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Fix bugs in python documentation #5

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Nov 23, 2021
Merged

Fix bugs in python documentation #5

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67 changes: 41 additions & 26 deletions src/python/adsorption/external_potential.rs
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Expand Up @@ -5,18 +5,21 @@ use pyo3::prelude::*;
use quantity::python::{PySIArray2, PySINumber};
use quantity::si::*;

/// A collection of external potentials.
#[pyclass(name = "ExternalPotential", unsendable)]
#[derive(Clone)]
pub struct PyExternalPotential(pub ExternalPotential<SIUnit>);

#[pymethods]
#[allow(non_snake_case)]
impl PyExternalPotential {
/// A hard wall potential
/// Hard wall potential
///
/// .. math:: V_i^\mathrm{ext}(z)=\begin{cases}\infty&z\leq\sigma_{si}\\\\0&z>\sigma_{si}\end{cases},~~~~\sigma_{si}=\frac{1}{2}\left(\sigma_{ss}+\sigma_{ii}\right)
///
/// Parameters
/// ----------
/// sigma_ss : f64
/// sigma_ss : float
/// Segment diameter of the solid.
///
/// Returns
Expand All @@ -30,15 +33,17 @@ impl PyExternalPotential {
Self(ExternalPotential::HardWall { sigma_ss })
}

/// Create a Lennard-Jones-9-3 potential.
/// 9-3 Lennard-Jones potential
///
/// .. math:: V_i^\mathrm{ext}(z)=\frac{2\pi}{45} m_i\varepsilon_{si}\sigma_{si}^3\rho_s\left(2\left(\frac{\sigma_{si}}{z}\right)^9-15\left(\frac{\sigma_{si}}{z}\right)^3\right),~~~~\varepsilon_{si}=\sqrt{\varepsilon_{ss}\varepsilon_{ii}},~~~~\sigma_{si}=\frac{1}{2}\left(\sigma_{ss}+\sigma_{ii}\right)
///
/// Parameters
/// ----------
/// sigma_ss : f64
/// sigma_ss : float
/// Segment diameter of the solid.
/// epsilon_k_ss : f64
/// epsilon_k_ss : float
/// Energy parameter of the solid.
/// rho_s : f64
/// rho_s : float
/// Density of the solid.
///
/// Returns
Expand All @@ -55,13 +60,15 @@ impl PyExternalPotential {
})
}

/// Create a simple Lennard-Jones-9-3 potential.
/// Simple 9-3 Lennard-Jones potential
///
/// .. math:: V_i^\mathrm{ext}(z)=\varepsilon_{si}\left(\left(\frac{\sigma_{si}}{z}\right)^9-\left(\frac{\sigma_{si}}{z}\right)^3\right),~~~~\varepsilon_{si}=\sqrt{\varepsilon_{ss}\varepsilon_{ii}},~~~~\sigma_{si}=\frac{1}{2}\left(\sigma_{ss}+\sigma_{ii}\right)
///
/// Parameters
/// ----------
/// sigma_ss : f64
/// sigma_ss : float
/// Segment diameter of the solid.
/// epsilon_k_ss : f64
/// epsilon_k_ss : float
/// Energy parameter of the solid.
///
/// Returns
Expand All @@ -77,13 +84,15 @@ impl PyExternalPotential {
})
}

/// Create a custom Lennard-Jones-9-3 potential.
/// Custom 9-3 Lennard-Jones potential
///
/// .. math:: V_i^\mathrm{ext}(z)=\varepsilon_{si}\left(\left(\frac{\sigma_{si}}{z}\right)^9-\left(\frac{\sigma_{si}}{z}\right)^3\right)
///
/// Parameters
/// ----------
/// sigma_sf : PyArray
/// sigma_sf : numpy.ndarray[float]
/// Solid-fluid interaction diameters.
/// epsilon_k_sf : PyArray
/// epsilon_k_sf : numpy.ndarray[float]
/// Solid-fluid interaction energies.
///
/// Returns
Expand All @@ -99,17 +108,19 @@ impl PyExternalPotential {
})
}

