
  ___ ___ ___ _ _ _  
 |   |   |_  | | | | 
 | | | | | . | | | | 
 |__ |  _|___|_____|  22.1.0
 |___|_|             

User:   thorkong@node063.cluster
Date:   Wed Sep 21 03:14:46 2022
Arch:   x86_64
Pid:    87043
Python: 3.10.5
gpaw:   /groups/kemi/thorkong/miniconda3/envs/gpaw22/lib/python3.10/site-packages/gpaw
_gpaw:  /groups/kemi/thorkong/miniconda3/envs/gpaw22/lib/python3.10/site-packages/
        _gpaw.cpython-310-x86_64-linux-gnu.so
ase:    /groups/kemi/thorkong/miniconda3/envs/gpaw22/lib/python3.10/site-packages/ase (version 3.22.1)
numpy:  /groups/kemi/thorkong/miniconda3/envs/gpaw22/lib/python3.10/site-packages/numpy (version 1.23.0)
scipy:  /groups/kemi/thorkong/miniconda3/envs/gpaw22/lib/python3.10/site-packages/scipy (version 1.8.1)
libxc:  5.2.3
units:  Angstrom and eV
cores: 32
OpenMP: True
OMP_NUM_THREADS: 1

Input parameters:
  basis: dzp
  kpts: [4 4 1]
  mode: {ecut: 600.0,
         name: pw}
  xc: BEEF-vdW

System changes: positions, numbers, cell, pbc, initial_charges, initial_magmoms 

Initialize ...

Cu-setup:
  name: Copper
  id: f1c4d45d90492f1bbfdcb091e8418fdf
  Z: 29.0
  valence: 11
  core: 18
  charge: 0.0
  file: /groups/kemi/thorkong/miniconda3/envs/gpaw22/share/gpaw/Cu.PBE.gz
  compensation charges: gauss, rc=0.33, lmax=2
  cutoffs: 2.06(filt), 2.43(core),
  valence states:
                energy  radius
    4s(1.00)    -4.609   1.164
    4p(0.00)    -0.698   1.164
    3d(10.00)    -5.039   1.058
    *s          22.603   1.164
    *p          26.513   1.164
    *d          22.172   1.058

  LCAO basis set for Cu:
    Name: dzp
    File: /groups/kemi/thorkong/miniconda3/envs/gpaw22/share/gpaw/Cu.dzp.basis.gz
    Number of radial functions: 5
    Number of spherical harmonics: 15
      l=0, rc=8.9688 Bohr: 4s-sz confined orbital
      l=2, rc=5.1719 Bohr: 3d-sz confined orbital
      l=0, rc=5.3281 Bohr: 4s-dz split-valence wave
      l=2, rc=3.1406 Bohr: 3d-dz split-valence wave
      l=1, rc=8.9688 Bohr: p-type Gaussian polarization

Reference energy: -2161029.688374

Spin-paired calculation

Convergence criteria:
 Maximum [total energy] change in last 3 cyles: 0.0005 eV / electron
 Maximum integral of absolute [dens]ity change: 0.0001 electrons / valence electron
 Maximum integral of absolute [eigenst]ate change: 4e-08 eV^2 / valence electron
 Maximum number of scf [iter]ations: 333
 (Square brackets indicate name in SCF output, whereas a 'c' in
 the SCF output indicates the quantity has converged.)

Symmetries present (total): 1

  ( 1  0  0)
  ( 0  1  0)
  ( 0  0  1)

16 k-points: 4 x 4 x 1 Monkhorst-Pack grid
8 k-points in the irreducible part of the Brillouin zone
       k-points in crystal coordinates                weights
   0:     0.12500000   -0.37500000    0.00000000          2/16
   1:     0.12500000   -0.12500000    0.00000000          2/16
   2:     0.12500000    0.12500000    0.00000000          2/16
   3:     0.12500000    0.37500000    0.00000000          2/16
   4:     0.37500000   -0.37500000    0.00000000          2/16
   5:     0.37500000   -0.12500000    0.00000000          2/16
   6:     0.37500000    0.12500000    0.00000000          2/16
   7:     0.37500000    0.37500000    0.00000000          2/16

