added figures into tutorials

Author: simongravelle

docs/sphinx/source/converter/main.rst

@@ -340,12 +340,20 @@ shows a non-linear increase with :math:`t` once the deformation starts, which is
 from the typical dependency of bond energy with bond distance,
 :math:`U_\text{b} = k_\text{b} \left( r - r_0 \right)^2`.
 
-INCLUDE FIGURE CNT-unbreakable-length-energy -- a) Evolution
-of the length :math:`L_\text{cnt}` of the CNT with time.  
-The CNT starts deforming at :math:`t = 5\,\text{ps}`, and :math:`L_\text{cnt-0}` is the  
-CNT initial length.
-b) Evolution of the total energy :math:`E` of the system with time :math:`t`.  
-Here, the potential is OPLS-AA, and the CNT is unbreakable.
+.. figure:: figures/CNT-unbreakable-length-energy-dm.png
+    :class: only-dark
+    :alt: Evolution of the CNT energy
+
+.. figure:: figures/CNT-unbreakable-length-energy.png
+    :class: only-light
+    :alt: Evolution of the CNT energy
+
+..  container:: figurelegend
+
+    a) Evolution of the length :math:`L_\text{cnt}` of the CNT with time.  
+    The CNT starts deforming at :math:`t = 5\,\text{ps}`, and :math:`L_\text{cnt-0}` is the  
+    CNT initial length.  b) Evolution of the total energy :math:`E` of the system with time :math:`t`.  
+    Here, the potential is OPLS-AA, and the CNT is unbreakable.
 
 Importing YAML log file into Python
 -----------------------------------
@@ -522,12 +530,22 @@ curve reveals a linear (elastic) regime where
 
     <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a>
 
-ADD FIGURE CNT-breakable-stress-energy -- a) Evolution of the total energy :math:`E` of the CNT with time :math:`t`.
-b) Stress applied on the CNT during deformation, :math:`F_\text{cnt}/A_\text{cnt}`,
-where :math:`F_\text{cnt}` is the force and :math:`A_\text{cnt}` the CNT surface area,
-as a function of the strain, :math:`\Delta L_\text{cnt} = (L_\text{cnt}-L_\text{cnt-0}/L_\text{cnt-0})`, where
-:math:`L_\text{cnt}` is the CNT length and :math:`L_\text{cnt-0}` the CNT initial length.
-Here, the potential is AIREBO, and the CNT is breakable.
+.. figure:: figures/CNT-breakable-stress-energy-dm.png
+    :class: only-dark
+    :alt: Evolution of the CNT energy
+
+.. figure:: figures/CNT-breakable-stress-energy.png
+    :class: only-light
+    :alt: Evolution of the CNT energy
+
+..  container:: figurelegend
+
+    a) Evolution of the total energy :math:`E` of the CNT with time :math:`t`.  b) Stress applied on the CNT
+    during deformation, :math:`F_\text{cnt}/A_\text{cnt}`,
+    where :math:`F_\text{cnt}` is the force and :math:`A_\text{cnt}` the CNT surface area,
+    as a function of the strain, :math:`\Delta L_\text{cnt} = (L_\text{cnt}-L_\text{cnt-0}/L_\text{cnt-0})`, where
+    :math:`L_\text{cnt}` is the CNT length and :math:`L_\text{cnt-0}` the CNT initial length.
+    Here, the potential is AIREBO, and the CNT is breakable.
 
 Tip: bonds representation with AIREBO
 -------------------------------------

docs/sphinx/source/converter/tex-to-rst.py

@@ -61,9 +61,9 @@ distances, etc).  Thus add to **water.lmp** the line:
 
     This tutorial uses type labels :cite:`typelabel_paper` to map each
     numeric atom type to a string (see the **parameters.inc** file):
-    \lmpcmdnote{labelmap atom 1 OE 2 C 3 HC 4 H 5 CPos 6 OAlc 7 OW 8 HW}
+    ``labelmap atom 1 OE 2 C 3 HC 4 H 5 CPos 6 OAlc 7 OW 8 HW``
     Therefore, the oxygen and hydrogen atoms of water (respectively types
-    7 and 8) can be referred to as `OW' and `HW', respectively.  Similar
+    7 and 8) can be referred to as ``OW`` and ``HW``, respectively.  Similar
     maps are used for the bond types, angle types, and dihedral types.
 
