Hi CP2K community,
I'm optimizing Au (111) 5 layers surface with aromatic thiols on the
surface.
But the charge on S atoms is +ve, and the first and last layers of Au have
-ve charge.
But S atoms should have +ve charge.
Please suggest how I can get the correct charges.
I have attached the Mulliken charges file and the coordinates file here,
just in case you'd like to have a look.
The input file is -
--------------------------------------------------------------------------------------------------------------------------------------------
&GLOBAL
PROJECT Au_2DMBT_tilt
RUN_TYPE GEO_OPT
PRINT_LEVEL MEDIUM
&END GLOBAL
&MOTION
&GEO_OPT
TYPE MINIMIZATION
OPTIMIZER BFGS
MAX_DR 3.00E-03
MAX_FORCE 4.50E-04
RMS_DR 1.50E-03
RMS_FORCE 3.00E-04
MAX_ITER 3000
&END GEO_OPT
&CONSTRAINT
&FIXED_ATOMS
COMPONENTS_TO_FIX XYZ
LIST 1..48
&END FIXED_ATOMS
&END CONSTRAINT
&END MOTION
&FORCE_EVAL
METHOD QS
&DFT
BASIS_SET_FILE_NAME /home/spremkumar.iitm/vikash/cp2k_pot/BASIS_MOLOPT
POTENTIAL_FILE_NAME /home/spremkumar.iitm/vikash/cp2k_pot/GTH_POTENTIALS
&QS
METHOD GPW
EXTRAPOLATION USE_GUESS
EPS_DEFAULT 1.0E-10
&END QS
&MGRID
CUTOFF 500
NGRIDS 4
REL_CUTOFF 60
&END MGRID
&SCF
SCF_GUESS ATOMIC
EPS_SCF 1.0E-05
MAX_SCF 200
ADDED_MOS 10
&DIAGONALIZATION T
ALGORITHM STANDARD
&END DIAGONALIZATION
&SMEAR ON
METHOD FERMI_DIRAC
ELECTRONIC_TEMPERATURE [K] 300
&END SMEAR
&MIXING T
METHOD BROYDEN_MIXING
ALPHA 0.4
NBROYDEN 8
&END MIXING
&END SCF
&XC
&XC_FUNCTIONAL PBE
&END XC_FUNCTIONAL
&vdW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
PARAMETER_FILE_NAME
/home/spremkumar.iitm/vikash/cp2k_pot/dftd3.dat
TYPE DFTD3
REFERENCE_FUNCTIONAL PBE
R_CUTOFF 25.0
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
&KPOINTS
SCHEME MONKHORST-PACK 2 3 1
FULL_GRID .TRUE.
PARALLEL_GROUP_SIZE 0
&END KPOINTS
&END DFT
&SUBSYS
&CELL
PERIODIC XYZ
A 17.3099747000000015 0.0000000000000000 0.0000000000000000
B 0.0000000000000000 9.9939184000000001 0.0000000000000000
C 0.0000000000000000 0.0000000000000000 35.0000000000000000
&END CELL
&COORD
@INCLUDE Au_2DMBT_tilt.xyz
&END COORD
&KIND Ag
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND Au
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND H
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND C
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE
&END KIND
&KIND S
BASIS_SET DZVP-MOLOPT-GTH
POTENTIAL GTH-PBE
&END KIND
&END SUBSYS
--------------------------------------------------------------------------------------------------------------------------------------------
Thank you
Vikash Khokhar
Project Assistant
Pradeep research group,
DST Unit of Nanoscience & Thematic Unit of Excellence,
Department of Chemistry
Indian Institute of Technology Madras, Chennai, India
Web: pradeepresearch.org
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp2k+unsubscribe at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/88426b13-9f34-4334-a802-c858ef161805n%40googlegroups.com.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230117/4cf56db8/attachment-0001.htm>
-------------- next part --------------
Mulliken Population Analysis
# Atom Element Kind Atomic population Net charge
1 Au 1 11.078601 -0.078601
2 Au 1 11.078872 -0.078872
3 Au 1 11.078642 -0.078642
4 Au 1 11.076928 -0.076928
5 Au 1 11.077847 -0.077847
6 Au 1 11.076760 -0.076760
7 Au 1 11.078438 -0.078438
8 Au 1 11.078316 -0.078316
9 Au 1 11.077848 -0.077848
10 Au 1 11.075978 -0.075978
11 Au 1 11.075713 -0.075713
12 Au 1 11.077867 -0.077867
13 Au 1 11.076746 -0.076746
14 Au 1 11.077706 -0.077706
15 Au 1 11.076854 -0.076854
16 Au 1 11.078482 -0.078482
17 Au 1 11.078802 -0.078802
18 Au 1 11.078687 -0.078687
19 Au 1 11.076101 -0.076101
20 Au 1 11.075708 -0.075708
21 Au 1 11.077902 -0.077902
22 Au 1 11.078385 -0.078385
23 Au 1 11.078344 -0.078344
24 Au 1 11.077773 -0.077773
