[Pw_forum] Magnetization on the Fe atom doped on the graphene
David Foster
davidfoster751 at yahoo.com
Sat Jul 18 20:51:27 CEST 2015
Dear Pang,
Thank you for your kindness. I will correct the input and report the corrected total_magnetization, as soon as possible.
However, I think total_magnetization should not be changed, due to the approach I took in my previous calculation (I have not fixed it, and the correct value calculated from SCF). So, output from start_magnetization=0 is equal to start_magnetization=0.5 or any other values.
I have a question about this subject:
In chemistry, we discuss about spin multiplicity for molecules (clusters). But, in solid state physics, we discuss about magnetic moment.
What is the relationship between spin multiplicity and magnetic moment, if we want to calculate a cluster model with QE?
I am not sure, but, I think, if we take Stot=sigma(Si) as the total spin of electrons, the spin multiplicity is 2Stot+1, and the magnetic moment is 2*Stot, which is summation of number of spin-up electrons minus summation of number of spin-down electrons.
See Stefano de Gironcoli comment:
(http://qe-forge.org/pipermail/pw_forum/2003-March/074663.html)
TM = \int (n_up-n_down) d^3r (from Stefano, TM is total_magnetization)
Am I right?
For, example, for triplet state (Stot=1) of a molecule, we should take the total_magnetization of 2 (which has 2*Stot relationship). For example, see following posts:
http://qe-forge.org/pipermail/pw_forum/2013-September/102317.html
http://qe-forge.org/pipermail/pw_forum/2006-May/078792.html
Now, about my run (4*4 graphene sheet+one Fe doped atom), I have 4 unpaired electron (d6 from Fe). So, I should get total_magnetization near to 4 bohr-magneton. Is it right?
=====================
Regards
David Foster
Ph.D. Student of Chemistry
=====================
--------------------------------------------
On Fri, 7/17/15, 庞瑞(PANG Rui) <pang.r at sustc.edu.cn> wrote:
Subject: Re: [Pw_forum] Magnetization on the Fe atom doped on the graphene
To: "PWSCF Forum" <pw_forum at pwscf.org>
Date: Friday, July 17, 2015, 11:54 PM
Dear David
You set
"starting_magnetization(3)=0.5", but you only have
two elements. Therefore , the starting_magnetization of Fe
is actually zero.
Best wishes.
Pang Rui
------------------庞瑞(PANG Rui)South
University of Science and Technology of China/Department of
PhysicsNo.1088,Xueyuan
Road, Shenzhen,Guangdong
------------------ Original ------------------From: "David
Foster"<davidfoster751 at yahoo.com>;Date:
Fri, Jul 17, 2015 08:44 PMTo:
"pw_forum"<pw_forum at pwscf.org>;
Subject:
[Pw_forum] Magnetization on the Fe atom doped on the
graphene Dear Users
I have doped one Fe atom in
the supercell of graphene, and used
"starting_magnetization" keyword (due to the
electronic configuration of Fe which is 4s2 3d6).
Here it is my input:
=====
&CONTROL
title = 'graph44'
calculation =
'vc-relax'
restart_mode =
'from_scratch'
outdir = './graph44_relax'
pseudo_dir =
'./'
prefix = 'graph44'
disk_io = 'default'
verbosity
= 'default'
etot_conv_thr=1.0D-6
forc_conv_thr=1.0D-2
nstep=1000
tstress=.true.
tprnfor=.true.
