def main():
parser = ArgumentParser()
parser.add_argument("--version", action="version",
version="%(prog)s " + sfepy.__version__)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=helps['debug'])
parser.add_argument("-o", metavar='filename', action="store",
dest="output_filename_trunk",
default=None, help=helps['filename'])
parser.add_argument('filename_in')
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
filename_in = options.filename_in
required, other = get_standard_keywords()
required.remove('equations')
conf = ProblemConf.from_file(filename_in, required, other)
app = HomogenizationApp(conf, options, 'homogen:')
opts = conf.options
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)
app()
def main():
parser = ArgumentParser(description=__doc__, formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("-v", "--version", action="version", version="%(prog)s " + sfepy.__version__)
parser.add_argument("--print-doc", action="store_true", dest="print_doc", default=False, help=helps["print-doc"])
parser.add_argument(
"-d", "--dir", metavar="directory", action="store", dest="test_dir", default=get_dir("tests"), help=helps["dir"]
)
parser.add_argument(
"-o",
"--output",
metavar="directory",
action="store",
dest="out_dir",
default=get_dir("output-tests"),
help=helps["out_dir"],
)
parser.add_argument(
"--raise", action="store_true", dest="raise_on_error", default=False, help=helps["raise_on_error"]
)
parser.add_argument("--debug", action="store_true", dest="debug", default=False, help=helps["debug"])
parser.add_argument(
"--filter-none", action="store_true", dest="filter_none", default=False, help=helps["filter-none"]
)
parser.add_argument(
"--filter-less", action="store_true", dest="filter_less", default=False, help=helps["filter-less"]
)
parser.add_argument(
"--filter-more", action="store_true", dest="filter_more", default=False, help=helps["filter-more"]
)
parser.add_argument("test_filename", nargs="*", default=[])
options = parser.parse_args()
if options.print_doc:
print(__doc__)
return
if options.debug:
options.raise_on_error = True
from sfepy.base.base import debug_on_error
debug_on_error()
run_tests = wrap_run_tests(options)
stats = [0, 0, 0, 0.0]
if len(options.test_filename) > 0:
for test_filename in options.test_filename:
dirname, filename = op.split(test_filename)
run_tests(stats, dirname, [filename])
else:
for dirpath, dirnames, filenames in os.walk(options.test_dir):
run_tests(stats, dirpath, filenames)
print("%d test file(s) executed in %.2f s, %d failure(s) of %d test(s)" % (stats[0], stats[3], stats[1], stats[2]))
return stats[1]
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version',
version='%(prog)s ' + sfepy.__version__)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=helps['debug'])
parser.add_argument('-o', metavar='filename',
action='store', dest='output_filename_trunk',
default=None, help=helps['filename'])
parser.add_argument('--auto-dir',
action='store_true', dest='auto_dir',
default=False, help=helps['auto_dir'])
parser.add_argument('--same-dir',
action='store_true', dest='same_dir',
default=False, help=helps['same_dir'])
parser.add_argument('-f', '--format', metavar='format',
action='store', dest='output_format',
default='png', help=helps['output_format'])
parser.add_argument('--only-names', metavar='list of names',
action='store', dest='only_names',
default=None, help=helps['only_names'])
parser.add_argument('-s', '--step', type=int, metavar='step',
action='store', dest='step',
default=0, help=helps['step'])
parser.add_argument('-c', '--close-limit', type=float, metavar='distance',
action='store', dest='close_limit',
default=0.1, help=helps['close_limit'])
parser.add_argument('-p', '--postprocess',
action='store_true', dest='postprocess',
default=False, help=helps['postprocess'])
parser.add_argument('--radial',
action='store_true', dest='radial',
default=False, help=helps['radial'])
parser.add_argument('filename_in')
parser.add_argument('filename_out')
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
filename_input = options.filename_in
filename_results = options.filename_out
if options.only_names is not None:
options.only_names = options.only_names.split(',')
output.prefix = 'probe:'
if options.postprocess:
postprocess(filename_input, filename_results, options)
else:
generate_probes(filename_input, filename_results, options)
def main():
parser = ArgumentParser()
parser.add_argument("--version", action="version",
version="%(prog)s " + sfepy.__version__)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=helps['debug'])
parser.add_argument("-o", metavar='filename',
action="store", dest="output_filename_trunk",
default=None, help=helps['filename'])
parser.add_argument("-b", "--band-gaps",
action="store_true", dest="detect_band_gaps",
default=False, help=helps['detect_band_gaps'])
parser.add_argument("-d", "--dispersion",
action="store_true", dest="analyze_dispersion",
default=False, help=helps['analyze_dispersion'])
parser.add_argument("-p", "--plot",
action="store_true", dest="plot",
default=False, help=helps['plot'])
parser.add_argument("--phase-velocity",
action="store_true", dest="phase_velocity",
default=False, help=helps['phase_velocity'])
parser.add_argument("filename_in")
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
if options.plot:
if plt is None:
output('matplotlib.pyplot cannot be imported, ignoring option -p!')
