# Initialize fiber discretization
NupsampleForDirect=128;
fibDisc = ChebyshevDiscretization(Lf,eps,Eb,mu,N,deltaLocal=0.1,nptsUniform=40,NupsampleForDirect=NupsampleForDirect);
fibList = makeFibBundle(nFib,N,fibDisc);
# Initialize the master list of fibers
allFibers = fiberCollection(nFib,10,fibDisc,nonLocal,mu,omega,gam0,Dom);
#allFibers.initFibList(fibList,Dom,pointsfileName='StiffLocs'+str(seed+1)+'.txt',tanvecfileName='StiffTanVecs'+str(seed+1)+'.txt');
allFibers.initFibList(fibList,Dom);
allFibers.fillPointArrays();
Ewald = GPUEwaldSplitter(allFibers.getaRPY()*eps*Lf,mu,xi*1.4*(fibDisc.getNumDirect()/N)**(1/3),Dom,NupsampleForDirect*nFib);
# Initialize the temporal integrator
TIntegrator = CrankNicolson(allFibers);
if (nonLocal==3):
nIts = 2;
TIntegrator.setMaxIters(nIts);
TIntegrator.setLargeTol(0.1);
# Prepare the output file and write initial locations
of = prepareOutFile('BundleTest/XLooseBundle'+str(nonLocal)+'.txt');
allFibers.writeFiberLocations(of);
stopcount = int(tf/dt+1e-10);
Lamstress = np.zeros(stopcount);
Elstress = np.zeros(stopcount);
nLinks =np.zeros(stopcount)
for iT in range(stopcount):
maxX, _, StressArray = TIntegrator.updateAllFibers(iT,dt,stopcount,Dom,Ewald,grav/Lf,write=1,outfile=of,stress=True);
Lamstress[iT]=StressArray[0];
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)
else:
TIntegrator = CrankNicolson(allFibers, CLNet)
TIntegrator.setMaxIters(nIts)
TIntegrator.setLargeTol(LargeTol)
# Prepare the output file and write initial locations
of = prepareOutFile('DynamicRheo/Locs' + outFile)
allFibers.writeFiberLocations(of)
saveCurvaturesAndStrains(allFibers, CLNet, outFile, wora='w')
ofCL = prepareOutFile('DynamicRheo/Step' + str(0) + 'Links' + outFile)
CLNet.writeLinks(ofCL)
ofCL.close()
# Run to steady state (no flow)
stopcount = int(tf / dt + 1e-10)
numSaves = stopcount // saveEvery + 1
numStress = stopcount // stressEvery
gam0,
Dom,
nThreads=4)
# Initialize the fiber list
fibList = [None] * nFib
allFibers.initFibList(fibList, Dom)
allFibers.fillPointArrays()
#of = prepareOutFile('PyLocs.txt');
#allFibers.writeFiberLocations(of);
# Initialize the temporal integrator
if (TemporalOrder == 1):
TIntegrator = BackwardEuler(allFibers, FPimp=ImpFP)
else:
TIntegrator = CrankNicolson(allFibers, FPimp=ImpFP)
TIntegrator.setMaxIters(giters)
TIntegrator.setLargeTol(1e-6)
# Compute the endtime and do the time loop
stopcount = int(tf / dt + 1e-10)
for iT in range(stopcount):
#print('Time %1.2E' %(float(iT)*dt));
maxX, _, _ = TIntegrator.updateAllFibers(iT,
dt,
stopcount,
Dom,
Ewald,
gravity,
write=0)
#print('Max x: %f' %maxX);
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);
# Initialize the temporal integrator
TIntegrator = CrankNicolson(allFibers, CLNet)
TIntegrator.setMaxIters(1)
# only 1 iteration since we do local drag
# Prepare the output file and write initial locations
of = prepareOutFile('PermanentLinkLocsF' + str(nFib) + 'C' + str(nCL) + 'rl' +
str(rl) + '.txt')
allFibers.writeFiberLocations(of)
saveCurvaturesAndStrains(nFib, nCL, allFibers, CLNet, rl, wora='w')
# Run to steady state
stopSS = int(tf / dt + 1e-10)
for iT in range(stopSS):
wr = 0
if ((iT % saveEvery) == (saveEvery - 1)):
print('Time %1.2E' % (float(iT) * dt))
