[QE-users] memory problem
Neelam Swarnkar
neelamswarnkar35 at gmail.com
Tue Jul 7 09:57:09 CEST 2020
Dear Expert and all
Here i am sharing my input file
&control
calculation = 'scf',
prefix = 'Zn4Sb3_exc1',
outdir = './tmp/'
pseudo_dir = './'
verbosity = 'low'
/
&system
ibrav = 4,
celldm(1)= 46.2264804,
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 0.5000000000000000 0.8660250000000000 0.0161070000000001
Zn 0.0000000000000000 0.8660250000000000 0.0161070000000001
Zn 0.5080535000000000 0.0000000000000000 0.8660250000000000
Zn 0.0080534999999999 0.0000000000000000 0.8660250000000000
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 0.5000000000000000
Zn 0.2419465000000000 0.6339750000000000 0.5000000000000000
Zn 0.7500000000000000 0.4838930000000000 0.6339750000000000
Zn 0.2500000000000000 0.4838930000000000 0.6339750000000000
Sb 0.5000000000000000 0.1339750000000000 0.9838929999999999
Sb 0.0000000000000000 0.1339750000000000 0.9838929999999999
Sb 0.4919465000000000 0.0000000000000000 0.1339750000000000
Sb 0.9919465000000000 0.0000000000000000 0.1339750000000000
Sb 0.5669875000000000 0.9838929999999999 0.0000000000000000
Sb 0.0669875000000000 0.9838929999999999 0.0000000000000000
Sb 0.1830125000000000 0.5000000000000000 0.5161070000000000
Sb 0.6830125000000000 0.5000000000000000 0.5161070000000000
Sb 0.2580535000000000 0.3660250000000000 0.5000000000000000
Sb 0.7580534999999999 0.3660250000000000 0.5000000000000000
Sb 0.2500000000000000 0.5161070000000000 0.3660250000000000
Sb 0.7500000000000000 0.5161070000000000 0.3660250000000000
K_POINTS (automatic)
2 1 1 0 0 0
On Mon, Jul 6, 2020 at 5:49 PM Neelam Swarnkar <neelamswarnkar35 at gmail.com>
wrote:
> I am sharing my input and output files here. also the screenshot of error .
>
> input file
>
> &control
> calculation = 'scf',
> prefix = 'Zn4Sb3_exc1',
> outdir = './tmp/'
> pseudo_dir = './'
> verbosity = 'low'
>
> /
> &system
> ibrav = 4,
> celldm(1)= 46.2264804,
> 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 0.5000000000000000 0.8660250000000000 0.0161070000000001
> Zn 0.0000000000000000 0.8660250000000000 0.0161070000000001
> Zn 0.5080535000000000 0.0000000000000000 0.8660250000000000
> Zn 0.0080534999999999 0.0000000000000000 0.8660250000000000
> 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 0.5000000000000000
> Zn 0.2419465000000000 0.6339750000000000 0.5000000000000000
> Zn 0.7500000000000000 0.4838930000000000 0.6339750000000000
> Zn 0.2500000000000000 0.4838930000000000 0.6339750000000000
> Sb 0.5000000000000000 0.1339750000000000 0.9838929999999999
> Sb 0.0000000000000000 0.1339750000000000 0.9838929999999999
> Sb 0.4919465000000000 0.0000000000000000 0.1339750000000000
> Sb 0.9919465000000000 0.0000000000000000 0.1339750000000000
> Sb 0.5669875000000000 0.9838929999999999 0.0000000000000000
> Sb 0.0669875000000000 0.9838929999999999 0.0000000000000000
> Sb 0.1830125000000000 0.5000000000000000 0.5161070000000000
> Sb 0.6830125000000000 0.5000000000000000 0.5161070000000000
> Sb 0.2580535000000000 0.3660250000000000 0.5000000000000000
> Sb 0.7580534999999999 0.3660250000000000 0.5000000000000000
> Sb 0.2500000000000000 0.5161070000000000 0.3660250000000000
> Sb 0.7500000000000000 0.5161070000000000 0.3660250000000000
>
>
> K_POINTS (automatic)
> 2 1 1 0 0 0
>
>
> output
> Program PWSCF v.6.3 starts on 6Jul2020 at 14:29:48
>
> 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
> file Zn.pbe-dnl-kjpaw_psl.1.0.0.UPF: wavefunction(s) 4S 3D
> renormalized
> file Sb.pbe-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 5S
> renormalized
>
> Subspace diagonalization in iterative solution of the eigenvalue
> problem:
> a serial algorithm will be used
>
> Found symmetry operation: I + ( 0.5000 0.0000 0.0000)
> This is a supercell, fractional translations are disabled
>
> G-vector sticks info
> --------------------
> sticks: dense smooth PW G-vecs: dense smooth PW
> Sum 20017 15937 4093 2328127 1647611 215359
>
>
>
> bravais-lattice index = 4
> lattice parameter (alat) = 46.2265 a.u.
