在OpenMX当中有一个NEGF范例，它得出的transmission图是沿0轴对称的，事实上却是应该是这样的。而我做出的却并不是。所以需要在原来的文件上修改，以逐步达成需要。
先来看左电极：
#
# File Name
#
System.CurrrentDirectory ./ # default=./
System.Name lead-l-8zgnr
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)
#
# Definition of Atomic Species
#
Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
H H5.0-s2 H_CA13
Definition.of.Atomic.Species>
NEGF.output_hks true
NEGF.filename.hks lead-l-8zgnr.hks
#
# Atoms
#
Atoms.Number 36
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0.0000005 0.0361626 0.0012037 2.5000000 1.5000000
2 C 0.0000005 0.7140385 1.2211879 2.5000000 1.5000000
3 C 0.0000004 2.1457201 1.2213117 2.5000000 1.5000000
4 C 0.0000001 2.8501725 0.0013209 2.5000000 1.5000000
5 C -0.0000001 4.2700744 0.0012023 2.5000000 1.5000000
6 C -0.0000002 4.9766306 1.2212146 2.5000000 1.5000000
7 C 0.0000001 6.3942050 1.2213979 2.5000000 1.5000000
8 C 0.0000001 7.1014018 0.0014044 2.5000000 1.5000000
9 C -0.0000001 8.5186603 0.0014042 2.5000000 1.5000000
10 C 0.0000001 9.2258519 1.2213977 2.5000000 1.5000000
11 C 0.0000004 10.6434033 1.2212143 2.5000000 1.5000000
12 C 0.0000003 11.3499296 0.0012020 2.5000000 1.5000000
13 C -0.0000002 12.7697977 0.0013211 2.5000000 1.5000000
14 C -0.0000004 13.4742418 1.2213119 2.5000000 1.5000000
15 C -0.0000004 14.9059644 1.2211875 2.5000000 1.5000000
16 C -0.0000004 15.5838921 0.0012032 2.5000000 1.5000000
17 H 0.0000003 -1.0818549 0.0012134 0.5000000 0.5000000
18 H -0.0000005 16.7019089 0.0012129 0.5000000 0.5000000
19 C 0.0000005 0.0361626 2.4412037 2.5000000 1.5000000
20 C 0.0000005 0.7140385 3.6611879 2.5000000 1.5000000
21 C 0.0000004 2.1457201 3.6613117 2.5000000 1.5000000
22 C 0.0000001 2.8501725 2.4413209 2.5000000 1.5000000
23 C -0.0000001 4.2700744 2.4412023 2.5000000 1.5000000
24 C -0.0000002 4.9766306 3.6612146 2.5000000 1.5000000
25 C 0.0000001 6.3942050 3.6613979 2.5000000 1.5000000
26 C 0.0000001 7.1014018 2.4414044 2.5000000 1.5000000
27 C -0.0000001 8.5186603 2.4414042 2.5000000 1.5000000
28 C 0.0000001 9.2258519 3.6613977 2.5000000 1.5000000
29 C 0.0000004 10.6434033 3.6612143 2.5000000 1.5000000
30 C 0.0000003 11.3499296 2.4412020 2.5000000 1.5000000
31 C -0.0000002 12.7697977 2.4413211 2.5000000 1.5000000
32 C -0.0000004 13.4742418 3.6613119 2.5000000 1.5000000
33 C -0.0000004 14.9059644 3.6611875 2.5000000 1.5000000
34 C -0.0000004 15.5838921 2.4412032 2.5000000 1.5000000
35 H 0.0000003 -1.0818549 2.4412134 0.5000000 0.5000000
36 H -0.0000005 16.7019089 2.4412129 0.5000000 0.5000000
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 1000 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 201 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 10.0 # default=1
scf.Init.Mixing.Weight 0.001 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.105 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)
#
# MD or Geometry Optimization
#
MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 18 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 2000 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)
#
# Band dispersion
#
Band.dispersion off # on|off, default=off
<Band.KPath.UnitCell
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Band.KPath.UnitCell>
Band.Nkpath 1
<Band.kpath
601 0.0 0.0 0.0 0.5 0.0 0.0 G X
Band.kpath>
#
# DOS and PDOS
#
Dos.fileout off # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 601 1 1 # default = Kgrid1 Kgrid2 Kgrid3
DosGauss.fileout off
DosGauss.Num.Mesh 4000
DosGauss.Width 0.01
MO.fileout off # on|off
num.HOMOs 1 # default=1
num.LUMOs 1 # default=1
MO.Nkpoint 1 # default=1
<MO.kpoint
0.0 0.0 0.0
MO.kpoint>
中间标红的一块区域为Central区域，左边有四个氢，右边也有四个氢。
由这个图出发，可以将现有的左右电极都化作中心，将现有的左右电极都复制分别向外侧移动，形成新的研究结构。为此需要确定坐标的轴与原子的实际关系。
通过简单分析，发现第一列全是0，这代表z轴。中心部分的第三列全是4.8812037，意味着第三列是x轴。剩下的第二列是y轴。
一、中心区域重构
经过一番研究。发现如果可以重构原子位置，进行一下剪接，可以避免原子数目急剧扩大的风险。
#
# File Name
#
System.CurrrentDirectory ./ # default=./
System.Name negf-8zgnr-0.3
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)
NEGF.filename.hks.l lead-l-8zgnr.hks
NEGF.filename.hks.r lead-r-8zgnr.hks
NEGF.SCF.Iter.Band 20
NEGF.Num.Poles 100 # defalut=150
NEGF.scf.Kgrid 1 1 # defalut=1 1
NEGF.bias.voltage -0.3 # default=0.0 (eV)
NEGF.bias.neq.im.energy 0.01 # default=0.01 (eV)
NEGF.bias.neq.energy.step 0.02 # default=0.02 (eV)
Dos.fileout off # on|off, default=off
NEGF.Dos.energyrange -20.0 20.0 1.0e-4 #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div 4000 # default=200
NEGF.Dos.Kgrid 1 1 # default=1 1
#
# Transmission & Eigen Channel Analysis
#
NEGF.tran.Analysis on # default on
NEGF.tran.energydiv 800 # default=200
NEGF.tran.energyrange -4 4 0.001 # default=-10.0 10.0 5.0e-3 (eV)
NEGF.tran.Kgrid 1 1 # default= 1 1
NEGF.tran.CurrentDensity on # default on
NEGF.tran.Channel on # default on
NEGF.Channel.Nkpoint 1 # default 1
<NEGF.Channel.kpoint
0.0 0.0
NEGF.Channel.kpoint>
# default 0.0 0.0
NEGF.Channel.Nenergy 1 # default 1
<NEGF.Channel.energy
0.0
NEGF.Channel.energy>
# default 0.0
NEGF.Channel.Num 5 # defualt=5(for collinear), 10(for Non-collinear)
#
# Definition of Atomic Species
#
Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
H H5.0-s2 H_CA13
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
Atoms.Number 10
<Atoms.SpeciesAndCoordinates
1 C 0.0000005 0.0361626 4.8812037 2.1000000 1.9000000
2 C 0.0000001 2.8501725 4.8813209 2.1000000 1.9000000
3 C -0.0000001 4.2700744 4.8812023 2.1000000 1.9000000
4 C 0.0000001 7.1014018 4.8814044 2.1000000 1.9000000
5 C -0.0000001 8.5186603 4.8814042 2.1000000 1.9000000
6 C 0.0000003 11.3499296 4.8812020 2.1000000 1.9000000
7 C -0.0000002 12.7697977 4.8813211 2.1000000 1.9000000
8 C -0.0000004 15.5838921 4.8812032 2.1000000 1.9000000
9 H 0.0000003 -1.0818549 4.8812134 0.5000000 0.5000000
10 H -0.0000005 16.7019089 4.8812129 0.5000000 0.5000000
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
#<Atoms.UnitVectors
# 0.000 0.000 4.88
# 10.000 0.000 0.000
# 0.000 24.000 0.000
#Atoms.UnitVectors>
#
# Lead-Left
#
LeftLeadAtoms.Number 36
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 0.0000005 0.0361626 0.0012037 2.1000000 1.9000000
2 C 0.0000005 0.7140385 1.2211879 2.1000000 1.9000000
3 C 0.0000004 2.1457201 1.2213117 2.1000000 1.9000000
4 C 0.0000001 2.8501725 0.0013209 2.1000000 1.9000000
5 C -0.0000001 4.2700744 0.0012023 2.1000000 1.9000000
6 C -0.0000002 4.9766306 1.2212146 2.1000000 1.9000000
