Problem while running bader charge Calculation

Bader charge density analysis

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sgy002
Posts: 4
Joined: Tue Nov 13, 2018 5:11 pm

Problem while running bader charge Calculation

Post by sgy002 » Tue Nov 13, 2018 11:22 pm

Dear Baders,

I tried to search if the problem i am having has been discussed previously. It has been discussed while the problem was fixed by downloading and installing new version of bader source code. I am new to this forum. I am trying to calculate bader charges for my system. I downloaded my bader source code yesterday and compiled it. My systems were optimized using PAW potentials. After getting the charge_sum file, and executing bader CHGCAR -ref CHGCAR_sum command, i get the following errors.

At line 89 of file chgcar_mod.f90 (unit = 100, file = 'CHGCAR')
Fortran runtime error: Bad real number in item 58996800 of list input.

I really do not know what's going on. I would highly appreciate for shading light on this problem. I am also attaching the CHGCAR and CHGCAR_sum file herewith.

Thank you
Suraj
Last edited by sgy002 on Wed Nov 14, 2018 4:54 pm, edited 1 time in total.

graeme
Site Admin
Posts: 1826
Joined: Tue Apr 26, 2005 4:25 am
Location: University of Texas at Austin
Contact:

Re: Problem while running bader charge Calculation

Post by graeme » Wed Nov 14, 2018 1:34 am

I don't see the CHGCAR or AECCAR0/2 files attached.

sgy002
Posts: 4
Joined: Tue Nov 13, 2018 5:11 pm

Re: Problem while running bader charge Calculation

Post by sgy002 » Wed Nov 14, 2018 6:10 pm

Attaching files here.[attachment=1]CHGCAR.zip[/attachment]
Attachments
AECCAR.zip
(1.25 GiB) Downloaded 210 times
CHGCAR.zip
(1.21 GiB) Downloaded 199 times

graeme
Site Admin
Posts: 1826
Joined: Tue Apr 26, 2005 4:25 am
Location: University of Texas at Austin
Contact:

Re: Problem while running bader charge Calculation

Post by graeme » Wed Nov 14, 2018 7:29 pm

My guess is that this is a memory issue or a system limitation, such as file size or memory allocation. It seems to work fine on my laptop. Try this on some linux machine with a reasonable amount of memory. You can also check my theory to see if it works fine on a smaller file, which you can generate by reducing NGXF, NGYF, and NGZF.

---------

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

OPEN ... CHGCAR
VASP5-STYLE INPUT FILE
DENSITY-GRID: 400 x 400 x 400
CLOSE ... CHGCAR
RUN TIME: 22.83 SECONDS

OPEN ... CHGCAR_sum
VASP5-STYLE INPUT FILE
DENSITY-GRID: 400 x 400 x 400
CLOSE ... CHGCAR_sum
RUN TIME: 26.25 SECONDS

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

REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 53075009
REASSIGNED POINTS: 2137511

RUN TIME: 337.16 SECONDS

CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************
RUN TIME: 17.27 SECONDS

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

NUMBER OF BADER MAXIMA FOUND: 1507478
SIGNIFICANT MAXIMA FOUND: 34061
VACUUM CHARGE: 0.0000
NUMBER OF ELECTRONS: 1088.00000

