def fixed_chill_command(folder_name='FixedChill-t2.0e-02-Ra1e+06-Da1.0e-04-C2.00-Rel1.0e-04-0'):
figure_directory = get_base_output_dir()
fixed_chill_data = os.path.join(get_base_output_dir(), folder_name)
cmd ='Fig9FixedChill(\'' + fixed_chill_data + '\', [1100,1500,2500], \'' + figure_directory + '\')'
return cmd
def no_flow_command():
figure_directory = get_base_output_dir()
no_flow_data = os.path.join(get_base_output_dir(), 'NoFlow')
cmd = 'Fig4NoFlow(\'' + no_flow_data + '\', \'' + figure_directory + 'Fig4BenchmarkNoFlow.eps\')'
return cmd
def fixed_porous_command():
figure_directory = get_base_output_dir()
cfl = get_default_cfl()
data_folder_nu = os.path.join(get_base_output_dir(), 'ConvectionDB-cfl%s' % cfl, 'chi0.4-Da1.0e-02-Ra1.0e+05')
data_folder_variable_porosity = os.path.join(get_base_output_dir(), 'FixedPorousHole-1proc')
cmd = 'Fig5FixedPorosityConvectionPlots(\'' + data_folder_nu + '\', \'' + data_folder_variable_porosity + '\', \'' + figure_directory + '\')'
return cmd
def test_fixed_porous_hole():
base_output_dir = get_base_output_dir()
# matlab_command = get_matlab_base_command()
print(Fore.GREEN + 'Setup tests for (fixed) porous hole' + Style.RESET_ALL)
physical_problem = 'DBVariablePorosity'
data_folder = os.path.join(
base_output_dir,
'FixedPorousHole-1proc-minPorosity%s' % get_min_porosity())
amr_setup, num_procs = get_setup()
# Setup up the post processing command
# uniform_prefix = 'Uniform-DBVariablePorosity-'
python_compare_file = os.path.join(get_mushy_layer_dir(), 'test',
'run_chombo_compare.py')
chombo_compare_analyse = 'python %s -f %s -a -v \'xDarcy velocity\' ' \
'-e L2 -r True -n 6 -d %s \n \n' % (python_compare_file,
data_folder,
base_output_dir)
# Just do analysis - make figures manually once we know the sidewall problem has also finished
analysis_command = chombo_compare_analyse
# Run
extra_params = {}
run_test(data_folder, physical_problem,
fixed_porous_resolution_specific_params, amr_setup, num_procs,
analysis_command, extra_params)
def fixed_chill_video_command(folder_name='FixedChill-t2.0e-02-Ra1e+06-Da1.0e-04-C2.00-Rel1.0e-04-0'):
# figure_directory = get_base_output_dir()
fixed_chill_data = os.path.join(get_base_output_dir(), folder_name)
cmd = 'Fig9MakeVideo(\'' + fixed_chill_data + '\')'
return cmd
def testDiffusiveSolidification():
base_output_dir = get_base_output_dir()
matlab_command = get_matlab_base_command()
print(Fore.GREEN + 'Setup tests for solidification without flow' + Style.RESET_ALL)
physicalProblem = 'noFlow'
AMRSetup = [{'max_level': 0, 'ref_rat': 1, 'run_types': ['uniform'], 'Nzs': [8, 16, 32, 64, 128, 256]},
{'max_level': 1, 'ref_rat': 2, 'run_types': ['amr'], 'Nzs': [8, 16, 32, 64, 128]},
{'max_level': 2, 'ref_rat': 2, 'run_types': ['amr'], 'Nzs': [8, 16, 32, 64]}]
# While testing:
# AMRSetup = [{'max_level': 0, 'ref_rat': 1, 'run_types': ['uniform']}];
# Nzs = [16, 32, 64]
num_procs = [1] * 6 # Needs to be as long as the longest Nzs
# Setup up the post processing command
dataFolder = os.path.join(base_output_dir, 'NoFlow')
figureName = os.path.join(base_output_dir, 'Fig4NoFlow.pdf')
analysis_command = matlab_command + ' "Fig4NoFlow(\'' + dataFolder + '\', \'' + figureName + '\'); exit;"'
# Run
extra_params = {'main.debug': 'true'}
