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csshermancssherman
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Adding pygeosx integrated test
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‎inputFiles/pygeos/modified_sedov.xml

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<?xml version="1.0" ?>
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<Problem>
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<Included>
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<File
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name="../solidMechanics/sedov_base.xml"/>
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</Included>
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<Mesh>
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<InternalMesh
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name="mesh1"
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elementTypes="{ C3D8 }"
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xCoords="{ 0, 10 }"
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yCoords="{ 0, 10 }"
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zCoords="{ 0, 10 }"
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nx="{ 10 }"
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ny="{ 10 }"
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nz="{ 10 }"
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cellBlockNames="{ cb1 }"/>
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</Mesh>
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<Solvers>
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<SolidMechanics_LagrangianFEM
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name="lagsolve"
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strainTheory="1"
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cflFactor="0.25"
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discretization="FE1"
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targetRegions="{ Region2 }"
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/>
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</Solvers>
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<Events
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maxTime="1.0e-3">
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<!-- This event is applied every cycle, and overrides the
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solver time-step request -->
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<PeriodicEvent
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name="solverApplications"
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forceDt="1.0e-5"
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target="/Solvers/lagsolve"/>
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<PeriodicEvent
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name="timeHistoryCollection"
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target="/Tasks/velocityCollection"/>
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<PeriodicEvent
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name="timeHistoryOutput"
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timeFrequency="5.0e-4"
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targetExactTimestep="0"
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target="/Outputs/timeHistoryOutput"/>
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<PeriodicEvent
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name="restarts"
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timeFrequency="5.0e-4"
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targetExactTimestep="0"
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target="/Outputs/restartOutput"/>
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<PeriodicEvent
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name="python"
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cycleFrequency="5"
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target="/Outputs/pythonOutput"/>
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</Events>
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</Problem>
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‎inputFiles/pygeos/pygeos.ats

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# Integrated Test Docs Begin Parameters
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import geos_ats
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from geos_ats.test_builder import generate_geos_tests, RestartcheckParameters, TestDeck, CurveCheckParameters
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restartcheck_params = {}
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restartcheck_params["atol"] = 2.0E-10
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restartcheck_params["rtol"] = 2.0E-13
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curvecheck_params = {}
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curvecheck_params['filename'] = 'veloc_history.hdf5'
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curvecheck_params['tolerance'] = 1e-10
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curvecheck_params['time_units'] = 'milliseconds'
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curvecheck_params['curves'] = [['velocity', 'source']]
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# Integrated Test Docs End Parameters
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# Integrated Test Docs Begin Test Loop
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partitions = ((1, 1, 1), (2, 2, 2), (3, 3, 3))
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decks = [
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TestDeck(
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name="modified_sedov",
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pygeos_script="run_sedov_problem.py",
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description="Sedov problem with initial conditions modified using pygeos",
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partitions=partitions,
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restart_step=50,
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check_step=100,
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restartcheck_params=RestartcheckParameters(**restartcheck_params),
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curvecheck_params=CurveCheckParameters(**curvecheck_params))
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]
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generate_geos_tests(decks)
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# Integrated Test Docs End Test Loop

‎inputFiles/pygeos/run_sedov_problem.py

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import numpy as np
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from mpi4py import MPI
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import pygeosx
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from pygeosx_tools import wrapper
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from geosx_xml_tools.main import preprocess_parallel
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# PYGEOSX_STRESS_FN
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def stress_fn(x):
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"""
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Function to set stress values
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Args:
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x (np.ndarray) the element centers
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Returns:
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np.ndarray: stress values
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"""
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R = x[:, 0]**2 + x[:, 1]**2 + x[:, 2]**2
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return np.sin(2.0 * np.pi * R / np.amax(R))
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# PYGEOSX_STRESS_FN_END
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def run_problem():
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"""
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Run the GEOSX problem
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"""
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# PYGEOSX_INITIALIZATION
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# Get the MPI rank
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comm = MPI.COMM_WORLD
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rank = comm.Get_rank()
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# Initialize the code and set initial conditions
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problem = pygeosx.initialize(rank, args)
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pygeosx.apply_initial_conditions()
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# Rather than specifying the wrapper paths explicitly,
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# search for them using a set of filters
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location_key = wrapper.get_matching_wrapper_path(problem, ['Level0', 'Region2', 'elementCenter'])
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stress_key = wrapper.get_matching_wrapper_path(problem, ['Level0', 'Region2', 'shale', 'stress'])
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ghost_key = wrapper.get_matching_wrapper_path(problem, ['Level0', 'Region2', 'cb1', 'ghostRank'])
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# PYGEOSX_INITIALIZATION_END
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# PYGEOSX_STRESS_IC
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# Print initial stress
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wrapper.print_global_value_range(problem, stress_key, 'stress')
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# Zero out stress
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wrapper.set_wrapper_to_value(problem, stress_key, 0.0)
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wrapper.print_global_value_range(problem, stress_key, 'stress')
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# Set stress via a function
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wrapper.set_wrapper_with_function(problem, stress_key, location_key, stress_fn, target_index=0)
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wrapper.set_wrapper_with_function(problem, stress_key, location_key, stress_fn, target_index=1)
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wrapper.set_wrapper_with_function(problem, stress_key, location_key, stress_fn, target_index=2)
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wrapper.print_global_value_range(problem, stress_key, 'stress')
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# PYGEOSX_STRESS_IC_END
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# PYGEOSX_MAIN_LOOP
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# Run the code
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while pygeosx.run() != pygeosx.COMPLETED:
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wrapper.print_global_value_range(problem, stress_key, 'stress')
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# Gather/allgather tests
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tmp = wrapper.gather_wrapper(problem, stress_key)
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print(wrapper.rank, 'gather', np.shape(tmp), flush=True)
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tmp = wrapper.allgather_wrapper(problem, stress_key)
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print(wrapper.rank, 'allgather', np.shape(tmp), flush=True)
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tmp = wrapper.allgather_wrapper(problem, stress_key, ghost_key=ghost_key)
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print(wrapper.rank, 'allgather_ghost_filtered', np.shape(tmp), flush=True)
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# PYGEOSX_MAIN_LOOP_END
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if __name__ == '__main__':
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run_problem()
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‎inputFiles/solidMechanics/sedov_base.xml

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</FieldSpecifications>
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<Outputs>
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<Blueprint
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name="blueprint"
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plotLevel="3"/>
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<Silo
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name="siloOutput"
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plotLevel="3"/>
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<Python
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name="pythonOutput"/>
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<Restart
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name="restartOutput"/>

‎src/CMakeLists.txt

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################################
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# message(WARNING "Temporarily changing the geosPythonBranch to cusini/fix-streak-cert-fail")
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# set(GEOS_PYTHON_PACKAGES_BRANCH "cusini/fix-streak-cert-fail" CACHE STRING "" FORCE)
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message(WARNING "Temporarily changing the geosPythonBranch to feature/sherman/addPygeosxIntegratedTests")
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set(GEOS_PYTHON_PACKAGES_BRANCH "cusini/fix-streak-cert-fail" CACHE STRING "" FORCE)
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if ( Python3_EXECUTABLE )

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