7 C 0.0000001 6.3942050 1.2213979 2.1000000 1.9000000
8 C 0.0000001 7.1014018 0.0014044 2.1000000 1.9000000
9 C -0.0000001 8.5186603 0.0014042 2.1000000 1.9000000
10 C 0.0000001 9.2258519 1.2213977 2.1000000 1.9000000
11 C 0.0000004 10.6434033 1.2212143 2.1000000 1.9000000
12 C 0.0000003 11.3499296 0.0012020 2.1000000 1.9000000
13 C -0.0000002 12.7697977 0.0013211 2.1000000 1.9000000
14 C -0.0000004 13.4742418 1.2213119 2.1000000 1.9000000
15 C -0.0000004 14.9059644 1.2211875 2.1000000 1.9000000
16 C -0.0000004 15.5838921 0.0012032 2.1000000 1.9000000
17 H 0.0000003 -1.0818549 0.0012134 0.5000000 0.5000000
18 H -0.0000005 16.7019089 0.0012129 0.5000000 0.5000000
19 C 0.0000005 0.0361626 2.4412037 2.1000000 1.9000000
20 C 0.0000005 0.7140385 3.6611879 2.1000000 1.9000000
21 C 0.0000004 2.1457201 3.6613117 2.1000000 1.9000000
22 C 0.0000001 2.8501725 2.4413209 2.1000000 1.9000000
23 C -0.0000001 4.2700744 2.4412023 2.1000000 1.9000000
24 C -0.0000002 4.9766306 3.6612146 2.1000000 1.9000000
25 C 0.0000001 6.3942050 3.6613979 2.1000000 1.9000000
26 C 0.0000001 7.1014018 2.4414044 2.1000000 1.9000000
27 C -0.0000001 8.5186603 2.4414042 2.1000000 1.9000000
28 C 0.0000001 9.2258519 3.6613977 2.1000000 1.9000000
29 C 0.0000004 10.6434033 3.6612143 2.1000000 1.9000000
30 C 0.0000003 11.3499296 2.4412020 2.1000000 1.9000000
31 C -0.0000002 12.7697977 2.4413211 2.1000000 1.9000000
32 C -0.0000004 13.4742418 3.6613119 2.1000000 1.9000000
33 C -0.0000004 14.9059644 3.6611875 2.1000000 1.9000000
34 C -0.0000004 15.5838921 2.4412032 2.1000000 1.9000000
35 H 0.0000003 -1.0818549 2.4412134 0.5000000 0.5000000
36 H -0.0000005 16.7019089 2.4412129 0.5000000 0.5000000
LeftLeadAtoms.SpeciesAndCoordinates>
#
# Lead-Right
#
RightLeadAtoms.Number 36
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 0.0000005 0.7140385 6.1011879 1.9000000 2.1000000
2 C 0.0000004 2.1457201 6.1013117 1.9000000 2.1000000
3 C -0.0000002 4.9766306 6.1012146 1.9000000 2.1000000
4 C 0.0000001 6.3942050 6.1013979 1.9000000 2.1000000
5 C 0.0000001 9.2258519 6.1013977 1.9000000 2.1000000
6 C 0.0000004 10.6434033 6.1012143 1.9000000 2.1000000
7 C -0.0000004 13.4742418 6.1013119 1.9000000 2.1000000
8 C -0.0000004 14.9059644 6.1011875 1.9000000 2.1000000
9 C 0.0000005 0.0361626 7.3212037 1.9000000 2.1000000
10 C 0.0000005 0.7140385 8.5411879 1.9000000 2.1000000
11 C 0.0000004 2.1457201 8.5413117 1.9000000 2.1000000
12 C 0.0000001 2.8501725 7.3213209 1.9000000 2.1000000
13 C -0.0000001 4.2700744 7.3212023 1.9000000 2.1000000
14 C -0.0000002 4.9766306 8.5412146 1.9000000 2.1000000
15 C 0.0000001 6.3942050 8.5413979 1.9000000 2.1000000
16 C 0.0000001 7.1014018 7.3214044 1.9000000 2.1000000
17 C -0.0000001 8.5186603 7.3214042 1.9000000 2.1000000
18 C 0.0000001 9.2258519 8.5413977 1.9000000 2.1000000
19 C 0.0000004 10.6434033 8.5412143 1.9000000 2.1000000
20 C 0.0000003 11.3499296 7.3212020 1.9000000 2.1000000
21 C -0.0000002 12.7697977 7.3213211 1.9000000 2.1000000
22 C -0.0000004 13.4742418 8.5413119 1.9000000 2.1000000
23 C -0.0000004 14.9059644 8.5411875 1.9000000 2.1000000
24 C -0.0000004 15.5838921 7.3212032 1.9000000 2.1000000
25 H 0.0000003 -1.0818549 7.3212134 0.5000000 0.5000000
26 H -0.0000005 16.7019089 7.3212129 0.5000000 0.5000000
27 C 0.0000005 0.0361626 9.7612037 1.9000000 2.1000000
28 C 0.0000001 2.8501725 9.7613209 1.9000000 2.1000000
29 C -0.0000001 4.2700744 9.7612023 1.9000000 2.1000000
30 C 0.0000001 7.1014018 9.7614044 1.9000000 2.1000000
31 C -0.0000001 8.5186603 9.7614042 1.9000000 2.1000000
32 C 0.0000003 11.3499296 9.7612020 1.9000000 2.1000000
33 C -0.0000002 12.7697977 9.7613211 1.9000000 2.1000000
34 C -0.0000004 15.5838921 9.7612032 1.9000000 2.1000000
35 H 0.0000003 -1.0818549 9.7612134 0.5000000 0.5000000
36 H -0.0000005 16.7019089 9.7612129 0.5000000 0.5000000
RightLeadAtoms.SpeciesAndCoordinates>
#
# SCF or Electronic System
#
scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 2000 # default=40
scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 1 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 20.0 # default=1
scf.Init.Mixing.Weight 0.1 # default=0.30
scf.Min.Mixing.Weight 0.04 # default=0.001
scf.Max.Mixing.Weight 0.4 # default=0.40
scf.Mixing.History 60 # default=5
scf.Mixing.StartPulay 20 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)
#
# MD or Geometry Optimization
#
MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 10 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 200 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)
方案如下图所示：
将黑色方框所标的设置为中心，并且补上三个氢原子或者直接删掉下面的三个氢原子。分别新增6个碳原子到左、右电极处，并且分别在左右电极上方补上一个氢原子。
为完成目标先进行第一步，分别将左右电极的12个原子放进中心区域。
在左电极当中，第三列坐标为3.66的8个碳原子选取第二列坐标较小的6个。这六个碳原子在左电极当中的编号为20、21、24、25、28、29。
在左电极当中，第三列坐标为2.44的8个碳原子选取第二列坐标较小的6个。这六个碳原子在左电极当中的编号为19、22、23、26、27、30。
在右电极当中，第三列坐标为6.1的8个碳原子选取第二列坐标较小的6个。这六个碳原子在左电极当中的编号为1~6。
在右电极当中，第三列坐标为7.32的8个碳原子选取第二列坐标较小的6个。这六个碳原子在左电极当中的编号为9、12、13、16、17、20。
将左右电极的碳原子放入中心区域后，还需要在中心区域增加氢原子。中心区域要保留的原有氢原子编号为距离最近的碳原子9，坐标为
9 H 0.0000003 -1.0818549 4.8812134 0.5000000 0.5000000与之相邻的碳原子编号为1，坐标为
1 C 0.0000005 0.0361626 4.8812037 2.1000000 1.9000000二者第二列坐标差为0.0361626-（-1.0818549）=1.1180。这也就是C-H键长。接下来需要在原中心区的8个碳原子去掉第二列坐标最高的两个编号为7、8的这两个碳原子。再去掉编号为10的氢原子。再在6号碳原子坐标为：
6 C 0.0000003 11.3499296 4.8812020 2.1000000 1.9000000头上构建一个第二列坐标与之距离1.118的氢原子。计算11.3499296+1.118=12.4679
新的氢原子坐标为：
7 H 0.0000003 12.4679 4.8812020 0.5000000 0.5000000接下来的工作需要按照上面计算出来的新氢原子坐标，在新的中心区域中补齐剩下的4个氢原子，它们的第二列坐标分别为2.44和7.32。
4个氢原子里面有两个是现成的，分别是原左电极的35号原子：
35 H 0.0000003 -1.0818549 2.4412134 0.5000000 0.5000000和右电极的25号氢原子：
25 H 0.0000003 -1.0818549 7.3212134 0.5000000 0.5000000我们可以直接把上面两个氢原子的第二列修改为需要的12.4679，即可完成剩下两个原子的构建。
36 H 0.0000003 12.4679 2.4412134 0.5000000 0.5000000
26 H 0.0000003 12.4679 7.3212134 0.5000000 0.5000000现在已经完成了，中心区域的重构，标号未修整的原子列表如下：
1 C 0.0000005 0.0361626 4.8812037 2.1000000 1.9000000
2 C 0.0000001 2.8501725 4.8813209 2.1000000 1.9000000
3 C -0.0000001 4.2700744 4.8812023 2.1000000 1.9000000
4 C 0.0000001 7.1014018 4.8814044 2.1000000 1.9000000
5 C -0.0000001 8.5186603 4.8814042 2.1000000 1.9000000
6 C 0.0000003 11.3499296 4.8812020 2.1000000 1.9000000
7 H 0.0000003 12.4679 4.8812020 0.5000000 0.5000000
9 H 0.0000003 -1.0818549 4.8812134 0.5000000 0.5000000
20 C 0.0000005 0.7140385 3.6611879 2.1000000 1.9000000
21 C 0.0000004 2.1457201 3.6613117 2.1000000 1.9000000
24 C -0.0000002 4.9766306 3.6612146 2.1000000 1.9000000
