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README for PHonon/examples added from main examples dir
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These are instructions on how to run some or all of the examples
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contained within the "examples" directory of the ESPRESSO distribution
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(the one where this file should be). These examples try to exercise
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all the programs and features of the ESPRESSO package: for details,
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see the "README" file in each example's directory. If you find that
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any relevant feature isn't being tested, please contact us (or even
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better, write and send us a new example).
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To run the examples, you should follow this procedure:
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1) Go to the "examples" directory and edit the "environment_variables"
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file, setting the following variables as needed:
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BIN_DIR = directory where ESPRESSO executables reside
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PSEUDO_DIR = directory where pseudopotential files reside
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TMP_DIR = directory to be used as temporary storage area
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If you have downloaded the full ESPRESSO distribution, you may set
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BIN_DIR=$TOPDIR/bin and PSEUDO_DIR=$TOPDIR/pseudo, where $TOPDIR is
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the root of the ESPRESSO source tree.
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TMP_DIR must be a directory you have read and write access to, with
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enough available space to host the temporary files produced by the
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example runs, and possibly offering high I/O performance (i.e.,
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don't use an NFS-mounted directory).
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2) If you want to test the parallel version of ESPRESSO, you will
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usually have to specify a driver program (such as "poe" or "mpirun")
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and the number of processors. This can be done by editing PARA_PREFIX
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and PARA_POSTFIX variables (in the "environment_variables" file).
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Parallel executables will be run by a command like this:
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$PARA_PREFIX pw.x $PARA_POSTFIX < file.in > file.out
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For example, if the command line is like this (as for an IBM SP):
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poe pw.x -procs 4 < file.in > file.out
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you should set PARA_PREFIX="poe", PARA_POSTFIX="-procs 4".
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See section "Running on parallel machines" of the user guide for details.
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Furthermore, if your machine does not support interactive use, you
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must run the commands specified below through the batch queueing
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system installed on that machine. Ask your system administrator
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for instructions.
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3) To run a single example, go to the corresponding directory (for
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instance, "example/example01") and execute:
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./run_example
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(except for example 21, see below)
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This will create a subdirectory "results", containing the input and
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output files generated by the calculation.
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Some examples take only a few seconds to run, while others may
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require several minutes depending on your system.
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To run all the examples in one go, execute:
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./run_all_examples
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from the "examples" directory. On a single-processor machine, this
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typically takes one to three hours.
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The "make_clean" script cleans the examples tree, by removing all
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the "results" subdirectories. However, if additional
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subdirectories have been created, they aren't deleted.
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4) In each example's directory, the "reference" subdirectory contains
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verified output files, that you can check your results against.
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The reference results were generated on a Linux PC with Intel compiler.
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On different architectures the precise numbers could be slightly
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different, in particular if different FFT dimensions are
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automatically selected. For this reason, a plain "diff" of your
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results against the reference data doesn't work, or at least, it
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requires human inspection of the results.
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-----------------------------------------------------------------------
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LIST AND CONTENT OF THE EXAMPLES
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example01:
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This example shows how to use pw.x to calculate the total energy
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and the band structure of four simple systems: Si, Al, Cu, Ni.
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example02:
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This example shows how to use pw.x and ph.x to calculate phonon
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frequencies at Gamma and X for Si and C in the diamond structure and
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for fcc-Ni.
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example03:
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This example shows how to use pw.x to compute the equilibrium
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geometry of a simple molecule, CO, and of an Al (001) slab.
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In the latter case the relaxation is performed in two ways:
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1) using the quasi-Newton BFGS algorithm
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2) using a damped dynamics algorithm.
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example04:
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This example shows how to use pw.x to perform molecular dynamics
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for 2- and 8-atom cells of Si starting with compressed bonds along
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(111).
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example05:
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This example shows how to use pw.x and postprocessing codes to
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make a contour plot in the [110] plane of the charge density for
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Si, and to plot the band structure of Si.
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example06:
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This example shows how to calculate interatomic force constants in
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real space for AlAs in zincblende structure.
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example07:
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This example shows how to calculate electron-phonon interaction
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coefficients at X for fcc Al.
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example08:
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This example shows how to use pw.x to calculate the DOS of Ni
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and how to plot the Fermi Surface using XCrysDen
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example09:
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This example shows how to use pw.x and phcg.x to calculate the
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normal modes of a molecule (SiH4) at Gamma. It shows also the
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use of ph.x for molecules (CH4) at Gamma.
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example10:
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This example shows how to calculate the polarization via Berry
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Phase in PBTiO3 (contributed by the Vanderbilt Group in Rutgers
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University).
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example11:
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This example shows how to calculate the total energy of an
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isolated atom in a supercell with fixed occupations.
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Two examples: LDA energy of Al and sigma-GGA energy of O.
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example12:
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This example shows how to use pw.x and pwcond.x to calculate the
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complex bands and the transmission coefficient of an open quantum
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system.
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example13:
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This example shows how to use pw.x to calculate the total energy
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and the band structure of four simple systems in the non-collinear
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case: Fe, Cu, Ni, O.
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example14:
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This example shows how to use pw.x, ph.x and d3.x to calculate the
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third-order expansion coefficients of the total energy of Si.
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example15:
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This example shows how to use pw.x and ph.x to calculate the Raman
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tensor for AlAs.
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example16:
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This example shows a calculation of STM maps.
