def test_build_terachem_constraint_string():
"""
Test build_geometric_constraint_string() function
Notes
-----
Atom indices in constraits_string is 1-indexed
Atom indices in dihedral_idxs is 0-indexed
"""
constraints_dict = {
'freeze': [{
'type': 'xyz',
'indices': [0, 1, 2, 5, 6],
}, {
'type': 'distance',
'indices': [0, 4],
}],
'set': [
{
'type': 'distance',
'indices': [0, 3],
'value': 1.0,
},
{
'type': 'angle',
'indices': [1, 0, 3],
'value': 30.0,
},
{
'type': 'dihedral',
'indices': [0, 1, 2, 3],
'value': 60.0,
},
]
}
constraints_string = build_terachem_constraint_string(constraints_dict)
# validate the constraints string
assert constraints_string.strip() == '\n'.join([
'$constraint_freeze', 'xyz 1-3,6-7', 'bond 1_5', '$end\n',
'$constraint_set', 'bond 1.0 1_4', 'angle 30.0 2_1_4',
'dihedral 60.0 1_2_3_4', '$end'
])
# test with dihedral_idx_values
dihedral_idx_values = [(1, 2, 3, 4, 90.0), (2, 3, 4, 5, 120.0)]
constraints_string2 = build_terachem_constraint_string(
constraints_dict, dihedral_idx_values=dihedral_idx_values)
assert constraints_string2.strip() == '\n'.join([
'$constraint_freeze', 'xyz 1-3,6-7', 'bond 1_5', '$end\n',
'$constraint_set', 'bond 1.0 1_4', 'angle 30.0 2_1_4',
'dihedral 60.0 1_2_3_4', 'dihedral 90.0 2_3_4_5',
'dihedral 120.0 3_4_5_6', '$end'
])
def optimize_native(self):
"""
Run the constrained optimization.
1. write a optimization job input file.
2. run the job
"""
assert self.temp_type == 'optimize', "To use native optimization, the input file be an opt job"
if self.extra_constraints is None:
self.constraintsStr = '\n$constraint_set\n'
for d1, d2, d3, d4, v in self.dihedral_idx_values:
# TeraChem use atom index starting from 1
self.constraintsStr += f"dihedral {float(v)} {d1 + 1}_{d2 + 1}_{d3 + 1}_{d4 + 1}\n"
self.constraintsStr += '$end\n'
else:
self.constraintsStr = build_terachem_constraint_string(
self.extra_constraints, self.dihedral_idx_values)
# write input file
self.write_input()
# run the job
self.run('terachem run.in > run.out',
input_files=['run.in', self.tera_geo_file],
output_files=['run.out', 'scr'])