peritheos 0.1.0__py3-none-any.whl

peritheos/eos/thermal/sokolova2016.py

@@ -0,0 +1,242 @@
+import numpy as np
+from scipy.integrate import quad
+from scipy.constants import R
+
+from ..rt.holzapfel import Holzapfel
+from .. import (
+    NumericType,
+    ThermalEOS,
+    validate_finite_scalar,
+    validate_positive_scalar,
+    validate_volume,
+)
+
+
+class Sokolova2016(ThermalEOS):
+    def __init__(
+        self,
+        rt_eos: Holzapfel,
+        Tr: float,
+        QE1o: float,
+        mE1: float,
+        QE2o: float,
+        mE2: float,
+        delta: float,
+        t: float,
+        a_0: float,
+        m: float,
+        g: float,
+        e_0: float,
+    ):
+        """
+        Original thermal pressure equation from sokolova et al. 2016.
+
+        Parameters
+        ----------
+        rt_eos : Holzapfel
+            Room temperature equation of state (Holzapfel EOS)
+        Tr : float
+            Reference temperature in [K] for the EOS (typically 298.15 K)
+        QE1o : float
+            Einstein characteristic temperature, Theta_1 in [K]
+        mE1 : float
+            The first Einstein number
+        QE2o : float
+            Einstein characteristic temperature, Theta_02 in [K]
+        mE2 : float
+            The second Einstein number
+        TK : float
+            Temperature in [K]
+        delta : float
+            Additive normalizing constant for the Gruneisen parameter
+        t : float
+            Generalized Gruneisen parameter
+        a_0 : float
+            Intrinsic anharmonicity parameter (10e-6 [K])
+        m : float
+            Anharmonic analogue of the Grüneisen parameter
+        g : float
+            Electronic analogue of the Grüneisen parameter
+        e_0 : float
+            Free electrons parameter (10e-6 [K])
+        """
+        if not isinstance(rt_eos, Holzapfel):
+            raise TypeError("Sokolova2016 requires a Holzapfel room-temperature EOS")
+        super().__init__(rt_eos)
+        self.Tr = validate_positive_scalar(Tr, "Tr")
+        self.QE1o = validate_positive_scalar(QE1o, "QE1o")
+        self.mE1 = validate_finite_scalar(mE1, "mE1")
+        self.QE2o = validate_positive_scalar(QE2o, "QE2o")
+        self.mE2 = validate_finite_scalar(mE2, "mE2")
+        if self.mE1 < 0 or self.mE2 < 0:
+            raise ValueError("Einstein multiplicities must not be negative")
+        self.delta = validate_finite_scalar(delta, "delta")
+        self.t = validate_finite_scalar(t, "t")
+        self.a_0 = validate_finite_scalar(a_0, "a_0")
+        self.m = validate_finite_scalar(m, "m")
+        self.g = validate_finite_scalar(g, "g")
+        self.e_0 = validate_finite_scalar(e_0, "e_0")
+
+    def thermal_pressure(self, V: NumericType, T: NumericType) -> NumericType:
+        """
+        Calculate the thermal pressure using the Sokolova et al. 2016 model.
+
+        Parameters
+        ----------
+        V : NumericType
+            Molar volume in [J bar^-1], equal to [cm^3/mol] / 10
+        T : NumericType
+            Temperature in [K]
+
+        Returns
+        -------
+        thermal_pressure : NumericType
+            Thermal pressure in [GPa]
+        """
+        V = validate_volume(V)
+        temperatures = np.asarray(T, dtype=float)
+        if not np.all(np.isfinite(temperatures)) or np.any(temperatures <= 0):
+            raise ValueError("Temperature must be finite and greater than zero")
+        try:
+            V, T = np.broadcast_arrays(np.asarray(V, dtype=float), temperatures)
+        except ValueError as error:
+            raise ValueError("V and T must have broadcast-compatible shapes") from error
+
+        x = V / self.rt_eos.V0  # fractional volume
+        Px = self.rt_eos.pressure(V)
+        KT = self.rt_eos.bulk_modulus(V)
+        kkx = self.rt_eos.bulk_modulus_derivative(V)
+
+        # Equation (10) - seems not the same as in the original paper
+        gamV = (-3 * KT + 2 * Px * self.t + 9 * KT * kkx - 6 * self.t * KT) / 6 / (
