# Set minimal log verbosity setVerbosity(MinimalLog) # %% Si_long # Set up lattice vector_a = [19.200070429558327, 0.0, 0.0]*Angstrom vector_b = [0.0, 19.200070429558327, 0.0]*Angstrom vector_c = [0.0, 0.0, 129.4731]*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, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, 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 = [[ 0.1 , 0. , 0.010485961949], [ 0.3 , 0. , 0.010485961949], [ 0.5 , 0. , 0.010485961949], [ 0.7 , 0. , 0.010485961949], [ 0.9 , 0. , 0.010485961949], [ 0.1 , 0.2 , 0.010485961949], [ 0.3 , 0.2 , 0.010485961949], [ 0.5 , 0.2 , 0.010485961949], [ 0.7 , 0.2 , 0.010485961949], [ 0.9 , 0.2 , 0.010485961949], [ 0.1 , 0.4 , 0.010485961949], [ 0.3 , 0.4 , 0.010485961949], [ 0.5 , 0.4 , 0.010485961949], [ 0.7 , 0.4 , 0.010485961949], [ 0.9 , 0.4 , 0.010485961949], [ 0.1 , 0.6 , 0.010485961949], [ 0.3 , 0.6 , 0.010485961949], [ 0.5 , 0.6 , 0.010485961949], [ 0.7 , 0.6 , 0.010485961949], [ 0.9 , 0.6 , 0.010485961949], [ 0.1 , 0.8 , 0.010485961949], [ 0.3 , 0.8 , 0.010485961949], [ 0.5 , 0.8 , 0.010485961949], [ 0.7 , 0.8 , 0.010485961949], [ 0.9 , 0.8 , 0.010485961949], [ 0.1 , 0.1 , 0.020971923898], [ 0.3 , 0.1 , 0.020971923898], [ 0.5 , 0.1 , 0.020971923898], [ 0.7 , 0.1 , 0.020971923898], [ 0.9 , 0.1 , 0.020971923898], [ 0.1 , 0.3 , 0.020971923898], [ 0.3 , 0.3 , 0.020971923898], [ 0.5 , 0.3 , 0.020971923898], [ 0.7 , 0.3 , 0.020971923898], [ 0.9 , 0.3 , 0.020971923898], [ 0.1 , 0.5 , 0.020971923898], [ 0.3 , 0.5 , 0.020971923898], [ 0.5 , 0.5 , 0.020971923898], [ 0.7 , 0.5 , 0.020971923898], [ 0.9 , 0.5 , 0.020971923898], [ 0.1 , 0.7 , 0.020971923898], [ 0.3 , 0.7 , 0.020971923898], [ 0.5 , 0.7 , 0.020971923898], [ 0.7 , 0.7 , 0.020971923898], [ 0.9 , 0.7 , 0.020971923898], [ 0.1 , 0.9 , 0.020971923898], [ 0.3 , 0.9 , 0.020971923898], [ 0.5 , 0.9 , 0.020971923898], [ 0.7 , 0.9 , 0.020971923898], [ 0.9 , 0.9 , 0.020971923898], [ 0. , 0.1 , 0.031457885847], [ 0.2 , 0.1 , 0.031457885847], [ 0.4 , 0.1 , 0.031457885847], [ 0.6 , 0.1 , 0.031457885847], [ 0.8 , 0.1 , 0.031457885847], [ 0. , 0.3 , 0.031457885847], [ 0.2 , 0.3 , 0.031457885847], [ 0.4 , 0.3 , 0.031457885847], [ 0.6 , 0.3 , 0.031457885847], [ 0.8 , 0.3 , 0.031457885847], [ 0. , 0.5 , 0.031457885847], [ 0.2 , 0.5 , 0.031457885847], [ 0.4 , 0.5 , 0.031457885847], [ 0.6 , 0.5 , 0.031457885847], [ 0.8 , 0.5 , 0.031457885847], [ 0. , 0.7 , 0.031457885847], [ 0.2 , 0.7 , 0.031457885847], [ 0.4 , 0.7 , 0.031457885847], [ 0.6 , 0.7 , 0.031457885847], [ 0.8 , 0.7 , 0.031457885847], [ 0. , 0.9 , 0.031457885847], [ 0.2 , 0.9 , 0.031457885847], [ 