def __init__(
self,
full_system,
primary_subsystem,
secondary_subsystem,
info):
"""
Parameters:
full_system: ASE Atoms
primary_subsystem: :class:`~pysic.subsystem.SubSystem`
secondary_subsystem: :class:`~pysic.subsystem.SubSystem`
info: :class:`~pysic.interaction.Interaction`
"""
self.info = info
self.full_system = full_system
self.primary_subsystem = primary_subsystem
self.secondary_subsystem = secondary_subsystem
self.uncorrected_interaction_energy = None
self.uncorrected_interaction_forces = None
self.link_atom_correction_energy = None
self.link_atom_correction_forces = None
self.interaction_energy = None
self.interaction_forces = None
# Determine if any potentials have been set
self.has_interaction_potentials = False
if self.info.comb_potential_enabled:
self.has_interaction_potentials = True
if self.info.coulomb_potential_enabled:
self.has_interaction_potentials = True
if len(self.info.potentials) != 0:
self.has_interaction_potentials = True
self.calculator = Pysic()
self.pbc_calculator = Pysic()
self.timer = Timer([
"Interaction",
"Interaction (PBC)",
"Forces",
"Forces (PBC)",
"Link atom correction energy",
"Link atom correction forces"])
# The interaction needs to know if PBC:s are on
pbc = primary_subsystem.atoms_for_interaction.get_pbc()
if pbc[0] or pbc[1] or pbc[2]:
self.has_pbc = True
else:
self.has_pbc = False
# Initialize hydrogen links
self.link_atoms = None
self.setup_hydrogen_links(info.links)
# Store the number of atoms in different systems
self.n_primary = len(primary_subsystem.atoms_for_interaction)
self.n_secondary = len(secondary_subsystem.atoms_for_interaction)
self.n_full = self.n_primary + self.n_secondary
if self.link_atoms is not None:
self.n_links = len(self.link_atoms)
else:
self.n_links = 0
# Initialize the COMB potential first (set_potentials(COMB) is used,
# because it isn' the same as add_potential(COMB))
if info.comb_potential_enabled:
self.setup_comb_potential()
# Initialize the coulomb interaction
if info.electrostatic_parameters is not None:
self.setup_coulomb_potential()
# Add the other potentials
self.setup_potentials()
# Can't enable link atom correction on system without link atoms
if len(info.links) == 0:
self.info.link_atom_correction_enabled = False
def __init__(self, full_system, primary_subsystem, secondary_subsystem, info):
"""
Parameters:
full_system: ASE Atoms
primary_subsystem: :class:`~pysic.subsystem.SubSystem`
secondary_subsystem: :class:`~pysic.subsystem.SubSystem`
info: :class:`~pysic.interaction.Interaction`
"""
self.info = info
self.full_system = full_system
self.primary_subsystem = primary_subsystem
self.secondary_subsystem = secondary_subsystem
self.uncorrected_interaction_energy = None
self.uncorrected_interaction_forces = None
self.link_atom_correction_energy = None
self.link_atom_correction_forces = None
self.interaction_energy = None
self.interaction_forces = None
# Determine if any potentials have been set
self.has_interaction_potentials = False
if self.info.comb_potential_enabled:
self.has_interaction_potentials = True
if self.info.coulomb_potential_enabled:
self.has_interaction_potentials = True
if len(self.info.potentials) != 0:
self.has_interaction_potentials = True
self.calculator = Pysic()
self.pbc_calculator = Pysic()
self.timer = Timer(
[
"Interaction",
"Interaction (PBC)",
"Forces",
"Forces (PBC)",
"Link atom correction energy",
"Link atom correction forces",
]
)
# The interaction needs to know if PBC:s are on
pbc = primary_subsystem.atoms_for_interaction.get_pbc()
if pbc[0] or pbc[1] or pbc[2]:
self.has_pbc = True
else:
self.has_pbc = False
# Initialize hydrogen links
self.link_atoms = None
self.setup_hydrogen_links(info.links)
# Store the number of atoms in different systems
self.n_primary = len(primary_subsystem.atoms_for_interaction)
self.n_secondary = len(secondary_subsystem.atoms_for_interaction)
self.n_full = self.n_primary + self.n_secondary
if self.link_atoms is not None:
self.n_links = len(self.link_atoms)
else:
self.n_links = 0
# Initialize the COMB potential first (set_potentials(COMB) is used,
# because it isn' the same as add_potential(COMB))
if info.comb_potential_enabled:
self.setup_comb_potential()
# Initialize the coulomb interaction
if info.electrostatic_parameters is not None:
self.setup_coulomb_potential()
# Add the other potentials
self.setup_potentials()
# Can't enable link atom correction on system without link atoms
if len(info.links) == 0:
self.info.link_atom_correction_enabled = False
class InteractionInternal(object):
"""The internal version of the Interaction-class.
