yaeos 4.0.0__cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl

yaeos/envelopes.py

@@ -0,0 +1,510 @@
+"""Envelopes.
+
+This module contains the classes that wrap the data structures used to
+represent different kinds of phase envelopes.
+"""
+
+from IPython.display import display
+
+import matplotlib.pyplot as plt
+
+import numpy as np
+
+import pandas as pd
+
+
+class PTEnvelope:
+    """PTEnvelope.
+    This class represents a pressure-temperature envelope.
+    Attributes
+    ----------
+    global_composition : np.ndarray
+        The global composition of the system. Shape is (n_components,).
+    main_phases_compositions : np.ndarray
+        The compositions of the main phases along the envelope.
+        Shape is (n_points, n_phases, n_components).
+    reference_phase_compositions : np.ndarray
+        The compositions of the reference phase along the envelope.
+        Shape is (n_points, n_components).
+    main_phases_molar_fractions : np.ndarray
+        The molar fractions of the main phases along the envelope.
+        Shape is (n_points, n_phases).
+    pressures : np.ndarray
+        The pressures along the envelope. [bar]
+    temperatures : np.ndarray
+        The temperatures along the envelope. [K]
+    iterations : np.ndarray
+        The number of iterations taken to compute the envelope at each point.
+        Shape is (n_points,).
+    specified_variable : np.ndarray
+        The specified variable used to compute the envelope at each point.
+        Shape is (n_points,).
+    reference_phase_kinds : np.ndarray
+        The kinds of the reference phase at each point.
+        Shape is (n_points,).
+    main_phases_kinds : np.ndarray
+        The kinds of the main phases at each point.
+        Shape is (n_points, n_phases).
+    cp : list
+        A list of lists containing the indices of the critical points for each
+        phase. Each sublist corresponds to a phase and contains the indices of
+        the critical points in the `temperatures` and `pressures` arrays.
+    df : pd.DataFrame
+        A DataFrame containing the data of the envelope. The columns are:
+        - 'T': Temperatures along the envelope.
+        - 'P': Pressures along the envelope.
+        - 'x_i^j': Compositions of the main phases, where `i` is the component index and `j` is the phase index.
+        - 'w_i': Compositions of the reference phase, where `i` is the component index.
+        - 'beta^j': Molar fractions of the main phases, where `j` is the phase index.
+    """
+
+    def __init__(
+        self,
+        global_composition,
+        main_phases_compositions,
+        reference_phase_compositions,
+        reference_phase_kinds,
+        main_phases_kinds,
+        main_phases_molar_fractions,
+        pressures,
+        temperatures,
+        iterations,
+        specified_variable,
+        critical_pressures,
+        critical_temperatures,
+    ):
+
+        msk = ~np.isnan(pressures)
+        msk_cp = ~np.isnan(critical_pressures)
+        self.number_of_components = len(global_composition)
+        self.number_of_phases = main_phases_compositions.shape[1]
+        self.global_composition = global_composition
+        self.main_phases_compositions = main_phases_compositions[msk, :, :]
+        self.reference_phase_compositions = reference_phase_compositions[
+            msk, :
+        ]
+        self.main_phases_molar_fractions = main_phases_molar_fractions[msk]
+        self.pressures = pressures[msk]
+        self.temperatures = temperatures[msk]
+        self.iterations = iterations[msk]
+        self.specified_variable = specified_variable[msk]
+        self.reference_phase_kinds = reference_phase_kinds[msk]
+        self.main_phases_kinds = main_phases_kinds[msk]
+        self.critical_pressures = critical_pressures[msk_cp]
+        self.critical_temperatures = critical_temperatures[msk_cp]
+
+        df = pd.DataFrame()
+
+        df["T"] = self.temperatures
+        df["P"] = self.pressures
+
+        for i in range(self.number_of_components):
+            for j in range(self.number_of_phases):
