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Merged
kfir4444 merged 5 commits into from
Nov 1, 2025
Merged

Supports scans with Orca 🐋 #805

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b70a92c
added parse_1d_scan_coords to orca
kfir4444 Oct 28, 2025
da17932
Test: parse scan coords Orca
kfir4444 Oct 28, 2025
55029fb
added orca parse_1d_scan_energies
kfir4444 Oct 28, 2025
0e161ec
Test: parse scan energies Orca
kfir4444 Oct 28, 2025
cbf0a7d
Test: added scan logs.
kfir4444 Oct 28, 2025
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48 changes: 43 additions & 5 deletions arc/parser/adapters/orca.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,11 @@

import numpy as np
import pandas as pd
import re

from arc.common import SYMBOL_BY_NUMBER
from arc.constants import E_h_kJmol, bohr_to_angstrom
from arc.species.converter import xyz_from_data
from arc.species.converter import str_to_xyz, xyz_from_data
from arc.parser.adapter import ESSAdapter
from arc.parser.factory import register_ess_adapter
from arc.parser.parser import _get_lines_from_file
Expand Down Expand Up @@ -238,8 +239,22 @@ def parse_1d_scan_energies(self) -> Tuple[Optional[List[float]], Optional[List[f
Returns: Tuple[Optional[List[float]], Optional[List[float]]]
The electronic energy in kJ/mol and the dihedral scan angle in degrees.
"""
# Not implemented for Orca.
return None, None
cs, es = [], []
with open(self.log_file_path, "r") as f:
flag_actual = False
for line in f.readlines():
if "The Calculated Surface using the 'Actual Energy'" in line:
flag_actual = True
elif flag_actual:
if not line.strip():
break
else:
c, e = line.split()
cs.append(float(c))
es.append(float(e))
if len(cs) != len(es) or not cs:
raise ValueError("Failed to parse 1D scan energies from Orca log file.")
return np.array(es), np.array(cs)

def parse_1d_scan_coords(self) -> Optional[List[Dict[str, tuple]]]:
"""
Expand All @@ -248,8 +263,31 @@ def parse_1d_scan_coords(self) -> Optional[List[Dict[str, tuple]]]:
Returns: List[Dict[str, tuple]]
The Cartesian coordinates for each scan point.
"""
# Not implemented for Orca.
return None
coords_list = []
with open(self.log_file_path, "r") as f:
flag_hurray, flag_coords = False, False
pat = re.compile(
r'^\s*([A-Z][a-z]?)\s+'
r'([+-]?(?:\d+(?:\.\d*)?|\.\d+)(?:[eE][+-]?\d+)?)\s+'
r'([+-]?(?:\d+(?:\.\d*)?|\.\d+)(?:[eE][+-]?\d+)?)\s+'
r'([+-]?(?:\d+(?:\.\d*)?|\.\d+)(?:[eE][+-]?\d+)?)\s*$',
re.MULTILINE
)
for line in f.readlines():
if "HURRAY" in line:
coords = """"""
flag_hurray = True
if flag_hurray and "CARTESIAN COORDINATES (ANGSTROEM)" in line:
flag_coords = True
if flag_hurray and flag_coords:
if not line.strip():
coords_list.append(str_to_xyz(coords))
flag_hurray, flag_coords = False, False
if bool(pat.match(line)):
coords += line
if not coords_list:
raise ValueError("Failed to parse 1D scan coordinates from Orca log file.")
return coords_list

def parse_irc_traj(self) -> Optional[List[Dict[str, tuple]]]:
"""
Expand Down
72 changes: 72 additions & 0 deletions arc/parser/parser_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -604,6 +604,24 @@ def test_parse_1d_scan_coords(self):
self.assertEqual(traj_4[0]['symbols'], ('C', 'C', 'H', 'H', 'H', 'H', 'H', 'C', 'C', 'C', 'C', 'C', 'C', 'C',
'C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H',
'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'))

path_5 = os.path.join(ARC_PATH, 'arc', 'testing', 'rotor_scans', 'orca', 'cc.txt')
traj_5 = parser.parse_1d_scan_coords(path_5)
self.assertEqual(len(traj_5), 45)
self.assertEqual(traj_5[0]['symbols'], ('O', 'N', 'O', 'H'))
self.assertEqual(traj_5[10]['coords'], ((-0.799556, -0.234171, 0.251428),
(0.64986, -0.41193, -0.121131),
(0.909042, 0.203539, -1.074932),
(-0.759345, 0.442562, 0.944635)))

path_6 = os.path.join(ARC_PATH, 'arc', 'testing', 'rotor_scans', 'orca', 'dft.txt')
traj_6 = parser.parse_1d_scan_coords(path_6)
self.assertEqual(len(traj_6), 40)
self.assertEqual(traj_6[0]['symbols'], ('N', 'O', 'O', 'H'))
self.assertEqual(traj_6[30]['coords'], ((0.002293, -0.673281, -0.26298),
(-0.138634, 0.590201, -0.397709),
(0.692562, 1.371759, 0.229642),
(-0.574929, -1.150836, 0.427339)))

