Error: Invalid decimal character . was detected

Bader charge density analysis

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ryu27
Posts: 2
Joined: Wed Jan 30, 2019 5:47 am

Error: Invalid decimal character . was detected

Post by ryu27 » Wed Jan 30, 2019 7:24 am

Dear all,

My CHGCAR file causes an error when I do valence charge analysis with Bader.
I want to analyse charge of the model such as various shapes of platinum on defective graphene.
but only models include graphene, message below was displayed and Bader didn't run.

-----------------------------------------------------------------------
Invalid decimal character . was detected (unit = 100).
(the relative position causing an error in a record = 3 )
0.950000 0.374935 0.442080
?
Error occurs at or near line 75 of
_chgcar_mod@_read_charge_chgcar_
Called from or near line 74 of _io_mod@_read_charge_
Called from or near line 64 of _MAIN__
-----------------------------------------------------------------------

I have already obtained some results of calculations in VASP code of these models, so I don't want to reconstruct models if possible.
Here attached one of CHGCARs. Are there any good solutions?

Thanks in advance.

Best regards,
Attachments
CHGCAR.txt
(264.62 MiB) Downloaded 129 times

graeme
Site Admin
Posts: 1862
Joined: Tue Apr 26, 2005 4:25 am
Location: University of Texas at Austin
Contact:

Re: Error: Invalid decimal character . was detected

Post by graeme » Wed Jan 30, 2019 1:24 pm

I'm not sure what is going wrong. I can run the analysis on my computer with your charge density file. Maybe build a clean version of the binary after removing all the object files. I'm puzzled about what could cause this error.
Graeme


------------
bader CHGCAR

GRID BASED BADER ANALYSIS (Version 1.03 11/13/17)

OPEN ... CHGCAR
VASP5-STYLE INPUT FILE
DENSITY-GRID: 252 x 168 x 360
CLOSE ... CHGCAR
RUN TIME: 5.29 SECONDS

CALCULATING BADER CHARGE DISTRIBUTION
0 10 25 50 75 100
PERCENT DONE: **********************

REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 10497145
REASSIGNED POINTS: 529266

RUN TIME: 124.36 SECONDS

CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************
RUN TIME: 3.33 SECONDS

