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muSpectre/dummy.py
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dummy.py
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import numpy as np
import scipy.sparse.linalg as sp
import itertools
import sys
# turn of warning for zero division
# (which occurs in the linearization of the logarithmic strain)
np.seterr(divide='ignore', invalid='ignore')
def reference_curve (tauy0_input, h_input, max_shear, E, nu,
shear_incr):
# ----------------------------------- GRID ------------------------------------
Nx = 5 # number of voxels in x-direction
Ny = 5 # number of voxels in y-direction
Nz = 3 # number of voxels in z-direction
shape = [Nx,Ny,Nz] # number of voxels as list: [Nx,Ny,Nz]
# ----------------------------- TENSOR OPERATIONS -----------------------------
# tensor operations / products: np.einsum enables index notation, avoiding loops
# e.g. ddot42 performs $C_ij = A_ijkl B_lk$ for the entire grid
trans2 = lambda A2 : np.einsum('ijxyz ->jixyz ',A2 )
ddot22 = lambda A2,B2: np.einsum('ijxyz ,jixyz ->xyz ',A2,B2)
ddot42 = lambda A4,B2: np.einsum('ijklxyz,lkxyz ->ijxyz ',A4,B2)
ddot44 = lambda A4,B4: np.einsum('ijklxyz,lkmnxyz->ijmnxyz',A4,B4)
dot11 = lambda A1,B1: np.einsum('ixyz ,ixyz ->xyz ',A1,B1)
dot22 = lambda A2,B2: np.einsum('ijxyz ,jkxyz ->ikxyz ',A2,B2)
dot24 = lambda A2,B4: np.einsum('ijxyz ,jkmnxyz->ikmnxyz',A2,B4)
dot42 = lambda A4,B2: np.einsum('ijklxyz,lmxyz ->ijkmxyz',A4,B2)
dyad22 = lambda A2,B2: np.einsum('ijxyz ,klxyz ->ijklxyz',A2,B2)
dyad11 = lambda A1,B1: np.einsum('ixyz ,jxyz ->ijxyz ',A1,B1)
# eigenvalue decomposition of 2nd-order tensor: return in convention i,j,x,y,z
# NB requires to swap default order of NumPy (in in/output)
def eig2(A2):
swap1i = lambda A1: np.einsum('xyzi ->ixyz ',A1)
swap2 = lambda A2: np.einsum('ijxyz->xyzij',A2)
swap2i = lambda A2: np.einsum('xyzij->ijxyz',A2)
vals,vecs = np.linalg.eig(swap2(A2))
vals = swap1i(vals)
vecs = swap2i(vecs)
return vals,vecs
# logarithm of grid of 2nd-order tensors
def ln2(A2):
vals,vecs = eig2(A2)
return sum([np.log(vals[i])*dyad11(vecs[:,i],vecs[:,i]) for i in range(3)])
# exponent of grid of 2nd-order tensors
def exp2(A2):
vals,vecs = eig2(A2)
return sum([np.exp(vals[i])*dyad11(vecs[:,i],vecs[:,i]) for i in range(3)])
# determinant of grid of 2nd-order tensors
def det2(A2):
return (A2[0,0]*A2[1,1]*A2[2,2]+A2[0,1]*A2[1,2]*A2[2,0]+A2[0,2]*A2[1,0]*A2[2,1])-\
(A2[0,2]*A2[1,1]*A2[2,0]+A2[0,1]*A2[1,0]*A2[2,2]+A2[0,0]*A2[1,2]*A2[2,1])
# inverse of grid of 2nd-order tensors
def inv2(A2):
A2det = det2(A2)
A2inv = np.empty([3,3,Nx,Ny,Nz])
A2inv[0,0] = (A2[1,1]*A2[2,2]-A2[1,2]*A2[2,1])/A2det
A2inv[0,1] = (A2[0,2]*A2[2,1]-A2[0,1]*A2[2,2])/A2det
A2inv[0,2] = (A2[0,1]*A2[1,2]-A2[0,2]*A2[1,1])/A2det
A2inv[1,0] = (A2[1,2]*A2[2,0]-A2[1,0]*A2[2,2])/A2det
A2inv[1,1] = (A2[0,0]*A2[2,2]-A2[0,2]*A2[2,0])/A2det
A2inv[1,2] = (A2[0,2]*A2[1,0]-A2[0,0]*A2[1,2])/A2det
A2inv[2,0] = (A2[1,0]*A2[2,1]-A2[1,1]*A2[2,0])/A2det
A2inv[2,1] = (A2[0,1]*A2[2,0]-A2[0,0]*A2[2,1])/A2det
A2inv[2,2] = (A2[0,0]*A2[1,1]-A2[0,1]*A2[1,0])/A2det
return A2inv
# ------------------------ INITIATE (IDENTITY) TENSORS ------------------------
# identity tensor (single tensor)
i = np.eye(3)
# identity tensors (grid)
I = np.einsum('ij,xyz' , i ,np.ones([Nx,Ny,Nz]))
I4 = np.einsum('ijkl,xyz->ijklxyz',np.einsum('il,jk',i,i),np.ones([Nx,Ny,Nz]))
I4rt = np.einsum('ijkl,xyz->ijklxyz',np.einsum('ik,jl',i,i),np.ones([Nx,Ny,Nz]))
I4s = (I4+I4rt)/2.
