gebpy 1.1.3__py3-none-any.whl

gebpy/core/minerals/phyllosilicates.py

@@ -0,0 +1,436 @@
+#!/usr/bin/env python
+# -*-coding: utf-8 -*-
+
+#-----------------------------------------------
+
+# Name:		phyllosilicates.py
+# Author:	Maximilian A. Beeskow
+# Version:	1.0
+# Date:		15.12.2025
+
+#-----------------------------------------------
+
+"""
+Module: phyllosilicates.py
+This module controls the generation of the synthetic data of the phyllosilicate minerals.
+"""
+
+# PACKAGES
+import yaml
+import numpy as np
+from pathlib import Path
+
+from asteval import Interpreter
+
+# MODULES
+from ..chemistry.common import PeriodicSystem
+from ..chemistry.geochemistry import MineralChemistry
+from ..physics.geophysics import WellLog as wg
+
+from .common import (
+    GeophysicalProperties,
+    CrystallographicProperties,
+    CrystalPhysics,
+    MineralGeneration as MinGen
+)
+
+# CODE
+BASE_PATH = Path(__file__).resolve().parents[2]
+DATA_PATH = BASE_PATH / "data_minerals"
+
+class Phyllosilicates:
+    _yaml_cache = {}
+    _formula_cache = {}
+    _minerals = {
+        "Annite", "Eastonite", "Illite", "Kaolinite", "Phlogopite", "Siderophyllite", "Chamosite", "Clinochlore",
+        "Pennantite", "Nimite", "Muscovite", "Talc", "Chrysotile", "Antigorite", "Pyrophyllite", "Montmorillonite",
+        "Nontronite", "Saponite", "Glauconite", "Vermiculite", "Chlorite", "Biotite", "FeChlorite", "MgChlorite",
+        "MnChlorite", "NiChlorite"}
+
+    def __init__(self, name, random_seed, rounding=3) -> None:
+        self.name = name
+        self.random_seed = random_seed
+        self.rng = np.random.default_rng(random_seed)
+        self.current_seed = int(np.round(self.rng.uniform(0, 1000), 0))
+        self.data_path = DATA_PATH
+        self.rounding = rounding
+        self.ae = Interpreter()
+        self.cache = {}
+
+        # Chemistry
+        self.elements = {
+            "H": PeriodicSystem(name="H").get_data(),
+            "O": PeriodicSystem(name="O").get_data(),
+            "Na": PeriodicSystem(name="Na").get_data(),
+            "Mg": PeriodicSystem(name="Mg").get_data(),
+            "Al": PeriodicSystem(name="Al").get_data(),
+            "Si": PeriodicSystem(name="Si").get_data(),
+            "K": PeriodicSystem(name="K").get_data(),
+            "Ca": PeriodicSystem(name="Ca").get_data(),
+            "Mn": PeriodicSystem(name="Mn").get_data(),
+            "Fe": PeriodicSystem(name="Fe").get_data(),
+            "Ni": PeriodicSystem(name="Ni").get_data(),
+        }
+
+        # Geophysics
+        self.geophysical_properties = GeophysicalProperties()
+        # Crystallography
+        self.crystallographic_properties = CrystallographicProperties()
+
+        # Mineral-specific data
+        if self.name in [
+            "Annite", "Eastonite", "Illite", "Kaolinite", "Phlogopite", "Siderophyllite", "Chamosite", "Clinochlore",
+            "Pennantite", "Nimite", "Muscovite", "Talc", "Chrysotile", "Antigorite", "Pyrophyllite", "Montmorillonite",
+            "Nontronite", "Saponite", "Glauconite", "Vermiculite", "Chlorite", "FeChlorite", "MgChlorite", "MnChlorite",
+            "NiChlorite"]:
+            self.yaml_data = self._load_yaml(self.name.lower())
+        if self.name == "Biotite":
+            self.yaml_data = {
+                mineral.lower(): self._load_yaml(mineral.lower())
+                for mineral in ["Annite", "Phlogopite", "Siderophyllite", "Eastonite"]}
+        elif self.name == "Chlorite":
+            self.yaml_data = {
+                mineral.lower(): self._load_yaml(mineral.lower())
+                for mineral in ["FeChlorite", "MgChlorite", "MnChlorite", "NiChlorite"]}
+
+    def _load_yaml(self, mineral_name: str) -> dict:
+        # 1) Cache-Hit
+        if mineral_name in Phyllosilicates._yaml_cache:
+            return Phyllosilicates._yaml_cache[mineral_name]
+
+        # 2) Laden von Disk
+        yaml_file = self.data_path/f"{mineral_name}.yaml"
+        if not yaml_file.exists():
+            raise FileNotFoundError(f"No YAML file found for {mineral_name}.")