25 C 0.0000001 6.3942050 3.6613979 2.1000000 1.9000000
28 C 0.0000001 9.2258519 3.6613977 2.1000000 1.9000000
29 C 0.0000004 10.6434033 3.6612143 2.1000000 1.9000000
19 C 0.0000005 0.0361626 2.4412037 2.1000000 1.9000000
22 C 0.0000001 2.8501725 2.4413209 2.1000000 1.9000000
23 C -0.0000001 4.2700744 2.4412023 2.1000000 1.9000000
26 C 0.0000001 7.1014018 2.42414044 2.1000000 1.9000000
27 C -0.0000001 8.5186603 2.4414042 2.1000000 1.9000000
30 C 0.0000003 11.3499296 2.4412020 2.1000000 1.9000000
1 C 0.0000005 0.7140385 6.1011879 1.9000000 2.1000000
2 C 0.0000004 2.1457201 6.1013117 1.9000000 2.1000000
3 C -0.0000002 4.9766306 6.1012146 1.9000000 2.1000000
4 C 0.0000001 6.3942050 6.1013979 1.9000000 2.1000000
5 C 0.0000001 9.2258519 6.1013977 1.9000000 2.1000000
6 C 0.0000004 10.6434033 6.1012143 1.9000000 2.1000000
9 C 0.0000005 0.0361626 7.3212037 1.9000000 2.1000000
12 C 0.0000001 2.8501725 7.3213209 1.9000000 2.1000000
13 C -0.0000001 4.2700744 7.3212023 1.9000000 2.1000000
16 C 0.0000001 7.1014018 7.3214044 1.9000000 2.1000000
17 C -0.0000001 8.5186603 7.3214042 1.9000000 2.1000000
20 C 0.0000003 11.3499296 7.3212020 1.9000000 2.1000000
35 H 0.0000003 -1.0818549 2.4412134 0.5000000 0.5000000
25 H 0.0000003 -1.0818549 7.3212134 0.5000000 0.5000000
36 H 0.0000003 12.4679 2.4412134 0.5000000 0.5000000
26 H 0.0000003 12.4679 7.3212134 0.5000000 0.5000000经过修改后的原子列表如下：
Atoms.Number 36
<Atoms.SpeciesAndCoordinates
1 C 0.0000005 0.0361626 4.8812037 2.1000000 1.9000000
2 C 0.0000001 2.8501725 4.8813209 2.1000000 1.9000000
3 C -0.0000001 4.2700744 4.8812023 2.1000000 1.9000000
4 C 0.0000001 7.1014018 4.8814044 2.1000000 1.9000000
5 C -0.0000001 8.5186603 4.8814042 2.1000000 1.9000000
6 C 0.0000003 11.3499296 4.8812020 2.1000000 1.9000000
7 H 0.0000003 12.4679 4.8812020 0.5000000 0.5000000
8 H 0.0000003 -1.0818549 4.8812134 0.5000000 0.5000000
9 C 0.0000005 0.7140385 3.6611879 2.1000000 1.9000000
10 C 0.0000004 2.1457201 3.6613117 2.1000000 1.9000000
11 C -0.0000002 4.9766306 3.6612146 2.1000000 1.9000000
12 C 0.0000001 6.3942050 3.6613979 2.1000000 1.9000000
13 C 0.0000001 9.2258519 3.6613977 2.1000000 1.9000000
14 C 0.0000004 10.6434033 3.6612143 2.1000000 1.9000000
15 C 0.0000005 0.0361626 2.4412037 2.1000000 1.9000000
16 C 0.0000001 2.8501725 2.4413209 2.1000000 1.9000000
17 C -0.0000001 4.2700744 2.4412023 2.1000000 1.9000000
18 C 0.0000001 7.1014018 2.42414044 2.1000000 1.9000000
19 C -0.0000001 8.5186603 2.4414042 2.1000000 1.9000000
20 C 0.0000003 11.3499296 2.4412020 2.1000000 1.9000000
21 C 0.0000005 0.7140385 6.1011879 1.9000000 2.1000000
22 C 0.0000004 2.1457201 6.1013117 1.9000000 2.1000000
23 C -0.0000002 4.9766306 6.1012146 1.9000000 2.1000000
24 C 0.0000001 6.3942050 6.1013979 1.9000000 2.1000000
25 C 0.0000001 9.2258519 6.1013977 1.9000000 2.1000000
26 C 0.0000004 10.6434033 6.1012143 1.9000000 2.1000000
27 C 0.0000005 0.0361626 7.3212037 1.9000000 2.1000000
28 C 0.0000001 2.8501725 7.3213209 1.9000000 2.1000000
29 C -0.0000001 4.2700744 7.3212023 1.9000000 2.1000000
30 C 0.0000001 7.1014018 7.3214044 1.9000000 2.1000000
31 C -0.0000001 8.5186603 7.3214042 1.9000000 2.1000000
32 C 0.0000003 11.3499296 7.3212020 1.9000000 2.1000000
33 H 0.0000003 -1.0818549 2.4412134 0.5000000 0.5000000
34 H 0.0000003 -1.0818549 7.3212134 0.5000000 0.5000000
35 H 0.0000003 12.4679 2.4412134 0.5000000 0.5000000
36 H 0.0000003 12.4679 7.3212134 0.5000000 0.5000000
Atoms.SpeciesAndCoordinates>一共36个原子，与我们设计的目标一致。
二、左电极
首先需要将橙色框内的六个碳原子复制到浅蓝色的位置，再删除原有的上方的6个碳原子和一个最靠近中心区的上方氢原子（右上角），并且把最上方的氢原子向下移动到12.4679。
在左电极原子列表当中，橙色框中的碳原子的第三列坐标为1.22。我们需要保留其中第二列坐标中较小的6个，被删除的两个碳原子编号为14号和15号。
14 C -0.0000004 13.4742418 1.2213119 2.1000000 1.9000000
15 C -0.0000004 14.9059644 1.2211875 2.1000000 1.9000000接下来需要做一道算术题目，石墨烯C-C键长为1.42埃，计算出需要平移的距离为2.4595埃。用1.2211879-2.4595=-1.2383。将编号为2、3、6、7、10、11这六个碳原子分别复制，并修改第三列为-1.2383。
将原18号氢原子的第二列坐标由16.7019089修改为12.4679。
18 H -0.0000005 12.4679 0.0012129 0.5000000 0.5000000要被删除的的6个碳原子和一个氢原子编号分别为：13、16、31、32、33 、34、36。
13 C -0.0000002 12.7697977 0.0013211 2.1000000 1.9000000
16 C -0.0000004 15.5838921 0.0012032 2.1000000 1.9000000
31 C -0.0000002 12.7697977 2.4413211 2.1000000 1.9000000
32 C -0.0000004 13.4742418 3.6613119 2.1000000 1.9000000
33 C -0.0000004 14.9059644 3.6611875 2.1000000 1.9000000
34 C -0.0000004 15.5838921 2.4412032 2.1000000 1.9000000
36 H -0.0000005 16.7019089 2.4412129 0.5000000 0.5000000完成后，未修改编号的左电极变为：
1 C 0.0000005 0.0361626 0.0012037 2.1000000 1.9000000
2 C 0.0000005 0.7140385 1.2211879 2.1000000 1.9000000
3 C 0.0000004 2.1457201 1.2213117 2.1000000 1.9000000
4 C 0.0000001 2.8501725 0.0013209 2.1000000 1.9000000
5 C -0.0000001 4.2700744 0.0012023 2.1000000 1.9000000
6 C -0.0000002 4.9766306 1.2212146 2.1000000 1.9000000
7 C 0.0000001 6.3942050 1.2213979 2.1000000 1.9000000
8 C 0.0000001 7.1014018 0.0014044 2.1000000 1.9000000
9 C -0.0000001 8.5186603 0.0014042 2.1000000 1.9000000
10 C 0.0000001 9.2258519 1.2213977 2.1000000 1.9000000
11 C 0.0000004 10.6434033 1.2212143 2.1000000 1.9000000
12 C 0.0000003 11.3499296 0.0012020 2.1000000 1.9000000
17 H 0.0000003 -1.0818549 0.0012134 0.5000000 0.5000000
18 H -0.0000005 12.4679 0.0012129 0.5000000 0.5000000
2 C 0.0000005 0.7140385 -1.2383 2.1000000 1.9000000
3 C 0.0000004 2.1457201 -1.2383 2.1000000 1.9000000
6 C -0.0000002 4.9766306 -1.2383 2.1000000 1.9000000
7 C 0.0000001 6.3942050 -1.2383 2.1000000 1.9000000
10 C 0.0000001 9.2258519 -1.2383 2.1000000 1.9000000
11 C 0.0000004 10.6434033 -1.2383 2.1000000 1.9000000进行修改编号，得到总共20个原子的列表：
LeftLeadAtoms.Number 20
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 0.0000005 0.0361626 0.0012037 2.1000000 1.9000000
2 C 0.0000005 0.7140385 1.2211879 2.1000000 1.9000000
3 C 0.0000004 2.1457201 1.2213117 2.1000000 1.9000000
4 C 0.0000001 2.8501725 0.0013209 2.1000000 1.9000000
5 C -0.0000001 4.2700744 0.0012023 2.1000000 1.9000000
6 C -0.0000002 4.9766306 1.2212146 2.1000000 1.9000000
7 C 0.0000001 6.3942050 1.2213979 2.1000000 1.9000000
8 C 0.0000001 7.1014018 0.0014044 2.1000000 1.9000000
9 C -0.0000001 8.5186603 0.0014042 2.1000000 1.9000000
10 C 0.0000001 9.2258519 1.2213977 2.1000000 1.9000000
11 C 0.0000004 10.6434033 1.2212143 2.1000000 1.9000000
12 C 0.0000003 11.3499296 0.0012020 2.1000000 1.9000000
13 H 0.0000003 -1.0818549 0.0012134 0.5000000 0.5000000
14 H -0.0000005 12.4679 0.0012129 0.5000000 0.5000000