/
&SYSTEM
ibrav = 4
nat = 32
celldm(1)=18.783876326
celldm(3)=2.004008
ntyp = 2
ecutwfc = 75
ecutrho = 500
starting_magnetization(1)=0.5
starting_magnetization(3)=0.5
nspin=2
occupations='smearing'
degauss=0.02
smearing='mv'
nbnd=160
/
&ELECTRONS
electron_maxstep =
1000
conv_thr = 1.0D-7
mixing_mode =
'plain'
mixing_beta =
0.5
mixing_ndim = 15
diagonalization = 'david'
/
&IONS
ion_dynamics =
'bfgs'
/
&CELL
cell_dynamics =
'bfgs'
cell_dofree='2Dxy'
/
ATOMIC_SPECIES
C
12.0107 C.pbe-n-rrkjus_psl.1.0.0.UPF
Fe 55.845
Fe.pbe-spn-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS crystal
C 0.0827257631375200 0.1654515262750400
0.0000000000000000 1 1 0
C
0.1654515262077270 0.0827257630794374
0.0000000000000000 1 1 0
C
0.3309030525741389 0.1654515262750400
0.0000000000000000 1 1 0
C
0.4136288157449489 0.0827257630794371
0.0000000000000000 1 1 0
C
0.5790803421113629 0.1654515262750400
0.0000000000000000 1 1 0
C
0.6618061051815698 0.0827257630794374
0.0000000000000000 1 1 0
C
0.8272576315479819 0.1654515262750410
0.0000000000000000 1 1 0
C
0.9099833946181889 0.0827257630794374
0.0000000000000000 1 1 0
C
0.0827257632048355 0.4136288157456879
0.0000000000000000 1 1 0
C
0.1654515263331270 0.3309030526662500
0.0000000000000000 1 1 0
C
0.3309030525408510 0.4136288157456870
0.0000000000000000 1 1 0
C
0.4136288157697440 0.3309030526662500
0.0000000000000000 1 1 0
C
0.5790803420780759 0.4136288157456880
0.0000000000000000 1 1 0
C
0.6618061053069669 0.3309030526662500
0.0000000000000000 1 1 0
C
0.8272576315146950 0.4136288157456880
0.0000000000000000 1 1 0
C
0.9099833947435888 0.3309030526662499
0.0000000000000000 1 1 0
C
0.0827257632296303 0.6618061053324988
0.0000000000000000 1 1 0
C
0.1654515264004400 0.5790803421368960
0.0000000000000000 1 1 0
C
0.3309030526662500 0.6618061053325008
0.0000000000000000 1 1 0
C
0.4136288157364559 0.5790803421368959
0.0000000000000000 1 1 0
C
0.5790803421028690 0.6618061053324990
0.0000000000000000 1 1 0
C
0.8272576316400939 0.6618061053324990
0.0000000000000000 1 1 0
C
0.9099833947102990 0.5790803421368960
0.0000000000000000 1 1 0
C
0.0827257631382572 0.9099833946869810
0.0000000000000000 1 1 0
C
0.1654515263090670 0.8272576314913760
0.0000000000000000 1 1 0
C
0.3309030526754809 0.9099833946869810
0.0000000000000000 1 1 0
C
0.4136288157456880 0.8272576314913770
0.0000000000000000 1 1 0
C
0.5790803420114971 0.9099833946869810
0.0000000000000000 1 1 0
C
0.6618061051823049 0.8272576314913748
0.0000000000000000 1 1 0
C
0.8272576315487209 0.9099833946869799
0.0000000000000000 1 1 0
C
0.9099833947195301 0.8272576314913750
0.0000000000000000 1 1 0
Fe
0.6618061052736799 0.5790803421368970
0.0000000000000000 1 1 0
K_POINTS
automatic
2 2 1 0 0 0
====================
and got following
scf-converged magnetization in the first step of geometry
optimization:
========
Program PWSCF v.5.1.1 starts on 17Jul2015 at
13:41:18
This
program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials;
please cite
"P.
