<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"><div><div><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><div><br style="font-size:14px"><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></font></span></div></div>
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