peritheos 0.1.0__py3-none-any.whl

peritheos/eos/_reference/sokolova2016.py

@@ -0,0 +1,527 @@
+"""
+Original thermal pressure equation of states formalisms from Sokolova et al. 2016.
+"""
+
+import numpy as np
+
+
+def P_thermal(
+    n,
+    z,
+    Vo,
+    Ko,
+    kk,
+    Tr,
+    x,
+    expp,
+    V,
+    QBo,
+    d,
+    mb,
+    QB1o,
+    d1,
+    mb1,
+    QE1o,
+    mE1,
+    QE2o,
+    mE2,
+    TK,
+    gamVo,
+    beta,
+    gb,
+    ao,
+    m,
+    mm,
+    ae,
+):
+    """
+    Original thermal pressure equation from sokolova et al. 2016.
+
+    Parameters
+    ----------
+    n : float
+        Number of atoms in the chemical formula
+    z : float
+        Atomic number of the chemical formula unit
+    Vo : float
+        Reference volume in [JBar^-1] (same as [cm^3/mol]/10)
+    Ko : float
+        Bulk modulus at reference volume [kbar]
+    kk : float
+        Bulk modulus derivative at reference volume
+    Tr : float
+        Reference temperature in [K] for the EOS (typically 298.15 K)
+    x : float
+        Fractional volume (V/Vo)
+    expp : float
+        unused in function
+    V : float
+        Volume in [JBar^-1] (same as [cm^3/mol]/10)
+    QBo : float
+        should be 1
+    d : float
+        should be 1
+    mb : float
+        should be 0
+    QB1o : float
+        should be 1
+    d1 : float
+        should be 1
+    mb1 : float
+        should be 0
+    QE1o : float
+        Einstein characteristic temperature, Theta_1 in [K]
+    mE1 : float
+        The first Einstein number
+    QE2o : float
+        Einstain characteristic temperature, Theta_02 in [K]
+    mE2 : float
+        The second Einstein number
+    TK : float
+        Temperature in [K]
+    gamVo : float
+        Additive normalizing constant for the Gruneisen parameter, (given as delta in Sokolova et al. 2016)
+    beta : float
+        Should be 0
+    gb : float
+        Generalized Gruneisen parameter, given as t in Sokolova et al. 2016
+    ao : float
+        Intrinsic anharmonicity parameter (10e-6 [K]), given as a_0 in Sokolova et al. 2016
+    m : float
+        Anharmonic analogue of the Grüneisen parameter
+    mm : float
+        Electronic analogue of the Grüneisen parameter, given as g in Sokolova et al. 2016
+    ae : float
+        Free electrons parameter (10e-6 [K]), given as e_0 in Sokolova et al. 2016
+
+    Returns
+    -------
+    Pth : float
+        Thermal pressure in [bar]
+    """
+    R = 8.31451
+
+    fw = -np.log(3 * Ko / 10 / (1003.6 * (z * n / (Vo * 10)) ** (5 / 3)))
+    ff = x ** (1 / 3)
+    aa = 1.5 * (kk - 3) - fw
+    Px = (
+        3
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff))
+        * (1 / ff**5 - 1 / ff**4)
+        * (1 + aa * ff - aa * ff**2)
+    )
+    KT = (
+        Ko
+        * 1000
+        / ff**6
+        * np.exp(fw * (1 - ff))
+        * (
+            (-5 / ff**2 + 4 / ff) * (1 + aa * ff - aa * ff**2)
+            + (1 / ff - 1) * (1 + aa * ff - aa * ff**2) * (-fw)
+            + (1 / ff - 1) * (aa - 2 * aa * ff)
+        )
+        * (-x)
+    )
+    ex = (
+        3
+        / ff**4
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff))
+        * (
+            (-5 / ff**2 + 4 / ff) * (1 + aa * ff - aa * ff**2)
+            - (1 / ff - 1) * (1 + aa * ff - aa * ff**2) * fw
+            + (1 / ff - 1) * (aa - 2 * aa * ff)
+        )
+    )
+    ex1 = (
+        1
+        / ff**3
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff))
+        * fw
+        * (
+            (-5 / ff**2 + 4 / ff) * (1 + aa * ff - aa * ff**2)
+            - (1 / ff - 1) * (1 + aa * ff - aa * ff**2) * fw
+            + (1 / ff - 1) * (aa - 2 * aa * ff)
+        )
+    )
+    ex2 = (
+        Ko
+        * 1000
+        * np.exp(fw * (1 - ff))
