# %% MoleculeConfiguration # Define elements elements = [Carbon, Carbon, Hydrogen, Hydrogen, Hydrogen, Oxygen, Carbon, Hydrogen, Carbon, Hydrogen, Hydrogen, Hydrogen, Carbon, Oxygen, Carbon, Hydrogen, Hydrogen, Oxygen, Carbon, Hydrogen, Carbon, Hydrogen, Hydrogen, Hydrogen, Carbon, Oxygen, Carbon, Hydrogen, Hydrogen, Oxygen, Carbon, Hydrogen, Carbon, Hydrogen, Hydrogen, Hydrogen, Carbon, Oxygen, Carbon, Hydrogen, Hydrogen, Oxygen, Carbon, Hydrogen, Carbon, Hydrogen, Hydrogen, Hydrogen, Carbon, Oxygen, Carbon, Hydrogen, Hydrogen, Oxygen, Carbon, Hydrogen, Carbon, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Oxygen, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen, Hydrogen] # Define coordinates cartesian_coordinates = [[ 0. , 0. , 0. ], [ 1.513 , 0. , 0. ], [ -0.363333307269, 0. , -1.027661781602], [ -0.363333307269, -0.889981209366, 0.513830890801], [ -0.363333307269, 0.889981209366, 0.513830890801], [ 1.924666666667, 1.008373277446, -0.582184583177], [ 2.017333333333, 0. , 1.426470079914], [ 1.876333307269, -0.889981209366, -0.513830890801], [ 3.530333333333, 0. , 1.426470079914], [ 1.654000026065, 0.889981209366, 1.940300970715], [ 1.654000026065, -0.889981209366, 1.940300970715], [ 3.893666640602, 0.889981209366, 0.912639189113], [ 4.034666666667, 0. , 2.852940159827], [ 3.942 , -1.008373277446, 0.844285496737], [ 5.547666666667, 0. , 2.852940159827], [ 3.671333359398, 0.889981209366, 3.366771050628], [ 3.671333359398, -0.889981209366, 3.366771050628], [ 5.959333333333, 1.008373277446, 2.27075557665 ], [ 6.052 , 0. , 4.279410239741], [ 5.910999973935, -0.889981209366, 2.339109269026], [ 7.565 , 0. , 4.279410239741], [ 5.688666692731, 0.889981209366, 4.793241130542], [ 5.688666692731, -0.889981209366, 4.793241130542], [ 7.928333307269, 0.889981209366, 3.76557934894 ], [ 8.069333333333, 0. , 5.705880319655], [ 7.976666666667, -1.008373277446, 3.697225656564], [ 9.582333333333, 0. , 5.705880319655], [ 7.706000026065, 0.889981209366, 6.219711210456], [ 7.706000026065, -0.889981209366, 6.219711210456], [ 9.994 , 1.008373277446, 5.123695736478], [ 10.086666666667, 0. , 7.132350399568], [ 9.945666640602, -0.889981209366, 5.192049428854], [ 11.599666666667, 0. , 7.132350399568], [ 9.723333359398, 0.889981209366, 7.646181290369], [ 9.723333359398, -0.889981209366, 7.646181290369], [ 11.962999973935, 0.889981209366, 6.618519508767], [ 12.104 , 0. , 8.558820479482], [ 12.011333333333, -1.008373277446, 6.550165816391], [ 13.617 , 0. , 8.558820479482], [ 11.740666692731, 0.889981209366, 9.072651370283], [ 11.740666692731, -0.889981209366, 9.072651370283], [ 14.028666666667, 1.008373277446, 7.976635896305], [ 14.121333333333, 0. , 9.985290559396], [ 13.980333307269, -0.889981209366, 8.044989588681], [ 15.634333333333, 0. , 9.985290559396], [ 13.758000026065, 0.889981209366, 10.499121450197], [ 13.758000026065, -0.889981209366, 10.499121450197], [ 15.997666640602, 0.889981209366, 9.471459668595], [ 16.138666666667, 0. , 11.411760639309], [ 16.046 , -1.008373277446, 9.403105976219], [ 17.651666666667, 0. , 11.411760639309], [ 15.775333359398, 0.889981209366, 11.92559153011 ], [ 15.775333359398, -0.889981209366, 11.92559153011 ], [ 18.063333333333, 1.008373277446, 10.829576056132], [ 18.156 , 0. , 12.838230719223], [ 18.014999973935, -0.889981209366, 10.897929748508], [ 19.669 , 0. , 12.838230719223], [ 17.792666692732, 0.889981209366, 13.352061610024], [ 17.792666692732, -0.889981209366, 13.352061610024], [ 20.032333307269, 0.889981209366, 12.324399828422], [ 20.032333307269, 0. , 13.865892500825], [ 