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Commit 54022b0c by Jigyasa Watwani
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extend code + visualising dldt

parent d7f785ec
Inline Side-by-side
Showing with 46 additions and 33 deletions
basic_model_only_density/parameters.json
{ {
"resolution": 1000, "resolution": 1000,
"system_size": 1.0, "system_size": 1.0,
"elasticity": 1, "elasticity": 0.5,
"viscosity": 1, "viscosity": 1,
"zero_rho_boundary": true, "zero_rho_boundary": true,
"friction": 1.0, "friction": 1.0,
"lamda": 1, "lamda": 1.5,
"diffusion_rho": 0.1, "diffusion_rho": 0.1,
"turnover_rho": 1, "turnover_rho": 1,
"active_death": false, "active_death": false,
...@@ -15,5 +15,5 @@ ...@@ -15,5 +15,5 @@
"noise_level": 0.0, "noise_level": 0.0,
"timestep": 0.01, "timestep": 0.01,
"savetime": 0.1, "savetime": 0.1,
"maxtime": 1.0 "maxtime": 600.0
} }
\ No newline at end of file
basic_model_only_density/run_tissue.py
...@@ -38,17 +38,12 @@ else: ...@@ -38,17 +38,12 @@ else:
mesh = df.IntervalMesh(parameters['resolution'], mesh = df.IntervalMesh(parameters['resolution'],
- parameters['system_size']/2, - parameters['system_size']/2,
parameters['system_size']/2) parameters['system_size']/2)
print('Before reading geometry the mesh:', mesh.coordinates()[:,0])
# read geometry from h5 file # read geometry from h5 file
var = 'density' var = 'density'
h5 = h5py.File( '%s_%s.h5' % (parameters['timestamp'], var,), 'a') h5 = h5py.File( '%s_%s.h5' % (parameters['timestamp'], var,), 'a')
# print("Name of the file: ", h5.filename)
# print('Details of the h5 file:', [(i,j) for i,j in h5.attrs.items()])
print(f'var {var}, savesteps {savesteps}')
geometry = np.array(h5['%s/%s_%d/mesh/geometry'%(var,var, savesteps)]) geometry = np.array(h5['%s/%s_%d/mesh/geometry'%(var,var, savesteps)])
mesh.coordinates()[:,0] = geometry[:,0] mesh.coordinates()[:,0] = geometry[:,0]
print('After reading geometry the mesh:',mesh.coordinates()[:,0])
# Read data # Read data
SFS = df.FunctionSpace(mesh, 'P', 1) SFS = df.FunctionSpace(mesh, 'P', 1)
...@@ -62,7 +57,6 @@ else: ...@@ -62,7 +57,6 @@ else:
rhoFile.close() rhoFile.close()
initTime = parameters['maxtime'] initTime = parameters['maxtime']
print('old max time=', initTime)
parameters['maxtime'] = args.time parameters['maxtime'] = args.time
tissue = Tissue(parameters, mesh) tissue = Tissue(parameters, mesh)
...@@ -74,5 +68,5 @@ if extend: ...@@ -74,5 +68,5 @@ if extend:
with open(parametersFile, "w") as jsonFile: with open(parametersFile, "w") as jsonFile:
json.dump(parameters, jsonFile, indent=4, sort_keys=True) json.dump(parameters, jsonFile, indent=4, sort_keys=True)
# from viz_tissue import visualize from viz_tissue import visualize
# visualize(parameters, DIR='') visualize(parameters, DIR='')
\ No newline at end of file \ No newline at end of file
basic_model_only_density/tissue.py
...@@ -17,7 +17,6 @@ class Tissue(object): ...@@ -17,7 +17,6 @@ class Tissue(object):
self.system_size/2) self.system_size/2)
else: else:
