added small description of folder with lammps example; added jupyter …

…notebook with inputs format example also in docs
sissaschool · Jun 28, 2022 · da390b6 · da390b6
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diff --git a/docs/source/LAMMPS_SILICA.md b/docs/source/LAMMPS_SILICA.md
@@ -0,0 +1 @@
+../../examples/data/Silica/lammps/README.md
diff --git a/docs/source/example_input_formats.ipynb b/docs/source/example_input_formats.ipynb
@@ -0,0 +1 @@
+../../examples/05_example_input_formats.ipynb
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -25,6 +25,7 @@ These examples show how to use the sportran package in a Python script, step by
 .. toctree::
    example_cepstrum_singlecomp_silica
    example_cepstrum_doublecomp_NaCl
+   example_input_formats
 
 Command line examples
 ---------------------
@@ -36,6 +37,11 @@ You can find the examples in the `repository <https://github.com/sissaschool/spo
    EXAMPLE_SILICA.md
    EXAMPLE_NACL.md
 
+LAMMPS input files for energy current generation
+------------------------------------------------
+
+.. toctree::
+   LAMMPS_SILICA.md
 
 API
 ===

diff --git a/examples/03_cmdline_example_silica/README.md b/examples/03_cmdline_example_silica/README.md
@@ -1,4 +1,4 @@
-# Command line example (silica)
+# Example 3: command line (silica)
 
 In this example we perform the same analysis that is performed in the correspondent [example notebook](../02_example_cepstrum_doublecomp_NaCl.ipynb), but using the command-line interface.
 

diff --git a/examples/04_cmdline_example_NaCl/README.md b/examples/04_cmdline_example_NaCl/README.md
@@ -1,4 +1,4 @@
-# Command line example (NaCl)
+# Example 4: command line (NaCl)
 
 In this example we perform the same analysis that is performed in the correspondent [example notebook](../02_example_cepstrum_doublecomp_NaCl.ipynb), but using the command-line interface.
 

diff --git a/examples/data/Silica/lammps/README.md b/examples/data/Silica/lammps/README.md
@@ -0,0 +1,9 @@
+# Example inputs for LAMMPS simulation of glass silica
+
+In the folder [examples/data/Silica/lammps](https://github.com/sissaschool/sportran/tree/develop/examples/data/Silica/lammps) you can find an example input file to generate some data that you can analyze with sportran.
+To run it you need a working LAMMPS installation and to run the file with, for example
+
+	mpirun -np 12 lmp_mpi -in silica.in -log silica.out
+
+After this it is possible to extract a simple table file by running the script `convert_lammps_log.sh`.
+This input generated the data used in the silica examples.