'front_distance': 0.05 + 0.15,
'bottom_distance': 0.05 + 0.15,
'jet_radius': 0.05,
'width': 0.41,
'jet_positions': [90, 270],
'jet_width': 10,
'clscale': 1.0
}
if not os.path.exists(mesh_path):
generate_mesh(geometry_params, template='geometry_2d.template_geo')
# Convert to H5
not os.path.exists(os.path.dirname(mesh_path)) and os.mkdir(
os.path.dirname(mesh_path))
convert('mesh.msh', 'mesh.h5')
cleanup(exts=('.msh', ))
shutil.move('mesh.xml', mesh_path)
shutil.move('mesh_facet_region.xml', surface_path)
# With same dt and duration as with RL make the base flow
dt = 0.0005
solver_params = {'dt': dt}
flow_params = {'mu': 1E-3, 'rho': 1}
T_final = 5.0
# Is there nonzero flow?
u0_file, p0_file = 'mesh/u_init000000.vtu', 'mesh/p_init000000.vtu'
if os.path.exists(u0_file) and os.path.exists(p0_file):
from msh_convert import convert
from dolfin import (Measure, assemble, File, SubsetIterator, sqrt, avg,
TestFunction, FunctionSpace)
import matplotlib.pyplot as plt
import subprocess, os
import numpy as np
ratios = []
exponents = [2, 3, 3.5, 4.0, 4.5, 5.0, 5.5]
for hein in exponents[-1:]:
subprocess.call(
['gmsh -3 -clscale 0.075 -setnumber Hein %d tile_1_hein.geo' % hein],
shell=True)
outputs = convert('tile_1_hein.msh', 'tile_1_hein.h5')
mesh, surfaces, volumes = outputs
dx = Measure('dx', domain=mesh, subdomain_data=volumes)
intra = assemble(1 * dx(1))
extra = assemble(1 * dx(0))
ratios.append(extra / (intra + extra))
print('Extracellular volume %.2f' % ratios[-1])
# Now want to get ratio of cell surface area to its volume
# Want to keep track of port areas - these are boundary integrals
ds = Measure('ds', domain=mesh, subdomain_data=surfaces)
dS = Measure('dS', domain=mesh, subdomain_data=surfaces)
area_no_port = assemble(1 * dS(1))
def start_class(self):
'''
Initialise attributes needed by the Environment object:
Initialise history buffers, remesh if necessary, load initialization quantities if not remesh, create flow solver
object, initialise probes, make converged flow if necessary, simulate to random position if random_start,
fill probes buffer if no. probes changed wrt last remesh
:return:
'''
self.solver_step = 0 # Numerical step
self.accumulated_drag = 0 # Sum of step drags so far
self.accumulated_lift = 0
self.initialized_vtu= False
self.resetted_number_probes = False
self.area_probe = None
# Create ring buffers to hold recent history of jet values, probe values, lift, drag, area
self.history_parameters = {}
for crrt_jet in range(2):
self.history_parameters["jet_{}".format(crrt_jet)] = RingBuffer(self.size_history)
self.history_parameters["number_of_jets"] = 2
for crrt_probe in range(len(self.output_params["locations"])):
if self.output_params["probe_type"] == 'pressure':
self.history_parameters["probe_{}".format(crrt_probe)] = RingBuffer(self.size_history)
elif self.output_params["probe_type"] == 'velocity':
self.history_parameters["probe_{}_u".format(crrt_probe)] = RingBuffer(self.size_history)
self.history_parameters["probe_{}_v".format(crrt_probe)] = RingBuffer(self.size_history)
self.history_parameters["number_of_probes"] = len(self.output_params["locations"])
print("Number of probes: {}".format(self.history_parameters["number_of_probes"]))
self.history_parameters["drag"] = RingBuffer(self.size_history)
self.history_parameters["lift"] = RingBuffer(self.size_history)
self.history_parameters["recirc_area"] = RingBuffer(self.size_history)
