Negative charge on Al in Al-doped AGNR |
- Date: 2019/07/13 17:04
- Name: Lovleen Kaur
<lovleenkaurkkr@gmail.com>
- Hello Developers,
I am doing doping of Al in Arm-chair graphene nano ribbon by replacing one C atom. In the optimized structure when i do Mulliken charge analysis i am getting a negative charge on Al (-0.66) but according to literature there should be positive charge on Al of order approx +1.6.
Q2. When i draw graphene.tden.cube in openMX viewer it is showing a hole near Al, is it showing lack of electron density? In this file also it is showing -0.66 charge on Al.
The input file for this system is as follows:
System.CurrrentDirectory ./
System.Name graphene
DATA.PATH ../../../../../../../DFT_DATA13
level.of.stdout 1
level.of.fileout 1
Species.Number 3
<Definition.of.Atomic.Species
H H6.0-s2p1 H_PBE13
C C6.0-s2p2d1 C_PBE13
Al Al8.0-s3p3d2 Al_PBE13
Definition.of.Atomic.Species>
Atoms.Number 110
Atoms.SpeciesAndCoordinates.Unit Ang
<Atoms.SpeciesAndCoordinates
1 C 0.75920 1.25294 -0.00676 2.0 2.0
2 C 2.13406 1.25131 -0.00795 2.0 2.0
3 C 5.07119 1.24934 -0.01366 2.0 2.0
4 C 9.39498 1.23448 -0.06859 2.0 2.0
5 C 6.44438 1.24787 -0.03697 2.0 2.0
6 C 10.77360 1.22292 -0.07368 2.0 2.0
7 C 0.01734 2.45862 -0.00655 2.0 2.0
8 C 0.01513 4.93099 -0.01135 2.0 2.0
9 C 0.01932 7.39352 -0.01171 2.0 2.0
10 C 0.03488 9.86418 -0.00646 2.0 2.0
11 C 2.88017 2.45552 -0.01067 2.0 2.0
12 C 2.89449 4.92872 -0.01752 2.0 2.0
13 C 2.89459 7.39023 -0.01251 2.0 2.0
14 C 2.87243 9.85800 -0.01064 2.0 2.0
15 C 0.73410 3.69022 -0.00744 2.0 2.0
16 C 0.73587 6.16044 -0.00893 2.0 2.0
17 C 0.73470 8.62923 -0.00631 2.0 2.0
18 C 0.74789 11.07028 -0.00559 2.0 2.0
19 C 2.17038 3.68933 -0.01053 2.0 2.0
20 C 2.17643 6.16183 -0.01053 2.0 2.0
21 C 2.17468 8.63404 -0.00722 2.0 2.0
22 C 2.15743 11.07233 -0.00831 2.0 2.0
23 C 4.32413 2.45322 -0.02215 2.0 2.0
24 C 4.32498 4.93142 -0.03663 2.0 2.0
25 C 4.32231 7.40179 -0.02496 2.0 2.0
26 C 4.30956 9.87471 -0.02701 2.0 2.0
27 C 8.64313 2.44288 -0.09170 2.0 2.0
28 C 8.60587 4.91292 -0.06570 2.0 2.0
29 C 8.63097 7.43542 0.12103 2.0 2.0
30 C 8.59189 9.95853 -0.07101 2.0 2.0
31 C 7.19409 2.44967 -0.07540 2.0 2.0
32 C 7.18485 4.92376 -0.08522 2.0 2.0
33 C 7.21106 7.42062 -0.00506 2.0 2.0
34 C 7.15572 9.92019 -0.08926 2.0 2.0
35 C 11.52816 2.42641 -0.09109 2.0 2.0
36 C 11.51288 4.87871 0.11349 2.0 2.0
37 Al 11.53521 7.45500 1.09550 1.5 1.5
38 C 11.49162 10.03896 0.12115 2.0 2.0
39 C 5.03948 3.68561 -0.04735 2.0 2.0
40 C 5.04834 6.16620 -0.04112 2.0 2.0
41 C 5.04368 8.64026 -0.03651 2.0 2.0
42 C 5.03727 11.08632 -0.03600 2.0 2.0
