Particle type map goes out of sync when clearing particles

[jngrad]

The particle type map is updated when removing individual particles, but not when clearing all particles. The type map remains desynchronized until new particles are created. Affects all ESPResSo versions since 4.0.

MWE for 4.3-dev (tested on 30c7c23):

import espressomd
import espressomd.reaction_methods
import numpy as np
np.random.seed(seed=42)
system = espressomd.System(box_l=3 * [10.])
system.time_step = 0.02
system.cell_system.skin = 0.4
# set particles
type_A = 0
type_B = 1
system.part.add(pos=np.random.random((10, 3)) * system.box_l, type=10 * [type_B])
# set reaction 1A <-> 1B
RE = espressomd.reaction_methods.ReactionEnsemble(kT=1., exclusion_range=0., seed=42)
RE.add_reaction(reactant_types=[type_A], reactant_coefficients=[1],
                product_types=[type_B], product_coefficients=[1],
                gamma=0.001, default_charges={type_A: 0, type_B: 0})
RE.set_non_interacting_type(type=2)
# clear particle list
system.part.clear()
# state tracking is now out of sync
print(f"n_A = {system.number_of_particles(type=type_A)}")
print(f"n_B = {system.number_of_particles(type=type_B)}")
# triggering a cell system reset has no effect on state tracking
system.cell_system.set_n_square()
system.cell_system.set_regular_decomposition()
# reaction fails
RE.reaction(reaction_steps=4)

Output:

n_A = 0
n_B = 10
Traceback (most recent call last):
  File "/work/jgrad/espresso/build/mwe.py", line 27, in <module>
    RE.reaction(reaction_steps=4)
  File "script_interface.pyx", line 425, in espressomd.script_interface.ScriptInterfaceHelper.generate_caller.template_method
  File "script_interface.pyx", line 159, in espressomd.script_interface.PScriptInterface.call_method
RuntimeError: Particle node for id 0 not found!

Expected output:

n_A = 0
n_B = 0