qrotor 4.0.2__py3-none-any.whl → 4.1.1__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__ = 'v4.0.2'
+__version__ = "v4.1.1"
 

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).
@@ -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/solve.py

@@ -100,7 +100,7 @@ def schrodinger(system:System) -> System:
     system.version = __version__
     system.runtime = time.time() - time_start
     system.eigenvalues = eigenvalues
-    system.energy_barrier = max(V) - min(eigenvalues)
+    system.E_activation = max(V) - min(eigenvalues)
     # Solve excitations and tunnel splittings, assuming triplet degeneracy
     system = excitations(system)
     # Do we really need to save eigenvectors?

qrotor/system.py

@@ -103,6 +103,8 @@ class System:
         """List of `eigenvalues` grouped by energy levels, found below `potential_max`."""
         self.deg: float = None
         """Estimated degeneracy of the `E_levels` found below `potential_max`."""
+        self.E_activation: float = None
+        """Activation energy or energy barrier, from the ground torsional state to the top of the potential barrier, `max(V) - min(eigenvalues)`"""
         self.excitations: list = []
         """Torsional excitations, as the difference between each energy level with respect to the ground state.
 
@@ -115,8 +117,6 @@ class System:
         the mean of the eigenvalues from A and the mean of the eigenvalues from E,
         see [R. M. Dimeo, American Journal of Physics 71, 885–893 (2003)](https://doi.org/10.1119/1.1538575).
         """
-        self.energy_barrier: float = None
-        """Activation energy or energy barrier, from the ground torsional state to the top of the potential barrier, `max(V) - min(eigenvalues)`"""
         self.runtime: float = None
         """Time taken to solve the eigenvalues."""
 
@@ -269,7 +269,7 @@ class System:
             'deg': self.deg,
             'excitations': self.excitations,
             'splittings': self.splittings,
-            'energy_barrier': self.energy_barrier,
+            'E_activation': self.E_activation,
             'runtime': self.runtime,
         }
 

{qrotor-4.0.2.dist-info → qrotor-4.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.0.2
+Version: 4.1.1
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

qrotor-4.1.1.dist-info/RECORD

@@ -0,0 +1,14 @@
+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,,

{qrotor-4.0.2.dist-info → qrotor-4.1.1.dist-info}/top_level.txt

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

qrotor-4.0.2.dist-info/RECORD

@@ -1,20 +0,0 @@
-qrotor/__init__.py,sha256=rG2dH4QjsVUOMBhFnv5gXs3QnrUg7fywd5pIDmMBXcQ,246
-qrotor/_version.py,sha256=WfMOkqINoRxtl94Yz6ro_Svh85CVtVc_kBhLMclRC4g,194
-qrotor/constants.py,sha256=l25-YHxWQPr5RFGl8e0Hpdkc0E4ER03Gj-P9Jmbqelc,3203
-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=tnkE5JYT8wW85gNbOEMgHTnzOZCb8q5xPcJbDI4uOB0,10724
-qrotor/system.py,sha256=onY3HfY2zpRLDJUjBJRX-nJu6YH_qhnPnCW6Uyam_Ws,11453
-qrotor/systems.py,sha256=Hcx0QvMWpaPMfC6HWpkZPPWDyHk9rxWKdAxWNnD2NMg,8184
-qrotor-4.0.2.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-4.0.2.dist-info/METADATA,sha256=T4uzj6bJ0bsRZ5pN5XO2i-i2SY1JoakroDGl1Za5zYU,8719
-qrotor-4.0.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-qrotor-4.0.2.dist-info/top_level.txt,sha256=mLnYs07-amqX4TqbDV2_XvgdpHfgrYmzmYb7dwoh6EQ,13
-qrotor-4.0.2.dist-info/RECORD,,

tests/test_constants.py

@@ -1,13 +0,0 @@
-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

@@ -1,37 +0,0 @@
-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

@@ -1,53 +0,0 @@
-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

@@ -1,28 +0,0 @@
-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

@@ -1,24 +0,0 @@
-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
-