options.plot = False
elif options.analyze_dispersion == False:
options.detect_band_gaps = True
required, other = get_standard_keywords()
required.remove('equations')
if not options.analyze_dispersion:
required.remove('solver_[0-9]+|solvers')
if options.phase_velocity:
required.remove('ebc_[0-9]+|ebcs')
conf = ProblemConf.from_file(options.filename_in, required, other)
app = AcousticBandGapsApp(conf, options, 'phonon:')
opts = conf.options
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)
app()
def main():
# if multi_mpi.cpu_count() < 2:
# raise ValueError('MPI mode - the number of nodes is less then 2!')
if multi_mpi.mpi_rank == multi_mpi.mpi_master:
# MPI master node - solve problem at macro scale
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=helps['debug'])
parser.add_argument('--debug_mpi',
action='store_true', dest='debug_mpi',
default=False, help=helps['debug_mpi'])
parser.add_argument('-c', '--conf', metavar='"key : value, ..."',
action='store', dest='conf', type=str,
default=None, help=helps['conf'])
parser.add_argument('-O', '--options', metavar='"key : value, ..."',
action='store', dest='app_options', type=str,
default=None, help=helps['options'])
parser.add_argument('-d', '--define', metavar='"key : value, ..."',
action='store', dest='define_args', type=str,
default=None, help=helps['define'])
parser.add_argument('-o', metavar='filename',
action='store', dest='output_filename_trunk',
default=None, help=helps['filename'])
parser.add_argument('--format', metavar='format',
action='store', dest='output_format',
default=None, help=helps['output_format'])
parser.add_argument('--log', metavar='file',
action='store', dest='log',
default=None, help=helps['log'])
parser.add_argument('-q', '--quiet',
action='store_true', dest='quiet',
default=False, help=helps['quiet'])
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument('filename_in', nargs='?')
options = parser.parse_args()
for k in ['save_ebc', 'save_ebc_nodes', 'save_regions',
'save_regions_as_groups', 'save_field_meshes', 'solve_not']:
setattr(options, k, False)
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
if options.debug_mpi:
multi_mpi.set_logging_level('debug')
filename_in = options.filename_in
output.set_output(filename=options.log,
quiet=options.quiet,
combined=options.log is not None)
required, other = get_standard_keywords()
conf = ProblemConf.from_file_and_options(filename_in, options,
required, other, define_args=options.define_args)
opts = conf.options
nslaves = multi_mpi.cpu_count() - 1
opts.n_mpi_homog_slaves = nslaves
output_prefix = opts.get('output_prefix', 'sfepy:')
app = PDESolverApp(conf, options, output_prefix)
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)
app()
multi_mpi.master_send_task('finalize', None)
else:
# MPI slave mode - calculate homogenized coefficients
homogen_app = None
done = False
rank = multi_mpi.mpi_rank
while not done:
task, data = multi_mpi.slave_get_task('main slave loop')
if task == 'init': # data: micro_file, n_micro
output.set_output(filename='homog_app_mpi_%d.log' % rank,
quiet=True)
micro_file, n_micro = data[:2]
required, other = get_standard_keywords()
required.remove('equations')
conf = ProblemConf.from_file(micro_file, required, other,
verbose=False)
options = Struct(output_filename_trunk=None)
homogen_app = HomogenizationApp(conf, options, 'micro:',
n_micro=n_micro,
update_micro_coors=True)
elif task == 'calculate': # data: rel_def_grad, ts, iteration
rel_def_grad, ts, iteration = data[:3]
homogen_app.setup_macro_deformation(rel_def_grad)
homogen_app(ret_all=True, itime=ts.step, iiter=iteration)
elif task == 'finalize':
done = True
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version',
version='%(prog)s ' + sfepy.__version__)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=helps['debug'])
parser.add_argument('-c', '--conf', metavar='"key : value, ..."',
action='store', dest='conf', type=str,
default=None, help= helps['conf'])
parser.add_argument('-O', '--options', metavar='"key : value, ..."',
action='store', dest='app_options', type=str,
default=None, help=helps['options'])
parser.add_argument('-o', metavar='filename',
action='store', dest='output_filename_trunk',
default=None, help=helps['filename'])
group = parser.add_mutually_exclusive_group()
group.add_argument('--oscillator',
action='store_true', dest='oscillator',
default=False, help=helps['oscillator'])
group.add_argument('--well',
action='store_true', dest='well',
default=False, help=helps['well'])
group.add_argument('--hydrogen',
action='store_true', dest='hydrogen',
default=False, help=helps['hydrogen'])
group.add_argument('--boron',
action='store_true', dest='boron',
default=False, help=helps['boron'])
parser.add_argument('-n', '--n-eigs', type=int, metavar='int',
action='store', dest='n_eigs',
default=None, help=helps['n_eigs'])
parser.add_argument('-t', '--tau', type=float, metavar='float',
action='store', dest='tau',
default=None, help=helps['tau'])
parser.add_argument('filename_in', nargs='?')
