[QE-users] supercell
Neelam Swarnkar
neelamswarnkar35 at gmail.com
Sat Jul 4 14:32:56 CEST 2020
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.
>>> >
>>> >
>>> >
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>>> --
>>> Lorenzo Paulatto - Paris
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
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>
>
> --
>
> ------------------------------------------------------------------------------------------------------------
> Yue-Wen FANG, PhD
> Tokyo Institute of Technology, Japan
>
>
>
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