<div>Hi Maricris,</div>
<div>As far as I know, at present code, we can not produce cube file by DFTB. Of course, a tool may need to help this but unfortunately there is no available such a tool now.</div>
<div><br> </div>
<div class="gmail_quote">On 22 December 2010 05:26, Maricris <span dir="ltr"><<a href="mailto:mlodr...@gmail.com">mlodr...@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi Radif,<br><br>I've tried following the relevant &PRINT part to my DFTB input but it<br>did not produce any cube file. Any ideas?<br>
<br><br>Maricris<br>
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<div></div>
<div class="h5"><br>On Dec 20, 10:16 pm, Muhammad Radifar <<a href="mailto:m.rad...@gmail.com">m.rad...@gmail.com</a>> wrote:<br>> Dear Macicris,<br>><br>> So far I've never done any DFTB calculation but I think the way to<br>
> produce the file that can show the electron density or molecular<br>> orbital should be the same with any other calculation. Here is the<br>> excerpt of input file to produce the electron density file:<br>> &FORCE_EVAL<br>
> METHOD Quickstep<br>> &DFT<br>> BASIS_SET_FILE_NAME ../BASIS_SET<br>> POTENTIAL_FILE_NAME ../POTENTIAL<br>> &MGRID<br>> CUTOFF 150<br>> &END MGRID<br>> &QS<br>
> EPS_DEFAULT 1.0E-8<br>> &END QS<br>> &SCF<br>> EPS_SCF 1.0E-4<br>> SCF_GUESS ATOMIC<br>> &END SCF<br>> &XC<br>> &XC_FUNCTIONAL Pade<br>
> &END XC_FUNCTIONAL<br>> &END XC<br>> &PRINT<br>> &E_DENSITY_CUBE<br>> # STRIDE 1 1 1<br>> &END E_DENSITY_CUBE<br>> &TOT_DENSITY_CUBE<br>> # STRIDE 1 1 1<br>
> &END TOT_DENSITY_CUBE<br>> &END PRINT<br>> &END DFT<br>> ......<br>><br>> Notice the sections and keywords inside the print section, the<br>> e_density_cube is used to produce the electron density cube, you can<br>
> view the cube file using any molecule viewer that support cube file,<br>> my favorite for this is VMD. While the tot_density_cube is used to<br>> produce the total density cube file, the total density is the density<br>
> of core + electron. The stride keyword is to adjust the smoothness of<br>> your cube file, the default is 2 2 2, 1 1 1 will produce the smoother<br>> one but it uses more harddisk space.<br>><br>> To produce the molecular orbital here is the excerpt of input file<br>
> that I use:<br>> &FORCE_EVAL<br>> METHOD Quickstep<br>> &DFT<br>> BASIS_SET_FILE_NAME ../BASIS_SET<br>> POTENTIAL_FILE_NAME ../POTENTIAL<br>> &MGRID<br>> CUTOFF 100<br>
> &END MGRID<br>> &QS<br>> EPS_DEFAULT 1.0E-8<br>> &END QS<br>> &SCF<br>> EPS_SCF 1.0E-4<br>> SCF_GUESS ATOMIC<br>> &END SCF<br>> &XC<br>
> &XC_FUNCTIONAL Pade<br>> &END XC_FUNCTIONAL<br>> &END XC<br>> &PRINT<br>> &MO_CUBES<br>> # STRIDE 1 1 1<br>> NHOMO 1<br>> NLUMO 1<br>
> &END MO_CUBES<br>> &END PRINT<br>> .....<br>><br>> With the mo_cubes I found that the result is the HOMO and LUMO for<br>> overall system, and I found that using the localized one can show the<br>
> HOMO and LUMO for individual molecule:<br>> &FORCE_EVAL<br>> METHOD Quickstep<br>> &DFT<br>> BASIS_SET_FILE_NAME ../BASIS_SET<br>> POTENTIAL_FILE_NAME ../POTENTIAL<br>> &MGRID<br>
> CUTOFF 100<br>> &END MGRID<br>> &QS<br>> EPS_DEFAULT 1.0E-8<br>> &END QS<br>> &SCF<br>> EPS_SCF 1.0E-4<br>> SCF_GUESS ATOMIC<br>> &END SCF<br>
> &XC<br>> &XC_FUNCTIONAL Pade<br>> &END XC_FUNCTIONAL<br>> &END XC<br>> &LOCALIZE<br>> &END LOCALIZE<br>> &PRINT<br>> &LOCALIZATION<br>
> &WANNIER_CUBES<br>> # STRIDE 1 1 1<br>> &END WANNIER_CUBES<br>> &END LOCALIZATION<br>> &END PRINT<br>><br>> Watch out that there will be so many orbital CUBE file produced,<br>
