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GUIDE / builder_device.py
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# -------------------------------------------------------------
# Left Electrode
# -------------------------------------------------------------
# Set up lattice
vector_a = [8.65127, 0.0, 0.0]*Angstrom
vector_b = [-4.32564, 7.49222, 0.0]*Angstrom
vector_c = [0.0, 0.0, 7.06373620597]*Angstrom
left_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
left_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold, Gold, Gold, Gold]
# Define coordinates
left_electrode_coordinates = [[ 0. , 0. , 1.177246838306],
 [ 2.883758230374, 0. , 1.177246838306],
 [ 5.767516460748, 0. , 1.177246838306],
 [-1.441879115187, 2.497407885876, 1.177246838306],
 [ 1.441879115187, 2.497407885876, 1.177246838306],
 [ 4.325637345561, 2.497407885876, 1.177246838306],
 [-2.883758230374, 4.994815771753, 1.177246838306],
 [-0. , 4.994815771753, 1.177246838306],
 [ 2.883758230374, 4.994815771753, 1.177246838306],
 [ 1.441879115187, 0.832469295292, 3.531825573629],
 [ 4.325637345561, 0.832469295292, 3.531825573629],
 [ 7.209395575935, 0.832469295292, 3.531825573629],
 [-0. , 3.329877181169, 3.531825573629],
 [ 2.883758230374, 3.329877181169, 3.531825573629],
 [ 5.767516460748, 3.329877181169, 3.531825573629],
 [-1.441879115187, 5.827285067045, 3.531825573629],
 [ 1.441879115187, 5.827285067045, 3.531825573629],
 [ 4.325637345561, 5.827285067045, 3.531825573629],
 [-0. , 1.664938590584, 5.886404308952],
 [ 2.883758230374, 1.664938590584, 5.886404308952],
 [ 5.767516460748, 1.664938590584, 5.886404308952],
 [-1.441879115187, 4.162346476461, 5.886404308952],
 [ 1.441879115187, 4.162346476461, 5.886404308952],
 [ 4.325637345561, 4.162346476461, 5.886404308952],
 [-2.883758230374, 6.659754362337, 5.886404308952],
 [-0. , 6.659754362337, 5.886404308952],
 [ 2.883758230374, 6.659754362337, 5.886404308952]]*Angstrom
# Set up configuration
left_electrode = BulkConfiguration(
 bravais_lattice=left_electrode_lattice,
 elements=left_electrode_elements,
 cartesian_coordinates=left_electrode_coordinates
 )
# -------------------------------------------------------------
# Right Electrode
# -------------------------------------------------------------
# Set up lattice
vector_a = [8.65127, 0.0, 0.0]*Angstrom
vector_b = [-4.32564, 7.49222, 0.0]*Angstrom
vector_c = [0.0, 0.0, 7.06373620597]*Angstrom
right_electrode_lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
right_electrode_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold, Gold, Gold, Gold]
# Define coordinates
right_electrode_coordinates = [[ 0. , 1.664938590584, 1.177331897016],
 [ 2.883758230374, 1.664938590584, 1.177331897016],
 [ 5.767516460748, 1.664938590584, 1.177331897016],
 [-1.441879115187, 4.162346476461, 1.177331897016],
 [ 1.441879115187, 4.162346476461, 1.177331897016],
 [ 4.325637345561, 4.162346476461, 1.177331897016],
 [-2.883758230374, 6.659754362337, 1.177331897016],
 [-0. , 6.659754362337, 1.177331897016],
 [ 2.883758230374, 6.659754362337, 1.177331897016],