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example17:
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This example shows how to use pw.x to calculate the minimum energy
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path (MEP) in the collinear proton transfer reaction H2+H => H+H2.
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example18:
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This example shows how to use cp.x to perform molecular dynamics
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simulation of SiO2.
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example19:
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This example shows how to use cp.x to perform molecular dynamics
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simulation of H2O.
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example20:
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This example shows how to use cp.x to perform molecular dynamics
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simulation of NH3.
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example21:
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This example shows how to use cp.x to perform molecular dynamics
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simulation of medium to large systems.
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This example consists in calculations with 32, 64, 128, 256 water
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molecules and takes a long time to execute. To run a calculation
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with up to N molecules, use:
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./run_example N
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Note that "./run_example" alone does nothing.
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example22:
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This example shows how to use pw.x to calculate the total energy
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and the band structure of fcc-Pt with a fully relativistic US-PP
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which includes spin-orbit effects. pwcond.x is used to calculate the
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complex bands including spin-orbit coupling. ph.x is used to calculate
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the phonon frequencies at Gamma and X of fcc-Pt.
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example23:
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This example shows how to use cp.x to calculate Wannier functions
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and to perform dynamics with an external electric field.
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(contributed by Manu Sharma)
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example24:
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This example tests pw.x and ph.x in several cases that require the
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noncollinear or the spin-orbit part of the code together with the gga.
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ph.x is used to calculate the phonons at X and Gamma of fcc-Pt with gga,
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and to calculate the phonons at X and Gamma of fcc-Ni to test the magnetic
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case with gga with or without spin-orbit (experimental stage).
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example25:
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This example shows how to use pw.x to perform LDA+U calculations.
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example26:
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Additional example of calculation of Wannier functions with cp.x,
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using the Jacobi Rotation algorithm for localizing Wannier functions
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(contributed by IRRMA, Lausanne)
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example27:
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This example shows how to use cp.x to perform TPSS metaGGA calculations
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for C4H6
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example28 REMOVED
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example29:
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This example shows how to perform Born-Oppenheimer molecular dynamics
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with conjugate gradient algorithm for the electronic states and
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ensemble-DFT for treating metallic systems.
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It is a simple Si dimer.
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example30:
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This example shows how to use cp.x to perform molecular dynamics
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in the presence of an electric field described through the
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modern theory of the polarization. The example shows how to
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calculate high-frequency and static dielectric constants and
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Born effective charges.
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example31:
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This example shows how to use pw.x to perform electronic structure
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calculations in the presence of a finite electric field described
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through the modern theory of the polarization. The example shows how to
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calculate the dielectric constant of silicon.
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example32:
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This example tests ph.x together with PAW.
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example33:
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This example illustrates how to use pw.x and ph.x to calculate
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dynamic polarizability of methane molecules (experimental stage)
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example34:
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This example illustrates how to use vdw.x to calculate
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dynamic polarizability of methane molecules (experimental stage).
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example35:
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This example tests pw.x and ph.x for the effective charges and
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dielectric constants with the noncollinear or the spin-orbit part of the
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code (experimental stage).
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example36:
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This example tests pw.x and ph.x for the noncollinear/spin-orbit case
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and PAW (still experimental).
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Additional feature-specific examples:
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autopilot-example:
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This example (a water molecule) shows how to use cp.x to perform
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molecular dynamics with variable parameters using AUTOPILOT.
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CLS_IS_example, CLS_FS_example
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These examples show how to calculate initial-state (IS) and final-state (FS)
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core-level-shift (CLS) using the core-excited pseudo-potential technique.
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EXX_example:
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Use experimental implementation of Hybrid Functional to compute
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total energy of Silicon using different values for nq and for
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calculation of binding energy of o2,co,n2 from calculations in a
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12 au cubic box and gamma sampling.
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ESM_example:
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This example shows how to use the Effective Screening Medium Method (ESM)
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in pw.x to calculate the total energy, charge density, force, and
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potential of a polarized or charged medium. Calculations are for a water
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molecule and an Al(111) electrode.
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GRID_example
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This example shows how to use ph.x on a GRID.
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Recover_example:
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This example tests the recover feature of ph.x.
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Restart_example:
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This example shows how to use cp.x together with pw.x
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to perform an electronic minimization at Gamma for SiO2.
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VCSexample:
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This example shows how to use pw.x to optimize crystal structures at two
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pressures for As.
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WorkFct_example:
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This example shows how to use pw.x, pp.x, and average.x to
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compute the work function of a metal using the slab-supercell
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approximation. This example is of a 4 layer unrelaxed Al(100) slab
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with 5 equivalent layers of vacuum between the surfaces.
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WAN90_example:
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This example shows how to use pw2wannier90.x in conjunction with
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Wannier90 (http://www.wannier.org) to obtain maximally-localised
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Wannier functions (MLWFs) for the valence bands of diamond.
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WannierHam_example:
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This example shows how to generate a model Hamiltonian in a
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Wannier functions basis, using pw.x and wannier_ham.x.
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XSpectra_example:
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This example tests K-edge X-ray absorption spectra calculation
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for diamond and NiO.
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QExml_example:
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The example shows how rto use qexml.f90 (in PP/) to read files
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written by pw.x and cp.x
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Note: additional documentation specific to pseudopotential generation,
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including examples, is available in the ../atomic_doc/ directory.
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