def create_simple_petsc_matrix(request):
vals_F = [3.2, 1.1, 6.3, 1., -5.1]
col_idx_F = [0, 1, 0, 1, 2]
row_idx_F = [0, 2, 4, 5]
num_v_unkwn = 3
petsc_matF = LAT.csr_2_petsc(size=(num_v_unkwn, num_v_unkwn),
csr=(row_idx_F, col_idx_F, vals_F))
yield petsc_matF
def create_simple_petsc_matrix(request):
vals_F = [3.2, 1.1, 6.3, 1., -5.1]
col_idx_F = [0, 1, 0, 1, 2]
row_idx_F = [0, 2, 4, 5]
num_v_unkwn = 3
petsc_matF = LAT.csr_2_petsc(size = (num_v_unkwn,num_v_unkwn),
csr = (row_idx_F,col_idx_F,vals_F))
yield petsc_matF
def test_lsc_shell(self):
''' Test for the lsc operator shell '''
vals_A = [5.5, 7.1, 1.0]
col_idx_A = [0, 1, 2]
row_idx_A = [0, 1, 2, 3]
vals_B = [1.1, 6.3, 7.3, 3.6, 6.3]
col_idx_B = [0, 2, 0, 1, 2]
row_idx_B = [0, 2, 5]
vals_Bt = [1.1, 7.3, 3.6, 6.3, 6.3]
col_idx_Bt = [0, 1, 1, 0, 1]
row_idx_Bt = [0, 2, 3, 5]
vals_F = [3.2, 1.1, 6.3, 1., -5.1]
col_idx_F = [0, 1, 0, 2, 0]
row_idx_F = [0, 2, 4, 5]
num_B_rows = len(row_idx_B) - 1
num_B_cols = len(row_idx_A) - 1
petsc_matA = LAT.csr_2_petsc(size=(num_B_cols, num_B_cols),
csr=(row_idx_A, col_idx_A, vals_A))
petsc_matB = LAT.csr_2_petsc(size=(num_B_rows, num_B_cols),
csr=(row_idx_B, col_idx_B, vals_B))
petsc_matBt = LAT.csr_2_petsc(size=(num_B_cols, num_B_rows),
csr=(row_idx_Bt, col_idx_Bt, vals_Bt))
petsc_matF = LAT.csr_2_petsc(size=(num_B_cols, num_B_cols),
csr=(row_idx_F, col_idx_F, vals_F))
self.petsc_options.setValue('innerLSCsolver_BTinvBt_ksp_type',
'preonly')
self.petsc_options.setValue('innerLSCsolver_T_ksp_type', 'preonly')
self.petsc_options.setValue('innerLSCsolver_BTinvBt_pc_type', 'lu')
self.petsc_options.setValue('innerLSCsolver_T_pc_type', 'lu')
LSC_shell = LAT.LSCInv_shell(petsc_matA, petsc_matB, petsc_matBt,
petsc_matF)
x_vec = np.ones(num_B_rows)
y_vec = np.zeros(num_B_rows)
x_PETSc_vec = p4pyPETSc.Vec().createWithArray(x_vec)
y_PETSc_vec = p4pyPETSc.Vec().createWithArray(y_vec)
A = None
LSC_shell.apply(A, x_PETSc_vec, y_PETSc_vec)
true_solu = np.mat('[-0.01096996,0.00983216]')
assert np.allclose(y_vec, true_solu)
def test_matrix_splitting_1(self):
vals_F = [3.2, 1.1, 5.4, 6.3, 1., -5.1, 1.2]
col_idx_F = [0, 1, 2, 0, 2, 0, 1]
row_idx_F = [0, 3, 5, 7]
num_v_unkwn = len(row_idx_F) - 1
petsc_matF = LAT.csr_2_petsc(size = (num_v_unkwn,num_v_unkwn),
csr = (row_idx_F,col_idx_F,vals_F))
A = LAT.split_PETSc_Mat(petsc_matF)
A[0].axpy(1.0,A[1])
assert np.allclose(A[0].getValuesCSR()[2], petsc_matF.getValuesCSR()[2])
def test_matrix_splitting_1(self):
vals_F = [3.2, 1.1, 5.4, 6.3, 1., -5.1, 1.2]
col_idx_F = [0, 1, 2, 0, 2, 0, 1]
row_idx_F = [0, 3, 5, 7]
num_v_unkwn = len(row_idx_F) - 1
petsc_matF = LAT.csr_2_petsc(size=(num_v_unkwn, num_v_unkwn),
csr=(row_idx_F, col_idx_F, vals_F))
A = LAT.split_PETSc_Mat(petsc_matF)
A[0].axpy(1.0, A[1])
assert np.allclose(A[0].getValuesCSR()[2],
petsc_matF.getValuesCSR()[2])
def test_petsc_load_matrix(tmpdir):
"""test petsc_load_matrix """
from petsc4py import PETSc as p4pyPETSc
from proteus import LinearAlgebraTools as LAT
vals_A = [5.5, 7.1, 1.0]
col_idx_A = [0, 1, 2]
row_idx_A = [0, 1, 2, 3]
A = LAT.csr_2_petsc(size=(3, 3), csr=(row_idx_A, col_idx_A, vals_A))
A_tmp = tmpdir.join('A.petsc_mat')
LAT._petsc_view(A, A_tmp.strpath)
