qrotor 4.0.0a2__tar.gz → 4.0.1__tar.gz

{qrotor-4.0.0a2 → qrotor-4.0.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.0.0a2
+Version: 4.0.1
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus
@@ -21,6 +21,7 @@ Requires-Dist: pandas
 Requires-Dist: numpy
 Requires-Dist: matplotlib
 Requires-Dist: aton
+Requires-Dist: periodictable
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -33,7 +34,7 @@ Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
 
-<p align="center"><img width="40.0%" src="pics/qrotor.png"></p>
+<p align="center"><img width="60.0%" src="pics/qrotor.png"></p>
  
 QRotor is a Python package used to study molecular rotations,
 such as those of methyl and amine groups.
@@ -44,10 +45,43 @@ These quantum systems are represented by the `qrotor.System()` object.
 QRotor can obtain custom potentials from DFT,
 which are used to solve the quantum system.
 
-Check the [full documentation online](https://pablogila.github.io/qrotor/).
 
+---
+
+
+# Installation
+
+As always, it is recommended to install your packages in a virtual environment:  
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+```
+
+
+## With pip
+
+Install or upgrade ATON with  
+```bash
+pip install qrotor -U
+```
+
+
+## From source
+
+Optionally, you can install ATON from the [GitHub repo](https://github.com/pablogila/qrotor/).
+Clone the repository or download the [latest stable release](https://github.com/pablogila/qrotor/tags)
+as a ZIP, unzip it, and run inside it:  
+```bash
+pip install .
+```
 
-# Index
+
+---
+
+
+# Documentation
+
+QRotor contains the following modules:
 
 | | |
 | --- | --- |
@@ -59,6 +93,11 @@ Check the [full documentation online](https://pablogila.github.io/qrotor/).
 | [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 |
 
+Check the [full documentation online](https://pablogila.github.io/qrotor/).
+
+
+---
+
 
 # Usage
 
@@ -165,3 +204,71 @@ See [R. M. Dimeo, American Journal of Physics 71, 885–893 (2003)](https://doi.
 and [A. J. Horsewill, Progress in Nuclear Magnetic Resonance Spectroscopy 35, 359–389 (1999)](https://doi.org/10.1016/S0079-6565(99)00016-3)
 for further reference.
 
+
+---
+
+
+# Contributing
+
+If you are interested in opening an issue or a pull request, please feel free to do so on [GitHub](https://github.com/pablogila/qrotor/).  
+For major changes, please get in touch first to discuss the details.  
+
+
+## Code style
+
+Please try to follow some general guidelines:  
+- Use a code style consistent with the rest of the project.  
+- Include docstrings to document new additions.  
+- Include automated tests for new features or modifications, see [automated testing](#automated-testing).  
+- Arrange function arguments by order of relevance.  
+
+
+## Automated testing
+
+If you are modifying the source code, you should run the automated tests of the [`tests/`](https://github.com/pablogila/qrotor/tree/main/tests) folder to check that everything works as intended.
+To do so, first install PyTest in your environment,
+```bash
+pip install pytest
+```
+
+And then run PyTest inside the main directory,
+```bash
+pytest -vv
+```
+
+
+## Compiling the documentation
+
+The documentation can be compiled automatically to `docs/qrotor.html` with [Pdoc](https://pdoc.dev/) and [ATON](https://pablogila.github.io/aton), by running:
+```shell
+python3 makedocs.py
+```
+
+This runs Pdoc, updating links and pictures, and using the custom theme CSS template from the `css/` folder.
+
+
+---
+
+
+# Citation
+
+QRotor is currently under development.
+Please cite it if you use it in your research,
+> Pablo Gila-Herranz, *QRotor*, https://pablogila.github.io/qrotor  
+
+
+---
+
+
+# License
+
+Copyright (C) 2025 Pablo Gila-Herranz  
+This program is free software: you can redistribute it and/or modify
+it under the terms of the **GNU Affero General Public License** as published
+by the Free Software Foundation, either version **3** of the License, or
+(at your option) any later version.  
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
+See the attached GNU Affero General Public License for more details.  
+

{qrotor-4.0.0a2 → qrotor-4.0.1}/README.md

@@ -1,4 +1,4 @@
-<p align="center"><img width="40.0%" src="pics/qrotor.png"></p>
+<p align="center"><img width="60.0%" src="pics/qrotor.png"></p>
  
 QRotor is a Python package used to study molecular rotations,
 such as those of methyl and amine groups.
@@ -9,10 +9,43 @@ These quantum systems are represented by the `qrotor.System()` object.
 QRotor can obtain custom potentials from DFT,
 which are used to solve the quantum system.
 
