qrotor 4.1.0__py3-none-any.whl → 4.1.2__py3-none-any.whl

qrotor/_version.py

@@ -8,7 +8,8 @@ Package version is defined here. Follows semantic versioning, as in:
 More about semantic versioning:
 https://semver.org/
 
+---
 """
 
-__version__ = 'v4.1.0'
+__version__ = "v4.1.2"
 

qrotor/constants.py

@@ -1,7 +1,7 @@
 """
 # Description
 
-Common constants and default inertia values used in the QRotor subpackage.
+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).
@@ -51,13 +51,13 @@ I_ND3 = 3 * (periodictable.D.mass * _amu * r_NH**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."""
 
 # Potential constants from titov2023 [C1, C2, C3, C4, C5]
 constants_titov2023 = [
@@ -75,11 +75,15 @@ In meV units.
 
 # Quick conversion factors
 Ry_to_eV = const.physical_constants['Rydberg constant times hc in eV'][0]
-"""Quick conversion factor from eV to Rydberg energy."""
+"""Quick conversion factor from Rydberg to eV energy."""
 Ry_to_meV = Ry_to_eV * 1000
-"""Quick conversion factor from meV to Rydberg energy."""
+"""Quick conversion factor from Rydberg to meV energy."""
 eV_to_Ry = 1 / Ry_to_eV
-"""Quick conversion factor from Rydberg to eV."""
+"""Quick conversion factor from eV to Rydberg."""
 meV_to_Ry = 1 / Ry_to_meV
-"""Quick conversion factor from Rydberg 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/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/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/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-4.1.0.dist-info → qrotor-4.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.1.0
+Version: 4.1.2
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

{qrotor-4.1.0.dist-info → qrotor-4.1.2.dist-info}/RECORD

@@ -1,20 +1,20 @@
 qrotor/__init__.py,sha256=rG2dH4QjsVUOMBhFnv5gXs3QnrUg7fywd5pIDmMBXcQ,246
-qrotor/_version.py,sha256=Nua4qsgx0bY8W7io9up8mEgvL_e9nuVunr--jEqP2LQ,194
-qrotor/constants.py,sha256=l25-YHxWQPr5RFGl8e0Hpdkc0E4ER03Gj-P9Jmbqelc,3203
-qrotor/plot.py,sha256=th6eDoTB01KaVjfH2uiKMjU4VJMfdv0yK97PwCJydKI,13479
-qrotor/potential.py,sha256=9NyekNIMbjiRtJ8G6CtCMHX5v-g7kKC8un2x3blq-2w,18320
+qrotor/_version.py,sha256=gtnQ4qGBlYQr4K9VzdiULHRclyxik47zCja1dRudtyk,198
+qrotor/constants.py,sha256=Q59CU5QrvOyCz-2TFP31GDKJYi7G7LUxbs10ZTMiKIE,3408
+qrotor/plot.py,sha256=s0XYMxQ7BxN_MngU-UAvX5mGk5R8c_Hznw2xFX9-8nI,14028
+qrotor/potential.py,sha256=2HjSDVJWSvwplyH5pq0MMPoQsLIBJbbTwkr350u949I,18491
 qrotor/rotate.py,sha256=Wje9Q9SFhDvizz58MzNGBwsmgV-3wN9z2SnUNTIXzeg,8107
 qrotor/solve.py,sha256=YkOR1SJlpk41PCNEhslv6X3wV1TWMNztT78qX3Pngf0,10722
-qrotor/system.py,sha256=v6BFA9Pm1HbYdfm-XrPP7iWlbcvjxX7ynGBMOxDR7yc,11447
+qrotor/system.py,sha256=ahYurNUmVOV7B6aZSe7rhcruagj5rW9UClqG-H1vVvY,11454
 qrotor/systems.py,sha256=Hcx0QvMWpaPMfC6HWpkZPPWDyHk9rxWKdAxWNnD2NMg,8184
-qrotor-4.1.0.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
+qrotor-4.1.2.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
 tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 tests/test_constants.py,sha256=YHKkPyZlzjchxxzON_VSNsQdKnpkknsFVoIA6TcUk70,399
 tests/test_potential.py,sha256=_Vq9t9Xm59kNbyYwXlRnvKcxwL7vntD2j14W2aUtF6I,1302
 tests/test_rotate.py,sha256=2On2d1E82hdisFC5DXpaqqYNnteX7ZP3PAnGa_oGm2M,1896
 tests/test_solve.py,sha256=tEjLUZC7oe6LCQD5b2xf2aaK9lu-zI4lzuPXOGR2GAs,861
 tests/test_system.py,sha256=36d-8AdoJdzq0O9_O3s8wwBPGa-M7A86YiHqhhAsCZ8,742
-qrotor-4.1.0.dist-info/METADATA,sha256=-_zFlV6XwLwo5Oxrrf8lo-srb06KI5sF1SMJCJqAVAk,8719
-qrotor-4.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-qrotor-4.1.0.dist-info/top_level.txt,sha256=mLnYs07-amqX4TqbDV2_XvgdpHfgrYmzmYb7dwoh6EQ,13
-qrotor-4.1.0.dist-info/RECORD,,
+qrotor-4.1.2.dist-info/METADATA,sha256=5oHcJpRWIUcYiIzE5ilaFOWfH0xVy_7klIULdL2WhH0,8719
+qrotor-4.1.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+qrotor-4.1.2.dist-info/top_level.txt,sha256=mLnYs07-amqX4TqbDV2_XvgdpHfgrYmzmYb7dwoh6EQ,13
+qrotor-4.1.2.dist-info/RECORD,,