Input File Description

Program: ph.x / PHonon / Quantum ESPRESSO

TABLE OF CONTENTS

INTRODUCTION

Line-of-input: title_line

&INPUTPH

amass | outdir | prefix | niter_ph | tr2_ph | alpha_mix(niter) | nmix_ph | verbosity | reduce_io | max_seconds | dftd3_hess | fildyn | fildrho | fildvscf | epsil | lrpa | lnoloc | trans | lraman | eth_rps | eth_ns | dek | recover | low_directory_check | only_init | qplot | q2d | q_in_band_form | electron_phonon | el_ph_nsigma | el_ph_sigma | ahc_dir | ahc_nbnd | ahc_nbndskip | skip_upperfan | lshift_q | zeu | zue | elop | fpol | ldisp | nogg | asr | ldiag | lqdir | search_sym | nq1 | nq2 | nq3 | nk1 | nk2 | nk3 | k1 | k2 | k3 | diagonalization | read_dns_bare | ldvscf_interpolate | wpot_dir | do_long_range | do_charge_neutral | start_irr | last_irr | nat_todo | modenum | start_q | last_q | dvscf_star | drho_star

Line-of-input: xq(1) xq(2) xq(3)

qPointsSpecs

nqs | xq1 | xq2 | xq3 | nq

Line-of-input: atom(1) atom(2) ... atom(nat_todo)

ADDITIONAL INFORMATION

INTRODUCTION

Input data format: { } = optional, [ ] = it depends, # = comment

Structure of the input data:
===============================================================================

title_line

&INPUTPH
   ...
/

[ xq(1) xq(2) xq(3) ]                        # if ldisp != .true.  and  qplot != .true.

[ nqs                                        # if qplot == .true. 
  xq(1,i)    xq(2,i)    xq(3,1)    nq(1)
  ...
  xq(1,nqs)  xq(2,nqs)  xq(3,nqs)  nq(nqs) ]

[ atom(1)  atom(2)  ... atom(nat_todo) ]     # if nat_todo was specified
   

Line of input

Syntax:

title_line  

Description of items:

title_line CHARACTER
Title of the job, i.e., a line that is reprinted on output.
         

Namelist: &INPUTPH

amass(i), i=1,ntyp REAL
Default: 0.0
Atomic mass [amu] of each atomic type.
If not specified, masses are read from data file.
         
outdir CHARACTER
Default: value of the ESPRESSO_TMPDIR environment variable if set;
current directory ('./') otherwise
Directory containing input, output, and scratch files;
must be the same as specified in the calculation of
the unperturbed system.
         
prefix CHARACTER
Default: 'pwscf'
Prepended to input/output filenames; must be the same
used in the calculation of unperturbed system.
         
niter_ph INTEGER
Default: maxter=100
Maximum number of iterations in a scf step. If you want
more than 100, edit variable "maxter" in PH/phcom.f90
         
tr2_ph REAL
Default: 1e-12
 Threshold for self-consistency.
         
alpha_mix(niter) REAL
Default: alpha_mix(1)=0.7
Mixing factor (for each iteration) for updating
the scf potential:

vnew(in) = alpha_mix*vold(out) + (1-alpha_mix)*vold(in)
         
nmix_ph INTEGER
Default: 4
Number of iterations used in potential mixing. Using a larger value (8~20)
can significantly speed up convergence, at the cost of using more memory.
         
verbosity CHARACTER
Default: 'default'
 Options are:
            
'debug', 'high', 'medium' :
 verbose output
            
'low', 'default', 'minimal' :
 short output
            
reduce_io LOGICAL
Default: .false.
Reduce I/O to the strict minimum.

