removed unused functions, fixed attribute function for solution fitting

refactored seismo output
updated tests

Author: bobmyhill

Readme.md

@@ -1,6 +1,6 @@
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.14238360.svg)](https://doi.org/10.5281/zenodo.14238360)
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.05389/status.svg)](https://doi.org/10.21105/joss.05389)
-[![coverage](https://img.shields.io/badge/coverage-%3E86%25-green")](https://github.com/geodynamics/burnman/actions/workflows/coverage.yml)
+[![coverage](https://img.shields.io/badge/coverage-%3E90%25-green")](https://github.com/geodynamics/burnman/actions/workflows/coverage.yml)
 
 # BurnMan - a Python toolkit for planetary geophysics, geochemistry and thermodynamics
 

burnman/eos/dks_solid.py

@@ -124,12 +124,6 @@ def _isotropic_eta_s(self, x, params):
 
         return eta_s
 
-    # calculate isotropic thermal pressure, see
-    # Matas et. al. (2007) eq B4
-    def _thermal_pressure(self, T, V, params):
-        gr = self.grueneisen_parameter(0.0, T, V, params)  # P not important
-        return params["Cv"] * (T - params["T_0"]) * gr
-
     def volume(self, pressure, temperature, params):
         """
         Returns molar volume. :math:`[m^3]`
@@ -202,16 +196,6 @@ def isothermal_bulk_modulus_reuss(self, pressure, temperature, volume, params):
 
         return K
 
-    def isentropic_bulk_modulus_reuss(self, pressure, temperature, volume, params):
-        """
-        Returns adiabatic bulk modulus. :math:`[Pa]`
-        """
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        alpha = self.thermal_expansivity(pressure, temperature, volume, params)
-        gr = self.grueneisen_parameter(pressure, temperature, volume, params)
-        K_S = K_T * (1.0 + gr * alpha * temperature)
-        return K_S
-
     def shear_modulus(self, pressure, temperature, volume, params):
         """
         Returns shear modulus. :math:`[Pa]`
@@ -260,14 +244,6 @@ def gibbs_free_energy(self, pressure, temperature, volume, params):
         )
         return G
 
-    def molar_internal_energy(self, pressure, temperature, volume, params):
-        """
-        Returns the internal energy at the pressure and temperature of the mineral [J/mol]
-        """
-        return self.helmholtz_free_energy(
-            pressure, temperature, volume, params
-        ) + temperature * self.entropy(pressure, temperature, volume, params)
-
     def entropy(self, pressure, temperature, volume, params):
         """
         Returns the entropy at the pressure and temperature of the mineral [J/K/mol]
@@ -282,17 +258,6 @@ def entropy(self, pressure, temperature, volume, params):
 
         return S_0 + S_th
 
-    def enthalpy(self, pressure, temperature, volume, params):
-        """
-        Returns the enthalpy at the pressure and temperature of the mineral [J/mol]
-        """
-
-        return (
-            self.helmholtz_free_energy(pressure, temperature, volume, params)
-            + temperature * self.entropy(pressure, temperature, volume, params)
-            + pressure * volume
-        )
-
     def helmholtz_free_energy(self, pressure, temperature, volume, params):
         """
         Returns the Helmholtz free energy at the pressure and temperature of the mineral [J/mol]

burnman/eos/hp.py

@@ -45,16 +45,6 @@ def pressure(self, temperature, volume, params):
         Pth = self.__relative_thermal_pressure(temperature, params)
         return mt.modified_tait(params["V_0"] / volume, params) + Pth
 
-    def grueneisen_parameter(self, pressure, temperature, volume, params):
-        """
-        Returns grueneisen parameter [unitless] as a function of pressure,
-        temperature, and volume.
-        """
-        alpha = self.thermal_expansivity(pressure, temperature, volume, params)
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        C_V = self.molar_heat_capacity_v(pressure, temperature, volume, params)
-        return alpha * K_T * volume / C_V
-
     def isothermal_bulk_modulus_reuss(self, pressure, temperature, volume, params):
         """
         Returns isothermal bulk modulus [Pa] as a function of pressure [Pa],
@@ -72,18 +62,6 @@ def shear_modulus(self, pressure, temperature, volume, params):
         """
         return 0.0
 
