qrotor 4.2.2__tar.gz → 4.4.0__tar.gz

{qrotor-4.2.2 → qrotor-4.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.2.2
+Version: 4.4.0
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

{qrotor-4.2.2 → qrotor-4.4.0}/qrotor/_version.py

@@ -11,5 +11,5 @@ https://semver.org/
 ---
 """
 
-__version__ = "v4.2.2"
+__version__ = "v4.4.0"
 

{qrotor-4.2.2 → qrotor-4.4.0}/qrotor/plot.py

@@ -98,7 +98,10 @@ def energies(
         data,
         title:str=None,
         ) -> None:
-    """Plot the eigenvalues of `data` (System or a list of System objects)."""
+    """Plot the eigenvalues of `data` (System or a list of System objects).
+
+    You can use up to 1 tag per system to differentiate between molecular groups.
+    """
     if isinstance(data, System):
         var = [data]
     else:  # Should be a list
@@ -137,14 +140,14 @@ def energies(
         # Plot eigenvalues
         if any(system.eigenvalues):
             text_offset = 3 * len(unique_groups)
-            if system.group not in unique_groups:
-                unique_groups.append(system.group)
+            if system.tags not in unique_groups:
+                unique_groups.append(system.tags)
             for j, energy in enumerate(system.eigenvalues):
                 plt.axhline(y=energy, color=E_color, linestyle=E_linestyle)
                 # Textbox positions are a bit weird when plotting more than 2 systems, but whatever...
                 plt.text(j%3*1.0 + text_offset, energy, f'$E_{{{j}}}$ = {round(energy,4):.04f}', va='top', bbox=dict(edgecolor=edgecolor, boxstyle='round,pad=0.2', facecolor='white', alpha=0.8))
             if len(systems.get_groups(var)) > 1:
-                plt.plot([], [], color=E_color, label=f'{system.group} Energies')  # Add to legend
+                plt.plot([], [], color=E_color, label=f'{system.tags} Energies')  # Add to legend
 
     if len(systems.get_groups(var)) > 1:
         plt.subplots_adjust(right=0.85)

{qrotor-4.2.2 → qrotor-4.4.0}/qrotor/potential.py

@@ -49,7 +49,7 @@ from copy import deepcopy
 from scipy.interpolate import CubicSpline
 import aton.alias as alias
 import aton.file as file
-import aton.api.qe as qe
+import aton.api.pwx as pwx
 from ._version import __version__
 
 
@@ -125,6 +125,7 @@ def save(
 def load(
         filepath:str='potential.csv',
         comment:str=None,
+        tags:str='',
         system:System=None,
         angle:str='deg',
         energy:str='meV',
@@ -184,6 +185,8 @@ def load(
         system.comment = loaded_comment
     else:
         system.comment = os.path.basename(os.path.dirname(file_path))
+    if tags:
+        system.tags = tags
     print(f"Loaded {filepath}")
     return system
 
@@ -196,8 +199,8 @@ def from_qe(
         energy:str='meV',
         comment:str=None,
         ) -> System:
-    """Compiles a rotational potential CSV file from Quantum ESPRESSO outputs,
-    created with `qrotor.rotate.structure_qe()`.
+    """Compiles a rotational potential CSV file from Quantum ESPRESSO pw.x outputs,
+    created with `qrotor.rotate.input_qe()`.
     Returns a `System` object with the new potential values.
 
     The angle in degrees is extracted from the output filenames,
@@ -227,7 +230,7 @@ def from_qe(
     # Set header
     potential_data = f'## {comment}\n' if comment else f'## {folder_name}\n'
     potential_data += '# Rotational potential dataset\n'
-    potential_data += f'# Calculated with QE using QRotor {__version__}\n'
+    potential_data += f'# Calculated with QE pw.x using QRotor {__version__}\n'
     potential_data += '# https://pablogila.github.io/qrotor\n'
     potential_data += '#\n'
     if energy.lower() in alias.units['eV']:
@@ -249,7 +252,7 @@ def from_qe(
         file_path = file.get(filepath=file_path, include='.out', return_anyway=True)
         if not file_path:  # Not an output file, skip it
             continue
-        content = qe.read_out(file_path)
+        content = pwx.read_out(file_path)
         if not content['Success']:  # Ignore unsuccessful calculations
             print(f'x   {filename}')
             counter_errors += 1

{qrotor-4.2.2 → qrotor-4.4.0}/qrotor/rotate.py

@@ -9,7 +9,7 @@ Works with Quantum ESPRESSO input files.
 
 | | |
 | --- | --- |
-| `structure_qe()`  | Rotate specific atoms from a Quantum ESPRESSO input file |
+| `input_qe()`      | Rotate specific atoms from a Quantum ESPRESSO input file |
 | `rotate_coords()` | Rotate a specific list of coordinates |
 
 ---
@@ -26,7 +26,7 @@ import aton.txt.extract as extract
 import aton.txt.edit as edit
 
 
-def structure_qe(
+def input_qe(
         filepath:str,
         positions:list,
         angle:float,
@@ -66,13 +66,13 @@ def structure_qe(
     lines = []
     full_positions = []
     for position in positions:
-        line = api.qe.get_atom(filepath, position, precision)
+        line = api.pwx.get_atom(filepath, position, precision)
         lines.append(line)
         pos = extract.coords(line)
         if len(pos) > 3:  # Keep only the first three coordinates
             pos = pos[:3]
         # Convert to cartesian
-        pos_cartesian = api.qe.to_cartesian(filepath, pos)
+        pos_cartesian = api.pwx.to_cartesian(filepath, pos)
         full_positions.append(pos_cartesian)
         print(f'Found atom: "{line}"')
     # Set the angles to rotate
@@ -92,7 +92,7 @@ def structure_qe(
         rotated_positions_cartesian = rotate_coords(full_positions, angle, use_centroid, show_axis)
         rotated_positions = []
         for coord in rotated_positions_cartesian:
-            pos = api.qe.from_cartesian(filepath, coord)
+            pos = api.pwx.from_cartesian(filepath, coord)
             rotated_positions.append(pos)
         _save_qe(filepath, output, lines, rotated_positions)
         outputs.append(output)
@@ -184,7 +184,7 @@ def _save_qe(
         additional_positions = positions[-2:]
         for pos in additional_positions:
             pos.insert(0, 'He')
-            api.qe.add_atom(output, pos)
+            api.pwx.add_atom(output, pos)
     elif len(lines) != len(positions):
         raise ValueError(f"What?!  len(lines)={len(lines)} and len(positions)={len(positions)}")
     # Add angle to calculation prefix
@@ -192,11 +192,11 @@ def _save_qe(
     splits = output_name.split('_')
     angle_str = splits[-1].replace('.in', '')
     prefix = ''
-    content = api.qe.read_in(output)
+    content = api.pwx.read_in(output)
     if 'prefix' in content.keys():
         prefix = content['prefix']
         prefix = prefix.strip("'")
     prefix = "'" + prefix + angle_str + "'"
-    api.qe.set_value(output, 'prefix', prefix)
+    api.pwx.set_value(output, 'prefix', prefix)
     return output
 

{qrotor-4.2.2 → qrotor-4.4.0}/qrotor/system.py

@@ -24,16 +24,14 @@ class System:
     def __init__(
             self,
             comment: str = None,
+            B: float = B_CH3,
+            gridsize: int = 200000,
             searched_E: int = 21,
             correct_potential_offset: bool = True,
             save_eigenvectors: bool = True,
-            group: str = '',
-            B: float = B_CH3,
-            gridsize: int = 200000,
-            grid = [],
             potential_name: str = '',
             potential_constants: list = None,
-            potential_values = [],
+            tags: str = '',
             ):
         """A new quantum system can be instantiated as `system = qrotor.System()`.
         This new system will contain the default values listed above.
@@ -49,17 +47,12 @@ class System:
         """Correct the potential offset as `V - min(V)` or not."""
         self.save_eigenvectors: bool = save_eigenvectors
         """Save or not the eigenvectors. Final file size will be bigger."""
-        self.group: str = group
-        """Chemical group, methyl or amine: `'CH3'`, `'CD3'`, `'NH3'`, `'ND3'`.
+        self.tags: str = tags
+        """Custom tags separated by spaces, such as the molecular group, etc.
 