This class is meant only for internal use, and should not be accessed by
the end-user.
Attributes:
info: :class:'~Pysic.interaction.Interaction'
Contains all the info about the interaction given by the user.
full_system: ASE Atoms
-
primary_subsystem: :class:`~pysic.subsystem.SubSystem`
-
secondary_subsystem: :class:`~pysic.subsystem.SubSystem`
-
uncorrected_interaction_energy: float
The interaction energy without the link atom correction.
uncorrected_interaction_forces: numpy array
The interaction forces without the link atom correction.
link_atom_correction_energy: float
-
link_atom_correction_forces: numpy array
-
interaction_energy: float
The total interaction energy = uncorrected_interaction_energy +
link_atom_correction_energy
interaction_forces: numpy array
The total interaction forces = uncorrected_interaction_forces +
link_atom_correction_forces
has_interaction_potentials: bool
True if any potentials are defined.
calculator: :class:'~pysic.calculator.Pysic'
The pysic calculator used for non-pbc systems.
pbc_calculator: :class:'~pysic.calculator.Pysic'
The pysic calculator used for pbc systems.
timer: :class:'~pysic.utility.timer.Timer'
Used for tracking time usage.
has_pbc: bool
-
link_atoms: ASE Atoms
Contains all the hydrogen link atoms. Needed when calculating link
atom correction.
n_primary: int
Number of atoms in primary subsystem.
n_secondary: int
Number of atoms in secondary subsystem.
n_full: int
Number of atoms in full system.
n_links: int
Number of link atoms.
"""
def __init__(
self,
full_system,
primary_subsystem,
secondary_subsystem,
info):
"""
Parameters:
full_system: ASE Atoms
primary_subsystem: :class:`~pysic.subsystem.SubSystem`
secondary_subsystem: :class:`~pysic.subsystem.SubSystem`
info: :class:`~pysic.interaction.Interaction`
"""
self.info = info
self.full_system = full_system
self.primary_subsystem = primary_subsystem
self.secondary_subsystem = secondary_subsystem
self.uncorrected_interaction_energy = None
self.uncorrected_interaction_forces = None
self.link_atom_correction_energy = None
self.link_atom_correction_forces = None
self.interaction_energy = None
self.interaction_forces = None
# Determine if any potentials have been set
self.has_interaction_potentials = False
if self.info.comb_potential_enabled:
self.has_interaction_potentials = True
if self.info.coulomb_potential_enabled:
self.has_interaction_potentials = True
if len(self.info.potentials) != 0:
self.has_interaction_potentials = True
self.calculator = Pysic()
self.pbc_calculator = Pysic()
self.timer = Timer([
"Interaction",
"Interaction (PBC)",
"Forces",
"Forces (PBC)",
"Link atom correction energy",
"Link atom correction forces"])
# The interaction needs to know if PBC:s are on
pbc = primary_subsystem.atoms_for_interaction.get_pbc()
if pbc[0] or pbc[1] or pbc[2]:
self.has_pbc = True
else:
self.has_pbc = False
# Initialize hydrogen links
self.link_atoms = None
self.setup_hydrogen_links(info.links)
# Store the number of atoms in different systems
self.n_primary = len(primary_subsystem.atoms_for_interaction)
self.n_secondary = len(secondary_subsystem.atoms_for_interaction)
self.n_full = self.n_primary + self.n_secondary
if self.link_atoms is not None:
self.n_links = len(self.link_atoms)
else:
self.n_links = 0
# Initialize the COMB potential first (set_potentials(COMB) is used,
# because it isn' the same as add_potential(COMB))
if info.comb_potential_enabled:
self.setup_comb_potential()
# Initialize the coulomb interaction
if info.electrostatic_parameters is not None:
self.setup_coulomb_potential()
# Add the other potentials
self.setup_potentials()
# Can't enable link atom correction on system without link atoms
if len(info.links) == 0:
self.info.link_atom_correction_enabled = False
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 update_hydrogen_link_positions(self):
"""Used to update the position of the hydrogen link atoms specified in
this interaction
It is assumed that the position of the host atoms have already been
updated.