+            3 * KT - 2 * Px * self.t
+        ) + self.delta
+
+        # Exponent part in equation (9) - However this is not the correct value - the Excel spreadsheet
+        # calculation has a more elaborate calculation included
+
+        # expp_test = np.exp(0.5 * ao * TK * 1e6 * (V / V0) ** (1 / 3))
+        expp = np.exp(I_gamV(x, self.delta, self.t, self.rt_eos))
+
+        # Equation (9)
+        QE1 = self.QE1o * expp
+        QE2 = self.QE2o * expp
+
+        # Equation (12) for the different Einstein contributions at the temperature TK
+        PE1 = self.mE1 * R * (_einstein_energy(QE1, T) * gamV / V)
+
+        PE2 = self.mE2 * R * (_einstein_energy(QE2, T) * gamV / V)
+
+        # Equation (12) for the different Einstein contributions at the reference temperature
+        PE1r = self.mE1 * R * (_einstein_energy(QE1, self.Tr) * gamV / V)
+
+        PE2r = self.mE2 * R * (_einstein_energy(QE2, self.Tr) * gamV / V)
+
+        # Equation (12) second additive term
+        Pea = (
+            3
+            / 2
+            * self.rt_eos.n
+            * R
+            * self.a_0
+            / 1000000
+            * x ** (self.m)
+            * (self.m)
+            / V
+            * (T**2 - self.Tr**2)
+        )
+        Pee = (
+            3
+            / 2
+            * self.rt_eos.n
+            * R
+            * self.e_0
+            / 1000000
+            * x ** (self.g)
+            * (self.g)
+            / V
+            * (T**2 - self.Tr**2)
+        )
+
+        # R [J mol^-1 K^-1] divided by V [J bar^-1 mol^-1] produces bar.
+        Pth_bar = PE1 + PE2 - PE1r - PE2r + Pee + Pea
+        Pth_gpa = Pth_bar / 10000
+        if Pth_gpa.ndim == 0:
+            return float(Pth_gpa)
+        return Pth_gpa
+
+
+def _einstein_energy(theta, temperature):
+    """Return Einstein oscillator energy in kelvin without exponential overflow."""
+    ratio = theta / temperature
+    decay = np.exp(-ratio)
+    thermal_part = theta * decay / (-np.expm1(-ratio))
+    return theta / 2 + thermal_part
+
+
+def I_gamV(x, delta, t, rt_eos):
+    """
+    Integral of the Gruneisen parameter over the volume ratio (from x to 1).
+
+    Parameters
+    ----------
+    x : float
+        Fractional volume (V/Vo)
+    delta : float
+        Additive normalizing constant for the Gruneisen parameter
+    t : float
+        Generalized Gruneisen parameter
+    rt_eos : RT_EOS
+        room temperature equation of state object used for the calculation
+
+    Returns
+    -------
+    I_gamV : float
+        Integral of the Gruneisen parameter over the volume ratio (from x to 1)
+    """
+
+    V0 = rt_eos.V0
+
+    def f_gamV_x(x):
+        Px_x = rt_eos.pressure(x * V0)
+        KT_x = rt_eos.bulk_modulus(x * V0)
+        kkx_x = rt_eos.bulk_modulus_derivative(x * V0)
+        return f_gamV(x, Px_x, KT_x, kkx_x, delta, t)
+
+    x_values = np.asarray(x, dtype=float)
+    if not np.all(np.isfinite(x_values)) or np.any(x_values <= 0):
+        raise ValueError("Volume ratio must be finite and greater than zero")
+    integrals = np.array(
+        [quad(f_gamV_x, float(x_i), 1)[0] for x_i in x_values.flat]
+    ).reshape(x_values.shape)
+    if integrals.ndim == 0:
+        return float(integrals)
+    return integrals
+
+
+def f_gamV(x, Px, KT, kkx, delta, t):
+    """
+    Helper function to calculate the Gruneisen parameter at a given temperature and pressure.
+
+    Parameters
+    ----------
+    x : float
+        Fractional volume (V/Vo)
+    Px : float
+        Pressure in [GPa]
+    KT: float
+        Bulk modulus at temperature in [GPa]
+    kkx: float
+        Bulk modulus derivative at temperature
+    delta: float
+        Additive normalizing constant for the Gruneisen parameter
+    gb: float
+        Generalized Gruneisen parameter
+    """
+    f_gamV_value = (
+        delta
+        + (-3 * KT + 2 * Px * t + 9 * KT * kkx - 6 * t * KT)
+        / (6 * (3 * KT - 2 * Px * t))
+    ) / x
+
+    return f_gamV_value