+
+        with open(yaml_file, "r") as f:
+            data = yaml.safe_load(f)
+
+        if "chemistry" in data and mineral_name not in Phyllosilicates._formula_cache:
+            self._compile_chemistry_formulas(mineral_name, data["chemistry"])
+
+        # 3) Cache schreiben
+        Phyllosilicates._yaml_cache[mineral_name] = data
+
+        return data
+
+    def _get_value(self, data: dict, path: list[str], default=None):
+        """Safely extract a float or string value from nested YAML data."""
+        try:
+            for key in path:
+                data = data[key]
+            if isinstance(data, dict) and "value" in data:
+                return float(data["value"])
+            else:
+                return data  # kann z.B. ein String oder eine Zahl sein
+        except (KeyError, TypeError):
+            return default
+
+    def _get_variables(self):
+        if self.name == "Glauconite":
+            x = round(self.rng.uniform(0, 1), 2)
+            y1 = round(self.rng.uniform(0, 1), 2)
+            y2 = round(self.rng.uniform(0, 1 - y1), 2)
+            z = round(self.rng.uniform(0, 1), 2)
+            return {"x": x, "y1": y1, "y2": y2, "z": z}
+        elif self.name == "Vermiculite":
+            x = round(self.rng.uniform(0, 1), 2)
+            y = round(self.rng.uniform(0, (1 - x)), 2)
+            z = round(self.rng.uniform(0, 1), 2)
+            return {"x": x, "y": y, "z": z}
+        elif self.name == "Chlorite":
+            x = round(self.rng.uniform(0, 1), 2)
+            y = round(self.rng.uniform(0, (1 - x)), 2)
+            upper = max(0, (1 - x - y))
+            z = round(self.rng.uniform(0, upper), 2)
+            return {"x": x, "y": y, "z": z}
+        else:
+            if "variables" not in self.yaml_data:
+                return {}
+            vars = {}
+            for k, v in self.yaml_data["variables"].items():
+                if isinstance(v[0], int):
+                    vars[k] = self.rng.integers(v[0], v[1])
+                else:
+                    vars[k] = round(self.rng.uniform(v[0], v[1]), 2)
+            return vars
+
+    def generate_dataset(self, number: int = 1, as_dataframe=False) -> None:
+        fixed = {
+            "Annite", "Eastonite", "Illite", "Kaolinite", "Phlogopite", "Siderophyllite",
+            "Chamosite", "Clinochlore", "Pennantite", "Nimite", "Muscovite",
+            "Talc", "Chrysotile", "Antigorite", "Pyrophyllite", "FeChlorite", "MgChlorite", "MnChlorite", "NiChlorite"}
+        variable = {"Montmorillonite", "Nontronite", "Saponite", "Glauconite", "Vermiculite"}
+        endmember = {"Biotite", "Chlorite"}
+        generators = {
+            **{m: MinGen(
+                name=self.name, yaml_data=self.yaml_data, elements=self.elements, cache=self.cache,
+                geophysical_properties=self.geophysical_properties, rounding=self.rounding
+            ).create_mineral_data_fixed_composition for m in fixed},
+            **{m: self.create_mineral_data_variable_composition for m in variable},
+            **{m: self.create_mineral_data_endmember_series for m in endmember},
+        }
+
+        if self.name not in generators:
+            raise ValueError(f"Mineral '{self.name}' not recognized.")