BEWARE: If the input flag reduce_io=.true. was
used, it is not allowed to restart from an interrupted
run.
         
max_seconds REAL
Default: 1.d7
 Maximum allowed run time before the job stops smoothly.
         
dftd3_hess CHARACTER
Default: 'prefix.hess'
File where the D3 dispersion hessian matrix is read. Set to
'automatic.hess' to enable automatic mode (experimental). In
this mode, D3 Hessian is computed if 'automatic.hess' file is
missing.
         
fildyn CHARACTER
Default: 'matdyn'
 File where the dynamical matrix is written.
         
fildrho CHARACTER
Default: ' '
File where the charge density responses are written. Note that the file
will actually be saved as ${outdir}/_ph0/${prefix}.${fildrho}1
where  ${outdir}, ${prefix} and ${fildrho} are the values of the
corresponding input variables
         
fildvscf CHARACTER
Default: ' '
File where the the potential variation is written
(for later use in electron-phonon calculation, see also fildrho).
         
epsil LOGICAL
Default: .false.
If .true. in a q=0 calculation for a non metal the
macroscopic dielectric constant of the system is
computed. Do not set epsil to .true. if you have a
metallic system or q/=0: the code will complain and stop.

Note: the input value of epsil will be ignored if ldisp=.true.
(the code will automatically set epsil to .false. for metals,
to .true. for insulators: see routine PHonon/PH/prepare_q.f90).
         
lrpa LOGICAL
Default: .false.
If .true. the dielectric constant is calculated at the
RPA level with DV_xc=0.
         
lnoloc LOGICAL
Default: .false.
If .true. the dielectric constant is calculated without
local fields, i.e. by setting DV_H=0 and DV_xc=0.
         
trans LOGICAL
Default: .true.
If .false. the phonons are not computed.
If trans .and. epsil are both .true.,
the effective charges are calculated.
If ldisp is .true., trans=.false. is overridden
(except for the case of electron-phonon calculations)
         
lraman LOGICAL
Default: .false.
If .true. calculate non-resonant Raman coefficients
using second-order response as in:
M. Lazzeri and F. Mauri, PRL 90, 036401 (2003).
         

Optional variables for Raman:

eth_rps REAL
Default: 1.0d-9
 Threshold for calculation of  Pc R |psi>.
            
eth_ns REAL
Default: 1.0e-12
 Threshold for non-scf wavefunction calculation.
            
dek REAL
Default: 1.0e-3
 Delta_xk used for wavefunction derivation wrt k.
            
recover LOGICAL
Default: .false.
 If .true. restart from an interrupted run.
         
low_directory_check LOGICAL
Default: .false.
If .true. search in the phsave directory only the
                 quantities requested in input.
         
only_init LOGICAL
Default: .false.
If .true. only the bands and other initialization quantities are calculated.
(used for GRID parallelization)
         
qplot LOGICAL
Default: .false.
 If .true. a list of q points is read from input.
         
q2d LOGICAL
Default: .false.
If .true. three q points and relative weights are
read from input. The three q points define the rectangle
q(:,1) + l (q(:,2)-q(:,1)) + m (q(:,3)-q(:,1)) where
0< l,m < 1. The weights are integer and those of points two
and three are the number of points in the two directions.
         
q_in_band_form LOGICAL
Default: .false.
This flag is used only when qplot is .true. and q2d is
.false.. When .true. each couple of q points q(:,i+1) and
q(:,i) define the line from q(:,i) to q(:,i+1) and nq
points are generated along that line. nq is the weigth of
q(:,i). When .false. only the list of q points given as
input is calculated. The weights are not used.
         
electron_phonon CHARACTER
Default: ' '
Options are:
            
'simple' :
Electron-phonon lambda coefficients are computed
for a given q and a grid of k-points specified by
the variables nk1, nk2, nk3, k1, k2, k3.
            
'interpolated' :
Electron-phonon is calculated by interpolation
over the Brillouin Zone as in M. Wierzbowska, et
al. arXiv:cond-mat/0504077
            
'lambda_tetra' :
The electron-phonon coefficient \lambda_{q \nu}
is calculated with the optimized tetrahedron method.
            
'gamma_tetra' :
The phonon linewidth \gamma_{q \nu} is calculated
from the electron-phonon interactions
using the optimized tetrahedron method.
            
