nonLocal,
mu,
omega,
gam0,
Dom,
nThreads=nThr)
# Initialize Ewald for non-local velocities
if (nonLocal > 0 and nonLocal < 4):
Ewald = GPUEwaldSplitter(
allFibers.getaRPY() * eps * Lf, mu,
xi * 1.4 * (fibDisc.getNumDirect() / N)**(1 / 3), Dom,
NupsampleForDirect * nFib)
else: # This is so it doesn't try to initialize a GPU code if there isn't a GPU
Ewald = EwaldSplitter(allFibers.getaRPY() * eps * Lf, mu,
xi * 1.4 * (fibDisc.getNumDirect() / N)**(1 / 3),
Dom, NupsampleForDirect * nFib)
# Initialize the fiber list (straight fibers)
fibList = [None] * nFib
print('Loading from steady state')
try:
XFile = 'DynamicStress/DynamicSSLocs' + inFile
XsFile = 'DynamicStress/DynamicSSTanVecs' + inFile
allFibers.initFibList(fibList,
Dom,
pointsfileName=XFile,
tanvecfileName=XsFile)
except:
print('Redirecting input file directory')
XFile = 'DynamicRheo/Time60Locs' + inFile
for giters in gits:
for dt in dts:
# Initialize the domain
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):
# We don't have dynamic cross linking, what we do is bind links
# at t = 0 by calling the dynamic method with high binding rate and
# zero unbinding rate
konCL = 1000
# cross linker binding rate
koffCL = 1e-16
# cross linker unbinding rate
np.random.seed(1)
# Initialize the domain and spatial database
Dom = PeriodicShearedDomain(Ld, Ld, Ld)
# Initialize Ewald for non-local velocities
Ewald = EwaldSplitter(np.exp(1.5) / 4 * eps * Lf, mu, xi, Dom, N * nFib)
# Initialize fiber discretization
fibDisc = ChebyshevDiscretization(Lf, eps, Eb, mu, N, deltaLocal=0.1)
# Initialize the master list of fibers
allFibers = fiberCollection(nFib,
fibDisc,
nonLocal,
mu,
omega,
gam0,
Dom,
nThreads=4)
# Initialize the fiber list (straight fibers)
# The hexagonal array calculation
# Initialization
g = 0.5
# strain for parallelepiped
Lx = 2.0
Ly = 2.0
Lz = 2.0
a = 1e-2
mu = 3.0
xi = 5.0
Npts = 4
pts = np.array([[0, 0, 0], [1, 0, 0], [0.5, 1, 0], [1.5, 1, 0]])
forces = np.array([[1.0, 1, 1], [-1, -1, -1], [2, 2, 2], [-2.0, -2, -2]])
ShearDom = PeriodicShearedDomain(Lx, Ly, Lz)
ShearDom.setg(g)
Ewald = EwaldSplitter(a, mu, xi, ShearDom, Npts)
SpatialkD = ckDSpatial(pts, ShearDom)
# Velocity of the blobs - parallelogram domain
uParallelogram = Ewald.calcBlobTotalVel(pts, forces, ShearDom, SpatialkD)
par = uammd.PSEParameters(psi=Ewald._xi,
viscosity=mu,
hydrodynamicRadius=a,
tolerance=1e-6,
Lx=Lx,
Ly=Ly,
Lz=Lz)
pse = uammd.UAMMD(par, Npts)
#pse.Mdot assumes interleaved positions and forces, that is x1,y1,z1,x2,y2,z2,...
shearedpts = pts.copy()
shearedpts[:, 0] -= g * shearedpts[:, 1]