom type and electronic configuration in a namelist, and using gnuplot to visualize the orbital wavefunctions from the output file. Comparisons can be made to literature data on atomic energies and properties like ionization energies.

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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    60 views3 pages

    Metnum Ex1

    Uploaded by

    baig79
    This document provides instructions for running atomic calculations using the Quantum ESPRESSO software distribution. It describes how to install the necessary software, run self-consistent atomic calculations, calculate atomic energies for different atoms and functionals, and plot the resulting Kohn-Sham orbitals. Key steps include compiling the atomic code, specifying input parameters like the atom type and electronic configuration in a namelist, and using gnuplot to visualize the orbital wavefunctions from the output file. Comparisons can be made to literature data on atomic energies and properties like ionization energies.

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    Chapter 8

    Computer exercises

    8.1 Needed software


    The computer exercises described in the following sections require a Unix machine (Mac
    OS-X is fine) or, for Windows machines, the Unix-like environment cygwin. The base
    software is contained in the Quantum ESPRESSO distribution, freely downloadable from
    http://www.quantum-espresso.org. A fortran-95 compiler is needed; if you do not have
    one, or if the one you have doesnt work or compile properly, download g95. The gnuplot
    visualization program will be useful. All the software mentioned above (and below) is
    freely downloadable from the net under an open-source or similar license.

    8.2 Atoms
    Software Installation Unpack the Quantum ESPRESSO distribution. The code will
    be created into a subdirectory espresso-x.y.z/ , where x.y.z is the version number. In
    the following, the path (relative or absolute) to the directory containing the executables
    will be referred to as $espresso dir.
    Move into $espresso dir. A package for atomic calculations and for pseudo-potential
    generation can be found in subdirectory atomic/; the relative tests, examples, and doc-
    umentation are in atomic doc/. Run the commands ./configure; make ld1: if every-
    thing goes well, an executable is produced in bin/ld1.x.

    How to run the code The atomic code is quite complex and its input has a lot of
    options. Let us start from the simple case of a self-consistent calculation for atoms. The
    essential data is contained in a namelist &input:

    &input
    atom=atomic symbol,
    config=electronic configuration,
    dft=density-functional theory identifier
    /

    where config is the electronic configuration in obvious format (example: config=[Ne]


    3s2 3p2, or config=1s2 2s2 2p6 3s2 3p2); dft can be for instance PZ, for the well-

    50
    known Perdew-Zunger formula for LDA; or a gradient-corrected functional like PW91
    (Perdew-Wang), BP (Becke-Perdew). PBE (Perdew, Becke and Ernzerhof), BLYP, ...
    More details and more optional variables are described in file atomic doc/INPUT LD1.txt
    (there is also a html version of this file, readable with a browser). An example:

    &input
    atom=Si,
    config=[Ne] 3s2 3p2,
    dft=PZ
    /

    For a short description of numerical methods used in atomic calculations, see Appendix
    A of atomic doc/pseudo-gen.pdf.

    Atomic energies As a first application, you can calculate atomic energies with various
    DFT approximations for a few light atoms and compare them with results known from
    the literature, for instance: table I of the paper by Dal Corso et al. (1996), and table IV
    of Jones and Gunnarsson (1989). How much is the effect of spin polarization (lsd=1)?
    Verify also the size of relativistic effects by comparing the nonrelativistic (rel=0) to scalar-
    relativistic (rel=1) and fully relativistic (rel=2) cases (in the latter case do not specify
    lsd=1).
    You may also try to reproduce data on ionization energies and transfer energies (figs.8-
    11 of Jones and Gunnarsson) by performing calculations with different electronic configu-
    rations. What should you do in order to calculate electron affinities of atoms? why doesnt
    it work ?

    Plot of the Kohn-Sham orbitals Kohn-Sham atomic orbitals are written to a file
    with name "prefix".wfc. If variable prefix is not specified, Kohn-Sham orbitals are
    written to file ld1.wfc. This contains up to 7 columns of numbers: the first column
    contains the radial grid (in a.u.), the following up to the last 6 wavefunctions in reversed
    order with respect to input (in case of doubt, see the first line of the file). These functions
    can be plotted using any plotting package, for instance gnuplot: type gnuplot, then at
    the prompt (gnuplot >) type commands like:

    gnuplot > plot [xmin:xmax] [ymin:ymax] ld1.wfc using 1:2 with lines

    to plot a y(x) line using columns 1 and 2 of file ld1.wfc. The specification of [xmin:xmax]
    [ymin:ymax] is optional. To plot points representing columns 1 and 3 over the existing
    graph:

    gnuplot > replot ld1.wfc using 1:3 with points

    Note that you cannot specify [xmin:xmax] [ymin:ymax] with replot. Type quit to
    leave gnuplot. For a better plot, use the following script plotwfc.gnu that writes to
    printable file gnuplot.ps:

    set encoding iso_8859_15


    set terminal postscript enhanced solid color "Helvetica" 20
    set output "gnuplot.ps"

    51
    set key off
    set xrange [0:5]
    set label "Si LDA" at 4.0,2.5
    set xlabel "a.u." ; set ylabel "{/Symbol y}_{nl} (r)"
    set label "1s" at 0.2,2.2
    set label "2s" at 0.8,-1.3
    set label "2p" at 0.6,1.3
    set label "3s" at 2.0,0.9
    set label "3p" at 2.7,-0.7
    plot "ld1.wfc" u 1:2 w l lw 2
    replot "ld1.wfc" u 1:3 w l lw 2
    replot "ld1.wfc" u 1:4 w l lw 2
    replot "ld1.wfc" u 1:5 w l lw 2
    replot "ld1.wfc" u 1:6 w l lw 2

    Remove or comment the three top lines to see the plot at the terminal. The script should
    be run from inside gnuplot as

    gnuplot> load plotwfc.gnu

    Note that what is plotted is rRnl (r), that is, r times the radial part of the wavefunction
    having n as principal quantum number and l as angular momentum number. Do they look
    like you expected ?

    52

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