aton 0.2.1__tar.gz → 0.2.2__tar.gz

{aton-0.2.1 → aton-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aton
-Version: 0.2.1
+Version: 0.2.2
 Summary: The Ab-iniTiO & Neutron research toolbox, or ATON, provides powerful and comprehensive tools for cutting-edge materials research, focused on (but not limited to) neutron science.
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

{aton-0.2.1 → aton-0.2.2}/aton/_version.py

@@ -10,5 +10,5 @@ https://semver.org/
 
 """
 
-__version__ = 'v0.2.1'
+__version__ = 'v0.2.2'
 

{aton-0.2.1 → aton-0.2.2}/aton/interface/__init__.py

@@ -33,7 +33,7 @@ To modify values from an input file,
 ```python
 from aton.interface import qe
 # Add a hydrogen atom to a specific position
-qe.add_atom('H  0.10  0.20  0.30')
+qe.add_atom('relax.in', 'H  0.10  0.20  0.30')
 # Set the input ecutwfc value
 qe.set_value('relax.in', 'ecutwfc', 60.0)
 ```

{aton-0.2.1 → aton-0.2.2}/aton/phys/atoms.py

@@ -22,7 +22,7 @@ The `atoms` dictionary can be loaded directly as `aton.phys.atoms`.
 ```python
 from aton import phys
 aluminium_neutron_cross_section = phys.atoms['Al'].cross_section  # 1.503
-He4_mass = phys.atoms['H'].isotope[4].mass  # 4.0026032497
+He4_mass = phys.atoms['He'].isotope[4].mass  # 4.0026032497
 ```
 
 ---

{aton-0.2.1 → aton-0.2.2}/aton/phys/functions.py

@@ -62,7 +62,7 @@ def export_atoms(
             "```python\n"
             "from aton import phys\n"
             "aluminium_neutron_cross_section = phys.atoms['Al'].cross_section  # 1.503\n"
-            "He4_mass = phys.atoms['H'].isotope[4].mass  # 4.0026032497\n\n"
+            "He4_mass = phys.atoms['He'].isotope[4].mass  # 4.0026032497\n\n"
             "```\n\n"
             "---\n"
             "'''\n\n\n"

{aton-0.2.1 → aton-0.2.2}/aton/qrotor/plot.py

@@ -25,7 +25,12 @@ import numpy as np
 from copy import deepcopy
 
 
-def potential(data, title:str=None, marker='', linestyle='-') -> None:
+def potential(
+        data,
+        title:str=None,
+        marker='',
+        linestyle='-',
+        ) -> None:
     """Plot the potential values of `data` (System object, or list of systems).
 
     Title can be customized with `title`.
@@ -52,7 +57,7 @@ def potential(data, title:str=None, marker='', linestyle='-') -> None:
     plt.title(title_str)
     plt.xlabel('Angle / rad')
     plt.ylabel('Potential energy / meV')
-    plt.xticks([0, np.pi/2, np.pi, 3*np.pi/2, 2*np.pi], ['0', r'$\frac{\pi}{2}$', r'$\pi$', r'$\frac{3\pi}{2}$', r'$2\pi$'])
+    plt.xticks([-2*np.pi, -3*np.pi/2, -np.pi, -np.pi/2, 0, np.pi/2, np.pi, 3*np.pi/2, 2*np.pi], [r'$-2\pi$', r'$-\frac{3\pi}{2}$', r'$-\pi$', r'$-\frac{\pi}{2}$', '0', r'$\frac{\pi}{2}$', r'$\pi$', r'$\frac{3\pi}{2}$', r'$2\pi$'])
 
     for i, s in enumerate(system):
         plt.plot(s.grid, s.potential_values, marker=marker[i], linestyle=linestyle[i], label=s.comment)
@@ -63,7 +68,10 @@ def potential(data, title:str=None, marker='', linestyle='-') -> None:
     plt.show()
 
 
-def energies(data, title:str=None) -> None:
+def energies(
+        data,
+        title:str=None,
+        ) -> None:
     """Plot the eigenvalues of `data` (System or a list of System objects)."""
     if isinstance(data, System):
         var = [data]
@@ -85,7 +93,7 @@ def energies(data, title:str=None) -> None:
     plt.xlabel(xlabel_text)
     plt.ylabel(ylabel_text)
     plt.title(title)
-    plt.xticks([0, np.pi/2, np.pi, 3*np.pi/2, 2*np.pi], ['0', r'$\frac{\pi}{2}$', r'$\pi$', r'$\frac{3\pi}{2}$', r'$2\pi$'])
+    plt.xticks([-2*np.pi, -3*np.pi/2, -np.pi, -np.pi/2, 0, np.pi/2, np.pi, 3*np.pi/2, 2*np.pi], [r'$-2\pi$', r'$-\frac{3\pi}{2}$', r'$-\pi$', r'$-\frac{\pi}{2}$', '0', r'$\frac{\pi}{2}$', r'$\pi$', r'$\frac{3\pi}{2}$', r'$2\pi$'])
 
     unique_potentials = []
     unique_groups = []
@@ -119,7 +127,12 @@ def energies(data, title:str=None) -> None:
     plt.show()
 