-Check the [full documentation online](https://pablogila.github.io/qrotor/).
 
+---
+
+
+# Installation
+
+As always, it is recommended to install your packages in a virtual environment:  
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+```
+
+
+## With pip
+
+Install or upgrade ATON with  
+```bash
+pip install qrotor -U
+```
+
+
+## From source
+
+Optionally, you can install ATON from the [GitHub repo](https://github.com/pablogila/qrotor/).
+Clone the repository or download the [latest stable release](https://github.com/pablogila/qrotor/tags)
+as a ZIP, unzip it, and run inside it:  
+```bash
+pip install .
+```
 
-# Index
+
+---
+
+
+# Documentation
+
+QRotor contains the following modules:
 
 | | |
 | --- | --- |
@@ -24,6 +57,11 @@ Check the [full documentation online](https://pablogila.github.io/qrotor/).
 | [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 |
 
+Check the [full documentation online](https://pablogila.github.io/qrotor/).
+
+
+---
+
 
 # Usage
 
@@ -130,3 +168,71 @@ See [R. M. Dimeo, American Journal of Physics 71, 885–893 (2003)](https://doi.
 and [A. J. Horsewill, Progress in Nuclear Magnetic Resonance Spectroscopy 35, 359–389 (1999)](https://doi.org/10.1016/S0079-6565(99)00016-3)
 for further reference.
 
+
+---
+
+
+# Contributing
+
+If you are interested in opening an issue or a pull request, please feel free to do so on [GitHub](https://github.com/pablogila/qrotor/).  
+For major changes, please get in touch first to discuss the details.  
+
+
+## Code style
+
+Please try to follow some general guidelines:  
+- Use a code style consistent with the rest of the project.  
+- Include docstrings to document new additions.  
+- Include automated tests for new features or modifications, see [automated testing](#automated-testing).  
+- Arrange function arguments by order of relevance.  
+
+
+## Automated testing
+
+If you are modifying the source code, you should run the automated tests of the [`tests/`](https://github.com/pablogila/qrotor/tree/main/tests) folder to check that everything works as intended.
+To do so, first install PyTest in your environment,
+```bash
+pip install pytest
+```
+
+And then run PyTest inside the main directory,
+```bash
+pytest -vv
+```
+
+
+## Compiling the documentation
+
+The documentation can be compiled automatically to `docs/qrotor.html` with [Pdoc](https://pdoc.dev/) and [ATON](https://pablogila.github.io/aton), by running:
+```shell
+python3 makedocs.py
+```
+
+This runs Pdoc, updating links and pictures, and using the custom theme CSS template from the `css/` folder.
+
+
+---
+
+
+# Citation
+
+QRotor is currently under development.
+Please cite it if you use it in your research,
+> Pablo Gila-Herranz, *QRotor*, https://pablogila.github.io/qrotor  
+
+
+---
+
+
+# License
+
+Copyright (C) 2025 Pablo Gila-Herranz  
+This program is free software: you can redistribute it and/or modify
+it under the terms of the **GNU Affero General Public License** as published
+by the Free Software Foundation, either version **3** of the License, or
+(at your option) any later version.  
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
+See the attached GNU Affero General Public License for more details.  
+

{qrotor-4.0.0a2 → qrotor-4.0.1}/qrotor/_version.py

@@ -10,5 +10,5 @@ https://semver.org/
 
 """
 
-__version__ = 'v4.0.0a2'
+__version__ = 'v4.0.1'
 

{qrotor-4.0.0a2 → qrotor-4.0.1}/qrotor/constants.py

@@ -11,7 +11,8 @@ Bond lengths and angles were obtained from MAPbI3, see
 
 
 import numpy as np
-import aton.phys as phys
+import periodictable
+import scipy.constants as const
 
 
 # Distance between Carbon and Hydrogen atoms (measured from MAPbI3)
@@ -31,29 +32,31 @@ angle_NH = 180 - angle_NH_external
 """Internal angle of the X-N-H bond, in degrees."""
 
