Re: [Pw_forum] Force is fluctuating for water system
Dear Narendra Nath Ghosh,
Adding to Lorenzo's answer, a small note: You seem to have an odd number
of electrons but you do not specify 'nspin = 2' - are you sure that this
is what you intended to do (physically)? 70 Ry with a pseudo potential à
la Troullier-Martins for oxygen, it might be at the lower limit (it
depends on the core radii, usually I would go for 80-90 Ry minimum). And,
do you know if the electron gets localised or remains delocalised - this
is an open question to my knowledge, and might well depend on the kind of
exchange-correlation functional used (GGA like BLYP probably delocalise it
- with the highest occupied orbital in the conduction band - and hybrid
functionals might localise it).
Greetings from Helsinki/Finland,
apsi
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
Ari Paavo Seitsonen / ari.p.seitso...@iki.fi / http://www.iki.fi/~apsi/
Ecole Normale Supérieure (ENS), Département de Chimie, Paris
Mobile (F) : +33 789 37 24 25(CH) : +41 79 71 90 935
On Tue, 19 Dec 2017, Narendranath Ghosh wrote:
Dear all
I am relaxing a system of 128 water molecule with extra electron.The force is
fluctuating even after bfgs
steps = 48.
Input:
&CONTROL
calculation='relax',
outdir='/share_home/hpc/NEGATIVE_HYDRATED_ELECTRON/OUTPUT',
prefix='water-128-negative',
pseudo_dir='/share_home/hpc/RESEARCH_SCHOLAR/HYDRATED-ELECTRON/pseudo',
verbosity='high',
restart_mode='restart',
/
&SYSTEM
ibrav=0,
celldm(1)=29.8576727681d0,
nat=384,
tot_charge=-1,
ntyp=2,
ecutwfc=70,
ecutrho=280,
input_dft='BLYP',
occupations='smearing',
degauss=0.05d0,
/
&ELECTRONS
mixing_beta=0.500d0,
electron_maxstep=500,
/
&IONS
/
ATOMIC_SPECIES
O 16.0d0 O.blyp-mt.UPF
H 1.0079d0 H.blyp-vbc.UPF
K_POINTS {automatic}
1 1 1 0 0 0
CELL_PARAMETERS {alat}
1.d0 0.d0 0.d0
0.d0 1.d0 0.d0
0.d0 0.d0 1.d0
Output
Total force = 0.030447 Total SCF correction = 0.001115
Total force = 0.033732 Total SCF correction = 0.000223
Total force = 0.042921 Total SCF correction = 0.000171
Total force = 0.032971 Total SCF correction = 0.000165
Total force = 0.032983 Total SCF correction = 0.000266
Total force = 0.036132 Total SCF correction = 0.000252
Total force = 0.040191 Total SCF correction = 0.000833
Total force = 0.032897 Total SCF correction = 0.001663
Total force = 0.025425 Total SCF correction = 0.000288
Total force = 0.019869 Total SCF correction = 0.000279
Total force = 0.020382 Total SCF correction = 0.000102
Total force = 0.025164 Total SCF correction = 0.000109
Total force = 0.027580 Total SCF correction = 0.000141
Total force = 0.026211 Total SCF correction = 0.000188
Total force = 0.023574 Total SCF correction = 0.000139
Total force = 0.024877 Total SCF correction = 0.000103
Total force = 0.027597 Total SCF correction = 0.000131
Total force = 0.027563 Total SCF correction = 0.000169
Total force = 0.023015 Total SCF correction = 0.000195
Total force = 0.02 Total SCF correction = 0.000109
Total force = 0.021345 Total SCF correction = 0.92
Total force = 0.023793 Total SCF correction = 0.000129
Total force = 0.024400 Total SCF correction = 0.000145
Total force = 0.025073 Total SCF correction = 0.000243
Total force = 0.022300 Total SCF correction = 0.000376
Total force = 0.020060 Total SCF correction = 0.97
Total force = 0.021991 Total SCF correction = 0.000134
Total force = 0.022541 Total SCF correction = 0.000132
Total force = 0.023051 Total SCF correction = 0.000158
Total force = 0.023734 Total SCF correction = 0.000168
Total force = 0.023734 Total SCF correction = 0.000168
number of scf cycles = 49
number of bfgs steps = 48
energy old = -4400.3520443575 Ry
energy new = -4400.3528674259 Ry
CASE: energy _new < energy _old
new trust radius = 0.0602516409 bohr
new conv_thr = 0.000591 Ry
Please help me.
Dr. Narendra Nath Ghosh
Research Associate
University of Gour Banga
Malda-732102
India
Phone No : 09126667601
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Re: [Pw_forum] problem in relaxing gold cluster
Dear all,
As I said before, I steel have a problem with relaxing gold cluster. the output
was very messy and some of atoms take apart and the others have no structure.
I took advice which I received and Changed cut off , mixing beta , mixing mode
and put i-brave=0
this is my input file :.
&CONTROL
calculation = 'relax' ,
restart_mode = 'from_scratch' ,
outdir="/home/rahil/Desktop/zareyi/out",
pseudo_dir ="/home/rahil/Desktop/zareyi/pes",
tprnfor = .true.
tstress = .true.