A_test = LAT.petsc_load_matrix(A_tmp.strpath)
csr_values = A_test.getValuesCSR()
assert np.allclose(csr_values[0], row_idx_A)
assert np.allclose(csr_values[1], col_idx_A)
assert np.allclose(csr_values[2], vals_A)
A_test = LAT.petsc_load_matrix('dne.txt')
assert A_test is None
def test_petsc_load_matrix(tmpdir):
"""test petsc_load_matrix """
from petsc4py import PETSc as p4pyPETSc
from proteus import LinearAlgebraTools as LAT
vals_A = [5.5,7.1,1.0]
col_idx_A = [0 , 1 , 2 ]
row_idx_A = [0, 1, 2, 3]
A = LAT.csr_2_petsc(size = (3,3),
csr = (row_idx_A,col_idx_A,vals_A))
A_tmp = tmpdir.join('A.petsc_mat')
LAT._petsc_view(A,A_tmp.strpath)
A_test = LAT.petsc_load_matrix(A_tmp.strpath)
csr_values = A_test.getValuesCSR()
assert np.allclose(csr_values[0], row_idx_A)
assert np.allclose(csr_values[1], col_idx_A)
assert np.allclose(csr_values[2], vals_A)
A_test = LAT.petsc_load_matrix('dne.txt')
assert A_test is None
def create_simple_saddle_point_problem(request):
"""Builds simple matrices and vectors for saddle point shell tests.
Returns
-------
output_lst : lst
This function returns an output list with three sublists. See
the notes below for a description of these lists.
Notes
-----
The output of this function returns xxx sublists. The first
contains a list of matrices. The second returns a list
of vectors. The last returns a list of sizes.
"""
class Output_Storage(object):
"""Storage class for matrix objects. """
def __init__(self, petsc_matF, petsc_matD, petsc_matB, petsc_matBt,
petsc_matC, x_vec, y_vec, num_p_unkwn, num_v_unkwn):
self.petsc_matF = petsc_matF
self.petsc_matD = petsc_matD
self.petsc_matB = petsc_matB
self.petsc_matBt = petsc_matBt
self.petsc_matC = petsc_matC
self.x_vec = x_vec
self.y_vec = y_vec
self.num_p_unkwn = num_p_unkwn
self.num_v_unkwn = num_v_unkwn
vals_F = [3.2, 1.1, 6.3, 1., -5.1]
col_idx_F = [0, 1, 0, 2, 0]
row_idx_F = [0, 2, 4, 5]
vals_D = [5.5, 7.1, 1.0]
col_idx_D = [0, 1, 2]
row_idx_D = [0, 1, 2, 3]
vals_B = [1.1, 6.3, 7.3, 3.6, 6.3]
col_idx_B = [0, 2, 0, 1, 2]
row_idx_B = [0, 2, 5]
vals_Bt = [1.1, 7.3, 3.6, 6.3, 6.3]
col_idx_Bt = [0, 1, 1, 0, 1]
row_idx_Bt = [0, 2, 3, 5]
vals_C = [1.2, 2.1, 3.3]
col_idx_C = [0, 1, 1]
row_idx_C = [0, 2, 3]
num_p_unkwn = len(row_idx_B) - 1
num_v_unkwn = len(row_idx_F) - 1
petsc_matF = LAT.csr_2_petsc(size=(num_v_unkwn, num_v_unkwn),
csr=(row_idx_F, col_idx_F, vals_F))
petsc_matD = LAT.csr_2_petsc(size=(num_v_unkwn, num_v_unkwn),
csr=(row_idx_D, col_idx_D, vals_D))
petsc_matB = LAT.csr_2_petsc(size=(num_p_unkwn, num_v_unkwn),
csr=(row_idx_B, col_idx_B, vals_B))
petsc_matBt = LAT.csr_2_petsc(size=(num_v_unkwn, num_p_unkwn),
csr=(row_idx_Bt, col_idx_Bt, vals_Bt))
petsc_matC = LAT.csr_2_petsc(size=(num_p_unkwn, num_p_unkwn),
csr=(row_idx_C, col_idx_C, vals_C))
x_vec = np.ones(num_p_unkwn)
y_vec = np.zeros(num_p_unkwn)
x_PETSc_vec = p4pyPETSc.Vec().createWithArray(x_vec)
y_PETSc_vec = p4pyPETSc.Vec().createWithArray(y_vec)
output_data = Output_Storage(petsc_matF, petsc_matD, petsc_matB,
petsc_matBt, petsc_matC, x_PETSc_vec,
y_PETSc_vec, num_p_unkwn, num_v_unkwn)
yield output_data
def create_simple_saddle_point_problem(request):
"""Builds simple matrices and vectors for saddle point shell tests.
