User Guide

user_guide

User Manual:

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PHonon User’s Guide (v. 6.4)
(only partially updated)
Contents
1 Introduction 1
2 People 2
3 Installation 3
3.1 Compilation...................................... 4
4 Using PHonon 4
4.1 Single-qcalculation.................................. 5
4.2 Calculation of interatomic force constants in real space . . . . . . . . . . . . . . 5
4.3 Calculation of electron-phonon interaction coefficients . . . . . . . . . . . . . . . 6
4.4 DFPT with the tetrahedron method . . . . . . . . . . . . . . . . . . . . . . . . . 6
4.5 Calculation of electron-phonon interaction coefficients with the tetrahedron method 7
4.6 Phonons for two-dimensional crystals . . . . . . . . . . . . . . . . . . . . . . . . 7
4.7 Phonons from DFPT+U............................... 7
5 Parallelism 8
6 Troubleshooting 8
A Appendix: Electron-phonon coefficients 10
1 Introduction
This guide covers the usage of the PHonon package, a part of the Quantum ESPRESSO
distribution. Further documentation, beyond what is provided in this guide, can be found in
the directory PHonon/Doc/, containing a copy of this guide.
Important notice: due to the lack of time and of manpower, this manual is only partially
updated and may contain outdated information.
This guide assumes that you know the contents of the general User’s Guide for Quantum
ESPRESSO and of the User’s Guide for PWscf. It also assumes that you have already installed
1
Quantum ESPRESSO (PHonon is not a stand-alone package: it requires PWscf to be compiled
and used). If not, please locate the general User’s Guide in directory Doc/ two levels above the
one containing this guide, and the User’s Guide for PWscf in PW/Doc/; or consult the web site:
http://www.quantum-espresso.org. It is also assumed that you know the physics behind
Quantum ESPRESSO, the methods it implements, and in particular the physics and the
methods of PHonon.
PHonon has the following directory structure, contained in a subdirectory PHonon/ of the
main Quantum ESPRESSO tree:
Doc/ : contains the user guide and input data description
examples/ : some running examples
PH/ : source files for phonon calculations and analysis
Gamma/ : source files for Gamma-only phonon calculation
Important Notice: since v.5.4, many modules and routines that were common to all linear-
response Quantum ESPRESSO codes are moved into the new LR Modules subdirectory of
the main tree. Since v.6.0, the D3 code for anharmonic force constant calculations has been
superseded by the D3Q coda, available on http://www.qe-forge.org/gf/project/d3q/.
The codes available in the PHonon package can perform the following types of calculations:
•phonon frequencies and eigenvectors at a generic wave vector, using Density-Functional
Perturbation Theory;
•effective charges and dielectric tensors;
•electron-phonon interaction coefficients for metals;
•interatomic force constants in real space;
•Infrared and Raman (nonresonant) cross section.
Phonons can be plotted using the PlotPhon package. Calculations of the vibrational free
energy in the Quasi-Harmonic approximations can be performed using the QHA package. Note:
since v.5.4, these two packages are separately distributed and no longer bundled with PHonon.
Their latest version can be found in the tarballs of PHonon v.5.3.
2 People
The PHonon package was originally developed by Stefano Baroni, Stefano de Gironcoli, Andrea
Dal Corso (SISSA), Paolo Giannozzi (Univ. Udine), and many others. We quote in particular:
•Michele Lazzeri (Univ.Paris VI) for the 2n+1 code and Raman cross section calculation
with 2nd-order response;
•Andrea Dal Corso for the implementation of Ultrasoft, PAW, noncolinear, spin-orbit
extensions to PHonon;
•Mitsuaki Kawamura (U.Tokyo) for implementation of the optimized tetrahedron method
in phonon and electron-phonon calculations;
•Thibault Sohier, Matteo Calandra, Francesco Mauri, for phonons in two-dimensional
systems;
2
•Andrea Floris, Iurii Timrov, Burak Himmetoglu, Stefano de Gironcoli, Nicola Marzari,
and Matteo Cococcioni, for phonons using Hubbard-corrected DFPT (DFPT+U).