Dom = PeriodicShearedDomain(Ld,Ld,Ld);
# Initialize fiber discretization
fibDisc = ChebyshevDiscretization(Lf,eps,Eb,mu,N,deltaLocal=0.1,NupsampleForDirect=N,rigid=True);
# Initialize the master list of fibers
allFibers = fiberCollection(nFib,10,fibDisc,nonLocal,mu,omega,gam0,Dom);
fibList = makeThreeSheared(Lf,N,fibDisc);
allFibers.initFibList(fibList,Dom);
allFibers.fillPointArrays();
# Initialize Ewald for non-local velocities
Ewald = EwaldSplitter(allFibers.getaRPY()*eps*Lf,mu,xi,Dom,N*nFib);
# Initialize the temporal integrator
TIntegrator = CrankNicolson(allFibers);
# Number of GMRES iterations for nonlocal solves
# 1 = block diagonal solver
# N > 1 = N-1 extra iterations of GMRES
TIntegrator.setMaxIters(giters);
# Prepare the output file and write initial locations
of = prepareOutFile('New2LocationsN' +str(N)+'G'+str(giters)+str(dt)+'.txt');
allFibers.writeFiberLocations(of);
# Time loop
stopcount = int(tf/dt+1e-10);
for iT in range(stopcount):
print('Time %f' %(float(iT)*dt));
maxX = TIntegrator.updateAllFibers(iT,dt,stopcount,Dom,Ewald,gravity/Lf,of);
print(maxX)
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)
print('Number of links initially %d' % CLNet._nDoubleBoundLinks)
# Initialize the temporal integrator
if (BrownianFluct or useBackwardEuler):
TIntegrator = BackwardEuler(allFibers, CLNet, FPimp=ImplicitFinitePart)
else:
TIntegrator = CrankNicolson(allFibers, CLNet, FPimp=ImplicitFinitePart)
TIntegrator.setMaxIters(nIts)
TIntegrator.setLargeTol(LargeTol)
# Prepare the output file and write initial network information
of = prepareOutFile('BundlingBehavior/Locs' + OutputFileName)
allFibers.writeFiberLocations(of)
saveCurvaturesAndStrains(nFib,
konCL,
allFibers,
CLNet,
rl,
OutputFileName,
wora='w')
ofCL = prepareOutFile('BundlingBehavior/Step' + str(0) + 'Links' +
OutputFileName)
fibDisc.getNumUniform(),
Lf,
nCL,
Kspring,
rl,
konCL,
koffCL,
CLseed,
Dom,
fibDisc,
nThreads=4)
CLNet.setLinksFromFile('NetworkSteadyStates/F' + str(nFib) + 'C' +
str(nCL) + '.txt')
# Initialize the temporal integrator
TIntegrator = CrankNicolson(allFibers, CLNet)
TIntegrator.setMaxIters(nIts)
# Prepare the output file and write initial locations
of = prepareOutFile('Straining' + HydroStr + 'Om' + str(omHz) + 'LocsF' +
str(nFib) + 'C' + str(nCL) + 'REV.txt')
allFibers.writeFiberLocations(of)
#saveCurvaturesAndStrains(omHz,nFib,nCL,allFibers,CLNet,HydroStr,wora='w')
stopcount = int(tf / dt + 1e-10)
Lamstress = np.zeros(stopcount)
Elstress = np.zeros(stopcount)
CLstress = np.zeros(stopcount)
for iT in range(stopcount):
wr = 0
if ((iT % saveEvery) == (saveEvery - 1)):
nonLocal,
mu,
omega,
gam0,
Dom,
nThreads=4)
# Initialize the fiber list
fibList = [None] * nFib
allFibers.initFibList(fibList, Dom)
allFibers.fillPointArrays()
#of = prepareOutFile('PyLocs.txt');
#allFibers.writeFiberLocations(of);
# Initialize the temporal integrator
TIntegrator = CrankNicolson(allFibers)
TIntegrator.setMaxIters(giters)
# Compute the endtime and do the time loop
stopcount = int(tf / dt + 1e-10)
for iT in range(stopcount):
print('Time %1.2E' % (float(iT) * dt))
maxX = TIntegrator.updateAllFibers(iT,
dt,
stopcount,
Dom,
Ewald,
gravity,
write=0)
print('Max x: %f' % maxX)
if (maxX > 2 * Ld):