self.mesh = mesh self.mesh = mesh
print('Mesh passed as initial condition:', self.mesh.coordinates()[:,0])
scalar_element = df.FiniteElement('P', self.mesh.ufl_cell(), 1) 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)
...@@ -156,7 +155,6 @@ class Tissue(object): ...@@ -156,7 +155,6 @@ class Tissue(object):
self.rhoFile.write_checkpoint(rho, 'density', self.time) self.rhoFile.write_checkpoint(rho, 'density', self.time)
for steps in progressbar.progressbar(range(1, maxsteps + 1)): for steps in progressbar.progressbar(range(1, maxsteps + 1)):
print(self.time)
df.solve(self.form == 0, self.function, self.bc) df.solve(self.form == 0, self.function, self.bc)
self.function0.assign(self.function) self.function0.assign(self.function)
self.time += self.timestep self.time += self.timestep
...@@ -170,17 +168,13 @@ class Tissue(object): ...@@ -170,17 +168,13 @@ class Tissue(object):
self.time, append=True) self.time, append=True)
self.rhoFile.write_checkpoint(rho, 'density', self.rhoFile.write_checkpoint(rho, 'density',
self.time, append=True) self.time, append=True)
# move mesh # move mesh
dr = df.project(v*self.timestep, self.function_space.sub(0).collapse()) dr = df.project(v*self.timestep, self.function_space.sub(0).collapse())
df.ALE.move(self.mesh, dr) df.ALE.move(self.mesh, dr)
print('After solving till new maxtime, the mesh coordinates:',self.mesh.coordinates()[:,0])
self.uFile = None self.uFile.close()
self.vFile = None self.vFile.close()
self.rhoFile = None self.rhoFile.close()
# self.uFile.closed
# self.vFile.closed
# self.rhoFile.closed
basic_model_only_density/viz_tissue.py
...@@ -10,7 +10,6 @@ from tempfile import TemporaryDirectory ...@@ -10,7 +10,6 @@ from tempfile import TemporaryDirectory
def visualize(params, DIR=''): def visualize(params, DIR=''):
savesteps = int(params['maxtime']/params['savetime']) savesteps = int(params['maxtime']/params['savetime'])
times = np.arange(savesteps+1) * params['savetime'] times = np.arange(savesteps+1) * params['savetime']
print(times)
# Read mesh geometry from h5 file # Read mesh geometry from h5 file
var = 'density' var = 'density'
...@@ -21,7 +20,6 @@ def visualize(params, DIR=''): ...@@ -21,7 +20,6 @@ def visualize(params, DIR=''):
topology = np.array(h5['%s/%s_0/mesh/topology'%(var,var)]) topology = np.array(h5['%s/%s_0/mesh/topology'%(var,var)])
geometry = [] geometry = []
for i in progressbar.progressbar(range(len(times))): for i in progressbar.progressbar(range(len(times))):
print(times[i])
geometry.append(np.array(h5['%s/%s_%d/mesh/geometry'%(var,var,i)])) geometry.append(np.array(h5['%s/%s_%d/mesh/geometry'%(var,var,i)]))
h5.close() h5.close()
geometry = np.array(geometry) geometry = np.array(geometry)
...@@ -114,7 +112,7 @@ def visualize(params, DIR=''): ...@@ -114,7 +112,7 @@ def visualize(params, DIR=''):
fc='#999999') fc='#999999')
slider.drawon = False slider.drawon = False
slider.on_changed(update) slider.on_changed(update)
# plt.show()
print('Saving movie-...') print('Saving movie-...')