Giannozzi et al., J. Phys.:Condens. Matter 21 395502
(2009);
URL
http://www.quantum-espresso.org",
in publications or presentations
arising from this work. More details at
http://www.quantum-espresso.org/quote
Parallel version (MPI), running
on 12 processors
R & G
space division: proc/nbgrp/npool/nimage = 12
Reading input from graph44.in
Current dimensions of
program PWSCF are:
Max number of
different atomic species (ntypx) = 10
Max number of k-points (npk) =
40000
Max angular momentum in
pseudopotentials (lmaxx) = 3
Subspace diagonalization in iterative
solution of the eigenvalue problem:
scalapack distributed-memory algorithm (size of sub-group:
2* 2 procs)
Parallelization info
--------------------
sticks: dense smooth
PW G-vecs: dense smooth PW
Min 1011
606 159 180960
84085 11235
Max
1013 607 160
180966 84119 11239
Sum 12145 7279
1915 2171547 1009209 134837
Generating
pointlists ...
new r_m : 0.0591
(alat units) 1.1102 (a.u.) for type 1
new r_m : 0.0591 (alat units)
1.1102 (a.u.) for type 2
Title:
graph44
bravais-lattice index = 4
lattice parameter (alat) =
18.7839 a.u.
unit-cell
volume = 11502.3279 (a.u.)^3
number of atoms/cell
= 32
number of
atomic types = 2
number of electrons
= 140.00
number of
Kohn-Sham states= 160
kinetic-energy cutoff
= 75.0000 Ry
charge
density cutoff = 500.0000 Ry
convergence threshold
= 1.0E-07
mixing
beta = 0.5000
number of iterations used
= 15 plain mixing
Exchange-correlation = PBE (
1 4 3 4 0 0)
nstep
= 1000
celldm(1)= 18.783876
celldm(2)= 0.000000 celldm(3)= 2.004008
celldm(4)= 0.000000
celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart.
coord. in units of alat)
a(1) = (
1.000000 0.000000 0.000000 )
a(2) = (
-0.500000 0.866025 0.000000 )
a(3) = (
0.000000 0.000000 2.004008 )
reciprocal axes: (cart. coord. in
units 2 pi/alat)
b(1) = (
1.000000 0.577350 0.000000 )
b(2) = (
0.000000 1.154701 0.000000 )
b(3) = (
0.000000 0.000000 0.499000 )
PseudoPot. # 1 for
C read from file:
./C.pbe-n-rrkjus_psl.1.0.0.UPF
MD5
check sum: d965a6b284613baf0982652bb1fc1f03
Pseudo is Ultrasoft + core correction,
Zval = 4.0
Generated using
"atomic" code by A. Dal Corso v.5.1.1
Using radial grid of 1073 points, 4
beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
PseudoPot. # 2 for Fe read from file:
./Fe.pbe-spn-rrkjus_psl.1.0.0.UPF
MD5 check sum:
12c5fd6419f2a80ca8ce5aff3429efb6
Pseudo is Ultrasoft + core correction, Zval = 16.0
Generated using "atomic"
code by A. Dal Corso v.5.1.1
Using radial grid of 1191 points, 6 beta functions with:
l(1) =
0
l(2) =
0
l(3) =
1
l(4) =
1
l(5) =
2
l(6) =
2
Q(r) pseudized with 0
coefficients
atomic species valence
mass pseudopotential
C 4.00 12.01070 C(
1.00)
Fe 16.00 55.84500 Fe(
1.00)
Starting
magnetic structure
atomic
species magnetization
C 0.500
Fe 0.000
2 Sym. Ops. (no inversion) found
Cartesian axes
site n.