"""
print "UPDATE"
counter = 0
for bond in self.info.links:
pairs = bond[0]
CHL = bond[1]
for i, link in enumerate(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)
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
print frq1
print frm1
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
# Update hydrogen atom positions
j = i + counter
self.link_atoms[j].position = r_link
self.primary_subsystem.atoms_for_subsystem[self.n_primary+j].position = r_primary
# Add the number of links in this bond type to the counter
counter += len(pairs)
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_comb_potential(self):
"""Setups a COMB-potential between the subsystems.
"""
COMB = CombPotential(excludes=[])
COMB.set_calculator(self.pbc_calculator, True)
# Notice that set_potentials is used here instead of add_potential.
# This means that enable_comb_potential has to be called first in the
# constructor.
self.pbc_calculator.set_potentials(COMB)
def setup_potentials(self):
"""Setups the additional Pysic potentials given in the
Interaction-object.
"""
# If pbcs are not on, the targets of the potential are modified and the
# calculator for finite systems is used
if not self.has_pbc:
primary_atoms = self.primary_subsystem.atoms_for_interaction
secondary_atoms = self.secondary_subsystem.atoms_for_interaction
# Make the interaction potentials
for potential in self.info.potentials:
symbols = potential.get_symbols()
for pair in symbols:
element1 = pair[0]
element2 = pair[1]
pairs = []
for i_a, a in enumerate(primary_atoms):
for i_b, b in enumerate(secondary_atoms):
if (a.symbol == element1 and b.symbol == element2) or (a.symbol == element2 and b.symbol == element2):
pairs.append([i_a, i_b])
trimmed_potential = copy(potential)
trimmed_potential.set_symbols(None)
trimmed_potential.set_indices(pairs)
self.calculator.add_potential(trimmed_potential)
# If pbcs are on, the interactions need to be calculated with pbc
# calculator
else:
for potential in self.info.potentials:
self.pbc_calculator.add_potential(potential)
def calculate_link_atom_correction_energy(self):
"""Calculates the link atom interaction energy defined as
.. math::
E^\\text{link} = -E^\\text{tot}_\\text{MM}(\\text{HL})-E^\\text{int}_\\text{MM}(\\text{PS, HL})
"""
self.timer.start("Link atom correction energy")
primary_atoms = self.primary_subsystem.atoms_for_interaction
link_atoms = self.link_atoms
primary_and_link_atoms = primary_atoms + link_atoms
secondary_calculator = self.secondary_subsystem.calculator
# The Pysic calculators in one simulation all share one CoreMirror
# object that contains the data about the Atoms. This object should be
# automatically updated if the number of atoms changes. This is however
# not happening for some reason, so we temporarily force the updation here. TODO:
# Find out why this is the case
secondary_calculator.force_core_initialization = True
E1 = secondary_calculator.get_potential_energy(link_atoms)
E2 = secondary_calculator.get_potential_energy(primary_and_link_atoms)
E3 = secondary_calculator.get_potential_energy(primary_atoms)
secondary_calculator.force_core_initialization = False
link_atom_correction_energy = -E1 - (E2 - E1 - E3)
self.link_atom_correction_energy = link_atom_correction_energy
self.timer.stop()
return copy(self.link_atom_correction_energy)
def calculate_link_atom_correction_forces(self):
"""Calculates the link atom correction forces defined as
.. math::
F^\\text{link} = -\\nabla(-E^\\text{tot}_\\text{MM}(\\text{HL})-E^\\text{int}_\\text{MM}(\\text{PS, HL}))
"""
self.timer.start("Link atom correction forces")
primary_atoms = self.primary_subsystem.atoms_for_interaction
link_atoms = self.link_atoms
primary_and_link_atoms = primary_atoms + link_atoms
secondary_calculator = self.secondary_subsystem.calculator
# The Pysic calculators in one simulation all share one CoreMirror
# object that contains the data about the Atoms. This object should be
# automatically updated if the number of atoms changes. This is however
# not happening for some reason, so we temporarily force the updation here. TODO:
# Find out why this is the case
secondary_calculator.force_core_initialization = True
# The force arrays from the individual subsystems need to be extended
# to the size of the combined system
forces = np.zeros((len(primary_and_link_atoms), 3))
primary_postfix = np.zeros((len(link_atoms), 3))
link_prefix = np.zeros((len(primary_atoms), 3))
