Merge pull request #101 from lammpstutorials/fix-links

fixed href links

Author: simongravelle

.dependencies/lammpstutorials-inputs

@@ -77,7 +77,7 @@ as well as the identity of the atoms that are linked by ``bonds``, ``angles``,
 
 .. |unbreakable_data| raw:: html
 
-   <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/unbreakable.data" target="_blank">unbreakable.data</a>
+   <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/unbreakable.data" target="_blank">unbreakable.data</a>
 
 .. 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
 
-   <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a>
+   <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a>
 
 .. 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
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/breakable.lmp" target="_blank">breakable.lmp</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/breakable.lmp" target="_blank">breakable.lmp</a>
 
 .. |CH_airebo| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/CH.airebo" target="_blank">CH.airebo</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/CH.airebo" target="_blank">CH.airebo</a>
 
 .. 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
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/breakable.data" target="_blank">breakable.data</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/breakable.data" target="_blank">breakable.data</a>
 
 Start the simulation
 --------------------
@@ -546,7 +546,7 @@ curve reveals a linear (elastic) regime where
 
 .. |unbreakable_yaml_reader| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/unbreakable-yaml-reader.py" target="_blank">unbreakable-yaml-reader.py</a>
 
 .. 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
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial2/breakable-with-tip.lmp" target="_blank">breakable-with-tip.lmp</a>,
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial2/breakable-with-tip.lmp" target="_blank">breakable-with-tip.lmp</a>,

docs/sphinx/source/tutorial2/tutorial.rst

@@ -59,7 +59,7 @@ 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>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial3/parameters.inc" target="_blank">parameters.inc</a>
 
 .. 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
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/water.mol" target="_blank">water.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial3/water.mol" target="_blank">water.mol</a>
 
 .. figure:: figures/PEG-density-dm.png
     :class: only-dark
@@ -271,7 +271,7 @@ commands to **merge.lmp**:
 
 .. |peg_mol_3| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial3/peg.mol" target="_blank">peg.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial3/peg.mol" target="_blank">peg.mol</a>
 
 .. code-block:: lammps
         
@@ -500,7 +500,7 @@ 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>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial3/pull-with-tip.lmp" target="_blank">pull-with-tip.lmp</a>
 
 .. code-block:: lammps
 

docs/sphinx/source/tutorial3/tutorial.rst

@@ -100,7 +100,7 @@ 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>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial4/water.mol" target="_blank">water.mol</a>
 
 .. 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
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial4/parameters.inc" target="_blank">parameters.inc</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial4/parameters.inc" target="_blank">parameters.inc</a>
 
 .. |groups_inc_4| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial4/groups.inc" target="_blank">groups.inc</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial4/groups.inc" target="_blank">groups.inc</a>
 
 .. code-block:: lammps
 

docs/sphinx/source/tutorial4/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
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial5/silica.data" target="_blank">silica.data</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial5/silica.data" target="_blank">silica.data</a>
 
 .. admonition:: Note
     :class: non-title-info
@@ -66,7 +66,7 @@ equilibrate the charge.
 
 .. |reaxCHOFe_inc_5| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial5/reaxCHOFe.inc" target="_blank">reaxCHOFe.inc</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/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/tutorial5/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
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial6/SiO.1990.vashishta" target="_blank">SiO.1990.vashishta</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial6/SiO.1990.vashishta" target="_blank">SiO.1990.vashishta</a>
 
 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
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial6/H2O.mol" target="_blank">H2O.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/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.

docs/sphinx/source/tutorial6/tutorial.rst

@@ -438,7 +438,7 @@ Then, run the WHAM algorithm by typing the following command in the terminal:
 
 .. |umbrella_sampling_meta| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial7/umbrella-sampling.meta" target="_blank">umbrella-sampling.meta</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial7/umbrella-sampling.meta" target="_blank">umbrella-sampling.meta</a>
 
 .. code-block:: bash
 

docs/sphinx/source/tutorial7/tutorial.rst

@@ -38,7 +38,7 @@ CNT.  Add the following line to **mixing.lmp**:
 
 .. |CNT_data_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/CNT.data" target="_blank">CNT.data</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/CNT.data" target="_blank">CNT.data</a>
 
 .. 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
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/styrene.mol" target="_blank">styrene.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/styrene.mol" target="_blank">styrene.mol</a>
 
 .. code-block:: lammps
 
@@ -175,39 +175,39 @@ for polymer.
 
 .. |M_M_pre_mol_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/M-M_pre.mol" target="_blank">M-M_pre.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/M-M_pre.mol" target="_blank">M-M_pre.mol</a>
 
 .. |M_M_post_mol_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/M-M_post.mol" target="_blank">M-M_post.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/M-M_post.mol" target="_blank">M-M_post.mol</a>
 
 .. |M_M_rxnmap_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/M-M.rxnmap" target="_blank">M-M.rxnmap</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/M-M.rxnmap" target="_blank">M-M.rxnmap</a>
 
 .. |M_P_pre_mol_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/M-P_pre.mol" target="_blank">M-P_pre.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/M-P_pre.mol" target="_blank">M-P_pre.mol</a>
 
 .. |M_P_post_mol_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/M-P_post.mol" target="_blank">M-P_post.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/M-P_post.mol" target="_blank">M-P_post.mol</a>
 
 .. |M_P_rxnmap_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/M-P.rxnmap" target="_blank">M-P.rxnmap</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/M-P.rxnmap" target="_blank">M-P.rxnmap</a>
 
 .. |P_P_pre_mol_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/P-P_pre.mol" target="_blank">P-P_pre.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/P-P_pre.mol" target="_blank">P-P_pre.mol</a>
 
 .. |P_P_post_mol_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/P-P_post.mol" target="_blank">P-P_post.mol</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/P-P_post.mol" target="_blank">P-P_post.mol</a>
 
 .. |P_P_rxnmap_8| raw:: html
 
-    <a href="../../../../../.dependencies/lammpstutorials-inputs/tutorial8/P-P.rxnmap" target="_blank">P-P.rxnmap</a>
+    <a href="https://raw.githubusercontent.com/lammpstutorials/lammpstutorials-inputs/refs/heads/main/tutorial8/P-P.rxnmap" target="_blank">P-P.rxnmap</a>
 
 Simulating the reaction
 -----------------------