[CP2K:3018] Re: visualizing dftb orbital density

Nguyen Ngoc Ha ha... at hnue.edu.vn
Tue Dec 21 22:33:48 UTC 2010
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Hi Maricris,
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.


On 22 December 2010 05:26, 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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>


-- 
Nguyen, Ngoc Ha
Hanoi National University of Education
Faculty of Chemistry
Department of Physical Chemistry
Tel: Office: 04/38330842
Home: 04/37891674
Mobile: 0989133436
E-mai... at hnue.edu.vn <E-mail... at hnue.edu.vn>
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