def test_DefaultProcess(self):
model = KratosMultiphysics.Model()
model_part = model.CreateModelPart('test')
parent_settings = KratosMultiphysics.Parameters('''
{
"list_of_controllers" : [
{
"model_part_name" : "test"
}
]
}
''')
process = core.Factory(
parent_settings['list_of_controllers'], model)
patcher1 = patch(
'KratosMultiphysics.HDF5Application.core.file_io.KratosHDF5.HDF5FileSerial', autospec=True)
patcher2 = patch(
'KratosMultiphysics.HDF5Application.core.operations.KratosHDF5.HDF5ModelPartIO', autospec=True)
patcher1.start()
MockHDF5ModelPartIO = patcher2.start()
process.ExecuteInitialize()
model_part_io = MockHDF5ModelPartIO.return_value
model_part_io.WriteModelPart.assert_called_once_with(model_part)
patcher1.stop()
patcher2.stop()
def test_DefaultSettings(self):
model = KratosMultiphysics.Model()
model.CreateModelPart('test')
parent_settings = KratosMultiphysics.Parameters('''
{
"list_of_controllers" : [
{
"model_part_name" : "test"
}
]
}
''')
parent_settings = ParametersWrapper(parent_settings)
core.Factory(parent_settings['list_of_controllers'], model)
settings = parent_settings['list_of_controllers'][0]
self.assertTrue(settings.Has('model_part_name'))
self.assertTrue(settings.Has('process_step'))
self.assertTrue(settings.Has('controller_settings'))
self.assertTrue(settings.Has('io_settings'))
self.assertTrue(settings.Has('list_of_operations'))
self.assertTrue(settings['list_of_operations'].IsArray())
self.assertEqual(settings['list_of_operations'].size(), 1)
self.assertTrue(
settings['list_of_operations'][0].Has('operation_type'))
self.assertTrue(settings['list_of_operations'][0].Has('prefix'))
def test_EmptyArraySettings(self):
model = KratosMultiphysics.Model()
settings = KratosMultiphysics.Parameters('''
{
"list_of_controllers" : []
}
''')
with self.assertRaisesRegex(RuntimeError, '"PLEASE_SPECIFY_MODEL_PART_NAME" was not found'):
core.Factory(settings['list_of_controllers'], model)
def Factory(process_settings, Model):
"""Return a process to read a transient solution from HDF5."""
default_settings = KratosMultiphysics.Parameters("""
{
"model_part_name" : "MainModelPart",
"file_settings" : {},
"nodal_solution_step_data_settings" : {},
"nodal_data_value_settings": {},
"element_data_value_settings" : {}
}
""")
new_settings = KratosMultiphysics.Parameters('''
{
"list_of_controllers": [{
"model_part_name" : "",
"process_step": "initialize_solution_step",
"io_settings": {
"io_type": "serial_hdf5_file_io",
"file_name": "<identifier>-<time>.h5",
"file_access_mode": "read_only"
},
"list_of_operations": [{
"operation_type": "nodal_solution_step_data_input"
},{
"operation_type": "nodal_data_value_input"
},{
"operation_type": "element_data_value_input"
}]
}]
}
''')
settings = process_settings["Parameters"]
if settings.Has('file_name'):
_utils.CheckForDeprecatedFilename(
settings, __name__,
new_settings["list_of_controllers"][0]["io_settings"])
settings.RemoveValue('file_name')
if settings.Has('time_tag_precision'):
depr_msg = '\nDEPRECATION-WARNING: "time_tag_precision" is ignored, please use "time_format" in "file_settings"!\n'
KratosMultiphysics.Logger.PrintWarning(__name__, depr_msg)
settings.RemoveValue('time_tag_precision')
settings.ValidateAndAssignDefaults(default_settings)
model_part_name = settings["model_part_name"].GetString()
results_settings = new_settings["list_of_controllers"][0]
results_settings["model_part_name"].SetString(model_part_name)
_utils.InsertSettings(settings["file_settings"],
results_settings["io_settings"])
if _utils.IsDistributed():
results_settings["io_settings"]["io_type"].SetString(
"parallel_hdf5_file_io")
_utils.InsertArrayOfSettings([
settings["nodal_solution_step_data_settings"],
settings["nodal_data_value_settings"],
settings["element_data_value_settings"]
], results_settings["list_of_operations"])
return _core.Factory(new_settings["list_of_controllers"], Model)
def Factory(process_settings, Model):
"""Return a process for initializing a model part from an existing HDF5 output file."""
