# ------------------------------------------------------------- # Bulk configuration # ------------------------------------------------------------- # Set up lattice vector_a = [25.3060712531, -3.61876975118e-12, 0.0]*Angstrom vector_b = [-5.0143120592e-12, 35.0651170803, 0.0]*Angstrom vector_c = [0.0, 0.0, 50.0]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon, Carbon] # Define coordinates fractional_coordinates = [[ 0.000000112616, 0.000000513907, 0.1 ], [ 0.000000112616, 0.250000288025, 0.1 ], [ 0.000000112616, 0.500000581275, 0.1 ], [ 0.000000112616, 0.750000874525, 0.1 ], [ 0.100000069502, 0.000000519132, 0.1 ], [ 0.100000069502, 0.25000029325 , 0.1 ], [ 0.100000069502, 0.5000005865 , 0.1 ], [ 0.100000069502, 0.75000087975 , 0.1 ], [ 0.200000139004, 0.000000519132, 0.1 ], [ 0.200000139004, 0.25000029325 , 0.1 ], [ 0.200000139004, 0.5000005865 , 0.1 ], [ 0.200000139004, 0.75000087975 , 0.1 ], [ 0.300000208506, 0.000000519132, 0.1 ], [ 0.300000208506, 0.25000029325 , 0.1 ], [ 0.300000208506, 0.5000005865 , 0.1 ], [ 0.300000208506, 0.75000087975 , 0.1 ], [ 0.400000278008, 0.000000519132, 0.1 ], [ 0.400000278008, 0.25000029325 , 0.1 ], [ 0.400000278008, 0.5000005865 , 0.1 ], [ 0.400000278008, 0.75000087975 , 0.1 ], [ 0.50000034751 , 0.000000519132, 0.1 ], [ 0.50000034751 , 0.25000029325 , 0.1 ], [ 0.50000034751 , 0.5000005865 , 0.1 ], [ 0.50000034751 , 0.75000087975 , 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0.200000139004, 0.041666728068, 0.1 ], [ 0.200000139004, 0.291667008792, 0.1 ], [ 0.200000139004, 0.541667302042, 0.1 ], [ 0.200000139004, 0.791667595292, 0.1 ], [ 0.300000208506, 0.041666728068, 0.1 ], [ 0.300000208506, 0.291667008792, 0.1 ], [ 0.300000208506, 0.541667302042, 0.1 ], [ 0.300000208506, 0.791667595292, 0.1 ], [ 0.400000278008, 0.041666728068, 0.1 ], [ 0.400000278008, 0.291667008792, 0.1 ], [ 0.400000278008, 0.541667302042, 0.1 ], [ 0.400000278008, 0.791667595292, 0.1 ], [ 0.50000034751 , 0.041666728068, 0.1 ], [ 0.50000034751 , 0.291667008792, 0.1 ], [ 0.50000034751 , 0.541667302042, 0.1 ], [ 0.50000034751 , 0.791667595292, 0.1 ], [ 0.600000417012, 0.041666728068, 0.1 ], [ 0.600000417012, 0.291667008792, 0.1 ], [ 0.600000417012, 0.541667302042, 0.1 ], [ 0.600000417012, 0.791667595292, 0.1 ], [ 0.700000486513, 0.041666728068, 0.1 ], [ 0.700000486513, 0.291667008792, 0.1 ], [ 0.700000486513, 0.541667302042, 0.1 ], [ 0.700000486513, 0.791667595292, 0.1 ], [ 0.800000556015, 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0.1 ], [ 0.050000046011, 0.937501076178, 0.1 ], [ 0.150000104253, 0.187500219937, 0.1 ], [ 0.150000104253, 0.437500513187, 0.1 ], [ 0.150000104253, 0.687500806437, 0.1 ], [ 0.150000104253, 0.937501087161, 0.1 ], [ 0.250000173755, 0.187500219937, 0.1 ], [ 0.250000173755, 0.437500513187, 0.1 ], [ 0.250000173755, 0.687500806437, 0.1 ], [ 0.250000173755, 0.937501087161, 0.1 ], [ 0.350000243257, 