0.4 , 0.9 , 0.031457885847], [ 0.6 , 0.9 , 0.031457885847], [ 0.8 , 0.9 , 0.031457885847], [ 0. , 0. , 0.041943847796], [ 0.2 , 0. , 0.041943847796], [ 0.4 , 0. , 0.041943847796], [ 0.6 , 0. , 0.041943847796], [ 0.8 , 0. , 0.041943847796], [ 0. , 0.2 , 0.041943847796], [ 0.2 , 0.2 , 0.041943847796], [ 0.4 , 0.2 , 0.041943847796], [ 0.6 , 0.2 , 0.041943847796], [ 0.8 , 0.2 , 0.041943847796], [ 0. , 0.4 , 0.041943847796], [ 0.2 , 0.4 , 0.041943847796], [ 0.4 , 0.4 , 0.041943847796], [ 0.6 , 0.4 , 0.041943847796], [ 0.8 , 0.4 , 0.041943847796], [ 0. , 0.6 , 0.041943847796], [ 0.2 , 0.6 , 0.041943847796], [ 0.4 , 0.6 , 0.041943847796], [ 0.6 , 0.6 , 0.041943847796], [ 0.8 , 0.6 , 0.041943847796], [ 0. , 0.8 , 0.041943847796], [ 0.2 , 0.8 , 0.041943847796], [ 0.4 , 0.8 , 0.041943847796], [ 0.6 , 0.8 , 0.041943847796], [ 0.8 , 0.8 , 0.041943847796], [ 0.1 , 0. , 0.052429809745], [ 0.3 , 0. , 0.052429809745], [ 0.5 , 0. , 0.052429809745], [ 0.7 , 0. , 0.052429809745], [ 0.9 , 0. , 0.052429809745], [ 0.1 , 0.2 , 0.052429809745], [ 0.3 , 0.2 , 0.052429809745], [ 0.5 , 0.2 , 0.052429809745], [ 0.7 , 0.2 , 0.052429809745], [ 0.9 , 0.2 , 0.052429809745], [ 0.1 , 0.4 , 0.052429809745], [ 0.3 , 0.4 , 0.052429809745], [ 0.5 , 0.4 , 0.052429809745], [ 0.7 , 0.4 , 0.052429809745], [ 0.9 , 0.4 , 0.052429809745], [ 0.1 , 0.6 , 0.052429809745], [ 0.3 , 0.6 , 0.052429809745], [ 0.5 , 0.6 , 0.052429809745], [ 0.7 , 0.6 , 0.052429809745], [ 0.9 , 0.6 , 0.052429809745], [ 0.1 , 0.8 , 0.052429809745], [ 0.3 , 0.8 , 0.052429809745], [ 0.5 , 0.8 , 0.052429809745], [ 0.7 , 0.8 , 0.052429809745], [ 0.9 , 0.8 , 0.052429809745], [ 0.1 , 0.1 , 0.062915771694], [ 0.3 , 0.1 , 0.062915771694], [ 0.5 , 0.1 , 0.062915771694], [ 0.7 , 0.1 , 0.062915771694], [ 0.9 , 0.1 , 0.062915771694], [ 0.1 , 0.3 , 0.062915771694], [ 0.3 , 0.3 , 0.062915771694], [ 0.5 , 0.3 , 0.062915771694], [ 0.7 , 0.3 , 0.062915771694], [ 0.9 , 0.3 , 0.062915771694], [ 0.1 , 0.5 , 0.062915771694], [ 0.3 , 0.5 , 0.062915771694], [ 0.5 , 0.5 , 0.062915771694], [ 0.7 , 0.5 , 0.062915771694], [ 0.9 , 0.5 , 0.062915771694], [ 0.1 , 0.7 , 0.062915771694], [ 0.3 , 0.7 , 0.062915771694], [ 0.5 , 0.7 , 0.062915771694], [ 0.7 , 0.7 , 0.062915771694], [ 0.9 , 0.7 , 0.062915771694], [ 0.1 , 0.9 , 0.062915771694], [ 0.3 , 0.9 , 0.062915771694], [ 0.5 , 0.9 , 0.062915771694], [ 0.7 , 0.9 , 0.062915771694], [ 0.9 , 0.9 , 0.062915771694], [ 0. , 0.1 , 0.073401733642], [ 0.2 , 0.1 , 0.073401733642], [ 0.4 , 0.1 , 0.073401733642], [ 0.6 , 0.1 , 0.073401733642], [ 0.8 , 0.1 , 0.073401733642], [ 0. , 0.3 , 0.073401733642], [ 0.2 , 0.3 , 