Re: [Phonopy-users] eigenvectors with phonopy - quantum espresso
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Re: [Phonopy-users] eigenvectors with phonopy - quantum espresso
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From: Antonio C. <cam...@fe...> - 2023-02-24 15:37:09
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Hi Patrizio, On 24. 02. 23 15:26, Patrizio Graziosi wrote: > Hi Antonio, > > Thanks for your patience. I based on this website > https://github.com/AdityaRoy-1996/Phonopy_VESTA > because I could not find an example on how to properly set the .conf > file in the doc. the setting file is just what you did, it's a file where each line contains a command with its options > > So, I used the following setting.conf file: > > DIM = 2 3 2 > > > FORCE_CONSTANTS = WRITE > > > EIGENVECTORS = .TRUE. > > > BAND = 0 0 0 0.5 0.5 0.5 > > > BAND_POINTS = 2 > > > > and I got the eigenvectors for two q points (Thank you Antonio!). > > Now, two questions to understand, please: > 1) I run > 1. phonopy --qe -d --dim.... > 2. all the qe calc. with displacement > 3. phonopy -f qe1.out qe2.out ... > 4. phonopy --qe -c qe.in <http://qe.in> setting.conf -s > after point 4 I got the eigenvectors, is this correct, i.e. at point > 4. phonopy diagonalizes the dynamical matrix? yes > > > 2) I got a band.yaml file with, for example > > q-position: [0.5000000,0.5000000,0.5000000 ] > > distance:0.0809338 > > band: > > - # 1 > > frequency:1.2842851749 > > eigenvector: > > - # atom 1 > > - [0.00000000000000,0.00000000000000 ] > > - [0.03436018597771, -0.10282855212023 ] > > - [ -0.00127405302119,0.00381281485376 ] > > - # atom 2 > > - [0.00118915921850, -0.01067693613962 ] > > - [0.00734798360164, -0.06597430390448 ] > > - [ -0.00446519610236,0.04009102641115 ] > > > How to interpret the numbers in the square brackets? I understand that > the first is the real part and the second is the imaginary part of the > displacement, is my understanding correct? > they are real and imaginary part of the eigenvector, not of the whole displacement. The whole displacement is defined, for example, in eq 10.40 of Duane Wallace "Thermodynamics of Crystals" or analogously in any other textbook on phonons. The displacement is an observable and, as such, it must be a real quantity. > > If I want to displace each atom along the eigenvector to make further > calculations, shall I use only the real part, the norm, or...? > You should learn the physics underlying the phonon theory to correctly use the eigenvectors. I want to stress once more that the displacement is an observable and, as such, it must be a real quantity. Check eq. 10.40 from the book that I mentioned: the sum runs over the complete q-set. Remember that in the sum q=Gamma is unique, the q-points at the BZ border are unique, while for all the other q-points, there must be couples complying with the complex conjugation relation, otherwise the displacement is not a real quantity. The MODULATION tag https://phonopy.github.io/phonopy/setting-tags.html#create-modulated-structure does this job but use it with care, as the amplitude factor, which is set by the user, does not automatically take into account that the q-set must be complete; unless you want to do specific tests and you don't care about the physical meaning of the amplitude. > What are the default units for the eigenvectors? > Eigenvectors are unitless. Check again equation 10.40 of the same book. On the l.h.s you have a displacement, then on the r.h.s. you must have a displacement; since you know the units of all the other quantities, then you can obtain the units of the eigenvectors, that is, that they are unitless. > > > > Thanks again, > > Patrizio > Best Antonio > > > > > /*--*/ > /*Patrizio Graziosi, PhD > <https://scholar.google.de/citations?user=asbZXssAAAAJ&hl=en>*/ > scholar.google profile > <https://scholar.google.it/citations?user=asbZXssAAAAJ&hl=en>, > ResearcherID: F-8225-2014 <http://www.researcherid.com/rid/F-8225-2014> > > *Research Scientist* > * > * > *_CNR - ISMN_* > *Institute for the Study of Nanostructured Materials* > > > > > > Il giorno ven 24 feb 2023 alle ore 13:17 Antonio Cammarata > <cam...@fe...> ha scritto: > > Hi Patrizio, > > no, the tag is for phonopy, it is not specific of VASP. If you go > through the phonopy website > > https://phonopy.github.io/phonopy/ > > there is a section "setting tags" > > https://phonopy.github.io/phonopy/setting-tags.html > > which lists all the possible options that you can customize for > you phonon postprocessing with the related syntax. If the use of > some tag is restricted for some of the calculators (e.g. qe, VASP, > ABINIT...) it is specified in the documentation. I strongly > suggest you to read all the documentation before asking questions > to the mailing list, it will save you a lot of time. > > Best > > Antonio > > On 24. 