default_settings = KratosMultiphysics.Parameters("""
{
"model_part_name" : "MainModelPart",
"file_settings" : {},
"nodal_solution_step_data_settings" : {},
"nodal_data_value_settings": {},
"element_data_value_settings" : {}
}
""")
settings = process_settings["Parameters"]
settings.ValidateAndAssignDefaults(default_settings)
new_settings = KratosMultiphysics.Parameters('''
{
"list_of_controllers": [{
"model_part_name" : "",
"process_step": "initialize",
"io_settings": {
"io_type": "serial_hdf5_file_io",
"file_name": "<identifier>.h5",
"file_access_mode": "read_only"
},
"list_of_operations": [{
"operation_type": "nodal_solution_step_data_input"
},{
"operation_type": "nodal_data_value_input"
},{
"operation_type": "element_data_value_input"
}]
}]
}
''')
model_part_name = settings["model_part_name"].GetString()
new_settings["list_of_controllers"][0]["model_part_name"].SetString(
model_part_name)
results_settings = new_settings["list_of_controllers"][0]
_utils.InsertSettings(settings["file_settings"],
results_settings["io_settings"])
if _utils.IsDistributed():
results_settings["io_settings"]["io_type"].SetString(
"parallel_hdf5_file_io")
_utils.InsertArrayOfSettings([
settings["nodal_solution_step_data_settings"],
settings["nodal_data_value_settings"],
settings["element_data_value_settings"]
], results_settings["list_of_operations"])
return _core.Factory(new_settings["list_of_controllers"], Model)
def SingleMeshTemporalOutputProcessFactory(core_settings, Model):
return core.Factory(core_settings, Model)
def SingleMeshXdmfOutputProcessFactory(core_settings, Model):
return core.Factory(core_settings, Model)
def test_NonArraySettings(self):
model = KratosMultiphysics.Model()
settings = KratosMultiphysics.Parameters()
with self.assertRaisesRegex(ValueError, r'Expected settings as an array'):
core.Factory(settings, model)
def InitializationFromHDF5ProcessFactory(core_settings, Model):
return core.Factory(core_settings, Model)
def Factory(process_settings, Model):
"""Return a process for writing simulation results for a single mesh to HDF5.
It also creates the xdmf-file on the fly
"""
if not isinstance(process_settings, KratosMultiphysics.Parameters):
raise Exception(
"expected input shall be a Parameters object, encapsulating a json string"
)
default_settings = KratosMultiphysics.Parameters("""
{
"model_part_name" : "MainModelPart",
"file_settings" : {},
"model_part_output_settings" : {},
"nodal_solution_step_data_settings" : {},
"nodal_data_value_settings": {},
"element_data_value_settings" : {},
"output_time_settings" : {}
}
""")
settings = process_settings["Parameters"]
settings.ValidateAndAssignDefaults(default_settings)
new_settings = KratosMultiphysics.Parameters('''
{
"list_of_controllers": [{
"model_part_name" : "",
"process_step": "initialize",
"io_settings": {
"io_type": "mock_hdf5_file_io",
"file_name": "<identifier>.h5"
},
"list_of_operations": [{
"module_name": "operations.system",
"operation_type": "delete_old_h5_files"
}]
},{
"model_part_name" : "",
"process_step": "before_solution_loop",
"io_settings": {
"io_type": "serial_hdf5_file_io",
"file_name": "<identifier>.h5",
"file_access_mode": "truncate"
},
"list_of_operations": [{
"operation_type": "model_part_output"
},{
"operation_type": "nodal_solution_step_data_output"
},{
"operation_type": "nodal_data_value_output"
},{
"operation_type": "element_data_value_output"
}]
},{
"model_part_name" : "",
"process_step": "finalize_solution_step",
"controller_settings": {
"controller_type": "temporal_controller"
},
"io_settings": {
"io_type": "serial_hdf5_file_io",
"file_name": "<identifier>-<time>.h5",
"file_access_mode": "truncate"
},
"list_of_operations": [{
"operation_type": "nodal_solution_step_data_output"
},{
"operation_type": "nodal_data_value_output"
},{
"operation_type": "element_data_value_output"
}]
},{
"model_part_name" : "",
"process_step": "finalize_solution_step",
"controller_settings": {
"controller_type": "temporal_controller"
},
"io_settings": {
"io_type": "mock_hdf5_file_io",
"file_name": "<identifier>.h5"
},
"list_of_operations": [{
"module_name": "operations.xdmf",
"operation_type": "xdmf_output"
}]
}]
}
''')
model_part_name = settings["model_part_name"].GetString()
for current_settings in new_settings["list_of_controllers"]:
