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Commit e9ee584d by Jigyasa Watwani
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project the IC, not interpolate. Computing errornorm

parent f0ead902
Inline Side-by-side
Showing with 68 additions and 29 deletions
simple_extend_code/111223-235806_parameters.json 0 → 100644
{
"D": 0.1,
"L": 1.0,
"maxtime": 1.0,
"resolution": 128,
"timestamp": "111223-235806",
"timestep": 0.1
}
\ No newline at end of file
simple_extend_code/111223-235856_parameters.json 0 → 100644
{
"D": 0.1,
"L": 1.0,
"maxtime": 1,
"resolution": 128,
"timestamp": "111223-235856",
"timestep": 0.1
}
\ No newline at end of file
simple_extend_code/121223-065829_parameters.json 0 → 100644
{
"D": 0.1,
"L": 1.0,
"maxtime": 1.0,
"resolution": 128,
"timestamp": "121223-065829",
"timestep": 0.1
}
\ No newline at end of file
simple_extend_code/121223-065916_parameters.json 0 → 100644
{
"D": 0.1,
"L": 1.0,
"maxtime": 1,
"resolution": 128,
"timestamp": "121223-065916",
"timestep": 0.1
}
\ No newline at end of file
simple_extend_code/compare.py 0 → 100644
import dolfin as df
import numpy as np
c1File = df.XDMFFile('121223-065916_concentration.xdmf')
c2File = df.XDMFFile('121223-065829_concentration.xdmf')
mesh = df.IntervalMesh(128, -0.5, 0.5)
times = np.arange(0.0, 1.1, 0.1)
SFS = df.FunctionSpace(mesh, 'P', 1)
for steps in range(len(times)):
c1 = df.Function(SFS)
c2 = df.Function(SFS)
c1File.read_checkpoint(c1, 'concentration', steps)
c2File.read_checkpoint(c2, 'concentration', steps)
print(df.assemble((c2 - c1)**2 * df.dx(mesh))**0.5)
c1File.close()
c2File.close()
simple_extend_code/extend_for_diffusion.py
import numpy as np import numpy as np
import dolfin as df import dolfin as df
import progressbar import progressbar
import os
df.set_log_level(df.LogLevel.ERROR) df.set_log_level(df.LogLevel.ERROR)
df.parameters['form_compiler']['optimize'] = True df.parameters['form_compiler']['optimize'] = True
...@@ -25,21 +24,19 @@ class diffusion(object): ...@@ -25,21 +24,19 @@ class diffusion(object):
if initc is None: if initc is None:
self.c0.interpolate(df.Expression('1 + 0.2 * cos(pi*x[0]/L)', pi=np.pi, L=self.L, degree=1)) self.c0.interpolate(df.Expression('1 + 0.2 * cos(pi*x[0]/L)', pi=np.pi, L=self.L, degree=1))
else: else:
self.c0.interpolate(initc) self.c0 = df.project(initc, self.function_space)
print('c0[-1]=', self.c0.compute_vertex_values(self.mesh)[-1])
def setup_weak_forms(self): def setup_weak_forms(self):
self.form = (df.inner((self.c - self.c0)/self.timestep, self.tc) self.form = (df.inner((self.c - self.c0)/self.timestep, self.tc)
+ self.D * df.inner(df.nabla_grad(self.c), df.nabla_grad(self.tc)) + self.D * df.inner(df.nabla_grad(self.c), df.nabla_grad(self.tc))
) * df.dx ) * df.dx
def solve(self, initc=None, initTime=0.0, extend=False): def solve(self, initc=None, initTime=0.0, extend=False):
# create file if it doesn't exist, open if it exists
self.cFile = df.XDMFFile('%s_concentration.xdmf' % self.timestamp) self.cFile = df.XDMFFile('%s_concentration.xdmf' % self.timestamp)
# time-variables # time-variables
self.time = initTime self.time = initTime
print('time=', self.time)
maxsteps = int(self.maxtime/self.timestep) maxsteps = int(self.maxtime/self.timestep)
self.setup_initial_conditions(initc) self.setup_initial_conditions(initc)
...@@ -51,12 +48,9 @@ class diffusion(object): ...@@ -51,12 +48,9 @@ class diffusion(object):
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
print('time=', self.time)
df.solve(self.form == 0, self.c) df.solve(self.form == 0, self.c)
print('c[-1]=', self.c.compute_vertex_values(self.mesh)[-1]) self.cFile.write_checkpoint(self.c, 'concentration', self.time, append=True)
self.c0.assign(self.c) self.c0.assign(self.c)
self.cFile.write_checkpoint(self.c, 'concentration',
self.time, append=True)
self.cFile.close() self.cFile.close()
......