The PlotPhon and QHA packages were contribute by the late Prof. Eyvaz Isaev.
Other contributors include: Lorenzo Paulatto (Univ. Paris VI) for PAW, 2n+1 code;
William Parker (Argonne) for phonon terms in dielectric tensor; Tobias Wassmann (Univ.
Paris VI) for third-order derivatives of GGA potential. Weicheng Bao (Nanjing University)
and Norge Cruz Hernandez (Universidad de Sevilla) helped debugging the phonon code.
We shall greatly appreciate if scientific work done using the Quantum ESPRESSO dis-
tribution will contain an acknowledgment to the following references:
P. Giannozzi, S. Baroni, N. Bonini, M. Calandra, R. Car, C. Cavazzoni, D. Ceresoli,
G. L. Chiarotti, M. Cococcioni, I. Dabo, A. Dal Corso, S. Fabris, G. Fratesi, S. de
Gironcoli, R. Gebauer, U. Gerstmann, C. Gougoussis, A. Kokalj, M. Lazzeri, L.
Martin-Samos, N. Marzari, F. Mauri, R. Mazzarello, S. Paolini, A. Pasquarello, L.
Paulatto, C. Sbraccia, S. Scandolo, G. Sclauzero, A. P. Seitsonen, A. Smogunov, P.
Umari, R. M. Wentzcovitch, J.Phys.: Condens.Matter 21, 395502 (2009)
and
P. Giannozzi, O. Andreussi, T. Brumme, O. Bunau, M. Buongiorno Nardelli, M.
Calandra, R. Car, C. Cavazzoni, D. Ceresoli, M. Cococcioni, N. Colonna, I. Carn-
imeo, A. Dal Corso, S. de Gironcoli, P. Delugas, R. A. DiStasio Jr, A. Ferretti, A.
Floris, G. Fratesi, G. Fugallo, R. Gebauer, U. Gerstmann, F. Giustino, T. Gorni, J
Jia, M. Kawamura, H.-Y. Ko, A. Kokalj, E. K¨u¸c¨ukbenli, M .Lazzeri, M. Marsili, N.
Marzari, F. Mauri, N. L. Nguyen, H.-V. Nguyen, A. Otero-de-la-Roza, L. Paulatto,
S. Ponc´e, D. Rocca, R. Sabatini, B. Santra, M. Schlipf, A. P. Seitsonen, A. Smo-
gunov, I. Timrov, T. Thonhauser, P. Umari, N. Vast, X. Wu, S. Baroni J.Phys.:
Condens.Matter 29, 465901 (2017)
Note the form Quantum ESPRESSO for textual citations of the code. Please also see
package-specific documentation for further recommended citations. Pseudopotentials should
be cited as (for instance)
[ ] We used the pseudopotentials C.pbe-rrjkus.UPF and O.pbe-vbc.UPF from
http://www.quantum-espresso.org.
3 Installation
PHonon is a package tightly bound to Quantum ESPRESSO. For instruction on how to down-
load and compile Quantum ESPRESSO, please refer to the general Users’ Guide, available
in file Doc/user guide.pdf under the main Quantum ESPRESSO directory, or in web site
http://www.quantum-espresso.org.
Once Quantum ESPRESSO is correctly configured, PHonon can be automatically down-
loaded, unpacked and compiled by just typing make ph, from the main Quantum ESPRESSO
directory.
3
3.1 Compilation
Typing make ph from the root Quantum ESPRESSO directory, or make from the PHonon
directory, produces the following codes:
•PH/ph.x: Calculates phonon frequencies and displacement patterns, dielectric tensors,
effective charges (uses data produced by pw.x).
•PH/dynmat.x: applies various kinds of Acoustic Sum Rule (ASR), calculates LO-TO
splitting at q= 0 in insulators, IR and Raman cross sections (if the coefficients have been
properly calculated), from the dynamical matrix produced by ph.x
•PH/q2r.x: calculates Interatomic Force Constants (IFC) in real space from dynamical
matrices produced by ph.x on a regular q-grid
•PH/matdyn.x: produces phonon frequencies at a generic wave vector using the IFC file
calculated by q2r.x; may also calculate phonon DOS, the electron-phonon coefficient λ,
the function α2F(ω)
•PH/lambda.x: also calculates λand α2F(ω), plus Tcfor superconductivity using the
McMillan formula
•PH/alpha2f.x: also calculates λand α2F(ω). It is used together with the optimized tetra-
hedron method (occupations="tetrahedra_opt" in pw.x) and shifted q-grid (lshiftq=.true.
in ph.x).
