[QE-users] supercell
Yue-Wen Fang
yuewen.fang at gmail.com
Mon Jul 6 02:16:26 CEST 2020
This error info. has already told you how to fix this problem:
ibrav=0: must read cell parameters
So you must use CELL PARAMETERS in the input file.
Neelam Swarnkar <neelamswarnkar35 at gmail.com> 于2020年7月4日周六 下午9:33写道：
> Thanks for reply Yue-Wen
>
> I used the supercell 001 file to further calculation of SCF. in QE-6.3
>
> But it has an error .
>
> input file
> &control
> calculation = 'scf',
> prefix = '2d_exc1',
> outdir = './tmp/'
> pseudo_dir = './'
> verbosity = 'high'
>
> /
> &system
> ibrav = 0,
> celldm(1)= 23.1132402,
> celldm(3)= 1.016106614,
> nat = 24,
> ntyp = 2,
> occupations='smearing', degauss=0.02,
> ecutwfc = 27,
> ecutrho = 136
>
> /
> &electrons
> mixing_beta = 0.6
> /
>
> ATOMIC_SPECIES
> Zn 60.00 Zn.pbe-dnl-kjpaw_psl.1.0.0.UPF
> Sb 102.00 Sb.pbe-n-kjpaw_psl.1.0.0.UPF
>
> ATOMIC_POSITIONS crystal
> Zn 0.5004326526196012 0.8660250000000002 0.0161070000000001
> Zn 0.0000000000000000 0.8660250000000002 0.0161070000000001
> Zn 0.5080535000000000 0.0000000000000000 0.8660249999999999
> Zn 0.0080534999999999 0.0000000000000000 0.8660249999999999
> Zn 0.4330125000000000 0.0161070000000001 0.0000000000000000
> Zn 0.9330125000000000 0.0161070000000001 0.0000000000000000
> Zn 0.8169875000000000 0.5000000000000000 0.4838930000000000
> Zn 0.3169875000000000 0.5000000000000000 0.4838930000000000
> Zn 0.7419465000000001 0.6339750000000000 0.4999999999999999
> Zn 0.2419465000000000 0.6339750000000000 0.4999999999999999
> Zn 0.7500000000000000 0.4838930000000000 0.6339749999999998
> Zn 0.2500000000000000 0.4838930000000000 0.6339749999999998
> Sb 0.5000000000000000 0.1339750000000000 0.9838929999999998
> Sb 0.0000000000000000 0.1339750000000000 0.9838929999999998
> Sb 0.4919465000000000 0.0000000000000000 0.1339750000000000
> Sb 0.9919465000000000 0.0000000000000000 0.1339750000000000
> Sb 0.5669875000000000 0.9838930000000000 0.0000000000000000
> Sb 0.0669875000000000 0.9838930000000000 0.0000000000000000
> Sb 0.1830125000000000 0.5000000000000000 0.5161070000000000
> Sb 0.6830124999999999 0.5000000000000000 0.5161070000000000
> Sb 0.2580535000000000 0.3660250000000000 0.4999999999999999
> Sb 0.7580534999999998 0.3660250000000000 0.4999999999999999
> Sb 0.2500000000000000 0.5161070000000000 0.3660250000000000
> Sb 0.7500000000000000 0.5161070000000000 0.3660250000000000
>
>
> K_POINTS (automatic)
> 4 4 4 0 0 0
>
>
> output file.
> Program PWSCF v.6.3 starts on 4Jul2020 at 17:54:48
>
> This program is part of the open-source Quantum ESPRESSO suite
> for quantum simulation of materials; please cite
> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
> URL http://www.quantum-espresso.org",
> in publications or presentations arising from this work. More details
> at
> http://www.quantum-espresso.org/quote
>
> Parallel version (MPI), running on 1 processors
>
> MPI processes distributed on 1 nodes
> Waiting for input...
