spn density problem

Rizwan Nabi rizwan... at gmail.com
Tue Jun 16 12:34:30 UTC 2015

```Hi Marcella

Thank you for your guidance and valuable inputs!

On Tuesday, June 16, 2015 at 2:08:46 PM UTC+5:30, Marcella Iannuzzi wrote:
>
> Hi,
>
> compile it, then run it without any input and you get the following hints:
>
> Usage: cubecruncher.x -i input.cube -o output.cube [options]
>
>
>
>
>
>          transforms 'input.cube' into 'output.cube' doing
>
>
>          transformations based on the specified options.
>
>
>          The following options are available and can normally
>
>
>          be combined:
>
>
>
>
>
>   -xyz coords.xyz         : merge in a xyz coordinate file
>
>
>                                (e.g. for VMD usage)
>
>
>   -subtract min.cube      : subtract min.cube from input.cube
>
>
>   -center {#|geo|point}   : #=1..Natom center the cube around atom #
>
>
>                             geo        center the cube so that the cell
>
>
>                                boundaries are as far as possible from the
>
>
>                                molecule
>
>
>                             point      center around a fixed point
>
>
>   -fold                   : fold atoms inside the box defined by the cube
>
>
>   -point x y z            : coordinates of the center point
>
>
>   -foldsmart              : idem, but place hydrogens near heavier atoms
>
>
>   -stride #               : reduces resolution writing grids with stride #
>
>
>   -multiply #             : multiply all values of cube by the given
> factor
>
>   -1d_profile dir delta   : compute the profile along the cartesian axis
> dir
>
>                            and a smoothed profile with smoothing interval
> delta
>
>   -slice h1 h2 h3         : extract the values of the cube slice at height
> h#,
>
>                             along the cartesian axis #, if h#/=0,
>
>
>                             reads three reals, takes the first /=0
>
>
>   -iso l1 l2 l3           : compute the isosurface at level l#, recording
> height
>
>                             along the axis #, if l#/=0,
>
>
>                             reads three reals, takes the first /=0
>
>
>   -iso_delta_grid  delta  : step of the regular grid to output the
> iso-surface
>
>   -isocurrent W           : correct the iso-density surface to approximate
> the
>
>                             iso-current surface, where
>
>
>                              I(z) \propto
> rho(z)*exp(alpha*W*sqrt(ES-pot(z)))
>
>                             The ES-pot cube must be loaded
>
>
>   -espot                  : assign ES-pot values to the calculated
> iso-surface
>
>                             The ES-pot cube must be loaded
>
>
>   -espot_cube             : name cube file of the electrostatic potential
>
>
>   -help                   : print this message
>
>
>   -v                      : print a version string
>
>
> On Tuesday, June 16, 2015 at 9:51:32 AM UTC+2, Rizwan Nabi wrote:
>>
>> Hi CP2K users and developers
>> I am trying to do geometry optimization of my complex system and after
>> obtaining SPIN_DENSITY_CUBE FILE, the spin density is shifted away from
>> complex itself only a part of the spin density is retained on the central
>> metal ion. Is there any problem with my input file? Any solution to the
>> issue?
>> Here I am attaching my input file and snapshot of the spin density plot.
>>
>>
>> Regards
>>
>>
>> Rizwan
>>
>>
>>
>>
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