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IshaanDesaiIshaanDesai
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Conform to naming standard in precice/tutorials (#215)
* Conform to naming standard in precice/tutorials for quantities relevant to adaptivity * Conform to naming standard in the dummy * Conform to data naming nomenclature in all configs and code * Try to fix HDF5 test * Fix tests * Fix snapshot tests
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‎CHANGELOG.md‎

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## latest
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- Conformed to naming standard in precice/tutorials [#215](https://github.com/precice/micro-manager/pull/215)
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- Changed default values of adaptivity metrics output and similarity distance calculation norm [#213](https://github.com/precice/micro-manager/pull/213)
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- Fixed ordering of global IDs of micro simulation for load balancing to ensure consistency [#210](https://github.com/precice/micro-manager/pull/210)
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- Initiated triggering of load balancing at the start of the simulation when adaptivity is triggered [#207](https://github.com/precice/micro-manager/pull/207)

‎docs/configuration.md‎

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### Adding adaptivity in the preCICE XML configuration
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If adaptivity is used, the Micro Manager will attempt to write two scalar data per micro simulation to preCICE, called `active_state` and `active_steps`.
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If adaptivity is used, the Micro Manager will attempt to write two scalar data per micro simulation to preCICE, called `Active-State` and `Active-Steps`.
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- `active_state` is `1` if the micro simulation is active in the time window, and `0` if inactive.
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- `active_steps` is summation of `active_state` up to the current time window.
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- `Active-State` is `1` if the micro simulation is active in the time window, and `0` if inactive.
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- `Active-Steps` is summation of `Active-State` up to the current time window.
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The Micro Manager uses the output functionality of preCICE, hence these data sets need to be manually added to the preCICE configuration file. In the mesh and the participant Micro-Manager add the following lines:
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```xml
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<data:scalar name="active_state"/>
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<data:scalar name="active_steps"/>
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<data:scalar name="Active-State"/>
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<data:scalar name="Active-Steps"/>
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<mesh name="macro-mesh">
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<use-data name="active_state"/>
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<use-data name="active_steps"/>
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<use-data name="Active-State"/>
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<use-data name="Active-Steps"/>
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</mesh>
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<participant name="Micro-Manager">
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<write-data name="active_state" mesh="macro-mesh"/>
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<write-data name="active_steps" mesh="macro-mesh"/>
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<write-data name="Active-State" mesh="macro-mesh"/>
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<write-data name="Active-Steps" mesh="macro-mesh"/>
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</participant>
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```
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‎examples/cpp-dummy/micro_cpp_dummy.cpp‎

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{
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//! Code below shows how to convert input macro data and use it in your C++ solver
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// Create a double from macro_data["micro_scalar_data"], which is a Python float
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double macro_scalar_data = macro_data["macro-scalar-data"].cast<double>();
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// Create a double from macro_data["Macro-Scalar"], which is a Python float
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double macro_scalar_data = macro_data["Macro-Scalar"].cast<double>();
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// Create a pybind style Numpy array from macro_write_data["micro_vector_data"], which is a Numpy array
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py::array_t<double> macro_vector_data = macro_data["macro-vector-data"].cast<py::array_t<double>>();
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// Create a pybind style Numpy array from macro_write_data["Macro-Vector"], which is a Numpy array
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py::array_t<double> macro_vector_data = macro_data["Macro-Vector"].cast<py::array_t<double>>();
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_micro_vector_data = std::vector<double>(macro_vector_data.data(), macro_vector_data.data() + macro_vector_data.size()); // convert numpy array to std::vector.
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// Change data
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py::dict micro_write_data;
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// add micro_scalar_data and micro_vector_data to micro_write_data
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micro_write_data["micro-scalar-data"] = _micro_scalar_data;
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micro_write_data["micro-vector-data"] = _micro_vector_data; // numpy array is automatically converted to python list
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micro_write_data["Micro-Scalar"] = _micro_scalar_data;
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micro_write_data["Micro-Vector"] = _micro_vector_data; // numpy array is automatically converted to python list
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return micro_write_data;
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}