•PH/fqha.x: a simple code to calculate vibrational entropy with the quasi-harmonic ap-
proximation
•Gamma/phcg.x: a version of ph.x that calculates phonons at q= 0 using conjugate-
gradient minimization of the density functional expanded to second-order. Only the Γ
(k= 0) point is used for Brillouin zone integration. It is faster and takes less memory
than ph.x, but does not support USPP and PAW.
Links to the main Quantum ESPRESSO bin/ directory are automatically generated.
4 Using PHonon
Phonon calculation is presently a two-step process. First, you have to find the ground-
state atomic and electronic configuration; Second, you can calculate phonons using Density-
Functional Perturbation Theory. Further processing to calculate Interatomic Force Constants,
to add macroscopic electric field and impose Acoustic Sum Rules at q= 0 may be needed. In
the following, we will indicate by qthe phonon wavevectors, while kwill indicate Bloch vectors
used for summing over the Brillouin Zone.
The main code ph.x can be used whenever PWscf can be used, with the exceptions of
DFT+U, hybrid functionals, external electric fields, constraints on magnetization, nonperiodic
boundary conditions. USPP and PAW are not implemented for higher-order response calcula-
tions. See the header of file PHonon/PH/phonon.f90 for a complete and updated list of what
PHonon can and cannot do.
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Since version 4.0 it is possible to safely stop execution of ph.x code using the same mecha-
nism of the pw.x code, i.e. by creating a file prefix.EXIT in the working directory. Execution
can be resumed by setting recover=.true. in the subsequent input data. Moreover the exe-
cution can be (cleanly) stopped after a given time is elapsed, using variable max seconds. See
example/Recover example/.
4.1 Single-q calculation
The phonon code ph.x calculates normal modes at a given q-vector, starting from data files
produced by pw.x with a simple SCF calculation. NOTE: the alternative procedure in which a
band-structure calculation with calculation=’phonon’ was performed as an intermediate step
is no longer implemented since version 4.1. It is also no longer needed to specify lnscf=.true.
for q6= 0.
The output data files appear in the directory specified by the variable outdir, with names
specified by the variable prefix. After the output file(s) has been produced (do not remove
any of the files, unless you know which are used and which are not), you can run ph.x.
The first input line of ph.x is a job identifier. At the second line the namelist &INPUTPH
starts. The meaning of the variables in the namelist (most of them having a default value) is
described in file Doc/INPUT PH.*. Variables outdir and prefix must be the same as in the
input data of pw.x. Presently you can specify amass(i) (a real variable) the atomic mass of
atomic type ior you can use the default one deduced from the periodic table on the basis of
the element name. If amass(i) is not given as input of ph.x, the one given as input in pw.x is
used. When this is 0the default one is used.
After the namelist you must specify the q-vector of the phonon mode, in Cartesian coordi-
nates and in units of 2π/a.
Notice that the dynamical matrix calculated by ph.x at q= 0 does not contain the non-
analytic term occurring in polar materials, i.e. there is no LO-TO splitting in insulators.
Moreover no Acoustic Sum Rule (ASR) is applied. In order to have the complete dynamical
matrix at q= 0 including the non-analytic terms, you need to calculate effective charges by
specifying option epsil=.true. to ph.x. This is however not possible (because not physical!)
for metals (i.e. any system subject to a broadening).
At q= 0, use program dynmat.x to calculate the correct LO-TO splitting, IR cross sections,
and to impose various forms of ASR. If ph.x was instructed to calculate Raman coefficients,
dynmat.x will also calculate Raman cross sections for a typical experimental setup. Input
documentation in the header of PHonon/PH/dynmat.f90.
See Example 01 for a simple phonon calculations in Si, Example 06 for fully-relativistic
calculations (LDA) on Pt, Example 07 for fully-relativistic GGA calculations.
