crunchflow 2.0.2__tar.gz → 2.0.3__tar.gz

{crunchflow-2.0.2 → crunchflow-2.0.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: crunchflow
-Version: 2.0.2
+Version: 2.0.3
 Summary: A Python toolbox for working with the CrunchFlow reactive transport code
 License: GPL-3.0-or-later
 Author: Zach Perzan

{crunchflow-2.0.2 → crunchflow-2.0.3}/crunchflow/input/blocks.py

@@ -476,7 +476,7 @@ class Gases(SpeciesBlock):
     pass
 
 
-class KineticsBlock(KeywordBlock):
+class SurfaceComplexation(KeywordBlock):
     def __init__(self):
         super().__init__()
         self.species = []
@@ -494,8 +494,43 @@ class KineticsBlock(KeywordBlock):
         return "\n".join(result)
 
 
-class SurfaceComplexation(KineticsBlock):
-    pass
+class KineticsBlock(KeywordBlock):
+    def __init__(self):
+        super().__init__()
+        self.species_dict = {}
+        self.species = []
+
+    def set_parameters(self, parameters):
+        for species, details in parameters.items():
+            label = details.pop('label', None)
+            if species not in self.species_dict:
+                self.species_dict[species] = {}
+                self.species.append(species)
+            if label:
+                self.species_dict[species][label] = details
+            else:
+                self.species_dict[species]['default'] = details
+
+    def update_parameters(self, species, label, new_details):
+        if species in self.species_dict and label in self.species_dict[species]:
+            self.species_dict[species][label].update(new_details)
+        else:
+            print(f"Species '{species}' with label '{label}' not found.")
+
+    def __str__(self):
+        result = []
+        for species, labels in self.species_dict.items():
+            if 'default' in labels and not labels['default']:
+                result.append(f"{species:<20}")
+            else:
+                for label, details in labels.items():
+                    if label == 'default' and not details:
+                        result.append(f"{species:<20}")
+                    else:
+                        details_str = ' '.join(f'-{k} {v}' for k, v in details.items())
+                        label_str = f"-label {label} " if label != 'default' else ""
+                        result.append(f"{species:<20} {label_str}{details_str}")
+        return "\n".join(result)
 
 
 class Minerals(KineticsBlock):

{crunchflow-2.0.2 → crunchflow-2.0.3}/crunchflow/input/inputfile.py

@@ -63,7 +63,7 @@ class InputFile:
         # Initialize other blocks as needed
 
     def set_block(self, block_name, parameters):
-        """Set the parameters for a block in the Run instance.
+        """Set the parameters of a block in an InputFile instance.
 
         Parameters
         ----------
@@ -93,11 +93,9 @@ class InputFile:
                         # Note that the "CONDITION  <name>" is included in
                         # Condition.__str__ method, so it is omitted here
                         result.append(f"{str(condition)}\nEND")
-            # elif isinstance(value, list):
-            #     for item in value:
-            #         if any(val for val in item.__dict__.values() if val):
-            #             block_name = format_class_name(item.__class__.__name__)
-            #             result.append(f"{block_name}\n{str(item)}\nEND")
+
+            # Otherwise, check if the block has any attributes set
+            # and if so, format the block name then print it
             elif any(val for val in value.__dict__.values() if val):
                 block_name = format_class_name(value.__class__.__name__)
                 result.append(f"{block_name}\n{str(value)}\nEND")
@@ -114,7 +112,12 @@ class InputFile:
             The path to the output file. Default is the current directory.
         update_pestcontrol : bool, optional
             Whether to update PestControl.ant with the name of the
-            CrunchFlow input file. Default is False."""
+            CrunchFlow input file. Default is False.
+
+        Returns
+        -------
+        None
+            The CrunchFlow input file is saved to disk."""
 
         full_path = os.path.join(path, filename)
         with open(full_path, 'w') as file:
@@ -127,7 +130,7 @@ class InputFile:
         if update_pestcontrol:
             folder = os.path.dirname(full_path)
             pestfile = os.path.join(folder, 'PestControl.ant')
-            with open('PestControl.ant', 'w') as file:
+            with open(pestfile, 'w') as file:
                 file.write('%s \n' % os.path.basename(full_path))
 
