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Commit d7d0c907 authored by Martin Deimel's avatar Martin Deimel
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MAINT Update 'workflows.rst'

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Modelling Workflows Modelling Workflows
=================== ===================
At the core of modelling lies the art to capture At the core of modelling lies the art to capture the most important features of a system and leave
the most important features of a system and leave all others out. Kmos3 is designed around the fact that modeling is a creative and iterative
all others out. kmos3 is designed around the fact process.
that modelling is a creative and iterative process.
A typical type of approach for modelling could be: A typical type of approach for modeling could be:
#. start with educated guess #. start with educated guess
#. calculate outcome #. calculate outcome
#. compare various observables and qualitative #. compare various observables and qualitative behavior with reference system
behavior with reference system #. adapt model, go to 2. or publish model
#. adapt model, goto 2. or publish model
So while this procedure is quite generic it may help So while this procedure is quite generic, it may help to illustrate that the chances to find and
to illustrate that the chances to find and capture capture the relevant features of a system are enhanced if the trial/learn loop is as short as
the relevant features of a system are enhanced possible.
if the trial/learn loop is as short as possible.
KMC Modeling
kMC Modeling
^^^^^^^^^^^^ ^^^^^^^^^^^^
A good way to define a model is to use a paper and pencil to draw A good way to define a model is to use a paper and pencil to draw your lattice, choose the species
your lattice, choose the species that you will need, draw that you will need, draw each process and write down an expression for each rate constant, and
each process and write down an expression for each rate constant, and finally fix all energy barriers and external parameters that you will need. Putting a model
finally fix all energy barriers and external parameters that you will need. prepared like this into a computer is a simple exercise. You enter a new model by filling in
Putting a model prepared like this into a computer is a simple exercise.
You enter a new model by filling in
* meta information * meta information
* lattice * lattice
...@@ -36,31 +30,27 @@ You enter a new model by filling in ...@@ -36,31 +30,27 @@ You enter a new model by filling in
* parameters * parameters
* processes * processes
in roughly this order or open an existing one by opening a kMC XML file. in roughly this order or adapt an existing one by opening a KMC XML file.
If you want to see the model run
`kmos3 export <xml-file>` and you will get a subfolder with a self-contained
Fortran90 code, which solves the model. If all necessary dependencies are
installed you can simply run `kmos3 view` in the export folder.
If you want to see the model run `kmos3 export <xml-file>`. You will get a subfolder with a
self-contained Fortran90 code, which represents the model and you can simply run
`kmos3 view` in this export folder as described in detail in the :ref:`API tutorial
<api-tutorial>`.
kmos3 workflows Kmos3 Workflows
^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^
Since `kmos3` has several entry points, there are several ways of using it. Since kmos3 has several entry points, there are several ways of using it. This section will
This section will outline different ways of using kmos3: outline different ways of using kmos3:
- *the render script* - *the render script*
Just write complete scripts as outlined in Just write complete scripts as outlined in :ref:`api-tutorial`. Compile source from there or
:ref:`api-tutorial`. Export inspect the XML file with one of the next methods below.
source from there or inspect XML file with one
of the next methods below.
- *the CLI editor* - *the CLI editor*
Open an existing project \*.xml file with :: Open an existing project XML file with ::
kmos3 import <project_name>.xml kmos3 import <project_name>.xml
...@@ -68,9 +58,7 @@ This section will outline different ways of using kmos3: ...@@ -68,9 +58,7 @@ This section will outline different ways of using kmos3:
- *edit the XML file* - *edit the XML file*
Just open the XML file of your kmos3 project with a text Just open the XML file of your kmos3 project with a text editor of your choice and inspect or
editor of your choice and inspect or your model right edit your model right there. This might only be a last resort to figure out what is going on.
there. This might only be a last resort to figure out XML is often not considered very readable and note that changing variable names in one place
what is going on. XML is often not considered very might cause inconsistencies in other places.
readable and note that changing variable names in
one place might often break inconsistencies in other.
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