added href links

Author: simongravelle

docs/sphinx/source/journal-article.bib

@@ -27,6 +27,25 @@ @article{mills1955remeasurement
   publisher={ACS Publications}
 }
 
+@article{typelabel_paper,
+  author =       {Gissinger, Jacob R. and Nikiforov, Ilia and Afshar,
+                  Yaser and Waters, Brendon and Choi, Moon-ki and Karls,
+                  Daniel S. and Stukowski, Alexander and Im, Wonpil and
+                  Heinz, Hendrik and Kohlmeyer, Axel and Tadmor, Ellad
+                  B.},
+  title =        {Type Label Framework for Bonded Force Fields in
+                  LAMMPS},
+  journal =      {The Journal of Physical Chemistry B},
+  volume =       {128},
+  number =       {13},
+  pages =        {3282-3297},
+  year =         {2024},
+  doi =          {10.1021/acs.jpcb.3c08419},
+  note =         {PMID: 38506668},
+  URL =          { https://doi.org/10.1021/acs.jpcb.3c08419 },
+  eprint =       { https://doi.org/10.1021/acs.jpcb.3c08419 }
+}
+
 @misc{lammps_docs,
   title = {{LAMMPS} Online Documentation for latest stable version},
   howpublished = {\url{https://docs.lammps.org/stable}},

docs/sphinx/source/tutorial3/tutorial.rst

@@ -5,9 +5,7 @@ In this tutorial, the water reservoir is first prepared in the absence of the po
 A rectangular box of water is created and equilibrated at ambient temperature and
 pressure.  The SPC/Fw water model is used :cite:`wu2006flexible`, which is
 a flexible variant of the rigid SPC (simple point charge) model :cite:`berendsen1981interaction`.
-To set up this tutorial, select ``Start Tutorial 3`` from the
-``Tutorials`` menu of LAMMPS--GUI and follow the instructions.
-The editor should display the following content corresponding to **water.lmp**:
+Create a file named **water.lmp**, and copy the following lines into it:
 
 .. code-block:: lammps
 
@@ -20,6 +18,13 @@ The editor should display the following content corresponding to **water.lmp**:
     kspace_style ewald 1e-5
     special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 1.0 angle yes
 
+.. admonition:: Optional: follow this tutorial using LAMMPS-GUI
+    :class: gui
+
+    To set up this tutorial, select ``Start Tutorial 3`` from the
+    ``Tutorials`` menu of LAMMPS--GUI and follow the instructions.
+    The editor should display the content corresponding to **water.lmp**.
+
 With the unit style ``real``, masses are in g/mol, distances in Å,
 time in fs, and energies in kcal/mol.  With the ``atom_style full``,
 each atom is a dot with a mass and a charge that can be linked
@@ -44,14 +49,18 @@ and 4 dihedral types (only for the polymer).  Copy the following lines into **wa
 .. code-block:: lammps
 
     region box block -30 30 -15 15 -15 15
-    create_box 8 box bond/types 7 angle/types 8 dihedral/types 4 &
-        extra/bond/per/atom 3 extra/angle/per/atom 6 extra/dihedral/per/atom 10 extra/special/per/atom 14
+    create_box 8 box bond/types 7 angle/types 8 dihedral/types 4 extra/bond/per/atom 3 &
+        extra/angle/per/atom 6 extra/dihedral/per/atom 10 extra/special/per/atom 14
 
 The ``extra/x/per/atom`` commands reserve memory for adding bond topology
-data later. We use the file \href{\filepath tutorial3/parameters.inc}{\dwlcmd{parameters.inc}}
+data later. We use the file |parameters_inc_3|
 to set all the parameters (masses, interaction energies, bond equilibrium
 distances, etc).  Thus add to **water.lmp** the line:
 
+.. |parameters_inc_3| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/parameters.inc" target="_blank">parameters.inc</a>
+
 .. code-block:: lammps
 
     include parameters.inc
@@ -89,13 +98,15 @@ of molecules.  Always check the number of created atoms in the **log** file
     Created 2100 atoms
 
 When LAMMPS fails to create the desired number of molecules, a WARNING
-appears.  The molecule template called 
-\href{\filepath tutorial3/water.mol}{\dwlcmd{water.mol}}
-must be downloaded and saved
+appears.  The molecule template called |water_mol_3| must be downloaded and saved
 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.
 
