The command "chgsplit.pl CHGCAR" freezes

Bader charge density analysis

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jianmin
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The command "chgsplit.pl CHGCAR" freezes

Post by jianmin » Thu Oct 18, 2018 12:35 am

Dear Prof. Graeme and all,

I have built the rutile-TiO2(110) 3x1x4 surface slab and tried to do the spin number analysis by the following steps:
step 1: chgsum.pl AECCAR0 AECCAR2
step 2: chgsplit.pl CHGCAR
step 3: bader CHGCAR_mag -ref CHGCAR_sum

At step 2, after I issued the command, it freezes there without any standard ouput. It occasionally happened to other surface models, usually large systems. Could it be that it exceeds the memory limit of the computer the script is running on? I usually run this chgsplit.pl script on the login node of a supercomputing center.

Thanks a million.

graeme
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Re: The command "chgsplit.pl CHGCAR" freezes

Post by graeme » Thu Oct 18, 2018 1:19 am

Maybe; if you post the files, I can check.

jianmin
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Joined: Fri Jan 15, 2010 2:39 am

Re: The command "chgsplit.pl CHGCAR" freezes

Post by jianmin » Thu Oct 18, 2018 3:09 am

Dear Prof. Graeme, thanks for your quick reply. And in the attachment please find the CHGCAR file I mentioned.

Thanks again.
Attachments
CHGCAR.txt
(34.71 MiB) Downloaded 22 times

graeme
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Re: The command "chgsplit.pl CHGCAR" freezes

Post by graeme » Thu Oct 18, 2018 12:57 pm

also the AECCAR0 and AECCAR2 please

and these are relatively small files - there should not be any problems with memory.

jianmin
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Joined: Fri Jan 15, 2010 2:39 am

Re: The command "chgsplit.pl CHGCAR" freezes

Post by jianmin » Fri Oct 19, 2018 12:56 am

Thanks. The AECCAR0 and ACECAR2 are attached.
Attachments
AECCAR2.txt
(34.55 MiB) Downloaded 17 times
AECCAR0.txt
(34.55 MiB) Downloaded 18 times

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Re: The command "chgsplit.pl CHGCAR" freezes

Post by graeme » Fri Oct 19, 2018 1:44 am

I don't see any problem. Here is the output of my calculations and the ACF.dat file, following that.

graeme@fri:~/tmp> bader CHGCAR -ref CHGCAR_sum

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

OPEN ... CHGCAR
VASP5-STYLE INPUT FILE
DENSITY-GRID: 96 x 72 x 288
CLOSE ... CHGCAR
RUN TIME: 1.67 SECONDS

OPEN ... CHGCAR_sum
VASP5-STYLE INPUT FILE
DENSITY-GRID: 96 x 72 x 288
CLOSE ... CHGCAR_sum
RUN TIME: 1.75 SECONDS

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

REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 862651
REASSIGNED POINTS: 33349

RUN TIME: 11.13 SECONDS

CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************
RUN TIME: 1.64 SECONDS