4.2 Calculation of interatomic force constants in real space
First, dynamical matrices are calculated and saved for a suitable uniform grid of q-vectors
(only those in the Irreducible Brillouin Zone of the crystal are needed). Although this can be
done one q-vector at the time, a simpler procedure is to specify variable ldisp=.true. and to
set variables nq1,nq2,nq3 to some suitable Monkhorst-Pack grid, that will be automatically
generated, centered at q= 0.
Second, code q2r.x reads the dynamical matrices produced in the preceding step and
Fourier-transform them, writing a file of Interatomic Force Constants in real space, up to a
5
distance that depends on the size of the grid of q-vectors. Input documentation in the header
of PHonon/PH/q2r.f90.
Program matdyn.x may be used to produce phonon modes and frequencies at any qus-
ing the Interatomic Force Constants file as input. Input documentation in the header of
PHonon/PH/matdyn.f90.
See Example 02 for a complete calculation of phonon dispersions in AlAs.
4.3 Calculation of electron-phonon interaction coefficients
Since v.5.0, there are two ways of calculating electron-phonon coefficients, distinguished accord-
ing to the value of variable electron phonon. The following holds for the case electron phonon=
’interpolated’ (see also Example 03).
The calculation of electron-phonon coefficients in metals is made difficult by the slow conver-
gence of the sum at the Fermi energy. It is convenient to use a coarse k-point grid to calculate
phonons on a suitable wavevector grid; a dense k-point grid to calculate the sum at the Fermi
energy. The calculation proceeds in this way:
1. a scf calculation for the dense k-point grid (or a scf calculation followed by a non-scf
one on the dense k-point grid); specify option la2f=.true. to pw.x in order to save a
file with the eigenvalues on the dense k-point grid. The latter MUST contain all kand
k+qgrid points used in the subsequent electron-phonon calculation. All grids MUST
be unshifted, i.e. include k= 0.
2. a normal scf + phonon dispersion calculation on the coarse k-point grid, specifying option
electron phonon=’interpolated’, and the file name where the self-consistent first-order
variation of the potential is to be stored: variable fildvscf). The electron-phonon coeffi-
cients are calculated using several values of Gaussian broadening (see PHonon/PH/elphon.f90)
because this quickly shows whether results are converged or not with respect to the k-
point grid and Gaussian broadening.
3. Finally, you can use matdyn.x and lambda.x (input documentation in the header of
PHonon/PH/lambda.f90) to get the α2F(ω) function, the electron-phonon coefficient λ,
and an estimate of the critical temperature Tc.
See the appendix for the relevant formulae. Important notice: the q→0 limit of the con-
tribution to the electron-phonon coefficient diverges for optical modes! please be very careful,
consult the relevant literature. .
4.4 DFPT with the tetrahedron method
In order to use the tetrahedron method for phonon calculations, you should run pw.x and ph.x
as follows:
1. Run pw.x with occupation = "tetrahedra_opt" and K_POINT automatic.
2. Run ph.x.
There is an example in PHonon/example/tetra_example/.
6
4.5 Calculation of electron-phonon interaction coefficients with the
tetrahedron method
When you perform a calculation of electron-phonon interaction coefficients with the tetrahedron
method, you have to use an offset q-point grid in order to avoid a singularity at q= Γ; you can
perform this calculation as follows:
1. Run pw.x with occupation = "tetrahedra_opt" and K_POINT automatic.
2. Run ph.x with lshift_q = .true. and electron_phonon = "" (or unset it) to generate
the dynamical matrix and the deformation potential (in _ph*/{prefix}_q*/) of each q.
3. Run ph.x with electron_phonon = "lambda_tetra". You should use a denser kgrid
by setting nk1,nk2, and nk3. Then lambda*.dat are generated; they contain λqν .
4. Run alpha2f.x with an input file as follows:
&INPUTPH
! The same as that for the electron-phonon calculation with ph.x
:
/
&INPUTA2F
nfreq = Number of frequency-points for a2F(omega),
/
Then λ, and ωln are computed and they are printed to the standard output. α2F(ω) and
(partial) phonon-DOS are also computed; they are printed to a file prefix .a2F.dat.
