def run_test():
#meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh'))
meshfile = "../data/amr-quad.mesh"
mesh = mfem.Mesh(meshfile, 1, 1)
dim = mesh.Dimension()
sdim = mesh.SpaceDimension()
fec = mfem.H1_FECollection(1, dim)
fespace = mfem.FiniteElementSpace(mesh, fec, 1)
print('Number of finite element unknowns: ' + str(fespace.GetTrueVSize()))
c = mfem.ConstantCoefficient(1.0)
gf = mfem.GridFunction(fespace)
gf.ProjectCoefficient(c)
print("write mesh to STDOUT")
mesh.Print(mfem.STDOUT)
print("creat VTK file to file")
mesh.PrintVTK('mesh.vtk', 1)
print("creat VTK to STDOUT")
mesh.PrintVTK(mfem.STDOUT, 1)
print("save GridFunction to file")
gf.Save('out_test_gridfunc.gf')
gf.SaveVTK(mfem.wFILE('out_test_gridfunc1.vtk'), 'data', 1)
print("save GridFunction to file in VTK format")
gf.SaveVTK('out_test_gridfunc2.vtk', 'data', 1)
print("Gridfunction to STDOUT")
gf.Save(mfem.STDOUT)
o = io.StringIO()
count = gf.Save(o)
count2 = gf.SaveVTK(o, 'data', 1)
print("length of data ", count, count2)
print('result: ', o.getvalue())
def save_scaled_jacobian(filename, mesh, sd=-1):
sj = get_scaled_jacobian(mesh, sd=sd)
fec = mfem.L2_FECollection(0, mesh.Dimension())
fes = mfem.FiniteElementSpace(mesh, fec)
vec = mfem.Vector(sj)
gf = mfem.GridFunction(fes, vec.GetData())
gf.Save(filename)
def run_test():
#meshfile =expanduser(join(mfem_path, 'data', 'beam-tri.mesh'))
meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh'))
mesh = mfem.Mesh(meshfile, 1, 1)
dim = mesh.Dimension()
sdim = mesh.SpaceDimension()
fec = mfem.H1_FECollection(1, dim)
fespace = mfem.FiniteElementSpace(mesh, fec, 1)
print('Number of finite element unknowns: ' + str(fespace.GetTrueVSize()))
c = mfem.ConstantCoefficient(1.0)
gf = mfem.GridFunction(fespace)
gf.ProjectCoefficient(c)
gf.Save('out_test_gridfunc.gf')
def run_test():
#meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh'))
meshfile = "../data/amr-quad.mesh"
mesh = mfem.Mesh(meshfile, 1, 1)
dim = mesh.Dimension()
sdim = mesh.SpaceDimension()
fec = mfem.H1_FECollection(1, dim)
fespace = mfem.FiniteElementSpace(mesh, fec, 1)
print('Number of finite element unknowns: ' + str(fespace.GetTrueVSize()))
c = mfem.ConstantCoefficient(1.0)
gf = mfem.GridFunction(fespace)
gf.ProjectCoefficient(c)
odata = gf.GetDataArray().copy()
gf.Save("out_test_gz.gf")
gf2 = mfem.GridFunction(mesh, "out_test_gz.gf")
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, "text file does not agree with original")
gf.Save("out_test_gz.gz")
gf2.Assign(0.0)
gf2 = mfem.GridFunction(mesh, "out_test_gz.gz")
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, ".gz file does not agree with original")
gf.Print("out_test_gz.dat")
gf2.Assign(0.0)
gf2.Load("out_test_gz.dat", gf.Size())
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, ".dat file does not agree with original")
gf.Print("out_test_gz.dat.gz")
gf2.Assign(0.0)
gf2.Load("out_test_gz.dat.gz", gf.Size())
