[CP2K:6126] Re: Issue with symmetry
S Ling
lingsa... at gmail.com
Tue Feb 17 17:28:52 UTC 2015
I don't have problem with the latter setting. I am not sure why you didn't
get the same.
SL
On Tuesday, February 17, 2015 at 5:20:04 PM UTC, Laszlo Ryan Seress wrote:
>
> 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 <ling... at gmail.com <javascript:>
> > 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 <javascript:>
>
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