[ase-users] Unable to read the created .nc file

[Marcin Dulak]

Hi,

the jacapo handling of restart has been fixed in the development version 
of ase: https://wiki.fysik.dtu.dk/ase/download.html#id8
Please use the ase trunk.

Best regards,

Marcin

c cook wrote:
> Hello again,
>
> I started to do some simple testing:
>
> http://beowulf.cheme.cmu.edu/jacapo/2-bulk/2.2-unitcell-optimization/2.2.0-unit-cell-optimization.html#simple-total-energy-calculation
>
>
> the first step to calculate the energy seen below worked 
> #!/usr/bin/env python
> from ase import *
> from ase.calculators.jacapo import *
>
>
> a = 3.8  # approximate lattice constant
> b = a / 2.
> bulk = Atoms([Atom('Al',(0.0,0.0,0.0))], 
>              cell=[(0,b,b),
>                    (b,0,b),
>                    (b,b,0)])
>
> calc = Jacapo('2.2.1-Al.nc <http://2.2.1-Al.nc>',
>               pw=350,
>               kpts=(4,4,4),
>               calculate_stress=True,
>               atoms=bulk)
>
> print bulk.get_stress()
> the 2.2.1-Al.nc <http://2.2.1-Al.nc> and the corresponding .txt  file 
> were created,
>
> but when I went further to:
>
> #!/usr/bin/env python
> from ase.calculators.jacapo import *
>
> bulk = Jacapo.read_atoms('2.2.1-Al.nc <http://2.2.1-Al.nc>')
>
> print  'energy: ' ,bulk.get_potential_energy()
>
>
> sxx, syy, szz, syz, sxz, sxy = bulk.get_stress()
>
> import numpy as np
> from ase.units import GPa
> print 'Stress (GPa) = '
> print np.array([[sxx, sxy, sxz],
>                 [sxy, syy, syz],
>                 [sxz, syz, szz]])/GPa
> I' ve got the following error:
>
> File "./bulkAl2.sh", line 4, in <module>
>     bulk = Jacapo.read_atoms('2.2.1-Al.nc <http://2.2.1-Al.nc>')
>   File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 3059, 
> in read_atoms
>     calc = Jacapo(filename)
>   File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 231, 
> in __init__
>     self.set_nc(nc)
>   File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 1135, 
> in set_nc
>     self.update_input_parameters()
>   File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 383, 
> in update_input_parameters
>     self.pars[key] = eval(getf)
>   File "<string>", line 1, in <module>
>   File "/home/csaba/ase/ase/calculators/jacapo/jacapo.py", line 2257, 
> in get_psp
>     raise Exception, 'You can only specify Z or sym!'
> Exception: You can only specify Z or sym!
>
>
> I've checked in the jacapo.py and the only reference to the error is this:
>
> *def set_psp(self,*
> *                sym=None,*
> *                z=None,*
> *                psp=None):*
> *        '''*
> *        set the pseudopotential file for a species or an atomic number.*
> *
> *
> *        :Parameters:*
> *
> *
> *         sym : string*
> *           chemical symbol of the species*
> *
> *
> *          z : integer*
> *            the atomic number of the species*
> *
> *
> *          psp : string*
> *            filename of the pseudopotential*
> *
> *
> *        *
> *        you can only set sym or z.*
> *
> *
> *        examples::*
> *        *
> *          set_psp('N',psp='pspfile')*
> *          set_psp(z=6,psp='pspfile')*
> *        '''*
> *        log.debug(str([sym, z, psp]))*
> *        if (sym, z, psp) == (None, None, None):*
> *            return*
> *        *
> *        if (sym is None and z is not None):*
> *            from ase.data import chemical_symbols*
> *            sym = chemical_symbols[z]*
> *        elif (sym is not None and z is None):*
> *            pass*
> *        else:*
> *            raise Exception, 'You can only specify Z or sym!'*
>
>
> But, I am stuck here. The DACAPOPATH is correctly pointing to the psp 
> directory, and anyways, why it didn't complain when he did the energy 
> calculation?
>
> And this is happening every time there is a need to read an already 
> created .nc file (I 've tried couple of more examples and I got the 
> same error)
>
> What am I doing wrong?
>
> Thanks,
> Csaba 
>
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>
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-- 
***********************************
 
Marcin Dulak
Technical University of Denmark
Department of Physics
Building 307, Room 229
DK-2800 Kongens Lyngby
Denmark
Tel.: (+45) 4525 3157
Fax.: (+45) 4593 2399
email: Marcin.Dulak at fysik.dtu.dk

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