simple_extend_code/parameters.json
{ {
"resolution": 1000, "resolution": 128,
"L": 1.0, "L": 1.0,
"D": 0.1, "D": 0.1,
"timestep": 0.1, "timestep": 0.1,
"maxtime": 0.5 "maxtime": 1
} }
\ No newline at end of file
simple_extend_code/run_extend_for_diffusion.py
import json, datetime import json, datetime
import os import os
from extend_for_diffusion import diffusion from extend_for_diffusion import diffusion
from viz_extend_for_diffusion import visualize
import argparse import argparse
import dolfin as df import dolfin as df
import h5py
parser = argparse.ArgumentParser() parser = argparse.ArgumentParser()
parser.add_argument('-j','--jsonfile', help='data file', parser.add_argument('-j','--jsonfile', help ='data file',
default='parameters.json') default='parameters.json')
parser.add_argument('-t','--time', help='time to run', type=float) parser.add_argument('-t','--time', help ='time to run', type=float)
args = parser.parse_args() args = parser.parse_args()
assert os.path.isfile(args.jsonfile), '%s file not found' % args.jsonfile assert os.path.isfile(args.jsonfile), '%s file not found' % args.jsonfile
...@@ -18,7 +16,7 @@ assert os.path.isfile(args.jsonfile), '%s file not found' % args.jsonfile ...@@ -18,7 +16,7 @@ assert os.path.isfile(args.jsonfile), '%s file not found' % args.jsonfile
with open(args.jsonfile) as jsonFile: with open(args.jsonfile) as jsonFile:
parameters = json.load(jsonFile) parameters = json.load(jsonFile)
if args.jsonfile=='parameters.json': if args.jsonfile == 'parameters.json':
extend = False extend = False
print('Fresh run...') print('Fresh run...')
timestamp = datetime.datetime.now().strftime("%d%m%y-%H%M%S") timestamp = datetime.datetime.now().strftime("%d%m%y-%H%M%S")
...@@ -29,7 +27,7 @@ if args.jsonfile=='parameters.json': ...@@ -29,7 +27,7 @@ if args.jsonfile=='parameters.json':
else: else:
extend = True extend = True
print('Extending run') print('Extending run...')
parametersFile = args.jsonfile parametersFile = args.jsonfile
steps = int(parameters['maxtime']/parameters['timestep']) steps = int(parameters['maxtime']/parameters['timestep'])
...@@ -38,10 +36,6 @@ else: ...@@ -38,10 +36,6 @@ else:
- parameters['L']/2, - parameters['L']/2,
parameters['L']/2) parameters['L']/2)
# read geometry from h5 file
var = 'concentration'
h5 = h5py.File( '%s_%s.h5' % (parameters['timestamp'], var,), 'r+')
# Read data # Read data
SFS = df.FunctionSpace(mesh, 'P', 1) SFS = df.FunctionSpace(mesh, 'P', 1)
initc = df.Function(SFS) initc = df.Function(SFS)
......
simple_extend_code/viz_extend_for_diffusion.py
import dolfin as df import dolfin as df
import numpy as np import numpy as np
import os import os
import h5py
from matplotlib.widgets import Slider from matplotlib.widgets import Slider
import progressbar import progressbar
import matplotlib.pyplot as plt import matplotlib.pyplot as plt
from tempfile import TemporaryDirectory
def visualize(params, DIR=''): def visualize(params, DIR=''):
savesteps = int(params['maxtime']/params['timestep']) savesteps = int(params['maxtime']/params['timestep'])
...@@ -16,16 +14,13 @@ def visualize(params, DIR=''): ...@@ -16,16 +14,13 @@ def visualize(params, DIR=''):
params['L']/2) params['L']/2)
# Read data # Read data
c = np.zeros((len(times), mesh.num_vertices())) c = np.zeros((len(times), mesh.num_vertices()))
cFile = df.XDMFFile(os.path.join(DIR, '%s_concentration.xdmf' % params['timestamp']))
cFile = df.XDMFFile(os.path.join(DIR,
'%s_concentration.xdmf' % params['timestamp']))
# Reading data # Reading data
print('Reading data...') print('Reading data...')
for steps in progressbar.progressbar(range(savesteps+1)): for steps in progressbar.progressbar(range(savesteps+1)):
SFS = df.FunctionSpace(mesh, 'P', 1) SFS = df.FunctionSpace(mesh, 'P', 1)
ci= df.Function(SFS) ci = df.Function(SFS)
cFile.read_checkpoint(ci, 'concentration', steps) cFile.read_checkpoint(ci, 'concentration', steps)
c[steps] = ci.compute_vertex_values(mesh) c[steps] = ci.compute_vertex_values(mesh)
...@@ -57,7 +52,6 @@ if __name__ == '__main__': ...@@ -57,7 +52,6 @@ if __name__ == '__main__':
import argparse, json import argparse, json
parser = argparse.ArgumentParser() parser = argparse.ArgumentParser()
parser.add_argument('-j','--jsonfile', help='parameters file', required=True) parser.add_argument('-j','--jsonfile', help='parameters file', required=True)
parser.add_argument('--onscreen', action=argparse.BooleanOptionalAction)
args = parser.parse_args() args = parser.parse_args()
with open(args.jsonfile) as jsonFile: with open(args.jsonfile) as jsonFile:
......
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