def test_example_07():
from hermes2d.examples.c07 import set_bc, set_forms
set_verbose(False)
mesh = Mesh()
mesh.load(sample_mesh)
#mesh.refine_element(0)
#mesh.refine_all_elements()
#mesh.refine_towards_boundary(5, 3)
shapeset = H1Shapeset()
pss = PrecalcShapeset(shapeset)
# create an H1 space
xdisp = H1Space(mesh, shapeset)
ydisp = H1Space(mesh, shapeset)
xdisp.set_uniform_order(8)
ydisp.set_uniform_order(8)
set_bc(xdisp, ydisp)
ndofs = xdisp.assign_dofs(0)
ndofs += ydisp.assign_dofs(ndofs)
# initialize the discrete problem
wf = WeakForm(2)
set_forms(wf)
solver = DummySolver()
sys = LinSystem(wf, solver)
sys.set_spaces(xdisp, ydisp)
sys.set_pss(pss)
xsln = Solution()
ysln = Solution()
old_flag = set_warn_integration(False)
sys.assemble()
set_warn_integration(old_flag)
sys.solve_system(xsln, ysln)
E = float(200e9)
nu = 0.3
stress = VonMisesFilter(xsln, ysln, E / (2*(1 + nu)),
(E * nu) / ((1 + nu) * (1 - 2*nu)))
from numpy import array
from hermes2d import Mesh, H1Shapeset, PrecalcShapeset, H1Space, \
WeakForm, Solution, ScalarView, set_verbose, LinSystem, DummySolver, \
set_warn_integration
from hermes2d.forms import set_forms
from hermes2d.examples import get_example_mesh
domain_mesh = get_example_mesh()
set_warn_integration(False)
def equal_arrays(a, b, prec=1e-10):
if len(a) == len(b):
d = a - b
s = sum(d**2)
if s < prec:
return True
return False
def test_matrix():
set_verbose(False)
mesh = Mesh()
mesh.load(domain_mesh)
mesh.refine_element(0)
shapeset = H1Shapeset()
pss = PrecalcShapeset(shapeset)
# create an H1 space
space = H1Space(mesh, shapeset)
space.set_uniform_order(5)
from numpy import array
from hermes2d import Mesh, H1Shapeset, PrecalcShapeset, H1Space, \
WeakForm, Solution, ScalarView, set_verbose, LinSystem, DummySolver, \
set_warn_integration
from hermes2d.forms import set_forms
from hermes2d.examples import get_example_mesh
domain_mesh = get_example_mesh()
set_warn_integration(False)
def equal_arrays(a, b, prec=1e-10):
if len(a) == len(b):
d = a - b
s = sum(d**2)
if s < prec:
return True
return False
def test_matrix():
set_verbose(False)
mesh = Mesh()
mesh.load(domain_mesh)
mesh.refine_element_id(0)
# create an H1 space with default shapeset
space = H1Space(mesh, 1)
def schroedinger_solver(n_eigs=4, iter=2, verbose_level=1, plot=False,
potential="hydrogen", report=False, report_filename="report.h5",
force=False, sim_name="sim", potential2=None):
"""
One particle Schroedinger equation solver.
n_eigs ... the number of the lowest eigenvectors to calculate
iter ... the number of adaptive iterations to do
verbose_level ...
0 ... quiet
1 ... only moderate output (default)
2 ... lot's of output
plot ........ plot the progress (solutions, refined solutions, errors)
potential ... the V(x) for which to solve, one of:
well, oscillator, hydrogen
potential2 .. other terms that should be added to potential
report ...... it will save raw data to a file, useful for creating graphs
etc.
Returns the eigenvalues and eigenvectors.
