def run_mopac(self, mol):
cur_dir = os.getcwd()
all_errors = set()
energy = 0.0
with tempfile.TemporaryDirectory() as scratch_dir:
order_text = ["st", "nd", "th"]
title = "Salt Alignment {}{} Calculation".format(
self.run_number,
order_text[self.run_number - 1 if self.run_number < 3 else 2])
self.run_number += 1
mop = MopTask(mol, self.total_charge, "opt", title, "PM7",
{"CYCLES": 2000})
mop.write_file("mol.mop")
job = MopacJob(backup=False)
handler = MopacErrorHandler()
c = Custodian(handlers=[handler], jobs=[job], max_errors=50)
custodian_out = c.run()
mopout = MopOutput("mol.out")
final_pmg_mol = mopout.data["molecules"][-1]
final_ob_mol = BabelMolAdaptor(final_pmg_mol)._obmol
energy = Energy(mopout.data["energies"][-1][-1], "eV").to("Ha")
if energy < self.global_best_energy:
self.global_best_energy = energy
shutil.copy("mol.out", os.path.join(cur_dir, "best_mol.out"))
for run in custodian_out:
for correction in run['corrections']:
all_errors.update(correction['errors'])
if len(all_errors) > 0:
out_error_logs_file = os.path.join(cur_dir,
"out_error_logs.txt")
bak_cmd = "cat {} >> {}".format("mol.out", out_error_logs_file)
os.system(bak_cmd)
return energy, final_ob_mol
def check(self):
self.outdata = MopOutput(self.output_file).data
self.mopinp = MopTask.from_file(self.input_file)
self.errors = None
if self.outdata["has_error"]:
self.errors = self.outdata["errors"]
return True
return False
def test_parse_structures(self):
moo = MopOutput(os.path.join(test_dir, "ch3cl_ef.out"))
ans_mol1 = """Molecule Summary (H9 C4 N1 O3)
Reduced Formula: H9C4NO3
Charge = 0, Spin Mult = 1
Sites (17)
1 C -1.500500 1.510500 -0.753900
2 C -2.618000 0.880700 0.073000
3 C -3.572900 1.988900 0.611400
4 H -4.132700 2.465100 -0.227600
5 O -2.857300 3.085300 1.127500
6 H -2.369800 2.782000 1.884000
7 C -4.534800 1.408600 1.645800
8 H -5.165800 0.626600 1.204800
9 H -5.200800 2.185700 2.043700
10 H -4.003400 0.963000 2.498200
11 N -3.390800 -0.115500 -0.704200
12 O -1.498900 1.782200 -1.940900
13 O -0.358100 1.767200 -0.079200
14 H -2.169800 0.329600 0.939000
15 H -2.775300 -0.817100 -1.055900
16 H -3.863300 0.327900 -1.464000
17 H 0.271500 2.195900 -0.650900"""
self.assertEqual(ans_mol1, str(moo.data["molecules"][0]))
ans_mol2 = """Molecule Summary (H9 C4 N1 O3)
Reduced Formula: H9C4NO3
Charge = 0, Spin Mult = 1
Sites (17)
1 C -1.517682 1.490044 -0.707280
2 C -2.693150 0.817317 -0.013378
3 C -3.626038 1.922600 0.582224
4 H -4.351657 2.287764 -0.183361
5 O -2.880302 3.079022 0.858364
6 H -2.121236 2.897494 1.451907
7 C -4.328070 1.419830 1.836240
8 H -4.915870 0.516629 1.620984
9 H -5.016872 2.181694 2.224643
10 H -3.625366 1.180514 2.640740
11 N -3.473778 -0.006085 -0.940194
12 O -1.354202 1.649287 -1.885729
13 O -0.581079 1.866540 0.201170
14 H -2.306531 0.161269 0.812776
15 H -2.960140 -0.811422 -1.264447
16 H -3.793316 0.519019 -1.743723
17 H 0.183750 2.356539 -0.192487"""
self.assertEqual(ans_mol2, str(moo.data["molecules"][1]))
def main():
parser = argparse.ArgumentParser(
description="Convert a MOPAC output file to an XYZ file")
parser.add_argument("-i",
"--moo",
dest="moo_file",
type=str,
required=True,
help="the MOPAC output file")
parser.add_argument("-o",
"--xyz",
dest="xyz_file",
type=str,
required=True,
help="The XYZ file to write to")
options = parser.parse_args()
moo = MopOutput(options.moo_file)
moo.data["molecules"][-1].to("xyz", options.xyz_file)
def test_not_accurate_enough(self):
moo = MopOutput(os.path.join(test_dir, "not_accurate_enough.out"))
self.assertTrue(moo.data["has_error"])
self.assertEqual(moo.data["errors"], ['Not Accurate Enough'])
def test_scf_failed(self):
moo = MopOutput(os.path.join(test_dir, "quino_salt_scf_failed.out"))
self.assertTrue(moo.data["has_error"])
self.assertTrue(moo.data["errors"], ['Bad SCF convergence'])
def test_geom_opt_failed(self):
moo = MopOutput(os.path.join(test_dir, "quino_salt_geom_failed.out"))
self.assertTrue(moo.data["has_error"])
self.assertTrue(moo.data["errors"], ['Geometry optimization failed'])
def test_energies(self):
moo = MopOutput(os.path.join(test_dir, "ch3cl_ef.out"))
self.assertAlmostEqual(moo.data["energies"][0][1], -6.34798632251, 3)
self.assertAlmostEqual(moo.data["energies"][1][1], -1685.76391, 3)
def test_successful_message(self):
moo = MopOutput(os.path.join(test_dir, "ch3cl_ef.out"))
self.assertFalse(moo.data["has_error"])
self.assertEqual(moo.data["jobtype"], "OPT")
self.assertTrue(moo.data["gracefully_terminated"])