-        Can be used to set the value of `B` automatically at startup.
-        It can also be configured afterwards with `System.set_group()`.
-        This group can be used as metadata to analyse different datasets.
+        Can be used to filter between datasets.
         """
-        self.set_group(group)  # Normalise the group name, and set the value of B
         ## Potential
-        if not B:
-            B = self.B
         self.B: float = B
         """Kinetic rotational energy, as in $B=\\frac{\\hbar^2}{2I}$.
 
@@ -67,7 +60,7 @@ class System:
         """
         self.gridsize: int = gridsize
         """Number of points in the grid."""
-        self.grid = grid
+        self.grid = []
         """The grid with the points to be used in the calculation.
 
         Can be set automatically over $2 \\pi$ with `System.set_grid()`.
@@ -80,7 +73,7 @@ class System:
         """
         self.potential_constants: list = potential_constants
         """List of constants to be used in the calculation of the potential energy, in the `qrotor.potential` module."""
-        self.potential_values = potential_values
+        self.potential_values = []
         """Numpy [ndarray](https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html) with the potential values for each point in the grid.
 
         Can be calculated with a function available in the `qrotor.potential` module,
@@ -205,40 +198,6 @@ class System:
         else:
             raise ValueError('gridsize must be provided if there is no System.gridsize')
         return self
-    
-    def set_group(self, group:str=None, B:float=None):
-        """Normalise `System.group` name, and set `System.B` based on it."""
-        for name in alias.chemical['CH3']:
-            if group.lower() == name:
-                self.group = 'CH3'
-                if not B:
-                    B = B_CH3
-                self.B = B
-                return self
-        for name in alias.chemical['CD3']:
-            if group.lower() == name:
-                self.group = 'CD3'
-                if not B:
-                    B = B_CD3
-                self.B = B
-                return self
-        for name in alias.chemical['NH3']:
-            if group.lower() == name:
-                self.group = 'NH3'
-                if not B:
-                    B = B_NH3
-                self.B = B
-                return self
-        for name in alias.chemical['ND3']:
-            if group.lower() == name:
-                self.group = 'ND3'
-                if not B:
-                    B = B_ND3
-                self.B = B
-                return self
-        self.group = group  # No match was found
-        self.B = None
-        return self
 
     def reduce_size(self):
         """Discard data that takes too much space,
@@ -256,7 +215,7 @@ class System:
             'searched_E': self.searched_E,
             'correct_potential_offset': self.correct_potential_offset,
             'save_eigenvectors': self.save_eigenvectors,
-            'group': self.group,
+            'tags': self.tags,
             'B': self.B,
             'gridsize': self.gridsize,
             'potential_name': self.potential_name,

{qrotor-4.2.2 → qrotor-4.4.0}/qrotor/systems.py

@@ -12,14 +12,16 @@ These are commonly used as a list of `System` objects.
 | `as_list()`          | Ensures that a list only contains System objects |
 | `save_energies()`    | Save the energy eigenvalues for all systems to a CSV |
 | `save_splittings()`  | Save the tunnel splitting energies for all systems to a CSV |
+| `save_summary()`     | Save a summary of some relevant parameters for all systems to a CSV |
 | `get_energies()`     | Get the eigenvalues from all systems |
 | `get_gridsizes()`    | Get all gridsizes |
 | `get_runtimes()`     | Get all runtimes |
-| `get_groups()`       | Get the chemical groups in use |
 | `get_ideal_E()`      | Calculate the ideal energy for a specified level |
 | `sort_by_gridsize()` | Sort systems by gridsize |
 | `reduce_size()`      | Discard data that takes too much space |
 | `summary()`          | Print a summary of a System or list of Systems |
+| `list_tags()`        | Get a list with all system tags |
+| `filter_tags()`      | Filter the systems with or without specific tags |
 
