def allocate(self):
NeedsGD.allocate(self)
self.eps_gradeps = []
eps_g = self.gd.empty()
eps_g.fill(1.0)
self.eps_gradeps.append(eps_g)
self.eps_gradeps.extend([gd.zeros() for gd in (self.gd, ) * 3])
self.del_eps_del_g_g = self.gd.empty()
def allocate(self):
NeedsGD.allocate(self)
self.g_g = self.gd.empty()
self.grad_g_vg = self.gd.empty(3)
if self.depends_on_el_density:
self.del_g_del_n_g = self.gd.empty()
if self.surface_calculator is not None:
self.surface_calculator.allocate()
if self.volume_calculator is not None:
self.volume_calculator.allocate()
def __init__(self, epsinf):
"""Constructor for the Dielectric class.
Arguments:
epsinf -- Static dielectric constant
at infinite distance from the solute.
"""
NeedsGD.__init__(self)
self.epsinf = float(epsinf)
self.eps_gradeps = None # eps_g, dxeps_g, dyeps_g, dzeps_g
self.del_eps_del_g_g = None
def __init__(self, surface_calculator=None, volume_calculator=None):
"""Constructor for the Cavity class.
Arguments:
surface_calculator -- A SurfaceCalculator instance or None
volume_calculator -- A VolumeCalculator instance or None
"""
NeedsGD.__init__(self)
self.g_g = None
self.del_g_del_n_g = None
self.grad_g_vg = None
self.surface_calculator = surface_calculator
self.volume_calculator = volume_calculator
self.V = None # global Volume
self.A = None # global Surface
def allocate(self):
NeedsGD.allocate(self)
self.delta_E_delta_g_g = self.gd.empty()
if self.depends_on_el_density:
self.delta_E_delta_n_g = self.gd.empty()
def __init__(self):
NeedsGD.__init__(self)
self.E = None
self.delta_E_delta_n_g = None
self.delta_E_delta_g_g = None
def allocate(self):
NeedsGD.allocate(self)
self.delta_V_delta_g_g = self.gd.empty()
def __init__(self):
NeedsGD.__init__(self)
self.V = None
self.delta_V_delta_g_g = None
def __init__(self):
NeedsGD.__init__(self)
self.A = None
self.delta_A_delta_g_g = None
def allocate(self):
NeedsGD.allocate(self)
self.rho_g = self.gd.empty()
if self.depends_on_el_density:
self.del_rho_del_n_g = self.gd.empty()
self.grad_rho_vg = self.gd.empty(3)
def __init__(self):
NeedsGD.__init__(self)
self.rho_g = None
self.del_rho_del_n_g = None
self.grad_rho_vg = None
def __init__(self):
NeedsGD.__init__(self)
self.u_g = None
self.del_u_del_n_g = None
self.grad_u_vg = None
def set_grid_descriptor(self, gd):
NeedsGD.set_grid_descriptor(self, gd)
if self.surface_calculator is not None:
self.surface_calculator.set_grid_descriptor(gd)
if self.volume_calculator is not None:
self.volume_calculator.set_grid_descriptor(gd)