 Let us create water molecules.  To do so, let us import a molecule template called
@@ -96,9 +96,19 @@ next to **water.lmp**.  This template contains the necessary
 structural information of a water molecule, such as the number of atoms,
 or the IDs of the atoms that are connected by bonds and angles.
 
-INSERT-FIGURE PEG-density a) Temperature, :math:`T`, of the water reservoir from :ref:`all-atom-label`
-as a function of the time, :math:`t`.  The horizontal dashed line is the target temperature of 300\,K.
-b) Evolution of the system density, :math:`\rho`, with :math:`t`
+.. figure:: figures/PEG-density-dm.png
+    :class: only-dark
+    :alt: Evolution of the water reservoir density
+
+.. figure:: figures/PEG-density.png
+    :class: only-light
+    :alt: Evolution of the water reservoir density
+
+..  container:: figurelegend
+
+    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`
 
 Then, let us organize the atoms of types OW and HW of the water
 molecules in a group named ``H2O`` and perform a small energy
@@ -130,7 +140,6 @@ 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. 
 
@@ -361,11 +370,19 @@ the following lines to **pull.lmp**:
     fix mynvt all nvt temp 300 300 100
     fix myrct PEG recenter 0 0 0 shift all
 
-Add figure PEG-distance - a) Evolution of
-the radius of gyration :math:`R_\text{gyr}` of the PEG molecule
-from \hyperref[all-atom-label]{Tutorial 3}, 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.
+.. figure:: figures/PEG-distance-dm.png
+    :class: only-dark
+    :alt: Evolution of the polymer radius of gyration
+
+.. figure:: figures/PEG-distance.png
+    :class: only-light
+    :alt: Evolution of the polymer radius of gyration
+
+..  container:: figurelegend
+
+    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.
 
 To investigate the stretching of the PEG molecule, let us compute its radius of
 gyration :cite:`fixmanRadiusGyrationPolymer1962a` and the angles of its dihedral

docs/sphinx/source/tutorial2/figures/CNT-breakable-stress-energy-dm.png

@@ -400,8 +400,19 @@ the end of the simulation (Fig.~\ref{fig:NANOSHEAR-equilibration}).
     temperature :cite:`mills1955remeasurement`, one finds that the equilibration
     should be on the order of one nanosecond.
 
-ADD figure NANOSHEAR-equilibration 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`.
+.. figure:: figures/NANOSHEAR-equilibration-dm.png
+    :class: only-dark
+    :alt: Evolution of the pressure and distance for the elecrolyte
+
+.. figure:: figures/NANOSHEAR-equilibration.png
+    :class: only-light
+    :alt: Evolution of the pressure and distance for the elecrolyte
+
+..  container:: figurelegend
+
+    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`.
 
 Imposed shearing
 ----------------
@@ -468,8 +479,17 @@ experience any forces from the rest of the system.  Consequently, in the absence
 external forces, these atoms will conserve the initial velocities imposed by the
 two ``velocity`` commands.
 
-Add figure NANOSHEAR-profiles Velocity profiles for water (blue) and walls (orange) along the :math:`z`-axis.
+.. figure:: figures/NANOSHEAR-profiles-dm.png
+    :class: only-dark
+    :alt: Velocity profiles for the elecrolyte
+
+.. figure:: figures/NANOSHEAR-profiles.png
+    :class: only-light
+    :alt: Velocity profiles for the elecrolyte
+
+..  container:: figurelegend
 
+    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/tutorial2/figures/CNT-breakable-stress-energy.png