     @classmethod
@@ -160,7 +163,7 @@ class InputFile:
         # Define attributes and blocks to be handled as special cases
         # SpeciesBlock and KineticsBlock instances are handled differently below
         species_blocks = ['primary_species', 'secondary_species', 'gases']
-        kinetics_blocks = ['minerals', 'aqueous_kinetics', 'surface_complexation']
+        kinetics_blocks = ['minerals', 'aqueous_kinetics']
 
         # Some attributes can be set multiple times within a single block
         multiply_defined = ['time_series', 'pressure', 'mineral',
@@ -229,13 +232,35 @@ class InputFile:
                     parts = line.split()
                     current_block.species.append(parts[0])
 
-                elif current_block_name in kinetics_blocks:
+                elif current_block_name == 'surface_complexation':
                     parts = line.split()
                     species = parts[0]
                     details = " ".join(parts[1:]) if len(parts) > 1 else ""
                     current_block.species.append(species)
                     current_block.species_dict[species] = details
 
+                elif current_block_name in kinetics_blocks:
+                    parts = line.split()
+                    species = parts[0]
+                    details = {}
+
+                    # Assume the default label
+                    # This will be updated below if it is included in details
+                    label = 'default'
+
+                    # If there are details associated with the species_dict, then parse them
+                    if len(parts) > 1:
+                        # Loop through kinetic options (e.g., -activation, -rate, etc.)
+                        # and store this information in a dictionary
+                        for i in range(1, len(parts), 2):
+                            key = parts[i].lstrip('-')
+                            value = parts[i+1] if (i+1) < len(parts) else None
+                            if key == 'label':
+                                label = value
+                            else:
+                                details[key] = value
+                    current_block.set_parameters({species: {**details, 'label': label}})
+
                 # All other blocks, split on whitespace
                 else:
                     parts = line.split()

{crunchflow-2.0.2 → crunchflow-2.0.3}/crunchflow/output/spatial.py

@@ -197,6 +197,29 @@ class SpatialProfile:
         Get line segments that outline all the regions equal to 
         the provided value.
 
+    __init__(fileprefix, folder, output_times, suffix)
+    Read in and get basic info about all .tec files matching `fileprefix`.
+        For example, `tec('volume')` will read in all files matching
+        'volume[0-9]+.tec'
+
+        Parameters
+        ----------
+        fileprefix : str
+            file prefix of the tec file to read in, without the timestep
+            number or ".tec" file ending. For example, if your files are
+            "volume1.tec", "volume2.tec", etc., then fileprefix should be
+            "volume".
+        folder : str, optional
+            folder in which the .tec files are located. The default is the
+            current directory
+        output_times : list of float, optional
+            list of the actual output times at which the .tec files were
+            output, in CrunchFlow time units
+        suffix : str, optional
+            file ending of the tec files to read in. This can vary depending on the
+            version of CrunchTope used. The default is '.tec', but '.out' is also
+            tried if '.tec' files are not found.
+
     Examples
     --------
     >>> vol = SpatialProfile('volume')
@@ -207,7 +230,7 @@ class SpatialProfile:
     
     def __init__(self, fileprefix, folder='.', output_times=None, suffix='.tec'):
         """Read in and get basic info about all .tec files matching `fileprefix`.
-        For example, `tec('volume')` will read in all files matching 
+        For example, `SpatialProfile('volume')` will read in all files matching
         'volume[0-9]+.tec'
         
         Parameters
@@ -217,13 +240,13 @@ class SpatialProfile:
             number or ".tec" file ending. For example, if your files are
             "volume1.tec", "volume2.tec", etc., then fileprefix should be
             "volume".
-        folder : str
+        folder : str, optional
             folder in which the .tec files are located. The default is the 
             current directory
-        output_times : list of float 
+        output_times : list of float, optional
             list of the actual output times at which the .tec files were 
             output, in CrunchFlow time units
-        suffix : str
+        suffix : str, optional
             file ending of the tec files to read in. This can vary depending on the
             version of CrunchTope used. The default is '.tec', but '.out' is also
             tried if '.tec' files are not found.

{crunchflow-2.0.2 → crunchflow-2.0.3}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "crunchflow"
-version = "2.0.2"
+version = "2.0.3"
 description = "A Python toolbox for working with the CrunchFlow reactive transport code"
 authors = ["Zach Perzan <zach.perzan@unlv.edu>"]
 license = "GPL-3.0-or-later"