def addRestraint(self,restraint):
g1 = restraint[0]
g2 = restraint[1]
k_compound = N.float64(restraint[2])
r0_compound = N.float64(restraint[3])
option = restraint[4]
energy_exp = CreateRestraintString(g1,g2,k_compound,r0_compound,option)
print energy_exp
num_of_particles = len(g1) + len(g2)
MMTK_langevin.addRestraint(N.array(restraint[0]+restraint[1], dtype=N.int32),
energy_exp,num_of_particles)
def addRestraint(self, restraint):
g1 = restraint[0]
g2 = restraint[1]
k_compound = N.float64(restraint[2])
r0_compound = N.float64(restraint[3])
option = restraint[4]
energy_exp = CreateRestraintString(g1, g2, k_compound, r0_compound,
option)
print energy_exp
num_of_particles = len(g1) + len(g2)
MMTK_langevin.addRestraint(
N.array(restraint[0] + restraint[1], dtype=N.int32), energy_exp,
num_of_particles)
def __call__(self, **options):
# Process the keyword arguments
self.setCallOptions(options)
# Check if the universe has features not supported by the integrator
Features.checkFeatures(self, self.universe)
# Get the universe variables needed by the integrator
configuration = self.universe.configuration()
masses = self.universe.masses()
velocities = self.universe.velocities()
if velocities is None:
raise ValueError("no velocities")
# Get the friction coefficients. First check if a keyword argument
# 'friction' was given to the integrator. Its value can be a
# ParticleScalar or a plain number (used for all atoms). If no
# such argument is given, collect the values of the attribute
# 'friction' from all atoms (default is zero).
try:
friction = self.getOption('friction')
except KeyError:
friction = self.universe.getParticleScalar('friction')
if not ParticleProperties.isParticleProperty(friction):
var = ParticleProperties.ParticleScalar(self.universe)
var.array[:] = friction
friction = var
# Construct a C evaluator object for the force field, using
# the specified number of threads or the default value
nt = self.getOption('threads')
evaluator = self.universe.energyEvaluator(threads=nt).CEvaluator()
# Run the C integrator
MMTK_langevin.integrateLD(self.universe,
configuration.array, velocities.array,
masses.array, friction.array, evaluator,
self.getOption('temperature'),
self.getOption('delta_t'),
self.getOption('steps'),
self.getActions())
def createOmmForces(self):
params = self.universe.energyEvaluatorParameters()
natoms = len(self.universe.atomList())
nbeads = self.nbeads
#here we convert MMTK's internal representation of the forcefield parameters
#to OpenMM. For a new MMTK forcefield to work, it must implement the
#energyEvaluatorParameters method, and this code must be modified to make use
#of those parameters
#first, lets start with the bonded forcefield
bonds = params['harmonic_distance_term']
atom_index_1 = []
atom_index_2 = []
eq_distance = []
spring_k = []
for bond in bonds:
if ((bond[0] % nbeads == 0) and (bond[1] % nbeads == 0)):
atom_index_1.append(bond[0]/nbeads)
atom_index_2.append(bond[1]/nbeads)
eq_distance.append(bond[2])
spring_k.append(2.*bond[3]) # OpenMM divides by 2 so must counteract here by multiplying by 2
MMTK_langevin.makeOmmBondedForce(N.array(atom_index_1, dtype=N.int32),
N.array(atom_index_2, dtype=N.int32),
N.array(eq_distance, dtype=N.float64),
N.array(spring_k, dtype=N.float64),
len(atom_index_1))
#angles
angles = params['harmonic_angle_term']
atom_index_1 = []
atom_index_2 = []
atom_index_3 = []
eq_angle = []
spring_k = []
for angle in angles:
if ((angle[0] % nbeads == 0) and (angle[1] % nbeads == 0) and (angle[2] % nbeads == 0)):
atom_index_1.append(angle[0]/nbeads)
