====== Jacapoマニュアル ======
Python interface to the Fortran DACAPO code
[[seminar:jacapo_manj|日本語旧版]]
===== コンストラクタ =====
Initialize the Jacapo calculator

<code python>
__init__(self, nc = 'out.nc', outnc = None, deletenc = False, 
               debug = 30, stay_alive = False, **kwargs)
</code>

==== Parameters ====

 
^ [[ase:nc|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.((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))|
| stay_alive | Boolean |  |
^ kwargs | dictionary | various keywords |



==== Valid kwargs ====
 
| [[ase:atoms|atoms]] | ASE.Atoms instance | atoms is an ase.Atoms object that will be attached to this calculator.|
^ [[ase:cutoff |pw]] | integer | sets planewave cutoff |
^ [[[[ase:cutoff |dw]] | integer | sets density cutoff |
^ [[ase:kpts|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 | set the magnetic moment of the unit cell. only used in spin polarize calculations
| [[ase:ft|ft]] | float | set the Fermi temperature used in occupation smearing |
| [[ase:xc|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} |
^ [[ase:nbands|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
 
<code python>
calc = Jacapo('CO.nc')
</code> 
reads the calculator from CO.nc if it exists or
minimally initializes CO.nc with dimensions if it does not exist.
 
<code python>
calc = Jacapo('CO.nc', pw=300)
</code>
 
reads the calculator from CO.nc or initializes it if
it does not exist and changes the planewave cutoff energy to
300eV

<code python>
atoms = Jacapo.read_atoms('CO.nc')
</code>
 
returns the atoms in the netcdffile CO.nc, with the calculator
attached to it.
 
<code python>
atoms, calc = read('CO.nc')
</code>
===== 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 ====
<code python>
atoms = Jacapo.read_atoms(ncfile)
calc = atoms.get_calculator()
</code>
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 ====

<code python>
atoms, calc = read('co.nc')
</code>