[CP2K:6129] Re: Issue with symmetry
Laszlo Ryan Seress
laszlo... at gmail.com
Wed Feb 18 11:15:12 UTC 2015
Hi,
As usual, human error is to blame. I realized that the previous run was
input using separate A, B, and C commands, not the ABC command. I did get
it to run (although not to converge, probably because the coordinates need
to be adjusted).
Thanks for all your help,
Laszlo
On Tue, Feb 17, 2015 at 7:22 PM, Matt W <MattWa... at gmail.com> wrote:
> 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
>>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> You received this message because you are subscribed to the
>>>>>>>>>> Google Groups "cp2k" group.
>>>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>>>>>> send an email to cp2k+... at googlegroups.com.
>>>>>>>>>> To post to this group, send email to cp... at googlegroups.com.
>>>>>>>>>> Visit this group at http://groups.google.com/group/cp2k.
>>>>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> László Ryan Seress
>>>>>>>>> las... at laszloseress.com
>>>>>>>>>
>>>>>>>> --
>>>>>>>> You received this message because you are subscribed to the Google
>>>>>>>> Groups "cp2k" group.
>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>>>> send an email to cp2k+... at googlegroups.com.
>>>>>>>> To post to this group, send email to cp... at googlegroups.com.
>>>>>>>> Visit this group at http://groups.google.com/group/cp2k.
>>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> László Ryan Seress
>>>>>>> las... at laszloseress.com
>>>>>>>
>>>>>>> --
>>>>>>> You received this message because you are subscribed to the Google
>>>>>>> Groups "cp2k" group.
>>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>>> send an email to cp2k+... at googlegroups.com.
>>>>>>> To post to this group, send email to cp... at googlegroups.com.
>>>>>>> Visit this group at http://groups.google.com/group/cp2k.
>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>
>>>>>>
>>>>>> --
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "cp2k" group.
>>>>>> To unsubscribe from this group and stop receiving emails from it,
>>>>>> send an email to cp2k+... at googlegroups.com.
>>>>>> To post to this group, send email to cp... at googlegroups.com.
>>>>>> Visit this group at http://groups.google.com/group/cp2k.
>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> László Ryan Seress
>>>>> las... at laszloseress.com
>>>>>
>>>> --
>>>> You received this message because you are subscribed to the Google
>>>> Groups "cp2k" group.
>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to cp2k+... at googlegroups.com.
>>>> To post to this group, send email to cp... at googlegroups.com.
>>>> Visit this group at http://groups.google.com/group/cp2k.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>>
>>>
>>> --
>>> László Ryan Seress
>>> las... at laszloseress.com
>>>
>> --
> You received this message because you are subscribed to the Google Groups
> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to cp2k+uns... at googlegroups.com.
> To post to this group, send email to cp... at googlegroups.com.
> Visit this group at http://groups.google.com/group/cp2k.
> For more options, visit https://groups.google.com/d/optout.
>
--
László Ryan Seress
las... at laszloseress.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20150218/878deed3/attachment.htm>
More information about the CP2K-user
mailing list