qrotor 4.0.1__py3-none-any.whl → 4.0.2__py3-none-any.whl

qrotor/_version.py

@@ -10,5 +10,5 @@ https://semver.org/
 
 """
 
-__version__ = 'v4.0.1'
+__version__ = 'v4.0.2'
 

qrotor/plot.py

@@ -271,7 +271,7 @@ def splittings(
     The different `System.comment` are shown in the horizontal axis.
     An optional `title` can be specified.
     Default units shown are $\\mu$eV (`'ueV'`).
-    Available units are: `'ueV'`, `'meV'`, `'Ry'`.
+    Available units are: `'ueV'`, `'meV'`, `'Ry'`, or `'B'` (free rotor units).
     """
     title = title if title != None else 'Tunnel splitting energies'
     calcs = deepcopy(data)
@@ -289,6 +289,9 @@ def splittings(
     elif units.lower() in alias.units['Ry']:
         y = [j * constants.meV_to_Ry for j in y]
         ax.set_ylabel("Energy / Ry")
+    elif units.upper() == 'B':
+        y = [j / c.B for j, c in zip(y, calcs)]
+        ax.set_ylabel("Energy / B")
     #else:  # It's okay let's use meV
 
     ax.bar(range(len(y)), y)

qrotor/potential.py

@@ -66,6 +66,7 @@ def save(
     in degrees and meVs by default.
     The units can be changed with `angle` and `energy`,
     but only change these defaults if you know what you are doing.
+    An optional `comment` can be included in the header of the file.
     """
     print('Saving potential data file...')
     # Check if a previous potential.dat file exists, and ask to overwrite it
@@ -77,7 +78,7 @@ def save(
             print("Aborted.")
             return None
     # Set header
-    potential_data = f'# {comment}\n' if comment else f'# {system.comment}\n' if system.comment else ''
+    potential_data = f'## {comment}\n' if comment else f'## {system.comment}\n' if system.comment else ''
     potential_data += '# Rotational potential dataset\n'
     potential_data += f'# Saved with QRotor {__version__}\n'
     potential_data += '# https://pablogila.github.io/qrotor\n'
@@ -143,6 +144,11 @@ def load(
     system = System() if system is None else system
     with open(file_path, 'r') as f:
         lines = f.readlines()
+    # Read the comment
+    loaded_comment = ''
+    if lines[0].startswith('## '):
+        loaded_comment = lines[0][3:].strip()
+    # Read data
     positions = []
     potentials = []
     for line in lines:
@@ -171,8 +177,13 @@ def load(
     system.grid = np.array(positions)
     system.gridsize = len(positions)
     system.potential_values = np.array(potentials)
-    # System comment as the parent folder name
-    system.comment = os.path.basename(os.path.dirname(file_path)) if comment==None else comment
+    # System comment as the loaded comment or the parent folder name
+    if comment:
+        system.comment = comment
+    elif loaded_comment:
+        system.comment = loaded_comment
+    else:
+        system.comment = os.path.basename(os.path.dirname(file_path))
     print(f"Loaded {filepath}")
     return system
 
@@ -184,9 +195,10 @@ def from_qe(
         exclude:list=['slurm-'],
         energy:str='meV',
         comment:str=None,
-        ) -> None:
+        ) -> System:
     """Compiles a rotational potential CSV file from Quantum ESPRESSO outputs,
     created with `qrotor.rotate.structure_qe()`.
+    Returns a `System` object with the new potential values.
 
     The angle in degrees is extracted from the output filenames,
     which must follow `whatever_ANGLE.out`.
@@ -213,7 +225,7 @@ def from_qe(
     files = file.get_list(folder=folder, include=include, exclude=exclude, abspath=True)
     folder_name = os.path.basename(folder)
     # Set header
-    potential_data = f'# {comment}\n' if comment else f'# {folder_name}\n'
+    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 += '# https://pablogila.github.io/qrotor\n'
@@ -273,7 +285,12 @@ def from_qe(
     # Warn the user if not in default units
     if energy.lower() not in alias.units['meV']:
         print(f"WARNING: You saved the potential in '{energy}' units! Remember that QRotor works in meVs!")
-    return None
+    new_system = None
+    try:
+        new_system = load(filepath=filepath, comment=comment, energy=energy)
+    except:
+        pass
+    return new_system
 
 
 def merge(

{qrotor-4.0.1.dist-info → qrotor-4.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.0.1
+Version: 4.0.2
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus
@@ -85,13 +85,13 @@ 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)     | Functions to manage several System objects, such as a list of systems |
+| [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.constants](https://pablogila.github.io/qrotor/qrotor/constants.html) | Common bond lengths and inertias |
 | [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 functions |
+| [qrotor.plot](https://pablogila.github.io/qrotor/qrotor/plot.html)           | Plotting utilities |
 
 Check the [full documentation online](https://pablogila.github.io/qrotor/).
 
@@ -103,7 +103,8 @@ Check the [full documentation online](https://pablogila.github.io/qrotor/).
 
