[CP2K:6126] Re: Issue with symmetry

Laszlo Ryan Seress laszlo... at gmail.com
Tue Feb 17 17:19:30 UTC 2015
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I did the latter before I tried to manually dictate the symmetry, the same
issue of changing all angles to 90 occurred.  That file is attached here.

Apropos, I think that using the former would do the calculation on a
reflected version of my system (because b and c are the same length, if I
switch the y and z coordinates, wouldn't I luck out and still have a
functional structure?  Maybe I am picturing this in my head wrong).  I will
still probably have to do the rotation to check.

Any ideas as to why the latter is failing?  I still don't understand why it
is overwriting my inputted angles.

Thanks, as always,
Laszlo



On Tue, Feb 17, 2015 at 5:12 PM, S Ling <lingsa... at gmail.com> wrote:

> 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> 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>
>>> 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> 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/SUBSY
>>>>>>> S/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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>>>
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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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