0.073401733642], [ 0.4 , 0.3 , 0.073401733642], [ 0.6 , 0.3 , 0.073401733642], [ 0.8 , 0.3 , 0.073401733642], [ 0. , 0.5 , 0.073401733642], [ 0.2 , 0.5 , 0.073401733642], [ 0.4 , 0.5 , 0.073401733642], [ 0.6 , 0.5 , 0.073401733642], [ 0.8 , 0.5 , 0.073401733642], [ 0. , 0.7 , 0.073401733642], [ 0.2 , 0.7 , 0.073401733642], [ 0.4 , 0.7 , 0.073401733642], [ 0.6 , 0.7 , 0.073401733642], [ 0.8 , 0.7 , 0.073401733642], [ 0. , 0.9 , 0.073401733642], [ 0.2 , 0.9 , 0.073401733642], [ 0.4 , 0.9 , 0.073401733642], [ 0.6 , 0.9 , 0.073401733642], [ 0.8 , 0.9 , 0.073401733642], [ 0. , 0. , 0.083887695591], [ 0.2 , 0. , 0.083887695591], [ 0.4 , 0. , 0.083887695591], [ 0.6 , 0. , 0.083887695591], [ 0.8 , 0. , 0.083887695591], [ 0. , 0.2 , 0.083887695591], [ 0.2 , 0.2 , 0.083887695591], [ 0.4 , 0.2 , 0.083887695591], [ 0.6 , 0.2 , 0.083887695591], [ 0.8 , 0.2 , 0.083887695591], [ 0. , 0.4 , 0.083887695591], [ 0.2 , 0.4 , 0.083887695591], [ 0.4 , 0.4 , 0.083887695591], [ 0.6 , 0.4 , 0.083887695591], [ 0.8 , 0.4 , 0.083887695591], [ 0. , 0.6 , 0.083887695591], [ 0.2 , 0.6 , 0.083887695591], [ 0.4 , 0.6 , 0.083887695591], [ 0.6 , 0.6 , 0.083887695591], [ 0.8 , 0.6 , 0.083887695591], [ 0. , 0.8 , 0.083887695591], [ 0.2 , 0.8 , 0.083887695591], [ 0.4 , 0.8 , 0.083887695591], [ 0.6 , 0.8 , 0.083887695591], [ 0.8 , 0.8 , 0.083887695591], [ 0.1 , 0. , 0.09437365754 ], [ 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0.618671754983], [ 0.4 , 0.5 , 0.618671754983], [ 0.6 , 0.5 , 0.618671754983], [ 0.8 , 0.5 , 0.618671754983], [ 0. , 0.7 , 0.618671754983], [ 0.2 , 0.7 , 0.618671754983], [ 0.4 , 0.7 , 0.618671754983], [ 0.6 , 0.7 , 0.618671754983], [ 0.8 , 0.7 , 0.618671754983], [ 0. , 0.9 , 0.618671754983], [ 0.2 , 0.9 , 0.618671754983], [ 0.4 , 0.9 , 0.618671754983], [ 0.6 , 0.9 , 0.618671754983], [ 0.8 , 0.9 , 0.618671754983], [ 0. , 0. , 0.629157716932], [ 0.2 , 0. , 0.629157716932], [ 0.4 , 0. , 0.629157716932], [ 0.6 , 0. , 0.629157716932], [ 0.8 , 0. , 0.629157716932], [ 0. , 0.2 , 0.629157716932], [ 0.2 , 0.2 , 0.629157716932], [ 0.4 , 0.2 , 0.629157716932], [ 0.6 , 0.2 , 0.629157716932], [ 0.8 , 0.2 , 0.629157716932], [ 0. , 0.4 , 0.629157716932], [ 0.2 , 0.4 , 0.629157716932], [ 0.4 , 0.4 , 0.629157716932], [ 0.6 , 0.4 , 0.629157716932], [ 0.8 , 0.4 , 0.629157716932], [ 0. , 0.6 , 0.629157716932], [ 0.2 , 0.6 , 0.629157716932], [ 0.4 , 0.6 , 0.629157716932], [ 0.6 , 0.6 , 0.629157716932], [ 0.8 , 0.6 , 0.629157716932], [ 0. , 0.8 , 0.629157716932], [ 0.2 , 0.8 , 0.629157716932], [ 0.4 , 0.8 , 0.629157716932], [ 0.6 , 0.8 , 0.629157716932], [ 0.8 , 0.8 , 0.629157716932], [ 0.1 , 