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Commit 4b3965bb by Vijay Kumar Krishnamurthy
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Almost there

parent 7519b35d
Inline Side-by-side
Showing with 135 additions and 82 deletions
fixed_boundaries.json
...@@ -21,6 +21,6 @@ ...@@ -21,6 +21,6 @@
"noise_level": 0.1, "noise_level": 0.1,
"timestep" : 0.05, "timestep" : 0.05,
"maxtime" : 200.0 "maxtime" : 10.0
} }
fixed_boundaries.py
...@@ -60,8 +60,18 @@ class FixedBoundaries(object): ...@@ -60,8 +60,18 @@ class FixedBoundaries(object):
def diffusion_reaction_c(self, c, tc): def diffusion_reaction_c(self, c, tc):
return (self.diffusion_c * df.inner(c.dx(0), tc.dx(0)) + self.reaction_c(c, tc)) return (self.diffusion_c * df.inner(c.dx(0), tc.dx(0)) + self.reaction_c(c, tc))
def setup_initial_conditions(self, u0=None, rho0=None, c0=None): def setup_initial_conditions(self, ui=None, rhoi=None, ci=None):
if u0==None and rho0==None and c0==None: if (ui is not None) and (rhoi is not None):
u0 = df.Function(self.function_space.sub(0).collapse())
u0.vector()[:] = ui
rho0 = df.Function(self.function_space.sub(2).collapse())
rho0.vector()[:] = rhoi
if self.morphogen:
c0 = df.Function(self.function_space.sub(3).collapse())
c0.vector()[:] = ci
else:
c0 = df.Constant(1.0)
else:
u0 = df.interpolate(df.Constant(0), self.function_space.sub(0).collapse()) u0 = df.interpolate(df.Constant(0), self.function_space.sub(0).collapse())
rho0 = df.interpolate(df.Constant(self.average_rho), self.function_space.sub(2).collapse()) rho0 = df.interpolate(df.Constant(self.average_rho), self.function_space.sub(2).collapse())
# add noise # add noise
...@@ -76,13 +86,7 @@ class FixedBoundaries(object): ...@@ -76,13 +86,7 @@ class FixedBoundaries(object):
c0.vector()[:] = c0.vector()[:] + noise_c c0.vector()[:] = c0.vector()[:] + noise_c
else: else:
c0 = df.Constant(1.0) c0 = df.Constant(1.0)
else:
u0 = df.interpolate(u0, self.function_space.sub(0).collapse())
rho0 = df.interpolate(rho0, self.function_space.sub(2).collapse())
if self.morphogen:
c0 = df.interpolate(c0, self.function_space.sub(3).collapse())
else:
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)
...@@ -145,13 +149,7 @@ class FixedBoundaries(object): ...@@ -145,13 +149,7 @@ class FixedBoundaries(object):
Z = f.split(deepcopy=True) Z = f.split(deepcopy=True)
return np.array([z.compute_vertex_values(self.mesh) for z in Z]).T return np.array([z.compute_vertex_values(self.mesh) for z in Z]).T
def solve(self, extend=None, DIR=''): def solve(self, u0=None, rho0=None, c0=None):
if extend:
# read the last time point of earlier simulation
# u0, rho0, c0
pass
else:
u0, rho0, c0 = None, None, None
self.setup_initial_conditions(u0, rho0, c0) self.setup_initial_conditions(u0, rho0, c0)
self.setup_weak_forms() self.setup_weak_forms()
...@@ -165,69 +163,5 @@ class FixedBoundaries(object): ...@@ -165,69 +163,5 @@ class FixedBoundaries(object):
data.append(self.get_data(self.f)) data.append(self.get_data(self.f))
self.f0.assign(self.f) self.f0.assign(self.f)
self.f1.assign(self.f0) self.f1.assign(self.f0)
# parse data
data = np.array(data)
if self.morphogen:
# u, v, rho, c
return np.split(data, 4, axis=2)
else:
# u, v, rho
return np.split(data, 3, axis=2)
if __name__ == '__main__': return np.array(data)
import json \ No newline at end of file
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider
with open('fixed_boundaries.json') as jsonFile:
params = json.load(jsonFile)
fb = FixedBoundaries(params)
Z = fb.solve()
if params['morphogen']:
u, v, rho, c = Z
else:
u, v, rho = Z
x = fb.mesh.coordinates()
times = np.arange(0, fb.maxtime, fb.timestep)
if params['morphogen']:
fig, (axu, axv, axrho, axc) = plt.subplots(4,1, sharex=True, figsize=(8,8))
axc.set_xlabel(r'$x$')
axc.set_ylim(np.min(c), np.max(c))
else:
