[CP2K:6123] Re: Issue with symmetry
S Ling
lingsa... at gmail.com
Tue Feb 17 17:12:24 UTC 2015
Either
&CELL
ABC 16.000 15.600 15.600
ALPHA_BETA_GAMMA 90.00000000 86.40000000 90.00000000
SYMMETRY MONOCLINIC
&END CELL
or
&CELL
ABC 16.000 15.600 15.600
ALPHA_BETA_GAMMA 90.00000000 90.00000000 86.40000000
&END CELL
should give you correct "BETA" angle. You need to rotate the whole lattice
system for the first setting. Since you are not doing a CELL_OPT, I would
suggest you to use the second setting, in which you don't need to change
the coordinate system.
SL
On Tuesday, February 17, 2015 at 4:50:12 PM UTC, Laszlo Ryan Seress wrote:
>
> Hi,
>
> I've attached my input and coordinate files. There is some "overflow"
> beyond the edges of the box, but I have been told this is ok because of
> periodic boundary conditions. I got the coordinates from the SI of a
> paper, which I have not attached due to size, but can be found at this
> link, in case it is of interest. dx.doi.org/10.1021/ma100551m In the
> SI, they have gamma = 86.4, which is why I have it set up that way.
>
> I am aware that since I didn't rotate the coordinates yet there could be
> (i.e. almost definitely are) issues with the accuracy of the results, but I
> suppose I'm surprised that the geometry is still being set to 90 degrees.
> From what I understand, the program is immediately setting it to an
> orthorhomic box and so the errors are occurring on calculations that aren't
> in the right symmetry anyways.
>
> Thanks again for taking the time to help out with this.
>
> Laszlo
>
> On Tue, Feb 17, 2015 at 4:38 PM, S Ling <ling... at gmail.com <javascript:>
> > wrote:
>
>> It would be more useful if you can provide your full input file.
>>
>> As I said in the first post, you need to rotate your lattice if you swap
>> BETA and GAMMA angles, i.e. you need to change the whole coordinate system
>> and coordiantes of all the atoms. The "ERRORL2 in
>> cp_fm_cholesky:cp_fm_cholesky_decompose processor" error message might mean
>> you have a very bad geometry, which is related to the way you set your CELL
>> section.
>>
>> SL
>>
>>
>>
>> On 17 February 2015 at 16:11, Laszlo Ryan Seress <lasz... at gmail.com
>> <javascript:>> wrote:
>>
>>> Thank you again for the reply. I thought this was a really good
>>> suggestion so I was surprised to see that it didn't work (and also felt
>>> silly that I didn't think of it myself).
>>>
>>> I ran the program twice, with inputs:
>>>
>>> (run *759)
>>>
>>> &CELL
>>> ABC 16.000 15.600 15.600
>>> ALPHA_BETA_GAMMA 90.00000000 86.40000000 90.00000000
>>> SYMMETRY MONOCLINIC
>>> &END CELL
>>>
>>> and
>>>
>>> (run *762)
>>>
>>> &CELL
>>> ABC 16.000 15.600 15.600
>>> ALPHA_BETA_GAMMA 90.00000000 90.00000000 86.40000000
>>> SYMMETRY MONOCLINIC
>>> &END CELL
>>>
>>> Both runs ended with errors.
>>>
>>> Interestingly, in both cases, the output has the following information
>>> in the beginning:
>>>
>>> CELL_TOP| Volume [angstrom^3]:
>>> 3886.077
>>> CELL_TOP| Vector a [angstrom 16.000 0.000 0.000 |a| =
>>> 16.000
>>> CELL_TOP| Vector b [angstrom 0.000 15.600 0.000 |b| =
>>> 15.600
>>> CELL_TOP| Vector c [angstrom 0.000 0.000 15.600 |c| =
>>> 15.600
>>> CELL_TOP| Angle (b,c), alpha [degree]:
>>> 90.000
>>> CELL_TOP| Angle (a,c), beta [degree]:
>>> 90.000
>>> CELL_TOP| Angle (a,b), gamma [degree]:
>>> 90.000
>>> CELL_TOP| Requested initial symmetry:
>>> MONOCLINIC
>>> CELL_TOP| Numerically orthorhombic:
>>> YES
>>>
>>> So still the angles are being overwritten. However, something else is
>>> clearly breaking because the program is ending with errors. I don't really
>>> know how to interpret the error reports in great detail, but I have
>>> attached them in case they prove useful.
>>>
>>> Any thoughts?
>>>
>>> Laszlo
>>>
>>>
>>> On Tue, Feb 17, 2015 at 2:32 PM, S Ling <ling... at gmail.com
>>> <javascript:>> wrote:
>>>
>>>> Please remove the three A/B/C cell vectors, and set your CELL section
>>>> like this:
>>>>
>>>> &CELL
>>>> ABC 16.0 15.6 15.6
>>>> ALPHA_BETA_GAMMA 90.00000000 86.40000000 90.00000000
>>>> SYMMETRY MONOCLINIC
>>>> &END CELL
>>>>
>>>> SL
>>>>
>>>> On Tuesday, February 17, 2015 at 2:18:00 PM UTC, Laszlo Ryan Seress
>>>> wrote:
>>>>>
>>>>> Thank you for your reply.
