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Update type map when clearing the particle list #4648

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Jan 12, 2023
Merged

Update type map when clearing the particle list #4648

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4b290de
tests: Modernize test cases
jngrad Jan 9, 2023
8c8e6c0
core: Reset type tracker on particle clear
jngrad Jan 10, 2023
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7 changes: 7 additions & 0 deletions src/core/particle_node.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -322,6 +322,12 @@ int get_particle_node(int p_id) {

void clear_particle_node() { particle_node.clear(); }

static void clear_particle_type_map() {
for (auto &kv : ::particle_type_map) {
kv.second.clear();
}
}

/**
* @brief Calculate the largest particle id.
* Traversing the @ref particle_node to find the largest particle id
Expand Down Expand Up @@ -404,6 +410,7 @@ REGISTER_CALLBACK(mpi_remove_all_particles_local)
void remove_all_particles() {
mpi_call_all(mpi_remove_all_particles_local);
clear_particle_node();
clear_particle_type_map();
}

void remove_particle(int p_id) {
Expand Down
8 changes: 6 additions & 2 deletions testsuite/python/ek_eof_one_species.py
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Expand Up @@ -421,7 +421,9 @@ def test_vtk(self):
ek.write_vtk_velocity(str(path_vtk_velocity))
ek.write_vtk_potential(str(path_vtk_potential))
ek.write_vtk_density(str(path_vtk_lbdensity))
ek.write_vtk_lbforce(str(path_vtk_lbforce))
if espressomd.has_features('EK_DEBUG') or espressomd.has_features(
'VIRTUAL_SITES_INERTIALESS_TRACERS'):
ek.write_vtk_lbforce(str(path_vtk_lbforce))
counterions.write_vtk_density(str(path_vtk_density))
counterions.write_vtk_flux(str(path_vtk_flux))
if espressomd.has_features('EK_DEBUG'):
Expand All @@ -436,7 +438,9 @@ def test_vtk(self):
vtk_potential = get_vtk(path_vtk_potential, "potential", grid_dims)
vtk_lbdensity = get_vtk(
path_vtk_lbdensity, "density_lb", grid_dims)
get_vtk(path_vtk_lbforce, "lbforce", grid_dims + [3])
if espressomd.has_features('EK_DEBUG') or espressomd.has_features(
'VIRTUAL_SITES_INERTIALESS_TRACERS'):
get_vtk(path_vtk_lbforce, "lbforce", grid_dims + [3])
vtk_density = get_vtk(path_vtk_density, "density_1", grid_dims)
vtk_flux = get_vtk(path_vtk_flux, "flux_1", grid_dims + [3])
if espressomd.has_features('EK_DEBUG'):
Expand Down
10 changes: 3 additions & 7 deletions testsuite/python/particle.py
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Expand Up @@ -290,13 +290,9 @@ def test_particle_selection(self):
np.testing.assert_equal(sorted(res.id), np.arange(0, 16, 2, dtype=int))

def test_image_box(self):
s = self.system
s.part.clear()

pos = 1.5 * s.box_l

p = s.part.add(pos=pos)

self.system.part.clear()
pos = 1.5 * self.system.box_l
p = self.system.part.add(pos=pos)
np.testing.assert_equal(np.copy(p.image_box), [1, 1, 1])

def test_particle_numbering(self):
Expand Down
6 changes: 2 additions & 4 deletions testsuite/python/reaction_bookkeeping.py
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Expand Up @@ -94,10 +94,8 @@ def test_reaction_bookeeping(self):
for _ in range(50):
self.widom.calculate_particle_insertion_potential_energy(
reaction_id=0)
charge = 0.
for p in self.system.part:
charge += p.q
self.assertEqual(charge, 0.)
total_charge = sum(self.system.part.all().q)
self.assertEqual(total_charge, 0.)


if __name__ == "__main__":
Expand Down
43 changes: 27 additions & 16 deletions testsuite/python/reaction_methods_interface.py
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Expand Up @@ -45,6 +45,9 @@ def check_reaction_parameters(reactions, parameters):
else:
self.assertEqual(getattr(reaction, key), params[key])

def count_by_type(types):
return [self.system.number_of_particles(type=x) for x in types]

reaction_forward = {
'gamma': gamma,
'reactant_types': [5],
Expand Down Expand Up @@ -156,11 +159,15 @@ def check_reaction_parameters(reactions, parameters):
potential_energy = method.calculate_particle_insertion_potential_energy(
reaction_id=0)
self.assertEqual(potential_energy, 0.)
self.assertEqual(count_by_type([5, 2, 3, 0]), [1, 1, 1, 0])
method.delete_particle(p_id=p3.id)
self.assertEqual(count_by_type([5, 2, 3, 0]), [1, 1, 0, 0])
self.assertEqual(len(self.system.part), 2)
method.delete_particle(p_id=p1.id)
p1.remove()
self.assertEqual(count_by_type([5, 2, 3, 0]), [0, 1, 0, 0])
self.assertEqual(len(self.system.part), 1)
self.system.part.clear()
self.assertEqual(count_by_type([5, 2, 3, 0]), [0, 0, 0, 0])

# check reaction deletion
method.delete_reaction(reaction_id=0)
Expand All @@ -171,21 +178,25 @@ def test_interface(self):
'exclusion_radius_per_type': {1: 0.1}}

# reaction ensemble
method = espressomd.reaction_methods.ReactionEnsemble(
kT=1.4, seed=12, search_algorithm="order_n", **params)
self.check_interface(method, kT=1.4, gamma=1.2,
search_algorithm="order_n", **params)

# constant pH ensemble
method = espressomd.reaction_methods.ConstantpHEnsemble(
kT=1.5, seed=14, search_algorithm="parallel", constant_pH=10., **params)
self.check_interface(method, kT=1.5, gamma=1.2,
search_algorithm="parallel", **params)

# Widom insertion
method = espressomd.reaction_methods.WidomInsertion(kT=1.6, seed=16)
self.check_interface(method, kT=1.6, gamma=1., exclusion_range=0.,
exclusion_radius_per_type={}, search_algorithm=None)
with self.subTest(msg="reaction ensemble"):
method = espressomd.reaction_methods.ReactionEnsemble(
kT=1.4, seed=12, search_algorithm="order_n", **params)
self.check_interface(method, kT=1.4, gamma=1.2,
search_algorithm="order_n", **params)

with self.subTest(msg="constant pH ensemble"):
method = espressomd.reaction_methods.ConstantpHEnsemble(
kT=1.5, seed=14, search_algorithm="parallel", constant_pH=10.,
**params)
self.check_interface(method, kT=1.5, gamma=1.2,
search_algorithm="parallel", **params)

with self.subTest(msg="Widom insertion"):
method = espressomd.reaction_methods.WidomInsertion(
kT=1.6, seed=16)
self.check_interface(method, kT=1.6, gamma=1., exclusion_range=0.,
exclusion_radius_per_type={},
search_algorithm=None)

def test_exceptions(self):
single_reaction_params = {
Expand Down
42 changes: 26 additions & 16 deletions testsuite/python/virtual_sites_relative.py
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Expand Up @@ -32,6 +32,8 @@ class VirtualSites(ut.TestCase):

def setUp(self):
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()
Expand Down Expand Up @@ -266,10 +268,7 @@ 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 +299,12 @@ 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 +315,7 @@ 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 +326,33 @@ 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