 [ 1.441879115187, 0.832469295292, 3.531910632339],
 [ 4.325637345561, 0.832469295292, 3.531910632339],
 [ 7.209395575935, 0.832469295292, 3.531910632339],
 [-0. , 3.329877181169, 3.531910632339],
 [ 2.883758230374, 3.329877181169, 3.531910632339],
 [ 5.767516460748, 3.329877181169, 3.531910632339],
 [-1.441879115187, 5.827285067045, 3.531910632339],
 [ 1.441879115187, 5.827285067045, 3.531910632339],
 [ 4.325637345561, 5.827285067045, 3.531910632339],
 [ 0. , 0. , 5.886489367661],
 [ 2.883758230374, 0. , 5.886489367661],
 [ 5.767516460748, 0. , 5.886489367661],
 [-1.441879115187, 2.497407885876, 5.886489367661],
 [ 1.441879115187, 2.497407885876, 5.886489367661],
 [ 4.325637345561, 2.497407885876, 5.886489367661],
 [-2.883758230374, 4.994815771753, 5.886489367661],
 [-0. , 4.994815771753, 5.886489367661],
 [ 2.883758230374, 4.994815771753, 5.886489367661]]*Angstrom
# Set up configuration
right_electrode = BulkConfiguration(
 bravais_lattice=right_electrode_lattice,
 elements=right_electrode_elements,
 cartesian_coordinates=right_electrode_coordinates
 )
# -------------------------------------------------------------
# Central Region
# -------------------------------------------------------------
# Set up lattice
vector_a = [8.65127, 0.0, 0.0]*Angstrom
vector_b = [-4.32564, 7.49222, 0.0]*Angstrom
vector_c = [0.0, 0.0, 26.1842542284]*Angstrom
central_region_lattice = UnitCell(vector_a, vector_b, vector_c)
# Define elements
central_region_elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold, Gold, Sulfur, Carbon, Hydrogen, Hydrogen, Carbon,
 Carbon, Carbon, Carbon, Hydrogen, Hydrogen, Carbon, Sulfur, Gold,
 Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
 Gold, Gold]
# Define coordinates
central_region_coordinates = [[ 0. , 0. , 1.177246838306],
 [ 2.883758230374, 0. , 1.177246838306],
 [ 5.767516460748, 0. , 1.177246838306],
 [ -1.441879115187, 2.497407885876, 1.177246838306],
 [ 1.441879115187, 2.497407885876, 1.177246838306],
 [ 4.325637345561, 2.497407885876, 1.177246838306],
 [ -2.883758230374, 4.994815771753, 1.177246838306],
 [ -0. , 4.994815771753, 1.177246838306],
 [ 2.883758230374, 4.994815771753, 1.177246838306],
 [ 1.441879115187, 0.832469295292, 3.531825573629],
 [ 4.325637345561, 0.832469295292, 3.531825573629],
 [ 7.209395575935, 0.832469295292, 3.531825573629],
 [ -0. , 3.329877181169, 3.531825573629],
 [ 2.883758230374, 3.329877181169, 3.531825573629],
 [ 5.767516460748, 3.329877181169, 3.531825573629],
 [ -1.441879115187, 5.827285067045, 3.531825573629],
 [ 1.441879115187, 5.827285067045, 3.531825573629],
 [ 4.325637345561, 5.827285067045, 3.531825573629],
 [ -0. , 1.664938590584, 5.886404308952],
 [ 2.883758230374, 1.664938590584, 5.886404308952],
 [ 5.767516460748, 1.664938590584, 5.886404308952],
 [ -1.441879115187, 4.162346476461, 5.886404308952],
 [ 1.441879115187, 4.162346476461, 5.886404308952],
 [ 4.325637345561, 4.162346476461, 5.886404308952],
 [ -2.883758230374, 6.659754362337, 5.886404308952],
 [ -0. , 6.659754362337, 5.886404308952],
 [ 2.883758230374, 6.659754362337, 5.886404308952],
 [ 0. , 0. , 8.240983044274],
