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<H1><A ID="SECTION00060000000000000000">
5 Files produced by ph.x</A>
</H1>
<P>
The output files of the <TT>pw.x</TT> code are not modified by the <TT>ph.x</TT> code.
Each image of <TT>ph.x</TT> creates a new directory called <TT>outdir/_ph#</TT>
where it writes its files. <TT>#</TT> is an integer equal to <TT>0</TT>
in a calculation with one image or to the image number when the
<TT>-nimage</TT> flag is used.
There are two sets of files written
by <TT>ph.x</TT> in the <TT>outdir/_ph#</TT> directories: unformatted files
containing internal arrays, and <TT>.xml</TT>
files containing partial results or tensors. The former are in
<TT>outdir/_ph#</TT> if the input flag <TT>lqdir=.false.</TT>, or in
separate subdirectories <TT>outdir/_ph#/prefix.q_#iq</TT>,
where <TT>#iq</TT> is the number of the <B>q</B> point. Note that if
<TT>lqdir=.false.</TT> (default is <TT>lqdir=elph</TT>)
the disk occupation is reduced but the files of each <B>q</B> point are
rewritten by the following <B>q</B> so it is not possible to run an
electron-phonon calculation with <TT>trans=.false.</TT> and
<TT>ldisp=.true.</TT> after generating the induced potentials for a mesh of
<B>q</B> points.
The <TT>.xml</TT> files calculated by each image are in the
<TT>outdir/_ph#/prefix.phsave</TT> directory for all <B>q</B>-vectors and
irreps calculated by that images. Before closing the image calculation
the content of all the <TT>outdir/_ph#/prefix.phsave</TT>
directories are copied into <TT>outdir/_ph0/prefix.phsave</TT> directory, so
it is possible to recover the calculation without using images.
The <TT>ph.x</TT> code reads the output of <TT>pw.x</TT> from the <TT>outdir</TT> directory.
The wavefunctions are in <TT>outdir/prefix.wfc</TT> files
while information on the structure of the solid and on the <TT>pw.x</TT>
run are in the <TT>outdir/prefix.save</TT> directory. The wavefunctions are
also in this directory if <TT>pw.x</TT> was run with the <TT>wf_collect=.true.</TT>
flag. These files are not modified by <TT>ph.x</TT>.
At a finite <B>q</B> vector, <TT>ph.x</TT> runs its own instance of <TT>pw.x</TT> to compute the bands and saves the results into
the <TT>outdir/_ph#/prefix.q_#iq</TT> directory (<TT>lqdir=.true.</TT>) or
in <TT>outdir/_ph#</TT>. The charge density is copied inside
these directories before calculating the bands. The output of <TT>pw.x</TT> is
in files called <TT>outdir/_ph#/prefix.q_#iq/prefix.wfc</TT> and in
the directory
<TT>outdir/_ph#/prefix.q_#iq/prefix.save</TT> (<TT>lqdir=.true.</TT>),
or in <TT>outdir/_ph#/prefix.wfc</TT> and in
<TT>outdir/_ph#/prefix.save</TT> (<TT>lqdir=.false.</TT>). With
<TT>lqdir=.false.</TT> <TT>ph.x</TT> saves in
<TT>outdir/_ph#/prefix.bar</TT> the
non self-consistent part of the right hand side of the linear system,
in <TT>outdir/_ph#/prefix.dwf</TT> the change of the wavefunctions.
The files <TT>outdir/_ph#/</TT> <TT>prefix.igk</TT> contain the <!-- MATH
${\bf k}+{\bf G}$
-->
<IMG STYLE="height: 1.63ex; vertical-align: -0.10ex; " SRC="img3.png"
ALT="$\bf k$"> + <IMG STYLE="height: 1.69ex; vertical-align: -0.10ex; " SRC="img4.png"
ALT="$\bf G$">
lists as in the <TT>pw.x</TT> run.
With US or PAW, files called <TT>outdir/_ph#/prefix.prd</TT>
contain the induced charge density, for all modes.
Only the part that does not depend on the perturbed wavefunctions
is contained in these files. With electric field perturbations
there are also files called <TT>outdir/_ph#/prefix.com</TT> that
contain <!-- MATH
$P_c x |\psi\rangle$
-->
<I>P</I><SUB>c</SUB><I>x</I>| <I>ψ</I>〉 and are needed for the calculation
of the Born effective charges.
The mixing routine saves its data in files called
<TT>outdir/_ph#/prefix.mixd</TT>.
The status of <TT>ph.x</TT> is saved at each iteration in files called
<TT>outdir/_ph#/prefix.recover</TT>. These files can be used
to recover the run. All these unformatted files are saved in
<TT>outdir/_ph#/prefix.q_#iq</TT> directory when <TT>lqdir=.true.</TT>.
Using the input flag <TT>reduce_io=.true.</TT> these files can be
kept in memory and saved only at the end of the run if necessary.
<P>
In parallel calculations, previous files are split into several files
that have a final number. Each number labels the processor that wrote the
file. There are as many files as processors per image.
<P>
The files with the dynamical matrices are written in the directory in
which <TT>ph.x</TT> is started and are called <TT>fildyn#iq</TT> where
<TT>#iq</TT> is the <B>q</B>-vector number in a dispersion calculation,
or is not added in a single-<B>q</B> calculation. Only one copy of this
file is written in a parallel run. When the <TT>-nimage</TT> option
is used some of these files might be empty (if the corresponding <B>q</B>
point has been divided between two or more images). The results are
collected running <TT>ph.x</TT> another time (with <TT>recover=.true.</TT>)
without images.
