def index_msd(VW,index,L,t,save='msd_index'):
#skip = VW.shape[0]/len(surface)
skip = 1
spheres = np.zeros((t,len(index),3))
for f in range(t):
for i,j in enumerate(index):
spheres[f][i] = VW[f*skip][j]
x, MSD = msd_no_drift(spheres,L)
pyplot_eps.plot(x,MSD,xlabel='t',ylabel=r'$\sqrt{<(r(t)-r(0))^2>}$',save=save)
return x,MSDj
def find_lifetime(M,L,steps,temp,step_range=30,delta=4,rcut=1.0,step=5e4):
import MD.analysis.lifetime as life
try:
C = util.pickle_load('C.pkl')
G = util.pickle_load('G.pkl')
except:
C=M.cord_auto(['C'])
G=M.cord_auto(['G'])
util.pickle_dump(C,'C.pkl')
util.pickle_dump(G,'G.pkl')
#The total number of frames we are going to look at
for i in steps:
try:
print 'Frame',i,'Temp',temp[i]
except:
print i
x=np.arange(i,step_range+i,delta)
#Find he number of connections at specific points x
remain = life.lifetime(C[x],G[x],L)
x=np.arange(i,step_range+i,delta)*50000
print remain
pyplot_eps.plot(x,remain,xlabel='time', ylabel='remaining connections',
save='lifetime%i'%i)
plt.close()
def find_networks(M, VW, L, n_finish=1, n_start=0, delta=30, rcut=1.0, ndna=25):
#The total number of frames we are going to look at
x=np.arange(n_start,n_finish,delta)
print len(x)
#Find the number of connections at specific points x
import MD.canalysis.connections as con
import MD.analysis.connections as conn
import MD.analysis.graph as graph
try:
connections = util.pickle_load('con.pkl')
except:
try:
C = util.pickle_load('C.pkl')
G = util.pickle_load('G.pkl')
except:
G=M.cord_auto(['G'])
C=M.cord_auto(['C'])
util.pickle_dump(C,'C.pkl')
util.pickle_dump(G,'G.pkl')
connections = con.connections(C[x],G[x],L,rcut=rcut)
util.pickle_dump(connections,'con.pkl')
#plot total number of connections
num_connections=conn.num_connections(connections,VW.shape[1])
con_all = []
for i in range(len(connections)):
con_all.append(len(connections[i])/2.)
pyplot.plot(x,num_connections,xlabel='Time',
ylabel='hyrbid. density', save='connections')
pyplot.plot(x,con_all,xlabel='Time',
ylabel='hyrbid', save='connections_all')
plt.close()
#get the info
networks, num_networks, deg, neighbors, num_n, gr = graph.grapher(connections,VW.shape[1],ndna)
util.pickle_dump(networks,'net.pkl')
#plot the number of neighbors at each timesteps
pyplot_eps.plot(x,num_n,xlabel='Time',
ylabel='num neighbors', save='neighbors')
plt.close()
print 'making plot'
net = []
for i in networks:
net.append(len(i))
pyplot_eps.plot(x,net,xlabel='t',ylabel='networks',save='net')
label = ['networks','1','2','3','4','5','6','7','8','9']
pyplot_eps.plot(x,networks,xlabel='t',ylabel='Networks',save='net')
pyplot.plot_multi(x,deg,label,xlabel='time',ylabel='number',save='con_net')
return x, networks, connections