 # Rotation radius (calculated from distance and angle)
-r_CH = distance_CH * np.sin(np.deg2rad(angle_CH)) * phys.AA_to_m
+r_CH = distance_CH * np.sin(np.deg2rad(angle_CH)) * 1e-10
 """Rotation radius of the methyl group, in meters."""
-r_NH = distance_NH * np.sin(np.deg2rad(angle_NH)) * phys.AA_to_m
+r_NH = distance_NH * np.sin(np.deg2rad(angle_NH)) * 1e-10
 """Rotation radius of the amine group, in meters."""
 
 # Inertia, SI units
-I_CH3 = 3 * (phys.atoms['H'].mass * phys.amu_to_kg * r_CH**2)
+_amu = const.physical_constants['atomic mass constant'][0]
+I_CH3 = 3 * (periodictable.H.mass * _amu * r_CH**2)
 """Inertia of CH3, in kg·m^2."""
-I_CD3 = 3 * (phys.atoms['H'].isotope[2].mass * phys.amu_to_kg * r_CH**2)
+I_CD3 = 3 * (periodictable.D.mass * _amu * r_CH**2)
 """Inertia of CD3, in kg·m^2."""
-I_NH3 = 3 * (phys.atoms['H'].mass * phys.amu_to_kg * r_NH**2)
+I_NH3 = 3 * (periodictable.H.mass * _amu * r_NH**2)
 """Inertia of NH3, in kg·m^2."""
-I_ND3 = 3 * (phys.atoms['H'].isotope[2].mass * phys.amu_to_kg * r_NH**2)
+I_ND3 = 3 * (periodictable.D.mass * _amu * r_NH**2)
 """Inertia of ND3, in kg·m^2."""
 
-# Rotational energy.
-B_CH3 = ((phys.hbar**2) / (2 * I_CH3)) * phys.J_to_meV
+# Rotational energy
+_hbar = const.physical_constants['reduced Planck constant'][0]
+B_CH3 = ((_hbar**2) / (2 * I_CH3)) * (1000 / const.eV)
 """Rotational energy of CH3, in meV·s/kg·m^2."""
-B_CD3 = ((phys.hbar**2) / (2 * I_CD3)) * phys.J_to_meV
+B_CD3 = ((_hbar**2) / (2 * I_CD3)) * (1000 / const.eV)
 """Rotational energy of CD3, in meV·s/kg·m^2."""
-B_NH3 = ((phys.hbar**2) / (2 * I_NH3)) * phys.J_to_meV
+B_NH3 = ((_hbar**2) / (2 * I_NH3)) * (1000 / const.eV)
 """Rotational energy of NH3, in meV·s/kg·m^2."""
-B_ND3 = ((phys.hbar**2) / (2 * I_ND3)) * phys.J_to_meV
+B_ND3 = ((_hbar**2) / (2 * I_ND3)) * (1000 / const.eV)
 """Rotational energy of ND3, in meV·s/kg·m^2."""
 
 # Potential constants from titov2023 [C1, C2, C3, C4, C5]
@@ -70,3 +73,13 @@ for the `qrotor.potential.titov2023` potential.
 In meV units.
 """
 
+# Quick conversion factors
+Ry_to_eV = const.physical_constants['Rydberg constant times hc in eV'][0]
+"""Quick conversion factor from eV to Rydberg energy."""
+Ry_to_meV = Ry_to_eV * 1000
+"""Quick conversion factor from meV to Rydberg energy."""
+eV_to_Ry = 1 / Ry_to_eV
+"""Quick conversion factor from Rydberg to eV."""
+meV_to_Ry = 1 / Ry_to_meV
+"""Quick conversion factor from Rydberg to meV."""
+

{qrotor-4.0.0a2 → qrotor-4.0.1}/qrotor/plot.py

@@ -21,11 +21,11 @@ This module provides straightforward functions to plot QRotor data.
 