-    # Cv, heat capacity at constant volume
-    def molar_heat_capacity_v(self, pressure, temperature, volume, params):
-        """
-        Returns heat capacity at constant volume at the pressure, temperature,
-        and volume [J/K/mol].
-        """
-        C_p = self.molar_heat_capacity_p(pressure, temperature, volume, params)
-        V = self.volume(pressure, temperature, params)
-        alpha = self.thermal_expansivity(pressure, temperature, volume, params)
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        return C_p - V * temperature * alpha * alpha * K_T
-
     def thermal_expansivity(self, pressure, temperature, volume, params):
         """
         Returns thermal expansivity at the pressure, temperature,
@@ -121,29 +99,6 @@ def molar_heat_capacity_p0(self, temperature, params):
         )
         return Cp
 
-    def molar_heat_capacity_p_einstein(self, pressure, temperature, volume, params):
-        """
-        Returns heat capacity at constant pressure at the pressure,
-        temperature, and volume, using the C_v and Einstein model [J/K/mol]
-        WARNING: Only for comparison with internally self-consistent C_p
-        """
-        alpha = self.thermal_expansivity(pressure, temperature, volume, params)
-        gr = self.grueneisen_parameter(pressure, temperature, volume, params)
-        C_v = self.molar_heat_capacity_v(pressure, temperature, volume, params)
-        C_p = C_v * (1.0 + gr * alpha * temperature)
-        return C_p
-
-    def isentropic_bulk_modulus_reuss(self, pressure, temperature, volume, params):
-        """
-        Returns adiabatic bulk modulus [Pa] as a function of pressure [Pa],
-        temperature [K], and volume [m^3].
-        """
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        C_p = self.molar_heat_capacity_p(pressure, temperature, volume, params)
-        C_v = self.molar_heat_capacity_v(pressure, temperature, volume, params)
-        K_S = K_T * C_p / C_v
-        return K_S
-
     def gibbs_free_energy(self, pressure, temperature, volume, params):
         """
         Returns the gibbs free energy [J/mol] as a function of pressure [Pa]
@@ -182,11 +137,6 @@ def gibbs_free_energy(self, pressure, temperature, volume, params):
             + intVdP
         )
 
-    def helmholtz_free_energy(self, pressure, temperature, volume, params):
-        return self.gibbs_free_energy(
-            pressure, temperature, volume, params
-        ) - pressure * self.volume(pressure, temperature, params)
-
     def entropy(self, pressure, temperature, volume, params):
         """
         Returns the entropy [J/K/mol] as a function of pressure [Pa]
@@ -209,15 +159,6 @@ def entropy(self, pressure, temperature, volume, params):
         )
         return params["S_0"] + self.__intCpoverTdT(temperature, params) + dintVdpdT
 
-    def enthalpy(self, pressure, temperature, volume, params):
-        """
-        Returns the enthalpy [J/mol] as a function of pressure [Pa]
-        and temperature [K].
-        """
-        gibbs = self.gibbs_free_energy(pressure, temperature, volume, params)
-        entropy = self.entropy(pressure, temperature, volume, params)
-        return gibbs + temperature * entropy
-
     def molar_heat_capacity_p(self, pressure, temperature, volume, params):
         """
         Returns the heat capacity [J/K/mol] as a function of pressure [Pa]
@@ -422,24 +363,6 @@ def volume(self, pressure, temperature, params):
         self.static_params["K_0"] = self._K_T_1bar(temperature, params)
         return mt.volume(pressure, self.static_params)
 