current_settings["model_part_name"].SetString(model_part_name)
model_part_settings = new_settings["list_of_controllers"][1]
results_settings = new_settings["list_of_controllers"][2]
for io_settings in [
model_part_settings["io_settings"], results_settings["io_settings"]
]:
_utils.InsertSettings(settings["file_settings"], io_settings)
if _utils.IsDistributed():
io_settings["io_type"].SetString("parallel_hdf5_file_io")
_utils.InsertArrayOfSettings([
settings["model_part_output_settings"],
settings["nodal_solution_step_data_settings"],
settings["nodal_data_value_settings"],
settings["element_data_value_settings"]
], model_part_settings["list_of_operations"])
_utils.InsertArrayOfSettings([
settings["nodal_solution_step_data_settings"],
settings["nodal_data_value_settings"],
settings["element_data_value_settings"]
], results_settings["list_of_operations"])
output_time_settings = settings["output_time_settings"]
_utils.InsertSettings(output_time_settings,
results_settings["controller_settings"])
_utils.CheckForDeprecatedFilename(output_time_settings, __name__,
model_part_settings["io_settings"],
results_settings["io_settings"])
_utils.CheckForDeprecatedTemporalSettings(
output_time_settings, __name__,
results_settings["controller_settings"])
return _core.Factory(new_settings["list_of_controllers"], Model)
def Factory(process_settings, Model):
"""Return a process for writing simulation results for multiple meshes to HDF5."""
default_settings = KratosMultiphysics.Parameters("""
{
"model_part_name" : "MainModelPart",
"file_settings" : {},
"model_part_output_settings" : {},
"nodal_solution_step_data_settings" : {},
"nodal_data_value_settings": {},
"element_data_value_settings" : {},
"output_time_settings" : {}
}
""")
settings = process_settings["Parameters"]
settings.ValidateAndAssignDefaults(default_settings)
new_settings = KratosMultiphysics.Parameters('''
{
"list_of_controllers": [{
"model_part_name" : "",
"process_step": "before_solution_loop",
"io_settings": {
"io_type": "serial_hdf5_file_io",
"file_name": "<identifier>-<time>.h5"
},
"list_of_operations": [{
"operation_type": "model_part_output"
},{
"operation_type": "nodal_solution_step_data_output"
},{
"operation_type": "nodal_data_value_output"
},{
"operation_type": "element_data_value_output"
}]
},{
"model_part_name" : "",
"process_step": "finalize_solution_step",
"controller_settings": {
"controller_type": "temporal_controller"
},
"io_settings": {
"io_type": "serial_hdf5_file_io",
"file_name": "<identifier>-<time>.h5"
},
"list_of_operations": [{
"operation_type": "model_part_output"
},{
"operation_type": "nodal_solution_step_data_output"
},{
"operation_type": "nodal_data_value_output"
},{
"operation_type": "element_data_value_output"
}]
}]
}
''')
model_part_name = settings["model_part_name"].GetString()
for current_settings in new_settings["list_of_controllers"]:
current_settings["model_part_name"].SetString(model_part_name)
model_part_settings = new_settings["list_of_controllers"][0]
results_settings = new_settings["list_of_controllers"][1]
for io_settings in [
model_part_settings["io_settings"], results_settings["io_settings"]
]:
_utils.InsertSettings(settings["file_settings"], io_settings)
if _utils.IsDistributed():
io_settings["io_type"].SetString("parallel_hdf5_file_io")
list_of_operations_settings = [
settings["model_part_output_settings"],
settings["nodal_solution_step_data_settings"],
settings["nodal_data_value_settings"],
settings["element_data_value_settings"]
]
_utils.InsertArrayOfSettings(list_of_operations_settings,
model_part_settings["list_of_operations"])
_utils.InsertArrayOfSettings(list_of_operations_settings,
results_settings["list_of_operations"])
output_time_settings = settings["output_time_settings"]
_utils.InsertSettings(output_time_settings,
results_settings["controller_settings"])
_utils.CheckForDeprecatedFilename(output_time_settings, __name__,
model_part_settings["io_settings"],
results_settings["io_settings"])
_utils.CheckForDeprecatedTemporalSettings(
output_time_settings, __name__,
results_settings["controller_settings"])
return _core.Factory(new_settings["list_of_controllers"], Model)
def Factory(settings, Model):
"""Return a user-defined input/output process for HDF5.