20.080666666667, -1.008373277446, 12.256046136046], [ 2.974666591342, 1.008373277446, -0.582184583177], [ 4.991999924675, -1.008373277446, 0.844285496737], [ 7.009333258008, 1.008373277446, 2.27075557665 ], [ 9.026666591342, -1.008373277446, 3.697225656564], [ 11.043999924675, 1.008373277446, 5.123695736478], [ 13.061333258009, -1.008373277446, 6.550165816391], [ 15.078666591342, 1.008373277446, 7.976635896305], [ 17.095999924675, -1.008373277446, 9.403105976219], [ 19.113333258009, 1.008373277446, 10.829576056132], [ 21.130666591342, -1.008373277446, 12.256046136046]]*Angstrom # Set up configuration polyvinyl_alcohol = MoleculeConfiguration( elements=elements, cartesian_coordinates=cartesian_coordinates ) # Add tags polyvinyl_alcohol.addTags('H_C', [ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]) polyvinyl_alcohol.addTags('H_O', [62, 63, 64, 65, 66, 67, 68, 69, 70, 71]) # Add bonds bonds = [[ 0, 1], [ 0, 2], [ 0, 3], [ 0, 4], [ 1, 5], [ 1, 6], [ 1, 7], [ 5, 62], [ 6, 8], [ 6, 9], [ 6, 10], [ 8, 11], [ 8, 12], [ 8, 13], [12, 14], [12, 15], [12, 16], [13, 63], [14, 17], [14, 18], [14, 19], [17, 64], [18, 20], [18, 21], [18, 22], [20, 23], [20, 24], [20, 25], [24, 26], [24, 27], [24, 28], [25, 65], [26, 29], [26, 30], [26, 31], [29, 66], [30, 32], [30, 33], [30, 34], [32, 35], [32, 36], [32, 37], [36, 38], [36, 39], [36, 40], [37, 67], [38, 41], [38, 42], [38, 43], [41, 68], [42, 44], [42, 45], [42, 46], [44, 47], [44, 48], [44, 49], [48, 50], [48, 51], [48, 52], [49, 69], [50, 53], [50, 54], [50, 55], [53, 70], [54, 56], [54, 57], [54, 58], [56, 59], [56, 60], [56, 61], [61, 71]] polyvinyl_alcohol.setBonds(bonds) polyvinyl_alcohol_name = "polyvinyl_alcohol" # %% Create united atom configuration def create_united_atom_configuration(all_atom_configuration): # This custom script supports atkpython syntax # and can perform almost any procedure. united_atom_configuration = unitedAtomsConfiguration( all_atom_configuration, atom_list=[Carbon], min_hydrogen=1, max_hydrogen=4 ) return united_atom_configuration united_atom_configuration = create_united_atom_configuration(polyvinyl_alcohol) nlsave('UnitedAtom_Example_results.hdf5', united_atom_configuration) # %% Set ForceFieldCalculator # %% ForceFieldCalculator DREIDING = DreidingPotentialBuilder() DREIDING.assignAtomTypes(united_atom_configuration, overwrite=True) atomic_partial_charges = QEqAtomicCharges().charges(united_atom_configuration) calculator = DREIDING.createCalculator( united_atom_configuration, atomic_charges=atomic_partial_charges, ) # %% Set Calculator united_atom_configuration.setCalculator(calculator) nlsave('UnitedAtom_Example_results.hdf5', united_atom_configuration) # %% OptimizeGeometry restart_strategy = RestartFromTrajectory( trajectory_filename='UnitedAtom_Example_results.hdf5', object_id='optimize_trajectory' ) optimized_configuration = OptimizeGeometry( configuration=united_atom_configuration, trajectory_filename='UnitedAtom_Example_results.hdf5', trajectory_object_id='optimize_trajectory', restart_strategy=restart_strategy, ) nlsave('UnitedAtom_Example_results.hdf5', optimized_configuration, object_id='optgeom') # %% Create all-atom configuration def create_allatom_configuration(united_atom_configuration): # This custom script supports atkpython syntax # and can perform almost any procedure. final_configuration = explicitHydrogenConfiguration(united_atom_configuration) return final_configuration final_configuration = create_allatom_configuration(optimized_configuration) nlsave('UnitedAtom_Example_results.hdf5', final_configuration)