Re: [QE-users] Local charge

2018-08-11 Thread Robert Molt 
Without knowing your system, it is impossible to comment on whether the 
concept of local charge exists, meaningfully. Can you specify your system?


For example, there is no such thing as a widely-accepted method to 
calculate local charge because the concept of local charge does not 
exist, rigorously. No law of physics demands that electrons are "owned" 
by a certain atom (Coulomb's law neither knows nor cares about the human 
concept of atoms). In some cases, electrons' positions happen to be 
relatively localized (like, say average organic molecules), and the term 
has more meaning. If we are talking about a highly delocalized system, 
the term has no meaning (because the electrons don't "belong" to anyone).



On 8/11/18 3:25 PM, Comer, Benjamin M wrote:


Mr. Hosseini,

I am not sure what type the local charges and magnetizations QE prints 
by default, but you should use a widely accepted method to calculate 
local charges, such as Bader analysis. I should note that there is no 
“correct” way to calculate a local charge. However, there are many 
ways to calculate charges developed by the community, each with it’s 
own drawbacks (see Wikipedia link below.) I’d recommend using Bader 
charges, DDEC6, or the lowden charges printed out from the projwfc.x 
code in the quantum espresso suite(links below.)


https://en.wikipedia.org/wiki/Partial_charge

http://theory.cm.utexas.edu/henkelman/code/bader/

https://sourceforge.net/projects/ddec/files/

http://phya.snu.ac.kr/~nmcuong/board/physics/INPUT_PROJWFC.html 



Hope it helps,

Ben Comer

Georgia Tech

>Dear All

>

>I need to compute local charge of atoms in my unit cell. As I checked, the 
output of SCF provides local charge with the corresponding 
>magnetization. The numbers are confusing. How can I compute the local 
charge?


>

>M.R.Hosseini

>Tarbiat Modares University, Department of Chemistry, Iran



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--
Dr. Robert Molt Jr.
r.molt.chemical.phys...@gmail.com

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Re: [QE-users] Local charge

2018-08-11 Thread Comer, Benjamin M 
Mr. Hosseini,



I am not sure what type the local charges and magnetizations QE prints by 
default, but you should use a widely accepted method to calculate local 
charges, such as Bader analysis. I should note that there is no "correct" way 
to calculate a local charge. However, there are many ways to calculate charges 
developed by the community, each with it's own drawbacks (see Wikipedia link 
below.) I'd recommend using Bader charges, DDEC6, or the lowden charges printed 
out from the projwfc.x code in the quantum espresso suite(links below.)



https://en.wikipedia.org/wiki/Partial_charge



http://theory.cm.utexas.edu/henkelman/code/bader/

https://sourceforge.net/projects/ddec/files/

http://phya.snu.ac.kr/~nmcuong/board/physics/INPUT_PROJWFC.html



Hope it helps,

Ben Comer

Georgia Tech



>Dear All

>

>I need to compute local charge of atoms in my unit cell. As I checked, the 
>output of SCF provides local charge with the corresponding >magnetization. The 
>numbers are confusing. How can I compute the local charge?

>

>M.R.Hosseini

>Tarbiat Modares University, Department of Chemistry, Iran

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Re: [QE-users] Oxygen missing in CoFe2O4 input file

2018-08-11 Thread Lars Blumenthal 

Dear Hamed,

Your oxygen atoms are positioned more or less exactly on top of the 
other atoms, that's why you don't see them.


E.g.