atom_index_2.append(angle[1]/nbeads)
atom_index_3.append(angle[2]/nbeads)
eq_angle.append(angle[3])
spring_k.append(2.*angle[4]) # OpenMM divides by 2 so must counteract here by multiplying by 2
MMTK_langevin.makeOmmAngleForce(N.array(atom_index_1, dtype=N.int32),
N.array(atom_index_2, dtype=N.int32),
N.array(atom_index_3, dtype=N.int32),
N.array(eq_angle, dtype=N.float64),
N.array(spring_k, dtype=N.float64),
len(atom_index_1))
#dihedrals
dihedrals = params['cosine_dihedral_term']
atom_index_1 = []
atom_index_2 = []
atom_index_3 = []
atom_index_4 = []
periodicity = []
eq_dihedral = []
spring_k = []
for dihedral in dihedrals:
if ((dihedral[0] % nbeads == 0) and (dihedral[1] % nbeads == 0) and (dihedral[2] % nbeads == 0) and (dihedral[3] % nbeads == 0)):
atom_index_1.append(dihedral[0]/nbeads)
atom_index_2.append(dihedral[1]/nbeads)
atom_index_3.append(dihedral[2]/nbeads)
atom_index_4.append(dihedral[3]/nbeads)
periodicity.append(dihedral[4])
eq_dihedral.append(dihedral[5])
spring_k.append(dihedral[6])
MMTK_langevin.makeOmmDihedralForce(N.array(atom_index_1, dtype=N.int32),
N.array(atom_index_2, dtype=N.int32),
N.array(atom_index_3, dtype=N.int32),
N.array(atom_index_4, dtype=N.int32),
N.array(periodicity, dtype=N.int32),
N.array(eq_dihedral, dtype=N.float64),
N.array(spring_k, dtype=N.float64),
len(atom_index_1))
#now, nonbonded forces
lj = params['lennard_jones']
lj_14_factor = lj['one_four_factor']
lj_cutoff = lj['cutoff']
e_s_matrix = lj['epsilon_sigma']
epsilon_list = []
sigma_list = []
for i in range(0, len(e_s_matrix)):
epsilon, sigma = e_s_matrix[i][i]
epsilon_list.append(epsilon)
sigma_list.append(sigma)
#contains per-particle information, but we want per-atom
e_s_types = lj['type']
epsilon_p = [] # per-particle epsilons
sigma_p = [] # per-particle sigmas
for type in e_s_types:
epsilon_p.append(epsilon_list[type])
sigma_p.append(sigma_list[type])
epsilon = [] # per-atom epsilons
sigma = [] # per-atom sigmas
for i in range(0,natoms*self.nbeads,self.nbeads):
epsilon.append(epsilon_p[i])
sigma.append(sigma_p[i])
#now epsilon and sigma contain the correct values in the correct order
elec = params['electrostatic']
elec_14_factor = elec['one_four_factor']
#check if periodic universe so that Ewald and proper cutoff is set
is_periodic = (1,0)[isinstance(self.universe, Universe.InfiniteUniverse)]
#print "periodicity: ", is_periodic
if is_periodic:
elec_cutoff = elec['real_cutoff'] #for step_0_
else:
elec_cutoff = elec['cutoff'] #for example
charge_p = elec['charge'] # per-particle charges
elec_method = elec['algorithm']
charge = [] # per-atom charges
for i in range(0,natoms*self.nbeads,self.nbeads):
charge.append(charge_p[i])
MMTK_langevin.makeOmmEsAndLjForce(is_periodic,
N.array(sigma, dtype=N.float64),
N.array(epsilon, dtype=N.float64),
N.array(charge, dtype=N.float64),
elec_14_factor,
lj_14_factor,
elec_cutoff,
len(sigma))
def addOmmCMRemover(self, skip):
MMTK_langevin.addCMRemover(skip)
def destroyOmmSystem(self): MMTK_langevin.destroyOpenMM()
def initOmmSystem(self):
atoms = copy.copy(self.universe.atomList())
atoms.sort(key=operator.attrgetter('index'))
masses = [atom.mass() for atom in atoms]
MMTK_langevin.initOpenMM(N.array(masses, dtype=N.float64), len(atoms))
def __call__(self, **options):
# Process the keyword arguments
self.setCallOptions(options)
# Check if the universe has features not supported by the integrator
Features.checkFeatures(self, self.universe)
#the following two lines are required due to MMTK mixing up atom indices. This sorts them.
