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driven_cavity_noslip.shml
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driven_cavity_noslip.shml
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<?xml version='1.0' encoding='utf-8'?>
<harness_options>
<length>
<string_value lines="1">short</string_value>
</length>
<owner>
<string_value lines="1">cwilson</string_value>
</owner>
<description>
<string_value lines="1">A driven cavity example for stokes</string_value>
</description>
<simulations>
<simulation name="DrivenCavity">
<input_file>
<string_value lines="1" type="filename">driven_cavity/noslip/driven_cavity.tfml</string_value>
</input_file>
<run_when name="input_changed_or_output_missing"/>
<parameter_sweep>
<parameter name="dmu">
<values>
<string_value lines="1">1.0</string_value>
</values>
<update>
<string_value lines="20" type="code" language="python">import libspud
if float(dmu) <= 0.0:
import sys
print "ERROR: dmu must be greater than 0!"
sys.exit(1)
libspud.set_option("/system::Stokes/coefficient::ViscosityJumpFactor/type/rank/value/constant", float(dmu))</string_value>
<single_build/>
</update>
</parameter>
<parameter name="ncells">
<values>
<string_value lines="1">32</string_value>
</values>
</parameter>
</parameter_sweep>
<dependencies>
<run name="Mesh">
<input_file>
<string_value lines="1" type="filename">driven_cavity/unitsquare.geo</string_value>
</input_file>
<run_when name="input_changed_or_output_missing"/>
<parameter_sweep>
<parameter name="ncells">
<update>
<string_value lines="20" type="code" language="python">from string import Template as template
if int(ncells) <= 0:
import sys
print "ERROR: ncells must be greater than 0!"
sys.exit(1)
input_file = template(input_file).safe_substitute({'ncells':ncells})</string_value>
</update>
</parameter>
</parameter_sweep>
<required_output>
<filenames name="Mesh">
<string>
<string_value lines="1" type="filename">unitsquare.xml.gz</string_value>
</string>
</filenames>
</required_output>
<commands>
<command name="GMsh">
<string_value lines="1">gmsh -2 unitsquare.geo</string_value>
</command>
<command name="Convert">
<string_value lines="1">dolfin-convert unitsquare.msh unitsquare.xml</string_value>
</command>
<command name="GZip">
<string_value lines="1">gzip unitsquare.xml</string_value>
</command>
</commands>
</run>
</dependencies>
<variables>
<variable name="vtudata">
<string_value lines="20" type="code" language="python">import buckettools.vtktools as vtktools
import os
from lxml import etree
from buckettools.threadlibspud import *
from matplotlib.tri import Triangulation
def lastvtuinpvd(filename):
assert(filename[-4:]==".pvd")
dirname = os.path.dirname(filename)
tree = etree.parse(filename)
vtunames = [[element.attrib['timestep'], os.path.join(dirname, element.attrib['file'])] for element in tree.getroot().iterdescendants(tag="DataSet")]
sortedvtunames = sorted(vtunames, key=lambda entry: float(entry[0]))
return sortedvtunames[-1][-1]
filename = os.path.split(input_filename)[-1]
threadlibspud.load_options(filename)
basename = libspud.get_option("/io/output_base_name")
threadlibspud.clear_options()
vtufilename = lastvtuinpvd(basename+".pvd")
vtu = vtktools.vtu(vtufilename)
vtulocations = vtu.GetLocations()
triangles = []
for c in xrange(vtu.ugrid.GetNumberOfCells()):
points = vtu.GetCellPoints(c)
triangles.append(points)
triang = Triangulation(vtulocations[:,0], vtulocations[:,1], triangles)
v = vtu.GetField("Stokes::Velocity")
p = vtu.GetField("Stokes::Pressure")
vtudata = [triang, vtulocations, v, p]</string_value>
</variable>
<variable name="rmsvelocities">
<string_value lines="20" type="code" language="python">from buckettools.statfile import parser
