About Bader charge analysis in Quantum Espresso

Bader charge density analysis

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PPK
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About Bader charge analysis in Quantum Espresso

Post by PPK » Wed Aug 19, 2015 10:18 am

Hello my dear colleagues ....

I am working on Quantum Espresso. Is it possible to find out Bader charge analysis after relax calculations from Quantum Espresso (i.e creation of charge density file) ?? because except VASP and GAUSSIAN I found only 4 posts related to Quantum Espresso. If it is......Please specify which number (0 or 17) to specify in processing of PP.X input for creation of charge density file in PLOT_NUM (0- indicating PSEUDO electron charge density and 17- indicating charge density for only done for PAW type pseudo potential calculations) I am confused with both of these two options. Also how to increase grid size??

Thanks in advance

Regards
Phanikumar

graeme
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Re: About Bader charge analysis in Quantum Espresso

Post by graeme » Thu Aug 27, 2015 7:00 pm

I have not done this myself but I see references to using the pp.x script to generate a cube file from the output of Quantum Espresso. Then, hopefully, you can run the bader code directly with that cube file.

As far as increasing the grid density, that would have to be done in the input file, presumably using variables that determine the FFT grid size.

PPK
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Re: About Bader charge analysis in Quantum Espresso

Post by PPK » Fri Aug 28, 2015 12:48 pm

Thank you graeme and jijum for your reply

I found answer in pw.x forum for number in pp.x that is 17 we have to put for charge density extraction. But type of output form (weather it is applicable for PAW or not) I am not sure.......

I have some more doubts regarding Bader analysis

My FFT Grid size was 120 x 120 x 216, is it required to put grid size same in all three directions??

Also

In graeme paper (ref: Compt. Mat. Sci. 36(2006), 354-360) While explaining of NaCl Crystal Bader charge analysis you took 9 valance electrons for Na and 7 valance electrons for Cl. What is the reason for taking 9 valance electrons for Na instead of 1 , but 7 for Cl as usual?? If it is because of mathematical problem for small valance type atoms....what is the bench mark (minimum) of valance to take valance like that ??

Thanks in advance


Regards
Phanikumar

graeme
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Re: About Bader charge analysis in Quantum Espresso

Post by graeme » Fri Aug 28, 2015 1:46 pm

It is not required to have the same grid size or density along the different cell vectors.

The Bader analysis can become completely crazy if you only use the valence electrons for some elements. Na, for example, in an ionic crystal will have little valence charge at the atomic center. Having a charge density maximum at the atoms, however, is essential for defining the Bader volumes. In vasp, we are now able to include the core charge into the charge density. We can also, in some cases, treat core electrons explicitly as valence, so, in the case of Na, the explicit 8 core electrons allow for a proper representation of the charge density maximum at that atom.

PPK
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Re: About Bader charge analysis in Quantum Espresso

Post by PPK » Fri Aug 28, 2015 6:26 pm

My doubt was if you take 9 electrons in Na and 7 electrons for Cl, There will be chance of showing more charge on Na atom or not ??

Suppose if our material contain following five atoms Mg (2), Al (3), Si (4), P (5) , S (6) having less valance

for what value of valance (like previous Na (1) you added 8 extra core atoms) you will add core electrons for getting maximum charge density at center of atom ?? (example: if valance is 5 or 6 then i think its not required of adding core electrons)


Thanks in advance


Regards
Phanikumar

graeme
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Re: About Bader charge analysis in Quantum Espresso

Post by graeme » Fri Aug 28, 2015 6:30 pm

The definition of the Bader surfaces involves the total charge density; that is, with all the core electrons. The boundary between volumes, however, is in the bonding region between atoms. To the extent that the core charges do not extend to the surface of the Bader volumes, they will not be needed in the analysis. The relative importance of core electrons will be, of course, system dependent.

PPK
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Re: About Bader charge analysis in Quantum Espresso

Post by PPK » Fri Aug 28, 2015 6:51 pm

no words for your patience graeme ........now its time to generate Gaussian cube file......

