def check_c0q1(self,
test_hexMesh_3x3=False,
use_petsc=False,
name="_hexMesh_"):
poisson_3d_p = load_physics('poisson_3d_p', modulepath)
poisson_3d_c0q1_n = load_numerics('poisson_3d_c0q1_n', modulepath)
poisson_3d_c0q1_n.hex = True
if test_hexMesh_3x3 == True:
poisson_3d_p.meshfile = 'hexMesh_3x3'
poisson_3d_p.domain = Domain.MeshHexDomain(poisson_3d_p.meshfile)
poisson_3d_p.x0 = (-3., -3., -3.)
poisson_3d_p.L = (6., 6., 6.)
pList = [poisson_3d_p]
nList = [poisson_3d_c0q1_n]
so = System_base()
so.name = pList[0].name = "poisson_3d_c0q1" + name + "pe" + repr(
comm.size())
so.sList = [default_s]
opts.logLevel = 7
opts.verbose = True
if use_petsc == True:
nList[0].linearSolver = default_n.KSP_petsc4py
nList[0].multilevelLinearSolver = default_n.KSP_petsc4py
ns = NumericalSolution.NS_base(so, pList, nList, so.sList, opts)
ns.calculateSolution('poisson_3d_c0q1')
del ns
assert (True)
def example_setting(self, pre_setting):
Context.contextOptionsString = pre_setting
my_so = defaults.load_system("cylinder_so", modulepath)
opts.profile = False
opts.gatherArchive = True
pList = []
nList = []
sList = []
for (pModule, nModule) in my_so.pnList:
pList.append(defaults.load_physics(pModule, modulepath))
nList.append(defaults.load_numerics(nModule, modulepath))
if pList[-1].name == None:
pList[-1].name = pModule
if my_so.sList == []:
for i in range(len(my_so.pnList)):
s = default_s
sList.append(s)
else:
sList = my_so.sList
my_so.name += "_sbm_mesh3D_" + self.compare_name #save data with different filename
ns = proteus.NumericalSolution.NS_base(my_so, pList, nList, sList,
opts)
ns.calculateSolution(my_so.name)
expected_path = 'comparison_files/' + self.compare_name + '.h5'
with tables.open_file(os.path.join(self._scriptdir, expected_path)) as expected, \
tables.open_file( my_so.name + '.h5') as actual:
assert np.allclose(expected.root.u_t2,
actual.root.u_t2,
atol=1e-10)
def test_01_FullRun(self):
stokesDrivenCavity_2d_p = defaults.load_physics(
'stokesDrivenCavity_2d_p', import_modules)
stokesDrivenCavity_2d_n = defaults.load_numerics(
'stokesDrivenCavity_2d_n', import_modules)
self.pList = [stokesDrivenCavity_2d_p]
self.nList = [stokesDrivenCavity_2d_n]
self.nList[0].linearSmoother = proteus.LinearSolvers.Schur_Qp
self.pList = [stokesDrivenCavity_2d_p]
self.nList = [stokesDrivenCavity_2d_n]
defaults.reset_default_so()
self.so = default_so
self.so.tnList = [0., 1.]
self.so.name = self.pList[0].name
self.so.sList = self.pList[0].name
self.so.sList = [default_s]
self._setPETSc()
self._runTest()
relpath = 'comparison_files/Qp_expected.log'
actual_log = TestTools.NumericResults.build_from_proteus_log(
'proteus.log')
expected_log = TestTools.NumericResults.build_from_proteus_log(
os.path.join(self._scriptdir, relpath))
plot_lst = [(1.0, 0, 0), (1.0, 1, 0), (1.0, 2, 0)]
L1 = expected_log.get_ksp_resid_it_info(plot_lst)
L2 = actual_log.get_ksp_resid_it_info(plot_lst)
assert L1 == L2
def check_c0q1(self,test_hexMesh_3x3=False,use_petsc=False,name="_hexMesh_"):
poisson_3d_p = load_physics('poisson_3d_p',
modulepath)
poisson_3d_c0q1_n = load_numerics('poisson_3d_c0q1_n',
modulepath)
poisson_3d_c0q1_n.hex=True
if test_hexMesh_3x3 == True:
poisson_3d_p.meshfile='hexMesh_3x3'
poisson_3d_p.domain = Domain.MeshHexDomain(poisson_3d_p.meshfile)
poisson_3d_p.x0 = (-3.,-3.,-3.)
poisson_3d_p.L = ( 6., 6., 6.)