43 C 9.35508 3.67344 -0.08930 2.0 2.0
44 C 9.31546 6.13477 0.12980 2.0 2.0
45 C 9.30603 8.75605 0.14508 2.0 2.0
46 C 9.34874 11.17037 -0.17004 2.0 2.0
47 C 6.47059 3.68257 -0.07976 2.0 2.0
48 C 6.48285 6.17329 -0.04810 2.0 2.0
49 C 6.46724 8.66209 -0.04599 2.0 2.0
50 C 6.38594 11.10978 -0.07930 2.0 2.0
51 C 10.80423 3.64932 -0.07256 2.0 2.0
52 C 10.69636 5.99858 0.38469 2.0 2.0
53 C 10.69298 8.91050 0.39321 2.0 2.0
54 C 10.74064 11.22040 -0.15258 2.0 2.0
55 H 0.24216 0.29500 -0.00936 0.5 0.5
56 H 2.64837 0.29231 -0.01152 0.5 0.5
57 H 4.55471 0.29047 0.01255 0.5 0.5
58 H 6.95969 0.28799 -0.02373 0.5 0.5
59 H 8.87812 0.27754 -0.03045 0.5 0.5
60 H 11.27765 0.25793 -0.03604 0.5 0.5
61 H 11.21429 12.19330 -0.30149 0.5 0.5
62 H 8.81932 12.11435 -0.28531 0.5 0.5
63 H 6.90824 12.07995 -0.07458 0.5 0.5
64 H 4.49005 12.04326 -0.00365 0.5 0.5
65 H 2.65065 12.02538 -0.01396 0.5 0.5
66 H 0.25316 12.02557 -0.00941 0.5 0.5
67 C 13.73683 1.26320 -0.04639 2.0 2.0
68 C 15.11199 1.26848 -0.02300 2.0 2.0
69 C 18.05105 1.26777 -0.01427 2.0 2.0
70 C 19.42516 1.26388 -0.00679 2.0 2.0
71 C 12.97820 2.46130 -0.06078 2.0 2.0
72 C 12.97573 4.94227 0.09121 2.0 2.0
73 C 13.20430 7.43379 0.37230 2.0 2.0
74 C 12.99605 9.94053 0.10607 2.0 2.0
75 C 15.85755 2.47793 -0.04018 2.0 2.0
76 C 15.89318 4.93984 -0.09118 2.0 2.0
77 C 15.89993 7.42892 -0.08360 2.0 2.0
78 C 15.91009 9.92462 -0.08949 2.0 2.0
79 C 13.69399 3.71048 -0.02747 2.0 2.0
80 C 13.77437 6.18258 0.11546 2.0 2.0
81 C 13.78068 8.70128 0.12469 2.0 2.0
82 C 13.76304 11.11750 -0.00667 2.0 2.0
83 C 15.14501 3.70712 -0.05733 2.0 2.0
84 C 15.19404 6.17418 -0.07461 2.0 2.0
85 C 15.20024 8.69312 -0.05555 2.0 2.0
86 C 15.15191 11.11725 -0.06554 2.0 2.0
87 C 17.30611 2.47388 -0.03297 2.0 2.0
88 C 17.31890 4.94092 -0.07790 2.0 2.0
89 C 17.32722 7.41693 -0.09070 2.0 2.0
90 C 17.35453 9.90248 -0.08364 2.0 2.0
91 C 20.17748 2.46556 -0.01010 2.0 2.0
92 C 20.19061 4.93828 -0.02385 2.0 2.0
93 C 20.19562 7.40267 -0.02945 2.0 2.0
94 C 20.19629 9.87431 -0.01846 2.0 2.0
97 C 18.04937 8.65934 -0.07481 2.0 2.0
98 C 18.09386 11.10107 -0.04530 2.0 2.0
99 C 19.46721 3.69807 -0.02404 2.0 2.0
100 C 19.47441 6.17193 -0.04259 2.0 2.0
101 C 19.48277 8.64668 -0.04116 2.0 2.0
102 C 19.47923 11.08975 -0.01443 2.0 2.0
103 H 13.22608 0.30200 -0.04620 0.5 0.5
104 H 15.62861 0.31096 0.00219 0.5 0.5
105 H 17.53397 0.30939 -0.01019 0.5 0.5
106 H 19.93699 0.30265 0.00071 0.5 0.5
107 H 19.99746 12.03905 0.01248 0.5 0.5
108 H 17.58746 12.05912 -0.03493 0.5 0.5
109 H 15.65947 12.08035 -0.08450 0.5 0.5