15 C 0.0000005 0.7140385 -1.2383 2.1000000 1.9000000
16 C 0.0000004 2.1457201 -1.2383 2.1000000 1.9000000
17 C -0.0000002 4.9766306 -1.2383 2.1000000 1.9000000
18 C 0.0000001 6.3942050 -1.2383 2.1000000 1.9000000
19 C 0.0000001 9.2258519 -1.2383 2.1000000 1.9000000
20 C 0.0000004 10.6434033 -1.2383 2.1000000 1.9000000
LeftLeadAtoms.SpeciesAndCoordinates>三、右电极
按照左电极的制作方法制作右电极。
应该删除的8个碳原子为：7、8、21、22、23、24、33、34。要删除的氢原子编号为26。它们的坐标如下：
7 C -0.0000004 13.4742418 6.1013119 1.9000000 2.1000000
8 C -0.0000004 14.9059644 6.1011875 1.9000000 2.1000000
21 C -0.0000002 12.7697977 7.3213211 1.9000000 2.1000000
22 C -0.0000004 13.4742418 8.5413119 1.9000000 2.1000000
23 C -0.0000004 14.9059644 8.5411875 1.9000000 2.1000000
24 C -0.0000004 15.5838921 7.3212032 1.9000000 2.1000000
33 C -0.0000002 12.7697977 9.7613211 1.9000000 2.1000000
34 C -0.0000004 15.5838921 9.7612032 1.9000000 2.1000000
26 H -0.0000005 16.7019089 7.3212129 0.5000000 0.5000000将编号为26的氢原子第二列的16.7019089修改为12.4679。
将6个碳原子复制，并将第三列坐标由8.5411879修改为8.5411879+2.4595=11.0007。这六个碳原子原来的编号为10、11、14、15、18、19。
修改编号之前，原子列表如下：
10 C 0.0000005 0.7140385 8.5411879 1.9000000 2.1000000
11 C 0.0000004 2.1457201 8.5413117 1.9000000 2.1000000
14 C -0.0000002 4.9766306 8.5412146 1.9000000 2.1000000
15 C 0.0000001 6.3942050 8.5413979 1.9000000 2.1000000
18 C 0.0000001 9.2258519 8.5413977 1.9000000 2.1000000
19 C 0.0000004 10.6434033 8.5412143 1.9000000 2.1000000
27 C 0.0000005 0.0361626 9.7612037 1.9000000 2.1000000
28 C 0.0000001 2.8501725 9.7613209 1.9000000 2.1000000
29 C -0.0000001 4.2700744 9.7612023 1.9000000 2.1000000
30 C 0.0000001 7.1014018 9.7614044 1.9000000 2.1000000
31 C -0.0000001 8.5186603 9.7614042 1.9000000 2.1000000
32 C 0.0000003 11.3499296 9.7612020 1.9000000 2.1000000
35 H 0.0000003 -1.0818549 9.7612134 0.5000000 0.5000000
36 H -0.0000005 12.4679 9.7612129 0.5000000 0.5000000
10 C 0.0000005 0.7140385 11.0007 1.9000000 2.1000000
11 C 0.0000004 2.1457201 11.0007 1.9000000 2.1000000
14 C -0.0000002 4.9766306 11.0007 1.9000000 2.1000000
15 C 0.0000001 6.3942050 11.0007 1.9000000 2.1000000
18 C 0.0000001 9.2258519 11.0007 1.9000000 2.1000000
19 C 0.0000004 10.6434033 11.0007 1.9000000 2.1000000修改编号之后，原子列表如下，总共20个原子：
1 C 0.0000005 0.7140385 8.5411879 1.9000000 2.1000000
2 C 0.0000004 2.1457201 8.5413117 1.9000000 2.1000000
3 C -0.0000002 4.9766306 8.5412146 1.9000000 2.1000000
4 C 0.0000001 6.3942050 8.5413979 1.9000000 2.1000000
5 C 0.0000001 9.2258519 8.5413977 1.9000000 2.1000000
6 C 0.0000004 10.6434033 8.5412143 1.9000000 2.1000000
7 C 0.0000005 0.0361626 9.7612037 1.9000000 2.1000000
8 C 0.0000001 2.8501725 9.7613209 1.9000000 2.1000000
9 C -0.0000001 4.2700744 9.7612023 1.9000000 2.1000000
10 C 0.0000001 7.1014018 9.7614044 1.9000000 2.1000000
11 C -0.0000001 8.5186603 9.7614042 1.9000000 2.1000000
12 C 0.0000003 11.3499296 9.7612020 1.9000000 2.1000000
13 H 0.0000003 -1.0818549 9.7612134 0.5000000 0.5000000
14 H -0.0000005 12.4679 9.7612129 0.5000000 0.5000000
15 C 0.0000005 0.7140385 11.0007 1.9000000 2.1000000
16 C 0.0000004 2.1457201 11.0007 1.9000000 2.1000000
17 C -0.0000002 4.9766306 11.0007 1.9000000 2.1000000
18 C 0.0000001 6.3942050 11.0007 1.9000000 2.1000000
19 C 0.0000001 9.2258519 11.0007 1.9000000 2.1000000
20 C 0.0000004 10.6434033 11.0007 1.9000000 2.1000000Atoms.UnitVectors
在原来的左电极和右电极文件中的晶格矢量为
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Atoms.UnitVectors>在原NEGF-8ZGNR-0.3.dat文件中的晶格矢量为
#<Atoms.UnitVectors
# 0.000 0.000 4.88
# 10.000 0.000 0.000
# 0.000 24.000 0.000
#Atoms.UnitVectors>看来前两个一样，最后一个影响不大。参考Openmx用户手册第139页
现在沿着第三列的方向模型整体变宽了，原来的半宽恰好是4.88，而现在的半宽是6.1，所以，将Atoms.UnitVectors改成
<Atoms.UnitVectors
0.000 0.000 6.1
10.000 0.000 0.000
0.000 24.000 0.000
Atoms.UnitVectors>四、左右电极文件
上面仅仅完成了NEGF-8ZGNR-0.3.dat的修改，要想开始仿真还要修改Lead-L-8ZGNR.dat和Lead-R-8ZGNR.dat文件。
修改的地方就是原子个数，原子坐标。
新的左电极文件如下。
#
# File Name
#
System.CurrrentDirectory ./ # default=./
System.Name lead-l-8zgnr
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)
#
# Definition of Atomic Species
#
Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
H H5.0-s2 H_CA13
Definition.of.Atomic.Species>
NEGF.output_hks true
NEGF.filename.hks lead-l-8zgnr.hks
#
# Atoms
#
Atoms.Number 20
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0.0000005 0.0361626 0.0012037 2.1000000 1.9000000
2 C 0.0000005 0.7140385 1.2211879 2.1000000 1.9000000
3 C 0.0000004 2.1457201 1.2213117 2.1000000 1.9000000
4 C 0.0000001 2.8501725 0.0013209 2.1000000 1.9000000
5 C -0.0000001 4.2700744 0.0012023 2.1000000 1.9000000
6 C -0.0000002 4.9766306 1.2212146 2.1000000 1.9000000
7 C 0.0000001 6.3942050 1.2213979 2.1000000 1.9000000
8 C 0.0000001 7.1014018 0.0014044 2.1000000 1.9000000
9 C -0.0000001 8.5186603 0.0014042 2.1000000 1.9000000
10 C 0.0000001 9.2258519 1.2213977 2.1000000 1.9000000
11 C 0.0000004 10.6434033 1.2212143 2.1000000 1.9000000
12 C 0.0000003 11.3499296 0.0012020 2.1000000 1.9000000
13 H 0.0000003 -1.0818549 0.0012134 0.5000000 0.5000000
14 H -0.0000005 12.4679 0.0012129 0.5000000 0.5000000
15 C 0.0000005 0.7140385 -1.2383 2.1000000 1.9000000
16 C 0.0000004 2.1457201 -1.2383 2.1000000 1.9000000
17 C -0.0000002 4.9766306 -1.2383 2.1000000 1.9000000
18 C 0.0000001 6.3942050 -1.2383 2.1000000 1.9000000
19 C 0.0000001 9.2258519 -1.2383 2.1000000 1.9000000
20 C 0.0000004 10.6434033 -1.2383 2.1000000 1.9000000
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
0.000 0.000 6.1
10.000 0.000 0.000
0.000 27.000 0.000
Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 1000 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 201 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 10.0 # default=1
scf.Init.Mixing.Weight 0.001 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.105 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)
#
# MD or Geometry Optimization
#
MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 18 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 2000 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)
#
# Band dispersion
#
Band.dispersion off # on|off, default=off
<Band.KPath.UnitCell
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Band.KPath.UnitCell>
Band.Nkpath 1
<Band.kpath
601 0.0 0.0 0.0 0.5 0.0 0.0 G X
Band.kpath>
#
# DOS and PDOS
#
Dos.fileout off # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 601 1 1 # default = Kgrid1 Kgrid2 Kgrid3
