def proteus_runner(expr, problem_kws, numerics_kws, *args, **kws):
opts, args = get_prog_opts(args, __doc__)
log = kws.get('log', None)
if log is None: log = Profiling.logEvent
comm = init_mpi_petsc(opts, log)
problem_list = [ProteusProblem(**problem_kws),]
simulation_list = [default_s]
numerics_list = [ProteusNumerics(**numerics_kws),]
numerics_list[0].periodicDirichletConditions = problem_list[0].periodicDirichletConditions
numerics_list[0].T = problem_list[0].T
simulation_name = problem_list[0].name + "_" + numerics_list[0].__class__.__name__
simulation_name_proc = simulation_name + "_" + repr(comm.rank())
simFlagsList = [{ 'simulationName': simulation_name,
'simulationNameProc': simulation_name_proc,
'dataFile': simulation_name_proc + '.dat',
'components' : [ci for ci in range(problem_list[0].coefficients.nc)],
}]
so = default_so
so.name = problem_list[0].name
so.pnList = problem_list
so.sList = [default_s]
try:
so.systemStepControllerType = numerics_list[0].systemStepControllerType
except AttributeError:
pass
try:
so.tnList = numerics_list[0].tnList
so.archiveFlag = numerics_list[0].archiveFlag
except AttributeError:
pass
runNumber = 0
runName = so.name + repr(runNumber)
Profiling.procID=comm.rank()
if simulation_list[0].logAllProcesses or opts.logAllProcesses:
Profiling.logAllProcesses = True
Profiling.flushBuffer=simulation_list[0].flushBuffer
if opts.logLevel > 0:
Profiling.openLog(runName+".log",opts.logLevel)
ns = NumericalSolution.NS_base(default_so, problem_list, numerics_list, simulation_list,
opts, simFlagsList)
ns.calculateSolution(runName)
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
line = line[:line.index('#')]
return line
stripped_data = [strip_comments(line) for line in data]
petsc_argv += '\n'.join(stripped_data).split()
log("PETSc options from commandline")
log(str(petsc_argv))
Comm.argv = petsc_argv
comm = Comm.init()
Profiling.procID=comm.rank()
if opts.logLevel > 0:
#mwf looks like just gets .py.log if no sso file given
#Profiling.openLog(args[0][-3:]+".log",opts.logLevel)
if len(args) == 0:
Profiling.openLog("proteus.log",opts.logLevel)
elif len(args[0].split(' ')) == 1:
Profiling.openLog(args[0].split('.')[0]+".log",opts.logLevel)
else:
Profiling.openLog(args[0][-3:]+".log",opts.logLevel)
if opts.logAllProcesses:
Profiling.logAllProcesses = True
#blanket import statements can go below here now that petsc4py should be initialized
from proteus import *
try:
from proteusGraphical import *
except:
pass
log("Adding "+str(opts.probDir)+" to path for loading modules")
line = line[:line.index('#')]
return line
stripped_data = [strip_comments(line) for line in data]
petsc_argv += '\n'.join(stripped_data).split()
log("PETSc options from commandline")
log(str(petsc_argv))
Comm.argv = petsc_argv
comm = Comm.init()
Profiling.procID = comm.rank()
if opts.logLevel > 0:
#mwf looks like just gets .py.log if no sso file given
#Profiling.openLog(args[0][-3:]+".log",opts.logLevel)
if len(args) == 0:
Profiling.openLog("proteus.log", opts.logLevel)
elif len(args[0].split(' ')) == 1:
Profiling.openLog(args[0].split('.')[0] + ".log", opts.logLevel)
else:
Profiling.openLog(args[0][-3:] + ".log", opts.logLevel)
if opts.logAllProcesses:
Profiling.logAllProcesses = True
#blanket import statements can go below here now that petsc4py should be initialized
from proteus import *
try:
from proteusGraphical import *
except:
pass
log("Adding " + str(opts.probDir) + " to path for loading modules")
from __future__ import print_function
#import sys
#from proteus import Comm
from future import standard_library
standard_library.install_aliases()
import os
import sys
import socket
import pickle
import numpy
import proteus
#remove blankent import statements until after Comm initialized for petsc4py
# from proteus import *
from proteus import Profiling, Comm
from warnings import *
import optparse
import sys
import pstats
import pdb
import petsc4py
Profiling.openLog("proteus.log", 7)
print(sys.argv[:1])
Comm.argv = sys.argv[:1]
comm = Comm.init()
comm = Comm.init()
#petsc4py.init(sys.argv[:1])
print(comm.rank(), comm.size())
print("Hello World from", comm.rank())
from proteus import *
Profiling.procID = comm.rank()
def getpath():
path = sys.path[0]+'/'
return path
def remove_files(filenames):
''' delete files in filenames list '''
for f in filenames:
if os.path.exists(f):
try:
os.remove(f)
except OSError as e:
print ("Error: %s - %s" %(e.filename,e.strerror))
else:
pass
Profiling.logEvent("Testing Bodydynamics")
class TestAuxFunctions(unittest.TestCase):
def testForwardEler(self):
from proteus.mprans.BodyDynamics import forward_euler
p0 = 5.0
v0 = 2.0
a = 0.5
dt = 0.01
v = v0 + a*dt
p = p0 + v*dt
p1, v1 = forward_euler(p0, v0, a, dt)
self.assertTrue(p==p1)
self.assertTrue(v==v1)
def testRungeKutta(self):
from proteus import Comm, Profiling
import numpy as np
import numpy.testing as npt
import unittest
import pytest
comm = Comm.init()
Profiling.procID = comm.rank()
Profiling.logEvent("Testing SedClosure")
class GlobalVariables():
def __init__(self):
from proteus.mprans.SedClosure import HsuSedStress
self.C4e = 1.
