[QE-users] higher total energy in the last stage of vc-relax
mehrdad zamzamian
mehrdad.zamzamian at gmail.com
Tue Jun 18 17:53:48 CEST 2019
Dear Kevin
Hi again
Sorry i bothered you many times for asking many questions, but i am really
confused about my case
After using the paw-pp that you suggested, i obtained E(f-vacancy)~2.0 eV!!
here in attachment, i gave my input. i used a 128-atom supercell for a
perfect crystal (E=32199.76950786 Ry) and by removing a Fe atom, i had
E=31870.37251766 Ry and isolated Fe E=329.18792433 Ry. It seems that i
cannot obtain a better result than 2 eV. I appreciated if you give me any
suggestions. the paper that you mentioned talked about "Ecorr". what
exactly is this parameter?
On Sat, Jun 1, 2019 at 11:27 PM Kevin May <kmay at mit.edu> wrote:
> Hi Mehrdad,
>
> On Sat, Jun 1, 2019 at 1:58 PM mehrdad zamzamian <
> mehrdad.zamzamian at gmail.com> wrote:
>
>> With regard
>> Dear Kevin
>> 1) Actually, my reference is computational material science 44(2008)
>> 690-694 (although they reported delta(E)= -0.456 eV/atom that i don't know
>> what it is. because i said that it must be 1.6 eV according to
>> https://doi.org/10.1080/09506608.2018.1560984). i also used
>> spin-polarized (0.2 for Fe) but the same result was obtained (not better
>> than 2.2 eV). I also used constant volume (by using relax calculation not
>> vc_relax), but i had the same results.
>>
>
> The first paper you mention does not calculate vacancy formation energy,
> the -0.456 eV/atom is the bulk formation energy of orthorhombic Fe3C from
> GGA. The second paper is a review article that cites the paper by Jiang et
> al. that I mentioned in my last email for their ~1.6 eV formation energy of
> a Fe vacancy.
>
>> 2) thanks for the proposed links, but in that reference they offered two
>> non-consistent pps (C.pbe-n-kjpaw_psl.1.0.0.UPF
>> and Fe.pbe-spn-kjpaw_psl.0.2.1.UPF) that i cannot use for Fe3C. i used
>> these pp:
>> C.pbe-n-rrkjus_psl.1.0.0.UPF
>> Fe.pbe-spn-rrkjus_psl.1.0.0.UPF
>>
>
> I'm not sure what you mean by "non-consistent", or why you can't use those
> PAW datasets for your calculation. If you need to use ultrasoft for another
> reason, I'd still recommend using Fe.pbe-spn-rrkjus_psl.0.2.1.UPF instead
> of the psl.1.0.0 version.
>
> I am really confused about how can i calculate this rather simple
>> parameter. i should mention that i calculate the Fe vacancy with:
>> E(Fe-vacancy)=E(perfect Fe3C)- E(Fe3C with lack of one Fe atom)- E(single
>> Fe)
>>
>
> By E(single Fe) you mean 1/2 the energy of ferromagnetic BCC Fe (2 Fe per
> unit cell), rather than an isolated Fe atom, right? That is the chemical
> potential reference for Fe that was used in calculating the 1.6 eV
> formation energy value. And for what it's worth I don't think point defect
> calculations are that trivial.
>
>> 3) thanks very much for the reference Rev. Mod. Phys. 86, 253 (2014).
>>
>
> Regarding chemical potential reference, see section II.B.2 of this article.