110 H 13.25835 12.08480 -0.02277 0.5 0.5
Atoms.SpeciesAndCoordinates>
Atoms.UnitVectors.Unit Ang
<Atoms.UnitVectors
21.60574 0.00425 0.00027
0.00305 30.06117 -0.00175
0.00021 -0.00177 29.97588
Atoms.UnitVectors>
scf.XcType GGA-PBE
scf.SpinPolarization on
scf.ElectronicTemperature 300.0
scf.energycutoff 250.0
scf.maxIter 100
scf.EigenvalueSolver band
scf.Kgrid 5 1 1
scf.Mixing.Type rmm-diisk
scf.Init.Mixing.Weight 0.05
scf.Min.Mixing.Weight 0.01
scf.Max.Mixing.Weight 0.30
scf.Mixing.History 25
scf.Mixing.StartPulay 15#
scf.criterion 1.0e-7
# MD or Geometry Optimization
#
MD.Type RF # Opt|EF|BFGS|RF|DIIS
MD.Opt.DIIS.History 3 # default=3
MD.Opt.StartDIIS 10 # default=5
#MD.Opt.EveryDIIS 10000 # default=10
MD.maxIter 500 #
MD.Opt.criterion 1.0e-4 # default=1.0e-4 (a.u.)
Q3. I have also done the NPA analysis of the final structure and the result is shown below. Up to my interpretation as it is shoowing 0.73481704 population for Al in up-spin and 0.73481704 in downspin so at total of approx 1.5 population which is showing that Al has a positive charge of 1.5 but Mulliken is showing negative charge and how it is showing Total natural pop. of target atoms = 19.54637 as the sum of up-spin and down-spin is not equal to this value. Is my interpretation correct? Please suggest it will be very helpful to me.
NATURAL ATOMIC ORBITAL (NAO) Analysis
***********************************************
## Threshold for occupied or Rydberg orbital in NAO calc.: 0.850000 elec.
<< 1 >> NAO calculation
***********************************************
for up-spin
***********************************************
<< 2 >> Sending & Receiving atom data
<< 3 >> Collection of NAO data
### Natural populations of target atoms ###
(1) 37 Al : 0.73481704
(2) 52 C : 2.23194178
(3) 53 C : 2.25635983
(4) 73 C : 2.22935052
### Total natural pop. of target atoms = 19.54637
### NAO for each target atom (details) ###
#### Global atom num.: 37 ( Al ) / NP = 0.7348
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
NP in NAO 0.0000 0.0021 0.2747 0.0001 0.0004 0.1699 0.0001 0.0005 0.1722 0.0002 0.0012 0.1037 0.0005 0.0007 0.0003 0.0022 0.0003 0.0023 0.0000 0.0015 0.0001 0.0017
Energy (Hartree) 1.4133 1.3965 0.0801 1.7120 1.3985 0.2465 1.7230 1.3975 0.2471 0.7664 1.4554 0.1570 0.5429 1.1398 0.8541 1.5641 0.8693 1.5548 0.7133 1.3485 0.7200 1.3436
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
1 s -2.7445 -6.1637 -2.3305 0.0456 0.0215 0.0041 -0.0960 -0.1246 -0.0213 -1.9938 -7.9676 -0.9072 -2.1959 -2.3290 0.0722 -0.0234 0.0105 -0.0766 0.0431 -0.0241 -0.0960 0.0217
