visualizing dftb orbital density

eft rsd rashe... at gmail.com
Wed Apr 6 12:57:35 CEST 2016


Thanks Radif, this is really helpful.
eftrsd

On Tuesday, December 21, 2010 at 4:16:59 AM UTC, Muhammad Radifar wrote:
>
> Dear Macicris, 
>
> So far I've never done any DFTB calculation but I think the way to 
> produce the file that can show the electron density or molecular 
> orbital should be the same with any other calculation. Here is the 
> excerpt of input file to produce the electron density file: 
> &FORCE_EVAL 
>   METHOD Quickstep 
>   &DFT 
>     BASIS_SET_FILE_NAME ../BASIS_SET 
>     POTENTIAL_FILE_NAME ../POTENTIAL 
>     &MGRID 
>       CUTOFF 150 
>     &END MGRID 
>     &QS 
>       EPS_DEFAULT 1.0E-8 
>     &END QS 
>     &SCF 
>       EPS_SCF 1.0E-4 
>       SCF_GUESS ATOMIC 
>     &END SCF 
>     &XC 
>       &XC_FUNCTIONAL Pade 
>       &END XC_FUNCTIONAL 
>     &END XC 
>     &PRINT 
>       &E_DENSITY_CUBE 
> #      STRIDE 1 1 1 
>       &END E_DENSITY_CUBE 
>       &TOT_DENSITY_CUBE 
> #      STRIDE 1 1 1 
>       &END TOT_DENSITY_CUBE 
>     &END PRINT 
>   &END DFT 
> ...... 
>
> Notice the sections and keywords inside the print section, the 
> e_density_cube is used to produce the electron density cube, you can 
> view the cube file using any molecule viewer that support cube file, 
> my favorite for this is VMD. While the tot_density_cube is used to 
> produce the total density cube file, the total density is the density 
> of core + electron. The stride keyword is to adjust the smoothness of 
> your cube file, the default is 2 2 2, 1 1 1 will produce the smoother 
> one but it uses more harddisk space. 
>
> To produce the molecular orbital here is the excerpt of input file 
> that I use: 
> &FORCE_EVAL 
>   METHOD Quickstep 
>   &DFT 
>     BASIS_SET_FILE_NAME ../BASIS_SET 
>     POTENTIAL_FILE_NAME ../POTENTIAL 
>     &MGRID 
>       CUTOFF 100 
>     &END MGRID 
>     &QS 
>       EPS_DEFAULT 1.0E-8 
>     &END QS 
>     &SCF 
>       EPS_SCF 1.0E-4 
>       SCF_GUESS ATOMIC 
>     &END SCF 
>     &XC 
>       &XC_FUNCTIONAL Pade 
>       &END XC_FUNCTIONAL 
>     &END XC 
>     &PRINT 
>       &MO_CUBES 
> #      STRIDE 1 1 1 
>         NHOMO 1 
>         NLUMO 1 
>       &END MO_CUBES 
>     &END PRINT 
> ..... 
>
> With the mo_cubes I found that the result is the HOMO and LUMO for 
> overall system, and I found that using the localized one can show the 
> HOMO and LUMO for individual molecule: 
> &FORCE_EVAL 
>   METHOD Quickstep 
>   &DFT 
>     BASIS_SET_FILE_NAME ../BASIS_SET 
>     POTENTIAL_FILE_NAME ../POTENTIAL 
>     &MGRID 
>       CUTOFF 100 
>     &END MGRID 
>     &QS 
>       EPS_DEFAULT 1.0E-8 
>     &END QS 
>     &SCF 
>       EPS_SCF 1.0E-4 
>       SCF_GUESS ATOMIC 
>     &END SCF 
>     &XC 
>       &XC_FUNCTIONAL Pade 
>       &END XC_FUNCTIONAL 
>     &END XC 
>     &LOCALIZE 
>     &END LOCALIZE 
>     &PRINT 
>       &LOCALIZATION 
>         &WANNIER_CUBES 
> #         STRIDE 1 1 1 
>         &END WANNIER_CUBES 
>       &END LOCALIZATION 
>     &END PRINT 
>
> Watch out that there will be so many orbital CUBE file produced, 
> usually the HOMO(or LUMO) is the one that we're interested with. So I 
