diff --git a/.dependencies/lammpstutorials-inputs b/.dependencies/lammpstutorials-inputs index 5cf1ff47..f1592294 160000 --- a/.dependencies/lammpstutorials-inputs +++ b/.dependencies/lammpstutorials-inputs @@ -1 +1 @@ -Subproject commit 5cf1ff474d31a377d1cb96e4dbc838b908e48f19 +Subproject commit f1592294274e5d9c368349f0e7381d1cc7d37cf7 diff --git a/docs/sphinx/source/tutorial2/tutorial.rst b/docs/sphinx/source/tutorial2/tutorial.rst index 98fcb744..6eb1e8d1 100644 --- a/docs/sphinx/source/tutorial2/tutorial.rst +++ b/docs/sphinx/source/tutorial2/tutorial.rst @@ -77,7 +77,7 @@ as well as the identity of the atoms that are linked by ``bonds``, ``angles``, .. |unbreakable_data| raw:: html - unbreakable.data + unbreakable.data .. admonition:: Note :class: non-title-info @@ -381,7 +381,7 @@ the **unbreakable.yaml** file can then be used to plot the stress-strain curve. .. |yaml_reader| raw:: html - unbreakable-yaml-reader.py + unbreakable-yaml-reader.py .. figure:: figures/CNT-unbreakable-stress-strain-dm.png :class: only-dark @@ -430,11 +430,11 @@ and must be placed next to **breakable.lmp**. .. |breakable_lmp| raw:: html - breakable.lmp + breakable.lmp .. |CH_airebo| raw:: html - CH.airebo + CH.airebo .. admonition:: Note :class: non-title-info @@ -458,7 +458,7 @@ the :math:`x`-axis, to allow for larger deformation of the CNT. .. |breakable_data| raw:: html - breakable.data + breakable.data Start the simulation -------------------- @@ -546,7 +546,7 @@ curve reveals a linear (elastic) regime where .. |unbreakable_yaml_reader| raw:: html - unbreakable-yaml-reader.py + unbreakable-yaml-reader.py .. figure:: figures/CNT-breakable-stress-energy-dm.png :class: only-dark @@ -597,4 +597,4 @@ force fields with explicit bonds. .. |breakable_with_tip| raw:: html - breakable-with-tip.lmp, + breakable-with-tip.lmp, diff --git a/docs/sphinx/source/tutorial3/tutorial.rst b/docs/sphinx/source/tutorial3/tutorial.rst index 28ae9dc9..7c965fc4 100644 --- a/docs/sphinx/source/tutorial3/tutorial.rst +++ b/docs/sphinx/source/tutorial3/tutorial.rst @@ -59,7 +59,7 @@ distances, etc). Thus add to **water.lmp** the line: .. |parameters_inc_3| raw:: html - parameters.inc + parameters.inc .. code-block:: lammps @@ -105,7 +105,7 @@ or the IDs of the atoms that are connected by bonds and angles. .. |water_mol_3| raw:: html - water.mol + water.mol .. figure:: figures/PEG-density-dm.png :class: only-dark @@ -271,7 +271,7 @@ commands to **merge.lmp**: .. |peg_mol_3| raw:: html - peg.mol + peg.mol .. code-block:: lammps @@ -500,7 +500,7 @@ Then, replace the existing ``dump`` and ``dump_modify`` commands with: .. |pull_with_tip_lmp_3| raw:: html - pull-with-tip.lmp + pull-with-tip.lmp .. code-block:: lammps diff --git a/docs/sphinx/source/tutorial4/tutorial.rst b/docs/sphinx/source/tutorial4/tutorial.rst index 807ca1cc..dc133cec 100644 --- a/docs/sphinx/source/tutorial4/tutorial.rst +++ b/docs/sphinx/source/tutorial4/tutorial.rst @@ -100,7 +100,7 @@ bonds, and angles. Add the following lines to **create.lmp**: .. |water_mol_4| raw:: html - water.mol + water.mol .. code-block:: lammps @@ -152,11 +152,11 @@ must be