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

NUMBER OF BADER MAXIMA FOUND: 1155
SIGNIFICANT MAXIMA FOUND: 78
VACUUM CHARGE: 0.0000
NUMBER OF ELECTRONS: 589.99991

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

# X Y Z CHARGE MIN DIST ATOMIC VOL
--------------------------------------------------------------------------------
1 3.915729 3.590465 20.504695 0.915101 0.247323 184.368901
2 2.114797 3.612136 20.496109 0.979122 0.287766 148.418773
3 3.032633 4.815434 19.536881 0.892741 0.261237 16.707379
4 3.013192 1.972117 18.913790 0.307472 0.067007 4.002656
5 3.019793 3.780965 19.897459 3.604416 0.392858 20.540354
6 3.015010 2.933718 18.744405 7.238672 0.740990 17.977113
7 0.000000 3.289460 5.486162 7.111256 0.897927 81.871238
8 3.013997 3.289460 5.486162 7.111762 0.897925 127.763659
9 6.028003 3.289460 5.486162 7.111501 0.897925 111.509581
10 1.507003 1.281212 6.767373 7.185029 0.858753 20.737905
11 4.521000 1.281212 6.767373 7.185029 0.858755 20.736265
12 7.534997 1.281212 6.767373 7.184893 0.858753 20.001803
13 1.507003 5.297708 6.767373 7.194375 0.858753 19.607521
14 4.521000 5.297708 6.767373 7.194375 0.858755 19.607521
15 7.534997 5.297708 6.767373 7.194378 0.858753 19.901798
16 0.000000 3.289460 8.048584 7.250609 0.904631 12.793252
17 3.013997 3.289460 8.048584 7.249889 0.904629 12.794072
18 6.028003 3.289460 8.048584 7.250608 0.904629 12.793252
19 0.000000 0.000000 8.775610 7.155642 0.864059 12.512910
20 3.013997 0.000000 8.775610 7.155471 0.864057 12.508812
21 6.028003 0.000000 8.775610 7.155643 0.864057 12.512910
22 1.507003 2.008248 10.056848 7.182811 0.859633 12.594882
23 4.521000 2.008248 10.056848 7.182763 0.859636 12.594062
24 7.534997 2.008248 10.056848 7.186473 0.859633 12.603898
25 1.507003 4.570672 10.056848 7.190585 0.859633 12.618653
26 4.521000 4.570672 10.056848 7.190587 0.859636 12.618653
27 7.534997 4.570672 10.056848 7.194122 0.859633 12.621112
28 0.000000 0.000000 11.338059 7.192602 0.875006 12.898995
29 3.013997 0.000000 11.338059 7.189588 0.875004 12.947358
30 6.028003 0.000000 11.338059 7.192667 0.875004 12.898995
31 0.016465 3.304480 12.078279 7.182416 0.828185 12.435857
32 3.013798 3.304802 12.092187 7.184281 0.875145 12.440776
33 6.012785 3.304157 12.077950 7.181921 0.827536 12.433398
34 1.506904 1.325889 13.374522 7.193621 0.888863 12.741610
35 1.506659 5.300873 13.363193 7.193441 0.883369 12.656360
36 4.520864 1.325639 13.374495 7.193936 0.888666 12.743249
37 4.522655 5.301202 13.364044 7.193521 0.884258 12.656360
38 7.534952 1.329159 13.357378 7.202092 0.890484 12.811286
39 7.535603 5.302998 13.342977 7.190972 0.883223 12.582586
40 9.025290 3.343670 14.621609 7.195729 0.894035 12.509631
41 3.013662 3.334335 14.674112 7.200561 0.877511 12.823581
42 6.045969 3.343973 14.621170 7.195751 0.892812 12.508812
43 9.033410 0.009349 15.358373 7.191670 0.881093 13.176058
44 3.014205 6.575144 15.362598 7.183302 0.885234 13.157204
45 6.037877 0.008039 15.356892 7.191839 0.879612 13.176877
46 1.501144 4.558849 16.814949 7.216788 0.848262 15.465514
47 1.460862 2.078991 16.678124 7.211285 0.837828 14.326114
48 4.527004 4.559330 16.816595 7.216373 0.848555 15.441743
49 4.569022 2.079827 16.678344 7.211482 0.835883 14.317097
50 7.535983 4.561869 16.810259 7.227993 0.849052 21.206780
51 7.536290 2.106531 16.779893 7.222100 0.853497 20.753479
52 0.009304 0.057954 17.914102 7.091715 0.803557 45.794055
53 3.014567 0.160545 17.929107 7.153724 0.820050 21.978949
54 6.019151 0.058046 17.913032 7.090634 0.803098 40.079839
55 0.000000 0.000000 6.767373 9.693978 0.881201 14.938439
56 3.013997 0.000000 6.767373 9.694052 0.881199 14.108071
57 6.028003 0.000000 6.767373 9.693978 0.881199 14.938439
58 1.507003 3.289460 6.767373 9.622796 0.869297 8.160237
59 4.521000 3.289460 6.767373 9.622796 0.869300 8.157778
60 7.534997 3.289460 6.767373 9.622955 0.869297 8.201223
61 1.507003 0.000000 10.056848 9.629787 0.881885 7.405282
62 4.521000 0.000000 10.056848 9.629790 0.881887 7.405282
63 7.534997 0.000000 10.056848 9.629768 0.881885 7.406102
64 0.000000 3.289460 10.056848 9.624926 0.882060 7.449547
65 3.013997 3.289460 10.056848 9.628355 0.882057 7.505287
66 6.028003 3.289460 10.056848 9.624859 0.882057 7.449547
67 9.040598 0.024164 13.444334 9.616939 0.870980 7.459383
68 3.013789 0.018770 13.452974 9.625639 0.867839 7.518402
69 6.029323 0.022789 13.443895 9.616641 0.869976 7.459383
70 1.527284 3.315177 13.323775 9.609183 0.850616 7.304457
71 4.500637 3.313934 13.323611 9.609517 0.850412 7.306097
72 7.534120 3.319670 13.246064 9.631328 0.848895 7.402003
73 1.495285 0.041224 16.795967 9.632774 0.830140 7.680706
74 4.534283 0.040671 16.795336 9.632393 0.828916 7.676607
75 7.535006 0.040474 16.822054 9.617697 0.830031 8.234831
76 9.037841 3.336670 16.465837 9.626237 0.840076 9.404561
77 3.014115 3.310394 16.619779 9.589557 0.870502 7.509386
78 6.032795 3.337512 16.466221 9.626640 0.841035 9.402921
--------------------------------------------------------------------------------
VACUUM CHARGE: 0.0000
VACUUM VOLUME: 0.0000
NUMBER OF ELECTRONS: 589.9999

jianmin
Posts: 63
Joined: Fri Jan 15, 2010 2:39 am

Re: The command "chgsplit.pl CHGCAR" freezes

Post by jianmin » Fri Oct 19, 2018 2:21 am

Prof. Graeme, Yes, it has no problem for that.

But, in order to get the spin charges of the system, I issued the command "chgsplit.pl CHGCAR". It showed the following two lines:
Atoms in file: 78
Points in total charge density: 1990656

and then freezed there.

I can wait for it to finish, but I do not think it should take that long to finish, right?

graeme
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Re: The command "chgsplit.pl CHGCAR" freezes

Post by graeme » Fri Oct 19, 2018 2:43 am

It doesn't look like a spin polarized charge density; there is only one data set in the CHGCAR file corresponding to the total charge.

jianmin
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Re: The command "chgsplit.pl CHGCAR" freezes

Post by jianmin » Sun Oct 21, 2018 11:48 pm

I did not set ISPIN=2. Is that the problem?
Last edited by jianmin on Mon Oct 22, 2018 12:22 am, edited 1 time in total.

graeme
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Re: The command "chgsplit.pl CHGCAR" freezes

Post by graeme » Mon Oct 22, 2018 12:07 am

yes

jianmin
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Re: The command "chgsplit.pl CHGCAR" freezes

Post by jianmin » Thu Oct 25, 2018 12:38 am

Thanks, Prof. Graeme. You are right. The problem vanishes when I set ISPIN=2.

graeme
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Re: The command "chgsplit.pl CHGCAR" freezes

Post by graeme » Thu Oct 25, 2018 1:59 am

And clearly, we need a print statement to indicate this problem!

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