Adding pygeosx integrated test #3174
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| <?xml version="1.0" ?> | ||
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| <Problem> | ||
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| <Included> | ||
| <File | ||
| name="../solidMechanics/sedov_base.xml"/> | ||
| </Included> | ||
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| <Mesh> | ||
| <InternalMesh | ||
| name="mesh1" | ||
| elementTypes="{ C3D8 }" | ||
| xCoords="{ 0, 10 }" | ||
| yCoords="{ 0, 10 }" | ||
| zCoords="{ 0, 10 }" | ||
| nx="{ 10 }" | ||
| ny="{ 10 }" | ||
| nz="{ 10 }" | ||
| cellBlockNames="{ cb1 }"/> | ||
| </Mesh> | ||
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| <Solvers> | ||
| <SolidMechanics_LagrangianFEM | ||
| name="lagsolve" | ||
| strainTheory="1" | ||
| cflFactor="0.25" | ||
| discretization="FE1" | ||
| targetRegions="{ Region2 }" | ||
| /> | ||
| </Solvers> | ||
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| <Events | ||
| maxTime="1.0e-3"> | ||
| <!-- This event is applied every cycle, and overrides the | ||
| solver time-step request --> | ||
| <PeriodicEvent | ||
| name="solverApplications" | ||
| forceDt="1.0e-5" | ||
| target="/Solvers/lagsolve"/> | ||
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| <PeriodicEvent | ||
| name="timeHistoryCollection" | ||
| target="/Tasks/velocityCollection"/> | ||
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| <PeriodicEvent | ||
| name="timeHistoryOutput" | ||
| timeFrequency="5.0e-4" | ||
| targetExactTimestep="0" | ||
| target="/Outputs/timeHistoryOutput"/> | ||
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| <PeriodicEvent | ||
| name="restarts" | ||
| timeFrequency="5.0e-4" | ||
| targetExactTimestep="0" | ||
| target="/Outputs/restartOutput"/> | ||
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| <PeriodicEvent | ||
| name="python" | ||
| cycleFrequency="5" | ||
| target="/Outputs/pythonOutput"/> | ||
| </Events> | ||
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| </Problem> | ||
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| # Integrated Test Docs Begin Parameters | ||
| import geos_ats | ||
| from geos_ats.test_builder import generate_geos_tests, RestartcheckParameters, TestDeck, CurveCheckParameters | ||
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| restartcheck_params = {} | ||
| restartcheck_params["atol"] = 2.0E-10 | ||
| restartcheck_params["rtol"] = 2.0E-13 | ||
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| curvecheck_params = {} | ||
| curvecheck_params['filename'] = 'veloc_history.hdf5' | ||
| curvecheck_params['tolerance'] = 1e-10 | ||
| curvecheck_params['time_units'] = 'milliseconds' | ||
| curvecheck_params['curves'] = [['velocity', 'source']] | ||
| # Integrated Test Docs End Parameters | ||
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| # Integrated Test Docs Begin Test Loop | ||
| partitions = ((1, 1, 1), (2, 2, 2), (3, 3, 3)) | ||
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| decks = [ | ||
| TestDeck( | ||
| name="modified_sedov", | ||
| pygeos_script="run_sedov_problem.py", | ||
| description="Sedov problem with initial conditions modified using pygeos", | ||
| partitions=partitions, | ||
| restart_step=50, | ||
| check_step=100, | ||
| restartcheck_params=RestartcheckParameters(**restartcheck_params), | ||
| curvecheck_params=CurveCheckParameters(**curvecheck_params)) | ||
| ] | ||
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| generate_geos_tests(decks) | ||
| # Integrated Test Docs End Test Loop |
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| @@ -0,0 +1,80 @@ | ||||||
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| import numpy as np | ||||||
| from mpi4py import MPI | ||||||
| import pygeosx | ||||||
| from pygeosx_tools import wrapper | ||||||
| from geosx_xml_tools.main import preprocess_parallel | ||||||
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| # PYGEOSX_STRESS_FN | ||||||
| def stress_fn(x): | ||||||
