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<p>Dear Sunghwan Choi,</p>
<p><br>
</p>
<p>First some general comments:</p>
<p><br>
</p>
<p>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
</p>
<p><a href="http://www.quantum-espresso.org/forum/">http://www.quantum-espresso.org/forum/)</a></p>
<p>2. Your problem is different from the one discussed before in this thread. You should open new threads to ask your questions.</p>
<p><br>
</p>
<p>Now about your problem.</p>
<p><br>
</p>
<p>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.</p>
<p><br>
</p>
<p>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').</p>
<p><br>
</p>
<p>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".</p>
<p><br>
</p>
<p>Thank you for reporting about your problem, because it helped to find a bug.<br>
</p>
<p><br>
</p>
<p>HTH <br>
</p>
<p><br>
</p>
<p>Best regards,</p>
<p>Iurii<br>
</p>
<p><br>
</p>
<p><br>
</p>
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<font color="808080" face="'Times New Roman', Times, serif" size="3">--<br>
Dr. Iurii Timrov<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" color="#000000" face="Calibri, sans-serif"><b>From:</b> pw_forum-bounces@pwscf.org <pw_forum-bounces@pwscf.org> on behalf of SungHwan Choi <sunghwanchoi91@gmail.com><br>
<b>Sent:</b> Friday, July 22, 2016 7:00 AM<br>
<b>To:</b> PWSCF Forum<br>
<b>Subject:</b> Re: [Pw_forum] absorption spectrum &dielectric constant of turboTDDFT</font>
<div> </div>
</div>
<div>
<div dir="ltr">Dear all,
<div>As a one of newbies, I am happy to see active discussion.</div>
<div>I am now trying to obtain some spectrum of metallic quantum dot. </div>
<div>For a test, I put two gold atoms but I failed to run it</div>
<div><br>
</div>
<div>
<div>pwscf/Au2> cat <a href="http://input.pw">input.pw</a> </div>
<div>&control</div>
<div>calculation='scf'</div>
<div>pseudo_dir ='./',</div>
<div>outdir='./'</div>
<div>title='scf Au'</div>
<div>prefix='Au'</div>
<div>tprnfor=.true.</div>
<div>disk_io='low', restart_mode='from_scratch'</div>
<div>/</div>
<div>&system</div>
<div>ibrav=1, celldm(1) =30.0, nat=2, ntyp= 1, nbnd=50, smearing='fermi-dirac'</div>
<div>ecutwfc =24.0, nosym=.true.</div>
<div>/</div>
<div>&electrons</div>
<div>mixing_mode='plain'</div>
<div>mixing_beta = 0.5,</div>
<div>electron_maxstep=500,</div>
<div>diago_david_ndim=30,</div>
<div>conv_thr = 1.0d-6</div>
<div>/</div>
<div>ATOMIC_SPECIES</div>
<div>Au 196.97 Au.pbe-theos.UPF</div>
<div>ATOMIC_POSITIONS {bohr}</div>
<div> Au 13.0 15.0 15.0</div>
<div> Au 17.0 15.0 15.0</div>
<div>K_POINTS {gamma}</div>
<div><br>
</div>
<div>pwscf/Au2> cat <a href="http://input.lr">input.lr</a> </div>
<div>&lr_input</div>
<div>restart=.false.</div>
<div>restart_step=100</div>
<div>prefix='Au'</div>
<div>outdir='./'</div>
<div>lr_verbosity=1</div>
<div>/</div>
<div>&lr_control</div>
<div>itermax=1000</div>
<div>ipol=4</div>
<div>/</div>
<div><br>
</div>
</div>
<div><a href="http://input.pw">input.pw</a> work fine but <a href="http://input.lr">
input.lr</a> failed to run. output firstly work fine but at some point it just ended.</div>
<div><br>
</div>
<div>
<div><br>
</div>
<div> Program turboTDDFT v.5.4.0 starts on 22Jul2016 at 13:49:57 </div>
<div><br>
</div>
<div> This program is part of the open-source Quantum ESPRESSO suite</div>
<div> for quantum simulation of materials; please cite</div>
<div> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);</div>
<div> URL <a href="http://www.quantum-espresso.org">http://www.quantum-espresso.org</a>", </div>
<div> in publications or presentations arising from this work. More details at</div>
<div> <a href="http://www.quantum-espresso.org/quote">http://www.quantum-espresso.org/quote</a></div>
<div><br>
</div>
<div> Parallel version (MPI), running on 48 processors</div>
<div> R & G space division: proc/nbgrp/npool/nimage = 48</div>
<div><br>
</div>
<div> Reading data from directory:</div>
<div> ./Au.save</div>
<div><br>
</div>
<div> Info: using nr1, nr2, nr3 values from input</div>
<div><br>
</div>
<div> Info: using nr1, nr2, nr3 values from input</div>
<div><br>
</div>
<div> IMPORTANT: XC functional enforced from input :</div>
