[gpaw-users] gpaw-users Digest, Vol 6, Issue 9
xiao.jianping at bccms.uni-bremen.de
xiao.jianping at bccms.uni-bremen.de
Wed Jul 14 10:19:47 CEST 2010
Hi Jibiao
The examples in gpaw website have three steps. The second step is to
obtain the energy scale between full core hole and no core hole
approximation. If this step is necessary for XAS calculation? I skiped
this step and set energy scale in plot.py directly, it should work
also. But I obtained the following error :
"
File "/home/jxiao/localsoftware/GPAW_install/lib/python/gpaw/xas.py", line
15, in __init__
assert wfs.gd.orthogonal
AssertionError
"
Any suggestion? What meaning of this error?
Best
Jianping
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> Today's Topics:
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> 1. X-ray adsorption calculation-convergence (Xiao Jianping)
> 2. Re: Need help - gpaw test fails (ksaha at physics.udel.edu)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 12 Jul 2010 16:38:37 +0200
> From: Xiao Jianping <xiao.jianping at bccms.uni-bremen.de>
> Subject: [gpaw-users] X-ray adsorption calculation-convergence
> To: gpaw-users at listserv.fysik.dtu.dk
> Message-ID: <4C3B28ED.20902 at bccms.uni-bremen.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear gpaw-users,
>
> I want to calculate XAS of ZnO. Firstly I setup core hole paw files for
> Zinc and oxygen (fch1s). In this case I want to implement Zinc K-shell
> transition. I am unclear on the occupation. The Zn2O2 primitive
> structure has 30*2+8*2=76 electrons. How I should set occupation
> parameters? (occupation is for valence electrons or core electrons and
> both ?) The following case I calculated is not converged. Thank you very
> much!
> ----------------------------------------------------------------------------------
> /atoms = Atoms(symbols='Zn2O2',/
> / positions=[/
> / (-0.949,-1.643,0),/
> / (-1.89,0,2.621),/
> / (-0.945,-1.643,2.006),/
> / (-1.89,0,-0.615)],/
> / cell=[(2.85,-1.64,0),(0,3.29,0),(0,0,5.24)],/
> / pbc=(1,1,1))/
> /calc = GPAW(h=0.2,/
> / txt='ZnO_exc.txt',/
> / xc='PBE',/
> / kpts=(4, 4, 4),/
> / nbands = -30,/
> / maxiter=120,/
> / charge=-2,/
> / spinpol=True,/
> / occupations=FermiDirac(74.0, fixmagmom=True),/
> / convergence={'energy': 0.001, # eV/
> / 'density': 1.0e-5,/
> / 'eigenstates': 1.0e-9},/
> / mixer=Mixer(beta=0.5, nmaxold=5, weight=70.0),/
> / setups={0: 'fch1s',1: 'fch1s'})/
>
> /atoms[0].magmom = 1/
> /atoms[1].magmom = 1/
> ----------------------------------------------------------------------------------
>
> Best regards
> Jianping
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> ------------------------------
>
> Message: 2
> Date: Mon, 12 Jul 2010 20:56:49 -0400 (EDT)
> From: ksaha at physics.udel.edu
> Subject: Re: [gpaw-users] Need help - gpaw test fails
> To: jensj at fysik.dtu.dk
> Cc: gpaw-users at listserv.fysik.dtu.dk, ksaha at physics.udel.edu
> Message-ID:
> <57593.128.175.112.15.1278982609.squirrel at physics.udel.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear jens and others,
>
> By adding "PYTHONPATH" as the environment variable with "mpiexec", I see
> that the gpaw runs well for the following:
>
> [gpaw]$ mpiexec -machinefile $TMPDIR/machines -n $NSLOTS -envlist
> PYTHONPATH ~/bin/gpaw-python -c "import gpaw.mpi as mpi; print mpi.rank"
>
> [examples]$ mpiexec -machinefile $TMPDIR/machines -n $NSLOTS -envlist
> PYTHONPATH -envlist GPAW_SETUP_PATH ~/bin/gpaw-python H.py
>
> -------------------------
>
> However, while running "bee.py", I get the following message:
>
> Traceback (most recent call last):
> File "bee.py", line 2, in ?
> from ASE.Utilities.BEE import GetEnsembleEnergies
> ImportError: No module named ASE.Utilities.BEE
>
> -------------------------
>
> Also, while running "lcao.py", I get the following message:
>
> ___ ___ ___ _ _ _
> | | |_ | | | |
> | | | | | . | | | |
> |__ | _|___|_____| 0.8.6806
> |___|_|
>
> User: ksaha at compute-0-6.local
> Date: Mon Jul 12 20:43:12 2010
> Arch: x86_64
> Pid: 3210
> Dir: /home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw
> ase: /home/ksaha/ase/ase version: 3.5.0
> numpy: /usr/lib64/python2.4/site-packages/numpy
> units: Angstrom and eV
> Using default value for grid spacing.