 [ 2.883758230374, 0. , 8.240983044274],
 [ 5.767516460748, 0. , 8.240983044274],
 [ -1.441879115187, 2.497407885876, 8.240983044274],
 [ 1.441879115187, 2.497407885876, 8.240983044274],
 [ 4.325637345561, 2.497407885876, 8.240983044274],
 [ -2.883758230374, 4.994815771753, 8.240983044274],
 [ -0. , 4.994815771753, 8.240983044274],
 [ 2.883758230374, 4.994815771753, 8.240983044274],
 [ -0. , 3.329877181169, 9.950983044274],
 [ 0.000167598274, 3.330000988149, 11.700983031869],
 [ 2.141113495536, 3.104457648599, 11.849212743505],
 [ -2.140744100558, 3.555570150149, 11.849240681067],
 [ 1.19830836185 , 3.203799621127, 12.396521536067],
 [ -1.19793542389 , 3.456256114907, 12.39656493323 ],
 [ 1.198435435614, 3.203780838187, 13.787656477468],
 [ -1.197806007547, 3.456195085679, 13.787696164708],
 [ 2.141237198973, 3.10441690481 , 14.335054536015],
 [ -2.140622838979, 3.555422091299, 14.335071137123],
 [ 0.000320116744, 3.329990265468, 14.483271217051],
 [ -0. , 3.329877181169, 16.233271184118],
 [ 0. , 0. , 17.943271184118],
 [ 2.883758230374, 0. , 17.943271184118],
 [ 5.767516460748, 0. , 17.943271184118],
 [ -1.441879115187, 2.497407885876, 17.943271184118],
 [ 1.441879115187, 2.497407885876, 17.943271184118],
 [ 4.325637345561, 2.497407885876, 17.943271184118],
 [ -2.883758230374, 4.994815771753, 17.943271184118],
 [ -0. , 4.994815771753, 17.943271184118],
 [ 2.883758230374, 4.994815771753, 17.943271184118],
 [ 0. , 1.664938590584, 20.297849919441],
 [ 2.883758230374, 1.664938590584, 20.297849919441],
 [ 5.767516460748, 1.664938590584, 20.297849919441],
 [ -1.441879115187, 4.162346476461, 20.297849919441],
 [ 1.441879115187, 4.162346476461, 20.297849919441],
 [ 4.325637345561, 4.162346476461, 20.297849919441],
 [ -2.883758230374, 6.659754362337, 20.297849919441],
 [ -0. , 6.659754362337, 20.297849919441],
 [ 2.883758230374, 6.659754362337, 20.297849919441],
 [ 1.441879115187, 0.832469295292, 22.652428654764],
 [ 4.325637345561, 0.832469295292, 22.652428654764],
 [ 7.209395575935, 0.832469295292, 22.652428654764],
 [ -0. , 3.329877181169, 22.652428654764],
 [ 2.883758230374, 3.329877181169, 22.652428654764],
 [ 5.767516460748, 3.329877181169, 22.652428654764],
 [ -1.441879115187, 5.827285067045, 22.652428654764],
 [ 1.441879115187, 5.827285067045, 22.652428654764],
 [ 4.325637345561, 5.827285067045, 22.652428654764],
 [ 0. , 0. , 25.007007390086],
 [ 2.883758230374, 0. , 25.007007390086],
 [ 5.767516460748, 0. , 25.007007390086],
 [ -1.441879115187, 2.497407885876, 25.007007390086],
 [ 1.441879115187, 2.497407885876, 25.007007390086],
 [ 4.325637345561, 2.497407885876, 25.007007390086],
 [ -2.883758230374, 4.994815771753, 25.007007390086],
 [ -0. , 4.994815771753, 25.007007390086],
 [ 2.883758230374, 4.994815771753, 25.007007390086]]*Angstrom
# Set up configuration
central_region = BulkConfiguration(
 bravais_lattice=central_region_lattice,
 elements=central_region_elements,
 cartesian_coordinates=central_region_coordinates
 )
device_configuration = DeviceConfiguration(
 central_region,
 [left_electrode, right_electrode]
 )