0. , 0.63964367888 ], [ 0.3 , 0. , 0.63964367888 ], [ 0.5 , 0. , 0.63964367888 ], [ 0.7 , 0. , 0.63964367888 ], [ 0.9 , 0. , 0.63964367888 ], [ 0.1 , 0.2 , 0.63964367888 ], [ 0.3 , 0.2 , 0.63964367888 ], [ 0.5 , 0.2 , 0.63964367888 ], [ 0.7 , 0.2 , 0.63964367888 ], [ 0.9 , 0.2 , 0.63964367888 ], [ 0.1 , 0.4 , 0.63964367888 ], [ 0.3 , 0.4 , 0.63964367888 ], [ 0.5 , 0.4 , 0.63964367888 ], [ 0.7 , 0.4 , 0.63964367888 ], [ 0.9 , 0.4 , 0.63964367888 ], [ 0.1 , 0.6 , 0.63964367888 ], [ 0.3 , 0.6 , 0.63964367888 ], [ 0.5 , 0.6 , 0.63964367888 ], [ 0.7 , 0.6 , 0.63964367888 ], [ 0.9 , 0.6 , 0.63964367888 ], [ 0.1 , 0.8 , 0.63964367888 ], [ 0.3 , 0.8 , 0.63964367888 ], [ 0.5 , 0.8 , 0.63964367888 ], [ 0.7 , 0.8 , 0.63964367888 ], [ 0.9 , 0.8 , 0.63964367888 ], [ 0.1 , 0.1 , 0.650129640829], [ 0.3 , 0.1 , 0.650129640829], [ 0.5 , 0.1 , 0.650129640829], [ 0.7 , 0.1 , 0.650129640829], [ 0.9 , 0.1 , 0.650129640829], [ 0.1 , 0.3 , 0.650129640829], [ 0.3 , 0.3 , 0.650129640829], [ 0.5 , 0.3 , 0.650129640829], [ 0.7 , 0.3 , 0.650129640829], [ 0.9 , 0.3 , 0.650129640829], [ 0.1 , 0.5 , 0.650129640829], [ 0.3 , 0.5 , 0.650129640829], [ 0.5 , 0.5 , 0.650129640829], [ 0.7 , 0.5 , 0.650129640829], [ 0.9 , 0.5 , 0.650129640829], [ 0.1 , 0.7 , 0.650129640829], [ 0.3 , 0.7 , 0.650129640829], [ 0.5 , 0.7 , 0.650129640829], [ 0.7 , 0.7 , 0.650129640829], [ 0.9 , 0.7 , 0.650129640829], [ 0.1 , 0.9 , 0.650129640829], [ 0.3 , 0.9 , 0.650129640829], [ 0.5 , 0.9 , 0.650129640829], [ 0.7 , 0.9 , 0.650129640829], [ 0.9 , 0.9 , 0.650129640829], [ 0. , 0.1 , 0.660615602778], [ 0.2 , 0.1 , 0.660615602778], [ 0.4 , 0.1 , 0.660615602778], [ 0.6 , 0.1 , 0.660615602778], [ 0.8 , 0.1 , 0.660615602778], [ 0. , 0.3 , 0.660615602778], [ 0.2 , 0.3 , 0.660615602778], [ 0.4 , 0.3 , 0.660615602778], [ 0.6 , 0.3 , 0.660615602778], [ 0.8 , 0.3 , 0.660615602778], [ 0. , 0.5 , 0.660615602778], [ 0.2 , 0.5 , 0.660615602778], [ 0.4 , 0.5 , 0.660615602778], [ 0.6 , 0.5 , 0.660615602778], [ 0.8 , 0.5 , 0.660615602778], [ 0. , 0.7 , 0.660615602778], [ 0.2 , 0.7 , 0.660615602778], [ 0.4 , 0.7 , 0.660615602778], [ 0.6 , 0.7 , 0.660615602778], [ 0.8 , 0.7 , 0.660615602778], [ 0. , 0.9 , 0.660615602778], [ 0.2 , 0.9 , 0.660615602778], [ 0.4 , 0.9 , 0.660615602778], [ 0.6 , 0.9 , 0.660615602778], [ 0.8 , 0.9 , 0.660615602778], [ 0. , 0. , 0.671101564727], [ 0.2 , 0. , 0.671101564727], [ 0.4 , 0. , 0.671101564727], [ 0.6 , 0. , 0.671101564727], [ 0.8 , 0. , 0.671101564727], [ 0. , 0.2 , 0.671101564727], [ 0.2 , 0.2 , 0.671101564727], [ 0.4 , 0.2 , 0.671101564727], [ 0.6 , 0.2 , 0.671101564727], [ 0.8 , 0.2 , 0.671101564727], [ 