DosGauss.fileout off
DosGauss.Num.Mesh 4000
DosGauss.Width 0.01
MO.fileout off # on|off
num.HOMOs 1 # default=1
num.LUMOs 1 # default=1
MO.Nkpoint 1 # default=1
<MO.kpoint
0.0 0.0 0.0
MO.kpoint>
五、输入效果图
这个是一个仿真结束之后的图，是我们的输入文件的原子排布的xyz文件。用xcrysden画出来
六、仿真结果
得到文件negf-8zgnr-0.3.dat，文件的第六列就是transmission。
#/************************************************************/
#
# Current:
#
# convert the unit from a.u to ampere
#
# The unit of current is given by eEh/bar{h} in
# atomic unit, where e is the elementary charge,
# Eh Hartree, and bar{h} h/{2pi} given by
#
# e = 1.60217653 * 10^{-19} C
# Eh = 4.35974417 * 10^{-18} J
# bar{h} = 1.05457168 * 10^{-34} J s
#
# Therefore,
#
# 1 a.u.
# = 1.60217653 * 10^{-19} C * 4.35974417 * 10^{-18} J
# / (1.05457168 * 10^{-34} J s )
# = 6.6236178 * 10^{-3} [Cs^{-1}=ampere]
#
# Electric potential:
#
# convert the unit from a.u to volt
#
# The unit of electric potential is given by Eh/e in
# atomic unit.
#
# Therefore,
#
# 1 a.u.
# = 4.35974417 * 10^{-18} J/ (1.60217653 * 10^{-19} C)
# = 27.21138 [JC^{-1}=volt]
#
# This allows us to consider that the difference of 1 eV in
# the chemical potential of leads can be regarded as 1 volt.
#
#***********************************************************/
#
# k2= 0.0000 k3= -0.0000
# SpinP_switch= 1
# Chemical potential (eV) Left, Right Leads=-7.092117e+00 -7.382248e+00
# Chemical potential (Hartree) Left, Right Leads=-2.606305e-01 -2.712926e-01
# diff Chemical potential (eV) = 2.901306e-01
# diff Chemical potential (Hartree)= 1.066210e-02
# tran_transmission_energydiv= 800
#
# iw w.real(au) w.imag(au) w.real(eV) w.imag(eV) trans.real(up) trans.imag(up) trans.real(down) trans.imag(down)
#
0 -1.469973e-01 3.674932e-05 -4.000000e+00 1.000000e-03 1.504455e-10 1.521637e-24 1.071494e-10 1.816968e-25
1 -1.466293e-01 3.674932e-05 -3.989987e+00 1.000000e-03 1.158592e-10 1.305401e-24 1.056194e-10 5.332574e-25
2 -1.462614e-01 3.674932e-05 -3.979975e+00 1.000000e-03 9.618697e-11 1.190603e-24 1.508025e-10 1.605111e-24
3 -1.458934e-01 3.674932e-05 -3.969962e+00 1.000000e-03 8.818859e-11 1.187069e-24 4.791283e-10 9.338231e-24
4 -1.455255e-01 3.674932e-05 -3.959950e+00 1.000000e-03 1.072549e-10 1.517041e-24 1.124427e-08 3.594742e-22
5 -1.451575e-01 3.674932e-05 -3.949937e+00 1.000000e-03 1.522907e-09 2.749582e-23 4.817887e-08 3.401657e-22
6 -1.447896e-01 3.674932e-05 -3.939925e+00 1.000000e-03 1.626574e-10 8.560909e-24 2.177308e-08 -8.016507e-22
7 -1.444216e-01 3.674932e-05 -3.929912e+00 1.000000e-03 9.518922e-10 1.539321e-22 6.147583e-09 2.502252e-22
8 -1.440537e-01 3.674932e-05 -3.919900e+00 1.000000e-03 5.208821e-11 2.141974e-24 5.415061e-11 5.973337e-24
9 -1.436857e-01 3.674932e-05 -3.909887e+00 1.000000e-03 4.604393e-11 1.121868e-24 1.741657e-11 1.166194e-24
10 -1.433178e-01 3.674932e-05 -3.899875e+00 1.000000e-03 4.730882e-11 1.079651e-24 1.339429e-11 4.096322e-25
11 -1.429498e-01 3.674932e-05 -3.889862e+00 1.000000e-03 5.243957e-11 1.253502e-24 1.152121e-11 2.036732e-25
12 -1.425819e-01 3.674932e-05 -3.879850e+00 1.000000e-03 6.327638e-11 1.629360e-24 1.014272e-11 1.311523e-25
13 -1.422139e-01 3.674932e-05 -3.869837e+00 1.000000e-03 8.614049e-11 2.396678e-24 9.064420e-12 1.020612e-25
14 -1.418460e-01 3.674932e-05 -3.859825e+00 1.000000e-03 1.434529e-10 4.338940e-24 8.225351e-12 9.068025e-26
15 -1.414780e-01 3.674932e-05 -3.849812e+00 1.000000e-03 3.665718e-10 1.168167e-23 7.588897e-12 8.751189e-26
16 -1.411100e-01 3.674932e-05 -3.839800e+00 1.000000e-03 5.329663e-09 1.670105e-22 7.132836e-12 8.934003e-26
17 -1.407421e-01 3.674932e-05 -3.829787e+00 1.000000e-03 8.216993e-10 3.142963e-23 6.849852e-12 9.587737e-26
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687 1.057865e-01 3.674932e-05 2.878598e+00 1.000000e-03 4.720981e-08 1.274375e-23 1.215647e-08 1.242063e-23
688 1.061545e-01 3.674932e-05 2.888611e+00 1.000000e-03 3.113387e-08 2.102202e-23 1.148966e-08 3.083833e-23
689 1.065224e-01 3.674932e-05 2.898623e+00 1.000000e-03 1.811602e-08 2.338724e-23 1.066136e-08 4.023458e-23
690 1.068904e-01 3.674932e-05 2.908636e+00 1.000000e-03 2.519707e-09 1.283947e-23 9.558444e-09 4.867441e-23
691 1.072584e-01 3.674932e-05 2.918648e+00 1.000000e-03 4.695473e-10 8.753611e-25 8.824775e-09 4.919140e-23
692 1.076263e-01 3.674932e-05 2.928661e+00 1.000000e-03 2.537167e-10 4.301911e-25 8.166028e-09 4.882304e-23
693 1.079943e-01 3.674932e-05 2.938673e+00 1.000000e-03 1.640624e-10 2.818545e-25 7.461891e-09 3.895504e-23
694 1.083622e-01 3.674932e-05 2.948686e+00 1.000000e-03 1.153528e-10 2.056900e-25 6.545025e-09 9.234696e-24
695 1.087302e-01 3.674932e-05 2.958698e+00 1.000000e-03 8.534227e-11 1.608298e-25 6.034599e-09 8.853417e-25
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698 1.098340e-01 3.674932e-05 2.988736e+00 1.000000e-03 4.136931e-11 9.435329e-26 4.909795e-09 1.938705e-25
699 1.102020e-01 3.674932e-05 2.998748e+00 1.000000e-03 3.382768e-11 8.280722e-26 4.571948e-09 1.486340e-25
700 1.105699e-01 3.674932e-05 3.008761e+00 1.000000e-03 2.807171e-11 7.439787e-26 4.248731e-09 5.040632e-25
701 1.109379e-01 3.674932e-05 3.018773e+00 1.000000e-03 2.359792e-11 6.794203e-26 3.938475e-09 8.368741e-25
702 1.113058e-01 3.674932e-05 3.028786e+00 1.000000e-03 2.006844e-11 6.331343e-26 3.639592e-09 5.299126e-25
703 1.116738e-01 3.674932e-05 3.038798e+00 1.000000e-03 1.724967e-11 5.932988e-26 3.350495e-09 3.554292e-26
704 1.120417e-01 3.674932e-05 3.048811e+00 1.000000e-03 1.497601e-11 5.680730e-26 3.069529e-09 1.260158e-25
705 1.124097e-01 3.674932e-05 3.058824e+00 1.000000e-03 1.312771e-11 5.551249e-26 2.794888e-09 5.961517e-25
706 1.127777e-01 3.674932e-05 3.068836e+00 1.000000e-03 1.161675e-11 5.452067e-26 2.524488e-09 3.812786e-25
707 1.131456e-01 3.674932e-05 3.078849e+00 1.000000e-03 1.037769e-11 5.444743e-26 2.255760e-09 2.689953e-25
708 1.135136e-01 3.674932e-05 3.088861e+00 1.000000e-03 9.361512e-12 5.561442e-26 1.985277e-09 4.660969e-25
709 1.138815e-01 3.674932e-05 3.098874e+00 1.000000e-03 8.531609e-12 5.709107e-26 1.707992e-09 4.362085e-26
710 1.142495e-01 3.674932e-05 3.108886e+00 1.000000e-03 7.861056e-12 5.997118e-26 1.415448e-09 1.712522e-25
711 1.146174e-01 3.674932e-05 3.118899e+00 1.000000e-03 7.330989e-12 6.419762e-26 1.090431e-09 1.657996e-25
712 1.149854e-01 3.674932e-05 3.128911e+00 1.000000e-03 6.929868e-12 6.993153e-26 6.821414e-10 2.244656e-25
713 1.153533e-01 3.674932e-05 3.138924e+00 1.000000e-03 6.653764e-12 7.814292e-26 6.461532e-11 2.048049e-25
714 1.157213e-01 3.674932e-05 3.148936e+00 1.000000e-03 6.508067e-12 8.923570e-26 2.715370e-11 2.490785e-25
715 1.160892e-01 3.674932e-05 3.158949e+00 1.000000e-03 6.511792e-12 1.050394e-25 1.972204e-11 3.198980e-25
716 1.164572e-01 3.674932e-05 3.168961e+00 1.000000e-03 6.707380e-12 1.288015e-25 1.728053e-11 4.520914e-25
717 1.168251e-01 3.674932e-05 3.178974e+00 1.000000e-03 7.184015e-12 1.653669e-25 1.796458e-11 7.157694e-25
718 1.171931e-01 3.674932e-05 3.188986e+00 1.000000e-03 8.139425e-12 2.228429e-25 2.426308e-11 1.376499e-24
719 1.175610e-01 3.674932e-05 3.198999e+00 1.000000e-03 1.007433e-11 3.295577e-25 5.779362e-11 4.176669e-24
720 1.179290e-01 3.674932e-05 3.209011e+00 1.000000e-03 1.458779e-11 5.545447e-25 1.440692e-09 1.071257e-22
721 1.182969e-01 3.674932e-05 3.219024e+00 1.000000e-03 2.947165e-11 1.204336e-24 1.315603e-10 7.209739e-24
722 1.186649e-01 3.674932e-05 3.229036e+00 1.000000e-03 1.643038e-10 5.829298e-24 3.814975e-11 1.088881e-24
723 1.190329e-01 3.674932e-05 3.239049e+00 1.000000e-03 4.713177e-10 6.419514e-24 2.729174e-11 2.113689e-25
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725 1.197688e-01 3.674932e-05 3.259074e+00 1.000000e-03 4.676878e-11 -1.542572e-24 4.993282e-11 -5.540681e-25
726 1.201367e-01 3.674932e-05 3.269086e+00 1.000000e-03 9.261972e-11 -3.017177e-24 1.562091e-10 -1.974774e-24
