def update_energy(self, torschange, angchange, dict):
QSimulation.k_Qpin = dict['k_Qpin']
Simulation.nsigma2 = dict['nsigma2']
Simulation.totnc = dict['totnc']
SurfaceSimulation.update_energy(self, torschange, angchange, dict)
self.newQ = energyfunc.nativecontact(self.r2new, Simulation.nativeparam, Simulation.nsigma2) / Simulation.totnc
self.u1 += QSimulation.k_Qpin*(self.newQ - self.Qpin)**2
def loadextend(self, extenddirec):
self.coord = numpy.load('%s/coord%s.npy' % (extenddirec, self.suffix))
self.setenergy()
self.energyarray[0] = self.u0
self.nc[0] = energyfunc.nativecontact(
self.r2, Simulation.nativeparam,
Simulation.nsigma2) / Simulation.totnc
def setenergy(self):
# sets the u0, r2, torsE, angE from the current configuration
# called when restarting from a checkpoint
Simulation.setenergy(self)
self.Q = energyfunc.nativecontact(
self.r2, Simulation.nativeparam,
Simulation.nsigma2) / Simulation.totnc
self.u0 += QSimulation.k_Qpin * (self.Q - self.Qpin)**2
def save(self):
index = self.move / Simulation.save
self.energyarray[index] = self.u0
self.surfE_array[index, :] = self.surfE
self.nc[index] = energyfunc.nativecontact(self.r2, Simulation.nativeparam,
Simulation.nsigma2)
self.z_array[index] = numpy.sum(
self.mass * self.coord[:, 2]) / self.totmass
if (Simulation.writetraj):
f = open('%s/trajectory%i' % (self.out, int(self.T)), 'ab')
numpy.save(f, self.coord)
f.close()
return self
def save_state(self, dict):
Simulation.save = dict['save']
Simulation.nativeparam = dict['nativeparam']
Simulation.nsigma2 = dict['nsigma2']
Simulation.writetraj = dict['writetraj']
Simulation.totnc = dict['totnc']
self.energyarray[self.move / Simulation.save] = self.u0
self.nc[self.move / Simulation.save] = energyfunc.nativecontact(
self.r2, Simulation.nativeparam,
Simulation.nsigma2) / Simulation.totnc
if (Simulation.writetraj):
f = open('%s/trajectory%s' % (self.out, self.suffix), 'ab')
numpy.save(f, self.coord)
f.close()
def __init__(self, name, outputdirectory, coord, temp):
self.name = name
self.out = outputdirectory
self.suffix = str(int(temp)) # affixed at end of file names
self.coord = coord
self.energyarray = numpy.empty(Simulation.totmoves / Simulation.save +
1)
self.nc = numpy.empty(Simulation.totmoves / Simulation.save +
1) #native contacts
self.move = 0
self.T = temp
self.maxtheta = numpy.array([
5., # bend
10., # torsion
1. / self.T * 500, # global crankshaft
5.
]) # ParRot move
self.maxtheta = self.maxtheta * numpy.pi / 180 * self.T**1.5 / 5250. * 50 / Simulation.numbeads
self.setenergy()
self.energyarray[0] = self.u0
self.nc[0] = energyfunc.nativecontact(
self.r2, Simulation.nativeparam,
Simulation.nsigma2) / Simulation.totnc
# Instantiate constants for move stats
self.amoves = 0
self.atmoves = 0
self.gcmoves = 0
self.pmoves = 0
self.mdmoves = 0
self.acceptedgc = 0
self.acceptedp = 0
self.acceptedmd = 0
self.acceptedat = 0
self.accepteda = 0
self.pclosure = 0
self.accepted = 0
self.rejected = 0
self.movetype = ''
def setenergy(self):
SurfaceSimulation.setenergy(self)
self.Q = energyfunc.nativecontact(self.r2, Simulation.nativeparam, Simulation.nsigma2) / Simulation.totnc
self.u0 += QSimulation.k_Qpin*(self.Q - self.Qpin)**2
def setenergy(self):
# sets the u0, r2, torsE, angE from the current configuration
# called when restarting from a checkpoint
Simulation.setenergy(self)
self.Q = energyfunc.nativecontact(self.r2, Simulation.nativeparam, Simulation.nsigma2) / Simulation.totnc
self.u0 += QSimulation.k_Qpin*(self.Q - self.Qpin)**2