文書の過去の版を表示しています。

Jacapo

– Dacapoに対するASEのpythonインターフェイス – このページは本家サイトの日本語訳である。

Introduction

JacapoはDacapoのためのASEのインターフェイスで、ASE¹⁾と完全な互換性がある。JacapoはNumeric pythonとASE第2版を用いていた古いDacapoインターフェイスを置き換えるものである。プログラムは元々John Kitchinによって開発され、詳細な説明書が多くの例題とともにネットに公開されていた。²⁾

¹⁾

訳注：第３版

²⁾

訳注：このURLは現在存在しない）) JacapoはASEのオプション的な計算エンジンといった位置付けであり、前述の説明書とは若干の差異が生じており、説明書ももうメンテナンスをされていない。 ===== Jacapo calculator ===== The Jacapo interface is automatically installed with ase and can be imported using: from ase.calculators.jacapo import Jacapo (You will need to have a working installation of Dacapo, however.) class ase.calculators.jacapo.Jacapo Here is a list of available keywords to initialize the calculator:

keyword	type	description
nc	str	Output NetCDF file, or input file if nc already exists.
outnc	str	Output file. By default equal to nc.
atoms	object	Atoms object
pw	float	Planewave cutoff in eV
dw	float	Density cutoff in eV
xc	str	Exchange-correlation functional. One of [‘PZ’,’VWN’,’PW91’,’PBE’,’RPBE’,’revPBE’]
nbands	int	Number of bands
ft	float	Fermi temperature
kpts	list	K-point grid, e.g. kpts = (2,2,1)
spinpol	boolean	Turn on/off spin-polarization
fixmagmom	str	Magnetic moment of the unit cell
symmetry	boolean	Turn on/off symmetry reduction
stress	boolean	Turn on/off stress calculation
dipole	boolean	Turn on/off dipole correction
ados	dict	Atom-projected density of states
stay_alive	boolean	Turn on/off stay alive
debug	int	Set debug level (0=off, 10=extreme)
deletenc	boolean	If the nc file exists, delete it (to ensure a fresh run). Default is False.

===== Example ===== Here is an example of how to calculate the total energy of a H atom. Warning This is an example only - the parameters are not physically meaningful!

from ase import Atoms, Atom
from ase.io import write
from ase.calculators.jacapo import Jacapo
 
atoms = Atoms([Atom('H',[0,0,0])],
              cell=(2,2,2),
              pbc=True)
 
calc = Jacapo('Jacapo-test.nc',
              pw=200,
              nbands=2,
              kpts=(1,1,1),
              spinpol=False,
              dipole=False,
              symmetry=False,
              ft=0.01)
 
atoms.set_calculator(calc)
 
print(atoms.get_potential_energy())
write('Jacapo-test.traj', atoms)

Note that all calculator parameters should be set in the calculator definition itself. Do not attempt to use the calc.set_* commands as they are intended to be internal to the calculator. Note also that Dacapo can only operate with periodic boundary conditions, so be sure that pbc is set to True. ===== Restarting from an old calculation ===== If the file you specify to Jacapo with the nc keyword exists, Jacapo will assume you are attempting to restart an existing calculation. If you do not want this behavior, turn the flag deletenc to True in your calculator definition. For example, it is possible to continue a geometry optimization with something like this:

calc = Jacapo('old.nc', stay_alive=True)
atoms = calc.get_atoms()
dyn = QuasiNewton(atoms, logfile='qn.log')
dyn.run(fmax=0.05)

Note, that the stay_alive flag is not stored in the .nc file and must be set when the calculator instance is created. ===== Atom-projected density of states ===== To find the atom-projected density of states with Jacapo, first specify the ados dictionary in your calculator definition, as in:

calc = Jacapo( ... ,
              ados={'energywindow': (-10., 5.),
                    'energywidth': 0.2,
                    'npoints': 250,
                    'cutoff': 1.0})

After this is established, you can use the get_ados command to get the desired ADOS data. For example:

energies, dos = calc.get_ados(atoms=[0],
                              orbitals=['d'],
                              cutoff='short',
                              spin=[0])