727 1.205047e-01 3.674932e-05 3.279099e+00 1.000000e-03 7.962439e-10 -1.993506e-23 8.679693e-09 -9.194913e-23
728 1.208726e-01 3.674932e-05 3.289111e+00 1.000000e-03 6.228309e-10 -1.017160e-23 2.569537e-10 -2.001835e-24
729 1.212406e-01 3.674932e-05 3.299124e+00 1.000000e-03 8.916435e-11 -8.526522e-25 6.809849e-11 -3.379646e-25
730 1.216085e-01 3.674932e-05 3.309136e+00 1.000000e-03 4.001840e-11 -1.827192e-25 3.664703e-11 -1.067328e-25
731 1.219765e-01 3.674932e-05 3.319149e+00 1.000000e-03 2.637131e-11 -4.347240e-26 2.646977e-11 -4.335402e-26
732 1.223444e-01 3.674932e-05 3.329161e+00 1.000000e-03 2.123156e-11 1.671606e-27 2.250137e-11 -2.398808e-26
733 1.227124e-01 3.674932e-05 3.339174e+00 1.000000e-03 1.936121e-11 1.880574e-26 2.121719e-11 -2.039464e-26
734 1.230803e-01 3.674932e-05 3.349186e+00 1.000000e-03 1.926076e-11 2.653984e-26 2.152869e-11 -2.653611e-26
735 1.234483e-01 3.674932e-05 3.359199e+00 1.000000e-03 2.050554e-11 3.099939e-26 2.314394e-11 -4.027397e-26
736 1.238162e-01 3.674932e-05 3.369212e+00 1.000000e-03 2.317630e-11 3.568787e-26 2.619401e-11 -6.500804e-26
737 1.241842e-01 3.674932e-05 3.379224e+00 1.000000e-03 2.783274e-11 4.282013e-26 3.124924e-11 -1.084401e-25
738 1.245522e-01 3.674932e-05 3.389237e+00 1.000000e-03 3.589293e-11 5.658937e-26 3.968410e-11 -1.892964e-25
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740 1.252881e-01 3.674932e-05 3.409262e+00 1.000000e-03 8.436903e-11 1.485787e-25 8.711658e-11 -7.654339e-25
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744 1.267599e-01 3.674932e-05 3.449312e+00 1.000000e-03 3.904914e-10 -8.994207e-25 5.054969e-10 -1.158615e-23
745 1.271278e-01 3.674932e-05 3.459324e+00 1.000000e-03 1.520057e-10 -1.321419e-24 1.712195e-10 -4.054437e-24
746 1.274958e-01 3.674932e-05 3.469337e+00 1.000000e-03 1.234138e-10 -2.257872e-24 1.128313e-10 -2.479110e-24
747 1.278637e-01 3.674932e-05 3.479349e+00 1.000000e-03 1.982078e-10 -5.479317e-24 1.055850e-10 -1.959762e-24
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749 1.285996e-01 3.674932e-05 3.499374e+00 1.000000e-03 1.303906e-08 -3.506335e-22 1.921939e-10 -2.229819e-24
750 1.289676e-01 3.674932e-05 3.509387e+00 1.000000e-03 7.676050e-10 -1.602489e-23 4.317026e-10 -2.583485e-24
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752 1.297035e-01 3.674932e-05 3.529412e+00 1.000000e-03 3.328642e-10 -4.373515e-24 2.875034e-08 1.796640e-22
753 1.300715e-01 3.674932e-05 3.539424e+00 1.000000e-03 3.674758e-10 -4.366952e-24 2.286519e-09 3.066425e-23
754 1.304394e-01 3.674932e-05 3.549437e+00 1.000000e-03 5.013331e-10 -6.000626e-24 1.518282e-09 2.719243e-23
755 1.308074e-01 3.674932e-05 3.559449e+00 1.000000e-03 9.051672e-10 -1.275567e-23 1.933642e-09 4.246474e-23
756 1.311753e-01 3.674932e-05 3.569462e+00 1.000000e-03 3.041848e-09 -5.342153e-23 4.818846e-09 1.371507e-22
757 1.315433e-01 3.674932e-05 3.579474e+00 1.000000e-03 2.624562e-07 -5.782613e-21 1.938011e-07 6.617801e-21
758 1.319112e-01 3.674932e-05 3.589487e+00 1.000000e-03 2.791507e-09 -6.865899e-23 6.775196e-09 2.350874e-22
759 1.322792e-01 3.674932e-05 3.599499e+00 1.000000e-03 9.953545e-10 -2.244314e-23 2.271780e-09 5.741077e-23
760 1.326471e-01 3.674932e-05 3.609512e+00 1.000000e-03 7.655837e-10 -1.341885e-23 1.943860e-09 2.900775e-23
761 1.330151e-01 3.674932e-05 3.619524e+00 1.000000e-03 8.275581e-10 -1.050661e-23 2.396218e-09 1.918292e-23
762 1.333830e-01 3.674932e-05 3.629537e+00 1.000000e-03 1.060165e-09 -9.787099e-24 3.499396e-09 1.502298e-23
763 1.337510e-01 3.674932e-05 3.639549e+00 1.000000e-03 1.503902e-09 -1.032946e-23 5.690400e-09 1.297651e-23
764 1.341189e-01 3.674932e-05 3.649562e+00 1.000000e-03 2.314114e-09 -1.234072e-23 1.020410e-08 1.199336e-23
765 1.344869e-01 3.674932e-05 3.659574e+00 1.000000e-03 3.881040e-09 -1.648472e-23 2.054497e-08 1.052554e-23
766 1.348548e-01 3.674932e-05 3.669587e+00 1.000000e-03 7.289639e-09 -2.536924e-23 4.868694e-08 6.814458e-24
767 1.352228e-01 3.674932e-05 3.679599e+00 1.000000e-03 1.636717e-08 -4.831601e-23 1.509845e-07 -2.121709e-23
768 1.355907e-01 3.674932e-05 3.689612e+00 1.000000e-03 5.227449e-08 -1.343003e-22 8.269503e-07 -1.868824e-22
769 1.359587e-01 3.674932e-05 3.699625e+00 1.000000e-03 5.204287e-07 -1.197995e-21 5.688304e-05 -2.697602e-20
770 1.363267e-01 3.674932e-05 3.709637e+00 1.000000e-03 6.458411e-07 -1.324443e-21 3.101231e-05 -1.331659e-20
771 1.366946e-01 3.674932e-05 3.719650e+00 1.000000e-03 8.632297e-08 -1.545684e-22 3.045666e-05 -1.307342e-20
772 1.370626e-01 3.674932e-05 3.729662e+00 1.000000e-03 3.702972e-08 -6.182842e-23 2.104830e-05 -9.999926e-21
773 1.374305e-01 3.674932e-05 3.739675e+00 1.000000e-03 2.271001e-08 -3.554679e-23 1.489760e-05 -8.909320e-21
774 1.377985e-01 3.674932e-05 3.749687e+00 1.000000e-03 1.667577e-08 -2.455133e-23 1.063399e-05 -7.035196e-21
775 1.381664e-01 3.674932e-05 3.759700e+00 1.000000e-03 1.369605e-08 -1.935310e-23 7.335843e-06 -4.436391e-21
776 1.385344e-01 3.674932e-05 3.769712e+00 1.000000e-03 1.217578e-08 -1.654883e-23 4.250848e-06 -2.606491e-21
777 1.389023e-01 3.674932e-05 3.779725e+00 1.000000e-03 1.151028e-08 -1.518213e-23 2.571681e-07 -1.577984e-22
778 1.392703e-01 3.674932e-05 3.789737e+00 1.000000e-03 1.145558e-08 -1.470505e-23 5.571531e-08 -3.053818e-23
779 1.396382e-01 3.674932e-05 3.799750e+00 1.000000e-03 1.193857e-08 -1.499423e-23 2.502531e-08 -1.145753e-23
780 1.400062e-01 3.674932e-05 3.809762e+00 1.000000e-03 1.300077e-08 -1.620618e-23 1.400739e-08 -4.138332e-24
781 1.403741e-01 3.674932e-05 3.819775e+00 1.000000e-03 1.480360e-08 -1.830546e-23 8.879886e-09 4.788995e-25
782 1.407421e-01 3.674932e-05 3.829787e+00 1.000000e-03 1.769251e-08 -2.201223e-23 6.191191e-09 6.064529e-24
783 1.411100e-01 3.674932e-05 3.839800e+00 1.000000e-03 2.237492e-08 -2.814109e-23 5.119885e-09 3.330776e-23
784 1.414780e-01 3.674932e-05 3.849812e+00 1.000000e-03 3.041820e-08 -3.838269e-23 1.156713e-08 3.823049e-22
785 1.418460e-01 3.674932e-05 3.859825e+00 1.000000e-03 4.594176e-08 -5.912364e-23 1.262449e-08 4.363928e-22
786 1.422139e-01 3.674932e-05 3.869837e+00 1.000000e-03 8.409808e-08 -1.111886e-22 1.231210e-08 4.257914e-22
787 1.425819e-01 3.674932e-05 3.879850e+00 1.000000e-03 3.031398e-07 -4.110469e-22 1.155114e-08 3.893799e-22
788 1.429498e-01 3.674932e-05 3.889862e+00 1.000000e-03 3.807021e-06 -5.213947e-21 1.055913e-08 3.546546e-22
789 1.433178e-01 3.674932e-05 3.899875e+00 1.000000e-03 5.809968e-06 -8.171151e-21 9.307613e-09 3.054008e-22
790 1.436857e-01 3.674932e-05 3.909887e+00 1.000000e-03 7.176932e-06 -1.019868e-20 7.001269e-09 1.975998e-22
791 1.440537e-01 3.674932e-05 3.919900e+00 1.000000e-03 8.112722e-06 -1.218669e-20 3.472513e-09 -7.225933e-25
792 1.444216e-01 3.674932e-05 3.929912e+00 1.000000e-03 8.455338e-06 -1.363785e-20 6.168728e-09 -2.162496e-23
793 1.447896e-01 3.674932e-05 3.939925e+00 1.000000e-03 7.241001e-06 -1.377718e-20 8.057683e-08 -4.233631e-22
794 1.451575e-01 3.674932e-05 3.949937e+00 1.000000e-03 6.777021e-06 -4.819164e-21 2.203196e-07 -1.054760e-21
795 1.455255e-01 3.674932e-05 3.959950e+00 1.000000e-03 1.988081e-06 3.694937e-21 2.909059e-07 -1.341085e-21
796 1.458934e-01 3.674932e-05 3.969962e+00 1.000000e-03 1.370780e-06 4.299847e-21 3.319833e-07 -1.515685e-21
797 1.462614e-01 3.674932e-05 3.979975e+00 1.000000e-03 1.323759e-06 5.660296e-21 3.464341e-07 -1.591605e-21
798 1.466293e-01 3.674932e-05 3.989987e+00 1.000000e-03 1.686891e-06 9.339370e-21 3.260666e-07 -1.529987e-21
799 1.469973e-01 3.674932e-05 4.000000e+00 1.000000e-03 6.734467e-06 4.725014e-20 2.411280e-07 -1.169342e-21
这就是修改之后的transmission，跟修改之前的变化还是挺大滴，下面把原来的transmission图粘贴出来，进行对比一下。
为了验证是否是晶格矢量不匹配的问题，必须要对原来的NEGF-8ZGNR-0.3这个例子的晶格矢量修改，修改的内容是把4.88都改为6.1。仅改此一处，发现仿真结果如下：
从结果来看，确实变化非常大，而起没什么规律，这也就是说，必须将晶格匹配做到很好才行。
如果把原子的Atoms.UnitVectors修改为4.88的两倍，即9.76，transmission就全部成为0。可见，这个单位矢量对于这个非平衡格林函数的透射谱的影响之大。4.88就正好，6.1就很小，而到了9.76就到了全0.
