spn density problem

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


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  


                            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 

  -1d_profile dir delta   : compute the profile along the cartesian axis 

                           and a smoothed profile with smoothing interval 

  -slice h1 h2 h3         : extract the values of the cube slice at height 

                            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 

                            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 

  -isocurrent W           : correct the iso-density surface to approximate 

                            iso-current surface, where                     

                             I(z) \propto 

                            The ES-pot cube must be loaded                 

  -espot                  : assign ES-pot values to the calculated 

                            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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20150616/7fa1a352/attachment.htm>

More information about the CP2K-user mailing list