test_smoothing_length_computation_3D.py

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import os
import argparse
import numpy as np
import h5py
 
import peano4.api
import exaparty
import exaparty.api.sphtools
import dastgen2
 
import shutil
 
 
 
 
parser = argparse.ArgumentParser(description="SPH benchmarking script")
parser.add_argument(
    "-j", "--parallel-builds", dest="j", type=int, default=-1, help="Parallel builds"
)
parser.add_argument(
    "-v",
    "--verbose",
    dest="verbose",
    action="store_true",
    default=False,
    help="Verbose",
)
parser.add_argument(
    "-c",
    "--clean",
    dest="clean_temporary_directories",
    action="store_true",
    help="Remove temporary directories before script starts",
)
parser.add_argument(
    "-cs",
    "--cell-size",
    dest="cell_size",
    type=float,
    default=0.3,
    help="Cell size (default 0.3)",
)
parser.add_argument(
    "-pd",
    "--peano-dir",
    dest="peanodir",
    default="../../../..",
    help="Peano4 directory",
)
parser.add_argument(
    "-asserts",
    "--asserts",
    dest="asserts",
    action="store_true",
    default=False,
    help="Switch on assertions",
)
parser.add_argument(
    "-debug",
    "--debug",
    dest="debug",
    action="store_true",
    default=False,
    help="Switch on assertions",
)
parser.add_argument(
    "-ic",
    "--ic-file",
    dest="ic_filename",
    default="test_sml_3D.hdf5",
    help="Initial conditions hdf5 file",
)
parser.add_argument(
    "-n",
    "--neighbours",
    dest="nneigh",
    type=int,
    default=5,
    help="Number of neighbours to search for",
)
parser.add_argument(
    "-ht",
    "--h-tolerance",
    dest="h_tol",
    type=float,
    default=1.0e-6,
    help="Threshold for convergence of smoothing length",
)
parser.add_argument(
    "-k",
    "--kernel",
    dest="kernel",
    type=str,
    default="quartic_spline",
    help="SPH kernel function to use.",
    choices=exaparty.api.sphtools.sph_kernel_list,
)
 
args = parser.parse_args()
nneigh = args.nneigh
kernel = args.kernel
h_tol = args.h_tol
 
 
 
project_namespace = ["tests", "exaparty", "testSML3D"]
 
project = exaparty.api.Project(
    namespace=project_namespace, project_name="TestSML3D", executable="testSML"
)
 
cfl_factor = 0.2
init_dt = 1.0e-16
 
offset = [0, 0, 0]
domain_size = [1, 1, 1]
periodic_boundary_conditions = [False, False, False]
 
 
# Initialise the SPH particle --------------------------------------------------
# If multiple particle species are present, we can specify the parameters
# independently for each case.
 
name = "HydroPart"
 
dimensions = 3  # peano needs this for whatever reason...
hydro_dimensions = 3  # dimensions for the hydro
 
particle = exaparty.api.particle.SPHLeapfrogFixedSearchRadius(
    name,
    dimensions_hydro=hydro_dimensions,
    cfl_factor=cfl_factor,
    initial_time_step_size=init_dt,
    constant_time_step_size=True,
    exaparty_project_namespace=project_namespace,
    particles_per_cell=20,
    min_h=args.cell_size,
    max_h=args.cell_size,
)
 
 
 
 
 
# HYDRO_DIMENSION can be smaller than the Peano4 dimensions
HYDRO_DIMENSIONS = hydro_dimensions
 
# Particle number along 1 dimension
hfile = h5py.File(args.ic_filename, "r")
header = hfile["Header"]
npart = header.attrs["NumPart_ThisFile"][0]
npart_base = header.attrs["NumPart_base"][0]
hfile.close()
HYDRO_PART_NUMBER = npart
 
# Time integration parameters
GLOBAL_TIME_STEP_SIZE = init_dt  # make some stuff up and hope it'll be stable enough
CFL_CONSTANT = cfl_factor  # make some stuff up and hope it'll be stable enough
 
# EoS parameter ---------------------------------------------------------------
gamma_hydro_list = [str(5 / 3), str(7 / 5), str(4 / 3), str(2 / 1)]
gamma_hydro_list_symbols = [
    "HYDRO_GAMMA_5_3",
    "HYDRO_GAMMA_7_5",
    "HYDRO_GAMMA_4_3",
    "HYDRO_GAMMA_2_1",
]
GAMMA = gamma_hydro_list[0]
GAMMA_HYDRO_SYMBOL = gamma_hydro_list_symbols[0]
 
# SPH kernel -------------------------------------------------------
KERNEL_SYMBOL = exaparty.api.sphtools.sph_kernel_macro_name[kernel]
 
# Additional Particle Parameters -----------------------------------------------
dx = domain_size[0] / npart_base
hydro_H_max = 4 * dx
hydro_h_max = exaparty.api.sphtools.sph_kernel_get_smoothing_length_from_search_radius(
    hydro_H_max, kernel, hydro_dimensions
)
particle.h_hydro_max = hydro_h_max
 