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, ".dat file does not agree with original (gz)")
import gzip
import io
gf.Print("out_test_gz.dat2.gz")
with gzip.open("out_test_gz.dat2.gz", 'rt') as f:
sio = io.StringIO(f.read())
gf3 = mfem.GridFunction(fespace)
gf3.Load(sio, gf.Size())
odata3 = gf3.GetDataArray().copy()
check(odata, odata3, ".dat file does not agree with original(gz-io)")
c = mfem.ConstantCoefficient(2.0)
gf.ProjectCoefficient(c)
odata = gf.GetDataArray().copy()
o = io.StringIO()
gf.Print(o)
gf2.Load(o, gf.Size())
odata2 = gf2.GetDataArray().copy()
check(odata, odata2, "StringIO does not agree with original")
print("GridFunction .gf, .gz .dat and StringIO agree with original")
mesh2 = mfem.Mesh()
mesh.Print("out_test_gz.mesh")
mesh2.Load("out_test_gz.mesh")
check_mesh(mesh, mesh2, ".mesh does not agree with original")
mesh2 = mfem.Mesh()
mesh.Print("out_test_gz.mesh.gz")
mesh2.Load("out_test_gz.mesh.gz")
check_mesh(mesh, mesh2, ".mesh.gz does not agree with original")
mesh3 = mfem.Mesh()
mesh.PrintGZ("out_test_gz3.mesh")
mesh3.Load("out_test_gz3.mesh")
check_mesh(mesh, mesh3,
".mesh (w/o .gz exntension) does not agree with original")
o = io.StringIO()
mesh2 = mfem.Mesh()
mesh.Print(o)
mesh2.Load(o)
check_mesh(mesh, mesh2, ".mesh.gz does not agree with original")
print("Mesh .mesh, .mesh.gz and StringIO agree with original")
print("PASSED")
for i in range(dim - 1):
f.Set(i, mfem.ConstantCoefficient(0.0))
pull_force = mfem.Vector([0] * pmesh.bdr_attributes.Max())
pull_force[1] = -1.0e-2
f.Set(dim - 1, mfem.PWConstCoefficient(pull_force))
b = mfem.ParLinearForm(fespace)
b.AddBoundaryIntegrator(mfem.VectorBoundaryLFIntegrator(f))
print('r.h.s. ...')
b.Assemble()
# 10. Define the solution vector x as a parallel finite element grid
# function corresponding to fespace. Initialize x with initial guess of
# zero, which satisfies the boundary conditions.
x = mfem.GridFunction(fespace)
x.Assign(0.0)
# 11. Set up the parallel bilinear form a(.,.) on the finite element space
# corresponding to the linear elasticity integrator with piece-wise
# constants coefficient lambda and mu.
lamb = mfem.Vector(pmesh.attributes.Max())
lamb.Assign(1.0)
lamb[0] = lamb[1] * 50
lambda_func = mfem.PWConstCoefficient(lamb)
mu = mfem.Vector(pmesh.attributes.Max())
mu.Assign(1.0)
mu[0] = mu[1] * 50
mu_func = mfem.PWConstCoefficient(mu)
a = mfem.ParBilinearForm(fespace)
def eval_shape(order = 1, refine = 5, elem_type = 0,
fec = 'ND'):
if fec == 'ND':
fec_type = mfem.ND_FECollection
if order < 1: assert False, "ND order is 1 and above"
elif fec == 'RT':
fec_type = mfem.RT_FECollection
elif fec == 'H1':
fec_type = mfem.H1_FECollection
if order < 1: assert False, "H1 order is 1 and above"
elif fec == 'L2':
fec_type = mfem.L2_FECollection
else:
assert False, "unknown basis"
if elem_type == 0:
Nvert = 3; Nelem = 1; spaceDim = 2
elif elem_type == 1:
Nvert = 4; Nelem = 1; spaceDim = 2
mesh = mfem.Mesh(2, Nvert, Nelem, 0, spaceDim)