2 s -1.0131 2.8784 -0.0156 -0.0063 -0.0126 -0.0008 0.0154 0.0332 0.0022 0.2655 1.6650 0.1037 0.5349 0.2263 -0.0179 0.0104 -0.0063 0.0124 -0.0085 -0.0030 0.0227 0.0089
3 s 1.3822 1.2692 -0.0621 0.0015 -0.0140 -0.0005 0.0214 0.0254 0.0001 0.4876 0.6459 -0.0081 -0.0407 0.2025 0.0043 -0.0035 -0.0019 0.0026 0.0051 -0.0135 -0.0017 0.0106
1 px -0.0222 -0.0168 -0.0040 1.1782 6.5668 1.6792 -0.0441 -0.0986 -0.0103 -0.0396 -0.0210 -0.0006 -0.0327 0.0102 0.7077 2.6363 -0.0346 -0.1035 -2.1648 -3.6609 0.0308 0.0498
2 px 0.0061 0.0084 -0.0003 2.3308 -2.0769 0.5245 -0.0089 -0.0092 -0.0028 0.0110 -0.0208 -0.0008 0.0125 0.0084 -0.1145 0.5698 0.0313 -0.0500 1.3158 -0.5263 -0.0088 0.0072
3 px -0.0007 0.0045 -0.0003 -2.1865 -0.4791 0.1422 0.0053 0.0054 -0.0003 -0.0081 0.0023 0.0002 -0.0062 0.0038 -0.0678 -0.2456 -0.0122 0.0229 -0.4020 0.6621 -0.0001 -0.0072
1 py 0.0586 0.0601 0.0153 -0.0390 -0.0881 -0.0097 1.1579 6.6558 1.6836 0.0624 0.0228 0.0003 0.0812 0.0607 0.0442 0.0510 -0.6747 -2.5810 0.0294 0.0525 -2.2301 -3.6411
2 py 0.0138 -0.0095 0.0057 -0.0028 -0.0028 -0.0024 2.3466 -2.0874 0.5237 -0.0383 0.0331 0.0012 -0.0454 0.0271 -0.0332 0.0361 0.0923 -0.5193 -0.0072 0.0047 1.3475 -0.5370
3 py -0.0174 -0.0112 -0.0004 0.0068 0.0054 -0.0003 -2.1725 -0.4638 0.1430 0.0158 -0.0116 -0.0008 0.0217 -0.0278 0.0169 -0.0201 0.0735 0.2364 0.0006 -0.0096 -0.4100 0.6733
1 pz 1.0854 2.9193 0.4341 -0.0142 0.0162 0.0016 0.0327 -0.0179 -0.0020 1.1811 4.7873 1.3865 0.0270 -0.1566 -0.0268 0.0269 0.0042 0.0599 -0.0193 0.0055 0.0520 0.0191
2 pz 0.4071 -0.6208 0.1795 0.0178 -0.0048 0.0001 -0.0471 0.0154 0.0002 0.4580 -1.3573 0.4663 0.1081 0.1029 -0.0090 0.0085 -0.0059 0.0101 0.0110 -0.0007 -0.0286 0.0078
3 pz -0.4327 -0.2552 -0.0003 -0.0059 0.0092 0.0006 0.0130 -0.0190 -0.0012 -1.3522 -0.7453 0.1036 0.0233 0.0611 0.0045 0.0010 0.0016 -0.0006 -0.0074 0.0025 0.0146 -0.0082
1 d3z^2-r^2 0.0195 0.2780 0.0045 0.0046 -0.0079 -0.0004 0.0001 0.0264 0.0015 -0.0243 -0.0832 -0.0047 0.7440 1.8691 -0.0057 -0.0002 -0.0030 0.0043 0.0025 0.0005 -0.0061 -0.0120
2 d3z^2-r^2 0.4213 -0.3947 0.0339 -0.0125 0.0140 0.0007 0.0515 -0.0376 -0.0020 -0.0098 0.0445 0.0024 -1.4878 0.4624 0.0200 -0.0086 0.0074 -0.0002 -0.0083 -0.0041 0.0271 -0.0072
1 dx^2-y^2 0.0021 -0.0033 0.0002 0.3008 0.4263 0.0244 0.0011 0.0141 0.0008 -0.0041 -0.0015 -0.0001 -0.0059 -0.0000 0.9245 2.4513 -0.0037 -0.0222 -0.0424 -0.2658 0.0013 0.0012
2 dx^2-y^2 -0.0190 0.0145 -0.0016 -0.0090 -0.2467 -0.0137 0.0404 -0.0227 -0.0012 0.0112 0.0070 0.0004 0.0199 -0.0091 -2.0266 0.8299 -0.0056 0.0081 0.0282 -0.1456 0.0059 -0.0047