‎examples/macro_dummy.py‎

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# preCICE setup
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if args.adaptivity == "no_adaptivity":
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interface = precice.Participant("Macro-dummy", "precice-config.xml", 0, 1)
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interface = precice.Participant("Macro-Dummy", "precice-config.xml", 0, 1)
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elif args.adaptivity == "adaptivity":
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interface = precice.Participant(
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"Macro-dummy", "precice-config-adaptivity.xml", 0, 1
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"Macro-Dummy", "precice-config-adaptivity.xml", 0, 1
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)
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else:
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raise ValueError("Unknown adaptivity setting")
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# define coupling meshes
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read_mesh_name = write_mesh_name = "macro-mesh"
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read_data_names = {"micro-scalar-data": 0, "micro-vector-data": 1}
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read_mesh_name = write_mesh_name = "Macro-Mesh"
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read_data_names = {"Micro-Scalar": 0, "Micro-Vector": 1}
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write_data_names = {"macro-scalar-data": 0, "macro-vector-data": 1}
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write_data_names = {"Macro-Scalar": 0, "Macro-Vector": 1}
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# Coupling mesh
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coords = np.zeros((nv, interface.get_mesh_dimensions(write_mesh_name)))
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write_scalar_data = np.zeros(nv)
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write_vector_data = np.zeros(
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(nv, interface.get_data_dimensions(write_mesh_name, "macro-vector-data"))
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(nv, interface.get_data_dimensions(write_mesh_name, "Macro-Vector"))
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)
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for i in range(nv):
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write_scalar_data[i] = i
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for d in range(
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interface.get_data_dimensions(write_mesh_name, "macro-vector-data")
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):
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for d in range(interface.get_data_dimensions(write_mesh_name, "Macro-Vector")):
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write_vector_data[i, d] = i
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if interface.requires_initial_data():
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write_scalar_data[:] = read_scalar_data[:]
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for i in range(nv):
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for d in range(
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interface.get_data_dimensions(read_mesh_name, "micro-vector-data")
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interface.get_data_dimensions(read_mesh_name, "Micro-Vector")
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):
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write_vector_data[i, d] = read_vector_data[i, d]
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if t > 1: # to trigger adaptivity after some time

‎examples/micro-manager-cpp-adaptivity-config.json‎

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"micro_file_name": "cpp-dummy/micro_dummy",
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"coupling_params": {
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"precice_config_file_name": "precice-config-adaptivity.xml",
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"macro_mesh_name": "macro-mesh",
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"read_data_names": ["macro-scalar-data", "macro-vector-data"],
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"write_data_names": ["micro-scalar-data", "micro-vector-data"]
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"macro_mesh_name": "Macro-Mesh",
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"read_data_names": ["Macro-Scalar", "Macro-Vector"],
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"write_data_names": ["Micro-Scalar", "Micro-Vector"]
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},
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"simulation_params": {
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"micro_dt": 1.0,
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"macro_domain_bounds": [0.0, 25.0, 0.0, 25.0, 0.0, 25.0],
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"adaptivity": true,
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"adaptivity_settings": {
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"type": "local",
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"data": ["macro-scalar-data", "macro-vector-data"],
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"data": ["Macro-Scalar", "Macro-Vector"],
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"history_param": 0.5,
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"coarsening_constant": 0.3,
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"refining_constant": 0.4,

‎examples/micro-manager-cpp-config.json‎

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"micro_file_name": "cpp-dummy/micro_dummy",
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"coupling_params": {
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"precice_config_file_name": "precice-config.xml",
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"macro_mesh_name": "macro-mesh",
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"read_data_names": ["macro-scalar-data", "macro-vector-data"],
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"write_data_names": ["micro-scalar-data", "micro-vector-data"]
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"macro_mesh_name": "Macro-Mesh",
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"read_data_names": ["Macro-Scalar", "Macro-Vector"],
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"write_data_names": ["Micro-Scalar", "Micro-Vector"]
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},
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"simulation_params": {
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"micro_dt": 1.0,

