[QE-users] memory problem
Neelam Swarnkar
neelamswarnkar35 at gmail.com
Tue Jul 7 14:20:03 CEST 2020
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
>
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