def test_parse_t1(self):
"""Test T1 diagnostic parsing"""
Expand Down Expand Up @@ -712,6 +730,60 @@ def test_parse_1d_scan_energies(self):
104.0, 112.0, 120.0, 128.0, 136.0, 144.0, 152.0, 160.0, 168.0, 176.0, 184.0, 192.0,
200.0, 208.0, 216.0, 224.0, 232.0, 240.0, 248.0, 256.0, 264.0, 272.0, 280.0, 288.0,
296.0, 304.0, 312.0, 320.0, 328.0, 336.0, 344.0, 352.0])

path_4 = os.path.join(ARC_PATH, 'arc', 'testing', 'rotor_scans', 'orca', 'cc.txt')
energies_4, angles_4 = parser.parse_1d_scan_energies(log_file_path=path_4)
self.assertEqual(energies_4.shape, (45,))
energies_4, angles_4 = energies_4.tolist(), angles_4.tolist()
self.assertEqual(angles_4, [-180. , -171.81818182, -163.63636364, -155.45454545,
-147.27272727, -139.09090909, -130.90909091, -122.72727273,
-114.54545455, -106.36363636, -98.18181818, -90. ,
-81.81818182, -73.63636364, -65.45454545, -57.27272727,
-49.09090909, -40.90909091, -32.72727273, -24.54545455,
-16.36363636, -8.18181818, 0. , 8.18181818,
16.36363636, 24.54545455, 32.72727273, 40.90909091,
49.09090909, 57.27272727, 65.45454545, 73.63636364,
81.81818182, 90. , 98.18181818, 106.36363636,
114.54545455, 122.72727273, 130.90909091, 139.09090909,
147.27272727, 155.45454545, 163.63636364, 171.81818182,
180. ])
self.assertEqual(energies_4, [-205.45224799, -205.45190811, -205.45091275, -205.44933274,
-205.44728671, -205.4449269 , -205.44243238, -205.43999284,
-205.43779528, -205.43600588, -205.434757 , -205.43414239,
-205.43420969, -205.43496112, -205.4363512 , -205.43828268,
-205.44061138, -205.44315299, -205.44569266, -205.44800238,
-205.4498563 , -205.4510646 , -205.45148293, -205.45106459,
-205.44985629, -205.44800238, -205.44569265, -205.44315298,
-205.44061136, -205.43828268, -205.43635116, -205.43496113,
-205.43420969, -205.43414239, -205.434757 , -205.43600587,
-205.43779528, -205.43999284, -205.44243239, -205.44492691,
-205.44728671, -205.44933274, -205.45091284, -205.45190811,
-205.45224799])

path_5 = os.path.join(ARC_PATH, 'arc', 'testing', 'rotor_scans', 'orca', 'dft.txt')
energies_5, angles_5 = parser.parse_1d_scan_energies(log_file_path=path_5)
self.assertEqual(energies_5.shape, (40,))
energies_5, angles_5 = energies_5.tolist(), angles_5.tolist()
self.assertEqual(angles_5, [-180. , -170.76923077, -161.53846154, -152.30769231,
-143.07692308, -133.84615385, -124.61538462, -115.38461538,
-106.15384615, -96.92307692, -87.69230769, -78.46153846,
-69.23076923, -60. , -50.76923077, -41.53846154,
-32.30769231, -23.07692308, -13.84615385, -4.61538462,
4.61538462, 13.84615385, 23.07692308, 32.30769231,
41.53846154, 50.76923077, 60. , 69.23076923,
78.46153846, 87.69230769, 96.92307692, 106.15384615,
115.38461538, 124.61538462, 133.84615385, 143.07692308,
152.30769231, 161.53846154, 170.76923077, 180. ])
self.assertEqual(energies_5, [-205.56412863, -205.56304415, -205.55981277, -205.55449922,
-205.54721698, -205.53811775, -205.5274174 , -205.51539728,
-205.50245689, -205.49000818, -205.49181718, -205.50275068,
-205.51519265, -205.52710432, -205.53796901, -205.54748809,
-205.55543296, -205.56160894, -205.56584894, -205.5680131 ,
-205.56801483, -205.56585336, -205.56161212, -205.55542977,
-205.54748298, -205.53796909, -205.52710778, -205.51519567,
-205.50275147, -205.49181828, -205.49000878, -205.50245773,
-205.51540006, -205.52742038, -205.53811826, -205.5472153 ,
-205.55449977, -205.55981412, -205.56304759, -205.56413261])

def test_parse_nd_scan_energies(self):
"""Test parsing an ND scan output file"""
Expand Down
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