---------
ACF.dat
---------

# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 2.992969 3.280805 1.668839 1.721867 0.747520 6.094082
2 2.977109 0.067698 4.940896 1.741707 0.738560 6.264882
3 2.953674 3.327582 8.511532 1.799310 0.719126 6.519159
4 2.866324 0.155146 11.998089 1.935175 0.791028 9.699794
5 1.504474 0.082121 1.593374 1.883995 0.792906 7.219112
6 1.501515 3.318227 5.199281 1.658475 0.792811 5.455235
7 1.479027 0.081211 8.641955 1.643735 0.775653 5.404872
8 1.484234 3.404116 11.908270 1.891700 0.775453 12.314022
9 5.948892 3.298216 1.666789 1.714764 0.745649 6.034160
10 5.932558 0.063670 4.929413 1.753989 0.725676 6.379799
11 5.929007 3.328492 8.517274 1.816940 0.724949 6.610029
12 5.969487 0.037162 11.977172 1.885202 0.807506 9.429255
13 4.463829 0.064709 1.579430 1.679605 0.785563 5.855475
14 4.460042 3.315628 5.212816 1.702078 0.791383 5.840396
15 4.443234 0.134486 8.673125 1.764679 0.761472 6.162284
16 4.530702 3.318487 12.002191 2.243785 0.778578 9.333852
17 8.907300 3.296007 1.666789 1.740646 0.744138 6.228120
18 8.893097 0.070686 4.926952 1.805459 0.726640 6.767129
19 8.891322 3.314459 8.488564 1.751375 0.802511 6.150063
20 8.874396 12.966123 11.992347 1.894941 0.794439 9.173204
21 7.424723 0.069257 1.569997 1.634588 0.776925 5.482338
22 7.413360 3.314848 5.199281 1.703928 0.774499 5.788752
23 7.406140 0.072635 8.625549 1.735483 0.790429 5.964578
24 7.348972 3.159313 11.904989 2.250062 0.798326 8.499467
25 0.055274 3.327972 1.649973 1.756894 0.829840 6.235413
26 0.013730 0.076923 4.941717 1.739998 0.694565 6.296913
27 11.833633 3.323944 8.487334 1.724452 0.779244 6.038989
28 0.024027 0.074974 12.015725 1.864535 0.781668 9.215682
29 10.387274 0.080821 1.568356 1.651198 0.785034 5.570744
30 10.373307 3.321475 5.184927 1.852013 0.804506 6.829811
31 10.360998 0.097973 8.658360 1.651997 0.787491 5.422810
32 10.239324 3.259495 12.027209 2.045325 0.753688 12.792812
33 2.970481 9.793167 1.672531 1.820890 0.749971 6.884018
34 2.980542 6.565767 5.003237 1.779709 0.813068 6.567945
35 2.879817 9.753536 8.434016 1.790241 0.748232 6.430162
36 3.055582 6.903086 11.958306 2.223126 0.801624 9.446897
37 1.505894 6.545107 1.655715 1.715703 0.783124 6.241524
38 1.534419 9.820714 5.215277 1.628726 0.791516 5.322873
39 1.534182 6.540949 8.600121 1.803847 0.782117 6.358511
40 1.441743 9.861515 11.968560 1.920856 0.771290 12.155739
41 5.935044 9.803562 1.660637 1.732739 0.737970 6.170563
42 5.932558 6.562389 4.981910 1.796094 0.805284 6.699913
43 6.009256 9.740282 8.420072 1.796363 0.739048 6.541729
44 5.914094 6.602670 12.176908 2.272439 0.853271 8.760249
45 4.463119 6.552643 1.627006 1.785220 0.766077 6.484368
46 4.466078 9.816296 5.132429 1.710099 0.777216 5.946936
47 4.484069 6.559140 8.748180 1.873353 0.797722 6.818674
48 4.446548 10.282124 10.918204 2.166545 0.782845 9.020834
49 8.894517 9.801873 1.652844 1.794917 0.832704 6.594062
50 8.886350 6.565897 4.994624 1.794757 0.805398 6.741898
51 8.905288 9.846572 8.458624 1.752474 0.789135 6.105909
52 9.045426 6.461817 11.934518 2.178421 0.771461 8.860679
53 7.423539 6.558361 1.624135 1.724555 0.764310 6.168887
54 7.406614 9.819934 5.143913 1.701759 0.758440 5.779882
55 7.353115 6.537571 8.714959 1.903581 0.802319 7.065658
56 7.430759 9.801613 12.017366 2.042014 0.753988 11.820251
57 0.016097 9.819675 2.079384 1.783193 0.814300 6.903630
58 0.015032 6.558621 5.009389 1.745949 0.790188 6.383347
59 11.819075 9.842803 8.437707 1.698828 0.765220 5.673835
60 0.095517 6.590845 11.952564 1.995020 0.774553 9.831565
61 10.384315 6.551214 1.633568 1.686749 0.784567 5.919636
62 10.320992 9.817855 5.218968 1.685860 0.791254 5.859911
63 10.312944 6.564598 8.573462 1.840529 0.773017 6.648466
64 10.365495 9.790049 11.755289 2.013332 0.771920 11.125226
65 2.976399 0.071856 0.497494 6.925248 0.774056 53.407511
66 2.980660 3.318746 4.064028 7.096599 0.796498 13.372427
67 2.993324 0.011824 7.535000 7.061851 0.775178 13.952633
68 2.906922 3.226880 10.852992 7.093033 0.799762 13.785775
69 2.980186 0.039891 3.142454 7.096111 0.754292 13.288259
