[CP2K-user] What is the principle of &fixed_atoms?
Daeyun Lee
kamak... at gmail.com
Thu Aug 6 13:01:48 UTC 2020
Dear Fabian
Thanks for your advice.
However, I still have a question.
I read information of the fractional coordinates in wikipedia, and it says
that the fractional coordinates can be converted into cartesian coordinates
(and in the opposite case too).
If they correspond one-to-one, isn't it the same in terms of result?
I mean, if the fractional coordinates is fixed, the cartesian coordinates
will also be fixed because they can be converted each other. Am I wrong?
By any chance, does fixing fractional coordinates mean that the shape of
the crystal lattice will be fixed?
For example, does the orthorhombic unit cell retains orthorhombic, the
rhombohedral unit cell retains rhombohedral and so on?
sincerely
2020년 8월 6일 목요일 오후 8시 53분 35초 UTC+9, fa... at gmail.com 님의 말:
>
> &fixed_atoms does not fix the cartesian but the fractional coordinates. In
> a geo_top, nvt, nvt this is the same, but if you perform a cell_opt or npt
> the cartesian coordinate of atoms can still change.
>
> Best,
> Fabian
>
> On Thursday, 6 August 2020 at 13:08:19 UTC+2 ka... at gmail.com wrote:
>
>> Dear Matt
>>
>> First of all, I'm sorry.
>> Now I noticed that coordination is wrong.
>> I mean "coordinates".
>>
>>
>>
>> Do you mean &fixed_atoms and cell parameters are independent?
>>
>> Well, in my case, xyz lengths of the cell and the distances among atoms
>> are the same, because all fixed atoms form the cell frame(a cube shape).
>> I have already checked and confirmed that they are the same length.
>>
>> The coordinates should have been fixed with &fixed_atoms, according to
>> manual.
>> Nevertheless coordinates of atoms were changed at the output.
>>
>> I don't understand this.
>>
>>
>> 2020년 8월 6일 목요일 오후 6시 51분 6초 UTC+9, Matt W 님의 말:
>>
>>> To my knowledge it fixes the cartesian position of the atoms listed. The
>>> cell parameters are free to adjust if you perform a cell optimization.
>>>
>>> Matt
>>>
>>> On Wednesday, August 5, 2020 at 11:49:06 AM UTC+1 ka... at gmail.com
>>> wrote:
>>>
>>>> Hello, everyone
>>>>
>>>>
>>>> I try to optimize cell coordinate with &fixed_atoms.
>>>> I thought that it will be optimized not to change coordination because
>>>> of the word "fix"
>>>> and I read the manual says that "specifies a list of atoms to freeze".
>>>>
>>>> But I noticed that the coordination is changed somewhat at the output
>>>> file.
>>>> What is the principle of the &fixed_atoms?
>>>> Doesn't it just freeze or fix the coordination?
>>>>
>>>> This is a part of my input.
>>>> &MOTION
>>>> &CELL_OPT
>>>> KEEP_ANGLES .T.
>>>> &END CELL_OPT
>>>> &CONSTRAINT
>>>> &FIXED_ATOMS
>>>> LIST 1..56
>>>> &END FIXED_ATOMS
>>>> &END CONSTRAINT
>>>> ...(omission)...
>>>>
>>>> &SUBSYS
>>>> &CELL
>>>> ABC 10.166 10.166 10.166
>>>> ALPHA_BETA_GAMMA 90.0 90.0 90.0
>>>> PERIODIC XYZ
>>>> MULTIPLE_UNIT_CELL 1 1 1
>>>> &END CELL
>>>> ...(omission)...
>>>>
>>>> And, at the output file, the cell vector ABC was changed to 10.436 at
>>>> the Fe2+ lattice, to 10.447 at the Zn2+ lattice and so on.
>>>>
>>>> If anyone understands about this, please tell me.
>>>>
>>>>
>>>> Thanks for your attention.
>>>>
>>>
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