[Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
Timrov Iurii
iurii.timrov at epfl.ch
Fri Jul 22 12:45:41 CEST 2016
Dear Sunghwan Choi,
First some general comments:
1. Please always remember to sign your posts by indicating your affiliation (more information about how to make a post on the pw_forum can be found here
http://www.quantum-espresso.org/forum/)<http://www.quantum-espresso.org/forum/>
2. Your problem is different from the one discussed before in this thread. You should open new threads to ask your questions.
Now about your problem.
1. In order to solve your problem, do not specify the parameter "nbnd" in the input file for PWscf calculation. In this case, the code will compute only occupied states. The turboTDDFPT code (turbo_lanczos.x) needs only occupied states. But if one still includes some empty states in the calculations, the turbo_lanczos.x code still must work, but it does not in 5.4.0 version (and probably in some older versions), because there is a bug. This bug will be fixed soon and it will be committed to the SVN trunk on qe-forge.org. In your case, just do not specify "nbnd" and everything should be fine.
2. Your input for the PWscf code requires careful inspection, because there are several weird things. I comment only about one of them. Namely, you specified just "smearing='fermi-dirac'" probably thinking that your system is metallic. But your system is not metallic (and you can realize this by inspecting the output of the PWscf calculation), because in the PWscf you must also specify occupations = 'smearing', and of course the value of the broadening parameter "degauss = XXX" for the Fermi-Dirac smearing (because in your case you have smearing='fermi-dirac').
3. Even when you solve the problem in step 2, the turboTDDFT code does not currently support metallic systems. If you try to run it you will get an error message "turboTDDFT is not extended to metals".
Thank you for reporting about your problem, because it helped to find a bug.
HTH
Best regards,
Iurii
--
Dr. Iurii Timrov
Postdoctoral Researcher
Swiss Federal Institute of Technology Lausanne (EPFL)
Laboratory of Theory and Simulation of Materials (THEOS)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of SungHwan Choi <sunghwanchoi91 at gmail.com>
Sent: Friday, July 22, 2016 7:00 AM
To: PWSCF Forum
Subject: Re: [Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
Dear all,
As a one of newbies, I am happy to see active discussion.
I am now trying to obtain some spectrum of metallic quantum dot.
For a test, I put two gold atoms but I failed to run it
pwscf/Au2> cat input.pw<http://input.pw>
&control
calculation='scf'
pseudo_dir ='./',
outdir='./'
title='scf Au'
prefix='Au'
tprnfor=.true.
disk_io='low', restart_mode='from_scratch'
/
&system
ibrav=1, celldm(1) =30.0, nat=2, ntyp= 1, nbnd=50, smearing='fermi-dirac'
ecutwfc =24.0, nosym=.true.
/
&electrons
mixing_mode='plain'
mixing_beta = 0.5,
electron_maxstep=500,
diago_david_ndim=30,
conv_thr = 1.0d-6
/
ATOMIC_SPECIES
Au 196.97 Au.pbe-theos.UPF
ATOMIC_POSITIONS {bohr}
Au 13.0 15.0 15.0
Au 17.0 15.0 15.0
K_POINTS {gamma}
pwscf/Au2> cat input.lr<http://input.lr>
&lr_input
restart=.false.
restart_step=100
prefix='Au'
outdir='./'
lr_verbosity=1
/
&lr_control
itermax=1000
ipol=4
/
input.pw<http://input.pw> work fine but input.lr<http://input.lr> failed to run. output firstly work fine but at some point it just ended.
Program turboTDDFT v.5.4.0 starts on 22Jul2016 at 13:49:57
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Parallel version (MPI), running on 48 processors
R & G space division: proc/nbgrp/npool/nimage = 48
Reading data from directory:
./Au.save
Info: using nr1, nr2, nr3 values from input
Info: using nr1, nr2, nr3 values from input
IMPORTANT: XC functional enforced from input :
Exchange-correlation = SLA PW PBX PBC ( 1 4 3 4 0 0)
Any further DFT definition will be discarded
Please, verify this is what you really want
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 142 142 34 8926 8926 1110
Max 144 144 36 8936 8936 1124
Sum 6869 6869 1725 428689 428689 53715
Tot 3435 3435 863
Subspace diagonalization in iterative solution of the eigenvalue problem:
one sub-group per k-point group (pool) will be used
scalapack distributed-memory algorithm (size of sub-group: 4* 4 procs)
Warning: There are virtual states in the input file, trying to disregard in response calculation
Normal read
Gamma point algorithm
with such a error message
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
Stack trace terminated abnormally.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
turbo_lanczos.x 0000000000AC5C31 Unknown Unknown Unknown
turbo_lanczos.x 0000000000AC4387 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A6A554 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A6A366 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A00E8F Unknown Unknown Unknown
turbo_lanczos.x 0000000000A081BD Unknown Unknown Unknown
libpthread.so.0 00002AAAAF38C850 Unknown Unknown Unknown
libc.so.6 00002AAAAF88F0B8 Unknown Unknown Unknown
libc.so.6 00002AAAAF8911F7 Unknown Unknown Unknown
libmkl_core.so 00002AAAACAC3460 Unknown Unknown Unknown
libmkl_core.so 00002AAAADCC5E76 Unknown Unknown Unknown
Stack trace terminated abnormally.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
turbo_lanczos.x 0000000000AC5C31 Unknown Unknown Unknown
