Use in samples and tests.

samples/chamber_game.py

@@ -156,7 +156,7 @@
 # CELLSYSTEM
 
 system.cell_system.skin = 3.0
-system.cell_system.set_domain_decomposition(use_verlet_lists=False)
+system.cell_system.set_regular_decomposition(use_verlet_lists=False)
 
 # BONDS
 

samples/visualization_cellsystem.py

@@ -42,7 +42,7 @@
     draw_cells=True)
 
 system.time_step = 0.0005
-system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+system.cell_system.set_regular_decomposition(use_verlet_lists=True)
 system.cell_system.skin = 0.4
 #system.cell_system.node_grid = [i, j, k]
 

samples/visualization_charged.py

@@ -29,7 +29,7 @@
 
 box = [40, 40, 40]
 system = espressomd.System(box_l=box)
-system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+system.cell_system.set_regular_decomposition(use_verlet_lists=True)
 visualizer = espressomd.visualization_opengl.openGLLive(
     system, background_color=[1, 1, 1], drag_enabled=True, drag_force=10)
 

testsuite/python/CMakeLists.txt

@@ -143,7 +143,7 @@ python_test(FILE nsquare.py MAX_NUM_PROC 4)
 python_test(FILE virtual_sites_relative.py MAX_NUM_PROC 2)
 python_test(FILE virtual_sites_tracers.py MAX_NUM_PROC 2)
 python_test(FILE virtual_sites_tracers_gpu.py MAX_NUM_PROC 2 LABELS gpu)
-python_test(FILE domain_decomposition.py MAX_NUM_PROC 4)
+python_test(FILE regular_decomposition.py MAX_NUM_PROC 4)
 python_test(FILE integrator_npt.py MAX_NUM_PROC 4)
 python_test(FILE integrator_npt_stats.py MAX_NUM_PROC 4 LABELS long)
 python_test(FILE integrator_steepest_descent.py MAX_NUM_PROC 4)

testsuite/python/brownian_dynamics.py

@@ -26,7 +26,7 @@ class BrownianThermostat(ut.TestCase):
 
     """Test Brownian Dynamics"""
     system = espressomd.System(box_l=[1.0, 1.0, 1.0])
-    system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+    system.cell_system.set_regular_decomposition(use_verlet_lists=True)
     system.cell_system.skin = 0
     system.periodicity = [0, 0, 0]
 

testsuite/python/brownian_dynamics_stats.py

@@ -30,7 +30,7 @@ class BrownianThermostat(ut.TestCase, thermostats_common.ThermostatsCommon):
 
     """Tests velocity distributions and diffusion for Brownian Dynamics"""
     system = espressomd.System(box_l=[1.0, 1.0, 1.0])
-    system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+    system.cell_system.set_regular_decomposition(use_verlet_lists=True)
     system.cell_system.skin = 0
     system.periodicity = [0, 0, 0]
 

testsuite/python/cellsystem.py

@@ -30,14 +30,15 @@ def test_cell_system(self):
         self.system.cell_system.set_n_square(use_verlet_lists=False)
         s = self.system.cell_system.get_state()
         self.assertEqual([s['use_verlet_list'], s['type']], [0, "nsquare"])
-        self.system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+        self.system.cell_system.set_regular_decomposition(
+            use_verlet_lists=True)
         s = self.system.cell_system.get_state()
         self.assertEqual(
-            [s['use_verlet_list'], s['type']], [1, "domain_decomposition"])
+            [s['use_verlet_list'], s['type']], [1, "regular_decomposition"])
 
     @ut.skipIf(n_nodes == 1, "Skipping test: only runs for n_nodes >= 2")
     def test_node_grid(self):
-        self.system.cell_system.set_domain_decomposition()
+        self.system.cell_system.set_regular_decomposition()
         for i in range(3):
             node_grid_ref = [1, 1, 1]
             node_grid_ref[i] = self.n_nodes

testsuite/python/collision_detection.py

@@ -637,7 +637,7 @@ def test_bind_three_particles(self):
 
         system.part.add(id=4, pos=e)
         system.part.add(id=1, pos=b)
-        system.cell_system.set_domain_decomposition()
+        system.cell_system.set_regular_decomposition()
         system.integrator.run(1, recalc_forces=True)
         self.verify_triangle_binding(cutoff, system.bonded_inter[2], res)
         system.cell_system.set_n_square()

testsuite/python/coulomb_mixed_periodicity.py

@@ -76,7 +76,7 @@ def test_elc(self):
         for p in self.system.part:
             assert p.pos[2] >= 0. and p.pos[2] <= 9., f'particle {p.id} in gap'
 
