[CP2K:6126] Re: Issue with symmetry
Matt W
MattWa... at gmail.com
Tue Feb 17 19:22:55 UTC 2015
Hi,
Are guys you running the same input on the same machine, with the same
executable?
Then that would be really weird.
Laszlo, what I am hinting at is could you try a different cp2k module just
to check that it isn't somehow a bug of
CP2K| version string: CP2K version 2.6 (Development
Version)
CP2K| source code revision number:
svn:14482
CP2K| is freely available from
http://www.cp2k.org/
You don't need to run the whole big system, just see if anything with a
monoclinic cell gives you the same problems.
Matt
On Tuesday, February 17, 2015 at 5:28:52 PM UTC, S Ling wrote:
>
> 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> 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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