# ------------------------------------------------------------- # Nudged Elastic Band Configuration # ------------------------------------------------------------- # Setup the configuration list configuration_list = [] # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [11.4894163263, 6.878080409e-07, -5.86872437369e-08]*Angstrom vector_b = [2.87235421464, 2.87142020372, 4.72476889627e-07]*Angstrom vector_c = [-2.8867564457e-08, 9.74556142711e-07, 5.74568489455]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Cadmium, Cadmium, Cadmium, Cadmium, Selenium, Selenium, Selenium, Selenium] # Define coordinates fractional_coordinates = [[ 0.125008063924, 0.49996633744 , 0.249999773655], [ 0.625009594535, 0.499963292276, 0.249999763731], [ 0.374991699745, 0.50003405177 , 0.749995473668], [ 0.87499121277 , 0.50003473766 , 0.749995659537], [ 0.375002038846, 0.499991844314, 0.250003463042], [ 0.875002415953, 0.499990827322, 0.250002564712], [ 0.125000202945, 0.50000370022 , 0.750009316336], [ 0.624995940539, 0.500011964325, 0.750008396313]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [11.0987285699, 5.89549749342e-07, -5.03033517745e-08]*Angstrom vector_b = [2.77468222923, 3.00276790684, 4.04980191109e-07]*Angstrom vector_c = [5.20820332257e-09, 8.0338330661e-07, 5.9190210633]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Cadmium, Cadmium, Cadmium, Cadmium, Selenium, Selenium, Selenium, Selenium] # Define coordinates fractional_coordinates = [[ 0.130959330474, 0.476161538826, 0.241632602883], [ 0.630960616185, 0.476158963462, 0.241630281176], [ 0.36904050333 , 0.523838676757, 0.74162737097 ], [ 0.869040119214, 0.523839236116, 0.741627178371], [ 0.36904953618 , 0.523802323991, 0.258372353278], [ 0.869049576758, 0.523801741042, 0.258371199736], [ 0.130952543695, 0.476193620326, 0.758377501739], [ 0.63094894342 , 0.476200654806, 0.758375922844]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [10.7080408135, 4.91291457785e-07, -4.19194598121e-08]*Angstrom vector_b = [2.67701024381, 3.13411560997, 3.37483492591e-07]*Angstrom vector_c = [3.92839711021e-08, 6.32210470508e-07, 6.09235723205]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Cadmium, Cadmium, Cadmium, Cadmium, Selenium, Selenium, Selenium, Selenium] # Define coordinates fractional_coordinates = [[ 0.136910597024, 0.452356740213, 0.233265432111], [ 0.636911637836, 0.452354634649, 0.233260798621], [ 0.363089306914, 0.547643301743, 0.733259268271], [ 0.863089025657, 0.547643734573, 0.733258697204], [ 0.363097033515, 0.547612803668, 0.266741243514], [ 0.863096737564, 0.547612654761, 0.26673983476 ], [ 0.136904884446, 0.452383540432, 0.766745687142], [ 0.636901946301, 0.452389345288, 0.766743449374]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [10.3173530572, 3.93033166228e-07, -3.35355678497e-08]*Angstrom vector_b = [2.57933825839, 3.2654633131, 2.69986794073e-07]*Angstrom vector_c = [7.33597388817e-08, 4.61037634406e-07, 6.2656934008]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Cadmium, Cadmium, Cadmium, Cadmium, Selenium, Selenium, Selenium, Selenium] # Define coordinates fractional_coordinates = [[ 0.142861863574, 0.428551941599, 0.224898261338], [ 0.642862659486, 0.428550305836, 0.224891316065], [ 0.357138110499, 0.571447926729, 0.724891165573], [ 0.8571379321 , 0.571448233029, 0.724890216038], [ 0.35714453085 , 0.571423283345, 0.27511013375 ], [ 0.857143898369, 0.571423568481, 0.275108469783], [ 0.142857225196, 0.428573460539, 0.775113872545], [ 0.642854949182, 0.42857803577 , 0.775110975904]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [9.92666530078, 2.94774874671e-07, -2.51516758872e-08]*Angstrom vector_b = [2.48166627298, 3.39681101622, 2.02490095555e-07]*Angstrom vector_c = [1.07435506661e-07, 2.89864798305e-07, 6.43902956955]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Cadmium, Cadmium, Cadmium, Cadmium, Selenium, Selenium, Selenium, Selenium] # Define coordinates fractional_coordinates = [[ 0.148813130124, 0.404747142985, 0.216531090566], [ 0.648813681137, 0.404745977023, 0.21652183351 ], [ 0.351186914083, 0.595252551716, 0.716523062874], [ 0.851186838544, 0.595252731485, 0.716521734871], [ 0.351192028185, 0.595233763022, 0.283479023986], [ 0.851191059174, 0.5952344822 , 0.283477104807], [ 0.148809565946, 0.404763380645, 0.783482057947], [ 0.648807952064, 0.404766726251, 0.783478502434]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [9.5359775444, 1.96516583114e-07, -1.67677839248e-08]*Angstrom