Updates

Author: calvinp0

arc/job/adapters/qchem.py

@@ -380,85 +380,80 @@ def write_input_file(self) -> None:
         with open(os.path.join(self.local_path, input_filenames[self.job_adapter]), 'w') as f:
             f.write(Template(input_template).render(**input_dict))
     def generate_qchem_scan_angles(self,start_angle: int, step: int) -> (int, int, int, int):
-            """
-            Generates the angles for a Q-Chem scan. The scan is split into two parts, one from start_angle to 180, and one from -180 to end_angle.
-
-            Parameters
-            ----------
-            start_angle : int
-                The starting angle for the scan
-            step : int
-                The step size for the scan
-
-            Returns
-            -------
-            scan1_start : int
-                The starting angle for the first part of the scan
-            scan1_end : int
-                The ending angle for the first part of the scan
-            scan2_start : int
-                The starting angle for the second part of the scan
-            scan2_end : int
-                The ending angle for the second part of the scan
-            """
-
-            # First, we need to check that the start_angle is within the range of -180 to 180, and if not, convert it to be within that range
-            if start_angle > 180:
-                start_angle = start_angle - 360
-
-
-            # This sets the end angle but does not take into account the limit of -180 to 180
-            end_angle = start_angle - step
-
-            # This function wraps the scan2_start within the range of -180 to 180
-            wrap_within_range = lambda number, addition: (number + addition) % 360 - 360 if (number + addition) % 360 > 180 else (number + addition) % 360
-
-            # This function converts the angles to be within the range of -180 to 180
-            convert_angle = lambda angle: angle % 360 if angle >= 0 else ( angle % 360 if angle <= -180 else (angle % 360) - 360)
-
-            # This converts the angles to be within the range of -180 to 180
-            start_angle = convert_angle(start_angle)
-            end_angle = convert_angle(end_angle)
+        """Generates angles for a Q-Chem dihedral scan, split into two segments.
+
+        This function computes the angles for a Q-Chem dihedral scan. The scan is
+        divided into two parts: one spanning from the start_angle to 180 degrees,
+        and the other from -180 degrees to the calculated end_angle based on the
+        step size.
+
+        Args:
+            start_angle (int): The initial angle for the scan.
+            step (int): The incremental step size for the scan.
+
+        Returns:
+            tuple of int: A tuple containing the start and end angles for both
+                        scan segments. It includes scan1_start, scan1_end,
+                        scan2_start, and scan2_end.
+        """
+
+        # First, we need to check that the start_angle is within the range of -180 to 180, and if not, convert it to be within that range
+        if start_angle > 180:
+            start_angle = start_angle - 360
+
+
+        # This sets the end angle but does not take into account the limit of -180 to 180
+        end_angle = start_angle - step
+
+        # This function wraps the scan2_start within the range of -180 to 180
+        wrap_within_range = lambda number, addition: (number + addition) % 360 - 360 if (number + addition) % 360 > 180 else (number + addition) % 360
+
+        # This function converts the angles to be within the range of -180 to 180
+        convert_angle = lambda angle: angle % 360 if angle >= 0 else ( angle % 360 if angle <= -180 else (angle % 360) - 360)
+
+        # This converts the angles to be within the range of -180 to 180
+        start_angle = convert_angle(start_angle)
+        end_angle = convert_angle(end_angle)
+
+        if start_angle == 0 and end_angle == 0:
+            scan1_start = start_angle
+            scan1_end = 180
+            scan2_start = -180
+            scan2_end = end_angle
+        elif start_angle == 180:
+            # This is a special case because the scan will be from 180 to 180
+            # This is not allowed in Q-Chem so we split it into two scans
+            # Arguably this could be done in one scan but it is easier to do it this way
+            # We will need to find the starting angle that when added by the step size will be 180
+            target_sum = 180
+            quotient = target_sum // step
+            starting_number = target_sum - (quotient * step)
+            scan1_start = starting_number
+            scan1_end = 180
+            scan2_start = -180
+            scan2_end = scan1_start - step
+        elif start_angle <= end_angle:
+            scan1_start = start_angle
+            scan1_end =  start_angle + (step * ((180 - start_angle)//step))
+            scan2_start = convert_angle(scan1_end)
+            scan2_end = end_angle
+        elif (start_angle + step) > 180:
+            # This is a special case because the scan will be from, for example, 178 to 178 for the first scan. Therefore, we should make it a single scan from end angle, 178, step size
+            scan1_end = start_angle
+            scan1_start = wrap_within_range(scan1_end, step)
+            scan2_start = 0
+            scan2_end = 0
+        else:
+            scan1_start = start_angle
+            scan1_end = start_angle + (step * ((180 - start_angle)//step))
+            scan2_start = wrap_within_range(scan1_end, step)
+            scan2_end = end_angle
 
