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Merge pull request #36 from bhourahine/surfaces
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Si100 tilted dimer NEGF surface
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@bhourahine
bhourahine committed Jun 7, 2022
2 parents 20fa6a0 + bd7902a commit 354f95b
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140 changes: 140 additions & 0 deletions docs/_archives/recipes/boundaryconditions/surfaces/Si100/Si100_slab.hsd
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Geometry = GenFormat {
# 2x1 Si (100) surface slab
96 S
Si
1 1 0.1436314505E+01 0.7721161954E+01 0.3152529009E+02
2 1 0.1436314501E+01 0.3860580980E+01 0.3152529008E+02
3 1 -0.8433493145E+00 0.7721161833E+01 0.3086532941E+02
4 1 -0.8433493165E+00 0.3860580865E+01 0.3086532940E+02
5 1 0.1826707360E+01 0.5790871476E+01 0.3011449699E+02
6 1 0.1826707359E+01 0.9651452446E+01 0.3011449699E+02
7 1 -0.1865461371E+01 0.5790871321E+01 0.3003687950E+02
8 1 -0.1865461380E+01 0.9651452291E+01 0.3003687950E+02
9 1 -0.3903088044E+01 0.5790871513E+01 0.2878226154E+02
10 1 -0.3903088040E+01 0.9651452486E+01 0.2878226154E+02
11 1 0.3659555512E-01 0.9651452624E+01 0.2855097092E+02
12 1 0.3659555324E-01 0.5790871654E+01 0.2855097092E+02
13 1 -0.3862315933E+01 0.3860581030E+01 0.2738160408E+02
14 1 -0.3862315934E+01 0.7721162002E+01 0.2738160408E+02
15 1 -0.7722844854E-02 0.3860581039E+01 0.2720322729E+02
16 1 -0.7722845712E-02 0.7721162014E+01 0.2720322728E+02
17 1 0.1969086931E+01 0.3860581155E+01 0.2593009425E+02
18 1 0.1969086932E+01 0.7721162128E+01 0.2593009425E+02
19 1 -0.1978861438E+01 0.3860581161E+01 0.2592525725E+02
20 1 -0.1978861439E+01 0.7721162133E+01 0.2592525725E+02
21 1 0.1951966836E+01 0.5790871541E+01 0.2456439506E+02
22 1 0.1951966834E+01 0.9651452517E+01 0.2456439506E+02
23 1 -0.1955355459E+01 0.5790871534E+01 0.2456125776E+02
24 1 -0.1955355461E+01 0.9651452510E+01 0.2456125776E+02
25 1 -0.6490551224E-03 0.5790871684E+01 0.2322037260E+02
26 1 -0.6490530300E-03 0.9651452657E+01 0.2322037260E+02
27 1 -0.3863177407E+01 0.5790871713E+01 0.2317670825E+02
28 1 -0.3863177405E+01 0.9651452687E+01 0.2317670825E+02
29 1 0.6561823872E-04 0.3860581037E+01 0.2184958561E+02
30 1 0.6561836540E-04 0.7721162009E+01 0.2184958561E+02
31 1 -0.3861643171E+01 0.3860581024E+01 0.2181953111E+02
32 1 -0.3861643171E+01 0.7721161996E+01 0.2181953111E+02
33 1 -0.1923346569E+01 0.3860581245E+01 0.2047112421E+02
34 1 -0.1923346569E+01 0.7721162218E+01 0.2047112421E+02
35 1 0.1922433180E+01 0.3860581253E+01 0.2047016538E+02
36 1 0.1922433180E+01 0.7721162225E+01 0.2047016538E+02
37 1 -0.1926378505E+01 0.5790871455E+01 0.1910680358E+02
38 1 -0.1926378505E+01 0.9651452428E+01 0.1910680358E+02
39 1 0.1926266392E+01 0.5790871448E+01 0.1910658064E+02
40 1 0.1926266392E+01 0.9651452421E+01 0.1910658064E+02
41 1 -0.3860874406E+01 0.5790871713E+01 0.1774643182E+02
42 1 -0.3860874407E+01 0.9651452686E+01 0.1774643182E+02
43 1 0.2076942562E-03 0.5790871718E+01 0.1773894183E+02
44 1 0.2076937993E-03 0.9651452691E+01 0.1773894183E+02
45 1 -0.3861537035E+01 0.3860580928E+01 0.1638132278E+02