Fe    5.2187500    5.2187500    5.2187500
O    5.1185500    5.3189500    5.3189500


Fe    3.1312500    7.3062500    7.3062500
O    3.0310500    7.2060500    7.4064500

Best wishes,

Lars
PhD Student
Imperial College London


On 11/08/18 14:00, hamed asadi wrote:


Dear users;
I have faced a tricky problem to construction of CoFe2O4 input file, 
in the following input, When I open the structure with Xcrysden, there 
are no oxygen in it.
I'll appreciate any helps in this problem. Indeed, if anyone has the 
correct structure, I'm grateful to give it to me.




calculation = 'scf' ,
restart_mode = 'from_scratch' ,
etot_conv_thr = 1.0E-8  ,
forc_conv_thr = 1.0D-8 ,
outdir='/home/asa/Desktop/drgerami/out',
pseudo_dir = '/home/asa/Desktop/drgerami/pp',
wf_collect=.true.
tprnfor   = .true.
tstress = .true.
verbosity= 'low',

 /
 
ibrav = 1,
celldm(1) =15.86667684,
nbnd = 400,
nat = 56,
ntyp = 3,
ecutwfc = 40 ,
ecutrho = 400,
occupations = 'smearing' ,
degauss= 0.01 ,
smearing= 'gaussian',

 /
 
mixing_beta = 0.7
conv_thr = 1.D-8 ,
 /

ion_dynamics= 'bfgs'

/
 
cell_dynamics = 'bfgs' ,
cell_factor = 2
 /
ATOMIC_SPECIES
Co    58.933   Co.pbe-spn-rrkjus_psl.0.3.1.UPF
Fe    55.845   Fe.pbe-spn-rrkjus_psl.0.2.1.UPF
O 15.999    O.pbe-n-rrkjus_psl.0.1.UPF
ATOMIC_POSITIONS (angstrom)
Co 0.000    0.000  0.000
Fe 5.2187500    5.2187500  5.2187500
O 3.2314500    3.2314500  3.2314500
Co 0.000    2.0875000  2.0875000
Co 6.2625000    2.0875000  4.175
Co 6.2625000    0.000  6.2625000
Co 4.175    6.2625000  2.0875000
Co 2.0875000    6.2625000  4.175
Co 2.0875000    4.175  6.2625000
Co 0.000    4.175  4.175
Co 2.0875000    2.0875000  0.000
Co 2.0875000    0.000  2.0875000
Co 4.175    2.0875000  6.2625000
Co 0.000    6.2625000  6.2625000
Co 6.2625000    4.175  2.0875000
Co 6.2625000    6.2625000  0.000
Co 4.175    0.000  4.175
Co 4.175    4.175  0.000
Fe 3.1312500    7.3062500  7.3062500
Fe 1.0437500    5.2187500  1.0437500
Fe 3.1312500    3.1312500  3.1312500
Fe 1.0437500    1.0437500  5.2187500
Fe 7.3062500    3.1312500  7.3062500
Fe 5.2187500    1.0437500  1.0437500
Fe 7.3062500    7.3062500  3.1312500
O 5.1185500    5.3189500  5.3189500
O 3.0310500    7.2060500  7.4064500
O 1.1439500    5.1185500  1.1439500
O 3.2314500    7.2060500  7.2060500
O 1.1439500    5.3189500  0.9435500
O 3.0310500    3.2314500  3.0310500
O 5.1185500    5.1185500  5.1185500
O 7.4064500    3.0310500  7.2060500
O 5.3189500    1.1439500  0.9435500
O 7.2060500    7.4064500  3.0310500
O 5.1185500    0.9435500  0.9435500
O 7.2060500    7.2060500  3.2314500
O 5.3189500    5.1185500  5.3189500
O 0.9435500    5.3189500  1.1439500
O 3.2314500    3.0310500  3.0310500
O 7.2060500    3.2314500  7.2060500
O 5.1185500    1.1439500  1.1439500
O 7.2060500    3.0310500  7.4064500
O 1.1439500    0.9435500  5.3189500
O 3.2314500    7.4064500  7.4064500
O 1.1439500    1.1439500  5.1185500
O 3.0310500    3.0310500  3.2314500
O 3.0310500    7.4064500  7.2060500
O 7.4064500    7.2060500  3.0310500
O 5.3189500    5.3189500  5.1185500
O 5.3189500    0.9435500  1.1439500
O 0.9435500    1.1439500  5.3189500
O 7.4064500    3.2314500  7.4064500
O 0.9435500    5.1185500  0.9435500
O 0.9435500    0.9435500  5.1185500
O 7.4064500    7.4064500  3.2314500
K_POINTS {automatic}
6 6 6   0 0 0 

best regards,
Hamed Asadi,
KN Toosi university of Technology, Faculty of physics



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[QE-users] Oxygen missing in CoFe2O4 input file

