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rt_timed.py
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rt_timed.py
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import os
os.environ["UW_ENABLE_TIMING"] = "1"
import underworld as uw
from underworld import function as fn
import glucifer
import math
import numpy as np
import time
time_post_import = time.time()
time_launch_srun = float(os.environ["TIME_LAUNCH_SRUN"])/1000.
time_launch_python = float(os.environ["TIME_LAUNCH_PYTHON"])/1000.
uw.timing.start()
if os.environ["UW_ENABLE_IO"] == "1":
do_IO=True
else:
do_IO=False
other_timing = {}
other_timing["Python_Import_Time"] = time_post_import - time_launch_python
other_timing["Container_Launch_Time"] = time_launch_python - time_launch_srun
res = 64
RESKEY = "UW_RESOLUTION"
if RESKEY in os.environ:
res = int(os.environ[RESKEY])
PREFIX = os.environ["PREFIXSTRING"]
mesh = uw.mesh.FeMesh_Cartesian(elementRes = (res, res, res),
minCoord = ( 0., 0., 0., ),
maxCoord = ( 1., 1., 1., ))
velocityField = uw.mesh.MeshVariable( mesh=mesh, nodeDofCount=3 )
pressureField = uw.mesh.MeshVariable( mesh=mesh.subMesh, nodeDofCount=1 )
temperatureField = uw.mesh.MeshVariable( mesh=mesh, nodeDofCount=1 )
temperatureFieldDeriv = uw.mesh.MeshVariable( mesh=mesh, nodeDofCount=1 )
# initialise
velocityField.data[:] = [0.,0.,0.]
pressureField.data[:] = 0.
for index, coord in enumerate(mesh.data):
temperatureField.data[index] = coord[2]
temperatureFieldDeriv.data[:] = 0.
# Create a swarm.
swarm = uw.swarm.Swarm( mesh=mesh )
# Create a data variable. It will be used to store the material index of each particle.
materialIndex = swarm.add_variable( dataType="int", count=1 )
# Create a layout object, populate the swarm with particles.
swarmLayout = uw.swarm.layouts.PerCellSpaceFillerLayout( swarm=swarm, particlesPerCell=40 )
swarm.populate_using_layout( layout=swarmLayout )
# define these for convience.
denseIndex = 0
lightIndex = 1
# material perturbation from van Keken et al. 1997
wavelength = 2.0
amplitude = 0.02
offset = 0.2
k = 2. * math.pi / wavelength
# Create function to return particle's coordinate
coord = fn.coord()
# Define the material perturbation, a function of the x coordinate (accessed by `coord[0]`).
perturbationFn = offset + amplitude*fn.math.cos( k*coord[0] )
# Setup the conditions list.
# If z is less than the perturbation, set to lightIndex.
conditions = [ ( perturbationFn > coord[1] , lightIndex ),
( True , denseIndex ) ]
# The swarm is passed as an argument to the evaluation, providing evaluation on each particle.
# Results are written to the materialIndex swarm variable.
fnc = fn.branching.conditional( conditions )
matdat = fnc.evaluate(swarm)
materialIndex.data[:] = matdat
store = glucifer.Store('{}_RT'.format(PREFIX),compress=False)
fig = glucifer.Figure( store, name="firstFig" )
fig.append( glucifer.objects.Points(swarm, materialIndex, pointSize=2, colourBar=False) )
fig.append( glucifer.objects.Surface(mesh, pressureField))
fig.append( glucifer.objects.VectorArrows( mesh, velocityField, scaling=1.0e2))
# Set a density of '0.' for light material, '1.' for dense material.
densityMap = { lightIndex:0., denseIndex:1. }
densityFn = fn.branching.map( fn_key = materialIndex, mapping = densityMap )
# Set a viscosity value of '1.' for both materials.
viscosityMap = { lightIndex:1., denseIndex:1. }
fn_viscosity = fn.branching.map( fn_key = materialIndex, mapping = viscosityMap )
# Define a vertical unit vector using a python tuple.
z_hat = ( 0., 0., 1. )
# Create buoyancy force vector
buoyancyFn = -densityFn*z_hat
# Construct node sets using the mesh specialSets
iWalls = mesh.specialSets["MinI_VertexSet"] + mesh.specialSets["MaxI_VertexSet"]
jWalls = mesh.specialSets["MinJ_VertexSet"] + mesh.specialSets["MaxJ_VertexSet"]
kWalls = mesh.specialSets["MinK_VertexSet"] + mesh.specialSets["MaxK_VertexSet"]
allWalls = iWalls + jWalls + kWalls
# Prescribe degrees of freedom on each node to be considered Dirichlet conditions.
# In the x direction on allWalls flag as Dirichlet
# In the y direction on jWalls (horizontal) flag as Dirichlet
stokesBC = uw.conditions.DirichletCondition( variable = velocityField,
indexSetsPerDof = (allWalls, allWalls, kWalls))
advdiffBc = uw.conditions.DirichletCondition( variable = temperatureField,
indexSetsPerDof = kWalls )
stokes = uw.systems.Stokes( velocityField = velocityField,
pressureField = pressureField,
# voronoi_swarm = swarm,
conditions = stokesBC,
fn_viscosity = fn_viscosity,
fn_bodyforce = buoyancyFn )
solver = uw.systems.Solver( stokes )
# Create a system to advect the swarm
advector = uw.systems.SwarmAdvector( swarm=swarm, velocityField=velocityField, order=2 )
# Create a dummy temperature field.
advdiff = uw.systems.AdvectionDiffusion(velocityField=velocityField, phiField=temperatureField, phiDotField=temperatureFieldDeriv,
fn_diffusivity=1.,conditions=advdiffBc)
# functions for calculating RMS velocity
vdotv = fn.math.dot(velocityField,velocityField)
v2sum_integral = uw.utils.Integral( mesh=mesh, fn=vdotv )
volume_integral = uw.utils.Integral( mesh=mesh, fn=1. )
# Get instantaneous Stokes solution
solver.solve()
# Calculate the RMS velocity.
vrms = math.sqrt( v2sum_integral.evaluate()[0] )
# update
dt1 = advector.get_max_dt()
dt2 = advdiff.get_max_dt()
dt = min(dt1,dt2)
# Advect using this timestep size.
advector.integrate(dt)
advdiff.integrate(dt)
# Save things
if do_IO:
meshFileHandle = mesh.save("{}_Mesh.h5".format(PREFIX))
vFH = velocityField.save("{}_velocityField.h5".format(PREFIX))
velocityField.xdmf( "{}_velocityField".format(PREFIX), vFH, "velocity", meshFileHandle, "Mesh" )
swarmFileHandle = swarm.save("{}_Swarm.h5".format(PREFIX))
mH = materialIndex.save("{}_materialIndex.h5".format(PREFIX))
materialIndex.xdmf("{}_materialIndex".format(PREFIX), mH, "material", swarmFileHandle, "Swarm" )
fig.save()
# load things
# first create analogues
mesh_copy = uw.mesh.FeMesh_Cartesian(
elementRes = (res, res, res),
minCoord = (20., 20., 20.),
maxCoord = (33., 33., 33.))
velocityField_copy = uw.mesh.MeshVariable( mesh=mesh_copy, nodeDofCount=3 )
swarm_copy = uw.swarm.Swarm(mesh = mesh_copy)
materialIndex_copy = swarm_copy.add_variable( dataType="int", count=1 )
# now load data and check loaded versions are identical to originals
mesh_copy.load("{}_Mesh.h5".format(PREFIX))
# test
if not np.allclose(mesh_copy.data, mesh.data):
raise RuntimeError("Loaded mesh data does not appear to be identical to previous data.")
velocityField_copy.load("{}_velocityField.h5".format(PREFIX))
if not np.allclose(velocityField_copy.data, velocityField.data):
raise RuntimeError("Loaded velocity data does not appear to be identical to previous data.")
swarm_copy.load("{}_Swarm.h5".format(PREFIX))
if not np.allclose(swarm_copy.particleCoordinates.data, swarm.particleCoordinates.data):
raise RuntimeError("Loaded swarm data does not appear to be identical to previous data.")
materialIndex_copy.load("{}_materialIndex.h5".format(PREFIX))
if not np.allclose(materialIndex_copy.data, materialIndex.data):
raise RuntimeError("Loaded material data does not appear to be identical to previous data.")
uw.timing.stop()
module_timing_data_orig = uw.timing.get_data(group_by="routine")
# write out data
filename = "{}_Res_{}_Nproc_{}_SlurmID_{}".format(os.environ["SLURM_JOB_NAME"],res,uw.mpi.size,os.environ["SLURM_JOB_ID"])
import json
if module_timing_data_orig:
module_timing_data = {}
for key,val in module_timing_data_orig.items():
module_timing_data[key[0]] = val
other_timing["Total_Runtime"] = uw.timing._endtime-uw.timing._starttime
module_timing_data["Other_timing"] = other_timing
module_timing_data["Other_data"] = {"vrms":vrms, "res":res, "nproc":uw.mpi.size}
with open(filename+".json", 'w') as fp:
json.dump(module_timing_data, fp,sort_keys=True, indent=4)
uw.timing.print_table(group_by="routine", output_file=filename+".txt", display_fraction=0.99)