Wave functions: Plane wave expansion
  Cutoff energy: 600.000 eV
  Number of coefficients (min, max): 44425, 44535
  Pulay-stress correction: 0.000000 eV/Ang^3 (de/decut=0.000000)
  Using FFTW library
  ScaLapack parameters: grid=2x2, blocksize=64
  Wavefunction extrapolation:
    Improved wavefunction reuse through dual PAW basis 

Occupation numbers: Fermi-Dirac: width=0.1000 eV
 

Eigensolver
   Davidson(niter=2) 

Densities:
  Coarse grid: 30*42*196 grid
  Fine grid: 60*84*392 grid
  Total Charge: 0.000000 

Density mixing:
  Method: separate
  Backend: pulay
  Linear mixing parameter: 0.05
  Mixing with 5 old densities
  Damping of long wave oscillations: 50 

Hamiltonian:
  XC and Coulomb potentials evaluated on a 60*84*392 grid
  Using the BEEF-vdW Exchange-Correlation functional
  External potential:
    NoExternalPotential
 

XC parameters: BEEF-vdW with 2 nearest neighbor stencil

Memory estimate:
  Process memory now: 192.52 MiB
  Calculator: 504.42 MiB
    Density: 28.72 MiB
      Arrays: 12.25 MiB
      Localized functions: 11.76 MiB
      Mixer: 4.71 MiB
    Hamiltonian: 8.25 MiB
      Arrays: 8.01 MiB
      XC: 0.00 MiB
      Poisson: 0.00 MiB
      vbar: 0.24 MiB
    Wavefunctions: 467.45 MiB
      Arrays psit_nG: 218.14 MiB
      Eigensolver: 237.27 MiB
      Projections: 1.06 MiB
      Projectors: 1.27 MiB
      PW-descriptor: 9.72 MiB

Total number of cores used: 32
Parallelization over k-points: 8
Domain decomposition: 1 x 1 x 4
                      2 x 2 x 8 (xc only)

Number of atoms: 48
Number of atomic orbitals: 720
Number of bands in calculation: 321
Number of valence electrons: 528
Bands to converge: occupied

... initialized

Initializing position-dependent things.

Density initialized from atomic densities
Creating initial wave functions:
  321 bands from LCAO basis set

      .------------.  
     /|            |  
    / |            |  
   /  |            |  
  /   |            |  
 *    |            |  
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 |    |            |  
 |    |            |  
 |    |            |  
 |    |            |  
 |    |  Cu    Cu  |  
 |    |            |  
 |  Cu|    Cu      |  
 |    |  Cu    Cu  |  
 |    |            |  
 |Cu  CuCu   Cu    |  
 |  Cu|CuCuCuCuCu  |  
 |    |            |  
 |Cu  CuCu   Cu    |  
 |  Cu|  CuCu  Cu  |  
 |    |            |  
 |    |            |  
 |  CuCu CuCuCuCu  |  
 |    |Cu    Cu    |  
 |Cu  | Cu         |  
 |  CuCu   CuCu    |  
 |    |CuCu  CuCu  |  
 |    |            |  
 |  CuCu   CuCu    |  
 |    |            |  
 |    |            |  
 |    Cu     Cu    |  
 |    |            |  
 |    |            |  
 |    |            |  
 |    |            |  
 |    |            |  
 |    |            |  
 |    .------------.  
 |   /            /   
 |  /            /    
 | /            /     
 |/            /      
 *------------*       