-            if start_angle == 0 and end_angle == 0:
-                scan1_start = start_angle
-                scan1_end = 180
-                scan2_start = -180
-                scan2_end = end_angle
-            elif start_angle == 180:
-                # This is a special case because the scan will be from 180 to 180
-                # This is not allowed in Q-Chem so we split it into two scans
-                # Arguably this could be done in one scan but it is easier to do it this way
-                # We will need to find the starting angle that when added by the step size will be 180
-                target_sum = 180
-                quotient = target_sum // step
-                starting_number = target_sum - (quotient * step)
-                scan1_start = starting_number
-                scan1_end = 180
-                scan2_start = -180
-                scan2_end = scan1_start - step
-            elif start_angle <= end_angle:
-                scan1_start = start_angle
-                scan1_end =  start_angle + (step * ((180 - start_angle)//step))
-                scan2_start = convert_angle(scan1_end)
-                scan2_end = end_angle
-            elif (start_angle + step) > 180:
-                # This is a special case because the scan will be from, for example, 178 to 178 for the first scan. Therefore, we should make it a single scan from end angle, 178, step size 
-                scan1_end = start_angle
-                scan1_start = wrap_within_range(scan1_end, step)
-                scan2_start = 0
-                scan2_end = 0
-            else:
-                scan1_start = start_angle
-                scan1_end = start_angle + (step * ((180 - start_angle)//step))
-                scan2_start = wrap_within_range(scan1_end, step)
-                scan2_end = end_angle
-                
-            if scan2_start == scan2_end:
-                scan2_start = 0
-                scan2_end = 0
-
-            return int(scan1_start), int(scan1_end), int(scan2_start), int(scan2_end)
+        if scan2_start == scan2_end:
+            scan2_start = 0
+            scan2_end = 0
+
+        return int(scan1_start), int(scan1_end), int(scan2_start), int(scan2_end)
 
     def generate_scan_angles(self, req_angle: int, step: int) -> (int, int):
 

arc/level_test.py

@@ -70,11 +70,18 @@ def test_deduce_software_irc_with_both(self):
         self.assertEqual(level.software, 'gaussian')  # gaussian is also available
 
     @patch('arc.level.supported_ess', new=['qchem'])
-    def test_deduce_software_irc_with_only_gaussian(self):
+    def test_deduce_software_irc_with_only_qchem(self):
         """Test deducing software for IRC job when only gaussian is supported."""
         level = Level(method='B3LYP', basis='6-311g+(d,f)')
         level.deduce_software(job_type='irc')
         self.assertEqual(level.software, 'qchem')  # Only qchem is available
+    
+    @patch('arc.level.supported_ess', new=['gaussian'])
+    def test_deduce_software_irc_with_only_gaussian(self):
+        """Test deducing software for IRC job when only qchem is supported."""
+        level = Level(method='B3LYP', basis='6-311g+(d,f)')
+        level.deduce_software(job_type='irc')
+        self.assertEqual(level.software, 'gaussian')
 
     @patch('arc.level.supported_ess', new=[])
     def test_deduce_software_value_errors(self):

arc/parser.py

@@ -149,7 +149,7 @@ def parse_frequencies(path: str,
 
 def parse_normal_mode_displacement(path: str,
                                    software: Optional[str] = None,
-                                   raise_error: bool = False, # TODO: Why is this true? What is it supposed to do?
+                                   raise_error: bool = False,
                                    ) -> Tuple[np.ndarray, np.ndarray]:
     """
     Parse frequencies and normal mode displacement.

arc/parser_test.py

@@ -244,6 +244,23 @@ def test_parse_normal_mode_displacement(self):
              [-0.16184923713199378, -0.3376354950974596, 0.787886990928027]], np.float64)
         np.testing.assert_almost_equal(normal_modes_disp[0], expected_normal_modes_disp_4_0)
 
+        # QChem
+        path = os.path.join(ARC_PATH, 'arc', 'testing', 'normal_mode', 'HO2', 'qchem-freq.out')
+        freqs, normal_modes_disp = parser.parse_normal_mode_displacement(path=path, software='qchem', raise_error=False)
+        print(freqs)
+        expected_freqs = np.array([1164.75, 1431.41, 3582.24], np.float64)
+        np.testing.assert_allclose(freqs, expected_freqs, rtol=1e-5, atol=1e-8)
+        expected_normal_modes_disp_3 = np.array([[[-0.584,  0.091, -0.   ],
+                                                [ 0.612, -0.107,  0.   ],
+                                                [-0.448,  0.253,  0.   ]],
+                                                [[-0.065, -0.039, -0.   ],
+                                                [ 0.005,  0.057,  0.   ],
+                                                [ 0.951, -0.294, -0.   ]],
+                                                [[-0.001,  0.001,  0.   ],
+                                                [-0.021, -0.06 , -0.   ],
+                                                [ 0.348,  0.935,  0.   ]]])
+        np.testing.assert_allclose(normal_modes_disp, expected_normal_modes_disp_3, rtol=1e-5, atol=1e-8)
+
     def test_parse_xyz_from_file(self):
         """Test parsing xyz from a file"""
         path1 = os.path.join(ARC_PATH, 'arc', 'testing', 'xyz', 'CH3C(O)O.gjf')
@@ -428,6 +445,12 @@ def test_parse_1d_scan_coords(self):
                                                 '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', 'qchem-pes.out')
+        traj_5 = parser.parse_1d_scan_coords(path_5)
+        self.assertEqual(len(traj_5), 25)
+        self.assertEqual(traj_5[0]['symbols'], ('C', 'C', 'C', 'C', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'))
+        self.assertEqual(traj_5[0]['coords'][13], (-2.1002861161, 0.7502495424, -0.8796160845))
+
     def test_parse_t1(self):
         """Test T1 diagnostic parsing"""
         path = os.path.join(ARC_PATH, 'arc', 'testing', 'sp', 'mehylamine_CCSD(T).out')

arc/settings/submit_test.py

@@ -18,7 +18,7 @@ class TestSubmit(unittest.TestCase):
     def test_servers(self):
         """Test server keys in submit_scripts"""
         for server in submit_scripts.keys():
-            self.assertTrue(server in ['local', 'atlas', 'txe1', 'pbs_sample', 'server1', 'server2', 'azure'])
+            self.assertIn(server, ['local', 'atlas', 'txe1', 'pbs_sample', 'server1', 'server2', 'azure'])
 
 
 if __name__ == '__main__':