2018-08-11 Thread hamed asadi 

Dear users; 
I have faced a tricky problem to construction of CoFe2O4 input file, in the 
following input, When I open the structure with Xcrysden, there are no oxygen 
in it. 
I'll appreciate any helps in this problem. Indeed, if anyone has the correct 
structure, I'm grateful to give it to me. 


 
calculation = 'scf' , 
restart_mode = 'from_scratch' , 
etot_conv_thr = 1.0E-8 , 
forc_conv_thr = 1.0D-8 , 
outdir='/home/asa/Desktop/drgerami/out', 
pseudo_dir = '/home/asa/Desktop/drgerami/pp', 
wf_collect=.true. 
tprnfor = .true. 
tstress = .true. 
verbosity= 'low', 

/ 
 
ibrav = 1, 
celldm(1) =15.86667684, 
nbnd = 400, 
nat = 56, 
ntyp = 3, 
ecutwfc = 40 , 
ecutrho = 400, 
occupations = 'smearing' , 
degauss= 0.01 , 
smearing= 'gaussian', 

/ 
 
mixing_beta = 0.7 
conv_thr = 1.D-8 , 
/ 
 
ion_dynamics= 'bfgs' 

/ 
 
cell_dynamics = 'bfgs' , 
cell_factor = 2 
/ 
ATOMIC_SPECIES 
Co 58.933 Co.pbe-spn-rrkjus_psl.0.3.1.UPF 
Fe 55.845 Fe.pbe-spn-rrkjus_psl.0.2.1.UPF 
O 15.999 O.pbe-n-rrkjus_psl.0.1.UPF 
ATOMIC_POSITIONS (angstrom) 
Co [ callto:0.000 0.000 | 0.000    0.000 ] 0.000 
Fe [ callto:5.2187500 5.2187500 | 5.2187500    5.2187500 ] 5.2187500 
O [ callto:3.2314500 3.2314500 | 3.2314500    3.2314500 ] 3.2314500 
Co [ callto:0.000 2.0875000 | 0.000    2.0875000 ] 2.0875000 
Co [ callto:6.2625000 2.0875000 | 6.2625000    2.0875000 ] 4.175 
Co [ callto:6.2625000 0.000 | 6.2625000    0.000 ] 6.2625000 
Co [ callto:4.175 6.2625000 | 4.175    6.2625000 ] 2.0875000 
Co [ callto:2.0875000 6.2625000 | 2.0875000    6.2625000 ] 4.175 
Co [ callto:2.0875000 4.175 | 2.0875000    4.175 ] 6.2625000 
Co [ callto:0.000 4.175 | 0.000    4.175 ] 4.175 
Co [ callto:2.0875000 2.0875000 | 2.0875000    2.0875000 ] 0.000 
Co [ callto:2.0875000 0.000 | 2.0875000    0.000 ] 2.0875000 
Co [ callto:4.175 2.0875000 | 4.175    2.0875000 ] 6.2625000 
Co [ callto:0.000 6.2625000 | 0.000    6.2625000 ] 6.2625000 
Co [ callto:6.2625000 4.175 | 6.2625000    4.175 ] 2.0875000 
Co [ callto:6.2625000 6.2625000 | 6.2625000    6.2625000 ] 0.000 
Co [ callto:4.175 0.000 | 4.175    0.000 ] 4.175 
Co [ callto:4.175 4.175 | 4.175    4.175 ] 0.000 
Fe [ callto:3.1312500 7.3062500 | 3.1312500    7.3062500 ] 7.3062500 
Fe [ callto:1.0437500 5.2187500 | 1.0437500    5.2187500 ] 1.0437500 
Fe [ callto:3.1312500 3.1312500 | 3.1312500    3.1312500 ] 3.1312500 
Fe [ callto:1.0437500 1.0437500 | 1.0437500    1.0437500 ] 5.2187500 
