def test_tppcd_shell_with_chebyshev_iteration(self):
''' Test for the lsc operator shell '''
Qp_visc = LAT.petsc_load_matrix(os.path.join(self._scriptdir,'import_modules/Qp_visc.bin'))
Qp_dens = LAT.petsc_load_matrix(os.path.join(self._scriptdir,'import_modules/Qp_dens.bin'))
Ap_rho = LAT.petsc_load_matrix(os.path.join(self._scriptdir, 'import_modules/Ap_rho.bin'))
Np_rho = LAT.petsc_load_matrix(os.path.join(self._scriptdir, 'import_modules/Np_rho.bin'))
alpha = True
delta_t = 0.001
x_vec = LAT.petsc_load_vector(os.path.join(self._scriptdir,'import_modules/input_vec_tppcd.bin'))
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_ksp_type','preonly')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_ksp_constant_null_space', '')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_type','hypre')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_hypre_type','boomeramg')
TPPCD_shell = LAT.TwoPhase_PCDInv_shell(Qp_visc,
Qp_dens,
Ap_rho,
Np_rho,
alpha,
delta_t,
5,
laplace_null_space=True)
y_vec = x_vec.copy()
y_vec.zeroEntries()
A = None
TPPCD_shell.apply(A,x_vec,y_vec)
true_solu = LAT.petsc_load_vector(os.path.join(self._scriptdir, 'import_modules/tp_pcd_y_output.bin'))
assert np.allclose(y_vec.getArray(),true_solu.getArray())
def test_tppcd_shell(self):
''' Test for the lsc operator shell '''
Qp_visc = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Qp_visc'))
Qp_dens = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Qp_dens'))
Ap_rho = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Ap_rho'))
Np_rho = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Np_rho'))
alpha = True
delta_t = 0.001
x_vec = LAT.petsc_load_vector(
os.path.join(self._scriptdir, 'import_modules/input_vec_tppcd'))
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_ksp_type',
'preonly')
self.petsc_options.setValue(
'innerTPPCDsolver_Ap_rho_ksp_constant_null_space', '')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_type', 'hypre')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_hypre_type',
'boomeramg')
TPPCD_shell = LAT.TwoPhase_PCDInv_shell(Qp_visc, Qp_dens, Ap_rho,
Np_rho, alpha, delta_t, 5)
y_vec = x_vec.copy()
y_vec.zeroEntries()
A = None
TPPCD_shell.apply(A, x_vec, y_vec)
true_solu = LAT.petsc_load_vector(
os.path.join(self._scriptdir, 'import_modules/tp_pcd_y_output'))
assert np.allclose(y_vec.getArray(), true_solu.getArray())
def test_tppcd_shell_with_dirichlet_pressure(self):
''' Test for the lsc operator shell '''
Qp_visc = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Qp_visc.bin'))
Qp_dens = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Qp_dens.bin'))
Ap_rho = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Ap_rho.bin'))
Np_rho = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Np_rho.bin'))
alpha = True
delta_t = 0.001
x_vec = LAT.petsc_load_vector(
os.path.join(self._scriptdir,
'import_modules/input_vec_tppcd.bin'))
self.petsc_options.clear()
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_ksp_type',
'preonly')
self.petsc_options.setValue(
'innerTPPCDsolver_Ap_rho_ksp_constant_null_space', '')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_type', 'hypre')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_hypre_type',
'boomeramg')
dirichlet_nodes = [3, 12, 15, 21, 33]
TPPCD_shell = LAT.TwoPhase_PCDInv_shell(
Qp_visc,
Qp_dens,
Ap_rho,
Np_rho,
alpha=alpha,
delta_t=delta_t,
num_chebyshev_its=5,
strong_dirichlet_DOF=dirichlet_nodes)
# Test the index set is set correctly
unknown_indices = np.arange(TPPCD_shell.getSize())
known_indices_mask = np.ones(TPPCD_shell.getSize(), dtype=bool)
known_indices_mask[dirichlet_nodes] = False
unknown_is = unknown_indices[known_indices_mask]
np.testing.assert_equal(unknown_is,
TPPCD_shell.unknown_dof_is.getIndices())
y_vec = x_vec.copy()
y_vec.zeroEntries()
A = None
TPPCD_shell.apply(A, x_vec, y_vec)
assert np.array_equal(y_vec[dirichlet_nodes], [0., 0., 0., 0., 0.])
