Add MLIP Tutorial (#4982)

Add a Tutorial on Machine-Learning Interatomic Potentials.

doc/tutorials/CMakeLists.txt

@@ -108,6 +108,7 @@ add_subdirectory(constant_pH)
 add_subdirectory(widom_insertion)
 add_subdirectory(electrodes)
 add_subdirectory(grand_canonical_monte_carlo)
+add_subdirectory(mlip)
 
 configure_file(Readme.md ${CMAKE_CURRENT_BINARY_DIR} COPYONLY)
 configure_file(convert.py ${CMAKE_CURRENT_BINARY_DIR})

doc/tutorials/Readme.md

@@ -50,6 +50,9 @@ physical systems.
 * **Raspberry electrophoresis**  
   Extended objects in a Lattice-Boltzmann fluid, raspberry particles.  
   [Guide](raspberry_electrophoresis/raspberry_electrophoresis.ipynb)
+* **Machine-learned interatomic potential**  
+  Atomistic simulations using the MACE-MP-0 model.  
+  [Guide](mlip/mlip.ipynb)
 
 ### Advanced tutorials
 

doc/tutorials/mlip/CMakeLists.txt

@@ -0,0 +1,22 @@
+#
+# Copyright (C) 2016-2024 The ESPResSo project
+#
+# This file is part of ESPResSo.
+#
+# ESPResSo is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# ESPResSo is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+
+configure_tutorial_target(TARGET tutorial_mlip DEPENDS mlip.ipynb)
+
+nb_export(TARGET tutorial_mlip SUFFIX "" FILE "mlip.ipynb")

doc/tutorials/mlip/NotesForTutor.md

@@ -0,0 +1,22 @@
+# Machine-learned interatomic potential
+
+## Physics learning goals
+
+* Short introduction to how machine-learned inter-atomic potentials (MLPs) work.
+* Visualisation of dissociation of sulfuric acid in water.
+* Ground state calculations of small molecules MLPs
+* Learn about the shortcomings of the lack of interpretability of MLPs.
+
+After the tutorial, students should be able to:
+
+* Explain how MLP derived results can be hard to explain, e.g., is the dissociation real or an artifact.
+* Understand how to use the ESPResSo engine with MLPs.
+* Perform ground state calculations and small quantum mechanically accurate simulations.
+
+## ESPResSo learning goals
+
+* Interfacing ESPResSo with an MLP.
+* Interfacing ESPResSo with ASE.
+* Performing geometry minimisation.
+* Creating and filling simulation boxes.
+* Setting thermostats and running MD.