0. , 0.4 , 0.671101564727], [ 0.2 , 0.4 , 0.671101564727], [ 0.4 , 0.4 , 0.671101564727], [ 0.6 , 0.4 , 0.671101564727], [ 0.8 , 0.4 , 0.671101564727], [ 0. , 0.6 , 0.671101564727], [ 0.2 , 0.6 , 0.671101564727], [ 0.4 , 0.6 , 0.671101564727], [ 0.6 , 0.6 , 0.671101564727], [ 0.8 , 0.6 , 0.671101564727], [ 0. , 0.8 , 0.671101564727], [ 0.2 , 0.8 , 0.671101564727], [ 0.4 , 0.8 , 0.671101564727], [ 0.6 , 0.8 , 0.671101564727], [ 0.8 , 0.8 , 0.671101564727]] # Set up configuration si_long = BulkConfiguration( bravais_lattice=lattice, elements=elements, fractional_coordinates=fractional_coordinates ) # Add tags si_long.addTags('apply_heat', [1050, 1051, 1052, 1053, 1054, 1055, 1056, 1057, 1058, 1059, 1060, 1061, 1062, 1063, 1064, 1065, 1066, 1067, 1068, 1069, 1070, 1071, 1072, 1073, 1074, 1075, 1076, 1077, 1078, 1079, 1080, 1081, 1082, 1083, 1084, 1085, 1086, 1087, 1088, 1089, 1090, 1091, 1092, 1093, 1094, 1095, 1096, 1097, 1098, 1099, 1100, 1101, 1102, 1103, 1104, 1105, 1106, 1107, 1108, 1109, 1110, 1111, 1112, 1113, 1114, 1115, 1116, 1117, 1118, 1119, 1120, 1121, 1122, 1123, 1124, 1125, 1126, 1127, 1128, 1129, 1130, 1131, 1132, 1133, 1134, 1135, 1136, 1137, 1138, 1139, 1140, 1141, 1142, 1143, 1144, 1145, 1146, 1147, 1148, 1149, 1150, 1151, 1152, 1153, 1154, 1155, 1156, 1157, 1158, 1159, 1160, 1161, 1162, 1163, 1164, 1165, 1166, 1167, 1168, 1169, 1170, 1171, 1172, 1173, 1174, 1175, 1176, 1177, 1178, 1179, 1180, 1181, 1182, 1183, 1184, 1185, 1186, 1187, 1188, 1189, 1190, 1191, 1192, 1193, 1194, 1195, 1196, 1197, 1198, 1199, 1200, 1201, 1202, 1203, 1204, 1205, 1206, 1207, 1208, 1209, 1210, 1211, 1212, 1213, 1214, 1215, 1216, 1217, 1218, 1219, 1220, 1221, 1222, 1223, 1224, 1225, 1226, 1227, 1228, 1229, 1230, 1231, 1232, 1233, 1234, 1235, 1236, 1237, 1238, 1239, 1240, 1241, 1242, 1243, 1244, 1245, 1246, 1247, 1248, 1249, 1250, 1251, 1252, 1253, 1254, 1255, 1256, 1257, 1258, 1259, 1260, 1261, 1262, 1263, 1264, 1265, 1266, 1267, 1268, 1269, 1270, 1271, 1272, 1273, 1274, 1275, 1276, 1277, 1278, 1279, 1280, 1281, 1282, 1283, 1284, 1285, 1286, 1287, 1288, 1289, 1290, 1291, 1292, 1293, 1294, 1295, 1296, 1297, 1298, 1299, 1300, 1301, 1302, 1303, 1304, 1305, 1306, 1307, 1308, 1309, 1310, 1311, 1312, 1313, 1314, 1315, 1316, 1317, 1318, 1319, 1320, 1321, 1322, 1323, 1324, 1325, 1326, 1327, 1328, 1329, 1330, 1331, 1332, 1333, 1334, 1335, 1336, 1337, 1338, 1339, 1340, 1341, 1342, 1343, 1344, 1345, 1346, 1347, 1348, 1349, 1350, 1351, 1352, 1353, 1354, 1355, 1356, 1357, 1358, 1359, 1360, 1361, 1362, 1363, 1364, 1365, 1366, 1367, 1368, 1369, 1370, 1371, 1372, 1373, 1374, 1375, 