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
filename_in = options.filename_in
if not filename_in:
if options.oscillator:
filename_in = fix_path("examples/quantum/oscillator.py")
elif options.well:
filename_in = fix_path("examples/quantum/well.py")
elif options.hydrogen:
filename_in = fix_path("examples/quantum/hydrogen.py")
elif options.boron:
filename_in = fix_path("examples/quantum/boron.py")
else:
parser.print_help()
return
define_args = {}
if options.n_eigs is not None:
define_args['n_eigs'] = options.n_eigs
if options.tau is not None:
define_args['tau'] = options.tau
required, other = get_standard_keywords()
conf = ProblemConf.from_file_and_options(filename_in, options,
required, other,
define_args=define_args)
app = SchroedingerApp(conf, options, 'schroedinger:')
opts = conf.options
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)
app()
def main():
parser = ArgumentParser(description=__doc__, formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("--version", action="version", version="%(prog)s " + sfepy.__version__)
parser.add_argument("--debug", action="store_true", dest="debug", default=False, help=helps["debug"])
parser.add_argument(
"-o", metavar="filename", action="store", dest="output_filename_trunk", default=None, help=helps["filename"]
)
parser.add_argument("-d", "--dump", action="store_true", dest="dump", default=False, help=helps["dump"])
parser.add_argument("--same-dir", action="store_true", dest="same_dir", default=False, help=helps["same_dir"])
parser.add_argument(
"-l",
"--linearization",
metavar="options",
action="store",
dest="linearization",
default=None,
help=helps["linearization"],
)
parser.add_argument("--times", action="store_true", dest="times", default=False, help=helps["times"])
parser.add_argument(
"-f", "--from", type=int, metavar="ii", action="store", dest="step_from", default=0, help=helps["from"]
)
parser.add_argument(
"-t", "--to", type=int, metavar="ii", action="store", dest="step_to", default=None, help=helps["to"]
)
parser.add_argument(
"-s", "--step", type=int, metavar="ii", action="store", dest="step_by", default=1, help=helps["step"]
)
parser.add_argument(
"-e", "--extract", metavar="list", action="store", dest="extract", default=None, help=helps["extract"]
)
parser.add_argument("-a", "--average", action="store_true", dest="average", default=False, help=helps["average"])
parser.add_argument("input_file", nargs="?", default=None)
parser.add_argument("results_file")
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error
debug_on_error()
filename_in = options.input_file
filename_results = options.results_file
if filename_in is None:
linearize = False
else:
linearize = True
options.dump = True
if options.times:
steps, times, nts, dts = th.extract_times(filename_results)
for ii, time in enumerate(times):
step = steps[ii]
print("%d %e %e %e" % (step, time, nts[ii], dts[ii]))
if options.dump:
trunk = get_default(options.output_filename_trunk, get_trunk(filename_results))
if options.same_dir:
trunk = os.path.join(os.path.dirname(filename_results), os.path.basename(trunk))
args = {}
if linearize:
problem = create_problem(filename_in)
linearization = Struct(kind="adaptive", min_level=0, max_level=2, eps=1e-2)
aux = problem.conf.options.get("linearization", None)
linearization.update(aux)
if options.linearization is not None:
aux = parse_linearization(options.linearization)
linearization.update(aux)
args.update({"fields": problem.fields, "linearization": linearization})
if options.step_to is None:
args.update({"step0": options.step_from})
else:
args.update({"steps": nm.arange(options.step_from, options.step_to + 1, options.step_by, dtype=nm.int)})
th.dump_to_vtk(filename_results, output_filename_trunk=trunk, **args)
if options.extract:
ths, ts = th.extract_time_history(filename_results, options.extract)
if options.average:
ths = th.average_vertex_var_in_cells(ths)
if options.output_filename_trunk:
th.save_time_history(ths, ts, options.output_filename_trunk + ".h5")
else:
print(dict_to_struct(ths, flag=(1, 1, 1)).str_all())
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version',
version='%(prog)s ' + sfepy.__version__)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=helps['debug'])
parser.add_argument('-c', '--conf', metavar='"key : value, ..."',
action='store', dest='conf', type=str,
default=None, help= helps['conf'])
parser.add_argument('-O', '--options', metavar='"key : value, ..."',
action='store', dest='app_options', type=str,
default=None, help=helps['options'])
parser.add_argument('-d', '--define', metavar='"key : value, ..."',
action='store', dest='define_args', type=str,
default=None, help=helps['define'])
parser.add_argument('-o', metavar='filename',
action='store', dest='output_filename_trunk',
default=None, help=helps['filename'])
parser.add_argument('--format', metavar='format',
action='store', dest='output_format',
default=None, help=helps['output_format'])
parser.add_argument('--save-restart', metavar='mode', type=int,
action='store', dest='save_restart',
default=None, help=helps['save_restart'])
parser.add_argument('--load-restart', metavar='filename',
action='store', dest='load_restart',
default=None, help=helps['load_restart'])
parser.add_argument('--log', metavar='file',
action='store', dest='log',
default=None, help=helps['log'])
parser.add_argument('-q', '--quiet',
action='store_true', dest='quiet',
default=False, help=helps['quiet'])
parser.add_argument('--save-ebc',
action='store_true', dest='save_ebc',
default=False, help=helps['save_ebc'])
parser.add_argument('--save-ebc-nodes',
action='store_true', dest='save_ebc_nodes',
default=False, help=helps['save_ebc_nodes'])
parser.add_argument('--save-regions',
action='store_true', dest='save_regions',
default=False, help=helps['save_regions'])
parser.add_argument('--save-regions-as-groups',
action='store_true', dest='save_regions_as_groups',
default=False, help=helps['save_regions_as_groups'])
parser.add_argument('--save-field-meshes',
action='store_true', dest='save_field_meshes',
default=False, help=helps['save_field_meshes'])
parser.add_argument('--solve-not',
action='store_true', dest='solve_not',
default=False, help=helps['solve_not'])
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument('--list', metavar='what',
action='store', dest='_list',
default=None, help=helps['list'])
group.add_argument('filename_in', nargs='?')
