first stable release!

aton/_version.py

@@ -10,5 +10,5 @@
 
 """
 
-__version__ = 'v0.0.1rc34'
+__version__ = 'v0.0.1'
 

aton/qrotor/classes.py

@@ -30,7 +30,7 @@ def __init__(
             comment: str = None,
             group: str = 'CH3',
             E_levels: int = 5,
-            units = None,               ################ TODO CHECK THAT THIS WORKS. previously = []
+            units = None,            ################ TODO CHECK THAT THIS WORKS. previously = []
             correct_potential_offset: bool = True,
             save_eigenvectors: bool = False,
             gridsize: int = None,
@@ -122,7 +122,11 @@ def summary(self):
         }
 
     def set_grid(self, gridsize:int=None):
-        """Sets the `QSys.grid` to the specified `gridsize`."""
+        """Sets the `QSys.grid` to the specified `gridsize`.
+
+        It removes the previous grid,
+        do **not** use this method if the potential was loaded externally!
+        """
         if gridsize is not None:
             self.gridsize = gridsize
         if self.gridsize is None:

aton/qrotor/constants.py

@@ -37,17 +37,17 @@
 """Rotation radius of the amine group, in meters."""
 
 # Inertia, SI units
-I_CH = 3 * (phys.atoms['H'].mass * r_CH**2)
+I_CH = 3 * (phys.atoms['H'].mass * phys.amu_to_kg * r_CH**2)
 """Inertia of CH3, in uma·m^2."""
-I_CD = 3 * (phys.atoms['H'].isotope[2].mass * r_CH**2)
+I_CD = 3 * (phys.atoms['H'].isotope[2].mass * phys.amu_to_kg * r_CH**2)
 """Inertia of CD3, in uma·m^2."""
-I_NH = 3 * (phys.atoms['H'].mass * r_NH**2)
+I_NH = 3 * (phys.atoms['H'].mass * phys.amu_to_kg * r_NH**2)
 """Inertia of NH3, in uma·m^2."""
-I_ND = 3 * (phys.atoms['H'].isotope[2].mass * r_NH**2)
+I_ND = 3 * (phys.atoms['H'].isotope[2].mass * phys.amu_to_kg * r_NH**2)
 """Inertia of ND3, in uma·m^2."""
 
 # Rotational energy.
-B_CH = ((phys.hbar_eV**2) / (2 * I_CH)) * phys.J_to_eV
+B_CH = ((phys.hbar**2) / (2 * I_CH)) * phys.J_to_eV
 """Rotational energy of CH3, in eV·s/uma·m^2."""
 B_CD = ((phys.hbar**2) / (2 * I_CD)) * phys.J_to_eV
 """Rotational energy of CD3, in eV·s/uma·m^2."""

aton/qrotor/potential.py

@@ -35,13 +35,13 @@
 def load(
         filepath:str='potential.dat',
         system:QSys=None,
-        angle:str='deg',
-        energy:str='eV',
+        angle_unit:str='deg',
+        energy_unit:str='eV',
         ) -> QSys:
     """Read a potential rotational energy dataset.
 
-    The file in `filepath` should contain two columns with `angle` and `potential` values.
-    Degrees and eV are assumed as default units unless stated in `angle` and `energy`.
+    The file in `filepath` should contain two columns with angle and potential energy values.
+    Degrees and eV are assumed as default units unless stated in `angle_unit` and `energy_unit`.
     Units will be converted automatically to radians and eV.
     """
     file_path = file.get(filepath)
@@ -57,21 +57,21 @@ def load(
         positions.append(float(position.strip()))
         potentials.append(float(potential.strip()))
     # Save angles to numpy arrays
-    if angle.lower() in alias.units['deg']:
+    if angle_unit.lower() in alias.units['deg']:
         positions = np.radians(positions)
-    elif angle.lower() in alias.units['rad']:
+    elif angle_unit.lower() in alias.units['rad']:
         positions = np.array(positions)
     else:
-        raise ValueError(f"Angle unit '{angle}' not recognized.")
+        raise ValueError(f"Angle unit '{angle_unit}' not recognized.")
     # Save energies to numpy arrays
-    if energy.lower() in alias.units['meV']:
+    if energy_unit.lower() in alias.units['meV']:
         potentials = np.array(potentials) * 1000
-    elif energy.lower() in alias.units['eV']:
+    elif energy_unit.lower() in alias.units['eV']:
         potentials = np.array(potentials)
-    elif energy.lower() in alias.units['Ry']:
+    elif energy_unit.lower() in alias.units['Ry']:
         potentials = np.array(potentials) * phys.Ry_to_eV
     else:
-        raise ValueError(f"Energy unit '{energy}' not recognized.")
+        raise ValueError(f"Energy unit '{energy_unit}' not recognized.")
     # Set the system
     system.grid = np.array(positions)
     system.gridsize = len(positions)
@@ -81,45 +81,56 @@ def load(
 
