[gpaw-users] optB88-vdW
Jess Wellendorff
jewe at slac.stanford.edu
Wed Nov 27 19:10:44 CET 2013
no problem!
On 11/27/2013 10:07 AM, Glen Jenness wrote:
> Jess,
> It is working now. Thanks!
>
> Glen
>
>
> On Wed, Nov 27, 2013 at 12:36 PM, Jess Wellendorff
> <jewe at slac.stanford.edu <mailto:jewe at slac.stanford.edu>> wrote:
>
> Hi Glen, I have committed the revision to GPAW trunk along with
> other changes, please try it out.
>
> - Jess
>
>
> On 11/27/2013 08:52 AM, Jess Wellendorff wrote:
>> All right, I will attempt to fix this issue in gpaw then.
>>
>> On 11/27/2013 08:49 AM, Glen Jenness wrote:
>>> We're running libxc v.2.0.2, so it has the B88 exchange functional.
>>>
>>>
>>> On Wed, Nov 27, 2013 at 11:47 AM, Jess Wellendorff
>>> <jewe at slac.stanford.edu <mailto:jewe at slac.stanford.edu>> wrote:
>>>
>>> Hmm, in order to use optB88-vdW in GPAW trunk you need your
>>> LibXC to supply the optB88 exchange. I do not know when this
>>> exchange functional was committed to LibXC, but the
>>> following link to the relevant file in the LibXC trunk shows
>>> how it should look if the LibXC you use does supply optB88:
>>> http://www.tddft.org/svn/octopus/trunk/libxc/src/gga_x_b88.c
>>>
>>> - Jess
>>>
>>> On 11/27/2013 08:42 AM, Glen Jenness wrote:
>>>> Jess,
>>>> I have my own gpaw installation from the trunk (updated
>>>> yesterday in fact), but I am currently using a system
>>>> installed LibXC. But LibXC is easy to install, so it
>>>> shouldn't be a problem to link to that.
>>>>
>>>> Glen
>>>>
>>>>
>>>> On Wed, Nov 27, 2013 at 11:24 AM, Jess Wellendorff
>>>> <jewe at slac.stanford.edu <mailto:jewe at slac.stanford.edu>> wrote:
>>>>
>>>> Dear Glen,
>>>>
>>>> I see that optB88-vdW might be broken due to our recent
>>>> transition to a never LibXC, where the optB88 exchange
>>>> for optB88-vdW calculations has a slightly different
>>>> name than the previous local GPAW implementation of
>>>> that exchange had.
>>>>
>>>> Have you compiled LibXC yourself for use with the GPAW
>>>> trunk? If so, I might be persuaded to fix the naming in
>>>> gpaw/xc/vdw.py and let you test the fix.
>>>>
>>>> Best,
>>>> Jess Wellendorff
>>>>
>>>>
>>>> On 11/26/2013 12:16 PM, Glen Jenness wrote:
>>>>
>>>> Dear users,
>>>> Is optB88-vdW available in the svn branch? I tried
>>>> running the following:
>>>>
>>>> import time
>>>>
>>>> from ase.atoms import Atoms
>>>> from ase.lattice.surface import fcc111, add_adsorbate
>>>> from ase.constraints import FixAtoms
>>>> from ase.optimize.lbfgs import LBFGS
>>>> from ase.parallel import parprint
>>>>
>>>> from gpaw import GPAW, Mixer, FermiDirac
>>>>
>>>> verb = False
>>>> mix = Mixer(beta=0.05, nmaxold=5, weight=100.0)
>>>> occ = FermiDirac(0.1)
>>>> convergence = {'energy': 1e-05,
>>>> 'density': 1e-04}
>>>>
>>>> parprint('Mixer = %s' % str(mix))
>>>> parprint('Occupations = %s' % str(occ))
>>>>
>>>> functionals = ['optB88-vdW']
>>>>
>>>> for functional in functionals:
>>>> calc = GPAW(mode='lcao', basis='dzp',
>>>> txt='%s.txt' % functional.lower(), kpts=(3,3,1),
>>>> occupations=occ, xc=functional,
>>>> mixer=mix, maxiter=500, spinpol=False)
>>>>
>>>> rhodium = fcc111('Rh', (1,1,4), vacuum=8.0)
>>>> constraint = FixAtoms([0, 1])
>>>> rhodium.set_constraint(constraint)
>>>> rhodium *= (2,2,1)