#atoms = self.universe.atomList()
#atoms.sort(key=operator.attrgetter('index'))
# Get the universe variables needed by the integrator
configuration = self.universe.configuration()
velocities = self.universe.velocities()
if velocities is None:
raise ValueError("no velocities")
# Get the friction coefficients. First check if a keyword argument
# 'friction' was given to the integrator. Its value can be a
# ParticleScalar or a plain number (used for all atoms). If no
# such argument is given, collect the values of the attribute
# 'friction' from all atoms (default is zero).
friction = self.getOption('friction')
#call this method to create the OpenMM System. Without this, creating
#the forces will fail!!
self.initOmmSystem()
#call this method to ensure that the forcefield parameters get
#passed to OpenMM. Without this, there will be no forces to integrate!
self.createOmmForces()
#The restraint option must be included in the creation of the integrator for this part to be executed
try:
restraint = self.getOption('restraint')
except ValueError:
restraint = None
print 'No restraints (Value Error)'
except:
print sys.exc_info()[0]
if restraint != None:
self.addRestraint(restraint)
#ugly hack to get timestep skip information
skip = -1
if ('actions' in self.call_options):
actions = self.call_options['actions']
for action in actions:
if isinstance(action, Dynamics.TranslationRemover):
self.addOmmCMRemover(action.skip)
if isinstance(action, Trajectory.LogOutput):
break # to avoid Logoutput skip setting problem PNR NFF SJC
if isinstance(action, Trajectory.TrajectoryOutput):
skip = action.skip
action.skip = 1
if skip < 0 :
for action in actions:
if issubclass(action.__class__, Trajectory.TrajectoryOutput):
skip = action.skip
action.skip = 1
break
#we are not logging anything, so we don't have to report any intermediate values
if skip < 0:
skip = 100
steps = 1
# Run the C integrator
atoms = self.universe.atomList()
masses = [atom.mass() for atom in atoms]
natoms = len(atoms)
nmolecules = len(self.universe.objectList(Molecule))
molecule_lengths = N.zeros(nmolecules, dtype=N.int32, order='C')
for i in range(0,len(self.universe.objectList(Molecule))):
molecule_lengths[i] = len(self.universe.objectList(Molecule)[i].atomList())
MMTK_langevin.integrateLD(self.universe, configuration.array,
velocities.array, N.array(masses, dtype=N.float64),
friction,
self.getOption('temperature'),
self.getOption('delta_t'),
self.getOption('steps'), skip, natoms, self.nbeads,
nmolecules, molecule_lengths,
self.getActions())
#call this to clean up after ourselves
self.destroyOmmSystem()
def createOmmForces(self):
params = self.universe.energyEvaluatorParameters()
natoms = len(self.universe.atomList())
nbeads = self.nbeads
#here we convert MMTK's internal representation of the forcefield parameters
#to OpenMM. For a new MMTK forcefield to work, it must implement the
#energyEvaluatorParameters method, and this code must be modified to make use
#of those parameters
#first, lets start with the bonded forcefield
bonds = params['harmonic_distance_term']
atom_index_1 = []
atom_index_2 = []
eq_distance = []
spring_k = []
for bond in bonds:
if ((bond[0] % nbeads == 0) and (bond[1] % nbeads == 0)):
atom_index_1.append(bond[0] / nbeads)
atom_index_2.append(bond[1] / nbeads)
eq_distance.append(bond[2])
spring_k.append(
2. * bond[3]
