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Commit de69b4f0 by Jigyasa Watwani
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test

parents 9f9d07da c9aa2b3e
Inline Side-by-side
Showing with 157 additions and 46 deletions
fixed_boundaries.py
...@@ -18,9 +18,11 @@ class FixedBoundaries(object): ...@@ -18,9 +18,11 @@ class FixedBoundaries(object):
# u, v, rho, c # u, v, rho, c
mixed_element = df.MixedElement([scalar_element, scalar_element, mixed_element = df.MixedElement([scalar_element, scalar_element,
scalar_element, scalar_element]) scalar_element, scalar_element])
self.savedata = self.save_data_uvrhoc
else: else:
# u, v, rho # u, v, rho
mixed_element = df.MixedElement([scalar_element, scalar_element, scalar_element]) mixed_element = df.MixedElement([scalar_element, scalar_element, scalar_element])
self.savedata = self.save_data_uvrho
# define function space with this mixed element # define function space with this mixed element
self.function_space = df.FunctionSpace(self.mesh, mixed_element) self.function_space = df.FunctionSpace(self.mesh, mixed_element)
...@@ -62,13 +64,10 @@ class FixedBoundaries(object): ...@@ -62,13 +64,10 @@ class FixedBoundaries(object):
def setup_initial_conditions(self, ui=None, rhoi=None, ci=None): def setup_initial_conditions(self, ui=None, rhoi=None, ci=None):
if (ui is not None) and (rhoi is not None): if (ui is not None) and (rhoi is not None):
u0 = df.Function(self.function_space.sub(0).collapse()) u0 = df.interpolate(ui, self.function_space.sub(0).collapse())
u0.vector()[:] = ui rho0 = df.interpolate(rhoi, self.function_space.sub(2).collapse())
rho0 = df.Function(self.function_space.sub(2).collapse())
rho0.vector()[:] = rhoi
if self.morphogen: if self.morphogen:
c0 = df.Function(self.function_space.sub(3).collapse()) c0 = df.interpolate(ci, self.function_space.sub(3).collapse())
c0.vector()[:] = ci
else: else:
c0 = df.Constant(1.0) c0 = df.Constant(1.0)
else: else:
...@@ -87,7 +86,6 @@ class FixedBoundaries(object): ...@@ -87,7 +86,6 @@ class FixedBoundaries(object):
else: else:
c0 = df.Constant(1.0) c0 = df.Constant(1.0)
VFS = self.function_space.sub(1).collapse() VFS = self.function_space.sub(1).collapse()
v0 = df.Function(VFS) v0 = df.Function(VFS)
tv = df.TestFunction(VFS) tv = df.TestFunction(VFS)
...@@ -145,23 +143,54 @@ class FixedBoundaries(object): ...@@ -145,23 +143,54 @@ class FixedBoundaries(object):
else: else:
self.form = (uform + vform + rhoform) * df.dx self.form = (uform + vform + rhoform) * df.dx
def get_data(self, f): def save_data_uvrho(self):
Z = f.split(deepcopy=True) u, v, rho = self.f0.split(deepcopy=True)
return np.array([z.compute_vertex_values(self.mesh) for z in Z]).T self.uFile.write_checkpoint(u, 'displacement', self.time, append=True)
self.vFile.write_checkpoint(v, 'velocity', self.time, append=True)
self.rhoFile.write_checkpoint(rho, 'density', self.time, append=True)
def save_data_uvrhoc(self):
u, v, rho, c = self.f0.split(deepcopy=True)
self.uFile.write_checkpoint(u, 'displacement', self.time, append=True)
self.vFile.write_checkpoint(v, 'velocity', self.time, append=True)
self.rhoFile.write_checkpoint(rho, 'density', self.time, append=True)