70 2.969889 3.313419 6.688482 7.125890 0.898720 13.476207
71 2.897808 0.109668 10.186113 7.152816 0.887618 13.739848
72 1.527554 4.574337 1.853400 7.218606 0.915644 16.098615
73 1.498201 1.328616 5.280078 7.195922 0.946729 14.107367
74 1.482104 4.574207 8.787553 7.150456 0.916180 13.486063
75 1.441270 1.478435 12.533315 7.280994 0.890511 34.907551
76 1.495360 2.036648 1.875547 7.176627 0.867831 14.320546
77 1.500923 5.306018 5.316580 7.213954 0.944270 14.089528
78 1.477014 2.040157 8.745719 7.188375 0.938467 13.570527
79 1.529448 5.277042 12.426680 7.223365 0.856831 22.299336
80 5.939542 0.071856 0.486010 7.011755 0.777301 60.960041
81 5.931848 3.321995 4.056645 7.114684 0.756081 13.784790
82 5.886280 0.017282 7.527618 7.077004 0.755578 14.127177
83 5.888883 3.249619 10.754560 7.068475 0.822829 12.748265
84 5.940488 0.034304 3.128510 7.122345 0.870337 13.497496
85 5.926285 3.309391 6.685201 7.135661 0.805564 13.417172
86 5.968776 0.069127 10.168067 7.131017 0.803099 13.512674
87 4.460515 4.559654 1.741433 7.133141 0.836723 14.838957
88 4.455070 1.326017 5.271875 7.197166 0.948946 14.115055
89 4.434712 4.582523 8.787553 7.070687 0.875658 12.801880
90 4.449034 1.290154 12.452109 7.243397 0.923865 22.988842
91 4.465249 2.034959 1.856681 7.209414 0.957699 14.635042
92 4.455544 5.305109 5.303866 7.187540 0.923311 13.849345
93 4.433884 2.037428 8.776479 7.121926 0.868986 13.258988
94 4.359199 5.355655 11.836496 7.110109 0.693083 11.685228
95 8.905761 0.067438 0.480268 7.028804 0.819513 76.291980
96 8.888954 3.323684 4.043931 7.043934 0.788458 13.183690
97 8.896411 0.074714 7.511623 7.035870 0.764382 13.604332
98 8.944820 3.224411 10.795163 7.040232 0.787225 13.192856
99 8.907182 0.044569 3.124408 7.129064 0.874492 13.533075
100 8.891440 3.301335 6.666334 7.082788 0.818846 13.117065
101 8.865519 0.021180 10.172578 7.137155 0.877364 13.690865
102 7.423658 4.566151 1.763580 7.172032 0.891170 15.417191
103 7.410993 1.327577 5.263673 7.182777 0.943085 13.996195
104 7.410165 4.567451 8.764585 7.083838 0.785620 13.016833
105 7.435730 1.283658 12.446367 7.263593 0.903037 20.403787
106 7.428155 2.036258 1.842737 7.220481 0.922938 15.320310
107 7.409928 5.303290 5.297304 7.165204 0.932012 13.617144
108 7.400696 2.033010 8.751461 7.152423 0.930923 13.515138
109 7.396080 5.273924 11.884482 7.090649 0.545191 11.537096
110 0.036337 0.062500 0.486010 6.949585 0.778798 73.466151
111 0.021423 3.329401 4.050493 7.068245 0.791187 13.354391
112 11.829609 0.070686 7.520235 7.089343 0.772303 13.788141
113 11.781554 3.293798 10.916153 7.128378 0.803813 14.552648
114 0.009350 0.047947 3.139994 7.100504 0.756538 13.218283
115 0.006983 3.310041 6.668795 7.086965 0.713677 13.183000
116 0.017754 0.059512 10.195136 7.158359 0.776085 14.213020
117 10.384196 4.566931 1.754968 7.207857 0.957224 16.003705
118 10.368218 1.332124 5.261622 7.170263 0.879700 13.920996
119 10.365850 4.571479 8.758433 7.164380 0.951377 13.755420
120 10.333301 1.346547 12.489431 7.272730 0.868847 29.411119
121 10.405146 2.049902 1.775064 7.191828 0.913565 15.535756
122 10.365140 5.304719 5.307557 7.169759 0.887199 13.713730
123 10.370703 2.040936 8.768276 7.219666 0.937885 13.991464
124 10.566116 5.227666 12.349985 7.285698 0.908022 21.504867
125 2.970718 6.580320 0.549991 6.956893 0.791838 56.079493
126 2.955568 9.818375 4.011120 7.084405 0.802241 13.078529
127 3.007173 6.595003 7.497678 7.015745 0.760408 13.603740
128 2.700502 9.718843 10.685247 7.061687 0.774859 12.896396
129 2.985631 6.558491 3.194952 7.093999 0.749818 13.441121
130 2.995218 9.845012 6.615888 7.135475 0.775790 13.448217
131 2.917929 6.688169 10.089731 7.081000 0.664918 12.814988
132 1.480210 11.069678 1.804184 7.156799 0.832195 14.994973
133 1.486838 7.860339 5.291562 7.202177 0.976300 14.014724
134 1.488850 11.088779 8.693221 7.176700 0.916490 13.343254
135 1.470978 8.025101 12.559154 7.243159 0.856487 34.284177
136 1.465178 8.549401 1.875957 7.188726 0.948621 15.264034
137 1.486010 11.789145 5.270235 7.191393 0.972693 13.896356
138 1.443637 8.560575 8.626369 7.174712 0.942377 13.283331