> think you have to find out which one is the HOMO by try to run it with 
> run_type energy then open the orbital file one by one. And then you 
> specify which is the HOMO you're looking for, like this: 
>     &LOCALIZE 
>     &END LOCALIZE 
>     &PRINT 
>       &LOCALIZATION 
>         &WANNIER_CUBES 
> #        STRIDE 1 1 1 
>           CUBES_LIST 13 14 15 16 
>         &END WANNIER_CUBES 
>       &END LOCALIZATION 
>     &END PRINT 
>
> The cubes_list specify which HOMO that you want. If you don't get it, 
> you might want to run this input file and view the cube file it 
> produce: 
> &FORCE_EVAL 
>   METHOD Quickstep 
>   &DFT 
>     BASIS_SET_FILE_NAME ../BASIS_SET 
>     POTENTIAL_FILE_NAME ../POTENTIAL 
>     CHARGE +1 
>     &MGRID 
>       CUTOFF 100 
>     &END MGRID 
>     &QS 
>       EPS_DEFAULT 1.0E-8 
>     &END QS 
>     &SCF 
>       EPS_SCF 1.0E-4 
>       SCF_GUESS ATOMIC 
>     &END SCF 
>     &XC 
>       &XC_FUNCTIONAL Pade 
>       &END XC_FUNCTIONAL 
>     &END XC 
>     &LOCALIZE 
>     &END LOCALIZE 
>     &PRINT 
>       &LOCALIZATION 
>         &WANNIER_CUBES 
> #        STRIDE 1 1 1 
>           CUBES_LIST 13 14 15 16 
>         &END WANNIER_CUBES 
>       &END LOCALIZATION 
>     &END PRINT 
>   &END DFT 
>   &SUBSYS 
>     &CELL 
>       ABC 8.0 8.0 8.0 
>     &END CELL 
>     &COORD 
>  O         4.972295        2.976983        4.667921 
>  H         5.092295        3.036983        3.677921 
>  H         4.012295        2.726983        4.827922 
>  O         5.112295        5.365985        5.587922 
>  H         5.452294        5.585985        6.457922 
>  H         4.932295        6.245984        5.207923 
>  O         2.522294        2.386984        5.077923 
>  H         2.098294        2.915983        5.602922 
>  H         2.212294        1.496982        5.287923 
>  O         4.832295        3.230984        2.240921 
>  H         3.929295        3.330984        2.052921 
>  H         5.224295        3.257984        1.286921 
>  H         5.072295        3.906982        5.017922 
>     &END COORD 
>     &KIND H 
>       BASIS_SET DZVP-GTH-PADE 
>       POTENTIAL GTH-PADE-q1 
>     &END KIND 
>     &KIND O 
>       BASIS_SET DZVP-GTH-PADE 
>       POTENTIAL GTH-PADE-q6 
>     &END KIND 
>   &END SUBSYS 
> &END FORCE_EVAL 
> &GLOBAL 
>   PROJECT H2O 
>   RUN_TYPE MD 
>   PRINT_LEVEL LOW 
> &END GLOBAL 
> &MOTION 
>   &MD 
>     ENSEMBLE NVE 
>     STEPS 2 
>     TIMESTEP 0.5 
>     TEMPERATURE 300.0 
>   &END MD 
> &END MOTION 
>
> One more thing, there is one caveat in cube file printing, read this: 
> http://groups.google.com/group/cp2k/browse_thread/thread/f94b4924e091443b 
>
> I hope that can help :) 
>
> Best regards, 
>
> Radif 
>
>
> On Dec 21, 4:10 am, Maricris <mlodr... at gmail.com> wrote: 
> > Hi, 
> > 
> > I would like to know how to view the electron density from DFTB 
> > results. How can I generate the file that contains the charge 
> > distribution, molecular orbitals, etc from the DFTB calculation? Is 
> > this possible? 
> > 
> > Any input would be highly appreciated. 
> > 
> > Best, 
> > Maricris

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