def test_check_conflict_constraints():
"""
Test the check_conflict_constraints() function
Notes
-----
Atom indices in constraits_string is 1-indexed
Atom indices in dihedral_idxs is 0-indexed
"""
constraits_string = '''
$freeze
xyz 1-3,6-7
distance 1 5
$set
distance 1 4 1.0
angle 4 1 2 30.0
dihedral 1 2 3 4 60.0
'''
constraints_dict = make_constraints_dict(constraits_string)
# empty check
check_conflict_constraints(constraints_dict, [])
# test valid constraints_dict when not conflicting
dihedral_idxs = [[1, 2, 3, 4], [2, 3, 4, 5]]
check_conflict_constraints(constraints_dict, dihedral_idxs)
# test conflicting
with pytest.raises(ValueError):
# dihedral conflict (same as scanning)
check_conflict_constraints(constraints_dict, [[0, 1, 2, 3]])
with pytest.raises(ValueError):
# dihedral conflict (share the same center atoms 1, 2)
check_conflict_constraints(constraints_dict, [[5, 2, 1, 6]])
with pytest.raises(ValueError):
# xyz conflict
check_conflict_constraints(constraints_dict, [[0, 1, 2, 5]])
def main():
import argparse, sys
parser = argparse.ArgumentParser(description="Potential energy scan of dihedral angle from 1 to 360 degree", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('inputfile', type=str, help='Input template file for QMEngine. Geometry will be used as starting point for scanning.')
parser.add_argument('dihedralfile', type=str, help='File defining all dihedral angles to be scanned.')
parser.add_argument('--init_coords', type=str, help='File contain a list of geometries, that will be used as multiple starting points, overwriting the geometry in input file.')
parser.add_argument('-g', '--grid_spacing', type=int, nargs='*', default=[15], help='Grid spacing for dihedral scan, i.e. every 15 degrees, multiple values will be mapped to each dihedral angle')
parser.add_argument('-e', '--engine', type=str, default="psi4", choices=['qchem', 'psi4', 'terachem', 'openmm', "gaussian"], help='Engine for running scan')
parser.add_argument('-c', '--constraints', type=str, default=None, help='Provide a constraints file in geomeTRIC format for additional freeze or set constraints (geomeTRIC or TeraChem only)')
parser.add_argument('--native_opt', action='store_true', default=False, help='Use QM program native constrained optimization algorithm. This will turn off geomeTRIC package.')
parser.add_argument('--energy_thresh', type=float, default=1e-5, help='Only activate grid points if the new optimization is <thre> lower than the previous lowest energy (in a.u.).')
parser.add_argument('--energy_upper_limit', type=float, default=None, help='Only activate grid points if the new optimization is less than <thre> higher than the global lowest energy (in a.u.).')
parser.add_argument('--wq_port', type=int, default=None, help='Specify port number to use Work Queue to distribute optimization jobs.')
parser.add_argument('--zero_based_numbering', action='store_true', help='Use zero_based_numbering in dihedrals file.')
parser.add_argument('-v', '--verbose', action='store_true', default=False, help='Print more information while running.')