runTest(dataFolder, physicalProblem, diffusive_solidification_resolution_specific_params,
AMRSetup, num_procs, analysis_command, extra_params)
def make_figures():
base_output_dir = get_base_output_dir()
#matlab_command = get_matlab_base_command()
print(Fore.GREEN + 'Make figures' + Style.RESET_ALL)
#data_folder_nu = os.path.join(base_output_dir, 'ConvectionDB-cfl0.2','chi0.4-Da1.0e-02-Ra1.0e+05')
#data_folder_variable_porosity = os.path.join(base_output_dir, 'FixedPorousHole-1proc')
#porous_mushy_hole_folder = os.path.join(base_output_dir, 'PorousMushyHole-t0.00015')
#no_flow_data = os.path.join(base_output_dir, 'NoFlow')
#fixed_chill_data = os.path.join(base_output_dir, 'FixedChill-t5.0e-02-Ra1e+06-Da5.0e-04-C2.00-Rel1.0e-04-0')
#fig_commands = ['Fig4NoFlow(\'' + no_flow_data + '\', \'' + figure_directory + 'Fig4BenchmarkNoFlow.eps\')',
# 'Fig5FixedPorosityConvectionPlots(\'' + data_folder_nu + '\', \'' + data_folder_variable_porosity + '\', \'' + figure_directory + '\')',
# 'Fig7PorousHole(\'' + porous_mushy_hole_folder + '\', \'' + figure_directory + '\')',
# 'Fig9FixedChill(\'' + fixed_chill_data + '\', [3000, 4000, 7000], \'' + figure_directory + '\')',
# 'Fig9MakeVideo(\'' + fixed_chill_data + '\')']
fig_commands = [no_flow_command(),
fixed_porous_command(),
porous_hole_command(),
fixed_chill_command(),
fixed_chill_video_command()]
full_matlab_command = ''
for c in fig_commands:
full_matlab_command = full_matlab_command + 'try \n' + c + '; \ncatch e \n fprintf(\'Plotting failed\'); \nend \n'
# Write out as a script then run that
scriptFile = os.path.join(base_output_dir, 'makeFigureScript.m')
f = open(scriptFile, "w")
full_matlab_command = "set(groot, 'defaultAxesFontName', 'Latin Modern Math'); \nset(groot, 'defaultTextFontName', 'Latin Modern Math'); \n" + full_matlab_command
f.write(full_matlab_command)
f.close()
slurm_command = ' matlab -nodisplay -nosplash -nodesktop -r " makeFigureScript; exit; "'
#slurmCommand = matlab_command + ' "' + full_matlab_command + ' exit;"'
# + makeFig5 + '; ' + makeFig6 + '; exit ;"'
job_name = 'makeFigures'
s = BatchJob(base_output_dir, job_name, '', 4)
#s.setDependency(job_ids)
s.set_custom_command(slurm_command)
# s.write_slurm_file(job_name + '.sh')
s.run_task(job_name + '.sh')
print(Fore.GREEN + 'Submitted make figures job \n' + Fore.RESET)
def test_porous_mushy_hole(argv):
# Defaults:
max_time = 1.5e-4
hole_radius = 0.04
plot_interval = None
try:
opts, _ = getopt.getopt(argv, "t:h:p:")
except getopt.GetoptError as err:
print(str(err))
print('testPorousMushyHole.py -t<max time> -h<hole radius=0.02>')
sys.exit(2)
for opt, arg in opts:
if opt in "-t":
max_time = float(arg)
elif opt in "-h":
hole_radius = float(arg)
elif opt in "-p":
plot_interval = int(arg)
base_output_dir = get_base_output_dir()
matlab_command = get_matlab_base_command()
print(Fore.GREEN + 'Setup tests for porous mushy hole' + Style.RESET_ALL)
physical_problem = 'PorousMushyHole'
min_concentration = -5.0 # default -5
folder_name = 'PorousMushyHole-t%s-minC%s' % (max_time, min_concentration)
data_folder = os.path.join(base_output_dir, folder_name)
amr_setup, num_procs = get_setup()
# Setup up the post processing command
python_compare_file = os.path.join(get_mushy_layer_dir(), 'test', 'run_chombo_compare.py')