# Modify the eta factor to look for a precise number of neighbours.
# Then round it up a little to avoid round-down errors.
# In 1D, N_neigh = 2 * kernel_gamma * eta; see Price 2012
particle.eta_factor = exaparty.api.sphtools.eta_from_number_of_neighbours(
    nneigh, kernel=kernel, ndim=hydro_dimensions
)
 
particle.h_hydro_min = 1e-10
particle.h_max_iterations = 50
particle.h_tolerance = h_tol
# particle.beta_av = 3.0
# particle.alpha_av = 0.8
# Optional: Reduce the mantissa size for particle attributes -------------------
# Native size is 53 (double precision)
# particle.mantissa_size = 23
 
 
# deploy particle properties
particle.set_parameters()
 
 
# Add particle to the ExaParty project --------------------------------------------
# Notice that you any change to the particle will not take effect after adding
# the particle_set to the project
particle_set = project.add_particle_species(particle)
 
if args.debug:
    build_mode = peano4.api.output.CompileMode.DEBUG
elif args.asserts:
    build_mode = peano4.api.output.CompileMode.ASSERTS
else:
    build_mode = peano4.api.output.CompileMode.RELEASE
 
# Set Peano4 simulation parameters ---------------------------------------------
project.set_global_simulation_parameters(
    dimensions=dimensions,
    offset=offset,
    domain_size=domain_size,
    min_end_time=init_dt,
    max_end_time=init_dt,
    first_plot_time_stamp=0.0,
    time_in_between_plots=init_dt,
    periodic_BC=periodic_boundary_conditions,
    plotter_precision=8,
)
 
project.set_Peano4_installation(args.peanodir, build_mode)
 
#  project.set_load_balancing(
#      "toolbox::loadbalancing::strategies::RecursiveBipartition",
#      "new toolbox::loadbalancing::DefaultConfiguration()",
#  )
 
 
 
 
project.algorithm_step_initial_conditions.add_action_set(
    exaparty.api.input.InsertParticlesFromHDF5File(
        particle_set=particle_set, filename=args.ic_filename
    )
)
 
 
 
particle_plotter = peano4.api.toolbox.particles.PlotParticlesInVTKFormat(
    "particles",
    particle_set,
    "globaldata::{}::getSpecies().getMinTimeStamp()".format(particle.name),
)
# for some reason, using hydro_dimensions here writes wrong output.
particle_plotter.add_attribute_to_plot(particle.velocity, dimensions)
particle_plotter.add_attribute_to_plot(particle.acceleration, dimensions)
particle_plotter.add_attribute_to_plot(particle.mass, 1)
particle_plotter.add_attribute_to_plot(particle.density, 1)
particle_plotter.add_attribute_to_plot(particle.pressure, 1)
particle_plotter.add_attribute_to_plot(particle.u, 1)
particle_plotter.add_attribute_to_plot(particle.smoothL, 1)
if args.asserts or args.debug:
    particle_plotter.add_attribute_to_plot(particle.partid, 1)
project.algorithm_step_plot.add_action_set(particle_plotter)
 
 
 
 
peano4_project = project.generate_Peano4_project(verbose=args.verbose)
 
# Some sanity checks ----------------------------------------------------------
if GAMMA not in gamma_hydro_list:
    print(f"Please check the value of GAMMA. You have chosen: {GAMMA}")
 
print("-----------------------------------------------------------------------")
print("SPH parameters summary:")
print(f"Effective dimensions of the Simulation: {HYDRO_DIMENSIONS}")
print(f"Global time-step size: {GLOBAL_TIME_STEP_SIZE}")
print(f"Number of particles (1D): {HYDRO_PART_NUMBER}")
print(f"Adiabatic index: {GAMMA}")
print(f"Smoothing length free factor: {particle.eta_factor}")
print("-----------------------------------------------------------------------")
 
 
# Export Constants.h file ------------------------------------------------------
peano4_project.constants.export_const_with_type(
    "HYDRO_DIMENSIONS", str(HYDRO_DIMENSIONS), "double"
)
peano4_project.constants.export_const_with_type(
    "HYDRO_PART_NUMBER", str(HYDRO_PART_NUMBER), "double"
)
peano4_project.constants.export_const_with_type(
    "GLOBAL_TIME_STEP_SIZE", str(GLOBAL_TIME_STEP_SIZE), "double"
)
peano4_project.constants.export_const_with_type("GAMMA", GAMMA, "double")
 
# Export symbols for compilation (e.g. for SPH kernel) -----------------------
peano4_project.output.makefile.add_CXX_flag(
    "-D" + "HYDRO_DIMENSION=" + str(HYDRO_DIMENSIONS)
)
peano4_project.output.makefile.add_CXX_flag("-D" + GAMMA_HYDRO_SYMBOL)
peano4_project.output.makefile.add_CXX_flag("-D" + KERNEL_SYMBOL)
 
 
 
 
# If we want to start a project from scratch, we may want to remove some of the generated code
if args.clean_temporary_directories:
    dirs = ["vertexdata/", "repositories/", "globaldata/", "observers/"]
    for dir in dirs:
        shutil.rmtree(dir)
 
# It is safe (and recommended) to overwrite any existing main file, since this
# is generated automatically by the ExaParty graph compiler.
peano4_project.generate(
    overwrite=peano4.api.output.Overwrite.Always, throw_away_data_after_generation=True
)
peano4_project.build(make_clean_first=True, number_of_parallel_builds=args.j)
 
# remove output files from previous runs
output_files = [
    f
    for f in os.listdir(".")
    if f.endswith(".peano-patch-file") or f.endswith(".vtu") or f.endswith(".pvd")
]
for f in output_files:
    os.remove(f)