 ---
 """
@@ -51,9 +53,9 @@ def as_list(systems) -> None:
 def save_energies(
         systems:list,
         comment:str='',
-        filepath:str='eigenvalues.csv',
+        filepath:str='qrotor_eigenvalues.csv',
         ) -> pd.DataFrame:
-    """Save the energy eigenvalues for all `systems` to a eigenvalues.csv file.
+    """Save the energy eigenvalues for all `systems` to a qrotor_eigenvalues.csv file.
 
     Returns a Pandas Dataset with `System.comment` columns and `System.eigenvalues` values.
 
@@ -62,7 +64,7 @@ def save_energies(
     A `comment` can be included at the top of the file.
     Note that `System.comment` must not include commas (`,`).
     """
-    as_list(systems)
+    systems = as_list(systems)
     version = systems[0].version
     E = {}
     # Find max length of eigenvalues
@@ -81,7 +83,7 @@ def save_energies(
     # Else save to file
     df.to_csv(filepath, sep=',', index=False)
     # Include a comment at the top of the file
-    file_comment = f'# {comment}\n' if comment else f''
+    file_comment = f'## {comment}\n' if comment else f''
     file_comment += f'# Energy eigenvalues\n'
     file_comment += f'# Calculated with QRotor {version}\n'
     file_comment += f'# https://pablogila.github.io/qrotor\n#'
@@ -93,9 +95,9 @@ def save_energies(
 def save_splittings(
     systems:list,
     comment:str='',
-    filepath:str='splittings.csv',
+    filepath:str='qrotor_splittings.csv',
     ) -> pd.DataFrame:
-    """Save the tunnel splitting energies for all `systems` to a splittings.csv file.
+    """Save the tunnel splitting energies for all `systems` to a qrotor_splittings.csv file.
 
     Returns a Pandas Dataset with `System.comment` columns and `System.splittings` values.
 
@@ -105,7 +107,7 @@ def save_splittings(
     Note that `System.comment` must not include commas (`,`).
     Different splitting lengths across systems are allowed - missing values will be NaN.
     """
-    as_list(systems)
+    systems = as_list(systems)
     version = systems[0].version
     tunnelling_E = {}
     # Find max length of splittings
@@ -119,7 +121,7 @@ def save_splittings(
     # Else save to file
     df.to_csv(filepath, sep=',', index=False)
     # Include a comment at the top of the file 
-    file_comment = f'# {comment}\n' if comment else f''
+    file_comment = f'## {comment}\n' if comment else f''
     file_comment += f'# Tunnel splitting energies\n'
     file_comment += f'# Calculated with QRotor {version}\n'
     file_comment += f'# https://pablogila.github.io/qrotor\n#'
@@ -128,12 +130,80 @@ def save_splittings(
     return df
 
