notebook.community

Edit and run



In [1]:

    
%matplotlib inline
import openpathsampling as paths
import numpy as np

As always, we load things from files so we don't have to set them up again.



In [2]:

    
old = paths.AnalysisStorage("mistis.nc")
engine = old.engines[0]
network = old.networks[0]
states = set(network.initial_states + network.final_states)

The flux_pairs variable is a list of 2-tuples, where the first element is the state we're calculating the flux out of, and the second element is the interface we're calculating the flux through.



In [3]:

    
flux_pairs = [(trans.stateA, trans.interfaces[0]) for trans in network.transitions.values()]

Set up the simulation and run it!



In [4]:

    
sim = paths.DirectSimulation(
    storage=None,
    engine=engine,
    states=states,
    flux_pairs=flux_pairs,
    initial_snapshot=old.snapshots[0]
)



In [5]:

    
%%time
sim.run(150000)









    



CPU times: user 6min 6s, sys: 1.13 s, total: 6min 7s
Wall time: 6min 10s

Now we move on to the analysis.



In [6]:

    
sim.rate_matrix









    Out[6]:






  
    
      
      ({x|opX(x) in [-inf, -0.3]} and {x|opY(x) in [-inf, -0.3]})
      ({x|opX(x) in [-inf, -0.3]} and {x|opY(x) in [0.3, inf]})
      ({x|opX(x) in [0.3, inf]} and {x|opY(x) in [-inf, -0.3]})
    
  
  
    
      ({x|opX(x) in [-inf, -0.3]} and {x|opY(x) in [-inf, -0.3]})
      NaN
      0.000113593
      7.93139e-05
    
    
      ({x|opX(x) in [-inf, -0.3]} and {x|opY(x) in [0.3, inf]})
      5.23322e-05
      NaN
      5.16412e-05
    
    
      ({x|opX(x) in [0.3, inf]} and {x|opY(x) in [-inf, -0.3]})
      5.8578e-05
      4.93234e-05
      NaN



In [7]:

    
sim.n_transitions









    Out[7]:





{(<openpathsampling.volume.IntersectionVolume at 0x11595a290>,
  <openpathsampling.volume.IntersectionVolume at 0x11595a390>): 20,
 (<openpathsampling.volume.IntersectionVolume at 0x11595a290>,
  <openpathsampling.volume.IntersectionVolume at 0x11595a990>): 10,
 (<openpathsampling.volume.IntersectionVolume at 0x11595a390>,
  <openpathsampling.volume.IntersectionVolume at 0x11595a290>): 19,
 (<openpathsampling.volume.IntersectionVolume at 0x11595a390>,
  <openpathsampling.volume.IntersectionVolume at 0x11595a990>): 16,
 (<openpathsampling.volume.IntersectionVolume at 0x11595a990>,
  <openpathsampling.volume.IntersectionVolume at 0x11595a290>): 11,
 (<openpathsampling.volume.IntersectionVolume at 0x11595a990>,
  <openpathsampling.volume.IntersectionVolume at 0x11595a390>): 16}



In [8]:

    
fluxes = sim.fluxes
for f in fluxes:
    print f[0].name, f[1].name, fluxes[f]









    



A -inf<opY<-0.3 0.00130918783318
B -inf<opXprime<-0.3 0.00129306050463
A -inf<opX<-0.3 0.00134206626387



In [9]:

    
sim.n_flux_events









    Out[9]:





{(<openpathsampling.volume.IntersectionVolume at 0x11595a390>,
  <openpathsampling.volume.CVDefinedVolume at 0x11593e9d0>): 501,
 (<openpathsampling.volume.IntersectionVolume at 0x11595a390>,
  <openpathsampling.volume.CVDefinedVolume at 0x115952cd0>): 518,
 (<openpathsampling.volume.IntersectionVolume at 0x11595a990>,
  <openpathsampling.volume.CVDefinedVolume at 0x115945b90>): 610}



In [ ]:

	({x\|opX(x) in [-inf, -0.3]} and {x\|opY(x) in [-inf, -0.3]})	({x\|opX(x) in [-inf, -0.3]} and {x\|opY(x) in [0.3, inf]})	({x\|opX(x) in [0.3, inf]} and {x\|opY(x) in [-inf, -0.3]})
({x\|opX(x) in [-inf, -0.3]} and {x\|opY(x) in [-inf, -0.3]})	NaN	0.000113593	7.93139e-05
({x\|opX(x) in [-inf, -0.3]} and {x\|opY(x) in [0.3, inf]})	5.23322e-05	NaN	5.16412e-05
({x\|opX(x) in [0.3, inf]} and {x\|opY(x) in [-inf, -0.3]})	5.8578e-05	4.93234e-05	NaN