options = parser.parse_args()
if options._list is not None:
if options._list == 'terms':
print_terms()
elif options._list == 'solvers':
print_solvers()
return
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
filename_in = options.filename_in
output.set_output(filename=options.log,
quiet=options.quiet,
combined=options.log is not None)
required, other = get_standard_keywords()
if options.solve_not:
required.remove('equations')
required.remove('solver_[0-9]+|solvers')
other.extend(['equations'])
conf = ProblemConf.from_file_and_options(filename_in, options,
required, other,
define_args=options.define_args)
opts = conf.options
output_prefix = opts.get('output_prefix', 'sfepy:')
opts.save_restart = options.save_restart
opts.load_restart = options.load_restart
app = PDESolverApp(conf, options, output_prefix)
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)
app()
def main():
parser = ArgumentParser()
parser.add_argument("--version",
action="version",
version="%(prog)s " + sfepy.__version__)
parser.add_argument('--debug',
action='store_true',
dest='debug',
default=False,
help=help['debug'])
parser.add_argument("-o",
metavar='filename',
action="store",
dest="output_filename_trunk",
default=None,
help=help['filename'])
parser.add_argument("-b",
"--band-gaps",
action="store_true",
dest="detect_band_gaps",
default=False,
help=help['detect_band_gaps'])
parser.add_argument("-d",
"--dispersion",
action="store_true",
dest="analyze_dispersion",
default=False,
help=help['analyze_dispersion'])
parser.add_argument("-p",
"--plot",
action="store_true",
dest="plot",
default=False,
help=help['plot'])
parser.add_argument("--phase-velocity",
action="store_true",
dest="phase_velocity",
default=False,
help=help['phase_velocity'])
parser.add_argument("filename_in")
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error
debug_on_error()
if options.plot:
if plt is None:
output('matplotlib.pyplot cannot be imported, ignoring option -p!')
options.plot = False
elif options.analyze_dispersion == False:
options.detect_band_gaps = True
required, other = get_standard_keywords()
required.remove('equations')
if not options.analyze_dispersion:
required.remove('solver_[0-9]+|solvers')
if options.phase_velocity:
required.remove('ebc_[0-9]+|ebcs')
conf = ProblemConf.from_file(options.filename_in, required, other)
app = AcousticBandGapsApp(conf, options, 'phonon:')
opts = conf.options
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)
app()
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version',
version='%(prog)s ' + sfepy.__version__)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=helps['debug'])
group = parser.add_argument_group('Output Options')
group.add_argument('-o', '--output', metavar='filename',
action='store', dest='filename',
default=None, help=helps['filename'])
group.add_argument('--output-dir', metavar='directory',
action='store', dest='output_dir',
default=None, help=helps['output_dir'])
group.add_argument('-n', '--no-show',
action='store_false', dest='show',
default=True, help=helps['no_show'])
group.add_argument('--no-offscreen',
action='store_false', dest='offscreen',
default=None, help=helps['no_offscreen'])
group.add_argument('-a', '--animation',
metavar='<ffmpeg-supported format>', action='store',
dest='anim_format', default=None,
help=helps['anim_format'])
group.add_argument('--ffmpeg-options', metavar='<ffmpeg options>',
action='store', dest='ffmpeg_options',
default='-r 10 -sameq',
help=helps['ffmpeg_options'])
group = parser.add_argument_group('Data Options')
group.add_argument('--step', type=int, metavar='step',
action='store', dest='step',
default=None, help=helps['step'])
group.add_argument('--time', type=float, metavar='time',
action='store', dest='time',
default=None, help=helps['time'])
group.add_argument('-w', '--watch',
action='store_true', dest='watch',
default=False, help=helps['watch'])
group.add_argument('--all',
action='store_true', dest='all',
default=False, help=helps['all'])
group.add_argument('--only-names', metavar='list of names',
action='store', dest='only_names',
default=None, help=helps['only_names'])
group.add_argument('-l', '--list-ranges',
action='store_true', dest='list_ranges',
default=False, help=helps['list_ranges'])
group.add_argument('--ranges', type=str,
metavar='name1,min1,max1:name2,min2,max2:...',
action=ParseRanges, dest='ranges',
help=helps['ranges'])
group = parser.add_argument_group('View Options')
group.add_argument('-r', '--resolution', type=str, metavar='resolution',
action=ParseResolution, dest='resolution',
help=helps['resolution'])
group.add_argument('--layout', metavar='layout',
action='store', dest='layout',
default='rowcol', help=helps['layout'])
group.add_argument('--3d',
action='store_true', dest='is_3d',
default=False, help=helps['is_3d'])
group.add_argument('--view', type=str,
metavar='angle,angle[,distance[,focal_point]]',
action=ParseView, dest='view',
help=helps['view'])
group.add_argument('--roll', type=float, metavar='angle',
action='store', dest='roll',
default=0.0, help=helps['roll'])
group.add_argument('--parallel-projection',
action='store_true', dest='parallel_projection',
