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Commit ead15c37 by Jigyasa Watwani
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ditch density field altogether

parent cdb5a46c
Inline Side-by-side
Showing with 26 additions and 81 deletions
u_v_rho/1D/check_response_curves_without_activity/parameters.json
...@@ -12,6 +12,6 @@ ...@@ -12,6 +12,6 @@
"timestep": 0.01, "timestep": 0.01,
"turnover_rho": 1, "turnover_rho": 1,
"viscosity": 1, "viscosity": 1,
"applied_boundary_stress": 2.0, "applied_boundary_stress": 1.5,
"zero_rho_boundary": true "zero_rho_boundary": true
} }
\ No newline at end of file
u_v_rho/1D/check_response_curves_without_activity/run_tissue.py
...@@ -25,7 +25,6 @@ if args.jsonfile=='parameters.json': ...@@ -25,7 +25,6 @@ if args.jsonfile=='parameters.json':
parametersFile = timestamp + '_parameters.json' parametersFile = timestamp + '_parameters.json'
initu = None initu = None
initv = None initv = None
initrho = None
initTime = 0.0 initTime = 0.0
mesh = None mesh = None
...@@ -74,7 +73,7 @@ else: ...@@ -74,7 +73,7 @@ else:
parameters['maxtime'] = args.time parameters['maxtime'] = args.time
tissue = OneDimTissue(parameters, mesh) tissue = OneDimTissue(parameters, mesh)
tissue.solve(initu, initv, initrho, initTime, extend) tissue.solve(initu, initv, initTime, extend)
if extend: if extend:
parameters['maxtime'] = initTime + parameters['maxtime'] parameters['maxtime'] = initTime + parameters['maxtime']
......
u_v_rho/1D/check_response_curves_without_activity/tissue.py
...@@ -37,25 +37,14 @@ class OneDimTissue(object): ...@@ -37,25 +37,14 @@ class OneDimTissue(object):
def setup(self): def setup(self):
scalar_element = df.FiniteElement('P', self.mesh.ufl_cell(), 1)
vector_element = df.VectorElement('P', self.mesh.ufl_cell(), 1) vector_element = df.VectorElement('P', self.mesh.ufl_cell(), 1)
# u, v, rho # u, v
self.mixed_element = df.MixedElement([vector_element, vector_element, scalar_element]) self.mixed_element = df.MixedElement([vector_element, vector_element])
# define function space with this mixed element # define function space with this mixed element
self.function_space = df.FunctionSpace(self.mesh, self.mixed_element) self.function_space = df.FunctionSpace(self.mesh, self.mixed_element)
# boundary condition on rho
if self.zero_rho_boundary:
self.rho_boundary = 0.0
else:
self.rho_boundary = self.average_rho
self.bc = df.DirichletBC(self.function_space.sub(2),
df.Constant(self.rho_boundary),
'on_boundary')
# define functions on function space # define functions on function space
self.function0 = df.Function(self.function_space) self.function0 = df.Function(self.function_space)
self.function = df.Function(self.function_space) self.function = df.Function(self.function_space)
...@@ -100,30 +89,11 @@ class OneDimTissue(object): ...@@ -100,30 +89,11 @@ class OneDimTissue(object):
viscous_stress = self.viscosity * 2 * eps_v viscous_stress = self.viscosity * 2 * eps_v
return (elastic_stress + viscous_stress) return (elastic_stress + viscous_stress)
def diffusion_reaction_rho(self, rho, trho):
return (self.diffusion_rho * df.inner(df.nabla_grad(rho),
df.nabla_grad(trho))
- self.turnover_rho * df.inner(rho*(1 - rho/self.average_rho),
trho)
)
def setup_initial_conditions(self): def setup_initial_conditions(self):
# ic for u # ic for u
zero_vector = df.Constant((0.0,)) zero_vector = df.Constant((0.0,))
u0 = df.interpolate(zero_vector, u0 = df.interpolate(zero_vector,
self.function_space.sub(0).collapse()) self.function_space.sub(0).collapse())
# ic for rho
if self.zero_rho_boundary:
base_rho = 0.0
else:
base_rho = self.average_rho
