zoomy-core 0.1.11__py3-none-any.whl

zoomy_core/model/models/core.py

@@ -0,0 +1,564 @@
+try:
+    import jax.numpy as jnp
+    _HAVE_JAX = True
+except ImportError:
+    _HAVE_JAX = False
+    import numpy as jnp
+
+import numpy as np
+
+import sympy
+
+from sympy import (
+    Matrix,
+    lambdify,
+    powsimp,
+    init_printing,
+    zeros
+)
+
+from typing import Union, Callable
+from types import SimpleNamespace
+from attrs import define, field
+
+
+
+from library.model.boundary_conditions import BoundaryConditions
+from library.model.initial_conditions import InitialConditions, Constant
+from library.python.misc.misc import Zstruct
+
+init_printing()
+
+
+def vectorize_constant_sympy_expressions(expr, Q, Qaux):
+    symbol_list = Q.get_list() + Qaux.get_list()
+    q0 = Q[0]
+
+    rows, cols = expr.shape
+
+    new_data = []
+
+    for i in range(rows):
+        row = []
+        for j in range(cols):
+            entry = expr[i, j]
+            if not any(symbol in entry.free_symbols for symbol in symbol_list):
+                if entry == 0:
+                    row.append(10 ** (-20) * q0)
+                else:
+                    row.append(entry + 10 ** (-20) * q0)
+            else:
+                row.append(entry)
+        new_data.append(row)
+
+    return Matrix(new_data)
+
+def default_simplify(expr):
+    return powsimp(expr, combine="all", force=False, deep=True)
+
+def get_default_function_arguments():
+    return Zstruct(
+        time=sympy.symbols("t", real=True),
+        position=register_sympy_attribute(3, "X"),
+        distance=sympy.symbols("dX", real=True),
+        p=register_sympy_attribute(0, "p_"),
+        n=register_sympy_attribute(3, "n"),
+    )
+
+@define(frozen=True, slots=True, kw_only=True)
+class Core:
+    """
+    Generic (virtual) model implementation.
+    """
+    
+    boundary_conditions: BoundaryConditions 
+    
+    name: str = "Model"
+    dimension: int = 1
+
+    initial_conditions: InitialConditions = field(factory=Constant)
+    aux_initial_conditions: InitialConditions = field(factory=Constant)
+    
+    parameters: Zstruct = field(factory=lambda: Zstruct())
+    
+    function_arguments: Zstruct = field(factory=lambda: get_default_function_arguments())
+    variables: Zstruct = field(init=False, default=1)
+    positive_variables: Union[dict, list, None] = field(default=None)
+    aux_variables: Zstruct = field(default=0)
+
+
+
+    _simplify: Callable = field(factory=lambda: default_simplify)
+
+    # Derived fields initialized in __attrs_post_init__
+    _default_parameters: dict = field(init=False, factory=dict)
+    n_variables: int = field(init=False)
+    n_aux_variables: int = field(init=False)
+    n_parameters: int = field(init=False)
+    parameter_symbols: Zstruct = field(init=False)
+    
+
+
+    def __attrs_post_init__(self):
+        
+        # Use object.__setattr__ because class is frozen
+        object.__setattr__(self, "variables", register_sympy_attribute(self.variables, "q", self.positive_variables))
+        object.__setattr__(self, "aux_variables", register_sympy_attribute(self.aux_variables, "qaux"))
+        # object.__setattr__(self, "position", register_sympy_attribute(self.dimension, "X"))
+
+        object.__setattr__(self, "parameters_symbols", register_sympy_attribute(self.parameters, "p"))
+        object.__setattr__(self, "parameters", register_parameter_values(self.parameters))
+        object.__setattr__(
+            self, "normal",
+            register_sympy_attribute(["n" + str(i) for i in range(self.dimension)], "n")
+        )
+
+        object.__setattr__(self, "n_variables", self.variables.length())
+        object.__setattr__(self, "n_aux_variables", self.aux_variables.length())
+        object.__setattr__(self, "n_parameters", self.parameters.length())
+        
+    def initialize_boundary_conditions(self, mesh):
+        self.boundary_conditions.initialize(
+            mesh,
+            self.time,
+            self.position,
+            self.distance,
+            self.variables,
+            self.aux_variables,
+            self.parameters,
+            self.normal,
+        )
+        
+    def print_boundary_conditions(self):
+        inputs = self.get_boundary_conditions_matrix_inputs()
+        return self.boundary_conditions.get_boundary_function_matrix(*inputs)
+    
+    def squeeze(self, printer='jax'):
+        if printer == 'jax':
+            return jnp.squeeze
+        elif printer == 'numpy':
+            return np.squeeze
+        else:
+            assert False
+    
+    def array(self, printer='jax'):
+        if printer == 'jax':
+            return jnp.array
+        elif printer == 'numpy':
+            return np.array
+        else:
+            assert False
+    
+        
+    def get_boundary_conditions_matrix_inputs(self):
+        """
+        Returns the inputs for the boundary conditions matrix.