Fe [ callto:7.3062500 3.1312500 | 7.3062500    3.1312500 ] 7.3062500 
Fe [ callto:5.2187500 1.0437500 | 5.2187500    1.0437500 ] 1.0437500 
Fe [ callto:7.3062500 7.3062500 | 7.3062500    7.3062500 ] 3.1312500 
O [ callto:5.1185500 5.3189500 | 5.1185500    5.3189500 ] 5.3189500 
O [ callto:3.0310500 7.2060500 | 3.0310500    7.2060500 ] 7.4064500 
O [ callto:1.1439500 5.1185500 | 1.1439500    5.1185500 ] 1.1439500 
O [ callto:3.2314500 7.2060500 | 3.2314500    7.2060500 ] 7.2060500 
O [ callto:1.1439500 5.3189500 | 1.1439500    5.3189500 ] 0.9435500 
O [ callto:3.0310500 3.2314500 | 3.0310500    3.2314500 ] 3.0310500 
O [ callto:5.1185500 5.1185500 | 5.1185500    5.1185500 ] 5.1185500 
O [ callto:7.4064500 3.0310500 | 7.4064500    3.0310500 ] 7.2060500 
O [ callto:5.3189500 1.1439500 | 5.3189500    1.1439500 ] 0.9435500 
O [ callto:7.2060500 7.4064500 | 7.2060500    7.4064500 ] 3.0310500 
O [ callto:5.1185500 0.9435500 | 5.1185500    0.9435500 ] 0.9435500 
O [ callto:7.2060500 7.2060500 | 7.2060500    7.2060500 ] 3.2314500 
O [ callto:5.3189500 5.1185500 | 5.3189500    5.1185500 ] 5.3189500 
O [ callto:0.9435500 5.3189500 | 0.9435500    5.3189500 ] 1.1439500 
O [ callto:3.2314500 3.0310500 | 3.2314500    3.0310500 ] 3.0310500 
O [ callto:7.2060500 3.2314500 | 7.2060500    3.2314500 ] 7.2060500 
O [ callto:5.1185500 1.1439500 | 5.1185500    1.1439500 ] 1.1439500 
O [ callto:7.2060500 3.0310500 | 7.2060500    3.0310500 ] 7.4064500 
O [ callto:1.1439500 0.9435500 | 1.1439500    0.9435500 ] 5.3189500 
O [ callto:3.2314500 7.4064500 | 3.2314500    7.4064500 ] 7.4064500 
O [ callto:1.1439500 1.1439500 | 1.1439500    1.1439500 ] 5.1185500 
O [ callto:3.0310500 3.0310500 | 3.0310500    3.0310500 ] 3.2314500 
O [ callto:3.0310500 7.4064500 | 3.0310500    7.4064500 ] 7.2060500 
O [ callto:7.4064500 7.2060500 | 7.4064500    7.2060500 ] 3.0310500 
O [ callto:5.3189500 5.3189500 | 5.3189500    5.3189500 ] 5.1185500 
O [ callto:5.3189500 0.9435500 | 5.3189500    0.9435500 ] 1.1439500 
O [ callto:0.9435500 1.1439500 | 0.9435500    1.1439500 ] 5.3189500 
O [ callto:7.4064500 3.2314500 | 7.4064500    3.2314500 ] 7.4064500 
O [ callto:0.9435500 5.1185500 | 0.9435500    5.1185500 ] 0.9435500 
O [ callto:0.9435500 0.9435500 | 0.9435500    0.9435500 ] 5.1185500 
O [ callto:7.4064500 7.4064500 | 7.4064500    7.4064500 ] 3.2314500 
K_POINTS {automatic} 
[ callto:6 6 6 0 0 0 | 6 6 6   0 0 0 ]

