zoomy-core 0.1.11__py3-none-any.whl

zoomy_core/__init__.py

@@ -0,0 +1,7 @@
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version("zoomy-core")
+except PackageNotFoundError:
+    # Package not installed, e.g. running from source
+    __version__ = "0.0.0"

zoomy_core/decorators/decorators.py

@@ -0,0 +1,25 @@
+
+def require(requirement):
+    """
+    Decorator to check if a requirement is met before executing the decorated function.
+
+    Parameters:
+    - requirement (str): The requirement string to evaluate. Should evaluate to True or False.
+
+    Returns:
+    - wrapper: The decorated function that will check the requirement before executing.
+    """
+
+    # decorator to check the assertion given in requirements given the settings
+    def req_decorator(func):
+        @wraps(func)
+        def wrapper(settings, *args, **kwargs):
+            requirement_evaluated = eval(requirement)
+            if not requirement_evaluated:
+                print("Requirement {}: {}".format(requirement, requirement_evaluated))
+                assert requirement_evaluated
+            return func(settings, *args, **kwargs)
+
+        return wrapper
+
+    return req_decorator

zoomy_core/fvm/flux.py

@@ -0,0 +1,52 @@
+import numpy as np
+
+
+class Flux:
+    def get_flux_operator(self, model):
+        pass
+
+
+class Zero(Flux):
+    def get_flux_operator(self, model):
+        def compute(Qi, Qj, Qauxi, Qauxj, parameters, normal, Vi, Vj, Vij, dt):
+            return np.zeros_like(Qi)
+
+        return compute
+
+
+class LaxFriedrichs(Flux):    
+    """
+    Lax-Friedrichs flux implementation
+    """
+    def get_flux_operator(self, model):
+        def compute(Qi, Qj, Qauxi, Qauxj, parameters, normal, Vi, Vj, Vij, dt):
+            Fi = np.einsum("id..., d...-> i...", model.flux(Qi, Qauxi, parameters), normal)
+            Fj = np.einsum("id..., d...-> i...", model.flux(Qj, Qauxj, parameters), normal)
+            Qout = 0.5 * (Fi + Fj)
+            Qout -= 0.5 * dt / (Vi + Vj) * (Qj - Qi)
+            return Qout
+        return compute
+    
+class Rusanov(Flux):
+    def __init__(self, identity_matrix=None):
+        if not identity_matrix:
+            self.Id = lambda n: np.eye(n)
+        else:
+            self.Id = identity_matrix
+    """
+    Rusanov (local Lax-Friedrichs) flux implementation
+    """
+    def get_flux_operator(self, model):
+        Id_single = self.Id(model.n_variables)
+        def compute(Qi, Qj, Qauxi, Qauxj, parameters, normal, Vi, Vj, Vij, dt):
+            EVi = model.eigenvalues(Qi, Qauxi, parameters, normal)
+            EVj = model.eigenvalues(Qj, Qauxj, parameters, normal)
+            smax = np.max(np.abs(np.hstack([EVi, EVj])))
+            Id = np.stack([Id_single]*Qi.shape[1], axis=2)  # (n_eq, n_eq, n_points)
+            Fi = np.einsum("id..., d...-> i...", model.flux(Qi, Qauxi, parameters), normal)
+            Fj = np.einsum("id..., d...-> i...", model.flux(Qj, Qauxj, parameters), normal)
+            Qout = 0.5 * (Fi + Fj)
+            Qout -= 0.5 * smax * np.einsum("ij..., jk...-> ik...", Id, (Qj - Qi))
+            return Qout
+        return compute 
+            

