Python Constants.boltzmann方法代码示例

# 需要导入模块: import Constants [as 别名]
# 或者: from Constants import boltzmann [as 别名]
    def metropolis( self, new, curr, phys ):
        """
        Metropolis function which computes an acceptance probability
        for sets of positions depending on energy change dE.
        P = e^-dE/kt

        @type new: float
        @param new: Hypothetical new energy with flip.

        @type curr: float
        @param curr: Current energy.

        @type phys: Physical
        @param phys: The physical system.

        @rtype: int
        @return: 0 for reject, 1 for accept
        """
        deltaE = new - curr
        
        if( deltaE < 0 ):
            return 1

        acceptProb = exp( -deltaE / ( Constants.boltzmann() * phys.getTemperature() ) )

        randNum = random()

        if( randNum < acceptProb ):
            print "\n****    Move accepted\n"
            return 1
        else:
            print "\n****    Move rejected\n"
            return 0

# 需要导入模块: import Constants [as 别名]
# 或者: from Constants import boltzmann [as 别名]
 def init(self, phys, forces, prop):
    """
    Initialize propagator.
    
    @type phys: Physical
    @param phys: The physical system.
    
    @type forces: Forces
    @param forces: MDL Forces object.
    
    @type prop: Propagator
    @param prop: MDL Propagator object.
    """
    self.bathPold = self.bathP #: Old thermostat value as system stores rescaled velocity number of Dof of system, momentum conserved so atoms*3D-3
    self.gkT = 3.0*(phys.numAtoms()-1.0)*Constants.boltzmann()*self.temp #: Product of degrees of freedom, boltzmann constant and Kelvin temperature
    self.KEtoT = 2.0 / (3.0*(phys.numAtoms()-1.0)*Constants.boltzmann()) #: Kinetic to temp. conversion
    prop.calculateForces(forces)
    self.Potnl = forces.energies.potentialEnergy(phys)  #: Potential energy
    self.h0 = self.Potnl + forces.energies.kineticEnergy(phys)  #: Initial 'internal' Hamiltonian value so that total Hamiltonian allways 0
    self.stepsdone = 0 #: Number of steps completed
    self.avTemp = 0 #: Average Kelvin temperature
    self.tempers = [] #: Holds pairs of step numbers and average temperatures
    self.Hamiltonian = [] #: Holds pairs of step numbers and total energies

# 需要导入模块: import Constants [as 别名]
# 或者: from Constants import boltzmann [as 别名]
    def run(self, phys, forces, prop):
       """
       Execute the propagator.
       
       @type phys: Physical
       @param phys: The physical system.
       
       @type forces: Forces
       @param forces: MDL Forces object

       @type prop: Propagator
       @param prop: MDL Propagator object
       """
       forceconstant = 2*Constants.boltzmann()*self.temp*self.gamma/self.dt      # assign random force
       forces.force += forces.randomForce(phys,self.seed)*numpy.sqrt(forceconstant*phys.masses)
       phys.velocities *= (1.0-0.5*self.dt*self.gamma)         # first half kick
       phys.velocities += forces.force*0.5*self.dt*phys.invmasses
       phys.positions += phys.velocities*self.dt                # drift
       prop.calculateForces(forces)
       forceconstant = 2*Constants.boltzmann()*self.temp*self.gamma/self.dt      # assign random force
       forces.force += forces.randomForce(phys,self.seed)*numpy.sqrt(forceconstant*phys.masses)
       phys.velocities += forces.force*0.5*self.dt*phys.invmasses   # second first kick
       phys.velocities *= (1.0/(1.0+0.5*self.dt*self.gamma))

# 需要导入模块: import Constants [as 别名]
# 或者: from Constants import boltzmann [as 别名]
 def init(self, phys, forces, prop):
    """
    Initialize propagator.
    
    @type phys: Physical
    @param phys: The physical system.
    
    @type forces: Forces
    @param forces: MDL Forces object.
    
    @type prop: Propagator
    @param prop: MDL Propagator object.
    """
    prop.calculateForces(forces)
    self.Potnl = forces.energies.potentialEnergy(phys) #: Potential energy
    self.gkT = 3.0*(phys.numAtoms()-1.0)*Constants.boltzmann()*self.temp #: Number of Dof*kT, momentum conserved so number of atoms * 3D - 3 
    self.KEtoT = 2.0 / (3.0*(phys.numAtoms()-1.0)*Constants.boltzmann()) #: Convertion of kinetic energy to temperature
    self.Nf = 3.0*(phys.numAtoms()-1.0)   #: number of Dof
    self.kT = Constants.boltzmann()*self.temp    #: Boltzmann constant times Kelvin temperature
    self.h0 = self.totalEnergy(0,phys,forces)    #: Initial total energy
    self.stepsdone = 0 #: Number of steps completed
    self.avTemp = 0 #: Average Kelvin temperature
    self.tempers = [] #: Holds pairs of step numbers and average temperatures
    self.Hamiltonian = [] #: Holds pairs of step numbers and total energies

# 需要导入模块: import Constants [as 别名]
# 或者: from Constants import boltzmann [as 别名]
def metropolis( u_i, u_j, t_i, t_j ):
    # Metropolis for replicas i with potential energy u_i
    #                         temperature t_i
    #                    and  j with potential energy u_j
    #                         temperature t_j
    K_b = Constants.boltzmann()
    deltaE = (1 / (K_b * t_i) - 1/ (K_b * t_j) ) - (u_j - u_i)
    if( deltaE < 0 ):
        return True
    acceptProb = np.exp( -deltaE )
    randNum = nr.random()
    if( randNum < acceptProb ):
        return True
    else:
        return False

# 需要导入模块: import Constants [as 别名]
# 或者: from Constants import boltzmann [as 别名]
def friction(phys, forces, prop, obj):
   """
    Modify the force vector to include a frictional force.
    This can be used for incorporation of Langevin dynamics.
    
    @type phys: Physical
    @param phys: The physical system.

    @type forces: Forces
    @param forces: MDL Forces object
    
    @type prop: Propagator
    @param prop: MDL Propagator object

    @type obj: STS/MTS
    @param obj: Prototyped propagator object
   """
   targetKE = 3.0/2.0*phys.numAtoms()*Constants.boltzmann()*obj.temp
   obj.thermal = 0
   obj.bathpos = (forces.energies.kineticEnergy(phys) - targetKE)*obj.thermal/(obj.dt*phys.numAtoms())
   forces.force -= phys.velocities*obj.bathpos*phys.masses