'epa' :
Electron-phonon coupling matrix elements are written
to file prefix.epa.k for further processing by program
epa.x which implements electron-phonon averaged (EPA)
approximation as described in G. Samsonidze & B. Kozinsky,
Adv. Energy Mater. 2018, 1800246 doi:10.1002/aenm.201800246
arXiv:1511.08115
            
'ahc' :
Quantities required for the calculation of phonon-induced
electron self-energy are computed and written to the directory
ahc_dir. The output files can be read by postahc.x for
the calculation of electron self-energy.
Available for both metals and insulators.
trans=.false. is required.
            
For metals only, requires gaussian smearing (except for 'ahc').

If trans=.true., the lambdas are calculated in the same
run, using the same k-point grid for phonons and lambdas.
If trans=.false., the lambdas are calculated using
previously saved DeltaVscf in fildvscf, previously saved
dynamical matrix, and the present punch file. This allows
the use of a different (larger) k-point grid.
            
el_ph_nsigma INTEGER
Default: 10
The number of double-delta smearing values used in an
electron-phonon coupling calculation.
         
el_ph_sigma REAL
Default: 0.02
The spacing between double-delta smearing values used in
an electron-phonon coupling calculation.
         

Variables for electron_phonon = 'ahc':

ahc_dir CHARACTER
Default: outdir // 'ahc_dir/'
Directory where the output binary files are written.
            
ahc_nbnd INTEGER
Status: REQUIRED
Number of bands for which the electron self-energy is to be computed.
            
ahc_nbndskip INTEGER
Default: 0
Number of bands to exclude when computing the self-energy. Self-energy
is computed for bands with indices from ahc_nbndskip+1 to
ahc_nbndskip+ahc_nbnd. ahc_nbndskip+ahc_nbnd cannot
exceed nbnd of the preceding SCF or NSCF calculation.
            
skip_upperfan LOGICAL
Default: .false.
If .true., skip calculation of the upper Fan self-energy, which
involves solving the Sternheimer equation.
            
lshift_q LOGICAL
Default: .false.
Use a wave-vector grid displaced by half a grid step
in each direction - meaningful only when ldisp is .true.
When this option is set, the q2r.x code cannot be used.
         
zeu LOGICAL
Default: zeu=epsil
If .true. in a q=0 calculation for a non metal the
effective charges are computed from the dielectric
response. This is the default algorithm. If epsil=.true.
and zeu=.false. only the dielectric tensor is calculated.
         
zue LOGICAL
Default: .false.
If .true. in a q=0 calculation for a non metal the
effective charges are computed from the phonon
density responses. This is an alternative algorithm,
different from the default one (if trans .and. epsil )
The results should be the same within numerical noise.
         
elop LOGICAL
Default: .false.
If .true. calculate electro-optic tensor.
         
fpol LOGICAL
Default: .false.
If .true. calculate dynamic polarizabilities
Requires epsil=.true. ( experimental stage:
see example09 for calculation of methane ).
         
ldisp LOGICAL
Default: .false.
If .true. the run calculates phonons for a grid of
q-points specified by nq1, nq2, nq3 - for direct
calculation of the entire phonon dispersion.
         
nogg LOGICAL
Default: .false.
If .true. disable the "gamma_gamma" trick used to speed
up calculations at q=0 (phonon wavevector) if the sum over
the Brillouin Zone includes k=0 only. The gamma_gamma
trick exploits symmetry and acoustic sum rule to reduce
the number of linear response calculations to the strict
minimum, as it is done in code phcg.x.
         
asr LOGICAL
Default: .false.
Apply Acoustic Sum Rule to dynamical matrix, effective charges
Works only in conjunction with "gamma_gamma" tricks (see above)
         
ldiag LOGICAL
Default: .false.
If .true. forces the diagonalization of the dynamical
matrix also when only a part of the dynamical matrix
has been calculated. It is used together with start_irr
and last_irr. If all modes corresponding to a
given irreducible representation have been calculated,
the phonon frequencies of that representation are
correct. The others are zero or wrong. Use with care.
         
