qrotor 4.4.0__py3-none-any.whl → 4.5.0__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__ = "v4.4.0"
+__version__ = "v4.5.0"
 

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/systems.py

@@ -324,11 +324,13 @@ def filter_tags(
         systems:list,
         include:str='',
         exclude:str='',
+        strict:bool=False,
         ) -> list:
     """Returns a filtered list of systems with or without specific tags.
-    
-    Tags are separated by blank spaces.
-    Include tags from `include`, exclude tags from `exclude`.
+
+    You can `include` or `exclude` any number of tags, separated by blank spaces.
+    By default, the filters are triggered if any tag is found, i.e. *tag1 OR tag2*.
+    Set `strict=True` to require all tags to match, i.e. *tag1 AND tag2*.
     """
     systems = as_list(systems)
     included_tags = include.split()
@@ -336,12 +338,16 @@ def filter_tags(
     filtered_systems = []
     for i in systems:
         tags_found = list_tags(i)
-        if excluded_tags and any(tag in excluded_tags for tag in tags_found):
-            continue
+        if excluded_tags:
+            if strict and all(tag in tags_found for tag in excluded_tags):
+                continue
+            elif not strict and any(tag in tags_found for tag in excluded_tags):
+                continue
         if included_tags:
-            if any(tag in included_tags for tag in tags_found):
-                filtered_systems.append(i)
-        else:
-            filtered_systems.append(i)
+            if strict and not all(tag in tags_found for tag in included_tags):
+                continue
+            elif not strict and not any(tag in tags_found for tag in included_tags):
+                continue
+        filtered_systems.append(i)
     return filtered_systems
 

{qrotor-4.4.0.dist-info → qrotor-4.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.4.0
+Version: 4.5.0
 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-4.5.0.dist-info/RECORD

@@ -0,0 +1,21 @@
+qrotor/__init__.py,sha256=FgB2-SglHK-hAzjctoVqzJSBA1rLBQH2nv0o3LWuh5A,248
+qrotor/_version.py,sha256=TtdvqIyM9prSdLh_gm1u2NzWAHa0f2sK482XiKtEmyo,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=NQ7fcSo2R1QY1D0k9ymjJT9i9BSvuAOE7zqt5NJxFCQ,9946
+qrotor/systems.py,sha256=KbeaomvMcmQluJW2VMzQounu4qB42_jX2CU0ablDNCI,12389
+qrotor-4.5.0.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-4.5.0.dist-info/METADATA,sha256=z96837SiDPa-FoSfs3rGVYQMvT3f_Hp3h_oqpFmzgRA,9648
+qrotor-4.5.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+qrotor-4.5.0.dist-info/top_level.txt,sha256=mLnYs07-amqX4TqbDV2_XvgdpHfgrYmzmYb7dwoh6EQ,13
+qrotor-4.5.0.dist-info/RECORD,,

{qrotor-4.4.0.dist-info → qrotor-4.5.0.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_rotation.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_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.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)
+        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.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)
+        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
+

tests/test_systems.py

@@ -0,0 +1,30 @@
+import qrotor as qr
+
+
+def test_tags():
+    sys1 = qr.System(tags='tag1 tag2 tag3', comment='sys1', potential_name='zero')
+    sys2 = qr.System(tags='tag2 tag3 tag4', comment='sys2')
+    sys3 = qr.System(tags='tag4 tag5 tag6', comment='sys3')
+    sys1.solve(100)
+    test1 = qr.systems.filter_tags(sys1, include='tag4')
+    assert test1 == []
+    test2 = qr.systems.filter_tags([sys1, sys2], include='tag4 tag5', strict=False)
+    assert len(test2) == 1
+    assert test2[0].comment == 'sys2'
+    test3 = qr.systems.filter_tags([sys1, sys2], include='tag4 tag5', strict=True)
+    assert test3 == []
+    test4 = qr.systems.filter_tags([sys1, sys2, sys3], include='tag3 tag4', strict=False)
+    assert len(test4) == 3
+    test5 = qr.systems.filter_tags([sys1, sys2, sys3], include='tag3 tag4', strict=True)
+    assert len(test5) == 1
+    assert test5[0].comment == 'sys2'
+    test6 = qr.systems.filter_tags([sys1, sys2, sys3], include='tag3 tag4', exclude='tag6', strict=False)
+    assert len(test6) == 2
+    test7 = qr.systems.filter_tags([sys1, sys2, sys3], include='tag4', exclude='tag5 tag6', strict=True)
+    assert len(test7) == 1
+    assert test7[0].comment == 'sys2'
+    test8 = qr.systems.filter_tags([sys1, sys2, sys3], include='', exclude='tag1 tag2', strict=True)
+    assert len(test8) == 2
+    test9 = qr.systems.filter_tags([sys1, sys2, sys3], include='', exclude='tag1 tag2', strict=False)
+    assert test9[0].comment == 'sys3'
+

qrotor-4.4.0.dist-info/RECORD

@@ -1,14 +0,0 @@
-qrotor/__init__.py,sha256=rG2dH4QjsVUOMBhFnv5gXs3QnrUg7fywd5pIDmMBXcQ,246
-qrotor/_version.py,sha256=ROJNaCCcVwCHHX73Jf2tvmDGOerQZHlj_2VO-tE-DCw,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=h2e5cP0GKaXbnbbna5dyCbRYHWloSrQXVs_wrV69Mto,12006
-qrotor-4.4.0.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
-qrotor-4.4.0.dist-info/METADATA,sha256=ZJwODdQbVnxqiLEPZ3Iid_guIiWcw500ou-67Sn7oh8,9649
-qrotor-4.4.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-qrotor-4.4.0.dist-info/top_level.txt,sha256=SFRMgcJiR1GiEtZ4aLo-x5TdfSCo7Igxezp2qyI0u5A,7
-qrotor-4.4.0.dist-info/RECORD,,