added GUI possibility to tutorial 1

Author: simongravelle

docs/sphinx/source/_static/custom.css

@@ -66,6 +66,8 @@
     content: '';  /* No icon needed, as there's no title */
   }
 
+  
+
 :root { /*https://fontawesomeicons.com/svg/icons/info*/
   --icon--patreon: url('data:image/svg+xml;charset=utf-8,   <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"> <g> <path fill="none" d="M0 0h24v24H0z"/> <path d="M15 17a7.5 7.5 0 1 1 0-15 7.5 7.5 0 0 1 0 15zM2 2h4v20H2V2z"/> </g> </svg>')
 }
@@ -133,6 +135,23 @@
           mask-image: var(--icon--solution);
 }
 
+:root {
+  --icon--gui: url('data:image/svg+xml;charset=utf-8, <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 16 16"><path d="M4.5 0A1.5 1.5 0 0 0 3 1.5v13A1.5 1.5 0 0 0 4.5 16h7a1.5 1.5 0 0 0 1.5-1.5v-13A1.5 1.5 0 0 0 11.5 0h-7zM4 1.5a.5.5 0 0 1 .5-.5h7a.5.5 0 0 1 .5.5v13a.5.5 0 0 1-.5.5h-7a.5.5 0 0 1-.5-.5v-13zM7.5 14a.5.5 0 1 0 1 0 .5.5 0 0 0-1 0z"/></svg>')
+}
+
+.admonition.gui > .admonition-title {
+  background-color: #2962ff10;
+  border-color: #2963ff;
+  font-size: 13pt;
+}
+
+.admonition.gui > .admonition-title::before {
+  background-color: #2963ff;
+  -webkit-mask-image: var(--icon--gui);
+          mask-image: var(--icon--gui);
+}
+
+
 a:link { 
     text-decoration: none; 
 } 
@@ -150,14 +169,3 @@ a:active {
 section {
   text-align: justify;
 }
-
-
-/* Add more specific parent selectors */
-body .sphinx-tabs .tab-button {
-  background-color: red !important;
-}
-
-/* If tabs are inside a specific section or container */
-section div.sphinx-tabs .tab-button {
-  background-color: red !important;
-}

docs/sphinx/source/conf.py

@@ -5,8 +5,7 @@
 
 extensions = ['sphinx_togglebutton',
               'sphinx_favicon',
-              'sphinxcontrib.bibtex',
-              'sphinx_tabs.tabs']
+              'sphinxcontrib.bibtex']
 
 templates_path = ['_templates']
 

docs/sphinx/source/journal-article.bib

@@ -17,6 +17,12 @@ @misc{lammps_run_basics
   note = {Accessed: 2025-03-22}
 }
 
+@misc{lammps_gui_docs,
+  title = {{LAMMPS-GUI} Online Documentation for latest stable version},
+  howpublished = {\url{https://docs.lammps.org/stable/Howto_lammps_gui.html}},
+  note = {Accessed: 2024-07-15}
+}
+
 @article{gravelle2025tutorials,
   author    = {Simon Gravelle and Jacob R. Gissinger and Axel Kohlmeyer},
   title     = {A Set of Tutorials for the LAMMPS Simulation Package},
@@ -322,6 +328,36 @@ @book{van1995python
   publisher={Centrum voor Wiskunde en Informatica Amsterdam}
 } 
 
+@misc{vmd_home,
+  title = {{VMD} Homepage},
+  howpublished = {\url{https://www.ks.uiuc.edu/Research/vmd}},
+  note = {Accessed: 2024-07-15}
+}
+
+@misc{ovito_home,
+  title = {{OVITO} Homepage},
+  howpublished = {\url{https://ovito.org}},
+  note = {Accessed: 2024-07-15}
+}
+
+@article{ovito_paper,
+Author = {Stukowski, Alexander},
+Title = {{Visualization and analysis of atomistic simulation data with OVITO - the
+   Open Visualization Tool}},
+Journal = {Modelling and Simulation in Materials Science and Engineering},
+Year = {{2010}},
+Volume = {{18}},
+Number = {{1}},
+pages = {015012},
+DOI = {{10.1088/0965-0393/18/1/015012}},
+Article-Number = {{015012}},
+ISSN = {{0965-0393}},
+EISSN = {{1361-651X}},
+ResearcherID-Numbers = {{Stukowski, Alexander/G-9695-2017}},
+ORCID-Numbers = {{Stukowski, Alexander/0000-0001-6750-3401}},
+Unique-ID = {{ISI:000272791800012}},
+}
+
 @article{humphrey1996vmd,
   title={{{VMD}}: visual molecular dynamics},
   author={Humphrey, William and Dalke, Andrew and Schulten, Klaus},

docs/sphinx/source/tutorial1/exercises.rst

@@ -1,7 +1,42 @@
-
 Going further with exercises
 ============================
 
+Experiments
+-----------
+
+Here are some suggestions for further experiments with this system that  
+may lead to additional insights into how different systems are configured  
+and how various features function:  
+
+- Use a Nosé-Hoover thermostat (*fix nvt*) instead of a Langevin thermostat  
+  (*fix nve* + *fix langevin*).  
+- Omit the energy minimization step before starting the MD simulation using either  
+  the Nosé-Hoover or the Langevin thermostat.  
+- Apply a thermostat to only one type of atoms and observe the  
+  temperature for each type separately.  
+- Append an NVE run (i.e., without any thermostat) and observe the energy levels.  
+
+.. admonition:: If you are using LAMMPS-GUI
+    :class: gui
+
+    An useful experiment is coloring the atoms in the *Slide Show* according
+    to an observable, such as their respective coordination numbers. To do this,
+    replace the *dump* and *dump_modify* commands with the following lines:
+
+    .. code-block:: lammps
+
+        variable coor12 atom (type==1)*(c_coor12)+(type==2)*-1
+        dump viz all image 1000 myimage-*.ppm v_coor12 type &
+        shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes size 800 800
+        dump_modify viz adiam 1 1 adiam 2 3 backcolor white &
+        amap -1 2 ca 0.0 4 min royalblue 0 turquoise 1 yellow max red
+
+    Run LAMMPS again.  Atoms of type 1 are now colored based on the value
+    of *c_coor12*, which is mapped continuously from turquoise to yellow
+    and red for atoms with the highest coordination.
+    In the definition of the variable *v_coor12*, atoms of type 2 are
+    all assigned a value of -1, and will therefore always be colored their default blue.
+
 Solve Lost atoms error
 ----------------------