46 1 -0.3861537035E+01 0.7721161901E+01 0.1638132278E+02
47 1 0.1023484509E-02 0.3860580925E+01 0.1637598788E+02
48 1 0.1023484455E-02 0.7721161898E+01 0.1637598788E+02
49 1 -0.1931686958E+01 0.3860581158E+01 0.1501686898E+02
50 1 -0.1931686958E+01 0.7721162131E+01 0.1501686898E+02
51 1 0.1931756445E+01 0.3860581155E+01 0.1501230420E+02
52 1 0.1931756445E+01 0.7721162128E+01 0.1501230420E+02
53 1 -0.1931405862E+01 0.5790871414E+01 0.1365406302E+02
54 1 -0.1931405862E+01 0.9651452387E+01 0.1365406302E+02
55 1 0.1931317338E+01 0.5790871417E+01 0.1364704683E+02
56 1 0.1931317338E+01 0.9651452390E+01 0.1364704683E+02
57 1 -0.3914987540E-02 0.5790871564E+01 0.1228788973E+02
58 1 -0.3914987522E-02 0.9651452537E+01 0.1228788973E+02
59 1 -0.3856771930E+01 0.5790871564E+01 0.1228520978E+02
60 1 -0.3856771930E+01 0.9651452537E+01 0.1228520978E+02
61 1 -0.7793233570E-02 0.3860580947E+01 0.1092392135E+02
62 1 -0.7793233562E-02 0.7721161920E+01 0.1092392135E+02
63 1 -0.3853697224E+01 0.3860580947E+01 0.1092127495E+02
64 1 -0.3853697224E+01 0.7721161921E+01 0.1092127495E+02
65 1 0.1928815091E+01 0.3860581022E+01 0.9573661002E+01
66 1 0.1928815091E+01 0.7721161995E+01 0.9573661002E+01
67 1 -0.1929803726E+01 0.7721161993E+01 0.9543711870E+01
68 1 -0.1929803726E+01 0.3860581020E+01 0.9543711869E+01
69 1 0.1927464554E+01 0.5790871448E+01 0.8216505026E+01
70 1 0.1927464554E+01 0.9651452420E+01 0.8216505026E+01
71 1 -0.1930698327E+01 0.5790871450E+01 0.8172910165E+01
72 1 -0.1930698327E+01 0.9651452422E+01 0.8172910165E+01
73 1 -0.3885616512E+01 0.5790871478E+01 0.6832204921E+01
74 1 -0.3885616512E+01 0.9651452451E+01 0.6832204921E+01
75 1 0.2165786407E-01 0.5790871478E+01 0.6828622279E+01
76 1 0.2165786406E-01 0.9651452451E+01 0.6828622279E+01
77 1 -0.3909094618E+01 0.3860580969E+01 0.5468091287E+01
78 1 -0.3909094618E+01 0.7721161942E+01 0.5468091287E+01
79 1 0.3877161955E-01 0.3860580970E+01 0.5462959994E+01
80 1 0.3877161958E-01 0.7721161943E+01 0.5462959993E+01
81 1 -0.1938080446E+01 0.3860580978E+01 0.4189852683E+01
82 1 -0.1938080446E+01 0.7721161951E+01 0.4189852683E+01
83 1 0.1928620889E+01 0.3860580978E+01 0.4011643231E+01
84 1 0.1928620889E+01 0.7721161952E+01 0.4011643231E+01
85 1 -0.1893690090E+01 0.5790871460E+01 0.2842212694E+01
86 1 -0.1893690090E+01 0.9651452433E+01 0.2842212694E+01
87 1 0.1887872876E+01 0.5790871459E+01 0.2610822405E+01
88 1 0.1887872876E+01 0.9651452432E+01 0.2610822405E+01
89 1 -0.3795849463E+01 0.5790871460E+01 0.1356212853E+01
90 1 -0.3795849463E+01 0.9651452433E+01 0.1356212853E+01
91 1 -0.1035843276E+00 0.5790871460E+01 0.1278651205E+01
92 1 -0.1035843276E+00 0.9651452433E+01 0.1278651205E+01
93 1 -0.2773526523E+01 0.3860580971E+01 0.5276939096E+00
94 1 -0.2773526523E+01 0.7721161944E+01 0.5276939095E+00
95 1 -0.4939387955E+00 0.3860580973E+01 -0.1321721785E+00
96 1 -0.4939387955E+00 0.7721161946E+01 -0.1321721785E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.7721161946E+01 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.7721161946E+01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.1000000000E+04
}

