def test_parameteric_constr():
import numpy as np
from ase.build import bulk
from ase.constraints import (
dict2constraint,
FixScaledParametricRelations,
FixCartesianParametricRelations,
)
from ase.calculators.emt import EMT
# Build the atoms object and attach a calculator
a = bulk("Ni", cubic=True)
a.calc = EMT()
# Get adjusted cell
cell = a.cell + 0.01
# Generate lattice constraint
param_lat = ["a"]
expr_lat = [
"a",
"0",
"0",
"0",
"a",
"0",
"0",
"0",
"a",
]
constr_lat = FixCartesianParametricRelations.from_expressions(
indices=[0, 1, 2],
params=param_lat,
expressions=expr_lat,
use_cell=True,
)
# Check expression generator
for const_expr, passed_expr in zip(constr_lat.expressions.flatten(),
expr_lat):
assert const_expr == passed_expr
# Check adjust_cell
constr_lat.adjust_cell(a, cell)
# Check serialization and construction from dict
constr_lat_dict = constr_lat.todict()
dict2constraint(constr_lat_dict)
cell_diff = (cell - a.cell).flatten()
expected_cell_diff = np.array(
[0.01, 0.0, 0.0, 0.0, 0.01, 0.0, 0.0, 0.0, 0.01])
assert np.max(np.abs(cell_diff - expected_cell_diff)) < 1e-12
# Check adjust_stress
a.cell += 0.01
stress = a.get_stress().copy()
constr_lat.adjust_stress(a, stress)
stress_rat = stress / a.get_stress()
assert np.max(
np.abs(stress_rat - np.array([1., 1., 1., 0., 0., 0.]))) < 1e-12
# Reset cell
a.cell -= 0.01
# Get adjusted cell/positions for the system
pos = a.get_positions().copy() + 0.01
# Generate proper atomic constraints
constr_atom = FixScaledParametricRelations(
[0, 1, 2, 3],
np.ndarray((12, 0)),
a.get_scaled_positions().flatten(),
)
# Check serialization and construction from dict
constr_atom_dict = constr_atom.todict()
dict2constraint(constr_atom_dict)
# Check adjust_positions
constr_atom.adjust_positions(a, pos)
assert np.max(np.abs(a.get_positions() - pos)) < 1e-12
# Check adjust_forces
assert np.max(np.abs(a.get_forces())) < 1e-12
# Check non-empty constraint
param_atom = ["dis"]
expr_atom = [
"dis",
"dis",
"dis",
"dis",
"-0.5",
"0.5",
"0.5",
"dis",
"0.5",
"0.5",
"0.5",
"dis",
]
constr_atom = FixScaledParametricRelations.from_expressions(
indices=[0, 1, 2, 3],
params=param_atom,
expressions=expr_atom,
)
# Restart position adjustment
pos += 0.01 * a.cell[0, 0]
# Check adjust_positions
constr_atom.adjust_positions(a, pos)
scaled_pos = a.cell.scaled_positions(pos)
pos_diff = (scaled_pos - a.get_scaled_positions()).flatten()
expected_pos_diff = np.array(
[0.01, 0.01, 0.01, 0.01, 0.0, 0.0, 0.0, 0.01, 0.0, 0.0, 0.0, 0.01])
assert np.max(np.abs(pos_diff - expected_pos_diff)) < 1e-12
# Check adjust_forces
a.set_positions(pos + 0.3)
forces = a.get_forces()
constr_atom.adjust_forces(a, forces)
forces_rat = forces / a.get_forces()
assert np.max(
np.abs(forces_rat.flatten() / 100.0 - expected_pos_diff)) < 1e-12
# Check auto-remapping/expression generation, the -0.5 should now be 0.5
expr_atom[4] = "0.5"
current_expression = constr_atom.expressions.flatten()
for const_expr, passed_expr in zip(current_expression, expr_atom):
assert const_expr == passed_expr
# Check with Cartesian parametric constraints now
expr_atom = [
"dis",
"dis",
"dis",
"dis",
"1.76",
"1.76",
"1.76",
"dis",
"1.76",
"1.76",
"1.76",
"dis",
]
constr_atom = FixCartesianParametricRelations.from_expressions(
indices=[0, 1, 2, 3],
params=param_atom,
expressions=expr_atom,
)
# Restart position adjustment
a.set_positions(pos)
pos += 0.01
# Check adjust_positions
constr_atom.adjust_positions(a, pos)
pos_diff = (pos - a.get_positions()).flatten()
expected_pos_diff = np.array(
[0.01, 0.01, 0.01, 0.01, 0.0, 0.0, 0.0, 0.01, 0.0, 0.0, 0.0, 0.01])
assert np.max(np.abs(pos_diff - expected_pos_diff)) < 1e-12
# Check adjust_forces
a.set_positions(pos + 0.3)
forces = a.get_forces()
constr_atom.adjust_forces(a, forces)
forces_rat = forces / a.get_forces()
assert np.max(
np.abs(forces_rat.flatten() / 100.0 - expected_pos_diff)) < 1e-12
stress = a.get_stress().copy()
constr_lat.adjust_stress(a, stress)
stress_rat = stress / a.get_stress()
assert np.max(np.abs(stress_rat - np.array([1., 1., 1., 0., 0., 0.]))) < 1e-12
# Reset cell
a.cell -= 0.01
# Get adjusted cell/positions for the system
pos = a.get_positions().copy() + 0.01
# Generate proper atomic constraints
constr_atom = FixScaledParametricRelations(
[0, 1, 2, 3],
np.ndarray((12, 0)),
a.get_scaled_positions().flatten(),
)
# Check serialization and construction from dict
constr_atom_dict = constr_atom.todict()
dict2constraint(constr_atom_dict)
# Check adjust_positions
constr_atom.adjust_positions(a, pos)
assert np.max(np.abs(a.get_positions() - pos)) < 1e-12
# Check adjust_forces
assert np.max(np.abs(a.get_forces())) < 1e-12
# Check non-empty constraint