work on tutorial 1

Author: simongravelle

dependencies/.github

@@ -0,0 +1,53 @@
+import subprocess
+import re
+
+# Define ANSI escape codes for colors
+RED = '\033[91m'
+GREEN = '\033[92m'
+GRAY = '\033[90m'
+RESET = '\033[0m'
+
+def filter_make_output():
+
+    # Define multiple patterns to ignore
+    ignore_patterns = [
+        "Pygments lexer name 'bw' is not known",
+        "Pygments lexer name 'lammps' is not known",
+        ".. label:: start_",
+        ".. label:: end_",
+        "Unknown directive type"
+    ]
+    
+    # Define a pattern to identify warnings (example pattern, adjust as needed)
+    warning_pattern = re.compile('|'.join(re.escape(p) for p in ["WARNING:", "ERROR:"]))
+    
+    # Combine ignore patterns into a single regex pattern
+    ignore_pattern = re.compile('|'.join(re.escape(p) for p in ignore_patterns))
+    
+    # Run 'make clean'
+    subprocess.run(['make', 'clean'], check=True)
+    
+    # Run 'make html' and capture output
+    process = subprocess.Popen(['make', 'html'],
+                               stdout=subprocess.PIPE,
+                               stderr=subprocess.STDOUT, text=True)
+    
+    # Read and filter output
+    output_lines = []
+    for line in process.stdout:
+        if len(line) > 1:
+            if not ignore_pattern.search(line):
+                # Determine the color based on whether the line matches the warning pattern
+                if warning_pattern.search(line):
+                    output_lines.append(RED + line + RESET)
+                else:
+                    output_lines.append(GRAY + line + RESET)
+
+    # Wait for the process to complete
+    process.wait()
+
+    # Print the filtered output
+    print(''.join(output_lines), end='')
+
+if __name__ == "__main__":
+    filter_make_output()

docs/sphinx/compile.py

@@ -5,6 +5,30 @@ @book{barrat2003basic
   publisher={Cambridge University Press}
 }
 
+@article{gravelle2025tutorials,
+  author    = {Simon Gravelle and Jacob R. Gissinger and Axel Kohlmeyer},
+  title     = {A Set of Tutorials for the LAMMPS Simulation Package},
+  journal   = {arXiv preprint},
+  year      = {2025},
+  archivePrefix = {arXiv},
+  eprint    = {2503.14020},
+  primaryClass = {physics.comp-ph},
+  doi       = {10.48550/arXiv.2503.14020},
+  note      = {Submitted on 18 Mar 2025}
+}
+
+@misc{lammps_code,
+  author       = {Plimpton, Steven J. and Kohlmeyer, Axel and Thompson, Aidan P. and Moore, Stan G. and Berger, Richard},
+  title        = {{LAMMPS: Large-scale Atomic/Molecular Massively
+                   Parallel Simulator}},
+  month        = aug,
+  year         = 2024,
+  publisher    = {Zenodo},
+  version      = {stable\_XXAug2024},
+  doi          = {10.5281/zenodo.3726416},
+  url          = {https://doi.org/10.5281/zenodo.3726416}
+}
+
 @article{sulpizi2012silica,
   title={The silica--water interface: how the silanols determine the surface acidity and modulate the water properties},
   author={Sulpizi, Marialore and Gaigeot, Marie-Pierre and Sprik, Michiel},

docs/sphinx/source/journal-article.bib

@@ -0,0 +1 @@
+If these tutorials are useful to you, please cite Ref. :cite:`gravelle2025tutorials`.

docs/sphinx/source/shared/cite.rst

@@ -1,3 +1,3 @@
 .. container:: version
 
-    This tutorial is compatible with the XXXX2024 LAMMPS version.
+    This tutorial is compatible with the 29Aug2024 (update 2) LAMMPS version.

docs/sphinx/source/shared/versionLAMMPS.rst

@@ -12,15 +12,10 @@
     :align: right
     :class: only-light
 
-The objective of this tutorial is to perform the simulation of a binary
-fluid using LAMMPS.
-
-The system is a Lennard-Jones fluid composed of neutral particles with two
-different diameters, contained within a cubic box with periodic boundary conditions 
-In this tutorial, the temperature of the system is maintained using a Langevin
-thermostat :cite:`schneider1978molecular`, and basic quantities are extracted
-from the system, including the potential and kinetic energies. 
-
-This tutorial illustrates several key ingredients of molecular dynamics
-simulations, such as system initialization, energy minimization, integration
-of the equations of motion, and trajectory visualization.
+The objective of this tutorial is to perform simple MD simulations
+using LAMMPS.  The system consists of a Lennard-Jones fluid composed of
+neutral particles with two different effective diameters, contained
+within a cubic box with periodic boundary conditions.  In this tutorial, basic MD simulations in
+the microcanonical (NVE) and canonical (NVT) ensembles are performed,
+and basic quantities are calculated, including the potential and kinetic
+energies.

docs/sphinx/source/tutorial1/introduction.rst

@@ -10,6 +10,7 @@ Lennard-Jones fluid
 .. include:: introduction.rst
 .. include:: ../../non-tutorials/needhelp.rst
 .. include:: ../shared/versionLAMMPS.rst
+.. include:: ../shared/cite.rst
 .. include:: tutorial.rst
 .. include:: ../shared/access-the-files.rst
 .. include:: exercises.rst