def __init__(self, mode, *args, **kwargs):
super(SlicedDatabaseWindow, self).__init__(*args, **kwargs)
self.setupUi(self)
self._setup_tree()
self._connect()
# Setup database
path = __directory__ / config.get_key('paths', 'database')
self.database = Database(str(path))
# Open Options Window
if mode == 'binding-energy':
self.options = SlicedDataBaseOptions()
elif mode == 'photon-energy':
self.options = SlicedDataBaseOptions2()
elif mode == 'cubefile':
self.options = SlicedCubefileOptions()
# URLs (with extra information if available) chosen
self.URLs = []
self.fill_tree()
self.show()
self.options.show()
def __init__(self, *args, **kwargs):
super(OrbitalDatabase, self).__init__(*args, **kwargs)
self.setupUi(self)
self._setup_tree()
self._connect()
# Setup database
path = __directory__ / config.get_key('paths', 'database')
self.database = Database(path)
# URLs (with extra information if available) chosen
self.URLs = []
self.fill_tree()
self.show()
# kMap.py Imports
from kmap.library.database import Database
from kmap.library.orbital import Orbital
from kmap.library.misc import energy_to_k
from kmap.library.orbital2povray import Orbital2Povray
# here are other possible choices
#E_kin = 30; ID = 406; orbital_name = 'H**O'; # bisanthene (gas phase geometry) PBE-GGA,
#E_kin = 30; ID = 406; orbital_name = 'LUMO'; # bisanthene (gas phase geometry) PBE-GGA,
#E_kin = 60; ID = 406; orbital_name = 'H**O-8';# bisanthene (gas phase geometry) PBE-GGA,
#E_kin = 60; ID = 406; orbital_name = 'H**O-9';# bisanthene (gas phase geometry) PBE-GGA,
#E_kin = 30; ID = 406; orbital_name = 'H**O-5';# bisanthene (gas phase geometry) PBE-GGA,
# define paths and select orbital ID
db = Database('../../kmap/resources/misc/molecules.txt') # define path to molecules.txt file
# add more elements in povray-image
FT_stuff = '''
// x-axis
#declare l = 5;
union{
cylinder { <0,0,0>,<l,0,0>,0.075 }
cone { <l,0,0>, 0.15, <l+0.5,0,0>,0.0 }
pigment { rgb<0,0,0>}
}
// y-axis
#declare l = 7.5;
union{
cylinder { <0,0,0>,<0,-l,0>,0.075 }
cone { <0,-l,0>, 0.15, <0,-l-0.5,0>,0.0 }
# Python Imports
from pathlib import Path
# Third Party Imports
import matplotlib.pyplot as plt
# kMap.py Imports
from kmap.library.database import Database
from kmap.library.sliceddata import SlicedData
# Path to data folder; replace with your own; use '/' instead of '+'
# when concatenating with strings
data_path = Path(__file__).parent / Path('../../kmap/resources/misc')
db = Database(data_path / 'molecules.txt')
molecule = db.get_molecule_by_ID(
11) # choose pentacene molecule for testing ...
# set name and select list of orbitals
name = 'pentacene' # set name for SlicedData Object
orbitals = []
for orbital in molecule.orbitals[7:-4]:
orbitals.append(
[orbital.URL, {
'energy': orbital.energy,
'name': orbital.name
}])
# set parameters
parameters = [
# Third Party Imports
# kMap.py Imports
from kmap.library.database import Database
from kmap.library.orbital2povray import Orbital2Povray
# set path to molecules.txt file containing the summary of the OrganicMoelculeDatabase at http://143.50.77.12:5000/
molecules_path = '../../kmap/resources/misc/molecules.txt'
# set path to povray settings file
settings = Path('settings_povray.ini')
ID = 406 # choose molecule ID from database
########################################################
db = Database(molecules_path)
molecule = db.get_molecule_by_ID(ID)
chosen_orbitals = ['H**O', 'LUMO'
] # give list of orbitals or set choose_orbitals = 'all'
for orbital in molecule.orbitals:
name = orbital.name.split()[-1]
if type(chosen_orbitals) == str or name in chosen_orbitals:
with urllib.request.urlopen(orbital.URL) as f:
file = f.read().decode('utf-8') # read cube from online-database
povray = Orbital2Povray.init_from_cube(
file, domain='real',
settingsfile=settings) # convert to povray
povray.write_povfile('%04i_%s.pov' %
(ID, name)) # write povray-file
povray.run_povray(executable='povray +W1600 +H1200')
# Python Imports
from pathlib import Path
# Third Party Imports
import matplotlib.pyplot as plt
# kMap.py Imports
from kmap.library.database import Database
from kmap.library.sliceddata import SlicedData
# Path to data folder; replace with your own; use '/' instead of '+'
# when concatenating with strings
data_path = Path(__file__).parent / Path('../../kmap/resources/misc')
db = Database(data_path / 'molecules.txt')
molecule = db.get_molecule_by_ID(
406) # choose ID from database (406 = bisanthene, PBE-functional)
# set name and select list of orbitals
name = 'bisanthene' # set name for SlicedData Object
hdf5_name = 'bisanthene_ID406.hdf5' # choose name fpr hdf5-file to be written
energy_range = [-13, -2] # select a binding energy range
pi = ['au', 'b2g', 'b3g', 'b1u']
sigma = ['ag', 'b1g', 'b2u', 'b3u']
selected_symmetry = pi + sigma # choose between pi or sigma orbitals
orbitals = []
for orbital in molecule.orbitals:
if (energy_range[0] <= orbital.energy <= energy_range[1]) and \
orbital.symmetry in selected_symmetry: