diff --git a/doc/source/tutorials/development.rst b/doc/source/tutorials/development.rst
index f4b6f3d7d7c47fde21f5e5c0fe26853f8800d273..f385c54dd75205acb17175cf3b43d54f0c0004af 100644
--- a/doc/source/tutorials/development.rst
+++ b/doc/source/tutorials/development.rst
@@ -1,5 +1,5 @@
Development
-===========
+^^^^^^^^^^^
Contributions of any sort are of course quite welcome.
diff --git a/doc/source/tutorials/first_model_api.rst b/doc/source/tutorials/first_model_api.rst
index 5572b3cc24489a0b13fde30d7be398f2057103cc..224082bb9f1374325aa88be1fdef3cc9516310d5 100644
--- a/doc/source/tutorials/first_model_api.rst
+++ b/doc/source/tutorials/first_model_api.rst
@@ -1,7 +1,7 @@
.. _api-tutorial:
A first kMC Model--the API way
-==============================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In general there are two interfaces to *defining* a new
model: A GUI and an API. While the GUI can be quite
@@ -15,10 +15,10 @@ do this will also pay-off especially if you starting tinkering
with your existing models and make little changes here and there.
-Construct the model
-^^^^^^^^^^^^^^^^^^^
+Build the model
+===============
-You may also look at MyFirstDiffusion.py in the examples directory.
+You may also look at MyFirstDiffusion__build.py in the examples directory.
We start by making the necessary import statements (in `*python* <http://python.org>`_ or better `*ipython* <http://ipython.org>`_)::
@@ -32,11 +32,8 @@ from `kmcos.io` will only be needed at the end to save the project
or to export compilable code.
The example sketched out here leads you to a kMC model for CO adsorption
-and desorption on Pd(100) including a simple lateral interaction. Granted
-this hardly excites surface scientists but we need to start somewhere, right?
-
-
-First you should instantiate a new project and fill in meta information ::
+and desorption on Pd(100). First you should instantiate a new project
+and fill in meta information ::
pt = Project()
pt.set_meta(author = 'Your Name',
@@ -99,7 +96,7 @@ Ok, let us see what we managed so far: you have a *lattice* with a
Populate process list and parameter list
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+========================================
The remaining work is to populate the `process list` and the
`parameter list`. The parameter list defines the parameters
@@ -205,7 +202,7 @@ coordinate is ::
check :ref:`manual_coord_generation` for details.
Export, save, compile
-^^^^^^^^^^^^^^^^^^^^^
+=====================
Next, it's a good idea to save your work ::
@@ -256,7 +253,7 @@ for some hints. To learn more about the kmcos approach
and methods you should into :ref:`topic guides <topic-guides>`.
Taking it home
-^^^^^^^^^^^^^^^
+==============
Despite its simplicity you have now seen all elements needed
to implement a kMC model and hopefully gotten a first feeling for
@@ -279,7 +276,7 @@ the workflow.
An alternative way using .ini files
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+===================================
Presently, a full description of the .ini capability is not being provided because this way is not the standard way of using kmcos. However, it is available. This method is an alternative to making an xml file, and can be used instead of kmcos export.
diff --git a/doc/source/tutorials/index.rst b/doc/source/tutorials/index.rst
index c31082cf55fc64a81966efbde227596acaa38674..3f903d5131d3cab3d340d1b4783a75842df4141e 100644
--- a/doc/source/tutorials/index.rst
+++ b/doc/source/tutorials/index.rst
@@ -17,6 +17,4 @@ Tutorials
.. include:: run_model_gui.rst
-
-.. include:: development.rst
-
+.. include:: development.rst
\ No newline at end of file
diff --git a/doc/source/tutorials/model_editor.rst b/doc/source/tutorials/model_editor.rst
index ec102fbbb8ac21124b8998da414f7a83af8273e8..84a69d88682df58c7ea12ef78e4a6efb7415c5ed 100644
--- a/doc/source/tutorials/model_editor.rst
+++ b/doc/source/tutorials/model_editor.rst
@@ -1,5 +1,5 @@
The Model Editor (Deprecated -- glade migration is required to revive this feature)
-^^^^^^^^^^^^^^
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -31,8 +31,4 @@ The Model Editor (Deprecated -- glade migration is required to revive this featu
:width: 1000px
Processes can be added by point and click or by entering
- a chemical expression.
-
-
-
-
+ a chemical expression.
\ No newline at end of file
diff --git a/doc/source/tutorials/run_model_api.rst b/doc/source/tutorials/run_model_api.rst
index 119a13e19e948f9ba577fc41a0c88cbe2cc850eb..9cda489816a7328fc995c59a9770ef99a34b2de1 100644
--- a/doc/source/tutorials/run_model_api.rst
+++ b/doc/source/tutorials/run_model_api.rst
@@ -1,3 +1,6 @@
+Running the Model From Runfiles
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
Running the Model--the API way
==============================
diff --git a/doc/source/tutorials/run_model_gui.rst b/doc/source/tutorials/run_model_gui.rst
index a2d40d264351e5d24de6643e62218979a0a13a70..2e475ea40c65b17210bfd96db8100f93fff7e942 100644
--- a/doc/source/tutorials/run_model_gui.rst
+++ b/doc/source/tutorials/run_model_gui.rst
@@ -6,10 +6,10 @@ two files: kmc_model.so and kmc_settings.py. These two files
are really all you need for simulations. So a simple
way to view the model is the ::
- kmcos view
+ python3 kmcos view
command from the command line. For this two work you need to
-be in the same directory as these two file (more precisely
+be in the same directory as these two files (more precisely
these two files need to be in the python import path) and
you should see an instance of your model running.
This feature can be quite useful to quickly obtain an
diff --git a/kmcos/io.py b/kmcos/io.py
index d3fc25affb31259394d0561f5a28a89910c231c2..ecc48682d313cb548e2dfc4973c7e1d6328ebd62 100644
--- a/kmcos/io.py
+++ b/kmcos/io.py
@@ -3070,8 +3070,9 @@ class ProcListWriter():
# XML
out.write('xml = """%s"""\n' % data)
- #benchmark if run directly, else cli.
+ #benchmark if kmc_settings.py is run without additional arguments, else call cli with additional argument provided.
out.write('if __name__ == "__main__":\n')
+ out.write(' #benchmark if kmc_settings.py is run without additional arguments, else call cli with additional argument provided.\n')
out.write(' import sys\n')
out.write(' if len(sys.argv) == 1:\n')
out.write(' from kmcos import cli\n')