[CP2K:7846] Printing Core Charges for Bader analysis

Satish Kumar satis... at gmail.com
Sun Jun 12 01:07:21 CEST 2016


Will try it out. Thank you.
On Jun 11, 2016 6:44 PM, "S Ling" <lingsa... at gmail.com> wrote:

> Hi
>
> You may try this tool, see:
>
> https://sourceforge.net/projects/ddec/
>
> Although the tool was originally developed to perform partial charge
> analysis using another method (see
> http://pubs.acs.org/doi/abs/10.1021/ct100125x), the tool can produce a
> cube file which contains the core electron density based on some reference
> densities (included in the DDEC program). You can then perform Bader charge
> analysis on this new cube file using the tool developed by Henkelman.
> Please have a look at the manual included in the DDEC program. You may need
> to change some of the parameters (number of core electrons) in the DDEC
> program, as the GTH pseudopotentials used by CP2K may correspond to
> different numbers of core electrons.
>
> SL
>
>
> On 10 June 2016 at 23:21, Satish Kumar <satis... at gmail.com> wrote:
>
>> Hello CP2K users
>>
>> I was trying to obtain "proper?" Bader charges (Using Henkelman's
>> program) for a CO2 molecule. Right now, I am getting the charge associated
>> with C atom to be zero. In VASP, we can add the LAECHG=TRUE tag that will
>> print the core charges too (
>> http://theory.cm.utexas.edu/henkelman/code/bader/). Doing so in VASP
>> gives a reasonable (around 2 electrons) charge associated with C atom.
>> After looking up the CP2K Google group I tried a couple of other options in
>> an attempt to get the total (valence + core) charge density. I tried the
>> following print sections:
>>
>> 1)
>>
>>
>> &PRINT
>>
>>     &E_DENSITY_CUBE
>>
>>       STRIDE 1
>>
>>     &END E_DENSITY_CUBE
>>
>> &END PRINT
>>
>> 2)
>>   &PRINT
>>    &E_DENSITY_CUBE
>>       STRIDE 1
>>       TOTAL_DENSITY .TRUE.
>>     &END E_DENSITY_CUBE
>>   &END PRINT
>>
>> 3) This one gave wrong results I think (number of electrons estimated
>> from Bader was 0).
>>   &PRINT
>>     &TOT_DENSITY_CUBE
>>       STRIDE 1
>>     &END TOT_DENSITY_CUBE
>>   &END PRINT
>> Input file:
>>
>> &FORCE_EVAL
>>
>>   METHOD Quickstep
>>
>>   &DFT
>>
>>     UKS
>>
>>     BASIS_SET_FILE_NAME /home/siyemperumal/GTH_BASIS_SETS_5-12-10
>>
>>     POTENTIAL_FILE_NAME /home/siyemperumal/GTH_POTENTIALS_5-12-10
>>
>>     WFN_RESTART_FILE_NAME co2-RESTART.wfn
>>
>>     &MGRID
>>
>>       CUTOFF 1600
>>
>>     &END MGRID
>>
>>     &QS
>>
>>       WF_INTERPOLATION ASPC
>>
>>       EXTRAPOLATION_ORDER 3
>>
>>     &END QS
>>
>>     &SCF
>>
>>      EPS_SCF 1.E-6
>>
>>      SCF_GUESS RESTART
>>
>>      MAX_SCF 500
>>
>>      &OT T
>>
>>        PRECONDITIONER FULL_SINGLE_INVERSE
>>
>>        MINIMIZER DIIS
>>
>>        LINESEARCH 3PNT
>>
>>      &END OT
>>
>>     &END SCF
>>
>>     &XC
>>
>>       &XC_FUNCTIONAL PBE
>>
>>       &END XC_FUNCTIONAL
>>
>>       &VDW_POTENTIAL
>>
>>          DISPERSION_FUNCTIONAL PAIR_POTENTIAL
>>
>>          &PAIR_POTENTIAL
>>
>>             TYPE DFTD3(BJ)
>>
>>             PARAMETER_FILE_NAME
>> /home/siyemperumal/Research/cp2k/package/cp2k/data/dftd3.dat
>>
>>             REFERENCE_FUNCTIONAL PBE
>>
>>     &PRINT_DFTD MEDIUM
>>
>>     &END PRINT_DFTD
>>
>>          &END PAIR_POTENTIAL
>>
>>       &END VDW_POTENTIAL
>>
>>     &END XC
>>
>>   &PRINT
>>
>> #Tried the above three combinations
>>
>>   &END PRINT
>>
>>   &END DFT
>>
>>   &SUBSYS
>>
>>     &CELL
>>
>>       ABC 12.00 13.00 14.00
>>
>>     &END CELL
>>
>>     &TOPOLOGY
>>
>>     &END TOPOLOGY
>>
>>     &COORD
>>
>> C         0.0000153980        0.0000010425        0.0006891492
>>
>> O         1.1762907217        0.0000004039        0.0006107401
>>
>> O        -1.1763057650       -0.0000013603        0.0006092107
>>
>>     &END COORD
>>
>>     &KIND O
>>
>>       BASIS_SET DZVP-MOLOPT-GTH
>>
>>       POTENTIAL GTH-PBE-q6
>>
>>     &END KIND
>>
>>     &KIND C
>>
>>       BASIS_SET DZVP-MOLOPT-GTH
>>
>>       POTENTIAL GTH-PBE-q4
>>
>>     &END KIND
>>
>>   &END SUBSYS
>>
>> &END FORCE_EVAL
>>
>> &GLOBAL
>>
>>   PROJECT co2
>>
>>   RUN_TYPE ENERGY
>>
>>   #RUN_TYPE GEO_OPT
>>
>>   PRINT_LEVEL LOW
>>
>> &END GLOBAL
>>
>>  &MOTION
>>
>>   &GEO_OPT
>>
>>     MAX_ITER 200
>>
>>     MAX_FORCE 0.0009725  #0.05 eV/A
>>
>>     OPTIMIZER BFGS
>>
>>   &END GEO_OPT
>>
>>  &END MOTION
>>
>>
>> Related Output that is printed:
>>
>>
>>   Electronic density on regular grids:        -15.9999999999
>> 0.0000000001
>>
>>   Core density on regular grids:               15.9999999994
>> -0.0000000006
>>
>>   Total charge density on r-space grids:       -0.0000000005
>>
>>   Total charge density g-space grids:          -0.0000000005
>>
>>
>> Thank you for any ideas.
>>
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