added figures

Author: simongravelle

docs/sphinx/source/tutorial3/tutorial.rst

@@ -117,7 +117,7 @@ or the IDs of the atoms that are connected by bonds and angles.
 
 ..  container:: figurelegend
 
-    a) Temperature, :math:`T`, of the water reservoir as a function of the
+    Figure: a) Temperature, :math:`T`, of the water reservoir as a function of the
     time, :math:`t`.  The horizontal dashed line is the target temperature
     of :math:`300 \text{K}`. b) Evolution of the system density, :math:`\rho`, with :math:`t`
 
@@ -151,8 +151,18 @@ 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.
 
-INSERT FIGURE PEG-water The water reservoir from \hyperref[all-atom-label]{Tutorial 3}
-after equilibration.  Oxygen atoms are in red, and hydrogen atoms are in white. 
+.. 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**:
 
@@ -222,11 +232,20 @@ Now that the water reservoir is equilibrated, we can safely add the PEG polymer
 to the water.  The PEG molecule topology was downloaded from the ATB repository
 :cite:`malde2011automated, oostenbrink2004biomolecular`.  It has a formula
 :math:`\text{C}_{16}\text{H}_{34}\text{O}_{9}`, and the parameters are taken from
-the {GROMOS} 54A7 force field :cite:`schmid2011definition` (Fig.~\ref{fig:PEG-in-vacuum}).
+the GROMOS 54A7 force field :cite:`schmid2011definition`.
+
+.. figure:: figures/singlePEG-light.png
+    :alt: PEG in vacuum as simulated with LAMMPS
+    :class: only-light
+
+.. figure:: figures/singlePEG-dark.png
+    :alt: PEG in vacuum as simulated with LAMMPS
+    :class: only-dark
+
+..  container:: figurelegend
 
-INSERT FIGURE PEG-in-vacuum
-The PEG molecule from \hyperref[all-atom-label]{Tutorial 3}.
-The carbon atoms are in gray, the oxygen atoms in red, and the hydrogen atoms in white.
+    Figure: The PEG molecule with carbon atoms in gray, oxygen atoms in red,
+    and hydrogen atoms in white.
 
 Open the file named **merge.lmp** that was downloaded
 alongside **water.lmp** during the tutorial setup.  It only contain one line:
@@ -311,9 +330,20 @@ Let us create images of the systems:
         acolor OAlc darkred adiam OAlc 2.6
     thermo 500
 
-Inlude PEG-solvated figure : The PEG molecule solvated in water.
+.. 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.
 
-inally, to perform a short equilibration and save the final state to
+Finally, to perform a short equilibration and save the final state to
 a **.restart** file, add the following lines to the input:
 
 .. code-block:: lammps
@@ -363,7 +393,17 @@ 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.
 
-Add figure PEG-in-water PEG molecule stretched along the :math:`x` direction in water.
+.. 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:
 
@@ -394,7 +434,7 @@ the following lines to **pull.lmp**:
 
 ..  container:: figurelegend
 
-    a) Evolution of the radius of gyration :math:`R_\text{gyr}` of the PEG molecule,
+    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.
 

docs/sphinx/source/tutorial4/tutorial.rst

@@ -261,10 +261,20 @@ file.  With the ``nocoeff`` option, the parameters from the force field are
 not included in the **.data** file.  Run the **create.lmp** file using LAMMPS,
 and a file named **create.data** will be created alongside **create.lmp**.
 