# ------------------------------------------------------------------------
# Remesh if necessary
h5_file = '.'.join([self.path_root, 'h5']) # mesh/turek_2d.h5
msh_file = '.'.join([self.path_root, 'msh']) # mesh/turek_2d.msh
self.geometry_params['mesh'] = h5_file
# Regenerate mesh?
if self.geometry_params['remesh']:
if self.verbose > 0:
print("Remesh")
generate_mesh(self.geometry_params, template=self.geometry_params['template'])
if self.verbose > 0:
print("Generate .msh done")
print(msh_file)
assert os.path.exists(msh_file)
convert(msh_file, h5_file)
if self.verbose > 0:
print("Convert to .h5 done")
print(h5_file)
assert os.path.exists(h5_file)
# ------------------------------------------------------------------------
# If no remesh, load initialization fields and buffers
if self.n_iter_make_ready is None:
if self.verbose > 0:
print("Load initial flow state")
# Load initial fields
self.flow_params['u_init'] = 'mesh/u_init.xdmf'
self.flow_params['p_init'] = 'mesh/p_init.xdmf'
if self.verbose > 0:
print("Load buffer history")
# Load ring buffers
with open('mesh/dict_history_parameters.pkl', 'rb') as f:
self.history_parameters = pickle.load(f)
# Check everything is good to go
if not "number_of_probes" in self.history_parameters:
self.history_parameters["number_of_probes"] = 0
print("Warning!! The number of probes was not set in the loaded hdf5 file")
if not "number_of_jets" in self.history_parameters:
self.history_parameters["number_of_jets"] = 2
print("Warning!! The number of jets was not set in the loaded hdf5 file")
if not "lift" in self.history_parameters:
self.history_parameters["lift"] = RingBuffer(self.size_history)
print("Warning!! No lift history found in the loaded hdf5 file")
if not "drag" in self.history_parameters:
self.history_parameters["drag"] = RingBuffer(self.size_history)
print("Warning!! No lift history found in the loaded hdf5 file")
if not "recirc_area" in self.history_parameters:
self.history_parameters["recirc_area"] = RingBuffer(self.size_history)
print("Warning!! No recirculation area history found in the loaded hdf5 file")
# if not the same number of probes, reset
if not self.history_parameters["number_of_probes"] == len(self.output_params["locations"]):
for crrt_probe in range(len(self.output_params["locations"])):
if self.output_params["probe_type"] == 'pressure':
self.history_parameters["probe_{}".format(crrt_probe)] = RingBuffer(self.size_history)
elif self.output_params["probe_type"] == 'velocity':
self.history_parameters["probe_{}_u".format(crrt_probe)] = RingBuffer(self.size_history)
self.history_parameters["probe_{}_v".format(crrt_probe)] = RingBuffer(self.size_history)
self.history_parameters["number_of_probes"] = len(self.output_params["locations"])
print("Warning!! Number of probes was changed! Probes buffer content reset")
self.resetted_number_probes = True
# ------------------------------------------------------------------------
# create the flow simulation object
self.flow = FlowSolver(self.flow_params, self.geometry_params, self.solver_params)
# ------------------------------------------------------------------------
# Setup probes
if self.output_params["probe_type"] == 'pressure':
self.ann_probes = PressureProbeANN(self.flow, self.output_params['locations'])
elif self.output_params["probe_type"] == 'velocity':
self.ann_probes = VelocityProbeANN(self.flow, self.output_params['locations'])
else:
raise RuntimeError("Unknown probe type")
# Setup drag and lift measurement
self.drag_probe = PenetratedDragProbeANN(self.flow)
self.lift_probe = PenetratedLiftProbeANN(self.flow)
