# -*- coding: utf-8 -*- # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [10.8612, 0.0, 0.0]*Angstrom vector_b = [0.0, 10.8612, 0.0]*Angstrom vector_c = [0.0, 0.0, 10.8612]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Germanium] # Define coordinates fractional_coordinates = [[-0.000438773566, -0.000719753172, -0.000719753172], [-0.002567048046, -0.001436533687, 0.50015398949 ], [-0.008628223743, 0.500646899944, 0.005181769839], [-0.0075336859 , 0.497981444601, 0.486430774944], [ 0.500947655116, 0.000236291602, 0.000236291602], [ 0.502080702598, -0.001824159557, 0.500665469201], [ 0.518447274743, 0.514068709243, -0.006784361843], [ 0.511361534119, 0.500099626911, 0.503369081493], [ 0.126304289587, 0.120387604013, 0.126194042761], [ 0.119803525236, 0.12140203436 , 0.625643203194], [ 0.121637174382, 0.640795577302, 0.107830922561], [ 0.132228965017, 0.599709200801, 0.632560083983], [ 0.627996589671, 0.121347176542, 0.12739156124 ], [ 0.626723079448, 0.123615776954, 0.634476381168], [ 0.638449772262, 0.62809984021 , 0.129458995897], [ 0.623996092286, 0.626673326408, 0.63053904907 ], [ 0.247732322928, 0.247759417158, 0.004033366315], [ 0.255813345952, 0.234052465179, 0.502071751904], [ 0.256924293433, 0.757864733252, -0.004023557598], [ 0.244043574545, 0.763392164623, 0.499390018214], [ 0.757660078175, 0.252993826265, 0.01242439574 ], [ 0.747275861645, 0.245805761335, 0.497488191514], [ 0.748752048167, 0.754616111697, 0.006968396435], [ 0.749465186978, 0.750778035671, 0.507097984283], [ 0.383297090569, 0.378411943075, 0.117078347839], [ 0.386895271843, 0.361603875376, 0.665954534059], [ 0.375768933433, 0.881381989707, 0.134128894587], [ 0.375450534638, 0.884870867409, 0.624301009322], [ 0.877267610466, 0.375600169127, 0.134683434724], [ 0.880017948779, 0.374726354547, 0.622983560028], [ 0.876934361933, 0.876309323754, 0.124004249147], [ 0.880190661062, 0.868783642201, 0.627818056869], [ 0.249334530799, -0.001824159557, 0.247919297402], [ 0.24984601051 , -0.001436533687, 0.752567048046], [ 0.252382932107, 0.507317270523, 0.226019615003], [ 0.254034523691, 0.486863176266, 0.780703223454], [ 0.749763708398, 0.000236291602, 0.249052344884], [ 0.750719753172, -0.000719753172, 0.750438773566], [ 0.744409970307, 0.500248028737, 0.261677208202], [ 0.753224929162, 0.492908956765, 0.750065335811], [ 0.386243582096, 0.120577430322, 0.36912588949 ], [ 0.37104959195 , 0.120496097796, 0.878816392485], [ 0.373859204094, 0.630988069354, 0.370842085067], [ 0.383936750184, 0.640407295974, 0.8807181055 ], [ 0.874472280166, 0.123065685306, 0.373792120428], [ 0.881336896269, 0.124737714042, 0.875651089351], [ 0.87040350098 , 0.631757056472, 0.375732222511], [ 0.873444355028, 0.62875525013 , 0.879987148288], [ 0.000547060768, 0.244865594023, 0.245135009438], [-0.002370899126, 0.249077176039, 0.747221218407], [ 0.000785605524, 0.751563758165, 0.248855845989], [ 0.003820039246, 0.741458808826, 0.746663154452], [ 0.501791393177, 0.254559526194, 0.244945866766], [ 0.514179054395, 0.234997867078, 0.772582018458], [ 0.509142333917, 0.759435774818, 0.24910901912 ], [ 0.496488935193, 0.756656132044, 0.743838608308], [ 0.12783948924 , 0.374562229753, 0.355849101595], [ 0.111806210406, 0.370994314737, 0.884575319845], [ 0.118594912684, 0.876396904879, 0.379030927804], [ 0.131713793498, 0.876581832571, 0.870688416455], [ 0.623406366889, 0.371467869653, 0.376299967382], [ 0.637884519093, 0.37277842172 , 0.888032135701], [ 0.634029995114, 0.873114427964, 0.375773533933], [ 0.624840105207, 0.873606322327, 0.874844769765], [ 0.272667812509, 0.473592064854, 0.503720963815]] # Set up configuration bulk_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates, ) # ------------------------------------------------------------- # Calculator # ------------------------------------------------------------- potentialSet = Tersoff_SiGe_1989() calculator = TremoloXCalculator(parameters=potentialSet) calculator.setVerletListsDelta(0.25*Angstrom) 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, heating_rate=0*Kelvin/picoSecond, ) # The bottom layer of atoms will be fixed to provide an absolute reference frame. fix_atom_indices_0 = [0, 1, 4, 5, 32, 33, 36, 37] constraints = [FixAtomConstraints(fix_atom_indices_0)] # Set up the PLUMED command plumed_command = """\ # Change the units to Ang, fs, eV UNITS LENGTH=A TIME=fs ENERGY=96.48533645956869 # Use the cartesian position of the Ge interstitial atom as CV. p: POSITION ATOM=65 # Put a metadynamics bias on the x component of the position CV p. METAD ARG=p.x SIGMA=0.2 HEIGHT=0.05 PACE=50 LABEL=restraint # Print the current position and bias potential value every 10 steps. PRINT ARG=p.x,p.y,p.z,restraint.bias STRIDE=10 FILE=COLVAR """ # Set up the Plumed hook-class. plumed_hook = PlumedMetadynamics( configuration=bulk_configuration, timestep=1.0*fs, plumed_commands=plumed_command, logfile='plumed_example.log', ) md_trajectory = MolecularDynamics( bulk_configuration, constraints=constraints, trajectory_filename='si_ge_metadynamics_md.hdf5', steps=30000, log_interval=200, post_step_hook=plumed_hook, method=method ) bulk_configuration = md_trajectory.lastImage()