default=False, help=helps['parallel_projection'])
group.add_argument('--fgcolor', metavar='R,G,B',
action='store', dest='fgcolor',
default='0.0,0.0,0.0', help=helps['fgcolor'])
group.add_argument('--bgcolor', metavar='R,G,B',
action='store', dest='bgcolor',
default='1.0,1.0,1.0', help=helps['bgcolor'])
group.add_argument('--colormap', metavar='colormap',
action='store', dest='colormap',
default='blue-red', help=helps['colormap'])
group.add_argument('--anti-aliasing', type=int, metavar='value',
action='store', dest='anti_aliasing',
default=None, help=helps['anti_aliasing'])
group = parser.add_argument_group('Custom Plots Options')
group.add_argument('-b', '--scalar-bar',
action='store_true', dest='is_scalar_bar',
default=False, help=helps['is_scalar_bar'])
group.add_argument('--wireframe',
action='store_true', dest='is_wireframe',
default=False, help=helps['is_wireframe'])
group.add_argument('--group-names', type=str,
metavar='name1,...,nameN:...', action=ParseGroupNames,
dest='group_names', help=helps['group_names'])
group.add_argument('--subdomains', type=str,
metavar='mat_id_name,threshold_limits,single_color',
action=ParseSubdomains, dest='subdomains_args',
default=None,
help=helps['subdomains'])
group.add_argument('-d', '--domain-specific', type=str,
metavar='"var_name0,function_name0,' \
'par0=val0,par1=val1,...:var_name1,..."',
action=ParseDomainSpecific, dest='domain_specific',
default=None,
help=helps['domain_specific'])
group = parser.add_argument_group('Mayavi Options')
group.add_argument('--scalar-mode', metavar='mode',
action='store', dest='scalar_mode',
default='iso_surface', help=helps['scalar_mode'])
group.add_argument('--vector-mode', metavar='mode',
action='store', dest='vector_mode',
default='arrows_norm', help=helps['vector_mode'])
group.add_argument('-s', '--scale-glyphs', type=float, metavar='scale',
action='store', dest='rel_scaling',
default=0.05, help=helps['rel_scaling'])
group.add_argument('--clamping',
action='store_true', dest='clamping',
default=False, help=helps['clamping'])
group.add_argument('--opacity', type=str, metavar='opacity',
action=ParseOpacity, dest='opacity',
help=helps['opacity'])
group.add_argument('--rel-text-width', type=float, metavar='width',
action='store', dest='rel_text_width',
default=0.02, help=helps['rel_text_width'])
parser.add_argument('filenames', nargs='+')
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
filenames = options.filenames
options.fgcolor = tuple([float(ii) for ii in
options.fgcolor.split(',')])
assert_(len(options.fgcolor) == 3)
options.bgcolor = tuple([float(ii) for ii in
options.bgcolor.split(',')])
assert_(len(options.bgcolor) == 3)
can_save = not options.show
# Output dir / file names.
if options.filename is None:
can_save = False
options.filename = 'view.png'
if options.output_dir is None:
options.output_dir = '.'
else:
options.output_dir, options.filename = os.path.split(options.filename)
# Data filtering,
if not options.all:
filter_names = ['node_groups', 'mat_id']
else:
filter_names = []
if options.anim_format is not None:
# Do not call show when saving an animation.
options.show = False
if options.list_ranges:
all_ranges = {}
for ii, filename in enumerate(filenames):
output('%d: %s' % (ii, filename))
file_source = create_file_source(filename)
if (options.step is None) and (options.time is None):
steps, _ = file_source.get_ts_info()
else:
if options.step is not None:
step, _ = file_source.get_step_time(step=options.step)
else:
step, _ = file_source.get_step_time(time=options.time)
steps = [step]
if not len(steps):
steps = [0]
for iis, step in enumerate(steps):
output('%d: step %d' %(iis, step))
file_source.get_step_time(step=step)
source = file_source.create_source()
ranges = get_data_ranges(source, return_only=True)
for key, val in six.iteritems(ranges):
all_ranges.setdefault(key, []).append(val[3:])
if (len(filenames) > 1) or (len(steps) > 1):
output('union of ranges:')
else:
output('ranges:')
for key, ranges in six.iteritems(all_ranges):
aux = nm.array(ranges)
mins = aux[:, [0, 2]].min(axis=0)
maxs = aux[:, [1, 3]].max(axis=0)
output(' items: %s,%e,%e' % (key, mins[0], maxs[0]))
output(' norms: %s,%e,%e' % (key, mins[1], maxs[1]))
else:
if len(filenames) == 1:
filenames = filenames[0]
view = view_file(filenames, filter_names, options)
if can_save:
view.save_image(options.filename)
if options.anim_format is not None:
view.save_animation(options.filename)
view.encode_animation(options.filename, options.anim_format,
options.ffmpeg_options)
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("-v",
"--version",
action="version",
version="%(prog)s " + sfepy.__version__)
parser.add_argument("--print-doc",
action="store_true",
dest="print_doc",
default=False,
help=helps['print-doc'])
parser.add_argument("-d",
"--dir",
metavar='directory',
action="store",
dest="test_dir",
default=get_dir('tests'),
help=helps['dir'])
parser.add_argument("-o",
"--output",
metavar='directory',
action="store",
dest="out_dir",
default=get_dir('output-tests'),
help=helps['out_dir'])
parser.add_argument("--raise",
action="store_true",
dest="raise_on_error",