atom positions (alat
units)
1 C tau( 1) = (
0.0000000 0.1432852 0.0000000 )
2 C
tau( 2) = ( 0.1240886 0.0716426 0.0000000
)
3
C tau( 3) = ( 0.2481773 0.1432852
0.0000000 )
4 C tau( 4) = (
0.3722659 0.0716426 0.0000000 )
5 C
tau( 5) = ( 0.4963546 0.1432852 0.0000000
)
6
C tau( 6) = ( 0.6204432 0.0716426
0.0000000 )
7 C tau( 7) = (
0.7445319 0.1432852 0.0000000 )
8 C
tau( 8) = ( 0.8686205 0.0716426 0.0000000
)
9
C tau( 9) = ( -0.1240886 0.3582131
0.0000000 )
10 C tau( 10) = (
0.0000000 0.2865704 0.0000000 )
11 C
tau( 11) = ( 0.1240886 0.3582131 0.0000000
)
12
C tau( 12) = ( 0.2481773 0.2865704
0.0000000 )
13 C tau( 13) = (
0.3722659 0.3582131 0.0000000 )
14 C
tau( 14) = ( 0.4963546 0.2865704 0.0000000
)
15
C tau( 15) = ( 0.6204432 0.3582131
0.0000000 )
16 C tau( 16) = (
0.7445319 0.2865704 0.0000000 )
17 C
tau( 17) = ( -0.2481773 0.5731409 0.0000000
)
18
C tau( 18) = ( -0.1240886 0.5014983
0.0000000 )
19 C tau( 19) = ( -0.0000000
0.5731409 0.0000000 )
20 C tau( 20) = (
0.1240886 0.5014983 0.0000000 )
21 C
tau( 21) = ( 0.2481773 0.5731409 0.0000000
)
22
C tau( 22) = ( 0.4963546 0.5731409
0.0000000 )
23 C tau( 23) = (
0.6204432 0.5014983 0.0000000 )
24 C
tau( 24) = ( -0.3722659 0.7880687 0.0000000
)
25
C tau( 25) = ( -0.2481773 0.7164261
0.0000000 )
26 C tau( 26) = ( -0.1240886
0.7880687 0.0000000 )
27 C tau( 27) = ( -0.0000000
0.7164261 0.0000000 )
28 C tau( 28) = (
0.1240886 0.7880687 0.0000000 )
29 C
tau( 29) = ( 0.2481773 0.7164261 0.0000000
)
30
C tau( 30) = ( 0.3722659 0.7880687
0.0000000 )
31 C tau( 31) = (
0.4963546 0.7164261 0.0000000 )
32 Fe
tau( 32) = ( 0.3722659 0.5014983 0.0000000
)
number of k
points= 8 Marzari-Vanderbilt smearing, width
(Ry)= 0.0200
cart. coord. in units 2pi/alat
k( 1) = (
0.0000000 0.0000000 0.0000000), wk =
0.2500000
k( 2) = (
0.0000000 -0.5773503 0.0000000), wk = 0.2500000
k( 3) = ( 0.5000000
-0.2886751 0.0000000), wk = 0.2500000
k( 4) = ( -0.5000000
-0.2886751 0.0000000), wk = 0.2500000
k( 5) = (
0.0000000 0.0000000 0.0000000), wk =
0.2500000
k( 6) = (
0.0000000 -0.5773503 0.0000000), wk = 0.2500000
k( 7) = ( 0.5000000
-0.2886751 0.0000000), wk = 0.2500000
k( 8) = ( -0.5000000
-0.2886751 0.0000000), wk = 0.2500000
Dense grid:
2171547 G-vectors FFT dimensions: ( 135, 135,
270)
Smooth
grid: 1009209 G-vectors FFT dimensions: ( 108,
108, 216)
Largest
allocated arrays est. size (Mb)
dimensions
Kohn-Sham
Wavefunctions 25.76 Mb ( 10552,
160)
NL
pseudopotentials 42.83 Mb
( 10552, 266)
Each
V/rho on FFT grid 12.79 Mb (
419175, 2)
Each G-vector
array 1.38 Mb ( 180962)
G-vector
shells 1.38 Mb (
180962)
Largest temporary
arrays est. size (Mb) dimensions
Auxiliary
wavefunctions 103.05 Mb ( 10552,
640)
Each subspace H/S
matrix 1.56 Mb ( 320,
320)
Each
<psi_i|beta_j> matrix 0.65 Mb
( 266, 160)
Arrays
