spn density problem

Marcella Iannuzzi marci... at gmail.com
Tue Jun 16 08:38:46 UTC 2015

```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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