if elem_type == 0:
tri_v = [[1., 0.3 ], [0., 1.,], [0, 0]]
tri_e = [[0, 1, 2], ]
for j in range(Nvert):
mesh.AddVertex(tri_v[j])
for j in range(Nelem):
mesh.AddTriangle(tri_e[j], j+1)
mesh.FinalizeTriMesh(1,1, True)
else:
quad_v = [[-1, -1.3, ], [+1, -1, ], [+1, +1, ], [-1, +1,]]
quad_e = [[0, 1, 2, 3]]
for j in range(Nvert):
mesh.AddVertex(quad_v[j])
for j in range(Nelem):
mesh.AddQuad(quad_e[j], j+1)
mesh.FinalizeQuadMesh(1,1, True)
#mesh.PrintToFile('plot_basis.mesh', 8)
fe_coll = fec_type(order, spaceDim)
fespace = mfem.FiniteElementSpace(mesh, fe_coll)
x = mfem.GridFunction(fespace)
x.Assign(0.0)
x[0] = 1.0
idx = 0
geom = mesh.GetElementBaseGeometry(idx)
T = mesh.GetElementTransformation(idx)
fe = fespace.GetFE(idx)
fe_nd = fe.GetDof()
ir = fe.GetNodes()
npt = ir.GetNPoints()
dof = np.vstack([T.Transform(ir.IntPoint(i)) for i in range(npt)])
RefG = mfem.GlobGeometryRefiner.Refine(geom, refine, 1);
ir = RefG.RefPts
npt = ir.GetNPoints()
ptx = np.vstack([T.Transform(ir.IntPoint(i)) for i in range(npt)])
shape = []
if fec == 'ND' or fec == 'RT':
mat = mfem.DenseMatrix(fe_nd, spaceDim)
shape_func = fe.CalcVShape
for i in range(npt):
ip = ir.IntPoint(i)
T.SetIntPoint(ip)
fe.CalcVShape(T, mat)
shape.append(mat.GetDataArray().copy())
else:
vec = mfem.Vector(fe_nd)
for i in range(npt):
ip = ir.IntPoint(i)
fe.CalcShape(ip, vec)
shape.append(vec.GetDataArray().copy())
return dof, ptx, np.stack(shape)
def run_test():
#meshfile = expanduser(join(mfem_path, 'data', 'semi_circle.mesh'))
mesh = mfem.Mesh(3, 3, 3, "TETRAHEDRON")
mesh.ReorientTetMesh()
order = 1
dim = mesh.Dimension()
sdim = mesh.SpaceDimension()
fec1 = mfem.H1_FECollection(order, dim)
fespace1 = mfem.FiniteElementSpace(mesh, fec1, 1)
fec2 = mfem.ND_FECollection(order, dim)
fespace2 = mfem.FiniteElementSpace(mesh, fec2, 1)
print("Element order :", order)
print('Number of H1 finite element unknowns: ' +
str(fespace1.GetTrueVSize()))
print('Number of ND finite element unknowns: ' +
str(fespace2.GetTrueVSize()))
print("Checking scalar")
gf = mfem.GridFunction(fespace1)
c1 = mfem.NumbaFunction(s_func, sdim).GenerateCoefficient()
c2 = s_coeff()
gf.Assign(0.0)
start = time.time()
gf.ProjectCoefficient(c1)
end = time.time()
data1 = gf.GetDataArray().copy()
print("Numba time (scalar)", end - start)
gf.Assign(0.0)
start = time.time()
gf.ProjectCoefficient(c2)
end = time.time()
data2 = gf.GetDataArray().copy()
print("Python time (scalar)", end - start)
check(data1, data2, "scalar coefficient does not agree with original")
print("Checking vector")
gf = mfem.GridFunction(fespace2)
c3 = mfem.VectorNumbaFunction(v_func, sdim, dim).GenerateCoefficient()
c4 = v_coeff(dim)
gf.Assign(0.0)
start = time.time()
gf.ProjectCoefficient(c3)
end = time.time()
data1 = gf.GetDataArray().copy()
print("Numba time (vector)", end - start)
gf.Assign(0.0)
start = time.time()
gf.ProjectCoefficient(c4)
end = time.time()
data2 = gf.GetDataArray().copy()