self.cFile.write_checkpoint(c, 'concentration', self.time, append=True)
def solve(self, extend=False):
# for saving data
self.uFile = df.XDMFFile('%s_displacement.xdmf' % self.timestamp)
self.vFile = df.XDMFFile('%s_velocity.xdmf' % self.timestamp)
self.rhoFile = df.XDMFFile('%s_density.xdmf' % self.timestamp)
if self.morphogen:
self.cFile = df.XDMFFile('%s_concentration.xdmf' % self.timestamp)
if extend:
SFS = df.FunctionSpace(self.mesh, 'P', 1)
ui, vi, rhoi, ci = df.Function(SFS), df.Function(SFS), df.Function(SFS), df.Function(SFS)
self.uFile.read_checkpoint(ui, 'displacement', -1)
self.vFile.read_checkpoint(vi, 'velocity', -1)
self.rhoFile.read_checkpoint(rhoi, 'density', -1)
if self.morphogen:
self.cFile.read_checkpoint(ci, 'concentration', -1)
else:
ci.interpolate(df.Constant(1.0))
else:
ui, vi, rhoi, ci = None, None, None, None
def solve(self, u0=None, rho0=None, c0=None): self.setup_initial_conditions(ui, rhoi, ci)
self.setup_initial_conditions(u0, rho0, c0)
self.setup_weak_forms() self.setup_weak_forms()
# store self.time = 0.0
data = [] self.savedata()
data.append(self.get_data(self.f0)) for i in progressbar.progressbar(range(1, int(self.maxtime/self.timestep))):
times = np.arange(0.0, self.maxtime, self.timestep)
for i in progressbar.progressbar(range(0, len(times))):
df.solve(self.form == 0, self.f, self.bc) df.solve(self.form == 0, self.f, self.bc)
data.append(self.get_data(self.f)) self.time += self.timestep
self.f0.assign(self.f) df.assign(self.f1, self.f0)
self.f1.assign(self.f0) df.assign(self.f0, self.f)
self.savedata()
return np.array(data)
\ No newline at end of file self.uFile.close()
self.vFile.close()
self.rhoFile.close()
if self.morphogen:
self.cFile.close()
\ No newline at end of file
run_fixed_boundaries.py
...@@ -3,8 +3,6 @@ import json ...@@ -3,8 +3,6 @@ import json
import os import os
import argparse import argparse
import numpy as np
from fixed_boundaries import FixedBoundaries from fixed_boundaries import FixedBoundaries
parser = argparse.ArgumentParser() parser = argparse.ArgumentParser()
...@@ -32,24 +30,13 @@ else: ...@@ -32,24 +30,13 @@ else:
DIR = os.path.dirname(args.jsonfile) DIR = os.path.dirname(args.jsonfile)
oldMaxTime = params['maxtime'] oldMaxTime = params['maxtime']
params['maxtime'] = args.time params['maxtime'] = args.time
dataFile = params['timestamp'] + '_fixed_boundaries.npy'
assert os.path.isfile(dataFile), '%s not found' % dataFile
old_data = np.load(dataFile)
print(old_data.shape)
u0, rho0 = old_data[-1, :, 0], old_data[-1, :, 2]
if params['morphogen']:
c0 = old_data[-1, :, 3]
# solve # solve
fb = FixedBoundaries(params) fb = FixedBoundaries(params)
data = fb.solve(u0=u0, rho0=rho0, c0=c0) fb.solve(extend=extend)
if extend: if extend:
params['maxtime'] = oldMaxTime + params['maxtime'] params['maxtime'] = oldMaxTime + params['maxtime']
data = np.concatenate((old_data, data[1:]), axis=0)
# save data
np.save('%s_fixed_boundaries.npy' % params['timestamp'], data)
with open(os.path.join(DIR, with open(os.path.join(DIR,
params['timestamp'] + '_fixed_boundaries.json'), "w") as fp: params['timestamp'] + '_fixed_boundaries.json'), "w") as fp:
......