[QE-users] Fwd: Oxygen missing in CoFe2O4 input file

2018-08-11 Thread hamed asadi 




Dear users; 
I have faced a tricky problem to construction of CoFe2O4 input file, in the 
following input, When I open the structure with Xcrysden, there are no oxygen 
in it. 
I'll appreciate any helps in this problem. Indeed, if anyone has the correct 
structure, I'm grateful to give it to me. 


 
calculation = 'scf' , 
restart_mode = 'from_scratch' , 
etot_conv_thr = 1.0E-8 , 
forc_conv_thr = 1.0D-8 , 
outdir='/home/asa/Desktop/drgerami/out', 
pseudo_dir = '/home/asa/Desktop/drgerami/pp', 
wf_collect=.true. 
tprnfor = .true. 
tstress = .true. 
verbosity= 'low', 

/ 
 
ibrav = 1, 
celldm(1) =15.86667684, 
nbnd = 400, 
nat = 56, 
ntyp = 3, 
ecutwfc = 40 , 
ecutrho = 400, 
occupations = 'smearing' , 
degauss= 0.01 , 
smearing= 'gaussian', 

/ 
 
mixing_beta = 0.7 
conv_thr = 1.D-8 , 
/ 
 
ion_dynamics= 'bfgs' 

/ 
 
cell_dynamics = 'bfgs' , 
cell_factor = 2 
/ 
ATOMIC_SPECIES 
Co 58.933 Co.pbe-spn-rrkjus_psl.0.3.1.UPF 
Fe 55.845 Fe.pbe-spn-rrkjus_psl.0.2.1.UPF 
O 15.999 O.pbe-n-rrkjus_psl.0.1.UPF 
ATOMIC_POSITIONS (angstrom) 
Co [ callto:0.000 0.000 | 0.000    0.000 ] 0.000 
Fe [ callto:5.2187500 5.2187500 | 5.2187500    5.2187500 ] 5.2187500 
O [ callto:3.2314500 3.2314500 | 3.2314500    3.2314500 ] 3.2314500 
Co [ callto:0.000 2.0875000 | 0.000    2.0875000 ] 2.0875000 
Co [ callto:6.2625000 2.0875000 | 6.2625000    2.0875000 ] 4.175 
Co [ callto:6.2625000 0.000 | 6.2625000    0.000 ] 6.2625000 
Co [ callto:4.175 6.2625000 | 4.175    6.2625000 ] 2.0875000 
Co [ callto:2.0875000 6.2625000 | 2.0875000    6.2625000 ] 4.175 
Co [ callto:2.0875000 4.175 | 2.0875000    4.175 ] 6.2625000 
Co [ callto:0.000 4.175 | 0.000    4.175 ] 4.175 
Co [ callto:2.0875000 2.0875000 | 2.0875000    2.0875000 ] 0.000 
Co [ callto:2.0875000 0.000 | 2.0875000    0.000 ] 2.0875000 
Co [ callto:4.175 2.0875000 | 4.175    2.0875000 ] 6.2625000 
Co [ callto:0.000 6.2625000 | 0.000    6.2625000 ] 6.2625000 
Co [ callto:6.2625000 4.175 | 6.2625000    4.175 ] 2.0875000 
Co [ callto:6.2625000 6.2625000 | 6.2625000    6.2625000 ] 0.000 
Co [ callto:4.175 0.000 | 4.175    0.000 ] 4.175 
Co [ callto:4.175 4.175 | 4.175    4.175 ] 0.000 
Fe [ callto:3.1312500 7.3062500 | 3.1312500    7.3062500 ] 7.3062500 
Fe [ callto:1.0437500 5.2187500 | 1.0437500    5.2187500 ] 1.0437500 
Fe [ callto:3.1312500 3.1312500 | 3.1312500    3.1312500 ] 3.1312500 
Fe [ callto:1.0437500 1.0437500 | 1.0437500    1.0437500 ] 5.2187500 
Fe [ callto:7.3062500 3.1312500 | 7.3062500    3.1312500 ] 7.3062500 
Fe [ callto:5.2187500 1.0437500 | 5.2187500    1.0437500 ] 1.0437500 