25 Au 1 10.930837 0.069163
26 Au 1 10.928079 0.071921
27 Au 1 10.930112 0.069888
28 Au 1 10.926798 0.073202
29 Au 1 10.933421 0.066579
30 Au 1 10.926761 0.073239
31 Au 1 10.932970 0.067030
32 Au 1 10.931232 0.068768
33 Au 1 10.931763 0.068237
34 Au 1 10.927891 0.072109
35 Au 1 10.928861 0.071139
36 Au 1 10.930430 0.069570
37 Au 1 10.926601 0.073399
38 Au 1 10.933409 0.066591
39 Au 1 10.926760 0.073240
40 Au 1 10.930941 0.069059
41 Au 1 10.928075 0.071925
42 Au 1 10.930313 0.069687
43 Au 1 10.927699 0.072301
44 Au 1 10.928889 0.071111
45 Au 1 10.930477 0.069523
46 Au 1 10.932917 0.067083
47 Au 1 10.931196 0.068804
48 Au 1 10.931854 0.068146
49 Au 1 10.971541 0.028459
50 Au 1 10.967572 0.032428
51 Au 1 10.973628 0.026372
52 Au 1 10.966383 0.033617
53 Au 1 10.973056 0.026944
54 Au 1 10.967978 0.032022
55 Au 1 10.981303 0.018697
56 Au 1 10.978774 0.021226
57 Au 1 10.980300 0.019700
58 Au 1 10.977722 0.022278
59 Au 1 10.979203 0.020797
60 Au 1 10.976578 0.023422
61 Au 1 10.965437 0.034563
62 Au 1 10.973712 0.026288
63 Au 1 10.969183 0.030817
64 Au 1 10.971149 0.028851
65 Au 1 10.968391 0.031609
66 Au 1 10.973623 0.026377
67 Au 1 10.977934 0.022066
68 Au 1 10.979052 0.020948
69 Au 1 10.976256 0.023744
70 Au 1 10.981363 0.018637
71 Au 1 10.978794 0.021206
72 Au 1 10.980196 0.019804
73 Au 1 10.944983 0.055017
74 Au 1 10.959422 0.040578
75 Au 1 10.964375 0.035625
76 Au 1 10.942758 0.057242
77 Au 1 10.946143 0.053857
78 Au 1 10.942752 0.057248
79 Au 1 10.941946 0.058054
80 Au 1 10.959449 0.040551
81 Au 1 10.935498 0.064502
82 Au 1 10.958684 0.041316
83 Au 1 10.949995 0.050005
84 Au 1 10.938172 0.061828
85 Au 1 10.943733 0.056267
86 Au 1 10.946606 0.053394
87 Au 1 10.941834 0.058166
88 Au 1 10.946835 0.053165
89 Au 1 10.960552 0.039448
90 Au 1 10.963386 0.036614
91 Au 1 10.960126 0.039874
92 Au 1 10.950542 0.049458
93 Au 1 10.936963 0.063037
94 Au 1 10.943489 0.056511
95 Au 1 10.957209 0.042791
96 Au 1 10.936065 0.063935
97 Au 1 11.106663 -0.106663
98 Au 1 11.065301 -0.065301
99 Au 1 11.055915 -0.055915
100 Au 1 11.069891 -0.069891
101 Au 1 11.073365 -0.073365
102 Au 1 11.057951 -0.057951
103 Au 1 11.223663 -0.223663
104 Au 1 11.281920 -0.281920
105 Au 1 11.118282 -0.118282
106 Au 1 11.082623 -0.082623
107 Au 1 11.055284 -0.055284
108 Au 1 11.100624 -0.100624
109 Au 1 11.072137 -0.072137
110 Au 1 11.074051 -0.074051
111 Au 1 11.056209 -0.056209
112 Au 1 11.106221 -0.106221
113 Au 1 11.062730 -0.062730
114 Au 1 11.058722 -0.058722
115 Au 1 11.082963 -0.082963
116 Au 1 11.053166 -0.053166
117 Au 1 11.098224 -0.098224
118 Au 1 11.231771 -0.231771
119 Au 1 11.280871 -0.280871
120 Au 1 11.116461 -0.116461
121 C 2 4.028684 -0.028684
122 C 2 4.129367 -0.129367
123 C 2 4.009662 -0.009662
124 C 2 4.024941 -0.024941
125 C 2 4.018537 -0.018537
126 C 2 4.034982 -0.034982
127 C 2 4.198266 -0.198266
128 C 2 4.202241 -0.202241
129 H 3 0.914233 0.085767
130 H 3 0.936225 0.063775
131 H 3 0.930568 0.069432
132 H 3 0.910985 0.089015
133 H 3 0.912059 0.087941
134 H 3 0.917790 0.082210
135 H 3 0.899833 0.100167
136 H 3 0.906082 0.093918
137 H 3 0.922653 0.077347
138 S 4 5.638430 0.361570
139 C 2 4.028313 -0.028313
140 C 2 4.130261 -0.130261
141 C 2 4.009055 -0.009055
142 C 2 4.025445 -0.025445
143 C 2 4.017937 -0.017937
144 C 2 4.035439 -0.035439
145 C 2 4.198143 -0.198143
146 C 2 4.202002 -0.202002
147 H 3 0.915076 0.084924
148 H 3 0.936026 0.063974
149 H 3 0.930845 0.069155
150 H 3 0.911047 0.088953
151 H 3 0.912775 0.087225
152 H 3 0.917255 0.082745
153 H 3 0.899763 0.100237
154 H 3 0.905961 0.094039
155 H 3 0.922474 0.077526
156 S 4 5.639407 0.360593
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Au_2DMBT_tilt.xyz
Type: chemical/x-xyz
Size: 8424 bytes
Desc: not available
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20230117/4cf56db8/attachment-0001.xyz>