1 dxy 0.0025 0.0015 0.0002 -0.0087 -0.0178 -0.0010 -0.2949 -0.4186 -0.0239 0.0006 0.0075 0.0004 -0.0028 0.0041 -0.0034 -0.0226 0.9298 2.4411 -0.0023 0.0056 0.0471 0.2601
2 dxy -0.0030 0.0067 -0.0002 -0.0346 0.0195 0.0010 0.0279 0.2261 0.0126 0.0050 -0.0019 -0.0001 0.0074 0.0002 -0.0055 0.0088 -2.0572 0.8495 -0.0019 0.0076 -0.0307 0.1358
1 dxz 0.0001 -0.0046 -0.0000 -0.0709 -1.0629 -0.0592 0.0061 0.0139 0.0008 0.0050 -0.0035 -0.0002 0.0051 -0.0025 0.0025 -0.3195 -0.0015 0.0047 0.9467 2.1883 -0.0039 -0.0133
2 dxz -0.0133 0.0053 -0.0011 -1.1258 1.0599 0.0562 0.0044 -0.0109 -0.0006 -0.0146 0.0086 0.0004 -0.0075 0.0025 0.0430 -0.0289 -0.0016 0.0097 -2.0103 0.6658 0.0085 -0.0040 #### Global atom num.: 52 ( C ) / NP = 2.2319
-------------------------------------------------------------------------------------------------------------------------
NP in NAO 0.0026 0.5014 0.0021 0.5657 0.0040 0.6223 0.0025 0.5292 0.0003 0.0003 0.0004 0.0005 0.0004
Energy (Hartree) 3.0986 -0.0631 1.7141 -0.0106 1.5803 -0.0576 0.8733 -0.1023 1.6026 2.1358 2.1394 1.6632 1.5608
-------------------------------------------------------------------------------------------------------------------------
1 s -10.6702 1.1047 0.7265 0.0422 1.2565 0.0734 1.3242 0.0814 -1.6641 1.0366 -1.7278 0.6750 1.2570
2 s 5.7373 0.4279 -0.2395 -0.0328 -0.4152 -0.0570 -0.5840 -0.0836 0.8743 -0.3504 0.5892 -0.3813 -0.7016
1 px 0.5001 -0.0137 -5.9270 0.8706 0.8366 0.0327 -0.5639 -0.0085 0.0733 -2.5894 -1.0057 -1.7516 1.0031
2 px -0.3060 -0.0182 4.7840 0.3987 -0.4867 -0.0573 0.3475 0.0390 -0.0344 1.4947 0.5730 1.0601 -0.6012
1 py 0.8701 -0.0229 0.8324 0.0320 -4.8902 0.9128 -1.0563 -0.0158 0.1061 0.8621 1.4724 1.0152 -0.5587
2 py -0.5314 -0.0318 -0.4859 -0.0572 4.1732 0.3261 0.6489 0.0728 -0.0484 -0.4839 -0.8598 -0.6072 0.3436
1 pz 1.1546 0.0036 -0.5585 -0.0076 -1.0447 -0.0139 -1.8048 1.0321 -0.2606 -0.4108 0.7314 -0.0712 -0.1581
2 pz -0.7681 -0.0554 0.3464 0.0389 0.6466 0.0724 2.2261 0.0907 0.1874 0.2521 -0.4461 0.0431 0.0942
1 d3z^2-r^2 0.0668 0.0068 -0.0016 -0.0003 -0.0022 -0.0003 0.0109 0.0017 1.3590 -0.0725 0.1141 -0.0101 -0.0175
1 dx^2-y^2 -0.0245 -0.0025 0.0788 0.0125 -0.0251 -0.0040 0.0137 0.0022 -0.0725 1.7739 -0.0240 0.0866 -0.1428
1 dxy 0.0412 0.0042 0.0300 0.0048 -0.0456 -0.0072 -0.0242 -0.0038 0.1141 -0.0240 1.7993 0.1419 0.0699
1 dxz -0.0295 -0.0030 0.0572 0.0091 -0.0326 -0.0052 0.0023 0.0004 -0.0101 0.0866 0.1419 1.4451 -0.0667
1 dyz -0.0541 -0.0055 -0.0323 -0.0051 0.0187 0.0030 0.0050 0.0008 -0.0175 -0.1428 0.0699 -0.0667 1.3679
