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Correct over-squaring in internal coordinate objective function for adding an atom to XYZ #802

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Correct over-squaring in internal coordinate objective function for adding an atom to XYZ #802

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11 changes: 8 additions & 3 deletions arc/species/converter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,9 @@
ob.obErrorLog.SetOutputLevel(0)
logger = get_logger()

DIST_PRECISION = 0.01 # Angstrom
ANGL_PRECISION = 0.1 # rad (for both bond angle and dihedral)


def str_to_xyz(xyz_str: str,
project_directory: Optional[str] = None,
Expand Down Expand Up @@ -2074,7 +2077,7 @@ def calculate_errors(result_coords):

def meets_precision(result_coords):
r_error, a_error, d_error = calculate_errors(result_coords)
return r_error < 0.01 and a_error < 0.1 and d_error < 0.1
return r_error < DIST_PRECISION and a_error < ANGL_PRECISION and d_error < ANGL_PRECISION

guess_functions = [
generate_initial_guess_r_a,
Expand Down Expand Up @@ -2262,7 +2265,9 @@ def angle_eq(x, y, z):
cross_product_length = np.linalg.norm(np.cross(BA, BX))
dot_product = np.dot(BA, BX)
calc_angle = math.atan2(cross_product_length, dot_product)
return (calc_angle - target_angle) ** 2
angle_diff = calc_angle - target_angle
wrapped_diff = np.arctan2(np.sin(angle_diff), np.cos(angle_diff)) # wrapped to the range (-pi, pi]
return wrapped_diff

return angle_eq

Expand Down Expand Up @@ -2310,7 +2315,7 @@ def dihedral_eq(x, y, z):
BC_norm = np.linalg.norm(BC)
cos_calc = np.dot(N1, N2) / (N1_norm * N2_norm)
sin_calc = np.dot(BC, np.cross(N1, N2)) / (BC_norm * N1_norm * N2_norm)
return (cos_calc - cos_d) ** 2 + (sin_calc - sin_d) ** 2
return np.sqrt((cos_calc - cos_d) ** 2 + (sin_calc - sin_d) ** 2)

return dihedral_eq

Expand Down
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