def main():
nnodes = 100
# an easy way to set up the graph is to make
# a dictionary of rates
rates = dict()
for i in range(nnodes):
for j in range(i+1,nnodes):
rates[(i,j)] = float(i+j) / (i+1)
rates[(j,i)] = float(i+j) / (j+1)
# we want to compute rates from node 0 to node 1
A = [0 ,1, 2]
B = [3, 4]
x = 2
weights=dict([(a,1.) for a in A+B])
weights[2] = 5e3
ngt = NGT(rates, A, B)
ngt.compute()
kAB = ngt.get_rate_AB()
kBA = ngt.get_rate_BA()
print "rate AB", kAB
print "rate BA", kBA
graph = kmcgraph_from_rates(rates)
pyngt = GraphReduction(graph, A, B)
pyngt.compute_rates()
print "pyngt rate AB", pyngt.get_rate_AB()
print "pyngt rate AB", pyngt.get_rate_BA()
def main():
"""the main loop"""
tstart = time.clock()
parser = argparse.ArgumentParser(description=description)
parser.add_argument("-d", type=str, default=".",
help="directory with the min.data, ts.data files")
parser.add_argument("-T", type=float, default=1., help="Temperature")
args = parser.parse_args()
print "temperature", args.T
directory = args.d
print "reading from directory:", os.path.abspath(directory)
A = read_minA(directory+"/min.A")
B = read_minA(directory+"/min.B")
rate_constants, Peq, knorm = make_rates(args.d, args.T)
if True:
fname = "out.rate_consts"
print "saving rate constants to", fname
with open(fname, "w") as fout:
for (u,v), k in sorted(rate_constants.iteritems()):
fout.write("%6d %6d %s\n" % (u,v,k/knorm))
print "checking and reducing the graph structure"
try:
rate_constants = reduce_rates(rate_constants, B, A=A)
except Exception:
analyze_graph_error(rate_constants, A, B)
raise
write_dat_files(rate_constants, A, B, Peq)
print "computing mean first passage times"
calculator = NGT(rate_constants, A, B, weights=Peq)#, check_rates=False)
calculator.compute()
print "computing rates"
kAB = calculator.get_rate_AB()
print "k(B<-A)", kAB / knorm
kBA = calculator.get_rate_BA()
print "k(A<-B)", kBA / knorm
# if True:
# fname = "out.mfpt"
# print "saving mean first passage times for all minima to reach B to file", fname
# mfpt = sorted([(m, t) for m, t in
# calculator.mfpt_computer.mfpt_dict.iteritems()])
# with open(fname, "w") as fout:
# for i, t in mfpt:
# fout.write("%d %.12g\n" % (i, t * knorm))
#
# print "computing committor probabilities"
# sys.stdout.flush()
# calculator.compute_committors()
# print "computing steady state rates"
# kSS = calculator.get_rate_AB_SS() / knorm
# print "kSS(B<-A)", kSS
#
# if True:
# fname = "out.committors"
# print "saving committor probabilities for all minima to file", fname
# coms = sorted([(m, c) for m, c in
# calculator.committor_computer.committor_dict.iteritems()])
# with open(fname, "w") as fout:
# for i, c in coms:
# fout.write("%d %.12g\n" % (i, c))
#
time_solve = calculator.time_solve #+ calculator.committor_computer.time_solve
print "time spent solving linear equations", time_solve, "seconds"
print "total time", time.clock() - tstart