Returns
-------
output_lst : lst
This function returns an output list with three sublists. See
the notes below for a description of these lists.
Notes
-----
The output of this function returns xxx sublists. The first
contains a list of matrices. The second returns a list
of vectors. The last returns a list of sizes.
"""
class Output_Storage(object):
"""Storage class for matrix objects. """
def __init__(self,
petsc_matF,
petsc_matD,
petsc_matB,
petsc_matBt,
petsc_matC,
x_vec,
y_vec,
num_p_unkwn,
num_v_unkwn):
self.petsc_matF = petsc_matF
self.petsc_matD = petsc_matD
self.petsc_matB = petsc_matB
self.petsc_matBt = petsc_matBt
self.petsc_matC = petsc_matC
self.x_vec = x_vec
self.y_vec = y_vec
self.num_p_unkwn = num_p_unkwn
self.num_v_unkwn = num_v_unkwn
vals_F = [3.2, 1.1, 6.3, 1., -5.1]
col_idx_F = [0, 1, 0, 2, 0]
row_idx_F = [0, 2, 4, 5]
vals_D = [5.5,7.1,1.0]
col_idx_D = [0 , 1 , 2 ]
row_idx_D = [0, 1, 2, 3]
vals_B = [1.1, 6.3, 7.3, 3.6, 6.3]
col_idx_B = [0 , 2 , 0 , 1 , 2 ]
row_idx_B = [0, 2, 5]
vals_Bt = [1.1, 7.3, 3.6, 6.3, 6.3]
col_idx_Bt = [0, 1, 1, 0, 1]
row_idx_Bt = [0, 2, 3, 5]
vals_C = [1.2, 2.1, 3.3]
col_idx_C = [0, 1, 1]
row_idx_C = [0, 2, 3]
num_p_unkwn = len(row_idx_B) - 1
num_v_unkwn = len(row_idx_F) - 1
petsc_matF = LAT.csr_2_petsc(size = (num_v_unkwn,num_v_unkwn),
csr = (row_idx_F,col_idx_F,vals_F))
petsc_matD = LAT.csr_2_petsc(size = (num_v_unkwn,num_v_unkwn),
csr = (row_idx_D,col_idx_D,vals_D))
petsc_matB = LAT.csr_2_petsc(size = (num_p_unkwn,num_v_unkwn),
csr = (row_idx_B,col_idx_B,vals_B))
petsc_matBt = LAT.csr_2_petsc(size = (num_v_unkwn,num_p_unkwn),
csr = (row_idx_Bt,col_idx_Bt,vals_Bt))
petsc_matC = LAT.csr_2_petsc(size = (num_p_unkwn,num_p_unkwn),
csr = (row_idx_C,col_idx_C,vals_C))
x_vec = np.ones(num_p_unkwn)
y_vec = np.zeros(num_p_unkwn)
x_PETSc_vec = p4pyPETSc.Vec().createWithArray(x_vec)
y_PETSc_vec = p4pyPETSc.Vec().createWithArray(y_vec)
output_data = Output_Storage(petsc_matF,
petsc_matD,
petsc_matB,
petsc_matBt,
petsc_matC,
x_PETSc_vec,
y_PETSc_vec,
num_p_unkwn,
num_v_unkwn)
yield output_data
