import os
import numpy as np
import readdy


system = readdy.ReactionDiffusionSystem(box_size=[10., 10., 10.])

system.add_species("A", 1.0)

sim = system.simulation("SingleCPU")

sim.output_file = "out.h5"

if os.path.exists("checkpoints/"):
    # load checkpoint
    sim.load_particles_from_latest_checkpoint("checkpoints/")
else:
    # new positions
    init_pos = np.random.uniform(size=(100, 3)) * 10. - 5.
    sim.add_particles("A", init_pos)

# this also creates the directory, if it does not exist
sim.make_checkpoints(100, output_directory="checkpoints/", max_n_saves=5)

if os.path.exists(sim.output_file):
    os.remove(sim.output_file)

sim.run(1000, 0.1)