qrotor 4.4.1__py3-none-any.whl → 4.5.1__py3-none-any.whl

qrotor/__init__.py

@@ -7,7 +7,7 @@ from ._version import __version__ as version
 from .system import System
 from .constants import *
 from . import systems
-from . import rotate
+from . import rotation
 from . import potential
 from . import solve
 from . import plot

qrotor/_version.py

@@ -11,5 +11,5 @@ https://semver.org/
 ---
 """
 
-__version__ = "v4.4.1"
+__version__ = "v4.5.1"
 

qrotor/potential.py

@@ -200,7 +200,7 @@ def from_qe(
         comment:str=None,
         ) -> System:
     """Compiles a rotational potential CSV file from Quantum ESPRESSO pw.x outputs,
-    created with `qrotor.rotate.input_qe()`.
+    created with `qrotor.rotation.rotate_qe()`.
     Returns a `System` object with the new potential values.
 
     The angle in degrees is extracted from the output filenames,

qrotor/{rotate.py → rotation.py}

@@ -9,7 +9,7 @@ Works with Quantum ESPRESSO input files.
 
 | | |
 | --- | --- |
-| `input_qe()`      | Rotate specific atoms from a Quantum ESPRESSO input file |
+| `rotate_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 input_qe(
+def rotate_qe(
         filepath:str,
         positions:list,
         angle:float,
@@ -35,7 +35,7 @@ def input_qe(
         use_centroid:bool=True,
         show_axis:bool=False,
     ) -> list:
-    """Rotates atoms from a Quantum ESPRESSO input file.
+    """Rotates atoms from a Quantum ESPRESSO pw.x input file.
 
     Takes a `filepath` with a molecular structure, and three or more atomic `positions` (list).
     These input positions can be approximate, and are used to identify the target atoms.

qrotor/system.py

@@ -212,10 +212,10 @@ class System:
         return {
             'version': self.version,
             'comment': self.comment,
+            'tags': self.tags,
             'searched_E': self.searched_E,
             'correct_potential_offset': self.correct_potential_offset,
             'save_eigenvectors': self.save_eigenvectors,
-            'tags': self.tags,
             'B': self.B,
             'gridsize': self.gridsize,
             'potential_name': self.potential_name,

qrotor/systems.py

@@ -288,6 +288,7 @@ def summary(
     """
     print('--------------------')
     systems = as_list(systems)
+    
     for system in systems:
         dictionary = system.summary()
         if verbose:
@@ -299,10 +300,16 @@ def summary(
             if len(system.eigenvalues) > 6:
                 eigenvalues = eigenvalues[:6]
                 extra = '...'
-            print('comment     ' + str(system.comment))
-            print('B           ' + str(system.B))
-            print('eigenvalues ' + str([float(round(e, 4)) for e in eigenvalues]) + extra)
-            print('version     ' + str(system.version))
+            print('comment         ' + str(system.comment))
+            print('ZPE             ' + str(system.eigenvalues[0]))
+            print('E activation    ' + str(system.E_activation))
+            print('V max           ' + str(system.potential_max))
+            print('1st splitting   ' + str(system.splittings[0]))
+            print('1st excitation  ' + str(system.excitations[0]))
+            print('B               ' + str(system.B))
+            print('eigenvalues     ' + str([float(round(e, 4)) for e in eigenvalues]) + extra)
+            print('tags            ' + str(system.tags))
+            print('version         ' + str(system.version))
         print('--------------------')
     return None
 

