[DFTB-Plus-User] Waveplot - CUBEMANIP .different size fragments.

[R.Perez Garcia]

for future users:
using for all three fragments 
PlottedR‚egion = {
Origin a { -0.2606880915E+01  0.1501589201E+02  0.3227004719E+01}
Box ‘[angstrom“] = {
   0.1002160145E+01  0.0000000000E+00  0.0000000000E+00
  0.0000000000E+00  0.5433932370E+00  0.0000000000E+00
  0.0000000000E+00  0.0000000000E+00  0.5449127867E+00
}
}
does not work!
the box is all weird  and misplaced.

On 16-10-12, "R.Perez Garcia"  <r.perez.garcia at student.rug.nl> wrote:
> 
> Thank you for the answer Mr. Jakowski,
> Unfortunately I do not master the use of awk either, it would be very helpful an example, supposing I manage to make all start at the same 3D mesh origin (i believe if I use for all three fragments
> PottedR‚egion = {
> Origin a { -0.2606880915E+01  0.1501589201E+02  0.3227004719E+01}
> Box ‘angstrom“ a {
>    0.1002160145E+01  0.0000000000E+00  0.0000000000E+00
>   0.0000000000E+00  0.5433932370E+00  0.0000000000E+00
>   99  0.0000000000E+00  0.0000000000E+00  0.5449127867E+00
> }
> }
> it should work as this data is the one for the complex so it is big enough to host all three). 
> because up to now they look like these:
> Complex: Cube file generated by WAVEPLOT from data created by DFTB+
> Calc-Id: 2060768639, abs2
>        424 -0.2606880915E+01  0.1501589201E+02  0.3227004719E+01
>         99  0.1002160145E+01  0.0000000000E+00  0.0000000000E+00
>         99  0.0000000000E+00  0.5433932370E+00  0.0000000000E+00
>         99  0.0000000000E+00  0.0000000000E+00  0.5449127867E+00
> ....
> PCBM: Cube file generated by WAVEPLOT from data created by DFTB+
> Calc-Id:  315999360, abs2
>        176  0.3073172503E+02  0.1691896450E+02  0.3196952235E+01
>         99  0.3255996063E+00  0.0000000000E+00  0.0000000000E+00
>         99  0.0000000000E+00  0.4414185834E+00  0.0000000000E+00
>         99  0.0000000000E+00  0.0000000000E+00  0.4848078183E+00
> Polymer: Cube file generated by WAVEPLOT from data created by DFTB+
> Calc-Id:   12057984, abs2
>        248 -0.2606880915E+01  0.1501589201E+02  0.1159444599E+02
>         99  0.1002160145E+01  0.0000000000E+00  0.0000000000E+00
>         99  0.0000000000E+00  0.5433932370E+00  0.0000000000E+00
>         99  0.0000000000E+00  0.0000000000E+00  0.4599641443E+00
> 
> Thank you again! R
> 
> On 16-10-12, Jacek Jakowski  <jjakowski at gmail.com> wrote:
> > I did not use cubemanip.py  but I used awk.  You can ignore different number of atoms, but you need to make sure  that the origin  (of the 3D mesh) generated by waveplot in all cube  files is the same.  You need to rerun waveplot and make sure that all three files  generate the same mesh.  
> > 
> > 
> > Jacek
> > 
> > 
> > On Tue, Oct 16, 2012 at 1:23 AM, R.Perez Garcia <r.perez.garcia at student.rug.nl> wrote:
> > 
> > 
> > > Dear DFTB list,
> > > I am wondering if any of you did use the cubemanip.py written by prof. Aradi? In my system I have two parts and I would like to see what is the difference of charge between the whole system and the sum of the two independent parts.
> > > 
> > > By doing something similar to this:
> > > cubemanip '(($1)-(($2)+($3)))' total/WP/wp-abs2.cube parts/COPOLYM/WP/wp-abs2.cube parts/PCBM/WP/wp-abs2.cube >> finalDiff_b4.cube
> > > I believe I can not get the right output as I get several warnings:
> > > 
> > > Warning: Nr. of atoms in 'total/WP/wp-abs2.cube' and 'parts/COPOLYM/WP/wp-abs2.cube' differ
> > > Warning: Origins in 'total/WP/wp-abs2.cube' and 'parts/COPOLYM/WP/wp-abs2.cube' differ!
> > > 
> > > Warning: Grid vectors in 'total/WP/wp-abs2.cube' and 'parts/COPOLYM/WP/wp-abs2.cube' differ!
> > > Warning: Grid vectors in 'total/WP/wp-abs2.cube' and 'parts/COPOLYM/WP/wp-abs2.cube' differ!
> > > 
> > > Warning: Nr. of atoms in 'total/WP/wp-abs2.cube' and 'parts/PCBM/WP/wp-abs2.cube' differ
> > > Warning: Origins in 'total/WP/wp-abs2.cube' and 'parts/PCBM/WP/wp-abs2.cube' differ!
> > > Warning: Grid vectors in 'total/WP/wp-abs2.cube' and 'parts/PCBM/WP/wp-abs2.cube' differ!
> > > 
> > > Warning: Grid vectors in 'total/WP/wp-abs2.cube' and 'parts/PCBM/WP/wp-abs2.cube' differ!
> > > Do you have any idea how to tackle this issue? i.e. solve it within VMD, I mean performing the operations with the visualization tool..
> > > 
> > > Thank you very much for your attention.
> > > Best regards: Rodrigo
> > > 
> > > 
> > > 
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