keep applying reviewers commentaries

Author: simongravelle

docs/sphinx/source/tutorial2/introduction.rst

@@ -16,6 +16,7 @@ by imposing a constant velocity on the edge atoms.  To illustrate the
 difference between conventional and reactive force fields, this tutorial
 is divided into two parts: in the first part, a conventional molecular
 force field (called OPLS-AA :cite:`jorgensenDevelopmentTestingOPLS1996`)
-is used and the bonds between the atoms of the CNT are unbreakable.  In
+is used and the form of the bonded potential ensure that the bonds between the
+atoms of the CNT are unbreakable.  In
 the second part, a reactive force field (called AIREBO :cite:`stuart2000reactive`)
 is used, which allows chemical bonds to break under large strain.

docs/sphinx/source/tutorial2/tutorial.rst

@@ -3,7 +3,9 @@ Unbreakable bonds
 
 With most conventional molecular force fields, the chemical bonds between
 atoms are defined at the start of the simulation and remain fixed, regardless
-of the forces applied to the atoms.  These bonds are typically modeled as springs
+of the forces applied to the atoms.  In this tutorial, these bonds are
+explicitly specified in the **.data** file, which is read using the ``read_data`` command (see below).
+Bonds are typically modeled as springs
 with equilibrium distances :math:`r_0` and force constants :math:`k_\text{b}`:
 :math:`U_\text{b} = k_\text{b} \left( r - r_0 \right)^2`.  Additionally, angular and
 dihedral constraints are often imposed to preserve the molecular structure
@@ -48,7 +50,7 @@ the scripts required for the second part of the tutorial.
     file in a text editor of your choice, and copy the previous lines into it.
 
 The chosen unit system is ``real`` (therefore distances are in
-Ångströms (Å), times in femtoseconds (fs), and energies in kcal/mol), the
+Ångströms (Å), times in femtoseconds (fs), and energies in (kcal/mol)), the
 ``atom_style`` is ``molecular`` (therefore atoms are point
 particles that can form bonds with each other), and the boundary
 conditions are fixed.  The boundary conditions do not matter here, as
@@ -64,8 +66,8 @@ potential.
 The ``bond_style``, ``angle_style``, ``dihedral_style``, and ``improper_style``
 commands specify the different potentials used to constrain the relative
 positions of the atoms.  The ``special_bonds`` command sets the weighting factors
-for the Lennard-Jones interactions between atoms directly connected by
-one bond, two bonds, and three bonds, respectively.  This is done for
+for the Lennard-Jones interactions between atoms sitting one,
+two, or three bonds away from each other, respectively. This is done for
 convenience when parameterizing the force constants for bonds, angles, and
 so on.  By excluding the non-bonded (Lennard-Jones) interactions for
 these pairs, those interactions do not need to be considered when determining
@@ -174,7 +176,9 @@ just before the ``run 0`` command:
     set group cnt_mid mol 3
 
 With the three ``set`` commands, we assign unique, otherwise unused
-molecule IDs to atoms in those three groups.  We will use this IDs later to
+molecule IDs to atoms in those three groups.  A molecule ID is an
+integer that groups atoms into a *molecule* for bookkeeping purposes, and can be
+useful for tracking and post-processing.  We will use this IDs later to
 assign different colors to these groups of atoms.
 
 Run the simulation using LAMMPS.  The number of atoms in each group is given in
@@ -235,6 +239,14 @@ The ``fix nve`` commands are applied to the atoms of ``cnt_top`` and
 from these groups are recalculated at every step.  The ``fix nvt`` does the  
 same for the ``cnt_mid`` group, while also applying a Nosé-Hoover thermostat  
 with desired temperature of 300 K :cite:`nose1984unified, hoover1985canonical`.  
+
+.. admonition:: Note
+    :class: non-title-info
+
+    The Nosé-Hoover thermostat only controls the temperature of
+    the atoms belonging to the specified ``cnt_mid`` group.  Atoms outside
+    this group are not affected by the thermostat.
+
 To restrain the motion of the atoms at the edges, let us add the following  
 commands to **unbreakable.lmp**:
 
@@ -248,7 +260,10 @@ commands to **unbreakable.lmp**:
 The two ``setforce`` commands cancel the forces applied on the atoms of the  
 two edges, respectively.  The cancellation of the forces is done at every step,  
 and along all 3 directions of space, :math:`x`, :math:`y`, and :math:`z`, due to the use of  
-``0 0 0``.  The two ``velocity`` commands set the initial velocities  
+``0 0 0``.  Although the forces on these atoms is set to zero,
+the ``fix`` still stores the forces acting on the group before
+cancellation, which can later be extracted for analysis (see below).
+The two ``velocity`` commands set the initial velocities  
 along :math:`x`, :math:`y`, and :math:`z` to 0 for the atoms of ``cnt_top`` and  
 ``cnt_bot``, respectively.  As a consequence of these last four commands,  
 the atoms of the edges will remain immobile during the simulation (or at least  

docs/sphinx/source/tutorial3/tutorial.rst

@@ -151,7 +151,8 @@ Add the following line into **water.lmp**:
 The ``fix npt`` allows us to impose both a temperature of :math:`300\,\text{K}`
 (with a damping constant of :math:`100\,\text{fs}`), and a pressure of 1 atmosphere
 (with a damping constant of :math:`1000\,\text{fs}`).  With the ``iso`` keyword,
-the three dimensions of the box will be re-scaled simultaneously.
+the three dimensions of the box will be re-scaled isotropically,
+maintaining the same proportion in all directions.
 
 Let us output the system into images by adding the following commands to **water.lmp**:
 

docs/sphinx/source/tutorial4/tutorial.rst

@@ -32,7 +32,7 @@ file in a text editor of your choice, and copy the following into it:
     The editor should display the following content corresponding to **create.lmp**
 
 These lines are used to define the most basic parameters, including the
-atom, bond, and angle styles, as well as interaction
+atom, bond, and angle styles, as well as the non-bonded interaction
 potential.  Here, ``lj/cut/tip4p/long`` imposes a Lennard-Jones potential with
 a cut-off at :math:`12\,\text{Å}` and a long-range Coulomb potential.
 The parameters ``O``, ``H``, ``O-H``, and ``H-O-H`` correspond
@@ -217,7 +217,7 @@ the force constant of the angular harmonic potential to 0 and the equilibrium
 angle to :math:`104.52^\circ`.
 
 Alongside **parameters.inc**, the **groups.inc** file contains
-several ``group`` commands to selects atoms based on their types:
+several ``group`` commands to define groups of atoms based on their types:
 
 .. code-block:: lammps
 
@@ -334,6 +334,16 @@ used to apply a restraint force when used during minimization.  This last keywor
 here, because the spring constants of the rigid water molecules were set
 to 0 (see the **parameters.inc** file).
 
+.. admonition:: Note
+    :class: non-title-info
+
+    LAMMPS provides several ways to maintain molecules rigid during a simulation. 
+    The ``fix shake`` command is appropriate for constraining bond lengths 
+    and angles within small molecules like water. 
+    However, it may fail for linear molecules like :math:`\text{CO}_2` or more complex rigid bodies. 
+    In such cases, the ``fix rigid`` family of commands can be used instead to
+    treat entire molecules or groups of atoms as rigid bodies.
+
 Let us also create images of the system and control
 the printing of thermodynamic outputs by adding the following lines
 to **equilibrate.lmp**: