[Phonopy-users] Fwd: Need help to used modulation command
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From: Naveena P.S. <nav...@gm...> - 2026-02-24 12:17:39
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Hi, I have included the required files in the attached .zip folder. I am attempting to modulate (i.e., displace) the atomic positions in a 2×2×1 supercell of a TiS₂ monolayer. For this purpose, I started from the optimised unit cell input file (TiS2_primitive_scf.in). Since I obtained a soft phonon mode at the M high-symmetry point (0.5, 0, 0), I need to construct a 2×2×1 supercell and modulate the atomic positions according to the eigenvector of this soft mode. I have included the phonon output files from Quantum ESPRESSO, which contain information about the soft mode and its eigenvectors. However, I am unsure which file should be used for this purpose, whether I should refer to the .modesfile or the corresponding .dyn* file of the soft mode. For reference, I have included all the relevant files in the folder. So far, I have used the following command: phonopy --qe -c TiS2_primitive_scf.in --readfc --dim="2 2 1" --qpoints 0.5000 0.2887 0.0000 --bi 1 --amplitude 0.03 --modulation 2 2 1, 0.5000 0.2887 0.0000 1 0.03 0 -v However, this results in an error. I would like to use the modulation command correctly, but I am not sure how to configure it properly within Phonopy. I hope this clarifies my issue and helps you understand the problem. With regards, Naveena TiS2_1.zip <https://drive.google.com/file/d/1yPfp2CqdeS0bFJOPuDqOcOOozTB8HtP1/view?usp=drive_web> On Fri, Feb 13, 2026 at 9:00 AM Atsushi Togo <atz...@gm...> wrote: > Hi, > > > Do you need the input files? > > Maybe. Please think about how you could motivate me to solve your problem. > > Togo > > On Fri, Feb 13, 2026 at 4:18 PM Naveena P.Sivam <nav...@gm...> > wrote: > >> Hi >> >> I followed the instructions in the document, but I am unable to modulate >> the atom. It shows errors. Do you need the input files? >> >> -naveena >> >> On Fri 13 Feb 2026 at 08:16, Atsushi Togo <atz...@gm...> wrote: >> >>> Hi, >>> >>> > How to perform this? >>> >>> It is written in the documentation. >>> >>> > if you need any additional input, let me know. >>> >>> I need to reproduce your issue. >>> >>> Togo >>> >>> On Fri, Feb 13, 2026 at 1:59 PM Naveena P.Sivam <nav...@gm...> >>> wrote: >>> >>>> Hi, >>>> >>>> I need help to perform atomic modulation with a specific q-point >>>> (pre-processing after DFPT calculation using QE) using phonopy. MODULATION >>>> = (command). How to perform this? >>>> >>>> if you need any additional input, let me know. >>>> >>>> with regards >>>> Naveena >>>> >>>> On Fri, Feb 13, 2026 at 4:38 AM Atsushi Togo <atz...@gm...> >>>> wrote: >>>> >>>>> Hi, >>>>> >>>>> Information is too little to see the issue. So it is difficult to >>>>> answer. >>>>> >>>>> > I found your youtube videos >>>>> >>>>> I think those are not my youtube videos. >>>>> >>>>> Togo >>>>> >>>>> >>>>> On Fri, Feb 13, 2026 at 1:22 AM Naveena P.Sivam <nav...@gm...> >>>>> wrote: >>>>> >>>>>> Hello >>>>>> I am trying to do atomic modulation (atomic displacement) with >>>>>> respect to the normal mode at the specific q point. I tried to use this >>>>>> command line: >>>>>> phonopy --qe --modulation 2 2 1, 0.000000000 0.433012702 >>>>>> 0.000000000 1 0.03 0 -c TiS2_primitive_scf.in --dim 2 2 1 -v. >>>>>> >>>>>> But it provides error like this: >>>>>> >>>>>> phonopy --qe --modulation 2 2 1, 0.000000000 0.433012702 >>>>>> 0.000000000 1 0.03 0 -c TiS2_primitive_scf.in --dim 2 2 1 -v >>>>>> _ >>>>>> _ __ | |__ ___ _ __ ___ _ __ _ _ >>>>>> | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | >>>>>> | |_) | | | | (_) | | | | (_) || |_) | |_| | >>>>>> | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | >>>>>> |_| |_| |___/ >>>>>> 2.47.1 >>>>>> >>>>>> -------------------------[time 2026-02-06 >>>>>> 16:53:41]------------------------- >>>>>> Compiled with OpenMP support (max 8 threads). >>>>>> Python version 3.11.11 >>>>>> Spglib version 2.7.0 >>>>>> >>>>>> Calculator interface: qe >>>>>> Crystal