[Phonopy-users] Fwd: Need help to used modulation command

[Naveena P.S. <nav...@gm...>]

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
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>>>>>
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>>>>
>>>
>>>
>>> --
>>> Atsushi Togo
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>
>
> --
> Atsushi Togo
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