updated tutorial 1

Author: simongravelle

.dependencies/gromacstutorials-inputs

@@ -1,3 +1,8 @@
 [submodule ".dependencies/gromacstutorials-inputs"]
 	path = .dependencies/gromacstutorials-inputs
 	url = git@github.com:gromacstutorials/gromacstutorials-inputs.git
+	branch = main
+[submodule ".dependencies/pyplot-perso"]
+	path = .dependencies/pyplot-perso
+	url = git@github.com:simongravelle/pyplot-perso.git
+	branch = LAMMPS-livecom

.dependencies/pyplot-perso

@@ -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()

.gitmodules

@@ -7,13 +7,13 @@ Bulk salt solution
 
     The very basics of GROMACS through a simple example
 
-.. figure:: ../figures/level1/bulk-solution/video-solution-white.webp
+.. figure:: figures/video-solution-white.webp
     :alt: Water solution of SO\ :sub:`4`\ :sup:`2-` and Na\ :sup:`+` ions visualized with VMD
     :class: only-light
     :height: 250
     :align: right
 
-.. figure:: ../figures/level1/bulk-solution/video-solution-dark.webp
+.. figure:: figures/video-solution-dark.webp
     :alt: Water solution of SO\ :sub:`4`\ :sup:`2-` and Na\ :sup:`+` ions visualized with VMD
     :class: only-dark
     :height: 250
@@ -79,7 +79,7 @@ into it:
 
 The first line, *Cubic box*, is a comment, the second line is the
 total number of atoms (0), and the last line is the box dimension in nanometer,
-here 3.5 nm by 3.5 nm by 3.5 nm. This **.gro** file is written in |Gromos87 format.
+here 3.5 nm by 3.5 nm by 3.5 nm. This **.gro** file is written in Gromos87 format.
 
 .. |Gromos87| raw:: html
 
@@ -496,12 +496,12 @@ minimization step using VMD by typing in the terminal:
 
     vmd conf.gro min.trr
 
-.. figure:: ../figures/level1/bulk-solution/solution-light.webp
+.. figure:: figures/solution-light.webp
     :alt: Gromacs tutorial : Movie showing the motion of the atoms during the energy minimization.
     :class: only-light
     :height: 330
 
-.. figure:: ../figures/level1/bulk-solution/solution-dark.webp
+.. figure:: figures/solution-dark.webp
     :alt: Gromacs tutorial : Movie showing the motion of the atoms during the energy minimization.
     :class: only-dark
     :height: 330
@@ -548,11 +548,11 @@ can be oppened with the Grace software (or equivalent) :cite:`grace`:
 
     xmgrace min-pe.xvg
 
-.. figure:: ../figures/level1/bulk-solution/potential-energy-min-light.png
+.. figure:: figures/potential-energy-min-light.png
     :alt: Gromacs tutorial : plot of the energy versus time.
     :class: only-light
 
-.. figure:: ../figures/level1/bulk-solution/potential-energy-min-dark.png
+.. figure:: figures/potential-energy-min-dark.png
     :alt: Gromacs tutorial : plot of the energy versus time.
     :class: only-dark
 
@@ -720,16 +720,14 @@ thermostat that is removing the extra energy from the system,
 the temperature reaches the requested temperature of
 :math:`360~\text{K}` after a duration of a few picoseconds.
 
-.. 
-
 In general, it is better to perform a longer equilibration, but simulation
 durations are kept as short as possible for these tutorials. 
 
-.. figure:: ../figures/level1/bulk-solution/temperature-nvt-light.png
+.. figure:: figures/temperature-nvt-light.png
     :alt: Gromacs tutorial : temperature versus time.
     :class: only-light
 
-.. figure:: ../figures/level1/bulk-solution/temperature-nvt-dark.png
+.. figure:: figures/temperature-nvt-dark.png
     :alt: Gromacs tutorial : temperature versus time.
     :class: only-dark
 
@@ -821,11 +819,11 @@ command 3 consecutive times:
 Choose respectively ``temperature`` (10), ``pressure`` (11) and
 ``density`` (16).
 
-.. figure:: ../figures/level1/bulk-solution/temperature-npt-light.png
+.. figure:: figures/temperature-npt-light.png
     :alt: Gromacs tutorial : NPT equilibration
     :class: only-light
 
-.. figure:: ../figures/level1/bulk-solution/temperature-npt-dark.png
+.. figure:: figures/temperature-npt-dark.png
     :alt: Gromacs tutorial : NPT equilibration
     :class: only-dark
 
@@ -938,6 +936,20 @@ and then by typing 2 and 4.
 
 The results show...
 
+.. figure:: figures/rdf-plain.png
+    :alt: Gromacs tutorial RDF radial distribution function
+    :class: only-light
+
+.. figure:: figures/rdf-plain-dm.png
+    :alt: Gromacs tutorial RDF radial distribution function
+    :class: only-dark
+
+.. container:: figurelegend
+
+    Figure: Radial distribution functions (RDF) as calculated between sodium
+    and water (:math:`\text{Na}^+ - \text{H}_2\text{O}`), between sulfate and
+    water (:math:`\text{SO}_4^{2-} - \text{H}_2\text{O}`).
+
 The main issue with the calculated rdf, is that it includes all the atoms from 
 thr :math:`\text{H}_2\text{O}` molecules (including the hydrogen atoms) and all
 the atoms from the :math:`\text{SO}_4^{2-}`, leading to more peaks and dephts
@@ -993,19 +1005,20 @@ and select 3 and 7.
 
 and select 8 and 7.
 
-    
-.. figure:: ../figures/level1/bulk-solution/rdf-production-light.png
+.. figure:: figures/rdf-filtered.png
     :alt: Gromacs tutorial RDF radial distribution function
     :class: only-light
 
-.. figure:: ../figures/level1/bulk-solution/rdf-production-dark.png
+.. figure:: figures/rdf-filtered-dm.png
     :alt: Gromacs tutorial RDF radial distribution function
     :class: only-dark
 
 .. container:: figurelegend
 
     Figure: Radial distribution functions (RDF) as calculated between sodium
-    and water, between sulfate and water, and finally between water and water.
+    and water oxygens (:math:`\text{Na}^+ - \text{OW1}`), between sulfur and
+    water oxygens  (:math:`\text{S1} - \text{OW1}`), and in between water oxygens
+    (:math:`\text{OW1} - \text{OW1}`),.
 
 The radial distribution functions highlight the typical distance between
 the different species of the fluid. For instance, it can be seen that
@@ -1014,9 +1027,6 @@ distance of :math:`2.4 ~ \text{Å}` from the center of the sodium ion.
 
 .. include:: ../../non-tutorials/accessfile.rst
 
-
-
-
 ..
     Mean square displacement
     ========================