> usually the HOMO(or LUMO) is the one that we're interested with. So I<br>> think you have to find out which one is the HOMO by try to run it with<br>> run_type energy then open the orbital file one by one. And then you<br>
> specify which is the HOMO you're looking for, like this:<br>> &LOCALIZE<br>> &END LOCALIZE<br>> &PRINT<br>> &LOCALIZATION<br>> &WANNIER_CUBES<br>> # STRIDE 1 1 1<br>
> CUBES_LIST 13 14 15 16<br>> &END WANNIER_CUBES<br>> &END LOCALIZATION<br>> &END PRINT<br>><br>> The cubes_list specify which HOMO that you want. If you don't get it,<br>
> you might want to run this input file and view the cube file it<br>> produce:<br>> &FORCE_EVAL<br>> METHOD Quickstep<br>> &DFT<br>> BASIS_SET_FILE_NAME ../BASIS_SET<br>> POTENTIAL_FILE_NAME ../POTENTIAL<br>
> CHARGE +1<br>> &MGRID<br>> CUTOFF 100<br>> &END MGRID<br>> &QS<br>> EPS_DEFAULT 1.0E-8<br>> &END QS<br>> &SCF<br>> EPS_SCF 1.0E-4<br>
> SCF_GUESS ATOMIC<br>> &END SCF<br>> &XC<br>> &XC_FUNCTIONAL Pade<br>> &END XC_FUNCTIONAL<br>> &END XC<br>> &LOCALIZE<br>> &END LOCALIZE<br>
> &PRINT<br>> &LOCALIZATION<br>> &WANNIER_CUBES<br>> # STRIDE 1 1 1<br>> CUBES_LIST 13 14 15 16<br>> &END WANNIER_CUBES<br>> &END LOCALIZATION<br>
> &END PRINT<br>> &END DFT<br>> &SUBSYS<br>> &CELL<br>> ABC 8.0 8.0 8.0<br>> &END CELL<br>> &COORD<br>> O 4.972295 2.976983 4.667921<br>
> H 5.092295 3.036983 3.677921<br>> H 4.012295 2.726983 4.827922<br>> O 5.112295 5.365985 5.587922<br>> H 5.452294 5.585985 6.457922<br>
> H 4.932295 6.245984 5.207923<br>> O 2.522294 2.386984 5.077923<br>> H 2.098294 2.915983 5.602922<br>> H 2.212294 1.496982 5.287923<br>
> O 4.832295 3.230984 2.240921<br>> H 3.929295 3.330984 2.052921<br>> H 5.224295 3.257984 1.286921<br>> H 5.072295 3.906982 5.017922<br>
> &END COORD<br>> &KIND H<br>> BASIS_SET DZVP-GTH-PADE<br>> POTENTIAL GTH-PADE-q1<br>> &END KIND<br>> &KIND O<br>> BASIS_SET DZVP-GTH-PADE<br>> POTENTIAL GTH-PADE-q6<br>
> &END KIND<br>> &END SUBSYS<br>> &END FORCE_EVAL<br>> &GLOBAL<br>> PROJECT H2O<br>> RUN_TYPE MD<br>> PRINT_LEVEL LOW<br>> &END GLOBAL<br>> &MOTION<br>> &MD<br>
> ENSEMBLE NVE<br>> STEPS 2<br>> TIMESTEP 0.5<br>> TEMPERATURE 300.0<br>> &END MD<br>> &END MOTION<br>><br></div></div>> One more thing, there is one caveat in cube file printing, read this:<a href="http://groups.google.com/group/cp2k/browse_thread/thread/f94b4924e091." target="_blank">http://groups.google.com/group/cp2k/browse_thread/thread/f94b4924e091.</a>..<br>
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<div class="h5">><br>> I hope that can help :)<br>><br>> Best regards,<br>><br>> Radif<br>><br>> On Dec 21, 4:10 am, Maricris <<a href="mailto:mlodr...@gmail.com">mlodr...@gmail.com</a>> wrote:<br>
><br>> > Hi,<br>><br>> > I would like to know how to view the electron density from DFTB<br>> > results. How can I generate the file that contains the charge<br>> > distribution, molecular orbitals, etc from the DFTB calculation? Is<br>
> > this possible?<br>><br>> > Any input would be highly appreciated.<br>><br>> > Best,<br>> > Maricris<br><br>--<br>You received this message because you are subscribed to the Google Groups "cp2k" group.<br>
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Nguyen, Ngoc Ha<br>Hanoi National University of Education<br>Faculty of Chemistry<br>Department of Physical Chemistry<br>Tel: Office: 04/38330842<br>Home: 04/37891674<br>Mobile: 0989133436<br><a href="mailto:E-mail...@hnue.edu.vn">E-mai...@hnue.edu.vn</a><br>