 from .system import System
 from . import systems
+from . import constants
 import matplotlib.pyplot as plt
 import numpy as np
 from copy import deepcopy
 import aton.alias as alias
-import aton.phys as phys
 
 
 def potential(
@@ -284,10 +284,10 @@ def splittings(
     x = [c.comment for c in calcs]
     # What units do we want?
     if units.lower() in alias.units['ueV']:
-        y = [j * phys.meV_to_ueV for j in y]
+        y = [j * 1000 for j in y]  # Convert meV to micro eV
         ax.set_ylabel("Energy / $\\mu$eV")
     elif units.lower() in alias.units['Ry']:
-        y = [j * phys.meV_to_Ry for j in y]
+        y = [j * constants.meV_to_Ry for j in y]
         ax.set_ylabel("Energy / Ry")
     #else:  # It's okay let's use meV
 

{qrotor-4.0.0a2 → qrotor-4.0.1}/qrotor/potential.py

@@ -50,7 +50,6 @@ from scipy.interpolate import CubicSpline
 import aton.alias as alias
 import aton.file as file
 import aton.api.qe as qe
-import aton.phys as phys
 from ._version import __version__
 
 
@@ -100,10 +99,10 @@ def save(
     if energy.lower() in alias.units['meV']:
         potential_data += 'Potential/meV\n'
     elif energy.lower() in alias.units['eV']:
-        potential_values = potential_values * phys.meV_to_eV
+        potential_values = potential_values * 1e-3
         potential_data += 'Potential/eV\n'
     elif energy.lower() in alias.units['Ry']:
-        potential_values = potential_values * phys.meV_to_Ry
+        potential_values = potential_values * constants.meV_to_Ry
         potential_data += 'Potential/Ry\n'
     else:
         print(f"WARNING:  Unrecognised '{energy}' energy units, using meV instead")
@@ -161,11 +160,11 @@ def load(
         raise ValueError(f"Angle unit '{angle}' not recognized.")
     # Save energies to numpy arrays
     if energy.lower() in alias.units['eV']:
-        potentials = np.array(potentials) * phys.eV_to_meV
+        potentials = np.array(potentials) * 1000
     elif energy.lower() in alias.units['meV']:
         potentials = np.array(potentials)
     elif energy.lower() in alias.units['Ry']:
-        potentials = np.array(potentials) * phys.Ry_to_meV
+        potentials = np.array(potentials) * constants.Ry_to_meV
     else:
         raise ValueError(f"Energy unit '{energy}' not recognized.")
     # Set the system
@@ -244,15 +243,15 @@ def from_qe(
             counter_errors += 1
             continue
         if energy.lower() in alias.units['eV']:
-            energy_value = content['Energy'] * phys.Ry_to_eV
+            energy_value = content['Energy'] * constants.Ry_to_eV
         elif energy.lower() in alias.units['meV']:
-            energy_value = content['Energy'] * phys.Ry_to_meV
+            energy_value = content['Energy'] * constants.Ry_to_meV
         elif energy.lower() in alias.units['Ry']:
             energy_value = content['Energy']
         else:
             print(f"WARNING: Energy unit '{energy}' not recognized, using meV instead.")
             energy = 'meV'
-            energy_value = content['Energy'] * phys.Ry_to_meV
+            energy_value = content['Energy'] * constants.Ry_to_meV
         splits = filename.split('_')
         angle_value = splits[-1].replace('.out', '')
         angle_value = float(angle_value)

{qrotor-4.0.0a2 → qrotor-4.0.1}/qrotor.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.0.0a2
+Version: 4.0.1
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus
@@ -21,6 +21,7 @@ Requires-Dist: pandas
 Requires-Dist: numpy
 Requires-Dist: matplotlib
 Requires-Dist: aton
+Requires-Dist: periodictable
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier
@@ -33,7 +34,7 @@ Dynamic: requires-dist
 Dynamic: requires-python
 Dynamic: summary
 
-<p align="center"><img width="40.0%" src="pics/qrotor.png"></p>
+<p align="center"><img width="60.0%" src="pics/qrotor.png"></p>
  
 QRotor is a Python package used to study molecular rotations,
 such as those of methyl and amine groups.
@@ -44,10 +45,43 @@ These quantum systems are represented by the `qrotor.System()` object.
 QRotor can obtain custom potentials from DFT,
 which are used to solve the quantum system.
 
-Check the [full documentation online](https://pablogila.github.io/qrotor/).
 