chombo_compare_analyse = 'python %s -f %s -a -v Porosity -e L2 -r True -n 8 -d %s \n \n' % (python_compare_file,
data_folder,
base_output_dir)
make_figures = porous_hole_command(folder_name=folder_name)
analysis_command = '%s\n\n%s" %s; exit;"' % (chombo_compare_analyse, matlab_command, make_figures)
# Run
extra_params = {'main.max_time': max_time,
'main.radius': hole_radius,
'bc.bulkConcentrationHiVal': [-1, min_concentration]}
if plot_interval:
extra_params['main.plot_interval'] = plot_interval
run_test(data_folder, physical_problem, porous_mushy_hole_resolution_specific_params, amr_setup, num_procs,
analysis_command, extra_params)
def test_get_base_output_dir(self):
with mock.patch("socket.gethostname", return_value="atmlxmaster"):
self.assertEqual(
util.get_base_output_dir(),
'/network/group/aopp/oceans/AW002_PARKINSON_MUSH/TestDevelopment-19Dec/'
)
with mock.patch("socket.gethostname", return_value="atmlxlap005"):
self.assertEqual(util.get_base_output_dir(),
'/home/parkinsonjl/mushy-layer/test/output/')
with mock.patch("socket.gethostname", return_value="somethingelse"):
with mock.patch.dict('os.environ',
{'MUSHY_LAYER_TEST_PATH': 'testing'}):
self.assertEqual(util.get_base_output_dir(), 'testing')
# Check that with no mushy layer path available we raise an error
with mock.patch.dict('os.environ', {}):
with self.assertRaises(SystemExit) as cm:
util.get_base_output_dir()()
self.assertEqual(cm.exception.code, -1)
def test_uniform_porous_convection(argv):
# Default vals:
cfl = get_default_cfl()
nz_uniform = 64 # don't do uniform mesh simulations by default
nz_vm = 64
chi = 0.4
bc_accuracy = 2
u_del_u_method = 0
advection_method = 1
fixed_da = -1.0
fixed_ra = -1.0
try:
opts, _ = getopt.getopt(argv, "n:v:c:p:b:u:a:d:r:")
except getopt.GetoptError as err:
print(str(err))
print(
'test_uniform_porous_convection.py -n<num uniform mesh grid points> -v<num variable mesh points>'
' -c<cfl> -p <chi> -b <BC accuracy> -u <u del u method> -a <advection method> '
'-d<fixed darcy> -r<fixed Ra>')
sys.exit(2)
for opt, arg in opts:
if opt in "-n":
nz_uniform = int(arg)
elif opt in "-c":
cfl = float(arg)
elif opt in "-v":
nz_vm = int(arg)
elif opt in "-p":
chi = float(arg)
elif opt in "-b":
bc_accuracy = int(arg)
elif opt in "-u":
u_del_u_method = int(arg)
elif opt in "-a":
advection_method = int(arg)
elif opt in "-d":
fixed_da = float(arg)
elif opt in "-r":
fixed_ra = float(arg)
base_output_dir = get_base_output_dir()
matlab_command = get_matlab_base_command()
# Check we have the executables needed to run this test
success = check_exec_exists(
os.path.join(get_mushy_layer_dir(), 'execSubcycle'), 'mushyLayer')
success = success and check_exec_exists(
os.path.join(get_mushy_layer_dir(), 'setupNewRun'), 'setupnewrun')
if not success:
sys.exit(-1)
print(Fore.GREEN +
'Setup tests for convection in a fixed uniform porous medium' +
Style.RESET_ALL)
physical_problem = 'convectionDB'
# Nz_uniform = 128
# if Nz_vm <= 0:
# Nz_vm = Nz_uniform #int(float(Nz_uniform) / 2)
amr_setup = []
if nz_uniform > 0:
amr_setup.append({
'max_level':
0,
'ref_rat':
2,
'run_types': ['uniform'],
'Nzs': [int(nz_uniform / 2), nz_uniform, 2 * nz_uniform]
})
if nz_vm > 0:
these_nzs = [nz_vm, 2 * nz_vm, 4 * nz_vm]
amr_setup.append({
'max_level': 1,
