firther refinment

Author: simongravelle

docs/lammpstutorials-inputs

@@ -0,0 +1 @@
+Subproject commit 4e249a6f7a0f8f8057bf72c07d39841a297e69a6

docs/sphinx/source/index.rst

@@ -20,7 +20,6 @@ lammpstutorials by Simon Gravelle : LAMMPS courses for beginners
     tutorial5/reactive-silicon-dioxide.rst
     tutorial6/water-adsorption-in-silica.rst
     tutorial7/free-energy-calculation.rst
-    tutorial8/reactive-molecular-dynamics.rst
 
 .. toctree::
     :maxdepth: 2

docs/sphinx/source/tutorial1/tutorial.rst

@@ -403,7 +403,7 @@ a plateau value of about 1.5.
 
 ..  container:: figurelegend
 
-    (a) Potential energy, :math:`U`, of the binary mixture as a function of the
+    Figure: (a) Potential energy, :math:`U`, of the binary mixture as a function of the
     step during energy minimization.
     (b) Potential energy, :math:`U`, as a function of time, :math:`t`, during molecular dynamics in
     the NVT ensemble.  (c) Kinetic energy, :math:`K`, during energy minimization.
@@ -749,7 +749,7 @@ over time.
 
 ..  container:: figurelegend
 
-    Evolution of the system during mixing. The
+    Figure: Evolution of the system during mixing. The
     three snapshots show respectively the system at :math:`t = 0` (left panel),
     :math:`t = 75` (middle panel), and :math:`t = 1500` (right panel). The atoms of type
     1 are represented as small green spheres and the atoms of type 2 as large cyan spheres.
@@ -775,7 +775,7 @@ expected during mixing.  This can be observed using the entry
 
 ..  container:: figurelegend
 
-    a) Evolution of the numbers :math:`N_\text{1, in}$` and :math:`N_\text{2, in}` of atoms
+    Figure: a) Evolution of the numbers :math:`N_\text{1, in}$` and :math:`N_\text{2, in}` of atoms
     of types 1 and 2, respectively, within the ``cyl_in`` region as functions
     of time :math:`t`.  b) Evolution of the coordination number :math:`C_{1-2}`
     (compute ``sumcoor12``) between atoms of types 1 and 2.

docs/sphinx/source/tutorial2/figures/CNT-unbreakable-stress-strain-dm.png

@@ -5,7 +5,16 @@
    "execution_count": 1,
    "id": "7c8c9669",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/home/simon/.local/lib/python3.12/site-packages/matplotlib/projections/__init__.py:63: UserWarning: Unable to import Axes3D. This may be due to multiple versions of Matplotlib being installed (e.g. as a system package and as a pip package). As a result, the 3D projection is not available.\n",
+      "  warnings.warn(\"Unable to import Axes3D. This may be due to multiple versions of \"\n"
+     ]
+    }
+   ],
    "source": [
     "import numpy as np\n",
     "import sys, os, git, lammps_logfile\n",

docs/sphinx/source/tutorial2/figures/CNT-unbreakable-stress-strain.png

@@ -308,16 +308,6 @@ which makes the average temperature of the entire system less relevant.
 The ``thermo_modify`` command also imposes the use of the YAML format that can easily be read by  
 Python (see below).
 
-.. figure:: figures/colored-edge-def-dark.png
-    :class: only-dark
-    :alt: Evolution of the CNT energy
-
-.. figure:: figures/colored-edge-def-light.png
-    :class: only-light
-    :alt: Evolution of the CNT energy
-
-    The unbreakable CNT before (top) and after deformation (bottom).
-
 Let us impose a constant velocity deformation on the CNT  
 by combining the ``velocity set`` command with previously defined  
 ``fix setforce``.  Add the following lines in the **unbreakable.lmp**  
@@ -331,12 +321,23 @@ file, right after the last ``run 5000`` command:
    run 10000
 
