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simongravelle merged 1 commit into from
Sep 14, 2026
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Change input links to GitHub URLs #110

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46 changes: 23 additions & 23 deletions docs/sphinx/source/non-tutorials/solutions.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ working |input_broken_solution| I wrote. These are the main commands:

.. |input_broken_solution| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial1/exercises/broken/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial1/exercises/broken/input.lammps" target="_blank">input</a>

.. code-block:: lammps

Expand Down Expand Up @@ -70,7 +70,7 @@ I use large numbers of particles: 8000 for each type.

.. |input_demixed_solution| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial1/exercises/demixion/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial1/exercises/demixion/input.lammps" target="_blank">input</a>

.. container:: justify

Expand Down Expand Up @@ -109,7 +109,7 @@ dumbell molecules.

.. |input_dumbbell_solution| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial1/exercises/dumbbell/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial1/exercises/dumbbell/input.lammps" target="_blank">input</a>

The first important change to make to the inputs from the
tutorial is the *atom_style*: an *atom_style* that allows for the atoms
Expand Down Expand Up @@ -149,19 +149,19 @@ length (2.5) need to be specified:

.. |mol_dumbbell_solution| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial1/exercises/dumbbell/dumbell.mol" target="_blank">here</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial1/exercises/dumbbell/dumbell.mol" target="_blank">here</a>

For the polymer, the angular potential must be defined to give its
rigidity to the polymer. You can download the |input_polymer_solution| and
|mol_polymer_solution|.

.. |input_polymer_solution| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial1/exercises/polymer/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial1/exercises/polymer/input.lammps" target="_blank">input</a>

.. |mol_polymer_solution| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial1/exercises/polymer/polymer.mol" target="_blank">molecule template</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial1/exercises/polymer/polymer.mol" target="_blank">molecule template</a>

Pulling on a carbon nanotube
============================
Expand All @@ -174,11 +174,11 @@ and |input_stress_strain_solution2| I wrote.

.. |input_stress_strain_solution1| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/exercises/stress-strain/breakable-bonds/input.lammps" target="_blank">input for the breakable CNT</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial2/exercises/stress-strain/breakable-bonds/input.lammps" target="_blank">input for the breakable CNT</a>

.. |input_stress_strain_solution2| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/exercises/stress-strain/unbreakable-bonds/input.lammps" target="_blank">input for the unbreakable CNT</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial2/exercises/stress-strain/unbreakable-bonds/input.lammps" target="_blank">input for the unbreakable CNT</a>

The stress is calculated as the total force
induced on the CNT by the pulling divided by the
Expand Down Expand Up @@ -228,7 +228,7 @@ You can download the |input_gas_cnt| I wrote.

.. |input_gas_cnt| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/exercises/gas/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial2/exercises/gas/input.lammps" target="_blank">input</a>

The key is to modify the *.data* file
to make space for the second atom type 2.
Expand Down Expand Up @@ -290,7 +290,7 @@ You can download the |input_membrane_solution1| I wrote.

.. |input_membrane_solution1| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/exercises/membrane/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial2/exercises/membrane/input.lammps" target="_blank">input</a>

The CNT can be replicated using the *replicate* command.
It is recommended to adjust the box size before replicating,
Expand Down Expand Up @@ -319,7 +319,7 @@ You can download the |input_PEG_RDF| file I wrote.

.. |input_PEG_RDF| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/exercises/radial-distribution-function/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial3/exercises/radial-distribution-function/input.lammps" target="_blank">input</a>

I use the *compute rdf* command of LAMMPS
to extract the RDF between atoms of type 8 (oxygen from water)
Expand All @@ -342,15 +342,15 @@ and |parm_PEG_salt| files I wrote.

.. |input_PEG_salt| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/exercises/salt/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial3/exercises/salt/input.lammps" target="_blank">input</a>

.. |data_PEG_salt| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/exercises/salt/mix-with-salt.data" target="_blank">data</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial3/exercises/salt/mix-with-salt.data" target="_blank">data</a>

.. |parm_PEG_salt| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/exercises/salt/PARM-with-salt.lammps" target="_blank">parm</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial3/exercises/salt/PARM-with-salt.lammps" target="_blank">parm</a>

It is important to
make space for the two salt atoms by modifying the data file as follows:
Expand Down Expand Up @@ -389,7 +389,7 @@ You can download the |input_PEG_dihedral| file I wrote.

.. |input_PEG_dihedral| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/exercises/structurePEG/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial3/exercises/structurePEG/input.lammps" target="_blank">input</a>

The key is to combine the *compute dihedral/local*,
which computes the angles of the dihedrals and returns
Expand Down Expand Up @@ -611,7 +611,7 @@ progressive adsorption of both species.

.. |input_mixture| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial6/Exercises/MixtureH2OCO2/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial6/Exercises/MixtureH2OCO2/input.lammps" target="_blank">input</a>

Adsorb water in ZIF-8 nanopores
-------------------------------
Expand All @@ -622,7 +622,7 @@ which you have to place in the same folder as the *zif-8.data*,

.. |input_zif| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial6/Exercises/Zif-8/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial6/Exercises/Zif-8/input.lammps" target="_blank">input</a>

Apart from the parameters and topology, the *input* is
quite similar to the one developed in the case of the crack
Expand Down Expand Up @@ -654,7 +654,7 @@ You can download the |input_binary_wont_mix| here.

.. |input_binary_wont_mix| raw:: html

<a href=".../../../../../.dependencies/lammpstutorials-inputs/tutorial7/Exercises/BinaryFluid/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial7/Exercises/BinaryFluid/input.lammps" target="_blank">input</a>

The solution chosen here was to create two groups (*t1* and *t2*)
and apply the two potentials *U1* and *U2* to each group, respectively.
Expand Down Expand Up @@ -714,7 +714,7 @@ You can download the |input_adsorption_ethanol| here.

.. |input_adsorption_ethanol| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial7/Exercises/MoleculeAdsorption/input.lammps" target="_blank">input</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial7/Exercises/MoleculeAdsorption/input.lammps" target="_blank">input</a>

Reactive silicon dioxide
========================
Expand Down Expand Up @@ -942,7 +942,7 @@ Then, download the proposed input |input_reax_water|.

.. |input_reax_water| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial5/Exercices/Hydrate/input.lammps" target="_blank">here</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial5/Exercices/Hydrate/input.lammps" target="_blank">here</a>

As seen in the *input.lammps* file, the molecules are added to the system
using the *create_atoms* command:
Expand Down Expand Up @@ -973,11 +973,11 @@ file. In addition, create a molecule template named *H2O.mol*:

.. |input_reax_water_2| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial5/Exercices/BulkWater/input.lammps" target="_blank">here</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial5/Exercices/BulkWater/input.lammps" target="_blank">here</a>

.. |reaxCHOFe_ff_ex| raw:: html

<a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial5/Exercices/BulkWater/reaxCHOFe.ff" target="_blank">reaxff force field</a>
<a href="https://github.com/lammpstutorials/lammpstutorials-inputs/tree/main/tutorial5/Exercices/BulkWater/reaxCHOFe.ff" target="_blank">reaxff force field</a>

.. code-block:: lammps

Expand Down Expand Up @@ -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.
the reactive force field.
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