aton 0.3.0__tar.gz → 0.3.2__tar.gz

{aton-0.3.0 → aton-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aton
-Version: 0.3.0
+Version: 0.3.2
 Summary: The Ab-iniTiO & Neutron research toolbox, or ATON, provides powerful and comprehensive tools for cutting-edge materials research, focused on (but not limited to) neutron science.
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus
@@ -16,9 +16,9 @@ Classifier: Operating System :: Other OS
 Requires-Python: >=3
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
+Requires-Dist: scipy>=1.15.2
 Requires-Dist: pandas
-Requires-Dist: scipy
+Requires-Dist: numpy
 Requires-Dist: matplotlib
 Dynamic: author
 Dynamic: author-email

{aton-0.3.0 → aton-0.3.2}/aton/_version.py

@@ -10,5 +10,5 @@ https://semver.org/
 
 """
 
-__version__ = 'v0.3.0'
+__version__ = 'v0.3.2'
 

{aton-0.3.0 → aton-0.3.2}/aton/phys/__init__.py

@@ -38,22 +38,23 @@ See the API reference of the specific modules for more information.
 Constant values come from the [2022 CODATA](https://doi.org/10.48550/arXiv.2409.03787) Recommended Values of the Fundamental Physical Constants.
 
 Conversion factors for neutron scattering come from
-[M. Bée, "Quasielastic Neutron scattering", Adam Hilger, Bristol and Philadelphia, 1988](https://www.ncnr.nist.gov/instruments/dcs/dcs_usersguide/Conversion_Factors.pdf).
+[David L. Price and Felix Fernandez-Alonso, *Neutron Scattering Fundamentals*, Experimental methods in the physical sciences, Elsevier Academic Press (2013)](https://doi.org/10.1016/B978-0-12-398374-9.00001-2),
+and from
+[M. Bée, "Quasielastic Neutron scattering", Adam Hilger, Bristol and Philadelphia (1988)](https://www.ncnr.nist.gov/instruments/dcs/dcs_usersguide/Conversion_Factors.pdf);
 
 
 ## `aton.phys.atoms`
 
 Atomic `mass` are in atomic mass units (amu), and come from:
-Pure Appl. Chem., Vol. 78, No. 11, pp. 2051-2066, 2006.
+[M. E. Wieser, *Atomic weights of the elements 2005*, Pure and Applied Chemistry 78, 2051–2066 (2006)](https://doi.org/10.1351/pac200678112051).
 The following masses are obtained from Wikipedia:
 Ac: 227, Np: 237, Pm: 145, Tc: 98.
 
-Isotope `mass`, `mass_number` and `abundance` come from:
-J. R. de Laeter, J. K. Böhlke, P. De Bièvre, H. Hidaka, H. S. Peiser, K. J. R. Rosman
-and P. D. P. Taylor (2003). *"Atomic weights of the elements. Review 2000 (IUPAC Technical Report)"*.
+Isotope `mass`, `mass_number` and `abundance` come from
+[J. R. de Laeter *et al*., *Atomic weights of the elements 2000*, Pure and Applied Chemistry 75, 683–800 (2003)](https://doi.org/10.1351/pac200375060683).
 
-Total bound scattering `cross_sections` $\\sigma_s$ are in barns (1 b = 100 fm$^2$).
-From Felix Fernandez-Alonso, *"Neutron Scattering Fundamentals"*, 2013.
+Total bound scattering `cross_sections` $\\sigma_s$ are in barns (1 b = 100 fm$^2$ = 10e-28 m$^2$). From
+[David L. Price and Felix Fernandez-Alonso, *Neutron Scattering Fundamentals*, Experimental methods in the physical sciences, Elsevier Academic Press (2013)](https://doi.org/10.1016/B978-0-12-398374-9.00001-2).
 
 """
 

{aton-0.3.0 → aton-0.3.2}/aton/phys/units.py

@@ -5,8 +5,10 @@ This module contains the constants from the
 [2022 CODATA](https://doi.org/10.48550/arXiv.2409.03787)
 Recommended Values of the Fundamental Physical Constants.
 