#np.savetxt(os.path.join(self._scriptdir,'comparison_files/tppcd_y_dirichlet_dof.csv'),y_vec.getArray(),delimiter=',')
true_solu = np.loadtxt(os.path.join(
self._scriptdir, 'comparison_files/tppcd_y_dirichlet_dof.csv'),
delimiter=',')
np.testing.assert_allclose(y_vec.getArray(),
true_solu,
rtol=1e-8,
atol=1e-8)
def load_matrix_step_noslip():
"""
Loads a medium sized backwards facing step matrix for studying
different AMG preconditioners.
"""
A = LAT.petsc_load_matrix('dump_test_2_step2d_1.0par_j_0')
return A
def load_saddle_point_matrix_1(request):
"""
Loads a small example of a backwards facing step matrix for
testing purposes. (Note: this matrix does not have advection)
"""
A = LAT.petsc_load_matrix(os.path.join
(os.path.dirname(__file__),
'import_modules/saddle_point_mat_1'))
yield A
def load_small_step_matrix(request):
"""
Loads a small example of a backwards facing step matrix for
testing purposes. (Note: this matrix does not have advection)
"""
A = LAT.petsc_load_matrix(
os.path.join(os.path.dirname(__file__),
'import_modules/saddle_point_small.bin'))
yield A
def load_nse_step_matrix(request):
"""
Loads a Navier-Stokes matrix for the backwards step problem from
the MPRANS module. This matrix is constructed using no-slip
boundary conditions, and weakly enforced Dirichlet conditions.
"""
A = LAT.petsc_load_matrix(os.path.join
(os.path.dirname(__file__),
'import_modules/NSE_step_no_slip.bin'))
yield A
def load_nse_step_matrix(request):
"""
Loads a Navier-Stokes matrix for the backwards step problem from
the MPRANS module. This matrix is constructed using no-slip
boundary conditions, and weakly enforced Dirichlet conditions.
"""
A = LAT.petsc_load_matrix(
os.path.join(os.path.dirname(__file__),
'import_modules/NSE_step_no_slip.bin'))
yield A
def load_medium_step_matrix(request):
"""
Loads a medium sized backwards facing step matrix for studying
different AMG preconditioners. (Note: this matrix does not have
advection)
"""
A = LAT.petsc_load_matrix(
os.path.join(os.path.dirname(__file__),
'import_modules/saddle_point_matrix.bin'))
yield A
def load_medium_step_matrix(request):
"""
Loads a medium sized backwards facing step matrix for studying
different AMG preconditioners. (Note: this matrix does not have
advection)
"""
A = LAT.petsc_load_matrix(os.path.join
(os.path.dirname(__file__),
'import_modules/saddle_point_matrix'))
yield A
def test_tppcd_shell_with_chebyshev_iteration(self):
''' Test for the lsc operator shell '''
Qp_visc = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Qp_visc.bin'))
Qp_dens = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Qp_dens.bin'))
Ap_rho = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Ap_rho.bin'))
Np_rho = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/Np_rho.bin'))
alpha = True
delta_t = 0.001
x_vec = LAT.petsc_load_vector(
os.path.join(self._scriptdir,
'import_modules/input_vec_tppcd.bin'))
self.petsc_options.clear()
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_ksp_type',
'preonly')
self.petsc_options.setValue(
'innerTPPCDsolver_Ap_rho_ksp_constant_null_space', '')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_type', 'hypre')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_hypre_type',
'boomeramg')
TPPCD_shell = LAT.TwoPhase_PCDInv_shell(Qp_visc,
Qp_dens,
Ap_rho,
Np_rho,
alpha,
delta_t,
5,
laplace_null_space=True)
y_vec = x_vec.copy()
y_vec.zeroEntries()
A = None
TPPCD_shell.apply(A, x_vec, y_vec)
#np.savetxt(os.path.join(self._scriptdir,'comparison_files/tp_pcd_y_output_cheb.csv'),y_vec.getArray(),delimiter=',')
true_solu = np.loadtxt(os.path.join(
self._scriptdir, 'comparison_files/tp_pcd_y_output_cheb.csv'),
delimiter=',')
np.testing.assert_allclose(y_vec.getArray(),
true_solu,
rtol=1e-8,
atol=1e-8)
