Some problems about the grid point of pot.cube file in the EXTERNAL_POTENTIAL subsection
Nico Holmberg
holmbe... at gmail.com
Mon Dec 4 06:53:08 UTC 2017
Hi,
That's correct. You need to output the potential V(i*dx,j*dy,k*dz) for i,
j, k between [1, 108] with dx=dy=dz=(12.4138/108). See e.g. this link
<http://paulbourke.net/dataformats/cube/> for information on how to prepare
the cube file so that it is in the correct format.
BR,
Nico
lauantai 2. joulukuuta 2017 14.52.17 UTC+2 Tianshu Jiang in Beijing
kirjoitti:
>
> Hi, Nico, sorry to bother you again.
>
> I have checked the PW grid as you have suggested, and in my simulation the
> finest grid has 108 grid points.
>
> PW_GRID| Information for grid
> number 1
> PW_GRID| Grid distributed over 12
> processors
> PW_GRID| Real space group dimensions
> 12 1
> PW_GRID| the grid is
> blocked: NO
> PW_GRID| Cutoff [a.u.]
> 100.0
> PW_GRID| spherical
> cutoff: NO
> PW_GRID| Bounds 1 -54 53
> Points: 108
> PW_GRID| Bounds 2 -54 53
> Points: 108
> PW_GRID| Bounds 3 -54 53
> Points: 108
> PW_GRID| Volume element (a.u.^3) 0.1025E-01 Volume (a.u.^3)
> 12909.5421
> PW_GRID| Grid span
> FULLSPACE
> PW_GRID| Distribution Average
> Max Min
> PW_GRID| G-Vectors 104976.0 104976
> 104976
> PW_GRID| G-Rays 972.0
> 972 972
> PW_GRID| Real Space Points 104976.0 104976
> 104976
>
> And the simulation box is a cube with length 12.4138.
>
> &FORCE_EVAL
> METHOD QS
> &SUBSYS
> &CELL
> ABC 12.4138 12.4138 12.4138
> &END CELL
>
> The next thing I need to do is to distribute 108^3 grid points in the
> simulation box uniformly. And specify the potential atoms can feel at each
> grid point.
> Is it right ?
>
> Expecting your reply!
>
> 在 2017年12月1日星期五 UTC+8下午6:31:14，Nico Holmberg写道：
>>
>> Hi,
>>
>> You need to supply a cube file that contains as many grid points as the
>> grid that holds the real space electron density in your simulation system
>> (depends on the PW_CUTOFF and cell size). You can check the size of this
>> grid by turning on the print key FORCE_EVAL/PRINT/GRID_INFORMATION (see
>> example below). When you print out a cube file, unless you explicitly
>> specify otherwise, only every second value along each axis is printed out
>> (keyword STRIDE). You need to take this into account when you supply a file
>> for READ_FROM_CUBE, because as far as I understand no
>> interpolation/extrapolation from tighter/looser grids is possible.
>>
>> An example output is given below. In this case, the grid contains 350^3
>> points at a planewave cutoff of 500 Ry. So to summarize, if your system
>> contains 54 data points along each direction (at STRIDE 1), then you need
>> to provide a cube with 54^3 grid points. You need a larger cube file with
>> (2*54)^3 grid points if you printed out the cube file with STRIDE 2.
>>
>> PW_GRID| Information for grid
>> number 1
>> PW_GRID| Grid distributed over 192
>> processors
>> PW_GRID| Real space group dimensions
>> 192 1
>> PW_GRID| the grid is
>> blocked: NO
>> PW_GRID| Cutoff
>> [a.u.] 250.0
>> PW_GRID| spherical
>> cutoff: NO
>> PW_GRID| Bounds 1 -175 174
>> Points: 350
>> PW_GRID| Bounds 2 -175 174
>> Points: 350
>> PW_GRID| Bounds 3 -175 174
>> Points: 350
>> PW_GRID| Volume element (a.u.^3) 0.2459E-02 Volume (a.u.^3)
>> 105442.7279
>> PW_GRID| Grid span
>> FULLSPACE
>> PW_GRID| Distribution Average
>> Max Min
>> PW_GRID| G-Vectors 223307.3 223650
>> 223300
>> PW_GRID| G-Rays 638.0
>> 639 638
>> PW_GRID| Real Space Points 223307.3 245000
>> 122500
>>
>> RS_GRID| Information for grid
>> number 1
>> RS_GRID| Bounds 1 -175 174
>> Points: 350
>> RS_GRID| Bounds 2 -175 174
>> Points: 350
>> RS_GRID| Bounds 3 -175 174
>> Points: 350
>> RS_GRID| Real space distribution over 4
>> groups
>> RS_GRID| Real space distribution along
>> direction 1
>> RS_GRID| Border
>> size 29
>> RS_GRID| Real space distribution over 6
>> groups
>> RS_GRID| Real space distribution along
>> direction 2
>> RS_GRID| Border
>> size 29
>> RS_GRID| Real space distribution over 8
>> groups
>> RS_GRID| Real space distribution along
>> direction 3
>> RS_GRID| Border
>> size 29
>> RS_GRID| Distribution Average
>> Max Min
>> RS_GRID| Planes 145.5
>> 146 145
>> RS_GRID| Distribution Average
>> Max Min
>> RS_GRID| Planes 116.3
>> 117 116
>> RS_GRID| Distribution Average
>> Max Min
>> RS_GRID| Planes 101.8
>> 102 101
>>
>> BR,
>>
>> Nico
>>
>>
>> perjantai 1. joulukuuta 2017 11.19.13 UTC+2 jts2... at gmail.com kirjoitti:
>>>
>>> Hi everyone,
>>>
>>> I have asked several questions about the same subject. Until yesterday,
>>> I have figured out the meaning of the *.cube file generated by CP2K.
>>> What I want to do is to add potential to my simulation system, but the
>>> potential is calculated from Poisson equation using finite element method.
>>> Hence I only have grid point values of the potential.
>>>
>>> So the solution is adding the potential from pot.cube file using
>>> READ_FROM_CUBE option. I will try this in a simple simulation to figure the
>>> structure.
>>> The simulation box in my simulation is a cube, whose length of a side is
>>> 12.4138 (Angstrom, I think). And from the *.cube file I know the length
>>> of the
>>> vector along x, y and z direction is 0.434420(Angstrom, maybe). What's
>>> more, the number of data points along each direction is 54.
>>>
>>> Now I need to supply the pot.cube file to CP2K. I wonder how many grid
>>> point value should be given?
>>> (54*12.4138 / 0.434420) ^3 ?
>>>
>>> I major in mathematic, so the easy thing for you may be a problem for me.
>>>
>>> Thanks for your reply !
>>>
>>
>>
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