"""
set_verbose(verbose_level == 2)
set_warn_integration(False)
pot = {"well": 0, "oscillator": 1, "hydrogen": 2, "three-points": 3}
pot_type = pot[potential]
if report:
from timeit import default_timer as clock
from tables import IsDescription, UInt32Col, Float32Col, openFile, \
Float64Col, Float64Atom, Col, ObjectAtom
class Iteration(IsDescription):
n = UInt32Col()
DOF = UInt32Col()
DOF_reference = UInt32Col()
cpu_solve = Float32Col()
cpu_solve_reference = Float32Col()
eig_errors = Float64Col(shape=(n_eigs,))
eigenvalues = Float64Col(shape=(n_eigs,))
eigenvalues_reference = Float64Col(shape=(n_eigs,))
h5file = openFile(report_filename, mode = "a",
title = "Simulation data")
if hasattr(h5file.root, sim_name):
if force:
h5file.removeNode(getattr(h5file.root, sim_name),
recursive=True)
else:
print "The group '%s' already exists. Use -f to overwrite it." \
% sim_name
return
group = h5file.createGroup("/", sim_name, 'Simulation run')
table = h5file.createTable(group, "iterations", Iteration,
"Iterations info")
h5eigs = h5file.createVLArray(group, 'eigenvectors', ObjectAtom())
h5eigs_ref = h5file.createVLArray(group, 'eigenvectors_reference',
ObjectAtom())
iteration = table.row
mesh = Mesh()
mesh.load("square.mesh")
if potential == "well":
# Read the width of the mesh automatically. This assumes there is just
# one square element:
a = sqrt(mesh.get_element(0).get_area())
# set N high enough, so that we get enough analytical eigenvalues:
N = 10
levels = []
for n1 in range(1, N):
for n2 in range(1, N):
levels.append(n1**2 + n2**2)
levels.sort()
E_exact = [pi**2/(2.*a**2) * m for m in levels]
elif potential == "oscillator":
E_exact = [1] + [2]*2 + [3]*3 + [4]*4 + [5]*5 + [6]*6
elif potential == "hydrogen":
Z = 1 # atom number
E_exact = [-float(Z)**2/2/(n-0.5)**2/4 for n in [1]+[2]*3+[3]*5 +\
[4]*8 + [5]*15]
else:
E_exact = [1.]*50
if len(E_exact) < n_eigs:
print n_eigs
print E_exact
raise Exception("We don't have enough analytical eigenvalues.")
#mesh.refine_element(0)
mesh.refine_all_elements()
#mesh.refine_all_elements()
#mesh.refine_all_elements()
#mesh.refine_all_elements()
#mview = MeshView()
#mview.show(mesh)
shapeset = H1Shapeset()
space = H1Space(mesh, shapeset)
space.set_uniform_order(2)
space.assign_dofs()
pss = PrecalcShapeset(shapeset)
#bview = BaseView()
#bview.show(space)
wf1 = WeakForm(1)
# this is induced by set_verbose():
#dp1.set_quiet(not verbose)
set_forms8(wf1, pot_type, potential2)
wf2 = WeakForm(1)
# this is induced by set_verbose():
#dp2.set_quiet(not verbose)
set_forms7(wf2)
solver = DummySolver()
w = 320
h = 320
views = [ScalarView("", i*w, 0, w, h) for i in range(4)]
viewsm = [ScalarView("", i*w, h, w, h) for i in range(4)]
viewse = [ScalarView("", i*w, 2*h, w, h) for i in range(4)]
#for v in viewse:
# v.set_min_max_range(0, 10**-4)
ord = OrderView("Polynomial Orders", 0, 2*h, w, h)
rs = None
precision = 30.0
if verbose_level >= 1:
print "Problem initialized. Starting calculation."
for it in range(iter):
if verbose_level >= 1:
print "-"*80
print "Starting iteration %d." % it
if report:
iteration["n"] = it
#mesh.save("refined2.mesh")
sys1 = LinSystem(wf1, solver)
sys1.set_spaces(space)
sys1.set_pss(pss)
sys2 = LinSystem(wf2, solver)
sys2.set_spaces(space)
sys2.set_pss(pss)
if verbose_level >= 1:
print "Assembling the matrices A, B."
sys1.assemble()
sys2.assemble()
if verbose_level == 2:
print "converting matrices A, B"
A = sys1.get_matrix()
B = sys2.get_matrix()
if verbose_level >= 1:
n = A.shape[0]
print "Solving the problem Ax=EBx (%d x %d)." % (n, n)
if report:
n = A.shape[0]
iteration["DOF"] = n
if report:
t = clock()
eigs, sols = solve(A, B, n_eigs, verbose_level == 2)
if report:
t = clock() - t
iteration["cpu_solve"] = t
iteration["eigenvalues"] = array(eigs)
#h5eigs.append(sols)
if verbose_level >= 1:
print " \-Done."
print_eigs(eigs, E_exact)
s = []
n = sols.shape[1]
for i in range(n):
sln = Solution()
vec = sols[:, i]
sln.set_fe_solution(space, pss, vec)
s.append(sln)
if verbose_level >= 1:
print "Matching solutions."