139 1.504001 11.735610 12.538237 7.279109 0.822399 55.197604
140 5.940133 6.583439 0.535226 6.989206 0.805532 59.914646
141 5.938950 9.823183 3.986512 7.104385 0.828790 13.334877
142 5.906756 6.585388 7.520645 7.034840 0.816173 13.670661
143 6.183363 9.714945 10.710676 7.036383 0.761824 12.756445
144 5.934570 6.543678 3.172394 7.096069 0.630383 13.563135
145 5.906164 9.835267 6.613427 7.096065 0.865776 12.993967
146 5.959071 6.678553 10.103676 7.095739 0.865877 12.815875
147 4.439092 11.062402 1.744304 7.205723 0.954455 16.208704
148 4.458384 7.850724 5.270645 7.165238 0.921074 13.647401
149 4.440986 11.057984 9.122223 7.146931 0.561883 12.721851
150 4.466315 8.174919 12.130563 7.134401 0.912010 15.788357
151 4.442879 8.549271 1.828382 7.163119 0.940205 14.416935
152 4.453532 11.791873 5.253829 7.191313 0.937698 13.991661
153 4.442643 8.637369 8.831437 7.182559 0.910119 12.970708
154 4.403347 11.672720 12.155991 7.149878 0.782546 29.978710
155 8.907537 6.585388 0.539738 6.973084 0.813018 55.924462
156 8.897476 9.819675 4.009890 7.074368 0.819130 13.025013
157 8.869307 6.560310 7.467328 6.994549 0.696503 13.051229
158 8.822673 9.861645 10.773426 7.090679 0.716863 13.603642
159 8.900909 6.556282 3.182237 7.087978 0.714090 13.360994
160 8.899488 9.847091 6.615888 7.134169 0.766587 13.096861
161 8.935707 6.569275 10.074556 7.101818 0.691527 13.087892
162 7.426380 11.067339 1.745945 7.214433 0.951930 16.854745
163 7.406969 7.850464 5.276797 7.170910 0.921628 13.769908
164 7.396435 11.081373 8.688710 7.149287 0.911635 13.275939
165 7.627947 7.892564 12.315124 7.203399 0.637908 12.437317
166 7.424249 8.549271 1.834944 7.156430 0.947962 14.461877
167 7.414544 11.795512 5.265313 7.161069 0.941911 13.770499
168 7.458219 8.555898 8.641134 7.126879 0.907843 13.016241
169 7.376432 11.674020 12.545620 7.273821 0.900011 35.648701
170 0.035035 6.572004 0.551632 6.977220 0.801338 53.339506
171 0.015624 9.830719 3.989383 7.134468 0.811047 12.642316
172 0.012073 6.551604 7.491116 7.032902 0.760864 13.174524
173 0.068057 9.847481 10.740205 7.114686 0.784954 13.852104
174 0.007812 6.550045 3.200694 7.119704 0.846027 13.246766
175 11.831502 9.847611 6.610146 7.134584 0.772312 13.036544
176 0.063678 6.625669 10.163555 7.041543 0.705037 13.531301
177 10.409525 11.058893 1.736101 7.184946 0.927934 17.467475
178 10.376621 7.856831 5.279258 7.196532 0.954025 14.036110
179 10.363365 11.100214 8.766636 7.209591 0.915320 13.785381
180 10.423728 7.946228 12.359828 7.220829 0.837989 23.204386
181 10.418639 8.562135 1.807465 7.172519 0.961523 15.635200
182 10.375793 11.794212 5.255470 7.198940 0.950914 14.032070
183 10.362655 8.576818 8.734645 7.219591 0.943177 13.926712
184 10.388812 11.634129 12.438574 7.279013 0.766222 40.093627
185 2.839930 9.648936 0.001641 1.396582 0.468668 144.735562
186 2.904909 3.045097 0.008203 1.428571 0.616189 165.541857
187 5.894920 9.671935 41.010219 1.448732 0.516060 178.337527
188 5.937529 3.090705 0.002871 1.451852 0.509919 184.041126
189 8.814861 9.673364 41.011039 1.436608 0.516205 211.382053
190 8.858062 3.159572 41.010629 1.461883 0.517282 205.040198
191 0.580319 9.819545 40.987251 1.005726 0.708006 189.738812
192 0.426214 3.323034 0.009023 1.435611 0.602421 163.054571
193 5.809819 3.397099 14.118897 8.296992 1.068167 24.210359
194 7.989655 4.786136 13.792430 7.992083 0.899028 17.613438
195 6.141582 5.498067 15.412463 7.930394 0.877091 12.611073
196 4.162011 5.384371 13.879379 7.899258 0.714154 19.167881
197 7.505563 7.408545 14.288283 7.820921 0.897805 22.026037
198 8.016049 3.688030 15.961224 8.091277 0.718048 123.861263
199 5.115519 7.704024 14.661916 8.014536 1.057116 44.743749
200 3.692595 5.594091 16.249549 8.206382 0.773065 100.459861
201 7.040526 7.995475 16.634665 7.897126 0.820313 267.618449
202 8.481441 6.070573 16.107642 8.053503 1.013997 96.541822
203 6.494532 4.515865 17.685841 7.940625 0.922806 678.480896
204 4.730257 3.536003 16.492349 7.926572 0.897408 197.236347
205 5.395559 6.623590 17.563621 7.856639 1.009258 563.828021
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 1088.0000

