## phonopy-users

 [Phonopy-users] analysis modulation From: 김수란 - 2013-05-13 04:25:33 Attachments: Message as HTML ```Hello I analysis the eigenvector and modulation of phonon and I have some questions In phonopy-workshop.pdf which can be obtained in phonopy homepage, eigenvector(w(qs)) is sqrt(M1)* U_x(1,q,s) Therefore I thought, displacement of atom is w(qs)/sqrt(M1) (w(qs) is the output data of phononpy in band.yaml, right?) However, I used the moulation-tag. I found that displacement is e^(i*q*r)*w(qs)/sqrt(M1) not w(qs)/sqrt(M1) (r=atom position, q=q point) So I am confused. Many reference which I obtained said displacement is w(qs)/sqrt(M1). if I want to draw the displacement by phonon mode, should I use e^(i*q*r)*w(qs)/sqrt(M1) not w(qs)/sqrt(M1)? Thank you for your concern Best regards Sooran Kim ```
 Re: [Phonopy-users] analysis modulation From: Atsushi Togo - 2013-05-13 05:07:27 ```Hello, An expression of atomic displacement operator is shown here, http://phonopy.sourceforge.net/theory.html#dynamical-matrix (the last formula in this section). On the position dependence: In the old phonopy, only gamma point modulation was supported. Therefore phase factor was irrelevant. Now general q-point is supported. On the time dependence: There is also a time dependent phase factor. Therefore we may have to specify this also to represent a snapshot of a normal mode. Togo On Mon, May 13, 2013 at 1:25 PM, 김수란 wrote: > Hello > > I analysis the eigenvector and modulation of phonon and I have some > questions > > In phonopy-workshop.pdf which can be obtained in phonopy homepage, > eigenvector(w(qs)) is sqrt(M1)* U_x(1,q,s) > > Therefore I thought, displacement of atom is w(qs)/sqrt(M1) > (w(qs) is the output data of phononpy in band.yaml, right?) > > However, > > I used the moulation-tag. I found that > displacement is e^(i*q*r)*w(qs)/sqrt(M1) not w(qs)/sqrt(M1) > (r=atom position, q=q point) > > So I am confused. > Many reference which I obtained said displacement is w(qs)/sqrt(M1). > > if I want to draw the displacement by phonon mode, should I use > e^(i*q*r)*w(qs)/sqrt(M1) not w(qs)/sqrt(M1)? > > Thank you for your concern > > Best regards > > Sooran Kim > > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and > their applications. This 200-page book is written by three acclaimed > leaders in the field. The early access version is available now. > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > _______________________________________________ > Phonopy-users mailing list > Phonopy-users@... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > -- Atsushi Togo http://atztogo.github.com/ atz.togo@... ```
 Re: [Phonopy-users] analysis modulation From: 김수란 - 2013-05-13 05:19:23 Attachments: Message as HTML ```Hello Thank you for your answer. I checked the formulation in that page. I thought that w(qs) contains the e^(iqr) So, that formulation can be rewritten as u=w(qs)/sqrt(M) (w(qs) is phononpy output) But you mean u=w(qs)/sqrt(M)*e^(iqr) is it right? 2013/5/13 Atsushi Togo > Hello, > > An expression of atomic displacement operator is shown here, > http://phonopy.sourceforge.net/theory.html#dynamical-matrix > (the last formula in this section). > > On the position dependence: > In the old phonopy, only gamma point modulation was supported. > Therefore phase factor was irrelevant. Now general q-point is > supported. > > On the time dependence: > There is also a time dependent phase factor. Therefore we may have to > specify this also to represent a snapshot of a normal mode. > > Togo > > On Mon, May 13, 2013 at 1:25 PM, 김수란 wrote: > > Hello > > > > I analysis the eigenvector and modulation of phonon and I have some > > questions > > > > In phonopy-workshop.pdf which can be obtained in phonopy homepage, > > eigenvector(w(qs)) is sqrt(M1)* U_x(1,q,s) > > > > Therefore I thought, displacement of atom is w(qs)/sqrt(M1) > > (w(qs) is the output data of phononpy in band.yaml, right?) > > > > However, > > > > I used the moulation-tag. I found that > > displacement is e^(i*q*r)*w(qs)/sqrt(M1) not w(qs)/sqrt(M1) > > (r=atom position, q=q point) > > > > So I am confused. > > Many reference which I obtained said displacement is