Hi
I have coordinates of the central region.Based on the central region I define the electrodes.The left electrode has no problem with it as the coordinates of my first 30 atoms make up the coordinates of my electrodes.But my right electrode shows some conflict.Here is my central region coordinates
cartesian_coordinates = numpy.array([[ 11.78410677, 8.39205339, 0. ],
[ 11.49084835, 9.77172579, 0. ],
[ 11.13628222, 10.38585234, 1.23050086],
[ 10.08808008, 11.32965779, 1.23050086],
[ 9.44025553, 11.61808786, 0. ],
[ 8.03748726, 11.76552475, 0. ],
[ 7.34385124, 11.61808786, 1.23050086],
[ 6.12232665, 10.91284031, 1.23050086],
[ 5.64782455, 10.38585234, 0. ],
[ 5.0741245 , 9.09730094, 0. ],
[ 5. , 8.39205339, 1.23050086],
[ 5.29325842, 7.01238098, 1.23050086],
[ 5.64782455, 6.39825443, 0. ],
[ 6.69602669, 5.45444898, 0. ],
[ 7.34385124, 5.16601891, 1.23050086],
[ 8.74661951, 5.01858202, 1.23050086],
[ 9.44025553, 5.16601891, 0. ],
[ 10.66178013, 5.87126646, 0. ],
[ 11.13628222, 6.39825443, 1.23050086],
[ 11.70998227, 7.68680583, 1.23050086],
[ 11.78410677, 8.39205339, 2.46100171],
[ 11.49084835, 9.77172579, 2.46100171],
[ 11.13628222, 10.38585234, 3.69150257],
[ 9.44025553, 11.61808786, 2.46100171],
[ 8.03748726, 11.76552475, 2.46100171],
[ 7.34385124, 11.61808786, 3.69150257],
[ 5.64782455, 10.38585234, 2.46100171],
[ 5.0741245 , 9.09730094, 2.46100171],
[ 5. , 8.39205339, 3.69150257],
[ 5.64782455, 6.39825443, 2.46100171],
[ 6.69602669, 5.45444898, 2.46100171],
[ 8.74661951, 5.01858202, 3.69150257],
[ 9.44025553, 5.16601891, 2.46100171],
[ 10.66178013, 5.87126646, 2.46100171],
[ 11.70998227, 7.68680583, 3.69150257],
[ 10.40042677, 8.88880475, 6.96812],
[ 11.30777677, 8.45569475, 5.191936],
[ 9.51582677, 7.98203475, 7.54074],
[ 11.29134677, 7.13432475, 5.48832],
[ 11.39062677, 6.83183475, 4.07066257],
[ 11.42394677, 9.53401475, 4.95221],
[ 7.72150677, 9.66815475, 7.51415],
[ 8.64598677, 10.61579475, 6.91579],
[ 8.14669677, 8.38042475, 7.81981],
[ 9.95586677, 10.23483475, 6.64888],
[ 10.58825677, 10.63352475, 5.40304],
[ 7.90947677, 11.41236475, 5.949],
[ 8.51457677, 11.79387475, 4.75709257],
[ 9.88366677, 11.39586475, 4.47817257],
[ 6.03219677, 7.44738475, 6.97001],
[ 5.58782677, 8.79318475, 6.65067],
[ 7.28322677, 7.24547475, 7.54167],
[ 6.41376677, 9.87907475, 6.9168],
[ 6.52994677, 10.95687475, 5.94947],
[ 4.84106677, 8.73603475, 5.40539],
[ 4.95214677, 9.76732475, 4.47995257],
[ 5.81524677, 10.90237475, 4.75816257],
[ 7.66702677, 5.29566475, 6.08772],
[ 6.35955677, 5.50656475, 5.4904],
[ 8.11872677, 6.14570475, 7.09069],
[ 5.56009677, 6.55864475, 5.92184],
[ 4.82410677, 7.35499475, 4.95483],
[ 6.45916677, 5.20353475, 4.07273257],
[ 5.75485677, 5.96538475, 3.14755257],
[ 4.91914677, 7.06490475, 3.59846257],
[ 10.36669677, 6.18659475, 6.08648],
[ 9.89460677, 5.29812475, 5.03836],
[ 9.49850677, 6.60097475, 7.09004],
[ 8.57462677, 4.86238475, 5.03899],
[ 7.82823677, 4.80552475, 3.79374257],
[ 10.52758677, 5.69679475, 3.79263257],
[ 6.44770677, 11.30104475, 3.51245257],
[ 9.98296677, 11.09329475, 3.06063257]])
