review/test/typos

alexruiz95 · Nov 26, 2019 · d3a2707 · d3a2707
1 parent 8929740
commit d3a2707
Show file tree

Hide file tree

Showing 4 changed files with 20 additions and 25 deletions.
diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -29,7 +29,7 @@ through the terminal by typing::
     $ turtleFSI
 
 followed by any additional options, for instance, which problem to run and the time step size.
-Use ``-h`` to see all availeble options. A detailed explanation for usage of turtleFSI can be found
+Use ``-h`` to see all available options. A detailed explanation for usage of turtleFSI can be found
 `here <https://turtlefsi2.readthedocs.io/en/latest/using_turtleFSI.html>`.
 
 

diff --git a/docs/source/using_turtleFSI.rst b/docs/source/using_turtleFSI.rst
@@ -26,35 +26,32 @@ To get an overview of all parameters, please run::
 
 Built-in functionality
 ======================
-We have designed turtleFSI to be lightweight and focus around solving the equiations, not additional 
-functionality. However, we have added two functions: checkpointing/restart, and storing files for visualization.
+Two important functions are available in the current version of turtleFSI: checkpointing/restart, and storing files for visualization.
 
 For checkpointing you can set the variable ``--checkpoint-step`` to set how often a checkpoint should
-be stored. To restart the from a previous run set ``--restart-folder [folder/sub-folder]``. Note that 
+be stored. To restart from a previous checkpoint step use the command ``--restart-folder [folder/sub-folder]``. Note that
 the variables from the previous simulation will overwrite any parameters set in the ``set_problem_parameters``
-or on the commandline. To overwrite any parameters from the previous run, for instance, end time ``T``, you can
-use the ``initiate`` function.
+or on the commandline. If you need to change a parameter from the previous checkpoint file (for instance, end time ``T``), you can
+still do it by explicitly redefining it within the ``initiate`` function.
 
 To set how often you save files for visualization you can set ``--save-step``. Note that the default is ``1``.
 
 
 Setting parameters
 ==================
-All the the default parameters are set in the ``problem/__init__.py`` file. Problem specific parameters
-are then overwritten in the problem file under ``set_problem_parameters``. Then any parameters given on the
-command line overwrites those given in the problem file. In summary; we have that defualt parameters <
-problem file < command line.
+All the default parameters are set in the ``problem/__init__.py`` file. Problem specific parameters
+are then overwritten in the problem file under ``set_problem_parameters`` or by defining them in the command line. In summary;
+the priority is as follow: default parameters < problem file < command line < (checkpointing).
 
 
 Create your own problem file
 ============================
 
-The number of problem files in turtleFSI is somewhat limited. We have, therefore, created a step-by-step
-explanation, see the below, on how you can create your own problem file.
+We have created a step-by-step explanation, see the below, on how you can create your own problem file.
 
 For all numerical problems we have to specify a set parameters, provide a mesh and boundary conditions,
 how to solve the equations, and finally specify which metric we are interested in measuring.
-In turtleFSI problem file you can define upto seven functions which provides the solver with
+In turtleFSI problem file you can define up to seven functions which provides the solver with
 the above mentioned information. Listed in the order they are first executed:
 
 - ``set_problem_parameters``

diff --git a/turtleFSI/problems/__init__.py b/turtleFSI/problems/__init__.py
@@ -49,9 +49,9 @@
     Um=0.8,          # Maximum velocity at inlet
 
     # Variational formulations
-    fluid="fluid",                      # ["fluid", "no-fluid"] Turn off fluid and only solve the solid problem
-    solid="solid",                      # ["solid", "no-solid"] Turn off solid and only solve the fluid problem
-    extrapolation="laplace",            # laplace, elastic, biharmonic, no-extrapolation
+    fluid="fluid",                      # ["fluid", "no_fluid"] Turn off fluid and only solve the solid problem
+    solid="solid",                      # ["solid", "no_solid"] Turn off solid and only solve the fluid problem
+    extrapolation="laplace",            # laplace, elastic, biharmonic, no_extrapolation
     extrapolation_sub_type="constant",  # small_constant, volume, constant, constrained_disp, constrained_disp_vel
     bc_ids=[],                          # List of ids for weak form of biharmonic mesh lifting operator with 'constrained_disp_vel'
 
@@ -104,8 +104,7 @@ def create_folders(folder, sub_folder, restart_folder, **namespace):
 
 
 def checkpoint(dvp_, default_variables, checkpoint_folder, mesh, **namespace):
-    """Utility function for storing the current parameters and the last two timesteps to
-    restart from later"""
+    """Utility function for storing the current parameters and the last two timesteps"""
     # Only update variables that exists in default_variables
     default_variables.update((k, namespace[k]) for k in (default_variables.keys() & namespace.keys()))
 

diff --git a/turtleFSI/utils/argpar.py b/turtleFSI/utils/argpar.py
@@ -73,7 +73,7 @@ def return_typed(self, s):
                 tmp_dict[k] = return_types(v)
             return tmp_dict
 
-        else: # A string
+        else:  # A string
             return s
 
     def __call__(self, parser, namespace, values, option_string=None):
@@ -146,11 +146,11 @@ def parse():
                         choices=["fluid", "no_fluid"], metavar="Fluid",
                         help="Turn off fluid and only solve the solid problem")
     parser.add_argument("-s", "--solid", type=str, default=None, metavar="Solid",
-                        choices=["solid", "no-solid"],
+                        choices=["solid", "no_solid"],
                         help="Turn off solid and only solve the fluid problem")
     parser.add_argument("-e", "--extrapolation", type=str, default=None,
                         metavar="Extrapolation method",
-                        choices=["laplace", "elastic", "biharmonic", "no-extrapolation"],
+                        choices=["laplace", "elastic", "biharmonic", "no_extrapolation"],
                         help="Set approach for extrapolating the deformation into the fluid" +
                         "domain")
     parser.add_argument("-et", "--extrapolation-sub-type", type=str,
@@ -223,15 +223,14 @@ def parse():
     parser.add_argument("--save-step", type=int, default=None,
                         help="Saving frequency of the files defined in the problem file")
     parser.add_argument("--checkpoint-step", type=int, default=None,
-                         help="How often to store a checkpoint to restart the simulation from")
+                        help="How often to store a checkpoint (use to later restart a simulation)")
     parser.add_argument("--folder", type=str, default=None,
                         help="Path to store the results. You can store multiple" +
                         " simulations in one folder")
     parser.add_argument("--sub-folder", type=str, default=None,
-                         help="Over write the standard 1, 2, 3 name of the sub folders")
+                        help="Over write the standard 1, 2, 3 name of the sub folders")
     parser.add_argument("--restart-folder", type=str, default=None,
-                         help="Path to subfolder to restart from.")
-
+                        help="Path to subfolder to restart from")
 
     # Set spatial and temporal resolution
     parser.add_argument("-dt", metavar="Time step", type=float,