qrotor 4.2.1__py3-none-any.whl → 4.3.0__py3-none-any.whl

qrotor/_version.py

@@ -11,5 +11,5 @@ https://semver.org/
 ---
 """
 
-__version__ = "v4.2.1"
+__version__ = "v4.3.0"
 

qrotor/constants.py

@@ -53,7 +53,7 @@ r_CH = distance_CH * np.sin(np.deg2rad(angle_CH)) * 1e-10
 r_NH = distance_NH * np.sin(np.deg2rad(angle_NH)) * 1e-10
 """Rotation radius of the amine group, in meters."""
 
-# Inertia, SI units
+# Inertias, SI units
 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_to_kg * r_CH**2)
@@ -63,6 +63,7 @@ I_NH3 = 3 * (periodictable.H.mass * amu_to_kg * r_NH**2)
 I_ND3 = 3 * (periodictable.D.mass * amu_to_kg * r_NH**2)
 """Inertia of ND3, in kg·m^2."""
 
+# Inertias of the co-rotation, SI units
 I_CH3NH3 = I_CH3 + I_NH3
 """Inertia of CH3NH3+, in kg·m^2."""
 I_CD3NH3 = I_CD3 + I_NH3
@@ -72,7 +73,17 @@ I_CH3ND3 = I_CH3 + I_ND3
 I_CD3ND3 = I_CD3 + I_ND3
 """Inertia of CD3ND3+, in kg·m^2."""
 
-# Inertia, atomic units
+# Inertias of the dis-rotation, SI units
+I_CH3NH3_dis = 1 / ((1/I_CH3) + (1/I_NH3))
+"""Inertia of the disrotatory torsion of CH3NH3+, in kg·m^2."""
+I_CD3NH3_dis = 1 / ((1/I_CD3) + (1/I_NH3))
+"""Inertia of the disrotatory torsion of CD3NH3+, in kg·m^2."""
+I_CH3ND3_dis = 1 / ((1/I_CH3) + (1/I_ND3))
+"""Inertia of the disrotatory torsion of CH3ND3+, in kg·m^2."""
+I_CD3ND3_dis = 1 / ((1/I_CD3) + (1/I_ND3))
+"""Inertia of the disrotatory torsion of CD3ND3+, in kg·m^2."""
+
+# Inertias, 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)
@@ -82,6 +93,7 @@ I_NH3_amu = I_NH3 / (amu_to_kg * 1e-20)
 I_ND3_amu = I_ND3 / (amu_to_kg * 1e-20)
 """Inertia of ND3, in amu·AA^2."""
 
+# Inertias of the co-rotation, amu units
 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
@@ -91,6 +103,16 @@ I_CH3ND3_amu = I_CH3_amu + I_ND3_amu
 I_CD3ND3_amu = I_CD3_amu + I_ND3_amu
 """Inertia of CD3ND3+, in amu·AA^2."""
 
+# Inertias of the dis-rotation, amu units
+I_CH3NH3_dis_amu = I_CH3NH3_dis / (amu_to_kg * 1e-20)
+"""Inertia of the disrotatory torsion of CH3NH3+, in amu·AA^2."""
+I_CD3NH3_dis_amu = I_CD3NH3_dis / (amu_to_kg * 1e-20)
+"""Inertia of the disrotatory torsion of CD3NH3+, in amu·AA^2."""
+I_CH3ND3_dis_amu = I_CH3ND3_dis / (amu_to_kg * 1e-20)
+"""Inertia of the disrotatory torsion of CH3ND3+, in amu·AA^2."""
+I_CD3ND3_dis_amu = I_CD3ND3_dis / (amu_to_kg * 1e-20)
+"""Inertia of the disrotatory torsion 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)
@@ -111,6 +133,15 @@ B_CH3ND3 = ((_hbar**2) / (2 * I_CH3ND3)) * (1000 / const.eV)
 B_CD3ND3 = ((_hbar**2) / (2 * I_CD3ND3)) * (1000 / const.eV)
 """Kinetic rotational energy of CD3ND3+, in meV·s/kg·m^2."""
 
