Source code for gpaw.solvation.calculator

from ase.units import Bohr, Hartree

from gpaw.calculator import GPAW
from gpaw.io import Reader
from gpaw.solvation.hamiltonian import SolvationRealSpaceHamiltonian


[docs]class SolvationGPAW(GPAW): """Subclass of gpaw.GPAW calculator with continuum solvent model. See also Section III of A. Held and M. Walter, J. Chem. Phys. 141, 174108 (2014). """ def __init__(self, restart=None, cavity=None, dielectric=None, interactions=None, **gpaw_kwargs): """Constructor for SolvationGPAW class. Additional arguments not present in GPAW class: cavity -- A Cavity instance. dielectric -- A Dielectric instance. interactions -- A list of Interaction instances. """ if interactions is None: interactions = [] # if not all([cavity, dielectric]): # raise IOError('Cavity and dielectric modules need to be ' # 'defined in the calculator') self.stuff_for_hamiltonian = (cavity, dielectric, interactions) GPAW.__init__(self, restart, **gpaw_kwargs) def read(self, filename): """Read yourself from a file""" self.reader = reader = Reader(filename) if 'implicit_solvent' in reader: impl_in = reader.implicit_solvent if 'name' in impl_in.cavity.effective_potential: efpot = impl_in.cavity.effective_potential def atomic_radii(atoms): return efpot.atomic_radii if efpot.name == 'SJMPower12Potential': from gpaw.solvation.sjm import SJMPower12Potential effective_potential = SJMPower12Potential( atomic_radii=atomic_radii, u0=efpot.u0, H2O_layer=efpot.H2O_layer, unsolv_backside=efpot.unsolv_backside) elif efpot.name == 'Power12Potential': from gpaw.solvation.sjm import Power12Potential effective_potential = Power12Potential( atomic_radii=atomic_radii, u0=efpot.u0) else: raise IOError('Reading the given effective potential ' 'is not implemented yet') if 'name' in impl_in.cavity.surface_calculator: suca = impl_in.cavity.surface_calculator if suca.name == 'GradientSurface': from gpaw.solvation.cavity import GradientSurface surface_calculator = GradientSurface(suca.nn) else: raise IOError('Reading in the given used surface ' 'calculator is not implemented') T = impl_in.cavity.temperature from gpaw.solvation.cavity import EffectivePotentialCavity cavity = EffectivePotentialCavity( effective_potential=effective_potential, temperature=T, surface_calculator=surface_calculator) if impl_in.dielectric.name == 'LinearDielectric': from gpaw.solvation.dielectric import LinearDielectric dielectric = LinearDielectric(epsinf=impl_in.dielectric.epsinf) if impl_in.interactions.name == 'SurfaceInteraction': suin = impl_in.interactions from gpaw.solvation.interactions import SurfaceInteraction interactions = [SurfaceInteraction(suin.surface_tension)] self.stuff_for_hamiltonian = (cavity, dielectric, interactions) reader = GPAW.read(self, filename) return reader def _write(self, writer, mode): GPAW._write(self, writer, mode) stuff = self.stuff_for_hamiltonian writer.child('implicit_solvent').write(cavity=stuff[0], dielectric=stuff[1], interactions=stuff[2][0]) def create_hamiltonian(self, realspace, mode, xc): if not realspace: raise NotImplementedError( 'SolvationGPAW does not support ' 'calculations in reciprocal space yet.') dens = self.density self.hamiltonian = SolvationRealSpaceHamiltonian( *self.stuff_for_hamiltonian, gd=dens.gd, finegd=dens.finegd, nspins=dens.nspins, collinear=dens.collinear, setups=dens.setups, timer=self.timer, xc=xc, world=self.world, redistributor=dens.redistributor, vext=self.parameters.external, psolver=self.parameters.poissonsolver, stencil=mode.interpolation) self.log(self.hamiltonian) xc.set_grid_descriptor(self.hamiltonian.finegd) def initialize_positions(self, atoms=None): spos_ac = GPAW.initialize_positions(self, atoms) self.hamiltonian.update_atoms(self.atoms, self.log) return spos_ac def get_electrostatic_energy(self): """Return electrostatic part of the total energy. The electrostatic part consists of everything except the short-range interactions defined in the interactions list. """ # Energy extrapolated to zero width: return Hartree * self.hamiltonian.e_el_extrapolated def get_solvation_interaction_energy(self, subscript, atoms=None): """Return a specific part of the solvation interaction energy. The subscript parameter defines which part is to be returned. It has to match the value of a subscript attribute of one of the interactions in the interactions list. """ return Hartree * getattr(self.hamiltonian, 'e_' + subscript) def get_cavity_volume(self, atoms=None): """Return the cavity volume in Angstrom ** 3. In case no volume calculator has been set for the cavity, None is returned. """ V = self.hamiltonian.cavity.V return V and V * Bohr ** 3 def get_cavity_surface(self, atoms=None): """Return the cavity surface area in Angstrom ** 2. In case no surface calculator has been set for the cavity, None is returned. """ A = self.hamiltonian.cavity.A return A and A * Bohr ** 2