[gpaw-users] Calculations in LCAO mode

[Ulrik Grønbjerg]

Hi Ask

Thanks for your answers, they were very helpful. However, your fix for the
fprojectors does not seem to work in version 0.8. I have inserted the lines
outside the calculator object, but I get the following error when I try to
run it. I ahve attached the script. can you please tell me what I am doing
wrong?

Best wishes
Ulrik


Traceback (most recent call last):
  File "lcao-relax-structure.py", line 68, in ?
    qn.run(fmax=0.20)
  File "/home/camp/s072139/niflheim/ase/ase/optimize/optimize.py", line
114, in run
  File "/home/camp/s072139/niflheim/ase/ase/atoms.py", line 590, in
get_forces
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/aseinterface.py",
line 71, in get_forces
    force_call_to_set_positions=force_call_to_set_positions)
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/paw.py",
line 221, in calculate
    self.initialize(atoms)
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/paw.py",
line 509, in initialize
    self.wfs = LCAOWaveFunctions(lcaoksl, *args)
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/wavefunctions/lcao.py",
line 39, in __init__
    self.tci = NewTCI(gd.cell_cv, gd.pbc_c, setups, kd.ibzk_qc, kd.gamma)
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/lcao/overlap.py",
line 663, in __init__
    self.calculate_expansions()
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/lcao/overlap.py",
line 691, in calculate_expansions
    l_Ij, phit_Ijq)
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/lcao/overlap.py",
line 519, in calculate_expansions
    tsoe = calc.calculate_expansions(l1_j, f1_jq, l2_j, f2_jq)
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/lcao/overlap.py",
line 482, in calculate_expansions
    oe = self.transformer.calculate_overlap_expansion(a_q, la, lb)
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/lcao/overlap.py",
line 450, in calculate_overlap_expansion
    a_g = (8 * fbt(l, a_q * k1**(-2 - lmax - l), self.k_q, R) /
  File
"/opt/campos-gpaw/0.8.0.8092/1.el5.fys.open64.4.2.4.python2.4.without_ase.openmpi.1.4.3.goto2.2.1.13.acml.4.4.0/lib64/python2.4/site-packages/gpaw/lcao/overlap.py",
line 98, in fbt
    g += (dr * 2 * m * k**(l - n) *
IndexError: list index out of range
GPAW CLEANUP for serial binary: exceptions.IndexError occured. Calling
sys.exit()



2012/2/21 Ask Hjorth Larsen <askhl at fysik.dtu.dk>

> Hi
>
>
> On Tue, 21 Feb 2012, Ulrik Grønbjerg wrote:
>
>  Dear GPAW users
>>
>> I am doing calculations on some rather large metal-slabs using LCAO, and I
>> would like some advice in this regard.
>>
>> I have been told that performance improves if ScaLAPACK is used for
>> systems
>> with more than 50 atoms, which is the case here. I have therefore inserted
>> "parallel=dict(sl_default=(4,**2,64))," in my GPAW-object. I then see the
>> following in my log-file:
>>
>> Total number of cores used: 32
>> Parallelization over k-points: 4
>> Domain Decomposition: 2 x 1 x 4
>> Diagonalizer layout: BLACS 4 x 2 grid with 64 x 64 blocksize
>>
>> Does this mean that I parallelize over both space and the diagonalization
>> operation? I think it might refer to different operations, but is this
>> true?
>> If yes, could someone maybe explain it a bit or refer me to the relevant
>> documentation?
>>
>
> Within each k-point, there are [domain decomposition] x [band
> parallelization] cpus available for the scalapack operations.  Some
> redistribution of arrays takes place in order for this to be possible, but
> it will work no matter the band/domain parallelization. (Performance-wise
> it is slightly entangled with band/domain parallelization, but with just 8
> CPUs/k-point you should probably not worry about band parallelization yet.)
>
>
>  I would also like to know if it is possible to set "fprojectors=True"
>> inside
>> the script or GPAW-object, or is must always be set at job
>> submission/execution?
>>
>
> Try doing this at the top of the script:
>
>  from gpaw import extra_parameters
>  extra_parameters['fprojectors'**] = True
>
> (This does not *in general* work for "extra parameters", but it will work
> for fprojectors)
>
>
>  I currently run GPAW version 0.8, but should I switch to version 0.9 to
>> get
>> the best performance for LCAO calculations?
>>
>
> Switch to 0.9 when it comes out.
>
> Regards
> Ask
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