WRITING BADER ATOMIC CHARGES TO ACF.dat
WRITING BADER VOLUME CHARGES TO BCF.dat

NUMBER OF BADER MAXIMA FOUND: 2096
SIGNIFICANT MAXIMA FOUND: 480
VACUUM CHARGE: 0.0000
NUMBER OF ELECTRONS: 639.99992

--------------
ACF.dat
--------------
# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 1.230408 2.136420 7.351426 4.089656 0.564886 44.552951
2 2.460816 0.001317 7.351426 3.893328 0.560183 46.768753
3 3.691224 2.136420 7.351426 4.146151 0.558848 43.493719
4 2.460816 1.426173 7.351426 4.145958 0.558842 44.503364
5 4.921633 0.001317 7.351426 3.836018 0.565767 46.096115
6 4.921633 1.426173 7.351426 4.089463 0.564882 45.357821
7 1.230408 6.411535 7.351426 4.089580 0.564892 47.299058
8 3.691224 6.411535 7.351426 4.146139 0.558858 46.822472
9 11.073673 3.563773 7.351426 3.836575 0.564864 38.350910
10 9.843265 5.701219 7.351426 4.146047 0.558870 50.724230
11 8.612857 3.563773 7.351426 3.893234 0.558814 37.070832
12 9.843265 4.273918 7.351426 3.893117 0.558820 40.120429
13 7.382449 5.701219 7.351426 4.089500 0.564900 50.091078
14 7.382449 4.273918 7.351426 3.836288 0.564868 39.115375
15 11.073673 7.838938 7.351426 3.836410 0.564839 40.160374
16 8.612857 7.838938 7.351426 3.893738 0.558777 40.095636
17 11.073673 2.136420 7.351426 4.089656 0.564886 44.552951
18 9.843265 0.001317 7.351426 3.893328 0.560183 46.768753
19 8.612857 2.136420 7.351426 4.146151 0.558848 43.493719
20 9.843265 1.426173 7.351426 4.145958 0.558842 44.503364
21 7.382449 0.001317 7.351426 3.836019 0.565767 45.405571
22 7.382449 1.426173 7.351426 4.089463 0.564882 45.422100
23 11.073673 6.411535 7.351426 4.089579 0.564892 48.212284
24 8.612857 6.411535 7.351426 4.146139 0.558858 46.822472
25 1.230408 3.563773 7.351426 3.836575 0.564864 38.350910
26 2.460816 5.701219 7.351426 4.146047 0.558870 50.724230
27 3.691224 3.563773 7.351426 3.893234 0.558814 37.070832
28 2.460816 4.273918 7.351426 3.893117 0.558820 40.120429
29 4.921633 5.701219 7.351426 4.089500 0.564900 50.783459
30 4.921633 4.273918 7.351426 3.836288 0.564868 39.176900
31 1.230408 7.838938 7.351426 3.836410 0.564839 40.752663
32 3.691224 7.838938 7.351426 3.893738 0.558777 40.095636
33 0.000000 0.001317 7.351426 3.909673 0.576624 45.234772
34 0.000000 1.426173 7.351426 4.162118 0.575321 45.694828
35 0.000000 5.701219 7.351426 4.159915 0.575348 49.549295
36 0.000000 4.273918 7.351426 3.906900 0.575300 36.821061
37 6.152041 2.136420 7.351426 4.159932 0.575327 42.719612
38 6.152041 6.411535 7.351426 4.162121 0.575336 44.965717
39 6.152041 3.563773 7.351426 3.907203 0.575294 39.742558
40 6.152041 7.838938 7.351426 3.909709 0.575258 41.980399
41 13.534490 2.136420 7.351426 4.089656 0.564886 44.234768
42 14.764898 0.001317 7.351426 3.893328 0.560183 46.768753
43 15.995306 2.136420 7.351426 4.146151 0.558848 43.493719
44 14.764898 1.426173 7.351426 4.145958 0.558842 44.503364
45 17.225714 0.001317 7.351426 3.836018 0.565767 46.096115
46 17.225714 1.426173 7.351426 4.089463 0.564882 45.357821
47 13.534490 6.411535 7.351426 4.089580 0.564892 47.299058
48 15.995306 6.411535 7.351426 4.146139 0.558858 46.822472
49 23.377755 3.563773 7.351426 3.836575 0.564864 38.508854
50 22.147347 5.701219 7.351426 4.146047 0.558870 50.724230
51 20.916939 3.563773 7.351426 3.893234 0.558814 37.070832
52 22.147347 4.273918 7.351426 3.893117 0.558820 40.120429
53 19.686530 5.701219 7.351426 4.089500 0.564900 50.783459
54 19.686530 4.273918 7.351426 3.836288 0.564868 39.176900