turbo_lanczos.x 0000000000AC4387 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A6A554 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A6A366 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A00E8F Unknown Unknown Unknown
turbo_lanczos.x 0000000000A081BD Unknown Unknown Unknown
libpthread.so.0 00002AAAAF38C850 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A1FC11 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A1D6A1 Unknown Unknown Unknown
turbo_lanczos.x 0000000000775A72 davcio_ 382 io_files.f90
turbo_lanczos.x 000000000041DD10 lr_read_wf_IP_nor 154 lr_read_wf.f90
turbo_lanczos.x 000000000041D63B lr_read_wf_ 66 lr_read_wf.f90
turbo_lanczos.x 0000000000406BD9 MAIN__ 118 lr_main.f90
turbo_lanczos.x 000000000040698E Unknown Unknown Unknown
libc.so.6 00002AAAAF831C36 Unknown Unknown Unknown
turbo_lanczos.x 0000000000406899 Unknown Unknown Unknown
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
turbo_lanczos.x 0000000000AC5C31 Unknown Unknown Unknown
turbo_lanczos.x 0000000000AC4387 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A6A554 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A6A366 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A00E8F Unknown Unknown Unknown
turbo_lanczos.x 0000000000A081BD Unknown Unknown Unknown
libpthread.so.0 00007FFFCA7ED850 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A1FC11 Unknown Unknown Unknown
turbo_lanczos.x 0000000000A1D6A1 Unknown Unknown Unknown
turbo_lanczos.x 0000000000775A72 davcio_ 382 io_files.f90
turbo_lanczos.x 000000000041DD10 lr_read_wf_IP_nor 154 lr_read_wf.f90
turbo_lanczos.x 000000000041D63B lr_read_wf_ 66 lr_read_wf.f90
turbo_lanczos.x 0000000000406BD9 MAIN__ 118 lr_main.f90
turbo_lanczos.x 000000000040698E Unknown Unknown Unknown
libc.so.6 00007FFFCA207C36 Unknown Unknown Unknown
turbo_lanczos.x 0000000000406899 Unknown Unknown Unknown
Could you help me? please do not hesitate to tell me if you have any clues
best,
Sunghwan Choi
2016-07-22 6:54 GMT+09:00 Manu Hegde <mhegde at uwaterloo.ca<mailto:mhegde at uwaterloo.ca>>:
Hi Dario,
Thanks. My unit cell already big contains 80 atoms, I will try to calculate using supercell.
Regards,
Manu
On Thu, Jul 21, 2016 at 4:02 PM, dario rocca <roccad at gmail.com<mailto:roccad at gmail.com>> wrote:
Hi Manu,
The last release of the code does not allow for k-point sampling, that's why you get an error message.
You would need to use a supercell. If you have done a gamma only calculation for your system that's probably why you get a spectrum
that does not match at all experiments.
Additionally, the Bethe-Salpeter equation is considered the most accurate method for bulk solids.
Best,
Dario
On Thu, Jul 21, 2016 at 9:42 AM, Manu Hegde <mhegde at uwaterloo.ca<mailto:mhegde at uwaterloo.ca>> wrote:
Hi Dario,
Thank you very much. I have done some calculations for UV-Vis (see attached) and it is no where matching my experimental results in case of bcc-In2O3. Is it due to pseudopotential (I have used PBE USPP)?. Also I am unable to BZ sampling on k-mesh and TDDFT shown me an error.
Regards,
Manu
(University of Waterloo)
On Wed, Jul 20, 2016 at 8:09 PM, dario rocca <roccad at gmail.com<mailto:roccad at gmail.com>> wrote:
Dear Manu,
You can simply extract it with the command
$ grep "S(E)" prefix.plot_chi.dat > file_for_plot
and use your favorite program to plot it.
Best,
Dario
On Wed, Jul 20, 2016 at 10:49 AM, Manu Hegde <mhegde at uwaterloo.ca<mailto:mhegde at uwaterloo.ca>> wrote:
Hello Dario,
I have done the similar calculations, it went well, after running turbo_spectrum.x Do you have any code to extract S(E) or I have to do it manually?
Manu
(University of Waterloo)
On Tue, Jul 19, 2016 at 8:24 PM, dario rocca <roccad at gmail.com<mailto:roccad at gmail.com>> wrote:
Dear SungHwan,
please refer to
http://arxiv.org/pdf/1402.0486.pdf
and
http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1
for more details.
In the output of the postprocessing chi_1_1 is the xx component of the dynamical polarizability, chi_1_2 the xy component, etc.
Often chi is indicated as \alpha in the papers.
Specifically you would have
Component energy of the perturbation real part of chi imaginary
(indicated either as E or \omega)
chi_1_1= 0.000000000000000E+00 0.955769346791472E+01 0.000000000000000E+00
.........
As you correctly say the absorption spectrum is related to the imaginary part of the average of chi multiplied by E (the energy E is often
indicated as \omega).
This averaged quantity is contained in S(E). Specifically S(E) is the strength function defined as
S(E)=2m/(\pi*e^2*\hbar) * E*Im[chi(E)], where chi has been averaged over the 3 spatial directions.
This definition is convenient because S(E) satisfies the f-sum rule.
So if you extract S(E) and plot it you will have the absorption spectrum.
Let me know if it's still not clear
Best,
Dario
On Tue, Jul 19, 2016 at 4:01 PM, SungHwan Choi <sunghwanchoi91 at gmail.com<mailto:sunghwanchoi91 at gmail.com>> wrote:
hi, I am a newbie for turboTDDFT. Now, I ran a simple example. It was assume. Now I have prefix.plot_chi.dat file. then I don't know how to generate absorption spectrum from that file and dielectric constant values. As far as I understood, the absorption spectrum is related to imaginary part of average \chi value. but in the file there are 9 values
chi_1_1
chi_2_1
chi_3_1
chi_1_2
chi_2_2
chi_3_2
chi_1_3
chi_2_3
chi_3_3
This is 3*3*3 tensor. how do I get an absorption spectrum and dieletric constant values? by the way S(E) means what?
Sincerely
Sunghwan Choi
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