# Initialize the fiber list (straight fibers)
fibList = [None] * nFib
#print('Loading from steady state')
#XFile = 'SSLocsF'+str(nFib)+'C'+str(nCL)+'REV.txt';
#XsFile = 'SSTanVecsF'+str(nFib)+'C'+str(nCL)+'REV.txt';
allFibers.initFibList(fibList, Dom)
#,pointsfileName=XFile,tanvecfileName=XsFile);
allFibers.fillPointArrays()
# Initialize the network of cross linkers (set links from file)
# New seed for CLs
CLseed = 2
np.random.seed(CLseed)
CLNet = KMCCrossLinkedNetwork(nFib,
N,
fibDisc.getNumUniform(),
Lf,
nCL,
Kspring,
rl,
konCL,
koffCL,
CLseed,
Dom,
fibDisc,
nThreads=4)
CLNet.updateNetwork(allFibers, Dom, 0.01)
ofCL = prepareOutFile('F' + str(nFib) + 'C' + str(nCL) + 'rl' + str(rl) +
'.txt')
CLNet.writeLinks(ofCL, allFibers.getUniformPoints(allFibers._ptsCheb), Dom)
#CLNet.setLinksFromFile('F'+str(nFib)+'C'+str(nCL)+'.txt',Dom);
tanvecfileName=XsFile)
except:
print('Redirecting input file directory')
XFile = 'DynamicRheo/Time60Locs' + inFile
XsFile = 'DynamicRheo/Time60TanVecs' + inFile
allFibers.initFibList(fibList,
Dom,
pointsfileName=XFile,
tanvecfileName=XsFile)
allFibers.fillPointArrays()
# Initialize the network of cross linkers
# New seed for CLs
np.random.seed(CLseed)
CLNet = DoubleEndedCrossLinkedNetwork(nFib,N,fibDisc.getNumUniform(),Lf,Kspring,\
rl,konCL,koffCL,konSecond,koffSecond,CLseed,Dom,fibDisc,nThreads=nThr)
print('Name of the input file: ' + inFile)
try:
CLNet.setLinksFromFile('DynamicStress/DynamicSSLinks' + inFile,
'DynamicStress/DynSSFreeLinkBound' + inFile)
except:
print('Redirecting CL infile')
CLNet.setLinksFromFile('DynamicRheo/Time60Links' + inFile,
'DynamicRheo/Time60FreeLinkBound' + inFile)
print('Number of links initially %d' % CLNet._nDoubleBoundLinks)
# Initialize the temporal integrator
if (useBackwardEuler):
TIntegrator = BackwardEuler(allFibers, CLNet)
print('Initializing fresh')
allFibers.initFibList(fibList, Dom)
else:
print('Initializing from file ' + initFile)
XFile = 'DynamicStress/DynamicSSLocs' + initFile
XsFile = 'DynamicStress/DynamicSSTanVecs' + initFile
allFibers.initFibList(fibList,
Dom,
pointsfileName=XFile,
tanvecfileName=XsFile)
# Initialize the network of cross linkers
# New seed for CLs
np.random.seed(CLseed)
# Initialize network
print('Number uniform sites %d' % fibDisc.getNumUniform())
if (BrownianFluct):
kBt = 4e-3
else:
kBt = 0
CLNet = DoubleEndedCrossLinkedNetwork(nFib,N,fibDisc.getNumUniform(),Lf,Kspring,\
rl,konCL,koffCL,konSecond,koffSecond,CLseed,Dom,fibDisc,nThreads=nThr,\
bindingSiteWidth=bindingSiteWidth,kT=kBt)
#Pairs, _ = CLNet.getPairsThatCanBind(allFibers,Dom);
#np.savetxt('PairsN'+str(fibDisc.getNumUniform())+'.txt',Pairs);
if (initFile is None):
CLNet.updateNetwork(allFibers, Dom, 100.0 / min(
konCL * Lf, konSecond * Lf, koffCL, koffSecond)) # just to load up CLs
else:
CLNet.setLinksFromFile('DynamicStress/DynamicSSLinks' + initFile,
'DynamicStress/DynSSFreeLinkBound' + initFile)