[QE-users] memory problem
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Tue Jul 7 15:45:22 CEST 2020
You must know, because this is the system you want to study, which I
do not know!
Best
Giuseppe
Quoting Neelam Swarnkar <neelamswarnkar35 at gmail.com>:
> So, how to reduce the vacuum, and choose the correct atomic positions.
>
> On Tue, Jul 7, 2020, 3:04 PM Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> wrote:
>
>>
>> Dear Neelam
>>
>> > bravais-lattice index = 4
>> > lattice parameter (alat) = 46.2265 a.u.
>> > unit-cell volume = 86924.5388 (a.u.)^3
>>
>> Your hexagonal (ibrav=4) supercell has a=46.2265 a.u. and c=46.9710
>> a.u., that is, a huge cell volume of 86924.5388 (a.u.)^3, as reported
>> in your output file. Not only this huge cell requires a lot of memory,
>> as stated in your output
>>
>> Estimated max dynamical RAM per process > 11.48 GB
>>
>> but your small bunch of atoms (24) is scattered in a meaningless
>> structure around this huge cell. If you have no supervisor that can
>> guide you, please at least check carefully with some visual
>> editor/viewer of atomic structures (xcrysden can be a good choice)
>> your input file before starting the calculation. 99% of weird errors
>> depend on very wrong atomic positions.
>> HTH
>> Giuseppe
>>
>> Quoting Neelam Swarnkar <neelamswarnkar35 at gmail.com>:
>>
>> > output file
>> > Program PWSCF v.6.3 starts on 7Jul2020 at 13:32:49
>> >
>> > 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= 102
>> > 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
>> > 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 > 11.17 GB
>> >
>> > Check: negative/imaginary core charge= -0.000002 0.000000
>> >
>> > Initial potential from superposition of free atoms
>> > Check: negative starting charge= -0.128417
>> >
>> > starting charge 203.94778, renormalised to 204.00000
>> >
>> > On Tue, Jul 7, 2020 at 1:47 PM Neelam Swarnkar <
>> neelamswarnkar35 at gmail.com>
>> > wrote:
>> >
>> >> 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,
>> >>
>> >> 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 Tue, Jul 7, 2020 at 1:28 PM Neelam Swarnkar <
>> neelamswarnkar35 at gmail.com>
>> >> wrote:
>> >>
>> >>>
>> >>> output file
>> >>>
>> >>> 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 Tue, Jul 7, 2020 at 1:27 PM Neelam Swarnkar <
>> >>> neelamswarnkar35 at gmail.com> wrote:
>> >>>
>> >>>> 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
>> >>>>>
>> >>>>>
>>
>>
>>
>> GIUSEPPE MATTIOLI
>> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
>> Via Salaria Km 29,300 - C.P. 10
>> I-00015 - Monterotondo Scalo (RM)
>> Mob (*preferred*) +39 373 7305625
>> Tel + 39 06 90672342 - Fax +39 06 90672316
>> E-mail: <giuseppe.mattioli at ism.cnr.it>
>>
>> _______________________________________________
>> 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
>>
>>
GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
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