-        self.system.cell_system.set_domain_decomposition()
+        self.system.cell_system.set_regular_decomposition()
         self.system.cell_system.node_grid = sorted(
             self.system.cell_system.node_grid, key=lambda x: -x)
         self.system.periodicity = [1, 1, 1]
@@ -95,7 +95,7 @@ def test_elc(self):
                'Skipping test: missing feature SCAFACOS or p2nfft method')
     def test_scafacos_p2nfft(self):
         self.system.periodicity = [1, 1, 0]
-        self.system.cell_system.set_domain_decomposition()
+        self.system.cell_system.set_regular_decomposition()
 
         scafacos = espressomd.electrostatics.Scafacos(
             prefactor=1,

testsuite/python/ek_eof_one_species.py

@@ -156,7 +156,7 @@ def bisection():
                 pntm = pnt0 + size
         else:
             sys.exit("Bisection method fails:\n"
-                     "Tuning of domain boundaries may be required.")
+                     "Tuning of regular boundaries may be required.")
     return pntm
 
 

testsuite/python/elc_vs_analytic.py

@@ -54,7 +54,7 @@ def test_elc(self):
                              q=-self.q[0])
 
         self.system.box_l = [self.box_l, self.box_l, self.box_l + self.elc_gap]
-        self.system.cell_system.set_domain_decomposition(
+        self.system.cell_system.set_regular_decomposition(
             use_verlet_lists=True)
         self.system.periodicity = [1, 1, 1]
         p3m = espressomd.electrostatics.P3M(prefactor=self.prefactor,

testsuite/python/langevin_thermostat.py

@@ -26,7 +26,7 @@ class LangevinThermostat(ut.TestCase):
 
     """Test Langevin Dynamics"""
     system = espressomd.System(box_l=[1.0, 1.0, 1.0])
-    system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+    system.cell_system.set_regular_decomposition(use_verlet_lists=True)
     system.cell_system.skin = 0
     system.periodicity = [0, 0, 0]
 

testsuite/python/langevin_thermostat_stats.py

@@ -30,7 +30,7 @@ class LangevinThermostat(ut.TestCase, thermostats_common.ThermostatsCommon):
 
     """Tests velocity distributions and diffusion for Langevin Dynamics"""
     system = espressomd.System(box_l=[1.0, 1.0, 1.0])
-    system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+    system.cell_system.set_regular_decomposition(use_verlet_lists=True)
     system.cell_system.skin = 0
     system.periodicity = [0, 0, 0]
 

testsuite/python/lj.py

@@ -54,14 +54,15 @@ def check(self):
         self.assertLess(max_deviation, 1e-5)
 
     def test_dd(self):
-        self.system.cell_system.set_domain_decomposition(
+        self.system.cell_system.set_regular_decomposition(
             use_verlet_lists=False)
         self.system.integrator.run(recalc_forces=True, steps=0)
 
         self.check()
 
     def test_dd_vl(self):
-        self.system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+        self.system.cell_system.set_regular_decomposition(
+            use_verlet_lists=True)
         # Build VL and calc ia
         self.system.integrator.run(recalc_forces=True, steps=0)
 

testsuite/python/mass-and-rinertia_per_particle.py

@@ -60,7 +60,7 @@ class ThermoTest(ut.TestCase):
     @classmethod
     def setUpClass(cls):
         np.random.seed(seed=15)
-        cls.system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+        cls.system.cell_system.set_regular_decomposition(use_verlet_lists=True)
         cls.system.cell_system.skin = 5.0
 
     def setUp(self):

testsuite/python/mmm1d.py

@@ -114,7 +114,7 @@ def test_exceptions(self):
         if self.MMM1D is espressomd.electrostatics.MMM1D:
             with self.assertRaisesRegex(Exception, "MMM1D requires the N-square cellsystem"):
                 mmm1d = self.MMM1D(prefactor=1.0, maxPWerror=1e-2)
-                self.system.cell_system.set_domain_decomposition()
+                self.system.cell_system.set_regular_decomposition()
                 self.system.actors.add(mmm1d)
             self.system.cell_system.set_n_square()
             self.system.actors.clear()

testsuite/python/p3m_tuning_exceptions.py

@@ -210,10 +210,10 @@ def test_04_invalid_params_p3m_cpu(self):
         self.system.periodicity = (1, 1, 1)
 
