Added changes from Paul: Remove extra indent in some pyzacros example…

…s. SCMSUITE-9003 SO--

doc/source/components/cluster.rst

@@ -50,9 +50,9 @@ The following lines illustrate an example:
 .. code-block:: python
   :linenos:
 
-   # Cluster Expansion
-   ce = pz.ClusterExpansion([CO_p, O_p])
-   print(ce)
+  # Cluster Expansion
+  ce = pz.ClusterExpansion([CO_p, O_p])
+  print(ce)
 
 which produce the following output:
 

doc/source/components/latticestate.rst

@@ -21,14 +21,14 @@ We are going to make the initial state as a randomly populated lattice by ``CO*`
 .. code-block:: python
   :linenos:
 
-   # LatticeState setup (initial state)
-   ist = pz.LatticeState(lat, surface_species=spl.surface_species())
-   ist.fill_sites_random(site_name='StTp1', species='CO*', coverage=0.1)
-   ist.fill_sites_random(site_name='StTp1', species='O*', coverage=0.1)
+  # LatticeState setup (initial state)
+  ist = pz.LatticeState(lat, surface_species=spl.surface_species())
+  ist.fill_sites_random(site_name='StTp1', species='CO*', coverage=0.1)
+  ist.fill_sites_random(site_name='StTp1', species='O*', coverage=0.1)
 
-   print(ist)
+  print(ist)
 
-   ist.plot()
+  ist.plot()
 
 Similarly to the other classes, the function ``print()`` (see line 6) allows taking a look at the Zacros code that
 will be internally generated, which for this example is the following:

doc/source/components/zacrosjob.rst

@@ -12,11 +12,11 @@ The ``ZacrosJob`` class constructor requires a Settings object, and the set of o
 .. code-block:: python
   :linenos:
 
-   job = pz.ZacrosJob( settings=sett, lattice=lat,
-                       mechanism=[CO_ads, O2_ads, CO_oxi],
-                       cluster_expansion=[CO_p, O_p] )
+  job = pz.ZacrosJob( settings=sett, lattice=lat,
+                      mechanism=[CO_ads, O2_ads, CO_oxi],
+                      cluster_expansion=[CO_p, O_p] )
 
-   print(job)
+  print(job)
 
 In the previous code, we used the function print() to see the content of the files that are going to be used with Zacros. This output information is separated into 4 sections, each corresponding to the zacros input files: ``simulation_input.dat``, ``lattice_input.dat``, ``energetics_input.dat``, and ``mechanism_input.dat``.
 

doc/source/components/zacrosresults.rst

@@ -10,17 +10,17 @@ For our example (see :ref:`use case system <use_case_model_zgb>`), the following
 .. code-block:: python
   :linenos:
 
-   results = job.run()
+  results = job.run()
 
-   if( job.ok() ):
-      provided_quantities = results.provided_quantities()
-      print("nCO2 =", provided_quantities['CO2'])
+  if( job.ok() ):
+     provided_quantities = results.provided_quantities()
+     print("nCO2 =", provided_quantities['CO2'])
 
-      results.plot_molecule_numbers( results.gas_species_names() )
-      results.plot_lattice_states( results.lattice_states() )
+     results.plot_molecule_numbers( results.gas_species_names() )
+     results.plot_lattice_states( results.lattice_states() )
 
-      pstat = results.get_process_statistics()
-      results.plot_process_statistics( pstat, key="number_of_events" )
+     pstat = results.get_process_statistics()
+     results.plot_process_statistics( pstat, key="number_of_events" )
 
 
 Here, the ``ZacrosResults`` object ``results`` is created by calling the method ``run()`` of the corresponding ``ZacrosJob`` job (line 1).

doc/source/extended_components/zacrosparametersscanresults.rst

@@ -10,24 +10,24 @@ The following lines of code show an example of how to use the ``ZacrosParameters
 .. code-block:: python
   :linenos:
 
-   ps_parameters = pz.ZacrosParametersScanJob.Parameters()
-   ps_parameters.add( 'x_CO', 'molar_fraction.CO', numpy.arange(0.1, 1.0, 0.1) )
-   ps_parameters.add( 'x_O2', 'molar_fraction.O2', lambda params: 1.0-params['x_CO'] )
-   ps_parameters.set_generator( pz.ZacrosParametersScanJob.zipGenerator )
-   print(ps_parameters)
-
-   ps_job = pz.ZacrosParametersScanJob( reference=z_job, parameters=ps_parameters )
-   results = ps_job.run()
-
-   if( ps_job.ok() ):
-      results_dict = results.turnover_frequency()
-      print(results_dict[0])
-
-      print("%4s"%"cond", "%8s"%"x_CO", "%10s"%"TOF_CO2")
-      for i,idx in enumerate(results.indices()):
-          print( '%4d'%i,
-                 '%8.2f'%results_dict[i]['x_CO'],
-                 '%10.6f'%results_dict[i]['turnover_frequency']['CO2'] )
+  ps_parameters = pz.ZacrosParametersScanJob.Parameters()
+  ps_parameters.add( 'x_CO', 'molar_fraction.CO', numpy.arange(0.1, 1.0, 0.1) )
+  ps_parameters.add( 'x_O2', 'molar_fraction.O2', lambda params: 1.0-params['x_CO'] )
+  ps_parameters.set_generator( pz.ZacrosParametersScanJob.zipGenerator )
+  print(ps_parameters)
+
+  ps_job = pz.ZacrosParametersScanJob( reference=z_job, parameters=ps_parameters )
+  results = ps_job.run()
+
+  if( ps_job.ok() ):
+     results_dict = results.turnover_frequency()
+     print(results_dict[0])
+
+     print("%4s"%"cond", "%8s"%"x_CO", "%10s"%"TOF_CO2")
+     for i,idx in enumerate(results.indices()):
+         print( '%4d'%i,
+                '%8.2f'%results_dict[i]['x_CO'],
+                '%10.6f'%results_dict[i]['turnover_frequency']['CO2'] )
 
 Lines 1-8 were already discusssed before (see :ref:`ZacrosParametersScanJob <zacrosparametersscanjob>`).
 Here, the ``ZacrosParametersScanResults`` object ``results`` is created by calling the method ``run()`` of the corresponding ``ZacrosParametersScanJob`` job (line 8).