>
>
>> regards
>>
>> Seyed Mehrdad Zamzamian
>> Sharif University of Technology, Tehran, Iran
>> Energy engineering department
>> E-mail: mehrdad.zamzamian at gmail.com
>>
> Good luck,
>
> Kevin May, PhD
> Postdoctoral Associate
> Department of Materials Science and Engineering
> Massachusetts Institute of Technology
>
>
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&CONTROL
calculation = "relax"
forc_conv_thr = 1.00000e-03
max_seconds = 6.32070e+16
nstep = 201
pseudo_dir = ""
/
&SYSTEM
a = 1.00604e+01
angle1(1) = 0.00000e+00
angle2(1) = 0.00000e+00
b = 1.34786e+01
c = 8.98169e+00
degauss = 1.00000e-02
ecutrho = 1.08000e+03
ecutwfc = 9.00000e+01
ibrav = 8
nat = 127
nspin = 2
ntyp = 2
occupations = "smearing"
smearing = "gaussian"
starting_magnetization(1) = 2.00000e-01
starting_magnetization(2) = 0.00000e+00
/
&ELECTRONS
conv_thr = 1.00000e-06
electron_maxstep = 200
mixing_beta = 4.51613e-02
startingpot = "atomic"
startingwfc = "atomic+random"
/
&IONS
ion_dynamics = "bfgs"
/
&CELL
cell_dofree = "xyz"
cell_dynamics = "bfgs"
press = 0.00000e+00
press_conv_thr = 5.00000e-01
/
K_POINTS {gamma}
ATOMIC_SPECIES
Fe 55.84500 Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
Fe 0.892203 0.460793 1.491414
Fe 4.137977 6.278514 2.999431
Fe 1.622887 6.278514 3.736836
Fe 3.407293 0.460793 0.754008
Fe 3.407293 2.908860 0.754008
Fe 1.622887 3.830447 3.736836
Fe 4.137977 3.830447 2.999431
Fe 0.892203 2.908860 1.491414
Fe 0.184411 1.684827 3.759376
Fe 4.845769 5.054480 0.731469
Fe 2.330679 5.054480 1.513954
Fe 2.699502 1.684827 2.976891
C 0.618742 5.054480 2.519058
C 4.411438 1.684827 1.971786
C 1.896348 1.684827 0.273636
C 3.133833 5.054480 4.217209
Fe 0.892203 0.460793 5.982259
Fe 4.137977 6.278514 7.490275
Fe 1.622887 6.278514 8.227681
Fe 3.407293 0.460793 5.244853
Fe 3.407293 2.908860 5.244853
Fe 1.622887 3.830447 8.227681
Fe 4.137977 3.830447 7.490275
Fe 0.892203 2.908860 5.982259
Fe 0.184411 1.684827 8.250221
Fe 4.845769 5.054480 5.222313
Fe 2.330679 5.054480 6.004798
Fe 2.699502 1.684827 7.467736
C 0.618742 5.054480 7.009903
C 4.411438 1.684827 6.462631
C 1.896348 1.684827 4.764481
C 3.133833 5.054480 8.708053
Fe 0.892203 7.200101 1.491414
Fe 4.137977 13.017821 2.999431
Fe 1.622887 13.017821 3.736836
Fe 3.407293 7.200101 0.754008
Fe 3.407293 9.648168 0.754008
Fe 1.622887 10.569754 3.736836
Fe 4.137977 10.569754 2.999431
Fe 0.892203 9.648168 1.491414
Fe 0.184411 8.424134 3.759376
Fe 4.845769 11.793788 0.731469
Fe 2.330679 11.793788 1.513954
Fe 2.699502 8.424134 2.976891
C 0.618742 11.793788 2.519058
C 4.411438 8.424134 1.971786
C 1.896348 8.424134 0.273636
C 3.133833 11.793788 4.217209
Fe 0.892203 7.200101 5.982259