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 test_tppcd_shell_with_dirichlet_pressure(self):
''' Test for the lsc operator shell '''
Qp_visc = LAT.petsc_load_matrix(os.path.join(self._scriptdir,'import_modules/Qp_visc.bin'))
Qp_dens = LAT.petsc_load_matrix(os.path.join(self._scriptdir,'import_modules/Qp_dens.bin'))
Ap_rho = LAT.petsc_load_matrix(os.path.join(self._scriptdir, 'import_modules/Ap_rho.bin'))
Np_rho = LAT.petsc_load_matrix(os.path.join(self._scriptdir, 'import_modules/Np_rho.bin'))
alpha = True
delta_t = 0.001
x_vec = LAT.petsc_load_vector(os.path.join(self._scriptdir,'import_modules/input_vec_tppcd.bin'))
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_ksp_type','preonly')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_ksp_constant_null_space', '')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_type','hypre')
self.petsc_options.setValue('innerTPPCDsolver_Ap_rho_pc_hypre_type','boomeramg')
dirichlet_nodes = [3, 12, 15, 21, 33]
TPPCD_shell = LAT.TwoPhase_PCDInv_shell(Qp_visc,
Qp_dens,
Ap_rho,
Np_rho,
alpha = alpha,
delta_t = delta_t,
num_chebyshev_its = 5,
strong_dirichlet_DOF = dirichlet_nodes)
# Test the index set is set correctly
unknown_indices = np.arange(TPPCD_shell.getSize())
known_indices_mask = np.ones(TPPCD_shell.getSize(),dtype=bool)
known_indices_mask[dirichlet_nodes] = False
unknown_is = unknown_indices[known_indices_mask]
assert np.array_equal(unknown_is, TPPCD_shell.unknown_dof_is.getIndices())
y_vec = x_vec.copy()
y_vec.zeroEntries()
A = None
TPPCD_shell.apply(A,x_vec,y_vec)
assert np.array_equal(y_vec[dirichlet_nodes], [0.,0.,0.,0.,0.])
true_solu = LAT.petsc_load_vector(os.path.join(self._scriptdir,
'import_modules/tppcd_y_dirichlet_dof.bin'))
assert np.allclose(y_vec.getArray(),true_solu.getArray())
def load_rans2p_step_newton_5(request):
A = LAT.petsc_load_matrix(
os.path.join(os.path.dirname(__file__),
'import_modules/rans2p_step_newton_5.bin'))
yield A
def med_petsc_with_const_pressure():
petsc_mat = LinearAlgebraTools.petsc_load_matrix(os.path.join(os.path.dirname(__file__),
'jac.bin'))
yield petsc_mat
def load_rans2p_step_newton_5(request):
A = LAT.petsc_load_matrix(os.path.join
(os.path.dirname(__file__),
'import_modules/rans2p_step_newton_5.bin'))
yield A
def med_petsc_with_const_pressure():
petsc_mat = LinearAlgebraTools.petsc_load_matrix(
os.path.join(os.path.dirname(__file__), 'jac.bin'))
yield petsc_mat
def load_nse_cavity_matrix(request):
"""Loads a Navier-Stokes matrix drawn from the MPRANS module. """
A = LAT.petsc_load_matrix(
os.path.join(os.path.dirname(__file__),
'import_modules/NSE_cavity_matrix.bin'))
yield A
def load_matrix(mat_file_name):
"""Load a matrix """
A = LAT.petsc_load_matrix(
os.path.join(os.path.dirname(__file__),
'import_modules/' + mat_file_name))
return A
def setup_method(self, method):
self._scriptdir = os.path.dirname(__file__)
self.saddle_point_matrix = LAT.petsc_load_matrix(
os.path.join(self._scriptdir, 'import_modules/saddle_point_small'))
def load_nse_cavity_matrix(request):
"""Loads a Navier-Stokes matrix drawn from the MPRANS module. """
A = LAT.petsc_load_matrix('dump_stokes_drivenCavityStokesTrial_1.0par_j_1')
yield A
def load_nse_cavity_matrix(request):
"""Loads a Navier-Stokes matrix drawn from the MPRANS module. """
A = LAT.petsc_load_matrix(os.path.join
(os.path.dirname(__file__),
'import_modules/NSE_cavity_matrix.bin'))
yield A
def load_matrix(mat_file_name):
"""Load a matrix """
A = LAT.petsc_load_matrix(os.path.join
(os.path.dirname(__file__),
'import_modules/'+mat_file_name))
return A
def setup_method(self,method):
self._scriptdir = os.path.dirname(__file__)
self.saddle_point_matrix=LAT.petsc_load_matrix(os.path.join(self._scriptdir,
'import_modules/saddle_point_small'))
