qrotor 4.1.2__py3-none-any.whl → 4.2.1__py3-none-any.whl

qrotor/_version.py

@@ -11,5 +11,5 @@ https://semver.org/
 ---
 """
 
-__version__ = "v4.1.2"
+__version__ = "v4.2.1"
 

qrotor/constants.py

@@ -5,8 +5,6 @@ Common constants and default inertia values used in QRotor.
 
 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).
-
----
 """
 
 
@@ -15,6 +13,24 @@ import periodictable
 import scipy.constants as const
 
 
+# Quick conversion factors
+Ry_to_eV = const.physical_constants['Rydberg constant times hc in eV'][0]
+"""Quick conversion factor from Rydberg to eV energy."""
+Ry_to_meV = Ry_to_eV * 1000
+"""Quick conversion factor from Rydberg to meV energy."""
+eV_to_Ry = 1 / Ry_to_eV
+"""Quick conversion factor from eV to Rydberg."""
+meV_to_Ry = 1 / Ry_to_meV
+"""Quick conversion factor from meV to Rydberg."""
+cm1_to_meV = (const.h * const.c * 100 / const.e) * 1000
+"""Quick conversion factor from cm$^{-1}$ to meV."""
+meV_to_cm1 = 1/cm1_to_meV
+"""Quick conversion factor from meV to cm$^{-1}$."""
+amu_to_kg = const.physical_constants['atomic mass constant'][0]
+"""Quick conversion factor from amu to kg."""
+kg_to_amu = 1 / amu_to_kg
+"""Quick conversion factor from kg to amu."""
+
 # Distance between Carbon and Hydrogen atoms (measured from MAPbI3)
 distance_CH = 1.09285   # Angstroms
 """Distance of the C-H bond, in Angstroms."""
@@ -38,16 +54,43 @@ r_NH = distance_NH * np.sin(np.deg2rad(angle_NH)) * 1e-10
 """Rotation radius of the amine group, in meters."""
 
 # Inertia, SI units
-_amu = const.physical_constants['atomic mass constant'][0]
-I_CH3 = 3 * (periodictable.H.mass * _amu * r_CH**2)
+I_CH3 = 3 * (periodictable.H.mass * amu_to_kg * r_CH**2)
 """Inertia of CH3, in kg·m^2."""
-I_CD3 = 3 * (periodictable.D.mass * _amu * r_CH**2)
+I_CD3 = 3 * (periodictable.D.mass * amu_to_kg * r_CH**2)
 """Inertia of CD3, in kg·m^2."""
-I_NH3 = 3 * (periodictable.H.mass * _amu * r_NH**2)
+I_NH3 = 3 * (periodictable.H.mass * amu_to_kg * r_NH**2)
 """Inertia of NH3, in kg·m^2."""
-I_ND3 = 3 * (periodictable.D.mass * _amu * r_NH**2)
+I_ND3 = 3 * (periodictable.D.mass * amu_to_kg * r_NH**2)
 """Inertia of ND3, in kg·m^2."""
 
+I_CH3NH3 = I_CH3 + I_NH3
+"""Inertia of CH3NH3+, in kg·m^2."""
+I_CD3NH3 = I_CD3 + I_NH3
+"""Inertia of CD3NH3+, in kg·m^2."""
+I_CH3ND3 = I_CH3 + I_ND3
+"""Inertia of CH3ND3+, in kg·m^2."""
+I_CD3ND3 = I_CD3 + I_ND3
+"""Inertia of CD3ND3+, in kg·m^2."""
+
+# Inertia, atomic units
+I_CH3_amu = I_CH3 / (amu_to_kg * 1e-20)
+"""Inertia of CH3, in amu·AA^2."""
+I_CD3_amu = I_CD3 / (amu_to_kg * 1e-20)
+"""Inertia of CD3, in amu·AA^2."""
+I_NH3_amu = I_NH3 / (amu_to_kg * 1e-20)
+"""Inertia of NH3, in amu·AA^2."""
+I_ND3_amu = I_ND3 / (amu_to_kg * 1e-20)
+"""Inertia of ND3, in amu·AA^2."""
+
+I_CH3NH3_amu = I_CH3_amu + I_NH3_amu
+"""Inertia of CH3NH3+, in amu·AA^2."""
+I_CD3NH3_amu = I_CD3_amu + I_NH3_amu
+"""Inertia of CD3NH3+, in amu·AA^2."""
+I_CH3ND3_amu = I_CH3_amu + I_ND3_amu
+"""Inertia of CH3ND3+, in amu·AA^2."""
+I_CD3ND3_amu = I_CD3_amu + I_ND3_amu
+"""Inertia of CD3ND3+, in amu·AA^2."""
+
 # Rotational energy
 _hbar = const.physical_constants['reduced Planck constant'][0]
 B_CH3 = ((_hbar**2) / (2 * I_CH3)) * (1000 / const.eV)
@@ -59,6 +102,15 @@ B_NH3 = ((_hbar**2) / (2 * I_NH3)) * (1000 / const.eV)
 B_ND3 = ((_hbar**2) / (2 * I_ND3)) * (1000 / const.eV)
 """Kinetic rotational energy of ND3, in meV·s/kg·m^2."""
 
