MAINT Update 'proc_syntax.rst'

doc/source/topic_guides/proc_syntax.rst

 .. _proc_mini_language:
 
 The Process Syntax
-=========================
+==================
 
+In KMC language a process is uniquely defined by a configuration `before` the process is executed,
+a configuration `after` the process is executed, and a rate constant. Here, this model is used to
+define a process by giving it a:
 
-In kMC language a process is uniquely defined by a
-configuration `before` the process is executed,
-a configuration `after` the process is executed,
-and a rate constant. Here this model is used to
-define a process by giving it a :
+- ``condition_list``
+- ``action_list``
+- ``rate_constant``
 
-- condition_list
-- action_list
-- rate_constant
+As you might guess, each `condition` corresponds to one `before`, and each `action` corresponds to
+one `after`. In fact, conditions and actions are actually of the same class or data type: each
+condition and action consists of a coordinate and a species which `has to be` or `will be` at the
+coordinate. This model of process definition also means that each process in one unit cell has to
+be defined explicitly. Typically, on a single crystal surface one will have not only one diffusion
+per species, but as many as there are equivalent directions:
 
+- ``species_diffusion_right``
+- ``species_diffusion_up``
+- ``species_diffusion_left``
+- ``species_diffusion_down``
 
-As you might guess, each `condition` corresponds to one
-`before`, and each `action` corresponds to one `after`.
-In fact conditions and actions are actually of the same
-class or data type: each condition and action consists of
-a coordinate and a species which has to `be` or `will be` at
-the coordinate. This model of process definition also
-means that each process in one unit cell has to be
-defined explicitly. Typically, on a single crystal
-surface one will have not only one diffusion per species, but
-as many as there are equivalent directions :
-
-  - species_diffusion_right
-  - species_diffusion_up
-  - species_diffusion_left
-  - species_diffusion_down
-
-
-While it may seem like a lot of work to define that
-many processes, it allows for a very clean and straightforward
-definition of a process itself.  Later you can use
-geometric measures to abstract these cases as you will see
-further down.
+While it may seem like a lot of work to define that many processes, it allows for a very clean and
+straightforward definition of a process itself. Later you can use geometric measures to abstract
+these cases as you will see further down.
 
 Adsorption
 ^^^^^^^^^^
 
-Let's start with a very simple and basic process: molecular
-adsorption of a gas phase species, let call it ``A`` on a
-surface site. For this we need a species ::
+Let's start with a very simple and basic process: molecular adsorption of a gas phase species,
+let's call it ``A``, on a surface site. For this we need a species ::
 
   from kmos3.types import *
   kmc_model = kmos3.create_kmc_model()
@@ -54,91 +42,73 @@ surface site. For this we need a species ::
   empty = Species(name='empty')
   kmc_model.add_species(empty)
 
-
-and the coordinate of a surface site ::
+and the coordinates of a surface site ::
 
   layer = Layer(name='default')
   kmc_model.add_layer(layer)
   layer.sites.append(Site(name='a'))
   coord = kmc_model.lattice.generate_coord('a.(0,0,0).default')
 
-which is for now all we need to define an adsorption
-process::
+which is for now all we need to define an adsorption process ::
 
-  adsorption = Process(name='adsorption_A_a',
-                      condition_list=[Condition(coord=coord,
-                                                species='empty')],
-                      action_list=[Action(coord=coord,
-                                          species='A')])
+  adsorption = Process(
+      name='adsorption_A_a',
+      condition_list=[Condition(coord=coord, species='empty')],
+      action_list=[Action(coord=coord, species='A')]
+      )
   kmc_model.add_process(adsorption)
 
 Now this wasn't hard, was it?
 
-
 Diffusion
 ^^^^^^^^^
 
-Let's move to another example, namely the `diffusion` of
-a particle to the next unit cell in the y-direction.
-Initially, you need the coordinate of the final site ::
+Let's move to another example, namely the `diffusion` of a particle to the next unit cell in the
+y-direction. Initially, you need the coordinate of the final site ::
 
   final = kmc_model.lattice.generate_coord('a.(0,1,0).default')
 
 and you are good to go ::
 
-  diffusion_up = Process('diffusion_A_up',
-                         condition_list=[Condition(coord=coord,
-                                                   species='A'),
-                                         Condition(coord=final,
-                                                   species='empty')],
-                         condition_list=[Condition(coord=coord,
-                                                   species='empty'),
-                                         Condition(coord=final,
-                                                   species='A')],
+  diffusion_up = Process(
+      name='diffusion_A_up',
+      condition_list=[Condition(coord=coord, species='A'),
+                      Condition(coord=final, species='empty')],
+      condition_list=[Condition(coord=coord, species='empty'),
+                      Condition(coord=final, species='A')],
+      )
   kmc_model.add_process(diffusion_up)
 
-You can complicate this `ad infinitum` but you already know all the elements
-necessary to define processes.
-
+You can complicate this ad infinitum but you already know all the elements necessary to define
+processes.
 
 Avoid Double Counting
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Finally a word of warning: `double counting` is a phenomenon
-that can arise for certain processes where there are more
-than one equivalent directions and coordinates.
-Consider, for example, the dissociative oxygen adsorption. 
-Novices typically collect all possible directions (e.g. right, up,
-left, down) and then define this process for each direction. 
-However, this approach may be incorrect depending on 
-how the rate constant value was defined.
-If the rate constant represents a net rate for
-adsorption/desorption from a pair of sites (from an average or 
-from a single transition state that bridges two sites),
-then the right, up, left, down procedures will result in `double counting`.
-This is because, for example, adsorption_up is the same process
-as adsorption_down, just executed from one site above or below. 
-To address this issue, one can compensate by dividing each 
-adsorption and desorption rate constant by 2.
-Alternatively, one can avoid double counting by only defining geometrically equivalent
-sites once per unit cell: a simple trick to achieve this is to
-only consider processes in the `positive` directions, for example.
-
-However, it's crucial to recognize that in cases where there are two
-transition state possibilities (one above each site) due to a 
-heterolytic cleavage transition state, it's essential to acknowledge 
-and include both processes. These processes should not be dismissed 
-as 'double counting' because they represent distinct pathways with
-unique transition states sharing the same reactants and products.
-
-Most rate constants in the literature for dissociative adsorption
-are defined as an average for the two sites,
-or involve a single homolytic transition state,
-and thus most cases of dissociate adsorption should have a single process
-between up and down as well as between left and right
+^^^^^^^^^^^^^^^^^^^^^
+
+Finally a word of warning: `double counting` is a phenomenon that can arise for certain processes
+where there are more than one equivalent directions and coordinates. Consider, for example, the
+dissociative oxygen adsorption. Novices typically collect all possible directions (e.g., right,
+up, left, down) and then define this process for each direction. However, this approach may be
+incorrect depending on how the rate constant value was defined. If the rate constant represents a
+net rate for adsorption/desorption from a pair of sites (from an average or from a single
+transition state that bridges two sites), then the right, up, left, down procedures will result in
+`double counting`. This is because, for example, ``adsorption_up`` is the same process as
+``adsorption_down``, just executed from one site above or below. To address this issue, one can
+compensate by dividing each adsorption and desorption rate constant by 2. Alternatively, one can
+avoid double counting by only defining geometrically equivalent sites once per unit cell: a simple
+trick to achieve this is to only consider processes in the `positive` directions, for example.
+
+However, it's crucial to recognize that in cases where there are two transition state
+possibilities (one above each site) due to a heterolytic cleavage transition state, it's essential
+to acknowledge and include both processes. These processes should not be dismissed as `double
+counting` because they represent distinct pathways with unique transition states sharing the same
+reactants and products.
+
+Most rate constants in the literature for dissociative adsorption are defined as an average for
+the two sites, or involve a single homolytic transition state, and thus most cases of dissociative
+adsorption should have a single process between up and down as well as between left and right
 (yielding two processes, not four, for a simple cubic system).
 
-
 Taking It Home
 ^^^^^^^^^^^^^^^