> Reading input from standard input
>
> Current dimensions of program PWSCF are:
> Max number of different atomic species (ntypx) = 10
> Max number of k-points (npk) = 40000
> Max angular momentum in pseudopotentials (lmaxx) = 3
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine cell_base_init (1):
> ibrav=0: must read cell parameters
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> stopping ...
>
> error in ibrav=0 , how to run scf calculation in QE.
>
> regards
> Neelam Swarnkar
> Phd scholar
> RGPV Bhopal.
>
>
> On Sat, Jul 4, 2020 at 1:06 PM Yue-Wen Fang <yuewen.fang at gmail.com> wrote:
>
>> You can refer to Phonopy's webpage directly in which Dr. Togo has already
>> shown several examples using Phonopy+QE.
>> You were using the "finite displacement method" of supercells to get the
>> force constants, thus the supercell structures used for force calculations
>> were defined with "finite displacements", that was why you saw the
>> reduction of symmetry.
>>
>> Neelam Swarnkar <neelamswarnkar35 at gmail.com> 于2020年7月3日周五 下午5:31写道：
>>
>>> Thanks for the reply .
>>>
>>> Can anyone share a user guide or tutorial of phonopy . which has working
>>> techniques of phonopy, how to define the structure, and how to obtain
>>> required parameters.
>>>
>>> On Thu, Jul 2, 2020 at 9:08 PM Lorenzo Paulatto <paulatz at gmail.com>
>>> wrote:
>>>
>>>> > I make a supercell of dim 2 1 1 . But in the unit cell , I define a
>>>> > space group R-3c (167) rhombohedral structure , but after making the
>>>> > supercell its space group changed to C2 (5) .
>>>>
>>>> This is not just a supercell, atoms are moved to phonons via force
>>>> constants. Symmetry is reduced.
>>>>
>>>> > so it can be possible or either error .
>>>> > I don't know about phonopy , that's why I have a doubt.
>>>> > also after running the above command. There are too many
>>>> supercell001.in
>>>> > <http://supercell001.in> upto supercell072.in <http://supercell072.in
>>>> >.
>>>> > which one is correct. for further scf, nscf, relax calculation in QE.
>>>>
>>>> All of them. I.e. phonopy needs 72 calculations of forces in order to
>>>> compute all the force constants. Btw a 2x1x1 supercell is very likely
>>>> going to be too small for whatever you want to compute.
>>>>
>>>> cheers
>>>>
>>>> >
>>>> >
>>>> > pl. Suggest me.
>>>> >
>>>> > On Thu, Jul 2, 2020 at 3:16 PM Neelam Swarnkar
>>>> > <neelamswarnkar35 at gmail.com <mailto:neelamswarnkar35 at gmail.com>>
>>>> wrote:
>>>> >
>>>> > Thanks for reply
>>>> >
>>>> >
>>>> > On Thu, Jul 2, 2020, 12:37 PM Saibabu Madas
>>>> > <Saibabu.Madas at eli-alps.hu <mailto:Saibabu.Madas at eli-alps.hu>>
>>>> wrote:
>>>> >
>>>> > Dear Neelam Swarnkar,
>>>> >
>>>> >
>>>> > I believe the space between "dim" and " =" in the phonopy
>>>> > command is causing the error. Please try the following
>>>> command:
>>>> >
>>>> > "phonopy --qe -d --dim="2 1 1" -c filename.in <
>>>> http://filename.in>"
>>>> >
>>>> >
>>>> > Best regards,
>>>> >
>>>> > *Madas Saibabu*
>>>> >
>>>> > Early Stage Researcher
>>>> >
>>>> >
>>>> > *ELI-HU Non-Profit Ltd.*
>>>> >
>>>> > Computational and Applied Materials Science Group
>>>> >
>>>> > Attosecond and Strong Field Science division
>>>> >
>>>> > HQ: H-6728 Szeged, Wolfgang Sandner utca 3.
