docs: how_to page for analysis

_reference/analysis.qmd

@@ -15,10 +15,10 @@ For command line usage, run `kimmdy-analysis -h`.
 | [get_analysis_dir](#kimmdy.analysis.get_analysis_dir) | Get analysis directory for a KIMMDY run. |
 | [plot_energy](#kimmdy.analysis.plot_energy) | Plot GROMACS energy for a KIMMDY run. |
 | [plot_rates](#kimmdy.analysis.plot_rates) | Plot rates of all possible reactions for each 'decide_recipe' step. |
-| [plot_runtime](#kimmdy.analysis.plot_runtime) | Plot runtime of all tasks. |
 | [radical_migration](#kimmdy.analysis.radical_migration) | Plot population of radicals for a KIMMDY run. |
 | [radical_population](#kimmdy.analysis.radical_population) | Plot population of radicals for a KIMMDY run. |
 | [reaction_participation](#kimmdy.analysis.reaction_participation) | Plot which atoms participate in reactions. |
+| [runtime_analysis](#kimmdy.analysis.runtime_analysis) | Plot which atoms participate in reactions. |
 
 ### concat_traj { #kimmdy.analysis.concat_traj }
 
@@ -101,21 +101,6 @@ Plot rates of all possible reactions for each 'decide_recipe' step.
 |--------|--------------|-------------------------|------------|
 | `dir`  | [str](`str`) | Directory of KIMMDY run | _required_ |
 
-### plot_runtime { #kimmdy.analysis.plot_runtime }
-
-`analysis.plot_runtime(dir, md_tasks, datefmt, open_plot=False)`
-
-Plot runtime of all tasks.
-
-#### Parameters
-
-| Name        | Type           | Description                         | Default    |
-|-------------|----------------|-------------------------------------|------------|
-| `dir`       | [str](`str`)   | Directory of KIMMDY run             | _required_ |
-| `md_tasks`  | [list](`list`) | Names of MD tasks to color          | _required_ |
-| `datefmt`   | [str](`str`)   | Date format in the KIMMDY logfile   | _required_ |
-| `open_plot` | [bool](`bool`) | Open plot in default system viewer. | `False`    |
-
 ### radical_migration { #kimmdy.analysis.radical_migration }
 
 `analysis.radical_migration(dirs, type='qualitative', cutoff=1)`
@@ -155,6 +140,19 @@ Plot which atoms participate in reactions.
 
 #### Parameters
 
+| Name        | Type           | Description                         | Default    |
+|-------------|----------------|-------------------------------------|------------|
+| `dir`       | [str](`str`)   | Directory of KIMMDY run             | _required_ |
+| `open_plot` | [bool](`bool`) | Open plot in default system viewer. | `False`    |
+
+### runtime_analysis { #kimmdy.analysis.runtime_analysis }
+
+`analysis.runtime_analysis(dir, open_plot=False)`
+
+Plot which atoms participate in reactions.
+
+#### Parameters
+
 | Name        | Type           | Description                         | Default    |
 |-------------|----------------|-------------------------------------|------------|
 | `dir`       | [str](`str`)   | Directory of KIMMDY run             | _required_ |

_reference/kmc.qmd

@@ -18,7 +18,7 @@ and because we have one reactant molecule
 
 ### KMCResult { #kimmdy.kmc.KMCResult }
 
-`kmc.KMCResult(self, recipe=lambda: Recipe([], [], [])(), reaction_probability=None, time_delta=None, time_start=None)`
+`kmc.KMCResult(recipe=field(default_factory=lambda : Recipe([], [], [])), reaction_probability=None, time_delta=None, time_start=None)`
 
 The result of a KMC step. Similar to a Recipe but for the concrete realization of a reaction.
 

_reference/recipe.qmd

@@ -77,7 +77,7 @@ Change topology to break a bond
 
 ### CustomTopMod { #kimmdy.recipe.CustomTopMod }
 
-`recipe.CustomTopMod(self, f)`
+`recipe.CustomTopMod(f)`
 
 A custom recipe step that can be used to define a custom topology modification.
 
@@ -105,7 +105,7 @@ Either provide the index (ix_to_place) or the ID (id_to_place) of the atom to pl
 
 ### Recipe { #kimmdy.recipe.Recipe }
 
-`recipe.Recipe(self, recipe_steps, rates, timespans)`
+`recipe.Recipe(recipe_steps, rates, timespans)`
 
 A reaction path defined by one series of RecipeSteps.
 Defines everything necessart to build the
@@ -146,7 +146,7 @@ Combines this Recipe with another with the same RecipeSteps.
 
 ### RecipeCollection { #kimmdy.recipe.RecipeCollection }
 
-`recipe.RecipeCollection(self, recipes)`
+`recipe.RecipeCollection(recipes)`
 
 A RecipeCollection encompasses a number of reaction paths.
 They can originate from multiple reaction plugins, but do not need to.
@@ -234,7 +234,7 @@ id: 1-based, str
 
 ### Relax { #kimmdy.recipe.Relax }
 
-`recipe.Relax(self)`
+`recipe.Relax()`
 
 Start a relaxation MD.