# Calculate the force that binds the link atoms and primary atoms. We
# don't need to calculate the force between the link atoms, although
# the associated energy had to be calculated.
F1 = secondary_calculator.get_forces(link_atoms)
F2 = secondary_calculator.get_forces(primary_and_link_atoms)
F3 = secondary_calculator.get_forces(primary_atoms)
secondary_calculator.force_core_initialization = False
forces += F2
forces -= np.concatenate((F3, primary_postfix), axis=0)
forces -= np.concatenate((link_prefix, F1), axis=0)
# Ignore the forces acting on link atoms, and negate the force
# direction. The energy can't be ignored, force can
forces = -forces[0:self.n_primary, :]
# Store the forces in a suitable numpy array that can be added to the
# forces of the whole system
link_atom_correction_forces = np.zeros((self.n_full, 3))
for sub_index in range(self.n_primary):
full_index = self.primary_subsystem.reverse_index_map[sub_index]
force = forces[sub_index, :]
link_atom_correction_forces[full_index, :] = force
self.link_atom_correction_forces = link_atom_correction_forces
self.timer.stop()
return copy(link_atom_correction_forces)
def calculate_uncorrected_interaction_energy(self):
"""Calculates the interaction energy of a non-pbc system without the
link atom correction.
"""
self.timer.start("Interaction")
finite_energy = 0
primary = self.primary_subsystem.atoms_for_interaction
secondary = self.secondary_subsystem.atoms_for_interaction
combined = primary + secondary
finite_energy = self.calculator.get_potential_energy(combined)
self.uncorrected_interaction_energy = finite_energy
self.timer.stop()
return copy(finite_energy)
def calculate_uncorrected_interaction_energy_pbc(self):
"""Calculates the interaction energy of a pbc system without the link
atom correction.
"""
self.timer.start("Interaction (PBC)")
pbc_energy = 0
primary = self.primary_subsystem.atoms_for_interaction
secondary = self.secondary_subsystem.atoms_for_interaction
combined = primary + secondary
pbc_energy += self.pbc_calculator.get_potential_energy(combined)
pbc_energy -= self.pbc_calculator.get_potential_energy(primary)
pbc_energy -= self.pbc_calculator.get_potential_energy(secondary)
self.uncorrected_interaction_energy = pbc_energy
self.timer.stop()
return copy(pbc_energy)
def calculate_uncorrected_interaction_forces(self):
"""Calculates the interaction forces of a non-pbc system without the
link atom correction.
"""
self.timer.start("Forces")
primary = self.primary_subsystem.atoms_for_interaction.copy()
secondary = self.secondary_subsystem.atoms_for_interaction.copy()
combined_system = primary + secondary
## Forces due to finite coulomb potential and other pysic potentials
forces = np.array(self.calculator.get_forces(combined_system))
self.uncorrected_interaction_forces = forces
self.timer.stop()
return copy(forces)
def calculate_uncorrected_interaction_forces_pbc(self):
"""Calculates the interaction forces of a pbc system without the link
atom correction.