# ------------------------------------------------------------------------
# No flux from jets for starting
self.Qs = np.zeros(2)
self.action = np.zeros(2)
# ------------------------------------------------------------------------
# prepare the arrays for plotting positions
self.compute_positions_for_plotting()
# ------------------------------------------------------------------------
# if necessary, make converge
if self.n_iter_make_ready is not None:
self.u_, self.p_ = self.flow.evolve(self.Qs)
path=''
if "dump_vtu" in self.inspection_params:
path = 'results/area_out.pvd'
self.area_probe = RecirculationAreaProbe(self.u_, 0, store_path=path)
if self.verbose > 0:
print("Compute initial flow for {} steps".format(self.n_iter_make_ready))
for _ in range(self.n_iter_make_ready):
self.u_, self.p_ = self.flow.evolve(self.Qs)
self.probes_values = self.ann_probes.sample(self.u_, self.p_).flatten()
self.drag = self.drag_probe.sample(self.u_, self.p_)
self.lift = self.lift_probe.sample(self.u_, self.p_)
self.recirc_area = self.area_probe.sample(self.u_, self.p_)
self.write_history_parameters() # Add new step data to history buffers
self.visual_inspection() # Create dynamic plots, show step data in command line and save it to saved_models/debug.csv
self.output_data() # Extend arrays of episode qtys, generate vtu files for area, u and p
self.solver_step += 1
encoding = XDMFFile.Encoding.HDF5
mesh = convert(msh_file, h5_file)
comm = mesh.mpi_comm()
# save field data
XDMFFile(comm, 'mesh/u_init.xdmf').write_checkpoint(self.u_, 'u0', 0, encoding)
XDMFFile(comm, 'mesh/p_init.xdmf').write_checkpoint(self.p_, 'p0', 0, encoding)
# save buffer dict
with open('mesh/dict_history_parameters.pkl', 'wb') as f:
pickle.dump(self.history_parameters, f, pickle.HIGHEST_PROTOCOL)
# ----------------------------------------------------------------------
# if reading from disk (no remesh), show to check everything ok
if self.n_iter_make_ready is None:
# If random_start == True, let's start in a random position of the vortex shedding
if self.optimization_params["random_start"]:
rd_advancement = np.random.randint(1712) # 1712 is the number of steps of a shedding period. Needs to be hardcoded
for j in range(rd_advancement):
self.flow.evolve(self.Qs)
print("Simulated {} iterations before starting the control".format(rd_advancement))
self.u_, self.p_ = self.flow.evolve(self.Qs) # Initial step with Qs = 0
path=''
if "dump_vtu" in self.inspection_params:
path = 'results/area_out.pvd'
self.area_probe = RecirculationAreaProbe(self.u_, 0, store_path=path)
self.probes_values = self.ann_probes.sample(self.u_, self.p_).flatten()
self.drag = self.drag_probe.sample(self.u_, self.p_)
self.lift = self.lift_probe.sample(self.u_, self.p_)
self.recirc_area = self.area_probe.sample(self.u_, self.p_)
self.write_history_parameters()
# ----------------------------------------------------------------------
# if necessary, fill the probes buffer
if self.resetted_number_probes:
print("Need to fill again the buffer; modified number of probes")
# TODO: Execute runs for 1 action step, so we would be running for (T/Nb)*size_history. While it should be just for size_history. In practice, remesh if probes change
for _ in range(self.size_history):
self.execute()
# ----------------------------------------------------------------------
# ready now
self.ready_to_use = True
positions = [0, 60, 120, 180, 240, 300]
geometry_params = {
'jet_positions': positions,
'output': '.'.join([root, 'geo']),
'jet_width': 10,
'clscale': 0.25
}
h5_file = '.'.join([root, 'h5'])