'ref_rat': 2,
'run_types': ['variable'],
'Nzs': these_nzs
})
num_procs = [1, 1, 1]
# chi = 0.4
# Try and speed things up for now, should eventually make this criteria smaller
# extra_params = {'main.steady_state': 1e-4}
extra_params = {
'main.BCAccuracy': bc_accuracy,
'main.uDeluMethod': u_del_u_method,
'main.advectionMethod': advection_method,
'main.cfl': cfl,
'main.initial_cfl': cfl / 10
}
base_data_folder = os.path.join(base_output_dir,
'ConvectionDB-cfl' + str(cfl))
da_ra_vals = [{
'Da': 1e-6,
'RaT': [1e7, 1e8, 1e9],
'lebars': [1.08, 3.07, 12.9]
}, {
'Da': 1e-2,
'RaT': [1e3, 1e4, 1e5, 5e5],
'lebars': [1.01, 1.41, 3.17, 5.24]
}]
if fixed_da > 0.0:
if fixed_ra > 0.0:
da_ra_vals = [{
'Da': fixed_da,
'RaT': [fixed_ra],
'lebars': [float('NaN')]
}]
elif fixed_da == 1e-6:
da_ra_vals = [{
'Da': 1e-6,
'RaT': [1e7, 1e8, 1e9],
'lebars': [1.08, 3.07, 12.9]
}]
elif fixed_da == 1e-2:
da_ra_vals = [{
'Da': 1e-2,
'RaT': [1e3, 1e4, 1e5, 5e5],
'lebars': [1.01, 1.41, 3.17, 5.24]
}]
# [1.01, 1.41, 3.17, 5.24];
# [1.08, 3.07, 12.9];
all_job_ids = []
analysis_command = matlab_command + ' " '
ra_format = "%1.1e"
da_format = "%1.1e"
chi_format = "%1.1f"
chi_str = chi_format % chi
for da_ra in da_ra_vals:
da = da_ra['Da']
da_str = da_format % da
nu_lebars = [str(a) for a in da_ra['lebars']]
# extra_params['main.max_time'] = 0.1 / float(Da)
# extra_params['main.max_dt'] = ?
for ra in da_ra['RaT']:
extra_params['parameters.rayleighTemp'] = ra
extra_params['main.plot_interval'] = -1
extra_params['main.plot_period'] = 0.05
extra_params['main.checkpoint_interval'] = 2000
# this is for testing purposes
# extra_params['main.max_step'] = 10
if chi < 1.0:
extra_params['parameters.darcy'] = da * pow(1 - chi, 2) / pow(
chi, 3.0)
else:
extra_params['parameters.darcy'] = da
extra_params['bc.porosityHiVal'] = str(chi) + ' ' + str(
chi) # 0.4 0.4
extra_params['bc.porosityLoVal'] = str(chi) + ' ' + str(chi)
# output_dir = 'chi' + str(chi) + '-Da' + str(Da) + '-Ra' + str(extra_params['parameters.rayleighTemp'])
ra_str = ra_format % ra
output_dir = "chi" + chi_str + "-Da" + da_str + "-Ra" + ra_str
this_data_folder = os.path.join(base_data_folder, output_dir)
job_ids = run_test(this_data_folder,
physical_problem,
uniform_porous_resolution_specific_params,
amr_setup,
num_procs,
'',
extra_params,
restart_from_low_res=False)
all_job_ids = all_job_ids + job_ids
ra_str_vals = [ra_format % a for a in da_ra['RaT']]
ra_str = '{\'' + '\',\''.join(ra_str_vals) + '\'}'
analysis_command += ' compileNu(\'' + base_data_folder + '\', \'' \
+ chi_str + '\', \'' + da_str + '\', ' + ra_str + ', ' \
+ str(nz_uniform) + ', ' + str(nz_vm) + ', [' + ','.join(nu_lebars) + ']);'
# Now do analysis
analysis_command = analysis_command + ' exit; " '
run_analysis_name = 'runAnalysis.sh'
job_name = physical_problem + '-analysis'
s = BatchJob(base_data_folder, job_name, '')
s.set_dependency(all_job_ids)
s.set_custom_command(analysis_command)
# s.write_slurm_file(run_analysis_name)
s.run_task(run_analysis_name)
print(Fore.GREEN + 'Submitted analysis job \n' + Fore.RESET)
def porous_hole_command(folder_name='PorousMushyHole-t0.00015'):
figure_directory = get_base_output_dir()
porous_mushy_hole_folder = os.path.join(get_base_output_dir(), folder_name)