"""
self.timer.start("Forces (PBC)")
primary = self.primary_subsystem.atoms_for_interaction
secondary = self.secondary_subsystem.atoms_for_interaction
combined = primary + secondary
primary_postfix = np.zeros((self.n_secondary, 3))
secondary_prefix = np.zeros((self.n_primary, 3))
# The force arrays from the individual subsystems need to be extended
# to the size of the combined system
forces = self.pbc_calculator.get_forces(combined)
forces -= np.concatenate((self.pbc_calculator.get_forces(primary), primary_postfix), axis=0)
forces -= np.concatenate((secondary_prefix, self.pbc_calculator.get_forces(secondary)), axis=0)
self.uncorrected_interaction_forces = forces
self.timer.stop()
return copy(forces)
def update_subsystem_charges(self):
"""Updates the charges in the subsystems involved in the interaction (if
charge update is enabled in them).
"""
if self.info.coulomb_potential_enabled:
self.primary_subsystem.update_charges()
self.secondary_subsystem.update_charges()
def get_interaction_energy(self):
"""Returns the total interaction energy which consists of the
uncorrected energies and possible the link atom correction.
Returns:
float: the interaction energy
"""
# Try to update the charges
self.update_subsystem_charges()
interaction_energy = 0
# Calculate the interaction energies
if self.has_interaction_potentials:
if self.has_pbc:
interaction_energy += self.calculate_uncorrected_interaction_energy_pbc()
else:
interaction_energy += self.calculate_uncorrected_interaction_energy()
# Calculate the link atom correction energy if needed
if self.info.link_atom_correction_enabled is True:
interaction_energy += self.calculate_link_atom_correction_energy()
self.interaction_energy = interaction_energy
return copy(self.interaction_energy)
def get_interaction_forces(self):
"""Return a numpy array of total 3D forces for each atom in the whole
system.
The forces consists of the uncorrected forces and possibly the link
atom correction forces. The row index refers to the atom index in the
original structure.
Returns:
numpy array: the forces for each atom in the full system
"""
# Try to update the charges
self.update_subsystem_charges()
interaction_forces = np.zeros((self.n_full, 3))
# Calculate the uncorrected interaction forces
if self.has_interaction_potentials:
if self.has_pbc:
interaction_forces += self.calculate_uncorrected_interaction_forces_pbc()
else:
interaction_forces += self.calculate_uncorrected_interaction_forces()
# Calculate the link atom correction forces if needed
if self.info.link_atom_correction_enabled is True:
interaction_forces += self.calculate_link_atom_correction_forces()
self.interaction_forces = interaction_forces
return copy(self.interaction_forces)
class InteractionInternal(object):
"""The internal version of the Interaction-class.
This class is meant only for internal use, and should not be accessed by
the end-user.
Attributes:
info: :class:'~Pysic.interaction.Interaction'
Contains all the info about the interaction given by the user.
full_system: ASE Atoms
-
primary_subsystem: :class:`~pysic.subsystem.SubSystem`
-
secondary_subsystem: :class:`~pysic.subsystem.SubSystem`
-
uncorrected_interaction_energy: float
The interaction energy without the link atom correction.
uncorrected_interaction_forces: numpy array
The interaction forces without the link atom correction.
link_atom_correction_energy: float
-
link_atom_correction_forces: numpy array
-
interaction_energy: float
The total interaction energy = uncorrected_interaction_energy +
link_atom_correction_energy
interaction_forces: numpy array
The total interaction forces = uncorrected_interaction_forces +
link_atom_correction_forces
has_interaction_potentials: bool
True if any potentials are defined.
calculator: :class:'~pysic.calculator.Pysic'
The pysic calculator used for non-pbc systems.
pbc_calculator: :class:'~pysic.calculator.Pysic'
The pysic calculator used for pbc systems.
timer: :class:'~pysic.utility.timer.Timer'
Used for tracking time usage.
has_pbc: bool
-
link_atoms: ASE Atoms
Contains all the hydrogen link atoms. Needed when calculating link
atom correction.
n_primary: int
Number of atoms in primary subsystem.
n_secondary: int
Number of atoms in secondary subsystem.
n_full: int
Number of atoms in full system.
n_links: int
Number of link atoms.