/// Create a Steele potential.
/// Steele potential
///
/// .. math:: V_i^\mathrm{ext}(z)=2\pi m_i\xi\varepsilon_{si}\sigma_{si}^2\Delta\rho_s\left(0.4\left(\frac{\sigma_{si}}{z}\right)^{10}-\left(\frac{\sigma_{si}}{z}\right)^4-\frac{\sigma_{si}^4}{3\Delta\left(z+0.61\Delta\right)^3}\right),~~~~\varepsilon_{si}=\sqrt{\varepsilon_{ss}\varepsilon_{ii}},~~~~\sigma_{si}=\frac{1}{2}\left(\sigma_{ss}+\sigma_{ii}\right),~~~~\Delta=3.35
///
/// Parameters
/// ----------
/// sigma_ss : f64
/// sigma_ss : float
/// Segment diameter of the solid.
/// epsilon_k_ss : f64
/// epsilon_k_ss : float
/// Energy parameter of the solid.
/// rho_s : f64
/// rho_s : float
/// Density of the solid.
/// xi : f64, optional
/// xi : float, optional
/// Binary wall-fluid interaction parameter.
///
/// Returns
Expand All @@ -127,17 +138,19 @@ impl PyExternalPotential {
})
}

/// Create a Double-Well potential.
/// Double well potential
///
/// .. math:: V_i^\mathrm{ext}(z)=\mathrm{min}\left(\frac{2\pi}{45} m_i\varepsilon_{2si}\sigma_{si}^3\rho_s\left(2\left(\frac{2\sigma_{si}}{z}\right)^9-15\left(\frac{2\sigma_{si}}{z}\right)^3\right),0\right)+\frac{2\pi}{45} m_i\varepsilon_{1si}\sigma_{si}^3\rho_s\left(2\left(\frac{\sigma_{si}}{z}\right)^9-15\left(\frac{\sigma_{si}}{z}\right)^3\right),~~~~\varepsilon_{1si}=\sqrt{\varepsilon_{1ss}\varepsilon_{ii}},~~~~\varepsilon_{2si}=\sqrt{\varepsilon_{2ss}\varepsilon_{ii}},~~~~\sigma_{si}=\frac{1}{2}\left(\sigma_{ss}+\sigma_{ii}\right)
///
/// Parameters
/// ----------
/// sigma_ss : f64
/// sigma_ss : float
/// Segment diameter of the solid.
/// epsilon1_k_ss : f64
/// epsilon1_k_ss : float
/// Energy parameter of the first well.
/// epsilon2_k_ss : f64
/// epsilon2_k_ss : float
/// Energy parameter of the second well.
/// rho_s : f64
/// rho_s : float
/// Density of the solid.
///
/// Returns
Expand All @@ -155,15 +168,17 @@ impl PyExternalPotential {
})
}

/// Create a Free-Energy averaged potential.
/// Free-energy averaged potential
///
/// for details see: `J. Eller, J. Gross (2021) <https://pubs.acs.org/doi/abs/10.1021/acs.langmuir.0c03287>`_
///
/// Parameters
/// ----------
/// coordinates: SIArray2
/// The positions of all interaction sites in the solid.
/// sigma_ss : Array1
/// sigma_ss : numpy.ndarray[float]
/// The size parameters of all interaction sites.
/// epsilon_k_ss : Array1
/// epsilon_k_ss : numpy.ndarray[float]
/// The energy parameter of all interaction sites.
/// pore_center : [SINumber; 3]
/// The cartesian coordinates of the center of the pore
Expand Down Expand Up @@ -202,7 +217,7 @@ impl PyExternalPotential {
}
}

