Clean up

MolarVerse · Sep 2, 2024 · fd14fae · fd14fae
1 parent c9054f5
commit fd14fae
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Showing 3 changed files with 11 additions and 41 deletions.
diff --git a/PQAnalysis/analysis/thermal_expansion/thermal_expansion.py b/PQAnalysis/analysis/thermal_expansion/thermal_expansion.py
@@ -17,7 +17,6 @@
 from PQAnalysis.utils import timeit_in_class
 from PQAnalysis.utils.custom_logging import setup_logger
 from PQAnalysis import __package_name__
-from PQAnalysis.core.cell import Cells
 
 from PQAnalysis.type_checking import runtime_type_checking
 # local relative imports
@@ -104,8 +103,6 @@ def __init__(
             )
 
         if boxes_avg is not None:
-            # reshape the boxes data so that the columns are the temperature points and the rows are the boxes data
-            # if the boxes data is not in the correct format, transpose it
             boxes_avg = np.array(boxes_avg)
             if np.shape(boxes_avg)[0] == 4:
                 self._boxes_avg = boxes_avg

diff --git a/PQAnalysis/analysis/thermal_expansion/thermal_expansion_input_file_reader.py b/PQAnalysis/analysis/thermal_expansion/thermal_expansion_input_file_reader.py
@@ -26,7 +26,6 @@ class ThermalExpansionInputFileReader(Reader):
 
     #: List[str]: The optional keys of the input file
     optional_keys = required_keys + [
-        Reader.unit_key,
         Reader.log_file_key,
     ]
 
@@ -97,7 +96,6 @@ def read(self):
 They are optional in the input file, but they might be required for
 the analysis. This means that if an optional keyword is specified
 other keywords might be required.
-- :code:`{Reader.unit_key}` is optional for the analysis.
 - :code:`{Reader.log_file_key}` is optional for the analysis.
 (for more information see
 :py:class:`~PQAnalysis.io.input_file_reader.pq_analysis.thermal_expansion.thermal_expansion.ThermalExpansion`).

diff --git a/PQAnalysis/analysis/thermal_expansion/thermal_expansion_output_file_writer.py b/PQAnalysis/analysis/thermal_expansion/thermal_expansion_output_file_writer.py
@@ -76,13 +76,21 @@ def write(
             file=self.file
         )
         print(
-            f"T a_avg a_std b_avg b_std c_avg c_std V_avg V_std thermal_expansion_a thermal_expansion_b thermal_expansion_c volumetric_expansion",
+            "T a_avg a_std b_avg b_std c_avg c_std V_avg V_std "
+            "thermal_expansion_a thermal_expansion_b "
+            "thermal_expansion_c volumetric_expansion",
             file=self.file
         )
 
         for i, temperature in enumerate(temperature_points):
             print(
-                f"{temperature:16.16f} {boxes_avg_data[0,i]:16.16f} {boxes_std_data[0,i]:16.16f} {boxes_avg_data[1,i]:16.16f} {boxes_std_data[1,i]:16.16f} {boxes_avg_data[2,i]:16.16f} {boxes_std_data[2,i]:16.16f} {boxes_avg_data[3,i]:16.16f} {boxes_std_data[3,i]:16.16f} {thermal_expansion_data_mega[0]:16.16f} {thermal_expansion_data_mega[1]:16.16f} {thermal_expansion_data_mega[2]:16.16f} {thermal_expansion_data_mega[3]:16.16f}",
+                f"{temperature:16.16f} "
+                f"{boxes_avg_data[0,i]:16.16f} {boxes_std_data[0,i]:16.16f} "
+                f"{boxes_avg_data[1,i]:16.16f} {boxes_std_data[1,i]:16.16f} "
+                f"{boxes_avg_data[2,i]:16.16f} {boxes_std_data[2,i]:16.16f} "
+                f"{boxes_avg_data[3,i]:16.16f} {boxes_std_data[3,i]:16.16f} "
+                f"{thermal_expansion_data_mega[0]:16.16f} {thermal_expansion_data_mega[1]:16.16f} "
+                f"{thermal_expansion_data_mega[2]:16.16f} {thermal_expansion_data_mega[3]:16.16f}",
                 file=self.file
             )
 
@@ -181,40 +189,7 @@ def write_after_run(self, thermal_expansion: ThermalExpansion) -> None:
             the linear thermal expansion coefficient object
         """
         super().open()
-        # angstrom = "\u212B".encode('utf-8')
-        # for i, box in enumerate(thermal_expansion.boxes_avg):
-        #     print(
-        #         (
-        #             f"    a : {box}{angstrom} +/- "
-        #             f"{thermal_expansion.boxes_std[0,i]}{angstrom} at "
-        #             f"{thermal_expansion.temperature_points[i]} K"
-        #         ),
-        #         file=self.file
-        #     )
-        #     print(
-        #         (
-        #             f"    b: {thermal_expansion.boxes_avg[i,1]}{angstrom} +/- "
-        #             f"{thermal_expansion.boxes_std[i,1]}{angstrom} at "
-        #             f"{thermal_expansion.temperature_points[i]} K"
-        #         ),
-        #         file=self.file
-        #     )
-        #     print(
-        #         (
-        #             f"    c: {thermal_expansion.boxes_avg[i,2]}{angstrom} +/- "
-        #             f"{thermal_expansion.boxes_std[i,2]}{angstrom} at "
-        #             f"{thermal_expansion.temperature_points[i]} K"
-        #         ),
-        #         file=self.file
-        #     )
-        #     print(
-        #         (
-        #             f"    Volume: {thermal_expansion.boxes_avg[i,3]}{angstrom}³ +/- "
-        #             f"{thermal_expansion.boxes_std[i,3]}{angstrom}³ at "
-        #             f"{thermal_expansion.temperature_points[i]} K"
-        #         ),
-        #         file=self.file
-        #     )
+
         print(
             f"    Linear thermal expansion a: {thermal_expansion.thermal_expansions[0]} 1/K",
             file=self.file