 The chosen velocity for the deformation is :math:`100\,\text{m/s}`, or  
-:math:`0.001\,\text{Å/fs}`.
-
-Run the simulation using LAMMPS.  As can be seen from the variable :math:`L_\text{cnt}`, the length
+:math:`0.001\,\text{Å/fs}`. Run the simulation using LAMMPS.  As can be seen
+from the variable :math:`L_\text{cnt}`, the length
 of the CNT increases linearly over time for :math:`t > 5\,\text{ps}`,
-as expected from the imposed constant velocity.  What you observe in the :guicmd{Slide Show}
-windows should resemble Fig.~\ref{fig:CNT-unbreakable}.  The total energy of the system
+as expected from the imposed constant velocity.  What you observe in the `Slide Show`
+windows should resemble the figure below.  
+
+.. figure:: figures/colored-edge-def-dark.png
+    :class: only-dark
+    :alt: Evolution of the CNT energy
+
+.. figure:: figures/colored-edge-def-light.png
+    :class: only-light
+    :alt: Evolution of the CNT energy
+
+    The unbreakable CNT before (top) and after deformation (bottom).
+
+The total energy of the system
 shows a non-linear increase with :math:`t` once the deformation starts, which is expected
 from the typical dependency of bond energy with bond distance,
 :math:`U_\text{b} = k_\text{b} \left( r - r_0 \right)^2`.
@@ -351,7 +352,7 @@ from the typical dependency of bond energy with bond distance,
 
 ..  container:: figurelegend
 
-    a) Evolution of the length :math:`L_\text{cnt}` of the CNT with time.  
+    Figure: a) Evolution of the length :math:`L_\text{cnt}` of the CNT with time.  
     The CNT starts deforming at :math:`t = 5\,\text{ps}`, and :math:`L_\text{cnt-0}` is the  
     CNT initial length.  b) Evolution of the total energy :math:`E` of the system with time :math:`t`.  
     Here, the potential is OPLS-AA, and the CNT is unbreakable.
@@ -383,11 +384,21 @@ the **unbreakable.yaml** file can then be used to plot the stress-strain curve.
 
    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a>
 
-ADD FIGURE CNT-unbreakable-stress-strain -- Stress applied on the CNT during deformation, :math:`F_\text{cnt}/A_\text{cnt}`,
-where :math:`F_\text{cnt}` is the force and :math:`A_\text{cnt}` the CNT surface area,
-as a function of the strain, :math:`\Delta L_\text{cnt} = (L_\text{cnt}-L_\text{cnt-0})/L_\text{cnt-0}`,
-where :math:`L_\text{cnt}` is the CNT length and :math:`L_\text{cnt-0}` the CNT initial length.
-Here, the potential is OPLS-AA, and the CNT is unbreakable.
+.. figure:: figures/CNT-unbreakable-stress-strain-dm.png
+    :class: only-dark
+    :alt: Evolution of the carbon nanotube stress strain as calculated with LAMMPS
+
+.. figure:: figures/CNT-unbreakable-stress-strain.png
+    :class: only-light
+    :alt: Evolution of the carbon nanotube stress strain as calculated with LAMMPS
+
+..  container:: figurelegend
+
+    Figure: Stress applied on the CNT during deformation, :math:`F_\text{cnt}/A_\text{cnt}`,
+    where :math:`F_\text{cnt}` is the force and :math:`A_\text{cnt}` the CNT surface area,
+    as a function of the strain, :math:`\Delta L_\text{cnt} = (L_\text{cnt}-L_\text{cnt-0})/L_\text{cnt-0}`,
+    where :math:`L_\text{cnt}` is the CNT length and :math:`L_\text{cnt-0}` the CNT initial length.
+    Here, the potential is OPLS-AA, and the CNT is unbreakable.
 
 Breakable bonds
 ===============
@@ -510,8 +521,18 @@ previously.  Add the following lines into **breakable.lmp**:
 Run the simulation.  Some bonds are expected to break before the end of the
 simulation.
 
-ADD FIGURE CNT-deformed-breakable -- CNT with broken bonds.  This image was generated using
-VMD :cite:`vmd_home,humphrey1996vmd` ``DynamicBonds`` representation.
+.. figure:: figures/deformed-dark.png
+    :class: only-dark
+    :alt: Carbon nanotube deformed using LAMMPS
+
+.. figure:: figures/deformed-light.png
+    :class: only-light
+    :alt: Carbon nanotube deformed using LAMMPS
+
+..  container:: figurelegend
+
+    Figure: Figure: CNT with broken bonds.  This image was generated using
+    VMD :cite:`vmd_home,humphrey1996vmd` ``DynamicBonds`` representation.
 