下面是conductance文件：
#/************************************************************/
#
# Conductance:
#
# G0 = e^2/h
# = (1.60217653 * 10^{-19})^2/(6.626076 * 10^{-34})
# = 3.87404194169 * 10^{-4} [C^2 J^{-1} s^{-1}]
# note that
# e = 1.60217653 * 10^{-19} C
# h = 6.626076 * 10^{-34} J s
#***********************************************************/
#
# SpinP_switch= 1
# Chemical potential (eV) Left, Right Leads=-7.092117e+00 -7.382248e+00
# Chemical potential (Hartree) Left, Right Leads=-2.606305e-01 -2.712926e-01
# diff Chemical potential (eV) = 2.901306e-01
# diff Chemical potential (Hartree)= 1.066210e-02
# Corresponding bias voltage (Volt)= 2.901305e-01
# average conductance for up and down spins (G0)= 1.022572e-04 2.338899e-05
#
# i2 i3 k2 k3 conductance (G0, up spin) conductance (G0, down spin)
#
0 0 0.0000 0.0000 1.022572e-04 2.338899e-05下面是未修改之前的结果conductance文件：
#/************************************************************/
#
# Conductance:
#
# G0 = e^2/h
# = (1.60217653 * 10^{-19})^2/(6.626076 * 10^{-34})
# = 3.87404194169 * 10^{-4} [C^2 J^{-1} s^{-1}]
# note that
# e = 1.60217653 * 10^{-19} C
# h = 6.626076 * 10^{-34} J s
#***********************************************************/
#
# SpinP_switch= 1
# Chemical potential (eV) Left, Right Leads=-4.864470e+00 -5.164470e+00
# Chemical potential (Hartree) Left, Right Leads=-1.787660e-01 -1.897908e-01
# diff Chemical potential (eV) = 2.999998e-01
# diff Chemical potential (Hartree)= 1.102479e-02
# Corresponding bias voltage (Volt)= 2.999998e-01
# average conductance for up and down spins (G0)= 3.095083e-03 4.359661e-02
#
# i2 i3 k2 k3 conductance (G0, up spin) conductance (G0, down spin)
#
0 0 0.0000 0.0000 3.095083e-03 4.359661e-02上面是直接修改NEGF-8ZGNR-0.3这个例子。接下来需要修改的是我们自己的例子。也就是前三节刚做的那个例子。我们把左右电极的晶格矢量改写成下面这样：
<Atoms.UnitVectors
0.000 0.000 4.92
10.000 0.000 0.000
0.000 27.000 0.000
Atoms.UnitVectors>因为两个电极的最大和最小的第三列坐标之差为2.4595，又因为2.4595*2=4.92，所以需要试2.4595和4.92这两个数。另外强调一下，0.3.dat文件里不需要Atoms.UnitVectors这个文件，只有左右电极的文件才需要。4.92仿真结果如下图所示：
2.4595这一组因为提示太近而跑不下去。3.5、3.6893也不行。4虽然能跑完电极，但跑不了NEGF主文件。4.5的结果如下
附录：
为方便查阅，现将原文档8ZGNR的三个文件粘贴出来：
#
# File Name
#
System.CurrrentDirectory ./ # default=./
System.Name lead-l-8zgnr
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)
#
# Definition of Atomic Species
#
Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
H H5.0-s2 H_CA13
Definition.of.Atomic.Species>
NEGF.output_hks true
NEGF.filename.hks lead-l-8zgnr.hks
#
# Atoms
#
Atoms.Number 36
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0.0000005 0.0361626 0.0012037 2.5000000 1.5000000
2 C 0.0000005 0.7140385 1.2211879 2.5000000 1.5000000
3 C 0.0000004 2.1457201 1.2213117 2.5000000 1.5000000
4 C 0.0000001 2.8501725 0.0013209 2.5000000 1.5000000
5 C -0.0000001 4.2700744 0.0012023 2.5000000 1.5000000
6 C -0.0000002 4.9766306 1.2212146 2.5000000 1.5000000
7 C 0.0000001 6.3942050 1.2213979 2.5000000 1.5000000
8 C 0.0000001 7.1014018 0.0014044 2.5000000 1.5000000
9 C -0.0000001 8.5186603 0.0014042 2.5000000 1.5000000
10 C 0.0000001 9.2258519 1.2213977 2.5000000 1.5000000
11 C 0.0000004 10.6434033 1.2212143 2.5000000 1.5000000
12 C 0.0000003 11.3499296 0.0012020 2.5000000 1.5000000
13 C -0.0000002 12.7697977 0.0013211 2.5000000 1.5000000
14 C -0.0000004 13.4742418 1.2213119 2.5000000 1.5000000
15 C -0.0000004 14.9059644 1.2211875 2.5000000 1.5000000
16 C -0.0000004 15.5838921 0.0012032 2.5000000 1.5000000
17 H 0.0000003 -1.0818549 0.0012134 0.5000000 0.5000000
18 H -0.0000005 16.7019089 0.0012129 0.5000000 0.5000000
19 C 0.0000005 0.0361626 2.4412037 2.5000000 1.5000000
20 C 0.0000005 0.7140385 3.6611879 2.5000000 1.5000000
21 C 0.0000004 2.1457201 3.6613117 2.5000000 1.5000000
22 C 0.0000001 2.8501725 2.4413209 2.5000000 1.5000000
23 C -0.0000001 4.2700744 2.4412023 2.5000000 1.5000000
24 C -0.0000002 4.9766306 3.6612146 2.5000000 1.5000000
25 C 0.0000001 6.3942050 3.6613979 2.5000000 1.5000000
26 C 0.0000001 7.1014018 2.4414044 2.5000000 1.5000000
27 C -0.0000001 8.5186603 2.4414042 2.5000000 1.5000000
28 C 0.0000001 9.2258519 3.6613977 2.5000000 1.5000000
29 C 0.0000004 10.6434033 3.6612143 2.5000000 1.5000000
30 C 0.0000003 11.3499296 2.4412020 2.5000000 1.5000000
31 C -0.0000002 12.7697977 2.4413211 2.5000000 1.5000000
32 C -0.0000004 13.4742418 3.6613119 2.5000000 1.5000000
33 C -0.0000004 14.9059644 3.6611875 2.5000000 1.5000000
34 C -0.0000004 15.5838921 2.4412032 2.5000000 1.5000000
35 H 0.0000003 -1.0818549 2.4412134 0.5000000 0.5000000
36 H -0.0000005 16.7019089 2.4412129 0.5000000 0.5000000
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 1000 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 201 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 10.0 # default=1
scf.Init.Mixing.Weight 0.001 # default=0.30
scf.Min.Mixing.Weight 0.001 # default=0.001
scf.Max.Mixing.Weight 0.105 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)
#
# MD or Geometry Optimization
#
MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 18 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 2000 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)
#
# Band dispersion
#
Band.dispersion off # on|off, default=off
<Band.KPath.UnitCell
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Band.KPath.UnitCell>
Band.Nkpath 1
<Band.kpath
601 0.0 0.0 0.0 0.5 0.0 0.0 G X
Band.kpath>
#
# DOS and PDOS
#
Dos.fileout off # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 601 1 1 # default = Kgrid1 Kgrid2 Kgrid3
DosGauss.fileout off
DosGauss.Num.Mesh 4000
DosGauss.Width 0.01
MO.fileout off # on|off
num.HOMOs 1 # default=1
num.LUMOs 1 # default=1
MO.Nkpoint 1 # default=1
<MO.kpoint
0.0 0.0 0.0
MO.kpoint>
#
# File Name
#
System.CurrrentDirectory ./ # default=./
System.Name lead-r-8zgnr
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 0 # default=1 (0-2)
#
# Definition of Atomic Species
#
Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
H H5.0-s2 H_CA13
Definition.of.Atomic.Species>
NEGF.output_hks true
NEGF.filename.hks lead-r-8zgnr.hks
#
# Atoms
#
Atoms.Number 36
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
<Atoms.SpeciesAndCoordinates
1 C 0.0000005 0.7140385 6.1011879 1.5000000 2.5000000
2 C 0.0000004 2.1457201 6.1013117 1.5000000 2.5000000
3 C -0.0000002 4.9766306 6.1012146 1.5000000 2.5000000
4 C 0.0000001 6.3942050 6.1013979 1.5000000 2.5000000
5 C 0.0000001 9.2258519 6.1013977 1.5000000 2.5000000
6 C 0.0000004 10.6434033 6.1012143 1.5000000 2.5000000
7 C -0.0000004 13.4742418 6.1013119 1.5000000 2.5000000
8 C -0.0000004 14.9059644 6.1011875 1.5000000 2.5000000
9 C 0.0000005 0.0361626 7.3212037 1.5000000 2.5000000
10 C 0.0000005 0.7140385 8.5411879 1.5000000 2.5000000
11 C 0.0000004 2.1457201 8.5413117 1.5000000 2.5000000
12 C 0.0000001 2.8501725 7.3213209 1.5000000 2.5000000
13 C -0.0000001 4.2700744 7.3212023 1.5000000 2.5000000
14 C -0.0000002 4.9766306 8.5412146 1.5000000 2.5000000
15 C 0.0000001 6.3942050 8.5413979 1.5000000 2.5000000
16 C 0.0000001 7.1014018 7.3214044 1.5000000 2.5000000
17 C -0.0000001 8.5186603 7.3214042 1.5000000 2.5000000
18 C 0.0000001 9.2258519 8.5413977 1.5000000 2.5000000
19 C 0.0000004 10.6434033 8.5412143 1.5000000 2.5000000
20 C 0.0000003 11.3499296 7.3212020 1.5000000 2.5000000
21 C -0.0000002 12.7697977 7.3213211 1.5000000 2.5000000
22 C -0.0000004 13.4742418 8.5413119 1.5000000 2.5000000
23 C -0.0000004 14.9059644 8.5411875 1.5000000 2.5000000
24 C -0.0000004 15.5838921 7.3212032 1.5000000 2.5000000
25 H 0.0000003 -1.0818549 7.3212134 0.5000000 0.5000000
26 H -0.0000005 16.7019089 7.3212129 0.5000000 0.5000000
27 C 0.0000005 0.0361626 9.7612037 1.5000000 2.5000000
28 C 0.0000001 2.8501725 9.7613209 1.5000000 2.5000000
29 C -0.0000001 4.2700744 9.7612023 1.5000000 2.5000000
30 C 0.0000001 7.1014018 9.7614044 1.5000000 2.5000000
31 C -0.0000001 8.5186603 9.7614042 1.5000000 2.5000000
32 C 0.0000003 11.3499296 9.7612020 1.5000000 2.5000000
33 C -0.0000002 12.7697977 9.7613211 1.5000000 2.5000000
34 C -0.0000004 15.5838921 9.7612032 1.5000000 2.5000000
35 H 0.0000003 -1.0818549 9.7612134 0.5000000 0.5000000
36 H -0.0000005 16.7019089 9.7612129 0.5000000 0.5000000
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
<Atoms.UnitVectors
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Atoms.UnitVectors>
#
# SCF or Electronic System
#
scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 1000 # default=40
scf.EigenvalueSolver Band # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 201 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 10.0 # default=1