fig, (axu, axv, axrho) = plt.subplots(3,1, sharex=True, figsize=(8,6))
axrho.set_xlabel(r'$x$')
axu.set_ylabel(r'$u(x,t)$')
axv.set_ylabel(r'$v(x,t)$')
axrho.set_ylabel(r'$\rho(x,t)$')
axu.set_ylim(np.min(u), np.max(u))
axv.set_ylim(np.min(v), np.max(v))
axrho.set_ylim(np.min(rho), np.max(rho))
uplot, = axu.plot(x, u[0])
vplot, = axv.plot(x, v[0])
rhoplot, = axrho.plot(x, rho[0])
if params['morphogen']:
cplot, = axc.plot(x, c[0])
def update(value):
ti = np.abs(times-value).argmin()
uplot.set_ydata(u[ti])
vplot.set_ydata(v[ti])
rhoplot.set_ydata(rho[ti])
if params['morphogen']:
cplot.set_ydata(c[ti])
plt.draw()
sax = plt.axes([0.1, 0.92, 0.7, 0.02])
slider = Slider(sax, r'$t/\tau$', min(times), max(times),
valinit=min(times), valfmt='%3.1f',
fc='#999999')
slider.drawon = False
slider.on_changed(update)
plt.show()
run_fixed_boundaries.py 0 → 100644
import datetime
import json
import os
import argparse
import numpy as np
from fixed_boundaries import FixedBoundaries
parser = argparse.ArgumentParser()
parser.add_argument('-j','--jsonfile', help='json file', default='fixed_boundaries.json')
parser.add_argument('-t','--time', help='time to extend', type=float, default=50)
parser.add_argument('-o','--outputdir', help='output directory', type=str, default='')
args = parser.parse_args()
assert os.path.isfile(args.jsonfile), '%s file not found' % args.jsonfile
with open(args.jsonfile) as jsonFile:
params = json.load(jsonFile)
u0, rho0, c0 = None, None, None
if args.jsonfile=='fixed_boundaries.json':
print('Fresh run')
extend = False
DIR = args.outputdir
timestamp = datetime.datetime.now().strftime("%d%m%y-%H%M%S")
# current timestamp is the jobID
params['timestamp'] = timestamp
else:
print('Extending %s' % params['timestamp'])
extend = True
DIR = os.path.dirname(args.jsonfile)
oldMaxTime = params['maxtime']
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
fb = FixedBoundaries(params)
data = fb.solve(u0=u0, rho0=rho0, c0=c0)
if extend:
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,
params['timestamp'] + '_fixed_boundaries.json'), "w") as fp:
json.dump(params, fp, indent=4)
\ No newline at end of file
viz_fixed_boundaries.py 0 → 100644
import numpy as np
import json
import matplotlib.pyplot as plt
from matplotlib.widgets import Slider
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-j','--jsonfile', help='json file', default='fixed_boundaries.json')
parser.add_argument('-o','--outputdir', help='output directory', type=str, default='')
args = parser.parse_args()
with open(args.jsonfile) as jsonFile:
params = json.load(jsonFile)
dataFile = params['timestamp'] + '_fixed_boundaries.npy'
data = np.load(dataFile)
u, v, rho = data[:,:,0], data[:,:,1], data[:,:,2]
if params['morphogen']:
c = data[:,:,3]
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']:
fig, (axu, axv, axrho, axc) = plt.subplots(4,1, sharex=True, figsize=(8,8))
axc.set_xlabel(r'$x$')
axc.set_ylim(np.min(c), np.max(c))
else:
fig, (axu, axv, axrho) = plt.subplots(3,1, sharex=True, figsize=(8,6))
axrho.set_xlabel(r'$x$')
axu.set_ylabel(r'$u(x,t)$')
axv.set_ylabel(r'$v(x,t)$')
axrho.set_ylabel(r'$\rho(x,t)$')
axu.set_ylim(np.min(u), np.max(u))
axv.set_ylim(np.min(v), np.max(v))
axrho.set_ylim(np.min(rho), np.max(rho))
uplot, = axu.plot(x, u[0])
vplot, = axv.plot(x, v[0])
rhoplot, = axrho.plot(x, rho[0])
if params['morphogen']:
cplot, = axc.plot(x, c[0])
def update(value):
ti = np.abs(times-value).argmin()
uplot.set_ydata(u[ti])
vplot.set_ydata(v[ti])
rhoplot.set_ydata(rho[ti])
if params['morphogen']:
cplot.set_ydata(c[ti])
plt.draw()
sax = plt.axes([0.1, 0.92, 0.7, 0.02])
slider = Slider(sax, r'$t/\tau$', min(times), max(times),
valinit=min(times), valfmt='%3.1f',
fc='#999999')
slider.drawon = False
slider.on_changed(update)
plt.show()
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