[ase-users] dftb+

[ricardo santos]

Thanks for the tip !

I used the MaxwellBoltzmannDistribution
and this part seems to be ok now.

Now the error has changed, and the code bellow
--------------------------------------------------------------------------------------
import os
from ase.io.dftb import read_dftb
from ase import Atoms
from ase.calculators.dftb import Dftb
from ase.optimize import QuasiNewton
from ase.io import read
from ase.io import write
from ase.md.verlet import VelocityVerlet
from ase import units
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution

atomos = read('H.xyz',index=0)
calc =
Dftb(label='dftb',write_dftb=True,include_dispersion=True,md_dftb=True\
       ,dftb_nsteps=3,md_restart_frequency=1,md_dftb_berendsen_nvt=True )
atomos.set_calculator(calc)
MaxwellBoltzmannDistribution(atomos,300*units.kB)
dyn = VelocityVerlet(atomos,dt=1.0*units.fs)
dyn.run(steps=10)
write('test.final.xyz', atomos)
---------------------------------------------------------------------------------------

Gives me, after some information about the velocities, the following error:

Traceback (most recent call last):
  File "gas_ase.py", line 27, in <module>
    dyn.run(steps=10)
  File "/usr/lib/python2.7/dist-packages/ase/md/md.py", line 29, in run
    f = self.atoms.get_forces()
  File "/usr/lib/python2.7/dist-packages/ase/atoms.py", line 590, in
get_forces
    forces = self._calc.get_forces(self)
  File "/usr/lib/python2.7/dist-packages/ase/calculators/dftb.py", line
237, in get_forces
    return self.forces.copy()
AttributeError: Dftb instance has no attribute 'forces'

What should be done now ?

Thanks again.



On Fri, Mar 7, 2014 at 2:21 PM, Glen Jenness <glenjenness at gmail.com> wrote:

> Have you tried initializing your velocities?
>
> i.e.
>
> velocities = ....
> atomos.set_velocities(velocities)
>
>
> On Fri, Mar 7, 2014 at 2:01 PM, ricardo santos <ricardopaupitz at gmail.com>wrote:
>
>> Hi,
>>
>> I am really new to ASE and would like to use it to make some simulations
>> using dftb+.
>> I tried to run a first simple code which is the following:
>>
>> -----------------------------------------------------
>> import os
>> from ase.io.dftb import read_dftb
>> from ase import Atoms
>> from ase.calculators.dftb import Dftb
>> from ase.optimize import QuasiNewton
>> from ase.io import read
>> from ase.io import write
>> from ase.md.verlet import VelocityVerlet
>> from ase import units
>>
>>
>> atomos = read('H.xyz',index=0)
>> calc =
>> Dftb(label='dftb',write_dftb=True,include_dispersion=True,md_dftb=True\
>>        ,dftb_nsteps=3,md_restart_frequency=1,md_dftb_berendsen_nvt=True )
>> atomos.set_calculator(calc)
>> dyn = VelocityVerlet(atomos,dt=1.0*units.fs)
>> dyn.run(steps=10)
>> write('test.final.xyz', atomos)
>> -----------------------------------------------------
>>
>> but got the error message:
>>
>> Traceback (most recent call last):
>>   File "gas_ase.py", line 22, in <module>
>>     dyn.run(steps=10)
>>   File "/usr/lib/python2.7/dist-packages/ase/md/md.py", line 29, in run
>>     f = self.atoms.get_forces()
>>   File "/usr/lib/python2.7/dist-packages/ase/atoms.py", line 590, in
>> get_forces
>>     forces = self._calc.get_forces(self)
>>   File "/usr/lib/python2.7/dist-packages/ase/calculators/dftb.py", line
>> 236, in get_forces
>>     self.update(atoms)
>>   File "/usr/lib/python2.7/dist-packages/ase/calculators/dftb.py", line
>> 188, in update
>>     self.initialize(atoms)
>>   File "/usr/lib/python2.7/dist-packages/ase/calculators/dftb.py", line
>> 228, in initialize
>>     self.write_dftb_input_file(atoms)
>>   File "/usr/lib/python2.7/dist-packages/ase/calculators/dftb.py", line
>> 442, in write_dftb_input_file
>>     tmpvelocities = atoms.get_velocities().copy()
>> AttributeError: 'NoneType' object has no attribute 'copy'
>>
>>
>> Could someone help me to figure out what is the problem ?
>>
>> Thank you in advance.
>>
>>
>> --
>> ==================================================
>> Ricardo Paupitz B. dos Santos
>> Assistant Professor
>> *http://scholar.google.com/citations?user=BZBtHU4AAAAJ
>> <http://scholar.google.com/citations?user=BZBtHU4AAAAJ>*
>> CV: *http://lattes.cnpq.br/5313696806283523
>> <http://lattes.cnpq.br/5313696806283523>*
>>
>> *Universidade Estadual Paulista - UNESP     *
>> IGCE - Instituto de Geociências e Ciências Exatas
>> Departamento de Física - Room 45
>> Av. 24-A n. 1515 Bela Vista
>> CEP 13506-900
>> Rio Claro (SP), Brasil
>> Phone: +55-19-3526 9156
>>  ==================================================
>>
>> _______________________________________________
>> ase-users mailing list
>> ase-users at listserv.fysik.dtu.dk
>> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>>
>
>
>
> --
> Dr. Glen Jenness
> Catalysis Center for Energy Innovation (CCEI)
> University of Delaware
>



-- 
==================================================
Ricardo Paupitz B. dos Santos
Assistant Professor
*http://scholar.google.com/citations?user=BZBtHU4AAAAJ
<http://scholar.google.com/citations?user=BZBtHU4AAAAJ>*
CV: *http://lattes.cnpq.br/5313696806283523
<http://lattes.cnpq.br/5313696806283523>*

*Universidade Estadual Paulista - UNESP     *
IGCE - Instituto de Geociências e Ciências Exatas
Departamento de Física - Room 45
Av. 24-A n. 1515 Bela Vista
CEP 13506-900
Rio Claro (SP), Brasil
Phone: +55-19-3526 9156
==================================================
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