[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>




More information about the users mailing list