>>>>>
>>>>> I tried the following input:
>>>>>
>>>>> &CELL
>>>>> A 16.00000000 0.000000000 0.000000000
>>>>> B 0.000000000 15.60000000 0.000000000
>>>>> C 0.000000000 0.000000000 15.60000000
>>>>> ALPHA_BETA_GAMMA 90.00000000 86.40000000 90.00000000
>>>>> SYMMETRY MONOCLINIC
>>>>> &END CELL
>>>>>
>>>>> but still got this output:
>>>>>
>>>>> CELL| Volume [angstrom^3]:
>>>>> 3893.760
>>>>> CELL| Vector a [angstrom]: 16.000 0.000 0.000 |a| =
>>>>> 16.000
>>>>> CELL| Vector b [angstrom]: 0.000 15.600 0.000 |b| =
>>>>> 15.600
>>>>> CELL| Vector c [angstrom]: 0.000 0.000 15.600 |c| =
>>>>> 15.600
>>>>> CELL| Angle (b,c), alpha [degree]:
>>>>> 90.000
>>>>> CELL| Angle (a,c), beta [degree]:
>>>>> 90.000
>>>>> CELL| Angle (a,b), gamma [degree]:
>>>>> 90.000
>>>>> CELL| Requested initial symmetry:
>>>>> MONOCLINIC
>>>>> CELL| Numerically orthorhombic:
>>>>> YES
>>>>>
>>>>> It seems to be overwriting my inputted angles and replacing them with
>>>>> 90 degrees.
>>>>>
>>>>> Best,
>>>>> Laszlo
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Feb 17, 2015 at 2:02 PM, S Ling <ling... at gmail.com> wrote:
>>>>>
>>>>>> You need to rotate your lattice so that your beta=86.4, not
>>>>>> gamma=86.4. This is the requirement of MONOCLINIC space symmetry in CP2K,
>>>>>> see http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/
>>>>>> SUBSYS/CELL.html#desc_SYMMETRY
>>>>>>
>>>>>> SL
>>>>>>
>>>>>>
>>>>>> On Tuesday, February 17, 2015 at 1:15:44 PM UTC, Laszlo Ryan Seress
>>>>>> wrote:
>>>>>>>
>>>>>>> Dear All,
>>>>>>>
>>>>>>> I have been having an issue with the symmetry command in the CELL
>>>>>>> section. My input has:
>>>>>>>
>>>>>>> &CELL
>>>>>>> A 16.00000000 0.000000000 0.000000000
>>>>>>> B 0.000000000 15.60000000 0.000000000
>>>>>>> C 0.000000000 0.000000000 15.60000000
>>>>>>> ALPHA_BETA_GAMMA 90.00000000 90.00000000 86.40000000
>>>>>>> SYMMETRY MONOCLINIC
>>>>>>> &END CELL
>>>>>>>
>>>>>>> but the output has:
>>>>>>>
>>>>>>> CELL_TOP| Volume [angstrom^3]:
>>>>>>> 3893.760
>>>>>>> CELL_TOP| Vector a [angstrom 16.000 0.000 0.000 |a| =
>>>>>>> 16.000
>>>>>>> CELL_TOP| Vector b [angstrom 0.000 15.600 0.000 |b| =
>>>>>>> 15.600
>>>>>>> CELL_TOP| Vector c [angstrom 0.000 0.000 15.600 |c| =
>>>>>>> 15.600
>>>>>>> CELL_TOP| Angle (b,c), alpha [degree]:
>>>>>>> 90.000
>>>>>>> CELL_TOP| Angle (a,c), beta [degree]:
>>>>>>> 90.000
>>>>>>> CELL_TOP| Angle (a,b), gamma [degree]:
>>>>>>> 90.000
>>>>>>> CELL_TOP| Requested initial symmetry:
>>>>>>> MONOCLINIC
>>>>>>> CELL_TOP| Numerically orthorhombic:
>>>>>>> YES
>>>>>>>
>>>>>>> Has anyone had a similar issue with getting the angles changed and
>>>>>>> the program changing the symmetry from monoclinic to orthorhombic?
>>>>>>>
>>>>>>> Thanks for any help you may be able to provide.
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Laszlo
>>>>>>>
>>>>>> --
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>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> László Ryan Seress
>>>>> las... at laszloseress.com
>>>>>
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>>>
>>>
>>>
>>> --
>>> László Ryan Seress
>>> las... at laszloseress.com <javascript:>
>>>
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>>
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>
>
>
> --
> László Ryan Seress
> las... at laszloseress.com <javascript:>
>
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