| """ | ||||||
| Function to set stress values | ||||||
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| Args: | ||||||
| x (np.ndarray) the element centers | ||||||
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| Returns: | ||||||
| np.ndarray: stress values | ||||||
| """ | ||||||
| R = x[:, 0]**2 + x[:, 1]**2 + x[:, 2]**2 | ||||||
| return np.sin(2.0 * np.pi * R / np.amax(R)) | ||||||
| # PYGEOSX_STRESS_FN_END | ||||||
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| def run_problem(): | ||||||
| """ | ||||||
| Run the GEOSX problem | ||||||
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| """ | ||||||
| # PYGEOSX_INITIALIZATION | ||||||
| # Get the MPI rank | ||||||
| comm = MPI.COMM_WORLD | ||||||
| rank = comm.Get_rank() | ||||||
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| # Initialize the code and set initial conditions | ||||||
| problem = pygeosx.initialize(rank, args) | ||||||
| pygeosx.apply_initial_conditions() | ||||||
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| # Rather than specifying the wrapper paths explicitly, | ||||||
| # search for them using a set of filters | ||||||
| location_key = wrapper.get_matching_wrapper_path(problem, ['Level0', 'Region2', 'elementCenter']) | ||||||
| stress_key = wrapper.get_matching_wrapper_path(problem, ['Level0', 'Region2', 'shale', 'stress']) | ||||||
| ghost_key = wrapper.get_matching_wrapper_path(problem, ['Level0', 'Region2', 'cb1', 'ghostRank']) | ||||||
| # PYGEOSX_INITIALIZATION_END | ||||||
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| # PYGEOSX_STRESS_IC | ||||||
| # Print initial stress | ||||||
| wrapper.print_global_value_range(problem, stress_key, 'stress') | ||||||
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| # Zero out stress | ||||||
| wrapper.set_wrapper_to_value(problem, stress_key, 0.0) | ||||||
| wrapper.print_global_value_range(problem, stress_key, 'stress') | ||||||
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| # Set stress via a function | ||||||
| wrapper.set_wrapper_with_function(problem, stress_key, location_key, stress_fn, target_index=0) | ||||||
| wrapper.set_wrapper_with_function(problem, stress_key, location_key, stress_fn, target_index=1) | ||||||
| wrapper.set_wrapper_with_function(problem, stress_key, location_key, stress_fn, target_index=2) | ||||||
| wrapper.print_global_value_range(problem, stress_key, 'stress') | ||||||
| # PYGEOSX_STRESS_IC_END | ||||||
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| # PYGEOSX_MAIN_LOOP | ||||||
| # Run the code | ||||||
| while pygeosx.run() != pygeosx.COMPLETED: | ||||||
| wrapper.print_global_value_range(problem, stress_key, 'stress') | ||||||
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| # Gather/allgather tests | ||||||
| tmp = wrapper.gather_wrapper(problem, stress_key) | ||||||
| print(wrapper.rank, 'gather', np.shape(tmp), flush=True) | ||||||
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| tmp = wrapper.allgather_wrapper(problem, stress_key) | ||||||
| print(wrapper.rank, 'allgather', np.shape(tmp), flush=True) | ||||||
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| tmp = wrapper.allgather_wrapper(problem, stress_key, ghost_key=ghost_key) | ||||||
| print(wrapper.rank, 'allgather_ghost_filtered', np.shape(tmp), flush=True) | ||||||
| # PYGEOSX_MAIN_LOOP_END | ||||||
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| if __name__ == '__main__': | ||||||
| run_problem() | ||||||
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@@ -90,13 +90,8 @@ | |
| </FieldSpecifications> | ||
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| <Outputs> | ||
| <Python | ||
| name="pythonOutput"/> | ||
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| <Restart | ||
| name="restartOutput"/> | ||
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do you need this? It does not seem to be used.
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No, I missed cleaning up the import list when I removed the pre-processor from this example