Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Restore LB boundaries during checkpointing #4649

Merged
merged 2 commits into from
Jan 12, 2023
Merged

Restore LB boundaries during checkpointing #4649

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
a7f7023
core: Restore LB boundaries during checkpointing
jngrad Jan 11, 2023
ce0df27
Merge branch 'python' into fix-4647
jngrad Jan 12, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions src/core/grid_based_algorithms/lb.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -32,6 +32,7 @@
#include "cell_system/CellStructureType.hpp"
#include "communication.hpp"
#include "errorhandling.hpp"
#include "event.hpp"
#include "grid.hpp"
#include "grid_based_algorithms/lb_boundaries.hpp"
#include "halo.hpp"
Expand Down Expand Up @@ -207,6 +208,7 @@ void lb_initialize_fields(std::vector<LB_FluidNode> &lb_fields,
field.boundary = false;
#endif // LB_BOUNDARIES
}
on_lbboundary_change();
}

/** (Re-)allocate memory for the fluid and initialize pointers. */
Expand Down
19 changes: 15 additions & 4 deletions testsuite/python/test_checkpoint.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -87,15 +87,19 @@ def test_lb_fluid(self):
Check serialization of the LB fluid. The checkpoint file only stores
population information, therefore calling ``lbf.load_checkpoint()``
erases all LBBoundaries information but doesn't remove the objects
contained in ``system.lbboundaries`. This test method is named such
that it is executed after ``self.test_lb_boundaries()``.
contained in ``system.lbboundaries``. A callback should re-introduce
the LB boundary flag after LB populations are reloaded.
'''
lbf = self.get_active_actor_of_type(
espressomd.lb.HydrodynamicInteraction)
cpt_mode = 0 if 'LB.ASCII' in modes else 1
cpt_root = pathlib.Path(self.checkpoint.checkpoint_dir)
cpt_path = str(cpt_root / "lb") + "{}.cpt"

if has_lbb:
# LB boundaries must be correct before LB populations are loaded
self.check_lb_boundaries()

# check exception mechanism with corrupted LB checkpoint files
with self.assertRaisesRegex(RuntimeError, 'EOF found'):
lbf.load_checkpoint(cpt_path.format("-missing-data"), cpt_mode)
Expand Down Expand Up @@ -133,6 +137,10 @@ def test_lb_fluid(self):
self.assertIn(key, state)
self.assertAlmostEqual(reference[key], state[key], delta=1E-7)

if has_lbb:
# LB boundaries must be correct after LB populations are loaded
self.check_lb_boundaries(remove_boundaries=True)

def test_system_variables(self):
cell_system_params = system.cell_system.get_state()
self.assertTrue(cell_system_params['use_verlet_lists'])
Expand Down Expand Up @@ -672,8 +680,7 @@ def test_exclusions(self):
self.assertEqual(list(system.part.by_id(1).exclusions), [2])
self.assertEqual(list(system.part.by_id(2).exclusions), [0, 1])

@ut.skipIf(not has_lbb, "Missing features")
def test_lb_boundaries(self):
def check_lb_boundaries(self, remove_boundaries=False):
# check boundary objects
self.assertEqual(len(system.lbboundaries), 2)
np.testing.assert_allclose(
Expand All @@ -684,14 +691,18 @@ def test_lb_boundaries(self):
system.lbboundaries[0].shape, espressomd.shapes.Wall)
self.assertIsInstance(
system.lbboundaries[1].shape, espressomd.shapes.Wall)

# check boundary flag
lbf = self.get_active_actor_of_type(
espressomd.lb.HydrodynamicInteraction)
np.testing.assert_equal(np.copy(lbf[0, :, :].boundary.astype(int)), 1)
np.testing.assert_equal(np.copy(lbf[-1, :, :].boundary.astype(int)), 2)
np.testing.assert_equal(
np.copy(lbf[1:-1, :, :].boundary.astype(int)), 0)

# remove boundaries
if not remove_boundaries:
return
system.lbboundaries.clear()
self.assertEqual(len(system.lbboundaries), 0)
np.testing.assert_equal(np.copy(lbf[:, :, :].boundary.astype(int)), 0)
Expand Down