default=False,
help=helps['raise_on_error'])
parser.add_argument("--debug",
action="store_true",
dest="debug",
default=False,
help=helps['debug'])
parser.add_argument("--filter-none",
action="store_true",
dest="filter_none",
default=False,
help=helps['filter-none'])
parser.add_argument("--filter-less",
action="store_true",
dest="filter_less",
default=False,
help=helps['filter-less'])
parser.add_argument("--filter-more",
action="store_true",
dest="filter_more",
default=False,
help=helps['filter-more'])
parser.add_argument("test_filename", nargs="*", default=[])
options = parser.parse_args()
if options.print_doc:
print(__doc__)
return
if options.debug:
options.raise_on_error = True
from sfepy.base.base import debug_on_error
debug_on_error()
run_tests = wrap_run_tests(options)
stats = [0, 0, 0, 0.0]
if len(options.test_filename) > 0:
for test_filename in options.test_filename:
dirname, filename = op.split(test_filename)
run_tests(stats, dirname, [filename])
else:
for dirpath, dirnames, filenames in os.walk(options.test_dir):
run_tests(stats, dirpath, filenames)
print('%d test file(s) executed in %.2f s, %d failure(s) of %d test(s)' %
(stats[0], stats[3], stats[1], stats[2]))
return stats[1]
def main():
# if multi_mpi.cpu_count() < 2:
# raise ValueError('MPI mode - the number of nodes is less then 2!')
if multi_mpi.mpi_rank == multi_mpi.mpi_master:
# MPI master node - solve problem at macro scale
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--debug',
action='store_true',
dest='debug',
default=False,
help=helps['debug'])
parser.add_argument('--debug_mpi',
action='store_true',
dest='debug_mpi',
default=False,
help=helps['debug_mpi'])
parser.add_argument('-c',
'--conf',
metavar='"key : value, ..."',
action='store',
dest='conf',
type=str,
default=None,
help=helps['conf'])
parser.add_argument('-O',
'--options',
metavar='"key : value, ..."',
action='store',
dest='app_options',
type=str,
default=None,
help=helps['options'])
parser.add_argument('-d',
'--define',
metavar='"key : value, ..."',
action='store',
dest='define_args',
type=str,
default=None,
help=helps['define'])
parser.add_argument('-o',
metavar='filename',
action='store',
dest='output_filename_trunk',
default=None,
help=helps['filename'])
parser.add_argument('--format',
metavar='format',
action='store',
dest='output_format',
default=None,
help=helps['output_format'])
parser.add_argument('--log',
metavar='file',
action='store',
dest='log',
default=None,
help=helps['log'])
parser.add_argument('-q',
'--quiet',
action='store_true',
dest='quiet',
default=False,
help=helps['quiet'])
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument('filename_in', nargs='?')
options = parser.parse_args()
for k in [
'save_ebc', 'save_ebc_nodes', 'save_regions',
'save_regions_as_groups', 'save_field_meshes', 'solve_not'
]:
setattr(options, k, False)
if options.debug:
from sfepy.base.base import debug_on_error
debug_on_error()
if options.debug_mpi:
multi_mpi.set_logging_level('debug')
filename_in = options.filename_in
output.set_output(filename=options.log,
quiet=options.quiet,
combined=options.log is not None)
required, other = get_standard_keywords()
conf = ProblemConf.from_file_and_options(
filename_in,
options,
required,
other,
define_args=options.define_args)
opts = conf.options
nslaves = multi_mpi.cpu_count() - 1
opts.n_mpi_homog_slaves = nslaves
output_prefix = opts.get('output_prefix', 'sfepy:')
app = PDESolverApp(conf, options, output_prefix)
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)
app()
multi_mpi.master_send_task('finalize', None)
else:
# MPI slave mode - calculate homogenized coefficients
homogen_app = None
done = False
rank = multi_mpi.mpi_rank
while not done:
task, data = multi_mpi.slave_get_task('main slave loop')
if task == 'init': # data: micro_file, n_micro
output.set_output(filename='homog_app_mpi_%d.log' % rank,
quiet=True)
micro_file, n_micro = data[:2]
required, other = get_standard_keywords()
required.remove('equations')
conf = ProblemConf.from_file(micro_file,
required,
other,
verbose=False)
options = Struct(output_filename_trunk=None)
homogen_app = HomogenizationApp(conf,
options,
'micro:',
n_micro=n_micro,
update_micro_coors=True)
elif task == 'calculate': # data: rel_def_grad, ts, iteration
rel_def_grad, ts, iteration = data[:3]
homogen_app.setup_macro_deformation(rel_def_grad)
homogen_app(ret_all=True, itime=ts.step, iiter=iteration)
elif task == 'finalize':
done = True
def main():
parser = ArgumentParser()
parser.add_argument("--version", action="version",
version = "%(prog)s " + sfepy.__version__)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=helps['debug'])
parser.add_argument("-s", "--server",
action = "store_true", dest = "server_mode",
default = False, help = helps['server_mode'])
parser.add_argument("-a", "--adjoint",
action = "store_true", dest = "adjoint",
default = False, help = helps['adjoint'])
parser.add_argument("-d", "--direct",
action = "store_true", dest = "direct",
default = False, help = helps['direct'])
parser.add_argument("-t", "--test", type = int, metavar = 'idsg',
action = "store", dest = "test",
default = None, help = helps['test'])