<div> Exchange-correlation = SLA PW PBX PBC ( 1 4 3 4 0 0)</div>
<div> Any further DFT definition will be discarded</div>
<div> Please, verify this is what you really want</div>
<div><br>
</div>
<div> </div>
<div> Parallelization info</div>
<div> --------------------</div>
<div> sticks: dense smooth PW G-vecs: dense smooth PW</div>
<div> Min 142 142 34 8926 8926 1110</div>
<div> Max 144 144 36 8936 8936 1124</div>
<div> Sum 6869 6869 1725 428689 428689 53715</div>
<div> Tot 3435 3435 863</div>
<div> </div>
<div><br>
</div>
<div> Subspace diagonalization in iterative solution of the eigenvalue problem:</div>
<div> one sub-group per k-point group (pool) will be used</div>
<div> scalapack distributed-memory algorithm (size of sub-group: 4* 4 procs)</div>
<div><br>
</div>
<div><br>
</div>
<div> Warning: There are virtual states in the input file, trying to disregard in response calculation</div>
<div><br>
</div>
<div> Normal read</div>
<div><br>
</div>
<div> Gamma point algorithm</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>with such a error message </div>
<div>
<div>forrtl: severe (174): SIGSEGV, segmentation fault occurred</div>
<div>Image PC Routine Line Source </div>
<div><br>
</div>
<div>Stack trace terminated abnormally.</div>
<div>forrtl: severe (174): SIGSEGV, segmentation fault occurred</div>
<div>Image PC Routine Line Source </div>
<div>turbo_lanczos.x 0000000000AC5C31 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000AC4387 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A6A554 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A6A366 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A00E8F Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A081BD Unknown Unknown Unknown</div>
<div>libpthread.so.0 00002AAAAF38C850 Unknown Unknown Unknown</div>
<div>libc.so.6 00002AAAAF88F0B8 Unknown Unknown Unknown</div>
<div>libc.so.6 00002AAAAF8911F7 Unknown Unknown Unknown</div>
<div>libmkl_core.so 00002AAAACAC3460 Unknown Unknown Unknown</div>
<div>libmkl_core.so 00002AAAADCC5E76 Unknown Unknown Unknown</div>
<div><br>
</div>
<div>Stack trace terminated abnormally.</div>
<div>forrtl: severe (174): SIGSEGV, segmentation fault occurred</div>
<div>Image PC Routine Line Source </div>
<div>turbo_lanczos.x 0000000000AC5C31 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000AC4387 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A6A554 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A6A366 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A00E8F Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A081BD Unknown Unknown Unknown</div>
<div>libpthread.so.0 00002AAAAF38C850 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A1FC11 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A1D6A1 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000775A72 davcio_ 382 io_files.f90</div>
<div>turbo_lanczos.x 000000000041DD10 lr_read_wf_IP_nor 154 lr_read_wf.f90</div>
<div>turbo_lanczos.x 000000000041D63B lr_read_wf_ 66 lr_read_wf.f90</div>
<div>turbo_lanczos.x 0000000000406BD9 MAIN__ 118 lr_main.f90</div>
<div>turbo_lanczos.x 000000000040698E Unknown Unknown Unknown</div>
<div>libc.so.6 00002AAAAF831C36 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000406899 Unknown Unknown Unknown</div>
<div>forrtl: severe (174): SIGSEGV, segmentation fault occurred</div>
<div>Image PC Routine Line Source </div>
<div>turbo_lanczos.x 0000000000AC5C31 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000AC4387 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A6A554 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A6A366 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A00E8F Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A081BD Unknown Unknown Unknown</div>
<div>libpthread.so.0 00007FFFCA7ED850 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A1FC11 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000A1D6A1 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000775A72 davcio_ 382 io_files.f90</div>
<div>turbo_lanczos.x 000000000041DD10 lr_read_wf_IP_nor 154 lr_read_wf.f90</div>
<div>turbo_lanczos.x 000000000041D63B lr_read_wf_ 66 lr_read_wf.f90</div>