> unit-cell volume = 86924.5388 (a.u.)^3
> number of atoms/cell = 24
> number of atomic types = 2
> number of electrons = 204.00
> number of Kohn-Sham states= 122
> kinetic-energy cutoff = 27.0000 Ry
> charge density cutoff = 136.0000 Ry
> convergence threshold = 1.0E-06
> mixing beta = 0.6000
> number of iterations used = 8 plain mixing
> Exchange-correlation = SLA PW PBX PBC ( 1 4 3 4 0 0)
>
> celldm(1)= 46.226480 celldm(2)= 0.000000 celldm(3)= 1.016107
> celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
>
> crystal axes: (cart. coord. in units of alat)
> a(1) = ( 1.000000 0.000000 0.000000 )
> a(2) = ( -0.500000 0.866025 0.000000 )
> a(3) = ( 0.000000 0.000000 1.016107 )
>
> reciprocal axes: (cart. coord. in units 2 pi/alat)
> b(1) = ( 1.000000 0.577350 -0.000000 )
> b(2) = ( 0.000000 1.154701 0.000000 )
> b(3) = ( 0.000000 -0.000000 0.984149 )
>
>
> PseudoPot. # 1 for Zn read from file:
> ./Zn.pbe-dnl-kjpaw_psl.1.0.0.UPF
> MD5 check sum: 7217f78799bfc6aaa3738bf4cd09bafd
> Pseudo is Projector augmented-wave + core cor, Zval = 12.0
> Generated using "atomic" code by A. Dal Corso v.6.2.2
> Shape of augmentation charge: PSQ
> Using radial grid of 1201 points, 6 beta functions with:
> l(1) = 0
> l(2) = 0
> l(3) = 1
> l(4) = 1
> l(5) = 2
> l(6) = 2
> Q(r) pseudized with 0 coefficients
>
>
> PseudoPot. # 2 for Sb read from file:
> ./Sb.pbe-n-kjpaw_psl.1.0.0.UPF
> MD5 check sum: 8701ebd98ea0ddfeeee3c5089d2d8acc
> Pseudo is Projector augmented-wave + core cor, Zval = 5.0
> Generated using "atomic" code by A. Dal Corso v.6.2.2
> Shape of augmentation charge: PSQ
> Using radial grid of 1243 points, 6 beta functions with:
> l(1) = 0
> l(2) = 0
> l(3) = 1
> l(4) = 1
> l(5) = 2
> l(6) = 2
> Q(r) pseudized with 0 coefficients
>
>
> atomic species valence mass pseudopotential
> Zn 12.00 60.00000 Zn( 1.00)
> Sb 5.00 102.00000 Sb( 1.00)
>
> No symmetry found
>
>
>
> Cartesian axes
>
> site n. atom positions (alat units)
> 1 Zn tau( 1) = ( 0.0669875 0.7499997 0.0163664
> )
> 2 Zn tau( 2) = ( -0.4330125 0.7499997 0.0163664
> )
> 3 Zn tau( 3) = ( 0.5080535 0.0000000 0.8799737
> )
> 4 Zn tau( 4) = ( 0.0080535 0.0000000 0.8799737
> )
> 5 Zn tau( 5) = ( 0.4249590 0.0139491 0.0000000
> )
> 6 Zn tau( 6) = ( 0.9249590 0.0139491 0.0000000
> )
> 7 Zn tau( 7) = ( 0.5669875 0.4330127 0.4916869
> )
> 8 Zn tau( 8) = ( 0.0669875 0.4330127 0.4916869
> )
> 9 Zn tau( 9) = ( 0.4249590 0.5490385 0.5080533
> )
> 10 Zn tau( 10) = ( -0.0750410 0.5490385 0.5080533
> )
> 11 Zn tau( 11) = ( 0.5080535 0.4190636 0.6441862
> )
> 12 Zn tau( 12) = ( 0.0080535 0.4190636 0.6441862
> )
> 13 Sb tau( 13) = ( 0.4330125 0.1160258 0.9997402
> )
> 14 Sb tau( 14) = ( -0.0669875 0.1160258 0.9997402
> )
> 15 Sb tau( 15) = ( 0.4919465 0.0000000 0.1361329
> )
> 16 Sb tau( 16) = ( 0.9919465 0.0000000 0.1361329
> )
> 17 Sb tau( 17) = ( 0.0750410 0.8520763 0.0000000
> )
