Implement on-the-fly descriptor calculation

docs/source/basic_usage/more_data.rst

@@ -99,16 +99,16 @@ and fill it with data, e.g., by
                                         descriptor_input_path=outfile,
                                         target_input_type=".cube",
                                         target_input_path=ldosfile,
-                                        additional_info_input_type="espresso-out",
-                                        additional_info_input_path=outfile,
+                                        simulation_output_type="espresso-out",
+                                        simulation_output_path=outfile,
                                         target_units="1/(Ry*Bohr^3)")
 
 The ``add_snapshot`` function can be called multiple times to add
 multiple snapshots to MALA.
 For regular Quantum ESPRESSO calculations, the ``descriptor_input_type``
 and ``target_input_type`` will always be ``"espresso-out"`` and ``".cube"``,
 respectively, and the ``target_units`` will always be ``"1/(Ry*Bohr^3)"``.
-The paths have to be modified accordingly. ``additional_info_input_*`` refers
+The paths have to be modified accordingly. ``simulation_output_*`` refers
 to the calculation output file - MALA provides an interface to condense
 the entire, verbose simulation output to ``.json`` files for further
 processing. In the preceding section, we had to specify calculation output
@@ -121,7 +121,7 @@ Once data is provided, the conversion itself is simple.
 
             data_converter.convert_snapshots(descriptor_save_path="./",
                                              target_save_path="./",
-                                             additional_info_save_path="./",
+                                             simulation_output_save_path="./",
                                              naming_scheme="Be_snapshot*.npy",
                                              descriptor_calculation_kwargs=
                                              {"working_directory": data_path})

examples/advanced/ex10_convert_numpy_openpmd.py

@@ -20,15 +20,15 @@
         target_input_path=os.path.join(
             data_path, "Be_snapshot{}.out.npy".format(snapshot)
         ),
-        additional_info_input_type=None,
-        additional_info_input_path=None,
+        simulation_output_type=None,
+        simulation_output_path=None,
         target_units=None,
     )
 
 data_converter.convert_snapshots(
     descriptor_save_path="./",
     target_save_path="./",
-    additional_info_save_path="./",
+    simulation_output_save_path="./",
     naming_scheme="converted_from_numpy_*.h5",
     descriptor_calculation_kwargs={"working_directory": "./"},
 )
@@ -43,15 +43,15 @@
         descriptor_input_path="converted_from_numpy_{}.in.h5".format(snapshot),
         target_input_type="openpmd",
         target_input_path="converted_from_numpy_{}.out.h5".format(snapshot),
-        additional_info_input_type=None,
-        additional_info_input_path=None,
+        simulation_output_type=None,
+        simulation_output_path=None,
         target_units=None,
     )
 
 data_converter.convert_snapshots(
     descriptor_save_path="./",
     target_save_path="./",
-    additional_info_save_path="./",
+    simulation_output_save_path="./",
     naming_scheme="verify_against_original_numpy_data_*.npy",
     descriptor_calculation_kwargs={"working_directory": "./"},
 )
@@ -84,15 +84,15 @@
         target_input_path=os.path.join(
             data_path, "Be_snapshot{}.out.h5".format(snapshot)
         ),
-        additional_info_input_type=None,
-        additional_info_input_path=None,
+        simulation_output_type=None,
+        simulation_output_path=None,
         target_units=None,
     )
 
 data_converter.convert_snapshots(
     descriptor_save_path="./",
     target_save_path="./",
-    additional_info_save_path="./",
+    simulation_output_save_path="./",
     naming_scheme="converted_from_openpmd_*.npy",
     descriptor_calculation_kwargs={"working_directory": "./"},
 )