"""
def __init__(self, full_system, primary_subsystem, secondary_subsystem, info):
"""
Parameters:
full_system: ASE Atoms
primary_subsystem: :class:`~pysic.subsystem.SubSystem`
secondary_subsystem: :class:`~pysic.subsystem.SubSystem`
info: :class:`~pysic.interaction.Interaction`
"""
self.info = info
self.full_system = full_system
self.primary_subsystem = primary_subsystem
self.secondary_subsystem = secondary_subsystem
self.uncorrected_interaction_energy = None
self.uncorrected_interaction_forces = None
self.link_atom_correction_energy = None
self.link_atom_correction_forces = None
self.interaction_energy = None
self.interaction_forces = None
# Determine if any potentials have been set
self.has_interaction_potentials = False
if self.info.comb_potential_enabled:
self.has_interaction_potentials = True
if self.info.coulomb_potential_enabled:
self.has_interaction_potentials = True
if len(self.info.potentials) != 0:
self.has_interaction_potentials = True
self.calculator = Pysic()
self.pbc_calculator = Pysic()
self.timer = Timer(
[
"Interaction",
"Interaction (PBC)",
"Forces",
"Forces (PBC)",
"Link atom correction energy",
"Link atom correction forces",
]
)
# The interaction needs to know if PBC:s are on
pbc = primary_subsystem.atoms_for_interaction.get_pbc()
if pbc[0] or pbc[1] or pbc[2]:
self.has_pbc = True
else:
self.has_pbc = False
# Initialize hydrogen links
self.link_atoms = None
self.setup_hydrogen_links(info.links)
# Store the number of atoms in different systems
self.n_primary = len(primary_subsystem.atoms_for_interaction)
self.n_secondary = len(secondary_subsystem.atoms_for_interaction)
self.n_full = self.n_primary + self.n_secondary
if self.link_atoms is not None:
self.n_links = len(self.link_atoms)
else:
self.n_links = 0
# Initialize the COMB potential first (set_potentials(COMB) is used,
# because it isn' the same as add_potential(COMB))
if info.comb_potential_enabled:
self.setup_comb_potential()
# Initialize the coulomb interaction
if info.electrostatic_parameters is not None:
self.setup_coulomb_potential()
# Add the other potentials
self.setup_potentials()
# Can't enable link atom correction on system without link atoms
if len(info.links) == 0:
self.info.link_atom_correction_enabled = False
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 update_hydrogen_link_positions(self):
"""Used to update the position of the hydrogen link atoms specified in
this interaction
It is assumed that the position of the host atoms have already been
updated.
"""
print "UPDATE"
counter = 0
for bond in self.info.links:
pairs = bond[0]
CHL = bond[1]
for i, link in enumerate(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)
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
print frq1
print frm1
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
# Update hydrogen atom positions
j = i + counter
self.link_atoms[j].position = r_link
self.primary_subsystem.atoms_for_subsystem[self.n_primary + j].position = r_primary
# Add the number of links in this bond type to the counter
counter += len(pairs)
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_comb_potential(self):
"""Setups a COMB-potential between the subsystems.
"""
COMB = CombPotential(excludes=[])
COMB.set_calculator(self.pbc_calculator, True)
# Notice that set_potentials is used here instead of add_potential.
# This means that enable_comb_potential has to be called first in the
# constructor.
self.pbc_calculator.set_potentials(COMB)
def setup_potentials(self):
"""Setups the additional Pysic potentials given in the
Interaction-object.
