[gpaw-users] need a help (khadija korichi)

Wed Jul 14 11:08:18 CEST 2010

Hi khadija,

Which gpaw version you installed ? Where did you obtain this package?

Jianping

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>    1. need a help (khadija korichi)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 14 Jul 2010 08:54:51 +0000 (GMT)
> From: khadija korichi <k0richi at yahoo.fr>
> Subject: [gpaw-users] need a help
> To: gpaw-users at listserv.fysik.dtu.dk
> Message-ID: <762914.81671.qm at web28105.mail.ukl.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> hello all
>
> I have installed the GPAW? and for? verify if it is installed correct
> I test the H.py and the transport example.
> good result for H.py
> but for the second example it give me an error .
> could you help me please
> thank you in advance
> /KHADIJA
>
> first example
>
> **********************************************************************************
> korichi at laptop:~/Bureau/GPAW$ python H.py
>
> ? ___ ___ ___ _ _ _?
> ?|?? |?? |_? | | | |
> ?| | | | | . | | | |
> ?|__ |? _|___|_____|? 0.8.6824
> ?|___|_|????????????
>
> User: korichi at laptop
> Date: Sun Jul 11 22:51:18 2010
> Arch: i686
> Pid:? 3248
> Dir:? /home/korichi/Cluster/gridpaw/gpaw/gpaw
> ase:?? /home/cluster/dacapo_env/lib/python2.6/site-packages/ase? version:?
> 3.3.1.export?
> numpy: /usr/lib/python2.6/dist-packages/numpy
> units: Angstrom and eV
>
> Memory estimate
> ---------------
> Calculator? 34.46 MiB
> ??? Initial overhead? 13.97 MiB
> ??? Density? 7.39 MiB
> ??????? Arrays? 3.45 MiB
> ??????? Localized functions? 0.22 MiB
> ??????? Mixer? 0.56 MiB
> ??????? Interpolator? 3.16 MiB
> ??? Hamiltonian? 12.07 MiB
> ??????? Arrays? 2.56 MiB
> ??????? Restrictor? 1.80 MiB
> ??????? XC 3D grid? 0.79 MiB
> ??????? Poisson? 6.90 MiB
> ??????? vbar? 0.02 MiB
> ??? Wavefunctions? 1.03 MiB
> ??????? Arrays psit_nG? 0.19 MiB
> ??????? Eigensolver? 0.56 MiB
> ??????? Projectors? 0.01 MiB
> ??????? Overlap op? 0.09 MiB
> ??????? Kinetic operator? 0.19 MiB
>
> Positions:
> ? 0 H???? 2.5000??? 2.5000??? 2.5000
>
> ??? .-----------.?
> ?? /|?????????? |?
> ? / |?????????? |?
> ?*? |?????????? |?
> ?|? |?????????? |?
> ?|? |??? H????? |?
> ?|? .-----------.?
> ?| /?????????? /??
> ?|/?????????? /???
> ?*-----------*????
>
> Unit Cell:
> ?????????? Periodic???? X?????????? Y?????????? Z????? Points? Spacing
> ? --------------------------------------------------------------------
> ? 1. axis:??? no???? 5.000000??? 0.000000??? 0.000000??? 24???? 0.2083
> ? 2. axis:??? no???? 0.000000??? 5.000000??? 0.000000??? 24???? 0.2083
> ? 3. axis:??? no???? 0.000000??? 0.000000??? 5.000000??? 24???? 0.2083
>
> H-setup:
> ? name?? : Hydrogen
> ? id???? : 4766778ce56282eaa64abeb28b7c1de3
> ? Z????? : 1
> ? valence: 1
> ? core?? : 0
> ? charge : 0.0
> ? file?? : /home/korichi/Cluster/gridpaw/gpaw-setups-0.6.6300/H.LDA.gz
> ? cutoffs: 0.48(comp), 0.85(filt), 0.53(core), lmax=2
> ? valence states:
> ??????????? energy?? radius
> ??? 1s(1)?? -6.353?? 0.476
> ??? *s????? 20.858?? 0.476
> ??? *p?????? 0.000?? 0.476
>
> Using partial waves for H as LCAO basis
>
> Using the LDA Exchange-Correlation Functional.
> Spin-Polarized Calculation.
> Magnetic Moment:?? 1.000000
> Total Charge:????? 0.000000
> Fermi Temperature: 0.000000
> Mode:????????????? fd
> Eigensolver:?????? rmm-diis
> ?????????????????? (3 nearest neighbors central finite-difference stencil)
> Poisson Solver:??? Jacobi
> ?????????????????? (3 nearest neighbors central finite-difference stencil)
> Interpolation:???? 6th Order
> Reference Energy:? -12.128963
>