-    def pressure(self, temperature, volume, params):
-        """
-        Returns pressure [Pa] as a function of temperature [K] and volume[m^3]
-        """
-        self.static_params["V_0"] = self._V_T_1bar(temperature, params)
-        self.static_params["K_0"] = self._K_T_1bar(temperature, params)
-        return mt.pressure(volume, self.static_params)
-
-    def grueneisen_parameter(self, pressure, temperature, volume, params):
-        """
-        Returns grueneisen parameter [unitless] as a function of pressure,
-        temperature, and volume.
-        """
-        alpha = self.thermal_expansivity(pressure, temperature, volume, params)
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        C_V = self.molar_heat_capacity_v(pressure, temperature, volume, params)
-        return alpha * K_T * volume / C_V
-
     def isothermal_bulk_modulus_reuss(self, pressure, temperature, volume, params):
         """
         Returns isothermal bulk modulus [Pa] as a function of pressure [Pa],
@@ -458,18 +381,6 @@ def shear_modulus(self, pressure, temperature, volume, params):
         """
         return 0.0
 
-    # Cv, heat capacity at constant volume
-    def molar_heat_capacity_v(self, pressure, temperature, volume, params):
-        """
-        Returns heat capacity at constant volume at the pressure, temperature,
-        and volume [J/K/mol].
-        """
-        C_p = self.molar_heat_capacity_p(pressure, temperature, volume, params)
-        V = self.volume(pressure, temperature, params)
-        alpha = self.thermal_expansivity(pressure, temperature, volume, params)
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        return C_p - V * temperature * alpha * alpha * K_T
-
     def thermal_expansivity(self, pressure, temperature, volume, params):
         """
         Returns thermal expansivity at the pressure, temperature,
@@ -502,17 +413,6 @@ def molar_heat_capacity_p0(self, temperature, params):
         )
         return Cp
 
-    def isentropic_bulk_modulus_reuss(self, pressure, temperature, volume, params):
-        """
-        Returns adiabatic bulk modulus [Pa] as a function of pressure [Pa],
-        temperature [K], and volume [m^3].
-        """
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        C_p = self.molar_heat_capacity_p(pressure, temperature, volume, params)
-        C_v = self.molar_heat_capacity_v(pressure, temperature, volume, params)
-        K_S = K_T * C_p / C_v
-        return K_S
-
     def gibbs_free_energy(self, pressure, temperature, volume, params):
         """
         Returns the gibbs free energy [J/mol] as a function of pressure [Pa]
@@ -527,11 +427,6 @@ def gibbs_free_energy(self, pressure, temperature, volume, params):
             + mt.intVdP(pressure, self.static_params)
         )
 
-    def helmholtz_free_energy(self, pressure, temperature, volume, params):
-        return self.gibbs_free_energy(
-            pressure, temperature, volume, params
-        ) - pressure * self.volume(pressure, temperature, params)
-
     def entropy(self, pressure, temperature, volume, params):
         """
         Returns the entropy [J/K/mol] as a function of pressure [Pa]
@@ -546,15 +441,6 @@ def entropy(self, pressure, temperature, volume, params):
 
         return (G0 - G1) / dT
 
-    def enthalpy(self, pressure, temperature, volume, params):
-        """
-        Returns the enthalpy [J/mol] as a function of pressure [Pa]
-        and temperature [K].
-        """
-        gibbs = self.gibbs_free_energy(pressure, temperature, volume, params)
-        entropy = self.entropy(pressure, temperature, volume, params)
-        return gibbs + temperature * entropy
-
     def molar_heat_capacity_p(self, pressure, temperature, volume, params):
         """
         Returns the heat capacity [J/K/mol] as a function of pressure [Pa]
@@ -697,27 +583,6 @@ def volume(self, pressure, temperature, params):
             params["Kprime_0"],
         )
 