"""
# If pbcs are not on, the targets of the potential are modified and the
# calculator for finite systems is used
if not self.has_pbc:
primary_atoms = self.primary_subsystem.atoms_for_interaction
secondary_atoms = self.secondary_subsystem.atoms_for_interaction
# Make the interaction potentials
for potential in self.info.potentials:
symbols = potential.get_symbols()
for pair in symbols:
element1 = pair[0]
element2 = pair[1]
pairs = []
for i_a, a in enumerate(primary_atoms):
for i_b, b in enumerate(secondary_atoms):
if (a.symbol == element1 and b.symbol == element2) or (
a.symbol == element2 and b.symbol == element2
):
pairs.append([i_a, i_b])
trimmed_potential = copy(potential)
trimmed_potential.set_symbols(None)
trimmed_potential.set_indices(pairs)
self.calculator.add_potential(trimmed_potential)
# If pbcs are on, the interactions need to be calculated with pbc
# calculator
else:
for potential in self.info.potentials:
self.pbc_calculator.add_potential(potential)
def calculate_link_atom_correction_energy(self):
"""Calculates the link atom interaction energy defined as
.. math::
E^\\text{link} = -E^\\text{tot}_\\text{MM}(\\text{HL})-E^\\text{int}_\\text{MM}(\\text{PS, HL})
"""
self.timer.start("Link atom correction energy")
primary_atoms = self.primary_subsystem.atoms_for_interaction
link_atoms = self.link_atoms
primary_and_link_atoms = primary_atoms + link_atoms
secondary_calculator = self.secondary_subsystem.calculator
# The Pysic calculators in one simulation all share one CoreMirror
# object that contains the data about the Atoms. This object should be
# automatically updated if the number of atoms changes. This is however
# not happening for some reason, so we temporarily force the updation here. TODO:
# Find out why this is the case
secondary_calculator.force_core_initialization = True
E1 = secondary_calculator.get_potential_energy(link_atoms)
E2 = secondary_calculator.get_potential_energy(primary_and_link_atoms)
E3 = secondary_calculator.get_potential_energy(primary_atoms)
secondary_calculator.force_core_initialization = False
link_atom_correction_energy = -E1 - (E2 - E1 - E3)
self.link_atom_correction_energy = link_atom_correction_energy
self.timer.stop()
return copy(self.link_atom_correction_energy)
def calculate_link_atom_correction_forces(self):
"""Calculates the link atom correction forces defined as
.. math::
F^\\text{link} = -\\nabla(-E^\\text{tot}_\\text{MM}(\\text{HL})-E^\\text{int}_\\text{MM}(\\text{PS, HL}))
"""
self.timer.start("Link atom correction forces")
primary_atoms = self.primary_subsystem.atoms_for_interaction
link_atoms = self.link_atoms
primary_and_link_atoms = primary_atoms + link_atoms
secondary_calculator = self.secondary_subsystem.calculator
# The Pysic calculators in one simulation all share one CoreMirror
# object that contains the data about the Atoms. This object should be
# automatically updated if the number of atoms changes. This is however
# not happening for some reason, so we temporarily force the updation here. TODO:
# Find out why this is the case
secondary_calculator.force_core_initialization = True
# The force arrays from the individual subsystems need to be extended
# to the size of the combined system
forces = np.zeros((len(primary_and_link_atoms), 3))
primary_postfix = np.zeros((len(link_atoms), 3))
link_prefix = np.zeros((len(primary_atoms), 3))
# Calculate the force that binds the link atoms and primary atoms. We
# don't need to calculate the force between the link atoms, although
# the associated energy had to be calculated.
F1 = secondary_calculator.get_forces(link_atoms)
F2 = secondary_calculator.get_forces(primary_and_link_atoms)
F3 = secondary_calculator.get_forces(primary_atoms)
secondary_calculator.force_core_initialization = False
forces += F2
forces -= np.concatenate((F3, primary_postfix), axis=0)
forces -= np.concatenate((link_prefix, F1), axis=0)
# Ignore the forces acting on link atoms, and negate the force
# direction. The energy can't be ignored, force can
forces = -forces[0 : self.n_primary, :]
# Store the forces in a suitable numpy array that can be added to the
# forces of the whole system
link_atom_correction_forces = np.zeros((self.n_full, 3))
for sub_index in range(self.n_primary):
full_index = self.primary_subsystem.reverse_index_map[sub_index]
force = forces[sub_index, :]
link_atom_correction_forces[full_index, :] = force
self.link_atom_correction_forces = link_atom_correction_forces
self.timer.stop()
return copy(link_atom_correction_forces)
def calculate_uncorrected_interaction_energy(self):
"""Calculates the interaction energy of a non-pbc system without the
link atom correction.
