[Pw_forum] Magnetization on the Fe atom doped on the graphene
庞瑞(PANG Rui)
pang.r at sustc.edu.cn
Sat Jul 18 08:54:26 CEST 2015
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 Physics
No.1088,Xueyuan Road, Shenzhen,Guangdong
------------------ Original ------------------
From: "David Foster"<davidfoster751 at yahoo.com>;
Date: Fri, Jul 17, 2015 08:44 PM
To: "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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