+B_CH3NH3 = ((_hbar**2) / (2 * I_CH3NH3)) * (1000 / const.eV)
+"""Kinetic rotational energy of CH3NH3+, in meV·s/kg·m^2."""
+B_CD3NH3 = ((_hbar**2) / (2 * I_CD3NH3)) * (1000 / const.eV)
+"""Kinetic rotational energy of CD3NH3+, in meV·s/kg·m^2."""
+B_CH3ND3 = ((_hbar**2) / (2 * I_CH3ND3)) * (1000 / const.eV)
+"""Kinetic rotational energy of CH3ND3+, in meV·s/kg·m^2."""
+B_CD3ND3 = ((_hbar**2) / (2 * I_CD3ND3)) * (1000 / const.eV)
+"""Kinetic rotational energy of CD3ND3+, in meV·s/kg·m^2."""
+
 # Potential constants from titov2023 [C1, C2, C3, C4, C5]
 constants_titov2023 = [
     [2.7860, 0.0130,-1.5284,-0.0037,-1.2791],  # ZIF-8
@@ -73,17 +125,3 @@ 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 Rydberg to eV energy."""
-Ry_to_meV = Ry_to_eV * 1000
-"""Quick conversion factor from Rydberg to meV energy."""
-eV_to_Ry = 1 / Ry_to_eV
-"""Quick conversion factor from eV to Rydberg."""
-meV_to_Ry = 1 / Ry_to_meV
-"""Quick conversion factor from meV to Rydberg."""
-cm1_to_meV = (const.h * const.c * 100 / const.e) * 1000
-"""Quick conversion factor from cm$^{-1}$ to meV."""
-meV_to_cm1 = 1/cm1_to_meV
-"""Quick conversion factor from meV to cm$^{-1}$."""
-

qrotor/plot.py

@@ -13,7 +13,7 @@ This module provides straightforward functions to plot QRotor data.
 | `reduced_energies()` | Reduced energies E/B as a function of the reduced potential V/B |
 | `wavefunction()`     | Selected wavefunctions or squared wavefunctions of a system |
 | `splittings()`       | Tunnel splitting energies of a list of systems |
-| `convergence()`      | Energy convergence |
+| `convergence()`      | Energy convergence of a list of systems calculated with different parameters |
 
 ---
 """

{qrotor-4.1.2.dist-info → qrotor-4.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: qrotor
-Version: 4.1.2
+Version: 4.2.1
 Summary: QRotor
 Author: Pablo Gila-Herranz
 Author-email: pgila001@ikasle.ehu.eus
@@ -36,14 +36,28 @@ Dynamic: summary
 
 <p align="center"><img width="60.0%" src="pics/qrotor.png"></p>
  
-QRotor is a Python package used to study molecular rotations,
+
+QRotor is a Python package used to study molecular rotations
+based on the one-dimensional hindered-rotor model,
 such as those of methyl and amine groups.
 It can calculate their quantum energy levels and wavefunctions,
 along with excitations and tunnel splittings.
-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.
+QRotor systematically produces Quantum ESPRESSO SCF calculations to obtain
+the rotational Potential Energy Surface (PES) of custom molecular structures.
+This potential is used to solve the quantum hamiltonian of the hindered rotor model:
+
+$$
+H = -B \frac{d^2}{d\varphi^2} + V(\varphi)
+$$
+
+where $B$ is the *kinetic rotational energy* constant,
+
+$$
+B = \frac{\hbar^2}{2I}=\frac{\hbar^2}{2\sum_{i}m_{i}r_{i}^{2}}
+$$
+
+Head to the [Usage](#usage) section for a quick hands-on introduction.
 
 
 ---
@@ -51,6 +65,7 @@ which are used to solve the quantum system.
 