sgy002
Posts: 4
Joined: Tue Nov 13, 2018 5:11 pm

Re: Problem while running bader charge Calculation

Post by sgy002 » Wed Nov 21, 2018 6:44 pm

Thank you so much. You were right. It's working now.

skureshi
Posts: 2
Joined: Thu Feb 28, 2019 1:37 am

Re: Problem while running bader charge Calculation

Post by skureshi » Thu Feb 28, 2019 6:56 am

I am having the same problem as mentioned by sgy002,

At line 89 of file chgcar_mod.f90 (unit = 100, file = 'CHGCAR')
Fortran runtime error: Bad real number in item 58996800 of list input.

I tried the suggestion and I am already running on linux machine with node of 8GB memory but it is still giving same error.

I am attaching here my CHGCAR and AECCAR file for your reference.

Regards,
SKureshi
PhD student
Simon Fraser University
BC, Canada
Attachments
CHGCAR.zip
(759.89 MiB) Downloaded 39 times
AECCAR.zip
(741.33 MiB) Downloaded 28 times

graeme
Site Admin
Posts: 1826
Joined: Tue Apr 26, 2005 4:25 am
Location: University of Texas at Austin
Contact:

Re: Problem while running bader charge Calculation

Post by graeme » Sat Mar 02, 2019 2:58 am

I appreciate that people are having some problems, but I don't understand what is going wrong. Using you files, I can run the bader analysis on my laptop.
Graeme

----------

bader CHGCAR -ref CHGCAR_sum

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

OPEN ... CHGCAR
VASP5-STYLE INPUT FILE
DENSITY-GRID: 448 x 480 x 300
CLOSE ... CHGCAR
RUN TIME: 23.37 SECONDS

OPEN ... CHGCAR_sum
VASP5-STYLE INPUT FILE
DENSITY-GRID: 448 x 480 x 300
CLOSE ... CHGCAR_sum
RUN TIME: 24.73 SECONDS

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

REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 22750126
REASSIGNED POINTS: 1239092

RUN TIME: 186.91 SECONDS

CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************
RUN TIME: 17.82 SECONDS