 
+def save_summary(
+    systems:list,
+    comment:str='',
+    filepath:str='qrotor_summary.csv',
+    ) -> pd.DataFrame:
+    """Save a summary for all `systems` to a qrotor_summary.csv file.
+
+    Produces one row per System with the columns:
+    `comment`, `ZPE`, `E_activation`, `potential_max`, `1st_splitting`,
+    `1st_excitation`, `B`, `degeneracy`, `gridsize`.
+
+    Set `filepath` to null to just return the DataFrame.
+    """
+    systems = as_list(systems)
+    version = systems[0].version
+    rows = []
+    for s in systems:
+        eigenvalues = getattr(s, 'eigenvalues', None)
+        if eigenvalues is not None and len(eigenvalues) > 0:
+            first_val = eigenvalues[0]
+            zpe = float('nan') if first_val is None else first_val
+        else:
+            zpe = float('nan')
+        splittings = getattr(s, 'splittings', None)
+        if splittings is not None and len(splittings) > 0:
+            first_splitting = float('nan') if splittings[0] is None else splittings[0]
+        else:
+            first_splitting = float('nan')
+        excitations = getattr(s, 'excitations', None)
+        if excitations is not None and len(excitations) > 0:
+            first_excitation = float('nan') if excitations[0] is None else excitations[0]
+        else:
+            first_excitation = float('nan')
+        system_comment = getattr(s, 'comment', None)
+        E_activation = getattr(s, 'E_activation', None)
+        B = getattr(s, 'B', None)
+        tags = getattr(s, 'tags', None)
+        deg = getattr(s, 'deg', None)
+        gridsize = getattr(s, 'gridsize', None)
+        potential_max = getattr(s, 'potential_max', None)
+        # Each row contains the following:
+        rows.append({
+            'comment': system_comment,
+            'ZPE': zpe,
+            'E_activation': E_activation,
+            'potential_max': potential_max,
+            '1st_splitting': first_splitting,
+            '1st_excitation': first_excitation,
+            'B': B,
+            'degeneracy': deg,
+            'gridsize': gridsize,
+            'tags': tags,
+        })
+    # Save to file or just return df
+    df = pd.DataFrame(rows)
+    if not filepath:
+        return df
+    df.to_csv(filepath, sep=',', index=False)
+    # Include a comment at the top of the file
+    file_comment = f'## {comment}\n' if comment else ''
+    file_comment += '# Summary of systems\n'
+    file_comment += f'# Calculated with QRotor {version}\n'
+    file_comment += '# https://pablogila.github.io/qrotor\n#'
+    txt.edit.insert_at(filepath, file_comment, 0)
+    print(f'Summary saved to {filepath}')
+    return df
+
+
 def get_energies(systems:list) -> list:
     """Get a list with all lists of eigenvalues from all systems.
 
     If no eigenvalues are present for a particular system, appends None.
     """
-    as_list(systems)
+    systems = as_list(systems)
     energies = []
     for i in systems:
         if all(i.eigenvalues):
@@ -148,7 +218,7 @@ def get_gridsizes(systems:list) -> list:
 
     If no gridsize value is present for a particular system, appends None.
     """
-    as_list(systems)
+    systems = as_list(systems)
     gridsizes = []
     for i in systems:
         if i.gridsize:
@@ -165,7 +235,7 @@ def get_runtimes(systems:list) -> list:
     
     If no runtime value is present for a particular system, appends None.
     """
-    as_list(systems)
+    systems = as_list(systems)
     runtimes = []
     for i in systems:
         if i.runtime:
@@ -175,16 +245,6 @@ def get_runtimes(systems:list) -> list:
     return runtimes
 
 
-def get_groups(systems:list) -> list:
-    """Returns a list with all `System.group` values."""
-    as_list(systems)
-    groups = []
-    for i in systems:
-        if i.group not in groups:
-            groups.append(i.group)
-    return groups
-
-
 def get_ideal_E(E_level:int) -> int:
     """Calculates the ideal energy for a specified `E_level`.
 
@@ -201,7 +261,7 @@ def get_ideal_E(E_level:int) -> int:
 
 def sort_by_gridsize(systems:list) -> list:
     """Sorts a list of System objects by `System.gridsize`."""
-    as_list(systems)
+    systems = as_list(systems)
     systems = sorted(systems, key=lambda sys: sys.gridsize)
     return systems
 
@@ -212,13 +272,16 @@ def reduce_size(systems:list) -> list:
     Removes eigenvectors, potential values and grids,
     for all System values inside the `systems` list.
     """
-    as_list(systems)
+    systems = as_list(systems)
     for dataset in systems:
         dataset = dataset.reduce_size()
     return systems
 
 
-def summary(systems, verbose:bool=False) -> None:
+def summary(
+        systems,
+        verbose:bool=False
+        ) -> None:
     """Print a summary of a System or list of Systems.
     