zoomy_core/fvm/nonconservative_flux.py

@@ -0,0 +1,97 @@
+import numpy as np
+from numpy.polynomial.legendre import leggauss
+from functools import partial
+
+class NonconservativeFlux:
+    def get_flux_operator(self, model):
+        pass
+
+
+class Zero(NonconservativeFlux):
+    def get_flux_operator(self, model):
+        def compute(Qi, Qj, Qauxi, Qauxj, parameters, normal, Vi, Vj, Vij, dt):
+            return np.zeros_like(Qi), np.zeros_like(Qi)
+
+        return compute
+    
+class Rusanov(NonconservativeFlux):
+    def __init__(self, integration_order=3, identity_matrix=None, eps=1e-10):
+        self.integration_order = integration_order
+        samples, weights = leggauss(integration_order)
+        # shift from [-1, 1] to [0,1]
+        samples = 0.5 * (samples + 1)
+        weights *= 0.5
+        self.wi = np.array(weights)
+        self.xi = np.array(samples)
+        self.Id = identity_matrix if identity_matrix else lambda n: np.eye(n)
+        self.eps = eps
+        
+    def _get_A(self, model):
+        def A(q, qaux, parameters, n):                      
+            # q : (n_dof,)
+            # evaluate the matrices A_d
+            _A = model.quasilinear_matrix(q, qaux, parameters)
+            return np.einsum('d...,ijd...->ij...', n, _A)
+        return A
+    
+    def _integrate_path(self, model):
+        compute_A = self._get_A(model)
+        def compute(Qi, Qj,
+                            Qauxi, Qauxj,
+                            parameters,
+                            normal):
+            dQ     =  Qj    - Qi
+            dQaux  =  Qauxj - Qauxi
+            
+            A_int = np.zeros((Qi.shape[0], Qi.shape[0], Qi.shape[1]))
+            
+            for xi, wi in zip(self.xi, self.wi):
+                q_path     = Qi   + xi * dQ
+                qaux_path  = Qauxi + xi * dQaux
+                A = compute_A(q_path, qaux_path, parameters, normal)
+                A_int += wi * A     
+            return A_int
+        return compute
+    
+    
+
+
+    def get_flux_operator(self, model):
+        compute_path_integral = self._integrate_path(model)
+        Id_single = self.Id(model.n_variables)
+        
+        def compute( 
+            Qi,
+            Qj,
+            Qauxi,
+            Qauxj,
+            parameters,
+            normal,
+            Vi,
+            Vj,
+            Vij,
+            dt
+        ):
+            """
+            Vectorised Rusanov fluctuation.
+
+            Shapes
+            ------
+            Qi, Qj            : (n_dof , N)        states for the two cells
+            Qauxi, Qauxj      : (n_aux , N)
+            parameters        : (n_param ,)
+            normal            : (dim   , N)  or (dim,)   oriented outward for cell "i"
+            Vi                : (N,)   or scalar         cell volume
+            Vij               : (N,)   or scalar         face measure
+            """
+            A_int = compute_path_integral(Qi, Qj, Qauxi, Qauxj, parameters, normal)
+            sM = np.maximum(np.abs(model.eigenvalues(Qi, Qauxi, parameters, normal)).max(axis=0), np.abs(model.eigenvalues(Qj, Qauxj, parameters, normal)).max(axis=0)) 
+            Id = np.stack([Id_single]*Qi.shape[1], axis=2)
+            
+            dQ = Qj - Qi
+            Dp = np.einsum("ij..., j...-> i...", 0.5 * (A_int + sM * Id), dQ)
+            Dm = np.einsum("ij..., j...-> i...", 0.5 * (A_int - sM * Id), dQ)
+            return Dp, Dm
+            
+        return compute
+    

zoomy_core/fvm/ode.py

@@ -0,0 +1,55 @@
+import numpy as np
+
+
+def RK1(func, Q, Qaux, param, dt, func_jac=None, func_bc=None):
+    dQ = np.zeros_like(Q)
+    dQ = func(dt, Q, Qaux, param, dQ)
+    return Q + dt * dQ
+
+
+def RK2(func, Q, Qaux, param, dt, func_jac=None, func_bc=None):
+    """
+    heun scheme
+    """
+    dQ = np.zeros_like(Q)
+    Q0 = np.array(Q)
+    dQ = func(dt, Q, Qaux, param, dQ)
+    Q1 = Q + dt * dQ
+    dQ = func(dt, Q1, Qaux, param, dQ)
+    Q2 = Q1 + dt * dQ
+    return 0.5 * (Q0 + Q2)
+
+
+def RK3(func, Q, Qaux, param, dt, func_jac=None, func_bc=None):
+    """ """
+    dQ = np.zeros_like(Q)
+    Q0 = np.array(Q)
+    dQ = func(dt, Q, Qaux, param, dQ)
+    Q1 = Q + dt * dQ
+    dQ = func(dt, Q1, Qaux, param, dQ)
+    Q2 = 3.0 / 4 * Q0 + 1.0 / 4 * (Q1 + dt * dQ)
+    dQ = func(dt, Q2, Qaux, param, dQ)
+    Q3 = 1.0 / 3 * Q0 + 2 / 3 * (Q2 + dt * dQ)
+    # TODO see old implementation
+    # func(dt, Q3, Qaux, param, dQ)
+    return Q3
+
+
+def RKimplicit(func, Q, Qaux, param, dt, func_jac=None, func_bc=None):
+    """
+    implicit euler
+    """
+    assert func_jac is not None
+    Jac = np.zeros((Q.shape[0], Q.shape[0], Q.shape[1]), dtype=float)
+    dQ = np.zeros_like(Q)
+    I = np.eye(Q.shape[0])
+
+    dQ = func(dt, Q, Qaux, param, dQ)
+    Jac = func_jac(dt, Q, Qaux, param, Jac)
+
+    b = Q + dt * dQ
+    for i in range(Q.shape[1]):
+        A = I - dt * Jac[:, :, i]
+        b[:, i] += -dt * np.dot(Jac[:, :, i], Q[:, i])
+        Q[:, i] = np.linalg.solve(A, b[:, i])
+    return Q