 def from_qe(
         folder=None,
-        filters:str=None,
         output:str='potential.dat',
+        include:list=['.out'],
+        ignore:list=['slurm-'],
         ) -> None:
     """Creates a potential data file from Quantum ESPRESSO outputs.
 
     The angle in degrees is extracted from the output filenames,
     which must follow `whatever_ANGLE.out`.
 
-    Outputs from SCF calculations must be located in the provided `folder` (CWD if None),
-    and can be filtered with `filters`.
+    Outputs from SCF calculations must be located in the provided `folder` (CWD if None).
+    Files can be filtered by those containing the specified `filters`,
+    excluding those containing any string from the `ignore` list. 
     The `output` name is `potential.dat` by default.
     """
     folder = file.get_dir(folder)
-    files = file.get_list(folder=folder, filters=filters, abspath=True)
+    files = file.get_list(folder=folder, include=include, ignore=ignore, abspath=True)
     potential_data = '# Angle/deg    Potential/eV\n'
     potential_data_list = []
     print('Extracting the potential as a function of the angle...')
+    print('----------------------------------')
+    counter_success = 0
+    counter_errors = 0
     for filepath in files:
         filename = os.path.basename(filepath)
         filepath = file.get(filepath=filepath, filters='.out', return_anyway=True)
         if not filepath:  # Not an output file, skip it
             continue
         content = qe.read_out(filepath)
         if not content['Success']:  # Ignore unsuccessful calculations
-            print(f'{filename} was unsuccessful :(')
+            print(f'x   {filename}')
+            counter_errors += 1
             continue
         energy = content['Energy'] * phys.Ry_to_eV
         splits = filename.split('_')
         angle = splits[-1].replace('.out', '')
         angle = float(angle)
         potential_data_list.append((angle, energy))
-        print(f'{filename} added')
+        print(f'OK  {filename}')
+        counter_success += 1
     # Sort by angle
     potential_data_list_sorted = sorted(potential_data_list, key=lambda x: x[0])
     # Append the sorted values as a string
     for angle, energy in potential_data_list_sorted:
         potential_data += f'{angle}    {energy}\n'
     with open(output, 'w') as f:
         f.write(potential_data)
+    print('----------------------------------')
+    print(f'Succesful calculations (OK): {counter_success}')
+    print(f'Faulty calculations     (x): {counter_errors}')
+    print('----------------------------------')
     print(f'Saved angles and potential values at {output}')
     return None
 
@@ -153,7 +164,7 @@ def solve(system:QSys):
     data = deepcopy(system)
     # Is there a potential_name?
     if not data.potential_name:
-        if not data.potential_values.any():
+        if not any(data.potential_values):
             raise ValueError(f'No potential_name and no potential_values found in the system!')
     elif data.potential_name.lower() == 'titov2023':
         data.potential_values = titov2023(data)
@@ -162,7 +173,7 @@ def solve(system:QSys):
     elif data.potential_name.lower() == 'sine':
         data.potential_values = sine(data)
     # At least there should be potential_values
-    elif not data.potential_values.any():
+    elif not any(data.potential_values):
         raise ValueError("Unrecognised potential_name '{data.potential_name}' and no potential_values found")
     return data.potential_values
 

aton/qrotor/solve.py

@@ -9,11 +9,11 @@
 
 | | |
 | --- | --- |
-| `laplacian_matrix()`      | Calculate the second derivative matrix for a given grid |
-| `hamiltonian_matrix()`    | Calculate the hamiltonian matrix of the system |
+| `energies()`              | Solve the system(s) for the `QSys` or `QExp` object |
 | `potential()`             | Solve the potential values of the system |
 | `schrodinger()`           | Solve the Schrödiger equation for the system |
-| `energies()`              | Solve the system(s) for the `QSys` or `QExp` object |
+| `hamiltonian_matrix()`    | Calculate the hamiltonian matrix of the system |
+| `laplacian_matrix()`      | Calculate the second derivative matrix for a given grid |
 
