N = 16;
Eb = 0.07;
dt = 1e-4;#[2.5e-3,1e-3,5e-4,2.5e-4]; # Max stable = 5e-3
omHz = 0;
tf = 1#5/omHz;
omega = 2*pi*omHz;
gam0 = 0.1;
for nonLocal in [0,3,4]:
# Initialize the domain and spatial database
Dom = PeriodicShearedDomain(Ld,Ld,Ld);
# 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);
nCyc = tf * omHz
stressdt = T / numStressPerCycle
# 50 times per cycle
saveEvery = int(savedt / dt + 1e-10)
stressEvery = int(stressdt / dt + 1e-10)
print('Omega %f: stopping time %f, saveEvery %f, stressEvery %f' %
(omHz, tf, saveEvery * dt, stressEvery * dt))
# Initialize the domain and spatial database
Dom = PeriodicShearedDomain(Ld, Ld, Ld)
# Initialize fiber discretization
fibDisc = ChebyshevDiscretization(Lf,
eps,
Eb,
mu,
N,
deltaLocal=0.1,
nptsUniform=Nuniformsites,
NupsampleForDirect=NupsampleForDirect)
# Initialize the master list of fibers
allFibers = fiberCollection(nFib,
turnovertime,
fibDisc,
nonLocal,
mu,
omega,
gam0,
Dom,
nThreads=nThr)
# begin with 1 iteration
done = 0
while (done == 0):
print('Iterations %d' % giters)
#try:
np.random.seed(1)
# Initialize the domain and spatial database
Dom = PeriodicShearedDomain(Ld, Ld, Ld)
# Initialize fiber discretization
fibDisc = ChebyshevDiscretization(
Lf,
eps,
Eb,
mu,
N,
deltaLocal=deltaLocal,
trueRPYMobility=RPYMob,
NupsampleForDirect=128)
# Initialize Ewald for non-local velocities
Ewald = GPUEwaldSplitter(
np.exp(1.5) / 4 * eps * Lf, mu, xi, Dom,
fibDisc._nptsDirect * nFib)
# Initialize the master list of fibers
allFibers = fiberCollection(nFib,
10,
fibDisc,
nonLocal,
# 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)
fibList = [None] * nFib
#print('Loading from steady state')
#XFile = 'SSLocsF'+str(nFib)+'C'+str(nCL)+'REV.txt';
gravity = 0.0 # gravity on the fibers
giters = 1;
Ns = [32];
dts = [0.01];
for N in Ns:
gits = [1];
if (N==16):
gits=[1,2,4];
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
copyInput.write('True RPY mob = ' + str(RPYMob) + '\n')
copyInput.close()
Input.close()
except:
raise ValueError(
'This file takes three command line arguments: the seed (for CL network),\
whether to do the finite part implicitly (0 or 1), and whether to use RPY mobility (0 or 1), in that order'
)
saveEvery = int(savedt / dt + 1e-10)
# Initialize the domain and spatial database
Dom = PeriodicShearedDomain(Ld, Ld, Ld)
# Initialize fiber discretization
fibDisc = ChebyshevDiscretization(Lf,eps,Eb,mu,N,deltaLocal=0.1,nptsUniform=Nuniformsites,\
NupsampleForDirect=NupsampleForDirect,rigid=rigidFibs,trueRPYMobility=RPYMob)
# Initialize the master list of fibers
allFibers = fiberCollection(nFib,
turnovertime,
fibDisc,
nonLocal,
mu,
1,
0,
Dom,
nThreads=nThr)
# No flow, no nonlocal hydro (nothing to OMP parallelize)
# Initialize Ewald for non-local velocities
if (nonLocal == 0 or nonLocal == 4):
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)
# Initialize the domain and spatial database
Dom = PeriodicShearedDomain(Ld,Ld,Ld);
# Initialize fiber discretization
fibDisc = ChebyshevDiscretization(Lf,eps,Eb,mu,N,deltaLocal=0.1,nptsUniform=Nuniformsites,NupsampleForDirect=NupsampleForDirect);
# Initialize the master list of fibers
allFibers = fiberCollection(nFib,turnovertime,fibDisc,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)
XFile = 'DynamicStress/DynamicSSLocs'+inFile;
XsFile = 'DynamicStress/DynamicSSTanVecs'+inFile
fibList = [None]*nFib;
allFibers.initFibList(fibList,Dom,pointsfileName=XFile,tanvecfileName=XsFile);
# begin with 1 iteration
done = 0
while (done == 0):
print('Iterations %d' % giters)
try:
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)
# Initialize the master list of fibers
allFibers = fiberCollection(nFib,
fibDisc,
nonLocal,
mu,
omega,
gam0,
Dom,
nThreads=4)
# Initialize the fiber list
fibList = [None] * nFib
allFibers.initFibList(fibList, Dom)
allFibers.fillPointArrays()