cartesian_coordinates1 = numpy.array([[ 11.78410677, 8.39205339, 7.27452],
[ 11.49084835, 9.77172579, 7.27452],
[ 11.13628222, 10.38585234, 6.04402],
[ 10.08808008, 11.32965779, 6.04402],
[ 9.44025553, 11.61808786, 7.27452],
[ 8.03748726, 11.76552475, 7.27452],
[ 7.34385124, 11.61808786, 6.04402],
[ 6.12232665, 10.91284031, 6.04402],
[ 5.64782455, 10.38585234, 7.27452],
[ 5.0741245 , 9.09730094, 7.27452],
[ 5. , 8.39205339, 6.04402],
[ 5.29325842, 7.01238098, 6.04402],
[ 5.64782455, 6.39825443, 7.27452],
[ 6.69602669, 5.45444898, 7.27452],
[ 7.34385124, 5.16601891, 6.04402],
[ 8.74661951, 5.01858202, 6.04402],
[ 9.44025553, 5.16601891, 7.27452],
[ 10.66178013, 5.87126646, 7.27452],
[ 11.13628222, 6.39825443, 6.04402],
[ 11.70998227, 7.68680583, 6.04402],
[ 11.78410677, 8.39205339, 4.81351829],
[ 11.49084835, 9.77172579, 4.81351829],
[ 11.13628222, 10.38585234, 3.58301743],
[ 9.44025553, 11.61808786, 4.81351829],
[ 8.03748726, 11.76552475, 4.81351829],
[ 7.34385124, 11.61808786, 3.58301743],
[ 5.64782455, 10.38585234, 4.81351829],
[ 5.0741245 , 9.09730094, 4.81351829],
[ 5. , 8.39205339, 3.58301743],
[ 5.64782455, 6.39825443, 4.81351829],
[ 6.69602669, 5.45444898, 4.81351829],
[ 8.74661951, 5.01858202, 3.58301743],
[ 9.44025553, 5.16601891, 4.81351829],
[ 10.66178013, 5.87126646, 4.81351829],
[ 11.70998227, 7.68680583, 3.58301743],
[ 10.40042677, 8.88880475, 0.3064 ],
[ 11.30777677, 8.45569475, 2.082584 ],
[ 9.51582677, 7.98203475, -0.26622],
[ 11.29134677, 7.13432475, 1.7862 ],
[ 11.39062677, 6.83183475, 3.20385743],
[ 11.42394677, 9.53401475, 2.32231 ],
[ 7.72150677, 9.66815475, -0.2396368237342],
[ 8.64598677, 10.61579475, 0.35873 ],
[ 8.14669677, 8.38042475, -0.54529],
[ 9.95586677, 10.23483475, 0.62564 ],
[ 10.58825677, 10.63352475, 1.87148 ],
[ 7.90947677, 11.41236475, 1.32552 ],
[ 8.51457677, 11.79387475, 2.51742743],
[ 9.88366677, 11.39586475, 2.79634743],
[ 6.03219677, 7.44738475, 0.30451 ],
[ 5.58782677, 8.79318475, 0.62385 ],
[ 7.28322677, 7.24547475, -0.26715],
[ 6.41376677, 9.87907475, 0.35772 ],
[ 6.52994677, 10.95687475, 1.32505 ],
[ 4.84106677, 8.73603475, 1.86913 ],
[ 4.95214677, 9.76732475, 2.79456743],
[ 5.81524677, 10.90237475, 2.51635743],
[ 7.66702677, 5.29566475, 1.1868 ],
[ 6.35955677, 5.50656475, 1.78412 ],
[ 8.11872677, 6.14570475, 0.18383 ],
[ 5.56009677, 6.55864475, 1.35268 ],
[ 4.82410677, 7.35499475, 2.31969 ],
[ 6.45916677, 5.20353475, 3.20178743],
[ 5.75485677, 5.96538475, 4.12696743],
[ 4.91914677, 7.06490475, 3.67605743],
[ 10.36669677, 6.18659475, 1.18804 ],
[ 9.89460677, 5.29812475, 2.23616 ],
[ 9.49850677, 6.60097475, 0.18448 ],
[ 8.57462677, 4.86238475, 2.23553 ],
[ 7.82823677, 4.80552475, 3.48077743],
[ 10.52758677, 5.69679475, 3.48188743],
[ 6.44770677, 11.30104475, 3.76206743],
[ 9.98296677, 11.09329475, 4.21388743]])
cartesian_coordinates=cartesian_coordinates+numpy.array([0,0,0])
cartesian_coordinates1=cartesian_coordinates1+numpy.array([0,0,10.5651])
cartesiand=cartesian_coordinates1
cartesian_coordinates=cartesian_coordinates.tolist()
cartesian_coordinates1=cartesian_coordinates1.tolist()
elements = [Carbon,]*len(cartesian_coordinates+cartesian_coordinates1)