 ---
 """
@@ -29,27 +29,21 @@
 import aton
 
 
-def laplacian_matrix(grid):
-    """Calculates the Laplacian (second derivative) matrix for a given `grid`."""
-    x = grid
-    diagonals = [-2*np.ones(len(x)), np.ones(len(x)), np.ones(len(x))]
-    laplacian_matrix = sparse.spdiags(diagonals, [0, -1, 1], format='lil')
-    # Periodic boundary conditions
-    laplacian_matrix[0, -1] = 1
-    laplacian_matrix[-1, 0] = 1
-    dx = x[1] - x[0]
-    laplacian_matrix /= dx**2
-    return laplacian_matrix
-
-
-def hamiltonian_matrix(system:QSys):
-    """Calculates the Hamiltonian matrix for a given `aton.qrotor.classes.QSys` object."""
-    V = system.potential_values.tolist()
-    potential = sparse.diags(V, format='lil')
-    B = system.B
-    x = system.grid
-    H = -B * laplacian_matrix(x) + potential
-    return H
+def energies(var, filename:str=None) -> QExp:
+    """Solves the Schrödinger equation for a given `aton.qrotor.classes.QSys` or `aton.qrotor.classes.QExp` object."""
+    if isinstance(var, QSys):
+        data = QExp()
+        data.systems = [deepcopy(var)]
+    elif isinstance(var, QExp):
+        data = deepcopy(var)
+    else:
+        raise TypeError('Input must be a QSys or QExp object.')
+    for system in data.systems:
+        system = potential(system)
+        system = schrodinger(system)
+    if filename:
+        aton.st.file.save(data, filename)
+    return data
 
 
 def potential(system:QSys) -> QSys:
@@ -97,19 +91,25 @@ def schrodinger(system:QSys) -> QSys:
     return system
 
 
-def energies(var, filename:str=None) -> QExp:
-    """Solves the Schrödinger equation for a given `aton.qrotor.classes.QSys` or `aton.qrotor.classes.QExp` object."""
-    if isinstance(var, QSys):
-        data = QExp()
-        data.systems = [deepcopy(var)]
-    elif isinstance(var, QExp):
-        data = deepcopy(var)
-    else:
-        raise TypeError('Input must be a QSys or QExp object.')
-    for system in data.systems:
-        system = potential(system)
-        system = schrodinger(system)
-    if filename:
-        aton.st.file.save(data, filename)
-    return data
+def hamiltonian_matrix(system:QSys):
+    """Calculates the Hamiltonian matrix for a given `aton.qrotor.classes.QSys` object."""
+    V = system.potential_values.tolist()
+    potential = sparse.diags(V, format='lil')
+    B = system.B
+    x = system.grid
+    H = -B * laplacian_matrix(x) + potential
+    return H
+
+
+def laplacian_matrix(grid):
+    """Calculates the Laplacian (second derivative) matrix for a given `grid`."""
+    x = grid
+    diagonals = [-2*np.ones(len(x)), np.ones(len(x)), np.ones(len(x))]
+    laplacian_matrix = sparse.spdiags(diagonals, [0, -1, 1], format='lil')
+    # Periodic boundary conditions
+    laplacian_matrix[0, -1] = 1
+    laplacian_matrix[-1, 0] = 1
+    dx = x[1] - x[0]
+    laplacian_matrix /= dx**2
+    return laplacian_matrix
 

aton/st/file.py

@@ -49,7 +49,7 @@ def get(
     if os.path.isfile(filepath):
         return os.path.abspath(filepath)
     elif os.path.isdir(filepath):
-        files = get_list(filepath, filters, abspath=True)
+        files = get_list(folder=filepath, include=filters, abspath=True)
     elif return_anyway:
         return None
     else:
@@ -66,36 +66,55 @@ def get(
 
 
 def get_list(
-        folder:str,
-        filters=None,
-        abspath:bool=True
+        folder:str=None,
+        include=None,
+        ignore=None,
+        abspath:bool=True,
+        also_folders:bool=False,
     ) -> list:
-    """Return the files inside a `folder`, applying optional `filters`.
+    """Return the files inside a `folder`, applying optional filters.
+
+    Only filenames containing all strings in the `include` list will be returned.
+    Filenames containing any string from the `ignore` list will be ignored.
 