Fe 4.137977 13.017821 7.490275
Fe 1.622887 13.017821 8.227681
Fe 3.407293 7.200101 5.244853
Fe 3.407293 9.648168 5.244853
Fe 1.622887 10.569754 8.227681
Fe 4.137977 10.569754 7.490275
Fe 0.892203 9.648168 5.982259
Fe 0.184411 8.424134 8.250221
Fe 4.845769 11.793788 5.222313
Fe 2.330679 11.793788 6.004798
Fe 2.699502 8.424134 7.467736
C 0.618742 11.793788 7.009903
C 4.411438 8.424134 6.462631
C 1.896348 8.424134 4.764481
C 3.133833 11.793788 8.708053
Fe 5.922384 0.460793 1.491414
Fe 9.168158 6.278514 2.999431
Fe 6.653068 6.278514 3.736836
Fe 8.437474 0.460793 0.754008
Fe 8.437474 2.908860 0.754008
Fe 6.653068 3.830447 3.736836
Fe 9.168158 3.830447 2.999431
Fe 5.922384 2.908860 1.491414
Fe 5.214592 1.684827 3.759376
Fe 9.875949 5.054480 0.731469
Fe 7.360859 5.054480 1.513954
Fe 7.729682 1.684827 2.976891
C 5.648923 5.054480 2.519058
C 9.441619 1.684827 1.971786
C 6.926528 1.684827 0.273636
C 8.164013 5.054480 4.217209
Fe 5.922384 0.460793 5.982259
Fe 9.168158 6.278514 7.490275
Fe 6.653068 6.278514 8.227681
Fe 8.437474 0.460793 5.244853
Fe 8.437474 2.908860 5.244853
Fe 6.653068 3.830447 8.227681
Fe 9.168158 3.830447 7.490275
Fe 5.922384 2.908860 5.982259
Fe 5.214592 1.684827 8.250221
Fe 9.875949 5.054480 5.222313
Fe 7.360859 5.054480 6.004798
Fe 7.729682 1.684827 7.467736
C 5.648923 5.054480 7.009903
C 9.441619 1.684827 6.462631
C 6.926528 1.684827 4.764481
C 8.164013 5.054480 8.708053
Fe 5.922384 7.200101 1.491414
Fe 9.168158 13.017821 2.999431
Fe 6.653068 13.017821 3.736836
Fe 8.437474 7.200101 0.754008
Fe 8.437474 9.648168 0.754008
Fe 6.653068 10.569754 3.736836
Fe 9.168158 10.569754 2.999431
Fe 5.922384 9.648168 1.491414
Fe 9.875949 11.793788 0.731469
Fe 7.360859 11.793788 1.513954
Fe 7.729682 8.424134 2.976891
C 5.648923 11.793788 2.519058
C 9.441619 8.424134 1.971786
C 6.926528 8.424134 0.273636
C 8.164013 11.793788 4.217209
Fe 5.922384 7.200101 5.982259
Fe 9.168158 13.017821 7.490275
Fe 6.653068 13.017821 8.227681
Fe 8.437474 7.200101 5.244853
Fe 8.437474 9.648168 5.244853
Fe 6.653068 10.569754 8.227681
Fe 9.168158 10.569754 7.490275
Fe 5.922384 9.648168 5.982259
Fe 5.214592 8.424134 8.250221
Fe 9.875949 11.793788 5.222313
Fe 7.360859 11.793788 6.004798
Fe 7.729682 8.424134 7.467736
C 5.648923 11.793788 7.009903
C 9.441619 8.424134 6.462631
C 6.926528 8.424134 4.764481
C 8.164013 11.793788 8.708053
-------------- next part --------------
&CONTROL
calculation = "vc-relax"
forc_conv_thr = 1.00000e-03
max_seconds = 1.72800e+05
nstep = 199
pseudo_dir = ""
/
&SYSTEM
a = 2.84812e+00
angle1(1) = 0.00000e+00
angle2(1) = 0.00000e+00
degauss = 1.00000e-02
ecutrho = 8.10000e+02
ecutwfc = 9.00000e+01
ibrav = 1
nat = 1
nspin = 2