pList = [poisson_3d_p]
nList = [poisson_3d_c0q1_n]
so = System_base()
so.name = pList[0].name = "poisson_3d_c0q1"+name+"pe"+`comm.size()`
so.sList=[default_s]
opts.logLevel=7
opts.verbose=True
if use_petsc == True:
nList[0].linearSolver=default_n.KSP_petsc4py
nList[0].multilevelLinearSolver=default_n.KSP_petsc4py
ns = NumericalSolution.NS_base(so,pList,nList,so.sList,opts)
ns.calculateSolution('poisson_3d_c0q1')
del ns
assert(True)
def setup_method(self):
nseDrivenCavity_2d_p = defaults.load_physics('nseDrivenCavity_2d_p',import_modules)
nseDrivenCavity_2d_n = defaults.load_numerics('nseDrivenCavity_2d_n',import_modules)
self.pList = [nseDrivenCavity_2d_p]
self.nList = [nseDrivenCavity_2d_n]
self.so = default_so
self.so.name = self.pList[0].name
self.so.sList = self.pList[0].name
self.so.sList = [default_s]
self._scriptdir = os.path.dirname(__file__)
Profiling.openLog("proteus.log",10)
Profiling.logAllProcesses = True
def test_c0q2(self):
pList = [load_physics('poisson_3d_p', modulepath)]
nList = [load_numerics('poisson_3d_c0q2_n', modulepath)]
so = System_base()
so.name = pList[0].name = "poisson_3d_c0q2" + "pe" + repr(comm.size())
so.sList = [default_s]
opts.logLevel = 7
opts.verbose = True
nList[0].linearSolver = default_n.KSP_petsc4py
nList[0].multilevelLinearSolver = default_n.KSP_petsc4py
ns = NumericalSolution.NS_base(so, pList, nList, so.sList, opts)
ns.calculateSolution('poisson_3d_c0q2')
del ns
assert (True)
def test_c0q2(self):
pList = [load_physics('poisson_3d_p',
modulepath)]
nList = [load_numerics('poisson_3d_c0q2_n',
modulepath)]
so = System_base()
so.name = pList[0].name = "poisson_3d_c0q2"+"pe"+`comm.size()`
so.sList=[default_s]
opts.logLevel=7
opts.verbose=True
nList[0].linearSolver=default_n.KSP_petsc4py
nList[0].multilevelLinearSolver=default_n.KSP_petsc4py
ns = NumericalSolution.NS_base(so,pList,nList,so.sList,opts)
ns.calculateSolution('poisson_3d_c0q2')
del ns
assert(True)
def example_setting(self, pre_setting):
Context.contextOptionsString = pre_setting
my_so = defaults.load_system("cylinder_so", modulepath)
opts.profile = False
opts.gatherArchive = True
pList = []
nList = []
sList = []
for (pModule, nModule) in my_so.pnList:
pList.append(defaults.load_physics(pModule, modulepath))
nList.append(defaults.load_numerics(nModule, modulepath))
if pList[-1].name == None:
pList[-1].name = pModule
if my_so.sList == []:
for i in range(len(my_so.pnList)):
s = default_s
sList.append(s)
else:
sList = my_so.sList
my_so.name += "_sbm_mesh3D_" + self.compare_name #save data with different filename
try:
ns = proteus.NumericalSolution.NS_base(my_so, pList, nList, sList,
opts)
except:
assert 0, "NS setup failed"
try:
ns.calculateSolution(my_so.name)
except:
assert 0, "NS calculation failed"
actual = tables.open_file(
'cylinder_sbm_mesh3D_T001_P1_sbm_3Dmesh' + '.h5', 'r')
expected_path = 'comparison_files/' + 'comparison_u_t2.csv'
#write comparison file
#np.array(actual.root.u_t2).tofile(os.path.join(self._scriptdir, expected_path),sep=",")
np.testing.assert_almost_equal(np.fromfile(os.path.join(
self._scriptdir, expected_path),
sep=","),
np.array(actual.root.u_t2),
decimal=10)
actual.close()
def test_02_FullRun(self):
stokesDrivenCavity_2d_p = defaults.load_physics(
'stokesDrivenCavity_2d_p', import_modules)
stokesDrivenCavity_2d_n = defaults.load_numerics(
'stokesDrivenCavity_2d_n', import_modules)
self.pList = [stokesDrivenCavity_2d_p]
self.nList = [stokesDrivenCavity_2d_n]
self.pList = [stokesDrivenCavity_2d_p]
self.nList = [stokesDrivenCavity_2d_n]
defaults.reset_default_so()
self.so = default_so
self.so.tnList = [0., 1.]