rho0 = df.interpolate(df.Expression(
'base_rho + 0.1 * cos(PI*x[0]/L)*cos(PI*x[0]/L)',
L=self.system_size,
base_rho=base_rho,
degree=1, PI=np.pi),
self.function_space.sub(2).collapse())
# velocity from u0 and rho0 # velocity from u0 and rho0
VFS = self.function_space.sub(1).collapse() VFS = self.function_space.sub(1).collapse()
...@@ -137,12 +107,12 @@ class OneDimTissue(object): ...@@ -137,12 +107,12 @@ class OneDimTissue(object):
- df.inner(tv0, self.imposed_boundary_stress_normal_component()) * self.ds(2) - df.inner(tv0, self.imposed_boundary_stress_normal_component()) * self.ds(2)
) )
df.solve(v0form == 0, v0) df.solve(v0form == 0, v0)
df.assign(self.function0, [u0, v0, rho0]) df.assign(self.function0, [u0, v0])
def setup_weak_forms(self): def setup_weak_forms(self):
u0, v0, rho0 = df.split(self.function0) u0, v0 = df.split(self.function0)
u, v, rho = df.split(self.function) u, v = df.split(self.function)
tu, tv, trho = df.TestFunctions(self.function_space) tu, tv = df.TestFunctions(self.function_space)
uform = (df.inner((u - u0)/self.timestep, tu) uform = (df.inner((u - u0)/self.timestep, tu)
- df.inner(v0, tu))* df.dx - df.inner(v0, tu))* df.dx
...@@ -152,14 +122,10 @@ class OneDimTissue(object): ...@@ -152,14 +122,10 @@ class OneDimTissue(object):
self.epsilon(tv))) * df.dx self.epsilon(tv))) * df.dx
+ df.inner(tv, self.imposed_boundary_stress_normal_component()) * self.ds(1) + df.inner(tv, self.imposed_boundary_stress_normal_component()) * self.ds(1)
- df.inner(tv, self.imposed_boundary_stress_normal_component()) * self.ds(2)) - df.inner(tv, self.imposed_boundary_stress_normal_component()) * self.ds(2))
rhoform = (df.inner((rho - rho0)/self.timestep, trho)
+ self.advection(rho0, v0, trho)
+ self.diffusion_reaction_rho(rho, trho))* df.dx
self.form = (uform + vform + rhoform) self.form = (uform + vform)
def solve(self, initu=None, initv=None, initrho=None, initTime=0, extend=False): def solve(self, initu=None, initv=None, initTime=0, extend=False):
# create function space, functions, bc # create function space, functions, bc
self.setup() self.setup()
...@@ -167,7 +133,6 @@ class OneDimTissue(object): ...@@ -167,7 +133,6 @@ class OneDimTissue(object):
# create files if they don't exist, open them if they do exist # create files if they don't exist, open them if they do exist
self.uFile = df.XDMFFile('%s_displacement.xdmf' % self.timestamp) self.uFile = df.XDMFFile('%s_displacement.xdmf' % self.timestamp)
self.vFile = df.XDMFFile('%s_velocity.xdmf' % self.timestamp) self.vFile = df.XDMFFile('%s_velocity.xdmf' % self.timestamp)
self.rhoFile = df.XDMFFile('%s_density.xdmf' % self.timestamp)
# time-variables # time-variables
self.time = initTime self.time = initTime
...@@ -179,10 +144,9 @@ class OneDimTissue(object): ...@@ -179,10 +144,9 @@ class OneDimTissue(object):
self.setup_initial_conditions() self.setup_initial_conditions()
# save the ic # save the ic
u0, v0, rho0 = self.function0.split(deepcopy=True) u0, v0 = self.function0.split(deepcopy=True)
self.uFile.write_checkpoint(u0, 'displacement', self.time) self.uFile.write_checkpoint(u0, 'displacement', self.time)
self.vFile.write_checkpoint(v0, 'velocity', self.time) self.vFile.write_checkpoint(v0, 'velocity', self.time)
self.rhoFile.write_checkpoint(rho0, 'density', self.time)
# move the mesh with this initial velocity # move the mesh with this initial velocity
dr0 = df.project(v0 * self.timestep, self.function_space.sub(0).collapse()) dr0 = df.project(v0 * self.timestep, self.function_space.sub(0).collapse())
...@@ -192,32 +156,26 @@ class OneDimTissue(object): ...@@ -192,32 +156,26 @@ class OneDimTissue(object):