+        * (
+            (10 / ff**3 - 4 / ff**2) * (1 + aa * ff - aa * ff**2)
+            + (-5 / ff**2 + 4 / ff) * (aa - 2 * aa * ff)
+            + fw / ff**2 * (1 + aa * ff - aa * ff**2)
+            - (1 / ff - 1) * (aa - 2 * aa * ff) * fw
+            - (aa - 2 * aa * ff) / ff**2
+            - 2 * aa * (1 / ff - 1)
+        )
+        / ff**3
+    )
+    kkx = (ex + ex1 - ex2) / (-KT / ff) / 3
+
+    gt = gb - beta * x ** (1 / 3)
+    gtx = -beta / 3 * x ** (-2 / 3)
+    gamV = (-3 * KT + 2 * Px * gt + 9 * KT * kkx - 6 * gt * KT) / 6 / (
+        3 * KT - 2 * Px * gt
+    ) + gamVo
+    ff2 = (x + 0.00001) ** (1 / 3)
+    KT2 = (
+        Ko
+        * 1000
+        / ff2**6
+        * np.exp(fw * (1 - ff2))
+        * (
+            (-5 / ff2**2 + 4 / ff2) * (1 + aa * ff2 - aa * ff2**2)
+            + (1 / ff2 - 1) * (1 + aa * ff2 - aa * ff2**2) * (-fw)
+            + (1 / ff2 - 1) * (aa - 2 * aa * ff2)
+        )
+        * (-(x + 0.00001))
+    )
+    ex = (
+        3
+        / ff2**4
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff2))
+        * (
+            (-5 / ff2**2 + 4 / ff2) * (1 + aa * ff2 - aa * ff2**2)
+            - (1 / ff2 - 1) * (1 + aa * ff2 - aa * ff2**2) * fw
+            + (1 / ff2 - 1) * (aa - 2 * aa * ff2)
+        )
+    )
+    ex1 = (
+        1
+        / ff2**3
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff2))
+        * fw
+        * (
+            (-5 / ff2**2 + 4 / ff2) * (1 + aa * ff2 - aa * ff2**2)
+            - (1 / ff2 - 1) * (1 + aa * ff2 - aa * ff2**2) * fw
+            + (1 / ff2 - 1) * (aa - 2 * aa * ff2)
+        )
+    )
+    ex2 = (
+        Ko
+        * 1000
+        * np.exp(fw * (1 - ff2))
+        * (
+            (10 / ff2**3 - 4 / ff2**2) * (1 + aa * ff2 - aa * ff2**2)
+            + (-5 / ff2**2 + 4 / ff2) * (aa - 2 * aa * ff2)
+            + fw / ff2**2 * (1 + aa * ff2 - aa * ff2**2)
+            - (1 / ff2 - 1) * (aa - 2 * aa * ff2) * fw
+            - (aa - 2 * aa * ff2) / ff2**2
+            - 2 * aa * (1 / ff2 - 1)
+        )
+        / ff2**3
+    )
+    kkx2 = (ex + ex1 - ex2) / (-KT2 / ff2) / 3
+    ff1 = (x - 0.00001) ** (1 / 3)
+    KT1 = (
+        Ko
+        * 1000
+        / ff1**6
+        * np.exp(fw * (1 - ff1))
+        * (
+            (-5 / ff1**2 + 4 / ff1) * (1 + aa * ff1 - aa * ff1**2)
+            + (1 / ff1 - 1) * (1 + aa * ff1 - aa * ff1**2) * (-fw)
+            + (1 / ff1 - 1) * (aa - 2 * aa * ff1)
+        )
+        * (-(x - 0.00001))
+    )
+    ex = (
+        3
+        / ff1**4
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff1))
+        * (
+            (-5 / ff1**2 + 4 / ff1) * (1 + aa * ff1 - aa * ff1**2)
+            - (1 / ff1 - 1) * (1 + aa * ff1 - aa * ff1**2) * fw
+            + (1 / ff1 - 1) * (aa - 2 * aa * ff1)
+        )
+    )
+    ex1 = (
+        1
+        / ff1**3
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff1))
+        * fw
+        * (
+            (-5 / ff1**2 + 4 / ff1) * (1 + aa * ff1 - aa * ff1**2)
+            - (1 / ff1 - 1) * (1 + aa * ff1 - aa * ff1**2) * fw
+            + (1 / ff1 - 1) * (aa - 2 * aa * ff1)
+        )
+    )
+    ex2 = (
+        Ko
+        * 1000
+        * np.exp(fw * (1 - ff1))
+        * (
+            (10 / ff1**3 - 4 / ff1**2) * (1 + aa * ff1 - aa * ff1**2)
+            + (-5 / ff1**2 + 4 / ff1) * (aa - 2 * aa * ff1)
+            + fw / ff1**2 * (1 + aa * ff1 - aa * ff1**2)
+            - (1 / ff1 - 1) * (aa - 2 * aa * ff1) * fw
+            - (aa - 2 * aa * ff1) / ff1**2
+            - 2 * aa * (1 / ff1 - 1)
+        )
+        / ff1**3
+    )
+    kkx1 = (ex + ex1 - ex2) / (-KT1 / ff1) / 3
+
+    dkkdx = (kkx2 - kkx1) / (0.00002)
+
+    qV = (
+        -1
+        / 2
+        * (
+            -6 * KT * kkx**2 * Px * gt / x