> Gamma Point Calculation
> Total number of cores used: 1
> Diagonalizer layout: Serial LAPACK
> Orthonormalizer layout: Serial LAPACK
>
> 1 k-point in the Irreducible Part of the Brillouin Zone (total: 1)
> Linear Mixing Parameter:?????????? 0.25
> Pulay Mixing with 3 Old Densities
> No Damping of Long Wave Oscillations
>
> Convergence Criteria:
> Total Energy Change per Atom:?????????? 0.001 eV / atom
> Integral of Absolute Density Change:??? 0.0001 electrons
> Integral of Absolute Eigenstate Change: 0.001
> Number of Bands in Calculation:???????? 1
> Bands to Converge:????????????????????? Occupied States Only
> Number of Valence Electrons:??????????? 1
> ???????????????????? log10-error:??? Total??????? Iterations:
> ?????????? Time????? WFS??? Density? Energy?????? Fermi? Poisson? MagMom
> iter:?? 1? 22:51:19? +0.2??????????? -0.53550???? 0????? 13?????? +1.0000
> iter:?? 2? 22:51:19? -0.9??????????? -0.77759???? 0?????????????? +1.0000
> iter:?? 3? 22:51:19? -2.5??????????? -0.78540???? 0?????????????? +1.0000
> iter:?? 4? 22:51:20? -3.0?? -1.0???? -0.89114???? 0????? 5??????? +1.0000
> iter:?? 5? 22:51:20? -3.0?? -1.1???? -0.78764???? 0????? 7??????? +1.0000
> iter:?? 6? 22:51:21? -3.9?? -1.6???? -0.78880???? 0????? 5??????? +1.0000
> iter:?? 7? 22:51:21? -4.0?? -1.9???? -0.79039???? 0????? 3??????? +1.0000
> iter:?? 8? 22:51:22? -4.6?? -1.9???? -0.78525???? 0????? 5??????? +1.0000
> iter:?? 9? 22:51:22? -5.6?? -2.4???? -0.78300???? 0????? 4??????? +1.0000
> iter:? 10? 22:51:23? -6.8?? -3.2???? -0.78244???? 0????? 3??????? +1.0000
> iter:? 11? 22:51:23? -7.7?? -3.4???? -0.78253???? 0????? 3??????? +1.0000
> iter:? 12? 22:51:24? -8.6?? -3.6???? -0.78232???? 0????? 2??????? +1.0000
> iter:? 13? 22:51:24? -9.2?? -3.9???? -0.78230???? 0????? 1??????? +1.0000
> iter:? 14? 22:51:24? -9.9?? -4.0???? -0.78231???? 0????? 1??????? +1.0000
> ------------------------------------
> Converged After 14 Iterations.
>
> Energy Contributions Relative to Reference Atom:(reference = -12.12896)
> -------------------------
> Kinetic:???????? +1.77997
> Potential:?????? -1.09116
> External:??????? +0.00000
> XC:????????????? -1.45432
> Entropy (-ST):?? -0.00000
> Local:?????????? -0.01680
> -------------------------
> Free Energy:???? -0.78231
> Zero Kelvin:???? -0.78231
>
> Fermi Level: -4.52708
> ????????????????? Up???????????????????? Down
> ?Band? Eigenvalues? Occupancy? Eigenvalues? Occupancy
> ??? 0???? -7.04439??? 1.00000???? -2.00978??? 0.00000
>
>
> Total Charge:? -0.000000 electrons
> Dipole Moment: [ -5.92271601e-15? -5.92051694e-15? -5.91095348e-15]
>
> Total Magnetic Moment: 1.000000
> Spin contamination: 0.000000 electrons
> Local Magnetic Moments:
> 0 1.0
>
> Memory usage: 34.92 MB
>
> ============================================================
> Timing:?????????????????????????????? incl.???? excl.
> ============================================================
> Initialization:?????????????????????? 0.988???? 0.138?? 2.3% ||
> ?Hamiltonian:???????????????????????? 0.827???? 0.001?? 0.0% |
> ? Atomic:???????????????????????????? 0.035???? 0.000?? 0.0% |
> ?? XC Correction:???????????????????? 0.035???? 0.035?? 0.6% |
> ? Communicate energies:?????????????? 0.000???? 0.000?? 0.0% |
> ? Hartree integrate/restrict:???????? 0.009???? 0.009?? 0.2% |
> ? Initialize Hamiltonian:???????????? 0.005???? 0.005?? 0.1% |
> ? Poisson:??????????????????????????? 0.538???? 0.538?? 8.8% |---|
> ? XC 3D grid:???????????????????????? 0.235???? 0.235?? 3.8% |-|
> ? vbar:?????????????????????????????? 0.004???? 0.004?? 0.1% |
> ?LCAO initialization:???????????????? 0.023???? 0.020?? 0.3% |
