<div dir="ltr">Hi Marcella<div><br><div>Thank you for your guidance and valuable inputs!</div><div><br><br>On Tuesday, June 16, 2015 at 2:08:46 PM UTC+5:30, Marcella Iannuzzi wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi,<div><br></div><div>compile it, then run it without any input and you get the following hints:</div><div><br></div><div><p style="font-size:11px;font-family:Menlo">Usage: cubecruncher.x -i input.cube -o output.cube [options]                   </p>
<p style="font-size:11px;font-family:Menlo;min-height:13px">                                                                                </p>
<p style="font-size:11px;font-family:Menlo">         transforms 'input.cube' into 'output.cube' doing                       </p>
<p style="font-size:11px;font-family:Menlo">         transformations based on the specified options.                        </p>
<p style="font-size:11px;font-family:Menlo">         The following options are available and can normally                   </p>
<p style="font-size:11px;font-family:Menlo">         be combined:                                                           </p>
<p style="font-size:11px;font-family:Menlo;min-height:13px">                                                                                </p>
<p style="font-size:11px;font-family:Menlo">  -xyz coords.xyz         : merge in a xyz coordinate file                      </p>
<p style="font-size:11px;font-family:Menlo">                               (e.g. for VMD usage)                             </p>
<p style="font-size:11px;font-family:Menlo">  -subtract min.cube      : subtract min.cube from input.cube                   </p>
<p style="font-size:11px;font-family:Menlo">  -center {#|geo|point}   : #=1..Natom center the cube around atom #            </p>
<p style="font-size:11px;font-family:Menlo">                            geo        center the cube so that the cell         </p>
<p style="font-size:11px;font-family:Menlo">                               boundaries are as far as possible from the       </p>
<p style="font-size:11px;font-family:Menlo">                               molecule                                         </p>
<p style="font-size:11px;font-family:Menlo">                            point      center around a fixed point              </p>
<p style="font-size:11px;font-family:Menlo">  -fold                   : fold atoms inside the box defined by the cube       </p>
<p style="font-size:11px;font-family:Menlo">  -point x y z            : coordinates of the center point                     </p>
<p style="font-size:11px;font-family:Menlo">  -foldsmart              : idem, but place hydrogens near heavier atoms        </p>
<p style="font-size:11px;font-family:Menlo">  -stride #               : reduces resolution writing grids with stride #      </p>
<p style="font-size:11px;font-family:Menlo">  -multiply #             : multiply all values of cube by the given factor     </p>
<p style="font-size:11px;font-family:Menlo">  -1d_profile dir delta   : compute the profile along the cartesian axis dir    </p>
<p style="font-size:11px;font-family:Menlo">                           and a smoothed profile with smoothing interval delta </p>
<p style="font-size:11px;font-family:Menlo">  -slice h1 h2 h3         : extract the values of the cube slice at height h#,  </p>
<p style="font-size:11px;font-family:Menlo">                            along the cartesian axis #, if h#/=0,               </p>
<p style="font-size:11px;font-family:Menlo">                            reads three reals, takes the first /=0              </p>
<p style="font-size:11px;font-family:Menlo">  -iso l1 l2 l3           : compute the isosurface at level l#, recording height</p>
<p style="font-size:11px;font-family:Menlo">                            along the axis #, if l#/=0,                         </p>
<p style="font-size:11px;font-family:Menlo">                            reads three reals, takes the first /=0              </p>
<p style="font-size:11px;font-family:Menlo">  -iso_delta_grid  delta  : step of the regular grid to output the iso-surface  </p>
<p style="font-size:11px;font-family:Menlo">  -isocurrent W           : correct the iso-density surface to approximate the  </p>
<p style="font-size:11px;font-family:Menlo">                            iso-current surface, where                          </p>
<p style="font-size:11px;font-family:Menlo">                             I(z) \propto rho(z)*exp(alpha*W*sqrt(ES-<wbr>pot(z)))   </p>
<p style="font-size:11px;font-family:Menlo">                            The ES-pot cube must be loaded                      </p>
<p style="font-size:11px;font-family:Menlo">  -espot                  : assign ES-pot values to the calculated iso-surface  </p>
<p style="font-size:11px;font-family:Menlo">                            The ES-pot cube must be loaded                      </p>
<p style="font-size:11px;font-family:Menlo">  -espot_cube             : name cube file of the electrostatic potential       </p>
<p style="font-size:11px;font-family:Menlo">  -help                   : print this message                                  </p>
<p style="font-size:11px;font-family:Menlo">  -v                      : print a version string  </p></div><div><br><br>On Tuesday, June 16, 2015 at 9:51:32 AM UTC+2, Rizwan Nabi wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi CP2K users and developers<div>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? </div><div>Here I am attaching my input file and snapshot of the spin density plot.</div><div><br></div><div><br></div><div>Regards</div><div><br></div><div><br></div><div>Rizwan</div><div><br></div><div><br></div><div><br></div></div></blockquote></div></div></blockquote></div></div></div>