+                df[f"x_{i+1}^{j+1}"] = self.main_phases_compositions[:, j, i]
+            df[f"w_{i+1}"] = self.reference_phase_compositions[:, i]
+
+        for i in range(self.number_of_phases):
+            df[f"beta^{i+1}"] = self.main_phases_molar_fractions[:, i]
+
+        self.df = df
+
+    def plot(self, **plot_kwargs):
+        if "ax" in plot_kwargs:
+            ax = plot_kwargs["ax"]
+            del plot_kwargs["ax"]
+        else:
+            ax = plt.gca()
+        ax.plot(self.temperatures, self.pressures, **plot_kwargs)
+        ax.set_xlabel("Temperature [K]")
+        ax.set_ylabel("Pressure [bar]")
+        ax.scatter(
+            self.critical_temperatures, self.critical_pressures, color="black"
+        )
+
+    def __getitem__(self, key):
+        if "key" in self.__dict__:
+            return self.__dict__["key"]
+        elif isinstance(key, np.ndarray) or isinstance(key, list):
+            return PTEnvelope(
+                global_composition=self.global_composition,
+                main_phases_compositions=self.main_phases_compositions[key],
+                reference_phase_compositions=self.reference_phase_compositions[
+                    key
+                ],
+                main_phases_molar_fractions=self.main_phases_molar_fractions[
+                    key
+                ],
+                main_phases_kinds=self.main_phases_kinds[key],
+                reference_phase_kinds=self.reference_phase_kinds[key],
+                pressures=self.pressures[key],
+                temperatures=self.temperatures[key],
+                iterations=self.iterations[key],
+                specified_variable=self.specified_variable[key],
+                critical_pressures=self.critical_pressures,
+                critical_temperatures=self.critical_temperatures,
+            )
+        elif key == "T":
+            return self.temperatures
+        elif key == "Tc":
+            return self.critical_temperatures
+        elif key == "Pc":
+            return self.critical_pressures
+        elif key == "P":
+            return self.pressures
+        elif key == "z":
+            return self.global_composition
+        elif key == "x":
+            return self.main_phases_compositions
+        elif key == "w":
+            return self.reference_phase_compositions
+
+    def __repr__(self):
+        display(self.df)
+        return ""
+
+    def __len__(self):
+        return len(self.temperatures)
+
+
+class PXEnvelope:
+    """PXEnvelope.
+
+    This class represents a pressure-composition envelope.
+
+    Attributes
+    ----------
+    temperature : float
+        The temperature at which the envelope is defined. [K]
+    global_composition_0 : np.ndarray
+        The global composition at the point where :math:`\alpha = 0`.
+    global_composition_i : np.ndarray
+        The global composition at the point where :math:`\alpha = 1`.
+    main_phases_compositions : np.ndarray
+        The compositions of the main phases along the envelope.
+        Shape is (n_points, n_phases, n_components).
+    reference_phase_compositions : np.ndarray
+        The compositions of the reference phase along the envelope.
+        Shape is (n_points, n_components).
+    main_phases_molar_fractions : np.ndarray
+        The molar fractions of the main phases along the envelope.
+        Shape is (n_points, n_phases).
+    pressures : np.ndarray
+        The pressures along the envelope. [bar]
+    alphas : np.ndarray
+        The molar fraction of the `global_composition_i`, :math:`\alpha`.
+        Shape is (n_points,).
+    critical_pressures : np.ndarray
+        The critical pressures of the envelope. Shape is (n_critical_points,).
+    critical_alphas : np.ndarray
+        The molar fractions of the `global_composition_i` at the critical
+        points, :math:`\alpha`.  Shape is (n_critical_points,).
+    iterations : np.ndarray
+        The number of iterations taken to compute the envelope at each point.
+        Shape is (n_points,).
+    specified_variable : np.ndarray
+        The specified variable used to compute the envelope at each point.
+        Shape is (n_points,).