1376, 1377, 1378, 1379, 1380, 1381, 1382, 1383, 1384, 1385, 1386, 1387, 1388, 1389, 1390, 1391, 1392, 1393, 1394, 1395, 1396, 1397, 1398, 1399, 1400, 1401, 1402, 1403, 1404, 1405, 1406, 1407, 1408, 1409, 1410, 1411, 1412, 1413, 1414, 1415, 1416, 1417, 1418, 1419, 1420, 1421, 1422, 1423, 1424, 1425, 1426, 1427, 1428, 1429, 1430, 1431, 1432, 1433, 1434, 1435, 1436, 1437, 1438, 1439, 1440, 1441, 1442, 1443, 1444, 1445, 1446, 1447, 1448, 1449, 1450, 1451, 1452, 1453, 1454, 1455, 1456, 1457, 1458, 1459, 1460, 1461, 1462, 1463, 1464, 1465, 1466, 1467, 1468, 1469, 1470, 1471, 1472, 1473, 1474, 1475, 1476, 1477, 1478, 1479, 1480, 1481, 1482, 1483, 1484, 1485, 1486, 1487, 1488, 1489, 1490, 1491, 1492, 1493, 1494, 1495, 1496, 1497, 1498, 1499, 1500, 1501, 1502, 1503, 1504, 1505, 1506, 1507, 1508, 1509, 1510, 1511, 1512, 1513, 1514, 1515, 1516, 1517, 1518, 1519, 1520, 1521, 1522, 1523, 1524, 1525, 1526, 1527, 1528, 1529, 1530, 1531, 1532, 1533, 1534, 1535, 1536, 1537, 1538, 1539, 1540, 1541, 1542, 1543, 1544, 1545, 1546, 1547, 1548, 1549, 1550, 1551, 1552, 1553, 1554, 1555, 1556, 1557, 1558, 1559, 1560, 1561, 1562, 1563, 1564, 1565, 1566, 1567, 1568, 1569, 1570, 1571, 1572, 1573, 1574, 1575, 1576, 1577, 1578, 1579, 1580, 1581, 1582, 1583, 1584, 1585, 1586, 1587, 1588, 1589, 1590, 1591, 1592, 1593, 1594, 1595, 1596, 1597, 1598, 1599]) si_long.addTags('fixed_layer', [ 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, 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, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124]) si_long.addTags('thermostat_layer', [ 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 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652, 653, 654, 655, 656, 657, 658, 659, 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 814, 815, 816, 817, 818, 819, 820, 821, 822, 823, 824, 825, 826, 827, 828, 829, 830, 831, 832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 842, 843, 844, 845, 846, 847, 848, 849, 850, 851, 852, 853, 854, 855, 856, 857, 858, 859, 860, 861, 862, 863, 864, 865, 866, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 882, 883, 884, 885, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 896, 897, 898, 899, 900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911, 912, 913, 914, 915, 916, 917, 918, 919, 920, 921, 922, 923, 924, 925, 926, 927, 928, 929, 930, 931, 932, 933, 934, 935, 936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 965, 966, 967, 968, 969, 970, 971, 972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995, 996, 997, 998, 999, 1000, 1001, 1002, 1003, 1004, 1005, 1006, 1007, 1008, 