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];
Elstress[iT]=StressArray[1];
np.savetxt('BundleTest/StresssLooseBundle'+str(nonLocal)+'.txt',Lamstress+Elstress);
del allFibers;
del fibDisc;
del Dom;
del TIntegrator;
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);
# 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
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
Lamstress = np.zeros(numStress)
Elstress = np.zeros(numStress)
CLstress = np.zeros(numStress)
NumFibsConnected = np.zeros((numSaves, nFib), dtype=np.int64)
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)
# Destruction and cleanup
of.close();
del Dom;
del Ewald;
del fibDisc;
del allFibers;
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)
CLNet.writeLinks(ofCL)
ofCL.close()
stopcount = int(tf / dt + 1e-10)
numSaves = stopcount // saveEvery + 1
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)):
print('Time %1.2E' % (float(iT) * dt))
wr = 1
maxX = TIntegrator.updateAllFibers(iT,
dt,
stopcount,
allFibers.fillPointArrays()
# Initialize Ewald for non-local velocities
Ewald = GPUEwaldSplitter(allFibers.getaRPY() * eps * Lf, mu, xi,
Dom, fibDisc._nptsDirect * nFib)
# Initialize the temporal integrator
TIntegrator = BackwardEuler(allFibers, FPimp=0)
# Number of GMRES iterations for nonlocal solves
# 1 = block diagonal solver
# N > 1 = N-1 extra iterations of GMRES
TIntegrator.setMaxIters(giters)
TIntegrator.setLargeTol(1e-6)
# Prepare the output file and write initial locations
of = prepareOutFile('ThreeSheared/BE_Eps2RPYExLocsN' + 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)
# Destruction and cleanup
of.close()
del Dom
del Ewald
del fibDisc
for omHz in omegasToDo:
omega = 2 * pi * omHz
if (omHz > 0):
T = 1 / omHz
# one period
gam0 = maxStrain * omega # strain amplitude
else:
gam0 = maxStrain
T = 4
# Set up simulation variables
stressEvery = 1
saveEvery = int(savedt / dt + 1e-10)
print('Omega %f: stopping time %f, saveEvery %f, stressEvery %f' %
(omHz, tf, saveEvery * dt, stressEvery * dt))
# Run to steady state (no flow)
of = prepareOutFile('DynamicRheo/Locs' + outFile)
stopcount = int(tf / dt + 1e-10)
numSaves = stopcount // saveEvery + 1
numStress = stopcount // stressEvery
Lamstress = np.zeros(numStress)
Elstress = np.zeros(numStress)
CLstress = np.zeros(numStress)
NumFibsConnected = np.zeros((numSaves, nFib), dtype=np.int64)
labels = np.zeros((numSaves, nFib), dtype=np.int64)
AllLocalAlignment = np.zeros((numSaves, nFib))
AvgTangentVectors = np.zeros((numSaves * nFib, 3))
numLinksByFib = np.zeros((numSaves, nFib), dtype=np.int64)
numBundlesSep = np.zeros(numSaves, dtype=np.int64)
avgBundleAlignment_Sep = np.zeros(numSaves)