Merge branch 'main' into review-livecoms

Author: simongravelle

docs/sphinx/source/tutorial1/tutorial.rst

@@ -495,7 +495,8 @@ the following:
         view 80 10 box yes 0.025 axes no 0.0 0.0 center s 0.483725 0.510373 0.510373
     dump_modify viz pad 9 boxcolor royalblue backcolor white adiam 1 1.6 adiam 2 4.8
 
-This command tells LAMMPS to generate NetPBM format images every 100  
+The $\&$ is used to continue the command on a new line.
+These commands tell LAMMPS to generate NetPBM format images every 100  
 steps.  The two ``type`` keywords are for *color* and  
 *diameter*, respectively.  Run the **initial.lmp** using  
 LAMMPS again, and a new window named ``Slide Show`` will pop up.  

docs/sphinx/source/tutorial3/tutorial.rst

@@ -86,6 +86,8 @@ lines into **water.lmp**:
     molecule h2omol water.mol
     create_atoms 0 random 700 87910 NULL mol h2omol 454756 overlap 1.0 maxtry 50
 
+The first parameter is 0, meaning that the atom IDs from
+the **water.mol** file will be used.
 The ``overlap 1.0`` option of the ``create_atoms`` command ensures
 that no atoms are placed exactly in the same position, as this would cause the
 simulation to crash.  The ``maxtry 50`` asks LAMMPS to try at most 50 times
@@ -139,7 +141,9 @@ Resetting the step of the simulation to 0 using the
 ``reset_timestep`` command is optional.
 It is used here because the number of iterations performed by the ``minimize``
 command is usually not a round number, since the minimization stops when one of
-four criteria is reached.  We will use ``fix npt`` to control the temperature
+four criteria is reached, which can disrupt the intended frequency
+of outputs such as ``dump`` commands that depend on the timestep count.
+We will use ``fix npt`` to control the temperature
 and pressure of the molecules with a Nosé-Hoover thermostat and barostat,
 respectively :cite:`nose1984unified, hoover1985canonical, martyna1994constant`.
 Add the following line into **water.lmp**:

docs/sphinx/source/tutorial4/tutorial.rst

@@ -48,7 +48,7 @@ of ``lj/cut/tip4p/long`` instead of ``lj/cut/coul/long``, and ``pppm/tip4p``
 instead of ``pppm``.  When using ``lj/cut/tip4p/long`` and ``pppm/tip4p``,
 the interactions resemble the conventional Lennard-Jones and Coulomb interactions,
 except that they are specifically designed for the four-point water model.  As a result,
-LAMMPS automatically creates a four-point water molecule, assigning type O
+LAMMPS automatically adds the fourth point to the water molecules, assigning type O
 atoms as oxygen and type H atoms as hydrogen.  The fourth massless atom (M) of the
 TIP4P water molecule does not have to be defined explicitly, and the value of
 :math:`0.1546\,\text{Å}` corresponds to the O-M distance of the
@@ -532,8 +532,8 @@ commands to **shearing.lmp**:
     velocity walltop set 2e-4 NULL NULL
 
 The ``setforce`` commands cancel the forces on ``walltop`` and
-``wallbot``.  As a result, the atoms in these two groups will not
-experience any forces from the rest of the system.  Consequently, in the absence of
+``wallbot`` in the :math:`x` direction.  As a result, the atoms in these two groups will not
+experience any forces along :math:`x` from the rest of the system.  Consequently, in the absence of
 external forces, these atoms will conserve the initial velocities imposed by the
 two ``velocity`` commands.  As seen previously, although the
 forces on these atoms are set to zero, the ``fix setforce`` still stores the

docs/sphinx/source/tutorial6/tutorial.rst

@@ -226,14 +226,17 @@ classical textbooks like Ref. :cite:`frenkel2023understanding`.
 Adapting the pair style
 -----------------------
 
-For this next step, we need to define the parameters for the water molecules and
-the cross-interactions between water and silica. The TIP4P/2005 model is employed
-for the water :cite:`abascal2005general`, while no specific parameters are set
-for the silica itself. The atoms of the silica will remain frozen during this part.
+For this next step, we need to specify the force field used to
+model the interactions in the system. The TIP4P/2005 model is employed
+for the water :cite:`abascal2005general`, while no interaction within
+silica is defined, as it will be seen farther below. This is be-
+cause atoms of the silica will remain frozen during this part of the simulation.
 Only the cross-interactions between water and silica need
 to be defined. Create a new file called **gcmc.lmp**, and copy the following
 lines into it:
 
+Create a new file called **gcmc.lmp**, and copy the following lines into it:
+
 .. code-block:: lammps
 
     units metal

docs/sphinx/source/tutorial7/tutorial.rst

@@ -388,15 +388,15 @@ central part of the box.
     Add FIGURE US-system-biased Snapshot of the system simulated during the umbrella sampling
     step of \hyperref[umbrella-sampling-label]{Tutorial 7}, showing type-1 atoms
     in cyan and the type-2 atom in red.  Only the type-2 atom explores the central part of the box,
-    ``mymes``, due to the additional biasing potential :math:`V`. Parmaeters are
+    ``mymes``, due to the additional biasing potential :math:`V`. Parameters are
     :math:`U_0 = 2.38~\text{kcal/mol}`, :math:`\delta = 1.0~\text{Å}`, and :math:`x_0 = 10~\text{Å}`.
 
 Now, we create a loop with 15 steps and progressively move the center of the
 bias potential by increments of 0.4 nm.  Add the following lines to **umbrella-sampling.lmp**:
 
 .. code-block:: lammps
 
-    variable a loop 25
+    variable a loop 15
     label loop
 
     variable xdes equal 4*${a}-32

docs/sphinx/source/tutorial8/figures/REACT-mixing-dm.png

@@ -124,7 +124,7 @@ For visualization purposes, the atoms from the CNT ``group`` is moved
 to the center of the box using ``fix recenter``.
 As the time progresses, the system density,
 :math:`\rho`, gradually converges toward the target value
-of :math:`0.8`\,g/cm:math:`^3`.
+of :math:`0.9`\,g/cm:math:`^3`.
 Meanwhile, the total energy of the system initially evolves rapidly, reflecting the
 densification process, and then eventually stabilizes.