 Looking at the evolution of the energy, one can see that the total
 energy :math:`E` is initially increasing with the deformation.  When bonds
@@ -538,7 +559,7 @@ curve reveals a linear (elastic) regime where
 
 ..  container:: figurelegend
 
-    a) Evolution of the total energy :math:`E` of the CNT with time :math:`t`.  b) Stress applied on the CNT
+    Figure: Figure: a) Evolution of the total energy :math:`E` of the CNT with time :math:`t`.  b) Stress applied on the CNT
     during deformation, :math:`F_\text{cnt}/A_\text{cnt}`,
     where :math:`F_\text{cnt}` is the force and :math:`A_\text{cnt}` the CNT surface area,
     as a function of the strain, :math:`\Delta L_\text{cnt} = (L_\text{cnt}-L_\text{cnt-0}/L_\text{cnt-0})`, where

docs/sphinx/source/tutorial2/figures/breakable.ipynb

@@ -151,19 +151,6 @@ The ``fix npt`` allows us to impose both a temperature of :math:`300\,\text{K}`
 (with a damping constant of :math:`1000\,\text{fs}`).  With the ``iso`` keyword,
 the three dimensions of the box will be re-scaled simultaneously.
 
-.. figure:: figures/water-light.png
-    :alt: Water reservoir from molecular dynamics simulations
-    :class: only-light
-
-.. figure:: figures/water-dark.png
-    :alt: Water reservoir from molecular dynamics simulations
-    :class: only-dark
-
-..  container:: figurelegend
-
-    Figure: The water reservoir after equilibration.  Oxygen atoms are in red, and
-    hydrogen atoms are in white. 
-
 Let us output the system into images by adding the following commands to **water.lmp**:
 
 .. code-block:: lammps
@@ -212,9 +199,20 @@ adding the following lines into **water.lmp**:
 The final state is saved in a binary file named **water.restart**.
 Run the input using LAMMPS.  The system reaches its equilibrium temperature
 after just a few picoseconds, and its equilibrium density after approximately
-10 picoseconds (Fig.~\ref{fig:PEG-density}).  A snapshot of the equilibrated
-system can also be seen in Fig.~\ref{fig:PEG-water}.
+10 picoseconds.
 
+.. figure:: figures/water-light.png
+    :alt: Water reservoir from molecular dynamics simulations
+    :class: only-light
+
+.. figure:: figures/water-dark.png
+    :alt: Water reservoir from molecular dynamics simulations
+    :class: only-dark
+
+..  container:: figurelegend
+
+    Figure: The water reservoir after equilibration.  Oxygen atoms are in red, and
+    hydrogen atoms are in white. 
 
 .. admonition:: Note
     :class: non-title-info
@@ -330,19 +328,6 @@ Let us create images of the systems:
         acolor OAlc darkred adiam OAlc 2.6
     thermo 500
 
-.. figure:: figures/solvatedPEG_light.png
-    :alt: PEG in water as simulated with LAMMPS
-    :class: only-light
-
-.. figure:: figures/solvatedPEG_dark.png
-    :alt: PEG in water as simulated with LAMMPS
-    :class: only-dark
-
-..  container:: figurelegend
-
-    Figure : The PEG molecule solvated in water.  Water is represented as a
-    transparent field for clarity.
-
 Finally, to perform a short equilibration and save the final state to
 a **.restart** file, add the following lines to the input:
 
@@ -358,7 +343,19 @@ sure that the temperature remains close to the
 target value of :math:`300~\text{K}` throughout the entire simulation, and that
 the volume and total energy are almost constant, indicating
 that the system was in a reasonable configuration from the start.
-See a snapshot of the system in Fig.~\ref{fig:PEG-solvated}.
+
+.. figure:: figures/solvatedPEG_light.png
+    :alt: PEG in water as simulated with LAMMPS
+    :class: only-light
+
+.. figure:: figures/solvatedPEG_dark.png
+    :alt: PEG in water as simulated with LAMMPS
+    :class: only-dark
+
+..  container:: figurelegend
+
+    Figure : The PEG molecule solvated in water.  Water is represented as a
+    transparent field for clarity.
 
 Stretching the PEG molecule
 ===========================
@@ -389,22 +386,10 @@ following lines to **pull.lmp**:
 
 These lines identify the oxygen atoms (type OAlc) at the ends of the PEG
 molecule and calculates their center of mass along the :math:`x`-axis.  It then
-divides these atoms into two groups, ``end1`` (i.e.,~the OAlc atom to
-the right of the center) and ``end2`` (i.e.,~the OAlc atom to the right
+divides these atoms into two groups, ``end1`` (i.e., the OAlc atom to
+the right of the center) and ``end2`` (i.e., the OAlc atom to the right
 of the center), for applying force during the stretching process.
 
