def setup_coulomb_potential(self):
"""Setups a Coulomb potential between the subsystems.
Ewald calculation is automatically used for pbc-systems. Non-pbc
systems use the ProductPotential to reproduce the Coulomb potential.
"""
parameters = self.info.electrostatic_parameters
# Check that that should Ewald summation be used and if so, that all the
# needed parameters are given
if self.has_pbc:
needed = ["k_cutoff", "real_cutoff", "sigma"]
for param in needed:
if param not in parameters:
error(
param
+ " not specified in Interaction.enable_coulomb_potential(). It is needed in order to calculate electrostatic interaction energy with Ewald summation in systems with periodic boundary conditions."
)
return
ewald = CoulombSummation()
ewald.set_parameter_value("epsilon", parameters["epsilon"])
ewald.set_parameter_value("k_cutoff", parameters["k_cutoff"])
ewald.set_parameter_value("real_cutoff", parameters["real_cutoff"])
ewald.set_parameter_value("sigma", parameters["sigma"])
self.pbc_calculator.set_coulomb_summation(ewald)
else:
# Add coulomb force between all charged particles in secondary
# system, and all atoms in primary system. It is assumed that the
# combined system will be made so that the primary system comes
# before the secondary in indexing.
coulomb_pairs = []
for i, ai in enumerate(self.primary_subsystem.atoms_for_interaction):
for j, aj in enumerate(self.secondary_subsystem.atoms_for_interaction):
if not np.allclose(aj.charge, 0):
coulomb_pairs.append([i, j + self.n_primary])
# There are no charges in the secondary system, and that can't
# change unlike the charges in primary system
if len(coulomb_pairs) is 0:
warn(
"There cannot be electrostatic interaction between the "
"subsystems, because the secondary system does not have "
"any initial charges",
2,
)
return
# The first potential given to the productpotential defines the
# targets and cutoff
kc = 1.0 / (4.0 * np.pi * parameters["epsilon"])
max_cutoff = np.linalg.norm(np.array(self.primary_subsystem.atoms_for_interaction.get_cell()))
coul1 = Potential("power", indices=coulomb_pairs, parameters=[1, 1, 1], cutoff=max_cutoff)
coul2 = Potential("charge_pair", parameters=[kc, 1, 1])
coulomb_potential = ProductPotential([coul1, coul2])
self.calculator.add_potential(coulomb_potential)
self.has_coulomb_interaction = True
def setup_hydrogen_links(self, links):
"""Setup the hydrogen link atoms to the primary system.
Parameters:
link_parameters: list of tuples
Contains the link atom parameters from the Interaction-object.
Each tuple in the list is a link atom specification for a
covalent bond of different type. The first item in the tuple is
a list of tuples containing atom index pairs. The second item
in the tuple is the CHL parameter for these links.
"""
self.link_atoms = Atoms(pbc=copy(self.full_system.get_pbc()),
cell=copy(self.full_system.get_cell()))
for bond in links:
pairs = bond[0]
CHL = bond[1]
for link in pairs:
# Extract the position of the boundary atoms
q1_index = link[0]
m1_index = link[1]
iq1 = self.primary_subsystem.index_map.get(q1_index)
im1 = self.secondary_subsystem.index_map.get(m1_index)
if iq1 is None:
error(("Invalid link: "+str(q1_index)+"-"+str(m1_index)+":\n"
"The first index does not point to an atom in the primary system."))
if im1 is None:
error(("Invalid link: "+str(q1_index)+"-"+str(m1_index)+":\n"
"The second index does not point to an atom in the secondary system."))
q1 = self.primary_subsystem.atoms_for_subsystem[iq1]
rq1 = q1.position
# Calculate the separation between the host atoms from the full
# system. We need to do this in the full system because the
# subsystems may not have the same coordinate systems due to cell
# size minimization.
frq1 = self.full_system[q1_index].position
frm1 = self.full_system[m1_index].position
distance = CHL*(frm1 - frq1)
# Calculate position for the hydrogen atom in both the primary
# subsystem and in the system containing only link atoms. The link
# atom system is used when calculating link atom corrections.
r_primary = rq1 + distance
r_link = frq1 + distance
# Create a hydrogen atom in the primary subsystem and in the
# full subsystem
hydrogen_primary = Atom('H', position=r_primary)
hydrogen_link = Atom('H', position=r_link)
self.primary_subsystem.atoms_for_subsystem.append(hydrogen_primary)
self.link_atoms.append(hydrogen_link)
# Update the cell size after adding link atoms
if self.primary_subsystem.cell_size_optimization_enabled:
self.primary_subsystem.optimize_cell()
def setup_coulomb_potential(self):
"""Setups a Coulomb potential between the subsystems.