0.187500219937, 0.1 ], [ 0.350000243257, 0.437500513187, 0.1 ], [ 0.350000243257, 0.687500806437, 0.1 ], [ 0.350000243257, 0.937501087161, 0.1 ], [ 0.450000312759, 0.187500219937, 0.1 ], [ 0.450000312759, 0.437500513187, 0.1 ], [ 0.450000312759, 0.687500806437, 0.1 ], [ 0.450000312759, 0.937501087161, 0.1 ], [ 0.550000382261, 0.187500219937, 0.1 ], [ 0.550000382261, 0.437500513187, 0.1 ], [ 0.550000382261, 0.687500806437, 0.1 ], [ 0.550000382261, 0.937501087161, 0.1 ], [ 0.650000451762, 0.187500219937, 0.1 ], [ 0.650000451762, 0.437500513187, 0.1 ], [ 0.650000451762, 0.687500806437, 0.1 ], [ 0.650000451762, 0.937501087161, 0.1 ], [ 0.750000521264, 0.187500219937, 0.1 ], [ 0.750000521264, 0.437500513187, 0.1 ], [ 0.750000521264, 0.687500806437, 0.1 ], [ 0.750000521264, 0.937501087161, 0.1 ], [ 0.850000590766, 0.187500219937, 0.1 ], [ 0.850000590766, 0.437500513187, 0.1 ], [ 0.850000590766, 0.687500806437, 0.1 ], [ 0.850000590766, 0.937501087161, 0.1 ], [ 0.950000547652, 0.187500214713, 0.1 ], [ 0.950000547652, 0.437500507963, 0.1 ], [ 0.950000547652, 0.687500801213, 0.1 ], [ 0.950000547647, 0.937501081936, 0.1 ], [ 0.050000046011, 0.229166946462, 0.1 ], [ 0.050000046011, 0.479167239712, 0.1 ], [ 0.050000046011, 0.729167532962, 0.1 ], [ 0.050000046012, 0.979167307084, 0.1 ], [ 0.150000104253, 0.229166935479, 0.1 ], [ 0.150000104253, 0.479167228729, 0.1 ], [ 0.150000104253, 0.729167521979, 0.1 ], [ 0.150000104253, 0.979167296097, 0.1 ], [ 0.250000173755, 0.229166935479, 0.1 ], [ 0.250000173755, 0.479167228729, 0.1 ], [ 0.250000173755, 0.729167521979, 0.1 ], [ 0.250000173755, 0.979167296097, 0.1 ], [ 0.350000243257, 0.229166935479, 0.1 ], [ 0.350000243257, 0.479167228729, 0.1 ], [ 0.350000243257, 0.729167521979, 0.1 ], [ 0.350000243257, 0.979167296097, 0.1 ], [ 0.450000312759, 0.229166935479, 0.1 ], [ 0.450000312759, 0.479167228729, 0.1 ], [ 0.450000312759, 0.729167521979, 0.1 ], [ 0.450000312759, 0.979167296097, 0.1 ], [ 0.550000382261, 0.229166935479, 0.1 ], [ 0.550000382261, 0.479167228729, 0.1 ], [ 0.550000382261, 0.729167521979, 0.1 ], [ 0.550000382261, 0.979167296097, 0.1 ], [ 0.650000451762, 0.229166935479, 0.1 ], [ 0.650000451762, 0.479167228729, 0.1 ], [ 0.650000451762, 0.729167521979, 0.1 ], [ 0.650000451762, 0.979167296097, 0.1 ], [ 0.750000521264, 0.229166935479, 0.1 ], [ 0.750000521264, 0.479167228729, 0.1 ], [ 0.750000521264, 0.729167521979, 0.1 ], [ 0.750000521264, 0.979167296097, 0.1 ], [ 0.850000590766, 0.229166935479, 0.1 ], [ 0.850000590766, 0.479167228729, 0.1 ], [ 0.850000590766, 0.729167521979, 0.1 ], [ 0.850000590766, 0.979167296097, 0.1 ], [ 0.950000547652, 0.229166940704, 0.1 ], [ 0.950000547652, 0.479167233954, 0.1 ], [ 0.950000547652, 0.729167527204, 0.1 ], [ 0.950000547652, 0.979167301322, 0.1 ], [ 0.50000034751 , 0.5000005865 , 0.5 ]] # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags bulk_configuration.addTags('Selection 