print("Python time (vector)", end - start)
check(data1, data2, "vector coefficient does not agree with original")
print("Checking matrix")
a1 = mfem.BilinearForm(fespace2)
a2 = mfem.BilinearForm(fespace2)
c4 = mfem.MatrixNumbaFunction(m_func, sdim, dim).GenerateCoefficient()
c5 = m_coeff(dim)
a1.AddDomainIntegrator(mfem.VectorFEMassIntegrator(c4))
a2.AddDomainIntegrator(mfem.VectorFEMassIntegrator(c5))
start = time.time()
a1.Assemble()
end = time.time()
a1.Finalize()
M1 = a1.SpMat()
print("Numba time (matrix)", end - start)
start = time.time()
a2.Assemble()
end = time.time()
a2.Finalize()
M2 = a2.SpMat()
print("Python time (matrix)", end - start)
#from mfem.commmon.sparse_utils import sparsemat_to_scipycsr
#csr1 = sparsemat_to_scipycsr(M1, float)
#csr2 = sparsemat_to_scipycsr(M2, float)
check(M1.GetDataArray(), M2.GetDataArray(),
"matrix coefficient does not agree with original")
check(M1.GetIArray(), M2.GetIArray(),
"matrix coefficient does not agree with original")
check(M1.GetJArray(), M2.GetJArray(),
"matrix coefficient does not agree with original")
print("PASSED")
def do_integration(expr, solvars, phys, mesh, kind, attrs,
order, num):
from petram.helper.variables import (Variable,
var_g,
NativeCoefficientGenBase,
CoefficientVariable)
from petram.phys.coefficient import SCoeff
st = parser.expr(expr)
code= st.compile('<string>')
names = code.co_names
g = {}
#print solvars.keys()
for key in phys._global_ns.keys():
g[key] = phys._global_ns[key]
for key in solvars.keys():
g[key] = solvars[key]
l = var_g.copy()
ind_vars = ','.join(phys.get_independent_variables())
if kind == 'Domain':
size = max(max(mesh.attributes.ToList()), max(attrs))
else:
size = max(max(mesh.bdr_attributes.ToList()), max(attrs))
arr = [0]*(size)
for k in attrs:
arr[k-1] = 1
flag = mfem.intArray(arr)
s = SCoeff(expr, ind_vars, l, g, return_complex=False)
## note L2 does not work for boundary....:D
if kind == 'Domain':
fec = mfem.L2_FECollection(order, mesh.Dimension())
else:
fec = mfem.H1_FECollection(order, mesh.Dimension())
fes = mfem.FiniteElementSpace(mesh, fec)
one = mfem.ConstantCoefficient(1)
gf = mfem.GridFunction(fes)
gf.Assign(0.0)
if kind == 'Domain':
gf.ProjectCoefficient(mfem.RestrictedCoefficient(s, flag))
else:
gf.ProjectBdrCoefficient(mfem.RestrictedCoefficient(s, flag), flag)
b = mfem.LinearForm(fes)
one = mfem.ConstantCoefficient(1)
if kind == 'Domain':
itg = mfem.DomainLFIntegrator(one)
b.AddDomainIntegrator(itg)
else:
itg = mfem.BoundaryLFIntegrator(one)
b.AddBoundaryIntegrator(itg)
b.Assemble()
from petram.engine import SerialEngine
en = SerialEngine()
ans = mfem.InnerProduct(en.x2X(gf), en.b2B(b))
if not np.isfinite(ans):
print("not finite", ans, arr)
print(size, mesh.bdr_attributes.ToList())
from mfem.common.chypre import LF2PyVec, PyVec2PyMat, Array2PyVec, IdentityPyMat
#print(list(gf.GetDataArray()))
print(len(gf.GetDataArray()), np.sum(gf.GetDataArray()))
print(np.sum(list(b.GetDataArray())))
return ans