<P>
Moreover <TT>ph.x</TT> opens a directory called <TT>outdir/_ph#/prefix.phsave</TT>.
This directory contains the partial information on the calculation.
These files can be used to recover a run also when the recover file
is corrupted. In the directory <TT>outdir/_ph#/prefix.phsave</TT> the
files are in <TT>.xml</TT> format. Note that this directory is
always in <TT>outdir/_ph#/</TT> also when <TT>lqdir=.true.</TT>.
There are several files:
<P>
<TT>control_ph.xml</TT> contains information on the flags that control
what <TT>ph.x</TT> calculates. The content of this file is used mainly for
checking purposes. The code reads these flags in input and does not need
to reread them from file, but a recover run in which these flags change
is not allowed. <TT>control_ph.xml</TT> contains also the mesh of
<B>q</B>-vectors and their coordinates. This file is written only in a non
recovered calculation from the routine <TT>check_initial_status</TT> after
the creation of the <B>q</B>-vector mesh. It is read, if
<TT>recover=.true.</TT>, at the beginning of
the run by <TT>phq_readin</TT>.
<P>
<TT>status_run.xml</TT> contains information that tell <TT>ph.x</TT>
at which point the code stopped. It has information on the current
<B>q</B> vector, the current frequency, and a recover code that tells
<TT>ph.x</TT> if it has to expect a recover file and which routine produced this
recover file.
<TT>status_run.xml</TT> file is rewritten each time the phonon code
reaches a point from which a new recover is possible.
It is read, if <TT>recover=.true.</TT>,
at the beginning of the run by <TT>phq_readin</TT>.
<P>
If some routine wrote it, <TT>tensors.xml</TT> contains the tensors that
have been calculated. Possible tensors are: dielectric constant,
Born effective charges calculated as derivative of the forces (EU),
Born effective charges calculated as derivative of the polarization (UE),
raman tensor, electro-optic coefficient. This file is written by the
routines that calculate the tensors.
It is read by the routine <TT>phq_recover</TT>, if <TT>recover=.true.</TT>
and the <B>q</B> vector is <I>Γ</I>.
<P>
If <TT>polariz</TT> wrote it, <TT>polariz.xml</TT> contains the frequency
dependent polarizabilities for the frequencies calculated so far.
It is read by the routine
<TT>phq_recover</TT>, if <TT>recover=.true.</TT> and the <B>q</B> vector
is <I>Γ</I>.
<P>
<TT>patterns.#iq.xml</TT> are files written for each <B>q</B> vector
(<TT>#iq</TT> is its number).
They contain the information on the displacement patterns that
transform according to irreducible representations of the small
group of <B>q</B>: number of irreducible representations, their dimensions,
the displacement patterns and the name of the irreducible representation
to which each mode belongs. It is written in nonrecover runs by the routine
<TT>init_representations</TT>.
It is read for each <B>q</B> vector by <TT>phq_setup</TT>. The routine
reads the data of the file with <TT>iq=current_iq</TT>.
<P>
<TT>dynmat.#iq.0.xml</TT> contains the part of the dynamical matrix
calculated by <TT>dynmat0</TT> that does not depend on the perturbed
wavefunctions. It is written by <TT>dynmat0</TT> and read only in recover runs
by <TT>phq_recover</TT>.
<P>
<TT>dynmat.#iq.#irr.xml</TT>
contains the contribution to the dynamical matrix at the
<B>q</B> vector <TT>#iq</TT> of
the representation <TT>#irr</TT>.
Note that these files can be calculated independently even on
different machines and collected in a single directory (see the GRID example),
but it is necessary to calculate the patterns file in a single machine and
send it to all the machine where the calculation is run to be sure that
all machines use the same displacement patterns.
When the files <TT>dynmat.#iq.#irr.xml</TT> are present for all
<TT>#irr</TT> of a given <TT>#iq</TT> the dynamical matrix for that
<IMG STYLE="height: 1.52ex; vertical-align: -0.55ex; " SRC="img5.png"
ALT="$\bf q$"> can be calculated. If all the <TT>#irr</TT> of a given symmetry
for a given <TT>#iq</TT> are present,
the partial dynamical matrix that can be constructed with this information
can be diagonalized and the frequencies of the modes of that symmetry can
be calculated (using the <TT>ldiag=.true.</TT> flag).
These files are written by <TT>phqscf</TT> after calculating the
contribution of the representation to the dynamical matrix by
<TT>drhodv</TT>. They are read only in recover runs by the routine
<TT>phq_recover</TT>.
<P>
<TT>elph.#iq.#irr.xml</TT> contains the contribution to the electron
phonon coefficients
at the <B>q</B> vector <TT>#iq</TT> of the representation <TT>#irr</TT>.
These files are written by <TT>elphel</TT> and contain the quantities
<!-- MATH
$g_{{\bf q}\nu} ({\bf k}, i, j)$
-->
<I>g</I><SUB><IMG STYLE="height: 1.05ex; vertical-align: -0.40ex; " SRC="img2.png"
ALT="$\scriptstyle \bf q$"><I>ν</I></SUB>(<IMG STYLE="height: 1.63ex; vertical-align: -0.10ex; " SRC="img3.png"
ALT="$\bf k$">, <I>i</I>, <I>j</I>)
(see User Manual). They are read in recover runs by the routine
<TT>phq_recover</TT>.
<P>
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