) # OpenMM divides by 2 so must counteract here by multiplying by 2
MMTK_langevin.makeOmmBondedForce(N.array(atom_index_1, dtype=N.int32),
N.array(atom_index_2, dtype=N.int32),
N.array(eq_distance, dtype=N.float64),
N.array(spring_k, dtype=N.float64),
len(atom_index_1))
#angles
angles = params['harmonic_angle_term']
atom_index_1 = []
atom_index_2 = []
atom_index_3 = []
eq_angle = []
spring_k = []
for angle in angles:
if ((angle[0] % nbeads == 0) and (angle[1] % nbeads == 0)
and (angle[2] % nbeads == 0)):
atom_index_1.append(angle[0] / nbeads)
atom_index_2.append(angle[1] / nbeads)
atom_index_3.append(angle[2] / nbeads)
eq_angle.append(angle[3])
spring_k.append(
2. * angle[4]
) # OpenMM divides by 2 so must counteract here by multiplying by 2
MMTK_langevin.makeOmmAngleForce(N.array(atom_index_1, dtype=N.int32),
N.array(atom_index_2, dtype=N.int32),
N.array(atom_index_3, dtype=N.int32),
N.array(eq_angle, dtype=N.float64),
N.array(spring_k, dtype=N.float64),
len(atom_index_1))
#dihedrals
dihedrals = params['cosine_dihedral_term']
atom_index_1 = []
atom_index_2 = []
atom_index_3 = []
atom_index_4 = []
periodicity = []
eq_dihedral = []
spring_k = []
for dihedral in dihedrals:
if ((dihedral[0] % nbeads == 0) and (dihedral[1] % nbeads == 0)
and (dihedral[2] % nbeads == 0)
and (dihedral[3] % nbeads == 0)):
atom_index_1.append(dihedral[0] / nbeads)
atom_index_2.append(dihedral[1] / nbeads)
atom_index_3.append(dihedral[2] / nbeads)
atom_index_4.append(dihedral[3] / nbeads)
periodicity.append(dihedral[4])
eq_dihedral.append(dihedral[5])
spring_k.append(dihedral[6])
MMTK_langevin.makeOmmDihedralForce(
N.array(atom_index_1, dtype=N.int32),
N.array(atom_index_2, dtype=N.int32),
N.array(atom_index_3, dtype=N.int32),
N.array(atom_index_4, dtype=N.int32),
N.array(periodicity, dtype=N.int32),
N.array(eq_dihedral, dtype=N.float64),
N.array(spring_k, dtype=N.float64), len(atom_index_1))
#now, nonbonded forces
lj = params['lennard_jones']
lj_14_factor = lj['one_four_factor']
lj_cutoff = lj['cutoff']
e_s_matrix = lj['epsilon_sigma']
epsilon_list = []
sigma_list = []
for i in range(0, len(e_s_matrix)):
epsilon, sigma = e_s_matrix[i][i]
epsilon_list.append(epsilon)
sigma_list.append(sigma)
#contains per-particle information, but we want per-atom
e_s_types = lj['type']
epsilon_p = [] # per-particle epsilons
sigma_p = [] # per-particle sigmas
for type in e_s_types:
epsilon_p.append(epsilon_list[type])
sigma_p.append(sigma_list[type])
epsilon = [] # per-atom epsilons
sigma = [] # per-atom sigmas
for i in range(0, natoms * self.nbeads, self.nbeads):
epsilon.append(epsilon_p[i])
sigma.append(sigma_p[i])
#now epsilon and sigma contain the correct values in the correct order
elec = params['electrostatic']
elec_14_factor = elec['one_four_factor']
#check if periodic universe so that Ewald and proper cutoff is set
is_periodic = (1, 0)[isinstance(self.universe,
Universe.InfiniteUniverse)]
#print "periodicity: ", is_periodic
if is_periodic:
elec_cutoff = elec['real_cutoff'] #for step_0_
else:
elec_cutoff = elec['cutoff'] #for example
charge_p = elec['charge'] # per-particle charges
elec_method = elec['algorithm']
charge = [] # per-atom charges
for i in range(0, natoms * self.nbeads, self.nbeads):
charge.append(charge_p[i])
MMTK_langevin.makeOmmEsAndLjForce(is_periodic,
N.array(sigma, dtype=N.float64),
N.array(epsilon, dtype=N.float64),
