mirror of https://gitlab.com/QEF/q-e.git
More updates to the user guide. Contributions are welcome...
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@6581 c92efa57-630b-4861-b058-cf58834340f0
This commit is contained in:
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@ -133,7 +133,7 @@ If you want to learn that, you should read a good textbook, such as e.g.
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the book by Richard Martin:
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{\em Electronic Structure: Basic Theory and Practical Methods},
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Cambridge University Press (2004). See also the bibliography
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section in the wiki.
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section in the Wiki.
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All trademarks mentioned in this guide belong to their respective owners.
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@ -306,12 +306,11 @@ Other relevant contributions to \qe:
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Alessandro Curioni (IBM Zurich);
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\item Gerardo Ballabio wrote the first \texttt{configure} for \qe
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\item Audrius Alkauskas (IRRMA),
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Simon Binnie (Univ. College London), Davide Ceresoli (MIT),
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Guido Fratesi, Axel Kohlmeyer (UPenn),
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Simon Binnie (Univ. College London), Guido Fratesi, Axel Kohlmeyer (UPenn),
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Konstantin Kudin (Princeton), Sergey Lisenkov (Univ.Arkansas),
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Nicolas Mounet (MIT), William Parker (Ohio State Univ),
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Guido Roma (CEA), Gabriele Sclauzero (SISSA), Sylvie Stucki (IRRMA),
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Pascal Thibaudeau (CEA),
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Pascal Thibaudeau (CEA), Vittorio Zecca
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answered questions on the mailing list, found bugs, helped in
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porting to new architectures, wrote some code.
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\end{itemize}
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@ -340,15 +339,11 @@ site or following the links contained in it. The main entry point for
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developers is the QE-forge web site:
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\texttt{http://www.qe-forge.org/}.
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Announcements about new versions of \qe\ are available
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via a low-traffic mailing list: \texttt{pw\_users@pwscf.org}.
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You can
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subscribe (but not post) to this list from the \qe\ web site.
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The recommended place where to ask questions about installation
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and usage of \qe, and to report bugs, is the \texttt{pw\_forum}
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mailing list: \texttt{pw\_forum@pwscf.org}. Here you can obtain
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help from the developers and many knowledgeable users.
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mailing list: \texttt{pw\_forum@pwscf.org}. Here you can receive
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news about \qe\ and obtain help from the developers and from
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knowledgeable users.
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You have to be subscribed in order to post to the list.
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Please browse or search the archive -- links are available
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in the "Tools" page of the \qe\ web site,
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@ -362,8 +357,15 @@ automatically deleted with no further processing (sorry, too
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much spam). In case of trouble, carefully check that your return
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e-mail is the correct one (i.e. the one you used to subscribe).
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The \texttt{pw\_forum} mailing list is also the recommanded place
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where to contact the developers of \qe.
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Since \texttt{pw\_forum} averages $\sim 10$ message a day, an alternative
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low-traffic mailing list: \texttt{pw\_users@pwscf.org}, is provided for
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those interested only in \qe-related news, such as e.g. announcements
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of new versions, tutorials, etc.. You can subscribe (but not post) to
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this list from the \qe\ web site.
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If you need to contact the developers for {\em specific} questions
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about coding, proposals, offers of help, etc., send a message to the
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developers' mailing list: \texttt{q-e-developers@qe-forge.org}.
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\subsection{Terms of use}
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@ -420,7 +422,8 @@ may be distributed as a "diff" file. In order to install a patch (for instance):
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If more than one patch is present, they should be applied in the correct order.
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Daily snapshots of the development version can be downloaded from the
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developers' site \texttt{qe-forge.org}: follow the link ''Quantum ESPRESSO'', then ''SCM''. Beware: the development version
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developers' site \texttt{qe-forge.org}: follow the link ''Quantum ESPRESSO'',
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then ''SCM''. Beware: the development version
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is, well, under development: use at your own risk! The bravest
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may access the development version via anonymous CVS
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(Concurrent Version System): see the Developer Manual
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@ -691,14 +694,14 @@ and to modify file \texttt{make.sys} accordingly (MKL must be linked {\em after}
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the FFTW-MKL interface)
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If everything else fails, you'll have to modify file \texttt{make.sys}
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manually: see Sect.\ref{manconf}.
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manually: see Sec.\ref{SubSec:manconf}.
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\paragraph{MPI libraries}
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MPI libraries are usually needed for parallel execution
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(unless you are happy with OpenMP multicore parallelization).
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In well-configured machines, \texttt{configure} should find the appropriate
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parallel compiler for you, and this should find the appropriate
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libraries. Since often this doesn't
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happen, especially on PC clusters, see Sec.\ref{Sec:LinuxPCMPI}.