structure was read from "TiS2_primitive_scf.in". >>>>>> Unit of length: au >>>>>> Modulation mode >>>>>> Settings: >>>>>> Supercell: [2 2 1] >>>>>> Spacegroup: P-3m1 (164) >>>>>> Number of symmetry operations in supercell: 48 >>>>>> ------------------------------ primitive cell >>>>>> ------------------------------ >>>>>> Lattice vectors: >>>>>> a 6.460973493253429 0.000000000000000 0.000000000000000 >>>>>> b -3.230486746626715 5.595367178253872 0.000000000000000 >>>>>> c 0.000000000000000 0.000000000000000 34.015070466894429 >>>>>> Atomic positions (fractional): >>>>>> *1 Ti 0.00000000000000 0.00000000000000 0.50000000000000 47.867 >>>>>> *2 S 0.66666700000000 0.33333300000000 0.57891028530000 32.065 >>>>>> 3 S 0.33333300000000 0.66666700000000 0.42108971470000 32.065 >>>>>> -------------------------------- unit cell >>>>>> --------------------------------- >>>>>> Lattice vectors: >>>>>> a 6.460973493253429 0.000000000000000 0.000000000000000 >>>>>> b -3.230486746626715 5.595367178253872 0.000000000000000 >>>>>> c 0.000000000000000 0.000000000000000 34.015070466894429 >>>>>> Atomic positions (fractional): >>>>>> *1 Ti 0.00000000000000 0.00000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> *2 S 0.66666700000000 0.33333300000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 3 S 0.33333300000000 0.66666700000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> -------------------------------- super cell >>>>>> -------------------------------- >>>>>> Lattice vectors: >>>>>> a 12.921946986506859 0.000000000000000 0.000000000000000 >>>>>> b -6.460973493253429 11.190734356507743 0.000000000000000 >>>>>> c 0.000000000000000 0.000000000000000 34.015070466894429 >>>>>> Atomic positions (fractional): >>>>>> *1 Ti 0.00000000000000 0.00000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> 2 Ti 0.50000000000000 0.00000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> 3 Ti 0.00000000000000 0.50000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> 4 Ti 0.50000000000000 0.50000000000000 0.50000000000000 >>>>>> 47.867 > 1 >>>>>> *5 S 0.33333350000000 0.16666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 6 S 0.83333350000000 0.16666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 7 S 0.33333350000000 0.66666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 8 S 0.83333350000000 0.66666650000000 0.57891028530000 >>>>>> 32.065 > 2 >>>>>> 9 S 0.16666650000000 0.33333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> 10 S 0.66666650000000 0.33333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> 11 S 0.16666650000000 0.83333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> 12 S 0.66666650000000 0.83333350000000 0.42108971470000 >>>>>> 32.065 > 3 >>>>>> >>>>>> ---------------------------------------------------------------------------- >>>>>> ___ _ __ _ __ ___ _ __ >>>>>> / _ \ '__| '__/ _ \| '__| >>>>>> | __/ | | | | (_) | | >>>>>> \___|_| |_| \___/|_|. >>>>>> >>>>>> Also, it creates modulation.conf which contains: >>>>>> DIM = 2 2 1 >>>>>> MODULATION = 2 2 1, 0 0.433012702 0 1 0.03 0. >>>>>> >>>>>> Also, I found this idea from: >>>>>> https://phonopy.github.io/phonopy/setting-tags.html. >>>>>> >>>>>> Just today I started to use this package and I found your youtube >>>>>> videos discussing how to use phonopy with qe. So I thought I could ask for >>>>>> some help. kindly help me if you have any ideas. >>>>>> >>>>>> with regards >>>>>> Naveena P. >>>>>> _______________________________________________ >>>>>> Phonopy-users mailing list >>>>>> Pho...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/phonopy-users >>>>>> >>>>> >>>>> >>>>> -- >>>>> Atsushi Togo >>>>> _______________________________________________ >>>>> 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 >>>> >>> >>> >>> -- >>> Atsushi Togo >>> _______________________________________________ >>> 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 >> > > > -- > Atsushi Togo > _______________________________________________ > Phonopy-users mailing list > Pho...@li... > https://lists.sourceforge.net/lists/listinfo/phonopy-users > |