-It also contains useful conversion factors for neutron scattering,
-from [M. Bée, "Quasielastic Neutron scattering", Adam Hilger, Bristol and Philadelphia, 1988](https://www.ncnr.nist.gov/instruments/dcs/dcs_usersguide/Conversion_Factors.pdf).
+It also contains useful conversion factors for neutron scattering, from
+[David L. Price and Felix Fernandez-Alonso, *Neutron Scattering Fundamentals*, Experimental methods in the physical sciences, Elsevier Academic Press (2013)](https://doi.org/10.1016/B978-0-12-398374-9.00001-2),
+and from
+[M. Bée, "Quasielastic Neutron scattering", Adam Hilger, Bristol and Philadelphia (1988)](https://www.ncnr.nist.gov/instruments/dcs/dcs_usersguide/Conversion_Factors.pdf);
 
 
 # Index

{aton-0.3.0 → aton-0.3.2}/aton/qrotor/__init__.py

@@ -97,9 +97,8 @@ qr.plot.energies(system)
 
 ## Tunnel splittings and excitations
 
-When the quantum System is solved, tunnel splittings,
-excitations and energy level degeneracy
-below the potential maximum are also calculated:
+Tunnel splittings, excitations and energy level degeneracy
+below the potential maximum are also calculated upon solving the system:
 
 ```python
 system.solve()
@@ -108,6 +107,11 @@ system.excitations
 system.deg
 ```
 
