qrotor 4.2.1__tar.gz → 4.3.0__tar.gz

{qrotor-4.2.1 → qrotor-4.3.0}/PKG-INFO

@@ -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-4.2.1 → qrotor-4.3.0}/qrotor/_version.py

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

{qrotor-4.2.1 → qrotor-4.3.0}/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-4.2.1 → qrotor-4.3.0}/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-4.2.1 → qrotor-4.3.0}/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 → qrotor-4.3.0}/qrotor.egg-info/PKG-INFO

@@ -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-4.2.1 → qrotor-4.3.0}/qrotor.egg-info/SOURCES.txt

@@ -15,7 +15,6 @@ 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-4.2.1 → qrotor-4.3.0}/qrotor.egg-info/top_level.txt

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

{qrotor-4.2.1 → qrotor-4.3.0}/tests/test_rotate.py

@@ -17,9 +17,9 @@ def test_rotate():
         '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)
+    qr.rotate.input_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 = api.pwx.get_atom(filepath=structure_120, position=coord, precision=2)
         rotated_coord = extract.coords(rotated_coord)
         coord = extract.coords(coord)
         rotated_coord_rounded = []
@@ -37,9 +37,9 @@ def test_rotate():
         '0.095062781582172   0.488975944606740   0.115053787468686',
         '0.128156574395412   0.205890189020629   0.680672454316303',
     ]
-    qr.rotate.structure_qe(filepath=structure, positions=CH3, angle=60, precision=2)
+    qr.rotate.input_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 = api.pwx.get_atom(filepath=structure_60, position=coord, precision=3)
         rotated_coord = extract.coords(rotated_coord)
         coord = extract.coords(coord)
         rotated_coord_rounded = []