+.. |water_mol_3| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/water.mol" target="_blank">water.mol</a>
+
 .. figure:: figures/PEG-density-dm.png
     :class: only-dark
     :alt: Evolution of the water reservoir density
@@ -237,11 +248,14 @@ of the tutorial.  Add the following command to **merge.lmp**:
 
     kspace_style pppm 1e-5
 
-Using the molecule template for the polymer called
-\href{\filepath tutorial3/peg.mol}{\dwlcmd{peg.mol}},
+Using the molecule template for the polymer called |peg_mol_3|,
 let us create a single molecule in the middle of the box by adding the following
 commands to **merge.lmp**:
 
+.. |peg_mol_3| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/peg.mol" target="_blank">peg.mol</a>
+
 .. code-block:: lammps
         
     molecule pegmol peg.mol
@@ -423,7 +437,7 @@ for an extra 15 ps:
     fix myaf2 topull2 addforce -10 0 0
     run 15000
 
-Each applied force has a magnitude of :math:`10 \text{kcal/mol/\AA{}}`, corresponding to :math:`0.67 \text{nN}`.
+Each applied force has a magnitude of :math:`10 \, \text{kcal/mol/Å}`, corresponding to :math:`0.67 \text{nN}`.
 This value was chosen to be sufficiently large to overcome both the thermal agitation and
 the entropic contributions from the molecules.
 
@@ -445,10 +459,13 @@ OVITO :cite:`humphrey1996vmd, ovito_paper`.  To do so, the IDs and
 positions of the atoms must be regularly written to a file during the
 simulation.  This can be accomplished by adding a ``dump`` command
 to the input file.  For instance, create a duplicate of
-**pull.lmp** and name it
-\href{\filepath tutorial3/solution/pull-with-tip.lmp}{\dwlcmd{pull-with-tip.lmp}}.
+**pull.lmp** and name it |pull_with_tip_lmp_3|.
 Then, replace the existing ``dump`` and ``dump_modify`` commands with:
 
+.. |pull_with_tip_lmp_3| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/pull-with-tip.lmp" target="_blank">pull-with-tip.lmp</a>
+
 .. code-block:: lammps
 
     dump mydmp all atom 1000 pull.lammpstrj

docs/sphinx/source/tutorial4/tutorial.rst

@@ -37,7 +37,7 @@ except that they are specifically designed for the four-point water model.  As a
 LAMMPS automatically creates a four-point water molecule, 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{\AA{}}` corresponds to the O-M distance of the
+:math:`0.1546\,\text{Å}` corresponds to the O-M distance of the
 TIP4P-2005 water model :cite:`abascal2005general`.  All other atoms in the simulation
 are treated as usual, with long-range Coulomb interactions.  Another novelty, here, is
 the use of ``kspace modify slab 3.0`` that is combined with the non-periodic
@@ -51,9 +51,8 @@ Let us create the box and the label maps by adding the following lines to **crea
 
     lattice fcc 4.04
     region box block -3 3 -3 3 -5 5
-    create_box 5 box bond/types 1 angle/types 1 &
-    extra/bond/per/atom 2 extra/angle/per/atom 1 &
-    extra/special/per/atom 2
+    create_box 5 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 &
+        extra/special/per/atom 2
     labelmap atom 1 O 2 H 3 Na+ 4 Cl- 5 WALL
     labelmap bond 1 O-H
     labelmap angle 1 H-O-H
@@ -62,7 +61,7 @@ The ``lattice`` command defines the unit cell.  Here, the face-centered cubic (f
 with a scale factor of 4.04 has been chosen for the future positioning of the atoms
 of the walls.  The ``region`` command defines a geometric region of space.  By choosing
 :math:`\text{xlo}=-3` and :math:`\text{xlo}=3`, and because we have previously chosen a lattice with a scale
-factor of 4.04, the region box extends from :math:`-12.12~\text{\AA{}}` to :math:`12.12~\text{\AA{}}`
+factor of 4.04, the region box extends from :math:`-12.12~\text{Å}` to :math:`12.12~\text{Å}`
 along the :math:`x` direction.  The ``create_box`` command creates a simulation box with
 5 types of atoms: the oxygen and hydrogen of the water molecules, the two ions (:math:`\text{Na}^+`,
 :math:`\text{Cl}^-`), and the atoms from the walls.  The simulation contains 1 type of bond
@@ -87,12 +86,15 @@ following lines to **create.lmp**:
 Atoms will be placed in the positions of the previously defined lattice, thus
 forming fcc solids.
 