+            + 6 * KT * dkkdx * Px * gt
+            + 6 * KT * kkx * KT * gt / x
+            - 6 * KT * kkx * Px * gtx
+            + 4 * gt**2 * KT * kkx * Px / x
+            - 4 * gt**2 * KT**2 / x
+            - 9 * KT**2 * dkkdx
+            + 6 * gtx * KT**2
+        )
+        / (3 * KT - 2 * Px * gt) ** 2
+        * x
+        / gamV
+    )
+    a = ao / 1000000 * x**m
+
+    QB = QBo * expp
+    QB1 = QB1o * expp
+    QE1 = QE1o * expp
+    QE2 = QE2o * expp
+
+    ggr = d * np.log(1 + QB / Tr / d)
+    br = 1 / (np.exp(ggr) - 1)
+    ex1r = np.exp(QB / Tr)
+    PBr = (
+        mb * R * ((QB * (d - 1) / 2 / d + Tr * QB * d * br / (Tr * d + QB)) * gamV / V)
+    )
+
+    gg = d * np.log(1 + QB / TK / d)
+    b = 1 / (np.exp(gg) - 1)
+    ex1 = np.exp(QB / TK)
+    PB = mb * R * ((QB * (d - 1) / 2 / d + TK * QB * d * b / (TK * d + QB)) * gamV / V)
+
+    gg1r = d1 * np.log(1 + QB1 / Tr / d1)
+    b1r = 1 / (np.exp(gg1r) - 1)
+    ex2r = np.exp(QB1 / Tr)
+    PB1r = (
+        mb1
+        * R
+        * ((QB1 * (d1 - 1) / 2 / d1 + Tr * QB1 * d1 * b1r / (Tr * d1 + QB1)) * gamV / V)
+    )
+
+    gg1 = d1 * np.log(1 + QB1 / TK / d1)
+    b1 = 1 / (np.exp(gg1) - 1)
+    ex2 = np.exp(QB1 / TK)
+    PB1 = (
+        mb1
+        * R
+        * ((QB1 * (d1 - 1) / 2 / d1 + TK * QB1 * d1 * b1 / (TK * d1 + QB1)) * gamV / V)
+    )
+
+    e1 = np.exp(QE1 / TK)
+    PE1 = mE1 * R * ((QE1 / 2 + QE1 / (e1 - 1)) * gamV / V)
+
+    e2 = np.exp(QE2 / TK)
+    PE2 = mE2 * R * ((QE2 / 2 + QE2 / (e2 - 1)) * gamV / V)
+
+    e1r = np.exp(QE1 / Tr)
+    PE1r = mE1 * R * ((QE1 / 2 + QE1 / (e1r - 1)) * gamV / V)
+
+    e2r = np.exp(QE2 / Tr)
+    PE2r = mE2 * R * ((QE2 / 2 + QE2 / (e2r - 1)) * gamV / V)
+    Pea = 3 / 2 * n * R * ao / 1000000 * x ** (m) * (m) / V * (TK**2 - Tr**2)
+    Pee = 3 / 2 * n * R * ae / 1000000 * x ** (mm) * (mm) / V * (TK**2 - Tr**2)
+
+    Pth = PB + PB1 + PE1 + PE2 - PBr - PB1r - PE1r - PE2r + Pee + Pea
+    return Pth
+
+
+def I_gamV(z, n, b, Vo, Ko, kk, gamVo, gb, beta, e=0.001):
+    """
+    Integral of the Gruneisen parameter over the volume.
+
+    Parameters
+    ----------
+    z : float
+        Atomic number of the chemical formula unit
+    n : float
+        Number of atoms in the chemical formula
+    b : float
+        Fractional volume (V/V0)
+    Vo : float
+        Reference volume in [JBar^-1] (same as [cm^3/mol]/10)
+    Ko : float
+        Bulk modulus at reference volume [kbar]
+    kk : float
+        Bulk modulus derivative at reference volume
+    gamVo : float
+        Additive normalizing constant for the Gruneisen parameter, (given as delta in Sokolova et al. 2016)
+    gb : float
+        Generalized Gruneisen parameter, given as t in Sokolova et al. 2016
+    beta : float
+        Anharmonic analogue of the Grüneisen parameter
+    e : float
+        Tolerance for the integration
+
+    Returns
+    -------
+    I_gamV : float
+        Integral of the Gruneisen parameter over the volume
+
+    """
+    # check whether b is greater than 1
+    a = min(b, 1)
+    b = max(b, 1)
+
+    # calculate the integral using the trapezoidal rule
+    s2 = 1
+    h = b - a
+    S = f_gamV(a, n, z, Vo, Ko, kk, gamVo, gb, beta) + f_gamV(
+        b, n, z, Vo, Ko, kk, gamVo, gb, beta
+    )
+
+    while True:
+        s3 = s2
+        h /= 2
+        s1 = 0
+        x = a + h
+
+        while x < b:
+            s1 += 2 * f_gamV(x, n, z, Vo, Ko, kk, gamVo, gb, beta)
+            x += 2 * h
+
+        S += s1
+        s2 = (S + s1) * h / 3
+        error = abs(s3 - s2) / 15
+
+        if error < e:
+            break
+
+    return -s2 if b > 1 else s2
+
+
+def f_gamV(x, n, z, Vo, Ko, kk, gamVo, gb, beta):
+    """
+    Helper function to calculate the Gruneisen parameter at a given temperature and pressure.