parser.add_argument("--dump", metavar = 'filename',
action = "store", dest = "dump_filename",
default = None, help = helps['dump'])
parser.add_argument("--pert-mesh", metavar = 'filename',
action = "store", dest = "pert_mesh_filename",
default = None, help = helps['pert'])
parser.add_argument("-f", "--full",
action = "store_true", dest = "optimize",
default = False, help = helps['optimize'])
parser.add_argument('filename_in')
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
if options.test is not None:
options.adjoint = options.direct = True
if options.optimize:
options.adjoint = options.direct = False
if (options.direct or options.adjoint or options.optimize):
filename_in = options.filename_in
else:
parser.print_help(),
return
required, other = get_standard_keywords()
required.remove('equations')
if options.adjoint:
required += ['equations_adjoint_.*', 'filename_vp',
'equations_direct_.*']
options.direct = True
elif options.direct:
required += ['equations_direct_.*']
elif options.optimize:
required += ['equations_direct_.*', 'equations_adjoint_.*',
'equations_sensitivity_.*',
'filename_vp']
conf = ProblemConf.from_file( filename_in, required, other )
if options.direct:
dpb, state_dp, data = solve_direct( conf, options )
else:
dpb, state_dp, data = None, None, None
if options.adjoint:
solve_adjoint( conf, options, dpb, state_dp, data )
if options.optimize:
solve_optimize( conf, options )
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version',
action='version',
version='%(prog)s ' + sfepy.__version__)
parser.add_argument('--debug',
action='store_true',
dest='debug',
default=False,
help=help['debug'])
parser.add_argument('-o',
metavar='filename',
action='store',
dest='output_filename_trunk',
default=None,
help=help['filename'])
parser.add_argument('-d',
'--dump',
action='store_true',
dest='dump',
default=False,
help=help['dump'])
parser.add_argument('--same-dir',
action='store_true',
dest='same_dir',
default=False,
help=help['same_dir'])
parser.add_argument('-l',
'--linearization',
metavar='options',
action='store',
dest='linearization',
default=None,
help=help['linearization'])
parser.add_argument('--times',
action='store_true',
dest='times',
default=False,
help=help['times'])
parser.add_argument('-f',
'--from',
type=int,
metavar='ii',
action='store',
dest='step_from',
default=0,
help=help['from'])
parser.add_argument('-t',
'--to',
type=int,
metavar='ii',
action='store',
dest='step_to',
default=None,
help=help['to'])
parser.add_argument('-s',
'--step',
type=int,
metavar='ii',
action='store',
dest='step_by',
default=1,
help=help['step'])
parser.add_argument('-e',
'--extract',
metavar='list',
action='store',
dest='extract',
default=None,
help=help['extract'])
parser.add_argument('-a',
'--average',
action='store_true',
dest='average',
default=False,
help=help['average'])
parser.add_argument('input_file', nargs='?', default=None)
parser.add_argument('results_file')
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error
debug_on_error()
filename_in = options.input_file
filename_results = options.results_file
if filename_in is None:
linearize = False
else:
linearize = True
options.dump = True
if options.times:
steps, times, nts, dts = th.extract_times(filename_results)
for ii, time in enumerate(times):
step = steps[ii]
print('%d %e %e %e' % (step, time, nts[ii], dts[ii]))
if options.dump:
trunk = get_default(options.output_filename_trunk,
get_trunk(filename_results))
if options.same_dir:
trunk = os.path.join(os.path.dirname(filename_results),
os.path.basename(trunk))
args = {}
if linearize:
problem = create_problem(filename_in)
linearization = Struct(kind='adaptive',
min_level=0,
max_level=2,
eps=1e-2)
aux = problem.conf.options.get('linearization', None)
linearization.update(aux)
if options.linearization is not None:
aux = parse_linearization(options.linearization)
linearization.update(aux)
args.update({
'fields': problem.fields,
'linearization': linearization
})
if options.step_to is None:
args.update({'step0': options.step_from})
else:
args.update({
'steps':
nm.arange(options.step_from,
options.step_to + 1,
options.step_by,
dtype=nm.int)
})
th.dump_to_vtk(filename_results, output_filename_trunk=trunk, **args)
if options.extract:
ths, ts = th.extract_time_history(filename_results, options.extract)
if options.average:
ths = th.average_vertex_var_in_cells(ths)
if options.output_filename_trunk:
th.save_time_history(ths, ts,
options.output_filename_trunk + '.h5')
else:
print(dict_to_struct(ths, flag=(1, 1, 1)).str_all())
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version',
version='%(prog)s ' + sfepy.__version__)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=helps['debug'])
parser.add_argument('-c', '--conf', metavar='"key : value, ..."',
action='store', dest='conf', type=str,
default=None, help= helps['conf'])
parser.add_argument('-O', '--options', metavar='"key : value, ..."',
action='store', dest='app_options', type=str,
default=None, help=helps['options'])
parser.add_argument('-d', '--define', metavar='"key : value, ..."',
action='store', dest='define_args', type=str,
default=None, help=helps['define'])
