updated tutorials

Author: simongravelle

docs/sphinx/source/_static/custom.css

@@ -169,3 +169,13 @@ a:active {
 section {
   text-align: justify;
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+code {
+  border: none;
+  box-shadow: none;
+  outline: none;
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+strong {
+  font-weight: 550;
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docs/sphinx/source/tutorial1/tutorial.rst

@@ -1,14 +1,13 @@
-
 Prepare and relax
 =================
 
 
 The first step is to relax the structure with ReaxFF, which which will be achieved using
 molecular dynamics.  To ensure the system equilibrates properly, we will monitor certain
 parameters over time, such as the system volume.  To set up this
-tutorial, select *Start Tutorial 5* from the
-*Tutorials* menu of LAMMPS--GUI and follow the instructions.
-The editor should display the following content corresponding to *relax.lmp*:
+tutorial, select ``Start Tutorial 5`` from the
+``Tutorials`` menu of LAMMPS--GUI and follow the instructions.
+The editor should display the following content corresponding to **relax.lmp**:
 
 .. code-block:: lammps
 
@@ -17,15 +16,14 @@ The editor should display the following content corresponding to *relax.lmp*:
 
     read_data silica.data
 
-
 So far, the input is very similar to what was seen in the previous tutorials.
-Some basic parameters are defined (*units* and *atom_style*),
-and a *.data* file is imported by the *read\ data* command.
+Some basic parameters are defined (``units`` and ``atom_style``),
+and a **.data** file is imported by the ``read_data`` command.
 
 The initial topology given by \href{\filepath tutorial5/silica.data}{\dwlcmd{silica.data}}
 is a small amorphous silica structure.  This structure was created using a force field called
-Vashishta :cite:`vashishta1990interaction`.  If you open the *silica.data*
-file, you will find in the *Atoms* section that all silicon atoms have a
+Vashishta :cite:`vashishta1990interaction`.  If you open the **silica.data**
+file, you will find in the ``Atoms`` section that all silicon atoms have a
 charge of :math:`q = 1.1\,\text{e}`, and all oxygen atoms have a charge of :math:`q = -0.55\,\text{e}`.
 
 .. admonition:: Note
@@ -36,28 +34,28 @@ charge of :math:`q = 1.1\,\text{e}`, and all oxygen atoms have a charge of :math
     changes once ReaxFF is used: the charge of each atom will adjust to its local
     environment.
 
-Next, copy the following three crucial lines into the *relax.lmp* file:
+Next, copy the following three crucial lines into the **relax.lmp** file:
 
 .. code-block:: lammps
 
     pair_style reaxff NULL safezone 3.0 mincap 150
     pair_coeff * * reaxCHOFe.inc Si O
     fix myqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
 
-In this case, the *pair\ style reaxff* is used without a control file.  The
-*safezone* and *mincap* keywords are added to prevent
+In this case, the ``pair_style reaxff`` is used without a control file.  The
+``safezone`` and ``mincap`` keywords are added to prevent
 allocation issues, which sometimes can trigger segmentation faults and
-*bondchk* errors.  The *pair\ coeff* command uses the
+``bondchk`` errors.  The ``pair_coeff`` command uses the
 \href{\filepath tutorial5/reaxCHOFe.inc}{\dwlcmd{reaxCHOFe.inc}}
 file, which should have been downloaded during the tutorial set up.  Finally, the
-*fix qeq/reaxff* is used to perform charge equilibration :cite:`rappe1991charge`,
+``fix qeq/reaxff`` is used to perform charge equilibration :cite:`rappe1991charge`,
 which occurs at every step.  The values 0.0 and 10.0 represent the
 low and the high cutoffs, respectively, and :math:`1.0 \text{e} -6` is the tolerance.
-The *maxiter* sets an upper limit to the number of attempts to
+The ``maxiter`` sets an upper limit to the number of attempts to
 equilibrate the charge.
 