lqdir LOGICAL
Default: .false.
If .true. ph.x creates inside outdir a separate subdirectory
for each q vector. The flag is set to .true. when ldisp=.true.
and fildvscf /= ' ' or when an electron-phonon
calculation is performed. The induced potential is saved
separately for each q inside the subdirectories.
         
search_sym LOGICAL
Default: .true.
Set it to .false. if you want to disable the mode
symmetry analysis.
         
nq1, nq2, nq3 INTEGER
Default: 0,0,0
Parameters of the Monkhorst-Pack grid (no offset) used
when ldisp=.true. Same meaning as for nk1, nk2, nk3
in the input of pw.x.
         
nk1, nk2, nk3, k1, k2, k3 INTEGER
Default: 0,0,0,0,0,0
When these parameters are specified the phonon program
runs a pw non-self consistent calculation with a different
k-point grid thant that used for the charge density.
This occurs even in the Gamma case.
nk1, nk2, nk3 are the parameters of the Monkhorst-Pack grid
with offset determined by k1, k2, k3.
         
diagonalization CHARACTER
Default: 'david'
Diagonalization method for the non-SCF calculations.
            
'david' :
Davidson iterative diagonalization with overlap matrix
(default). Fast, may in some rare cases fail.
            
'cg' :
Conjugate-gradient-like band-by-band diagonalization.
Slower than 'david' but uses less memory and is
(a little bit) more robust.
            
read_dns_bare LOGICAL
Default: .false.
If .true. the PH code tries to read three files in the DFPT+U
calculation: dns_orth, dns_bare, d2ns_bare.
dns_orth and dns_bare are the first-order variations of
the occupation matrix, while d2ns_bare is the second-order
variation of the occupation matrix. These matrices are
computed only once during the DFPT+U calculation. However,
their calculation (especially of d2ns_bare) is computationally
expensive, this is why they are written to file and then can be
read (e.g. for restart) in order to save time.
         
ldvscf_interpolate LOGICAL
Default: .false.
If .true., use Fourier interpolation of phonon potential
to compute the induced part of phonon potential at each
q point. Results of a dvscf_q2r.x run is needed.
Requires trans = .false..
         

Optional variables for dvscf interpolation:

wpot_dir CHARACTER
Default: outdir // 'w_pot/'
Directory where the w_pot binary files are written.
Must be the same with wpot_dir used in dvscf_q2r.x.
The real space potential files are stored in wpot_dir
with names ${prefix}.wpot.irc${irc}//"1".
            
do_long_range LOGICAL
Default: .false.
If .true., add the long-range part of the potential
to the Fourier interpolated potential as in:
S. Ponce et al, J. Chem. Phys. 143, 102813 (2015).
Reads dielectric matrix and Born effective charges from
the ${wpot_dir}/tensors.dat file, written in dvscf_q2r.x.
Currently, only the dipole (Frohlich) part is implemented.
The quadrupole part is not implemented.
            
do_charge_neutral LOGICAL
Default: .false.
If .true., impose charge neutrality on the Born effective
charges. Used only if do_long_range = .true..
            

Specification of irreducible representation

start_irr INTEGER
Default: 1
See: last_irr
Perform calculations only from start_irr to last_irr
irreducible representations.

IMPORTANT:
   * start_irr must be <= 3*nat
   * do not specify nat_todo together with
     start_irr, last_irr
            
last_irr INTEGER
Default: 3*nat
See: start_irr
Perform calculations only from start_irr to last_irr
irreducible representations.

IMPORTANT:
   * start_irr must be <= 3*nat
   * do not specify nat_todo together with
     start_irr, last_irr
            
nat_todo INTEGER
Default: 0, i.e. displace all atoms
Choose the subset of atoms to be used in the linear response
calculation: nat_todo atoms, specified in input (see below)
are displaced. Can be used to estimate modes for a molecule
adsorbed over a surface without performing a full fledged
calculation. Use with care, at your own risk, and be aware
that this is an approximation and may not work.
IMPORTANT:
   * nat_todo <= nat
   * if linear-response is calculated for a given atom, it
     should also be done for all symmetry-equivalent atoms,
     or else you will get incorrect results
            
modenum INTEGER
Default: 0
For single-mode phonon calculation : modenum is the index of the
irreducible representation (irrep) into which the reducible
representation formed by the 3*nat atomic displacements are
decomposed in order to perform the phonon calculation.
Note that a single-mode calculation will not give you the
frequency of a single phonon mode: in general, the selected
"modenum" is not an eigenvector. What you get on output is
a column of the dynamical matrix.
            

q-point specification

start_q INTEGER
Default: 1
See: last_q
Used only when ldisp=.true..
Computes only the q points from start_q to last_q.

IMPORTANT:
   * start_q must be <= nqs (number of q points found)
   * do not specify nat_todo together with
     start_q, last_q
            
last_q INTEGER
Default: number of q points
See: start_q
Used only when ldisp=.true..
Computes only the q points from start_q to last_q.

IMPORTANT
   * last_q must be <= nqs (number of q points)
   * do not specify nat_todo together with
     start_q, last_q
            
dvscf_star STRUCTURE
Default: disabled
It contains the following components:

dvscf_star%open  (logical, default: .false.)
dvscf_star%dir   (character, default: outdir//"Rotated_DVSCF" or the
                  ESPRESSO_FILDVSCF_DIR environment variable)
dvscf_star%ext   (character, default: "dvscf") the extension to use
                  for the name of the output files, see below
dvscf_star%basis (character, default: "cartesian") the basis on which
                  the rotated dvscf will be saved
dvscf_star%pat   (logical, default: false) save an optional file with the
                  displacement patterns and q vector for each dvscf file

IF dvscf_star%open is .true. use symmetry to compute and store the variation
of the self-consistent potential on every q* in the star of the present q.

The rotated dvscf will then be stored in directory dvscf_star%dir with name
prefix.dvscf_star%ext.q_name//"1". Where q_name is derived from the coordinates
of the q-point, expressed as fractions in crystalline coordinates
(notice that ph.x reads q-points in cartesian coordinates).
E.g. q_cryst= (0, 0.5, -0.25) -> q_name = "0_1o2_-1o4"

The dvscf can be represented on a basis of cartesian 1-atom displacements
(dvscf_star%basis='cartesian') or on the basis of the modes at the rotated q-point
(dvscf_star%basis='modes'). Notice that the el-ph wannier code requires 'cartesian'.
Each dvscf file comes with a corresponding pattern file with an additional ".pat"
suffix; this file contains information about the basis and the q-point of the dvscf.

Note: rotating dvscf can require a large amount of RAM memory and can be i/o
      intensive; in its current implementation all the operations are done
      on a single processor.
Note2: this feature is currently untested with image parallelisation.
            
drho_star STRUCTURE
Default: disabled
See: dvscf_star
It contains the following components:

drho_star%open  (logical, default: .false.)
drho_star%dir   (character, default: outdir//"Rotated_DRHO" or the
                 ESPRESSO_FILDRHO_DIR environment variable)
drho_star%ext   (character, default: "drho") the extension to use
                 for the name of the output files, see below
drho_star%basis (character, default: "modes") the basis on which
                 the rotated drho will be saved
drho_star%pat   (logical, default: true) save an optional file with the
                 displacement patterns and q vector for each drho file

Like dvscf_star, but for the perturbation of the charge density.
Notice that the defaults are different.
            
IF ldisp != .true. and qplot != .true. :

Line of input

Syntax:

xq(1) xq(2) xq(3)   

Description of items:

xq(1) xq(2) xq(3) REAL
The phonon wavevector, in units of 2pi/a0
(a0 = lattice parameter).
Not used if ldisp=.true. or qplot=.true.
               
