3d-plots using vis5d

Here is a step-by-step procedure to prepare an input file for vis5d program to generate charge density of wavefunction 3d-plots reads as follows:

• A binary of AIMPRO ~goss/bin/aimpro_511_bh is compiled for generating 3d plots. It has max dimensions nfitx=2000, ndimx=3400, natomx=540. Use this binary in the following runs.
  However, for big clusters (ndimx > 2000) with wavefunction plots, it is more reasonable to use a parallel version of the code with options
  /mulliken{a b}
  /energies{1}
  /movers{all}
  added.
• For wave function plots:
  Add your dat file following lines:
  /mulliken{a b}
  /energies{1}
  /movers{all}
  , where a is the lowest state to be plotted and b the highest.
  In the case of spin polarized calculation, both spin states are printed.
  Comment or delete line beginning with '//optimise '
  
  For charge density plot add lines:
  /energies{1}
  /movers{all}
  
• For wave function plots:
  Run '~goss/bin/aimpro_511_bh > wf.out'
  (You must have the modified dat file in your current directory.)
  
  For charge density plot run:
  '~goss/bin/aimpro_511_bh
  Unfortunately the binary must be in a similar maschine than the one you do the 3d-plot. This because the charge density is in binary format. The binary must also be such that it produces automatically the charge density.

• For wave function plots:
  Either
  1) Cut and paste the coefficients of the wave functions to file (for example file 'wfn.wf.out'
  or
  2) Use 'gres -wf wf.out' this produces file 'wfn.wf.out'
• For wave functions plots:
  add following lines to your dat file :
  /begin{cplot}
  /wfun
  /file{wfn.wf.out}
  /levels{a b}
  /volume
  -2 -2 -2
  4 0 0
  0 4 0
  0 0 4
  /end{cplot}
  
  

  For charge density plots:
  add following lines to your dat file :
  /begin{cplot}
  /chden
  /volume
  -2 -2 -2
  4 0 0
  0 4 0
  0 0 4
  /end{cplot}
  
  

  In both cases the visible box is defined in a.u., x y and z running from -2 to +2.
  So -2 -2 -2 is the lower left corner and following 3 lines
  
  If you want give the number of the small cubes in which the charge density is averaged for the plots add line:
  /ngridn1 n2 n3
  , where (n1+1), (n2+1) and (n3+1) are the numbers of small boxes in x,y, and z directions (default is nx=51, ny=51, nz=51). This line must come after '/volume ..'

• Run '~goss/bin/aimpro_511_bh'
  Last lines of the output tell you the file names produced.
  They should end up with '.xyzi'.
  Notice that a file 'nucleus.xyzi' is produced as well. It contains delta function like gaussians at atoms.

• Run 'xyzi_to_v5d'. It asks you to give some details, which are:
  1) The filename of the output file to be read by 'vis5d', for example 'allwf.v5d'.
  2) Number of files to be read
  With charge density plots: the file nucleus.xyzi + charge density file == 2.
  With wave function plots:the file nucleus.xyzi + the number of wavefunction files.
  3) variable names for the vis5d program. For example for wf-plots nuc, wf1, wf2, wf3 etc...
  4) The names of input files (ie. the ones ending with .xyzi).
  $\rightarrow$ The output file (ex. 'allwf.v5d') can now be used as input for program 'vis5d'

• Call program vis5d by '/usr/local/bin/vis5d -box 1 1 1 allwf.v5d' assuming that the file created by 'xyzi_to_v5d' is named 'allwf.v5d'.
  The '-box 1 1 1' yieds a cubic box.

• In vis5d select 'isosurface' to plot. The odd numbered nucleai have negative signs and the even ones positive values. To see all the nucleai you have to copy the variable using 'new var' option and thereafter selecting other sign for the isosurface.
  The copying of the wave function must also be performed using 'new var' if you want to see the positive and negative lobes of the wave function.