The input settings are a json array of parameters which maps to the
structure of the HDF5 IO python core.
The settings of each array item are given in the following table:
+-----------------------+------------+-------------------------------------------+
| Setting | Type | Default Value |
+-----------------------+------------+-------------------------------------------+
| "model_part_name" | String | "PLEASE_SPECIFY_MODEL_PART_NAME" |
+-----------------------+------------+-------------------------------------------+
| "process_step" | String | "initialize" |
+-----------------------+------------+-------------------------------------------+
| "controller_settings" | Parameters | { |
| | | "controller_type": "default_controller" |
| | | } |
+-----------------------+------------+-------------------------------------------+
| "io_settings" | Parameters | "echo_level": 0 |
| | | "file_access_mode": "exclusive" |
| | | "file_driver": "sec2" |
| | | "file_name": "kratos" |
| | | "max_files_to_keep": "unlimited" |
| | | "io_type": "serial_hdf5_file_io" |
+-----------------------+------------+-------------------------------------------+
| "list_of_operations" | Parameters | [{ |
| | Array | "operation_type": "model_part_output" |
| | | "prefix": "/ModelData" |
| | | }] |
+-----------------------+------------+-------------------------------------------+
For example:
'''
[{
"model_part_name" : "MainModelPart",
"process_step": "finalize_solution_step",
"controller_settings": {
"controller_type": "temporal_controller",
"time_frequency": 0.5
},
"io_settings": {
"file_name": "results/<model_part_name>-<time>.h5"
},
"list_of_operations": [{
"operation_type": "model_part_output"
},{
"operation_type": "nodal_solution_step_data_output",
"list_of_variables": ["DISPLACEMENT"]
}]
}]
'''
will store the model part and displacement every 0.5s in the following
directory tree structure:
./results/MainModelPart-0.000.h5
./results/MainModelPart-0.500.h5
./results/MainModelPart-1.000.h5
...
and internal file tree structure in each .h5 file:
/ModelData/Conditions
/ModelData/Elements
...
/ResultsData/NodalSolutionStepData/DISPLACEMENT
In the above example, the nonterminal symbols <model_part_name> and <time>
are automatically replaced by the name of the model part and the current
time.
Alternatively, the simulations results can be stored in a single .h5 file
containing the directory tree structure of the above example:
'''
[{
"model_part_name" : "MainModelPart",
"process_step": "finalize_solution_step",
"controller_settings": {
"controller_type": "temporal_controller",
"time_frequency": 0.5
},
"io_settings": {
"file_name": "results.h5",
"file_access_mode": "read_write"
},
"list_of_operations": [{
"prefix": "/<time>/<model_part_name>/ModelData",
"operation_type": "model_part_output"
},{
"prefix": "/<time>/<model_part_name>/ResultsData",
"operation_type": "nodal_solution_step_data_output",
"list_of_variables": ["DISPLACEMENT"]
}]
}]
'''
will store the model part and displacement every 0.5s in the following
directory tree structure:
./results.h5
and internal file tree structure in each .h5 file:
/0.000/MainModelPart/ModelData/...