+
+        dataset = {}
+        if self.name in fixed:
+            dataset = self._evaluate_mineral(index=1, generators=generators, dataset=dataset)
+        else:
+            for index in range(number):
+                dataset = self._evaluate_mineral(index=index, generators=generators, dataset=dataset)
+
+        if as_dataframe:
+            import pandas as pd
+            return pd.DataFrame(dataset)
+        else:
+            return dataset
+
+    def _evaluate_mineral(self, index, generators, dataset):
+        self.current_seed = np.uint32(self.random_seed + index)
+        data_mineral = generators[self.name]()
+
+        for key, value in data_mineral.items():
+            if key in ["M", "rho", "rho_e", "V", "vP", "vS", "vP/vS", "K", "G", "E", "nu", "GR", "PE", "U",
+                       "p"]:
+                if key not in dataset:
+                    dataset[key] = [value]
+                else:
+                    dataset[key].append(value)
+            elif key in ["mineral", "state", "trace elements"] and key not in dataset:
+                dataset[key] = value
+            elif key in ["chemistry", "compounds"]:
+                if key not in dataset:
+                    dataset[key] = {}
+                    for key_2, value_2 in value.items():
+                        dataset[key][key_2] = [value_2]
+                else:
+                    for key_2, value_2 in value.items():
+                        dataset[key][key_2].append(value_2)
+        return dataset
+
+    def _compile_chemistry_formulas(self, mineral_name: str, chemistry_dict: dict):
+        """
+        Extracts and compiles all chemistry formulas from the YAML file.
+        Stores the compiled ASTs in the global formula cache.
+        """
+
+        compiled = {}
+
+        for element, entry in chemistry_dict.items():
+
+            # Fall A: Einfache Zahl (z.B. 2, 3.5)
+            if isinstance(entry, (int, float)):
+                expr = str(entry)
+            # Fall B: dict mit 'formula'
+            elif isinstance(entry, dict) and "formula" in entry:
+                expr = str(entry["formula"])
+            # Fall C: Alles andere ist invalid
+            else:
+                raise ValueError(
+                    f"Invalid chemistry entry for element '{element}' in {mineral_name}.yaml: {entry}")
+            # AST kompilieren
+            compiled[element] = self.ae.parse(expr)
+        # Cache schreiben
+        Phyllosilicates._formula_cache[mineral_name] = compiled
+
+    def _evaluate_chemistry(self, chemistry_dict, **variables):
+        """
+        Evaluates algebraic expressions of element amounts defined in the YAML file.
+
+        Parameters:
+            chemistry_dict (dict): Dictionary from YAML containing element formulas as strings.