 # Installation
 
+
 As always, it is recommended to install your packages in a virtual environment:  
 ```bash
 python3 -m venv .venv
@@ -60,6 +75,7 @@ source .venv/bin/activate
 
 ## With pip
 
+
 Install or upgrade ATON with  
 ```bash
 pip install qrotor -U
@@ -68,6 +84,7 @@ 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:  
@@ -81,6 +98,7 @@ pip install .
 
 # Documentation
 
+
 QRotor contains the following modules:
 
 | | |
@@ -101,17 +119,18 @@ Check the [full documentation online](https://pablogila.github.io/qrotor/).
 
 # Usage
 
-## Solving quantum rotational systems
+
+## Solving quantum eigenvalues for one-dimensional rotor systems
+
 
 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
 import qrotor as qr
 system = qr.System()
 system.gridsize = 200000  # Size of the potential grid
-system.B = 1  # Rotational inertia
+system.B = 1              # Rotational inertia
 system.potential_name = 'zero'
 system.solve()
 print(system.eigenvalues)
@@ -121,8 +140,10 @@ print(system.eigenvalues)
 The accuracy of the calculation increases with bigger gridsizes,
 but note that the runtime increases exponentially.
 
-The same calculation can be performed for a methyl group,
-in a cosine potential of amplitude 30 meV:
+Predefined synthetic potentials can be used,
+see all available options in the [qrotor.potential](https://pablogila.github.io/qrotor/qrotor/potential.html) documentation.
+For example, we can solve the system for a hindered methyl group,
+in a [cosine potential](https://pablogila.github.io/qrotor/qrotor/potential.html#cosine) of amplitude 30 meV:
 
 ```python
 import qrotor as qr
@@ -139,10 +160,14 @@ qr.plot.wavefunction(system, levels=[0,1,2], square=True)
 ```
 
 
-## Custom potentials from DFT
+## Rotational PES from custom structures
+
+
+QRotor can be used to calculate the rotational Potential Energy Surface (PES) from DFT calculations.
+Currently only Quantum ESPRESSO is supported,
+although other DFT codes can be easily implemented through [ATON](https://pablogila.github.io/aton).
 
-QRotor can be used to obtain custom rotational potentials from DFT calculations.
-To run a Quantum ESPRESSO SCF calculation for a methyl rotation every 10 degrees:
+First, run a Quantum ESPRESSO SCF calculation for a methyl rotation every 10 degrees:
 
 ```python
 import qrotor as qr
@@ -159,10 +184,13 @@ scf_files = qr.rotate.structure_qe('molecule.in', positions=atoms, angle=10, rep
 api.slurm.sbatch(files=scf_files)
 ```
 
-To load the calculated potential to a QRotor System,
+You can compile a `potential.csv` file with the calculated potential as a function of the angle,
+and load it into a new [system](https://pablogila.github.io/qrotor/qrotor/system.html):
+
 ```python
-# 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()
+# Check the potential
+qr.plot.potential(system)
 # Solve the system, interpolating to a bigger gridsize
 system.B = qr.B_CH3
 system.solve(200000)
@@ -170,13 +198,15 @@ qr.plot.energies(system)
 ```
 
 
-## Tunnel splittings and excitations
+## Other quantum observables
+
 
-Tunnel splittings, excitations and energy level degeneracy
-below the potential maximum are also calculated upon solving the system:
+The Zero-Point Energies (ZPEs), quantum tunnel splittings, excitations and energy level degeneracy
+below the potential maximum are also calculated upon solving the [system](https://pablogila.github.io/qrotor/qrotor/system.html):
 
 ```python
 system.solve()
+print(system.eigenvalues[0])
 print(system.splittings)
 print(system.excitations)
 print(system.deg)
@@ -185,7 +215,7 @@ print(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.
+you might want to 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:
 
@@ -209,12 +239,14 @@ 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.  
@@ -224,6 +256,7 @@ Please try to follow some general guidelines:
 
 ## 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
@@ -253,7 +286,7 @@ This runs Pdoc, updating links and pictures, and using the custom theme CSS temp
 
 QRotor is currently under development.
 Please cite it if you use it in your research,
-> Pablo Gila-Herranz, *QRotor*, https://pablogila.github.io/qrotor  
+> Gila-Herranz, P. (2024). QRotor: Solving one-dimensional hindered-rotor quantum systems. https://pablogila.github.io/qrotor
 
 
 ---
@@ -261,6 +294,7 @@ Please cite it if you use it in your research,
 
 # 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

{qrotor-4.1.2.dist-info → qrotor-4.2.1.dist-info}/RECORD

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