ELSEIF qplot == .true. :

Specification of q points when qplot == .true.

Card: qPointsSpecs

Syntax:

nqs  
 xq1(1)   xq2(1)   xq3(1)   nq(1) 
 xq1(2)   xq2(2)   xq3(2)   nq(2) 
 . . .
 xq1(nqs)   xq2(nqs)   xq3(nqs)   nq(nqs) 

Description of items:

nqs INTEGER
Number of q points in the list. Used only if qplot=.true.
                     
xq1, xq2, xq3 REAL
q-point coordinates; used only with ldisp=.true. and qplot=.true.
The phonon wavevector, in units of 2pi/a0 (a0 = lattice parameter).
The meaning of these q points and their weights nq depend on the
flags q2d and q_in_band_form. (NB: nq is integer)
                        
nq INTEGER
The weight of the q-point; the meaning of nq depends
on the flags q2d and q_in_band_form.
                        
IF nat_todo was specified :

Line of input

Syntax:

atom(1) atom(2) ... atom(nat_todo)   

Description of items:

atom(1) atom(2) ... atom(nat_todo) INTEGER
Contains the list of indices of atoms used in the
calculation if nat_todo is specified.
               

ADDITIONAL INFORMATION

NB: The program ph.x writes on the tmp_dir/_ph0/{prefix}.phsave directory
a file for each representation of each q point. This file is called
dynmat.#iq.#irr.xml where #iq is the number of the q point and #irr
is the number of the representation. These files contain the
contribution to the dynamical matrix of the irr representation for the
iq point.

If recover=.true. ph.x does not recalculate the
representations already saved in the tmp_dir/_ph0/{prefix}.phsave
directory.  Moreover ph.x writes on the files patterns.#iq.xml in the
tmp_dir/_ph0/{prefix}.phsave directory the displacement patterns that it
is using. If recover=.true. ph.x does not recalculate the
displacement patterns found in the tmp_dir/_ph0/{prefix}.phsave directory.

This mechanism allows:

  1) To recover part of the ph.x calculation even if the recover file
     or files are corrupted. You just remove the _ph0/{prefix}.recover
     files from the tmp_dir directory. You can also remove all the _ph0
     files and keep only the _ph0/{prefix}.phsave directory.

  2) To split a phonon calculation into several jobs for different
     machines (or set of nodes). Each machine calculates a subset of
     the representations and saves its dynmat.#iq.#irr.xml files on
     its tmp_dir/_ph0/{prefix}.phsave directory. Then you collect all the
     dynmat.#iq.#irr.xml files in one directory and run ph.x to
     collect all the dynamical matrices and diagonalize them.

NB: To split the q points in different machines, use the input
variables start_q and last_q. To split the irreducible
representations, use the input variables start_irr, last_irr. Please
note that different machines will use, in general, different
displacement patterns and it is not possible to recollect partial
dynamical matrices generated with different displacement patterns.  A
calculation split into different machines will run as follows: A
preparatory run of ph.x with start_irr=0, last_irr=0 produces the sets
of displacement patterns and save them on the patterns.#iq.xml files.
These files are copied in all the tmp_dir/_ph0/{prefix}.phsave directories
of the machines where you plan to run ph.x. ph.x is run in different
machines with complementary sets of start_q, last_q, start_irr and
last_irr variables.  All the files dynmat.#iq.#irr.xml are
collected on a single tmp_dir/_ph0/{prefix}.phsave directory (remember to
collect also dynmat.#iq.0.xml).  A final run of ph.x in this
machine collects all the data contained in the files and diagonalizes
the dynamical matrices.  This is done requesting a complete dispersion
calculation without using start_q, last_q, start_irr, or last_irr.
See an example in examples/GRID_example.

On parallel machines the q point and the irreps calculations can be split
automatically using the -nimage flag. See the phonon user guide for further
information.
      
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