/// Geometry of the 1-dimensional pore.
/// Geometry of a one-dimensional pore.
///
/// Returns
/// -------
Expand Down
34 changes: 18 additions & 16 deletions src/python/adsorption/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,11 @@ pub use external_potential::{PyExternalPotential, PyGeometry};
#[macro_export]
macro_rules! impl_adsorption {
($func:ty, $py_func:ty) => {
/// Container structure for adsorption isotherms in 1D pores.
#[pyclass(name = "Adsorption1D", unsendable)]
pub struct PyAdsorption1D(Adsorption1D<SIUnit, $func>);

/// Container structure for adsorption isotherms in 3D pores.
#[pyclass(name = "Adsorption3D", unsendable)]
pub struct PyAdsorption3D(Adsorption3D<SIUnit, $func>);

Expand Down Expand Up @@ -44,24 +46,24 @@ macro_rules! impl_adsorption_isotherm {
///
/// Parameters
/// ----------
/// functional : $func
/// functional : HelmholtzEnergyFunctional
/// The Helmholtz energy functional.
/// temperature : SINumber
/// The temperature.
/// pressure : {(SINumber, SINumber, int), SIArray1}
/// The pressures for which the profiles are calculated. Either
/// a tuple containing the minimum pressure, the maximum pressure,
/// and the number of points, or an array containing specific values.
/// pore : $py_pore
/// pore : Pore
/// The pore parameters.
/// molefracs: PyArray, optional
/// molefracs: numpy.ndarray[float], optional
/// For a mixture, the molefracs of the bulk system.
/// solver: DFTSolver, optional
/// Custom solver options.
///
/// Returns
/// -------
/// $adsorption
/// Adsorption
///
#[staticmethod]
#[pyo3(text_signature = "(functional, temperature, pressure, pore, molefracs=None, solver=None)")]
Expand Down Expand Up @@ -89,24 +91,24 @@ macro_rules! impl_adsorption_isotherm {
///
/// Parameters
/// ----------
/// functional : $func
/// functional : HelmholtzEnergyFunctional
/// The Helmholtz energy functional.
/// temperature : SINumber
/// The temperature.
/// pressure : {(SINumber, SINumber, int), SIArray1}
/// The pressures for which the profiles are calculated. Either
/// a tuple containing the minimum pressure, the maximum pressure,
/// and the number of points, or an array containing specific values.
/// pore : $py_pore
/// pore : Pore
/// The pore parameters.
/// molefracs: PyArray, optional
/// molefracs: numpy.ndarray[float], optional
/// For a mixture, the molefracs of the bulk system.
/// solver: DFTSolver, optional
/// Custom solver options.
///
/// Returns
/// -------
/// $adsorption
/// Adsorption
///
#[staticmethod]
#[pyo3(text_signature = "(functional, temperature, pressure, pore, molefracs=None, solver=None)")]
Expand Down Expand Up @@ -137,24 +139,24 @@ macro_rules! impl_adsorption_isotherm {
///
/// Parameters
/// ----------
/// functional : $func
/// functional : HelmholtzEnergyFunctional
/// The Helmholtz energy functional.
/// temperature : SINumber
/// The temperature.
/// pressure : {(SINumber, SINumber, int), SIArray1}
/// The pressures for which the profiles are calculated. Either
/// a tuple containing the minimum pressure, the maximum pressure,
/// and the number of points, or an array containing specific values.
/// pore : $py_pore
/// pore : Pore
/// The pore parameters.
/// molefracs: PyArray, optional
/// molefracs: numpy.ndarray[float], optional
/// For a mixture, the molefracs of the bulk system.
/// solver: DFTSolver, optional
/// Custom solver options.
///
/// Returns
/// -------
/// $adsorption
/// Adsorption
///
#[staticmethod]
#[pyo3(text_signature = "(functional, temperature, pressure, pore, molefracs=None, solver=None)")]
Expand All @@ -180,17 +182,17 @@ macro_rules! impl_adsorption_isotherm {
///
/// Parameters
/// ----------
/// functional : $func
/// functional : HelmholtzEnergyFunctional
/// The Helmholtz energy functional.
/// temperature : SINumber
/// The temperature.
/// p_min : SINumber
/// A suitable lower limit for the pressure.
/// p_max : SINumber
/// A suitable upper limit for the pressure.
/// pore : $py_pore
/// pore : Pore
/// The pore parameters.
/// molefracs: PyArray, optional
/// molefracs: numpy.ndarray[float], optional
/// For a mixture, the molefracs of the bulk system.
/// solver: DFTSolver, optional
/// Custom solver options.
Expand All @@ -203,7 +205,7 @@ macro_rules! impl_adsorption_isotherm {
///
/// Returns
/// -------
/// $adsorption
/// Adsorption
///
#[staticmethod]
#[pyo3(text_signature = "(functional, temperature, p_min, p_max, pore, molefracs=None, solver=None, max_iter=None, tol=None, verbosity=None)")]
Expand Down
26 changes: 13 additions & 13 deletions src/python/adsorption/pore.rs
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
#[macro_export]
macro_rules! impl_pore {
($func:ty, $py_func:ty) => {
/// A one-dimensional density profile of a fluid in a pore.
/// Parameters required to specify a 1D pore.
///
/// Parameters
/// ----------
/// functional : $func
/// functional : HelmholtzEnergyFunctional
/// The Helmholtz energy functional.
/// geometry : Geometry
/// The pore geometry.
Expand Down Expand Up @@ -52,21 +52,21 @@ macro_rules! impl_pore {
))
}