> Traceback (most recent call last):
> File "lcao.py", line 12, in ?
> atoms.get_potential_energy()
> File "/home/ksaha/ase/ase/atoms.py", line 494, in get_potential_energy
> return self.calc.get_potential_energy(self)
> File "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/aseinterface.py",
> line 32, in get_potential_energy
> self.calculate(atoms, converge=True)
> File "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/paw.py", line
> 219, in calculate
> self.initialize(atoms)
> File "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/paw.py", line
> 573, in initialize
> par.convergence)
> File
> "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/eigensolvers/__init__.py",
> line 27, in get_eigensolver
> assert isinstance(eigensolver, LCAO) == (mode == 'lcao')
> AssertionError
> Memory usage: 17.42 MB
>
> ============================================================
> Timing: incl. excl.
> ============================================================
> Initialization: 0.408 0.408 99.7%
> |---------------------------------------|
> Other: 0.001 0.001 0.3% |
> ============================================================
> Total: 0.409 100.0%
> ============================================================
> date: Mon Jul 12 20:43:12 2010
>
>
>
> As I reported earlier, I am still getting the "AssertionError" as:
>
>
> [ksaha at ulam gpaw]$ gpaw-python `which gpaw-test`
> /usr/lib64/python2.4/site-packages/scipy/misc/__init__.py:25:
> DeprecationWarning: NumpyTest will be removed in the next release; please
> update your code to use nose or unittest
> test = NumpyTest().test
> Running tests in /tmp/gpaw-test-bu-LNc
> =============================================================================
> ase3k_version.py 0.023 OK
> numpy_core_multiarray_dot.py 0.023 OK
> gemm_complex.py 0.023 OK
> lapack.py 0.024 OK
> mpicomm.py 0.024 OK
> eigh.py 0.025 OK
> setups.py 0.024 OK
> xc.py 0.025 OK
> xcfunc.py 0.025 OK
> gradient.py 0.030 OK
> pbe_pw91.py 0.024 OK
> cg2.py 0.027 OK
> d2Excdn2.py 0.026 OK
> dot.py 0.028 OK
> blas.py 0.026 OK
> gp2.py 0.029 OK
> non_periodic.py 0.031 OK
> erf.py 0.024 OK
> lf.py 0.032 OK
> lxc_xc.py 0.018 FAILED!
> #############################################################################
> Traceback (most recent call last):
> File
> "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/test/__init__.py",
> line 332, in run_one
> execfile(filename, {})
> File "/home/ksaha/gpaw/build/lib.linux-x86_64-2.4/gpaw/test/lxc_xc.py",
> line 139, in ?
> assert error1[0] < 1.0e-9
> AssertionError
> #############################################################################
> lxc_fxc.py Segmentation fault
> [ksaha at ulam gpaw]$
>
>
> Also, please see the following:
>
> [ksaha at ulam test]$ python lxc_xc.py
> 2.0 1.0
> LDA 2.90274693171e-10 dExdnb 2.90274693171e-10 dExdnb
> 2.0 1.0
> PBE 6.32377831523e-10 dExcdsigma2 6.32377831523e-10 dExcdsigma2
> 2.0 1.0
> revPBE 4.1867442846e-10 dExcdnb 4.1867442846e-10 dExcdnb
> 2.0 1.0
> RPBE 2.94699376013e-10 dExcdna 2.94699376013e-10 dExcdna
> 2.0 1.0
> LDAx 2.90274693171e-10 dExcdnb 2.90274693171e-10 dExcdnb
> 2.0 1.0
> revPBEx 3.88416410146e-10 dExcdnb 3.88416410146e-10 dExcdnb
> 2.0 1.0
> RPBEx 2.81688260174e-10 dExcdsigma0 2.81688260174e-10 dExcdsigma0
> 2.0 1.0
> None-C_PW 3.09313685776e-11 dExcdna 3.09313685776e-11 dExcdna
> 2.0 1.0
> TPSS 0.070917846674 dExcdna 0.070917846674 dExcdna
> Traceback (most recent call last):
> File "lxc_xc.py", line 139, in ?
> assert error1[0] < 1.0e-9
> AssertionError
>
>
> Can anyone help me out of this problem. Many thanks in advance!
>
> Regards,
> Kamal
>
>
>
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