         # check cell system exceptions
-        with self.assertRaisesRegex(Exception, "P3M requires the domain decomposition cell system"):
+        with self.assertRaisesRegex(Exception, "P3M requires the regular decomposition cell system"):
             self.system.cell_system.set_n_square()
             self.system.analysis.energy()
-        self.system.cell_system.set_domain_decomposition()
+        self.system.cell_system.set_regular_decomposition()
         self.system.actors.clear()
 
     @utx.skipIfMissingGPU()
@@ -259,10 +259,10 @@ def test_04_invalid_params_dp3m_cpu(self):
         self.system.periodicity = (1, 1, 1)
 
         # check cell system exceptions
-        with self.assertRaisesRegex(Exception, "dipolar P3M requires the domain decomposition cell system"):
+        with self.assertRaisesRegex(Exception, "dipolar P3M requires the regular decomposition cell system"):
             self.system.cell_system.set_n_square()
             self.system.analysis.energy()
-        self.system.cell_system.set_domain_decomposition()
+        self.system.cell_system.set_regular_decomposition()
         self.system.actors.clear()
 
     @utx.skipIfMissingFeatures("P3M")

testsuite/python/pairs.py

@@ -104,13 +104,13 @@ def test_nsquare_partial_z(self):
         self.run_and_check()
 
     def test_dd(self):
-        self.system.cell_system.set_domain_decomposition()
+        self.system.cell_system.set_regular_decomposition()
         self.system.periodicity = [1, 1, 1]
         self.run_and_check()
         self.check_range_exception()
 
     def test_dd_partial_z(self):
-        self.system.cell_system.set_domain_decomposition()
+        self.system.cell_system.set_regular_decomposition()
         self.system.periodicity = [1, 1, 0]
         self.run_and_check()
         self.check_range_exception()

testsuite/python/particle.py

@@ -344,7 +344,7 @@ def test_zz_remove_all(self):
     def test_coord_fold_corner_cases(self):
         system = self.system
         system.time_step = .5
-        system.cell_system.set_domain_decomposition(use_verlet_lists=False)
+        system.cell_system.set_regular_decomposition(use_verlet_lists=False)
         system.cell_system.skin = 0
         system.min_global_cut = 3
         system.part.clear()

testsuite/python/random_pairs.py

@@ -82,7 +82,7 @@ def check_pairs(self, n2_pairs):
         self.assertEqual(n2_pairs ^ set(cs_pairs), set())
 
     def check_dd(self, n2_pairs):
-        self.system.cell_system.set_domain_decomposition()
+        self.system.cell_system.set_regular_decomposition()
         self.check_pairs(n2_pairs)
 
     def check_n_squared(self, n2_pairs):

testsuite/python/domain_decomposition.py → testsuite/python/regular_decomposition.py

@@ -23,12 +23,12 @@
 np.random.seed(42)
 
 
-class DomainDecomposition(ut.TestCase):
+class RegularDecomposition(ut.TestCase):
     system = espressomd.System(box_l=3 * [50.0])
     original_node_grid = tuple(system.cell_system.node_grid)
 
     def setUp(self):
-        self.system.cell_system.set_domain_decomposition(
+        self.system.cell_system.set_regular_decomposition(
             use_verlet_lists=False)
         self.system.cell_system.node_grid = self.original_node_grid
         self.system.time_step = 1e-3

testsuite/python/virtual_sites_relative.py

@@ -307,9 +307,9 @@ def test_lj(self):
         system.cell_system.skin = 0.4
         system.cell_system.set_n_square(use_verlet_lists=True)
         self.run_test_lj()
-        system.cell_system.set_domain_decomposition(use_verlet_lists=True)
+        system.cell_system.set_regular_decomposition(use_verlet_lists=True)
         self.run_test_lj()
-        system.cell_system.set_domain_decomposition(use_verlet_lists=False)
+        system.cell_system.set_regular_decomposition(use_verlet_lists=False)
         self.run_test_lj()
 
     @utx.skipIfMissingFeatures("EXTERNAL_FORCES")