‎examples/micro-manager-python-adaptivity-config.json‎

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"micro_file_name": "python-dummy/micro_dummy",
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"coupling_params": {
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"precice_config_file_name": "precice-config-adaptivity.xml",
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"macro_mesh_name": "macro-mesh",
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"read_data_names": ["macro-scalar-data", "macro-vector-data"],
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"write_data_names": ["micro-scalar-data", "micro-vector-data"]
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"macro_mesh_name": "Macro-Mesh",
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"read_data_names": ["Macro-Scalar", "Macro-Vector"],
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"write_data_names": ["Micro-Scalar", "Micro-Vector"]
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},
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"simulation_params": {
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"micro_dt": 1.0,
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"macro_domain_bounds": [0.0, 25.0, 0.0, 25.0, 0.0, 25.0],
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"adaptivity": true,
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"adaptivity_settings": {
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"type": "local",
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"data": ["macro-scalar-data", "macro-vector-data"],
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"data": ["Macro-Scalar", "Macro-Vector"],
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"history_param": 0.5,
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"coarsening_constant": 0.3,
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"refining_constant": 0.4,

‎examples/micro-manager-python-config.json‎

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"micro_file_name": "python-dummy/micro_dummy",
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"coupling_params": {
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"precice_config_file_name": "precice-config.xml",
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"macro_mesh_name": "macro-mesh",
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"read_data_names": ["macro-scalar-data", "macro-vector-data"],
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"write_data_names": ["micro-scalar-data", "micro-vector-data"]
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"macro_mesh_name": "Macro-Mesh",
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"read_data_names": ["Macro-Scalar", "Macro-Vector"],
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"write_data_names": ["Micro-Scalar", "Micro-Vector"]
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},
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"simulation_params": {
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"micro_dt": 1.0,

‎examples/micro-manager-python-mada-config.json‎

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"micro_file_name": "python-dummy/micro_dummy",
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"coupling_params": {
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"precice_config_file_name": "precice-config.xml",
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"macro_mesh_name": "macro-mesh",
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"read_data_names": ["macro-scalar-data", "macro-vector-data"],
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"write_data_names": ["micro-scalar-data", "micro-vector-data"]
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"macro_mesh_name": "Macro-Mesh",
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"read_data_names": ["Macro-Scalar", "Macro-Vector"],
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"write_data_names": ["Micro-Scalar", "Micro-Vector"]
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},
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"simulation_params": {
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"micro_dt": 1.0,