Ewald calculation is automatically used for pbc-systems. Non-pbc
systems use the ProductPotential to reproduce the Coulomb potential.
"""
parameters = self.info.electrostatic_parameters
# Check that that should Ewald summation be used and if so, that all the
# needed parameters are given
if self.has_pbc:
needed = ["k_cutoff", "real_cutoff", "sigma"]
for param in needed:
if param not in parameters:
error(param + " not specified in Interaction.enable_coulomb_potential(). It is needed in order to calculate electrostatic interaction energy with Ewald summation in systems with periodic boundary conditions.")
return
ewald = CoulombSummation()
ewald.set_parameter_value('epsilon', parameters['epsilon'])
ewald.set_parameter_value('k_cutoff', parameters['k_cutoff'])
ewald.set_parameter_value('real_cutoff', parameters['real_cutoff'])
ewald.set_parameter_value('sigma', parameters['sigma'])
self.pbc_calculator.set_coulomb_summation(ewald)
else:
# Add coulomb force between all charged particles in secondary
# system, and all atoms in primary system. It is assumed that the
# combined system will be made so that the primary system comes
# before the secondary in indexing.
coulomb_pairs = []
for i, ai in enumerate(self.primary_subsystem.atoms_for_interaction):
for j, aj in enumerate(self.secondary_subsystem.atoms_for_interaction):
if not np.allclose(aj.charge, 0):
coulomb_pairs.append([i, j+self.n_primary])
# There are no charges in the secondary system, and that can't
# change unlike the charges in primary system
if len(coulomb_pairs) is 0:
warn("There cannot be electrostatic interaction between the "
"subsystems, because the secondary system does not have "
"any initial charges", 2)
return
# The first potential given to the productpotential defines the
# targets and cutoff
kc = 1.0/(4.0*np.pi*parameters['epsilon'])
max_cutoff = np.linalg.norm(np.array(self.primary_subsystem.atoms_for_interaction.get_cell()))
coul1 = Potential('power', indices=coulomb_pairs, parameters=[1, 1, 1], cutoff=max_cutoff)
coul2 = Potential('charge_pair', parameters=[kc, 1, 1])
coulomb_potential = ProductPotential([coul1, coul2])
self.calculator.add_potential(coulomb_potential)
self.has_coulomb_interaction = True
def setup_hydrogen_links(self, links):
"""Setup the hydrogen link atoms to the primary system.
Parameters:
link_parameters: list of tuples
Contains the link atom parameters from the Interaction-object.
Each tuple in the list is a link atom specification for a
covalent bond of different type. The first item in the tuple is
a list of tuples containing atom index pairs. The second item
in the tuple is the CHL parameter for these links.
"""
self.link_atoms = Atoms(pbc=copy(self.full_system.get_pbc()), cell=copy(self.full_system.get_cell()))
for bond in links:
pairs = bond[0]
CHL = bond[1]
for link in pairs:
# Extract the position of the boundary atoms
q1_index = link[0]
m1_index = link[1]
iq1 = self.primary_subsystem.index_map.get(q1_index)
im1 = self.secondary_subsystem.index_map.get(m1_index)
if iq1 is None:
error(
(
"Invalid link: " + str(q1_index) + "-" + str(m1_index) + ":\n"
"The first index does not point to an atom in the primary system."
)
)
if im1 is None:
error(
(
"Invalid link: " + str(q1_index) + "-" + str(m1_index) + ":\n"
"The second index does not point to an atom in the secondary system."
)
)
q1 = self.primary_subsystem.atoms_for_subsystem[iq1]
rq1 = q1.position
# Calculate the separation between the host atoms from the full
# system. We need to do this in the full system because the
# subsystems may not have the same coordinate systems due to cell
# size minimization.
frq1 = self.full_system[q1_index].position
frm1 = self.full_system[m1_index].position
distance = CHL * (frm1 - frq1)
# Calculate position for the hydrogen atom in both the primary
# subsystem and in the system containing only link atoms. The link
# atom system is used when calculating link atom corrections.
r_primary = rq1 + distance
r_link = frq1 + distance
# Create a hydrogen atom in the primary subsystem and in the
# full subsystem
hydrogen_primary = Atom("H", position=r_primary)
hydrogen_link = Atom("H", position=r_link)
self.primary_subsystem.atoms_for_subsystem.append(hydrogen_primary)
self.link_atoms.append(hydrogen_link)
# Update the cell size after adding link atoms
if self.primary_subsystem.cell_size_optimization_enabled:
self.primary_subsystem.optimize_cell()