-ADD FIGURE NANOSHEAR-system -- Side view of the system.  Periodic images are represented in darker colors.
-Water molecules are in red and white, :math:`\text{Na}^+` ions in purple, :math:`\text{Cl}^-`
-ions in lime, and wall atoms in gray.  Note the absence of atomic defect at the
-cell boundaries.
+.. figure:: figures/systemcreation-light.png
+    :alt: LAMMPS: electrolyte made of water and salt between walls
+    :class: only-light
+
+.. figure:: figures/systemcreation-dark.png
+    :alt: LAMMPS: electrolyte made of water and salt between walls
+    :class: only-dark
+
+..  container:: figurelegend
+
+    Figure: Side view of the system.  Periodic images are represented in darker colors.
+    Water molecules are in red and white, :math:`\text{Na}^+` ions in purple, :math:`\text{Cl}^-`
+    ions in lime, and wall atoms in gray.  Note the absence of atomic defect at the
+    cell boundaries.
 
 \paragraph{Energy minimization}
 
@@ -417,7 +427,7 @@ the end of the simulation (Fig.~\ref{fig:NANOSHEAR-equilibration}).
 
 ..  container:: figurelegend
 
-    a) Pressure, :math:`p`, of the nanosheared electrolyte system as a function
+    Figure: a) Pressure, :math:`p`, of the nanosheared electrolyte system as a function
     of the time, :math:`t`.  b) Distance between the walls, :math:`\Delta z`, as a
     function of :math:`t`.
 
@@ -496,7 +506,7 @@ two ``velocity`` commands.
 
 ..  container:: figurelegend
 
-    Velocity profiles for water (blue) and walls (orange) along the :math:`z`-axis.
+    Figure: Velocity profiles for water (blue) and walls (orange) along the :math:`z`-axis.
 
 Finally, let us generate images of the systems and print the values of the
 forces exerted by the fluid on the walls, as given by ``f_mysf1[1]``

docs/sphinx/source/tutorial5/tutorial.rst

@@ -1,7 +1,6 @@
 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
@@ -86,11 +85,20 @@ following lines to **relax.lmp**:
 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.
-The atoms are colored by their
-charges.  Dangling oxygen groups appear in greenish, bulk Si atoms with a charge of
-about :math:`1.8~\text{e}`  appear in red/orange, and bulk O atoms with a charge of
-about :math:`-0.9 ~ \text{e}` appear in blue.
+.. figure:: figures/silicon-light.png
+    :alt: Amorphous silica colored by charges using VMD
+    :class: only-light
+
+.. figure:: figures/silicon-dark.png
+    :alt: Amorphous silica colored by charges using VMD
+    :class: only-dark
+
+..  container:: figurelegend
+
+    Figure: Amorphous silicon oxide. The atoms are colored by their
+    charges.  Dangling oxygen groups appear in greenish, bulk Si atoms with a charge of
+    about :math:`1.8~\text{e}`  appear in red/orange, and bulk O atoms with a charge of
+    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:
@@ -150,10 +158,20 @@ plot the probability distributions, :math:`P(q)` (see Fig.~\ref{fig:SIO-distribu
     a function of time, :math:`t`, during equilibration of the :math:`\text{SiO}_2`
     system.  b) Volume of the system, :math:`V`, as a function of :math:`t`.
 
-FIGURE SIO-slice A slice of the amorphous silica, where atoms are colored by their charges.
-Dangling oxygen groups appear in greenish, bulk Si atoms with a charge of about
-:math:`1.8~\text{e}`  appear in red/orange, and bulk O atoms with a charge of about
-:math:`-0.9~\text{e}` appear in blue.
+.. figure:: figures/deformed-light.png
+    :alt: Amorphous silica colored by charges using VMD
+    :class: only-light
+
+.. figure:: figures/deformed-dark.png
+    :alt: Amorphous silica colored by charges using VMD
+    :class: only-dark
+
+..  container:: figurelegend
+
+    Figure: A slice of the amorphous silica after deformation, where atoms are colored by their charges.
+    Dangling oxygen groups appear in greenish, bulk Si atoms with a charge of about
+    :math:`1.8~\text{e}`  appear in red/orange, and bulk O atoms with a charge of about
+    :math:`-0.9~\text{e}` appear in blue.
 
 .. figure:: figures/SIO-distribution-dm.png
     :class: only-dark