>>>>
>>>> parprint('%s' % str( rhodium))
>>>>
>>>> co = Atoms('CO', positions=[(0,0,0), (0,0,1.14)])
>>>> add_adsorbate(rhodium, co, 1.8, position='ontop')
>>>>
>>>> rhodium.set_calculator(calc)
>>>>
>>>> parprint('Doing %s xc:' % functional)
>>>> t1 = time.time()
>>>> old = rhodium.get_potential_energy()
>>>> t2 = time.time()
>>>> parprint('Energy = %f' % old)
>>>> diff = (t2 - t1) / 3600.0
>>>> parprint('Time = %f' % diff)
>>>>
>>>> and got:
>>>>
>>>> File
>>>> "/home/vlachos/glenjenness/programs/gpaw/build/lib.linux-x86_64-2.7/gpaw/xc/libxc.py",
>>>> line 62, in initialize
>>>> self.xc = _gpaw.lxcXCFunctional(xc, x, c, nspins)
>>>> TypeError: an integer is required
>>>>
>>>> Adding in some extra print statements to
>>>> xc/libxc.py reveals that the variable x is getting
>>>> returned as None.
>>>>
>>>> Is optB88-vdW still available?
>>>>
>>>> Glen
>>>>
>>>> --
>>>> Dr. Glen Jenness
>>>> Catalysis Center for Energy Innovation (CCEI)
>>>> University of Delaware
>>>>
>>>>
>>>> --
>>>> -------------------------------------------------------------
>>>> Jess Wellendorff
>>>> Postdoctoral Scholar
>>>> SUNCAT Center for Interface Science & Catalysis
>>>> SLAC National Accelerator Laboratory, U.S.A.
>>>> jewe at slac.stanford.edu <mailto:jewe at slac.stanford.edu>
>>>> -------------------------------------------------------------
>>>>
>>>> _______________________________________________
>>>> gpaw-users mailing list
>>>> gpaw-users at listserv.fysik.dtu.dk
>>>> <mailto:gpaw-users at listserv.fysik.dtu.dk>
>>>> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Dr. Glen Jenness
>>>> Catalysis Center for Energy Innovation (CCEI)
>>>> University of Delaware
>>>
>>> --
>>> -------------------------------------------------------------
>>> Jess Wellendorff
>>> Postdoctoral Scholar
>>> SUNCAT Center for Interface Science & Catalysis
>>> SLAC National Accelerator Laboratory, U.S.A.
>>> jewe at slac.stanford.edu <mailto:jewe at slac.stanford.edu>
>>> -------------------------------------------------------------
>>>
>>>
>>>
>>>
>>> --
>>> Dr. Glen Jenness
>>> Catalysis Center for Energy Innovation (CCEI)
>>> University of Delaware
>>
>> --
>> -------------------------------------------------------------
>> Jess Wellendorff
>> Postdoctoral Scholar
>> SUNCAT Center for Interface Science & Catalysis
>> SLAC National Accelerator Laboratory, U.S.A.
>> jewe at slac.stanford.edu <mailto:jewe at slac.stanford.edu>
>> -------------------------------------------------------------
>
> --
> -------------------------------------------------------------
> Jess Wellendorff
> Postdoctoral Scholar
> SUNCAT Center for Interface Science & Catalysis
> SLAC National Accelerator Laboratory, U.S.A.
> jewe at slac.stanford.edu <mailto:jewe at slac.stanford.edu>
> -------------------------------------------------------------
>
>
>
>
> --
> Dr. Glen Jenness
> Catalysis Center for Energy Innovation (CCEI)
> University of Delaware
--
-------------------------------------------------------------
Jess Wellendorff
Postdoctoral Scholar
SUNCAT Center for Interface Science & Catalysis
SLAC National Accelerator Laboratory, U.S.A.
jewe at slac.stanford.edu
-------------------------------------------------------------
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