The cubecruncher is a tool to do various operations on cube files. Its source code can be found at tools/cubecruncher within CP2K's tool-collection.

Before using it the tool has to be compiled:

$ git clone https://github.com/cp2k/cp2k.git
$ cd cp2k/tools/cubecruncher
$ make

Afterwards the binary cubecruncher.x offers the following options:

$ ./cubecruncher.x -help
 Writing help message 
                                                                                
 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