02. 23 13:08, Patrizio Graziosi wrote: >> Hi Antonio, >> >> I used the phonopy commands in the doc, at >> https://phonopy.github.io/phonopy/qe.html#supported-qe-pw-tags, >> to run phonopy in combination with quantum espresso (qe), and I >> never used a proper input file for phonopy, I always used qe >> input file and phonopy commands. >> >> The tag EIGENVECTORS = .TRUE. sounds like a VASP tag, but I want >> to use qe. Can you give me some hints on how, or where, can I >> use this tag, please? Or an example of a phonopy input file, >> interfacing with qe, where I can use the tag EIGENVECTORS? Sorry >> but in the doc I cannot find any example of >> computing eigenvectors from qe calc... >> >> Thanks >> Patrizio >> >> >> >> >> >> >> >> /*--*/ >> /*Patrizio Graziosi, PhD >> <https://scholar.google.de/citations?user=asbZXssAAAAJ&hl=en>*/ >> scholar.google profile >> <https://scholar.google.it/citations?user=asbZXssAAAAJ&hl=en>, >> ResearcherID: F-8225-2014 >> <http://www.researcherid.com/rid/F-8225-2014> >> >> *Research Scientist* >> * >> * >> *_CNR - ISMN_* >> *Institute for the Study of Nanostructured Materials* >> >> >> >> >> >> Il giorno ven 24 feb 2023 alle ore 10:25 Antonio Cammarata >> <cam...@fe...> ha scritto: >> >> Hi, >> >> what is your phonopy input? Did you try to add the tag >> EIGENVECTORS = .TRUE. to the input file? You can find more >> info in the documentation. >> >> Best >> >> Antonio >> >> On 24. 02. 23 9:56, Patrizio Graziosi wrote: >>> Hello, >>> >>> This is Patrizio from the National Research Council, Italy. >>> I have started to approach phonopy and I wonder if it is >>> possible to diagonalize the dynamical matrix and get the >>> phonon eigenvectors when interfacing with quantum espresso. >>> I know it is possible with VASP but I'm struggling in doing >>> this with quantum espresso. >>> >>> Thanks in advance, >>> Patrizio >>> >>> /*--*/ >>> /*Patrizio Graziosi, PhD >>> <https://scholar.google.de/citations?user=asbZXssAAAAJ&hl=en>*/ >>> scholar.google profile >>> <https://scholar.google.it/citations?user=asbZXssAAAAJ&hl=en>, >>> ResearcherID: F-8225-2014 >>> <http://www.researcherid.com/rid/F-8225-2014> >>> >>> *Research Scientist* >>> * >>> * >>> *_CNR - ISMN_* >>> *Institute for the Study of Nanostructured Materials* >>> >>> >>> >>> >>> >>> _______________________________________________ >>> Phonopy-users mailing list >>> Pho...@li... >>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >> >> -- >> _______________________________________________ >> Antonio Cammarata, PhD in Physics >> Assistant Professor in Applied Physics >> Advanced Materials Group >> Department of Control Engineering - KN:G-204 >> Faculty of Electrical Engineering >> Czech Technical University in Prague >> Karlovo Náměstí, 13 >> 121 35, Prague 2, Czech Republic >> Phone: +420 224 35 5711 >> Fax: +420 224 91 8646 >> ORCID:orcid.org/0000-0002-5691-0682 <http://orcid.org/0000-0002-5691-0682> >> WoS ResearcherID: A-4883-2014 >> >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users >> >> >> >> _______________________________________________ >> Phonopy-users mailing list >> Pho...@li... >> https://lists.sourceforge.net/lists/listinfo/phonopy-users > > -- > _______________________________________________ > Antonio Cammarata, PhD in Physics > Assistant Professor in Applied Physics > Advanced Materials Group > Department of Control Engineering - KN:G-204 > Faculty of Electrical Engineering > Czech Technical University in Prague > Karlovo Náměstí, 13 > 121 35, Prague 2, Czech Republic > Phone: +420 224 35 5711 > Fax: +420 224 91 8646 > ORCID:orcid.org/0000-0002-5691-0682 <http://orcid.org/0000-0002-5691-0682> > WoS ResearcherID: A-4883-2014 > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > > > > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users -- _______________________________________________ Antonio Cammarata, PhD in Physics Assistant Professor in Applied Physics Advanced Materials Group Department of Control Engineering - KN:G-204 Faculty of Electrical Engineering Czech Technical University in Prague Karlovo Náměstí, 13 121 35, Prague 2, Czech Republic Phone: +420 224 35 5711 Fax: +420 224 91 8646 ORCID: orcid.org/0000-0002-5691-0682 WoS ResearcherID: A-4883-2014 |