 
-def reduced_energies(data:list, title:str=None, values:list=[], legend:list=[]) -> None:
+def reduced_energies(
+        data:list,
+        title:str=None,
+        values:list=[],
+        legend:list=[],
+        ) -> None:
     """Plots the reduced energy of the system E/B vs the reduced potential energy V/B.
 
     Takes a `data` list of System objects as input.
@@ -167,7 +180,14 @@ def reduced_energies(data:list, title:str=None, values:list=[], legend:list=[])
     plt.show()
 
 
-def wavefunction(system:System, title:str=None, square:bool=True, levels=[0, 1, 2], overlap=False):
+def wavefunction(
+        system:System,
+        title:str=None,
+        square:bool=True,
+        levels=[0, 1, 2],
+        overlap=False,
+        yticks:bool=False,
+        ) -> None:
     """Plot the wavefunction of a `system` for the specified `levels`.
 
     Wavefunctions are squared by default, showing the probabilities;
@@ -181,6 +201,8 @@ def wavefunction(system:System, title:str=None, square:bool=True, levels=[0, 1,
     but note that this overlap is limited by the number of System.E_levels,
     that must be specified before solving the system.
     Setting `overlap` will ignore the `levels` argument.
+
+    Set `yticks = True` to plot the wavefunction yticks.
     """
     data = deepcopy(system)
     eigenvectors = data.eigenvectors
@@ -190,10 +212,11 @@ def wavefunction(system:System, title:str=None, square:bool=True, levels=[0, 1,
     plt.title(title)
     ax1.set_xlabel('Angle / radians')
     ax1.set_ylabel('Potential / meV')
-    ax1.set_xticks([0, np.pi/2, np.pi, 3*np.pi/2, 2*np.pi], ['0', r'$\frac{\pi}{2}$', r'$\pi$', r'$\frac{3\pi}{2}$', r'$2\pi$'])
+    ax1.set_xticks([-2*np.pi, -3*np.pi/2, -np.pi, -np.pi/2, 0, np.pi/2, np.pi, 3*np.pi/2, 2*np.pi], [r'$-2\pi$', r'$-\frac{3\pi}{2}$', r'$-\pi$', r'$-\frac{\pi}{2}$', '0', r'$\frac{\pi}{2}$', r'$\pi$', r'$\frac{3\pi}{2}$', r'$2\pi$'])
     ax1.plot(data.grid, data.potential_values, color='blue', linestyle='-')
     ax2 = ax1.twinx()
-    ax2.set_yticks([])
+    if not yticks:
+        ax2.set_yticks([])
     ax2.set_ylabel('Squared wavefunction' if square else 'Wavefunction')
 
     # Set levels list

{aton-0.2.1 → aton-0.2.2}/aton/qrotor/system.py

@@ -91,23 +91,52 @@ class System:
         self.runtime: float = None
         """Time taken to solve the eigenvalues."""
 