     Print extra info with `verbose=True`
@@ -243,3 +306,42 @@ def summary(systems, verbose:bool=False) -> None:
         print('--------------------')
     return None
 
+
+def list_tags(systems:list) -> list:
+    """Returns a list with all system tags."""
+    systems = as_list(systems)
+    tags = []
+    for i in systems:
+        # i.tags is guaranteed to exist and be a string (may be empty)
+        system_tags = i.tags.split()
+        for tag in system_tags:
+            if tag not in tags:
+                tags.append(tag)
+    return tags
+
+
+def filter_tags(
+        systems:list,
+        include:str='',
+        exclude:str='',
+        ) -> list:
+    """Returns a filtered list of systems with or without specific tags.
+    
+    Tags are separated by blank spaces.
+    Include tags from `include`, exclude tags from `exclude`.
+    """
+    systems = as_list(systems)
+    included_tags = include.split()
+    excluded_tags = exclude.split()
+    filtered_systems = []
+    for i in systems:
+        tags_found = list_tags(i)
+        if excluded_tags and any(tag in excluded_tags for tag in tags_found):
+            continue
+        if included_tags:
+            if any(tag in included_tags for tag in tags_found):
+                filtered_systems.append(i)
+        else:
+            filtered_systems.append(i)
+    return filtered_systems
+

{qrotor-4.2.2 → qrotor-4.4.0}/qrotor.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.2.2
+Version: 4.4.0
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

{qrotor-4.2.2 → qrotor-4.4.0}/qrotor.egg-info/SOURCES.txt

@@ -15,7 +15,6 @@ qrotor.egg-info/SOURCES.txt
 qrotor.egg-info/dependency_links.txt
 qrotor.egg-info/requires.txt
 qrotor.egg-info/top_level.txt
-tests/__init__.py
 tests/test_constants.py
 tests/test_potential.py
 tests/test_rotate.py

{qrotor-4.2.2 → qrotor-4.4.0}/qrotor.egg-info/top_level.txt

@@ -1,2 +1 @@
 qrotor
-tests

{qrotor-4.2.2 → qrotor-4.4.0}/tests/test_rotate.py

@@ -17,9 +17,9 @@ def test_rotate():
         '0.118   0.816   0.277',
     ]
     # 120 degrees (it should remain the same)
-    qr.rotate.structure_qe(filepath=structure, positions=CH3, angle=120, precision=2)
+    qr.rotate.input_qe(filepath=structure, positions=CH3, angle=120, precision=2)
     for coord in CH3:
-        rotated_coord = api.qe.get_atom(filepath=structure_120, position=coord, precision=2)
+        rotated_coord = api.pwx.get_atom(filepath=structure_120, position=coord, precision=2)
         rotated_coord = extract.coords(rotated_coord)
         coord = extract.coords(coord)
         rotated_coord_rounded = []
@@ -37,9 +37,9 @@ def test_rotate():
         '0.095062781582172   0.488975944606740   0.115053787468686',
         '0.128156574395412   0.205890189020629   0.680672454316303',
     ]
-    qr.rotate.structure_qe(filepath=structure, positions=CH3, angle=60, precision=2)
+    qr.rotate.input_qe(filepath=structure, positions=CH3, angle=60, precision=2)
     for coord in ideal:
-        rotated_coord = api.qe.get_atom(filepath=structure_60, position=coord, precision=3)
+        rotated_coord = api.pwx.get_atom(filepath=structure_60, position=coord, precision=3)
         rotated_coord = extract.coords(rotated_coord)
         coord = extract.coords(coord)
         rotated_coord_rounded = []