 
-Next, add the following commands to the *relax.lmp* file to track the
+Next, add the following commands to the **relax.lmp** file to track the
 evolution of the charges during the simulation:
 
 .. code-block:: lammps
@@ -68,20 +66,18 @@ evolution of the charges during the simulation:
     variable qO equal charge(grpO)/count(grpO)
     variable vq atom q
 
-To print the averaged charges *qSi* and *qO* using the
-*thermo_style* command, and create images of the system.  Add the
-following lines to *relax.lmp*:
+To print the averaged charges ``qSi`` and ``qO`` using the
+``thermo_style`` command, and create images of the system.  Add the
+following lines to **relax.lmp**:
 
 .. code-block:: lammps
 
     thermo 100
     thermo_style custom step temp etotal press vol v_qSi v_qO
-    dump viz all image 100 myimage-*.ppm q &
-    type shiny 0.1 box no 0.01 view 180 90 zoom 2.3 size 1200 500
-    dump_modify viz adiam Si 2.6 adiam O 2.3 backcolor white &
-    amap -1 2 ca 0.0 3 min royalblue 0 green max orangered
+    dump viz all image 100 myimage-*.ppm q type shiny 0.1 box no 0.01 view 180 90 zoom 2.3 size 1200 500
+    dump_modify viz adiam Si 2.6 adiam O 2.3 backcolor white amap -1 2 ca 0.0 3 min royalblue 0 green max orangered
 
-Here, the atoms are colored by their charges *q*, ranging from royal blue
+Here, the atoms are colored by their charges ``q``, ranging from royal blue
 (when :math:`q=-1\,\text{e}`) to orange-red (when :math:`q=2\,\text{e}`).
 
 ADD FIGURE SIO-deformed Amorphous silicon oxide after deformation.
@@ -91,24 +87,22 @@ about :math:`1.8~\text{e}`  appear in red/orange, and bulk O atoms with a charge
 about :math:`-0.9 ~ \text{e}` appear in blue.
 
 We can generate histograms of the charges for each atom type using
-*fix ave/histo* commands:
+``fix ave/histo`` commands:
 
 .. code-block:: lammps
 
-    fix myhis1 grpSi ave/histo 10 500 5000 -1.5 2.5 1000 v_vq &
-    file relax-Si.histo mode vector
-    fix myhis2 grpO ave/histo 10 500 5000 -1.5 2.5 1000 v_vq &
-    file relax-O.histo mode vector
+    fix myhis1 grpSi ave/histo 10 500 5000 -1.5 2.5 1000 v_vq file relax-Si.histo mode vector
+    fix myhis2 grpO ave/histo 10 500 5000 -1.5 2.5 1000 v_vq file relax-O.histo mode vector
 
-We can also use the *fix reaxff/species* to evaluate what species are
+We can also use the ``fix reaxff/species`` to evaluate what species are
 present within the simulation.  It will be useful later when the system is deformed,
 and bonds are broken:
 
 .. code-block:: lammps
 
     fix myspec all reaxff/species 5 1 5 relax.species element Si O
 
-Here, the information will be printed every 5 steps in a file called *relax.species*.
+Here, the information will be printed every 5 steps in a file called **relax.species**.
 Let us perform a very short run using the anisotropic NPT command and relax the
 density of the system:
 
@@ -122,8 +116,8 @@ density of the system:
 
     write_data relax.data
 
-Run the *relax.lmp* file using LAMMPS.  As seen from *relax.species*,
-only one species is detected, called *O384Si192*, representing the entire system.
+Run the **relax.lmp** file using LAMMPS.  As seen from **relax.species**,
+only one species is detected, called ``O384Si192``, representing the entire system.
 
 As the simulation progresses, the charge of every atom fluctuates
 because it is adjusting to the local environment of the atom (Fig.~\ref{fig:SIO-charge}\,a).
@@ -133,7 +127,7 @@ to a rapid change in the system volume, which causes interatomic distances to
 shift quickly (Fig.~\ref{fig:SIO-charge}\,b).  The atoms with the
 most extreme charges are located at structural defects,
 such as dangling oxygen groups (Fig.~\ref{fig:SIO-slice}).
-Finally, the generated *.histo* files can be used to
+Finally, the generated **.histo** files can be used to
 plot the probability distributions, :math:`P(q)` (see Fig.~\ref{fig:SIO-distribution}\,a).
 