@@ -130,19 +130,38 @@ such as dangling oxygen groups (Fig.~\ref{fig:SIO-slice}).
 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
-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:: figures/SIO-charge-dm.png
+    :class: only-dark
+    :alt: Average charge per atom of the silicon
+
+.. figure:: figures/SIO-charge.png
+    :class: only-light
+    :alt: Average charge per atom of the silicon
+
+..  container:: figurelegend
+
+    a) Average charge per atom of the silicon, :math:`q_\text{Si}`, atoms as
+    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 SIO-distribution a) Probability distributions of charge of silicon (positive, blue) and oxygen
-(negative, orange) atoms during the equilibration of the :math:`\text{SiO}_2` system
-from \hyperref[reactive-silicon-dioxide-label]{Tutorial 5}.  b) Same probability distributions
-as in panel (a) after the deformation.
+.. figure:: figures/SIO-distribution-dm.png
+    :class: only-dark
+    :alt: Average charge per atom of the silicon
+
+.. figure:: figures/SIO-distribution.png
+    :class: only-light
+    :alt: Average charge per atom of the silicon
+
+..  container:: figurelegend
+
+    a) Probability distributions of charge of silicon (positive, blue) and oxygen
+    (negative, orange) atoms during the equilibration of the :math:`\text{SiO}_2`
+    system.  b) Same probability distributions as in panel (a) after the deformation.
 
 Deform the structure
 --------------------
@@ -192,12 +211,21 @@ Nosé-Hoover thermostat without a barostat:
 Here, no barostat is used because the change in the box volume will be imposed
 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.
-The break down of the
-silica structure occurs near :math:`t = 11`\,ps.  b) Temperature, :math:`T`, of the
-system as a function of :math:`t`.
+.. figure:: figures/SIO-deformed-charge-dm.png
+    :class: only-dark
+    :alt: Evolution of the pressure and distance for the elecrolyte
+
+.. figure:: figures/SIO-deformed-charge.png
+    :class: only-light
+    :alt: Evolution of the pressure and distance for the elecrolyte
+
+..  container:: figurelegend
 
+    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.
+    The break down of the
+    silica structure occurs near :math:`t = 11`\,ps.  b) Temperature, :math:`T`, of the
+    system as a function of :math:`t`.
 
 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

docs/sphinx/source/tutorial2/figures/CNT-unbreakable-length-energy-dm.png

@@ -104,10 +104,19 @@ Here, an anisotropic barostat is used.
 Anisotropic barostats adjust the dimensions independently, which is
 generally suitable for a solid phase.
 
-FIGURE GCMC-dimension a) Temperature, :math:`T`, as a function of time, :math:`t`, during the annealing
-of the silica system.
-b) System density, :math:`\rho`, during the annealing process.  The vertical dashed lines
-mark the transition between the different phases of the simulation.
+.. figure:: figures/GCMC-dimension-dm.png
+    :class: only-dark
+    :alt: Temperature and density of the silicon
+
+.. figure:: figures/GCMC-dimension.png
+    :class: only-light
+    :alt: Temperature and density of the silicon
+
+..  container:: figurelegend
+
+    a) Temperature, :math:`T`, as a function of time, :math:`t`, during the annealing
+    of the silica system.  b) System density, :math:`\rho`, during the annealing process.  The vertical dashed lines
+    mark the transition between the different phases of the simulation.
 
 Run the simulation using LAMMPS.  From the ``Charts`` window, the temperature
 evolution can be observed, showing that it closely follows the desired annealing procedure (Fig.~\ref{fig:GCMC-dimension}\,a).
@@ -384,7 +393,17 @@ Finally, let us print some information and run for 25 ps:
 
     run 25000
 
-ADD FIGURE GCMC-number Number of water molecules, :math:`N_\text{H2O}`, as a function of time, :math:`t`.
+.. figure:: figures/GCMC-number-dm.png
+    :class: only-dark
+    :alt: Number of water molecules from GCMC somulations
+
+.. figure:: figures/GCMC-number.png
+    :class: only-light
+    :alt: Number of water molecules from GCMC somulations
+
+..  container:: figurelegend
+
+    Number of water molecules, :math:`N_\text{H2O}`, as a function of time, :math:`t`.
 
 Running this simulation using LAMMPS, one can see that the number of molecules is increasing
 progressively.  When using the pressure argument, LAMMPS ignores the value of the