cmd = 'Fig7PorousHole(\'' + porous_mushy_hole_folder + '\', \'' + figure_directory + '\')'
return cmd
def test_hele_shaw_fixed_chill(argv):
mushy_layer_base_dir = os.path.abspath(os.pardir)
# params_file = mushyLayerBaseDir + '/params/convergenceTest/FixedChill.parameters'
params_file = mushy_layer_base_dir + '/params/convergenceTest/FixedChill.parameters'
# Defaults
default_params = read_inputs(params_file)
extra_params = {
'main.max_time':
float(default_params['main.max_time']),
'parameters.rayleighComp':
float(default_params['parameters.rayleighComp']),
'parameters.darcy':
float(default_params['parameters.darcy']),
'parameters.compositionRatio':
float(default_params['parameters.compositionRatio']),
'parameters.nonDimReluctance':
float(default_params['parameters.nonDimReluctance']),
'parameters.prandtl':
float(default_params['parameters.prandtl'])
}
do_amr = True
# Pr = 10.0 # fix this for now
periodic = False
try:
opts, _ = getopt.getopt(argv, "t:R:D:C:P:N:A")
except getopt.GetoptError as err:
print(str(err))
print(
'testHeleShawFixedChill.py -t<max time> -R<Compositional Rayleigh Number> -D<Darcy number> '
'-C<Composition Ratio> -A<do amr> -P<true(1)/false(0) do plot files> -N<non dimensional reluctance>'
)
sys.exit(2)
for opt, arg in opts:
if opt in "-t":
extra_params['main.max_time'] = float(arg)
elif opt in "-R":
extra_params['parameters.rayleighComp'] = float(arg)
elif opt in "-D":
extra_params['parameters.darcy'] = float(arg)
elif opt in "-C":
extra_params['parameters.compositionRatio'] = float(arg)
elif opt in "-N":
extra_params['parameters.nonDimReluctance'] = float(arg)
elif opt in "-P":
do_plot_files = bool(int(arg))
print('Do plot files: ' + str(do_plot_files) + ', arg = ' +
str(arg))
if not do_plot_files:
extra_params['main.plot_interval'] = -1
elif opt in "-A":
do_amr = True
base_output_dir = get_base_output_dir()
print(Fore.GREEN + 'Setup tests for fixed chill in a Hele-Shaw cell' +
Style.RESET_ALL)
physical_problem = 'FixedChill'
folder_name = "FixedChill-t%1.1e-Ra%.0e-Da%1.1e-C%1.2f-Rel%1.1e" % (
extra_params['main.max_time'], extra_params['parameters.rayleighComp'],
extra_params['parameters.darcy'],
extra_params['parameters.compositionRatio'],
extra_params['parameters.nonDimReluctance'])
if periodic:
folder_name = folder_name + '-periodic'
data_folder = os.path.join(base_output_dir, folder_name)
analysis_command = get_matlab_base_command(
) + ' "%s; exit;"' % fixed_chill_command(folder_name + '-0')
single_run = True
if single_run:
num_proc = 1
default_params['concise_run_name'] = folder_name
default_params = add_params(default_params, extra_params)
# Overwrite default params with any extra params we've specified
default_params = add_params(default_params, extra_params)
allow_restarts = False
s = BatchJob('', default_params['concise_run_name'], '', num_proc)
s.set_post_process(analysis_command)
ml_run = MushyLayerRunSimple(base_output_dir, num_proc, default_params,
s, allow_restarts, get_executable_name())
ml_run.single_run(folder_name)
else:
# Nz_uniform = 256
# Nz_amr_2 = int(float(Nz_uniform) / 2)
# Nz_amr_4 = int(float(Nz_uniform) / 4)
# amr_setup = [{'max_level': 0, 'ref_rat': 1, 'run_types': ['uniform'], 'Nzs': [Nz_uniform]},
# {'max_level': 1, 'ref_rat': 2, 'run_types': ['amr'], 'Nzs': [Nz_amr_2]},
# {'max_level': 2, 'ref_rat': 2, 'run_types': ['amr'], 'Nzs': [Nz_amr_4]},
# {'max_level': 1, 'ref_rat': 4, 'run_types': ['amr'], 'Nzs': [Nz_amr_4]}]
# While testing:
nz_uniform = [64]