+    df : pd.DataFrame
+        A DataFrame containing the data of the envelope. The columns are:
+        - 'alpha': Molar fraction of the `global_composition_i`.
+        - 'P': Pressures along the envelope.
+        - 'x_i^j': Compositions of the main phases, where `i`
+        is the component index and `j` is the phase index.
+        - 'w_i': Compositions of the reference phase, where `i` is the
+        component index.
+        - 'beta^j': Molar fractions of the main phases, where `j`
+        is the phase index.
+    """
+
+    def __init__(
+        self,
+        temperature,
+        global_composition_0,
+        global_composition_i,
+        main_phases_compositions,
+        reference_phase_compositions,
+        main_phases_molar_fractions,
+        pressures,
+        alphas,
+        iterations,
+        specified_variable,
+        critical_pressures,
+        critical_alphas,
+        main_phases_kinds,
+        reference_phase_kinds,
+    ):
+
+        msk = ~np.isnan(pressures)
+        msk_cp = ~np.isnan(critical_pressures)
+
+        self.temperature = temperature
+        self.number_of_components = len(global_composition_0)
+        self.number_of_phases = main_phases_compositions.shape[1]
+        self.global_composition_0 = global_composition_0
+        self.global_composition_i = global_composition_i
+        self.main_phases_compositions = main_phases_compositions[msk, :, :]
+        self.reference_phase_compositions = reference_phase_compositions[
+            msk, :
+        ]
+        self.main_phases_molar_fractions = main_phases_molar_fractions[msk]
+        self.pressures = pressures[msk]
+        self.alphas = alphas[msk]
+        self.iterations = iterations[msk]
+        self.specified_variable = specified_variable[msk]
+        self.main_phases_kinds = main_phases_kinds[msk]
+        self.reference_phase_kinds = reference_phase_kinds[msk]
+        self.critical_pressures = critical_pressures[msk_cp]
+        self.critical_alphas = critical_alphas[msk_cp]
+
+        df = pd.DataFrame()
+
+        df["alpha"] = self.alphas
+        df["P"] = self.pressures
+
+        for i in range(self.number_of_components):
+            for j in range(self.number_of_phases):
+                df[f"x_{i+1}^{j+1}"] = self.main_phases_compositions[:, j, i]
+            df[f"w_{i+1}"] = self.reference_phase_compositions[:, i]
+
+        for i in range(self.number_of_phases):
+            df[f"beta^{i+1}"] = self.main_phases_molar_fractions[:, i]
+
+        self.df = df
+
+    def plot(self, **plot_kwargs):
+        """Plot the envelope.
+
+        Plot the envelope in a matplotlib axis. Using the natural variables of
+        the envelope (:math:`alpha` and pressure)  If the `ax` keyword argument
+        is provided, it will be used as the axis to plot on. Otherwise, the
+        current axis will be used.
+
+        Parameters
+        ----------
+        plot_kwargs : dict
+            Keyword arguments to pass to the `plot` method of the axis.
+            This can include line style, color, etc.
+        """
+        if "ax" in plot_kwargs:
+            ax = plot_kwargs["ax"]
+            del plot_kwargs["ax"]
+        else:
+            ax = plt.gca()
+        ax.plot(self.alphas, self.alphas, **plot_kwargs)
+        ax.set_xlabel(r"$\alpha$")
+        ax.set_ylabel("Pressure [bar]")
+        for cp in self.cp:
+            ax.scatter(self.pressures[cp], self.alphas[cp], color="black")
+
+    def __getitem__(self, key):
+        if "key" in self.__dict__:
+            return self.__dict__["key"]
+        elif isinstance(key, np.ndarray) or isinstance(key, list):
+            return PXEnvelope(
+                global_composition_0=self.global_composition_0,
+                global_composition_i=self.global_composition_i,
+                temperature=self.temperature,
+                main_phases_compositions=self.main_phases_compositions[key],
+                reference_phase_compositions=self.reference_phase_compositions[
+                    key
+                ],
+                main_phases_molar_fractions=self.main_phases_molar_fractions[
+                    key
+                ],
+                pressures=self.pressures[key],
+                alphas=self.alphas[key],
+                iterations=self.iterations[key],
+                specified_variable=self.specified_variable[key],
+                critical_pressures=self.critical_pressures,
+                critical_alphas=self.critical_alphas,
+            )
+        elif key == "alpha" or key == "a":
+            return self.alphas
+        elif key == "P":
+            return self.pressures
+        elif key == "z":
+            return self.global_composition
+        elif key == "x":
+            return self.main_phases_compositions
+        elif key == "w":
+            return self.reference_phase_compositions
+
+    def __repr__(self):
+        display(self.df)
+        return ""
+
+    def __len__(self):
+        return len(self.alphas)
+
+
+class TXEnvelope:
+    """TXEnvelope.