parser.add_argument('-o', metavar='filename',
action='store', dest='output_filename_trunk',
default=None, help=helps['filename'])
parser.add_argument('--format', metavar='format',
action='store', dest='output_format',
default=None, help=helps['output_format'])
parser.add_argument('--save-restart', metavar='mode', type=int,
action='store', dest='save_restart',
default=None, help=helps['save_restart'])
parser.add_argument('--load-restart', metavar='filename',
action='store', dest='load_restart',
default=None, help=helps['load_restart'])
parser.add_argument('--log', metavar='file',
action='store', dest='log',
default=None, help=helps['log'])
parser.add_argument('-q', '--quiet',
action='store_true', dest='quiet',
default=False, help=helps['quiet'])
parser.add_argument('--save-ebc',
action='store_true', dest='save_ebc',
default=False, help=helps['save_ebc'])
parser.add_argument('--save-ebc-nodes',
action='store_true', dest='save_ebc_nodes',
default=False, help=helps['save_ebc_nodes'])
parser.add_argument('--save-regions',
action='store_true', dest='save_regions',
default=False, help=helps['save_regions'])
parser.add_argument('--save-regions-as-groups',
action='store_true', dest='save_regions_as_groups',
default=False, help=helps['save_regions_as_groups'])
parser.add_argument('--save-field-meshes',
action='store_true', dest='save_field_meshes',
default=False, help=helps['save_field_meshes'])
parser.add_argument('--solve-not',
action='store_true', dest='solve_not',
default=False, help=helps['solve_not'])
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument('--list', metavar='what',
action='store', dest='_list',
default=None, help=helps['list'])
group.add_argument('filename_in', nargs='?')
options, petsc_opts = parser.parse_known_args()
if options._list is not None:
if options._list == 'terms':
print_terms()
elif options._list == 'solvers':
print_solvers()
return
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
filename_in = options.filename_in
output.set_output(filename=options.log,
quiet=options.quiet,
combined=options.log is not None)
required, other = get_standard_keywords()
if options.solve_not:
required.remove('equations')
required.remove('solver_[0-9]+|solvers')
other.extend(['equations'])
conf = ProblemConf.from_file_and_options(filename_in, options,
required, other,
define_args=options.define_args)
opts = conf.options
output_prefix = opts.get('output_prefix', 'sfepy:')
opts.save_restart = options.save_restart
opts.load_restart = options.load_restart
app = PDESolverApp(conf, options, output_prefix)
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)
app()
def main():
parser = ArgumentParser(description=__doc__,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument('--version', action='version',
version='%(prog)s ' + sfepy.__version__)
parser.add_argument('--debug',
action='store_true', dest='debug',
default=False, help=help['debug'])
parser.add_argument('-c', '--conf', metavar='"key : value, ..."',
action='store', dest='conf', type=str,
default=None, help= help['conf'])
parser.add_argument('-O', '--options', metavar='"key : value, ..."',
action='store', dest='app_options', type=str,
default=None, help=help['options'])
parser.add_argument('-o', metavar='filename',
action='store', dest='output_filename_trunk',
default=None, help=help['filename'])
group = parser.add_mutually_exclusive_group()
group.add_argument('--oscillator',
action='store_true', dest='oscillator',
default=False, help=help['oscillator'])
group.add_argument('--well',
action='store_true', dest='well',
default=False, help=help['well'])
group.add_argument('--hydrogen',
action='store_true', dest='hydrogen',
default=False, help=help['hydrogen'])
group.add_argument('--boron',
action='store_true', dest='boron',
default=False, help=help['boron'])
parser.add_argument('-n', '--n-eigs', type=int, metavar='int',
action='store', dest='n_eigs',
default=None, help=help['n_eigs'])
parser.add_argument('-t', '--tau', type=float, metavar='float',
action='store', dest='tau',
default=None, help=help['tau'])
parser.add_argument('filename_in', nargs='?')
options = parser.parse_args()
if options.debug:
from sfepy.base.base import debug_on_error; debug_on_error()
filename_in = options.filename_in
if not filename_in:
if options.oscillator:
filename_in = fix_path("examples/quantum/oscillator.py")
elif options.well:
filename_in = fix_path("examples/quantum/well.py")
elif options.hydrogen:
filename_in = fix_path("examples/quantum/hydrogen.py")
elif options.boron:
filename_in = fix_path("examples/quantum/boron.py")
else:
parser.print_help()
return
define_args = {}
if options.n_eigs is not None:
define_args['n_eigs'] = options.n_eigs
if options.tau is not None:
define_args['tau'] = options.tau
required, other = get_standard_keywords()
conf = ProblemConf.from_file_and_options(filename_in, options,
required, other,
define_args=define_args)
app = SchroedingerApp(conf, options, 'schroedinger:')
opts = conf.options
if hasattr(opts, 'parametric_hook'): # Parametric study.
parametric_hook = conf.get_function(opts.parametric_hook)
app.parametrize(parametric_hook)
app()