55 23.377755 7.838938 7.351426 3.836410 0.564839 40.160374
56 20.916939 7.838938 7.351426 3.893738 0.558777 40.095636
57 23.377755 2.136420 7.351426 4.089656 0.564886 44.234768
58 22.147347 0.001317 7.351426 3.893328 0.560183 46.768753
59 20.916939 2.136420 7.351426 4.146151 0.558848 43.493719
60 22.147347 1.426173 7.351426 4.145958 0.558842 44.503364
61 19.686530 0.001317 7.351426 3.836019 0.565767 45.405571
62 19.686530 1.426173 7.351426 4.089463 0.564882 45.422100
63 23.377755 6.411535 7.351426 4.089579 0.564892 48.212284
64 20.916939 6.411535 7.351426 4.146139 0.558858 46.822472
65 13.534490 3.563773 7.351426 3.836575 0.564864 38.508854
66 14.764898 5.701219 7.351426 4.146047 0.558870 50.724230
67 15.995306 3.563773 7.351426 3.893234 0.558814 37.070832
68 14.764898 4.273918 7.351426 3.893117 0.558820 40.120429
69 17.225714 5.701219 7.351426 4.089500 0.564900 50.091078
70 17.225714 4.273918 7.351426 3.836288 0.564868 39.115375
71 13.534490 7.838938 7.351426 3.836410 0.564839 40.752663
72 15.995306 7.838938 7.351426 3.893738 0.558777 40.095636
73 12.304082 0.001317 7.351426 3.909673 0.576624 45.234772
74 12.304082 1.426173 7.351426 4.162118 0.575321 45.694828
75 12.304082 5.701219 7.351426 4.159915 0.575348 49.549295
76 12.304082 4.273918 7.351426 3.906900 0.575300 36.821061
77 18.456122 2.136420 7.351426 4.159932 0.575327 42.719612
78 18.456122 6.411535 7.351426 4.162121 0.575336 44.965717
79 18.456122 3.563773 7.351426 3.907203 0.575294 39.742558
80 18.456122 7.838938 7.351426 3.909709 0.575258 41.980399
81 1.230408 10.686615 7.351426 4.089656 0.564886 44.234768
82 2.460816 8.548878 7.351426 3.893332 0.558746 41.227871
83 3.691224 10.686615 7.351426 4.146151 0.558848 43.493719
84 2.460816 9.976368 7.351426 4.145954 0.558842 50.044246
85 4.921633 8.548878 7.351426 3.836022 0.564819 40.319695
86 4.921633 9.976368 7.351426 4.089459 0.564882 51.198520
87 1.230408 14.961730 7.351426 4.089580 0.564892 47.619995
88 3.691224 14.961730 7.351426 4.146139 0.558858 46.822472
89 11.073673 12.113968 7.351426 3.836575 0.564864 38.350910
90 9.843265 14.251414 7.351426 4.146047 0.558870 50.724230
91 8.612857 12.113968 7.351426 3.893234 0.558814 37.070832
92 9.843265 12.824113 7.351426 3.893117 0.558820 40.120429
93 7.382449 14.251414 7.351426 4.089500 0.564900 50.783459
94 7.382449 12.824113 7.351426 3.836288 0.564868 39.115375
95 11.073673 16.389133 7.351426 3.836410 0.564839 40.160374
96 8.612857 16.389133 7.351426 3.893738 0.558777 40.095636
97 11.073673 10.686615 7.351426 4.089656 0.564886 44.552951
98 9.843265 8.548878 7.351426 3.893332 0.558746 41.227871
99 8.612857 10.686615 7.351426 4.146151 0.558848 43.493719
100 9.843265 9.976368 7.351426 4.145954 0.558842 50.044246
101 7.382449 8.548878 7.351426 3.836023 0.564819 39.629151
102 7.382449 9.976368 7.351426 4.089459 0.564882 51.134241
103 11.073673 14.961730 7.351426 4.089580 0.564892 47.619995
104 8.612857 14.961730 7.351426 4.146139 0.558858 46.822472
105 1.230408 12.113968 7.351426 3.836575 0.564864 38.508854
106 2.460816 14.251414 7.351426 4.146047 0.558870 50.724230
107 3.691224 12.113968 7.351426 3.893234 0.558814 37.070832
108 2.460816 12.824113 7.351426 3.893117 0.558820 40.120429
109 4.921633 14.251414 7.351426 4.089500 0.564900 50.091078
110 4.921633 12.824113 7.351426 3.836288 0.564868 39.176900
111 1.230408 16.389133 7.351426 3.836410 0.564839 40.752663