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happen, especially on PC clusters, see Sec.\ref{SubSec:LinuxPCMPI}.
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\paragraph{Other libraries}
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\qe\ can use the MASS vector math
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@ -732,7 +735,7 @@ know exactly which routines are affected by the changed settings and how to
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force their recompilation.
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\subsubsection{Manual configuration}
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\label{manconf}
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\label{SubSec:manconf}
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If \texttt{configure} stops before the end, and you don't find a way to fix
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it, you have to write working "make.sys", "include/fft\_defs.h" and
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"include/c\_defs.h" files.
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@ -772,9 +775,23 @@ Here is a list:
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\begin{itemize}
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\item \texttt{make pw} produces PW/pw.x\\
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pw.x calculates electronic structure, structural optimization, molecular dynamics, barriers with NEB.
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\item \texttt{make ph} produces PH/ph.x\\
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\item \texttt{make ph} produces the following codes for phonon calculations:
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\begin{itemize}
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\item PH/ph.x\\
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ph.x calculates phonon frequencies and displacement patterns,
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dielectric tensors, effective charges (uses data produced by pw.x).
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\item dynmat.x\\
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applies various kinds of Acoustic Sum Rule (ASR),
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calculates LO-TO splitting at q = 0 in insulators, IR and Raman
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cross sections (if the coefficients have been properly calculated),
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from the dynamical matrix produced by ph.x
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\item q2r.x\\
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calculates Interatomic Force Constants (IFC) in real space
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from dynamical matrices produced by ph.x on a regular q-grid
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\item matdyn.x\\
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produces phonon frequencies at a generic wave vector
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using the IFC file calculated by q2r.x; may also calculate phonon DOS
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\end{itemize}
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\item \texttt{make d3} produces D3/d3.x\\
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d3.x calculates anharmonic phonon lifetimes (third-order derivatives
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of the energy), using data produced by pw.x and ph.x (Ultrasoft
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@ -795,7 +812,7 @@ not support Ultrasoft pseudopotentials.
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\item \texttt{make ld1} produces code atomic/ld1.x\\
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for pseudopotential generation (see specific documentation in atomic\_doc/).
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\item \texttt{make upf} produces utilities for pseudopotential conversion in
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directory upftools/ (see section 4, ``Pseudopotentials'').
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directory upftools/.
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\item \texttt{make cp} produces the Car-Parrinello code CP in CPV/cp.x
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and the postprocessing code CPV/cppp.x.
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\item \texttt{make all} produces all of the above.
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@ -845,15 +862,6 @@ code voronoy.x (removed from distribution after v.4.1).
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The utility programs in pwtools/ are:
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\begin{itemize}
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\item dynmat.x applies various kinds of Acoustic Sum Rule (ASR),
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calculates LO-TO splitting at q = 0 in insulators, IR and Raman
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cross sections (if the coefficients have been properly calculated),
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from the dynamical matrix produced by ph.x
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\item q2r.x calculates Interatomic Force Constants (IFC) in real space
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from dynamical matrices produced by ph.x on a regular q-grid
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\item matdyn.x produces phonon frequencies at a generic wave vector
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using the IFC file calculated by q2r.x; may also calculate phonon DOS
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\item fqha.x for quasi-harmonic calculations
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\item lambda.x calculates the electron-phonon coefficient $\lambda$ and the
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function $\alpha^2F(\omega)$
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\item dist.x calculates distances and angles between atoms in a cell,
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@ -929,7 +937,7 @@ high I/O performance (i.e., don't use an NFS-mounted directory).
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2. If you have compiled the parallel version of \qe\ (this
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is the default if parallel libraries are detected), you will usually
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have to specify a driver program (such as poe or mpiexec) and the
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number of processors: see section ''Running on parallel machines' for
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number of processors: see Sec.\ref{SubSec:para} for
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details. 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. Parallel
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executables will be run by a command like this:
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@ -1232,7 +1240,7 @@ together with the compilers most frequently used on AMD systems:
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pgf90, pathscale, openf95, sunf95.
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\subsubsection{Linux PC clusters with MPI}
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\label{Sec:LinuxPCMPI}
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\label{SubSec:LinuxPCMPI}
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PC clusters running some version of MPI are a very popular
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computational platform nowadays. \qe\ is known to work
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with at least two of the major MPI implementations (MPICH, LAM-MPI),
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@ -1250,12 +1258,11 @@ http://www.democritos.it/pipermail/pw\_forum/2008April/008818.htm .
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If \qe\ does not work for some reason on a PC cluster,
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try first if it works in serial execution. A frequent problem with parallel
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execution is that \qe\ does not read from standard input,
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due to the configuration of MPI libraries: see section
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''Running on parallel machines''.
