mirror of https://gitlab.com/QEF/q-e.git
239 lines
8.9 KiB
Plaintext
239 lines
8.9 KiB
Plaintext
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
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distribution (the one where this file should be). Those examples try
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to exercise all the programs and features of the ESPRESSO package: for
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details, see the "README" file in each example's directory.
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If you find that any relevant feature isn't being tested, please
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contact us (or even better, write and send us a new example
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yourself!).
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If you haven't downloaded the full ESPRESSO distribution and don't
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have the examples, you can get them from the Test and Examples Page of
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the ESPRESSO web site (http://www.pwscf.org/tests.htm). The necessary
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pseudopotentials are included.
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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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The PSEUDO_DIR directory must contain the following files:
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Al.vbc.UPF, As.gon.UPF, C.pz-rrkjus.UPF, Cu.pz-d-rrkjus.UPF,
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Fe.pz-nd-rrkjus.UPF, H.fpmd.UPF, H.vbc.UPF, N.BLYP.UPF,
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Ni.pbe-nd-rrkjus.UPF, NiUS.RRKJ3.UPF, O.BLYP.UPF,
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O.LDA.US.RRKJ3.UPF, O.pbe-rrkjus.UPF, O.vdb.UPF, OPBE_nc.UPF,
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Pb.vdb.UPF, Ptrel.RRKJ3.UPF, Si.vbc.UPF, SiPBE_nc.UPF, Ti.vdb.UPF
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If any of these are missing, you may not be able to run some of the
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examples. You can download them from the Pseudopotentials Page of
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the ESPRESSO web site (http://www.pwscf.org/pseudo.htm).
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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 have compiled the parallel version of ESPRESSO (that is the
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default), you'll usually have to specify a driver program (such as
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"poe" or "mpiexec") and the number of processors: see the section
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``Running on parallel machines'' of the ESPRESSO manual for
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details.
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In order to do that, edit again the "environment_variables" file
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and set the PARA_PREFIX and PARA_POSTFIX variables as needed.
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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 SP4):
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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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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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(for examples 21 and 26, see their description 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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Instead, you can run the "check_example" script in the "examples"
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directory:
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./check_example example_dir
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where "example_dir" is the directory of the example that you want
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to check (e.g., "./check_example example01"). You can specify
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multiple directories.
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Note: at the moment "check_example" is in early development and
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(should be) guaranteed to work only on examples 01 to 04.
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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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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.
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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, ph.x, and ram.x to calculate
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the Raman 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 fpmd.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 fpmd.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 fpmd.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.
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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 shows how to use efg.x to calculate the electric field
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gradient, and to obtain the quadrupolar parameters of an NMR experiment.
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The solid in example is quartz.
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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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This example shows how to use cp.x to do String method (SMD) to find
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the minimum energy path (MEP) (contributed by Yosuke Kanai).
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This example consists in 7 calculations and takes a long time.
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In order to run calculations up to the N-th, use:
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./run_example N
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Note that "./run_example" alone does nothing.
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