+B_CH3NH3_dis = ((_hbar**2) / (2 * I_CH3NH3_dis)) * (1000 / const.eV)
+"""Kinetic rotational energy of the disrotatory torsion of CH3NH3+, in meV·s/kg·m^2."""
+B_CD3NH3_dis = ((_hbar**2) / (2 * I_CD3NH3_dis)) * (1000 / const.eV)
+"""Kinetic rotational energy of the disrotatory torsion of CD3NH3+, in meV·s/kg·m^2."""
+B_CH3ND3_dis = ((_hbar**2) / (2 * I_CH3ND3_dis)) * (1000 / const.eV)
+"""Kinetic rotational energy of the disrotatory torsion of CH3ND3+, in meV·s/kg·m^2."""
+B_CD3ND3_dis = ((_hbar**2) / (2 * I_CD3ND3_dis)) * (1000 / const.eV)
+"""Kinetic rotational energy of the disrotatory torsion of CD3ND3+, in meV·s/kg·m^2."""
+
 # Potential constants from titov2023 [C1, C2, C3, C4, C5]
 constants_titov2023 = [
     [2.7860, 0.0130,-1.5284,-0.0037,-1.2791],  # ZIF-8

qrotor/potential.py

@@ -49,7 +49,7 @@ from copy import deepcopy
 from scipy.interpolate import CubicSpline
 import aton.alias as alias
 import aton.file as file
-import aton.api.qe as qe
+import aton.api.pwx as pwx
 from ._version import __version__
 
 
@@ -196,8 +196,8 @@ def from_qe(
         energy:str='meV',
         comment:str=None,
         ) -> System:
-    """Compiles a rotational potential CSV file from Quantum ESPRESSO outputs,
-    created with `qrotor.rotate.structure_qe()`.
+    """Compiles a rotational potential CSV file from Quantum ESPRESSO pw.x outputs,
+    created with `qrotor.rotate.input_qe()`.
     Returns a `System` object with the new potential values.
 
     The angle in degrees is extracted from the output filenames,
@@ -227,7 +227,7 @@ def from_qe(
     # Set header
     potential_data = f'## {comment}\n' if comment else f'## {folder_name}\n'
     potential_data += '# Rotational potential dataset\n'
-    potential_data += f'# Calculated with QE using QRotor {__version__}\n'
+    potential_data += f'# Calculated with QE pw.x using QRotor {__version__}\n'
     potential_data += '# https://pablogila.github.io/qrotor\n'
     potential_data += '#\n'
     if energy.lower() in alias.units['eV']:
@@ -249,7 +249,7 @@ def from_qe(
         file_path = file.get(filepath=file_path, include='.out', return_anyway=True)
         if not file_path:  # Not an output file, skip it
             continue
-        content = qe.read_out(file_path)
+        content = pwx.read_out(file_path)
         if not content['Success']:  # Ignore unsuccessful calculations
             print(f'x   {filename}')
             counter_errors += 1

qrotor/rotate.py

@@ -9,7 +9,7 @@ Works with Quantum ESPRESSO input files.
 
 | | |
 | --- | --- |
-| `structure_qe()`  | Rotate specific atoms from a Quantum ESPRESSO input file |
+| `input_qe()`      | Rotate specific atoms from a Quantum ESPRESSO input file |
 | `rotate_coords()` | Rotate a specific list of coordinates |
 
 ---
@@ -26,7 +26,7 @@ import aton.txt.extract as extract
 import aton.txt.edit as edit
 
 
-def structure_qe(
+def input_qe(
         filepath:str,
         positions:list,
         angle:float,
@@ -66,13 +66,13 @@ def structure_qe(
     lines = []
     full_positions = []
     for position in positions:
-        line = api.qe.get_atom(filepath, position, precision)
+        line = api.pwx.get_atom(filepath, position, precision)
         lines.append(line)
         pos = extract.coords(line)
         if len(pos) > 3:  # Keep only the first three coordinates
             pos = pos[:3]
         # Convert to cartesian
-        pos_cartesian = api.qe.to_cartesian(filepath, pos)
+        pos_cartesian = api.pwx.to_cartesian(filepath, pos)
         full_positions.append(pos_cartesian)
         print(f'Found atom: "{line}"')
     # Set the angles to rotate
@@ -92,7 +92,7 @@ def structure_qe(
         rotated_positions_cartesian = rotate_coords(full_positions, angle, use_centroid, show_axis)
         rotated_positions = []
         for coord in rotated_positions_cartesian:
-            pos = api.qe.from_cartesian(filepath, coord)
+            pos = api.pwx.from_cartesian(filepath, coord)
             rotated_positions.append(pos)
         _save_qe(filepath, output, lines, rotated_positions)
         outputs.append(output)
@@ -184,7 +184,7 @@ def _save_qe(
         additional_positions = positions[-2:]
         for pos in additional_positions:
             pos.insert(0, 'He')
-            api.qe.add_atom(output, pos)
+            api.pwx.add_atom(output, pos)
     elif len(lines) != len(positions):
         raise ValueError(f"What?!  len(lines)={len(lines)} and len(positions)={len(positions)}")
     # Add angle to calculation prefix
@@ -192,11 +192,11 @@ def _save_qe(
     splits = output_name.split('_')
     angle_str = splits[-1].replace('.in', '')
     prefix = ''
-    content = api.qe.read_in(output)
+    content = api.pwx.read_in(output)
     if 'prefix' in content.keys():
         prefix = content['prefix']
         prefix = prefix.strip("'")
     prefix = "'" + prefix + angle_str + "'"
-    api.qe.set_value(output, 'prefix', prefix)
+    api.pwx.set_value(output, 'prefix', prefix)
     return output
 