There is an example in PHonon/example/tetra_example/.
4.6 Phonons for two-dimensional crystals
The extension of DFPT to two dimensional crystals, in particular gated two-dimensional het-
erostructure, s described in the following paper:
T. Sohier, M. Calandra, and F. Mauri, Phys. Rev. B 96, 075448 (2017), https://doi.org/10.1103/PhysRevB.96.075448
See example PHonon/example/example17/.
4.7 Phonons from DFPT+U
The extension of DFPT to inlcude Hubbard Ucorrection is described in the following papers:
A. Floris, S. de Gironcoli, E. K. U. Gross, M. Cococcioni, Phys. Rev. B 84, 161102(R),
(2011);
A. Floris, I. Timrov, B. Himmetoglu, N. Marzari, S. de Gironcoli, and M. Cococcioni, in
preparation.
See example PHonon/example/example18/.
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5 Parallelism
We refer to the corresponding section of the PWscf guide for an explanation of how parallelism
works.
ph.x may take advantage of MPI parallelization on images, plane waves (PW) and on k-
points (“pools”). Currently all other MPI and explicit OpenMP parallelizations have very
limited to nonexistent implementation. phcg.x implements only PW parallelization. All other
codes may be launched in parallel, but will execute on a single processor.
In “image” parallelization, processors can be divided into different “images”, corresponding
to one (or more than one) “irrep” or qvectors. Images are loosely coupled: processors com-
municate between different images only once in a while, so image parallelization is suitable for
cheap communication hardware (e.g. Gigabit Ethernet). Image parallelization is activated by
specifying the option -nimage N to ph.x. Inside an image, PW and k-point parallelization can
be performed: for instance,
mpirun -np 64 ph.x -ni 8 -nk 2 ...
will run 8 images on 8 processors each, subdivided into 2 pools of 4 processors for k-point
parallelization. In order to run the ph.x code with these flags the pw.x run has to be run with:
mpirun -np 8 pw.x -nk 2 ...
without any -nimage flag. After the phonon calculation with images the dynmical matrices
of q-vectors calculated in different images are not present in the working directory. To obtain
them you need to run ph.x again with:
mpirun -np 8 ph.x -nk 2 ...
and the recover=.true. flag. This scheme is quite automatic and does not require any
additional work by the user, but it wastes some CPU time because all images stops when
the image that requires the largest amount of time finishes the calculation. Load balancing
between images is still at an experimental stage. You can look into the routine image q irr
inside PHonon/PH/check initial status to see the present algorithm for work distribution
and modify it if you think that you can improve the load balancing.
A different paradigm is the usage of the GRID concept, instead of MPI, to achieve paral-
lelization over irreps and qvectors. Complete phonon dispersion calculation can be quite long
and expensive, but it can be split into a number of semi-independent calculations, using options
start q,last q,start irr,last irr. An example on how to distribute the calculations and
collect the results can be found in examples/GRID example. Reference:
Calculation of Phonon Dispersions on the GRID using Quantum ESPRESSO, R. di Meo, A.
Dal Corso, P. Giannozzi, and S. Cozzini, in Chemistry and Material Science Applications on
Grid Infrastructures, editors: S. Cozzini, A. Lagan`a, ICTP Lecture Notes Series, Vol. 24,
pp.165-183 (2009).
6 Troubleshooting
ph.x stops with error reading file The data file produced by pw.x is bad or incomplete
or produced by an incompatible version of the code. In parallel execution: if you did not set
wf collect=.true., the number of processors and pools for the phonon run should be the
same as for the self-consistent run; all files must be visible to all processors.
8
ph.x mumbles something like cannot recover or error reading recover file You have
a bad restart file from a preceding failed execution. Remove all files recover* in outdir.
ph.x says occupation numbers probably wrong and continues You have a metallic or
spin-polarized system but occupations are not set to ‘smearing’.
ph.x does not yield acoustic modes with zero frequency at q = 0 This may not be
an error: the Acoustic Sum Rule (ASR) is never exactly verified, because the system is never
exactly translationally invariant as it should be. The calculated frequency of the acoustic mode
is typically less than 10 cm−1, but in some cases it may be much higher, up to 100 cm−1. The
ultimate test is to diagonalize the dynamical matrix with program dynmat.x, imposing the
ASR. If you obtain an acoustic mode with a much smaller ω(let us say <1cm−1) with all
other modes virtually unchanged, you can trust your results.