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

NUMBER OF BADER MAXIMA FOUND: 112094
SIGNIFICANT MAXIMA FOUND: 72
VACUUM CHARGE: 0.0000
NUMBER OF ELECTRONS: 218.00000

----------

with an ACF.dat

-------------


# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 11.111314 13.113390 7.615937 4.017394 0.629890 30.502869
2 12.528197 13.160206 7.530564 3.998441 0.624726 30.089404
3 10.350247 14.303288 7.494866 4.014669 0.643334 37.092626
4 13.178484 14.408331 7.328784 4.008453 0.628696 32.114418
5 11.001992 15.546048 7.297259 4.022493 0.625814 40.839486
6 12.417323 15.596837 7.214906 3.960038 0.624700 37.823995
7 10.442348 11.839580 7.833084 4.029666 0.653359 28.407388
8 13.305333 11.948040 7.663683 3.963639 0.620840 26.288563
9 8.897182 14.249209 7.572982 4.015729 0.639365 37.788397
10 14.630373 14.462435 7.244138 4.015272 0.618829 32.016669
11 10.221046 16.768337 7.182907 3.973648 0.624958 38.892379
12 13.087865 16.874443 7.020145 3.967335 0.608124 39.308616
13 9.024595 11.778897 7.900908 4.018100 0.632305 36.046564
14 14.729815 11.988959 7.594831 4.043114 0.627852 24.675555
15 11.203040 10.648847 7.980258 4.030924 0.612301 25.323326
16 12.666126 10.700800 7.907849 4.030081 0.627021 22.611441
17 8.128916 15.437816 7.455104 4.008037 0.637819 39.114723
18 15.289505 15.702918 7.039180 3.991741 0.625301 34.147748
19 8.237744 13.006069 7.764043 4.000916 0.635002 37.603257
20 15.399133 13.273272 7.367565 4.021306 0.651665 27.223163
21 10.869898 18.017652 6.995435 4.014009 0.643341 40.208930
22 12.331032 18.072413 6.918109 4.072551 0.641226 40.769019
23 8.803528 16.722331 7.260407 4.018012 0.636903 39.736233
24 14.504207 16.933456 6.935199 4.034874 0.646506 37.843253
25 8.394540 10.538312 8.102847 4.055124 0.626311 93.684183
26 15.468251 10.816826 7.764533 4.053014 0.615895 29.555868
27 10.535109 9.428254 8.185643 4.013683 0.600483 49.910324
28 13.435334 9.543522 8.077235 4.124133 0.596625 22.571466
29 6.726595 15.364708 7.525394 4.071153 0.626936 98.215079
30 16.693144 15.734095 6.943642 4.112148 0.633722 97.205344
31 6.832929 12.971831 7.822745 4.081444 0.625187 97.180105
32 16.798890 13.347771 7.268391 4.117944 0.639563 65.401389
33 10.099796 19.188519 6.886347 4.010060 0.616310 96.703030
34 12.997339 19.297384 6.743269 4.027418 0.612570 95.741878
35 8.065468 17.914329 7.147035 4.018204 0.614024 99.498804
36 15.133768 18.179228 6.757735 4.003578 0.605336 100.885822
37 9.143304 9.370380 8.243744 4.066041 0.615365 105.925160
38 14.834784 9.570447 7.951895 4.727831 0.623461 15.080081
39 6.082377 14.141230 7.704930 4.004090 0.611296 127.769051
40 17.444519 14.566289 7.055607 3.967899 0.596382 111.441864
41 8.708485 19.136971 6.959673 4.094395 0.628470 145.472897
42 14.388627 19.353335 6.664125 4.107247 0.637727 130.262970
43 15.000991 7.409496 10.257199 3.862562 0.589213 26.379893
44 16.086684 5.873999 8.623858 3.842106 0.537156 55.829696
45 7.310211 10.481223 8.151588 0.963653 0.357061 179.613934
46 16.557685 10.872195 7.767853 0.994480 0.373162 21.108583
47 11.108491 8.511962 8.301007 0.969319 0.313669 36.827974
48 12.926081 8.608478 8.306414 1.007626 0.321118 11.925407
49 6.130863 16.270448 7.438188 0.956887 0.322082 186.754881
50 17.204043 16.679084 6.781544 0.941772 0.299232 207.238161
51 6.318783 12.024362 7.961855 0.954745 0.314606 163.343354
52 17.395492 12.442841 7.360799 0.940819 0.301650 56.692224
53 10.588699 20.148767 6.742035 0.956359 0.311633 132.320664
54 12.423674 20.217801 6.667002 0.954236 0.317138 110.101387
55 6.979680 17.890364 7.206416 0.979240 0.360699 224.281689
56 16.217273 18.231965 6.691428 0.966522 0.356842 242.046373
57 8.644779 8.420330 8.398664 0.938662 0.295950 522.632352
58 5.000001 14.099046 7.752597 0.962747 0.356985 357.123633
59 18.525319 14.603362 6.979704 0.963531 0.356978 303.355570
60 8.128045 20.047621 6.871012 0.948467 0.302724 744.898072
61 14.888210 20.305662 6.528840 0.933441 0.292754 315.080665
62 14.557515 6.572714 10.809782 0.966135 0.311749 167.671166
63 15.689154 4.999993 9.159810 0.954765 0.304326 270.290942
64 14.242346 6.818406 8.409984 0.590342 0.185972 28.720331
65 14.348987 8.289323 10.362919 0.905230 0.298128 43.697557
66 16.215133 5.594802 7.570674 0.939727 0.319977 221.305006
67 15.975598 7.654303 10.698450 0.927438 0.312832 100.037884
68 17.081570 6.104584 9.033095 0.922045 0.308235 302.425202
69 16.918540 8.450596 8.249862 1.649564 0.620108 150.993249
70 15.171549 7.072779 8.771917 6.136565 0.688718 13.998566
71 15.754083 8.349626 8.030090 1.662089 0.417698 181.626693
72 15.156164 8.491262 5.000003 8.383075 1.409466 1634.644176
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 218.0000

skureshi
Posts: 2
Joined: Thu Feb 28, 2019 1:37 am

Re: Problem while running bader charge Calculation

Post by skureshi » Mon Mar 04, 2019 5:50 pm

Dear Graeme,

Thanks for your prompt response. Well, I think it's memory problem only, because with lower grid I am also able to run the Bader analysis. If you don't mind can you please share the configuration of your laptop, you ran this analysis, specifically memory usage? This will help me to ask for resources on high performance cluster.

