[Pw_forum] absorption spectrum
Dear users I want opinion from experts in the area. I have a system consisting of 94 atoms (periodic with cell lengths of 16.5, 8.5 and 8.7). I want to calculate its absorption spectrum. Can anyone guide me which technique would be easy to run. Actually, we have 16 core machine and we can run a job for a maximum of 15 days only. Based upon this time limit, I would like to know which technique would be suitable. Epsilon.x, TDDFT or GW? any help in this regards would be highly appreciated. Thanks Adnan Bilknet U. Ankara ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
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-boun...@pwscf.org on behalf of
SungHwan Choi
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 13.015.015.0
Au 17.015.015.0
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 on48 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 89261110
Max 144 144 36 8936 89361124
Sum68696869 1725 428689 4
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
&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 13.015.015.0
Au 17.015.015.0
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 on48 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 89261110
Max 144 144 36 8936 89361124
Sum68696869 1725 428689 428689 53715
Tot34353435863
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 PCRoutineLineSource
Stack trace terminated abnormally.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PCRoutineLineSource
turbo_lanczos.x00AC5C31 Unknown Unknown Unknown
turbo_lanczos.x00AC4387 Unknown Unknown Unknown
turbo_lanczos.x00A6A554 Unknown Unknown Unknown
turbo_lanczos.x00A6A366 Unknown Unknown Unknown
turbo_lanczos.x00A00E8F Unknown Unknown Unknown
turbo_lanczos.x00A081BD Unknown Unknown Unknown
libpthread.so.02F38C850 Unknown Unknown Unknown
libc.so.6 2F88F0B8 Unknown Unknown Unknown
libc.so.6 2F8911F7 Unknown Unknown Unknown
libmkl_core.so 2CAC3460 Unknown Unknown Unknown
libmkl_core.so 2DCC5E76 Unknown Unknown Unknown
Stack trace terminated abnormally.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PCRoutineLineSource
turbo_lanczos.x00AC5C31 Unknown Unknown Unknown
turbo_lanczos.x00AC4387 Unknown Unknown Unknown
turbo_lanczos.x00A6A554 Unknown Unknown Unknown
turbo_lanczos.x00A6A366 Unknown Unknown Unknown
turbo_lanczos.x00A00E8F Unknown Unknown Unknown
turbo_lanczos.x00A081BD Unknown Unknown Unknown
libpthread.so.02F38C850 Unknown Unknown Unknown
turbo_lanczos.x00A1FC11 Unknown Unknown Unknown
turbo_lanczos.x00A1D6A1 Unknown Unknown Unknown
turbo_lanczos.x00775A72 davcio_ 382
io_files.f90
turbo_lanczos.x0041DD10 lr_read_wf_IP_nor 154
lr_read_wf.f90
turbo_lanczos.x0041D63B lr_read_wf_66
lr_read_wf.f90
turbo_lanczos.x00406BD9 MAIN__
Re: [Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
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 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 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 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 >>> 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 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= 0.000E+00 0.955769346791472E+01 > 0.000E+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 < > sunghwancho...@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@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.or
Re: [Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
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 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 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 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 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= 0.000E+00 0.955769346791472E+01 0.000E+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 < sunghwancho...@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@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
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 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 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 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= 0.000E+00 0.955769346791472E+01 >>> 0.000E+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 >> > 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@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
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 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 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= 0.000E+00 0.955769346791472E+01 >> 0.000E+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 >> 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@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
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 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= 0.000E+00 0.955769346791472E+01 > 0.000E+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 > 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@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
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= 0.000E+00 0.955769346791472E+01 0.000E+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 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@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] absorption spectrum &dielectric constant of turboTDDFT
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@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Absorption Spectra
You can find the answer in this paper: Osman Baris Malcioglu, Ralph Gebauer, Dario Rocca, Stefano Baroni, "turboTDDFT – A code for the simulation of molecular spectra using the Liouville–Lanczos approach to time-dependent density-functional perturbation theory", Computer Physics Communications 08/2011; 182(8):1744-1754. DOI:10.1016/j.cpc.2011.04.020 As I have previously reported in the '[Pw_forum] Optical Properties Problem', you have to perform Lanczos calculations in 3 directions (X,Y,Z) in order to obtain S (the oscillator strength) which is proportional to the absorption coefficient. See the documentation of TDDFPT and the examples provided together with the code. Use units=2 in order to obtain the absorption coefficient as a function of the wavelength in nm. HTH I. On 2015-06-10 09:49, Amreen Bano wrote: > I have got the Chi vs Omega plot but I want to calculate the > absorption spectra with wave number. > how do i get it. > Thanks in advance. > > -- > > Amreen Bano > Department of Physics, > Barkatullah University, > Bhopal-462 026 > INDIA > +91-9993515955 > banoamree...@gmail.com > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Dr. Iurii TIMROV Postdoctoral Researcher SISSA - International School for Advanced Studies Condensed Matter Sector Via Bonomea n. 265, Trieste 34151, Italy (+39) 04 03 78 74 77 http://people.sissa.it/~itimrov/ ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Absorption Spectra
I have got the Chi vs Omega plot but I want to calculate the absorption spectra with wave number. how do i get it. Thanks in advance. -- Amreen Bano Department of Physics, Barkatullah University, Bhopal-462 026 INDIA +91-9993515955 banoamree...@gmail.com ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] absorption
Dear all Which Bravais-lattice better for absorption hydrogen on BNNT "Hexagonal and Trigonal P" or "Tetragonal P (st)" ? thanks a lot Bani Adam Faculty of Science Egypt
[Pw_forum] absorption
If the cell is large enough that the nanotube can be considered isolated then the result should not depend on the chosen Bravais lattice. An hexagonal BL may optimize better the minimum distance between images. stefano On 05/01/2012 06:35 PM, bf azi wrote: > Dear all > > Which Bravais-lattice better for absorption hydrogen on BNNT > "Hexagonal and Trigonal P" or "Tetragonal P (st)" ? > > thanks a lot > > Bani Adam > Faculty of Science > Egypt > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] absorption
Dear all Which Bravais-lattice better for absorption hydrogen on BNNT "Hexagonal and Trigonal P" or "Tetragonal P (st)" ?
[Pw_forum] absorption spectrum calculation
Dear all, I am interested in absorption spectrum calculation of semiconductor materials am working on. I read from the example that came with the espresso package that after scf calculation, one need to run? upf2plotcore.sh to be able to extract the core electron from the pseudopotential of the system of interest. But i keep getting empty value in .wfc file. Please can anyone give me an idea. Adetunji Bamidele Ibrahim M.Sc/Ph.D Student, Department of physics, University of Agriculture, Abeokuta, Ogun State, Nigeria. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110610/83be5522/attachment.htm
