fixed tutorials 1 2 and 7

Author: simongravelle

docs/sphinx/source/tutorial1/tutorial.rst

@@ -31,9 +31,7 @@ file in a text editor of your choice, and copy the following into it:
     the LAMMPS--GUI Editor window.
 
 Everything that appears after a hash symbol (#) is a comment
-and ignored by LAMMPS.
-.. LAMMPS-GUI will color such comments in red.
-These five categories are not required in every input script an do not
+and ignored by LAMMPS. These five categories are not required in every input script an do not
 necessarily need to be in that exact order.  For instance, the ``Settings``
 and the ``Visualization`` categories could be inverted, or
 the ``Visualization`` category could be omitted.  However, note that

docs/sphinx/source/tutorial2/tutorial.rst

@@ -208,10 +208,6 @@ that starts at :math:`2 \, \text{Å}` from the CNT edges:
 The ``delete_atoms`` command randomly deletes :math:`2\,\%` of the atoms from
 the ``rdel`` group, here about 10 atoms.
 
-ADD FIGURE -- The unbreakable CNT before the removal of atoms (top),
-after the removal of 10 atoms from the *rmid*
-region (middle), and after deformation (bottom).
-
 The molecular dynamics
 ----------------------
 
@@ -242,7 +238,7 @@ The ``fix nve`` commands are applied to the atoms of ``cnt_top`` and
 ``cnt_bot``, respectively, and will ensure that the positions of the atoms  
 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`.  
+with desired temperature of 300 K :cite:`nose1984unified, hoover1985canonical`.  
 To restrain the motion of the atoms at the edges, let us add the following  
 commands to **unbreakable.lmp**:
 
@@ -312,11 +308,21 @@ command in **unbreakable.lmp** with the following lines:
 With the ``thermo_modify`` command, we specify to LAMMPS that the  
 temperature :math:`T_\mathrm{mid}` of the middle group, ``cnt_mid``,  
 must be outputted, instead of the temperature of the entire system.  
-This choice is motivated by the presence of frozen parts with an effective temperature of :math:`0 \text{K}`,  
+This choice is motivated by the presence of frozen parts with an effective temperature of :math:`0~\text{K}`,  
 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**  

docs/sphinx/source/tutorial7/tutorial.rst

@@ -30,9 +30,11 @@ favorable area to explore.
 Basic LAMMPS parameters
 -----------------------
 
-Create a folder if needed and
-place the initial input file, **free-energy.lmp**, into it. Then, open the 
-file in a text editor of your choice, and copy the following into it:
+To begin this tutorial, if you are using LAMMPS--GUI, select ``Start Tutorial 7``
+from the ``Tutorials`` menu and follow the instructions. Alternatively, if you are
+not using LAMMPS--GUI, create a new folder and add a file named
+**free-energy.lmp**. Open the file in a text editor and paste in the following
+content:
 
 .. code-block:: lammps
 
@@ -48,12 +50,6 @@ file in a text editor of your choice, and copy the following into it:
     pair_modify shift yes
     boundary p p p
 
-.. admonition:: If you are using LAMMPS-GUI
-    :class: gui
-
-    To begin this tutorial, select ``Start Tutorial 7`` from the
-    ``Tutorials`` menu of LAMMPS--GUI and follow the instructions.
-
 Here, we begin by defining variables for the Lennard-Jones interaction
 :math:`\sigma` and :math:`\epsilon` and for the repulsive potential
 :math:`U`, which are :math:`U_0`, :math:`\delta`, and
@@ -152,10 +148,18 @@ referred to as ``mymes``, using the ``n_center`` variable:
     thermo_style custom step temp etotal v_n_center
     thermo 10000
 
-    dump viz all image 50000 myimage-*.ppm type type shiny 0.1 box yes 0.01 view 180 90 zoom 6 size 1600 500 fsaa yes
-    dump_modify viz backcolor white acolor 1 cyan adiam 1 3 boxcolor black
+For visualization, use one of the following options: the ``dump image`` command to
+create .ppm images of the system, or the ``dump atom`` command to write a
+VMD-compatible trajectory to a file:
+
+.. code-block:: lammps
+
+    # Option 1
+    dump viz1 all image 50000 myimage-*.ppm type type shiny 0.1 box yes 0.01 view 180 90 zoom 6 size 1600 500 fsaa yes
+    dump_modify viz1 backcolor white acolor 1 cyan adiam 1 3 boxcolor black
 
-A ``dump image`` command was also added for system visualization.
+    # Option 2
+    dump viz2 all atom 50000 free-energy.lammpstrj
 
 Finally, let us perform an equilibration of 50000 steps,
 using a timestep of :math:`2\,\text{fs}`, corresponding to a total duration of :math:`100\,\text{ps}`:
@@ -213,6 +217,8 @@ LAMMPS.
     :class: only-light
     :alt: Density from umbrella sampling simulations
 
+..  container:: figurelegend
+
     Figure: Snapshot of the system simulated during the free sampling step of the tutorial.
     The atoms density is the lowest in the central part of the box, ``mymes``.  Here,
     :math:`U_0 = 0.36~\text{kcal/mol}`, :math:`\delta = 1.0~\text{Å}`, and :math:`x_0 = 10~\text{Å}`.
@@ -279,8 +285,9 @@ unbiased free energy profile.
 LAMMPS input script
 -------------------
 
-Open the file named **umbrella-sampling.lmp**, which should
-contain the following lines:
+If you are using LAMMPS--GUI, open the file named **free-energy.lmp**.  
+Alternatively, if you are not using LAMMPS--GUI, create a new input file  
+and paste in the following content:
 
 .. code-block:: lammps
 
@@ -341,9 +348,12 @@ umbrella sampling run:
 
     thermo 5000
 
-    dump viz all image 50000 myimage-*.ppm type type shiny 0.1 box yes 0.01 view 180 90 zoom 6 size 1600 500 fsaa yes
-    dump_modify viz backcolor white acolor 1 cyan &
-    acolor 2 red adiam 1 3 adiam 2 3 boxcolor black
+    # Option 1
+    dump viz1 all image 50000 myimage-*.ppm type type shiny 0.1 box yes 0.01 view 180 90 zoom 6 size 1600 500 fsaa yes
+    dump_modify viz1 backcolor white acolor 1 cyan acolor 2 red adiam 1 3 adiam 2 3 boxcolor black
+
+    # Option 2
+    dump viz2 all atom 50000 free-energy.lammpstrj
 
     timestep 2.0
     run 50000