Python interface to the Fortran DACAPO code
Initialize the Jacapo calculator
__init__(self, nc='out.nc', outnc=None, deletenc=False, debug=30, stay_alive=False, **kwargs)
| keyword | type | default value | notes |
|---|---|---|---|
nc | string | 'out.nc' | output netcdf file, or input file if nc already exists |
outnc | string | None | output file. by default equal to nc |
deletenc | Boolean | False | If True, the ncfile is deleted if it exists.1) |
debug | integer | 30 | logging debug level. 2)) |
stay_alive | Boolean | False | |
| kwargs | dictionary | Keyword arguments |
| keyword | type | notes |
|---|---|---|
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 | set the magnetic moment of the unit cell. only used in spin polarize calculations |
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 | parameters to fine-tune behavior | |
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)3) |
Sample of dipole dictionary (Default on True-case):
dipole = {'status':False,
'mixpar':0.2,
'initval':0.0,
'adddipfield':0.0,
'position':None}
read_atoms(filename)
read atoms and calculator from an existing netcdf file.
| keyword | type | notes |
|---|---|---|
| filename | string | name of file to read from. |
atoms = Jacapo.read_atoms(ncfile) calc = atoms.get_calculator()
this method is here for legacy purposes. I used to use it alot.
function read in module ase.calculators.jacapo.jacapo:
read(ncfile)
return atoms and calculator from ncfile
atoms, calc = read('co.nc')
Modification of the nc file only occurs at calculate time if needed
we read everything directly from the ncfile to prevent triggering any calculations
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')