> 18 Sb tau( 18) = ( -0.4249590 0.8520763 0.0000000
> )
> 19 Sb tau( 19) = ( -0.0669875 0.4330127 0.5244197
> )
> 20 Sb tau( 20) = ( 0.4330125 0.4330127 0.5244197
> )
> 21 Sb tau( 21) = ( 0.0750410 0.3169869 0.5080533
> )
> 22 Sb tau( 22) = ( 0.5750410 0.3169869 0.5080533
> )
> 23 Sb tau( 23) = ( -0.0080535 0.4469618 0.3719204
> )
> 24 Sb tau( 24) = ( 0.4919465 0.4469618 0.3719204
> )
>
> number of k points= 4 gaussian smearing, width (Ry)= 0.0200
> cart. coord. in units 2pi/alat
> k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 1.0000000
> k( 2) = ( -0.5000000 -0.2886751 0.0000000), wk = 0.3333333
> k( 3) = ( 0.5000000 -0.2886751 0.0000000), wk = 0.3333333
> k( 4) = ( 0.0000000 -0.5773503 0.0000000), wk = 0.3333333
>
> Dense grid: 2328127 G-vectors FFT dimensions: ( 180, 180, 180)
>
> Smooth grid: 1647611 G-vectors FFT dimensions: ( 160, 160, 160)
>
> Estimated max dynamical RAM per process > 11.48 GB
>
> Check: negative/imaginary core charge= -0.000002 0.000000
>
> Initial potential from superposition of free atoms
> Check: negative starting charge= -0.128417
>
>
> On Mon, Jul 6, 2020 at 3:39 PM Oleksandr Motornyi <
> oleksandr.motornyi at polytechnique.edu> wrote:
>
>> Dear Neelam
>>
>> Other than this, it would be useful if you could also show the in/output
>> files of your system. While it does not seem large the memory usage depends
>> on the atoms/pseudopotentials you are using, size of the vacuum (if any).
>>
>> Best
>>
>> Oleksandr
>> On 06/07/2020 11:52, Michal Krompiec wrote:
>>
>> Dear Neelam,
>> I am by no means an expert, but from my limited experience I can say that
>> 4GB of RAM is not a lot, to put it mildly - but at the same time, your
>> system isn't large. In this case, I wouldn't use any parallelization on
>> k-points (pw.x -npool 1) and make use of symmetry as much as possible
>> (correct ibrav instead of ibrav=0). You can save memory by reducing ecutwfc
>> (at the expense of accuracy) - so try choosing pseudopotentials which give
>> you desired accuracy at the lowest ecutwfc (use
>> https://www.materialscloud.org/discover/sssp to guide you).
>> Best,
>> Michal
>>
>> On Mon, 6 Jul 2020 at 10:27, Neelam Swarnkar <neelamswarnkar35 at gmail.com>
>> wrote:
>>
>>> Dear expert and all
>>>
>>> I am making the supercell of 2x1x1 total 24 no of atoms, and perform scf
>>> calculation .but there is memory related problem currently i am using 4gb
>>> RAM.
>>>
>>> What can i do to solve this problem?
>>>
>>> Thanks in advance
>>> Neelam
>>>
>>> _______________________________________________
>>> 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.orghttps://lists.quantum-espresso.org/mailman/listinfo/users
>>
>> --
>> Oleksandr Motornyi
>> PhD, Data Scientist
>>
>> France
>>
>> _______________________________________________
>> 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
>
>
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