-.. figure:: figures/pulled_peg_light.png
-    :alt: PEG in water as simulated with LAMMPS
-    :class: only-light
-
-.. figure:: figures/pulled_peg_dark.png
-    :alt: PEG in water as simulated with LAMMPS
-    :class: only-dark
-
-..  container:: figurelegend
-
-    Figure: PEG molecule stretched along the :math:`x` direction in water.
-
 Add the following ``dump`` command to create images of the system:
 
 .. code-block:: lammps
@@ -424,20 +409,6 @@ the following lines to **pull.lmp**:
     fix mynvt all nvt temp 300 300 100
     fix myrct PEG recenter 0 0 0 shift all
 
-.. figure:: figures/PEG-distance-dm.png
-    :class: only-dark
-    :alt: Evolution of the polymer radius of gyration
-
-.. figure:: figures/PEG-distance.png
-    :class: only-light
-    :alt: Evolution of the polymer radius of gyration
-
-..  container:: figurelegend
-
-    Figure: a) Evolution of the radius of gyration :math:`R_\text{gyr}` of the PEG molecule,
-    with the force applied starting at :math:`t = 15\,\text{ps}`.  b) Histograms of
-    the dihedral angles of type 1 in the absence (orange) and in the presence (blue) of the applied force.
-
 To investigate the stretching of the PEG molecule, let us compute its radius of
 gyration :cite:`fixmanRadiusGyrationPolymer1962a` and the angles of its dihedral
 constraints using the following commands:
@@ -481,15 +452,40 @@ Each applied force has a magnitude of :math:`10 \, \text{kcal/mol/Å}`, correspo
 This value was chosen to be sufficiently large to overcome both the thermal agitation and
 the entropic contributions from the molecules.
 
+.. figure:: figures/pulled_peg_light.png
+    :alt: PEG in water as simulated with LAMMPS
+    :class: only-light
+
+.. figure:: figures/pulled_peg_dark.png
+    :alt: PEG in water as simulated with LAMMPS
+    :class: only-dark
+
+..  container:: figurelegend
+
+    Figure: PEG molecule stretched along the :math:`x` direction in water.
+
 Run the **pull.lmp** file using LAMMPS.  From the generated images of the system,
-you should observe that the PEG molecule eventually aligns
-in the direction of the applied force (as seen in Fig.~\ref{fig:PEG-in-water}).
-The evolutions of the radius of gyration over
-time indicates that the PEG quickly adjusts to the external force
-(Fig.~\ref{fig:PEG-distance}\,a).  Additionally, from the values of the dihedral angles
+you should observe that the PEG molecule eventually aligns in the direction of
+the applied force. The evolutions of the radius of gyration over
+time indicates that the PEG quickly adjusts to the external force.  Additionally,
+from the values of the dihedral angles
 printed in the **pull.dat** file, you can create a histogram
 of dihedral angles for a specific type.  For example, the angle :math:`\phi` for dihedrals
-of type 1 (C-C-OE-C) is shown in Fig.~\ref{fig:PEG-distance}\,b.
+of type 1 (C-C-OE-C) is shown below.
+
+.. figure:: figures/PEG-distance-dm.png
+    :class: only-dark
+    :alt: Evolution of the polymer radius of gyration
+
+.. figure:: figures/PEG-distance.png
+    :class: only-light
+    :alt: Evolution of the polymer radius of gyration
+
+..  container:: figurelegend
+
+    Figure: a) Evolution of the radius of gyration :math:`R_\text{gyr}` of the PEG molecule,
+    with the force applied starting at :math:`t = 15\,\text{ps}`.  b) Histograms of
+    the dihedral angles of type 1 in the absence (orange) and in the presence (blue) of the applied force.
 
 Tip: using external visualization tools
 ---------------------------------------

docs/sphinx/source/tutorial2/figures/unbreakable.ipynb

@@ -399,7 +399,7 @@ the two walls.  Add the following lines to **equilibrate.lmp**:
 
 The first two variables extract the centers of mass of the two walls.  The
 ``deltaz`` variable is then used to calculate the difference between the two
-variables ``walltopz`` and ``wallbotz``, i.e.~the distance between the
+variables ``walltopz`` and ``wallbotz``, i.e. the distance between the
 two centers of mass of the walls.
 
 Finally, let us run the simulation for 30 ps by adding a ``run`` command