def compare_linalg(self, A, B, nnodes=20, nedges=20): from kmc_rates import TwoStateRates maker = _MakeRandomGraph(nnodes=20, nedges=20, node_set=A+B) maker.run() reducer = NGT(maker.rates, A, B) reducer.compute_rates_and_committors() committors = reducer.get_committors() la = TwoStateRates(maker.rates, A, B) # la.compute_rates() la.compute_committors() qla = la.committor_dict for n, qla in la.committor_dict.iteritems(): self.assertAlmostEqual(qla, committors[n], 7)
def compare(self, A, B, nnodes=10, nedges=20, weights=None, x=1): print "" maker = _MakeRandomGraph(nnodes=nnodes, nedges=nedges, node_set=A+B+[x]) graph = maker.run() graph_backup = graph.copy() reducer = GraphReduction(maker.rates, A, B, weights=weights) kmc = KineticMonteCarlo(graph_backup, debug=False) # test compute_committor_probability() PxB = reducer.compute_committor_probability(x) PxB_kmc = kmc.committor_probability(x, A, B, niter=1000) print "committor probability ", x, "->", B, "=", PxB print "committor probability kmc", x, "->", B, "=", PxB_kmc self.assertAlmostEqual(PxB, PxB_kmc, delta=.1) reducer.compute_rates() rAB = reducer.get_rate_AB() rBA = reducer.get_rate_BA() rAB_SS = reducer.get_rate_AB_SS() # compute rate via linalg lin = TwoStateRates(maker.rates, A, B, weights=weights) lin.compute_rates() rAB_LA = lin.get_rate_AB() lin.compute_committors() rAB_SS_LA = lin.get_rate_AB_SS() self.assertAlmostEqual(rAB_SS, rAB_SS_LA, 5) PxB_LA = lin.get_committor(x) if x not in A and x not in B: self.assertAlmostEqual(PxB, PxB_LA, 5) rAB_KMC = kmc.mean_rate(A, B, niter=1000, weights=weights) print "NGT rate A->B", rAB print "KMC rate A->B", rAB_KMC print "normalized difference", (rAB - rAB_KMC)/rAB print "normalized difference to linalg", (rAB - rAB_LA)/rAB self.assertLess(abs(rAB - rAB_KMC)/rAB, .1) self.assertLess(abs(rAB - rAB_LA)/rAB, .00001) rBA_KMC = kmc.mean_rate(B, A, niter=1000, weights=weights) print "NGT rate B->A", rBA print "KMC rate B->A", rBA_KMC print "normalized difference", (rBA - rBA_KMC)/rBA self.assertLess(abs(rBA - rBA_KMC)/rBA, .1) paB = kmc.committor_probability(A[0], [A[0]], B, niter=1000) print "the committor probability a->B", paB print "graph reduction committor prob", reducer.get_committor_probabilityAB(A[0]) self.assertAlmostEqual(paB, reducer.get_committor_probabilityAB(A[0]), delta=.1)