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Add monitoring to flaky virtual sites test case #4640

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Add monitoring to flaky virtual sites test case #4640

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83ff02f
tests: Modernize test case with subtests
jngrad Dec 23, 2022
514e395
tests: Add diagnostics to flaky test case
jngrad Dec 23, 2022
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47 changes: 31 additions & 16 deletions testsuite/python/virtual_sites_relative.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,8 @@
import espressomd.virtual_sites
import numpy as np
import tests_common
import time
import sys


@utx.skipIfMissingFeatures(["VIRTUAL_SITES_RELATIVE", "LENNARD_JONES"])
Expand All @@ -31,14 +33,19 @@ class VirtualSites(ut.TestCase):
np.random.seed(42)

def setUp(self):
print(f"setUp({time.ctime()})", end=" ", file=sys.stderr, flush=True)
self.system.box_l = [10.0, 10.0, 10.0]
self.system.cell_system.set_regular_decomposition(
use_verlet_lists=True)

def tearDown(self):
self.system.part.clear()
self.system.thermostat.turn_off()
self.system.integrator.set_vv()
self.system.non_bonded_inter[0, 0].lennard_jones.deactivate()
self.system.virtual_sites = espressomd.virtual_sites.VirtualSitesOff()
print(f"tearDown({time.ctime()})", end=" ", file=sys.stderr,
flush=True)

def multiply_quaternions(self, a, b):
return np.array(
Expand Down Expand Up @@ -266,10 +273,7 @@ def run_test_lj(self):
# Setup
system.box_l = [l, l, l]
system.min_global_cut = 0.501
system.part.clear()

system.time_step = 0.01
system.thermostat.turn_off()

# Dumbbells consist of 2 virtual lj spheres + central particle
# w/o interactions. For n spheres, n/2 dumbbells.
Expand Down Expand Up @@ -300,8 +304,12 @@ def run_test_lj(self):
# Remove overlap
system.integrator.set_steepest_descent(
f_max=0, gamma=0.1, max_displacement=0.1)
while system.analysis.energy()["total"] > 10 * n:
n_loops = 0
n_max = 10
while system.analysis.energy()["total"] > 10 * n and n_loops < n_max:
system.integrator.run(20)
n_loops += 1
assert n_loops < n_max, "Steepest descent didn't converge"
# Integrate
system.integrator.set_vv()
for i in range(10):
Expand All @@ -312,7 +320,7 @@ def run_test_lj(self):
# Constant energy to get rid of thermostat forces in the
# verification
system.integrator.run(2)
# Check the virtual sites config,pos and vel of the lj spheres
# Check the virtual sites config, pos and vel of the lj spheres
for j in range(int(n / 2)):
self.verify_vs(system.part.by_id(3 * j + 1))
self.verify_vs(system.part.by_id(3 * j + 2))
Expand All @@ -323,26 +331,33 @@ def run_test_lj(self):
tests_common.verify_lj_forces(system, 1E-10, 3 * np.arange(n // 2))

# Test applying changes
enegry_pre_change = system.analysis.energy()['total']
energy_pre_change = system.analysis.energy()['total']
pressure_pre_change = system.analysis.pressure()['total']
p0 = system.part.by_id(0)
p0.pos = p0.pos + (2.2, -1.4, 4.2)
enegry_post_change = system.analysis.energy()['total']
energy_post_change = system.analysis.energy()['total']
pressure_post_change = system.analysis.pressure()['total']
self.assertNotAlmostEqual(enegry_pre_change, enegry_post_change)
self.assertNotAlmostEqual(energy_pre_change, energy_post_change)
self.assertNotAlmostEqual(pressure_pre_change, pressure_post_change)

def test_lj(self):
"""Run LJ fluid test for different cell systems."""
system = self.system

system.cell_system.skin = 0.4
system.cell_system.set_n_square(use_verlet_lists=True)
self.run_test_lj()
system.cell_system.set_regular_decomposition(use_verlet_lists=True)
self.run_test_lj()
system.cell_system.set_regular_decomposition(use_verlet_lists=False)
self.run_test_lj()
self.system.cell_system.skin = 0.4
with self.subTest(msg='N-square cell system with Verlet lists'):
self.system.cell_system.set_n_square(use_verlet_lists=True)
self.run_test_lj()
self.tearDown()
with self.subTest(msg='regular decomposition cell system with Verlet lists'):
self.system.cell_system.set_regular_decomposition(
use_verlet_lists=True)
self.run_test_lj()
self.tearDown()
with self.subTest(msg='regular decomposition cell system without Verlet lists'):
self.system.cell_system.set_regular_decomposition(
use_verlet_lists=False)
self.run_test_lj()
self.tearDown()

@utx.skipIfMissingFeatures("EXTERNAL_FORCES")
def test_zz_pressure_tensor(self):
Expand Down