vector_b = [2.38399428756, 3.52815871935, 1.34993397036e-07]*Angstrom vector_c = [1.41511274441e-07, 1.18691962203e-07, 6.6123657383]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Cadmium, Cadmium, Cadmium, Cadmium, Selenium, Selenium, Selenium, Selenium] # Define coordinates fractional_coordinates = [[ 0.154764396674, 0.380942344371, 0.208163919794], [ 0.654764702787, 0.38094164821 , 0.208152350955], [ 0.345235717668, 0.619057176702, 0.708154960176], [ 0.845235744987, 0.619057229941, 0.708153253704], [ 0.345239525519, 0.619044242698, 0.291847914222], [ 0.84523821998 , 0.619045395919, 0.29184573983 ], [ 0.154761906696, 0.380953300751, 0.79185024335 ], [ 0.654760954945, 0.380955416733, 0.791846028964]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [9.14528978803, 9.82582915571e-08, -8.38389196241e-09]*Angstrom vector_b = [2.28632230215, 3.65950642248, 6.74966985182e-08]*Angstrom vector_c = [1.7558704222e-07, -5.24808738984e-08, 6.78570190705]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Cadmium, Cadmium, Cadmium, Cadmium, Selenium, Selenium, Selenium, Selenium] # Define coordinates fractional_coordinates = [[ 0.160715663224, 0.357137545757, 0.199796749021], [ 0.660715724438, 0.357137319396, 0.199782868399], [ 0.339284521252, 0.642861801689, 0.699786857478], [ 0.839284651431, 0.642861728398, 0.699784772538], [ 0.339287022854, 0.642854722375, 0.300216804457], [ 0.839285380785, 0.642856309639, 0.300214374854], [ 0.160714247447, 0.357143220857, 0.800218428753], [ 0.660713957826, 0.357144107215, 0.800213555495]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Append to the list of configurations configuration_list.append(configuration) # ------------------------------------------------------------- # Bulk Configuration # ------------------------------------------------------------- # Set up lattice vector_a = [8.75460203165, 0.0, 0.0]*Angstrom vector_b = [2.18865031673, 3.7908541256, 0.0]*Angstrom vector_c = [2.0966281e-07, -2.2365371e-07, 6.9590380758]*Angstrom lattice = UnitCell(vector_a, vector_b, vector_c) # Define elements elements = [Cadmium, Cadmium, Cadmium, Cadmium, Selenium, Selenium, Selenium, Selenium] # Define coordinates fractional_coordinates = [[ 0.166666929775, 0.333332747144, 0.191429578249], [ 0.666666746088, 0.333332990583, 0.191413385844], [ 0.333333324837, 0.666666426675, 0.691418754779], [ 0.833333557874, 0.666666226854, 0.691416291371], [ 0.333334520189, 0.666665202052, 0.308585694693], [ 0.833332541591, 0.666667223358, 0.308583009878], [ 0.166666588197, 0.333333140964, 0.808586614156], [ 0.666666960707, 0.333332797696, 0.808581082025]] # Set up configuration configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Append to the list of configurations configuration_list.append(configuration) # Construct the Nudged Elastic Band object neb_configuration = NudgedElasticBand( configuration_list, generate_images=False) # Unreference the temporary configuration variable del configuration # Define the Rabani potential. potentialSet = TremoloXPotentialSet(name = 'StillingerWeber_CdTeZnSeHgS_2013') potentialSet.addParticleType(ParticleType( symbol='Cd', mass=112.411*atomic_mass_unit, charge=1.18*elementary_charge, sigma=1.98*Ang, epsilon=(16.8*Kelvin*boltzmann_constant).convertTo(eV), atomicNumber=48)) potentialSet.addParticleType(ParticleType( symbol='Se', mass=78.96*atomic_mass_unit, charge=-1.18*elementary_charge, sigma=5.24*Ang, epsilon=(14.9*Kelvin*boltzmann_constant).convertTo(eV), atomicNumber=34)) potential = LennardJonesSplinePotential('Cd', 'Cd', r_cut=10.0*Ang, r_i=8.0*Ang) potentialSet.addPotential(potential) potential = LennardJonesSplinePotential('Cd', 'Se', r_cut=10.0*Ang, r_i=8.0*Ang) potentialSet.addPotential(potential) potential = LennardJonesSplinePotential('Se', 'Se', r_cut=10.0*Ang, r_i=8.0*Ang) potentialSet.addPotential(potential) potentialSet.setCoulombSolver(CoulombEwald(alpha=0.1*Angstrom**-1, epsilon=1.0e-10)) calculator = TremoloXCalculator(parameters=potentialSet) calculator.setInternalOrdering("default") calculator.setVerletListsDelta(0.0*Angstrom) neb_configuration.setCalculator(calculator) neb_configuration.update() nlsave('cdse_neb_concerted.hdf5', neb_configuration) # Perform a VC-NEB optimization neb_configuration = OptimizeNudgedElasticBand( neb_configuration, max_forces=0.01*eV/Ang, max_stress=0.01*GPa, max_steps=500, climbing_image=True, optimize_cell=True, ) nlsave('cdse_neb_concerted.hdf5', neb_configuration)