+        """
+        return (
+            self.time,
+            self.position,
+            self.distance,
+            self.variables,
+            self.aux_variables,
+            self.parameters,
+            self.normal,
+        )
+        
+    def get_boundary_conditions_matrix_inputs_as_list(self):
+        """
+        Returns the inputs for the boundary conditions matrix where the Zstructs are converted to lists.
+        """
+        return [
+            self.time,
+            self.position.get_list(),
+            self.distance,
+            self.variables.get_list(),
+            self.aux_variables.get_list(),
+            self.parameters.get_list(),
+            self.normal.get_list(),
+        ]
+
+
+    def _get_boundary_conditions(self, printer="jax"):
+        """Returns a runtime boundary_conditions for jax arrays from the symbolic model."""
+        n_boundary_functions = len(self.boundary_conditions.boundary_functions)
+        bcs = []
+        for i in range(n_boundary_functions):
+            func_bc = lambdify(
+                [
+                    self.time,
+                    self.position.get_list(),
+                    self.distance,
+                    self.variables.get_list(),
+                    self.aux_variables.get_list(),
+                    self.parameters.get_list(),
+                    self.normal.get_list(),
+                ],
+                vectorize_constant_sympy_expressions(self.boundary_conditions.boundary_functions[i], self.variables, self.aux_variables),
+                printer,
+            )
+            # the func=func part is necessary, because of https://stackoverflow.com/questions/46535577/initialising-a-list-of-lambda-functions-in-python/46535637#46535637
+            f = (
+                lambda time,
+                position,
+                distance,
+                q,
+                qaux,
+                p,
+                n,
+                func=func_bc: self.squeeze(printer=printer)(
+                    self.array(printer=printer)(func(time, position, distance, q, qaux, p, n)), axis=1
+                )
+            )
+            bcs.append(f)
+        return bcs
+
+    def _get_pde(self, printer="jax"):
+        """Returns a runtime model for numpy arrays from the symbolic model."""
+        l_flux = [
+            lambdify(
+                (
+                    self.variables.get_list(),
+                    self.aux_variables.get_list(),
+                    self.parameters.get_list(),
+                ),
+                vectorize_constant_sympy_expressions(
+                    self.flux()[d], self.variables, self.aux_variables
+                ),
+                printer,
+            )
+            for d in range(self.dimension)
+        ]
+        # the f=l_flux[d] part is necessary, because of https://stackoverflow.com/questions/46535577/initialising-a-list-of-lambda-functions-in-python/46535637#46535637
+        flux = [
+            lambda Q, Qaux, param, f=l_flux[d]: self.squeeze(printer=printer)(
+                self.array(printer=printer)(f(Q, Qaux, param)), axis=1
+            )
+            for d in range(self.dimension)
+        ]
+        l_flux_jacobian = lambdify(
+            [
+                self.variables.get_list(),
+                self.aux_variables.get_list(),
+                self.parameters.get_list(),
+            ],
+            self.flux_jacobian(),
+            printer,
+        )
+        flux_jacobian = l_flux_jacobian
+
+        l_nonconservative_matrix = [
+            lambdify(
+                [
+                    self.variables.get_list(),
+                    self.aux_variables.get_list(),
+                    self.parameters.get_list(),
+                ],
+                vectorize_constant_sympy_expressions(
+                    self.nonconservative_matrix()[d],
+                    self.variables,
+                    self.aux_variables,
+                ),
+                printer,
+            )
+            for d in range(self.dimension)
+        ]
+        nonconservative_matrix = [
+            lambda Q, Qaux, param, f=l_nonconservative_matrix[d]: f(Q, Qaux, param)
+            for d in range(self.dimension)
+        ]
+
+        l_quasilinear_matrix = [
+            lambdify(
+                [
+                    self.variables.get_list(),
+                    self.aux_variables.get_list(),
+                    self.parameters.get_list(),
+                ],
+                vectorize_constant_sympy_expressions(
