___ ___ ___ _ _ _ | | |_ | | | | | | | | | . | | | | |__ | _|___|_____| 1.5.1b1 |___|_| User: askhl@jormungandr Date: Tue Jan 15 13:50:37 2019 Arch: x86_64 Pid: 861 Python: 3.5.3 gpaw: /home/askhl/src/gpaw/gpaw (42c1d3ba10) _gpaw: /home/askhl/src/gpaw/build/bin.linux-x86_64-3.5/ gpaw-python (f07921f729) ase: /home/askhl/src/ase/ase (version 3.18.0b1-2d439913df) numpy: /home/askhl/.local/lib/python3.5/site-packages/numpy (version 1.15.4) scipy: /home/askhl/.local/lib/python3.5/site-packages/scipy (version 1.1.0) units: Angstrom and eV cores: 4 Input parameters: eigensolver: {name: dav, niter: 3} h: 0.13 xc: {backend: libvdwxc, name: BEEF-vdW} System changes: positions, numbers, cell, pbc, initial_charges, initial_magmoms Initialize ... C-setup: name: Carbon id: 4aa54d4b901d75f77cc0ea3eec22967b Z: 6 valence: 4 core: 2 charge: 0.0 file: /home/askhl/install/gpaw-setups-0.9.20000/C.PBE.gz cutoffs: 0.64(comp), 1.14(filt), 1.14(core), lmax=2 valence states: energy radius 2s(2.00) -13.751 0.635 2p(2.00) -5.284 0.635 *s 13.461 0.635 *p 21.927 0.635 *d 0.000 0.635 Using partial waves for C as LCAO basis S-setup: name: Sulfur id: ca434db9faa07220b7a1d8cb6886b7a9 Z: 16 valence: 6 core: 10 charge: 0.0 file: /home/askhl/install/gpaw-setups-0.9.20000/S.PBE.gz cutoffs: 0.76(comp), 1.77(filt), 1.66(core), lmax=2 valence states: energy radius 3s(2.00) -17.254 0.974 3p(4.00) -7.008 0.979 *s 9.957 0.974 *p 20.203 0.979 *d 0.000 0.900 Using partial waves for S as LCAO basis H-setup: name: Hydrogen id: d65de229564ff8ea4db303e23b6d1ecf Z: 1 valence: 1 core: 0 charge: 0.0 file: /home/askhl/install/gpaw-setups-0.9.20000/H.PBE.gz cutoffs: 0.48(comp), 0.85(filt), 0.53(core), lmax=2 valence states: energy radius 1s(1.00) -6.494 0.476 *s 20.717 0.476 *p 0.000 0.476 Using partial waves for H as LCAO basis O-setup: name: Oxygen id: 32ecd46bf208036f09c70b0ec9a88b78 Z: 8 valence: 6 core: 2 charge: 0.0 file: /home/askhl/install/gpaw-setups-0.9.20000/O.PBE.gz cutoffs: 0.67(comp), 1.17(filt), 0.83(core), lmax=2 valence states: energy radius 2s(2.00) -23.961 0.688 2p(4.00) -9.029 0.598 *s 3.251 0.688 *p 18.182 0.598 *d 0.000 0.619 Using partial waves for O as LCAO basis Reference energy: -22207.662282 Spin-paired calculation Occupation numbers: Fermi-Dirac: width=0.0000 eV Convergence criteria: Maximum total energy change: 0.0005 eV / electron Maximum integral of absolute density change: 0.0001 electrons Maximum integral of absolute eigenstate change: 4e-08 eV^2 Maximum number of iterations: 333 Symmetries present (total): 1 ( 1 0 0) ( 0 1 0) ( 0 0 1) 1 k-point (Gamma) 1 k-point in the irreducible part of the Brillouin zone k-points in crystal coordinates weights 0: 0.00000000 0.00000000 0.00000000 1/1 Wave functions: Uniform real-space grid Kinetic energy operator: 6*3+1=19 point O(h^6) finite-difference Laplacian