qrotor 4.1.1__py3-none-any.whl → 4.1.2__py3-none-any.whl

qrotor/_version.py

@@ -11,5 +11,5 @@ https://semver.org/
 ---
 """
 
-__version__ = "v4.1.1"
+__version__ = "v4.1.2"
 

qrotor/constants.py

@@ -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 = [

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-4.1.1.dist-info → qrotor-4.1.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.1.1
+Version: 4.1.2
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

qrotor-4.1.2.dist-info/RECORD

@@ -0,0 +1,20 @@
+qrotor/__init__.py,sha256=rG2dH4QjsVUOMBhFnv5gXs3QnrUg7fywd5pIDmMBXcQ,246
+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=ahYurNUmVOV7B6aZSe7rhcruagj5rW9UClqG-H1vVvY,11454
+qrotor/systems.py,sha256=Hcx0QvMWpaPMfC6HWpkZPPWDyHk9rxWKdAxWNnD2NMg,8184
+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-4.1.2.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,,

{qrotor-4.1.1.dist-info → qrotor-4.1.2.dist-info}/top_level.txt

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

tests/test_constants.py

@@ -0,0 +1,13 @@
+import qrotor as qr
+
+
+def test_constants():
+    assert round(qr.B_CH3, 5) == 0.64518
+    assert round(qr.B_CD3, 5) == 0.32289
+    assert round(qr.B_NH3, 5) == 0.73569
+    assert round(qr.B_ND3, 5) == 0.36819
+    assert round(qr.Ry_to_eV, 5)  == 13.60569
+    assert round(qr.Ry_to_meV, 5) == 13605.69312
+    assert round(qr.eV_to_Ry, 5)  == 0.07350
+    assert round(qr.meV_to_Ry, 10) == .0000734986
+

tests/test_potential.py

@@ -0,0 +1,37 @@
+import qrotor as qr
+import aton
+
+
+folder = 'tests/samples/'
+structure = folder + 'CH3NH3.in'
+structure_120 = folder + 'CH3NH3_120.in'
+structure_60 = folder + 'CH3NH3_60.in'
+
+
+def test_save_and_load():
+    system = qr.System()
+    system.gridsize = 36
+    system.potential_name = 'sin'
+    system.B = 1
+    system.solve_potential()
+    potential_file = folder + '_temp_potential.csv'
+    # Remove the file if it exists
+    try:
+        aton.file.remove(potential_file)
+    except:
+        pass
+    qr.potential.save(system, comment='hi', filepath=potential_file)
+    system_new = qr.potential.load(potential_file)
+    assert system_new.gridsize == system.gridsize
+    assert round(system_new.potential_values[0], 5) == round(system.potential_values[0], 5)
+    assert round(system_new.potential_values[5], 5) == round(system.potential_values[5], 5)
+    assert round(system_new.potential_values[13], 5) == round(system.potential_values[13], 5)
+    assert system_new.comment == 'hi'
+    aton.file.remove(potential_file)
+    # If we don't provide a comment, it should be the name of the folder
+    system.comment = None
+    qr.potential.save(system, filepath=potential_file)
+    system_new = qr.potential.load(potential_file)
+    assert system_new.comment == 'samples'
+    aton.file.remove(potential_file)
+

tests/test_rotate.py

@@ -0,0 +1,53 @@
+import qrotor as qr
+import aton.api as api
+import aton.txt.extract as extract
+import aton.file as file
+
+
+folder = 'tests/samples/'
+structure = folder + 'CH3NH3.in'
+structure_120 = folder + 'CH3NH3_120.in'
+structure_60 = folder + 'CH3NH3_60.in'
+
+
+def test_rotate():
+    CH3 = [
+        '0.100   0.183   0.316',
+        '0.151   0.532   0.842',
+        '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)
+    for coord in CH3:
+        rotated_coord = api.qe.get_atom(filepath=structure_120, position=coord, precision=2)
+        rotated_coord = extract.coords(rotated_coord)
+        coord = extract.coords(coord)
+        rotated_coord_rounded = []
+        coord_rounded = []
+        for i in rotated_coord:
+            rotated_coord_rounded.append(round(i, 2))
+        for i in coord:
+            coord_rounded.append(round(i, 2))
+        assert coord_rounded == rotated_coord_rounded
+    file.remove(structure_120)
+
+    # 60 degrees (it should change quite a lot)
+    ideal = [
+        '0.146468644022416   0.837865866372631   0.641449758215011',
+        '0.095062781582172   0.488975944606740   0.115053787468686',
+        '0.128156574395412   0.205890189020629   0.680672454316303',
+    ]
+    qr.rotate.structure_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 = extract.coords(rotated_coord)
+        coord = extract.coords(coord)
+        rotated_coord_rounded = []
+        coord_rounded = []
+        for i in rotated_coord:
+            rotated_coord_rounded.append(round(i, 2))
+        for i in coord:
+            coord_rounded.append(round(i, 2))
+        assert coord_rounded == rotated_coord_rounded
+    file.remove(structure_60)
+