II = dyad22(I,I)
# ------------------------------------ FFT ------------------------------------
# projection operator (only for non-zero frequency, associated with the mean)
# NB: vectorized version of "hyper-elasticity.py"
# - allocate / support function
Ghat4 = np.zeros([3,3,3,3,Nx,Ny,Nz]) # projection operator
x = np.zeros([3 ,Nx,Ny,Nz],dtype='int64') # position vectors
q = np.zeros([3 ,Nx,Ny,Nz],dtype='int64') # frequency vectors
delta = lambda i,j: np.float(i==j) # Dirac delta function
# - set "x" as position vector of all grid-points [grid of vector-components]
x[0],x[1],x[2] = np.mgrid[:Nx,:Ny,:Nz]
# - convert positions "x" to frequencies "q" [grid of vector-components]
for i in range(3):
freq = np.arange(-(shape[i]-1)/2,+(shape[i]+1)/2,dtype='int64')
q[i] = freq[x[i]]
# - compute "Q = ||q||", and "norm = 1/Q" being zero for the mean (Q==0)
# NB: avoid zero division
q = q.astype(np.float)
Q = dot11(q,q)
Z = Q==0
Q[Z] = 1.
norm = 1./Q
norm[Z] = 0.
# - set projection operator [grid of tensors]
for i, j, l, m in itertools.product(range(3), repeat=4):
Ghat4[i,j,l,m] = norm*delta(i,m)*q[j]*q[l]
# (inverse) Fourier transform (for each tensor component in each direction)
fft = lambda x: np.fft.fftshift(np.fft.fftn (np.fft.ifftshift(x),[Nx,Ny,Nz]))
ifft = lambda x: np.fft.fftshift(np.fft.ifftn(np.fft.ifftshift(x),[Nx,Ny,Nz]))
# functions for the projection 'G', and the product 'G : K^LT : (delta F)^T'
G = lambda A2 : np.real( ifft( ddot42(Ghat4,fft(A2)) ) ).reshape(-1)
K_dF = lambda dFm: trans2(ddot42(K4,trans2(dFm.reshape(3,3,Nx,Ny,Nz))))
G_K_dF = lambda dFm: G(K_dF(dFm))
# --------------------------- CONSTITUTIVE RESPONSE ---------------------------
# constitutive response to a certain loading and history
# NB: completely uncoupled from the FFT-solver, but implemented as a regular
# grid of quadrature points, to have an efficient code;
# each point is completely independent, just evaluated at the same time
def constitutive(F,F_t,be_t,ep_t):
# function to compute linearization of the logarithmic Finger tensor
def dln2_d2(A2):
vals,vecs = eig2(A2)
#vecs[:,1,0,0,0] = - vecs[:,1,0,0,0] # for debugging consistency
K4 = np.zeros([3,3,3,3,Nx,Ny,Nz])
for m, n in itertools.product(range(3),repeat=2):
gc = (np.log(vals[n])-np.log(vals[m]))/(vals[n]-vals[m])
gc[vals[n]==vals[m]] = (1.0/vals[m])[vals[n]==vals[m]]
K4 += gc*dyad22(dyad11(vecs[:,m],vecs[:,n]),dyad11(vecs[:,m],vecs[:,n]))
return K4
# elastic stiffness tensor
C4e = K*II+2.*mu*(I4s-1./3.*II)
# trial state
Fdelta = dot22(F,inv2(F_t))
be_s = dot22(Fdelta,dot22(be_t,trans2(Fdelta)))
lnbe_s = ln2(be_s)
tau_s = ddot42(C4e,lnbe_s)/2.
taum_s = ddot22(tau_s,I)/3.
taud_s = tau_s-taum_s*I
taueq_s = np.sqrt(3./2.*ddot22(taud_s,taud_s))
N_s = 3./2.*taud_s/taueq_s
phi_s = taueq_s-(tauy0+H*ep_t)
phi_s = 1./2.*(phi_s+np.abs(phi_s))
# return map
dgamma = phi_s/(H+3.*mu)
ep = ep_t + dgamma
tau = tau_s -2.*dgamma*N_s*mu
lnbe = lnbe_s-2.*dgamma*N_s
be = exp2(lnbe)
P = dot22(tau,trans2(inv2(F)))
# consistent tangent operator
a0 = dgamma*mu/taueq_s
a1 = mu/(H+3.*mu)
C4ep = ((K-2./3.*mu)/2.+a0*mu)*II+(1.-3.*a0)*mu*I4s+2.*mu*(a0-a1)*dyad22(N_s,N_s)
dlnbe4_s = dln2_d2(be_s)
dbe4_s = 2.*dot42(I4s,be_s)
K4a = (C4e/2.)*(phi_s<=0.).astype(np.float)+C4ep*(phi_s>0.).astype(np.float)
K4b = ddot44(K4a,ddot44(dlnbe4_s,dbe4_s))
K4c = dot42(-I4rt,tau)+K4b
K4 = dot42(dot24(inv2(F),K4c),trans2(inv2(F)))
return P,K4,be,ep
# phase indicator: square inclusion of volume fraction (3*3*15)/(11*13*15)
phase = np.zeros([Nx,Ny,Nz]); phase[:3,:3,:] = 1.