+                    self.quasilinear_matrix()[d], self.variables, self.aux_variables
+                ),
+                printer,
+            )
+            for d in range(self.dimension)
+        ]
+        quasilinear_matrix = l_quasilinear_matrix
+
+        l_eigenvalues = lambdify(
+            [
+                self.variables.get_list(),
+                self.aux_variables.get_list(),
+                self.parameters.get_list(),
+                self.normal.get_list(),
+            ],
+            vectorize_constant_sympy_expressions(
+                self.eigenvalues(), self.variables, self.aux_variables
+            ),
+            printer,
+        )
+
+        def eigenvalues(Q, Qaux, param, normal):
+            return jnp.squeeze(
+                jnp.array(l_eigenvalues(Q, Qaux, param, normal)), axis=1
+            )
+
+        l_left_eigenvectors = lambdify(
+            [
+                self.variables.get_list(),
+                self.aux_variables.get_list(),
+                self.parameters.get_list(),
+                self.normal.get_list(),
+            ],
+            vectorize_constant_sympy_expressions(
+                self.left_eigenvectors(), self.variables, self.aux_variables
+            ),
+            printer,
+        )
+
+        def left_eigenvectors(Q, Qaux, param, normal):
+            return self.squeeze(printer=printer)(
+                self.array(printer=printer)(l_left_eigenvectors(Q, Qaux, param, normal)), axis=1
+            )
+
+
+        l_right_eigenvectors = lambdify(
+            [
+                self.variables.get_list(),
+                self.aux_variables.get_list(),
+                self.parameters.get_list(),
+                self.normal.get_list(),
+            ],
+            vectorize_constant_sympy_expressions(
+                self.right_eigenvectors(), self.variables, self.aux_variables
+            ),
+            printer,
+        )
+
+        def right_eigenvectors(Q, Qaux, param, normal):
+            return self.squeeze(printer=printer)(
+                self.array(printer=printer)(l_right_eigenvectors(Q, Qaux, param, normal)), axis=1
+            )
+            
+        
+
+        l_source = lambdify(
+            [
+                self.variables.get_list(),
+                self.aux_variables.get_list(),
+                self.parameters.get_list(),
+            ],
+            vectorize_constant_sympy_expressions(
+                self.source(), self.variables, self.aux_variables
+            ),
+            printer,
+        )
+
+        def source(Q, Qaux, param):
+            return self.squeeze(printer=printer)(self.array(printer=printer)(l_source(Q, Qaux, param)), axis=1)
+
+
+        l_source_jacobian = lambdify(
+            [
+                self.variables.get_list(),
+                self.aux_variables.get_list(),
+                self.parameters.get_list(),
+            ],
+            vectorize_constant_sympy_expressions(
+                self.source_jacobian(), self.variables, self.aux_variables
+            ),
+            printer,
+        )
+        source_jacobian = l_source_jacobian
+
+        l_source_implicit = lambdify(
+            [
+                self.variables.get_list(),
+                self.aux_variables.get_list(),
+                self.parameters.get_list(),
+            ],
+            vectorize_constant_sympy_expressions(
+                self.source_implicit(), self.variables, self.aux_variables
+            ),
+            printer,
+        )
+        def source_implicit(Q, Qaux, param):
+            return self.squeeze(printer=printer)(self.array(printer=printer)(l_source_implicit(Q, Qaux, param)), axis=1)
+        
+        l_residual = lambdify(
+            [
+                self.variables.get_list(),
+                self.aux_variables.get_list(),
+                self.parameters.get_list(),
+            ],
+            vectorize_constant_sympy_expressions(
+                self.residual(), self.variables, self.aux_variables
+            ),
+            printer,
+        )
+        def residual(Q, Qaux, param):
+            return self.squeeze(printer=printer)(self.array(printer=printer)(l_residual(Q, Qaux, param)), axis=1)
+
+
+        l_interpolate_3d = lambdify(
+            [
+                self.position.get_list(),
+                self.variables.get_list(),
+                self.aux_variables.get_list(),
+                self.parameters.get_list(),
+            ],
+            vectorize_constant_sympy_expressions(