tests/test_solve.py

@@ -0,0 +1,28 @@
+import qrotor as qr
+
+
+def test_solve_zero():
+    system = qr.System()
+    system.gridsize = 50000
+    system.potential_name = 'zero'
+    system.B = 1
+    system.solve()
+    assert round(system.eigenvalues[0], 2) == 0.0
+    assert round(system.eigenvalues[1], 2) == 1.0
+    assert round(system.eigenvalues[2], 2) == 1.0
+    assert round(system.eigenvalues[3], 2) == 4.0
+    assert round(system.eigenvalues[4], 2) == 4.0
+    assert round(system.eigenvalues[5], 2) == 9.0
+    assert round(system.eigenvalues[6], 2) == 9.0
+    assert round(system.eigenvalues[7], 2) == 16.0
+    assert round(system.eigenvalues[8], 2) == 16.0
+
+
+def test_solve_potential():
+    system = qr.System()
+    system.gridsize = 500
+    system.potential_name = 'sin'
+    system.potential_constants = [0, 1, 3, 0]
+    system.solve_potential()
+    assert round(system.potential_max, 2) == 1.0
+

tests/test_system.py

@@ -0,0 +1,24 @@
+import qrotor as qr
+import numpy as np
+
+
+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
+    # Were eigenvalues calculated?
+    assert len(sys.eigenvalues) > 0
+

qrotor-4.1.1.dist-info/RECORD

@@ -1,14 +0,0 @@
-qrotor/__init__.py,sha256=rG2dH4QjsVUOMBhFnv5gXs3QnrUg7fywd5pIDmMBXcQ,246
-qrotor/_version.py,sha256=2MgvxBLj7nl20vruBp0VlxrcVaLnJcKclBipVBi68xM,198
-qrotor/constants.py,sha256=XjKlaHnquVtrpt0vtNS1UoXeI9EWf-wzz2QAByJp_Ck,3376
-qrotor/plot.py,sha256=th6eDoTB01KaVjfH2uiKMjU4VJMfdv0yK97PwCJydKI,13479
-qrotor/potential.py,sha256=9NyekNIMbjiRtJ8G6CtCMHX5v-g7kKC8un2x3blq-2w,18320
-qrotor/rotate.py,sha256=Wje9Q9SFhDvizz58MzNGBwsmgV-3wN9z2SnUNTIXzeg,8107
-qrotor/solve.py,sha256=YkOR1SJlpk41PCNEhslv6X3wV1TWMNztT78qX3Pngf0,10722
-qrotor/system.py,sha256=v6BFA9Pm1HbYdfm-XrPP7iWlbcvjxX7ynGBMOxDR7yc,11447
-qrotor/systems.py,sha256=Hcx0QvMWpaPMfC6HWpkZPPWDyHk9rxWKdAxWNnD2NMg,8184
-qrotor-4.1.1.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
-qrotor-4.1.1.dist-info/METADATA,sha256=k0oAqJRLC6Rr8au36Lj_cmJYiFJVYtqfbTkEn94KOXM,8719
-qrotor-4.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-qrotor-4.1.1.dist-info/top_level.txt,sha256=SFRMgcJiR1GiEtZ4aLo-x5TdfSCo7Igxezp2qyI0u5A,7
-qrotor-4.1.1.dist-info/RECORD,,