zoomy_core/fvm/solver_numpy.py

@@ -0,0 +1,297 @@
+import os
+from time import time as gettime
+
+import numpy as np
+from attr import define
+
+from typing import Callable
+from attrs import define, field
+
+from zoomy_core.misc.logger_config import logger
+
+
+
+import zoomy_core.fvm.flux as fvmflux
+import zoomy_core.fvm.nonconservative_flux as nonconservative_flux
+import zoomy_core.misc.io as io
+from zoomy_core.misc.misc import Zstruct, Settings
+import zoomy_core.fvm.ode as ode
+import zoomy_core.fvm.timestepping as timestepping
+from zoomy_core.transformation.to_numpy import NumpyRuntimeModel
+
+
+@define(frozen=True, slots=True, kw_only=True)            
+class Solver():
+    settings: Zstruct = field(factory=lambda: Settings.default())
+
+    def __attrs_post_init__(self):
+        defaults = Settings.default()
+        defaults.update(self.settings)
+        object.__setattr__(self, 'settings', defaults)
+        
+
+    def initialize(self, mesh, model):
+        # model.boundary_conditions.initialize(
+        #     mesh,
+        #     model.time,
+        #     model.position,
+        #     model.distance,
+        #     model.variables,
+        #     model.aux_variables,
+        #     model.parameters,
+        #     model.normal,
+        # )
+
+        n_variables = model.n_variables
+        n_cells = mesh.n_cells
+        n_aux_variables = model.aux_variables.length()
+
+        Q = np.empty((n_variables, n_cells), dtype=float)
+        Qaux = np.empty((n_aux_variables, n_cells), dtype=float)
+        return Q, Qaux
+        
+    def create_runtime(self, Q, Qaux, mesh, model):      
+        mesh.resolve_periodic_bcs(model.boundary_conditions)
+        Q, Qaux = np.asarray(Q), np.asarray(Qaux)
+        parameters = np.asarray(model.parameter_values)
+        runtime_model = NumpyRuntimeModel(model)        
+        return Q, Qaux, parameters, mesh, runtime_model
+
+    def get_compute_source(self, mesh, model):
+        def compute_source(dt, Q, Qaux, parameters, dQ):
+            dQ = model.source(
+                    Q[:, :],
+                    Qaux[:, :],
+                    parameters,
+            )
+            return dQ
+
+        return compute_source
+
+    def get_compute_source_jacobian_wrt_variables(self, mesh, model):
+        def compute_source(dt, Q, Qaux, parameters, dQ):
+            dQ = model.source_jacobian_wrt_variables(
+                    Q[:, : mesh.n_inner_cells],
+                    Qaux[:, : mesh.n_inner_cells],
+                    parameters,
+                )
+            return dQ
+
+        return compute_source
+    
+    def get_apply_boundary_conditions(self, mesh, model):
+        
+        def apply_boundary_conditions(time, Q, Qaux, parameters):
+            for i in range(mesh.n_boundary_faces):
+                i_face = mesh.boundary_face_face_indices[i]
+                i_bc_func = mesh.boundary_face_function_numbers[i]
+                q_cell = Q[:, mesh.boundary_face_cells[i]]  # Shape: (Q_dim,)
+                qaux_cell = Qaux[:, mesh.boundary_face_cells[i]]
+                normal = mesh.face_normals[:, i_face]
+                position = mesh.face_centers[i_face, :]
+                position_ghost = mesh.cell_centers[:, mesh.boundary_face_ghosts[i]]
+                distance = np.linalg.norm(position - position_ghost)
+                q_ghost = model.boundary_conditions(i_bc_func, time, position, distance, q_cell, qaux_cell, parameters, normal)
+                Q[:,  mesh.boundary_face_ghosts[i]] = q_ghost
+            return Q
+
+        return apply_boundary_conditions
+    
+    def update_q(self, Q, Qaux, mesh, model, parameters):
+        """
+        Update variables before the solve step.
+        """
+        # This is a placeholder implementation. Replace with actual logic as needed.
+        return Q
+    