0', [320]) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- # Set up a calculator with the Tersoff parameters from # Bellido, J. Phys. Chem. C 116, 4044 (2012) potential_set = TremoloXPotentialSet(name='Tersoff_Bellido_ZBL') potential_set.addParticleType(ParticleType.fromElement(Carbon)) potential_set.addPotential(TersoffSingleTypePotential('C', A=1393.6*eV, B=346.74*eV, R=1.8*Angstrom, S=2.1*Angstrom, l=3.4879*1/Angstrom, mu=2.2119*1/Angstrom, alpha=0.0*Angstrom**-1, beta=1.5724e-07, omega=1.0, chi=1.0, chiR=1.0, m=0, n=0.72751, c=38049.0, d=4.3484, h=-0.57058)) potential_set.addPotential(TersoffZBLPotential('C', 'C', type=2, Z1=6.0, Z2=6.0, a0=0.529*Angstrom, rf=0.95*Angstrom, bf=14.0*1/Angstrom)) calculator = TremoloXCalculator(parameters=potential_set) bulk_configuration.setCalculator(calculator) bulk_configuration.update() # ------------------------------------------------------------- # Molecular Dynamics # ------------------------------------------------------------- initial_velocity = MaxwellBoltzmannDistribution( temperature=300.0*Kelvin, remove_center_of_mass_momentum=True ) method = Langevin( time_step=1*femtoSecond, reservoir_temperature=300*Kelvin, friction=0.01*femtoSecond**-1, initial_velocity=initial_velocity ) md_trajectory = MolecularDynamics( bulk_configuration, constraints=[320], trajectory_filename='graphene_sheet_equilibrate.hdf5', steps=50000, log_interval=5000, method=method ) bulk_configuration = md_trajectory.lastImage() # Get the velocities from the bulk_configuration velocities = bulk_configuration.velocities() # Define the incident energy of the bombardment atom. incident_energy = 10.0*eV # Calculate the corresponding velocity and apply it to the last atom. incident_velocity = ((2.0*incident_energy/Carbon.atomicMass())**0.5).inUnitsOf(Ang/fs) velocities[-1, :] = [0.0, 0.0, -incident_velocity]*Ang/fs bulk_configuration.setVelocities(velocities) # ------------------------------------------------------------- # Molecular Dynamics # ------------------------------------------------------------- initial_velocity = ConfigurationVelocities( remove_center_of_mass_momentum=False ) method = NVEVelocityVerlet( time_step=0.05*femtoSecond, initial_velocity=initial_velocity ) # Get the velocities from the bulk_configuration velocities = bulk_configuration.velocities() # Define the incident energy of the bombardment atom. incident_energy = 10.0*eV # Calculate the corresponding velocity and apply it to the last atom. incident_velocity = ((2.0*incident_energy/Carbon.atomicMass())**0.5).inUnitsOf(Ang/fs) velocities[-1, :] = [0.0, 0.0, -incident_velocity]*Ang/fs bulk_configuration.setVelocities(velocities) md_trajectory = MolecularDynamics( bulk_configuration, constraints=[], trajectory_filename='ion_bombardment_md.hdf5', steps=50000, log_interval=100, method=method ) bulk_configuration = md_trajectory.lastImage()