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From: Atz Togo <atz.togo@gm...>  20110829 05:16:13

Hi, I modified the implementation of the "nosym" option. I think it became more intuitive like ISYM=0. So if you want to test it, I will send a development version of phonopy to you though it may contain bugs because of rewriting many lines. Togo On Thu, Aug 25, 2011 at 2:33 AM, Atz Togo <atz.togo@...> wrote: > Hi, > > There is no option disable symmetry finding like ISYM=0 in phonopy as > you write. If your defect supercell has no translational symmetry, > nosym option should work though no message is shown clearly. For > example, you can run > > % phonopy d dim="1 1 1" > > with and without nosym opton. Then you may find the different number > of POSCARxxx files. In the current implementation, the full symmetry > is anyway searched (and the space group is shown) for the supercell > (not the input unit cell), then all the rotation operations are > removed, and only pure translation operations are left. > > Togo > > > On Wed, Aug 24, 2011 at 10:05 PM, Espen FlageLarsen > <espen.flagelarsen@...> wrote: >> Hi, >> >> Is there a way to turn of the symmetry routines during phonopy runs? >> There was a version with nosym, but I could not located it in the >> archives. >> >> I got some imaginary frequencies (rather flat bands all over kspace). >> Defects could of course introduce imaginary frequencies, but these flat >> bands seems a bit troublesome. Hence I want to disable symmetry. >> Basically, VASP puts my structure (defects in a 64 atom supercell) into >> C1, while Phonopy wants it in SG 113 (or SG 35 with artificial low >> tolerance). I'm now rerunning VASP with IBRION = 7, ISYM = 0 (I believe >> phonopy should work with IBRION=7 as well, since the output is similar, >> but without symmetry). To make the analysis consistent, symmetry >> unrestricted calculations in phonopy would be greatly appreciated. >> >> Cheers >> Espen >> >> >>  >> EMC VNX: the world's simplest storage, starting under $10K >> The only unified storage solution that offers unified management >> Up to 160% more powerful than alternatives and 25% more efficient. >> Guaranteed. http://p.sf.net/sfu/emcvnxdev2dev >> _______________________________________________ >> Phonopyusers mailing list >> Phonopyusers@... >> https://lists.sourceforge.net/lists/listinfo/phonopyusers >> > > > >  > Atsushi Togo > http://atztogo.users.sourceforge.net/ > atz.togo@... >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Atz Togo <atz.togo@gm...>  20110824 17:35:26

Hi, There is no option disable symmetry finding like ISYM=0 in phonopy as you write. If your defect supercell has no translational symmetry, nosym option should work though no message is shown clearly. For example, you can run % phonopy d dim="1 1 1" with and without nosym opton. Then you may find the different number of POSCARxxx files. In the current implementation, the full symmetry is anyway searched (and the space group is shown) for the supercell (not the input unit cell), then all the rotation operations are removed, and only pure translation operations are left. Togo On Wed, Aug 24, 2011 at 10:05 PM, Espen FlageLarsen <espen.flagelarsen@...> wrote: > Hi, > > Is there a way to turn of the symmetry routines during phonopy runs? > There was a version with nosym, but I could not located it in the > archives. > > I got some imaginary frequencies (rather flat bands all over kspace). > Defects could of course introduce imaginary frequencies, but these flat > bands seems a bit troublesome. Hence I want to disable symmetry. > Basically, VASP puts my structure (defects in a 64 atom supercell) into > C1, while Phonopy wants it in SG 113 (or SG 35 with artificial low > tolerance). I'm now rerunning VASP with IBRION = 7, ISYM = 0 (I believe > phonopy should work with IBRION=7 as well, since the output is similar, > but without symmetry). To make the analysis consistent, symmetry > unrestricted calculations in phonopy would be greatly appreciated. > > Cheers > Espen > > >  > EMC VNX: the world's simplest storage, starting under $10K > The only unified storage solution that offers unified management > Up to 160% more powerful than alternatives and 25% more efficient. > Guaranteed. http://p.sf.net/sfu/emcvnxdev2dev > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Espen FlageLarsen <espen.flagelarsen@fy...>  20110824 13:24:14