Positions:
   0 Cu     2.845471   -0.037085    9.987708    ( 0.0000,  0.0000,  0.0000)
   1 Cu     1.546289    1.847322   11.317508    ( 0.0000,  0.0000,  0.0000)
   2 Cu     4.163292    1.847322   11.317508    ( 0.0000,  0.0000,  0.0000)
   3 Cu     0.228468   -0.037084    9.987708    ( 0.0000,  0.0000,  0.0000)
   4 Cu     0.252619   -0.019057   12.605603    ( 0.0000,  0.0000,  0.0000)
   5 Cu     4.195621    1.848115   13.912378    ( 0.0000,  0.0000,  0.0000)
   6 Cu     1.578618    1.848115   13.912378    ( 0.0000,  0.0000,  0.0000)
   7 Cu     2.869621   -0.019057   12.605603    ( 0.0000,  0.0000,  0.0000)
   8 Cu     2.894021    0.000488   15.228047    ( 0.0000,  0.0000,  0.0000)
   9 Cu     1.586326    1.849469   16.538611    ( 0.0000,  0.0000,  0.0000)
  10 Cu     4.203329    1.849469   16.538611    ( 0.0000,  0.0000,  0.0000)
  11 Cu     0.277019    0.000488   15.228047    ( 0.0000,  0.0000,  0.0000)
  12 Cu     0.277575   -0.002638   17.853011    ( 0.0000,  0.0000,  0.0000)
  13 Cu     4.202872    1.850359   19.169920    ( 0.0000,  0.0000,  0.0000)
  14 Cu     1.585870    1.850359   19.169920    ( 0.0000,  0.0000,  0.0000)
  15 Cu     2.894577   -0.002639   17.853012    ( 0.0000,  0.0000,  0.0000)
  16 Cu     2.894409    0.016060   20.478175    ( 0.0000,  0.0000,  0.0000)
  17 Cu     1.585964    1.850509   21.831812    ( 0.0000,  0.0000,  0.0000)
  18 Cu     4.202966    1.850510   21.831812    ( 0.0000,  0.0000,  0.0000)
  19 Cu     0.277407    0.016060   20.478175    ( 0.0000,  0.0000,  0.0000)
  20 Cu     0.277531    0.034916   23.097447    ( 0.0000,  0.0000,  0.0000)
  21 Cu     4.153742    1.847543    8.809743    ( 0.0000,  0.0000,  0.0000)
  22 Cu     1.536740    1.847543    8.809743    ( 0.0000,  0.0000,  0.0000)
  23 Cu     2.894533    0.034916   23.097447    ( 0.0000,  0.0000,  0.0000)
  24 Cu     2.843606    3.731639    9.988868    ( 0.0000,  0.0000,  0.0000)
  25 Cu     1.539810    5.548813   11.251232    ( 0.0000,  0.0000,  0.0000)
  26 Cu     4.156812    5.548813   11.251232    ( 0.0000,  0.0000,  0.0000)
  27 Cu     0.226604    3.731639    9.988868    ( 0.0000,  0.0000,  0.0000)
  28 Cu     0.252668    3.714664   12.605832    ( 0.0000,  0.0000,  0.0000)
  29 Cu     4.194752    5.549198   13.911914    ( 0.0000,  0.0000,  0.0000)
  30 Cu     1.577750    5.549198   13.911914    ( 0.0000,  0.0000,  0.0000)
  31 Cu     2.869670    3.714664   12.605832    ( 0.0000,  0.0000,  0.0000)
  32 Cu     2.894043    3.697032   15.228109    ( 0.0000,  0.0000,  0.0000)
  33 Cu     1.586527    5.550521   16.542170    ( 0.0000,  0.0000,  0.0000)
  34 Cu     4.203529    5.550521   16.542170    ( 0.0000,  0.0000,  0.0000)
  35 Cu     0.277041    3.697032   15.228109    ( 0.0000,  0.0000,  0.0000)
  36 Cu     0.277575    3.702760   17.853012    ( 0.0000,  0.0000,  0.0000)
  37 Cu     4.202831    5.551361   19.170615    ( 0.0000,  0.0000,  0.0000)
  38 Cu     1.585829    5.551361   19.170615    ( 0.0000,  0.0000,  0.0000)
  39 Cu     2.894577    3.702761   17.853012    ( 0.0000,  0.0000,  0.0000)
  40 Cu     2.894410    3.684877   20.478179    ( 0.0000,  0.0000,  0.0000)
  41 Cu     1.586004    5.551506   21.767488    ( 0.0000,  0.0000,  0.0000)
  42 Cu     4.203007    5.551506   21.767488    ( 0.0000,  0.0000,  0.0000)
  43 Cu     0.277407    3.684877   20.478179    ( 0.0000,  0.0000,  0.0000)
  44 Cu     0.277531    3.666118   23.097455    ( 0.0000,  0.0000,  0.0000)
  45 Cu     4.203065    5.551501   24.276740    ( 0.0000,  0.0000,  0.0000)
  46 Cu     1.586063    5.551501   24.276741    ( 0.0000,  0.0000,  0.0000)
  47 Cu     2.894533    3.666118   23.097455    ( 0.0000,  0.0000,  0.0000)