 FIGURE SIO-charge a) Average charge per atom of the silicon, :math:`q_\text{Si}`, atoms as
@@ -155,7 +149,7 @@ Deform the structure
 
 
 Let us apply a deformation to the structure to force some :math:`\text{Si}-\text{O}`
-bonds to break (and eventually re-assemble).  Open the *deform.lmp*
+bonds to break (and eventually re-assemble).  Open the **deform.lmp**
 file, which must contain the following lines:
 
 .. code-block:: lammps
@@ -177,21 +171,17 @@ file, which must contain the following lines:
 
     thermo 200
     thermo_style custom step temp etotal press vol v_qSi v_qO
-    dump viz all image 100 myimage-*.ppm q &
-    type shiny 0.1 box no 0.01 view 180 90 zoom 2.3 size 1200 500
-    dump_modify viz adiam Si 2.6 adiam O 2.3 backcolor white &
-    amap -1 2 ca 0.0 3 min royalblue 0 green max orangered
-
-    fix myhis1 grpSi ave/histo 10 500 5000 -1.5 2.5 1000 v_vq &
-    file deform-Si.histo mode vector
-    fix myhis2 grpO ave/histo 10 500 5000 -1.5 2.5 1000 v_vq &
-    file deform-O.histo mode vector
+    dump viz all image 100 myimage-*.ppm q type shiny 0.1 box no 0.01 view 180 90 zoom 2.3 size 1200 500
+    dump_modify viz adiam Si 2.6 adiam O 2.3 backcolor white amap -1 2 ca 0.0 3 min royalblue 0 green max orangered
+
+    fix myhis1 grpSi ave/histo 10 500 5000 -1.5 2.5 1000 v_vq file deform-Si.histo mode vector
+    fix myhis2 grpO ave/histo 10 500 5000 -1.5 2.5 1000 v_vq file deform-O.histo mode vector
     fix myspec all reaxff/species 5 1 5 deform.species element Si O
 
-The only difference with the previous *relax.lmp* file is the path to
-the *relax.data* file.
+The only difference with the previous **relax.lmp** file is the path to
+the **relax.data** file.
 
-Next, let us use *fix nvt* instead of *fix npt* to apply a
+Next, let us use ``fix nvt`` instead of ``fix npt`` to apply a
 Nosé-Hoover thermostat without a barostat:
 
 .. code-block:: lammps
@@ -200,7 +190,7 @@ Nosé-Hoover thermostat without a barostat:
     timestep 0.5
 
 Here, no barostat is used because the change in the box volume will be imposed
-by the *fix deform*.
+by the ``fix deform``.
 
 ADD FIGURE SIO-deformed-charge a) Average charge per atom of the silicon, :math:`q_\text{Si}`, atoms as
 a function of time, :math:`t`, during deformation of the :math:`\text{SiO}_2` system.
@@ -209,9 +199,9 @@ silica structure occurs near :math:`t = 11`\,ps.  b) Temperature, :math:`T`, of
 system as a function of :math:`t`.
 
 
-Let us run for 5000 steps without deformation, then apply the *fix deform*
+Let us run for 5000 steps without deformation, then apply the ``fix deform``
 to progressively elongate the box along the :math:`x`-axis during 25000 steps.  Add
-the following line to *deform.lmp*:
+the following line to **deform.lmp**:
 
 .. code-block:: lammps
 
@@ -223,7 +213,7 @@ the following line to *deform.lmp*:
 
     write_data deform.data
 
-Run the *deform.lmp* file using LAMMPS.  During the deformation, the charge
+Run the **deform.lmp** file using LAMMPS.  During the deformation, the charge
 values progressively evolve until the structure eventually breaks down.  After the
 structure breaks down, the charges equilibrate near new average values that differ
 from the initial averages (Fig.~\ref{fig:SIO-deformed-charge}\,a).  The difference
@@ -236,7 +226,7 @@ the material (Fig.~\ref{fig:SIO-deformed-charge}\,b).
 You can examine the charge distribution after deformation, as well as during
 deformation (Fig.~\ref{fig:SIO-distribution}\,b).  As expected, the final
 charge distribution slightly differs from the previously calculated one.  If
-no new species were formed during the simulation, the *deform.species* file
+no new species were formed during the simulation, the **deform.species** file
 should look like this:
 
 .. code-block:: lammps
@@ -248,7 +238,7 @@ should look like this:
         30000            1          1          1
 
 Sometimes, :math:`\text{O}_2` molecules are formed during the deformation.  If this occurs,
-a new column *O2* appears in the *deform.species* file.
+a new column ``O2`` appears in the **deform.species** file.
 