+
+    This class represents a temperature-composition envelope.
+
+    Attributes
+    ----------
+    pressure : float
+        The pressure at which the envelope is defined. [bar]
+    global_composition_0 : np.ndarray
+        The global composition at the point where :math:`\alpha = 0`.
+    global_composition_i : np.ndarray
+        The global composition at the point where :math:`\alpha = 1`.
+    main_phases_compositions : np.ndarray
+        The compositions of the main phases along the envelope.
+        Shape is (n_points, n_phases, n_components).
+    reference_phase_compositions : np.ndarray
+        The compositions of the reference phase along the envelope.
+        Shape is (n_points, n_components).
+    main_phases_molar_fractions : np.ndarray
+        The molar fractions of the main phases along the envelope.
+        Shape is (n_points, n_phases).
+    temperatures : np.ndarray
+        The temperatures along the envelope. [K]
+    alphas : np.ndarray
+        The molar fraction of the `global_composition_i`, :math:`\alpha`.
+        Shape is (n_points,).
+    iterations : np.ndarray
+        The number of iterations taken to compute the envelope at each point.
+        Shape is (n_points,).
+    specified_variable : np.ndarray
+        The specified variable used to compute the envelope at each point.
+        Shape is (n_points,).
+    temperature : float
+        The temperatures along envelope. [K]
+    critical_temperatures : np.ndarray
+        The critical temperatures of the envelope. Shape is (n_critical_points,).
+    critical_alphas : np.ndarray
+        The molar fractions of the `global_composition_i` at the critical
+        points, :math:`\alpha`.  Shape is (n_critical_points,).
+    df : pd.DataFrame
+        A DataFrame containing the data of the envelope. The columns are:
+        - 'alpha': Molar fraction of the `global_composition_i`.
+        - 'T': Temperatures along the envelope.
+        - 'x_i^j': Compositions of the main phases, where `i`
+        is the component index and `j` is the phase index.
+        - 'w_i': Compositions of the reference phase, where `i` is the
+        component index.
+        - 'beta^j': Molar fractions of the main phases, where `j`
+        is the phase index.