examples/basic/ex03_preprocess_data.py

@@ -46,12 +46,12 @@
 # Data conversion itself is simple. We select input and output data
 # to be converted, add this data snapshot-wise and tell MALA to
 # convert snapshots. Inputs and outputs can be processed individually.
-# Further, via the additional_info_input_* keywords, calculation output
+# Further, via the simulation_output_input_* keywords, calculation output
 # can be processed from the original simulation *.out output files into
 # more convenient *.json files that can be used in their stead. This saves
 # on disk space.
 # To only process parts of the data, omit/add descriptor_input*, target_input_*
-# and additional_info_input_* at your leisure.
+# and simulation_output_* at your leisure.
 # Make sure to set the correct units - for QE, this should always be
 # 1/(Ry*Bohr^3).
 ####################
@@ -65,8 +65,8 @@
     descriptor_input_path=outfile,
     target_input_type=".cube",
     target_input_path=ldosfile,
-    additional_info_input_type="espresso-out",
-    additional_info_input_path=outfile,
+    simulation_output_type="espresso-out",
+    simulation_output_path=outfile,
     target_units="1/(Ry*Bohr^3)",
 )
 
@@ -84,7 +84,7 @@
 data_converter.convert_snapshots(
     descriptor_save_path="./",
     target_save_path="./",
-    additional_info_save_path="./",
+    simulation_output_save_path="./",
     naming_scheme="Be_snapshot*.npy",
     descriptor_calculation_kwargs={"working_directory": data_path},
 )

mala/datahandling/data_converter.py

@@ -12,7 +12,7 @@
 
 descriptor_input_types = ["espresso-out", "openpmd", "numpy"]
 target_input_types = [".cube", ".xsf", "openpmd", "numpy"]
-additional_info_input_types = ["espresso-out"]
+simulation_output_types = ["espresso-out"]
 
 
 class DataConverter:
@@ -78,16 +78,16 @@ def __init__(
         # Keep track of what has to be done by this data converter.
         self.__process_descriptors = False
         self.__process_targets = False
-        self.__process_additional_info = False
+        self.__process_simulation_output = False
 
     def add_snapshot(
         self,
         descriptor_input_type=None,
         descriptor_input_path=None,
         target_input_type=None,
         target_input_path=None,
-        additional_info_input_type=None,
-        additional_info_input_path=None,
+        simulation_output_type=None,
+        simulation_output_path=None,
         descriptor_units=None,
         metadata_input_type=None,
         metadata_input_path=None,
@@ -114,22 +114,22 @@ def add_snapshot(
         target_input_path : string
             Path of target data to be processed.
 
-        additional_info_input_type : string
+        simulation_output_type : string
             Type of additional info data to be processed.
-            See mala.datahandling.data_converter.additional_info_input_types
+            See mala.datahandling.data_converter.simulation_output_types
             for options.
 
-        additional_info_input_path : string
+        simulation_output_path : string
             Path of additional info data to be processed.
 
         metadata_input_type : string
             Type of additional metadata to be processed.
-            See mala.datahandling.data_converter.additional_info_input_types
+            See mala.datahandling.data_converter.simulation_output_types
             for options.
-            This is essentially the same as additional_info_input_type,
+            This is essentially the same as simulation_output_type,
             but will not affect saving; i.e., the data given here will
             only be saved in OpenPMD files, not saved separately.
-            If additional_info_input_type is set, this argument will be
+            If simulation_output_type is set, this argument will be
             ignored.
 
         metadata_input_path : string
@@ -161,28 +161,28 @@ def add_snapshot(
                 raise Exception("Cannot process this type of target data.")
             self.__process_targets = True
 
-        if additional_info_input_type is not None:
-            metadata_input_type = additional_info_input_type
-            if additional_info_input_path is None:
+        if simulation_output_type is not None:
+            metadata_input_type = simulation_output_type
+            if simulation_output_path is None:
                 raise Exception(
                     "Cannot process additional info data with "
                     "no path given."
                 )
-            if additional_info_input_type not in additional_info_input_types:
+            if simulation_output_type not in simulation_output_types:
                 raise Exception(
                     "Cannot process this type of additional info data."
                 )
-            self.__process_additional_info = True
+            self.__process_simulation_output = True
 