+                self.interpolate_3d(), self.variables, self.aux_variables
+            ),
+            printer,
+        )
+        def interpolate_3d(X, Q, Qaux, param):
+            return self.squeeze(printer=printer)(self.array(printer=printer)(l_interpolate_3d(X, Q, Qaux, param)), axis=1)
+
+
+
+        left_eigenvectors = None
+        right_eigenvectors = None
+        d = {
+            "flux": flux,
+            "flux_jacobian": flux_jacobian,
+            "nonconservative_matrix": nonconservative_matrix,
+            "quasilinear_matrix": quasilinear_matrix,
+            "eigenvalues": eigenvalues,
+            "left_eigenvectors": left_eigenvectors,
+            "right_eigenvectors": right_eigenvectors,
+            "source": source,
+            "source_jacobian": source_jacobian,
+            "source_implicit": source_implicit,
+            "residual": residual,
+            "interpolate_3d": interpolate_3d,
+        }
+        return SimpleNamespace(**d)
+
+    def flux(self):
+        return [Matrix(self.variables[:]) for d in range(self.dimension)]
+
+    def nonconservative_matrix(self):
+        return [zeros(self.n_variables, self.n_variables) for d in range(self.dimension)]
+
+    def source(self):
+        return zeros(self.n_variables, 1)
+
+    def flux_jacobian(self):
+        """ generated automatically unless explicitly provided """
+        return [ self._simplify(
+                Matrix(self.flux()[d]).jacobian(self.variables),
+            ) for d in range(self.dimension) ]
+
+    def quasilinear_matrix(self):
+        """ generated automatically unless explicitly provided """
+        return [ self._simplify(
+                Matrix(self.flux_jacobian()[d] + self.nonconservative_matrix()[d],
+            )
+        ) for d in range(self.dimension) ]
+
+    def source_jacobian(self):
+        """ generated automatically unless explicitly provided """
+        return self._simplify(
+                Matrix(self.source()).jacobian(self.variables),
+            )
+
+    def source_implicit(self):
+        return zeros(self.n_variables, 1)
+
+    def residual(self):
+        return zeros(self.n_variables, 1)
+    
+    def interpolate_3d(self):
+        return zeros(6, 1)
+
+
+    def eigenvalues(self):
+        A = self.normal[0] * self.quasilinear_matrix()[0]
+        for d in range(1, self.dimension):
+            A += self.normal[d] * self.quasilinear_matrix()[d]
+        return self._simplify(eigenvalue_dict_to_matrix(A.eigenvals()))
+    
+    def left_eigenvectors(self):
+        return zeros(self.n_variables, self.n_variables)
+    
+    def right_eigenvectors(self):
+        return zeros(self.n_variables, self.n_variables)
+    
+    def substitute_precomputed_denominator(self, expr, sym, sym_inv):
+        if isinstance(expr, sympy.MatrixBase):
+            return expr.applyfunc(lambda e: self.substitute_precomputed_denominator(e, sym, sym_inv))
+
+        num, den = sympy.fraction(expr)
+        if den.has(sym):
+            # split into (part involving sym, part not involving sym)
+            den_sym, den_rest = den.as_independent(sym, as_Add=False)
+            # careful: as_independent returns (independent, dependent)
+            # so we need to swap naming
+            den_rest, den_sym = den_sym, den_rest
+
+            # replace sym by sym_inv in the sym-dependent part
+            den_sym_repl = den_sym.xreplace({sym: sym_inv})
+
+            return self.substitute_precomputed_denominator(num, sym, sym_inv) * den_sym_repl / den_rest
+        elif expr.args:
+            return expr.func(*[self.substitute_precomputed_denominator(arg, sym, sym_inv) for arg in expr.args])
+        else:
+            return expr
+
+def transform_positive_variable_intput_to_list(argument, positive, n_variables):
+    out = [False for _ in range(n_variables)]
+    if positive is None:
+        return out
+    if type(positive) == type({}):
+        assert type(argument) == type(positive)
+        for i, a in enumerate(argument.keys()):
+            if a in positive.keys():
+                out[i] = positive[a]
+    if type(positive) == list:
+        for i in positive:
+            out[i] = True
+    return out
+
+def register_sympy_attribute(argument, string_identifier="q_", positives=None):
+    if type(argument) == int:
+        positive = transform_positive_variable_intput_to_list(argument, positives, argument)
+        attributes = {
+            string_identifier + str(i): sympy.symbols(
