spn density problem

[Rizwan Nabi]

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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