Driver = LBFGS {
# Only the top and bottom layers of the slab relax
MovedAtoms = 1:16 81:96
AppendGeometries = Yes
}

Hamiltonian = DFTB {
SCC = Yes
MaxAngularMomentum {
Si = "p"
}
Filling = Fermi {
Temperature [K] = 500
}
SlaterKosterFiles = Type2FileNames {
Prefix = "slakos/origin/pbc-0-3/"
Separator = "-"
Suffix = ".skf"
}
KPointsAndWeights = SupercellFolding {
6 0 0
0 6 0
0 0 1
0.5 0.5 0.5
}
}

ParserOptions {
ParserVersion = 11
}

Parallel {
Groups = 4
}
118 changes: 118 additions & 0 deletions docs/_archives/recipes/boundaryconditions/surfaces/Si100/Si_2x1.gen
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@@ -0,0 +1,118 @@
112 S
Si
1 1 0.3699660218E+02 0.5303059988E+01 0.3860556141E+01
2 1 0.3699660199E+02 0.5303059924E+01 0.2890238761E-07
3 1 0.3634719225E+02 0.3008352276E+01 0.3860556162E+01
4 1 0.3634719208E+02 0.3008352293E+01 0.8446022230E-08
5 1 0.3558736918E+02 0.5704492034E+01 0.5790834196E+01
6 1 0.3558736908E+02 0.5704492036E+01 0.1930278150E+01
7 1 0.3550794256E+02 0.1988795046E+01 0.5790834223E+01
8 1 0.3550794243E+02 0.1988795088E+01 0.1930278123E+01
9 1 0.3404507852E+02 0.3902436234E+01 0.5790834250E+01
10 1 0.3404507839E+02 0.3902436256E+01 0.1930278096E+01
11 1 0.3422900026E+02 -0.3884486792E-01 0.5790834277E+01
12 1 0.3422900016E+02 -0.3884485797E-01 0.1930278069E+01
13 1 0.3270518749E+02 0.3858696042E+01 0.3860556222E+01
14 1 0.3270518754E+02 0.3858696046E+01 -0.5339082181E-07
15 1 0.3281683428E+02 0.1555220106E-02 0.3860556215E+01
16 1 0.3281683429E+02 0.1555226054E-02 -0.4491802506E-07
17 1 0.3139298268E+02 0.5790834284E+01 0.3860556170E+01
18 1 0.3139298268E+02 0.5790834284E+01 0.0000000000E+00
19 1 0.3139298268E+02 0.1930278095E+01 0.3860556170E+01
20 1 0.3139298268E+02 0.1930278095E+01 0.0000000000E+00
21 1 0.3002807038E+02 0.5790834284E+01 0.5790834260E+01
22 1 0.3002807038E+02 0.5790834284E+01 0.1930278080E+01
23 1 0.3002807038E+02 0.1930278095E+01 0.5790834260E+01
24 1 0.3002807038E+02 0.1930278095E+01 0.1930278080E+01
25 1 0.2866315812E+02 0.3860580973E+01 0.5790834260E+01
26 1 0.2866315812E+02 0.3860580973E+01 0.1930278080E+01
27 1 0.2866315812E+02 0.0000000000E+00 0.5790834260E+01
28 1 0.2866315812E+02 0.0000000000E+00 0.1930278080E+01
29 1 0.2729824581E+02 0.3860580973E+01 0.3860556170E+01
30 1 0.2729824581E+02 0.3860580973E+01 0.0000000000E+00
31 1 0.2729824581E+02 0.0000000000E+00 0.3860556170E+01
32 1 0.2729824581E+02 0.0000000000E+00 0.0000000000E+00
33 1 0.2593333352E+02 0.5790834284E+01 0.3860556170E+01
34 1 0.2593333352E+02 0.5790834284E+01 0.0000000000E+00
35 1 0.2593333352E+02 0.1930278095E+01 0.3860556170E+01
36 1 0.2593333352E+02 0.1930278095E+01 0.0000000000E+00
37 1 0.2456842122E+02 0.5790834284E+01 0.5790834260E+01
38 1 0.2456842122E+02 0.5790834284E+01 0.1930278080E+01
39 1 0.2456842122E+02 0.1930278095E+01 0.5790834260E+01
40 1 0.2456842122E+02 0.1930278095E+01 0.1930278080E+01
41 1 0.2320350895E+02 0.3860580973E+01 0.5790834260E+01
42 1 0.2320350895E+02 0.3860580973E+01 0.1930278080E+01
43 1 0.2320350895E+02 0.0000000000E+00 0.5790834260E+01
44 1 0.2320350895E+02 0.0000000000E+00 0.1930278080E+01
45 1 0.2183859665E+02 0.3860580973E+01 0.3860556170E+01
46 1 0.2183859665E+02 0.3860580973E+01 0.0000000000E+00
47 1 0.2183859665E+02 0.0000000000E+00 0.3860556170E+01
48 1 0.2183859665E+02 0.0000000000E+00 0.0000000000E+00
49 1 0.2047368436E+02 0.5790834284E+01 0.3860556170E+01
50 1 0.2047368436E+02 0.5790834284E+01 0.0000000000E+00
51 1 0.2047368436E+02 0.1930278095E+01 0.3860556170E+01
52 1 0.2047368436E+02 0.1930278095E+01 0.0000000000E+00
53 1 0.1910877206E+02 0.5790834284E+01 0.5790834260E+01