 ## Solving quantum rotational systems
 
-A basic calculation of the eigenvalues for a zero potential goes as follows.
+Let's start with a basic calculation of the eigenvalues for a zero potential, corresponding to a free rotor. 
+A predefined synthetic potential can be used, see all available options in the [qrotor.potential](https://pablogila.github.io/qrotor/qrotor/potential.html) documentation.
 Note that the default energy unit is meV unless stated otherwise.
 
 ```python
@@ -113,7 +114,7 @@ system.gridsize = 200000  # Size of the potential grid
 system.B = 1  # Rotational inertia
 system.potential_name = 'zero'
 system.solve()
-system.eigenvalues
+print(system.eigenvalues)
 # [0.0, 1.0, 1.0, 4.0, 4.0, 9.0, 9.0, ...]  # approx values
 ```
 
@@ -126,10 +127,10 @@ in a cosine potential of amplitude 30 meV:
 ```python
 import qrotor as qr
 system = qr.System()
-system.gridsize = 200000  # Size of the potential grid
+system.gridsize = 200000
 system.B = qr.B_CH3  # Rotational inertia of a methyl group
 system.potential_name = 'cosine'
-system.potential_constants = [0, 30, 3, 0]  # Offset, max, freq, phase (for cos pot.)
+system.potential_constants = [0, 30, 3, 0]  # Offset, max, freq, phase (for cosine potential)
 system.solve()
 # Plot potential and eigenvalues
 qr.plot.energies(system)
@@ -141,7 +142,7 @@ qr.plot.wavefunction(system, levels=[0,1,2], square=True)
 ## Custom potentials from DFT
 
 QRotor can be used to obtain custom rotational potentials from DFT calculations.
-Using Quantum ESPRESSO, running an SCF calculation for a methyl rotation every 10 degrees:
+To run a Quantum ESPRESSO SCF calculation for a methyl rotation every 10 degrees:
 
 ```python
 import qrotor as qr
@@ -160,10 +161,8 @@ api.slurm.sbatch(files=scf_files)
 
 To load the calculated potential to a QRotor System,
 ```python
-# Compile a 'potential.csv' file with the calculated potential as a function of the angle
-qr.potential.from_qe()
-# Load to the system
-system = qr.potential.load()
+# Compile a 'potential.csv' file with the calculated potential as a function of the angle, and load it into a new system
+system = qr.potential.from_qe()
 # Solve the system, interpolating to a bigger gridsize
 system.B = qr.B_CH3
 system.solve(200000)
@@ -178,9 +177,9 @@ below the potential maximum are also calculated upon solving the system:
 
 ```python
 system.solve()
-system.splittings
-system.excitations
-system.deg
+print(system.splittings)
+print(system.excitations)
+print(system.deg)
 ```
 
 An integer `System.deg` degeneracy (e.g. 3 for methyls)

qrotor-4.0.2.dist-info/RECORD

@@ -0,0 +1,20 @@
+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

@@ -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_qrotor.py → test_rotate.py}

@@ -2,7 +2,6 @@ import qrotor as qr
 import aton.api as api
 import aton.txt.extract as extract
 import aton.file as file
-import numpy as np
 
 
 folder = 'tests/samples/'
@@ -52,50 +51,3 @@ def test_rotate():
         assert coord_rounded == rotated_coord_rounded
     file.remove(structure_60)
 
-
-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
-
-
-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_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
+

qrotor-4.0.1.dist-info/RECORD

@@ -1,16 +0,0 @@
-qrotor/__init__.py,sha256=rG2dH4QjsVUOMBhFnv5gXs3QnrUg7fywd5pIDmMBXcQ,246
-qrotor/_version.py,sha256=MdOgAkUR9D2frTc3Jx8g9MXBZxTyDiIlBtprpKhAfes,194
-qrotor/constants.py,sha256=l25-YHxWQPr5RFGl8e0Hpdkc0E4ER03Gj-P9Jmbqelc,3203
-qrotor/plot.py,sha256=SeQX8PM5qPdedmo0DzfGFbA8m_sH2mcK50aTuWXN8HA,13335
-qrotor/potential.py,sha256=4sONrwnJkKy2zyquX6AFpNVLXrRMX9XUJUnuS6eZ9bc,17781
-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-4.0.1.dist-info/licenses/LICENSE,sha256=hIahDEOTzuHCU5J2nd07LWwkLW7Hko4UFO__ffsvB-8,34523
-tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-tests/test_qrotor.py,sha256=KL5i1YVFOB5cFc7BXCtbrbBKKMCHyGM-B20m4unz1q0,3457
-qrotor-4.0.1.dist-info/METADATA,sha256=Z92ghlFydfpFiI1XOZ15pfRwQt69_hf9KFP9fHMuDCA,8528
-qrotor-4.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-qrotor-4.0.1.dist-info/top_level.txt,sha256=mLnYs07-amqX4TqbDV2_XvgdpHfgrYmzmYb7dwoh6EQ,13
-qrotor-4.0.1.dist-info/RECORD,,