[CP2K:6123] Re: Issue with symmetry

Laszlo Ryan Seress laszlo... at gmail.com
Tue Feb 17 16:49:30 UTC 2015
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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 <lingsa... at gmail.com> 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 <laszlo... at gmail.com>
> 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 <lingsa... at gmail.com> 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
>>
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-- 
László Ryan Seress
las... at laszloseress.com
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