+    """
+
+    def __init__(
+        self,
+        pressure,
+        global_composition_0,
+        global_composition_i,
+        main_phases_compositions,
+        reference_phase_compositions,
+        main_phases_molar_fractions,
+        temperatures,
+        alphas,
+        iterations,
+        specified_variable,
+        critical_temperatures,
+        critical_alphas,
+        main_phases_kinds,
+        reference_phase_kinds,
+    ):
+
+        msk = ~np.isnan(temperatures)
+        msk_cp = ~np.isnan(critical_temperatures)
+
+        self.temperature = pressure
+        self.number_of_components = len(global_composition_0)
+        self.number_of_phases = main_phases_compositions.shape[1]
+        self.global_composition_0 = global_composition_0
+        self.global_composition_i = global_composition_i
+        self.main_phases_compositions = main_phases_compositions[msk, :, :]
+        self.reference_phase_compositions = reference_phase_compositions[
+            msk, :
+        ]
+        self.main_phases_molar_fractions = main_phases_molar_fractions[msk]
+        self.temperatures = temperatures[msk]
+        self.alphas = alphas[msk]
+        self.iterations = iterations[msk]
+        self.specified_variable = specified_variable[msk]
+        self.critical_temperatures = critical_temperatures[msk_cp]
+        self.critical_alphas = critical_alphas[msk_cp]
+        self.main_phases_kinds = main_phases_kinds[msk]
+        self.reference_phase_kinds = reference_phase_kinds[msk]
+
+        df = pd.DataFrame()
+
+        df["alpha"] = self.alphas
+        df["T"] = self.temperatures
+
+        for i in range(self.number_of_components):
+            for j in range(self.number_of_phases):
+                df[f"x_{i+1}^{j+1}"] = self.main_phases_compositions[:, j, i]
+            df[f"w_{i+1}"] = self.reference_phase_compositions[:, i]
+
+        for i in range(self.number_of_phases):
+            df[f"beta^{i+1}"] = self.main_phases_molar_fractions[:, i]
+
+        self.df = df
+
+    def plot(self, **plot_kwargs):
+        """Plot the envelope.
+
+        Plot the envelope in a matplotlib axis. Using the natural variables of
+        the envelope (:math:`alpha` and temperature)  If the `ax` keyword
+        argument is provided, it will be used as the axis to plot on.
+        Otherwise, the current axis will be used.
+
+        Parameters
+        ----------
+        plot_kwargs : dict
+            Keyword arguments to pass to the `plot` method of the axis.
+            This can include line style, color, etc.
+        """
+        if "ax" in plot_kwargs:
+            ax = plot_kwargs["ax"]
+            del plot_kwargs["ax"]
+        else:
+            ax = plt.gca()
+        ax.plot(self.alphas, self.temperatures, **plot_kwargs)
+        ax.set_xlabel(r"$\alpha$")
+        ax.set_ylabel("Temperature [K]")
+        for cp in self.cp:
+            ax.scatter(self.alphas[cp], self.temperatures[cp], color="black")
+
+    def __getitem__(self, key):
+        if "key" in self.__dict__:
+            return self.__dict__["key"]
+        elif isinstance(key, np.ndarray) or isinstance(key, list):
+            return TXEnvelope(
+                global_composition_0=self.global_composition_0,
+                global_composition_i=self.global_composition_i,
+                pressure=self.pressure,
+                main_phases_compositions=self.main_phases_compositions[key],
+                reference_phase_compositions=self.reference_phase_compositions[
+                    key
+                ],
+                main_phases_molar_fractions=self.main_phases_molar_fractions[
+                    key
+                ],
+                temperatures=self.temperatures[key],
+                alphas=self.alphas[key],
+                iterations=self.iterations[key],
+                specified_variable=self.specified_variable[key],
+                critical_temperatures=self.critical_temperatures,
+                critical_alphas=self.critical_alphas,
+            )
+        elif key == "alpha" or key == "a":
+            return self.alphas
+        elif key == "T":
+            return self.temperatures
+        elif key == "z":
+            return self.global_composition
+        elif key == "x":
+            return self.main_phases_compositions
+        elif key == "w":
+            return self.reference_phase_compositions
+
+    def __repr__(self):
+        display(self.df)
+        return ""
+
+    def __len__(self):
+        return len(self.alphas)

yaeos/fitting/__init__.py

@@ -0,0 +1,12 @@
+"""yaeos fitting module.
+
+This module provides classes and functions for fitting binary interaction
+parameters to experimental data.
+"""
+
+from yaeos.fitting.core import BinaryFitter
+from yaeos.fitting.model_setters import fit_kij_lij
+from yaeos.fitting.solvers import solve_pt
+
+
+__all__ = ["BinaryFitter", "fit_kij_lij", "solve_pt"]