self.C3e = 1.2
self.eR = 0.8
self.aDarcy = 1.
self.bForch = 1.
self.grain = 0.1
self.packFraction = 0.2
self.packMargin = 0.01
self.sigmaC = 1.1
self.maxFraction = 0.635
self.frFraction = 0.57
self.fContact = 0.02
self.mContact = 2.
self.nContact = 5.
self.angFriction = np.pi/6.
from proteus import Comm, Profiling
import numpy as np
import numpy.testing as npt
import unittest
import pytest
comm = Comm.init()
Profiling.procID = comm.rank()
Profiling.logEvent("Testing SedClosure")
class GlobalVariables():
def __init__(self):
from proteus.mprans.SedClosure import HsuSedStress
self.C4e = 1.
self.C3e = 1.2
self.eR = 0.8
self.aDarcy = 1.
self.bForch = 1.
self.grain = 0.1
self.packFraction = 0.2
self.packMargin = 0.01
self.sigmaC = 1.1
self.maxFraction = 0.635
self.frFraction = 0.57
self.fContact = 0.02
self.mContact = 2.
self.nContact = 5.
self.angFriction = np.pi / 6.
self.vos_limiter = 0.6
#import sys
#from proteus import Comm
import os
import sys
import socket
import cPickle
import numpy
import proteus
#remove blankent import statements until after Comm initialized for petsc4py
# from proteus import *
from proteus import Profiling,Comm
from warnings import *
import optparse
import sys
import pstats
import pdb
import petsc4py
Profiling.openLog("proteus.log",7)
print sys.argv[:1]
comm = Comm.init(argv=sys.argv[:1])
comm = Comm.init(argv=sys.argv[:1])
#petsc4py.init(sys.argv[:1])
print comm.rank(),comm.size()
print "Hellow World from",comm.rank()
from proteus import *
Profiling.procID=comm.rank()
def getpath():
path = sys.path[0]+'/'
return path
def remove_files(filenames):
''' delete files in filenames list '''
for f in filenames:
if os.path.exists(f):
try:
os.remove(f)
except OSError, e:
print ("Error: %s - %s" %(e.filename,e.strerror))
else:
pass
Profiling.logEvent("Testing Bodydynamics")
class TestAuxFunctions(unittest.TestCase):
def testForwardEler(self):
from proteus.mprans.BodyDynamics import forward_euler
p0 = 5.0
v0 = 2.0
a = 0.5
dt = 0.01
v = v0 + a*dt
p = p0 + v*dt
p1, v1 = forward_euler(p0, v0, a, dt)
self.assertTrue(p==p1)
self.assertTrue(v==v1)
def testRungeKutta(self):
import sys,os
import logging
comm = Comm.init()
Profiling.procID = comm.rank()
def getpath():
path =str(os.getcwd())
if "tests" in path[-6:]:
path =""
else:
path = path+"/proteus/tests/"
return path
Profiling.logEvent("Testing WaveTools")
class TestAuxFunctions(unittest.TestCase):
def testVDir(self):
from proteus.WaveTools import setVertDir
self.assertTrue(np.array_equal(setVertDir(np.array([0,-9.81,0])), np.array([0,1,0])))
def testDirVector(self):
from proteus.WaveTools import setDirVector
self.assertTrue(all(setDirVector(np.array([2.,2.,1.]))== np.array([2.,2.,1])/3.))
def testDirCheck(self):
from proteus.WaveTools import dirCheck
dirCheck(np.array([1.,2.,3.]),np.array([7.,4.,-5.]) )# Just loading the function with two vertical vectors
with self.assertRaises(SystemExit) as cm:
dirCheck(np.array([9,9,9]),np.array([4,5,6]))
self.assertEqual(cm.exception.code, 1)
def testReduceToIntervals(self):