+            **variables: Variable assignments (e.g. x=0.5, y=1, n=8)
+
+        Returns:
+            dict: {element: calculated_amount}
+        """
+        self.ae.symtable.clear()
+
+        # Variablen setzen
+        for k, v in variables.items():
+            self.ae.symtable[k] = v
+
+        results = {}
+        compiled = Phyllosilicates._formula_cache[self.name.lower()]
+
+        for el in chemistry_dict:
+            results[el] = self.ae.run(compiled[el])
+
+        return results
+
+    def _extract_values_from_yaml(self):
+        vals = {}
+        # Physical parameters
+        for key in ["K", "G", "a_K", "b_K", "a_G", "b_G"]:
+            if key in self.yaml_data.get("physical_properties", {}):
+                vals[key] = float(self.yaml_data["physical_properties"][key]["value"])
+        # Cell parameters
+        for key in ["a", "b", "c", "alpha", "beta", "gamma", "Z"]:
+            if key in self.yaml_data.get("cell_data", {}):
+                vals[key] = float(self.yaml_data["cell_data"][key]["value"])
+        # Meta data
+        vals["key"] = self.yaml_data["metadata"]["key"]
+        vals["crystal_system"] = self.yaml_data["metadata"]["crystal_system"]
+
+        return vals
+
+    def _determine_majors_data(self):
+        majors_data = []
+        molar_mass_pure = 0
+        vars = self._get_variables()
+        amounts_elements = self._evaluate_chemistry(self.yaml_data["chemistry"], **vars)
+        for element, amount in amounts_elements.items():
+            n_order = int(self.elements[element][1])
+            val_amount = float(amount)
+            molar_mass = float(self.elements[element][2])
+            majors_data.append([element, n_order, val_amount, molar_mass])
+            molar_mass_pure += val_amount*molar_mass
+        majors_data.sort(key=lambda x: x[1])
+        return majors_data, amounts_elements, molar_mass_pure, vars
+
+    def _calculate_molar_mass_amounts(self, amounts_elements):
+        molar_mass = 0
+        for element, amount in amounts_elements.items():
+            molar_mass += amount*float(self.elements[element][2])
+
+        amounts = []
+        for element, amount in amounts_elements.items():
+            value = amount*float(self.elements[element][2])/molar_mass
+            amounts.append([element, self.elements[element][1], value])
+        element = [self.elements[name] for name, *_ in amounts]
+        return molar_mass, amounts, element
+
+    def _determine_volume_constructor(self, vals):
+        val_a = vals["a"]
+        val_system = vals["crystal_system"]
+        if val_system in ["isometric", "cubic"]:
+            constr_vol = CrystalPhysics([[val_a], [], val_system])
+        elif val_system in ["tetragonal", "hexagonal", "trigonal"]:
+            val_c = vals["c"]
+            constr_vol = CrystalPhysics([[val_a, val_c], [], val_system])
+        elif val_system in ["orthorhombic"]:
+            val_b = vals["b"]
+            val_c = vals["c"]
+            constr_vol = CrystalPhysics([[val_a, val_b, val_c], [], val_system])
+        elif val_system in ["monoclinic"]:
+            val_b = vals["b"]
+            val_c = vals["c"]
+            val_beta = vals["beta"]
+            constr_vol = CrystalPhysics([[val_a, val_b, val_c], [val_beta], val_system])
+        elif val_system in ["triclinic"]:
+            val_b = vals["b"]
+            val_c = vals["c"]
+            val_alpha = vals["alpha"]
+            val_beta = vals["beta"]
+            val_gamma = vals["gamma"]
+            constr_vol = CrystalPhysics([[val_a, val_b, val_c], [val_alpha, val_beta, val_gamma], val_system])
+        return constr_vol
+
+    def create_mineral_data_variable_composition(self):
+        """
+        Synthetic mineral data generation for an user-selected mineral.
+        All mechanical properties (K, G, E) are stored in Pascals internally.
+        For output, they are converted to GPa.