w(qs)/sqrt(M1). > > > > if I want to draw the displacement by phonon mode, should I use > > e^(i*q*r)*w(qs)/sqrt(M1) not w(qs)/sqrt(M1)? > > > > Thank you for your concern > > > > Best regards > > > > Sooran Kim > > > > > > > ------------------------------------------------------------------------------ > > Learn Graph Databases - Download FREE O'Reilly Book > > "Graph Databases" is the definitive new guide to graph databases and > > their applications. This 200-page book is written by three acclaimed > > leaders in the field. The early access version is available now. > > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may > > _______________________________________________ > > Phonopy-users mailing list > > Phonopy-users@... > > https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > > > -- > Atsushi Togo > http://atztogo.github.com/ > atz.togo@... > ```
 Re: [Phonopy-users] analysis modulation From: Atsushi Togo - 2013-05-13 05:34:17 ```Now I see your point. It depends on how dynamical matrix is built. In phonopy's convention, dynamical matrix is written as found here http://phonopy.sourceforge.net/theory.html#dynamical-matrix . So the phase factor on atomic position is not included in eigenvector, i.e. you have to consider e^(iqr) to create modulation from eigenvector. However when using MODULATION tag, this term is included in the process to create modulation (see _get_delta method in modulation.py), so what you have to think is only time dependence. You can find the phase factor conventions for dynamical matrix in the Wallace's book, "Thermodynamics of crystals". I will improve phonopy document in the future. Togo On Mon, May 13, 2013 at 2:19 PM, 김수란 wrote: > Hello > > Thank you for your answer. > > I checked the formulation in that page. > > I thought that w(qs) contains the e^(iqr) > So, that formulation can be rewritten as u=w(qs)/sqrt(M) > (w(qs) is phononpy output) > > But you mean u=w(qs)/sqrt(M)*e^(iqr) > > is it right? > > > > > 2013/5/13 Atsushi Togo >> >> Hello, >> >> An expression of atomic displacement operator is shown here, >> http://phonopy.sourceforge.net/theory.html#dynamical-matrix >> (the last formula in this section). >> >> On the position dependence: >> In the old phonopy, only gamma point modulation was supported. >> Therefore phase factor was irrelevant. Now general q-point is >> supported. >> >> On the time dependence: >> There is also a time dependent phase factor. Therefore we may have to >> specify this also to represent a snapshot of a normal mode. >> >> Togo >> >> On Mon, May 13, 2013 at 1:25 PM, 김수란 wrote: >> > Hello >> > >> > I analysis the eigenvector and modulation of phonon and I have some >> > questions >> > >> > In phonopy-workshop.pdf which can be obtained in phonopy homepage, >> > eigenvector(w(qs)) is sqrt(M1)* U_x(1,q,s) >> > >> > Therefore I thought, displacement of atom is w(qs)/sqrt(M1) >> > (w(qs) is the output data of phononpy in band.yaml, right?) >> > >> > However, >> > >> > I used the moulation-tag. I found that >> > displacement is e^(i*q*r)*w(qs)/sqrt(M1) not w(qs)/sqrt(M1) >> > (r=atom position, q=q point) >> > >> > So I am confused. >> > Many reference which I obtained said displacement is w(qs)/sqrt(M1). >> > >> > if I want to draw the displacement by phonon mode, should I use >> > e^(i*q*r)*w(qs)/sqrt(M1) not w(qs)/sqrt(M1)? >> > >> > Thank you for your concern >> > >> > Best regards >> > >> > Sooran Kim >> > >> > >> > >> > ------------------------------------------------------------------------------ >> > Learn Graph Databases - Download FREE O'Reilly Book >> > "Graph Databases" is the definitive new guide to graph databases and >> > their applications. This 200-page book is written by three acclaimed >> > leaders in the field. The early access version is available now. >> > Download your free book today! http://p.sf.net/sfu/neotech_d2d_may >> > _______________________________________________ >> > Phonopy-users mailing list >> > Phonopy-users@... >> > https://lists.sourceforge.net/lists/listinfo/phonopy-users >> > >> >> >> >> -- >> Atsushi Togo >> http://atztogo.github.com/ >> atz.togo@... > > -- Atsushi Togo http://atztogo.github.com/ atz.togo@... ```