crunchflow 2.0.2__tar.gz → 2.0.4__tar.gz

{crunchflow-2.0.2 → crunchflow-2.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: crunchflow
-Version: 2.0.2
+Version: 2.0.4
 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-2.0.4}/crunchflow/input/blocks.py

@@ -62,7 +62,7 @@ class Runtime(KeywordBlock):
         self.coordinate = ''
         self.coordinates = ''
         self.correction_max = ''
-        self.Courant_number = ''
+        self.courant_number = ''
         self.database = ''
         self.database_sweep = ''
         self.debye_huckel = ''
@@ -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-2.0.4}/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-2.0.4}/crunchflow/output/spatial.py

@@ -42,21 +42,24 @@ def get_tec_metadata(file, folder='.'):
     # Open file and read line by line
     inpath = os.path.join(folder, file)
     with open(inpath) as f:
+        lines = f.readlines()
+
         # Read the first line to determine the format of the file
-        line = f.readline()
-        if "TITLE" in line:
-            title = line.split('"')[1]
+        if "TITLE" in lines[0]:
+            title = lines[0].split('"')[1]
             fmt = '.tec'
-        elif 'Time' in line:
+        elif 'Time' in lines[0]:
             title = ''
             fmt = '.out'
+        elif 'Units' in lines[0]:
+            title = ''
+            fmt = '.dat'
         else:
             raise ValueError("Could not determine the format of this file")
 
         # Read the rest of the header
         if fmt == '.tec':
-            line = f.readline()
-            columns = line.split('"')
+            columns = lines[1].split('"')
 
             # Remove x, y, z
             columns = [col.strip() for col in columns]
@@ -70,11 +73,14 @@ def get_tec_metadata(file, folder='.'):
             for col in remove_fields:
                 columns.remove(col)
         elif fmt == '.out':
-            line = f.readline()  # skip units line
-            line = f.readline()
+            # pH files do not have a units line
+            if 'pH' in file:
+                columns_line = lines[1]  # skip units line
+            else:
+                columns_line = lines[2]
 
             # Split on whitespace
-            raw_cols = line.split()
+            raw_cols = columns_line.split()
 
             # Some versions of CrunchFlow don't include column names
             # in this case, the column entries should be numeric and we'll
@@ -84,6 +90,35 @@ def get_tec_metadata(file, folder='.'):
             else:
                 columns = raw_cols
 
+        elif fmt == '.dat':
+            title = lines[1].split('"')[1]
+            columns = lines[2].split('"')
+
+            # Remove x, y, z
+            columns = [col.strip() for col in columns]
+            for col in ['VARIABLES =']:
+                if col in columns:
+                    columns.remove(col)
+
+            # Remove commas, which can be repeated so will not be removed with loop above
+            columns = [col.replace(',', '') for col in columns]
+
+            # Remove whitespace, which was reduced to len 0 via col.strip()
+            remove_fields = [col for col in columns if len(col) == 0]
+            for col in remove_fields:
+                columns.remove(col)
+
+            # With .dat files, the naming scheme for x, y and z varies
+            # depending on the spatial units
+            if len(lines[3].split(',')) == 3:
+                # then this is 2d, so remove first two columns
+                columns = columns[2:]
+            elif len(lines[3].split(',')) == 4:
+                # then this is 3d, so remove first three columns
+                columns = columns[3:]
+            else:
+                raise ValueError("Could not determine the format of this file")
+
     return columns, title, fmt
 
 
@@ -197,6 +232,29 @@ 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 +265,7 @@ 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
@@ -217,27 +275,30 @@ 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.
+            version of CrunchTope used. The default is '.tec', but '.out' and '.dat'
+            are also tried if '.tec' files are not found.
         """
              
         # Glob doesn't support regex, so match manually using re and os
         search_str = '^' + fileprefix + '[0-9]+%s' % suffix
         unsort_files = [f for f in os.listdir(folder) if re.search(search_str, f)]
 
+        # Try again with .out or .dat suffix
         if len(unsort_files) == 0:
-            # Try again with .out suffix
-            search_str = '^' + fileprefix + '[0-9]+.out'
-            unsort_files = [f for f in os.listdir(folder) if re.search(search_str, f)]
-            suffix = '.out'
+            for try_suffix in ['.out', '.dat']:
+                search_str = '^' + fileprefix + '[0-9]+' + try_suffix
+                unsort_files = [f for f in os.listdir(folder) if re.search(search_str, f)]
+                if len(unsort_files) > 0:
+                    suffix = try_suffix
+                    break
 
         if len(unsort_files) == 0:
             raise ValueError("No files found matching %s. Double check the suffix and\n "
@@ -263,7 +324,7 @@ class SpatialProfile:
             # Otherwise, try setting it by reading from each .out file
             if self.fmt == '.out':
                 self.output_times = [get_out_output_time(f) for f in self.files]
-            elif self.fmt == '.tec':
+            elif self.fmt in ['.tec', '.dat']:
                 self.output_times = None
 
         # Get the grid size
@@ -298,6 +359,24 @@ class SpatialProfile:
             else:
                 skiprows = 3
             self.coords = np.loadtxt(self.files[0], skiprows=skiprows, usecols=[0])
+        elif self.fmt == '.dat':
+            with open(self.files[0]) as f:
+                lines = f.readlines()
+
+                fields = lines[3].split(',')[1:]
+                if len(fields) == 2:
+                    self.nx = int(re.sub('\\D', '', fields[0]))
+                    self.ny = int(re.sub('\\D', '', fields[1]))
+                    self.nz = np.nan
+                elif len(fields) == 3:
+                    self.nx = int(re.sub('\\D', '', fields[0]))
+                    self.ny = int(re.sub('\\D', '', fields[1]))
+                    self.nz = int(re.sub('\\D', '', fields[2]))
+                else:
+                    raise ValueError("Could not determine the coordinates in this file")
+            self.coords = np.loadtxt(self.files[0], skiprows=4, usecols=[0, 1])
+            self.griddedX = self.coords[:, 0].reshape(self.ny, self.nx)
+            self.griddedY = self.coords[:, 1].reshape(self.ny, self.nx)
 
     def plot(self, var, time=None, plot_type='image', figsize=(12,3), 
              **kwargs):
@@ -561,6 +640,16 @@ class SpatialProfile:
                     skiprows = 3
             col_no = self.columns.index(var)
             data = np.loadtxt(self.files[time - 1], skiprows=skiprows, usecols=col_no)
+        elif self.fmt == '.dat':
+            if np.isnan(self.nz):
+                col_no = self.columns.index(var) + 2
+                data = np.loadtxt(self.files[time - 1], skiprows=4, usecols=col_no)
+                data = data.reshape(self.ny, self.nx)
+            else:
+                col_no = self.columns.index(var) + 3
+                data = np.loadtxt(self.files[time - 1], skiprows=4, usecols=col_no)
+                data = data.reshape(self.nz, self.ny, self.nx)
+
         else:
             raise ValueError("Could not determine the format of this file")
 

{crunchflow-2.0.2 → crunchflow-2.0.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "crunchflow"
-version = "2.0.2"
+version = "2.0.4"
 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"