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Remove infinite loop in linear polymer #3491

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merged 3 commits into from
Feb 17, 2020
Merged

Remove infinite loop in linear polymer #3491

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9e3b596
Break infinite loop
jngrad Feb 16, 2020
0e0d8e8
Remove debug print statement
jngrad Feb 16, 2020
ae2c1f8
Remove fixed seed
jngrad Feb 17, 2020
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6 changes: 6 additions & 0 deletions src/core/polymer.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -177,6 +177,7 @@ draw_polymer_positions(PartCfg &partCfg, int const n_polymers,
// create remaining monomers' positions by backtracking.
for (int p = 0; p < n_polymers; ++p) {
for (int attempts_poly = 0; attempts_poly < max_tries; attempts_poly++) {
int rejections = 0;
while (positions[p].size() < beads_per_chain) {
auto pos = draw_valid_monomer_position(p, positions[p].size());

Expand All @@ -186,6 +187,11 @@ draw_polymer_positions(PartCfg &partCfg, int const n_polymers,
} else if (not positions[p].empty()) {
/* Go back one position and try again */
positions[p].pop_back();
rejections++;
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Can you please explain why this is needed? Couldn't you just increase attempts_poly?

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Ah sorry, when the first one has fixed position. But there has to be a more elegant solution than this...

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this while loop doesn't increment attempts_poly, therefore in high density systems, you can get stuck in an infinite cycle of deleting the previous bead and adding a new one at the same position

if (rejections > max_tries) {
/* Give up for this try. */
break;
}
} else {
/* Give up for this try. */
break;
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5 changes: 2 additions & 3 deletions testsuite/python/polymer_linear.py
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Expand Up @@ -16,6 +16,7 @@
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import unittest as ut
import numpy as np
import random
import espressomd
from espressomd import polymer
import espressomd.shapes
Expand All @@ -33,10 +34,9 @@ class LinearPolymerPositions(ut.TestCase):
"""

box_l = 15
seed = 23
seed = random.randint(0, 1000)

system = espressomd.System(box_l=[box_l, box_l, box_l])
np.random.seed(1234)

def assertShape(self, positions, n_poly, n_mono):
"""
Expand Down Expand Up @@ -185,7 +185,6 @@ def test_respect_constraints_wall(self):

z_components = positions[:, :, 2][0]
for z in z_components:
print(z)
self.assertGreaterEqual(z, 0.5 * self.box_l)

# assert that illegal start position raises error
Expand Down