args = parser.parse_args()
# print input command for reproducibility
print(' '.join(sys.argv))
# parse the dihedral file
if args.zero_based_numbering is True:
print("The use of command line --zero_based_numbering is deprecated and will be removed in the future. Please use #zero_based_numbering in dihedralfile")
dihedral_idxs, dihedral_ranges = load_dihedralfile(args.dihedralfile, args.zero_based_numbering)
grid_dim = len(dihedral_idxs)
# parse additional constraints
constraints_dict = None
if args.constraints is not None:
with open(args.constraints) as fin:
constraints_dict = make_constraints_dict(fin.read())
# check if there are extra constraints conflict with the specified dihedral angles
check_conflict_constraints(constraints_dict, dihedral_idxs)
# format grid spacing
n_grid_spacing = len(args.grid_spacing)
if n_grid_spacing == grid_dim:
grid_spacing = args.grid_spacing
elif n_grid_spacing == 1:
grid_spacing = args.grid_spacing * grid_dim
else:
raise ValueError("Number of grid_spacing values %d is not consistent with number of dihedral angles %d" % (grid_dim, n_grid_spacing))
# create QM Engine, and WorkQueue object if provided port
engine = create_engine(args.engine, inputfile=args.inputfile, work_queue_port=args.wq_port, native_opt=args.native_opt)
# load init_coords if provided
init_coords_M = Molecule(args.init_coords) if args.init_coords else None
# create DihedralScanner object
scanner = DihedralScanner(engine, dihedrals=dihedral_idxs, dihedral_ranges=dihedral_ranges, grid_spacing=grid_spacing, init_coords_M=init_coords_M,
energy_decrease_thresh=args.energy_thresh, energy_upper_limit=args.energy_upper_limit, extra_constraints=constraints_dict, verbose=args.verbose)
# Run the scan!
scanner.master()
# After finish, print result
print("Dihedral scan is finished!")
print(" Grid ID Energy")
for grid_id in sorted(scanner.grid_energies.keys()):
print(" %-20s %.10f" % (str(grid_id), scanner.grid_energies[grid_id]))
def test_make_constraints_dict():
'''
Unit test for torsiondrive.qm_engine.make_constraints_dict() function
'''
constraits_string = '''
$freeze
xyz 1-3,6-7
distance 1 5
$set
distance 1 4 1.0
angle 4 1 2 30.0
dihedral 1 2 3 4 60.0
'''
constraints_dict = make_constraints_dict(constraits_string)
# test the freeze constraints
spec_list = constraints_dict['freeze']
assert len(spec_list) == 2
assert spec_list[0]['type'] == 'xyz'
assert spec_list[0]['indices'] == [0, 1, 2, 5, 6]
assert spec_list[1]['type'] == 'distance'
assert spec_list[1]['indices'] == [0, 4]
# test the set constraints
spec_list = constraints_dict['set']
assert len(spec_list) == 3
assert spec_list[0]['type'] == 'distance'
assert spec_list[0]['indices'] == [0, 3]
assert spec_list[0]['value'] == 1.0
assert spec_list[1]['type'] == 'angle'
assert spec_list[1]['indices'] == [3, 0, 1]
assert spec_list[1]['value'] == 30.0
assert spec_list[2]['type'] == 'dihedral'
assert spec_list[2]['indices'] == [0, 1, 2, 3]
assert spec_list[2]['value'] == 60.0
# test error handling for wrong inputs
# scan not supported
wrong_constraits_string = '''
$scan
distance 1 2 1.0 2.0 10
'''
with pytest.raises(ValueError):
make_constraints_dict(wrong_constraits_string)
# $unknown not supported
wrong_constraits_string = '''
$unknown
distance 1 2 1.0 2.0 10
'''
with pytest.raises(ValueError):
make_constraints_dict(wrong_constraits_string)
# rotation not supported
wrong_constraits_string = '''
$set
rotation 1-4 10.0
'''
with pytest.raises(ValueError):
make_constraints_dict(wrong_constraits_string)
# freezing x not supported
wrong_constraits_string = '''
$freeze
x 1 1.0
'''
with pytest.raises(ValueError):
make_constraints_dict(wrong_constraits_string)
# missing $set
wrong_constraits_string = '''
distance 1 2 1.0
'''
with pytest.raises(ValueError):
make_constraints_dict(wrong_constraits_string)
# setting xyz not supported
wrong_constraits_string = '''
$set
xyz 1-3 1.0 2.0 3.0
'''
with pytest.raises(ValueError):
make_constraints_dict(wrong_constraits_string)
# wrong index
wrong_constraits_string = '''
$set
distance 0 1 1.0
'''
with pytest.raises(AssertionError):
make_constraints_dict(wrong_constraits_string)