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due to the configuration of MPI libraries: see Sec.\ref{SubSec:para}.
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If you are dissatisfied with the performances in parallel execution,
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read the section on ''Parallelization issues''. See also the following
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post from Axel Kohlmeyer:\\
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see Sec.\ref{Sec:para} and in particular Sec.\ref{SubSec:badpara}.
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See also the following post from Axel Kohlmeyer:\\
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http://www.democritos.it/pipermail/pw\_forum/2008-April/008796.html
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\subsubsection{Intel Mac OS X}
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@ -1291,6 +1298,7 @@ no longer supported since v.\version.
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\newpage
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\section{Parallelism}
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\label{Sec:para}
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\subsection{Understanding Parallelism in \qe}
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@ -1342,6 +1350,7 @@ and OpenMP threads in a controlled manner, forget about mixed
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OpenMP-MPI parallelization.
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\subsection{Running on parallel machines}
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\label{SubSec:para}
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Parallel execution is strongly system- and installation-dependent.
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Typically one has to specify:
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@ -1905,7 +1914,30 @@ is the directory where the pw.x executable is! The advantage of this
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procedure is that all files are properly closed, whereas just killing
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the process may leave data and output files in unusable state.
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\subsection{Phonon calculations}
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\subsection{Hartree-Fock and Hybrid functionals}
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Calculations in the Hartree-Fock approximation, or using hybrid XC functionals
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that include some Hartree-Fock exchange, can be performed by adding
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\texttt{-DEXX} to the preprocessing options \texttt{DFLAGS} in file
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\texttt{make.sys}. Issue command \texttt{make clean} before recompiling.
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Documentation on usage can be found in subdirectory \texttt{EXX\_example/}
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of the \texttt{examples/} directory.
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The algorithm is quite standard: see for instance Chawla and Voth,
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JCP {bf 108}, 4697 (1998); Sorouri, Foulkes and Hine, JCP {\bf 124},
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064105 (2006); Spencer and Alavi, PRB {\bf 77}, 193110 (2008).
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Basically, one generates auxiliary densities $\rho_{-q}=\phi^{*}_{k+q}*\psi_k$
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in real space and transforms them to reciprocal space using FFT;
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the Poisson equation is solved and the resulting potential is transformed
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back to real space using FFT, then multiplied by $\phi_{k+q}$ and the
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results are accumulated.
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The only tricky point is the treatment of the $q\rightarrow 0$ limit,
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which is described in the Appendix A.5 of the \qe\ paper mentioned
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in the Introduction (note the reference to the Gygi and Baldereschi paper).
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See also J. Comp. Chem. {\bf 29}, 2098 (2008);
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JACS {\bf 129}, 10402 (2007) for examples of applications.
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\section{Phonon calculations}
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Phonon calculation is presently a two-step process:
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First, you have to find the ground-state atomic and electronic configuration;
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@ -1918,7 +1950,7 @@ the same mechanism of the pw.x code, i.e. by creating a file prefix.EXIT in the
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working directory. Execution can be resumed by setting 'recover=.true.' in the
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subsequent input data.
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\paragraph{Single-q calculation}
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\subsection{Single-q calculation}
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The phonon code ph.x calculates normal modes at a given q-vector, starting
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from data files produced by pw.x with a simple SCF calculation.
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@ -1956,7 +1988,7 @@ for a typical experimental setup.
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A sample phonon calculation is performed in Example 02.
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\paragraph{Calculation of interatomic force constants in real space}
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\subsection{Calculation of interatomic force constants in real space}
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First, dynamical matrices D(q) are calculated and saved for a suitable uniform
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grid of q-vectors (only those in the Irreducible Brillouin Zone of the
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@ -1974,7 +2006,7 @@ of q-vectors. Program matdyn.x may be used to produce phonon modes and
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frequencies at any q using the Interatomic Force Constants file as input.
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See Example 06.
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\paragraph{Calculation of electron-phonon interaction coefficients}
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\subsection{Calculation of electron-phonon interaction coefficients}
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The calculation of electron-phonon coefficients in metals is made difficult by
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the slow convergence of the sum at the Fermi energy. It is convenient to
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@ -1993,14 +2025,14 @@ All of the above must be repeated for all desired q-vectors and the final
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result is summed over all q-vectors, using pwtools/lambda.x. The input
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data for the latter is described in the header of pwtools/lambda.f90.
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\subsection{Post-processing}
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\section{Post-processing}
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There are a number of auxiliary codes performing postprocessing tasks such
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as plotting, averaging, and so on, on the various quantities calculated by
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pw.x. Such quantities are saved by pw.x into the output data file(s).
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Postprocessing codes are in the PP/ directory.
