Bug in cube file printing?

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Muhammad Radifar

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Dec 14, 2010, 7:22:42 AM12/14/10
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Dear CP2K developers,

I was using CP2K version 2.2.47 to simulate the hydronium ion and 3 water molecules with print electron density turned on. And when I open the cube files (with VMD 1.8.7) I found something weird, the box position is seems to be shifted far away that the electron density looks absurd and not all the atom is inside the box. When I open the example cube file from CPMD tutorial in VMD everything is just fine. I'm wondering if this is some sort of bug inside CP2K that I am using or am I not typing the input file correctly.

With this mail I also attach the input file that I'm using and some of the output files produced. Hope to get the answer and the solution soon.

Thanks,

Radif

PS : I compile the CP2K(sopt) under Ubuntu 10.04 i686 using gfortran 4.4.3, with math-atlas lib (with netlib lapack), FFTSG.
cube-shifted.jpg
H2O-2.inp
H2O-2.out
H2O-ELECTRON_DENSITY-1_0.cube
H2O-pos-1.xyz

Fawzi Mohamed

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Dec 14, 2010, 9:25:01 AM12/14/10
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the box is periodic, so everything looks correct, you either have to
wrap the cube file, or center the molecule at L/2 instead of 0.

Fawzi

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> <cube-shifted.jpg><H2O-2.inp><H2O-2.out><H2O-
> ELECTRON_DENSITY-1_0.cube><H2O-pos-1.xyz>

Muhammad Radifar

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Dec 15, 2010, 4:56:36 AM12/15/10
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Dear Fawzi,
I just center the molecule on coordinate 4,4,4 inside 8x8x8 cell, and
the result is perfectly fine. Thanks a lot Fawzi!
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