+        """
+        name_lower = self.name.lower()
+        # Chemistry
+        val_state = "variable"
+        traces_data = []
+        # Molar mass, elemental amounts
+        majors_data, amounts_elements, molar_mass_pure, vars = self._determine_majors_data()
+
+        if name_lower not in self.cache:
+            vals = self._extract_values_from_yaml()
+            self.cache[name_lower] = {"constants": vals}
+        else:
+            vals = self.cache[name_lower]["constants"]
+            constr_vol = self.cache[name_lower]["constr_vol"]
+
+        # Molar mass, element amounts
+        molar_mass, amounts, element = self._calculate_molar_mass_amounts(amounts_elements=amounts_elements)
+
+        # Reading and assigning the mineral-specific information from the YAML file
+        val_key = vals["key"]
+        val_Z = vals["Z"]
+        if "K" in vals:
+            val_K = vals["K"]
+            val_G = vals["G"]
+        else:
+            val_a_K = float(vals["a_K"])
+            val_b_K = float(vals["b_K"])
+            val_a_G = float(vals["a_G"])
+            val_b_G = float(vals["b_G"])
+
+        # (Molar) Volume
+        if "constr_vol" not in self.cache[name_lower]:
+            constr_vol = self._determine_volume_constructor(vals=vals)
+            self.cache[name_lower]["constr_vol"] = constr_vol
+
+        constr_minchem = MineralChemistry(w_traces=traces_data, molar_mass_pure=molar_mass_pure, majors=majors_data)
+        V, V_m = self.crystallographic_properties.calculate_molar_volume(
+            constr_volume=constr_vol, constr_molar_volume=constr_minchem, cell_z=val_Z)
+        # Density
+        constr_density = CrystalPhysics([molar_mass, val_Z, V])
+        rho = self.crystallographic_properties.calculate_mineral_density(constr_density=constr_density)
+        constr_electr_density = wg(amounts=amounts, elements=element, rho_b=rho)
+        rho_e = self.crystallographic_properties.calculate_electron_density(
+            constr_electron_density=constr_electr_density)
+
+        # Elastic properties
+        if "K" not in vals:
+            val_K = (val_a_K*rho + val_b_K)*10**9
+            val_G = (val_a_G*rho + val_b_G)*10**9
+        E, nu = self.geophysical_properties.calculate_elastic_properties(bulk_mod=val_K, shear_mod=val_G)
+        # Seismic properties
+        vPvS, vP, vS = self.geophysical_properties.calculate_seismic_velocities(
+            bulk_mod=val_K, shear_mod=val_G, rho=rho)
+        # Radiation properties
+        constr_radiation = wg(amounts=amounts, elements=element)
+        gamma_ray, pe, U = self.geophysical_properties.calculate_radiation_properties(
+            constr_radiation=constr_radiation, rho_electron=rho_e)
+        # Electrical resistivity
+        p = None
+        # Results
+        results = {
+            "mineral": val_key, "state": val_state, "M": round(molar_mass, self.rounding),
+            "chemistry": {name: round(val[1], 6) for name, *val in amounts}, "rho": round(rho, self.rounding),
+            "rho_e": round(rho_e, self.rounding), "V": round(V_m, self.rounding), "vP": round(vP, self.rounding),
+            "vS": round(vS, self.rounding), "vP/vS": round(vPvS, self.rounding),
+            "K": round(val_K*10**(-9), self.rounding), "G": round(val_G*10**(-9), self.rounding),
+            "E": round(E*10**(-9), self.rounding), "nu": round(nu, 6), "GR": round(gamma_ray, self.rounding),
+            "PE": round(pe, self.rounding), "U": round(U, self.rounding), "p": p}
+        return results
+
+    def create_mineral_data_endmember_series(self):
+        """
+        Synthetic mineral data generation for an user-selected mineral.
+        All mechanical properties (K, G, E) are stored in Pascals internally.
+        For output, they are converted to GPa.
+        """
+        endmember_series = {
+            "Biotite": {
+                "name_lower": "biotite",
+                "key": "Bt",
+                "endmembers": ["Annite", "Phlogopite", "Siderophyllite", "Eastonite"],
+                "oxides": ["K2O", "FeO", "MgO", "Al2O3", "SiO2", "H2O"]
+            },
+            "Chlorite": {
+                "name_lower": "chlorite",
+                "key": "Bt",
+                "endmembers": ["FeChlorite", "MgChlorite", "MnChlorite", "NiChlorite"],
+                "oxides": ["FeO", "MgO", "MnO", "NiO", "Al2O3", "SiO2", "H2O"]
+            }
+        }
+        results = MinGen(
+            name=self.name, yaml_data=self.yaml_data, elements=self.elements, cache=self.cache,
+            geophysical_properties=self.geophysical_properties,
+            rounding=self.rounding).create_mineral_data_endmember_series(
+            endmember_series=endmember_series, var_class=Phyllosilicates, current_seed=self.current_seed, rng=self.rng)
+
+        return results
+
+# TEST
+if __name__ == "__main__":
+    DEFAULT_DATA = Phyllosilicates(name="Annite", random_seed=42).generate_dataset(number=10)