bader_programme_stuck after beginneing

[vimal]

Dear Graeme,

I combined my AECCAR0 and AECCAR2 file to get the CHGCAR_sum.
when i typed bader CHGCAR -ref CHGCAR_sum, the programme
starts working as below, but there is no update for more than an hour.
---------------------------------
GRID BASED BADER ANALYSIS (v0.27a 07/23/10)
OPEN ... CHGCAR
VASP-STYLE INPUT FILE
FFT-grid: 0 x 0 x 0
CLOSE ... CHGCAR
---------------------------------

Is there any limitation on the number of systems.
My system has 250 atoms on it.

Please help.
vimal

[graeme]

There is some problem with the calculation. The FFT-grid line should report the number of grid points in your calculation -- it should not be 0x0x0.

First, update to the latest version. There were some issues with vasp5 files which have not been fixed.

Also, if you are using our chgsum.pl script, try using the chgsumf.pl. The issue is that the first uses perl-formatted numbers and the second uses fortran-formatted numbers. If any values are too large so that the number run into each other, the fortran formatting will deal with this properly.

If you try these two things and still have problems, I would like to see the files and understand the problem.

[vimal]

I used the new version 0.28 downloaded from http://theory.cm.utexas.edu/vtsttools/bader/
and now it works ok.

------------------------------------------------------------------
GRID BASED BADER ANALYSIS (Version 0.28 06/26/11)

OPEN ... CHGCAR
VASP-STYLE INPUT FILE
VASP5 format
FFT-grid: 162 x 162 x 512
CLOSE ... CHGCAR

RUN TIME: 3.93 SECONDS

OPEN ... CHGCAR_sum
VASP-STYLE INPUT FILE
VASP5 format
FFT-grid: 162 x 162 x 512
CLOSE ... CHGCAR_sum

RUN TIME: 3.89 SECONDS

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

REFINING AUTOMATICALLY
ITERATION: 1
EDGE POINTS: 10849505
REASSIGNED POINTS: 896181
ITERATION: 2
CHECKED POINTS: 7419318
REASSIGNED POINTS: 94
ITERATION: 3
CHECKED POINTS: 2287
REASSIGNED POINTS: 2
ITERATION: 4
CHECKED POINTS: 52
REASSIGNED POINTS: 0

RUN TIME: 129.31 SECONDS

CALCULATING MINIMUM DISTANCES TO ATOMS
0 10 25 50 75 100
PERCENT DONE: **********************

RUN TIME: 5.15 SECONDS

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

NUMBER OF BADER MAXIMA FOUND: 326114
SIGNIFICANT MAXIMA FOUND: 40059
NUMBER OF ELECTRONS: 1224.00003
---------------------------------------------------------------------

[graeme]

That was quick! Good to hear that it's working now.

[vimal]

Dear Grame,

I get the following error message.
what i did is the following.

chgsumf.pl AECCAR0 AECCAR2
bader CHGCAR -ref CHGCAR_sum

and got the following error message.

Please help.

Best,
VImal


GRID BASED BADER ANALYSIS (Version 0.28 06/26/11)

OPEN ... CHGCAR
VASP-STYLE INPUT FILE
VASP5 format
FFT-grid: 168 x 168 x 540
CLOSE ... CHGCAR

RUN TIME: 8.02 SECONDS

OPEN ... CHGCAR_sum
VASP-STYLE INPUT FILE
VASP5 format
forrtl: severe (59): list-directed I/O syntax error, unit 100, file CHGCAR_sum
Image PC Routine Line Source
bader 00000000004C004D Unknown Unknown Unknown
bader 00000000004BEB55 Unknown Unknown Unknown
bader 0000000000477239 Unknown Unknown Unknown
bader 000000000043550D Unknown Unknown Unknown
bader 0000000000434D5A Unknown Unknown Unknown
bader 0000000000459E5E Unknown Unknown Unknown
bader 000000000040C205 Unknown Unknown Unknown
bader 0000000000410F3F Unknown Unknown Unknown
bader 00000000004155DF Unknown Unknown Unknown
bader 0000000000400614 Unknown Unknown Unknown
bader 00000000004002EC Unknown Unknown Unknown
bader 00000000004CB3E0 Unknown Unknown Unknown
bader 00000000004001B9 Unknown Unknown Unknown

[graeme]

If you post the AECCAR0 and AECCAR2 files, we'll debug the problem.

[vimal]

Dear Grimme,

Many thanks for your help.

I uploaded the files, but i didn't get any confirmation.
Therefore, I doubt if it worked out our not.

If you didn't get the files,
You can also download the files from the following link.
http://depositfiles.com/files/hgas28r8l

If you have any problem in getting the files, please let me know.

best regards,
vimal

[graeme]

I do not see a problem analyzing these files. I do not, however, have the CHGCAR file, so I can not do the exact test that you did.

I'll suggest a few things:

1. Update to the latest bader program if you have not already.

2. See if you can analyze smaller charge density files for the same system (for example by setting NGXF,NGYF,NGZF) to 1/2 the values of what you have now. If this calculation works fine, it could be a problem with limited memory.

3. Upload the CHGCAR file. To deal with these large files, use a compressor such as gzip or bzip2 which will reduce the file size by ~80%. Uploads which are <500Mb can be attached to posts.

EDIT: I was able to reproduce this problem using the chgsumf.pl script and an old version of the bader code. With the current version, things appear to work fine.

[graeme]

Actually, the problem was with our chgsumf.pl script. For negative densities (which there should not be, but they can show up infrequently), no white space was allocated to separate values. An updated version of the script solves the problem. The change is the line:

print OUT Fortran::Format->new('5E18.11:')->write(@line1);

to

print OUT Fortran::Format->new('5(1X,E17.11):')->write(@line1);

I'll attach the modified script here.

[RB_Rankin]

Hello,

I am using Bader(v28) with VASP 5.2.12 outputted calculations .

I get the dreaded message below while reading my CHGCAR_sum file generated from chgsumf.pl (and also with chgsum.pl) script
" VASP-STYLE INPUT FILE
VASP5 format
FFT-grid: 0 x 0 x 0
"


this is the top of the CHGCAR_sum file
(with some atomic coordinates trimmed for brevity)

--------------------------
RANKIN TM SURFACE CALC
1.00000000000000
20.487000 8.875000 0.000000
2.516000 22.319000 0.000000
0.000000 0.000000 29.379276
C H N O Cu
126 42 0 0 228
Direct
0.990417 0.979722 0.528874
0.961741 0.945920 0.556491
<snip of several coordinates>
0.983614 0.142644 0.285715
0.985182 0.640647 0.285715

250 250 324
-----------------------------------------




Any suggestions?
Note that while I removed many coordinates (in this post) I did not insert the empty line, that is in the file.

Thank you for your help and in developing these tools.

[graeme]

It looks like there is a problem with how the file is being read. If you post the AECCAR0,2 files, or the CHCAR_sum file, I'll see what's going wrong.

[RB_Rankin]

Thank you very much for your quick response
I am attaching CHGCAR_sum
as a zip file

[graeme]

Try removing the atom types which do not have any atoms. This worked in my test.

If this turns out to be the problem, we could consider changing the bader code to deal with this case.

[RB_Rankin]

[quote="graeme"]Try removing the atom types which do not have any atoms. This worked in my test.

If this turns out to be the problem, we could consider changing the bader code to deal with this case.[/quote]


Yes, this makes the analysis work.

If it wouldn't be too much effort, that would be nice if you could allow for adapting the code to work accordingly.
I can't be the only one who likes to reuse files for closely related systems. :)


Your assistance is very much appreciated. Thank you.