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seminar:jacapo_man

Jacapoマニュアル

Python interface to the Fortran DACAPO code

コンストラクタ

Initialize the Jacapo calculator

__init__(self, nc = 'out.nc', outnc = None, deletenc = False, 
               debug = 30, stay_alive = False, **kwargs)

Parameters

nc string output netcdf file, or input file if nc already exists
outnc string output file. by default equal to nc
deletenc Boolean determines whether the ncfile is deleted on initialization so a fresh run occurs. If True, the ncfile is deleted if it exists.
debug integer logging debug level.1)
stay_alive Boolean
kwargs dictionary various keywords

Valid kwargs

atoms ASE.Atoms instance atoms is an ase.Atoms object that will be attached to this calculator.
pw integer sets planewave cutoff
dw integer sets density cutoff
kpts iterable set chadi-cohen, monkhorst-pack kpt grid, e.g. kpts = (2,2,1) or explicit list of kpts
spinpol Boolean sets whether spin-polarization is used or not.
fixmagmom float
ft float set the Fermi temperature used in occupation smearing
xc string set the exchange-correlation functional. one of ['PZ', 'VWN', 'PW91', PBE', 'RPBE', 'revPBE'],
dipole boolean turn the dipole correction on (True) or off (False)
dictionary of parameters to fine-tune behavior {'status': False, 'mixpar': 0.2, 'initval': 0.0, 'adddipfield': 0.0, 'position': None}
nbands integer set the number of bands
symmetry Boolean Turn symmetry reduction on (True) or off (False)
stress Boolean Turn stress calculation on (True) or off (False)

使用法

Modification of the nc file only occurs at calculate time if needed

calc = Jacapo('CO.nc')

reads the calculator from CO.nc if it exists or minimally initializes CO.nc with dimensions if it does not exist.

calc = Jacapo('CO.nc', pw=300)

reads the calculator from CO.nc or initializes it if it does not exist and changes the planewave cutoff energy to 300eV

atoms = Jacapo.read_atoms('CO.nc')

returns the atoms in the netcdffile CO.nc, with the calculator attached to it.

atoms, calc = read('CO.nc')

クラスメソッド

read_atoms(filename) 既に存在しているnetcdfファイルからAtomsクラスとCalculatorクラスの情報を読み込む

Parameters

filename 文字列 読み込むべきファイル名

example

atoms = Jacapo.read_atoms(ncfile)
calc = atoms.get_calculator()

先輩の作ったncファイルを見つけたら読み込んでみよ。もしかしたら幸せになれるかもしれない。

Functions

read(ncfile) : return atoms and calculator from ncfile

使用例

atoms, calc = read('co.nc')
1)
debug level for logging could be something like logging.DEBUG or an integer 0-50. The higher the integer, the less information you see set debug level (0 = off, 10 = extreme
seminar/jacapo_man.txt · 最終更新: 2019/05/21 19:12 by kimi