def get_HW14_water_kwargs():
"""Return kwargs for initializing a SolvationGPAW instance.
Parameters for water as a solvent as in
A. Held and M. Walter, J. Chem. Phys. 141, 174108 (2014).
"""
from ase.units import Pascal, m
from ase.data.vdw import vdw_radii
u0 = 0.180
epsinf = 78.36
st = 18.4 * 1e-3 * Pascal * m
T = 298.15
vdw_radii = vdw_radii.copy()
vdw_radii[1] = 1.09
atomic_radii = lambda atoms: [vdw_radii[n] for n in atoms.numbers]
kwargs = {
'cavity':
EffectivePotentialCavity(effective_potential=Power12Potential(
atomic_radii, u0),
temperature=T,
surface_calculator=GradientSurface()),
'dielectric':
LinearDielectric(epsinf=epsinf),
'interactions': [SurfaceInteraction(surface_tension=st)]
}
return kwargs
now = datetime.datetime
timestamp = now.now().strftime('%Y%-m%-d%-I%-M%-S')
pydir = os.path.dirname(os.path.abspath(__file__))
pj = os.path.join
shell = ase.io.read(pj(pydir, "xyz/{}4x.xyz".format(sv)))
solvent = ase.io.read(pj(pydir, "xyz/{}.xyz".format(sv)))
solventparams = pickle.load(open(pj(pydir, "parameters.pkl"), "r"))
#Solvent parameters for DMSO (J. Chem. Phys. 141, 174108 (2014))
params = solventparams[sv]
name, nd, u0, gamma, epsinf = params['name'], params['number density'], params[
'u0 (eV)'], params['gamma (dyne/cm)'], params['dielectric constant']
gamma = gamma * Pascal * m
T = 298.15 #Kelvin
vdw_radii = vdw_radii.copy()
vdw_radii[1] = 1.09
atomic_radii = lambda atoms: [vdw_radii[n] for n in atoms.numbers
] #create callable for GPAW calculator
#DFT calculation parameters
xc = 'PBE'
beef = 'BEEF-vdW'
cell = vac * np.array([1, 1, 1])
parprint('completed')
#Each calculation will be converged with PBE, then, using same calculator, be run with BEEF.
#This enables the PBE WFs to be used as initial guesses for BEEF convergence, hopefully enabling large box sizes.
#Data is stored in a dictionary with key: input sys.argv string "s" indicating ion-species. value : tuple of one value and one array,
#indicating Gsol and dGsol.
output = {}
import time
import numpy as np
from os.path import join, abspath
from ase.data.colors import cpk_colors, jmol_colors
from ase.data.vdw import vdw_radii
from CalcTrollASE.AtomUtilities import cellCenter
my_radii = vdw_radii.copy()
my_radii[74] = 2.50
VALENCE_DICT = {'H': 1, 'Si': 4, 'C':4, 'B':3, 'Ge':4, 'Ag': 11, 'O':6}
DEFAULT_FONTSIZE = 10
def chargeDifferenceScheme(
figure,
atoms,
charges,
max_charge_difference=None,
scale_factor=1,
):
charges = -np.array(charges)
max_charge = charges.max()
colors = np.ones((len(atoms), 3))
if max_charge_difference is None:
maxi = abs(charges).max()
else:
maxi = max_charge_difference
charges = charges.clip(-maxi, maxi)