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run_tevg_patient_specific.py
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import vessel
import pickle
import os
import time
import numpy as np
import pyvista as pv
def saveVessel(vess):
with open('vessel.temp', 'wb') as file:
pickle.dump(vess,file)
os.system('mv vessel.temp vessel.pickle')
return
def loadVessel():
with open('vessel.pickle', 'rb') as file:
vess = pickle.load(file)
return vess
os.system("mpiexec python3 utils_init_vessel.py")
startTime = time.time()
if os.path.exists('vessel.pickle'):
simulation_vessel = loadVessel()
simulation_vessel.startTime = simulation_vessel.currTime
else:
simulation_vessel = vessel.Vessel(vesselType="segmentation", segmentationName="line", numLen=42, numCirc=32, numRad=6, rotateSegmentation=True)
simulation_vessel.radius = 1.1
simulation_vessel.gnr_step_size = 2.0
simulation_vessel.zcenter = 0.895
simulation_vessel.estimateOuterSegmentation = True
simulation_vessel.constantThickness = True
simulation_vessel.thickness = 0.0743
#simulation_vessel.outletPressure = 13000
simulation_vessel.rotation_matrix = np.loadtxt('ivcRotationMatrix.dat')
simulation_vessel.tevg = 1
simulation_vessel.damping = 1e4
simulation_vessel.penalty = 1e9
simulation_vessel.simulationExecutable = "~/svFSI-build/svFSI-build/mysvfsi"
simulation_vessel.numProcessorsSolid = 48
simulation_vessel.numProcessorsFluid = 96
simulation_vessel.flipContours = True
simulation_vessel.flipInlet = True
simulation_vessel.smoothAttributesValue = 0.1
simulation_vessel.setInputFileValues()
os.system('mkdir -p ' + simulation_vessel.outputDir)
os.system('mkdir -p ' + 'meshIterations')
os.system('mkdir -p ' + 'meshResults')
os.system('mkdir -p ' + 'simulationResults')
os.system('mkdir -p ' + 'materialResults')
simulation_vessel.initializeVessel()
simulation_vessel.runFluidIteration()
simulation_vessel.runSolidIteration()
simulation_vessel.runMaterialIteration()
simulation_vessel.currTime = time.time() - startTime + simulation_vessel.startTime
simulation_vessel.writeStatus(simulation_vessel.currTime, "FSG")
simulation_vessel.incrementIteration()
saveVessel(simulation_vessel)
#simulation_vessel.vesselReference = pv.read('mesh_4_0.vtu')
#simulation_vessel.timeIter = 1
while simulation_vessel.timeStep < simulation_vessel.total_time_steps:
while simulation_vessel.residual > simulation_vessel.tolerance or simulation_vessel.timeIter < 3 or simulation_vessel.skippedFluid == True:
while simulation_vessel.residual > simulation_vessel.tolerance:
simulation_vessel.runSolidIteration()
simulation_vessel.skipFluidIteration()
simulation_vessel.runMaterialIteration()
simulation_vessel.currTime = time.time() - startTime + simulation_vessel.startTime
simulation_vessel.writeStatus(simulation_vessel.currTime, "SG")
simulation_vessel.incrementIteration()
saveVessel(simulation_vessel)
simulation_vessel.runFluidIteration()
simulation_vessel.runSolidIteration()
simulation_vessel.runMaterialIteration()
simulation_vessel.currTime = time.time() - startTime + simulation_vessel.startTime
simulation_vessel.writeStatus(simulation_vessel.currTime, "FSG")
simulation_vessel.incrementIteration()
saveVessel(simulation_vessel)
simulation_vessel.timeIter = 0
simulation_vessel.residual = simulation_vessel.tolerance*10.0
simulation_vessel.incrementTimestep()
saveVessel(simulation_vessel)