Hi, Is there a way to turn of the symmetry routines during phonopy runs? There was a version with nosym, but I could not located it in the archives. I got some imaginary frequencies (rather flat bands all over kspace). Defects could of course introduce imaginary frequencies, but these flat bands seems a bit troublesome. Hence I want to disable symmetry. Basically, VASP puts my structure (defects in a 64 atom supercell) into C1, while Phonopy wants it in SG 113 (or SG 35 with artificial low tolerance). I'm now rerunning VASP with IBRION = 7, ISYM = 0 (I believe phonopy should work with IBRION=7 as well, since the output is similar, but without symmetry). To make the analysis consistent, symmetry unrestricted calculations in phonopy would be greatly appreciated. Cheers Espen 
From: Atz Togo <atz.togo@gm...>  20110822 05:35:56

Hi, Probably the answer is yes. But if we need frequencies only at Gammapoint, we can use unit cell. Togo On Mon, Aug 22, 2011 at 2:12 PM, Caloma Trumica <spmmal@...> wrote: > Dear all, > > I have a very quick question: > > when calculating the force constants, we need to use supercell and then use > phonopy? > > Thanks >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Caloma Trumica <spmmal@gm...>  20110822 05:12:09

Dear all, I have a very quick question: when calculating the force constants, we need to use supercell and then use phonopy? Thanks 
From: Atz Togo <atz.togo@gm...>  20110803 08:16:57

Hi, You can apply group theory since a band except for the end points has the same site symmetry. As another solution, this may be also worth to read. http://prb.aps.org/abstract/PRB/v65/i20/e205117 Togo 2011/8/3 Xiaoliang Zhang <zhangxiaoliang@...>: > OK, thanks > > And because I want to obtain the individual phonon modes to compute the phonon velocity, I would like the phonon dispersion curves belong to corresponding phonon modes, as you said, I hope they are connected. > > What can I do to achieve this? Any solutions? > Thanks again > > Best wishes, > Xiaoliang > > >> 原始邮件 >> 发件人: "Atz Togo" <atz.togo@...> >> 发送时间: 2011年8月3日 星期三 >> 收件人: "Xiaoliang Zhang" <zhangxiaoliang@...> >> 抄送: phonopyusers <phonopyusers@...> >> 主题: Re: [Phonopyusers] Are the phonon frequencies sorted? >> >> Hi, >> >> As you wrote, the frequencies are sorted in ascending order. The band >> connection function is not implemented in phonopy. >> >> Togo >> >> 2011/8/3 Xiaoliang Zhang <zhangxiaoliang@...>: >> > Dear Togo, >> > >> > As attached is the phonon dispersion curves for NaCl in the example folder of phonopy. >> > >> > When the "Number" value is less than 50, the direction of the kvector is the same, but you can see that there is a suddenly corner for the blue and pink curves, I mean, from increasing to sudden decreasing, or from decreasing to sudden increasing. >> > >> > And I notice that in the whole range of kpoints, the frequencies always increases in the order of colours, i.e., black,red, blue, .... I think maybe this is because when outputing the frequencies at specific kpoints, phonopy sorted the frequency values, am I right? >> > >> > If this is true, how can I cancel the sorting,I did not find where is the codes for sorting, thanks >> > >> > Best regards, >> > Xiaoliang >> > >> > >> > >> > >> >  >> > BlackBerry® DevCon Americas, Oct. 1820, San Francisco, CA >> > The mustattend event for mobile developers. Connect with experts. >> > Get tools for creating Super Apps. See the latest technologies. >> > Sessions, handson labs, demos & much more. Register early & save! >> > http://p.sf.net/sfu/rimblackberry1 >> > _______________________________________________ >> > Phonopyusers mailing list >> > Phonopyusers@... >> > https://lists.sourceforge.net/lists/listinfo/phonopyusers >> > >> > >> >> >> >>  >> Atsushi Togo >> http://atztogo.users.sourceforge.net/ >> atz.togo@... > > > > > >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Xiaoliang Zhang <zhangxiaoliang@ie...>  20110803 06:06:55