>>>> >
>>>> > E-mail: Saibabu.Madas at eli-alps.hu
>>>> > <mailto:Saibabu.Madas at eli-alps.hu>
>>>> >
>>>> > Website: www.eli-alps.hu <http://www.eli-alps.hu>
>>>> >
>>>> >
>>>> ------------------------------------------------------------------------
>>>> > *From:* users <users-bounces at lists.quantum-espresso.org
>>>> > <mailto:users-bounces at lists.quantum-espresso.org>> on behalf
>>>> of
>>>> > Neelam Swarnkar <neelamswarnkar35 at gmail.com
>>>> > <mailto:neelamswarnkar35 at gmail.com>>
>>>> > *Sent:* Thursday, July 2, 2020 7:00
>>>> > *To:* Quantum ESPRESSO users Forum
>>>> > *Subject:* [QE-users] supercell
>>>> > Dear expert and all
>>>> >
>>>> > I am making a supercell of dim 2 1 1, i already installed
>>>> > phonopy-2.6.0 version , but it is showing me an error.
>>>> >
>>>> > this is my input file
>>>> >
>>>> >
>>>> > &control
>>>> > calculation = 'scf',
>>>> > prefix = '2d_exc1',
>>>> > outdir = './tmp/'
>>>> > pseudo_dir = './'
>>>> >
>>>> >
>>>> > /
>>>> > &system
>>>> > ibrav = 0,
>>>> > celldm(1)= 23.1132402,
>>>> > celldm(3)= 1.016106614,
>>>> > nat = 12,
>>>> > ntyp = 2,
>>>> > ecutwfc = 27,
>>>> > ecutrho = 136
>>>> >
>>>> > /
>>>> > &electrons
>>>> > mixing_beta = 0.6
>>>> > /
>>>> >
>>>> > ATOMIC_SPECIES
>>>> > Zn 60.00 Zn.pbe-dnl-kjpaw_psl.1.0.0.UPF
>>>> > Sb 102.00 Sb.pbe-n-kjpaw_psl.1.0.0.UPF
>>>> >
>>>> >
>>>> > ATOMIC_POSITIONS crystal
>>>> > Zn 1.000000 0.866025 1.016107
>>>> > Zn 1.016107 1.000000 0.866025
>>>> > Zn 0.866025 1.016107 1.000000
>>>> > Zn -0.366025 -0.500000 -0.516107
>>>> > Zn -0.516107 -0.366025 -0.500000
>>>> > Zn -0.500000 -0.516107 -0.366025
>>>> > Sb -1.000000 -0.866025 -1.016107
>>>> > Sb -1.016107 -1.000000 -0.866025
>>>> > Sb -0.866025 -1.016107 -1.000000
>>>> > Sb 0.366025 0.500000 0.516107
>>>> > Sb 0.516107 0.366025 0.500000
>>>> > Sb 0.500000 0.516107 0.366025
>>>> >
>>>> >
>>>> > K_POINTS (automatic)
>>>> >
>>>> > 4 4 4 0 0 0
>>>> >
>>>> >
>>>> > CELL_PARAMETERS angstrom
>>>> >
>>>> > 12.2309951090 0.0000000000 0.0000000000
>>>> > -6.1154975550 10.5923524780 0.0000000000
>>>> > 0.0000000000 0.0000000000 12.4279950260
>>>> >
>>>> > I don't know what's wrong in my input file.
>>>> >
>>>> >
>>>> >
>>>> ------------------------------------------------------------------------
>>>> >
>>>> > A jelen email útján megküldött vélemény vagy információ
>>>> > kizárólag a küldő személyéhez kapcsolódik és nem feltétlenül
>>>> > jeleníti meg az ELI-HU Nonprofit Kft. álláspontját is.
