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.