def setUp(self): ensembleSize=3 esim = EnsembleSimulation("ensemble",ensembleSize) print "ensemble size", esim.size(),"running on",esim.numThreads(),"processors." dyn = ivm.IVM(esim) protocol.torsionTopology(dyn) potList = PotList("test pot list") pot = PyEnsemblePot('test ensemble pot') potList.append(pot) protocol.initDynamics(dyn, bathTemp=400, initVelocities=1, potList=potList, finalTime=1, numSteps=1, printInterval=0) dyn.run()
# Give atoms uniform weights, except for the anisotropy axis # protocol.massSetup() # IVM setup # the IVM is used for performing dynamics and minimization in torsion-angle # space, and in Cartesian space. # from ivm import IVM dyn = IVM() # reset ivm topology for torsion-angle dynamics # dyn.reset() protocol.torsionTopology(dyn) # minc used for final cartesian minimization # minc = IVM() protocol.initMinimize(minc) protocol.cartesianTopology(minc) # object which performs simulated annealing # from simulationTools import AnnealIVM init_t = 3000. # Need high temp and slow annealing to converge cool = AnnealIVM(initTemp=init_t, finalTemp=25, tempStep=12.5,
# protocol.massSetup() # IVM setup # the IVM is used for performing dynamics and minimization in torsion-angle # space, and in Cartesian space. # dyn = IVM() # initialize ivm topology for torsion-angle dynamics #for m in media.values(): # m.setFreedom("fixDa, fixRh") #fix tensor Rh, Da, vary orientation ## m.setFreedom("varyDa, varyRh") #vary tensor Rh, Da, vary orientation protocol.torsionTopology(dyn) # minc used for final cartesian minimization # minc = IVM() protocol.initMinimize(minc) #for m in media.values(): # m.setFreedom("varyDa, varyRh") #allow all tensor parameters float here # pass protocol.cartesianTopology(minc) # object which performs simulated annealing #