# Set minimal log verbosity setVerbosity(MinimalLog) # %% Equilibrate Substrate # %% substrate_configuration # Set up lattice vector_a = [15.360056343646662, 0.0, 0.0]*Angstrom vector_b = [0.0, 15.360056343646662, 0.0]*Angstrom vector_c = [0.0, 0.0, 48.0141]*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, 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, 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, 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] # Define coordinates fractional_coordinates = [[ 0.125 , 0. , 0.028276068905], [ 0.375 , 0. , 0.028276068905], [ 0.625 , 0. , 0.028276068905], [ 0.875 , 0. , 0.028276068905], [ 0.125 , 0.25 , 0.028276068905], [ 0.375 , 0.25 , 0.028276068905], [ 0.625 , 0.25 , 0.028276068905], [ 0.875 , 0.25 , 0.028276068905], [ 0.125 , 0.5 , 0.028276068905], [ 0.375 , 0.5 , 0.028276068905], [ 0.625 , 0.5 , 0.028276068905], [ 0.875 , 0.5 , 0.028276068905], [ 0.125 , 0.75 , 0.028276068905], [ 0.375 , 0.75 , 0.028276068905], [ 0.625 , 0.75 , 0.028276068905], [ 0.875 , 0.75 , 0.028276068905], [ 0.125 , 0.125 , 0.056552137809], [ 0.375 , 0.125 , 0.056552137809], [ 0.625 , 0.125 , 0.056552137809], [ 0.875 , 0.125 , 0.056552137809], [ 0.125 , 0.375 , 0.056552137809], [ 0.375 , 0.375 , 0.056552137809], [ 0.625 , 0.375 , 0.056552137809], [ 0.875 , 0.375 , 0.056552137809], [ 0.125 , 0.625 , 0.056552137809], [ 0.375 , 0.625 , 0.056552137809], [ 0.625 , 0.625 , 0.056552137809], [ 0.875 , 0.625 , 0.056552137809], [ 0.125 , 0.875 , 0.056552137809], [ 0.375 , 0.875 , 0.056552137809], [ 0.625 , 0.875 , 0.056552137809], [ 0.875 , 0.875 , 0.056552137809], [ 0. , 0.125 , 0.084828206714], [ 0.25 , 0.125 , 0.084828206714], [ 0.5 , 0.125 , 0.084828206714], [ 0.75 , 0.125 , 0.084828206714], [ 0. , 0.375 , 0.084828206714], [ 0.25 , 0.375 , 0.084828206714], [ 0.5 , 0.375 , 0.084828206714], [ 0.75 , 0.375 , 0.084828206714], [ 0. , 0.625 , 0.084828206714], [ 0.25 , 0.625 , 0.084828206714], [ 0.5 , 0.625 , 0.084828206714], [ 0.75 , 0.625 , 0.084828206714], [ 0. , 0.875 , 0.084828206714], [ 0.25 , 0.875 , 0.084828206714], [ 0.5 , 0.875 , 0.084828206714], [ 0.75 , 0.875 , 0.084828206714], [ 0. , 0. , 0.113104275619], [ 0.25 , 0. , 0.113104275619], [ 0.5 , 0. , 0.113104275619], [ 0.75 , 0. , 0.113104275619], [ 0. , 0.25 , 0.113104275619], [ 0.25 , 0.25 , 0.113104275619], [ 0.5 , 0.25 , 0.113104275619], [ 0.75 , 0.25 , 0.113104275619], [ 0. , 0.5 , 0.113104275619], [ 0.25 , 0.5 , 0.113104275619], [ 0.5 , 0.5 , 0.113104275619], [ 0.75 , 0.5 , 0.113104275619], [ 0. , 0.75 , 0.113104275619], [ 0.25 , 0.75 , 0.113104275619], [ 0.5 , 0.75 , 0.113104275619], [ 0.75 , 0.75 , 0.113104275619], [ 0.125 , 0. , 0.141380344524], [ 0.375 , 0. , 0.141380344524], [ 0.625 , 0. , 0.141380344524], [ 0.875 , 0. , 0.141380344524], [ 0.125 , 0.25 , 0.141380344524], [ 0.375 , 0.25 , 0.141380344524], [ 0.625 , 0.25 , 0.141380344524], [ 0.875 , 0.25 , 0.141380344524], [ 0.125 , 0.5 , 0.141380344524], [ 0.375 , 0.5 , 0.141380344524], [ 0.625 , 0.5 , 0.141380344524], [ 0.875 , 0.5 , 0.141380344524], [ 0.125 , 0.75 , 0.141380344524], [ 0.375 , 0.75 , 0.141380344524], [ 0.625 , 0.75 , 0.141380344524], [ 0.875 , 0.75 , 0.141380344524], [ 0.125 , 0.125 , 0.169656413428], [ 0.375 , 0.125 , 0.169656413428], [ 0.625 , 0.125 , 0.169656413428], [ 0.875 , 0.125 , 0.169656413428], [ 0.125 , 0.375 , 0.169656413428], [ 0.375 , 0.375 , 0.169656413428], [ 0.625 , 0.375 , 0.169656413428], [ 0.875 , 0.375 , 0.169656413428], [ 0.125 , 0.625 , 0.169656413428], [ 0.375 , 0.625 , 0.169656413428], [ 0.625 , 0.625 , 0.169656413428], [ 0.875 , 0.625 , 0.169656413428], [ 0.125 , 0.875 , 0.169656413428], [ 0.375 , 0.875 , 0.169656413428], [ 0.625 , 0.875 , 0.169656413428], [ 0.875 , 0.875 , 0.169656413428], [ 0. , 0.125 , 0.197932482333], [ 0.25 , 0.125 , 0.197932482333], [ 0.5 , 0.125 , 0.197932482333], [ 0.75 , 0.125 , 0.197932482333], [ 0. , 0.375 , 0.197932482333], [ 0.25 , 0.375 , 0.197932482333], [ 0.5 , 0.375 , 0.197932482333], [ 0.75 , 0.375 , 0.197932482333], [ 0. , 0.625 , 0.197932482333], [ 0.25 , 0.625 , 0.197932482333], [ 0.5 , 0.625 , 0.197932482333], [ 0.75 , 0.625 , 0.197932482333], [ 0. , 0.875 , 0.197932482333], [ 0.25 , 0.875 , 0.197932482333], [ 0.5 , 0.875 , 0.197932482333], [ 0.75 , 0.875 , 0.197932482333], [ 0. , 0. , 0.226208551238], [ 0.25 , 0. , 0.226208551238], [ 0.5 , 0. , 0.226208551238], [ 0.75 , 0. , 0.226208551238], [ 0. , 0.25 , 0.226208551238], [ 0.25 , 0.25 , 0.226208551238], [ 0.5 , 0.25 , 0.226208551238], [ 0.75 , 0.25 , 0.226208551238], [ 0. , 0.5 , 0.226208551238], [ 0.25 , 0.5 , 0.226208551238], [ 0.5 , 0.5 , 0.226208551238], [ 0.75 , 0.5 , 0.226208551238], [ 0. , 0.75 , 0.226208551238], [ 0.25 , 0.75 , 0.226208551238], [ 0.5 , 0.75 , 0.226208551238], [ 0.75 , 0.75 , 0.226208551238], [ 0.125 , 0. , 0.254484620143], [ 0.375 , 0. , 0.254484620143], [ 0.625 , 0. , 0.254484620143], [ 0.875 , 0. , 0.254484620143], [ 0.125 , 0.25 , 0.254484620143], [ 0.375 , 0.25 , 0.254484620143], [ 0.625 , 0.25 , 0.254484620143], [ 0.875 , 0.25 , 0.254484620143], [ 0.125 , 0.5 , 0.254484620143], [ 0.375 , 0.5 , 0.254484620143], [ 0.625 , 0.5 , 0.254484620143], [ 0.875 , 0.5 , 0.254484620143], [ 0.125 , 0.75 , 0.254484620143], [ 0.375 , 0.75 , 0.254484620143], [ 0.625 , 0.75 , 0.254484620143], [ 0.875 , 0.75 , 0.254484620143], [ 0.125 , 0.125 , 0.282760689047], [ 0.375 , 0.125 , 0.282760689047], [ 0.625 , 0.125 , 0.282760689047], [ 0.875 , 0.125 , 0.282760689047], [ 0.125 , 0.375 , 0.282760689047], [ 0.375 , 0.375 , 0.282760689047], [ 0.625 , 0.375 , 0.282760689047], [ 0.875 , 0.375 , 0.282760689047], [ 0.125 , 0.625 , 0.282760689047], [ 0.375 , 0.625 , 0.282760689047], [ 0.625 , 0.625 , 0.282760689047], [ 0.875 , 0.625 , 0.282760689047], [ 0.125 , 0.875 , 0.282760689047], [ 0.375 , 0.875 , 0.282760689047], [ 0.625 , 0.875 , 0.282760689047], [ 0.875 , 0.875 , 0.282760689047], [ 0. , 0.125 , 0.311036757952], [ 0.25 , 0.125 , 0.311036757952], [ 0.5 , 0.125 , 0.311036757952], [ 0.75 , 0.125 , 0.311036757952], [ 0. , 0.375 , 0.311036757952], [ 0.25 , 0.375 , 0.311036757952], [ 0.5 , 0.375 , 0.311036757952], [ 0.75 , 0.375 , 0.311036757952], [ 0. , 0.625 , 0.311036757952], [ 0.25 , 0.625 , 0.311036757952], [ 0.5 , 0.625 , 0.311036757952], [ 0.75 , 0.625 , 0.311036757952], [ 0. , 0.875 , 0.311036757952], [ 0.25 , 0.875 , 0.311036757952], [ 0.5 , 0.875 , 0.311036757952], [ 0.75 , 0.875 , 0.311036757952], [ 0. , 0. , 0.339312826857], [ 0.25 , 0. , 0.339312826857], [ 0.5 , 0. , 0.339312826857], [ 0.75 , 0. , 0.339312826857], [ 0. , 0.25 , 0.339312826857], [ 0.25 , 0.25 , 0.339312826857], [ 0.5 , 0.25 , 0.339312826857], [ 0.75 , 0.25 , 0.339312826857], [ 0. , 0.5 , 0.339312826857], [ 0.25 , 0.5 , 0.339312826857], [ 0.5 , 0.5 , 0.339312826857], [ 0.75 , 0.5 , 0.339312826857], [ 0. , 0.75 , 0.339312826857], [ 0.25 , 0.75 , 0.339312826857], [ 0.5 , 0.75 , 0.339312826857], [ 0.75 , 0.75 , 0.339312826857], [ 0.125 , 0. , 0.367588895762], [ 0.375 , 0. , 0.367588895762], [ 0.625 , 0. , 0.367588895762], [ 0.875 , 0. , 0.367588895762], [ 0.125 , 0.25 , 0.367588895762], [ 0.375 , 0.25 , 0.367588895762], [ 0.625 , 0.25 , 0.367588895762], [ 0.875 , 0.25 , 0.367588895762], [ 0.125 , 0.5 , 0.367588895762], [ 0.375 , 0.5 , 0.367588895762], [ 0.625 , 0.5 , 0.367588895762], [ 0.875 , 0.5 , 0.367588895762], [ 0.125 , 0.75 , 0.367588895762], [ 0.375 , 0.75 , 0.367588895762], [ 0.625 , 0.75 , 0.367588895762], [ 0.875 , 0.75 , 0.367588895762], [ 0.125 , 0.125 , 0.395864964666], [ 0.375 , 0.125 , 0.395864964666], [ 0.625 , 0.125 , 0.395864964666], [ 0.875 , 0.125 , 0.395864964666], [ 0.125 , 0.375 , 0.395864964666], [ 0.375 , 0.375 , 0.395864964666], [ 0.625 , 0.375 , 0.395864964666], [ 0.875 , 0.375 , 0.395864964666], [ 0.125 , 0.625 , 0.395864964666], [ 0.375 , 0.625 , 0.395864964666], [ 0.625 , 0.625 , 0.395864964666], [ 0.875 , 0.625 , 0.395864964666], [ 0.125 , 0.875 , 0.395864964666], [ 0.375 , 0.875 , 0.395864964666], [ 0.625 , 0.875 , 0.395864964666], [ 0.875 , 0.875 , 0.395864964666], [ 0. , 0.125 , 0.424141033571], [ 0.25 , 0.125 , 0.424141033571], [ 0.5 , 0.125 , 0.424141033571], [ 0.75 , 0.125 , 0.424141033571], [ 0. , 0.375 , 0.424141033571], [ 0.25 , 0.375 , 0.424141033571], [ 0.5 , 0.375 , 0.424141033571], [ 0.75 , 0.375 , 0.424141033571], [ 0. , 0.625 , 0.424141033571], [ 0.25 , 0.625 , 0.424141033571], [ 0.5 , 0.625 , 0.424141033571], [ 0.75 , 0.625 , 0.424141033571], [ 0. , 0.875 , 0.424141033571], [ 0.25 , 0.875 , 0.424141033571], [ 0.5 , 0.875 , 0.424141033571], [ 0.75 , 0.875 , 0.424141033571], [ 0.039062356711, 0. , 0.452417102476], [ 0.182634258774, 0. , 0.443362646845], [ 0.539062356711, 0. , 0.452417102476], [ 0.682634258774, 0. , 0.443362646845], [ 0.039062356711, 0.25 , 0.452417102476], [ 0.182634258774, 0.25 , 0.443362646845], [ 0.539062356711, 0.25 , 0.452417102476], [ 0.682634258774, 0.25 , 0.443362646845], [ 0.039062356711, 0.5 , 0.452417102476], [ 0.182634258774, 0.5 , 0.443362646845], [ 0.539062356711, 0.5 , 0.452417102476], [ 0.682634258774, 0.5 , 0.443362646845], [ 0.039062356711, 0.75 , 0.452417102476], [ 0.182634258774, 0.75 , 0.443362646845], [ 0.539062356711, 0.75 , 0.452417102476], [ 0.682634258774, 0.75 , 0.443362646845]] # Set up configuration substrate_configuration = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags substrate_configuration.addTags('bulk', [ 0, 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]) substrate_configuration_name = "substrate_configuration" # %% Set ForceFieldCalculator # %% ForceFieldCalculator potentialSet = TremoloXPotentialSet(name='TersoffBrenner_ClFSi_2003+Moliere') potentialSet.addParticleType( ParticleType( symbol='Si', mass=28.0855 * atomicMassUnit, charge=None, sigma=3.82640999441 * Angstrom, sigma14=3.82640999441 * Angstrom, epsilon=0.402 * kiloCaloriePerMole, epsilon14=0.402 * kiloCaloriePerMole, atomicNumber=14, tags=[], ) ) potentialSet.addParticleType( ParticleType( symbol='Cl', mass=35.453 * atomicMassUnit, charge=None, sigma=3.5163772405 * Angstrom, sigma14=3.5163772405 * Angstrom, epsilon=0.227 * kiloCaloriePerMole, epsilon14=0.227 * kiloCaloriePerMole, atomicNumber=17, tags=[], ) ) potentialSet.addParticleType( ParticleType( symbol='F', mass=1.0 * atomicMassUnit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=None, tags=[], ) ) potentialSet.addParticleType( ParticleType( symbol='Ar', mass=39.948 * atomicMassUnit, charge=None, sigma=None, sigma14=None, epsilon=None, epsilon14=None, atomicNumber=18, tags=[], ) ) _potential = TersoffBrennerPairPotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Si', []), A=1830.8 * eV, B=471.18 * eV, l=2.4799 * 1 / Angstrom, mu=1.7322 * 1 / Angstrom, Re=2.35 * Angstrom, R1=2.7 * Angstrom, R2=3.0 * Angstrom, fType='HumbridGraves', ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('F', []), A=1046.953 * eV, B=155.9846 * eV, l=3.2447 * 1 / Angstrom, mu=1.6223 * 1 / Angstrom, Re=1.6008 * Angstrom, R1=1.83922 * Angstrom, R2=2.13922 * Angstrom, fType='HumbridGraves', ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('F', []), A=6379.15 * eV, B=2813.8185 * eV, l=4.6407 * 1 / Angstrom, mu=3.9462 * 1 / Angstrom, Re=1.4119 * Angstrom, R1=1.7 * Angstrom, R2=2.0 * Angstrom, fType='HumbridGraves', ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Cl', []), A=1234.01 * eV, B=142.6061 * eV, l=2.8229 * 1 / Angstrom, mu=1.4114 * 1 / Angstrom, Re=2.019 * Angstrom, R1=2.32 * Angstrom, R2=2.62 * Angstrom, fType='HumbridGraves', ) potentialSet.addPotential(_potential) _potential = TersoffBrennerPairPotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Cl', []), A=7248.247 * eV, B=269.7098 * eV, l=4.0088 * 1 / Angstrom, mu=2.0044 * 1 / Angstrom, Re=1.9878 * Angstrom, R1=2.284 * Angstrom, R2=2.584 * Angstrom, fType='HumbridGraves', ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Si', []), delta=0.63505, eta=0.78734, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('F', []), delta=0.80469, eta=1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Cl', []), delta=0.80469, eta=1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('Si', []), delta=0.5, eta=1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('F', []), delta=0.5, eta=1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('Cl', []), delta=0.5, eta=1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Si', []), delta=0.5, eta=1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Cl', []), delta=0.5, eta=1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerBOPairPotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('F', []), delta=0.5, eta=1.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Si', []), particleType3=ParticleIdentifier('Si', []), beta=3, alpha=5.197495 * 1 / Angstrom**3, g_c=0.0, g_d=0.16, g_h=-0.59826, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Si', []), particleType3=ParticleIdentifier('F', []), beta=3, alpha=5.197495 * 1 / Angstrom**3, g_c=0.0, g_d=0.16, g_h=-0.59826, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Si', []), particleType3=ParticleIdentifier('Cl', []), beta=3, alpha=5.197495 * 1 / Angstrom**3, g_c=0.0, g_d=0.16, g_h=-0.59826, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('F', []), particleType3=ParticleIdentifier('Si', []), beta=3, alpha=4.0 * 1 / Angstrom**3, g_c=0.0216, g_d=0.27, g_h=-0.47, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('F', []), particleType3=ParticleIdentifier('F', []), beta=3, alpha=4.0 * 1 / Angstrom**3, g_c=0.0216, g_d=0.27, g_h=-0.47, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('F', []), particleType3=ParticleIdentifier('Cl', []), beta=3, alpha=4.0 * 1 / Angstrom**3, g_c=0.0216, g_d=0.27, g_h=-0.47, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Cl', []), particleType3=ParticleIdentifier('Si', []), beta=3, alpha=4.0 * 1 / Angstrom**3, g_c=0.0216, g_d=0.27, g_h=-0.47, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Cl', []), particleType3=ParticleIdentifier('F', []), beta=3, alpha=4.0 * 1 / Angstrom**3, g_c=0.0216, g_d=0.27, g_h=-0.47, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Cl', []), particleType3=ParticleIdentifier('Cl', []), beta=3, alpha=4.0 * 1 / Angstrom**3, g_c=0.0216, g_d=0.27, g_h=-0.47, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('Si', []), particleType3=ParticleIdentifier('Si', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('Si', []), particleType3=ParticleIdentifier('F', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('Si', []), particleType3=ParticleIdentifier('Cl', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('F', []), particleType3=ParticleIdentifier('Si', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('F', []), particleType3=ParticleIdentifier('F', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('F', []), particleType3=ParticleIdentifier('Cl', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('Cl', []), particleType3=ParticleIdentifier('Si', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('Cl', []), particleType3=ParticleIdentifier('F', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('Cl', []), particleType3=ParticleIdentifier('Cl', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Si', []), particleType3=ParticleIdentifier('Si', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Si', []), particleType3=ParticleIdentifier('F', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Si', []), particleType3=ParticleIdentifier('Cl', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('F', []), particleType3=ParticleIdentifier('Si', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('F', []), particleType3=ParticleIdentifier('F', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('F', []), particleType3=ParticleIdentifier('Cl', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Cl', []), particleType3=ParticleIdentifier('Si', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Cl', []), particleType3=ParticleIdentifier('F', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerTriplePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Cl', []), particleType3=ParticleIdentifier('Cl', []), beta=1, alpha=6.0 * 1 / Angstrom, g_c=14.0, g_d=0.0, g_h=0.0, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerMolierePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Si', []), a=-7.155376 * 1 / Angstrom, b=9.502208, c=237.361562 * eV, d=1.0 * eV, f=0.122464808658 * Angstrom, c1=0.35, c2=0.55, c3=0.1, c4=0.0, d1=0.1, d2=1.2, d3=6.0, d4=0.0, Zi=14.0 * elementaryCharge, Zj=14.0 * elementaryCharge, s=296.792932 * eV, ra=0.286968 * Angstrom, rb=0.65522 * Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerMolierePotential( particleType1=ParticleIdentifier('F', []), particleType2=ParticleIdentifier('F', []), a=-3.811346 * 1 / Angstrom, b=8.416768, c=-67.291591 * eV, d=1.0 * eV, f=0.141896979319 * Angstrom, c1=0.35, c2=0.55, c3=0.1, c4=0.0, d1=0.1, d2=1.2, d3=6.0, d4=0.0, Zi=9.0 * elementaryCharge, Zj=9.0 * elementaryCharge, s=642.521743 * eV, ra=0.286968 * Angstrom, rb=0.65522 * Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerMolierePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('F', []), a=-6.966201045 * 1 / Angstrom, b=9.057239273, c=42.67175229 * eV, d=1.0 * eV, f=0.131289360256 * Angstrom, c1=0.35, c2=0.55, c3=0.1, c4=0.0, d1=0.1, d2=1.2, d3=6.0, d4=0.0, Zi=14.0 * elementaryCharge, Zj=9.0 * elementaryCharge, s=55.11209444 * eV, ra=0.3 * Angstrom, rb=0.8 * Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerMolierePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Cl', []), a=-7.108443546 * 1 / Angstrom, b=9.622960686, c=77.76670812 * eV, d=1.0 * eV, f=0.118472319189 * Angstrom, c1=0.35, c2=0.55, c3=0.1, c4=0.0, d1=0.1, d2=1.2, d3=6.0, d4=0.0, Zi=14.0 * elementaryCharge, Zj=17.0 * elementaryCharge, s=106.164425 * eV, ra=0.3 * Angstrom, rb=0.8 * Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerMolierePotential( particleType1=ParticleIdentifier('Cl', []), particleType2=ParticleIdentifier('Cl', []), a=-5.093518 * 1 / Angstrom, b=9.51683, c=62.482094 * eV, d=1.0 * eV, f=0.114790076782 * Angstrom, c1=0.35, c2=0.55, c3=0.1, c4=0.0, d1=0.1, d2=1.2, d3=6.0, d4=0.0, Zi=17.0 * elementaryCharge, Zj=17.0 * elementaryCharge, s=948.058599 * eV, ra=0.3 * Angstrom, rb=0.8 * Angstrom, ) potentialSet.addPotential(_potential) _potential = TersoffBrennerSplinePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('F', []), activeTypes1=[ ParticleIdentifier('F', []), ], activeTypes2=[ ParticleIdentifier('Si', []), ], x=numpy.array([0, 1, 2, 3, 4, 5]), y=numpy.array([0, 1, 2, 3, 4, 5]), f=numpy.array( [ [0.0, 0.0, 0.085, -0.12, 0.0, 0.0], [-0.1755, 0.0, -0.09, 0.0, 0.0, 0.0], [0.496, -0.07, 0.0, 0.0, 0.0, 0.0], [-0.181, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], ] ), ) potentialSet.addPotential(_potential) _potential = TersoffBrennerSplinePotential( particleType1=ParticleIdentifier('Si', []), particleType2=ParticleIdentifier('Cl', []), activeTypes1=[ ParticleIdentifier('Cl', []), ], activeTypes2=[ ParticleIdentifier('Si', []), ], x=numpy.array([0, 1, 2, 3, 4, 5]), y=numpy.array([0, 1, 2, 3, 4, 5]), f=numpy.array( [ [0.0, 0.0, -0.05, -0.11, 0.0, 0.0], [-0.088, 0.0, -0.06, 0.0, 0.0, 0.0], [1.09, 0.015, 0.0, 0.0, 0.0, 0.0], [-0.068, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], ] ), ) potentialSet.addPotential(_potential) _potential = MolierePotential( particleType1=ParticleIdentifier('Ar', []), particleType2=ParticleIdentifier('Si', []), f=0.117286895064 * Angstrom, c1=0.35, c2=0.55, c3=0.1, c4=0.0, d1=0.1, d2=1.2, d3=6.0, d4=0.0, Zi=18.0 * elementaryCharge, Zj=14.0 * elementaryCharge, s=0.0 * eV, r_i=5.0 * Angstrom, r_cut=7.5 * Angstrom, ) potentialSet.addPotential(_potential) _potential = MolierePotential( particleType1=ParticleIdentifier('Ar', []), particleType2=ParticleIdentifier('Cl', []), f=0.113693994066 * Angstrom, c1=0.35, c2=0.55, c3=0.1, c4=0.0, d1=0.1, d2=1.2, d3=6.0, d4=0.0, Zi=18.0 * elementaryCharge, Zj=17.0 * elementaryCharge, s=0.0 * eV, r_i=5.0 * Angstrom, r_cut=7.5 * Angstrom, ) potentialSet.addPotential(_potential) _potential = MolierePotential( particleType1=ParticleIdentifier('Ar', []), particleType2=ParticleIdentifier('Ar', []), f=0.112623707121 * Angstrom, c1=0.35, c2=0.55, c3=0.1, c4=0.0, d1=0.1, d2=1.2, d3=6.0, d4=0.0, Zi=18.0 * elementaryCharge, Zj=18.0 * elementaryCharge, s=0.0 * eV, r_i=5.0 * Angstrom, r_cut=7.5 * Angstrom, ) potentialSet.addPotential(_potential) calculator = TremoloXCalculator(parameters=potentialSet) # %% Set Calculator substrate_configuration.setCalculator(calculator) nlsave('SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', substrate_configuration) # %% OptimizeGeometry constraints = [FixStrain(True, True, True), FixAtomConstraints('bulk')] optimized_configuration = OptimizeGeometry( configuration=substrate_configuration, max_forces=0.01 * eV / Angstrom, constraints=constraints, trajectory_filename='SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', trajectory_object_id='optimize_trajectory', optimize_cell=False, trajectory_interval=10, restart_strategy=NoRestart, enable_optimization_stop_file=False, ) nlsave('SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', optimized_configuration) # %% MD 10K - 300K method = NVTBussiDonadioParrinello( initial_velocity=MaxwellBoltzmannDistribution( temperature=10.0 * Kelvin, remove_center_of_mass_momentum=True ), time_step=0.5 * femtoSecond, reservoir_temperature=10.0 * Kelvin, heating_rate=2.9 * Kelvin / picoSecond, ) constraints = [FixStrain(True, True, True), FixAtomConstraints('bulk')] md_trajectory = MolecularDynamics( configuration=optimized_configuration, constraints=constraints, trajectory_filename='SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', steps=200000, log_interval=1000, method=method, ) last_image = md_trajectory.lastImage() nlsave('SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', last_image) # %% MD 300K method = NVTNoseHoover( initial_velocity=ConfigurationVelocities(), time_step=0.5 * femtoSecond, reservoir_temperature=300.0 * Kelvin, heating_rate=0.0 * Kelvin / femtoSecond, ) constraints = [FixStrain(True, True, True), FixAtomConstraints('bulk')] md_trajectory_1 = MolecularDynamics( configuration=last_image, constraints=constraints, trajectory_filename='SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', steps=200000, log_interval=100, method=method, ) last_image_1 = md_trajectory_1.lastImage() nlsave('SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', last_image_1) # %% Load Substrate Candidate(s) def load_substrate_candidates(md_trajectory, substrate_configuration): # Defined variables. list_bulk = False # Script. bulk_configuration_list = [] if list_bulk: for i in range(0, md_trajectory.length()): bulk_configuration_list.append(md_trajectory.image(i)) else: bulk_configuration_list.append(md_trajectory.lastImage()) substrate_configuration = md_trajectory.lastImage() return bulk_configuration_list, substrate_configuration bulk_configuration_list, substrate_configuration = load_substrate_candidates( md_trajectory_1, substrate_configuration ) nlsave('SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', bulk_configuration_list) nlsave('SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', substrate_configuration) # %% Cycle Cl2 and Ar # Cycle Cl2 and Ar(preparation) ############################################################ # Iteration (cycle) # ############################################################ # Create iterator. cycles = range(1, 5) for cycle in cycles: # %% Cl2 pulse MultiSpecies SPS # %% Cl2 # Define elements elements = [Chlorine, Chlorine] # Define coordinates cartesian_coordinates = [[-3.408379825326, -0.085312376112, 0. ], [-1.340005230658, 0.200293184294, 0. ]]*Angstrom # Set up configuration cl2 = MoleculeConfiguration( elements=elements, cartesian_coordinates=cartesian_coordinates ) # Add tags cl2.addTags('H_Cl', [1]) cl2_name = "Cl2" # %% SurfaceProcessSimulation # ------------------------------------------------------------- # Surface Process Simulation # ------------------------------------------------------------- clean_vacuum_region_hook = CleanVacuumRegion() sps_hooks = [clean_vacuum_region_hook] surface_process_simulation = SurfaceProcessSimulation( substrate=substrate_configuration, filename='SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', object_id=f'surface_process_simulation_sps_cycle_{cycle}', random_seed=randomSeed(520782836, cl2), temperature=300.0 * Kelvin, fixed_thickness=1.0 * Angstrom, thermostat_thickness=5.0 * Angstrom, log_interval=1000, trajectory_interval=1000, fixed_directions=(2,), ) surface_process_simulation.addSequence( molecule=cl2, number_of_events=250, md_time=10.0 * picoSecond, time_step=1.0 * femtoSecond, mean_kinetic_energy=300.0 * kBK, mean_incident_angle=0.0 * Degrees, internal_energy=300.0 * Kelvin, post_md_hooks=sps_hooks, log_interval=1000, trajectory_interval=1000, stability_checks=False, ) surface_process_simulation.update() last_image_2 = surface_process_simulation.lastImage() nlsave( 'SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', last_image_2, object_id=f'last_image_2_sps_cycle_{cycle}', ) # %% Custom def custom(configuration, substrate_configuration, sps_cl): substrate_configuration = configuration nlsave(f'Cl_pulse_{cycle}.hdf5', sps_cl) return substrate_configuration substrate_configuration = custom( last_image_2, substrate_configuration, surface_process_simulation ) nlsave( 'SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', substrate_configuration, object_id=f'substrate_configuration_Custom_cycle_{cycle}_1', ) # %% Ar pulse MultiSpecies SPS # %% Ar # Define elements elements = [Argon] # Define coordinates cartesian_coordinates = [[ 0., 0., 0.]]*Angstrom # Set up configuration ar = MoleculeConfiguration( elements=elements, cartesian_coordinates=cartesian_coordinates ) ar_name = "Ar" # %% SurfaceProcessSimulation # ------------------------------------------------------------- # Surface Process Simulation # ------------------------------------------------------------- clean_vacuum_region_hook = CleanVacuumRegion() remove_element_hook_0 = RemoveElementFromSubstrate(element=Argon) sps_hooks = [clean_vacuum_region_hook, remove_element_hook_0] surface_process_simulation_1 = SurfaceProcessSimulation( substrate=substrate_configuration, filename='SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', object_id=f'surface_process_simulation_1_sps_cycle_{cycle}', random_seed=randomSeed(520782836, ar), temperature=300.0 * Kelvin, fixed_thickness=1.0 * Angstrom, thermostat_thickness=5.0 * Angstrom, log_interval=1000, trajectory_interval=1000, fixed_directions=(2,), ) surface_process_simulation_1.addSequence( molecule=ar, number_of_events=250, md_time=10.0 * picoSecond, time_step=1.0 * femtoSecond, mean_kinetic_energy=100.0 * eV, mean_incident_angle=0.0 * Degrees, internal_energy=300.0 * Kelvin, post_md_hooks=sps_hooks, log_interval=1000, trajectory_interval=1000, stability_checks=False, ) surface_process_simulation_1.update() last_image_3 = surface_process_simulation_1.lastImage() nlsave( 'SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', last_image_3, object_id=f'last_image_3_sps_cycle_{cycle}', ) # %% Custom def custom_1(configuration, substrate_configuration, sps_ar): substrate_configuration = configuration nlsave(f'Ar_pulse_{cycle}.hdf5', sps_ar) return substrate_configuration substrate_configuration = custom_1( last_image_3, substrate_configuration, surface_process_simulation_1 ) nlsave( 'SPS_Si100_Cl2_300K_Ar_100eV_ALE_results.hdf5', substrate_configuration, object_id=f'substrate_configuration_Custom_cycle_{cycle}_3', )