"""
self.timer.start("Interaction")
finite_energy = 0
primary = self.primary_subsystem.atoms_for_interaction
secondary = self.secondary_subsystem.atoms_for_interaction
combined = primary + secondary
finite_energy = self.calculator.get_potential_energy(combined)
self.uncorrected_interaction_energy = finite_energy
self.timer.stop()
return copy(finite_energy)
def calculate_uncorrected_interaction_energy_pbc(self):
"""Calculates the interaction energy of a pbc system without the link
atom correction.
"""
self.timer.start("Interaction (PBC)")
pbc_energy = 0
primary = self.primary_subsystem.atoms_for_interaction
secondary = self.secondary_subsystem.atoms_for_interaction
combined = primary + secondary
pbc_energy += self.pbc_calculator.get_potential_energy(combined)
pbc_energy -= self.pbc_calculator.get_potential_energy(primary)
pbc_energy -= self.pbc_calculator.get_potential_energy(secondary)
self.uncorrected_interaction_energy = pbc_energy
self.timer.stop()
return copy(pbc_energy)
def calculate_uncorrected_interaction_forces(self):
"""Calculates the interaction forces of a non-pbc system without the
link atom correction.
"""
self.timer.start("Forces")
primary = self.primary_subsystem.atoms_for_interaction.copy()
secondary = self.secondary_subsystem.atoms_for_interaction.copy()
combined_system = primary + secondary
## Forces due to finite coulomb potential and other pysic potentials
forces = np.array(self.calculator.get_forces(combined_system))
self.uncorrected_interaction_forces = forces
self.timer.stop()
return copy(forces)
def calculate_uncorrected_interaction_forces_pbc(self):
"""Calculates the interaction forces of a pbc system without the link
atom correction.
"""
self.timer.start("Forces (PBC)")
primary = self.primary_subsystem.atoms_for_interaction
secondary = self.secondary_subsystem.atoms_for_interaction
combined = primary + secondary
primary_postfix = np.zeros((self.n_secondary, 3))
secondary_prefix = np.zeros((self.n_primary, 3))
# The force arrays from the individual subsystems need to be extended
# to the size of the combined system
forces = self.pbc_calculator.get_forces(combined)
forces -= np.concatenate((self.pbc_calculator.get_forces(primary), primary_postfix), axis=0)
forces -= np.concatenate((secondary_prefix, self.pbc_calculator.get_forces(secondary)), axis=0)
self.uncorrected_interaction_forces = forces
self.timer.stop()
return copy(forces)
def update_subsystem_charges(self):
"""Updates the charges in the subsystems involved in the interaction (if
charge update is enabled in them).
"""
if self.info.coulomb_potential_enabled:
self.primary_subsystem.update_charges()
self.secondary_subsystem.update_charges()
def get_interaction_energy(self):
"""Returns the total interaction energy which consists of the
uncorrected energies and possible the link atom correction.
Returns:
float: the interaction energy
"""
# Try to update the charges
self.update_subsystem_charges()
interaction_energy = 0
# Calculate the interaction energies
if self.has_interaction_potentials:
if self.has_pbc:
interaction_energy += self.calculate_uncorrected_interaction_energy_pbc()
else:
interaction_energy += self.calculate_uncorrected_interaction_energy()
# Calculate the link atom correction energy if needed
if self.info.link_atom_correction_enabled is True:
interaction_energy += self.calculate_link_atom_correction_energy()
self.interaction_energy = interaction_energy
return copy(self.interaction_energy)
def get_interaction_forces(self):
"""Return a numpy array of total 3D forces for each atom in the whole
system.
The forces consists of the uncorrected forces and possibly the link
atom correction forces. The row index refers to the atom index in the
original structure.
Returns:
numpy array: the forces for each atom in the full system
"""
# Try to update the charges
self.update_subsystem_charges()
interaction_forces = np.zeros((self.n_full, 3))
# Calculate the uncorrected interaction forces
if self.has_interaction_potentials:
if self.has_pbc:
interaction_forces += self.calculate_uncorrected_interaction_forces_pbc()
else:
interaction_forces += self.calculate_uncorrected_interaction_forces()
# Calculate the link atom correction forces if needed
if self.info.link_atom_correction_enabled is True:
interaction_forces += self.calculate_link_atom_correction_forces()
self.interaction_forces = interaction_forces
return copy(self.interaction_forces)
