def loadextend(self, extenddirec):
SurfaceSimulation.loadextend(self, extenddirec)
self.z_array[0] = numpy.sum(
self.mass * self.coord[:, 2]) / self.totmass
self.u0 += energyfunc.umbrellaenergy(self.coord, self.z_pin, self.mass,
self.totmass)
self.energyarray[0] = self.u0
def __init__(self, name, outputdirectory, coord, temp, surf_coord, z_pin, mass):
self.z_pin = z_pin
SurfaceSimulation.__init__(self, name, outputdirectory, coord, temp, surf_coord)
self.mass = mass
self.totmass = numpy.sum(mass)
self.z_array = numpy.empty(Simulation.totmoves/Simulation.save + 1)
self.z_array[0] = numpy.sum(mass*self.coord[:,2])/self.totmass
self.u0 += energyfunc.umbrellaenergy(self.coord, self.z_pin, mass, self.totmass)
self.energyarray[0] = self.u0
def update_energy(self, torschange, angchange):
self.newtorsE = energyfunc.ctorsionenergy(self.newcoord, self.torsE,
Simulation.torsparam, torschange)
self.newangE = energyfunc.cangleenergy(self.newcoord, self.angE,
Simulation.angleparam, angchange)
self.newsurfE = energyfunc.csurfenergy(self.newcoord,
SurfaceSimulation.surface,
Simulation.numbeads,
SurfaceSimulation.nspint,
SurfaceSimulation.surfparam,
SurfaceSimulation.scale)
self.r2new, self.u1 = energyfunc.cgetLJenergy(
self.newcoord, Simulation.numint, Simulation.numbeads,
Simulation.nativeparam, Simulation.nonnativeparam, Simulation.nnepsil)
self.u1 += numpy.sum(self.newtorsE) + numpy.sum(self.newangE) + numpy.sum(
self.newsurfE)
self.u1 += energyfunc.umbrellaenergy(self.newcoord, self.z_pin, self.mass,
self.totmass)
return self
def update_energy(self, torschange, angchange, dict):
SurfaceSimulation.update_energy(self, torschange, angchange, dict)
self.u1 += energyfunc.umbrellaenergy(self.newcoord, self.z_pin, self.mass, self.totmass)
def loadextend(self,extenddirec):
SurfaceSimulation.loadextend(self,extenddirec)
self.z_array[0] = numpy.sum(self.mass*self.coord[:,2])/self.totmass
self.u0 += energyfunc.umbrellaenergy(self.coord, self.z_pin, self.mass, self.totmass)
self.energyarray[0] = self.u0
def loadstate(self):
SurfaceSimulation.loadstate(self)
self.z_array = numpy.load('%s/z_traj%i_%i.npy' %(self.out, int(self.z_pin), int(self.T)))
self.u0 += energyfunc.umbrellaenergy(self.coord, self.z_pin, self.mass, self.totmass)