Shallow Moments with topography and turbulence (Advanced)

Shallow Moments with topography and turbulence (Advanced)#

Imports#

# | code-fold: true
# | code-summary: "Load packages"
# | output: false

import os
import numpy as np
import jax
from jax import numpy as jnp
import pytest
from types import SimpleNamespace
from sympy import cos, pi, Piecewise, Matrix

from zoomy_jax.fvm.solver_jax import HyperbolicSolver, Settings
from zoomy_core.fvm.ode import RK1
import zoomy_core.fvm.timestepping as timestepping
import zoomy_core.fvm.flux as flux
import zoomy_core.fvm.nonconservative_flux as nc_flux
from zoomy_core.model.boundary_conditions import BoundaryCondition
from zoomy_core.model.models.basisfunctions import Basisfunction, Legendre_shifted
from zoomy_core.model.models.basismatrices import Basismatrices
from zoomy_core.misc.misc import Zstruct

from zoomy_core.model.models.shallow_moments_topo_turbulence import ShallowMomentsTopoTurbulence

import zoomy_core.model.initial_conditions as IC
import zoomy_core.model.boundary_conditions as BC
import zoomy_core.misc.io as io
from zoomy_core.mesh.lsq_reconstruction import compute_derivatives


from zoomy_core.mesh import BaseMesh
import argparse

Model#

level = 1
offset = 1+level
n_fields = 3 + 2 * level
settings = Settings(
    name="SMETT",
    output=Zstruct(
        directory=f"outputs/topo_{level}", filename="SMETT", snapshots=30, clean_directory=True
    ),
)

bcs = BC.BoundaryConditions(
    [
        BC.Periodic(tag="left", periodic_to_physical_tag="right"),
        BC.Periodic(tag="right", periodic_to_physical_tag="left"),
    ]
)

def custom_ic(x):
    Q = np.zeros(4 + 2 * level, dtype=float)
    Q[0] = x[0] * (0.01)
    Q[1] = np.where(x[0] < 0.35, 0.35, 0.35)
    return Q

# def custom_ic_aux(x):
#     Q = custom_ic(x)
#     h = Q[1]
#     # Qaux = np.zeros(1 + 2 + 2 * level, dtype=float)
#     Qaux = np.zeros(1, dtype=float)
#     Qaux[0] = np.where(h > 0, 1/h, 0.0)
#     return Qaux

ic = IC.UserFunction(custom_ic)
# ic_aux = IC.UserFunction(custom_ic_aux)


model = ShallowMomentsTopoTurbulence(
    level=level,
    boundary_conditions=bcs,
    initial_conditions=ic,
    # aux_initial_conditions=ic_aux,
    aux_variables = ['hinv'] + [f'dalpha_{i}_dx' for i in range(level+1)] + [f'dbeta_{i}_dy' for i in range(level+1)],
    # aux_variables = ['hinv'],
    
)

# main_dir = os.getenv("ZOOMY_DIR")
# mesh = petscMesh.Mesh.from_gmsh(
#     os.path.join(main_dir, "meshes/channel_junction/mesh_2d_coarse.msh")
#     # os.path.join(main_dir, "meshes/channel_junction/mesh_2d_fine.msh")
# )

mesh = petscMesh.Mesh.create_1d([0, 25, 250])


solver = HyperbolicSolver(settings=settings, time_end=0.1, compute_dt=timestepping.adaptive(CFL=0.9))

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[3], line 26
     22 ic = IC.UserFunction(custom_ic)
     23 # ic_aux = IC.UserFunction(custom_ic_aux)
---> 26 model = ShallowMomentsTopoTurbulence(
     27     level=level,
     28     boundary_conditions=bcs,
     29     initial_conditions=ic,
     30     # aux_initial_conditions=ic_aux,
     31     aux_variables = ['hinv'] + [f'dalpha_{i}_dx' for i in range(level+1)] + [f'dbeta_{i}_dy' for i in range(level+1)],
     32     # aux_variables = ['hinv'],
     33 
     34 )
     36 # main_dir = os.getenv("ZOOMY_DIR")
     37 # mesh = petscMesh.Mesh.from_gmsh(
     38 #     os.path.join(main_dir, "meshes/channel_junction/mesh_2d_coarse.msh")
     39 #     # os.path.join(main_dir, "meshes/channel_junction/mesh_2d_fine.msh")
     40 # )
     42 mesh = petscMesh.Mesh.create_1d([0, 25, 250])

File ~/Git/Zoomy/library/zoomy_core/zoomy_core/model/models/shallow_moments_topo.py:37, in ShallowMomentsTopo.__init__(self, init_functions, **kwargs)
     34 self.variables[1] = new_h
     36 if init_functions:
---> 37     self._initialize_functions()

File ~/Git/Zoomy/library/zoomy_core/zoomy_core/model/basemodel.py:186, in Model._initialize_functions(self)
    147 regs = [
    148     ("flux", self.flux, std_sig),
    149     ("dflux", self.dflux, std_sig),
   (...)    183     ),
    184 ]
    185 for name, method, sig in regs:
--> 186     self.register_symbolic_function(name, method, sig)
    188 # --- Boundary Conditions Setup ---
    189 
    190 # 1. Main Boundary Conditions
    191 self._boundary_conditions = (
    192     self.boundary_conditions.get_boundary_condition_function(
    193         self.time,
   (...)    201     )
    202 )

File ~/Git/Zoomy/library/zoomy_core/zoomy_core/model/basefunction.py:41, in SymbolicRegistrar.register_symbolic_function(self, name, method_ref, sig_struct)
     40 def register_symbolic_function(self, name, method_ref, sig_struct):
---> 41     definition = method_ref()
     42     self.functions[name] = Function(
     43         name=name, definition=definition, args=sig_struct
     44     )
     46     def proxy_caller(*input_args):

File ~/Git/Zoomy/library/zoomy_core/zoomy_core/model/basemodel.py:311, in Model.quasilinear_matrix(self)
    309 for d in range(self.dimension):
    310     JacF[:, :, d] = ZArray(JacF[:, :, d].tomatrix().T)
--> 311 return self._simplify(JacF + self.nonconservative_matrix())

File ~/Git/Zoomy/library/zoomy_core/zoomy_core/misc/misc.py:111, in ZArray.__add__(self, other)
    110 def __add__(self, other):
--> 111     return ZArray(super().__add__(self._to_array(other)))

File ~/miniforge3/envs/zoomy/lib/python3.11/site-packages/sympy/tensor/array/ndim_array.py:403, in NDimArray.__add__(self, other)
    400     return NotImplemented
    402 if self.shape != other.shape:
--> 403     raise ValueError("array shape mismatch")
    404 result_list = [i+j for i,j in zip(Flatten(self), Flatten(other))]
    406 return type(self)(result_list, self.shape)

ValueError: array shape mismatch

model.source()
../../../_images/f25f424372c3b690b44d0748fe506f5f3b31905b6afc4ccbb850d7a52708fcdf.png

Solve#

Qnew, Qaux = solver.solve(mesh, model)

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Visualization#

io.generate_vtk(os.path.join(settings.output.directory, f"{settings.output.filename}.h5"))
# postprocessing.vtk_project_2d_to_3d(model, settings, Nz=20, filename='out_3d')

# visu.pyvista_3d(settings.output.directory, scale=1.0)
Contents