peritheos/utils.py

@@ -0,0 +1,118 @@
+"""
+Utility functions for thermodynamic calculations
+"""
+
+from .constants import R, N_A, k_B
+
+
+def convert_pressure(value, from_unit, to_unit):
+    """
+    Convert pressure between different units
+    
+    Parameters
+    ----------
+    value : float
+        Pressure value to convert
+    from_unit : str
+        Original unit ('pa', 'mpa', 'gpa', 'bar', 'kbar', 'atm', 'torr', 'psi')
+    to_unit : str
+        Target unit ('pa', 'mpa', 'gpa', 'bar', 'kbar', 'atm', 'torr', 'psi')
+        
+    Returns
+    -------
+    float
+        Converted pressure value
+    """
+    # Conversion factors to Pa
+    to_pa = {
+        'pa': 1.0,
+        'mpa': 1e6,
+        'gpa': 1e9,
+        'bar': 1e5,
+        'kbar': 1e8,
+        'atm': 101325.0,
+        'torr': 133.322,
+        'psi': 6894.76
+    }
+    
+    from_unit = from_unit.lower()
+    to_unit = to_unit.lower()
+    if from_unit not in to_pa:
+        raise ValueError(f"Unsupported pressure unit: {from_unit}")
+    if to_unit not in to_pa:
+        raise ValueError(f"Unsupported pressure unit: {to_unit}")
+
+    # Convert to Pa first
+    pa_value = value * to_pa[from_unit]
+    
+    # Convert from Pa to target unit
+    return pa_value / to_pa[to_unit]
+
+
+def convert_temperature(value, from_unit, to_unit):
+    """
+    Convert temperature between different units
+    
+    Parameters
+    ----------
+    value : float
+        Temperature value to convert
+    from_unit : str
+        Original unit ('k', 'c', 'f')
+    to_unit : str
+        Target unit ('k', 'c', 'f')
+        
+    Returns
+    -------
+    float
+        Converted temperature value
+    """
+    from_unit = from_unit.lower()
+    to_unit = to_unit.lower()
+    
+    # Convert to Kelvin first
+    if from_unit == 'k':
+        kelvin = value
+    elif from_unit == 'c':
+        kelvin = value + 273.15
+    elif from_unit == 'f':
+        kelvin = (value - 32) * 5/9 + 273.15
+    else:
+        raise ValueError(f"Unsupported temperature unit: {from_unit}")
+    
+    # Convert from Kelvin to target unit
+    if to_unit == 'k':
+        return kelvin
+    elif to_unit == 'c':
+        return kelvin - 273.15
+    elif to_unit == 'f':
+        return (kelvin - 273.15) * 9/5 + 32
+    else:
+        raise ValueError(f"Unsupported temperature unit: {to_unit}")
+
+
+def compressibility_factor(pressure, volume, temperature, moles):
+    """
+    Calculate the compressibility factor Z = PV/nRT
+    
+    Parameters
+    ----------
+    pressure : float
+        Pressure in Pascal
+    volume : float
+        Volume in cubic meters
+    temperature : float
+        Temperature in Kelvin
+    moles : float
+        Number of moles
+        
+    Returns
+    -------
+    float
+        Compressibility factor (dimensionless)
+    """
+    return pressure * volume / (moles * R * temperature) 
+
+def derivative(f, x, dx=1e-6):
+    """Compute the derivative of f at x using finite differences"""
+    return (f(x + dx) - f(x - dx)) / (2 * dx)