ntyp = 1
occupations = "smearing"
smearing = "gaussian"
starting_magnetization(1) = 0.00000e+00
/
&ELECTRONS
conv_thr = 1.00000e-06
electron_maxstep = 200
mixing_beta = 4.83871e-02
startingpot = "atomic"
startingwfc = "atomic+random"
/
&IONS
ion_dynamics = "bfgs"
/
&CELL
cell_dofree = "all"
cell_dynamics = "bfgs"
press = 0.00000e+00
press_conv_thr = 5.00000e-01
/
K_POINTS {automatic}
4 4 4 0 0 0
ATOMIC_SPECIES
Fe 55.84500 Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
ATOMIC_POSITIONS {angstrom}
Fe 1.424058 1.424058 1.424058
-------------- next part --------------
&CONTROL
calculation = "relax"
forc_conv_thr = 1.00000e-03
max_seconds = 3.82276e+22
nstep = 201
pseudo_dir = ""
/
&SYSTEM
a = 1.00604e+01
b = 1.34786e+01
c = 8.98169e+00
degauss = 1.00000e-02
ecutrho = 1.08000e+03
ecutwfc = 9.00000e+01
ibrav = 8
nat = 128
nspin = 2
ntyp = 2
occupations = "smearing"
smearing = "gaussian"
starting_magnetization(1) = 2.00000e-01
starting_magnetization(2) = 0.00000e+00
/
&ELECTRONS
conv_thr = 1.00000e-06
electron_maxstep = 200
mixing_beta = 4.51613e-02
startingpot = "atomic"
startingwfc = "atomic+random"
/
&IONS
ion_dynamics = "bfgs"
/
&CELL
cell_dofree = "xyz"
cell_dynamics = "bfgs"
press = 0.00000e+00
press_conv_thr = 5.00000e-01
/
K_POINTS {gamma}
ATOMIC_SPECIES
Fe 55.84500 Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
C 12.01070 C.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS {angstrom}
Fe 0.892203 0.460793 1.491414
Fe 4.137977 6.278514 2.999431
Fe 1.622887 6.278514 3.736836
Fe 3.407293 0.460793 0.754008
Fe 3.407293 2.908860 0.754008
Fe 1.622887 3.830447 3.736836
Fe 4.137977 3.830447 2.999431
Fe 0.892203 2.908860 1.491414
Fe 0.184411 1.684827 3.759376
Fe 4.845769 5.054480 0.731469
Fe 2.330679 5.054480 1.513954
Fe 2.699502 1.684827 2.976891
C 0.618742 5.054480 2.519058
C 4.411438 1.684827 1.971786
C 1.896348 1.684827 0.273636
C 3.133833 5.054480 4.217209
Fe 0.892203 0.460793 5.982259
Fe 4.137977 6.278514 7.490275
Fe 1.622887 6.278514 8.227681
Fe 3.407293 0.460793 5.244853
Fe 3.407293 2.908860 5.244853
Fe 1.622887 3.830447 8.227681
Fe 4.137977 3.830447 7.490275
Fe 0.892203 2.908860 5.982259
Fe 0.184411 1.684827 8.250221
Fe 4.845769 5.054480 5.222313
Fe 2.330679 5.054480 6.004798
Fe 2.699502 1.684827 7.467736
C 0.618742 5.054480 7.009903
C 4.411438 1.684827 6.462631
C 1.896348 1.684827 4.764481
C 3.133833 5.054480 8.708053
Fe 0.892203 7.200101 1.491414
Fe 4.137977 13.017821 2.999431
Fe 1.622887 13.017821 3.736836
Fe 3.407293 7.200101 0.754008
Fe 3.407293 9.648168 0.754008
Fe 1.622887 10.569754 3.736836
Fe 4.137977 10.569754 2.999431
Fe 0.892203 9.648168 1.491414
Fe 0.184411 8.424134 3.759376
