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seminar:jacapo_man

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seminar:jacapo_man [2019/05/21 17:28] – [Parameters] kimiseminar:jacapo_man [2022/08/23 13:34] (現在) – 外部編集 127.0.0.1
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 ====== Jacapoマニュアル ====== ====== Jacapoマニュアル ======
 Python interface to the Fortran DACAPO code Python interface to the Fortran DACAPO code
 +[[seminar:jacapo_manj|日本語旧版]]
 ===== コンストラクタ ===== ===== コンストラクタ =====
 +Initialize the Jacapo calculator
  
 <code python> <code python>
-__init__(self, nc='out.nc', outnc=None, deletenc=False, debug=30, stay_alive=False, **kwargs) +__init__(self, nc = 'out.nc', outnc = None, deletenc = False,  
-Initialize the Jacapo calculator+               debug = 30, stay_alive = False, **kwargs)
 </code> </code>
  
行 11: 行 13:
  
    
-^ nc | string | output netcdf file, or input file if nc already exists |+[[ase:nc|nc]] | string | output netcdf file, or input file if nc already exists |
 | outnc | string | output file. by default equal to nc | | 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. | | deletenc | Boolean | determines whether the ncfile is deleted on initialization so a fresh run occurs. If True, the ncfile is deleted if it exists. |
行 22: 行 24:
 ==== Valid kwargs ==== ==== Valid kwargs ====
    
-| atoms | ASE.Atoms instance | atoms is an ase.Atoms object that will be attached to this calculator.| +| [[ase:atoms|atoms]] | ASE.Atoms instance | atoms is an ase.Atoms object that will be attached to this calculator.| 
-| pw | integer | sets planewave cutoff | +^ [[ase:cutoff |pw]] | integer | sets planewave cutoff | 
-| dw | integer | sets density cutoff | +^ [[[[ase: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 |+^ [[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. | | 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 | fixmagmom | float | set the magnetic moment of the unit cell. only used in spin polarize calculations
-| ft | float | set the Fermi temperature used in occupation smearing | +[[ase:ft|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'],+[[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) | | 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} | | | 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 |+^ [[ase:nbands|nbands]] | integer | set the number of bands |
 | symmetry | Boolean | Turn symmetry reduction on (True) or off (False) | | symmetry | Boolean | Turn symmetry reduction on (True) or off (False) |
 | stress | Boolean | Turn stress calculation 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 ===== ===== クラスメソッド =====
  
seminar/jacapo_man.1558427331.txt.gz · 最終更新: 2022/08/23 13:34 (外部編集)

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