scf.Init.Mixing.Weight 0.100 # default=0.30
scf.Min.Mixing.Weight 0.01 # default=0.001
scf.Max.Mixing.Weight 0.105 # default=0.40
scf.Mixing.History 40 # default=5
scf.Mixing.StartPulay 10 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-9 # default=1.0e-6 (Hartree)
#
# MD or Geometry Optimization
#
MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 18 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 2000 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)
#
# Band dispersion
#
Band.dispersion off # on|off, default=off
<Band.KPath.UnitCell
0.000 0.000 4.88
10.000 0.000 0.000
0.000 27.000 0.000
Band.KPath.UnitCell>
Band.Nkpath 1
<Band.kpath
601 0.0 0.0 0.0 0.5 0.0 0.0 G X
Band.kpath>
#
# DOS and PDOS
#
Dos.fileout off # on|off, default=off
Dos.Erange -20.0 20.0 # default = -20 20
Dos.Kgrid 601 1 1 # default = Kgrid1 Kgrid2 Kgrid3
DosGauss.fileout off
DosGauss.Num.Mesh 4000
DosGauss.Width 0.01
#
# File Name
#
System.CurrrentDirectory ./ # default=./
System.Name negf-8zgnr-0.3
level.of.stdout 1 # default=1 (1-3)
level.of.fileout 1 # default=1 (0-2)
NEGF.filename.hks.l lead-l-8zgnr.hks
NEGF.filename.hks.r lead-r-8zgnr.hks
NEGF.SCF.Iter.Band 20
NEGF.Num.Poles 100 # defalut=150
NEGF.scf.Kgrid 1 1 # defalut=1 1
NEGF.bias.voltage -0.3 # default=0.0 (eV)
NEGF.bias.neq.im.energy 0.01 # default=0.01 (eV)
NEGF.bias.neq.energy.step 0.02 # default=0.02 (eV)
Dos.fileout off # on|off, default=off
NEGF.Dos.energyrange -20.0 20.0 1.0e-4 #default=-10.0 10.0 5.0e-3 (eV)
NEGF.Dos.energy.div 4000 # default=200
NEGF.Dos.Kgrid 1 1 # default=1 1
#
# Transmission & Eigen Channel Analysis
#
NEGF.tran.Analysis on # default on
NEGF.tran.energydiv 800 # default=200
NEGF.tran.energyrange -4 4 0.001 # default=-10.0 10.0 5.0e-3 (eV)
NEGF.tran.Kgrid 1 1 # default= 1 1
NEGF.tran.CurrentDensity on # default on
NEGF.tran.Channel on # default on
NEGF.Channel.Nkpoint 1 # default 1
<NEGF.Channel.kpoint
0.0 0.0
NEGF.Channel.kpoint>
# default 0.0 0.0
NEGF.Channel.Nenergy 1 # default 1
<NEGF.Channel.energy
0.0
NEGF.Channel.energy>
# default 0.0
NEGF.Channel.Num 5 # defualt=5(for collinear), 10(for Non-collinear)
#
# Definition of Atomic Species
#
Species.Number 2
<Definition.of.Atomic.Species
C C5.0-s2p1 C_CA13
H H5.0-s2 H_CA13
Definition.of.Atomic.Species>
#
# Atoms
#
Atoms.SpeciesAndCoordinates.Unit Ang # Ang|AU
Atoms.Number 10
<Atoms.SpeciesAndCoordinates
1 C 0.0000005 0.0361626 4.8812037 2.1000000 1.9000000
2 C 0.0000001 2.8501725 4.8813209 2.1000000 1.9000000
3 C -0.0000001 4.2700744 4.8812023 2.1000000 1.9000000
4 C 0.0000001 7.1014018 4.8814044 2.1000000 1.9000000
5 C -0.0000001 8.5186603 4.8814042 2.1000000 1.9000000
6 C 0.0000003 11.3499296 4.8812020 2.1000000 1.9000000
7 C -0.0000002 12.7697977 4.8813211 2.1000000 1.9000000
8 C -0.0000004 15.5838921 4.8812032 2.1000000 1.9000000
9 H 0.0000003 -1.0818549 4.8812134 0.5000000 0.5000000
10 H -0.0000005 16.7019089 4.8812129 0.5000000 0.5000000
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang # Ang|AU
#<Atoms.UnitVectors
# 0.000 0.000 4.88
# 10.000 0.000 0.000
# 0.000 24.000 0.000
#Atoms.UnitVectors>
#
# Lead-Left
#
LeftLeadAtoms.Number 36
<LeftLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 0.0000005 0.0361626 0.0012037 2.1000000 1.9000000
2 C 0.0000005 0.7140385 1.2211879 2.1000000 1.9000000
3 C 0.0000004 2.1457201 1.2213117 2.1000000 1.9000000
4 C 0.0000001 2.8501725 0.0013209 2.1000000 1.9000000
5 C -0.0000001 4.2700744 0.0012023 2.1000000 1.9000000
6 C -0.0000002 4.9766306 1.2212146 2.1000000 1.9000000
7 C 0.0000001 6.3942050 1.2213979 2.1000000 1.9000000
8 C 0.0000001 7.1014018 0.0014044 2.1000000 1.9000000
9 C -0.0000001 8.5186603 0.0014042 2.1000000 1.9000000
10 C 0.0000001 9.2258519 1.2213977 2.1000000 1.9000000
11 C 0.0000004 10.6434033 1.2212143 2.1000000 1.9000000
12 C 0.0000003 11.3499296 0.0012020 2.1000000 1.9000000
13 C -0.0000002 12.7697977 0.0013211 2.1000000 1.9000000
14 C -0.0000004 13.4742418 1.2213119 2.1000000 1.9000000
15 C -0.0000004 14.9059644 1.2211875 2.1000000 1.9000000
16 C -0.0000004 15.5838921 0.0012032 2.1000000 1.9000000
17 H 0.0000003 -1.0818549 0.0012134 0.5000000 0.5000000
18 H -0.0000005 16.7019089 0.0012129 0.5000000 0.5000000
19 C 0.0000005 0.0361626 2.4412037 2.1000000 1.9000000
20 C 0.0000005 0.7140385 3.6611879 2.1000000 1.9000000
21 C 0.0000004 2.1457201 3.6613117 2.1000000 1.9000000
22 C 0.0000001 2.8501725 2.4413209 2.1000000 1.9000000
23 C -0.0000001 4.2700744 2.4412023 2.1000000 1.9000000
24 C -0.0000002 4.9766306 3.6612146 2.1000000 1.9000000
25 C 0.0000001 6.3942050 3.6613979 2.1000000 1.9000000
26 C 0.0000001 7.1014018 2.4414044 2.1000000 1.9000000
27 C -0.0000001 8.5186603 2.4414042 2.1000000 1.9000000
28 C 0.0000001 9.2258519 3.6613977 2.1000000 1.9000000
29 C 0.0000004 10.6434033 3.6612143 2.1000000 1.9000000
30 C 0.0000003 11.3499296 2.4412020 2.1000000 1.9000000
31 C -0.0000002 12.7697977 2.4413211 2.1000000 1.9000000
32 C -0.0000004 13.4742418 3.6613119 2.1000000 1.9000000
33 C -0.0000004 14.9059644 3.6611875 2.1000000 1.9000000
34 C -0.0000004 15.5838921 2.4412032 2.1000000 1.9000000
35 H 0.0000003 -1.0818549 2.4412134 0.5000000 0.5000000
36 H -0.0000005 16.7019089 2.4412129 0.5000000 0.5000000
LeftLeadAtoms.SpeciesAndCoordinates>
#
# Lead-Right
#
RightLeadAtoms.Number 36
<RightLeadAtoms.SpeciesAndCoordinates # Unit=Ang.
1 C 0.0000005 0.7140385 6.1011879 1.9000000 2.1000000
2 C 0.0000004 2.1457201 6.1013117 1.9000000 2.1000000
3 C -0.0000002 4.9766306 6.1012146 1.9000000 2.1000000
4 C 0.0000001 6.3942050 6.1013979 1.9000000 2.1000000
5 C 0.0000001 9.2258519 6.1013977 1.9000000 2.1000000
6 C 0.0000004 10.6434033 6.1012143 1.9000000 2.1000000
7 C -0.0000004 13.4742418 6.1013119 1.9000000 2.1000000
8 C -0.0000004 14.9059644 6.1011875 1.9000000 2.1000000
9 C 0.0000005 0.0361626 7.3212037 1.9000000 2.1000000
10 C 0.0000005 0.7140385 8.5411879 1.9000000 2.1000000
11 C 0.0000004 2.1457201 8.5413117 1.9000000 2.1000000
12 C 0.0000001 2.8501725 7.3213209 1.9000000 2.1000000
13 C -0.0000001 4.2700744 7.3212023 1.9000000 2.1000000
14 C -0.0000002 4.9766306 8.5412146 1.9000000 2.1000000
15 C 0.0000001 6.3942050 8.5413979 1.9000000 2.1000000
16 C 0.0000001 7.1014018 7.3214044 1.9000000 2.1000000
17 C -0.0000001 8.5186603 7.3214042 1.9000000 2.1000000
18 C 0.0000001 9.2258519 8.5413977 1.9000000 2.1000000
19 C 0.0000004 10.6434033 8.5412143 1.9000000 2.1000000
20 C 0.0000003 11.3499296 7.3212020 1.9000000 2.1000000
21 C -0.0000002 12.7697977 7.3213211 1.9000000 2.1000000
22 C -0.0000004 13.4742418 8.5413119 1.9000000 2.1000000
23 C -0.0000004 14.9059644 8.5411875 1.9000000 2.1000000
24 C -0.0000004 15.5838921 7.3212032 1.9000000 2.1000000
25 H 0.0000003 -1.0818549 7.3212134 0.5000000 0.5000000
26 H -0.0000005 16.7019089 7.3212129 0.5000000 0.5000000
27 C 0.0000005 0.0361626 9.7612037 1.9000000 2.1000000
28 C 0.0000001 2.8501725 9.7613209 1.9000000 2.1000000
29 C -0.0000001 4.2700744 9.7612023 1.9000000 2.1000000
30 C 0.0000001 7.1014018 9.7614044 1.9000000 2.1000000
31 C -0.0000001 8.5186603 9.7614042 1.9000000 2.1000000
32 C 0.0000003 11.3499296 9.7612020 1.9000000 2.1000000
33 C -0.0000002 12.7697977 9.7613211 1.9000000 2.1000000
34 C -0.0000004 15.5838921 9.7612032 1.9000000 2.1000000
35 H 0.0000003 -1.0818549 9.7612134 0.5000000 0.5000000
36 H -0.0000005 16.7019089 9.7612129 0.5000000 0.5000000
RightLeadAtoms.SpeciesAndCoordinates>
#
# SCF or Electronic System
#
scf.XcType LSDA-CA # LDA|LSDA-CA|LSDA-PW|GGA-PBE
scf.SpinPolarization on # On|Off|NC
scf.ElectronicTemperature 300.0 # default=300 (K)
scf.energycutoff 120.0 # default=150 (Ry)
#scf.Ngrid 140 140 100 # about=200 (Ry)
scf.maxIter 2000 # default=40
scf.EigenvalueSolver NEGF # DC|GDC|Cluster|Band
scf.lapack.dste dstevx # dstegr|dstedc|dstevx, default=dstegr
scf.Kgrid 1 1 1 # means n1 x n2 x n3
scf.Mixing.Type rmm-diisk # Simple|Rmm-Diis|Gr-Pulay|Kerker|Rmm-Diisk
scf.Kerker.factor 20.0 # default=1
scf.Init.Mixing.Weight 0.1 # default=0.30
scf.Min.Mixing.Weight 0.04 # default=0.001
scf.Max.Mixing.Weight 0.4 # default=0.40
scf.Mixing.History 60 # default=5
scf.Mixing.StartPulay 20 # default=6
scf.Mixing.EveryPulay 1 # default=6
scf.criterion 1.0e-7 # default=1.0e-6 (Hartree)
#
# MD or Geometry Optimization
#
MD.Type Nomd # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 10 # default=3
MD.Opt.StartDIIS 6 # default=5
MD.Opt.EveryDIIS 5 # default=10
MD.maxIter 200 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)