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| class GibbsSampler(object): | ||
| """Basic Markov chain Monte Carlo Gibbs sampler. | ||
| Parameters | ||
| ---------- | ||
| conditional_state : states.ConditionalDistribution | ||
| Initial conditional distribution. | ||
| move_set : container of MarkovChainMonteCarloMove objects | ||
| Moves to attempt during MCMC run. If list or tuple, will run all moves each | ||
| iteration in specified sequence (e.g. [move1, move2, move3]). If dict, will | ||
| use specified unnormalized weights (e.g. { move1 : 0.3, move2 : 0.5, move3, 0.9 }) | ||
| Examples | ||
| -------- | ||
| Create and run an alanine dipeptide simulation with a weighted move. | ||
| """ | ||
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| def __init__(self, conditional_state, move_set): | ||
| from copy import deepcopy | ||
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| # Make a deep copy of the state so that initial state is unchanged. | ||
| self.conditional_state = deepcopy(conditional_state) | ||
| self.move = move_set | ||
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| def run(self, n_iterations=1): | ||
| """ | ||
| Run the sampler for a specified number of iterations. | ||
| Parameters | ||
| ---------- | ||
| n_iterations : int | ||
| Number of iterations of the sampler to run. | ||
| """ | ||
| # Apply move for n_iterations. |
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| class ThermodynamicState(object): | ||
| """Thermodynamic state of a system which is defined through the following attributes: | ||
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| Attributes | ||
| ---------- | ||
| system | ||
| temperature | ||
| pressure | ||
| volume | ||
| n_particles | ||
| class JointDistribution(object): | ||
| """ | ||
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| @property | ||
| def temperature(self): | ||
| """Constant temperature of the thermodynamic state.""" | ||
| return self._temperature | ||
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| @temperature.setter | ||
| def temperature(self, value): | ||
| if value is None: | ||
| raise RuntimeError("Cannot set temperature to None") | ||
| self._temperature = value | ||
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| @property | ||
| def kT(self): | ||
| """Thermal energy per mole.""" | ||
| from openmm import unit | ||
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| kB = unit.BOLTZMANN_CONSTANT_kB * unit.AVOGADRO_CONSTANT_NA | ||
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| return kB * self.temperature | ||
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| @property | ||
| def beta(self): | ||
| """Thermodynamic beta in units of mole/energy.""" | ||
| return 1.0 / self.kT | ||
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| @property | ||
| def pressure(self): | ||
| """Constant pressure of the thermodynamic state. | ||
| If the pressure is allowed to fluctuate, this is None. Setting | ||
| this will automatically add/configure a barostat to the system. | ||
| If it is set to None, the barostat will be removed. | ||
| """ | ||
| return self._pressure | ||
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| @pressure.setter | ||
| def pressure(self, new_pressure): | ||
| old_pressure = self._pressure | ||
| self._pressure = new_pressure | ||
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| # If we change ensemble, we need to modify the standard system. | ||
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| @property | ||
| def default_box_vectors(self): | ||
| """The default box vectors of the System (read-only).""" | ||
| return self._standard_system.getDefaultPeriodicBoxVectors() | ||
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| @property | ||
| def volume(self): | ||
| """Constant volume of the thermodynamic state (read-only). | ||
| If the volume is allowed to fluctuate, or if the system is | ||
| not in a periodic box this is None. | ||
| """ | ||
| return self.get_volume() | ||
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| def get_volume(self, ignore_ensemble=False): | ||
| """Volume of the periodic box (read-only). | ||
| Parameters | ||
| ---------- | ||
| ignore_ensemble : bool, optional | ||
| If True, the volume of the periodic box vectors is returned | ||
| even if the volume fluctuates. | ||
| Returns | ||
| ------- | ||
| volume : openmm.unit.Quantity | ||