/0.000/MainModelPart/ResultsData/...
...
/0.500/MainModelPart/ModelData/...
/0.500/MainModelPart/ResultsData/...
...
/1.000/MainModelPart/ModelData/...
/1.000/MainModelPart/ResultsData/...
Different groupings of model parts, files, locations within the solution
algorithm, frequencies and IO operations can be configured by appending
additional parameters to the json array.
"""
return core.Factory(ParametersWrapper(settings["Parameters"]), Model)
def Factory(process_settings, Model):
"""Return a process for writing Bossak primal results for a single mesh to HDF5."""
default_settings = KratosMultiphysics.Parameters("""
{
"model_part_name" : "MainModelPart",
"file_settings" : {},
"model_part_output_settings" : {},
"nodal_solution_step_data_settings" : {},
"nodal_data_value_settings": {},
"element_data_value_settings" : {},
"output_time_settings" : {}
}
""")
settings = process_settings["Parameters"]
if settings.Has("alpha_bossak"):
depr_msg = '\nDEPRECATION-WARNING: "alpha_bossak" should be specified in "nodal_solution_step_data_settings". This will be removed in the future!\n'
KratosMultiphysics.Logger.PrintWarning(__name__, depr_msg)
_utils.InsertSingleSetting(
settings["nodal_solution_step_data_settings"], "alpha_bossak", settings["alpha_bossak"])
settings.RemoveValue("alpha_bossak")
settings.ValidateAndAssignDefaults(default_settings)
new_settings = KratosMultiphysics.Parameters('''
{
"list_of_controllers": [{
"model_part_name" : "",
"process_step": "before_solution_loop",
"io_settings": {
"io_type": "serial_hdf5_file_io",
"file_name": "<identifier>.h5"
},
"list_of_operations": [{
"operation_type": "model_part_output"
},{
"operation_type": "primal_bossak_output"
},{
"operation_type": "nodal_data_value_output"
},{
"operation_type": "element_data_value_output"
}]
},{
"model_part_name" : "",
"process_step": "finalize_solution_step",
"controller_settings": {
"controller_type": "temporal_controller"
},
"io_settings": {
"io_type": "serial_hdf5_file_io",
"file_name": "<identifier>-<time>.h5"
},
"list_of_operations": [{
"operation_type": "primal_bossak_output"
},{
"operation_type": "nodal_data_value_output"
},{
"operation_type": "element_data_value_output"
}]
}]
}
''')
model_part_name = settings["model_part_name"].GetString()
for current_settings in new_settings["list_of_controllers"]:
current_settings["model_part_name"].SetString(model_part_name)
model_part_settings = new_settings["list_of_controllers"][0]
results_settings = new_settings["list_of_controllers"][1]
for io_settings in [model_part_settings["io_settings"], results_settings["io_settings"]]:
_utils.InsertSettings(settings["file_settings"], io_settings)
if _utils.IsDistributed():
io_settings["io_type"].SetString("parallel_hdf5_file_io")
_utils.InsertArrayOfSettings(
[settings["model_part_output_settings"], settings["nodal_solution_step_data_settings"], settings["nodal_data_value_settings"],
settings["element_data_value_settings"]], model_part_settings["list_of_operations"])
_utils.InsertArrayOfSettings([settings["nodal_solution_step_data_settings"], settings["nodal_data_value_settings"],
settings["element_data_value_settings"]], results_settings["list_of_operations"])
output_time_settings = settings["output_time_settings"]
_utils.InsertSettings(output_time_settings,
results_settings["controller_settings"])
_utils.CheckForDeprecatedFilename(
output_time_settings, __name__, model_part_settings["io_settings"], results_settings["io_settings"])
_utils.CheckForDeprecatedTemporalSettings(
output_time_settings, __name__, results_settings["controller_settings"])
return _core.Factory(new_settings["list_of_controllers"], Model)
def Factory(process_settings, Model):
"""Construct a user-defined input/output process for HDF5."""
return _core.Factory(process_settings["Parameters"], Model)