Fe 4.845769 11.793788 0.731469
Fe 2.330679 11.793788 1.513954
Fe 2.699502 8.424134 2.976891
C 0.618742 11.793788 2.519058
C 4.411438 8.424134 1.971786
C 1.896348 8.424134 0.273636
C 3.133833 11.793788 4.217209
Fe 0.892203 7.200101 5.982259
Fe 4.137977 13.017821 7.490275
Fe 1.622887 13.017821 8.227681
Fe 3.407293 7.200101 5.244853
Fe 3.407293 9.648168 5.244853
Fe 1.622887 10.569754 8.227681
Fe 4.137977 10.569754 7.490275
Fe 0.892203 9.648168 5.982259
Fe 0.184411 8.424134 8.250221
Fe 4.845769 11.793788 5.222313
Fe 2.330679 11.793788 6.004798
Fe 2.699502 8.424134 7.467736
C 0.618742 11.793788 7.009903
C 4.411438 8.424134 6.462631
C 1.896348 8.424134 4.764481
C 3.133833 11.793788 8.708053
Fe 5.922384 0.460793 1.491414
Fe 9.168158 6.278514 2.999431
Fe 6.653068 6.278514 3.736836
Fe 8.437474 0.460793 0.754008
Fe 8.437474 2.908860 0.754008
Fe 6.653068 3.830447 3.736836
Fe 9.168158 3.830447 2.999431
Fe 5.922384 2.908860 1.491414
Fe 5.214592 1.684827 3.759376
Fe 9.875949 5.054480 0.731469
Fe 7.360859 5.054480 1.513954
Fe 7.729682 1.684827 2.976891
C 5.648923 5.054480 2.519058
C 9.441619 1.684827 1.971786
C 6.926528 1.684827 0.273636
C 8.164013 5.054480 4.217209
Fe 5.922384 0.460793 5.982259
Fe 9.168158 6.278514 7.490275
Fe 6.653068 6.278514 8.227681
Fe 8.437474 0.460793 5.244853
Fe 8.437474 2.908860 5.244853
Fe 6.653068 3.830447 8.227681
Fe 9.168158 3.830447 7.490275
Fe 5.922384 2.908860 5.982259
Fe 5.214592 1.684827 8.250221
Fe 9.875949 5.054480 5.222313
Fe 7.360859 5.054480 6.004798
Fe 7.729682 1.684827 7.467736
C 5.648923 5.054480 7.009903
C 9.441619 1.684827 6.462631
C 6.926528 1.684827 4.764481
C 8.164013 5.054480 8.708053
Fe 5.922384 7.200101 1.491414
Fe 9.168158 13.017821 2.999431
Fe 6.653068 13.017821 3.736836
Fe 8.437474 7.200101 0.754008
Fe 8.437474 9.648168 0.754008
Fe 6.653068 10.569754 3.736836
Fe 9.168158 10.569754 2.999431
Fe 5.922384 9.648168 1.491414
Fe 5.214592 8.424134 3.759376
Fe 9.875949 11.793788 0.731469
Fe 7.360859 11.793788 1.513954
Fe 7.729682 8.424134 2.976891
C 5.648923 11.793788 2.519058
C 9.441619 8.424134 1.971786
C 6.926528 8.424134 0.273636
C 8.164013 11.793788 4.217209
Fe 5.922384 7.200101 5.982259
Fe 9.168158 13.017821 7.490275
Fe 6.653068 13.017821 8.227681
Fe 8.437474 7.200101 5.244853
Fe 8.437474 9.648168 5.244853
Fe 6.653068 10.569754 8.227681
Fe 9.168158 10.569754 7.490275
Fe 5.922384 9.648168 5.982259
Fe 5.214592 8.424134 8.250221
Fe 9.875949 11.793788 5.222313
Fe 7.360859 11.793788 6.004798
Fe 7.729682 8.424134 7.467736
C 5.648923 11.793788 7.009903
C 9.441619 8.424134 6.462631
C 6.926528 8.424134 4.764481
C 8.164013 11.793788 8.708053
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