1009, 1010, 1011, 1012, 1013, 1014, 1015, 1016, 1017, 1018, 1019, 1020, 1021, 1022, 1023, 1024, 1025, 1026, 1027, 1028, 1029, 1030, 1031, 1032, 1033, 1034, 1035, 1036, 1037, 1038, 1039, 1040, 1041, 1042, 1043, 1044, 1045, 1046, 1047, 1048, 1049]) si_long_name = "Si_long" # %% Set ForceFieldCalculator # %% ForceFieldCalculator potentialSet = Tersoff_Si_2005() calculator = TremoloXCalculator(parameters=potentialSet) # %% Set Calculator si_long.setCalculator(calculator) nlsave('Apply_Heat_Z_Dep_Example_results.hdf5', si_long) # %% MolecularDynamics method = NVTNoseHoover() constraints = [FixStrain(True, True, True), FixAtomConstraints('fixed_layer')] md_trajectory = MolecularDynamics( configuration=si_long, constraints=constraints, trajectory_filename='Apply_Heat_Z_Dep_Example_results.hdf5', steps=10000, log_interval=100, method=method, trajectory_object_id='md', ) last_image = md_trajectory.lastImage() nlsave('Apply_Heat_Z_Dep_Example_results.hdf5', last_image, object_id='md_1') # %% HookFunctions # Pre-step hook functions def custom_hook_function(step, time, configuration): call_interval = 1 if step % call_interval != 0: return # Define a custom script to be run as a hook function in MolecularDynamics. # This custom script supports atkpython syntax and can perform almost any # procedure. from ApplyHeatHook import apply_heat_hook pulse_period = 50000 # steps pulse_duration = 5 # steps heating_rate = 1 * eV / fs time_step = 1 * fs ramp = True configuration = apply_heat_hook( configuration, step, time_step, heating_rate, pulse_period, pulse_duration, ramp ) return pre_step_hooks = [ custom_hook_function, ] post_step_hooks = [] measurement_hooks = [] hook_functions = HookFunctions( pre_step_hooks=pre_step_hooks, post_step_hooks=post_step_hooks, measurement_hooks=measurement_hooks, ) nlsave('Apply_Heat_Z_Dep_Example_results.hdf5', hook_functions) # %% MolecularDynamics method = NVTBussiDonadioParrinello( initial_velocity=ConfigurationVelocities(), reservoir_temperature=[ ('thermostat_layer', 300.0 * Kelvin), ], ) md_measurement_hook = MDMeasurement(measurements=['temperature']) constraints = [FixStrain(True, True, True), FixAtomConstraints('fixed_layer')] md_trajectory_1 = MolecularDynamics( configuration=last_image, constraints=constraints, trajectory_filename='Apply_Heat_Z_Dep_Example_results.hdf5', steps=50000, log_interval=100, method=method, hook_functions=hook_functions, trajectory_object_id='md_2', measurement_hook=md_measurement_hook, ) last_image_1 = md_trajectory_1.lastImage() nlsave('Apply_Heat_Z_Dep_Example_results.hdf5', last_image_1, object_id='md_3')