diff --git a/docs/sphinx/source/non-tutorials/solutions.rst b/docs/sphinx/source/non-tutorials/solutions.rst
index ef0f6f43..5655e416 100644
--- a/docs/sphinx/source/non-tutorials/solutions.rst
+++ b/docs/sphinx/source/non-tutorials/solutions.rst
@@ -16,7 +16,7 @@ working |input_broken_solution| I wrote. These are the main commands:
.. |input_broken_solution| raw:: html
- input
+ input
.. code-block:: lammps
@@ -70,7 +70,7 @@ I use large numbers of particles: 8000 for each type.
.. |input_demixed_solution| raw:: html
- input
+ input
.. container:: justify
@@ -109,7 +109,7 @@ dumbell molecules.
.. |input_dumbbell_solution| raw:: html
- input
+ input
The first important change to make to the inputs from the
tutorial is the *atom_style*: an *atom_style* that allows for the atoms
@@ -149,7 +149,7 @@ length (2.5) need to be specified:
.. |mol_dumbbell_solution| raw:: html
- here
+ here
For the polymer, the angular potential must be defined to give its
rigidity to the polymer. You can download the |input_polymer_solution| and
@@ -157,11 +157,11 @@ rigidity to the polymer. You can download the |input_polymer_solution| and
.. |input_polymer_solution| raw:: html
- input
+ input
.. |mol_polymer_solution| raw:: html
- molecule template
+ molecule template
Pulling on a carbon nanotube
============================
@@ -174,11 +174,11 @@ and |input_stress_strain_solution2| I wrote.
.. |input_stress_strain_solution1| raw:: html
- input for the breakable CNT
+ input for the breakable CNT
.. |input_stress_strain_solution2| raw:: html
- input for the unbreakable CNT
+ input for the unbreakable CNT
The stress is calculated as the total force
induced on the CNT by the pulling divided by the
@@ -228,7 +228,7 @@ You can download the |input_gas_cnt| I wrote.
.. |input_gas_cnt| raw:: html
- input
+ input
The key is to modify the *.data* file
to make space for the second atom type 2.
@@ -290,7 +290,7 @@ You can download the |input_membrane_solution1| I wrote.
.. |input_membrane_solution1| raw:: html
- input
+ input
The CNT can be replicated using the *replicate* command.
It is recommended to adjust the box size before replicating,
@@ -319,7 +319,7 @@ You can download the |input_PEG_RDF| file I wrote.
.. |input_PEG_RDF| raw:: html
- input
+ input
I use the *compute rdf* command of LAMMPS
to extract the RDF between atoms of type 8 (oxygen from water)
@@ -342,15 +342,15 @@ and |parm_PEG_salt| files I wrote.
.. |input_PEG_salt| raw:: html
- input
+ input
.. |data_PEG_salt| raw:: html
- data
+ data
.. |parm_PEG_salt| raw:: html
- parm
+ parm
It is important to
make space for the two salt atoms by modifying the data file as follows:
@@ -389,7 +389,7 @@ You can download the |input_PEG_dihedral| file I wrote.
.. |input_PEG_dihedral| raw:: html
- input
+ input
The key is to combine the *compute dihedral/local*,
which computes the angles of the dihedrals and returns
@@ -611,7 +611,7 @@ progressive adsorption of both species.
.. |input_mixture| raw:: html
- input
+ input
Adsorb water in ZIF-8 nanopores
-------------------------------
@@ -622,7 +622,7 @@ which you have to place in the same folder as the *zif-8.data*,
.. |input_zif| raw:: html
- input
+ input
Apart from the parameters and topology, the *input* is
quite similar to the one developed in the case of the crack
@@ -654,7 +654,7 @@ You can download the |input_binary_wont_mix| here.
.. |input_binary_wont_mix| raw:: html
- input
+ input
The solution chosen here was to create two groups (*t1* and *t2*)
and apply the two potentials *U1* and *U2* to each group, respectively.
@@ -714,7 +714,7 @@ You can download the |input_adsorption_ethanol| here.
.. |input_adsorption_ethanol| raw:: html
- input
+ input
Reactive silicon dioxide
========================
@@ -942,7 +942,7 @@ Then, download the proposed input |input_reax_water|.
.. |input_reax_water| raw:: html
- here
+ here
As seen in the *input.lammps* file, the molecules are added to the system
using the *create_atoms* command:
@@ -973,11 +973,11 @@ file. In addition, create a molecule template named *H2O.mol*:
.. |input_reax_water_2| raw:: html
- here
+ here
.. |reaxCHOFe_ff_ex| raw:: html
- reaxff force field
+ reaxff force field
.. code-block:: lammps
@@ -1016,4 +1016,4 @@ to make the solution slightly acidic:
create_atoms 2 random 1 305672 NULL overlap 0.5 maxtry 200
As the simulation progresses, some :math:`H_3O^+` ions will form thanks to
-the reactive force field.
\ No newline at end of file
+the reactive force field.