“The problem is [...] in the fact that the XC energy is computed in real space on a discrete
grid and hence the total energy is invariant (...) only for translation in the FFT grid. Increasing
the charge density cutoff increases the grid density thus making the integral more exact thus
reducing the problem, unfortunately rather slowly...This problem is usually more severe for
GGA than with LDA because the GGA functionals have functional forms that vary more
strongly with the position; particularly so for isolated molecules or system with significant
portions of “vacuum” because in the exponential tail of the charge density a) the finite cutoff
(hence there is an effect due to cutoff) induces oscillations in rho and b) the reduced gradient
is diverging.”(info by Stefano de Gironcoli, June 2008)
ph.x yields really lousy phonons, with bad or “negative” frequencies or wrong
symmetries or gross ASR violations Possible reasons:
•if this happens only for acoustic modes at q= 0 that should have ω= 0: Acoustic Sum
Rule violation, see the item before this one.
•wrong data file read.
•wrong atomic masses given in input will yield wrong frequencies (but the content of file
fildyn should be valid, since the force constants, not the dynamical matrix, are written
to file).
•convergence threshold for either SCF (conv thr) or phonon calculation (tr2 ph) too large:
try to reduce them.
•maybe your system does have negative or strange phonon frequencies, with the approx-
imations you used. A negative frequency signals a mechanical instability of the chosen
structure. Check that the structure is reasonable, and check the following parameters:
–The cutoff for wavefunctions, ecutwfc
–For USPP and PAW: the cutoff for the charge density, ecutrho
–The k-point grid, especially for metallic systems.
•For metallic systems: it has been observed that the convergence with respect to the
k-point grid and smearing is very slow in presence of semicore states, and for phonon
wave-vectors that are not commensurate i with the k-point grid (that is, q6=ki−kj)
9
Note that “negative” frequencies are actually imaginary: the negative sign flags eigenvalues of
the dynamical matrix for which ω2<0.
Wrong degeneracy error in star q Verify the q-vector for which you are calculating
phonons. In order to check whether a symmetry operation belongs to the small group of q,
the code compares qand the rotated q, with an acceptance tolerance of 10−5(set in routine
PW/eqvect.f90). You may run into trouble if your q-vector differs from a high-symmetry point
by an amount in that order of magnitude.
A Appendix: Electron-phonon coefficients
The electron-phonon coefficients gare defined as
gqν(k, i, j) = ¯h
2Mωqν!1/2
hψi,k|dVSCF
dˆuqν
·ˆqν|ψj,k+qi.(1)
The phonon linewidth γqνis defined by
γqν= 2πωqνX
ij Zd3k
ΩBZ
|gqν(k, i, j)|2δ(eq,i −eF)δ(ek+q,j −eF),(2)
while the electron-phonon coupling constant λqνfor mode νat wavevector qis defined as
λqν=γqν
π¯hN(eF)ω2
qν
(3)
where N(eF) is the DOS at the Fermi level. The spectral function is defined as
α2F(ω) = 1
2πN(eF)X
qν
δ(ω−ωqν)γqν
¯hωqν
.(4)
The electron-phonon mass enhancement parameter λcan also be defined as the first reciprocal
momentum of the spectral function:
λ=X
qν
λqν= 2 Zα2F(ω)
ωdω. (5)
Note that a factor M−1/2is hidden in the definition of normal modes as used in the code.
McMillan:
Tc=ΘD
1.45exp "−1.04(1 + λ)
λ(1 −0.62µ∗)−µ∗#(6)
or (better?)
Tc=ωlog
1.2exp "−1.04(1 + λ)
λ(1 −0.62µ∗)−µ∗#(7)
where
ωlog = exp "2
λZdω
ωα2F(ω)logω#(8)
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