ScaLapack parameters: grid=1x1, blocksize=None Wavefunction extrapolation: Improved wavefunction reuse through dual PAW basis Eigensolver Davidson(niter=3, smin=None, normalize=True) Densities: Coarse grid: 156*100*140 grid Fine grid: 312*200*280 grid Total Charge: 0.000000 Density mixing: Method: separate Backend: pulay Linear mixing parameter: 0.25 Mixing with 3 old densities No damping of long wave oscillations Hamiltonian: XC and Coulomb potentials evaluated on a 312*200*280 grid Using the vdW-BEEF Exchange-Correlation functional Interpolation: tri-quintic (5. degree polynomial) Poisson solver: FastPoissonSolver using 6*3+1=19 point O(h^6) finite-difference Laplacian stencil; FFT axes: []; FST axes: [1, 2, 0]. XC parameters: vdW-BEEF with libvdwxc Mode: mpi with 4 cores Semilocal: BEEVDW with 2 nearest neighbor stencil Corresponding non-local functional: vdW-DF2 Local blocksize: 78 x 200 x 280 PAW datasets: PBE Memory estimate: Process memory now: 530.62 MiB Calculator: 518.81 MiB Density: 138.66 MiB Arrays: 106.16 MiB Localized functions: 8.42 MiB Mixer: 24.08 MiB Hamiltonian: 70.09 MiB Arrays: 69.43 MiB XC: 0.00 MiB Poisson: 0.00 MiB vbar: 0.66 MiB Wavefunctions: 310.07 MiB Arrays psit_nG: 144.47 MiB Eigensolver: 164.63 MiB Projections: 0.01 MiB Projectors: 0.96 MiB Total number of cores used: 4 Domain decomposition: 2 x 1 x 2 Number of atoms: 16 Number of atomic orbitals: 46 Number of bands in calculation: 36 Bands to converge: occupied states only Number of valence electrons: 52 ... initialized Initializing position-dependent things. Density initialized from atomic densities Creating initial wave functions: 36 bands from LCAO basis set .-------------------------------------------------. /| | / | | / | | / | | / | | / | | / | | * | | | | | | | | | | | | | H O | | | | | | H C C H | | | C C O | | | C C | | | S C H | | | | | | H H | | | | | | | | | | | .-------------------------------------------------. | / / | / / | / / | / / | / / | / / |/ / *-------------------------------------------------* Positions: 0 C 8.088149 6.500073 8.568171 ( 0.0000, 0.0000, 0.0000) 1 C 8.114833 6.500017 9.980722 ( 0.0000, 0.0000, 0.0000) 2 C 9.305691 6.500026 7.855617 ( 0.0000, 0.0000, 0.0000) 3 C 9.333427 6.500052 10.659204 ( 0.0000, 0.0000, 0.0000) 4 C 10.554397 6.500000 9.952815 ( 0.0000, 0.0000, 0.0000) 5 C 10.522082 6.500064 8.542684 ( 0.0000, 0.0000, 0.0000) 6 S 6.500000 6.500128 7.772774 ( 0.0000, 0.0000, 0.0000) 7 H 6.957541 6.500023 6.500000 ( 0.0000, 0.0000, 0.0000) 8 C 11.830018 6.500144 10.728257 ( 0.0000, 0.0000, 0.0000) 9 O 11.918808 6.500059 11.947883 ( 0.0000, 0.0000, 0.0000) 10 O 12.950186 6.500043 9.924022 ( 0.0000, 0.0000, 0.0000) 11 H 13.705711 6.500071 10.545060 ( 0.0000, 0.0000, 0.0000) 12 H 9.355452 6.500026 11.749428 ( 0.0000, 0.0000, 0.0000) 13 H 7.180531 6.500008 