# Regenerate mesh?
if True:
generate_mesh(geometry_params, template='./geometry_2d.template_geo')
msh_file = '.'.join([root, 'msh'])
assert os.path.exists(msh_file)
convert(msh_file, h5_file)
assert os.path.exists(h5_file)
comm = mpi_comm_world()
h5 = HDF5File(comm, h5_file, 'r')
mesh = Mesh()
h5.read(mesh, 'mesh', False)
surfaces = MeshFunction('size_t', mesh, mesh.topology().dim() - 1)
h5.read(surfaces, 'facet')
positions = [0, 60, 120, 180, 240, 300]
cylinder_noslip_tag = 4
first_jet = cylinder_noslip_tag + 1
njets = len(positions)
def start_class(self):
self.solver_step = 0
self.accumulated_drag = 0
self.accumulated_lift = 0
self.initialized_output = False
self.resetted_number_probes = False
self.area_probe = None
self.history_parameters = {}
for crrt_jet in range(len(self.geometry_params["jet_positions"])):
self.history_parameters["jet_{}".format(crrt_jet)] = RingBuffer(self.size_history)
self.history_parameters["number_of_jets"] = len(self.geometry_params["jet_positions"])
for crrt_probe in range(len(self.output_params["locations"])):
if self.output_params["probe_type"] == 'pressure':
self.history_parameters["probe_{}".format(crrt_probe)] = RingBuffer(self.size_history)
elif self.output_params["probe_type"] == 'velocity':
self.history_parameters["probe_{}_u".format(crrt_probe)] = RingBuffer(self.size_history)
self.history_parameters["probe_{}_v".format(crrt_probe)] = RingBuffer(self.size_history)
self.history_parameters["number_of_probes"] = len(self.output_params["locations"])
self.history_parameters["drag"] = RingBuffer(self.size_history)
self.history_parameters["lift"] = RingBuffer(self.size_history)
self.history_parameters["recirc_area"] = RingBuffer(self.size_history)
# ------------------------------------------------------------------------
# remesh if necessary
h5_file = '.'.join([self.path_root, 'h5'])
msh_file = '.'.join([self.path_root, 'msh'])
self.geometry_params['mesh'] = h5_file
# Regenerate mesh?
if self.geometry_params['remesh']:
if self.verbose > 0:
printi("Remesh")
printi("generate_mesh start...")
generate_mesh(self.geometry_params, template=self.geometry_params['template'])
if self.verbose > 0:
printi("generate_mesh done!")
assert os.path.exists(msh_file)
convert(msh_file, h5_file)
assert os.path.exists(h5_file)
# ------------------------------------------------------------------------
# if necessary, load initialization fields
if self.n_iter_make_ready is None:
if self.verbose > 0:
printi("Load initial flow")
self.flow_params['u_init'] = 'mesh/u_init.xdmf'
self.flow_params['p_init'] = 'mesh/p_init.xdmf'
if self.verbose > 0:
printi("Load buffer history")
with open('mesh/dict_history_parameters.pkl', 'rb') as f:
self.history_parameters = pickle.load(f)
if not "number_of_probes" in self.history_parameters:
self.history_parameters["number_of_probes"] = 0
if not "number_of_jets" in self.history_parameters:
self.history_parameters["number_of_jets"] = len(self.geometry_params["jet_positions"])
printi("Warning!! The number of jets was not set in the loaded hdf5 file")
if not "lift" in self.history_parameters:
self.history_parameters["lift"] = RingBuffer(self.size_history)
printi("Warning!! No value for the lift founded")
if not "recirc_area" in self.history_parameters:
self.history_parameters["recirc_area"] = RingBuffer(self.size_history)
printi("Warning!! No value for the recirculation area founded")
# if not the same number of probes, reset
if not self.history_parameters["number_of_probes"] == len(self.output_params["locations"]):
for crrt_probe in range(len(self.output_params["locations"])):
if self.output_params["probe_type"] == 'pressure':
self.history_parameters["probe_{}".format(crrt_probe)] = RingBuffer(self.size_history)
elif self.output_params["probe_type"] == 'velocity':
self.history_parameters["probe_{}_u".format(crrt_probe)] = RingBuffer(self.size_history)
self.history_parameters["probe_{}_v".format(crrt_probe)] = RingBuffer(self.size_history)
self.history_parameters["number_of_probes"] = len(self.output_params["locations"])