54 1 0.1910877206E+02 0.5790834284E+01 0.1930278080E+01
55 1 0.1910877206E+02 0.1930278095E+01 0.5790834260E+01
56 1 0.1910877206E+02 0.1930278095E+01 0.1930278080E+01
57 1 0.1774385979E+02 0.3860580973E+01 0.5790834260E+01
58 1 0.1774385979E+02 0.3860580973E+01 0.1930278080E+01
59 1 0.1774385979E+02 0.0000000000E+00 0.5790834260E+01
60 1 0.1774385979E+02 0.0000000000E+00 0.1930278080E+01
61 1 0.1637894749E+02 0.3860580973E+01 0.3860556170E+01
62 1 0.1637894749E+02 0.3860580973E+01 0.0000000000E+00
63 1 0.1637894749E+02 0.0000000000E+00 0.3860556170E+01
64 1 0.1637894749E+02 0.0000000000E+00 0.0000000000E+00
65 1 0.1501403520E+02 0.5790834284E+01 0.3860556170E+01
66 1 0.1501403520E+02 0.5790834284E+01 0.0000000000E+00
67 1 0.1501403520E+02 0.1930278095E+01 0.3860556170E+01
68 1 0.1501403520E+02 0.1930278095E+01 0.0000000000E+00
69 1 0.1364912290E+02 0.5790834284E+01 0.5790834260E+01
70 1 0.1364912290E+02 0.5790834284E+01 0.1930278080E+01
71 1 0.1364912290E+02 0.1930278095E+01 0.5790834260E+01
72 1 0.1364912290E+02 0.1930278095E+01 0.1930278080E+01
73 1 0.1228421063E+02 0.3860580973E+01 0.5790834260E+01
74 1 0.1228421063E+02 0.3860580973E+01 0.1930278080E+01
75 1 0.1228421063E+02 0.0000000000E+00 0.5790834260E+01
76 1 0.1228421063E+02 0.0000000000E+00 0.1930278080E+01
77 1 0.1091929833E+02 0.3860580973E+01 0.3860556170E+01
78 1 0.1091929833E+02 0.3860580973E+01 0.0000000000E+00
79 1 0.1091929833E+02 0.0000000000E+00 0.3860556170E+01
80 1 0.1091929833E+02 0.0000000000E+00 0.0000000000E+00
81 1 0.9554386033E+01 0.5790834284E+01 0.3860556170E+01
82 1 0.9554386033E+01 0.5790834284E+01 0.0000000000E+00
83 1 0.9554386033E+01 0.1930278095E+01 0.3860556170E+01
84 1 0.9554386033E+01 0.1930278095E+01 0.0000000000E+00
85 1 0.8189473733E+01 0.5790834284E+01 0.5790834260E+01
86 1 0.8189473733E+01 0.5790834284E+01 0.1930278080E+01
87 1 0.8189473733E+01 0.1930278095E+01 0.5790834260E+01
88 1 0.8189473733E+01 0.1930278095E+01 0.1930278080E+01
89 1 0.6824561463E+01 0.3860580973E+01 0.5790834260E+01
90 1 0.6824561463E+01 0.3860580973E+01 0.1930278080E+01
91 1 0.6824561463E+01 0.0000000000E+00 0.5790834260E+01
92 1 0.6824561463E+01 0.0000000000E+00 0.1930278080E+01
93 1 0.5459649163E+01 0.3860580973E+01 0.3860556170E+01
94 1 0.5459649163E+01 0.3860580973E+01 0.0000000000E+00
95 1 0.5459649163E+01 0.0000000000E+00 0.3860556170E+01
96 1 0.5459649163E+01 0.0000000000E+00 0.0000000000E+00
97 1 0.4094736870E+01 0.5790834284E+01 0.3860556170E+01
98 1 0.4094736870E+01 0.5790834284E+01 0.0000000000E+00
99 1 0.4094736870E+01 0.1930278095E+01 0.3860556170E+01
100 1 0.4094736870E+01 0.1930278095E+01 0.0000000000E+00
101 1 0.2729824570E+01 0.5790834284E+01 0.5790834260E+01
102 1 0.2729824570E+01 0.5790834284E+01 0.1930278080E+01
103 1 0.2729824570E+01 0.1930278095E+01 0.5790834260E+01
104 1 0.2729824570E+01 0.1930278095E+01 0.1930278080E+01
105 1 0.1364912300E+01 0.3860580973E+01 0.5790834260E+01
106 1 0.1364912300E+01 0.3860580973E+01 0.1930278080E+01
107 1 0.1364912300E+01 0.0000000000E+00 0.5790834260E+01
108 1 0.1364912300E+01 0.0000000000E+00 0.1930278080E+01
109 1 0.0000000000E+00 0.3860580973E+01 0.3860556170E+01
110 1 0.0000000000E+00 0.3860580973E+01 0.0000000000E+00
111 1 0.0000000000E+00 0.0000000000E+00 0.3860556170E+01
112 1 0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.0000000000E+00
0.0000000000E+00 0.7721112379E+01 0.0000000000E+00
0.0000000000E+00 0.0000000000E+00 0.7721112352E+01
0.1000000000E+04 0.0000000000E+00 0.0000000000E+00
45 changes: 45 additions & 0 deletions docs/_archives/recipes/boundaryconditions/surfaces/Si100/bulk.hsd
View file
@@ -0,0 +1,45 @@
Geometry = GenFormat {
<<< Si_2x1.gen
}