10.545125 ( 0.0000, 0.0000, 0.0000) 14 H 11.454442 6.500052 7.977920 ( 0.0000, 0.0000, 0.0000) 15 H 9.303728 6.500038 6.763882 ( 0.0000, 0.0000, 0.0000) Unit cell: periodic x y z points spacing 1. axis: no 20.205711 0.000000 0.000000 156 0.1295 2. axis: no 0.000000 13.000144 0.000000 100 0.1300 3. axis: no 0.000000 0.000000 18.447883 140 0.1318 Lengths: 20.205711 13.000144 18.447883 Angles: 90.000000 90.000000 90.000000 Effective grid spacing dv^(1/3) = 0.1304 log10-error: total iterations: time wfs density energy fermi poisson iter: 1 13:52:08 +1.16 +inf -222.520046 0 1 iter: 2 13:53:26 +0.10 -0.75 -216.386257 0 1 iter: 3 13:54:45 -0.18 -0.93 -214.629857 0 1 iter: 4 13:56:03 -0.33 -1.24 -214.450511 0 1 iter: 5 13:57:21 -0.98 -1.63 -214.482956 0 1 iter: 6 13:58:40 -1.46 -2.03 -214.470163 0 1 iter: 7 13:59:58 -2.31 -2.43 -214.470498 0 1 iter: 8 14:01:17 -2.77 -2.70 -214.470166 0 1 iter: 9 14:02:36 -3.54 -2.95 -214.470202 0 1 iter: 10 14:03:54 -3.70 -3.32 -214.470216 0 1 iter: 11 14:05:13 -4.44 -3.62 -214.470230 0 1 iter: 12 14:06:31 -4.68 -3.88 -214.470233 0 1 iter: 13 14:07:50 -5.36 -4.08 -214.470234 0 1 iter: 14 14:09:09 -5.54 -4.42 -214.470234 0 1 iter: 15 14:10:27 -6.10 -4.71 -214.470235 0 1 iter: 16 14:11:46 -6.37 -4.87 -214.470235 0 1 iter: 17 14:13:04 -6.89 -5.04 -214.470235 0 1 iter: 18 14:14:23 -7.12 -5.37 -214.470235 0 1 iter: 19 14:15:42 -7.65 -5.52 -214.470235 0 1 Converged after 19 iterations. Dipole moment: (-0.096412, 0.000018, -0.532980) |e|*Ang Energy contributions relative to reference atoms: (reference = -22207.662282) Kinetic: +112.454926 Potential: -120.591544 External: +0.000000 XC: -207.025508 Entropy (-ST): +0.000000 Local: +0.691892 -------------------------- Free energy: -214.470235 Extrapolated: -214.470235 Non-local vdW-BEEF correlation energy: 9.604903 Semilocal BEEVDW energy: -650.802095 (Not including atomic contributions) Fermi level: -4.46987 Band Eigenvalues Occupancy 0 -27.94867 2.00000 1 -25.67446 2.00000 2 -22.32823 2.00000 3 -20.54481 2.00000 4 -19.39048 2.00000 5 -18.67030 2.00000 6 -16.54453 2.00000 7 -15.85429 2.00000 8 -14.97754 2.00000 9 -13.54110 2.00000 10 -12.39465 2.00000 11 -12.21962 2.00000 12 -11.70227 2.00000 13 -11.50511 2.00000 14 -11.26197 2.00000 15 -11.10479 2.00000 16 -10.34698 2.00000 17 -9.92872 2.00000 18 -9.91802 2.00000 19 -9.16551 2.00000 20 -8.99522 2.00000 21 -8.18592 2.00000 22 -7.91028 2.00000 23 -7.09039 2.00000 24 -6.90322 2.00000 25 -6.10994 2.00000 26 -2.82981 0.00000 27 -2.01598 0.00000 28 -1.64070 0.00000 29 -1.05257 0.00000 30 -0.89218 0.00000 31 -0.55646 0.00000 32 -0.51101 0.00000 33 -0.40136 0.00000 34 0.49228 0.00000 35 1.06702 0.00000 Timing: incl. excl. ----------------------------------------------------------- Hamiltonian: 15.683 0.000 0.0% | Atomic: 0.208 0.001 0.0% | XC Correction: 0.207 0.207 