if rs is not None:
def minus2(sols, i):
sln = Solution()
vec = sols[:, i]
sln.set_fe_solution(space, pss, -vec)
return sln
pairs, flips = make_pairs(rs, s, d1, d2)
#print "_"*40
#print pairs, flips
#print len(rs), len(s)
#from time import sleep
#sleep(3)
#stop
s2 = []
for j, flip in zip(pairs, flips):
if flip:
s2.append(minus2(sols,j))
else:
s2.append(s[j])
s = s2
if plot:
if verbose_level >= 1:
print "plotting: solution"
ord.show(space)
for i in range(min(len(s), 4)):
views[i].show(s[i])
views[i].set_title("Iter: %d, eig: %d" % (it, i))
#mat1.show(dp1)
if verbose_level >= 1:
print "reference: initializing mesh."
rsys1 = RefSystem(sys1)
rsys2 = RefSystem(sys2)
if verbose_level >= 1:
print "reference: assembling the matrices A, B."
rsys1.assemble()
rsys2.assemble()
if verbose_level == 2:
print "converting matrices A, B"
A = rsys1.get_matrix()
B = rsys2.get_matrix()
if verbose_level >= 1:
n = A.shape[0]
print "reference: solving the problem Ax=EBx (%d x %d)." % (n, n)
if report:
n = A.shape[0]
iteration["DOF_reference"] = n
if report:
t = clock()
eigs, sols = solve(A, B, n_eigs, verbose_level == 2)
if report:
t = clock() - t
iteration["cpu_solve_reference"] = t
iteration["eigenvalues_reference"] = array(eigs)
#h5eigs_ref.append(sols)
if verbose_level >= 1:
print " \-Done."
print_eigs(eigs, E_exact)
rs = []
rspace = rsys1.get_ref_space(0)
n = sols.shape[1]
for i in range(n):
sln = Solution()
vec = sols[:, i]
sln.set_fe_solution(rspace, pss, vec)
rs.append(sln)
if verbose_level >= 1:
print "reference: matching solutions."
def minus(sols, i):
sln = Solution()
vec = sols[:, i]
sln.set_fe_solution(rspace, pss, -vec)
return sln
# segfaults
#mat2.show(rp1)
def d1(x, y):
return (x-y).l2_norm()
def d2(x, y):
return (x+y).l2_norm()
from pairs import make_pairs
pairs, flips = make_pairs(s, rs, d1, d2)
rs2 = []
for j, flip in zip(pairs, flips):
if flip:
rs2.append(minus(sols,j))
else:
rs2.append(rs[j])
rs = rs2
if plot:
if verbose_level >= 1:
print "plotting: solution, reference solution, errors"
for i in range(min(len(s), len(rs), 4)):
#views[i].show(s[i])
#views[i].set_title("Iter: %d, eig: %d" % (it, i))
viewsm[i].show(rs[i])
viewsm[i].set_title("Ref. Iter: %d, eig: %d" % (it, i))
viewse[i].show((s[i]-rs[i])**2)
viewse[i].set_title("Error plot Iter: %d, eig: %d" % (it, i))
if verbose_level >= 1:
print "Calculating errors."
hp = H1OrthoHP(space)
if verbose_level == 2:
print "-"*60
print "calc error (iter=%d):" % it
eig_converging = 0
errors = []
for i in range(min(len(s), len(rs))):
error = hp.calc_error(s[i], rs[i]) * 100
errors.append(error)
prec = precision
if verbose_level >= 1:
print "eig %d: %g%% precision goal: %g%%" % (i, error, prec)
if report:
iteration["eig_errors"] = array(errors)
if errors[0] > precision:
eig_converging = 0
elif errors[3] > precision:
eig_converging = 3
elif errors[1] > precision:
eig_converging = 1
elif errors[2] > precision:
eig_converging = 2
else:
precision /= 2
# uncomment the following line to only converge to some eigenvalue:
#eig_converging = 3
if verbose_level >= 1:
print "picked: %d" % eig_converging
error = hp.calc_error(s[eig_converging], rs[eig_converging]) * 100
if verbose_level >= 1:
print "Adapting the mesh."
hp.adapt(0.3)
space.assign_dofs()
if report:
iteration.append()
table.flush()
if report:
h5file.close()
return s