#### Global atom num.: 53 ( C ) / NP = 2.2564
-------------------------------------------------------------------------------------------------------------------------
NP in NAO 0.0028 0.5031 0.0020 0.5649 0.0037 0.6158 0.0025 0.5598 0.0003 0.0003 0.0004 0.0005 0.0004
Energy (Hartree) 3.0951 -0.0600 1.6300 -0.0109 1.4513 -0.0584 0.9035 -0.0954 1.5826 1.9932 2.0497 1.7448 1.6363
-------------------------------------------------------------------------------------------------------------------------
1 s -10.5393 1.0909 0.6917 0.0556 -0.9310 -0.0505 1.6386 0.0914 -1.3250 1.0403 1.7201 0.6169 -1.3373
2 s 5.7049 0.4312 -0.2162 -0.0305 0.2587 0.0340 -0.7175 -0.1022 0.6894 -0.3675 -0.5817 -0.3748 0.7512
1 px 0.4464 -0.0025 -5.6799 0.8824 -0.8771 -0.0331 -0.5969 -0.01 #### Global atom num.: 73 ( C ) / NP = 2.2294
-------------------------------------------------------------------------------------------------------------------------
NP in NAO 0.0026 0.5017 0.0052 0.6580 0.0012 0.5385 0.0026 0.5175 0.0003 0.0004 0.0004 0.0003 0.0006
Energy (Hartree) 3.0800 -0.0601 1.5400 -0.0800 1.7760 0.0083 0.8623 -0.1063 1.6011 2.1459 2.1580 1.4995 1.6835
-------------------------------------------------------------------------------------------------------------------------
1 s -10.7438 1.1232 -1.5689 -0.0780 0.0948 0.0025 1.2124 0.0680 -1.7253 -1.9492 -0.0854 -1.4124 -0.0079
2 s 5.7475 0.4290 0.5304 0.0705 -0.0328 -0.0042 -0.5317 -0.0736 0.8963 0.6469 0.0283 0.7852 0.0060
1 px -1.1143 0.0315 -4.5030 0.9545 0.0265 -0.0034 1.1756 0.0110 -0.2420 -0.8581 0.0077 0.1055 -0.0443
2 px 0.6847 0.0404 3.9521 0.2820 -0.0130 -0.0005 -0.7221 -0.0774 0.1301 0.5022 -0.0139 -0.0651 0.0320
1 py 0.0669 -0.0039 0.0281 -0.0031 -6.4123 0.8868 0.0188 0.0023 0.0285 0.1013 3.2336 -0.0780 -2.1428
2 py -0.0421 -0.0021 -0.0133 -0.0006 5.0696 0.4090 -0.0113 -0.0016 -0.0111 -0.0562 -1.8615 0.0497 1.2869
1 pz 1.0556 0.0019 1.1661 0.0095 0.0181 0.0022 -1.7829 1.0443 -0.2226 0.8123 -0.0409 0.1644 0.0060
2 pz -0.7006 -0.0497 -0.7203 -0.0771 -0.0112 -0.0016 2.2111 0.0795 0.1603 -0.4916 0.0277 -0.0976 -0.0074
1 d3z^2-r^2 0.0702 0.0070 0.0068 0.0010 -0.0004 -0.0001 0.0096 0.0015 1.3613 0.1312 0.0064 0.0206 0.0000
1 dx^2-y^2 0.0464 0.0047 0.0274 << 2 >> Sending & Receiving atom data
<< 3 >> Collection of NAO data
### Natural populations of target atoms ###
(1) 37 Al : 0.73481704
(2) 52 C : 2.23194178
(3) 53 C : 2.25635983
(4) 73 C : 2.22935052
### Total natural pop. of target atoms = 19.54637
With regards,
Lovleen Kaur
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Re: Negative charge on Al in Al-doped AGNR