>>>> > Társaságunk nem vállal felelősséget az email tartalmáért, ide
>>>> > értve különösen, de nem kizárólagosan kötelezettségvállalást
>>>> > jogi kötő erővel bíró szerződések létrehozásáért,
>>>> módosításáért
>>>> > vagy megszűntetéséért, valamint az átadott információ alapján
>>>> > indult eljárásokért mindaddig, amíg az adott információt
>>>> utólag
>>>> > és írásban a megfelelően meghatalmazott vagy az ELI-HU
>>>> Nonprofit
>>>> > Kft. képviseleti jogával felruházott személy meg nem erősíti.
>>>> Az
>>>> > email bizalmas vagy jogilag védett információt tartalmazhat,
>>>> > amelyet kizárólag a címzett személy vagy szervezet, illetve az
>>>> > általuk felhatalmazottak használhatnak fel. Amennyiben Ön nem
>>>> az
>>>> > üzenet címzettje, kérjük, értesítse erről az üzenet küldőjét
>>>> és
>>>> > törölje az üzenetet rendszeréből. A jelen email tartalmának
>>>> nem
>>>> > a címzett általi bármilyen formában történő illetéktelen
>>>> > közzététele, terjesztése, másolása, illetve felhasználása vagy
>>>> > alkalmazása szigorúan tilos és jogszabályba ütközhet.
>>>> >
>>>> >
>>>> > Please note that any information or opinions presented in this
>>>> > email are solely those of the sender and do not necessarily
>>>> > represent those of ELI-HU Nonprofit Ltd. Our Company accepts
>>>> no
>>>> > liability or responsibility for the content of this email,
>>>> > especially, but not limited to commitment for establishing,
>>>> > modifying or terminating legally binding contracts, or for the
>>>> > consequences of any actions taken on the basis of the
>>>> > information provided, unless that information is subsequently
>>>> > confirmed in writing by a person duly authorized or endowed
>>>> with
>>>> > the right of representation of ELI-HU Nonprofit Ltd. This
>>>> email
>>>> > may contain confidential or legally protected information, and
>>>> > is intended solely for the use of the individual or entity to
>>>> > whom it is addressed and others authorized to receive it. If
>>>> you
>>>> > are not the intended recipient of this email, please inform
>>>> the
>>>> > sender immediately and delete it from your system. Any
>>>> > unauthorized disclosure, dissemination, copying or use of or
>>>> > reliance upon the content of this email by anyone other than
>>>> the
>>>> > intended recipient is strictly prohibited and may be unlawful.
>>>> >
>>>> > _______________________________________________
>>>> > Quantum ESPRESSO is supported by MaX
>>>> > (www.max-centre.eu/quantum-espresso
>>>> > <http://www.max-centre.eu/quantum-espresso>)
>>>> > users mailing list users at lists.quantum-espresso.org
>>>> > <mailto:users at lists.quantum-espresso.org>
>>>> > https://lists.quantum-espresso.org/mailman/listinfo/users
>>>> >
>>>> >
>>>> > _______________________________________________
>>>> > Quantum ESPRESSO is supported by MaX (
>>>> www.max-centre.eu/quantum-espresso)
>>>> > users mailing list users at lists.quantum-espresso.org
>>>> > https://lists.quantum-espresso.org/mailman/listinfo/users
>>>> >
>>>>
>>>> --
>>>> Lorenzo Paulatto - Paris
>>>> _______________________________________________
>>>> Quantum ESPRESSO is supported by MaX (
>>>> www.max-centre.eu/quantum-espresso)
>>>> users mailing list users at lists.quantum-espresso.org
>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
>>> )
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>
>>
>>
>> --
>>
>> ------------------------------------------------------------------------------------------------------------
>> Yue-Wen FANG, PhD
>> Tokyo Institute of Technology, Japan
>>
>>
>>
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
------------------------------------------------------------------------------------------------------------
Yue-Wen FANG, PhD
Tokyo Institute of Technology, Japan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20200706/3f2ea70b/attachment.html>
More information about the users
mailing list