Once again Thanks a lot......If any doubt I will contact you....




Regards
Phanikumar

Bibhas Manna
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Re: About Bader charge analysis in Quantum Espresso

Post by Bibhas Manna » Fri Aug 25, 2017 5:20 am

Dear All,
I am very new to bader charge analysis. I am using Quantum Espresso to produce the charge density cube file (Plot_num= 17 and output_format = 6 in pp.x ) which is probably suitable as bader input file as per your conversations. However, I got an error while executing the program:

forrtl: severe (59): list-directed I/O syntax error, unit 100
Image PC Routine Line Source
bader 0000000000436509 Unknown Unknown Unknown
bader 000000000046256D Unknown Unknown Unknown
bader 000000000040CC01 Unknown Unknown Unknown
bader 000000000040EC97 Unknown Unknown Unknown
bader 00000000004005B3 Unknown Unknown Unknown
bader 000000000040050E Unknown Unknown Unknown
bader 00000000004F7ABB Unknown Unknown Unknown
bader 00000000004003E9 Unknown Unknown Unknown

Is it related to improper output format (cube format)? Please help me to solve this problem.

My charge file input file for 36 atoms looks like :

108 108 192 108 108 192 36 3
0 18.66690000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000
1.0000000000000000 3.4000000000000000E-008 0.0000000000000000
-0.49991516100000000 0.86587937300000017 0.0000000000000000
0.0000000000000000 0.0000000000000000 1.8222140000000002
2647.9264627735 10.0000000000 30.0000000000 17
1 C 4.00
2 H 1.00
3 O 6.00
1 -0.000010927 -0.000283385 -0.006658020 1
2 -0.124965462 0.216200056 -0.006610739 1
3 -0.249957346 0.432651174 -0.006675209 1
4 -0.374958920 0.649109570 -0.006584075 1
5 0.250000025 -0.000270168 -0.006547926 1
6 0.125034621 0.216229263 -0.006578318 1
7 0.000091883 0.432647862 -0.006624367 1
8 -0.124913604 0.649109474 -0.006584042 1
9 0.500011098 -0.000283483 -0.006657947 1
10 0.375007714 0.216229268 -0.006578309 1
11 0.250042260 0.432651003 -0.006904857 1
12 0.125097449 0.649080076 -0.006638980 1
13 0.750000150 -0.000300991 -0.006630379 1
14 0.625008296 0.216200062 -0.006610704 1
15 0.499993052 0.432647965 -0.006624422 1
16 0.375029787 0.649080195 -0.006639022 1
17 0.000037355 0.144046574 -0.006624342 1
18 -0.124933402 0.360506936 -0.006656641 1
19 -0.249943455 0.576971716 -0.006591358 1
20 -0.374919854 0.793435153 -0.006575643 1
21 0.250014378 0.144066304 -0.006548828 1
22 0.125084392 0.360535229 -0.006713055 1
23 0.000087319 0.576949057 -0.006611723 1
24 -0.124924428 0.793435277 -0.006575592 1
25 0.499991046 0.144046622 -0.006624282 1
26 0.374986794 0.360535144 -0.006713082 1
27 0.250056747 0.576909587 -0.006750618 1
28 0.125083860 0.793397586 -0.006665932 1
29 0.750014036 0.144020677 -0.006557494 1
30 0.625003991 0.360506883 -0.006656686 1
31 0.500025984 0.576948869 -0.006611776 1
32 0.375071724 0.793397471 -0.006665983 1
33 0.153936746 0.431262300 0.537715748 2
34 0.250024436 0.435182638 0.477878112 1
35 0.346083605 0.431263870 0.537762222 2
36 0.250056285 0.443203323 0.355200520 3
9.511751766E-01 3.525181893E-01 2.020303047E-01 2.554624396E-01 2.817844508E-01
2.720093830E-01 2.442101087E-01 2.123484587E-01 1.838291782E-01 1.615109184E-01
1.454156982E-01 1.338867538E-01 1.258685255E-01 1.215506004E-01 1.215547775E-01
1.258809876E-01 1.339088790E-01 1.454504228E-01 1.615639913E-01 1.839074012E-01
2.124513242E-01 2.443324988E-01 2.721289172E-01 2.818455923E-01 2.553855869E-01
2.020648537E-01 3.574003841E-01 9.761425063E-01 3.573822387E-01 2.020640499E-01
2.554007000E-01 2.818684663E-01 2.721540583E-01 2.443567068E-01 2.124734111E-01
1.839270551E-01 1.615810353E-01 1.454644525E-01 1.339193436E-01 1.258874781E-01
1.215571598E-01 1.215487702E-01 1.258625186E-01 1.338766876E-01 1.454019484E-01
.......................................................................................................................................
.......................................................................................................................................