-To add the water molecules, the molecule
-template called \href{\filepath tutorial4/water.mol}{\dwlcmd{water.mol}}
+To add the water molecules, the molecule template called |water_mol_4|
 must be located next to **create.lmp**.  The template contains all the
 necessary information concerning the water molecule, such as atom positions,
 bonds, and angles.  Add the following lines to **create.lmp**:
 
+.. |water_mol_4| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial4/water.mol" target="_blank">water.mol</a>
+
 .. code-block:: lammps
 
     region rliquid block INF INF INF INF -2 2
@@ -138,11 +140,16 @@ lines into **create.lmp**:
     include parameters.inc
     include groups.inc
 
-Both \href{\filepath tutorial4/parameters.inc}{\dwlcmd{parameters.inc}}
-and \href{\filepath tutorial4/groups.inc}{\dwlcmd{groups.inc}} files
-must be located next to **create.lmp**.
+Both |parameters_inc_4| and |groups_inc_4| files
+must be located next to **create.lmp**. The **parameters.inc** file contains the masses, as follows:
+
+.. |parameters_inc_4| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial4/parameters.inc" target="_blank">parameters.inc</a>
 
-The **parameters.inc** file contains the masses, as follows:
+.. |groups_inc_4| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial4/groups.inc" target="_blank">groups.inc</a>
 
 .. code-block:: lammps
 
@@ -182,14 +189,15 @@ to make the walls less hydrophilic, the value of
 :math:`\epsilon_\text{O-WALL}` was reduced.
 
 Finally, the **parameters.inc** file contains the following two lines:
+
 .. code-block:: lammps
 
     bond_coeff O-H 0 0.9572
     angle_coeff H-O-H 0 104.52
 
 The ``bond_coeff`` command, used here for the O-H bond of the water
 molecule, sets both the spring constant of the harmonic potential and the
-equilibrium bond distance of :math:`0.9572~\text{\AA{}}`.  The constant can be 0 for a
+equilibrium bond distance of :math:`0.9572~\text{Å}`.  The constant can be 0 for a
 rigid water molecule because the SHAKE algorithm will maintain the rigid
 structure of the water molecule (see below) :cite:`ryckaert1977numerical, andersen1983rattle`.
 Similarly, the ``angle_coeff`` command for the H-O-H angle of the water molecule sets
@@ -208,7 +216,7 @@ several ``group`` commands to selects atoms based on their types:
     group fluid union H2O ions
 
 The **groups.inc** file also defines the ``walltop`` and ``wallbot``
-groups, which contain the WALL atoms located in the :math:`z > 0` and :math:`z < 0` regions, respectively::
+groups, which contain the WALL atoms located in the :math:`z > 0` and :math:`z < 0` regions, respectively:
 
 .. code-block:: lammps
 
@@ -228,7 +236,6 @@ to delete about :math:`15~\%` of the water molecules:
 
     delete_atoms random fraction 0.15 yes H2O NULL 482793 mol yes
 
-
 To create an image of the system, add the following ``dump`` image
 into **create.lmp** (see also Fig.~\ref{fig:NANOSHEAR-system}):
 