ccordinates=(cartesian_coordinates + cartesian_coordinates1)*Ang
my left electrode coordinates
left_electrode_coordinates = [[ 11.78410677, 8.39205339, 0. ],
[ 11.49084835, 9.77172579, 0. ],
[ 11.13628222, 10.38585234, 1.23050086],
[ 10.08808008, 11.32965779, 1.23050086],
[ 9.44025553, 11.61808786, 0. ],
[ 8.03748726, 11.76552475, 0. ],
[ 7.34385124, 11.61808786, 1.23050086],
[ 6.12232665, 10.91284031, 1.23050086],
[ 5.64782455, 10.38585234, 0. ],
[ 5.0741245 , 9.09730094, 0. ],
[ 5. , 8.39205339, 1.23050086],
[ 5.29325842, 7.01238098, 1.23050086],
[ 5.64782455, 6.39825443, 0. ],
[ 6.69602669, 5.45444898, 0. ],
[ 7.34385124, 5.16601891, 1.23050086],
[ 8.74661951, 5.01858202, 1.23050086],
[ 9.44025553, 5.16601891, 0. ],
[ 10.66178013, 5.87126646, 0. ],
[ 11.13628222, 6.39825443, 1.23050086],
[ 11.70998227, 7.68680583, 1.23050086],
[ 11.78410677, 8.39205339, 2.46100171],
[ 11.49084835, 9.77172579, 2.46100171],
[ 11.13628222, 10.38585234, 3.69150257],
[ 9.44025553, 11.61808786, 2.46100171],
[ 8.03748726, 11.76552475, 2.46100171],
[ 7.34385124, 11.61808786, 3.69150257],
[ 5.64782455, 10.38585234, 2.46100171],
[ 5.0741245 , 9.09730094, 2.46100171],
[ 5. , 8.39205339, 3.69150257],
[ 5.64782455, 6.39825443, 2.46100171]]*Angstrom
my right electrode
right_electrode_coordinates = numpy.array([[ 8.14669677, 8.38042475, -0.54529],
[ 9.95586677, 10.23483475, 0.62564 ],
[ 10.58825677, 10.63352475, 1.87148 ],
[ 7.90947677, 11.41236475, 1.32552 ],
[ 8.51457677, 11.79387475, 2.51742743],
[ 9.88366677, 11.39586475, 2.79634743],
[ 6.03219677, 7.44738475, 0.30451 ],
[ 5.58782677, 8.79318475, 0.62385 ],
[ 7.28322677, 7.24547475, -0.26715],
[ 6.41376677, 9.87907475, 0.35772 ],
[ 6.52994677, 10.95687475, 1.32505 ],
[ 4.84106677, 8.73603475, 1.86913 ],
[ 4.95214677, 9.76732475, 2.79456743],
[ 5.81524677, 10.90237475, 2.51635743],
[ 7.66702677, 5.29566475, 1.1868 ],
[ 6.35955677, 5.50656475, 1.78412 ],
[ 8.11872677, 6.14570475, 0.18383 ],
[ 5.56009677, 6.55864475, 1.35268 ],
[ 4.82410677, 7.35499475, 2.31969 ],
[ 6.45916677, 5.20353475, 3.20178743],
[ 5.75485677, 5.96538475, 4.12696743],
[ 4.91914677, 7.06490475, 3.67605743],
[ 10.36669677, 6.18659475, 1.18804 ],
[ 9.89460677, 5.29812475, 2.23616 ],
[ 9.49850677, 6.60097475, 0.18448 ],
[ 8.57462677, 4.86238475, 2.23553 ],
[ 7.82823677, 4.80552475, 3.48077743],
[ 10.52758677, 5.69679475, 3.48188743],
[ 6.44770677, 11.30104475, 3.76206743],
[ 9.98296677, 11.09329475, 4.21388743]])
right_electrode_coordinates=right_electrode_coordinates+numpy.array([0,0,10.5651])
right_electrode_coordinates=right_electrode_coordinates.tolist()
right_electrode_coordinates=right_electrode_coordinates*Angstrom
when I use the above coordinates the error comes out as
"The last 30 atoms of the central region must match the last 30 atoms of the right electrode region. Atom 116 of the central region was C at (8.14669677 Ang, 8.38042475 Ang, 10.01981 Ang), it should have been C at (8.14669677 Ang, 8.38042475 Ang, 25.39840829 Ang)"
But still my last 30 central region coordinates are same as my right electrode coordinates.