N.array(charge, dtype=N.float64),
elec_14_factor, lj_14_factor,
elec_cutoff, len(sigma))
def addOmmCMRemover(self, skip):
MMTK_langevin.addCMRemover(skip)
def destroyOmmSystem(self):
MMTK_langevin.destroyOpenMM()
def initOmmSystem(self):
atoms = copy.copy(self.universe.atomList())
atoms.sort(key=operator.attrgetter('index'))
masses = [atom.mass() for atom in atoms]
MMTK_langevin.initOpenMM(N.array(masses, dtype=N.float64), len(atoms))
def __call__(self, **options):
# Process the keyword arguments
self.setCallOptions(options)
# Check if the universe has features not supported by the integrator
Features.checkFeatures(self, self.universe)
#the following two lines are required due to MMTK mixing up atom indices. This sorts them.
#atoms = self.universe.atomList()
#atoms.sort(key=operator.attrgetter('index'))
# Get the universe variables needed by the integrator
configuration = self.universe.configuration()
velocities = self.universe.velocities()
if velocities is None:
raise ValueError("no velocities")
# Get the friction coefficients. First check if a keyword argument
# 'friction' was given to the integrator. Its value can be a
# ParticleScalar or a plain number (used for all atoms). If no
# such argument is given, collect the values of the attribute
# 'friction' from all atoms (default is zero).
friction = self.getOption('friction')
#call this method to create the OpenMM System. Without this, creating
#the forces will fail!!
self.initOmmSystem()
#call this method to ensure that the forcefield parameters get
#passed to OpenMM. Without this, there will be no forces to integrate!
self.createOmmForces()
#The restraint option must be included in the creation of the integrator for this part to be executed
try:
restraint = self.getOption('restraint')
except ValueError:
restraint = None
print 'No restraints (Value Error)'
except:
print sys.exc_info()[0]
if restraint != None:
self.addRestraint(restraint)
#ugly hack to get timestep skip information
skip = -1
if ('actions' in self.call_options):
actions = self.call_options['actions']
for action in actions:
if isinstance(action, Dynamics.TranslationRemover):
self.addOmmCMRemover(action.skip)
if isinstance(action, Trajectory.LogOutput):
break # to avoid Logoutput skip setting problem PNR NFF SJC
if isinstance(action, Trajectory.TrajectoryOutput):
skip = action.skip
action.skip = 1
if skip < 0:
for action in actions:
if issubclass(action.__class__,
Trajectory.TrajectoryOutput):
skip = action.skip
action.skip = 1
break
#we are not logging anything, so we don't have to report any intermediate values
if skip < 0:
skip = 100
steps = 1
# Run the C integrator
atoms = self.universe.atomList()
masses = [atom.mass() for atom in atoms]
natoms = len(atoms)
nmolecules = len(self.universe.objectList(Molecule))
molecule_lengths = N.zeros(nmolecules, dtype=N.int32, order='C')
for i in range(0, len(self.universe.objectList(Molecule))):
molecule_lengths[i] = len(
self.universe.objectList(Molecule)[i].atomList())
MMTK_langevin.integrateLD(self.universe, configuration.array,
velocities.array,
N.array(masses, dtype=N.float64), friction,
self.getOption('temperature'),
self.getOption('delta_t'),
self.getOption('steps'), skip, natoms,
self.nbeads, nmolecules, molecule_lengths,
self.getActions())
#call this to clean up after ourselves
self.destroyOmmSystem()