0.0% | Calculate atomic Hamiltonians: 0.005 0.005 0.0% | Communicate: 0.000 0.000 0.0% | Hartree integrate/restrict: 0.107 0.107 0.0% | Initialize Hamiltonian: 0.000 0.000 0.0% | Poisson: 1.251 0.103 0.0% | Communicate bwd 0: 0.106 0.106 0.0% | Communicate bwd 1: 0.289 0.289 0.0% | Communicate fwd 0: 0.248 0.248 0.0% | Communicate fwd 1: 0.109 0.109 0.0% | fft: 0.177 0.177 0.0% | fft2: 0.219 0.219 0.0% | XC 3D grid: 14.080 0.020 0.0% | van der Waals: 14.060 0.356 0.0% | libvdwxc nonlocal: 8.308 8.308 0.6% | redistribute: 0.742 0.742 0.0% | semilocal: 4.655 4.655 0.3% | vbar: 0.032 0.032 0.0% | LCAO initialization: 0.488 0.192 0.0% | LCAO eigensolver: 0.068 0.000 0.0% | Calculate projections: 0.000 0.000 0.0% | DenseAtomicCorrection: 0.000 0.000 0.0% | Distribute overlap matrix: 0.010 0.010 0.0% | Orbital Layouts: 0.001 0.001 0.0% | Potential matrix: 0.056 0.056 0.0% | LCAO to grid: 0.183 0.183 0.0% | Set positions (LCAO WFS): 0.045 0.022 0.0% | Basic WFS set positions: 0.001 0.001 0.0% | Basis functions set positions: 0.000 0.000 0.0% | P tci: 0.014 0.014 0.0% | ST tci: 0.005 0.005 0.0% | mktci: 0.003 0.003 0.0% | SCF-cycle: 1479.910 0.011 0.0% | Davidson: 1179.619 88.541 5.9% |-| Apply hamiltonian: 70.529 70.529 4.7% |-| Subspace diag: 181.743 0.003 0.0% | calc_h_matrix: 53.481 40.027 2.7% || Apply hamiltonian: 13.454 13.454 0.9% | diagonalize: 0.667 0.667 0.0% | rotate_psi: 127.593 127.593 8.5% |--| calc. matrices: 457.143 416.199 27.7% |----------| Apply hamiltonian: 40.943 40.943 2.7% || diagonalize: 0.116 0.116 0.0% | rotate_psi: 381.547 381.547 25.4% |---------| Density: 4.679 0.001 0.0% | Atomic density matrices: 0.079 0.079 0.0% | Mix: 2.788 2.788 0.2% | Multipole moments: 0.006 0.006 0.0% | Pseudo density: 1.805 1.804 0.1% | Symmetrize density: 0.001 0.001 0.0% | Hamiltonian: 291.231 0.003 0.0% | Atomic: 3.805 0.078 0.0% | XC Correction: 3.726 3.726 0.2% | Calculate atomic Hamiltonians: 0.077 0.077 0.0% | Communicate: 0.005 0.005 0.0% | Hartree integrate/restrict: 1.929 1.929 0.1% | Poisson: 22.468 1.816 0.1% | Communicate bwd 0: 1.886 1.886 0.1% | Communicate bwd 1: 5.366 5.366 0.4% | Communicate fwd 0: 4.523 4.523 0.3% | Communicate fwd 1: 1.939 1.939 0.1% | fft: 2.856 2.856 0.2% | fft2: 4.083 4.083 0.3% | XC 3D grid: 262.457 0.445 0.0% | van der Waals: 262.012 6.224 0.4% | libvdwxc nonlocal: 151.976 151.976 10.1% |---| redistribute: 13.643 13.643 0.9% | semilocal: 90.169 90.169 6.0% |-| vbar: 0.486 0.486 0.0% | Orthonormalize: 4.369 0.000 0.0% | calc_s_matrix: 0.992 0.992 0.1% | inverse-cholesky: 0.047 0.047 0.0% | projections: 0.013 0.013 0.0% | rotate_psi_s: 3.318 3.318 0.2% | Set symmetry: 0.001 0.001 0.0% | Other: 8.648 8.648 0.6% | ----------------------------------------------------------- Total: 1504.730 100.0% Memory usage: 1.99 GiB Date: Tue Jan 15 14:15:42 2019