-    def pressure(self, temperature, volume, params):
-        """
-        Returns pressure [Pa] as a function of temperature [K] and volume[m^3]
-        """
-        return murn.pressure(
-            volume,
-            self._V_T_1bar(temperature, params),
-            self._K_T_1bar(temperature, params),
-            params["Kprime_0"],
-        )
-
-    def grueneisen_parameter(self, pressure, temperature, volume, params):
-        """
-        Returns grueneisen parameter [unitless] as a function of pressure,
-        temperature, and volume.
-        """
-        alpha = self.thermal_expansivity(pressure, temperature, volume, params)
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        C_V = self.molar_heat_capacity_v(pressure, temperature, volume, params)
-        return alpha * K_T * volume / C_V
-
     def isothermal_bulk_modulus_reuss(self, pressure, temperature, volume, params):
         """
         Returns isothermal bulk modulus [Pa] as a function of pressure [Pa],
@@ -736,18 +601,6 @@ def shear_modulus(self, pressure, temperature, volume, params):
         """
         return 0.0
 
-    # Cv, heat capacity at constant volume
-    def molar_heat_capacity_v(self, pressure, temperature, volume, params):
-        """
-        Returns heat capacity at constant volume at the pressure, temperature,
-        and volume [J/K/mol].
-        """
-        C_p = self.molar_heat_capacity_p(pressure, temperature, volume, params)
-        V = self.volume(pressure, temperature, params)
-        alpha = self.thermal_expansivity(pressure, temperature, volume, params)
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        return C_p - V * temperature * alpha * alpha * K_T
-
     def thermal_expansivity(self, pressure, temperature, volume, params):
         """
         Returns thermal expansivity at the pressure, temperature,
@@ -782,17 +635,6 @@ def molar_heat_capacity_p0(self, temperature, params):
         )
         return Cp
 
-    def isentropic_bulk_modulus_reuss(self, pressure, temperature, volume, params):
-        """
-        Returns adiabatic bulk modulus [Pa] as a function of pressure [Pa],
-        temperature [K], and volume [m^3].
-        """
-        K_T = self.isothermal_bulk_modulus_reuss(pressure, temperature, volume, params)
-        C_p = self.molar_heat_capacity_p(pressure, temperature, volume, params)
-        C_v = self.molar_heat_capacity_v(pressure, temperature, volume, params)
-        K_S = K_T * C_p / C_v
-        return K_S
-
     def gibbs_free_energy(self, pressure, temperature, volume, params):
         """
         Returns the gibbs free energy [J/mol] as a function of pressure [Pa]
@@ -810,11 +652,6 @@ def gibbs_free_energy(self, pressure, temperature, volume, params):
             )
         )
 
-    def helmholtz_free_energy(self, pressure, temperature, volume, params):
-        return self.gibbs_free_energy(
-            pressure, temperature, volume, params
-        ) - pressure * self.volume(pressure, temperature, params)
-
     def entropy(self, pressure, temperature, volume, params):
         """
         Returns the entropy [J/K/mol] as a function of pressure [Pa]
@@ -838,15 +675,6 @@ def entropy(self, pressure, temperature, volume, params):
         dintVdpdT = dVTdT * g + VT * dgdKT * params["dKdT_0"]
         return params["S_0"] + self.__intCpoverTdT(temperature, params) - dintVdpdT
 
-    def enthalpy(self, pressure, temperature, volume, params):
-        """
-        Returns the enthalpy [J/mol] as a function of pressure [Pa]
-        and temperature [K].
-        """
-        gibbs = self.gibbs_free_energy(pressure, temperature, volume, params)
-        entropy = self.entropy(pressure, temperature, volume, params)
-        return gibbs + temperature * entropy
-
     def molar_heat_capacity_p(self, pressure, temperature, volume, params):
         """
         Returns the heat capacity [J/K/mol] as a function of pressure [Pa]

burnman/optimize/nonlinear_fitting.py

@@ -425,7 +425,7 @@ def corner_plot(popt, pcov, param_names=[], n_std=1.0):
                 )
             )
 
-    fig.set_tight_layout(True)
+    fig.set_layout_engine("tight")
 
     return fig, ax