{qrotor-4.4.1.dist-info → qrotor-4.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.4.1
+Version: 4.5.1
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus
@@ -106,7 +106,7 @@ QRotor contains the following modules:
 | [qrotor.constants](https://pablogila.github.io/qrotor/qrotor/constants.html) | Common bond lengths and inertias |
 | [qrotor.system](https://pablogila.github.io/qrotor/qrotor/system.html)       | Definition of the quantum `System` object |
 | [qrotor.systems](https://pablogila.github.io/qrotor/qrotor/systems.html)     | Utilities to manage several System objects, such as a list of systems |
-| [qrotor.rotate](https://pablogila.github.io/qrotor/qrotor/rotate.html)       | Rotate specific atoms from structural files |
+| [qrotor.rotation](https://pablogila.github.io/qrotor/qrotor/rotation.html)   | Rotate specific atoms from structural files |
 | [qrotor.potential](https://pablogila.github.io/qrotor/qrotor/potential.html) | Potential definitions and loading functions |
 | [qrotor.solve](https://pablogila.github.io/qrotor/qrotor/solve.html)         | Solve rotation eigenvalues and eigenvectors |
 | [qrotor.plot](https://pablogila.github.io/qrotor/qrotor/plot.html)           | Plotting utilities |
@@ -179,7 +179,7 @@ atoms = [
     '3.103   3.206   3.309'
 ]
 # Create the input SCF files, saving the filenames to a list
-scf_files = qr.rotate.structure_qe('molecule.in', positions=atoms, angle=10, repeat=True)
+scf_files = qr.rotation.rotate_qe('molecule.in', positions=atoms, angle=10, repeat=True)
 # Run the Quantum ESPRESSO calculations
 api.slurm.sbatch(files=scf_files)
 ```

qrotor-4.5.1.dist-info/RECORD

@@ -0,0 +1,21 @@
+qrotor/__init__.py,sha256=FgB2-SglHK-hAzjctoVqzJSBA1rLBQH2nv0o3LWuh5A,248
+qrotor/_version.py,sha256=wkrb4M-n9WOwWsoukOo63VpjZSaomNKHz1UD8XiFrTM,198
+qrotor/constants.py,sha256=YRri136Zg5dqqDS-180sxOB5ytBJW74msUbHYbrfiMc,6655
+qrotor/plot.py,sha256=iJWHohW8hvKGRUjoqLYyQXweqrahF0XOIyyhDJ05_bI,14171
+qrotor/potential.py,sha256=n6izUMbl2okMSg7xj_IV6rDr2B-RCWiqtSBcsTltL1M,18564
+qrotor/rotation.py,sha256=4pXcIcb6fY44haRB6HWGLqC0la1V91Tr3NW4DrUNTkw,8115
+qrotor/solve.py,sha256=YkOR1SJlpk41PCNEhslv6X3wV1TWMNztT78qX3Pngf0,10722
+qrotor/system.py,sha256=i2EP3egJFwLFL6570abHzR3Hhl0KiAu6vp2jmohlbPE,9946
+qrotor/systems.py,sha256=dk-4PqQI8G5CgZamP5zaNv3_hNPgBE2qjT4bJnlE9aM,12798
+qrotor-4.5.1.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_rotation.py,sha256=qW6HQHdPNteN6qZ5blVoTSQINU8m9wn8hTcOszrdulE,1898
+tests/test_solve.py,sha256=tEjLUZC7oe6LCQD5b2xf2aaK9lu-zI4lzuPXOGR2GAs,861
+tests/test_system.py,sha256=36d-8AdoJdzq0O9_O3s8wwBPGa-M7A86YiHqhhAsCZ8,742
+tests/test_systems.py,sha256=wKaBDaF2QIvJAux5tsuFecp8oGx4LGNhWVJaCxNlb4g,1440
+qrotor-4.5.1.dist-info/METADATA,sha256=yMS6pryPOv0uUBrhghJWPMTw4ISb48YoxZUdDx2bJFc,9648
+qrotor-4.5.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+qrotor-4.5.1.dist-info/top_level.txt,sha256=mLnYs07-amqX4TqbDV2_XvgdpHfgrYmzmYb7dwoh6EQ,13
+qrotor-4.5.1.dist-info/RECORD,,

tests/{test_rotate.py → test_rotation.py}

@@ -10,14 +10,14 @@ structure_120 = folder + 'CH3NH3_120.in'
 structure_60 = folder + 'CH3NH3_60.in'
 
 
-def test_rotate():
+def test_rotation():
     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.input_qe(filepath=structure, positions=CH3, angle=120, precision=2)
+    qr.rotation.rotate_qe(filepath=structure, positions=CH3, angle=120, precision=2)
     for coord in CH3:
         rotated_coord = api.pwx.get_atom(filepath=structure_120, position=coord, precision=2)
         rotated_coord = extract.coords(rotated_coord)
@@ -37,7 +37,7 @@ def test_rotate():
         '0.095062781582172   0.488975944606740   0.115053787468686',
         '0.128156574395412   0.205890189020629   0.680672454316303',
     ]
-    qr.rotate.input_qe(filepath=structure, positions=CH3, angle=60, precision=2)
+    qr.rotation.rotate_qe(filepath=structure, positions=CH3, angle=60, precision=2)
     for coord in ideal:
         rotated_coord = api.pwx.get_atom(filepath=structure_60, position=coord, precision=3)
         rotated_coord = extract.coords(rotated_coord)

qrotor-4.4.1.dist-info/RECORD

@@ -1,21 +0,0 @@
-qrotor/__init__.py,sha256=rG2dH4QjsVUOMBhFnv5gXs3QnrUg7fywd5pIDmMBXcQ,246
-qrotor/_version.py,sha256=-0UGWvfKUxLJlpnjNakdqSmawlKdSDhL09z5yQDtirE,198
-qrotor/constants.py,sha256=YRri136Zg5dqqDS-180sxOB5ytBJW74msUbHYbrfiMc,6655
-qrotor/plot.py,sha256=iJWHohW8hvKGRUjoqLYyQXweqrahF0XOIyyhDJ05_bI,14171
-qrotor/potential.py,sha256=MsmUoac3wRhlIprY8ipThy0HNYaO8iRnfF51VsUJ5HU,18561
-qrotor/rotate.py,sha256=FppTiAwE3c7JtPyOGBF4YHxq9JzE-YilN_lpaOgPm9Q,8109
-qrotor/solve.py,sha256=YkOR1SJlpk41PCNEhslv6X3wV1TWMNztT78qX3Pngf0,10722
-qrotor/system.py,sha256=NQ7fcSo2R1QY1D0k9ymjJT9i9BSvuAOE7zqt5NJxFCQ,9946
-qrotor/systems.py,sha256=KbeaomvMcmQluJW2VMzQounu4qB42_jX2CU0ablDNCI,12389
-qrotor-4.4.1.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=pbwLeET6mCw7x8nFFvwn5ZvONRzNsexjSB_SZq7cJ1s,1890
-tests/test_solve.py,sha256=tEjLUZC7oe6LCQD5b2xf2aaK9lu-zI4lzuPXOGR2GAs,861
-tests/test_system.py,sha256=36d-8AdoJdzq0O9_O3s8wwBPGa-M7A86YiHqhhAsCZ8,742
-tests/test_systems.py,sha256=wKaBDaF2QIvJAux5tsuFecp8oGx4LGNhWVJaCxNlb4g,1440
-qrotor-4.4.1.dist-info/METADATA,sha256=Nncza56dmFQXPwO-BjhSuj3uwE0wabhaxcdkt4SQp0I,9649
-qrotor-4.4.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-qrotor-4.4.1.dist-info/top_level.txt,sha256=mLnYs07-amqX4TqbDV2_XvgdpHfgrYmzmYb7dwoh6EQ,13
-qrotor-4.4.1.dist-info/RECORD,,