visualizing dftb orbital density

Maricris mlodr... at gmail.com
Tue Dec 21 23:26:31 CET 2010


Hi Radif,

I've tried following the relevant &PRINT part to my DFTB input but it
did not produce any cube file. Any ideas?


Maricris

On Dec 20, 10:16 pm, Muhammad Radifar <m.rad... at gmail.com> 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/f94b4924e091...
>
> 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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