# function to convert material parameters to grid of scalars
param = lambda M0,M1: M0*np.ones([Nx,Ny,Nz])*(1.-phase)+\
M1*np.ones([Nx,Ny,Nz])* phase
K_input = E/(3*(1-2*nu))
mu_input = E/(2*(1+nu))
print("K_input = {}, mu_input = {}".format(K_input, mu_input))
# material parameters
K = param(0.833,K_input) # bulk modulus
mu = param(0.386,mu_input) # shear modulus
H = param(0.004,h_input) # hardening modulus
tauy0 = param(0.003,tauy0_input) # initial yield stress
# ---------------------------------- LOADING ----------------------------------
# stress, deformation gradient, plastic strain, elastic Finger tensor
# NB "_t" signifies that it concerns the value at the previous increment
ep_t = np.zeros([ Nx,Ny,Nz])
P = np.zeros([3,3,Nx,Ny,Nz])
F = np.array(I,copy=True)
F_t = np.array(I,copy=True)
be_t = np.array(I,copy=True)
# initialize macroscopic incremental loading
ninc = int(max_shear/shear_incr)
lam = 0.0
# for directional stiffness in shear direction
del_tau = np.array(I,copy=True)*0
del_tau[0, 1] = 1.
# for directional stiffness in σₓₓ direction
del_sigxx = np.array(I,copy=True)*0
del_sigxx[0, 0] = 1.
barF = np.array(I,copy=True)
barF_t = np.array(I,copy=True)
# initial tangent operator: the elastic tangent
K4 = K*II+2.*mu*(I4s-1./3.*II)
# incremental deformation
gammas=np.zeros(ninc, dtype=float)
tau = np.zeros_like(gammas)
dtau = np.zeros_like(gammas)
sigma_xx = np.zeros_like(gammas)
dsigma_xx = np.zeros_like(gammas)
for inc in range(ninc):
#print('=============================')
#print('inc: {0:d}'.format(inc))
# set macroscopic deformation gradient (pure-shear)
lam += 0.2/float(ninc)
barF = np.array(I,copy=True)
barF[0,0] = (1.+lam)
barF[1,1] = 1./(1.+lam)
# store normalization
Fn = np.linalg.norm(F)
F[0,1] += shear_incr
P,K4,be,ep = constitutive(F,F_t,be_t,ep_t)
gammas[inc] = F[0,1, 0, 0, 0]
tau[inc] = P[0,1, 0, 0, 0]
dtau[inc] = K_dF(del_tau)[0,1,0,0,0]
sigma_xx[inc] = P[0, 0, 0, 0, 0]
dsigma_xx[inc] = K_dF(del_sigxx)[0,0,0,0,0]
### first iteration residual: distribute "barF" over grid using "K4"
##b = -G_K_dF(barF-barF_t)
##F += barF-barF_t
##
### parameters for Newton iterations: normalization and iteration counter
##Fn = np.linalg.norm(F)
##iiter = 0
##
### iterate as long as the iterative update does not vanish
##while True:
##
## # solve linear system using the Conjugate Gradient iterative solver
## dFm,_ = sp.cg(tol=1.e-8,
## A = sp.LinearOperator(shape=(F.size,F.size),matvec=G_K_dF,dtype='float'),
## b = b,
## )
##
## # add solution of linear system to DOFs
## F += dFm.reshape(3,3,Nx,Ny,Nz)
##
## # compute residual stress and tangent, convert to residual
## P,K4,be,ep = constitutive(F,F_t,be_t,ep_t)
## b = -G(P)
##
## # check for convergence, print convergence info to screen
## print('{0:10.2e}'.format(np.linalg.norm(dFm)/Fn))
## if np.linalg.norm(dFm)/Fn<1.e-5 and iiter>0: break
##
## # update Newton iteration counter
## iiter += 1
# end-of-increment: update history
barF_t = np.array(barF,copy=True)
F_t = np.array(F ,copy=True)
be_t = np.array(be ,copy=True)
ep_t = np.array(ep ,copy=True)
pass
return gammas, tau, sigma_xx, dtau, dsigma_xx
if __name__ == "__main__":
gammas, tau, sigma_xx, del_tau, del_sigxx = reference_curve(tauy0_input=.006,
h_input = .008*2,
max_shear = 5e-2,
E = 1.0030648180242636,
nu = 0.299306759098787,
shear_incr=5e-3)
import matplotlib.pyplot as plt
plt.plot(gammas, tau, "+-")
plt.show()
##print("K4:\n{}".format(K4[:,:,:,:, 0,0,0]))
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