+    def update_qaux(self, Q, Qaux, Qold, Qauxold, mesh, model, parameters, time, dt):
+        """
+        Update auxiliary variables
+        """
+        # This is a placeholder implementation. Replace with actual logic as needed.
+        return Qaux
+    
+    def solve(self, mesh, model):
+        logger.error(
+            "Solver.solve() is not implemented. Please implement this method in the derived class."
+        )
+        raise NotImplementedError("Solver.solve() must be implemented in derived classes.")
+
+ 
+@define(frozen=True, slots=True, kw_only=True)            
+class HyperbolicSolver(Solver):
+    settings: Zstruct = field(factory=lambda: Settings.default())
+    compute_dt: Callable = field(factory=lambda: timestepping.adaptive(CFL=0.45))
+    flux: fvmflux.Flux = field(factory=lambda: fvmflux.Zero())
+    nc_flux: nonconservative_flux.NonconservativeFlux = field(
+        factory=lambda: nonconservative_flux.Rusanov()
+    )
+    time_end: float = 0.1
+
+
+    def __attrs_post_init__(self):
+        super().__attrs_post_init__()
+        defaults = Settings.default()
+        defaults.output.update(Zstruct(snapshots=10))
+        defaults.update(self.settings)
+        object.__setattr__(self, 'settings', defaults)
+        
+
+    def initialize(self, mesh, model):
+        Q, Qaux = super().initialize(mesh, model)
+        Q = model.initial_conditions.apply(mesh.cell_centers, Q)
+        Qaux = model.aux_initial_conditions.apply(mesh.cell_centers, Qaux)
+        return Q, Qaux
+
+    def get_compute_max_abs_eigenvalue(self, mesh, model):
+        def compute_max_abs_eigenvalue(Q, Qaux, parameters):
+            max_abs_eigenvalue = -np.inf
+            i_cellA = mesh.face_cells[0]
+            i_cellB = mesh.face_cells[1]
+            qA = Q[:, i_cellA]
+            qB = Q[:, i_cellB]
+            qauxA = Qaux[:, i_cellA]
+            qauxB = Qaux[:, i_cellB]
+            normal = mesh.face_normals
+            evA = model.eigenvalues(qA, qauxA, parameters, normal)
+            evB = model.eigenvalues(qB, qauxB, parameters, normal)
+            max_abs_eigenvalue = np.maximum(np.abs(evA).max(axis=0), np.abs(evB).max(axis=0))
+            return max_abs_eigenvalue
+        return compute_max_abs_eigenvalue
+
+    def get_flux_operator(self, mesh, model):
+        compute_num_flux = self.flux.get_flux_operator(model)
+        compute_nc_flux = self.nc_flux.get_flux_operator(model)
+        def flux_operator(dt, Q, Qaux, parameters, dQ):
+
+            # Initialize dQ as zeros using jax.numpy
+            dQ = np.zeros_like(dQ)
+
+            iA = mesh.face_cells[0]
+            iB = mesh.face_cells[1]
+
+            qA = Q[:, iA]
+            qB = Q[:, iB]
+            qauxA = Qaux[:, iA]
+            qauxB = Qaux[:, iB]
+            normals = mesh.face_normals
+            face_volumes = mesh.face_volumes
+            cell_volumesA = mesh.cell_volumes[iA]
+            cell_volumesB = mesh.cell_volumes[iB]
+            svA = mesh.face_subvolumes[:, 0]
+            svB = mesh.face_subvolumes[:, 1]
+
+            Dp, Dm = compute_nc_flux(
+                qA,
+                qB,
+                qauxA,
+                qauxB,
+                parameters,
+                normals,
+                svA,
+                svB,
+                face_volumes,
+                dt,
+            )
+            flux_out = Dm * face_volumes / cell_volumesA
+            flux_in = Dp * face_volumes / cell_volumesB
+
+        
+            # dQ[:, iA]-= flux_out does not guarantee correct accumulation
+            # dQ[:, iB]-= flux_in
+            np.add.at(dQ, (slice(None), iA), -flux_out)
+            np.add.at(dQ, (slice(None), iB), -flux_in)
+            return dQ
+        return flux_operator
+
+    def solve(self, mesh, model, write_output=True):
+        Q, Qaux = self.initialize(mesh, model)
+        