# assign fields to func0 # assign fields to func0
u0 = df.project(initu, self.function_space.sub(0).collapse()) u0 = df.project(initu, self.function_space.sub(0).collapse())
v0 = df.project(initv, self.function_space.sub(1).collapse()) v0 = df.project(initv, self.function_space.sub(1).collapse())
rho0 = df.project(initrho, self.function_space.sub(2).collapse()) df.assign(self.function0, [u0, v0])
df.assign(self.function0, [u0, v0, rho0])
# move the mesh with initial v read from file # move the mesh with initial v read from file
dr0 = df.project(v0 * self.timestep, self.function_space.sub(0).collapse()) dr0 = df.project(v0 * self.timestep, self.function_space.sub(0).collapse())
df.ALE.move(self.mesh, dr0) df.ALE.move(self.mesh, dr0)
self.setup() # Builds space on moved, unrefined mesh
self.function0 = df.project(self.function0, self.function_space)
self.setup_weak_forms() self.setup_weak_forms()
for steps in progressbar.ProgressBar()(range(1, maxsteps + 1)): for steps in progressbar.ProgressBar()(range(1, maxsteps + 1)):
self.time += self.timestep self.time += self.timestep
# solve to get fields at next timestep # solve to get fields at next timestep
df.solve(self.form == 0, self.function, self.bc) df.solve(self.form == 0, self.function)
# save the fields # save the fields
u, v, rho = self.function.split(deepcopy=True) u, v = self.function.split(deepcopy=True)
if steps % savesteps == 0: if steps % savesteps == 0:
self.uFile.write_checkpoint(u, 'displacement', self.time, append=True) self.uFile.write_checkpoint(u, 'displacement', self.time, append=True)
self.vFile.write_checkpoint(v, 'velocity', self.time, append=True) self.vFile.write_checkpoint(v, 'velocity', self.time, append=True)
self.rhoFile.write_checkpoint(rho, 'density', self.time, append=True)
# assign the calculated function to a newly-defined function, to be used later # assign the calculated function to a newly-defined function, to be used later
old_function = df.Function(self.function_space) old_function = df.Function(self.function_space)
...@@ -241,5 +199,4 @@ class OneDimTissue(object): ...@@ -241,5 +199,4 @@ class OneDimTissue(object):
self.uFile.close() self.uFile.close()
self.vFile.close() self.vFile.close()
self.rhoFile.close()
\ No newline at end of file
u_v_rho/1D/check_response_curves_without_activity/viz_tissue.py
...@@ -16,7 +16,7 @@ def visualize(params, DIR=''): ...@@ -16,7 +16,7 @@ def visualize(params, DIR=''):
times = np.arange(savesteps + 1) * params['savetime'] times = np.arange(savesteps + 1) * params['savetime']
# Read mesh geometry and topology from h5 file # Read mesh geometry and topology from h5 file
var = 'density' var = 'displacement'
h5 = h5py.File(os.path.join(DIR, '%s_%s.h5' % (params['timestamp'], var)), "r") h5 = h5py.File(os.path.join(DIR, '%s_%s.h5' % (params['timestamp'], var)), "r")
geometry = [] geometry = []
...@@ -32,11 +32,9 @@ def visualize(params, DIR=''): ...@@ -32,11 +32,9 @@ def visualize(params, DIR=''):
# Initialize field storage # Initialize field storage
u = [] u = []
v = [] v = []
rho = []
uFile = df.XDMFFile(os.path.join(DIR, '%s_displacement.xdmf' % params['timestamp'])) uFile = df.XDMFFile(os.path.join(DIR, '%s_displacement.xdmf' % params['timestamp']))
vFile = df.XDMFFile(os.path.join(DIR, '%s_velocity.xdmf' % params['timestamp'])) vFile = df.XDMFFile(os.path.join(DIR, '%s_velocity.xdmf' % params['timestamp']))
rhoFile = df.XDMFFile(os.path.join(DIR, '%s_density.xdmf' % params['timestamp']))
for k in progressbar.ProgressBar()(range(len(times))): for k in progressbar.ProgressBar()(range(len(times))):