+---
+
+
+# Installation
+
+As always, it is recommended to install your packages in a virtual environment:  
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+```
+
+
+## With pip
+
+Install or upgrade ATON with  
+```bash
+pip install qrotor -U
+```
+
+
+## From source
+
+Optionally, you can install ATON from the [GitHub repo](https://github.com/pablogila/qrotor/).
+Clone the repository or download the [latest stable release](https://github.com/pablogila/qrotor/tags)
+as a ZIP, unzip it, and run inside it:  
+```bash
+pip install .
+```
 
-# Index
+
+---
+
+
+# Documentation
+
+QRotor contains the following modules:
 
 | | |
 | --- | --- |
@@ -59,6 +93,11 @@ Check the [full documentation online](https://pablogila.github.io/qrotor/).
 | [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 |
 
+Check the [full documentation online](https://pablogila.github.io/qrotor/).
+
+
+---
+
 
 # Usage
 
@@ -165,3 +204,71 @@ See [R. M. Dimeo, American Journal of Physics 71, 885–893 (2003)](https://doi.
 and [A. J. Horsewill, Progress in Nuclear Magnetic Resonance Spectroscopy 35, 359–389 (1999)](https://doi.org/10.1016/S0079-6565(99)00016-3)
 for further reference.
 
+
+---
+
+
+# Contributing
+
+If you are interested in opening an issue or a pull request, please feel free to do so on [GitHub](https://github.com/pablogila/qrotor/).  
+For major changes, please get in touch first to discuss the details.  
+
+
+## Code style
+
+Please try to follow some general guidelines:  
+- Use a code style consistent with the rest of the project.  
+- Include docstrings to document new additions.  
+- Include automated tests for new features or modifications, see [automated testing](#automated-testing).  
+- Arrange function arguments by order of relevance.  
+
+
+## Automated testing
+
+If you are modifying the source code, you should run the automated tests of the [`tests/`](https://github.com/pablogila/qrotor/tree/main/tests) folder to check that everything works as intended.
+To do so, first install PyTest in your environment,
+```bash
+pip install pytest
+```
+
+And then run PyTest inside the main directory,
+```bash
+pytest -vv
+```
+
+
+## Compiling the documentation
+
+The documentation can be compiled automatically to `docs/qrotor.html` with [Pdoc](https://pdoc.dev/) and [ATON](https://pablogila.github.io/aton), by running:
+```shell
+python3 makedocs.py
+```
+
+This runs Pdoc, updating links and pictures, and using the custom theme CSS template from the `css/` folder.
+
+
+---
+
+
+# Citation
+
+QRotor is currently under development.
+Please cite it if you use it in your research,
+> Pablo Gila-Herranz, *QRotor*, https://pablogila.github.io/qrotor  
+
+
+---
+
+
+# License
+
+Copyright (C) 2025 Pablo Gila-Herranz  
+This program is free software: you can redistribute it and/or modify
+it under the terms of the **GNU Affero General Public License** as published
+by the Free Software Foundation, either version **3** of the License, or
+(at your option) any later version.  
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  
+See the attached GNU Affero General Public License for more details.  
+

{qrotor-4.0.0a2 → qrotor-4.0.1}/qrotor.egg-info/requires.txt

@@ -3,3 +3,4 @@ pandas
 numpy
 matplotlib
 aton
+periodictable

{qrotor-4.0.0a2 → qrotor-4.0.1}/setup.py

@@ -1,7 +1,6 @@
 from setuptools import setup, find_packages
 
 DESCRIPTION = "QRotor"
-LONG_DESCRIPTION = "QRotor"
 
 exec(open('qrotor/_version.py').read())
 
@@ -17,7 +16,7 @@ setup(
     long_description = LONG_DESCRIPTION,
     long_description_content_type = 'text/markdown',
     packages = find_packages(),
-    install_requires = ['scipy', 'pandas', 'numpy', 'matplotlib', 'aton'],
+    install_requires = ['scipy', 'pandas', 'numpy', 'matplotlib', 'aton', 'periodictable'],
     extras_requires = {'dev': ['pytest', 'twine', 'build']},
     python_requires = '>=3',
     license = 'AGPL-3.0',

{qrotor-4.0.0a2 → qrotor-4.0.1}/tests/test_qrotor.py

@@ -1,4 +1,4 @@
-import aton.qrotor as qr
+import qrotor as qr
 import aton.api as api
 import aton.txt.extract as extract
 import aton.file as file