[CP2K:7915] Printing Core Charges for Bader analysis

[Satish Kumar]

I do not think there are any options in the job_control.txt file to write
the reconstructed cube files in DDEC6 program. I do not know if you want to
tweak the program to make it write these reconstructed files. If you have a
CP2K valence electron density file with you, some relevant files may be
module_format_valence_cube_density.f08
or module_add_missing_core_density.f08 (not sure)?

I believe there will a paper soon by Prof. Manz, which will provide you
with the core densities that you can use to generate your own reconstructed
cube files.

On a different note for interested users, when CP2K files are generated
with large cutoff values and if you end up getting Fortran runtime
error/End of file error, the default variable value of read_buffer_size in
module_global_parameters may need to be increased from its default value.

HTH.

On Jul 10, 2016 5:26 AM, "David T" <amazing... at gmail.com> wrote:

> Hi
> I downloaded the code but the documentation is a bit encrypted.
> I can use the code for calculating the charges but I can't write any
> reconstructed cube file.
>
> Do you know how to do it? Can you please explain it to me?
>
> Cheers
> Davide
>
>
> On Sunday, 12 June 2016 00:44:19 UTC+2, S Ling 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 <sati... 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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>>
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