scan_fixed_boundaries.py 0 → 100644
import datetime, time, json, os, itertools
import dolfin as df
import numpy as np
from fixed_boundaries import FixedBoundaries
df.set_log_level(df.LogLevel.ERROR)
df.parameters['form_compiler']['optimize'] = True
# base parameters
parameters = {
"morphogen" : True,
"resolution" : 32,
"system_size_by_2PI" : 1 ,
"elasticity" : 0.0,
"viscosity" : 1.0,
"friction" : 1.0,
"lamda": 1.75,
"diffusion_rho" : 1.0,
"turnover_rho" : 0.0,
"average_rho" : 1.0,
"saturation_rho" : 1.0,
"diffusion_c" : 1.0,
"turnover_c" : 0.0,
"average_c" : 1.0,
"noise_level": 0.1,
"timestep" : 0.05,
"maxtime" : 10.0
}
# parameters to scan
lamda_list = np.arange(0, 2.2, 0.2)
elasticity_list = np.arange(0, 1.1, 0.1)
plist = list(itertools.product(lamda_list, elasticity_list))
# scan parameters
for i in range(len(plist)):
lamda, elasticity = plist[i]
print('-'*50)
print('%d/%d' % (i, len(plist)))
print('lamda = %4.3f, elasticity = %4.3f' % (lamda, elasticity))
print('-'*50)
# timestamp as job-ID
timestamp = datetime.datetime.now().strftime("%d%m%y-%H%M%S")
params = parameters.copy()
params['timestamp'] = timestamp
params['lamda'] = lamda
params['elasticity'] = elasticity
try:
fb = FixedBoundaries(params)
fb.solve(extend=False)
with open(timestamp+'_polarity.json', "w") as fp:
json.dump(params, fp, indent=4)
except:
print('*** FAILED ****')
os.system("rm -f %s*" % timestamp)
time.sleep(2)
test 0 → 100644
yyy
\ No newline at end of file
viz_fixed_boundaries.py
...@@ -2,8 +2,8 @@ import numpy as np ...@@ -2,8 +2,8 @@ import numpy as np
import json import json
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from matplotlib.widgets import Slider from matplotlib.widgets import Slider
import argparse import argparse
import dolfin as df
parser = argparse.ArgumentParser() parser = argparse.ArgumentParser()
parser.add_argument('-j','--jsonfile', help='json file', default='fixed_boundaries.json') parser.add_argument('-j','--jsonfile', help='json file', default='fixed_boundaries.json')
...@@ -13,16 +13,38 @@ args = parser.parse_args() ...@@ -13,16 +13,38 @@ args = parser.parse_args()
with open(args.jsonfile) as jsonFile: with open(args.jsonfile) as jsonFile:
params = json.load(jsonFile) params = json.load(jsonFile)
dataFile = params['timestamp'] + '_fixed_boundaries.npy' mesh = df.IntervalMesh(params['resolution'], 0.0, 2.0*np.pi*params['system_size_by_2PI'])
data = np.load(dataFile) x = mesh.coordinates()
SFS = df.FunctionSpace(mesh, 'P', 1)
ui, vi, rhoi, ci = df.Function(SFS), df.Function(SFS), df.Function(SFS), df.Function(SFS)
u, v, rho = data[:,:,0], data[:,:,1], data[:,:,2] savesteps = int(params['maxtime']/params['timestep'])
if params['morphogen']: times = np.arange(savesteps+1) * params['timestep']
c = data[:,:,3]
u = np.zeros((len(times), len(x)))
v, rho = np.zeros_like(u), np.zeros_like(u)
uFile = df.XDMFFile('%s_displacement.xdmf' % params['timestamp'])
vFile = df.XDMFFile('%s_velocity.xdmf' % params['timestamp'])
rhoFile = df.XDMFFile('%s_density.xdmf' % params['timestamp'])
if params['morphogen']:
c = np.zeros_like(u)
cFile = df.XDMFFile('%s_concentration.xdmf' % params['timestamp'])
for steps in range(len(times)):
uFile.read_checkpoint(ui, 'displacement', steps)
vFile.read_checkpoint(vi, 'velocity', steps)
rhoFile.read_checkpoint(rhoi, 'density', steps)
u[steps] = ui.compute_vertex_values(mesh)
v[steps] = vi.compute_vertex_values(mesh)
rho[steps] = rhoi.compute_vertex_values(mesh)
if params['morphogen']:
cFile.read_checkpoint(ci, 'concentration', steps)
c[steps] = ci.compute_vertex_values(mesh)
uFile.close()
vFile.close()
rhoFile.close()
if params['morphogen']:
cFile.close()
x = np.linspace(0, params['system_size_by_2PI']*2*np.pi, params['resolution']+1)
times = np.arange(0, params['maxtime'], params['timestep'])
if params['morphogen']: if params['morphogen']:
fig, (axu, axv, axrho, axc) = plt.subplots(4,1, sharex=True, figsize=(8,8)) fig, (axu, axv, axrho, axc) = plt.subplots(4,1, sharex=True, figsize=(8,8))
axc.set_xlabel(r'$x$') axc.set_xlabel(r'$x$')
......
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