@@ -525,7 +532,7 @@ along :math:`x` (``vx``) within the bins.  Add the following lines to **shearing
 
     run 200000
 
-Here, a bin size of :math:`0.25\,\text{\AA{}}` is used for the density
+Here, a bin size of :math:`0.25\,\text{Å}` is used for the density
 profiles generated by the ``ave/chunk`` commands, and three
 **.dat** files are created for the water, the walls, and the ions,
 respectively.  With values of ``10 15000 200000``, the velocity
@@ -552,7 +559,7 @@ the fluid on the shearing wall, and :math:`\dot{\gamma}` the shear rate
 :cite:`gravelle2021violations`.  Here, the shear rate is
 approximately :math:`\dot{\gamma} = 20 \cdot 10^9\,\text{s}^{-1}` (Fig.~\ref{fig:NANOSHEAR-profiles}),
 the average force on each wall is given by ``f_mysf1[1]`` and ``f_mysf2[1]``
-and is approximately :math:`2.7\,\mathrm{kcal/mol/\AA}` in magnitude.  Using a surface area
+and is approximately :math:`2.7\,\mathrm{kcal/mol/Å}` in magnitude.  Using a surface area
 for the walls of :math:`A = 6 \cdot 10^{-18}\,\text{m}^2`, one obtains an estimate for
 the shear viscosity for the confined fluid of :math:`\eta = 3.1\,\text{mPa.s}` using Eq.~\eqref{eq:eta}.
 

docs/sphinx/source/tutorial5/tutorial.rst

@@ -20,12 +20,16 @@ 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.
 
-The initial topology given by \href{\filepath tutorial5/silica.data}{\dwlcmd{silica.data}}
+The initial topology given by |silica_data_5|
 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
 charge of :math:`q = 1.1\,\text{e}`, and all oxygen atoms have a charge of :math:`q = -0.55\,\text{e}`.
 
+.. |silica_data_5| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial5/silica.data" target="_blank">silica.data</a>
+
 .. admonition:: Note
     :class: non-title-info
 
@@ -45,15 +49,17 @@ Next, copy the following three crucial lines into the **relax.lmp** file:
 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
-\href{\filepath tutorial5/reaxCHOFe.inc}{\dwlcmd{reaxCHOFe.inc}}
+``bondchk`` errors.  The ``pair_coeff`` command uses the |reaxCHOFe_inc_5|
 file, which should have been downloaded during the tutorial set up.  Finally, the
 ``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
 equilibrate the charge.
 
+.. |reaxCHOFe_inc_5| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial5/reaxCHOFe.inc" target="_blank">reaxCHOFe.inc</a>
 
 Next, add the following commands to the **relax.lmp** file to track the
 evolution of the charges during the simulation:

docs/sphinx/source/tutorial6/tutorial.rst

@@ -44,8 +44,11 @@ is ``Si`` and the second is ``O``:
 
     pair_coeff * * SiO.1990.vashishta Si O
 
-Ensure that the \href{\filepath tutorial6/SiO.1990.vashishta}{\dwlcmd{SiO.1990.vashishta}}
-file is located in the same directory as **generate.lmp**.
+Ensure that the |SiO_1990_vashishta_6| file is located in the same directory as **generate.lmp**.
+
+.. |SiO_1990_vashishta_6| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial6/SiO.1990.vashishta" target="_blank">SiO.1990.vashishta</a>
 
 FIGURE GCMC-generate Amorphous silica (:math:`\text{SiO}_2`).
 Silicon atoms are
@@ -217,9 +220,13 @@ with ``tip4p/long``.  Finally, the style for the bonds
 and angles of the water molecules are defined; however, these specifications are
 not critical since TIP4P/2005 is a rigid water model.
 
-The water molecule template called \href{\filepath tutorial6/H2O.mol}{\dwlcmd{H2O.mol}}
+The water molecule template called |H2O_mol_6|
 must be downloaded and located next to **gcmc.lmp**.
 
+.. |H2O_mol_6| raw:: html
+
+    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial6/H2O.mol" target="_blank">H2O.mol</a>
+
 Before going further, we need to make a few changes to our data file.
 Currently, the **cracking.data** file includes only two atom types, but we require four.
 Copy the previously generated **cracking.data**, and name the duplicate **cracking-mod.data**.