printi("Warning!! Number of probes was changed! Probes buffer content reseted")
self.resetted_number_probes = True
# ------------------------------------------------------------------------
# create the flow simulation object
self.flow = FlowSolver(self.flow_params, self.geometry_params, self.solver_params)
# ------------------------------------------------------------------------
# Setup probes
if self.output_params["probe_type"] == 'pressure':
self.ann_probes = PressureProbeANN(self.flow, self.output_params['locations'])
elif self.output_params["probe_type"] == 'velocity':
self.ann_probes = VelocityProbeANN(self.flow, self.output_params['locations'])
else:
raise RuntimeError("unknown probe type")
# Setup drag measurement
self.drag_probe = PenetratedDragProbeANN(self.flow)
self.lift_probe = PenetratedLiftProbeANN(self.flow)
# ------------------------------------------------------------------------
# No flux from jets for starting
self.Qs = np.zeros(len(self.geometry_params['jet_positions']))
# ------------------------------------------------------------------------
# prepare the arrays for plotting positions
self.compute_positions_for_plotting()
# ------------------------------------------------------------------------
# if necessary, make converge
if self.n_iter_make_ready is not None:
self.u_, self.p_ = self.flow.evolve(self.Qs)
path=''
if "dump" in self.inspection_params:
path = 'results/area_out.pvd'
self.area_probe = RecirculationAreaProbe(self.u_, 0, store_path=path)
if self.verbose > 0:
printi("Compute initial flow")
printiv(self.n_iter_make_ready)
for _ in range(self.n_iter_make_ready):
self.u_, self.p_ = self.flow.evolve(self.Qs)
self.probes_values = self.ann_probes.sample(self.u_, self.p_).flatten()
self.drag = self.drag_probe.sample(self.u_, self.p_)
self.lift = self.lift_probe.sample(self.u_, self.p_)
self.recirc_area = self.area_probe.sample(self.u_, self.p_)
self.write_history_parameters()
self.visual_inspection()
self.output_data()
self.solver_step += 1
if self.n_iter_make_ready is not None:
encoding = XDMFFile.Encoding_HDF5
mesh = convert(msh_file, h5_file)
comm = mesh.mpi_comm()
# save field data
XDMFFile(comm, 'mesh/u_init.xdmf').write_checkpoint(self.u_, 'u0', 0, encoding)
XDMFFile(comm, 'mesh/p_init.xdmf').write_checkpoint(self.p_, 'p0', 0, encoding)
# save buffer dict
with open('mesh/dict_history_parameters.pkl', 'wb') as f:
pickle.dump(self.history_parameters, f, pickle.HIGHEST_PROTOCOL)
# ----------------------------------------------------------------------
# if reading from disk, show to check everything ok
if self.n_iter_make_ready is None:
#Let's start in a random position of the vortex shading
if self.optimization_params["random_start"]:
rd_advancement = np.random.randint(650)
for j in range(rd_advancement):
self.flow.evolve(self.Qs)
print("Simulated {} iterations before starting the control".format(rd_advancement))
self.u_, self.p_ = self.flow.evolve(self.Qs)
path=''
if "dump" in self.inspection_params:
path = 'results/area_out.pvd'
self.area_probe = RecirculationAreaProbe(self.u_, 0, store_path=path)
self.probes_values = self.ann_probes.sample(self.u_, self.p_).flatten()
self.drag = self.drag_probe.sample(self.u_, self.p_)
self.lift = self.lift_probe.sample(self.u_, self.p_)
self.recirc_area = self.area_probe.sample(self.u_, self.p_)
self.write_history_parameters()
# self.visual_inspection()
# self.output_data()
# self.solver_step += 1
# time.sleep(10)
# ----------------------------------------------------------------------
# if necessary, fill the probes buffer
if self.resetted_number_probes:
printi("Need to fill again the buffer; modified number of probes")
for _ in range(self.size_history):
self.execute()
# ----------------------------------------------------------------------
# ready now
#Initialisation du prob de recirculation area
#path=''
#if "dump" in self.inspection_params:
# path = 'results/area_out.pvd'
#self.area_probe = RecirculationAreaProbe(self.u_, 0, store_path=path)
self.ready_to_use = True