 Decorate the surface
 --------------------
@@ -257,9 +247,9 @@ Under ambient conditions, some of the surface :math:`\text{SiO}_2` atoms become
 passivated by forming covalent bonds with hydrogen (H) atoms :cite:`sulpizi2012silica`.
 We will add hydrogen atoms randomly to the cracked silica and observe how the
 system evolves.  To do so, we first need to modify the previously generated data
-file *deform.data* and make space for a third atom type.
-Copy *deform.data*, name the copy *deform-mod.data*, and modify the
-first lines of *deform-mod.data* as follows:
+file **deform.data** and make space for a third atom type.
+Copy **deform.data**, name the copy **deform-mod.data**, and modify the
+first lines of **deform-mod.data** as follows:
 
 .. code-block:: lammps
 
@@ -282,7 +272,7 @@ first lines of *deform-mod.data* as follows:
 
     (...)
 
-Open the *decorate.lmp* file, which must contain the following lines:
+Open the **decorate.lmp** file, which must contain the following lines:
 
 .. code-block:: lammps
 
@@ -296,12 +286,12 @@ Open the *decorate.lmp* file, which must contain the following lines:
     pair_coeff * * reaxCHOFe.inc Si O H
     fix myqeq all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
 
-The *displace_atoms* command is used to move the center of the
+The ``displace_atoms`` command is used to move the center of the
 crack near the center of the box.  This step is optional but makes for a nicer
 visualization.  A different value for the shift may be needed in
 your case, depending on the location of the crack.  A difference with the previous
-input is that three atom types are specified in the *pair_coeff* command, i.e.
-*Si O H*.
+input is that three atom types are specified in the ``pair_coeff`` command, i.e.
+``Si O H``.
 
 ADD FIGURE SIO-decorated Cracked silicon oxide after the addition of hydrogen atoms.
 The atoms are colored by their charges, with the newly added hydrogen atoms appearing as small
@@ -322,16 +312,12 @@ types of atoms, and output the charge values into log files:
     thermo 5
     thermo_style custom step temp etotal press v_qSi v_qO v_qH
 
-    dump viz all image 100 myimage-*.ppm q &
-    type shiny 0.1 box no 0.01 view 180 90 zoom 2.3 size 1200 500
-    dump_modify viz adiam Si 2.6 adiam O 2.3 adiam H 1.0 &
-    backcolor white amap -1 2 ca 0.0 3 min royalblue &
-    0 green max orangered
+    dump viz all image 100 myimage-*.ppm q type shiny 0.1 box no 0.01 view 180 90 zoom 2.3 size 1200 500
+    dump_modify viz adiam Si 2.6 adiam O 2.3 adiam H 1.0 backcolor white amap -1 2 ca 0.0 3 min royalblue 0 green max orangered
 
-    fix myspec all reaxff/species 5 1 5 decorate.species &
-    element Si O H
+    fix myspec all reaxff/species 5 1 5 decorate.species element Si O H
 
-Here, the :math:`+1 \mathrm{e}{-10}` was added to the denominator of the *variable qH*
+Here, the :math:`+1 \mathrm{e}{-10}` was added to the denominator of the ``variable qH``
 to avoid dividing by 0 at the beginning of the simulation.  Finally, let us
 create a loop with 10 steps, and create two hydrogen atoms at random locations at
 every step:
@@ -353,7 +339,7 @@ every step:
     jump SELF loop
 
 Run the simulation with LAMMPS.  When the simulation is over,
-it can be seen from the *decorate.species* file that
+it can be seen from the **decorate.species** file that
 all the created hydrogen atoms reacted with the :math:`\text{SiO}_{2}` structure to
 form surface groups (such as hydroxyl (-OH) groups).