<div>turbo_lanczos.x 0000000000406BD9 MAIN__ 118 lr_main.f90</div>
<div>turbo_lanczos.x 000000000040698E Unknown Unknown Unknown</div>
<div>libc.so.6 00007FFFCA207C36 Unknown Unknown Unknown</div>
<div>turbo_lanczos.x 0000000000406899 Unknown Unknown Unknown</div>
</div>
<div><br>
</div>
<div>Could you help me? please do not hesitate to tell me if you have any clues </div>
<div>best,</div>
<div>Sunghwan Choi</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">2016-07-22 6:54 GMT+09:00 Manu Hegde <span dir="ltr"><<a href="mailto:mhegde@uwaterloo.ca" target="_blank">mhegde@uwaterloo.ca</a>></span>:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Hi Dario,</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Thanks. My unit cell already big contains 80 atoms, I will try to calculate using supercell.</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Regards,</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Manu</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif"><br>
</div>
</div>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Jul 21, 2016 at 4:02 PM, dario rocca <span dir="ltr">
<<a href="mailto:roccad@gmail.com" target="_blank">roccad@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div>
<div>
<div>Hi Manu,<br>
</div>
The last release of the code does not allow for k-point sampling, that's why you get an error message.<br>
</div>
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<br>
</div>
<div>that does not match at all experiments.<br>
</div>
<div>Additionally, the Bethe-Salpeter equation is considered the most accurate method for bulk solids.<br>
</div>
<div>Best,<br>
</div>
<div>Dario <br>
</div>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Jul 21, 2016 at 9:42 AM, Manu Hegde <span dir="ltr">
<<a href="mailto:mhegde@uwaterloo.ca" target="_blank">mhegde@uwaterloo.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Hi Dario,<br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">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.<br>
<br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Regards,<br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Manu<br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">(University of Waterloo)<br>
</div>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jul 20, 2016 at 8:09 PM, dario rocca <span dir="ltr">
<<a href="mailto:roccad@gmail.com" target="_blank">roccad@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>Dear Manu,<br>
</div>
You can simply extract it with the command<br>
</div>
$ grep "S(E)" <span style="font-size:14px">prefix.plot_chi.dat </span> > file_for_plot
<br>
</div>
and use your favorite program to plot it.<br>
</div>
Best,<br>
</div>
Dario<br>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Jul 20, 2016 at 10:49 AM, Manu Hegde <span dir="ltr">
<<a href="mailto:mhegde@uwaterloo.ca" target="_blank">mhegde@uwaterloo.ca</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Hello Dario,<br>
<br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">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?<br>
<br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">Manu<br>
</div>
<div class="gmail_default" style="font-family:arial,helvetica,sans-serif">(University of Waterloo)<br>
</div>
</div>
<div>
<div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Jul 19, 2016 at 8:24 PM, dario rocca <span dir="ltr">
<<a href="mailto:roccad@gmail.com" target="_blank">roccad@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>Dear SungHwan,<br>
</div>
please refer to <br>
<a href="http://arxiv.org/pdf/1402.0486.pdf" target="_blank">http://arxiv.org/pdf/1402.0486.pdf</a><br>
</div>
and<br>
<a href="http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1" target="_blank">http://urania.sissa.it/xmlui/bitstream/handle/1963/5797/turboTDDFT-CPC.pdf?sequence=1</a><br>
</div>
for more details.<br>
<br>
</div>
In the output of the postprocessing chi_1_1 is the xx component of the dynamical polarizability, chi_1_2 the xy component, etc.<br>
</div>
<div>Often chi is indicated as \alpha in the papers.<br>
</div>
Specifically you would have<br>
<div>
<div><br>