Fe [ callto:7.3062500 7.3062500 | 7.3062500    7.3062500 ] 3.1312500 
O [ callto:5.1185500 5.3189500 | 5.1185500    5.3189500 ] 5.3189500 
O [ callto:3.0310500 7.2060500 | 3.0310500    7.2060500 ] 7.4064500 
O [ callto:1.1439500 5.1185500 | 1.1439500    5.1185500 ] 1.1439500 
O [ callto:3.2314500 7.2060500 | 3.2314500    7.2060500 ] 7.2060500 
O [ callto:1.1439500 5.3189500 | 1.1439500    5.3189500 ] 0.9435500 
O [ callto:3.0310500 3.2314500 | 3.0310500    3.2314500 ] 3.0310500 
O [ callto:5.1185500 5.1185500 | 5.1185500    5.1185500 ] 5.1185500 
O [ callto:7.4064500 3.0310500 | 7.4064500    3.0310500 ] 7.2060500 
O [ callto:5.3189500 1.1439500 | 5.3189500    1.1439500 ] 0.9435500 
O [ callto:7.2060500 7.4064500 | 7.2060500    7.4064500 ] 3.0310500 
O [ callto:5.1185500 0.9435500 | 5.1185500    0.9435500 ] 0.9435500 
O [ callto:7.2060500 7.2060500 | 7.2060500    7.2060500 ] 3.2314500 
O [ callto:5.3189500 5.1185500 | 5.3189500    5.1185500 ] 5.3189500 
O [ callto:0.9435500 5.3189500 | 0.9435500    5.3189500 ] 1.1439500 
O [ callto:3.2314500 3.0310500 | 3.2314500    3.0310500 ] 3.0310500 
O [ callto:7.2060500 3.2314500 | 7.2060500    3.2314500 ] 7.2060500 
O [ callto:5.1185500 1.1439500 | 5.1185500    1.1439500 ] 1.1439500 
O [ callto:7.2060500 3.0310500 | 7.2060500    3.0310500 ] 7.4064500 
O [ callto:1.1439500 0.9435500 | 1.1439500    0.9435500 ] 5.3189500 
O [ callto:3.2314500 7.4064500 | 3.2314500    7.4064500 ] 7.4064500 
O [ callto:1.1439500 1.1439500 | 1.1439500    1.1439500 ] 5.1185500 
O [ callto:3.0310500 3.0310500 | 3.0310500    3.0310500 ] 3.2314500 
O [ callto:3.0310500 7.4064500 | 3.0310500    7.4064500 ] 7.2060500 
O [ callto:7.4064500 7.2060500 | 7.4064500    7.2060500 ] 3.0310500 
O [ callto:5.3189500 5.3189500 | 5.3189500    5.3189500 ] 5.1185500 
O [ callto:5.3189500 0.9435500 | 5.3189500    0.9435500 ] 1.1439500 
O [ callto:0.9435500 1.1439500 | 0.9435500    1.1439500 ] 5.3189500 
O [ callto:7.4064500 3.2314500 | 7.4064500    3.2314500 ] 7.4064500 
O [ callto:0.9435500 5.1185500 | 0.9435500    5.1185500 ] 0.9435500 
O [ callto:0.9435500 0.9435500 | 0.9435500    0.9435500 ] 5.1185500 
O [ callto:7.4064500 7.4064500 | 7.4064500    7.4064500 ] 3.2314500 
K_POINTS {automatic} 
[ callto:6 6 6 0 0 0 | 6 6 6   0 0 0 ]

[QE-users] Local charge

2018-08-11 Thread Mohammadreza Hosseini 
Dear All


I need to compute local charge of atoms in my unit cell. As I checked, the 
output of SCF provides local charge with the corresponding magnetization. The 
numbers are confusing. How can I compute the local charge?


M.R.Hosseini

Tarbiat Modares University, Department of Chemistry, Iran
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