Merge branch 'precice:develop' into Relax_similarity_condition

.github/workflows/run-adaptivity-test.yml

@@ -1,4 +1,4 @@
-name: Test for functions in classes AdaptivityCalculator, LocalAdaptivityCalculator, GlobalAdaptivityCalculator
+name: Test adaptivity functionality
 on:
   push:
     branches:

CITATION.cff

@@ -0,0 +1,46 @@
+cff-version: "1.2.0"
+authors:
+- family-names: Desai
+  given-names: Ishaan
+  orcid: "https://orcid.org/0000-0002-2552-7509"
+- family-names: Scheurer
+  given-names: Erik
+  orcid: "https://orcid.org/0009-0000-9396-2994"
+- family-names: Bringedal
+  given-names: Carina
+  orcid: "https://orcid.org/0000-0003-0495-2634"
+- family-names: Uekermann
+  given-names: Benjamin
+  orcid: "https://orcid.org/0000-0002-1314-9969"
+doi: 10.18419/darus-3764
+message: If you use this software, please cite our article in the
+  Journal of Open Source Software.
+preferred-citation:
+  authors:
+  - family-names: Desai
+    given-names: Ishaan
+    orcid: "https://orcid.org/0000-0002-2552-7509"
+  - family-names: Scheurer
+    given-names: Erik
+    orcid: "https://orcid.org/0009-0000-9396-2994"
+  - family-names: Bringedal
+    given-names: Carina
+    orcid: "https://orcid.org/0000-0003-0495-2634"
+  - family-names: Uekermann
+    given-names: Benjamin
+    orcid: "https://orcid.org/0000-0002-1314-9969"
+  date-published: 2023-11-07
+  doi: 10.21105/joss.05842
+  issn: 2475-9066
+  issue: 91
+  journal: Journal of Open Source Software
+  publisher:
+    name: Open Journals
+  start: 5842
+  title: "Micro Manager: a Python package for adaptive and flexible
+    two-scale coupling"
+  type: article
+  url: "https://joss.theoj.org/papers/10.21105/joss.05842"
+  volume: 8
+title: "Micro Manager: a Python package for adaptive and flexible
+  two-scale coupling"

CONTRIBUTING.md

@@ -0,0 +1,11 @@
+# Contributing to the Micro Manager
+
+Contributions to the Micro Manager are most welcome! Please have a look at the page [contributing to preCICE](https://precice.org/community-contribute-to-precice.html) and also this page for more details.
+
+## Automatic checks
+
+We check every contribution with a few GitHub Actions workflows that report at the bottom of each pull request. For example, we have an Action to check if the contributed code is formatting correctly according to [autopep8](https://pypi.org/project/autopep8/).
+
+## Changelog
+
+We maintain a `CHANGELOG.md` where all major changes and contributions are entered.

README.md

@@ -12,10 +12,10 @@
     <img src="https://github.com/precice/micro-manager/actions/workflows/pythonpublish.yml/badge.svg" alt="Upload Python Package">
 </a>
 
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.05842/status.svg)](https://doi.org/10.21105/joss.05842)
+
 A tool to facilitate solving two-scale (macro-micro) coupled problems using the coupling library [preCICE](https://www.precice.org/).
 
 The main documentation is rendered on the [preCICE website](https://precice.org/tooling-micro-manager-overview.html).
 
 Please report any [issues](https://github.com/precice/micro-manager/issues) and give us feedback through [one of our community channels](https://precice.org/community-channels.html).
-
-The concept and initial design of the Micro Manager is described in *Desai, Ishaan, & Bringedal, Carina & Uekermann, Benjamin. A flexible software approach to simulate two-scale coupled problems. ECCOMAS Congress 2022. [10.23967/eccomas.2022.037](https://doi.org/10.23967/eccomas.2022.037)*.

examples/README.md

@@ -1,18 +1,25 @@
 # Solverdummies
 
-The `solverdummies` are minimal working examples for using the preCICE Micro Manager with different languages. At the moment, there are examples for Python, and C++. They can be coupled with any other solver, for example the `macro-dummy.py` in this directory.
+The `solverdummies` are minimal working examples for using the preCICE Micro Manager with different languages. At the moment, there are examples for Python, and C++. They can be coupled with any other solver, for example the `macro_dummy.py` in this directory.
 
 ## Python
 
 To run the Python solverdummies, run the following commands in the `examples/` directory in **two different terminals**:
 
 ```bash
-python macro-dummy.py
-python python-dummy/run_micro_manager.py
+python macro_dummy.py
+python python-dummy/run_micro_manager.py --config micro-manager-config.json
 ```
 
 Note that running `micro_manager micro-manager-config.json` from the terminal will not work, as the path in the configuration file is relative to the current working directory. See [#36](https://github.com/precice/micro-manager/issues/36) for more information.
 