Unit cell:
           periodic     x           y           z      points  spacing
  1. axis:    yes    5.234005    0.000000    0.000000    30     0.1745
  2. axis:    yes    0.000000    7.402000    0.000000    42     0.1762
  3. axis:    yes    0.000000    0.000000   34.393512   196     0.1755

  Lengths:   5.234005   7.402000  34.393512
  Angles:   90.000000  90.000000  90.000000

Effective grid spacing dv^(1/3) = 0.1754

     iter     time        total  log10-change:
                         energy  eigst   dens
iter:   1 03:17:40 -3659.616843
iter:   2 03:18:10 -3649.981622  -1.64  -1.21
iter:   3 03:18:44 -3648.839019  -1.00  -1.28
iter:   4 03:19:19 -3636.667078  -1.27  -1.42
iter:   5 03:20:08 -3638.077182  -2.34  -1.65
iter:   6 03:20:41 -3640.956553  -2.13  -1.64
iter:   7 03:21:15 -3641.343537  -1.54  -1.64
iter:   8 03:21:51 -3638.888961  -2.67  -1.71
iter:   9 03:22:27 -3634.724847  -2.31  -1.80
iter:  10 03:23:07 -3634.721817  -2.99  -2.15
iter:  11 03:23:54 -3634.469356c -3.38  -2.22
iter:  12 03:24:25 -3634.533289c -2.70  -2.34
iter:  13 03:24:56 -3634.315076c -3.94  -2.37
iter:  14 03:25:28 -3634.322613c -4.46  -2.59
iter:  15 03:26:02 -3634.220612c -3.51  -2.58
iter:  16 03:26:35 -3634.202773c -4.30  -2.98
iter:  17 03:27:09 -3634.199722c -5.53  -3.21
iter:  18 03:27:48 -3634.200793c -5.04  -3.32
iter:  19 03:28:24 -3634.198009c -5.06  -3.33
iter:  20 03:29:04 -3634.198033c -5.54  -3.65
iter:  21 03:29:36 -3634.197424c -5.94  -3.68
iter:  22 03:30:05 -3634.197442c -6.88  -3.87
iter:  23 03:30:37 -3634.197549c -6.16  -3.90
iter:  24 03:31:11 -3634.197412c -5.91  -3.85
iter:  25 03:31:40 -3634.197386c -7.19  -4.17c
iter:  26 03:32:09 -3634.197412c -6.72  -4.28c
iter:  27 03:32:40 -3634.197396c -7.08  -4.49c
iter:  28 03:33:13 -3634.197388c -7.21  -4.47c
iter:  29 03:33:43 -3634.197388c -8.64c -4.81c

Converged after 29 iterations.

Dipole moment: (-46.313257, 0.497173, -0.000072) |e|*Ang

Energy contributions relative to reference atoms: (reference = -2161029.688374)

Kinetic:       +325.855405
Potential:     -368.103543
External:        +0.000000
XC:            -3591.065246
Entropy (-ST):   -0.466968
Local:           -0.650521
--------------------------
Free energy:   -3634.430872
Extrapolated:  -3634.197388

Showing only first 2 kpts
 Kpt  Band  Eigenvalues  Occupancy
  0   262      0.67677    0.93312
  0   263      0.72021    0.72324
  0   264      0.92721    0.13341
  0   265      1.14351    0.01630

  1   262      0.45796    1.77272
  1   263      0.57429    1.41813
  1   264      0.64877    1.07289
  1   265      0.82270    0.33784