# amr_setup = [{'max_level': 0, 'ref_rat': 1, 'run_types': ['uniform'], 'Nzs': Nz_uniform},
# {'max_level': 1, 'ref_rat': 2, 'run_types': ['amr'], 'Nzs': [64]}]
amr_setup = [{
'max_level': 0,
'ref_rat': 1,
'run_types': ['uniform'],
'Nzs': nz_uniform
}]
if do_amr:
amr_setup.append({
'max_level': 1,
'ref_rat': 2,
'run_types': ['amr'],
'Nzs': nz_uniform
})
amr_setup.append({
'max_level': 2,
'ref_rat': 2,
'run_types': ['amr'],
'Nzs': nz_uniform
})
num_procs = [1] # Needs to be as long as the longest Nzs
run_test(data_folder, physical_problem,
hele_shaw_resolution_specific_params, amr_setup, num_procs,
analysis_command, extra_params, 0)
def testPorousMushyHole(argv):
# Defaults:
max_time = 1.5e-4
hole_radius = 0.04
try:
opts, args = getopt.getopt(argv, "t:h:")
except getopt.GetoptError as err:
print(str(err))
print('testPorousMushyHole.py -t<max time> -h<hole radius=0.02>')
sys.exit(2)
for opt, arg in opts:
if opt in "-t":
max_time = float(arg)
elif opt in "-h":
hole_radius = float(arg)
base_output_dir = get_base_output_dir()
matlab_command = get_matlab_base_command()
print(Fore.GREEN + 'Setup tests for porous mushy hole' + Style.RESET_ALL)
physicalProblem = 'PorousMushyHole'
# dataFolder = os.path.join(base_output_dir, 'PorousMushyHole-t' + str(max_time) + '-hole' + str(hole_radius) )
minC = -5.0 # default -5
dataFolder = os.path.join(base_output_dir, 'PorousMushyHole-t%s-minC%s' % (max_time, minC))
Nz_uniform = [16, 32, 64, 128, 256, 512]
AMRSetup = [{'max_level': 0, 'ref_rat': 1, 'run_types': ['uniform'], 'Nzs': Nz_uniform},
{'max_level': 1, 'ref_rat': 2, 'run_types': ['amr'], 'Nzs': [16, 32, 64, 128]},
{'max_level': 2, 'ref_rat': 2, 'run_types': ['amr'], 'Nzs': [8, 16, 32, 64]},
{'max_level': 1, 'ref_rat': 4, 'run_types': ['amr'], 'Nzs': [8, 16, 32, 64]}]
# While testing:
# Nz_uniform = [16, 32, 64]
# AMRSetup = [{'max_level': 0, 'ref_rat': 1, 'run_types': ['uniform'], 'Nzs': Nz_uniform}]
# Nzs = [16, 32, 64]
#num_procs = [1, 1, 1, 4, 4, 4] # Needs to be as long as the longest Nzs
num_procs = [1] * len(Nz_uniform)
# Setup up the post processing command
# figureName = os.path.join(dataFolder, 'noFlow.pdf')
uniform_prefix = 'Uniform-' + physicalProblem + '-'
python_compare_file = os.path.join(get_mushy_layer_dir(), 'test', 'run_chombo_compare.py')
chombo_compare_analyse ='python %s -f %s -a -v Porosity -e L2 -r True -n 8 \n \n' % (python_compare_file, dataFolder)
# make_figures = 'Fig7PorousHole(\'' + dataFolder + '\', \'' + dataFolder + '\')'
make_figures = porous_hole_command()
#analyse_in_matlab = 'analyseVariablePorosityTest(\'' + dataFolder + '\', [' + ','.join([str(a) for a in Nz_uniform]) + '],' \
# 'true, true, \'' + uniform_prefix + '\', \'Porosity\', \'L2\');'
analysis_command = chombo_compare_analyse + '\n\n' + \
matlab_command + ' " %s; exit;"' % make_figures
# Run
extra_params = {'main.max_time':max_time,
'main.radius': hole_radius,
'bc.bulkConcentrationHiVal' : [-1, minC]}
runTest(dataFolder, physicalProblem, porous_mushy_hole_resolution_specific_params,
AMRSetup, num_procs, analysis_command, extra_params)