+        Q, Qaux, parameters, mesh, model = self.create_runtime(Q, Qaux, mesh, model)
+        
+        # init once with dummy values for dt
+        Qaux = self.update_qaux(Q, Qaux, Q, Qaux, mesh, model, parameters, 0.0, 1.0)
+
+        
+        if write_output:
+            output_hdf5_path = os.path.join(
+                self.settings.output.directory, f"{self.settings.output.filename}.h5"
+            )
+            save_fields = io.get_save_fields(output_hdf5_path, write_all=False)
+        else:
+            def save_fields(time, time_stamp, i_snapshot, Q, Qaux):
+                return i_snapshot
+            
+
+        def run(Q, Qaux, parameters, model):
+            iteration = 0.0
+            time = 0.0
+
+            i_snapshot = 0.0
+            dt_snapshot = self.time_end / (self.settings.output.snapshots - 1)
+            if write_output:
+                io.init_output_directory(
+                    self.settings.output.directory, self.settings.output.clean_directory
+                )
+                mesh.write_to_hdf5(output_hdf5_path)
+                io.save_settings(self.settings)
+            i_snapshot = save_fields(time, 0.0, i_snapshot, Q, Qaux)
+
+            Qnew = Q
+            Qauxnew = Qaux
+
+            compute_max_abs_eigenvalue = self.get_compute_max_abs_eigenvalue(mesh, model)
+            flux_operator = self.get_flux_operator(mesh, model)
+            source_operator = self.get_compute_source(mesh, model)
+            boundary_operator = self.get_apply_boundary_conditions(mesh, model)
+            Qnew = boundary_operator(time, Qnew, Qaux, parameters)
+
+
+            cell_inradius_face = np.minimum(mesh.cell_inradius[mesh.face_cells[0, :]], mesh.cell_inradius[mesh.face_cells[1,:]])
+            cell_inradius_face = cell_inradius_face.min()
+
+            while time < self.time_end:
+                Q = Qnew
+                Qaux = Qauxnew
+                
+                dt = self.compute_dt(
+                    Q, Qaux, parameters, cell_inradius_face, compute_max_abs_eigenvalue
+                )
+
+                Q1 = ode.RK1(flux_operator, Q, Qaux, parameters, dt)
+                Q2 = ode.RK1(
+                    source_operator,
+                    Q1,
+                    Qaux,
+                    parameters,
+                    dt,
+                )
+
+                Q3 = boundary_operator(time, Q2, Qaux, parameters)
+                
+                # Update solution and time
+                time += dt
+                iteration += 1
+
+                time_stamp = (i_snapshot) * dt_snapshot
+                
+                Qnew = self.update_q(Q3, Qaux, mesh, model, parameters)
+                Qauxnew = self.update_qaux(Qnew, Qaux, Q, Qaux, mesh, model, parameters, time, dt)
+
+
+                i_snapshot = save_fields(time, time_stamp, i_snapshot, Qnew, Qauxnew)
+
+                if iteration % 10 == 0:
+                    logger.info(
+                        f"iteration: {int(iteration)}, time: {float(time):.6f}, "
+                        f"dt: {float(dt):.6f}, next write at time: {float(time_stamp):.6f}"
+                    )
+
+            return Qnew, Qaux
+
+        time_start = gettime()
+        Qnew, Qaux = run(Q, Qaux, parameters, model)
+        time = gettime() - time_start
+        logger.info(f"Finished simulation with in {time:.3f} seconds")
+        return Qnew, Qaux
+    

zoomy_core/fvm/timestepping.py

@@ -0,0 +1,13 @@
+def constant(dt=0.1):
+    def compute_dt(Q, Qaux, parameters, min_inradius, compute_max_abs_eigenvalue):
+        return dt
+
+    return compute_dt
+
+
+def adaptive(CFL=0.9):
+    def compute_dt(Q, Qaux, parameters, min_inradius, compute_max_abs_eigenvalue):
+        ev_abs_max = compute_max_abs_eigenvalue(Q, Qaux, parameters)
+        return (CFL * 2 * min_inradius / ev_abs_max).min()
+
+    return compute_dt