Fermi level: 0.66337

No gap

Forces in eV/Ang:
  0 Cu    0.00478    0.00777    0.00710
  1 Cu    0.00689    0.00064   -0.01078
  2 Cu    0.00689    0.00064   -0.01078
  3 Cu    0.00478    0.00776    0.00710
  4 Cu   -0.00067    0.00318   -0.00899
  5 Cu   -0.01062    0.00090   -0.00458
  6 Cu   -0.01061    0.00090   -0.00458
  7 Cu   -0.00067    0.00318   -0.00899
  8 Cu   -0.00638   -0.00824    0.00003
  9 Cu   -0.00055   -0.00039    0.00015
 10 Cu   -0.00056   -0.00039    0.00015
 11 Cu   -0.00639   -0.00825    0.00003
 12 Cu    0.00062    0.00596    0.00731
 13 Cu    0.00053   -0.00055    0.00894
 14 Cu    0.00052   -0.00054    0.00894
 15 Cu    0.00063    0.00597    0.00730
 16 Cu    0.00020   -0.00218    0.00520
 17 Cu    0.00011   -0.00009    0.00979
 18 Cu    0.00011   -0.00010    0.00979
 19 Cu    0.00019   -0.00218    0.00520
 20 Cu    0.00017   -0.01085   -0.00743
 21 Cu   -0.00326    0.00038    0.00385
 22 Cu   -0.00326    0.00038    0.00385
 23 Cu    0.00017   -0.01085   -0.00743
 24 Cu    0.00903   -0.00671    0.00490
 25 Cu    0.01906   -0.00039   -0.00709
 26 Cu    0.01907   -0.00039   -0.00709
 27 Cu    0.00903   -0.00671    0.00490
 28 Cu   -0.00058   -0.00222   -0.00953
 29 Cu   -0.01238    0.00068   -0.00645
 30 Cu   -0.01238    0.00068   -0.00645
 31 Cu   -0.00058   -0.00222   -0.00953
 32 Cu   -0.00643    0.00924   -0.00017
 33 Cu   -0.00062   -0.00049    0.00704
 34 Cu   -0.00062   -0.00049    0.00704
 35 Cu   -0.00644    0.00925   -0.00017
 36 Cu    0.00062   -0.00759    0.00729
 37 Cu    0.00029   -0.00057    0.00218
 38 Cu    0.00028   -0.00057    0.00218
 39 Cu    0.00062   -0.00760    0.00729
 40 Cu    0.00019    0.00166    0.00521
 41 Cu    0.00021   -0.00011    0.01451
 42 Cu    0.00021   -0.00011    0.01451
 43 Cu    0.00020    0.00166    0.00521
 44 Cu    0.00017    0.01080   -0.00744
 45 Cu    0.00013    0.00001   -0.01361
 46 Cu    0.00013    0.00001   -0.01361
 47 Cu    0.00017    0.01081   -0.00744