Component energy of the perturbation real part of chi imaginary<br>
</div>
<div> (indicated either as E or \omega)<br>
</div>
<div>chi_1_1= 0.000000000000000E+00 0.955769346791472E+01 0.000000000000000E+00<br>
.........<br>
<br>
</div>
<div>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<br>
indicated as \omega).<br>
</div>
<div>This averaged quantity is contained in S(E). Specifically S(E) is the strength function defined as<br>
<span style="color:rgb(34,34,34); font-family:arial,sans-serif; font-size:12.8px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; display:inline!important; float:none; background-color:rgb(255,255,255)">S(E)=2m/(\pi*e^2*\hbar)
* E*Im[chi(E)], where chi has been averaged over the 3 spatial directions. <br>
This definition is convenient because S(E) satisfies the f-sum rule.<br>
</span></div>
<div><span style="color:rgb(34,34,34); font-family:arial,sans-serif; font-size:12.8px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; display:inline!important; float:none; background-color:rgb(255,255,255)">So
if you extract S(E) and plot it you will have the absorption spectrum.<br>
</span></div>
<div><span style="color:rgb(34,34,34); font-family:arial,sans-serif; font-size:12.8px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; display:inline!important; float:none; background-color:rgb(255,255,255)">Let
me know if it's still not clear<br>
</span></div>
<div><span style="color:rgb(34,34,34); font-family:arial,sans-serif; font-size:12.8px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; display:inline!important; float:none; background-color:rgb(255,255,255)">Best,<br>
</span></div>
<div><span style="color:rgb(34,34,34); font-family:arial,sans-serif; font-size:12.8px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; display:inline!important; float:none; background-color:rgb(255,255,255)">Dario
<br style="color:rgb(34,34,34); font-family:arial,sans-serif; font-size:12.8px; font-style:normal; font-variant:normal; font-weight:normal; letter-spacing:normal; line-height:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; background-color:rgb(255,255,255)">
</span></div>
<div><br>
</div>
<div><br>
<br>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">
<div>
<div>On Tue, Jul 19, 2016 at 4:01 PM, SungHwan Choi <span dir="ltr"><<a href="mailto:sunghwanchoi91@gmail.com" target="_blank">sunghwanchoi91@gmail.com</a>></span> wrote:<br>
</div>
</div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
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<div dir="ltr"><span style="font-size:14px"> hi, I am a newbie for turboTDDFT. Now, I ran a simple example. It was </span><span style="font-size:14px">assume. Now I have prefix.plot_chi.dat file. then I don't know how to</span><span style="font-size:14px"> generate
absorption spectrum from that file and dielectric constant values. As far as I understood, the</span><span style="font-size:14px"> absorption spectrum is related to imaginary part of average \chi value. but in the file there are </span><span style="font-size:14px">9
values</span><br style="font-size:14px">
<span style="font-size:14px"> chi_1_1</span><br style="font-size:14px">
<span style="font-size:14px"> chi_2_1</span><br style="font-size:14px">
<span style="font-size:14px"> chi_3_1</span><br style="font-size:14px">
<span style="font-size:14px"> chi_1_2</span><br style="font-size:14px">
<span style="font-size:14px"> chi_2_2</span><br style="font-size:14px">
<span style="font-size:14px"> chi_3_2</span><br style="font-size:14px">
<span style="font-size:14px"> chi_1_3</span><br style="font-size:14px">
<span style="font-size:14px"> chi_2_3</span><br style="font-size:14px">
<span style="font-size:14px"> chi_3_3</span><br style="font-size:14px">
<span style="font-size:14px">This is 3*3*3 tensor. how do I get an absorption spectrum and dieletric constant values? by the way S(E) means what? </span>
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<span style="font-size:14px">Sincerely</span><span><font color="#888888"><br style="font-size:14px">
<span style="font-size:14px">Sunghwan Choi</span><br>
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