FPS = 50 FPS = 50
movFile = os.path.join(DIR, '%s_fields.mov' % params['timestamp']) movFile = os.path.join(DIR, '%s_fields.mov' % params['timestamp'])
...@@ -133,7 +131,7 @@ def visualize(params, DIR=''): ...@@ -133,7 +131,7 @@ def visualize(params, DIR=''):
tmp_dir.cleanup() tmp_dir.cleanup()
# plotting the stresses # plotting the stresses
fig2, axes1 = plt.subplots(3, 1, sharex=True, figsize=(8,8)) figure, axes1 = plt.subplots(3, 1, sharex=True, figsize=(8,8))
axes1[-1].set_xlabel(r'$x$') axes1[-1].set_xlabel(r'$x$')
axes1[2].set_ylabel('Elastic stress') axes1[2].set_ylabel('Elastic stress')
axes1[1].set_ylabel('Viscous stress') axes1[1].set_ylabel('Viscous stress')
...@@ -180,7 +178,7 @@ def visualize(params, DIR=''): ...@@ -180,7 +178,7 @@ def visualize(params, DIR=''):
for tt in progressbar.progressbar(range(len(times))): for tt in progressbar.progressbar(range(len(times))):
slider.set_val(times[tt]) slider.set_val(times[tt])
fr = get_filename("%03d.png" % tt) fr = get_filename("%03d.png" % tt)
fig2.savefig(fr, facecolor=fig2.get_facecolor(), dpi=100) figure.savefig(fr, facecolor=figure.get_facecolor(), dpi=100)
os.system(command + " " + str(fps) os.system(command + " " + str(fps)
+ " -i " + tmp_dir.name + os.sep + " -i " + tmp_dir.name + os.sep
+ "%03d.png " + options + " " + movFile) + "%03d.png " + options + " " + movFile)
...@@ -188,24 +186,50 @@ def visualize(params, DIR=''): ...@@ -188,24 +186,50 @@ def visualize(params, DIR=''):
# L(t) vs t # L(t) vs t
length = geometry[:,-1,0]-geometry[:,0,0] length = geometry[:,-1,0]-geometry[:,0,0]
print(length)
fig1, ax1 = plt.subplots(1, 1, figsize=(8, 8)) fig1, ax1 = plt.subplots(1, 1, figsize=(8, 8))
ax1.set_xlabel('$t$') ax1.set_xlabel('$t$')
ax1.set_ylabel('$L(t)$') ax1.set_ylabel('$L(t)$')
ax1.set_xlim(np.min(times), np.max(times)) ax1.set_xlim(np.min(times), np.max(times))
ax1.set_ylim(np.min(length), np.max(length)+1) ax1.set_ylim(np.min(length), np.max(length)+0.01)
ax1.plot(times, length) ax1.plot(times, length)
plt.savefig("%s.png" %params['timestamp']) plt.savefig("%s.png" %params['timestamp'])
# plt.show()
np.save('%s_length.npy' %params['timestamp'], length) np.save('%s_length.npy' %params['timestamp'], length)
fig2, ax2 = plt.subplots(1, 1, figsize=(8, 8)) fig2, ax2 = plt.subplots(1, 1, figsize=(8, 8))
ax2.set_xlabel('$t$') ax2.set_xlabel('$t$')
ax2.set_ylabel('$L(t)$') ax2.set_ylabel('$L(t)$')
# ax2.set_xlim(np.min(times), np.max(times))
# ax2.set_ylim(np.min(length), np.max(length)+1)
ax2.loglog(times, length) ax2.loglog(times, length)
plt.savefig("%s_loglog.png" %params['timestamp']) plt.savefig("%s_loglog.png" %params['timestamp'])
# plt.show()
fig3, ax3 = plt.subplots(1, 1, figsize=(8, 8))
ax3.set_xlabel('$t$')
ax3.set_ylabel('$L(t)$')
ax3.semilogy(times, length)
plt.savefig("%s_semilog.png" %params['timestamp'])
# dldt vs t
dldt = np.gradient(length, times)
print(dldt)
fig11, ax11 = plt.subplots(1, 1, figsize=(8, 8))
ax11.set_xlabel('$t$')
ax11.set_ylabel('$dL/dt$')
ax11.set_xlim(np.min(times), np.max(times))
ax11.set_ylim(np.min(dldt), np.max(dldt)+0.01)
ax11.plot(times, dldt)
plt.savefig("%s_dldt.png" %params['timestamp'])
fig21, ax21 = plt.subplots(1, 1, figsize=(8, 8))
ax21.set_xlabel('$t$')
ax21.set_ylabel('$dL/dt$')
ax21.loglog(times, dldt)
plt.savefig("%s_loglog_dldt.png" %params['timestamp'])
fig31, ax31 = plt.subplots(1, 1, figsize=(8, 8))
ax31.set_xlabel('$t$')
ax31.set_ylabel('$dL/dt$')
ax31.semilogy(times, dldt)
plt.savefig("%s_semilog_dldt.png" %params['timestamp'])
if __name__ == '__main__': if __name__ == '__main__':
import argparse, json import argparse, json
......
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