112 3.691224 16.389133 7.351426 3.893738 0.558777 40.095636
113 0.000000 8.548878 7.351426 3.909677 0.575228 40.623186
114 0.000000 9.976368 7.351426 4.162115 0.575321 50.306414
115 0.000000 14.251414 7.351426 4.159915 0.575348 49.549295
116 0.000000 12.824113 7.351426 3.906900 0.575300 36.821061
117 6.152041 10.686615 7.351426 4.159932 0.575327 42.719612
118 6.152041 14.961730 7.351426 4.162121 0.575336 44.965717
119 6.152041 12.113968 7.351426 3.907203 0.575294 39.742558
120 6.152041 16.389133 7.351426 3.909709 0.575258 41.980399
121 13.534490 10.686615 7.351426 4.089656 0.564886 44.234768
122 14.764898 8.548878 7.351426 3.893332 0.558746 41.227871
123 15.995306 10.686615 7.351426 4.146151 0.558848 43.493719
124 14.764898 9.976368 7.351426 4.145954 0.558842 50.044246
125 17.225714 8.548878 7.351426 3.836022 0.564819 40.319695
126 17.225714 9.976368 7.351426 4.089459 0.564882 51.198520
127 13.534490 14.961730 7.351426 4.089579 0.564892 47.891346
128 15.995306 14.961730 7.351426 4.146139 0.558858 46.822472
129 23.377755 12.113968 7.351426 3.836575 0.564864 38.350910
130 22.147347 14.251414 7.351426 4.146047 0.558870 50.724230
131 20.916939 12.113968 7.351426 3.893234 0.558814 37.070832
132 22.147347 12.824113 7.351426 3.893117 0.558820 40.120429
133 19.686530 14.251414 7.351426 4.089500 0.564900 50.091078
134 19.686530 12.824113 7.351426 3.836288 0.564868 39.176900
135 23.377755 16.389133 7.351426 3.836410 0.564839 40.160374
136 20.916939 16.389133 7.351426 3.893738 0.558777 40.095636
137 23.377755 10.686615 7.351426 4.089656 0.564886 44.552951
138 22.147347 8.548878 7.351426 3.893332 0.558746 41.227871
139 20.916939 10.686615 7.351426 4.146151 0.558848 43.493719
140 22.147347 9.976368 7.351426 4.145954 0.558842 50.044246
141 19.686530 8.548878 7.351426 3.836023 0.564819 39.629151
142 19.686530 9.976368 7.351426 4.089459 0.564882 51.134241
143 23.377755 14.961730 7.351426 4.089579 0.564892 47.891346
144 20.916939 14.961730 7.351426 4.146139 0.558858 46.822472
145 13.534490 12.113968 7.351426 3.836575 0.564864 38.508854
146 14.764898 14.251414 7.351426 4.146047 0.558870 50.724230
147 15.995306 12.113968 7.351426 3.893234 0.558814 37.070832
148 14.764898 12.824113 7.351426 3.893117 0.558820 40.120429
149 17.225714 14.251414 7.351426 4.089500 0.564900 50.783459
150 17.225714 12.824113 7.351426 3.836288 0.564868 39.115375
151 13.534490 16.389133 7.351426 3.836410 0.564839 40.752663
152 15.995306 16.389133 7.351426 3.893738 0.558777 40.095636
153 12.304082 8.548878 7.351426 3.909677 0.575228 40.623186
154 12.304082 9.976368 7.351426 4.162115 0.575321 50.306414
155 12.304082 14.251414 7.351426 4.159915 0.575348 49.549295
156 12.304082 12.824113 7.351426 3.906900 0.575300 36.821061
157 18.456122 10.686615 7.351426 4.159932 0.575327 42.719612
158 18.456122 14.961730 7.351426 4.162121 0.575336 44.965717
159 18.456122 12.113968 7.351426 3.907203 0.575294 39.742558
160 18.456122 16.389133 7.351426 3.909709 0.575258 41.980399
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 639.9999

ryu27
Posts: 2
Joined: Wed Jan 30, 2019 5:47 am

Re: Error: Invalid decimal character . was detected

Post by ryu27 » Fri Feb 22, 2019 10:30 am

I'm sorry it took me a while to get back to you.

I got the same result as you by recompiling Bader analysis program on Windows.
Thank you for your cooperation.

Best regards,

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