Regards,
Sahida K

graeme wrote:
> I appreciate that people are having some problems, but I don't understand
> what is going wrong. Using you files, I can run the bader analysis on my
> laptop.
> Graeme
>
> ----------
>
> bader CHGCAR -ref CHGCAR_sum
>
> GRID BASED BADER ANALYSIS (Version 1.03 11/13/17)
>
> OPEN ... CHGCAR
> VASP5-STYLE INPUT FILE
> DENSITY-GRID: 448 x 480 x 300
> CLOSE ... CHGCAR
> RUN TIME: 23.37 SECONDS
>
> OPEN ... CHGCAR_sum
> VASP5-STYLE INPUT FILE
> DENSITY-GRID: 448 x 480 x 300
> CLOSE ... CHGCAR_sum
> RUN TIME: 24.73 SECONDS
>
> CALCULATING BADER CHARGE DISTRIBUTION
> 0 10 25 50 75 100
> PERCENT DONE: **********************
>
> REFINING AUTOMATICALLY
> ITERATION: 1
> EDGE POINTS: 22750126
> REASSIGNED POINTS: 1239092
>
> RUN TIME: 186.91 SECONDS
>
> CALCULATING MINIMUM DISTANCES TO ATOMS
> 0 10 25 50 75 100
> PERCENT DONE: **********************
> RUN TIME: 17.82 SECONDS
>
> WRITING BADER ATOMIC CHARGES TO ACF.dat
> WRITING BADER VOLUME CHARGES TO BCF.dat
>
> NUMBER OF BADER MAXIMA FOUND: 112094
> SIGNIFICANT MAXIMA FOUND: 72
> VACUUM CHARGE: 0.0000
> NUMBER OF ELECTRONS: 218.00000
>
> ----------
>
> with an ACF.dat
>
> -------------
>
>
> # X Y Z CHARGE MIN DIST ATOMIC
> VOL
>
> --------------------------------------------------------------------------------
> 1 11.111314 13.113390 7.615937 4.017394 0.629890
> 30.502869
> 2 12.528197 13.160206 7.530564 3.998441 0.624726
> 30.089404
> 3 10.350247 14.303288 7.494866 4.014669 0.643334
> 37.092626
> 4 13.178484 14.408331 7.328784 4.008453 0.628696
> 32.114418
> 5 11.001992 15.546048 7.297259 4.022493 0.625814
> 40.839486
> 6 12.417323 15.596837 7.214906 3.960038 0.624700
> 37.823995
> 7 10.442348 11.839580 7.833084 4.029666 0.653359
> 28.407388
> 8 13.305333 11.948040 7.663683 3.963639 0.620840
> 26.288563
> 9 8.897182 14.249209 7.572982 4.015729 0.639365
> 37.788397
> 10 14.630373 14.462435 7.244138 4.015272 0.618829
> 32.016669
> 11 10.221046 16.768337 7.182907 3.973648 0.624958
> 38.892379
> 12 13.087865 16.874443 7.020145 3.967335 0.608124
> 39.308616
> 13 9.024595 11.778897 7.900908 4.018100 0.632305
> 36.046564
> 14 14.729815 11.988959 7.594831 4.043114 0.627852
> 24.675555
> 15 11.203040 10.648847 7.980258 4.030924 0.612301
> 25.323326
> 16 12.666126 10.700800 7.907849 4.030081 0.627021
> 22.611441
> 17 8.128916 15.437816 7.455104 4.008037 0.637819
> 39.114723
> 18 15.289505 15.702918 7.039180 3.991741 0.625301
> 34.147748
> 19 8.237744 13.006069 7.764043 4.000916 0.635002
> 37.603257
> 20 15.399133 13.273272 7.367565 4.021306 0.651665
> 27.223163
> 21 10.869898 18.017652 6.995435 4.014009 0.643341
> 40.208930
> 22 12.331032 18.072413 6.918109 4.072551 0.641226
> 40.769019
> 23 8.803528 16.722331 7.260407 4.018012 0.636903
> 39.736233
> 24 14.504207 16.933456 6.935199 4.034874 0.646506
> 37.843253
> 25 8.394540 10.538312 8.102847 4.055124 0.626311
> 93.684183
> 26 15.468251 10.816826 7.764533 4.053014 0.615895
> 29.555868
> 27 10.535109 9.428254 8.185643 4.013683 0.600483
> 49.910324
> 28 13.435334 9.543522 8.077235 4.124133 0.596625
> 22.571466
> 29 6.726595 15.364708 7.525394 4.071153 0.626936
> 98.215079
> 30 16.693144 15.734095 6.943642 4.112148 0.633722
