qrotor 4.1.1__tar.gz → 4.2.0__tar.gz

{qrotor-4.1.1 → qrotor-4.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.1.1
+Version: 4.2.0
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

{qrotor-4.1.1 → qrotor-4.2.0}/qrotor/_version.py

@@ -11,5 +11,5 @@ https://semver.org/
 ---
 """
 
-__version__ = "v4.1.1"
+__version__ = "v4.2.0"
 

{qrotor-4.1.1 → qrotor-4.2.0}/qrotor/constants.py

@@ -5,8 +5,6 @@ Common constants and default inertia values used in QRotor.
 
 Bond lengths and angles were obtained from MAPbI3, see
 [K. Drużbicki *et al*., Crystal Growth & Design 24, 391–404 (2024)](https://doi.org/10.1021/acs.cgd.3c01112).
-
----
 """
 
 
@@ -15,6 +13,24 @@ import periodictable
 import scipy.constants as const
 
 
+# Quick conversion factors
+Ry_to_eV = const.physical_constants['Rydberg constant times hc in eV'][0]
+"""Quick conversion factor from Rydberg to eV energy."""
+Ry_to_meV = Ry_to_eV * 1000
+"""Quick conversion factor from Rydberg to meV energy."""
+eV_to_Ry = 1 / Ry_to_eV
+"""Quick conversion factor from eV to Rydberg."""
+meV_to_Ry = 1 / Ry_to_meV
+"""Quick conversion factor from meV to Rydberg."""
+cm1_to_meV = (const.h * const.c * 100 / const.e) * 1000
+"""Quick conversion factor from cm$^{-1}$ to meV."""
+meV_to_cm1 = 1/cm1_to_meV
+"""Quick conversion factor from meV to cm$^{-1}$."""
+amu_to_kg = const.physical_constants['atomic mass constant'][0]
+"""Quick conversion factor from amu to kg."""
+kg_to_amu = 1 / amu_to_kg
+"""Quick conversion factor from kg to amu."""
+
 # Distance between Carbon and Hydrogen atoms (measured from MAPbI3)
 distance_CH = 1.09285   # Angstroms
 """Distance of the C-H bond, in Angstroms."""
@@ -38,26 +54,62 @@ r_NH = distance_NH * np.sin(np.deg2rad(angle_NH)) * 1e-10
 """Rotation radius of the amine group, in meters."""
 
 # Inertia, SI units
-_amu = const.physical_constants['atomic mass constant'][0]
-I_CH3 = 3 * (periodictable.H.mass * _amu * r_CH**2)
+I_CH3 = 3 * (periodictable.H.mass * amu_to_kg * r_CH**2)
 """Inertia of CH3, in kg·m^2."""
-I_CD3 = 3 * (periodictable.D.mass * _amu * r_CH**2)
+I_CD3 = 3 * (periodictable.D.mass * amu_to_kg * r_CH**2)
 """Inertia of CD3, in kg·m^2."""
-I_NH3 = 3 * (periodictable.H.mass * _amu * r_NH**2)
+I_NH3 = 3 * (periodictable.H.mass * amu_to_kg * r_NH**2)
 """Inertia of NH3, in kg·m^2."""
-I_ND3 = 3 * (periodictable.D.mass * _amu * r_NH**2)
+I_ND3 = 3 * (periodictable.D.mass * amu_to_kg * r_NH**2)
 """Inertia of ND3, in kg·m^2."""
 
+I_CH3NH3 = I_CH3 + I_NH3
+"""Inertia of CH3NH3+, in kg·m^2."""
+I_CD3NH3 = I_CD3 + I_NH3
+"""Inertia of CD3NH3+, in kg·m^2."""
+I_CH3ND3 = I_CH3 + I_ND3
+"""Inertia of CH3ND3+, in kg·m^2."""
+I_CD3ND3 = I_CD3 + I_ND3
+"""Inertia of CD3ND3+, in kg·m^2."""
+
+# Inertia, atomic units
+I_CH3_amu = I_CH3 / (amu_to_kg * 1e-20)
+"""Inertia of CH3, in amu·AA^2."""
+I_CD3_amu = I_CD3 / (amu_to_kg * 1e-20)
+"""Inertia of CD3, in amu·AA^2."""
+I_NH3_amu = I_NH3 / (amu_to_kg * 1e-20)
+"""Inertia of NH3, in amu·AA^2."""
+I_ND3_amu = I_ND3 / (amu_to_kg * 1e-20)
+"""Inertia of ND3, in amu·AA^2."""
+
+I_CH3NH3_amu = I_CH3_amu + I_NH3_amu
+"""Inertia of CH3NH3+, in amu·AA^2."""
+I_CD3NH3_amu = I_CD3_amu + I_NH3_amu
+"""Inertia of CD3NH3+, in amu·AA^2."""
+I_CH3ND3_amu = I_CH3_amu + I_ND3_amu
+"""Inertia of CH3ND3+, in amu·AA^2."""
+I_CD3ND3_amu = I_CD3_amu + I_ND3_amu
+"""Inertia of CD3ND3+, in amu·AA^2."""
+
 # Rotational energy
 _hbar = const.physical_constants['reduced Planck constant'][0]
 B_CH3 = ((_hbar**2) / (2 * I_CH3)) * (1000 / const.eV)
-"""Rotational energy of CH3, in meV·s/kg·m^2."""
+"""Kinetic rotational energy of CH3, in meV·s/kg·m^2."""
 B_CD3 = ((_hbar**2) / (2 * I_CD3)) * (1000 / const.eV)
-"""Rotational energy of CD3, in meV·s/kg·m^2."""
+"""Kinetic rotational energy of CD3, in meV·s/kg·m^2."""
 B_NH3 = ((_hbar**2) / (2 * I_NH3)) * (1000 / const.eV)
-"""Rotational energy of NH3, in meV·s/kg·m^2."""
+"""Kinetic rotational energy of NH3, in meV·s/kg·m^2."""
 B_ND3 = ((_hbar**2) / (2 * I_ND3)) * (1000 / const.eV)
-"""Rotational energy of ND3, in meV·s/kg·m^2."""
+"""Kinetic rotational energy of ND3, in meV·s/kg·m^2."""
+
+B_CH3NH3 = ((_hbar**2) / (2 * I_CH3NH3)) * (1000 / const.eV)
+"""Kinetic rotational energy of CH3NH3+, in meV·s/kg·m^2."""
+B_CD3NH3 = ((_hbar**2) / (2 * I_CD3NH3)) * (1000 / const.eV)
+"""Kinetic rotational energy of CD3NH3+, in meV·s/kg·m^2."""
+B_CH3ND3 = ((_hbar**2) / (2 * I_CH3ND3)) * (1000 / const.eV)
+"""Kinetic rotational energy of CH3ND3+, in meV·s/kg·m^2."""
+B_CD3ND3 = ((_hbar**2) / (2 * I_CD3ND3)) * (1000 / const.eV)
+"""Kinetic rotational energy of CD3ND3+, in meV·s/kg·m^2."""
 