OK, thanks And because I want to obtain the individual phonon modes to compute the phonon velocity, I would like the phonon dispersion curves belong to corresponding phonon modes, as you said, I hope they are connected. What can I do to achieve this? Any solutions? Thanks again Best wishes, Xiaoliang > 原始邮件 > 发件人: "Atz Togo" <atz.togo@...> > 发送时间: 2011年8月3日 星期三 > 收件人: "Xiaoliang Zhang" <zhangxiaoliang@...> > 抄送: phonopyusers <phonopyusers@...> > 主题: Re: [Phonopyusers] Are the phonon frequencies sorted? > > Hi, > > As you wrote, the frequencies are sorted in ascending order. The band > connection function is not implemented in phonopy. > > Togo > > 2011/8/3 Xiaoliang Zhang <zhangxiaoliang@...>: > > Dear Togo, > > > > As attached is the phonon dispersion curves for NaCl in the example folder of phonopy. > > > > When the "Number" value is less than 50, the direction of the kvector is the same, but you can see that there is a suddenly corner for the blue and pink curves, I mean, from increasing to sudden decreasing, or from decreasing to sudden increasing. > > > > And I notice that in the whole range of kpoints, the frequencies always increases in the order of colours, i.e., black,red, blue, .... I think maybe this is because when outputing the frequencies at specific kpoints, phonopy sorted the frequency values, am I right? > > > > If this is true, how can I cancel the sorting,I did not find where is the codes for sorting, thanks > > > > Best regards, > > Xiaoliang > > > > > > > > > >  > > BlackBerry® DevCon Americas, Oct. 1820, San Francisco, CA > > The mustattend event for mobile developers. Connect with experts. > > Get tools for creating Super Apps. See the latest technologies. > > Sessions, handson labs, demos & much more. Register early & save! > > http://p.sf.net/sfu/rimblackberry1 > > _______________________________________________ > > Phonopyusers mailing list > > Phonopyusers@... > > https://lists.sourceforge.net/lists/listinfo/phonopyusers > > > > > > > >  > Atsushi Togo > http://atztogo.users.sourceforge.net/ > atz.togo@... 
From: Atz Togo <atz.togo@gm...>  20110803 00:51:20

Hi, As you wrote, the frequencies are sorted in ascending order. The band connection function is not implemented in phonopy. Togo 2011/8/3 Xiaoliang Zhang <zhangxiaoliang@...>: > Dear Togo, > > As attached is the phonon dispersion curves for NaCl in the example folder of phonopy. > > When the "Number" value is less than 50, the direction of the kvector is the same, but you can see that there is a suddenly corner for the blue and pink curves, I mean, from increasing to sudden decreasing, or from decreasing to sudden increasing. > > And I notice that in the whole range of kpoints, the frequencies always increases in the order of colours, i.e., black,red, blue, .... I think maybe this is because when outputing the frequencies at specific kpoints, phonopy sorted the frequency values, am I right? > > If this is true, how can I cancel the sorting,I did not find where is the codes for sorting, thanks > > Best regards, > Xiaoliang > > > > >  > BlackBerry® DevCon Americas, Oct. 1820, San Francisco, CA > The mustattend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, handson labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rimblackberry1 > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers > >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Atz Togo <atz.togo@gm...>  20110803 00:40:01

Probably PYTHONPATH is incorrectly set. You can see if it is set or not by % echo $PYTHONPATH Togo On Thu, Jul 28, 2011 at 10:31 AM, Panson Pan <pansonh@...> wrote: > When I run the phonopy, I got the following error. > > Traceback (most recent call last): > File "./phonopy", line 23, in ? > from phonopy import * > ImportError: No module named phonopy > > Would anyone be kind to comment on the problem? > >  > BlackBerry® DevCon Americas, Oct. 1820, San Francisco, CA > The mustattend event for mobile developers. Connect with experts. > Get tools for creating Super Apps. See the latest technologies. > Sessions, handson labs, demos & much more. Register early & save! > http://p.sf.net/sfu/rimblackberry1 > _______________________________________________ > Phonopyusers mailing list > Phonopyusers@... > https://lists.sourceforge.net/lists/listinfo/phonopyusers > >  Atsushi Togo http://atztogo.users.sourceforge.net/ atz.togo@... 
From: Xiaoliang Zhang <zhangxiaoliang@ie...>  20110802 19:24:42

Dear Togo, As attached is the phonon dispersion curves for NaCl in the example folder of phonopy. When the "Number" value is less than 50, the direction of the kvector is the same, but you can see that there is a suddenly corner for the blue and pink curves, I mean, from increasing to sudden decreasing, or from decreasing to sudden increasing. And I notice that in the whole range of kpoints, the frequencies always increases in the order of colours, i.e., black,red, blue, .... I think maybe this is because when outputing the frequencies at specific kpoints, phonopy sorted the frequency values, am I right? If this is true, how can I cancel the sorting,I did not find where is the codes for sorting, thanks Best regards, Xiaoliang 