/// Initialize the pore for the given bulk state
/// Initialize the pore for the given bulk state.
///
/// Parameters
/// ----------
/// bulk : State
/// The bulk state in equilibrium with the pore.
/// external_potential : Array2, optional
/// external_potential : numpy.ndarray[float], optional
/// The external potential in the pore. Used to
/// save computation time in the case of costly
/// evaluations of external potentials.
///
/// Returns
/// -------
/// PoreProfile1D
#[pyo3(text_signature = "(bulk, external_potential=None)")]
#[pyo3(text_signature = "($self, bulk, external_potential=None)")]
fn initialize(
&self,
bulk: &PyState,
Expand All @@ -92,21 +92,21 @@ macro_rules! impl_pore {
}
}

/// A three-dimensional density profile of a fluid in a pore.
/// Parameters required to specify a 3D pore.
///
/// Parameters
/// ----------
/// functional : $func
/// functional : HelmholtzEnergyFunctional
/// The Helmholtz energy functional.
/// system_size : [SINumber; 3]
/// The size of the unit cell.
/// n_grid : [int; 3]
/// The number of grid points in each direction.
/// coordinates : SIArray2
/// coordinates : numpy.ndarray[float]
/// The positions of all interaction sites in the solid.
/// sigma_ss : Array1
/// sigma_ss : numpy.ndarray[float]
/// The size parameters of all interaction sites.
/// epsilon_k_ss : Array1
/// epsilon_k_ss : numpy.ndarray[float]
/// The energy parameter of all interaction sites.
/// potential_cutoff: float, optional
/// Maximum value for the external potential.
Expand Down Expand Up @@ -151,21 +151,21 @@ macro_rules! impl_pore {
))
}

/// Initialize the pore for the given bulk state
/// Initialize the pore for the given bulk state.
///
/// Parameters
/// ----------
/// bulk : State
/// The bulk state in equilibrium with the pore.
/// external_potential : Array4, optional
/// external_potential : numpy.ndarray[float], optional
/// The external potential in the pore. Used to
/// save computation time in the case of costly
/// evaluations of external potentials.
///
/// Returns
/// -------
/// PoreProfile3D
#[pyo3(text_signature = "(bulk, external_potential=None)")]
#[pyo3(text_signature = "($self, bulk, external_potential=None)")]
fn initialize(
&self,
bulk: &PyState,
Expand Down
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