peritheos-0.1.0.dist-info/METADATA

@@ -0,0 +1,145 @@
+Metadata-Version: 2.4
+Name: peritheos
+Version: 0.1.0
+Summary: A library for thermodynamic equations of state calculations
+Author-email: Clemens Prescher <clemens.prescher@gmail.com>
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/cprescher/peritheos
+Project-URL: Bug Tracker, https://github.com/cprescher/peritheos/issues
+Keywords: equation-of-state,high-pressure,thermodynamics
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Operating System :: OS Independent
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20.0
+Requires-Dist: scipy>=1.7.0
+Dynamic: license-file
+
+# Peritheos
+
+A Python library for thermodynamic equations of state calculations for solid materials.
+
+## Features
+
+- Room temperature equations of state (EOS) implementations
+  - Birch-Murnaghan
+  - Vinet
+  - Holzapfel
+- Thermal equations of state (EOS) implementations
+  - Sokolova 2016
+
+## Unit conventions
+
+- Public pressure and bulk-modulus values are in GPa.
+- Temperatures are in K.
+- Birch-Murnaghan and Vinet accept any consistent volume unit.
+- Holzapfel and Sokolova 2016 require molar volume in J bar^-1, which is
+  equivalent to cm^3/mol divided by 10.
+
+## Installation
+
+```bash
+pip install peritheos
+```
+
+The latest development version can instead be installed directly from GitHub:
+
+```bash
+pip install git+https://github.com/CPrescher/peritheos.git
+```
+
+## Usage
+
+### Room-temperature equations of state
+
+Third-order Birch-Murnaghan equation of state:
+
+```python
+from peritheos.eos.rt import BM3
+
+# V0 may use any volume unit for a room-temperature EOS; K0 is in GPa here.
+eos = BM3(V0=50, K0=130, K0_prime=4.3)
+
+# Calculate pressure and bulk modulus at a given volume.
+pressure = eos.pressure(V=40)
+bulk_modulus = eos.bulk_modulus(V=40)
+
+# Invert the EOS to calculate volume at a given pressure.
+volume = eos.volume(P=pressure)
+
+print(f"Pressure: {pressure} GPa")
+print(f"Bulk modulus: {bulk_modulus} GPa")
+print(f"Recovered volume: {volume}")
+```
+
+### Thermal equations of state
+
+Diamond thermal equation of state from sokolova et al. 2016
+
+```python
+from peritheos.eos.rt.holzapfel import Holzapfel
+from peritheos.eos.thermal.sokolova2016 import Sokolova2016
+
+# Diamond parameters from Sokolova et al. 2016.
+# The thermal model requires molar volume in J bar^-1 (= [cm^3/mol] / 10),
+# pressure parameters in GPa, and temperatures in K.
+V0 = 0.3414
+K0 = 441.5
+K0_prime = 3.9  # pressure derivative of bulk modulus at reference volume
+QE1o = 684  # first Einstein characteristic temperature
+mE1 = 0.564  # first Einstein number
+QE2o = 1561  # second Einstein characteristic temperature
+mE2 = 2.436  # second Einstein number
+delta = -0.506  # additive normalizing constant for the Gruneisen parameter
+t = 1.085  # generalized Gruneisen parameter
+a_0 = 0  # intrinsic anharmonicity parameter
+m = 0  # anharmonic analogue of the Grüneisen parameter
+e_0 = 0  # free electrons parameter
+g = 0  # electronic analogue of the Grüneisen parameter
+
+n = 1  # number of atoms in the formula unit
+z = 6  # atomic number of the formula unit
+Tr = 298.15  # in K - Reference temperature
+
+# Initialize the Holzapfel EOS
+holzapfel = Holzapfel(V0=V0, K0=K0, K0_prime=K0_prime, n=n, Z=z)
+
+# Initialize the Sokolova 2016 EOS
+sokolova = Sokolova2016(
+    rt_eos=holzapfel,
+    Tr=Tr,
+    QE1o=QE1o,
+    mE1=mE1,
+    QE2o=QE2o,
+    mE2=mE2,
+    delta=delta,
+    t=t,
+    a_0=a_0,
+    m=m,
+    g=g,
+    e_0=e_0,
+)
+
+# Calculate the thermal pressure at a given volume and temperature
+V = V0 * 0.8
+T = 3000  # in K
+thermal_pressure = sokolova.thermal_pressure(V, T)
+rt_pressure = holzapfel.pressure(V)
+pressure = sokolova.pressure(V, T)
+recovered_volume = sokolova.volume(pressure, T)
+
+print(f"Thermal pressure: {thermal_pressure} GPa")
+print(f"RT pressure: {rt_pressure} GPa")
+print(f"Total pressure: {pressure} GPa")
+print(f"Recovered volume: {recovered_volume} J bar^-1")
+```

peritheos-0.1.0.dist-info/RECORD

@@ -0,0 +1,17 @@
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+peritheos/utils.py,sha256=SL6KkLc5aEWi1QZABChgu0mVViW0qZEIuNF8eIjLRuw,2909
+peritheos/eos/__init__.py,sha256=W9Ls4PyN5HE99oI0k6ERINUAkS4KEkWSxfQgjBHrfF4,8253
+peritheos/eos/_reference/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+peritheos/eos/_reference/sokolova2016.py,sha256=OLuIzchEVW671q1ilC5OU-40e0Bp9SipEtkbuQDVJ_E,13618
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+peritheos/eos/thermal/__init__.py,sha256=A9UdhMQzNNuip6TL6BHzWSXVZ54TRqkGr8UC-1GfRqA,123
+peritheos/eos/thermal/sokolova2016.py,sha256=EKlNA6qLeIaTx4qY3JYGBhGadLEt-oiDw6sfQJytVos,7697
+peritheos-0.1.0.dist-info/licenses/LICENSE,sha256=Jv-O3-lgGTwh-_iFdgkgKJVlRumuV9pnYYbtxU9cV0A,1073
+peritheos-0.1.0.dist-info/METADATA,sha256=wdZ-NQvkEndzKxGJHTxhvkrC11AmoVAVZsEDEhYNgO8,4381
+peritheos-0.1.0.dist-info/WHEEL,sha256=K260EYznzXsJYBQGqmI8VTxEdiZYNvDZwW9cBh9-_MA,91
+peritheos-0.1.0.dist-info/top_level.txt,sha256=CdcVZr-nDIv7L-66y4zgjJMVzcDBFY1vVY27afjB9E0,10
+peritheos-0.1.0.dist-info/RECORD,,

peritheos-0.1.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (83.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

peritheos-0.1.0.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 Clemens Prescher
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

peritheos-0.1.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+peritheos