def kineticEnergy(self, phys):
"""
@type phys: Physical
@param phys: Physical system.
@rtype: float
@return: Kinetic energy, as a sum of 0.5*m*v^2 for each atom.
"""
return TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec)
def kineticEnergy(self, phys):
"""
@type phys: Physical
@param phys: Physical system.
@rtype: float
@return: Kinetic energy, as a sum of 0.5*m*v^2 for each atom.
"""
return TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec)
def totalEnergy(self, phys):
"""
@type phys: Physical
@param phys: Physical system.
@rtype: float
@return: Total energy, as a sum of potential and kinetic.
"""
# potentialEnergy() is a member function of ScalarStructure
return phys.app.energies.potentialEnergy()+TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec)
def totalEnergy(self, phys):
"""
@type phys: Physical
@param phys: Physical system.
@rtype: float
@return: Total energy, as a sum of potential and kinetic.
"""
# potentialEnergy() is a member function of ScalarStructure
return phys.app.energies.potentialEnergy(
) + TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec)
def plotTotal(self, phys, forces, step):
"""
Similar, for total energy
@type phys: Physical
@param phys: The physical system
@type forces: Forces
@param forces: MDL Forces object
@type step: int
@param step: Simulation step number
"""
self.plotQuantity(step, forces.energies.potentialEnergy(phys)+TopologyUtilities.kineticEnergy(phys.myTop, phys.velvec), 'totalenergy')