+                string_identifier + str(i), real=True, positive=positive[i]
+            )
+            for i in range(argument)
+        }
+    elif type(argument) == type({}):
+        positive = transform_positive_variable_intput_to_list(argument, positives, len(argument))
+        attributes = {
+            name: sympy.symbols(str(name), real=True, positive=pos) for name, pos in zip(argument.keys(), positive)
+        }
+    elif type(argument) == list:
+        positive = transform_positive_variable_intput_to_list(argument, positives, len(argument))
+        attributes = {name: sympy.symbols(str(name), real=True, positive=pos) for name, pos in zip(argument, positive)}
+    elif type(argument) == Zstruct:
+        d = argument.as_dict()
+        register_sympy_attribute(d, string_identifier, positives)
+    else:
+        assert False
+    return Zstruct(**attributes)
+
+
+def register_parameter_symbols(parameters):
+    if type(parameters) == type({}):
+        for k, v in parameters.items():
+            parameters[k] = sympy.symbols(str(k), real=True)
+    elif type(parameters) == Zstruct:
+        d = parameters.as_dict()
+        register_parameter_symbols(d)
+    else:
+        assert False
+    return register_sympy_attribute(parameters, "p_")
+
+
+def eigenvalue_dict_to_matrix(eigenvalues, simplify=default_simplify):
+    evs = []
+    for ev, mult in eigenvalues.items():
+        for i in range(mult):
+            evs.append(simplify(ev))
+    return Matrix(evs)

zoomy_core/model/models/coupled_constrained.py

@@ -0,0 +1,60 @@
+import numpy as np
+import numpy.polynomial.legendre as L
+import numpy.polynomial.chebyshev as C
+from scipy.optimize import least_squares as lsq
+import sympy
+from sympy import Matrix
+from sympy.abc import x
+
+from sympy import integrate, diff
+from sympy import legendre
+from sympy import lambdify
+
+from zoomy_core.model.basemodel import (
+    register_sympy_attribute,
+    eigenvalue_dict_to_matrix,
+)
+from zoomy_core.model.basemodel import Model
+import zoomy_core.model.initial_conditions as IC
+
+class CoupledConstrained(Model):
+    def __init__(
+        self,
+        boundary_conditions,
+        initial_conditions,
+        dimension=2,
+        fields=2,
+        aux_variables=4,
+        parameters={},
+        _default_parameters={},
+        settings={},
+        settings_default={},
+    ):
+        self.variables = register_sympy_attribute(fields, "q")
+        self.n_variables = self.variables.length()
+        super().__init__(
+            dimension=dimension,
+            fields=fields,
+            aux_variables=aux_variables,
+            parameters=parameters,
+            _default_parameters=_default_parameters,
+            boundary_conditions=boundary_conditions,
+            initial_conditions=initial_conditions,
+            settings={**settings_default, **settings},
+        )
+
+
+    def source_implicit(self):
+        out = Matrix([0 for i in range(2)])
+        u = self.variables[0]
+        p = self.variables[1]
+        param = self.parameters
+        dudt = self.aux_variables.dudx
+        dudx = self.aux_variables.dudx
+        dpdx = self.aux_variables.dpdx
+        f = self.aux_variables.f
+        out[0] = dudt + dpdx  + 1
+        out[1] = dudx + f
+        # out[0] = dudx -1.
+        # out[1] = dpdx
+        return out

zoomy_core/model/models/poisson.py

@@ -0,0 +1,41 @@
+import numpy as np
+import numpy.polynomial.legendre as L
+import numpy.polynomial.chebyshev as C
+from scipy.optimize import least_squares as lsq
+import sympy
+from sympy import Matrix, sqrt
+from sympy.abc import x
+from attr import define, field
+
+from sympy import integrate, diff
+from sympy import legendre
+from sympy import lambdify
+
+from zoomy_core.misc.misc import Zstruct
+from zoomy_core.model.basemodel import (
+    register_sympy_attribute,
+    eigenvalue_dict_to_matrix,
+)
+from zoomy_core.model.basemodel import Model
+import zoomy_core.model.initial_conditions as IC
+
+
+@define(kw_only=True, slots=True, frozen=True)
+class Poisson(Model):
+    dimension: int = 1
+    variables: Zstruct = field(init=False, default=1)
+    aux_variables: Zstruct = field(factory = lambda: ['ddTdxx', 'ddTdyy', 'ddTdzz'])
+    
+            
+    def residual(self):
+        R = Matrix([0 for i in range(self.n_variables)])
+        T = self.variables[0]
+        ddTdxx = self.aux_variables.ddTdxx
+        param = self.parameters
+
+        R[0] = - ddTdxx + 2
+        return R
+        
+
+    
+