from buckettools.threadlibspud import *
import os
filename = os.path.split(input_filename)[-1]
threadlibspud.load_options(filename)
basename = libspud.get_option("/io/output_base_name")
threadlibspud.clear_options()
stat = parser(basename+".stat")
vrms = stat["Stokes"]["VelocityL2NormSquared"]["functional_value"][-1]**0.5
vrmsu = stat["Stokes"]["VelocityL2NormSquaredUpper"]["functional_value"][-1]**0.5
vrmsl = stat["Stokes"]["VelocityL2NormSquaredLower"]["functional_value"][-1]**0.5
rmsvelocities = [vrms, vrmsu, vrmsl]</string_value>
</variable>
<variable name="errfile">
<string_value lines="20" type="code" language="python">err = file("terraferma.err-0", 'r')
errfile = [line for line in err.readlines() if not line.startswith("WARNING:")]</string_value>
</variable>
<variable name="havedisplay">
<string_value lines="20" type="code" language="python">import os
exitval = os.system('python -c "import matplotlib.pyplot as plt; plt.figure()"')
havedisplay = (exitval == 0) and "DISPLAY" in os.environ</string_value>
</variable>
</variables>
</simulation>
</simulations>
<tests>
<test name="errors">
<string_value lines="20" type="code" language="python">noerrors = True
for dmu in errfile.parameters['dmu']:
for ncells in errfile.parameters['ncells']:
if len(errfile[{'dmu':dmu, 'ncells':ncells}]) > 0:
print "ERROR: dmu = {}, ncells produced an unexpected error!".format(dmu, ncells)
noerrors = False
assert(noerrors)</string_value>
</test>
<test name="rmsvelocities">
<string_value lines="20" type="code" language="python">for dmu in rmsvelocities.parameters['dmu']:
for ncells in rmsvelocities.parameters['ncells']:
index = {'dmu':dmu, 'ncells':ncells}
print "dmu = {}, ncells = {}:".format(dmu, ncells)
print " rms velocity = {}".format(rmsvelocities[index][0])
print " rms velocity upper = {}".format(rmsvelocities[index][1])
print " rms velocity lower = {}".format(rmsvelocities[index][2])</string_value>
</test>
<test name="plot">
<string_value lines="20" type="code" language="python">import matplotlib
if havedisplay[0][0]:
matplotlib.use('GTKAgg')
else:
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
import os
for dmu in vtudata.parameters['dmu']:
for ncells in vtudata.parameters['ncells']:
index = {'dmu':dmu, 'ncells':ncells}
x = vtudata[index][1]
v = vtudata[index][2]
fig = plt.figure()
stride = 1
q = plt.quiver(x[:,0][::stride], x[:,1][::stride], v[:,0][::stride], v[:,1][::stride], width=0.005, units='x', scale_units='x', scale=10, color='k')
plt.quiverkey(q, 0.9, 0.9, 1, "1", labelpos='S', coordinates='figure', color='k')
plt.gca().set_aspect('equal')
plt.xlabel('x')
plt.ylabel('y')
plt.title('velocity (dmu = {}, ncells = {})'.format(dmu, ncells), y=1.05)
fig.savefig("driven_cavity_freeslip_dmu_{}_ncells_{}.png".format(dmu, ncells))</string_value>
</test>
<test name="convergence">
<string_value lines="20" type="code" language="python">import matplotlib
if havedisplay[0][0]:
matplotlib.use('GTKAgg')
else:
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import numpy as np
import os
if len(rmsvelocities.parameters["ncells"]) > 1:
for dmu in rmsvelocities.parameters["dmu"]:
index = {'dmu':dmu}
ncells = [int(nc) for nc in rmsvelocities.parameters["ncells"]]
fig1 = plt.figure()
plt.plot(ncells, np.asarray(rmsvelocities[index])[:,0])
plt.xlabel('ncells')
plt.ylabel('RMS velocity')
plt.title('RMS velocity (dmu = {})'.format(dmu,), y=1.05)</string_value>
</test>
<test name="display">
<string_value lines="20" type="code" language="python">import matplotlib
if havedisplay[0][0]:
matplotlib.use('GTKAgg')
else:
matplotlib.use('Agg')
import matplotlib.pyplot as plt
import os
if havedisplay[0][0]: plt.show()</string_value>
</test>
</tests>
</harness_options>