> ? LCAO eigensolver:?????????????????? 0.001???? 0.001?? 0.0% |
> ?? Atomic Hamiltonian:??????????????? 0.000???? 0.000?? 0.0% |
> ?? Calculate projections:???????????? 0.000???? 0.000?? 0.0% |
> ?? Distribute overlap matrix:???????? 0.000???? 0.000?? 0.0% |
> ?? Orbital Layouts:?????????????????? 0.000???? 0.000?? 0.0% |
> ?? Potential matrix:????????????????? 0.001???? 0.001?? 0.0% |
> ? LCAO to grid:?????????????????????? 0.000???? 0.000?? 0.0% |
> ? Set positions (LCAO WFS):?????????? 0.001???? 0.000?? 0.0% |
> ?? Basic WFS set positions:?????????? 0.000???? 0.000?? 0.0% |
> ?? Basis functions set positions:???? 0.000???? 0.000?? 0.0% |
> ?? TCI: Calculate S, T, P:??????????? 0.001???? 0.001?? 0.0% |
> SCF-cycle:??????????????????????????? 5.068???? 0.010?? 0.2% |
> ?Density:???????????????????????????? 0.200???? 0.000?? 0.0% |
> ? Atomic density matrices:??????????? 0.004???? 0.004?? 0.1% |
> ? Mix:??????????????????????????????? 0.192???? 0.192?? 3.1% ||
> ? Multipole moments:????????????????? 0.000???? 0.000?? 0.0% |
> ? Pseudo density:???????????????????? 0.004???? 0.004?? 0.1% |
> ?Hamiltonian:???????????????????????? 4.699???? 0.005?? 0.1% |
> ? Atomic:???????????????????????????? 0.389???? 0.004?? 0.1% |
> ?? XC Correction:???????????????????? 0.385???? 0.385?? 6.3% |--|
> ? Communicate energies:?????????????? 0.000???? 0.000?? 0.0% |
> ? Hartree integrate/restrict:???????? 0.089???? 0.089?? 1.5% ||
> ? Poisson:??????????????????????????? 1.604???? 1.604? 26.3% |----------|
> ? XC 3D grid:???????????????????????? 2.575???? 2.575? 42.2%
> |----------------|
> ? vbar:?????????????????????????????? 0.038???? 0.038?? 0.6% |
> ?Orthonormalize:????????????????????? 0.010???? 0.002?? 0.0% |
> ? Band Layouts:?????????????????????? 0.001???? 0.000?? 0.0% |
> ?? Distribute results:??????????????? 0.000???? 0.000?? 0.0% |
> ?? Inverse Cholesky:????????????????? 0.000???? 0.000?? 0.0% |
> ? calc_matrix:??????????????????????? 0.003???? 0.003?? 0.1% |
> ? rotate_psi:???????????????????????? 0.004???? 0.004?? 0.1% |
> ?RMM-DIIS:??????????????????????????? 0.108???? 0.041?? 0.7% |
> ? precondition:?????????????????????? 0.067???? 0.067?? 1.1% |
> ?Subspace diag:?????????????????????? 0.040???? 0.002?? 0.0% |
> ? Band Layouts:?????????????????????? 0.001???? 0.001?? 0.0% |
> ?? Diagonalize:?????????????????????? 0.000???? 0.000?? 0.0% |
> ?? Distribute results:??????????????? 0.000???? 0.000?? 0.0% |
> ? calc_matrix:??????????????????????? 0.030???? 0.030?? 0.5% |
> ? rotate_psi:???????????????????????? 0.006???? 0.006?? 0.1% |
> Other:??????????????????????????????? 0.045???? 0.045?? 0.7% |
> ============================================================
> Total:????????????????????????????????????????? 6.101 100.0%
> ============================================================
> date: Sun Jul 11 22:51:24 2010
> ************************************************************************************
> second example
>
> korichi at laptop:~/Bureau/GPAW$ python transport.py
> Traceback (most recent call last):
> ? File "transport.py", line 3, in <module>
> ??? from gpaw.transport.calculator import Transport
> ? File "/home/korichi/Cluster/gridpaw/gpaw/gpaw/transport/calculator.py",
> line 10, in <module>
> ??? from gpaw.lcao.tools import get_realspace_hs
> ? File "/home/korichi/Cluster/gridpaw/gpaw/gpaw/lcao/tools.py", line 9, in
> <module>
> ??? from ase.calculators.singlepoint import SinglePointCalculator
> ImportError: No module named singlepoint
> korichi at laptop:~/Bureau/GPAW$
>
>
>
>
>
>
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