[fixed?] clear_volume doesn't work on empty simulation

[Jintram]

Problem

You might think this is not such a big problem, as usually the simulation isn't empty.

But I'm working on the rebinding sample, which, depending on arguments from the user, contains or doesn't contain inert X particles.

At a certain moment particles A and B are added to certain location, and therefore the volume should be cleared.

Now, when the user has decided there shouldn't be any X-particles, the eGFRD simulation crashes.

I don't know if this is the only case in which clear_volume crashes, but it's certainly something we should look into IMO.

Crash report:

wehrens@amocf23:~/myfork_egfrd/samples/rebind$ LOGLEVEL=ERROR PYTHONPATH=../.. python -O run.py 1 0 [INF] 100

Traceback (most recent call last):
File "run.py", line 306, in
int(sys.argv[2]), T_list, int(sys.argv[4]))
File "run.py", line 74, in run
r_list, t_list = singlerun(T_list, N_B, N_X)
File "run.py", line 190, in singlerun
dd = s.clear_volume(A_pos, float(A['radius']))
File "/storage1/wehrens/myfork_egfrd/egfrd.py", line 544, in clear_volume
return self.burst_objs(neighbors)
File "/storage1/wehrens/myfork_egfrd/egfrd.py", line 521, in burst_objs
for obj in objs:
File "/storage1/wehrens/myfork_egfrd/egfrd.py", line 1484, in get_neighbors_within_radius_no_sort
for container in self.containers:
AttributeError: 'EGFRDSimulator' object has no attribute 'containers'

Proposed solution

Simply build in a check in clear_volume that checks if there are domains at all, if not, just pass and return emtpy output.

[Jintram]

Resolved

I've resolved the situation by updating egfrd.py as follows:

def get_neighbors_within_radius_no_sort(self, pos, radius, ignore=[]):
    # Get neighbor domains within given radius.
    #
    # ignore: domain ids.
    #
    # Only returns neighbors, not the distances towards their 
    # shells. Can for example be used to try to clear all objects 
    # from a certain volume.

    try:
        for container in self.containers:
            result = container.get_neighbors_within_radius(pos, radius)
            # result = [((shell_id_shell_pair), distance), ]
            # Since a domain can have more than 1 shell (multis for 
            # example), and for each shell there is an entry in the 
            # shell container, we make sure each domain occurs only once 
            # in the returned list here.
            for did in uniq(s[0][1].did for s in result):
                if did not in ignore:
                    yield self.domains[did]
    except AttributeError:
        pass

Everyone ok with this?

If this is ok someone can close the issue.

[Jintram]

Log?

Perhaps such an exception should be logged in case this masks some bug?