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Bug fix for constraints #403

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Merged
jan-janssen merged 1 commit into from
Nov 27, 2025
+92 −5
Merged

Bug fix for constraints #403

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2 changes: 1 addition & 1 deletion src/pylammpsmpi/wrapper/ase.py
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Original file line number Diff line number Diff line change
Expand Up @@ -561,7 +561,7 @@ def get_fixed_atom_boolean_vector(structure):
if c_dict["name"] == "FixAtoms":
fixed_atom_vector[c_dict["kwargs"]["indices"]] = [True, True, True]
elif c_dict["name"] == "FixedPlane":
if all(np.isin(c_dict["kwargs"]["direction"], [0, 1])):
if all(np.isin(c_dict["kwargs"]["direction"], [0, 1, 1 / np.sqrt(2)])):
if "indices" in c_dict["kwargs"]:
fixed_atom_vector[c_dict["kwargs"]["indices"]] = np.array(
c_dict["kwargs"]["direction"]
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95 changes: 91 additions & 4 deletions tests/test_ase_interface.py
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Original file line number Diff line number Diff line change
Expand Up @@ -416,7 +416,7 @@ def setUpClass(cls):
structure.symbols[2:] = "Al"
cls.structure = structure

def test_selective_dynamics_mixed_calcmd(self):
def test_selective_dynamics_mixed_calcmd_x(self):
atoms = self.structure.copy()
c1 = FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == "Cu"])
c2 = FixedPlane(
Expand All @@ -433,11 +433,98 @@ def test_selective_dynamics_mixed_calcmd(self):
self.assertTrue(control_dict["velocity constraintxyz"], "set 0.0 0.0 0.0")
self.assertTrue(control_dict["group constraintx"], "id 3 4")
self.assertTrue(
control_dict["fix constraintx"], "constraintx setforce 0.0 NULL NULL"
control_dict["fix constraintx"], "constraintx setforce NULL NULL 0.0"
)
self.assertTrue(control_dict["velocity constraintx"], "set NULL NULL 0.0")

def test_selective_dynamics_mixed_calcmd_y(self):
atoms = self.structure.copy()
c1 = FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == "Cu"])
c2 = FixedPlane(
[atom.index for atom in atoms if atom.symbol == "Al"],
[0, 1, 0],
)
atoms.set_constraint([c1, c2])
control_dict = set_selective_dynamics(structure=atoms, calc_md=True)
self.assertEqual(len(control_dict), 6)
self.assertTrue(control_dict["group constraintxyz"], "id 1 2")
self.assertTrue(
control_dict["fix constraintxyz"], "constraintxyz setforce 0.0 0.0 0.0"
)
self.assertTrue(control_dict["velocity constraintxyz"], "set 0.0 0.0 0.0")
self.assertTrue(control_dict["group constrainty"], "id 3 4")
self.assertTrue(
control_dict["fix constrainty"], "constrainty setforce NULL 0.0 NULL"
)
self.assertTrue(control_dict["velocity constrainty"], "set NULL 0.0 NULL")

def test_selective_dynamics_mixed_calcmd_z(self):
atoms = self.structure.copy()
c1 = FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == "Cu"])
c2 = FixedPlane(
[atom.index for atom in atoms if atom.symbol == "Al"],
[0, 0, 1],
)
atoms.set_constraint([c1, c2])
control_dict = set_selective_dynamics(structure=atoms, calc_md=True)
self.assertEqual(len(control_dict), 6)
self.assertTrue(control_dict["group constraintxyz"], "id 1 2")
self.assertTrue(
control_dict["fix constraintxyz"], "constraintxyz setforce 0.0 0.0 0.0"
)
self.assertTrue(control_dict["velocity constraintxyz"], "set 0.0 0.0 0.0")
self.assertTrue(control_dict["group constraintz"], "id 3 4")
self.assertTrue(
control_dict["fix constraintz"], "constraintz setforce NULL NULL 0.0"
)
self.assertTrue(control_dict["velocity constraintz"], "set NULL NULL 0.0")

def test_selective_dynamics_calcmd_xy(self):
atoms = self.structure.copy()
c1 = FixedPlane(
[atom.index for atom in atoms if atom.symbol == "Al"],
[1, 1, 0],
)
atoms.set_constraint([c1])
control_dict = set_selective_dynamics(structure=atoms, calc_md=True)
self.assertEqual(len(control_dict), 3)
self.assertTrue(control_dict["group constraintxy"], "id 3 4")
self.assertTrue(
control_dict["fix constraintxy"], "constraintxy setforce NULL 0.0 0.0"
)
self.assertTrue(control_dict["velocity constraintxy"], "set NULL 0.0 0.0")

def test_selective_dynamics_calcmd_xz(self):
atoms = self.structure.copy()
c1 = FixedPlane(
[atom.index for atom in atoms if atom.symbol == "Al"],
[1, 0, 1],
)
atoms.set_constraint([c1])
control_dict = set_selective_dynamics(structure=atoms, calc_md=True)
self.assertEqual(len(control_dict), 3)
self.assertTrue(control_dict["group constraintxz"], "id 3 4")
self.assertTrue(
control_dict["fix constraintxz"], "constraintxz setforce NULL 0.0 0.0"
)
self.assertTrue(control_dict["velocity constraintxz"], "set NULL 0.0 0.0")

def test_selective_dynamics_calcmd_yz(self):
atoms = self.structure.copy()
c1 = FixedPlane(
[atom.index for atom in atoms if atom.symbol == "Al"],
[0, 1, 1],
)
atoms.set_constraint([c1])
control_dict = set_selective_dynamics(structure=atoms, calc_md=True)
self.assertEqual(len(control_dict), 3)
self.assertTrue(control_dict["group constraintyz"], "id 3 4")
self.assertTrue(
control_dict["fix constraintyz"], "constraintyz setforce NULL 0.0 0.0"
)
self.assertTrue(control_dict["velocity constraintx"], "set 0.0 NULL NULL")
self.assertTrue(control_dict["velocity constraintyz"], "set NULL 0.0 0.0")

def test_selective_dynamics_mixed(self):
def test_selective_dynamics_mixed_x(self):
atoms = self.structure.copy()
c1 = FixAtoms(indices=[atom.index for atom in atoms if atom.symbol == "Cu"])
c2 = FixedPlane(
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