{qrotor-4.2.1.dist-info → qrotor-4.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.2.1
+Version: 4.3.0
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus

qrotor-4.3.0.dist-info/RECORD

@@ -0,0 +1,14 @@
+qrotor/__init__.py,sha256=rG2dH4QjsVUOMBhFnv5gXs3QnrUg7fywd5pIDmMBXcQ,246
+qrotor/_version.py,sha256=yUq4NMbgza_UQXUxL5adzghdHM9U2mboRIIQkw4VrwE,198
+qrotor/constants.py,sha256=YRri136Zg5dqqDS-180sxOB5ytBJW74msUbHYbrfiMc,6655
+qrotor/plot.py,sha256=loyd-1sXvfD8_PyHCThE3VQpRC0qs1iONGY4LXjJyZ4,14086
+qrotor/potential.py,sha256=hKlDKA50Umwk0Tfzx4mUXHSWTcHQNqhHLA7T2XedtCY,18500
+qrotor/rotate.py,sha256=FppTiAwE3c7JtPyOGBF4YHxq9JzE-YilN_lpaOgPm9Q,8109
+qrotor/solve.py,sha256=YkOR1SJlpk41PCNEhslv6X3wV1TWMNztT78qX3Pngf0,10722
+qrotor/system.py,sha256=ahYurNUmVOV7B6aZSe7rhcruagj5rW9UClqG-H1vVvY,11454
+qrotor/systems.py,sha256=Hcx0QvMWpaPMfC6HWpkZPPWDyHk9rxWKdAxWNnD2NMg,8184
+qrotor-4.3.0.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
+qrotor-4.3.0.dist-info/METADATA,sha256=MJWzR5gyk2x4-VIWl2K7ReaJYb0uKMnRrh-iUvywBsE,9649
+qrotor-4.3.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+qrotor-4.3.0.dist-info/top_level.txt,sha256=SFRMgcJiR1GiEtZ4aLo-x5TdfSCo7Igxezp2qyI0u5A,7
+qrotor-4.3.0.dist-info/RECORD,,

{qrotor-4.2.1.dist-info → qrotor-4.3.0.dist-info}/top_level.txt

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

qrotor-4.2.1.dist-info/RECORD

@@ -1,20 +0,0 @@
-qrotor/__init__.py,sha256=rG2dH4QjsVUOMBhFnv5gXs3QnrUg7fywd5pIDmMBXcQ,246
-qrotor/_version.py,sha256=YSHr6C919Wy5fXxFzjIN6vSskUpecEZNWKepHCIAsy4,198
-qrotor/constants.py,sha256=tX_mM7WmP2wN4WYaL551jPcI-0Ca5SNOHATUxiUJQCQ,4934
-qrotor/plot.py,sha256=loyd-1sXvfD8_PyHCThE3VQpRC0qs1iONGY4LXjJyZ4,14086
-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-4.2.1.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-4.2.1.dist-info/METADATA,sha256=pkuA9iv1jSYiOUhxf9aYdRlKNHHyaLwJaiuWZACJyg0,9649
-qrotor-4.2.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-qrotor-4.2.1.dist-info/top_level.txt,sha256=mLnYs07-amqX4TqbDV2_XvgdpHfgrYmzmYb7dwoh6EQ,13
-qrotor-4.2.1.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
-