.......................................................................................................................................

Thanks,
Bibhas

graeme
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Re: About Bader charge analysis in Quantum Espresso

Post by graeme » Fri Aug 25, 2017 11:53 am

please post the charge density file so I can debug

Bibhas Manna
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Re: About Bader charge analysis in Quantum Espresso

Post by Bibhas Manna » Fri Aug 25, 2017 1:15 pm

Dear Graeme,

Thank you very much for your kind reply. I am attaching the charge density file generated from Quantum Espresso (pp.x ) in cube format.

A Brief summary of my structure specifications:

Number of atoms: 36 (Carbon = 33, Hydrogen=2 and Oxygen=1).
Types of atom= 3
Lattice constant= 18.6669 a.u.
Lattice vectors (in alat)
1.0000000000000000 3.4000000000000000E-008 0.0000000000000000
-0.49991516100000000 0.86587937300000017 0.0000000000000000
0.0000000000000000 0.0000000000000000 1.8222140000000002
FFT grid size= 108x108x192

I am waiting for your positive response.

With thanks and regards,
Bibhas Manna

graeme
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Re: About Bader charge analysis in Quantum Espresso

Post by graeme » Fri Aug 25, 2017 2:52 pm

I don't see the attachment

Bibhas Manna
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Re: About Bader charge analysis in Quantum Espresso

Post by Bibhas Manna » Fri Aug 25, 2017 7:36 pm

Dear Graeme,
Sorry for my mistake. I am sending you the charge file in .zip format. I have copied and pasted my original cube file data in a ms word which you can find in the zip file attached.

Thanking you once again.

With thanks and regards,
Bibhas Manna
Attachments
Chargefile.zip
Charge data in microsoft Word file
(13.85 MiB) Downloaded 534 times

graeme
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Re: About Bader charge analysis in Quantum Espresso

Post by graeme » Fri Aug 25, 2017 9:05 pm

The header does not look like a standard cube file. Here is what is should look like:

Cubfile created from PWScf calculation
Total SCF Density
2 0.000000 0.000000 0.000000
24 0.193000 0.000000 0.000000
24 -0.096500 0.167143 0.000000
144 0.000000 0.000000 0.194448
6 6.000000 0.000000 2.674286 14.000220
6 6.000000 2.316000 1.337143 14.000220
0.67809E-09 0.13410E-08 0.60164E-09 0.11076E-08 0.98507E-09 0.12130E-08
0.92314E-09 0.91628E-09 0.10538E-08 0.11147E-08 0.14008E-08 0.66290E-09
....

Bibhas Manna
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Re: About Bader charge analysis in Quantum Espresso

Post by Bibhas Manna » Sat Aug 26, 2017 5:15 pm

Dear Graeme,
Thank you very much.
Let me try to edit my pwscf generated cubefile as per your suggestions.


With thanks and regards,
Bibhas Manna

graeme
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Re: About Bader charge analysis in Quantum Espresso

Post by graeme » Sat Aug 26, 2017 7:37 pm

You can check to see if a program such as vesta can read and display it. Then, you can also make sure that it looks reasonable.

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