Hello,
Can any one tell me what modifications I should make in the script to replace thiol(-S) anchoring group by dithiocrboxylate(-CS2) linking group in the given script (which is showing dithiol molecule sandwitched between two gold electrodes):
# Left electrode
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*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 = [[ 0.72107876, 1.24846289, 1.17728937],
[ 3.60483699, 1.24846289, 1.17728937],
[ 6.48859522, 1.24846289, 1.17728937],
[-0.72080035, 3.74587078, 1.17728937],
[ 5.04671611, 3.74587078, 1.17728937],
[ 2.16295788, 3.74587078, 1.17728937],
[ 3.60483699, 6.24327867, 1.17728937],
[-2.16267947, 6.24327867, 1.17728937],
[ 0.72107876, 6.24327867, 1.17728937],
[ 2.16295788, 2.08093219, 3.5318681 ],
[-0.72080035, 2.08093219, 3.5318681 ],
[ 5.04671611, 2.08093219, 3.5318681 ],
[-3.60455858, 7.07574796, 3.5318681 ],
[-2.16267947, 4.57834008, 3.5318681 ],
[ 2.16295788, 7.07574796, 3.5318681 ],
[ 3.60483699, 4.57834008, 3.5318681 ],
[ 0.72107876, 4.57834008, 3.5318681 ],
[-0.72080035, 7.07574796, 3.5318681 ],
[ 7.93047434, 0.4159936 , 5.88644684],
[ 0.72107876, 2.91340148, 5.88644684],
[ 2.16295788, 5.41080937, 5.88644684],
[-0.72080035, 5.41080937, 5.88644684],
[ 5.04671611, 5.41080937, 5.88644684],
[ 2.16295788, 0.4159936 , 5.88644684],
[ 3.60483699, 2.91340148, 5.88644684],
[ 5.04671611, 0.4159936 , 5.88644684],
[ 6.48859522, 2.91340148, 5.88644684]]*Angstrom
# Set up configuration
left_electrode = BulkConfiguration(
bravais_lattice=left_electrode_lattice,
elements=left_electrode_elements,
cartesian_coordinates=left_electrode_coordinates
)
# Right electrode
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*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 = [[ 0.72080035, 4.57882217, 1.17728937],
[-0.72107876, 7.07623006, 1.17728937],
[ 2.16267947, 7.07623006, 1.17728937],
[-2.16295788, 4.57882217, 1.17728937],
[-0.72107876, 2.08141429, 1.17728937],
[ 3.60455858, 4.57882217, 1.17728937],
[-3.60483699, 7.07623006, 1.17728937],
[ 5.0464377 , 2.08141429, 1.17728937],
[ 2.16267947, 2.08141429, 1.17728937],
[ 7.93019593, 0.4164757 , 3.5318681 ],
[ 3.60455858, 2.91388358, 3.5318681 ],
[ 6.48831681, 2.91388358, 3.5318681 ],
[ 2.16267947, 5.41129147, 3.5318681 ],
[ 5.0464377 , 0.4164757 , 3.5318681 ],
[ 5.0464377 , 5.41129147, 3.5318681 ],
[-0.72107876, 5.41129147, 3.5318681 ],
[ 0.72080035, 2.91388358, 3.5318681 ],
[ 2.16267947, 0.4164757 , 3.5318681 ],
[ 2.16267947, 3.74635288, 5.88644684],
[-2.16295788, 6.24376076, 5.88644684],
[ 0.72080035, 6.24376076, 5.88644684],
[-0.72107876, 3.74635288, 5.88644684],
[ 6.48831681, 1.24894499, 5.88644684],
[ 0.72080035, 1.24894499, 5.88644684],
[ 5.0464377 , 3.74635288, 5.88644684],
[ 3.60455858, 1.24894499, 5.88644684],
[ 3.60455858, 6.24376076, 5.88644684]]*Angstrom
# Set up configuration
right_electrode = BulkConfiguration(
bravais_lattice=right_electrode_lattice,
elements=right_electrode_elements,
cartesian_coordinates=right_electrode_coordinates
)