Transport{
Device{
AtomRange = 1 48
}
Contact{
Id = "bulk"
AtomRange = 49 112
}
Task= contactHamiltonian{
contactId = "bulk"
}
}

Hamiltonian = DFTB {
SCC = Yes
MaxAngularMomentum {
Si = "p"
}
Filling = Fermi {
Temperature [K] = 500
}
SlaterKosterFiles = Type2FileNames {
Prefix = "slakos/origin/pbc-0-3/"
Separator = "-"
Suffix = ".skf"
}
KPointsAndWeights = SupercellFolding {
10 0 0
0 10 0
0 0 10
0.5 0.5 0.5
}
}

ParserOptions {
ParserVersion = 11
}

Parallel {
Groups = 4
}
56 changes: 56 additions & 0 deletions docs/_archives/recipes/boundaryconditions/surfaces/Si100/surface.hsd
View file
@@ -0,0 +1,56 @@
Geometry = GenFormat {
<<< Si_2x1.gen
}

Driver = LBFGS {
# top layer of the surface only
MovedAtoms = 1:16
AppendGeometries = Yes
}

Transport{
Device{
AtomRange = 1 48
}
Contact{
Id = "bulk"
AtomRange = 49 112
}
}

Hamiltonian = DFTB {
SCC = Yes
MaxAngularMomentum {
Si = "p"
}
Filling = Fermi {
Temperature [K] = 500
}
SlaterKosterFiles = Type2FileNames {
Prefix = "slakos/origin/pbc-0-3/"
Separator = "-"
Suffix = ".skf"
}
KPointsAndWeights = SupercellFolding {
# x and y sampling too low for speed, use ~10 to be converged:
4 0 0
0 4 0
0 0 1
0.5 0.5 0.0
}
Solver = GreensFunction{
Verbosity = 1
}
Electrostatics = Poisson {
MinimalGrid [Angstrom] = 0.3 0.3 0.3
PoissonThickness [AA] = 50
}
}

ParserOptions {
ParserVersion = 11
}

Parallel {
Groups = 6
}
1 change: 1 addition & 0 deletions docs/boundaryconditions/index.rst
View file
Expand Up @@ -11,3 +11,4 @@ free space or periodic supercells.
:maxdepth: 1

helical.rst
surfaces.rst

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