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\paragraph{Plotting selected quantities}
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\subsection{Plotting selected quantities}
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The main postprocessing code pp.x reads data file(s), extracts or calculates
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the selected quantity, writes it into a format that is suitable for plotting.
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@ -2027,7 +2059,7 @@ or by advanced plotting software XCrySDen and gOpenMol (3D plots).
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See file INPUT\_PP.* for a detailed description of the input for code pp.x.
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See example05/ in the examples/ directory for a charge density plot.
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\paragraph{Band structure, Fermi surface}
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\subsection{Band structure, Fermi surface}
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The code bands.x reads data file(s), extracts eigenvalues,
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regroups them into bands (the algorithm used to order bands and to resolve
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@ -2044,7 +2076,7 @@ bands\_FS.x. The resulting file in .xsf format can be read and plotted
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using xcrysden. See example08/ for an example of Fermi surface
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visualization (Ni, including the spin-polarized case).
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\paragraph{Projection over atomic states, DOS}
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\subsection{Projection over atomic states, DOS}
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The code projwfc.x calculates projections of wavefunctions
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over atomic orbitals. The atomic wavefunctions are those contained
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@ -2075,29 +2107,6 @@ performed on a subsection of the old path. The input file needed by
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path\_int.x can be easily set up with the help of the self-explanatory
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path\_int.sh shell script.
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\subsection{Hartree-Fock and Hybrid functionals}
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Calculations in the Hartree-Fock approximation, or using hybrid XC functionals
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that include some Hartree-Fock exchange, can be performed by adding
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\texttt{-DEXX} to the preprocessing options \texttt{DFLAGS} in file
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\texttt{make.sys}. Issue command \texttt{make clean} before recompiling.
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Documentation on usage can be found in subdirectory \texttt{EXX\_example/}
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of the \texttt{examples/} directory.
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|
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The algorithm is quite standard: see for instance Chawla and Voth,
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JCP {bf 108}, 4697 (1998); Sorouri, Foulkes and Hine, JCP {\bf 124},
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064105 (2006); Spencer and Alavi, PRB {\bf 77}, 193110 (2008).
|
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Basically, one generates auxiliary densities $\rho_{-q}=\phi^{*}_{k+q}*\psi_k$
|
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in real space and transforms them to reciprocal space using FFT;
|
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the Poisson equation is solved and the resulting potential is transformed
|
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back to real space using FFT, then multiplied by $\phi_{k+q}$ and the
|
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results are accumulated.
|
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The only tricky point is the treatment of the $q\rightarrow 0$ limit,
|
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which is described in the Appendix A.5 of the \qe\ paper mentioned
|
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in the Introduction (note the reference to the Gygi and Baldereschi paper).
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See also J. Comp. Chem. {\bf 29}, 2098 (2008);
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JACS {\bf 129}, 10402 (2007) for examples of applications.
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\section{Using CP}
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This section is intended to explain how to perform basic Car-Parrinello (CP)
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@ -2779,6 +2788,7 @@ self-consistency, default value = 8) if disk\_io is set to 'high'
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or not specified; q = 0 if disk\_io='low' or 'minimal'.
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\subsection{Parallelization issues}
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\label{SubSec:badpara}
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pw.x and cp.x can run in principle on any number of processors.
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The effectiveness of parallelization is ultimately judged by the
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@ -2787,7 +2797,7 @@ The effectiveness of parallelization is ultimately judged by the
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\begin{itemize}
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\item the size and type of the system under study;
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\item the judicious choice of the various levels of parallelization
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(detailed in the "Running on parallel machines" sections);
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(detailed in Sec.\ref{SubSec:para});
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\item the availability of fast interprocess communications (or lack thereof).
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\end{itemize}
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Ideally one would like to have linear scaling, i.e. $T_N \sim T_0/N_p$ for
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@ -2900,7 +2910,7 @@ the "'" in the definitions of PARA\_PREFIX and PARA\_POSTFIX.
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(parallel execution)}
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If the code looks like it is not reading from input, maybe
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it isn't: the MPI libraries need to be properly configured to accept input
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redirection. See section "Running on parallel machines", or inquire with
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redirection. See Sec.\ref{SubSec:para}, or inquire with
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your local computer wizard (if any).
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\subsection{pw.x stops with error while reading data}
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@ -3482,7 +3492,7 @@ the generation of the PP is the same for all PP's. Note that
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it is the hardest atom that determines the cutoff.
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\paragraph{ ''Where can I find pseudopotentials for atom X?''}
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'''A:''' See the wiki page on [[Pseudopotentials]], follow those
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'''A:''' See the Wiki page on [[Pseudopotentials]], follow those
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links. New contributions to the PP table are appreciated.
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If X is one of the rare earths: please consider first if DFT is
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suitable for your system!
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Reference in New Issue