# Central region
vector_a = [8.65127469112, -6.75261456523e-33, 0.0]*Angstrom
vector_b = [-4.32563734556, 7.49222365763, 4.09015759516e-16]*Angstrom
vector_c = [0.0, 0.0, 21.4923367139]*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, 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]
# Define coordinates
central_region_coordinates = [[ 0.72107876, 1.24846289, 1.17728937],
[ 3.60483699, 1.24846289, 1.17728937],
[ 6.48859522, 1.24846289, 1.17728937],
[ -0.72080035, 3.74587078, 1.17728937],
[ 5.04671611, 3.74587078, 1.17728937],
[ 2.16295788, 3.74587078, 1.17728937],
[ 3.60483699, 6.24327867, 1.17728937],
[ -2.16267947, 6.24327867, 1.17728937],
[ 0.72107876, 6.24327867, 1.17728937],
[ 2.16295788, 2.08093219, 3.5318681 ],
[ -0.72080035, 2.08093219, 3.5318681 ],
[ 5.04671611, 2.08093219, 3.5318681 ],
[ -3.60455858, 7.07574796, 3.5318681 ],
[ -2.16267947, 4.57834008, 3.5318681 ],
[ 2.16295788, 7.07574796, 3.5318681 ],
[ 3.60483699, 4.57834008, 3.5318681 ],
[ 0.72107876, 4.57834008, 3.5318681 ],
[ -0.72080035, 7.07574796, 3.5318681 ],
[ 7.93047434, 0.4159936 , 5.88644684],
[ 0.72107876, 2.91340148, 5.88644684],
[ 2.16295788, 5.41080937, 5.88644684],
[ -0.72080035, 5.41080937, 5.88644684],
[ 5.04671611, 5.41080937, 5.88644684],
[ 2.16295788, 0.4159936 , 5.88644684],
[ 3.60483699, 2.91340148, 5.88644684],
[ 5.04671611, 0.4159936 , 5.88644684],
[ 6.48859522, 2.91340148, 5.88644684],
[ 2.16295788, 3.74587078, 7.59644684],
[ 2.16295788, 3.74587078, 9.34644649],
[ 1.07984884, 5.62136998, 9.49557904],
[ 3.24594854, 1.87057656, 9.49607409],
[ 1.55660877, 4.79581794, 10.04613074],
[ 2.76904869, 2.69637089, 10.04634658],
[ 1.55658866, 4.79585277, 11.44599014],
[ 2.76902857, 2.69640571, 11.44620598],
[ 1.0796888 , 5.6216471 , 11.99626262],
[ 3.24578851, 1.87085367, 11.99675768],
[ 2.16267947, 3.74635288, 12.14589023],
[ 2.16267947, 3.74635288, 13.89588988],
[ 0.72080035, 4.57882217, 15.60588988],
[ -0.72107876, 7.07623006, 15.60588988],
[ 2.16267947, 7.07623006, 15.60588988],
[ -2.16295788, 4.57882217, 15.60588988],
[ -0.72107876, 2.08141429, 15.60588988],
[ 3.60455858, 4.57882217, 15.60588988],
[ -3.60483699, 7.07623006, 15.60588988],
[ 5.0464377 , 2.08141429, 15.60588988],
[ 2.16267947, 2.08141429, 15.60588988],
[ 7.93019593, 0.4164757 , 17.96046861],
[ 3.60455858, 2.91388358, 17.96046861],
[ 6.48831681, 2.91388358, 17.96046861],
[ 2.16267947, 5.41129147, 17.96046861],
[ 5.0464377 , 0.4164757 , 17.96046861],
[ 5.0464377 , 5.41129147, 17.96046861],
[ -0.72107876, 5.41129147, 17.96046861],
[ 0.72080035, 2.91388358, 17.96046861],
[ 2.16267947, 0.4164757 , 17.96046861],
[ 2.16267947, 3.74635288, 20.31504735],
[ -2.16295788, 6.24376076, 20.31504735],
[ 0.72080035, 6.24376076, 20.31504735],
[ -0.72107876, 3.74635288, 20.31504735],
[ 6.48831681, 1.24894499, 20.31504735],
[ 0.72080035, 1.24894499, 20.31504735],
[ 5.0464377 , 3.74635288, 20.31504735],
[ 3.60455858, 1.24894499, 20.31504735],
[ 3.60455858, 6.24376076, 20.31504735]]*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]
)