| The volume of the periodic box (units of length^3) or | ||
| None if the system is not periodic or allowed to fluctuate. | ||
| """ | ||
| # Check if volume fluctuates | ||
| if self.pressure is not None and not ignore_ensemble: | ||
| return None | ||
| if not self._standard_system.usesPeriodicBoundaryConditions(): | ||
| return None | ||
| return _box_vectors_volume(self.default_box_vectors) | ||
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| @property | ||
| def n_particles(self): | ||
| """Number of particles (read-only).""" | ||
| return self._standard_system.getNumParticles() | ||
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| @property | ||
| def is_periodic(self): | ||
| """True if the system is in a periodic box (read-only).""" | ||
| return self._standard_system.usesPeriodicBoundaryConditions() | ||
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| class SamplerState(object): | ||
| """State carrying the configurational properties of a system. | ||
| Parameters | ||
| ---------- | ||
| positions : Nx3 unit.Quantity | ||
| Position vectors for N particles (length units). | ||
| velocities : Nx3 unit.Quantity, optional | ||
| Velocity vectors for N particles (velocity units). | ||
| box_vectors : 3x3 unit.Quantity | ||
| Current box vectors (length units). | ||
| Attributes | ||
| ---------- | ||
| positions | ||
| velocities | ||
| box_vectors : 3x3 unit.Quantity. | ||
| Current box vectors (length units). | ||
| potential_energy | ||
| kinetic_energy | ||
| total_energy | ||
| volume | ||
| n_particles | ||
| collective_variables | ||
| Defines the extended ensamble build from ConditionalDistribution objects. | ||
| """ | ||
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| def __init__(self, positions, velocities=None, box_vectors=None): | ||
| from openmm import unit | ||
| import numpy as np | ||
| from copy import deepcopy | ||
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| # Allocate variables, they get set in _initialize | ||
| self._positions = None | ||
| self._velocities = None | ||
| self._box_vectors = None | ||
| self._collective_variables = None | ||
| self._kinetic_energy = None | ||
| self._potential_energy = None | ||
| args = [] | ||
| for input in [positions, velocities, box_vectors]: | ||
| if isinstance(input, unit.Quantity) and not isinstance( | ||
| input._value, np.ndarray | ||
| ): | ||
| args.append(np.array(input / input.unit) * input.unit) | ||
| else: | ||
| args.append(deepcopy(input)) | ||
| self._initialize(*args) | ||
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| @property | ||
| def positions(self): | ||
| """Particle positions. | ||
| An Nx3 openmm.unit.Quantity object, where N is the number of | ||
| particles. | ||
| Raises | ||
| ------ | ||
| SamplerStateError | ||
| If set to an array with a number of particles different | ||
| than n_particles. | ||
| """ | ||
| return self._positions | ||
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| @positions.setter | ||
| def positions(self, value): | ||
| self._set_positions(value, from_context=False, check_consistency=True) | ||
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| @property | ||
| def velocities(self): | ||
| """Particle velocities. | ||
| An Nx3 openmm.unit.Quantity object, where N is the number of | ||
| particles. | ||
| Raises | ||
| ------ | ||
| SamplerStateError | ||
| If set to an array with a number of particles different | ||
| than n_particles. | ||
| """ | ||
| return self._velocities | ||
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| @velocities.setter | ||
| def velocities(self, value): | ||
| self._set_velocities(value, from_context=False) | ||
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| @property | ||
| def box_vectors(self): | ||
| """Box vectors. | ||
| An 3x3 openmm.unit.Quantity object. | ||
| """ | ||
| return self._box_vectors | ||
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| @box_vectors.setter | ||
| def box_vectors(self, value): | ||
| from openmm import unit | ||
| class ConditionalDistribution(object): | ||
| """D | ||
| # Make sure this is a Quantity. System.getDefaultPeriodicBoxVectors | ||
| # returns a list of Quantity objects instead for example. | ||
| if value is not None and not isinstance(value, unit.Quantity): | ||
| value = unit.Quantity(value) | ||
| self._box_vectors = value | ||
| Args: | ||
| object (_type_): _description_ | ||
| """ |
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