for rho mixing 95.94 Mb (
419175, 15)
Check: negative/imaginary core charge= -0.000001
0.000000
Initial
potential from superposition of free atoms
Check: negative starting
charge=(component1): -0.000923
Check: negative starting charge=(component2):
-0.000347
starting
charge 139.99827, renormalised to 140.00000
negative rho (up,
down): 9.232E-04 3.468E-04
Starting wfc are 134 randomized atomic wfcs + 26
random wfc
total
cpu time spent up to now is 85.0 secs
per-process dynamical
memory: 427.7 Mb
Self-consistent Calculation
iteration #
1 ecut= 75.00 Ry beta=0.50
Davidson diagonalization with
overlap
ethr = 1.00E-02, avg #
of iterations = 7.8
negative rho (up, down): 8.979E-04
5.715E-04
Magnetic moment per site:
atom: 1 charge: 1.6553 magn:
0.4208 constr: 0.0000
atom: 2 charge: 1.6564 magn:
0.4234 constr: 0.0000
atom: 3 charge: 1.6879 magn:
0.4233 constr: 0.0000
atom: 4 charge: 1.6476 magn:
0.4301 constr: 0.0000
atom: 5 charge: 1.6901 magn:
0.4219 constr: 0.0000
atom: 6 charge: 1.6540 magn:
0.4268 constr: 0.0000
atom: 7 charge: 1.6913 magn:
0.4182 constr: 0.0000
atom: 8 charge: 1.6145 magn:
0.4197 constr: 0.0000
atom: 9 charge: 1.6534 magn:
0.4214 constr: 0.0000
atom: 10 charge: 1.6897 magn:
0.4144 constr: 0.0000
atom: 11 charge: 1.6909 magn:
0.4336 constr: 0.0000
atom: 12 charge: 1.6847 magn:
0.4380 constr: 0.0000
atom: 13 charge: 1.8452 magn:
0.4414 constr: 0.0000
atom: 14 charge: 1.6811 magn:
0.4409 constr: 0.0000
atom: 15 charge: 1.6933 magn:
0.4303 constr: 0.0000
atom: 16 charge: 1.6533 magn:
0.4169 constr: 0.0000
atom: 17 charge: 1.6536 magn:
0.4270 constr: 0.0000
atom: 18 charge: 1.6926 magn:
0.4206 constr: 0.0000
atom: 19 charge: 1.6876 magn:
0.4265 constr: 0.0000
atom: 20 charge: 1.6853 magn:
0.4360 constr: 0.0000
atom: 21 charge: 1.8448 magn:
0.4443 constr: 0.0000
atom: 22 charge: 1.8439 magn:
0.4420 constr: 0.0000
atom: 23 charge: 1.6483 magn:
0.4396 constr: 0.0000
atom: 24 charge: 1.6135 magn:
0.4298 constr: 0.0000
atom: 25 charge: 1.6880 magn:
0.4233 constr: 0.0000
atom: 26 charge: 1.6520 magn:
0.4145 constr: 0.0000
atom: 27 charge: 1.6883 magn:
0.4244 constr: 0.0000
atom: 28 charge: 1.6521 magn:
0.4257 constr: 0.0000
atom: 29 charge: 1.6838 magn:
0.4368 constr: 0.0000
atom: 30 charge: 1.6563 magn:
0.4340 constr: 0.0000
atom: 31 charge: 1.6501 magn:
0.4374 constr: 0.0000
atom: 32 charge: 11.4685 magn:
-0.0036 constr: 0.0000
total cpu time spent up to now
is 378.9 secs
total energy
= -630.04480293 Ry
Harris-Foulkes estimate = -629.83142751 Ry
estimated scf accuracy
< 5.43017607 Ry
total magnetization
= 4.29 Bohr mag/cell
absolute magnetization = 4.85 Bohr mag/cell
iteration #
2 ecut= 75.00 Ry beta=0.50
Davidson diagonalization with
overlap
ethr = 3.88E-03, avg #
of iterations = 5.8
negative rho (up, down): 2.473E-03
2.683E-03
.
