calculator = Pyscf(method='hf', label="ase", atoms=atoms) calculator.run_qr(atoms, coordinates=None, charge=None, pointcharges=None, command=None, define_str=None) assert approx_equal(calculator.energy_free, -24894.129755) assert approx_equal(calculator.forces.tolist(), [[10.3539855, -109.02533792, -52.22553528], [-89.1104867, 135.541275, -63.22351153], [81.34525894, -32.53859855, 36.0316453], [17.81046893, 0.39223847, 28.47319708], [-20.39922667, 5.630423, 50.94420443]]) if (__name__ == "__main__"): pyscf_installed = False try: import pyscf from pyscf import gto, scf, grad, dft pyscf_installed = True except ImportError: #"Pyscf not installed. Please run: qrefine.python pip -m install pyscf" pass prefix = os.path.basename(__file__).replace(".py", "") run_tests.runner(function=run, prefix=prefix, disable=not pyscf_installed)
TER ''' def run(prefix): fn = 'expansion.pdb' f = open(fn, 'w') f.write(expansion) f.close() fn = 'test_alt_loc_original.pdb' f = open(fn, 'w') f.write(pdb_lines) f.close() cmd = 'phenix.python %s/completion.py %s model_completion=False original_pdb_filename=expansion.pdb' % ( qrefine_path, fn) if 0: print(cmd) easy_run.go(cmd) fnc = '%s_capping.pdb' % fn.replace('.pdb', '') cmd = 'phenix.pdb_interpretation %s' % fnc if 0: print(cmd) rc = easy_run.go(cmd) assert ' H 47 1.00' in rc.stdout_lines os.remove(fn) os.remove(fnc) return rc if (__name__ == '__main__'): prefix = os.path.basename(__file__).replace(".py", "") run_tests.runner(function=run, prefix=prefix, disable=False)
calculatorANIccx = TorchAni(method='ani-1ccx', label="ase", atoms=atoms) calculatorANIccx.run_qr(atoms=atoms, coordinates=atoms.get_positions(), charge=0, pointcharges=None) assert calculatorANIccx.method == 'ani-1ccx' assert approx_equal(calculatorANIccx.energy_free, -40.4256210327) assert approx_equal(calculatorANIccx.forces, [[0.0312, -0.1272, -0.0511], [-0.1200, 0.1628, -0.0761], [0.0856, -0.0448, 0.0407], [0.0219, 0.0044, 0.0343], [-0.0187, 0.0049, 0.0521]], 0.001) if (__name__ == "__main__"): torchani_installed = False try: import torch device = torch.device('cpu') import torchnani from qrefine.plugin.ase.torchani_qr import TorchAni torchani_installed = True except ImportError: pass prefix = os.path.basename(__file__).replace(".py", "") run_tests.runner(function=run, prefix=prefix, disable=not torchani_installed)
[3.224648029245346, 17.928547580646576, -4.524288383451061], [-14.150630324115214, 1.2147768632076443, 1.967302103238517], [-11.589212064363652, -6.444221705381739, -4.77406901682601], [-5.5705251392947135, -49.58353381805122, 17.851453490207053], [12.42994083133531, -31.32628534955386, 0.5620932081847977], [-15.209140041336132, 2.6841055262949185, 18.113311015189275], [-38.73187194009035, -15.72274317196305, -11.82050674146153], [36.242545183467506, -10.805354680557413, -12.277902260267444], [15.232739148782514, -4.663316010381281, 8.999606560034826], [59.63334514038209, 26.088864339029772, 11.30765051583584], [15.608156356402093, 27.943937629842292, -43.96675247210592], [18.13331849770548, 7.431414655697998, 16.906001192291857], [17.86199385016078, -8.699557589383213, 33.00195465513993], [-10.848074631757044, 39.029932538400196, -25.227204796906726], [-39.85554941979901, 1.527429754721101, -19.432085940661143], [31.92966974414988, -30.73366946479253, -4.944928236082764], [3.6813964573627045, -4.724979244557905, -38.6569203686534], [14.529074495458673, 6.242069503845828, 12.534003126275708]], 0.001) if(__name__ == "__main__"): tensormol_installed = False try: import TensorMol from qrefine.plugin.ase.tensormol_qr import TensormolCalculator tensormol_installed = True except ImportError: pass prefix = os.path.basename(__file__).replace(".py","") run_tests.runner(function=run, prefix=prefix, disable=not tensormol_installed)