-    def summary(self):
-        return {
-            'version': self.version,
-            'comment': self.comment,
-            'group': self.group,
-            'gridsize': self.gridsize,
-            'B': self.B,
-            'potential_name': self.potential_name,
-            'potential_constants': self.potential_constants.tolist() if isinstance(self.potential_constants, np.ndarray) else self.potential_constants,
-            'potential_offset': self.corrected_potential_offset,
-            'potential_min': self.potential_min,
-            'potential_max': self.potential_max,
-            'eigenvalues': self.eigenvalues.tolist() if isinstance(self.eigenvalues, np.ndarray) else self.eigenvalues,
-            'energy_barrier': self.energy_barrier,
-            'transitions': self.transitions,
-            'runtime': self.runtime,
-        }
+    def solve(self, new_gridsize:int=None):
+        """Solves the quantum system.
+
+        The potential can be interpolated to a `new_gridsize`.
+    
+        Same as running `aton.qrotor.solve.energies(System)`.
+        """
+        from .solve import energies
+        if new_gridsize:
+            self.gridsize = new_gridsize
+        return energies(self)
+
+    def change_phase(self, phase:float, calculate:bool=True):
+        """Apply a phase shift to the grid and potential values.
+
+        The `phase` should be a multiple of $\pi$ (e.g., 3/2 for $3\pi/2$).
+        The resulting grid will be expressed between $-2\pi$ and $2\pi$.
+
+        The System is solved immediately after the phase change.
+        This last step ensures that all eigenvalues and wavefunctions are correct.
+        You can override this step with `calculate = False`,
+        but remember to solve the System later!
+        """
+        if not any(self.potential_values) or not any(self.grid):
+            raise ValueError("System.potential_values and System.grid must be set before applying a phase shift.")
+        # Normalise the phase between 0 and 2
+        if abs(phase) >= 2:
+            phase = phase % 2
+        while phase < 0:
+            phase = phase + 2
+        # Shift the grid, between -2pi and 2pi
+        self.grid = (self.grid + (phase * np.pi))
+        # Apply the phase shift to potential values
+        phase_points = int((phase / 2) * self.gridsize)
+        self.potential_values = np.roll(self.potential_values, phase_points)
+        # Check that the grid is still within -2pi and 2pi, otherwise normalise it for a final time
+        while self.grid[0] <= (-2 * np.pi + 0.1):  # With a small tolerance
+            self.grid = self.grid + 2 * np.pi
+            print('plus 2')
+        while self.grid[-1] >= 2.5 * np.pi:  # It was not a problem until reaching 5/2 pi
+            self.grid = self.grid -2 * np.pi
+            print('minus 2')
+        print(f'Potential shifted by {phase}π')
+        if calculate:
+            self.solve()
+        return self
 
     def set_grid(self, gridsize:int=None):
         """Sets the `System.grid` to the specified `gridsize` from 0 to $2\\pi$.
@@ -163,18 +192,6 @@ class System:
                 return self
         self.group = group  # No match was found
         return self
-    
-    def solve(self, new_gridsize:int=None):
-        """Solves the quantum system.
-
-        The potential can be interpolated to a `new_gridsize`.
-    
-        Same as running `aton.qrotor.solve.energies(System)`.
-        """
-        from .solve import energies
-        if new_gridsize:
-            self.gridsize = new_gridsize
-        return energies(self)
 
     def reduce_size(self):
         """Discard data that takes too much space,
@@ -184,3 +201,21 @@ class System:
         self.grid = []
         return self
 
+    def summary(self):
+        return {
+            'version': self.version,
+            'comment': self.comment,
+            'group': self.group,
+            'gridsize': self.gridsize,
+            'B': self.B,
+            'potential_name': self.potential_name,
+            'potential_constants': self.potential_constants.tolist() if isinstance(self.potential_constants, np.ndarray) else self.potential_constants,
+            'potential_offset': self.potential_offset,
+            'potential_min': self.potential_min,
+            'potential_max': self.potential_max,
+            'eigenvalues': self.eigenvalues.tolist() if isinstance(self.eigenvalues, np.ndarray) else self.eigenvalues,
+            'energy_barrier': self.energy_barrier,
+            'transitions': self.transitions,
+            'runtime': self.runtime,
+        }
+

{aton-0.2.1 → aton-0.2.2}/aton.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aton
-Version: 0.2.1
+Version: 0.2.2
 Summary: The Ab-iniTiO & Neutron research toolbox, or ATON, provides powerful and comprehensive tools for cutting-edge materials research, focused on (but not limited to) neutron science.
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

{aton-0.2.1 → aton-0.2.2}/tests/test_qrotor.py

@@ -2,6 +2,7 @@ import aton.qrotor as qr
 import aton.interface as interface
 import aton.txt.extract as extract
 import aton.st.file as file
+import numpy as np
 
 
 folder = 'tests/samples/'
@@ -68,3 +69,22 @@ def test_solve_zero():
     assert round(system.eigenvalues[7], 2) == 16.0
     assert round(system.eigenvalues[8], 2) == 16.0
 
+
+def test_phase():
+    sys = qr.System()
+    sys.B = 1.0
+    sys.potential_name = 'cos'
+    sys.gridsize = 10000
+    sys.solve()
+    # plus pi/2, which will be -3pi/2
+    sys.change_phase(0.5)
+    assert round(sys.grid[0], 2) == round(-np.pi * 3/2, 2)
+    # The first potential value should be 0,
+    # but remember that the potential offset is corrected
+    # so it should be half potential_max, so 1.0/2
+    assert round(sys.potential_values[0], 2) == 0.5
+    # minus pi, which will become -pi/2
+    sys.change_phase(-1)
+    assert round(sys.grid[0], 2) == round(-np.pi/2, 2)
+    assert round(sys.potential_values[0], 2) == 0.5
+