self.so.name = self.pList[0].name
self.so.sList = self.pList[0].name
self.so.sList = [default_s]
self._setPETSc_LU()
self._runTest()
def test_c0p2(genMesh=True):
pList = [defaults.load_physics('poisson_3d_tetgen_p',
modulepath)]
nList = [defaults.load_numerics('poisson_3d_tetgen_c0p2_n',
modulepath)]
so = defaults.System_base()
so.name = pList[0].name = "poisson_3d_tetgen_c0p2"+"pe"+`comm.size()`
so.sList=[default_s]
Profiling.logLevel=7
Profiling.verbose=False
opts.generatePartitionedMeshFromFiles = True
opts.gatherArchive=True
pList[0].genMesh=genMesh
nList[0].linearSolver=default_n.KSP_petsc4py
nList[0].multilevelLinearSolver=default_n.KSP_petsc4py
ns = NumericalSolution.NS_base(so,pList,nList,so.sList,opts)
ns.calculateSolution('poisson_3d_c0p2')
assert(True)
def test_c0p2(genMesh=True):
pList = [defaults.load_physics('poisson_3d_tetgen_p',
modulepath)]
nList = [defaults.load_numerics('poisson_3d_tetgen_c0p2_n',
modulepath)]
so = defaults.System_base()
so.name = pList[0].name = "poisson_3d_tetgen_c0p2"+"pe"+repr(comm.size())
so.sList=[default_s]
Profiling.logLevel=7
Profiling.verbose=False
opts.generatePartitionedMeshFromFiles = True
opts.gatherArchive=True
pList[0].genMesh=genMesh
nList[0].linearSolver=default_n.KSP_petsc4py
nList[0].multilevelLinearSolver=default_n.KSP_petsc4py
ns = NumericalSolution.NS_base(so,pList,nList,so.sList,opts)
ns.calculateSolution('poisson_3d_c0p2')
assert(True)
def test_c0p1(self):
pList = [load_physics('poisson_3d_p', modulepath)]
nList = [load_numerics('poisson_3d_c0p1_n', modulepath)]
so = System_base()
so.name = pList[0].name = "poisson_3d_c0p1" + "pe" + ` comm.size() `
so.sList = [default_s]
opts.logLevel = 7
opts.verbose = True
opts.profile = True
opts.gatherArchive = True
nList[0].linearSolver = default_n.KSP_petsc4py
nList[0].multilevelLinearSolver = default_n.KSP_petsc4py
#nList[0].linearSolver=default_n.LU
#nList[0].multilevelLinearSolver=default_n.LU
ns = NumericalSolution.NS_base(so, pList, nList, so.sList, opts)
ns.calculateSolution('poisson_3d_c0p1')
del ns
assert (True)
def load_simulation(context_options_str=None):
"""
Loads a two-phase step problem with settings
Parameters
----------
settings:
Returns:
--------
"""
from proteus import Context
from proteus import default_s
reload(PETSc)
reload(iproteus)
reload(default_p)
reload(default_n)
reload(default_s)
Profiling.openLog("proteus.log",11)
Profiling.verbose=True
Context.contextOptionsString=context_options_str
step2d_so = defaults.load_system('step2d_so',import_modules)
twp_navier_stokes_step2d_p = defaults.load_physics('twp_navier_stokes_step2d_p',import_modules)
twp_navier_stokes_step2d_n = defaults.load_numerics('twp_navier_stokes_step2d_n',import_modules)
pList = [twp_navier_stokes_step2d_p]
nList = [twp_navier_stokes_step2d_n]
pList[0].name = 'step2d'
so = step2d_so
so.name = pList[0].name
so.sList = pList[0].name
so.sList = [default_s]
_scriptdir = os.path.dirname(__file__)
Profiling.logAllProcesses = False
ns = NumericalSolution.NS_base(so,
pList,
nList,
so.sList,
opts)
return ns
def example_setting(self, pre_setting):
Context.contextOptionsString = pre_setting
my_so = defaults.load_system("cylinder_so",modulepath)
opts.profile = False
opts.gatherArchive = True
pList=[]
nList=[]
sList=[]
for (pModule,nModule) in my_so.pnList:
pList.append(defaults.load_physics(pModule,modulepath))
nList.append(defaults.load_numerics(nModule,modulepath))
if pList[-1].name == None:
pList[-1].name = pModule
if my_so.sList == []:
for i in range(len(my_so.pnList)):
s = default_s
sList.append(s)
else:
sList = my_so.sList
my_so.name += "_sbm_mesh3D_"+self.compare_name #save data with different filename
ns = proteus.NumericalSolution.NS_base(my_so,
pList,
nList,
sList,
opts)
ns.calculateSolution(my_so.name)
expected_path = 'comparison_files/' + self.compare_name + '.h5'
with tables.open_file(os.path.join(self._scriptdir, expected_path)) as expected, \
tables.open_file( my_so.name + '.h5') as actual:
assert np.allclose(expected.root.u_t2,
actual.root.u_t2,
atol=1e-10)
def setup_method(self):
stokesDrivenCavity_2d_p = defaults.load_physics(
'stokesDrivenCavity_2d_p', import_modules)
stokesDrivenCavity_2d_n = defaults.load_numerics(
'stokesDrivenCavity_2d_n', import_modules)
import sys
import inspect
import numpy as np
import tables
import pickle
import pytest
from petsc4py import PETSc
TestTools.addSubFolders(inspect.currentframe())
from proteus import defaults
import_modules = os.path.join(os.path.dirname(os.path.abspath(__file__)),
'import_modules')
twp_navier_stokes_cavity_2d_so = defaults.load_system(
'twp_navier_stokes_cavity_2d_so', import_modules)
twp_navier_stokes_cavity_2d_p = defaults.load_physics(
'twp_navier_stokes_cavity_2d_p', import_modules)
twp_navier_stokes_cavity_2d_n = defaults.load_numerics(
'twp_navier_stokes_cavity_2d_n', import_modules)
def clean_up_directory():
FileList = [
'forceHistory_p',
'forceHistory_v',
#'cavity2D',
#'mesh',
'momentHistory',
'proteus',
'wettedAreaHistory',
'twp_navier_stokes_cavity_2d'
]