+
+    Parameters
+    ----------
+    x : float
+        Fractional volume (V/Vo)
+    n : float
+        Number of atoms in the chemical formula
+    z : float
+        Atomic number of the chemical formula unit
+    Vo : float
+        Reference volume in [JBar^-1] (same as [cm^3/mol]/10)
+    Ko : float
+        Bulk modulus at reference volume [kbar]
+    kk : float
+        Bulk modulus derivative at reference volume
+    gamVo : float
+        Additive normalizing constant for the Gruneisen parameter, (given as delta in Sokolova et al. 2016)
+    gb : float
+        Generalized Gruneisen parameter, given as t in Sokolova et al. 2016
+    beta : float
+        Anharmonic analogue of the Grüneisen parameter
+
+    Returns
+    -------
+    f_gamV_value : float
+        Gruneisen parameter at a given temperature and pressure
+    """
+    fw = -np.log(3 * Ko / 10 / (1003.6 * (z * n / (Vo * 10)) ** (5 / 3)))
+    ff = x ** (1 / 3)
+    aa = 1.5 * (kk - 3) - fw
+
+    KT = (
+        Ko
+        * 1000
+        / ff**6
+        * np.exp(fw * (1 - ff))
+        * (
+            (-5 / ff**2 + 4 / ff) * (1 + aa * ff - aa * ff**2)
+            + (1 / ff - 1) * (1 + aa * ff - aa * ff**2) * (-fw)
+            + (1 / ff - 1) * (aa - 2 * aa * ff)
+        )
+        * (-x)
+    )
+
+    Px = (
+        3
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff))
+        * (1 / ff**5 - 1 / ff**4)
+        * (1 + aa * ff - aa * ff**2)
+    )
+
+    ex = (
+        3
+        / ff**4
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff))
+        * (
+            (-5 / ff**2 + 4 / ff) * (1 + aa * ff - aa * ff**2)
+            - (1 / ff - 1) * (1 + aa * ff - aa * ff**2) * fw
+            + (1 / ff - 1) * (aa - 2 * aa * ff)
+        )
+    )
+
+    ex1 = (
+        1
+        / ff**3
+        * Ko
+        * 1000
+        * np.exp(fw * (1 - ff))
+        * fw
+        * (
+            (-5 / ff**2 + 4 / ff) * (1 + aa * ff - aa * ff**2)
+            - (1 / ff - 1) * (1 + aa * ff - aa * ff**2) * fw
+            + (1 / ff - 1) * (aa - 2 * aa * ff)
+        )
+    )
+
+    ex2 = (
+        Ko
+        * 1000
+        * np.exp(fw * (1 - ff))
+        * (
+            (10 / ff**3 - 4 / ff**2) * (1 + aa * ff - aa * ff**2)
+            + (-5 / ff**2 + 4 / ff) * (aa - 2 * aa * ff)
+            + fw / ff**2 * (1 + aa * ff - aa * ff**2)
+            - (1 / ff - 1) * (aa - 2 * aa * ff) * fw
+            - (aa - 2 * aa * ff) / ff**2
+            - 2 * aa * (1 / ff - 1)
+        )
+        / ff**3
+    )
+
+    kkx = (ex + ex1 - ex2) / (-KT / ff) / 3
+
+    gt = gb - beta * x ** (1 / 3)
+    gtx = -beta / 3 * x ** (-2 / 3)
+
+    f_gamV_value = (
+        gamVo
+        + (-3 * KT + 2 * Px * gt + 9 * KT * kkx - 6 * gt * KT)
+        / (6 * (3 * KT - 2 * Px * gt))
+    ) / x
+
+    return f_gamV_value

peritheos/eos/rt/__init__.py

@@ -0,0 +1,7 @@
+"""
+This module contains the room temperature equations of state (EOS) implementations.
+"""
+
+from .holzapfel import Holzapfel
+from .bm import BM2, BM3, BM4
+from .vinet import Vinet