[Pw_forum] absorption spectrum &dielectric constant of turboTDDFT

SungHwan Choi sunghwanchoi91 at gmail.com
Fri Jul 22 07:00:58 CEST 2016


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
&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
&lr_input
restart=.false.
restart_step=100
prefix='Au'
outdir='./'
lr_verbosity=1
/
&lr_control
itermax=1000
ipol=4
/

input.pw work fine but 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>:

> 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> 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> 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> 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>
>>>> 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> 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> 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
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Pw_forum mailing list
>>>>>>> Pw_forum at pwscf.org
>>>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Pw_forum mailing list
>>>>>> Pw_forum at pwscf.org
>>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Pw_forum mailing list
>>>>> Pw_forum at pwscf.org
>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org
>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20160722/5ca155c3/attachment.html>


More information about the users mailing list