> 97.205344
> 31 6.832929 12.971831 7.822745 4.081444 0.625187
> 97.180105
> 32 16.798890 13.347771 7.268391 4.117944 0.639563
> 65.401389
> 33 10.099796 19.188519 6.886347 4.010060 0.616310
> 96.703030
> 34 12.997339 19.297384 6.743269 4.027418 0.612570
> 95.741878
> 35 8.065468 17.914329 7.147035 4.018204 0.614024
> 99.498804
> 36 15.133768 18.179228 6.757735 4.003578 0.605336
> 100.885822
> 37 9.143304 9.370380 8.243744 4.066041 0.615365
> 105.925160
> 38 14.834784 9.570447 7.951895 4.727831 0.623461
> 15.080081
> 39 6.082377 14.141230 7.704930 4.004090 0.611296
> 127.769051
> 40 17.444519 14.566289 7.055607 3.967899 0.596382
> 111.441864
> 41 8.708485 19.136971 6.959673 4.094395 0.628470
> 145.472897
> 42 14.388627 19.353335 6.664125 4.107247 0.637727
> 130.262970
> 43 15.000991 7.409496 10.257199 3.862562 0.589213
> 26.379893
> 44 16.086684 5.873999 8.623858 3.842106 0.537156
> 55.829696
> 45 7.310211 10.481223 8.151588 0.963653 0.357061
> 179.613934
> 46 16.557685 10.872195 7.767853 0.994480 0.373162
> 21.108583
> 47 11.108491 8.511962 8.301007 0.969319 0.313669
> 36.827974
> 48 12.926081 8.608478 8.306414 1.007626 0.321118
> 11.925407
> 49 6.130863 16.270448 7.438188 0.956887 0.322082
> 186.754881
> 50 17.204043 16.679084 6.781544 0.941772 0.299232
> 207.238161
> 51 6.318783 12.024362 7.961855 0.954745 0.314606
> 163.343354
> 52 17.395492 12.442841 7.360799 0.940819 0.301650
> 56.692224
> 53 10.588699 20.148767 6.742035 0.956359 0.311633
> 132.320664
> 54 12.423674 20.217801 6.667002 0.954236 0.317138
> 110.101387
> 55 6.979680 17.890364 7.206416 0.979240 0.360699
> 224.281689
> 56 16.217273 18.231965 6.691428 0.966522 0.356842
> 242.046373
> 57 8.644779 8.420330 8.398664 0.938662 0.295950
> 522.632352
> 58 5.000001 14.099046 7.752597 0.962747 0.356985
> 357.123633
> 59 18.525319 14.603362 6.979704 0.963531 0.356978
> 303.355570
> 60 8.128045 20.047621 6.871012 0.948467 0.302724
> 744.898072
> 61 14.888210 20.305662 6.528840 0.933441 0.292754
> 315.080665
> 62 14.557515 6.572714 10.809782 0.966135 0.311749
> 167.671166
> 63 15.689154 4.999993 9.159810 0.954765 0.304326
> 270.290942
> 64 14.242346 6.818406 8.409984 0.590342 0.185972
> 28.720331
> 65 14.348987 8.289323 10.362919 0.905230 0.298128
> 43.697557
> 66 16.215133 5.594802 7.570674 0.939727 0.319977
> 221.305006
> 67 15.975598 7.654303 10.698450 0.927438 0.312832
> 100.037884
> 68 17.081570 6.104584 9.033095 0.922045 0.308235
> 302.425202
> 69 16.918540 8.450596 8.249862 1.649564 0.620108
> 150.993249
> 70 15.171549 7.072779 8.771917 6.136565 0.688718
> 13.998566
> 71 15.754083 8.349626 8.030090 1.662089 0.417698
> 181.626693
> 72 15.156164 8.491262 5.000003 8.383075 1.409466
> 1634.644176
>
> --------------------------------------------------------------------------------
> VACUUM CHARGE: 0.0000
> VACUUM VOLUME: 0.0000
> NUMBER OF ELECTRONS: 218.0000

graeme
Site Admin
Posts: 1826
Joined: Tue Apr 26, 2005 4:25 am
Location: University of Texas at Austin
Contact:

Re: Problem while running bader charge Calculation

Post by graeme » Mon Mar 04, 2019 6:03 pm

Hi Sahida, my laptop has 16GB of memory - nothing very special. - Graeme

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