‎examples/precice-config-adaptivity.xml‎

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<sink type="stream" output="stdout" filter= "%Severity% > debug" enabled="true" />
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</log>
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<data:scalar name="macro-scalar-data"/>
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<data:vector name="macro-vector-data"/>
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<data:scalar name="micro-scalar-data"/>
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<data:vector name="micro-vector-data"/>
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<data:scalar name="active_state"/>
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<data:scalar name="active_steps"/>
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<mesh name="macro-mesh" dimensions="3">
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<use-data name="macro-scalar-data"/>
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<use-data name="macro-vector-data"/>
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<use-data name="micro-scalar-data"/>
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<use-data name="micro-vector-data"/>
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<use-data name="active_state"/>
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<use-data name="active_steps"/>
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<data:scalar name="Macro-Scalar"/>
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<data:vector name="Macro-Vector"/>
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<data:scalar name="Micro-Scalar"/>
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<data:vector name="Micro-Vector"/>
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<data:scalar name="Active-State"/>
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<data:scalar name="Active-Steps"/>
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<mesh name="Macro-Mesh" dimensions="3">
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<use-data name="Macro-Scalar"/>
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<use-data name="Macro-Vector"/>
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<use-data name="Micro-Scalar"/>
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<use-data name="Micro-Vector"/>
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<use-data name="Active-State"/>
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<use-data name="Active-Steps"/>
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</mesh>
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<participant name="Macro-dummy">
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<provide-mesh name="macro-mesh"/>
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<read-data name="micro-scalar-data" mesh="macro-mesh"/>
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<read-data name="micro-vector-data" mesh="macro-mesh"/>
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<write-data name="macro-scalar-data" mesh="macro-mesh"/>
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<write-data name="macro-vector-data" mesh="macro-mesh"/>
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<participant name="Macro-Dummy">
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<provide-mesh name="Macro-Mesh"/>
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<read-data name="Micro-Scalar" mesh="Macro-Mesh"/>
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<read-data name="Micro-Vector" mesh="Macro-Mesh"/>
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<write-data name="Macro-Scalar" mesh="Macro-Mesh"/>
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<write-data name="Macro-Vector" mesh="Macro-Mesh"/>
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</participant>
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<participant name="Micro-Manager">
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<receive-mesh name="macro-mesh" from="Macro-dummy" direct-access="true" safety-factor="0.0"/>
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<read-data name="macro-scalar-data" mesh="macro-mesh"/>
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<read-data name="macro-vector-data" mesh="macro-mesh"/>
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<write-data name="micro-scalar-data" mesh="macro-mesh"/>
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<write-data name="micro-vector-data" mesh="macro-mesh"/>
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<write-data name="active_state" mesh="macro-mesh"/>
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<write-data name="active_steps" mesh="macro-mesh"/>
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<receive-mesh name="Macro-Mesh" from="Macro-Dummy" direct-access="true" safety-factor="0.0"/>
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<read-data name="Macro-Scalar" mesh="Macro-Mesh"/>
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<read-data name="Macro-Vector" mesh="Macro-Mesh"/>
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<write-data name="Micro-Scalar" mesh="Macro-Mesh"/>
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<write-data name="Micro-Vector" mesh="Macro-Mesh"/>
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<write-data name="Active-State" mesh="Macro-Mesh"/>
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<write-data name="Active-Steps" mesh="Macro-Mesh"/>
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</participant>
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<m2n:sockets acceptor="Micro-Manager" connector="Macro-dummy"/>
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<m2n:sockets acceptor="Micro-Manager" connector="Macro-Dummy"/>
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<coupling-scheme:serial-implicit>
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<participants first="Macro-dummy" second="Micro-Manager"/>
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<max-time value="3.0"/>
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<time-window-size value="1.0"/>
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<max-iterations value="5"/>
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<exchange data="micro-scalar-data" mesh="macro-mesh" from="Micro-Manager" to="Macro-dummy"/>
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<exchange data="micro-vector-data" mesh="macro-mesh" from="Micro-Manager" to="Macro-dummy"/>
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<exchange data="macro-scalar-data" mesh="macro-mesh" from="Macro-dummy" to="Micro-Manager"/>
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<exchange data="macro-vector-data" mesh="macro-mesh" from="Macro-dummy" to="Micro-Manager"/>
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<relative-convergence-measure limit="1e-5" data="macro-scalar-data" mesh="macro-mesh"/>
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<relative-convergence-measure limit="1e-5" data="micro-scalar-data" mesh="macro-mesh"/>
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<participants first="Macro-Dummy" second="Micro-Manager"/>
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<max-time value="3.0"/>
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<time-window-size value="1.0"/>
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<max-iterations value="5"/>
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<exchange data="Micro-Scalar" mesh="Macro-Mesh" from="Micro-Manager" to="Macro-Dummy"/>
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<exchange data="Micro-Vector" mesh="Macro-Mesh" from="Micro-Manager" to="Macro-Dummy"/>
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<exchange data="Macro-Scalar" mesh="Macro-Mesh" from="Macro-Dummy" to="Micro-Manager"/>
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<exchange data="Macro-Vector" mesh="Macro-Mesh" from="Macro-Dummy" to="Micro-Manager"/>
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<relative-convergence-measure limit="1e-5" data="Macro-Scalar" mesh="Macro-Mesh"/>
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<relative-convergence-measure limit="1e-5" data="Micro-Scalar" mesh="Macro-Mesh"/>
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</coupling-scheme:serial-implicit>
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</precice-configuration>

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