Reverted back. Convergence study is not accurate because of inability…

… to control mesh for now.

README.md

@@ -56,17 +56,20 @@ Or through the command line with
 
 ```
 mkdir <root folder>/cavsim2d/solver/ABCI
-copy <root folder>/ABCI_MP_12_5/ABCI_MP_12_5/ABCI_MP application for Windows/ABCI_MP64_12_5.exe <root folder>/cavsim2d/solver/ABCI
+tar -xf <root folder>/ABCI_MP_12_5.zip
+copy '<root folder>/ABCI_MP_12_5/ABCI_MP_12_5/ABCI_MP application for Windows/ABCI_MP64_12_5.exe' <root folder>/cavsim2d/solver/ABCI
 cd <root folder>/cavsim2d/solver/ABCI
 ren ABCI_MP64_12_5.exe ABCI.exe
 ```
 
-Before diving in, I would install `pprintpp`. It is not necessay but it sure does makes the print readable.
-```python
-import pprint
-pp = pprint.PrettyPrinter(indent=4)
+Before diving in, I would install `pprintpp`. It is not necessary but it sure does make the print readable.
+
+```
+pip install pprintpp
 ```
 
+If jupyter and ipywidgets are not already installed, now will be a good time to installl it.
+
 --------------------------------------------
 Examples - TESLA Elliptical Cavity
 ==================================
@@ -75,6 +78,9 @@ The core components of `cavsim2d` are `Cavities` and `Cavity` objects. `Cavities
 instances, each representing a single RF cavity and its associated data. These objects are instantiated as follows:
 
 ```python
+
+import pprint
+pp = pprint.PrettyPrinter(indent=4)
 from cavsim2d.cavity import Cavity, Cavities
 
 cavs = Cavities()

cavsim2d/analysis/tune/pyTuner.py

@@ -60,6 +60,7 @@ def tune(self, par_mid, par_end, tune_var, target_freq, cell_type, beampipes, bc
             right = tuned_cell
             beampipes = 'none'
         elif cell_type.lower() == 'mid-end cell' or cell_type.lower() == 'mid-end-cell' or cell_type.lower() == 'mid_end_cell':
+            print(par_mid)
             mid = par_mid
             left = par_mid
             tuned_cell = par_end

cavsim2d/analysis/tune/tuner.py

@@ -81,13 +81,17 @@ def tune_ngsolve(self, pseudo_shape_space, bc, parentDir, projectDir, filename,
                         tune_var, freq = 0, 0
 
                 if tune_var != 0 and freq != 0:
-                    if cell_type.lower() == 'mid cell' or cell_type.lower() == 'mid-cell' or cell_type.lower() == 'mid_cell':
+                    if (cell_type.lower() == 'mid cell' or cell_type.lower() == 'mid-cell'
+                            or cell_type.lower() == 'mid_cell'):
+                        print('it is in here', tune_variable, tune_var, freq)
                         tuned_mid_cell = pseudo_shape['IC'][:7]
                         tuned_mid_cell[VAR_TO_INDEX_DICT[tune_variable]] = tune_var
                         tuned_end_cell = pseudo_shape['OC'][:7]
                         # enforce equator continuity
                         tuned_end_cell[6] = tuned_mid_cell[6]
-                    elif cell_type.lower() == 'mid-end cell' or cell_type.lower() == 'mid-end-cell' or cell_type.lower() == 'mid_end_cell':
+                    elif (cell_type.lower() == 'mid-end cell' or cell_type.lower() == 'mid-end-cell'
+                          or cell_type.lower() == 'mid_end_cell'):
+                        print('it is in here', tune_variable, tune_var, freq)
                         tuned_mid_cell = pseudo_shape['IC'][:7]
                         tuned_end_cell = pseudo_shape['OC'][:7]
                         tuned_end_cell[VAR_TO_INDEX_DICT[tune_variable]] = tune_var
@@ -97,11 +101,18 @@ def tune_ngsolve(self, pseudo_shape_space, bc, parentDir, projectDir, filename,
                         tuned_end_cell = pseudo_shape['OC'][:7]
                         tuned_end_cell[VAR_TO_INDEX_DICT[tune_variable]] = tune_var
                         tuned_mid_cell = copy.deepcopy(tuned_end_cell)
-                    else:
+                    elif cell_type.lower() == 'single_cell' or cell_type.lower() == 'single cell':
                         tuned_mid_cell = pseudo_shape['IC'][:7]
                         tuned_end_cell = pseudo_shape['OC'][:7]
                         tuned_end_cell[VAR_TO_INDEX_DICT[tune_variable]] = tune_var
                         tuned_mid_cell = copy.deepcopy(tuned_end_cell)
+                    else:
+                        info('Valid cell_type not selected. Defaulting to end_cell')
+                        tuned_mid_cell = pseudo_shape['IC'][:7]
+                        tuned_mid_cell[VAR_TO_INDEX_DICT[tune_variable]] = tune_var
+                        tuned_end_cell = pseudo_shape['OC'][:7]
+                        # enforce equator continuity
+                        tuned_end_cell[6] = tuned_mid_cell[6]
 
                         # # enforce equator continuity
                         # tuned_mid_cell[6] = tuned_end_cell[6]
@@ -133,8 +144,8 @@ def tune_ngsolve(self, pseudo_shape_space, bc, parentDir, projectDir, filename,
                     tuned_shape_space[key] = {"IC": inner_cell, "OC": outer_cell, "OC_R": outer_cell, "BP": 'both', 'FREQ': freq}
 
                     # write tune results
-                    d_tune_res = {'IC': list(tuned_mid_cell), 'OC': list(tuned_end_cell),
-                                  'OC_R': list(tuned_end_cell),
+                    d_tune_res = {'IC': list(inner_cell), 'OC': list(outer_cell),
+                                  'OC_R': list(outer_cell),
                                   'TUNED VARIABLE': tune_variable, 'CELL TYPE': cell_type, 'FREQ': freq}
 
                     abs_err_dict = {'abs_err': abs_err_list}