located next to **create.lmp**. The **parameters.inc** file contains the .. |parameters_inc_4| raw:: html - parameters.inc + parameters.inc .. |groups_inc_4| raw:: html - groups.inc + groups.inc .. code-block:: lammps diff --git a/docs/sphinx/source/tutorial5/tutorial.rst b/docs/sphinx/source/tutorial5/tutorial.rst index 7bc5e57e..c26ffe35 100644 --- a/docs/sphinx/source/tutorial5/tutorial.rst +++ b/docs/sphinx/source/tutorial5/tutorial.rst @@ -35,7 +35,7 @@ charge of :math:`q = 1.1\,\text{e}`, and all oxygen atoms have a charge of :math .. |silica_data_5| raw:: html - silica.data + silica.data .. admonition:: Note :class: non-title-info @@ -66,7 +66,7 @@ equilibrate the charge. .. |reaxCHOFe_inc_5| raw:: html - reaxCHOFe.inc + reaxCHOFe.inc Next, add the following commands to the **relax.lmp** file to track the evolution of the charges during the simulation: diff --git a/docs/sphinx/source/tutorial6/tutorial.rst b/docs/sphinx/source/tutorial6/tutorial.rst index 3274cc24..cb14d4c5 100644 --- a/docs/sphinx/source/tutorial6/tutorial.rst +++ b/docs/sphinx/source/tutorial6/tutorial.rst @@ -50,7 +50,7 @@ Ensure that the |SiO_1990_vashishta_6| file is located in the same directory as .. |SiO_1990_vashishta_6| raw:: html - SiO.1990.vashishta + SiO.1990.vashishta Next, add a ``dump image`` command to **generate.lmp** to follow the evolution of the system with time: @@ -253,7 +253,7 @@ must be downloaded and located next to **gcmc.lmp**. .. |H2O_mol_6| raw:: html - H2O.mol + H2O.mol 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. diff --git a/docs/sphinx/source/tutorial7/tutorial.rst b/docs/sphinx/source/tutorial7/tutorial.rst index 7fd9c88f..6dafb98e 100644 --- a/docs/sphinx/source/tutorial7/tutorial.rst +++ b/docs/sphinx/source/tutorial7/tutorial.rst @@ -438,7 +438,7 @@ Then, run the WHAM algorithm by typing the following command in the terminal: .. |umbrella_sampling_meta| raw:: html - umbrella-sampling.meta + umbrella-sampling.meta .. code-block:: bash diff --git a/docs/sphinx/source/tutorial8/tutorial.rst b/docs/sphinx/source/tutorial8/tutorial.rst index b00b6d38..d14c4f3b 100644 --- a/docs/sphinx/source/tutorial8/tutorial.rst +++ b/docs/sphinx/source/tutorial8/tutorial.rst @@ -38,7 +38,7 @@ CNT. Add the following line to **mixing.lmp**: .. |CNT_data_8| raw:: html - CNT.data + CNT.data .. code-block:: lammps @@ -51,7 +51,7 @@ we will use the |styrene_mol_8| molecule template file. Include the following co .. |styrene_mol_8| raw:: html - styrene.mol + styrene.mol .. code-block:: lammps @@ -175,39 +175,39 @@ for polymer. .. |M_M_pre_mol_8| raw:: html - M-M_pre.mol + M-M_pre.mol .. |M_M_post_mol_8| raw:: html - M-M_post.mol + M-M_post.mol .. |M_M_rxnmap_8| raw:: html - M-M.rxnmap + M-M.rxnmap .. |M_P_pre_mol_8| raw:: html - M-P_pre.mol + M-P_pre.mol .. |M_P_post_mol_8| raw:: html - M-P_post.mol + M-P_post.mol .. |M_P_rxnmap_8| raw:: html - M-P.rxnmap + M-P.rxnmap .. |P_P_pre_mol_8| raw:: html - P-P_pre.mol + P-P_pre.mol .. |P_P_post_mol_8| raw:: html - P-P_post.mol + P-P_post.mol .. |P_P_rxnmap_8| raw:: html - P-P.rxnmap + P-P.rxnmap Simulating the reaction -----------------------