visualizing dftb orbital density

Muhammad Radifar m.rad... at gmail.com
Wed Dec 22 01:02:22 UTC 2010
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Hi Maricris,

Sorry, the input file that I'm using was wrong, I think what Nguyen
said could be correct. I can not get the cube file for DFTB
calculation.

On Dec 22, 7:46 am, Muhammad Radifar <m.rad... at gmail.com> wrote:
> Hi Maricris,
>
> I've tried to use DFTB and print the cube file and it worked, I wonder
> what's wrong. Could you paste your input file here?
>
> On Dec 22, 5:26 am, Maricris <mlodr... at gmail.com> wrote:
>
>
>
> > 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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