.
.
.
.
total cpu time spent up to
now is 3943.6 secs
total energy
= -632.02402317 Ry
Harris-Foulkes estimate = -632.02402327 Ry
estimated scf accuracy
< 0.00000019 Ry
total magnetization
= 0.01 Bohr mag/cell
absolute magnetization = 0.01 Bohr mag/cell
iteration #
25 ecut= 75.00 Ry beta=0.50
Davidson diagonalization with
overlap
ethr = 1.34E-10, avg #
of iterations = 2.4
negative rho (up, down): 8.601E-04
8.602E-04
Magnetic moment per site:
atom: 1 charge: 1.6815 magn:
-0.0001 constr: 0.0000
atom: 2 charge: 1.6811 magn:
0.0001 constr: 0.0000
atom: 3 charge: 1.7051 magn:
0.0000 constr: 0.0000
atom: 4 charge: 1.6858 magn:
-0.0000 constr: 0.0000
atom: 5 charge: 1.7065 magn:
0.0000 constr: 0.0000
atom: 6 charge: 1.6828 magn:
0.0001 constr: 0.0000
atom: 7 charge: 1.7076 magn:
-0.0001 constr: 0.0000
atom: 8 charge: 1.6525 magn:
0.0001 constr: 0.0000
atom: 9 charge: 1.6832 magn:
-0.0001 constr: 0.0000
atom: 10 charge: 1.7073 magn:
0.0001 constr: 0.0000
atom: 11 charge: 1.7140 magn:
-0.0001 constr: 0.0000
atom: 12 charge: 1.7107 magn:
0.0001 constr: 0.0000
atom: 13 charge: 1.8439 magn:
-0.0001 constr: 0.0000
atom: 14 charge: 1.7097 magn:
0.0000 constr: 0.0000
atom: 15 charge: 1.7123 magn:
-0.0000 constr: 0.0000
atom: 16 charge: 1.6812 magn:
0.0001 constr: 0.0000
atom: 17 charge: 1.6792 magn:
-0.0000 constr: 0.0000
atom: 18 charge: 1.7101 magn:
0.0001 constr: 0.0000
atom: 19 charge: 1.7064 magn:
-0.0000 constr: 0.0000
atom: 20 charge: 1.7108 magn:
0.0001 constr: 0.0000
atom: 21 charge: 1.8440 magn:
-0.0001 constr: 0.0000
atom: 22 charge: 1.8405 magn:
-0.0001 constr: 0.0000
atom: 23 charge: 1.6823 magn:
0.0001 constr: 0.0000
atom: 24 charge: 1.6504 magn:
-0.0000 constr: 0.0000
atom: 25 charge: 1.7100 magn:
0.0001 constr: 0.0000
atom: 26 charge: 1.6796 magn:
0.0000 constr: 0.0000
atom: 27 charge: 1.7138 magn:
0.0000 constr: 0.0000
atom: 28 charge: 1.6791 magn:
-0.0000 constr: 0.0000
atom: 29 charge: 1.7077 magn:
0.0001 constr: 0.0000
atom: 30 charge: 1.6835 magn:
-0.0001 constr: 0.0000
atom: 31 charge: 1.6800 magn:
0.0001 constr: 0.0000
atom: 32 charge: 11.1637 magn:
0.0012 constr: 0.0000
total cpu time spent up to now
is 4107.5 secs
End of self-consistent calculation
------ SPIN UP
------------
k = 0.0000 0.0000 0.0000
(126127 PWs) bands (ev):
===================================================================
we know that
for a single electron |μS| = √3 μB, or approximately
1.73 Bohr magnetons.
For
my supercell, I have only one Fe, so, I expected to get
magnetization greater than one (for Fe atom, there is 4
unpaired electron). But, I got 0.01 Bohr-magneton. Any
help?
Regards
David
Foster
Ph.D. Student of
Chemistry
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