-            metadata_input_path = additional_info_input_path
+            metadata_input_path = simulation_output_path
 
         if metadata_input_type is not None:
             if metadata_input_path is None:
                 raise Exception(
                     "Cannot process additional info data with "
                     "no path given."
                 )
-            if metadata_input_type not in additional_info_input_types:
+            if metadata_input_type not in simulation_output_types:
                 raise Exception(
                     "Cannot process this type of additional info data."
                 )
@@ -192,15 +192,15 @@ def add_snapshot(
             {
                 "input": descriptor_input_path,
                 "output": target_input_path,
-                "additional_info": additional_info_input_path,
+                "simulation_output": simulation_output_path,
                 "metadata": metadata_input_path,
             }
         )
         self.__snapshot_description.append(
             {
                 "input": descriptor_input_type,
                 "output": target_input_type,
-                "additional_info": additional_info_input_type,
+                "simulation_output": simulation_output_type,
                 "metadata": metadata_input_type,
             }
         )
@@ -213,7 +213,7 @@ def convert_snapshots(
         complete_save_path=None,
         descriptor_save_path=None,
         target_save_path=None,
-        additional_info_save_path=None,
+        simulation_output_save_path=None,
         naming_scheme="ELEM_snapshot*.npy",
         starts_at=0,
         file_based_communication=False,
@@ -231,15 +231,15 @@ def convert_snapshots(
         complete_save_path : string
             If not None: the directory in which all snapshots will be saved.
             Overwrites descriptor_save_path, target_save_path and
-            additional_info_save_path if set.
+            simulation_output_save_path if set.
 
         descriptor_save_path : string
             Directory in which to save descriptor data.
 
         target_save_path : string
             Directory in which to save target data.
 
-        additional_info_save_path : string
+        simulation_output_save_path : string
             Directory in which to save additional info data.
 
         naming_scheme : string
@@ -304,7 +304,7 @@ def convert_snapshots(
         if complete_save_path is not None:
             descriptor_save_path = complete_save_path
             target_save_path = complete_save_path
-            additional_info_save_path = complete_save_path
+            simulation_output_save_path = complete_save_path
         else:
             if self.__process_targets is True and target_save_path is None:
                 raise Exception(
@@ -318,8 +318,8 @@ def convert_snapshots(
                     "No descriptor path specified, cannot process data."
                 )
             if (
-                self.__process_additional_info is True
-                and additional_info_save_path is None
+                self.__process_simulation_output is True
+                and simulation_output_save_path is None
             ):
                 raise Exception(
                     "No additional info path specified, cannot "
@@ -393,9 +393,9 @@ def convert_snapshots(
             snapshot_name = snapshot_name.replace("*", str(snapshot_number))
 
             # Create the paths as needed.
-            if self.__process_additional_info:
+            if self.__process_simulation_output:
                 info_path = os.path.join(
-                    additional_info_save_path, snapshot_name + ".info.json"
+                    simulation_output_save_path, snapshot_name + ".info.json"
                 )
             else:
                 info_path = None
@@ -454,7 +454,7 @@ def convert_snapshots(
                 use_memmap=memmap,
                 input_iteration=input_iteration,
                 output_iteration=output_iteration,
-                additional_info_path=info_path,
+                simulation_output_info_path=info_path,
                 use_fp64=use_fp64,
             )
 
@@ -479,7 +479,7 @@ def __convert_single_snapshot(
         target_calculator_kwargs,
         input_path=None,
         output_path=None,
-        additional_info_path=None,
+        simulation_output_info_path=None,
         use_memmap=None,
         output_iteration=None,
         input_iteration=None,
@@ -719,11 +719,11 @@ def __convert_single_snapshot(
             del tmp_output
 
         # Parse and/or calculate the additional info.
-        if description["additional_info"] is not None:
+        if description["simulation_output"] is not None:
             # Parsing and saving is done using the target calculator.
             self.target_calculator.read_additional_calculation_data(
-                snapshot["additional_info"], description["additional_info"]
+                snapshot["simulation_output"], description["simulation_output"]
             )
             self.target_calculator.write_additional_calculation_data(
-                additional_info_path
+                simulation_output_info_path
             )