 # Potential constants from titov2023 [C1, C2, C3, C4, C5]
 constants_titov2023 = [
@@ -73,17 +125,3 @@ for the `qrotor.potential.titov2023` potential.
 In meV units.
 """
 
-# Quick conversion factors
-Ry_to_eV = const.physical_constants['Rydberg constant times hc in eV'][0]
-"""Quick conversion factor from Rydberg to eV energy."""
-Ry_to_meV = Ry_to_eV * 1000
-"""Quick conversion factor from Rydberg to meV energy."""
-eV_to_Ry = 1 / Ry_to_eV
-"""Quick conversion factor from eV to Rydberg."""
-meV_to_Ry = 1 / Ry_to_meV
-"""Quick conversion factor from meV to Rydberg."""
-cm1_to_meV = (const.h * const.c * 100 / const.e) * 1000
-"""Quick conversion factor from cm$^{-1}$ to meV."""
-meV_to_cm1 = 1/cm1_to_meV
-"""Quick conversion factor from meV to cm$^{-1}$."""
-

{qrotor-4.1.1 → qrotor-4.2.0}/qrotor/plot.py

@@ -34,6 +34,8 @@ def potential(
         marker='',
         linestyle='-',
         cm:bool=False,
+        normalize:bool=False,
+        ylim:tuple=None,
         ) -> None:
     """Plot the potential values of `data` (System object, or list of systems).
 
@@ -42,8 +44,13 @@ def potential(
 
     `marker` and `linestyle` can be a Matplotlib string or list of strings.
     Optionally, the Viridis colormap can be used with `cm = True`.
+
+    Set `normalize = True` to normalize by their respective `qrotor.system.System.potential_max`.
+    This can be useful if you have performed subtractions or similar operations.
+    In this case, you might also want to play with `ylim` to adjust the y-axis limits.
     """
-    system = systems.as_list(data)
+    data_copy = deepcopy(data)
+    system = systems.as_list(data_copy)
     title_str = title if title else (system[0].comment if (system[0].comment and (len(system) == 1 or not system[-1].comment)) else 'Rotational potential energy')
     # Marker as a list
     if isinstance(marker, list):
@@ -62,6 +69,15 @@ def potential(
     plt.title(title_str)
     plt.xlabel('Angle / rad')
     plt.ylabel('Potential energy / meV')
+
+    if normalize:
+        plt.ylabel('Energy / V$_{3}$')
+        for s in system:
+            s.potential_values = s.potential_values / s.potential_max
+
+    if ylim:
+        plt.ylim(ylim)
+
     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'$2\pi$'])
 
     if cm:  # Plot using a colormap

{qrotor-4.1.1 → qrotor-4.2.0}/qrotor/potential.py

@@ -372,7 +372,10 @@ def interpolate(system:System) -> System:
     grid = system.grid
     gridsize = system.gridsize
     new_grid = np.linspace(0, 2*np.pi, gridsize)
-    cubic_spline = CubicSpline(grid, V)
+    # Impose periodic boundary conditions
+    grid_periodic = np.append(grid, grid[0] + 2*np.pi)
+    V_periodic = np.append(V, V[0])
+    cubic_spline = CubicSpline(grid_periodic, V_periodic, bc_type='periodic')
     new_V = cubic_spline(new_grid)
     system.grid = new_grid
     system.potential_values = new_V

{qrotor-4.1.1 → qrotor-4.2.0}/qrotor/system.py

@@ -61,7 +61,7 @@ class System:
         if not B:
             B = self.B
         self.B: float = B
-        """Rotational inertia, as in $B=\\frac{\\hbar^2}{2I}$.
+        """Kinetic rotational energy, as in $B=\\frac{\\hbar^2}{2I}$.
 
         Defaults to the value for a methyl group.
         """

{qrotor-4.1.1 → qrotor-4.2.0}/qrotor.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.1.1
+Version: 4.2.0
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

{qrotor-4.1.1 → qrotor-4.2.0}/qrotor.egg-info/SOURCES.txt

@@ -15,6 +15,7 @@ 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-4.1.1 → qrotor-4.2.0}/qrotor.egg-info/top_level.txt

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