     The full paths are returned by default; to get only the base names, set `abspath = False`.
+    The CWD folder is used by default if no `folder` is provided.
+    It also returns folders if `also_folders = True`.
     """
+    if not folder:
+        folder = os.getcwd()
     if os.path.isfile(folder):
         folder = os.path.dirname(folder)
     if not os.path.isdir(folder):
         raise FileNotFoundError('Directory not found: ' + folder)
     folder = os.path.abspath(folder)
     files = os.listdir(folder)
-    # Apply filters or not
-    if filters is not None:
-        target_files = []
-        if not isinstance(filters, list):
-            filters = [str(filters)]
-        for filter_i in filters:
-            filter_i = os.path.basename(filter_i)
-            for f in files:
-                if filter_i in f:
-                    target_files.append(f)
-        files = target_files
+    if not files:
+        return []
+    # Absolute paths?
     if abspath:
-        filepaths = []
-        for f in files:
-            filepaths.append(os.path.join(folder, f))
-        files = filepaths
+        files = [os.path.join(folder, f) for f in files]
+    # Should we keep only files?
+    if not also_folders:
+        files = [f for f in files if not os.path.isdir(f if abspath else os.path.join(folder, f))]
+    # Apply filters if provided
+    if include is not None:
+        # Ensure include filters is always a list
+        if not isinstance(include, list):
+            include = [str(include)]
+        # Normalize filter names
+        include = [os.path.basename(i) for i in include]
+        # Only keep files that contain all filters
+        files = [f for f in files if all(filter_str in os.path.basename(f) for filter_str in include)]
+    # Remove files containing any string from the ignore list
+    if ignore is not None:
+        # Ensure ignore filters is always a list
+        if not isinstance(ignore, list):
+            ignore = [str(ignore)]
+        # Normalize ignoring filter names
+        ignore = [os.path.basename(i) for i in ignore]
+        # Exclude the corresponding files
+        files = [f for f in files if not any(filter_str in os.path.basename(f) for filter_str in ignore)]
     return files
 
 
@@ -223,7 +242,7 @@ def copy_to_folders(
     """
     if folder is None:
         folder = os.getcwd()
-    old_files = get_list(folder, extension)
+    old_files = get_list(folder=folder, include=extension)
     if old_files is None:
         raise ValueError('No ' + extension + ' files found in path!')
     for old_file in old_files:

docs/aton.html

@@ -98,7 +98,7 @@ <h2>Submodules</h2>
             </ul>
 
 
-            <footer>ATON v0.0.1rc34 documentation</footer>
+            <footer>ATON v0.0.1 documentation</footer>
 
         <a class="attribution" title="pdoc: Python API documentation generator" href="https://pdoc.dev" target="_blank">
             built with <span class="visually-hidden">pdoc</span><img

docs/aton/_version.html

@@ -76,7 +76,7 @@ <h2>API Documentation</h2>
     </ul>
 
 
-            <footer>ATON v0.0.1rc34 documentation</footer>
+            <footer>ATON v0.0.1 documentation</footer>
 
         <a class="attribution" title="pdoc: Python API documentation generator" href="https://pdoc.dev" target="_blank">
             built with <span class="visually-hidden">pdoc</span><img
@@ -116,7 +116,7 @@ <h1 class="modulename">
 </span><span id="L-10"><a href="#L-10"><span class="linenos">10</span></a>
 </span><span id="L-11"><a href="#L-11"><span class="linenos">11</span></a><span class="sd">&quot;&quot;&quot;</span>
 </span><span id="L-12"><a href="#L-12"><span class="linenos">12</span></a>
-</span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s1">&#39;v0.0.1rc34&#39;</span>
+</span><span id="L-13"><a href="#L-13"><span class="linenos">13</span></a><span class="n">__version__</span> <span class="o">=</span> <span class="s1">&#39;v0.0.1&#39;</span>
 </span></pre></div>