Timing:                              incl.     excl.
-----------------------------------------------------------
Forces:                             12.706    12.706   1.1% |
Hamiltonian:                        12.110     0.022   0.0% |
 Atomic:                             0.145     0.001   0.0% |
  XC Correction:                     0.144     0.144   0.0% |
 Calculate atomic Hamiltonians:      1.145     1.145   0.1% |
 Communicate:                        0.312     0.312   0.0% |
 Initialize Hamiltonian:             0.002     0.002   0.0% |
 Poisson:                            0.006     0.006   0.0% |
 XC 3D grid:                        10.478     1.834   0.2% |
  VdW-DF integral:                   8.644     0.153   0.0% |
   Convolution:                      0.324     0.324   0.0% |
   FFT:                              0.144     0.144   0.0% |
   gather:                           1.039     1.039   0.1% |
   hmm1:                             0.078     0.078   0.0% |
   hmm2:                             0.205     0.205   0.0% |
   iFFT:                             0.122     0.122   0.0% |
   potential:                        1.347     0.015   0.0% |
    collect:                         0.194     0.194   0.0% |
    p1:                              0.608     0.608   0.1% |
    p2:                              0.293     0.293   0.0% |
    sum:                             0.237     0.237   0.0% |
   splines:                          5.232     5.232   0.5% |
LCAO initialization:               109.884     0.186   0.0% |
 LCAO eigensolver:                   9.406     0.001   0.0% |
  Blacs Orbital Layouts:             0.347     0.000   0.0% |
   General diagonalize:              0.340     0.340   0.0% |
   Redistribute coefs:               0.004     0.004   0.0% |
   Send coefs to domains:            0.003     0.003   0.0% |
  Calculate projections:             0.004     0.004   0.0% |
  Distribute overlap matrix:         8.781     0.000   0.0% |
   Scalapack redistribute:           0.007     0.007   0.0% |
   blocked summation:                8.773     8.773   0.8% |
  Potential matrix:                  0.193     0.193   0.0% |
  SparseAtomicCorrection:            0.009     0.009   0.0% |
  Sum over cells:                    0.072     0.072   0.0% |
 LCAO to grid:                      98.341    98.341   8.6% |--|
 Set positions (LCAO WFS):           1.951     0.012   0.0% |
  Basic WFS set positions:           0.002     0.002   0.0% |
  Basis functions set positions:     0.000     0.000   0.0% |
  P tci:                             0.000     0.000   0.0% |
  ST tci:                            0.391     0.391   0.0% |
  Scalapack redistribute:            0.015     0.015   0.0% |
  blocked summation:                 1.384     1.384   0.1% |
  mktci:                             0.147     0.147   0.0% |
PWDescriptor:                        0.604     0.604   0.1% |
SCF-cycle:                         988.668    71.388   6.2% |-|
 Davidson:                         638.581   158.746  13.8% |-----|
  Apply H:                          73.561    72.137   6.3% |--|
   HMM T:                            1.423     1.423   0.1% |
  Subspace diag:                   115.337     0.007   0.0% |
   calc_h_matrix:                   88.650    13.411   1.2% |
    Apply H:                        75.239    73.692   6.4% |--|
     HMM T:                          1.547     1.547   0.1% |
   diagonalize:                      4.551     4.551   0.4% |
   rotate_psi:                      22.129    22.129   1.9% ||
  calc. matrices:                  228.174    89.907   7.8% |--|
   Apply H:                        138.267   135.520  11.8% |----|
    HMM T:                           2.747     2.747   0.2% |
  diagonalize:                      23.062    23.062   2.0% ||
  rotate_psi:                       39.700    39.700   3.5% ||
 Density:                           88.876     0.002   0.0% |
  Atomic density matrices:           1.642     1.642   0.1% |
  Mix:                              43.435    43.435   3.8% |-|
  Multipole moments:                 0.031     0.031   0.0% |
  Pseudo density:                   43.766    43.765   3.8% |-|
   Symmetrize density:               0.001     0.001   0.0% |
 Hamiltonian:                      188.039     0.338   0.0% |
  Atomic:                            4.921     0.912   0.1% |
   XC Correction:                    4.010     4.010   0.3% |
  Calculate atomic Hamiltonians:    33.764    33.764   2.9% ||
  Communicate:                       9.360     9.360   0.8% |
  Poisson:                           0.142     0.142   0.0% |
  XC 3D grid:                      139.513    22.096   1.9% ||
   VdW-DF integral:                117.417     3.095   0.3% |
    Convolution:                     6.350     6.350   0.6% |
    FFT:                             3.250     3.250   0.3% |
    gather:                         53.916    53.916   4.7% |-|
    hmm1:                            2.016     2.016   0.2% |
    hmm2:                            4.512     4.512   0.4% |
    iFFT:                            3.125     3.125   0.3% |
    potential:                      41.154     0.474   0.0% |
     collect:                        6.593     6.593   0.6% |
     p1:                            16.922    16.922   1.5% ||
     p2:                             6.531     6.531   0.6% |
     sum:                           10.633    10.633   0.9% |
    splines:                         0.000     0.000   0.0% |
 Orthonormalize:                     1.785     0.000   0.0% |
  calc_s_matrix:                     0.211     0.211   0.0% |
  inverse-cholesky:                  0.089     0.089   0.0% |
  projections:                       1.087     1.087   0.1% |
  rotate_psi_s:                      0.398     0.398   0.0% |
Set symmetry:                        0.001     0.001   0.0% |
Other:                              24.913    24.913   2.2% ||
-----------------------------------------------------------
Total:                                      1148.886 100.0%

Memory usage: 869.16 MiB
Date: Wed Sep 21 03:33:55 2022