+To run the Python solverdummies with adaptivity run the following commands in the `examples/` directory in **two different terminals**:
+
+```bash
+python macro_dummy.py
+python python-dummy/run_micro_manager.py --config micro-manager-adaptivity-config.json
+```
+
 ## C++
 
 The C++ solverdummies have to be compiled first using [`pybind11`](https://pybind11.readthedocs.io/en/stable/index.html). To do so, install `pybind11` using `pip`:
@@ -42,7 +49,14 @@ Then, run the following commands in the `examples/` directory, in **two differen
 
 ```bash
 python macro_dummy.py
-python cpp-dummy/run_micro_manager.py
+python cpp-dummy/run_micro_manager.py --config micro-manager-config.json
+```
+
+To run the C++ solverdummies with adaptivity run the following commands in the `examples/` directory in **two different terminals**:
+
+```bash
+python macro_dummy.py
+python cpp-dummy/run_micro_manager.py --config micro-manager-adaptivity-config.json
 ```
 
 When changing the C++ solverdummy to your own solver, make sure to change the `PYBIND11_MODULE` in `micro_cpp_dummy.cpp` to the name that you want to compile to.

micro_manager/micro_manager.py

@@ -116,7 +116,7 @@ def __init__(self, config_file: str) -> None:
                 if name in self._write_data_names:
                     self._adaptivity_micro_data_names[name] = is_data_vector
 
-            self._is_adaptivity_required_in_every_implicit_iteration = self._config.is_adaptivity_required_in_every_implicit_iteration()
+            self._adaptivity_in_every_implicit_step = self._config.is_adaptivity_required_in_every_implicit_iteration()
             self._micro_sims_active_steps = None
 
     # **************
@@ -149,6 +149,8 @@ def initialize(self) -> None:
 
         self._mesh_vertex_ids, mesh_vertex_coords = self._participant.get_mesh_vertex_ids_and_coordinates(
             self._macro_mesh_name)
+        assert (mesh_vertex_coords.size != 0), "Macro mesh has no vertices."
+
         self._local_number_of_sims, _ = mesh_vertex_coords.shape
         self._logger.info("Number of local micro simulations = {}".format(self._local_number_of_sims))
 
@@ -282,7 +284,7 @@ def solve(self) -> None:
                 n_checkpoint = n
 
                 if self._is_adaptivity_on:
-                    if not self._is_adaptivity_required_in_every_implicit_iteration:
+                    if not self._adaptivity_in_every_implicit_step:
                         similarity_dists, is_sim_active, sim_is_associated_to = self._adaptivity_controller.compute_adaptivity(
                             self._dt, self._micro_sims, similarity_dists, is_sim_active, sim_is_associated_to, self._data_for_adaptivity)
 
@@ -304,7 +306,7 @@ def solve(self) -> None:
             micro_sims_input = self._read_data_from_precice()
 
             if self._is_adaptivity_on:
-                if self._is_adaptivity_required_in_every_implicit_iteration:
+                if self._adaptivity_in_every_implicit_step:
                     similarity_dists, is_sim_active, sim_is_associated_to = self._adaptivity_controller.compute_adaptivity(
                         self._dt, self._micro_sims, similarity_dists, is_sim_active, sim_is_associated_to, self._data_for_adaptivity)
 
@@ -339,7 +341,7 @@ def solve(self) -> None:
 
                 # If adaptivity is computed only once per time window, the states of sims need to be reset too
                 if self._is_adaptivity_on:
-                    if not self._is_adaptivity_required_in_every_implicit_iteration:
+                    if not self._adaptivity_in_every_implicit_step:
                         similarity_dists = np.copy(similarity_dists_cp)
                         is_sim_active = np.copy(is_sim_active_cp)
                         sim_is_associated_to = np.copy(sim_is_associated_to_cp)

tests/unit/test_adaptivity_serial.py

@@ -102,13 +102,6 @@ def test_update_active_sims(self):
 
         is_sim_active = np.array([True, True, True, True, True])  # Activate all micro sims before calling functionality
 
-        class MicroSimulation():
-            pass
-
-        dummy_micro_sims = []
-        for _ in range(self._number_of_sims):
-            dummy_micro_sims.append(MicroSimulation())
-
         is_sim_active = adaptivity_controller._update_active_sims(
             self._similarity_dists, is_sim_active)
 
@@ -153,17 +146,6 @@ def test_associate_active_to_inactive(self):
         is_sim_active = np.array([True, False, False, True, False])
         expected_sim_is_associated_to = np.array([-2, 0, 0, -2, 3])
 
-        class MicroSimulation():
-            def __init__(self, global_id):
-                self._global_id = global_id
-
-            def get_global_id(self):
-                return self._global_id
-
-        dummy_micro_sims = []
-        for i in range(self._number_of_sims):
-            dummy_micro_sims.append(MicroSimulation(i))
-
         sim_is_associated_to = np.array([-2, -2, -2, -2, -2])
 
         sim_is_associated_to = adaptivity_controller._associate_inactive_to_active(