+An integer `System.deg` degeneracy (e.g. 3 for methyls)
+indicates that the energy levels have been properly estimated.
+However, if the degeneracy is a float instead,
+please check the splittings and excitations manually from the system eigenvalues.
+
 To export the energies and the tunnel splittings of several calculations to a CSV file:
 
 ```python

{aton-0.3.0 → aton-0.3.2}/aton/qrotor/constants.py

@@ -3,8 +3,8 @@
 
 Common constants and default inertia values used in the QRotor subpackage.
 
-Bond lengths and angles were obtained from MAPbI3,
-see [*Cryst. Growth Des.* 2024, 24, 391−404](https://doi.org/10.1021/acs.cgd.3c01112).
+Bond lengths and angles were obtained from MAPbI3, see
+[K. Drużbicki *et al*., Crystal Growth & Design 24, 391–404 (2024)](https://doi.org/10.1021/acs.cgd.3c01112).
 
 ---
 """

{aton-0.3.0 → aton-0.3.2}/aton/qrotor/potential.py

@@ -44,7 +44,8 @@ from aton._version import __version__
 
 def save(
         system:System,
-        filepath:str='potential.dat',
+        comment:str='',
+        filepath:str='potential.csv',
         angle:str='deg',
         energy:str='meV',
         ) -> None:
@@ -65,7 +66,7 @@ def save(
             print("Aborted.")
             return None
     # Set header
-    potential_data = 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 ATON {__version__}\n'
     potential_data += '# https://pablogila.github.io/ATON\n'
@@ -77,10 +78,10 @@ def save(
     potential_values = system.potential_values
     # Convert angle units
     if angle.lower() in alias.units['rad']:
-        potential_data += '# Angle/rad    '
+        potential_data += '# Angle/rad,    '
     else:
         grid = np.degrees(grid)
-        potential_data += '# Angle/deg    '
+        potential_data += '# Angle/deg,    '
         if not angle.lower() in alias.units['deg']:
             print(f"WARNING: Unrecognised '{angle}' angle units, using degrees instead")
     # Convert energy units
@@ -110,7 +111,7 @@ def save(
 
 
 def load(
-        filepath:str='potential.dat',
+        filepath:str='potential.csv',
         comment:str=None,
         system:System=None,
         angle:str='deg',
@@ -136,7 +137,7 @@ def load(
         if line.startswith('#'):
             continue
         position, potential = line.split()
-        positions.append(float(position.strip()))
+        positions.append(float(position.strip().strip(',').strip()))
         potentials.append(float(potential.strip()))
     # Save angles to numpy arrays
     if angle.lower() in alias.units['deg']:
@@ -166,7 +167,7 @@ def load(
 
 def from_qe(
         folder=None,
-        filepath:str='potential.dat',
+        filepath:str='potential.csv',
         include:list=['.out'],
         exclude:list=['slurm-'],
         energy:str='meV',

{aton-0.3.0 → aton-0.3.2}/aton/qrotor/solve.py

@@ -114,8 +114,9 @@ def hamiltonian_matrix(system:System):
 def laplacian_matrix(grid):
     """Calculates the Laplacian (second derivative) matrix for a given `grid`."""
     x = grid
-    diagonals = [-2*np.ones(len(x)), np.ones(len(x)), np.ones(len(x))]
-    laplacian_matrix = sparse.spdiags(diagonals, [0, -1, 1], format='lil')
+    n = len(x)
+    diagonals = [-2*np.ones(n), np.ones(n), np.ones(n)]
+    laplacian_matrix = sparse.spdiags(diagonals, [0, -1, 1], m=n, n=n, format='lil')
     # Periodic boundary conditions
     laplacian_matrix[0, -1] = 1
     laplacian_matrix[-1, 0] = 1

{aton-0.3.0 → aton-0.3.2}/aton/qrotor/systems.py

@@ -92,9 +92,9 @@ def save_energies(
 def save_splittings(
     systems:list,
     comment:str='',
-    filepath:str='tunnel_splittings.csv',
+    filepath:str='splittings.csv',
     ) -> pd.DataFrame:
-    """Save the tunnel splitting energies for all `systems` to a tunnel_splittings.csv file.
+    """Save the tunnel splitting energies for all `systems` to a splittings.csv file.
 
     Returns a Pandas Dataset with `System.comment` columns and `System.splittings` values.
 

{aton-0.3.0 → aton-0.3.2}/aton/spx/deuterium.py

@@ -32,7 +32,7 @@ def impulse_approx(
     ) -> tuple:
     """Calculate the deuteration levels from INS spectra
     with the *Impulse Approximation*, see
-    https://www.tandfonline.com/doi/full/10.1080/00018732.2017.1317963.
+    [Andreani et al., Advances in Physics 66, 1–73 (2017)](https://www.tandfonline.com/doi/full/10.1080/00018732.2017.1317963).
 
     Protonated and deuterated materials must be specified
     as `aton.spectra.classes.Material` objects.

{aton-0.3.0 → aton-0.3.2}/aton.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aton
-Version: 0.3.0
+Version: 0.3.2
 Summary: The Ab-iniTiO & Neutron research toolbox, or ATON, provides powerful and comprehensive tools for cutting-edge materials research, focused on (but not limited to) neutron science.
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus
@@ -16,9 +16,9 @@ Classifier: Operating System :: Other OS
 Requires-Python: >=3
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: numpy
+Requires-Dist: scipy>=1.15.2
 Requires-Dist: pandas
-Requires-Dist: scipy
+Requires-Dist: numpy
 Requires-Dist: matplotlib
 Dynamic: author
 Dynamic: author-email

{aton-0.3.0 → aton-0.3.2}/aton.egg-info/requires.txt

@@ -1,4 +1,4 @@
-numpy
+scipy>=1.15.2
 pandas
-scipy
+numpy
 matplotlib

{aton-0.3.0 → aton-0.3.2}/setup.py

@@ -16,7 +16,7 @@ setup(
     long_description = LONG_DESCRIPTION,
     long_description_content_type = 'text/markdown',
     packages = find_packages(),
-    install_requires = ['numpy', 'pandas', 'scipy', 'matplotlib'],
+    install_requires = ['scipy>=1.15.2', 'pandas', 'numpy', 'matplotlib'],
     extras_requires = {
         'dev': ['pytest', 'twine', 'build']
     },