# Create and process the mesh # Create and process the mesh
...@@ -59,21 +57,18 @@ def visualize(params, DIR=''): ...@@ -59,21 +57,18 @@ def visualize(params, DIR=''):
# Read field values for the current mesh # Read field values for the current mesh
SFS = df.FunctionSpace(mesh, 'P', 1) SFS = df.FunctionSpace(mesh, 'P', 1)
VFS = df.VectorFunctionSpace(mesh, 'P', 1) VFS = df.VectorFunctionSpace(mesh, 'P', 1)
ui, vi, rhoi = df.Function(VFS), df.Function(VFS), df.Function(SFS) ui, vi = df.Function(VFS), df.Function(VFS)
uFile.read_checkpoint(ui, 'displacement', k) uFile.read_checkpoint(ui, 'displacement', k)
vFile.read_checkpoint(vi, 'velocity', k) vFile.read_checkpoint(vi, 'velocity', k)
rhoFile.read_checkpoint(rhoi, 'density', k)
u.append(ui.compute_vertex_values(mesh)) u.append(ui.compute_vertex_values(mesh))
v.append(vi.compute_vertex_values(mesh)) v.append(vi.compute_vertex_values(mesh))
rho.append(rhoi.compute_vertex_values(mesh))
del mesh del mesh
uFile.close() uFile.close()
vFile.close() vFile.close()
rhoFile.close()
# Sort the geometry and fields # Sort the geometry and fields
for k in range(len(times)): for k in range(len(times)):
...@@ -81,32 +76,26 @@ def visualize(params, DIR=''): ...@@ -81,32 +76,26 @@ def visualize(params, DIR=''):
geometry[k] = geometry[k][sorted_indices] geometry[k] = geometry[k][sorted_indices]
u[k] = u[k][sorted_indices] u[k] = u[k][sorted_indices]
v[k] = v[k][sorted_indices] v[k] = v[k][sorted_indices]
rho[k] = rho[k][sorted_indices]
# minima and maxima of the fields # minima and maxima of the fields
min_rho, min_u, min_v = map(lambda x: min(min(sublist) for sublist in x), [rho, u, v]) min_u, min_v = map(lambda x: min(min(sublist) for sublist in x), [u, v])
max_rho, max_u, max_v = map(lambda x: max(max(sublist) for sublist in x), [rho, u, v]) max_u, max_v = map(lambda x: max(max(sublist) for sublist in x), [u, v])
min_geometry = min(min(sublist) for sublist in geometry) min_geometry = min(min(sublist) for sublist in geometry)
max_geometry = max(max(sublist) for sublist in geometry) max_geometry = max(max(sublist) for sublist in geometry)
# interactive plot # interactive plot
fig, axes = plt.subplots(3, 1, sharex=True, figsize=(8,8)) fig, axes = plt.subplots(2, 1, sharex=True, figsize=(8,8))
axes[-1].set_xlabel(r'$x$') axes[-1].set_xlabel(r'$x$')
axes[0].set_ylabel(r'$\rho/\rho_0$') axes[0].set_ylabel(r'$v/\ell \kappa$')
axes[1].set_ylabel(r'$v/\ell \kappa$') axes[1].set_ylabel(r'$u/\ell$')
axes[2].set_ylabel(r'$u/\ell$')
axes[0].set_xlim(min_geometry, max_geometry) axes[0].set_xlim(min_geometry, max_geometry)
axes[0].set_ylim(min_rho-0.1, max_rho+0.1) axes[0].set_ylim(min_v-0.1, max_v+0.1)
axes[1].set_ylim(min_v-0.1, max_v+0.1) axes[1].set_ylim(min_u-0.1, max_u+0.1)
axes[2].set_ylim(min_u-0.1, max_u+0.1)
rhoplot, = axes[0].plot(geometry[0], rho[0], ms=3, color='g', lw = 2, marker = 'o') velplot, = axes[0].plot(geometry[0], v[0], ms=3, color='r', lw = 2, marker = 'o')
velplot, = axes[1].plot(geometry[0], v[0], ms=3, color='r', lw = 2, marker = 'o') uplot, = axes[1].plot(geometry[0], u[0], ms=3, color='b', lw = 2, marker = 'o')
uplot, = axes[2].plot(geometry[0], u[0], ms=3, color='b', lw = 2, marker = 'o')
def update(value): def update(value):
ti = np.abs(times-value).argmin() ti = np.abs(times-value).argmin()
rhoplot.set_ydata(rho[ti])
rhoplot.set_xdata(geometry[ti])
velplot.set_ydata(v[ti]) velplot.set_ydata(v[ti])
velplot.set_xdata(geometry[ti]) velplot.set_xdata(geometry[ti])
uplot.set_ydata(u[ti]) uplot.set_ydata(u[ti])
......
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