visualizing dftb orbital density
eft rsd
rashe... at gmail.com
Wed Apr 6 10:57:35 UTC 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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