/
&SYSTEM
ibrav = 0,
celldm(1) = 34.75,
nat = 13,
ntyp = 1,
ecutwfc = 120 ,
occupations = 'smearing' ,
degauss= 0.001 ,
smearing= 'gaussian',
nspin = 2 ,
starting_magnetization(1) = 0.5,
/
&ELECTRONS
mixing_beta = 0.1
conv_thr = 1.D-6 ,
/
&IONS
/
&CELL
/
ATOMIC_SPECIES
Au196.966657 Au.blyp-d-hgh.UPF
ATOMIC_POSITIONS (angstrom)
Au 7.000 10.000 10.000
Au 8.360 7.644 10.000
Au 11.080 7.644 10.000
Au 12.440 10.000 10.000
Au 11.080 12.356 10.000
Au 8.360 12.356 10.000
Au 9.720 10.000 10.000
Au 9.7238155 8.4315277 7.777622
Au 8.3424810 10.7842271 7.780175
Au 11.0523480 10.8179223 7.78000
Au 9.7238155 8.4315277 12.2223780
Au 8.3328179 10.7673656 12.220
Au 11.0523480 10.8179223 12.220
K_POINTS gamma
CELL_PARAMETERS { alat }
1 0 0
0 1 0
0 0 1
...and atom position out put is :
Cartesian axes
site n. atom positions (alat units)
1 Au tau( 1) = ( 0.3806643 0.5438061 0.5438061 )
2 Au tau( 2) = ( 0.4546219 0.4156854 0.5438061 )
3 Au tau( 3) = ( 0.6025371 0.4156854 0.5438061 )
4 Au tau( 4) = ( 0.6764948 0.5438061 0.5438061 )
5 Au tau( 5) = ( 0.6025371 0.6719268 0.5438061 )
6 Au tau( 6) = ( 0.4546219 0.6719268 0.5438061 )
7 Au tau( 7) = ( 0.5285795 0.5438061 0.5438061 )
8 Au tau( 8) = ( 0.5287870 0.4585116 0.4229518 )
9 Au tau( 9) = ( 0.4536692 0.5864528 0.4230906 )
10 Au tau( 10) = ( 0.6010334 0.5882852 0.4230811 )
11 Au tau( 11) = ( 0.5287870 0.4585116 0.6646603 )
12 Au tau( 12) = ( 0.4531437 0.5855359 0.6645310 )
13 Au tau( 13) = ( 0.6010334 0.5882852 0.6645310 )
total energy =-855.74288431 Ry
Harris-Foulkes estimate =-855.31185040 Ry
estimated scf accuracy< 3.28072580 Ry
is there anyone who knows about such problem ?
Hajar Zareyi
K.N.Toosi university
Tehran Iran
- Original Message -
From: "hajar zareyi"
To: "pw forum"
Sent: Tuesday, December 5, 2017 8:32:02 PM
Subject: Re: problem in relaxing gold cluster
Dear all
thank you for your attention and your quick answer especially "Ari P Seitsonen
and David Foster" .I will test your advice
and I will keep you posted about the result.
I add my affiliation too .
best regards
Hajar zarei
PHd student solid state physics
K.N.Toosi university
- Original Message -
From: "pw forum-request"
To: "pw forum"
Sent: Monday, December 4, 2017 2:30:02 PM
Subject: Pw_forum Digest, Vol 125, Issue 4
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Today's Topics:
1. Re: problem in relaxing gold cluster (Ari P Seitsonen)
2. Re: Error in routine sym_rho_init_shell (4): lone vector
(Manoar Hossain)
3. Re: (no subject) (Mitsuaki Kawamura)
4. Re: problem in relaxing gold cluster (David Foster)
5. SOC pseudopotential (Eliya Asmani)
6. Re: Phonon dispersion with LO-TO splitting (Barnali Bhattacharya)
7. Re: SOC pseudopotential (Lorenzo Paulatto)
8. Re: Error in routine sym_rho_init_shell (4): lone vector
(Paolo Giannozzi)
--
Message: 1
Date: Sun, 3 Dec 2017 12:38:03 +0100 (CET)
From: Ari P Seitsonen
Subject: Re: [Pw_forum] problem in relaxing gold cluster
To: PWSCF Forum
Message-ID:
Content-Type: text/plain; charset="iso-8859-15"
Dear Haja Zareyi,
[Next time with affiliation please :) ]
'hgh' in the name of the pseudo potential => it is norm-conserving, no
need to specify 'ecutrho'. Did you check that the 'ecutwfc' was
sufficient for a reasonable convergence?
Greetings from Lviv/Lemberg,
apsi
-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=
Re: [Pw_forum] error- dE0s is positive which should never happen
Ok... I have rerun the calculation... surprisingly, it completed without any error. Any way... Thank you Dr. Ullah for your kind reply. On Wed, Dec 20, 2017 at 4:32 PM, Saif Ullah wrote: > Dear Bhushan, > > It means that you have already achieved (nearly achieved) the convergence > as can be concluded from the following sentence by prof. Paolo > (This kind of errors invariably happens when you are very close > > to the minimum and you have some numerical noise on forces. It > is useless in my opinion to insist: your system is sufficiently > relaxed > > > Paolo) > > I'm surely not a QE expert but when I have this kind of problem, I usually > change (a bit) the positions of few atoms and do a relax calculation > following by an scf-calc. > > Regards > Saif > > Saif Ullah > Departamento de Física > Instituto de Ciências Exatas - ICE > Universidade Federal de Juiz de Fora - UFJF > Juiz de Fora - MG - Brazil - CEP 36036-330 > sul...@fisica.ufjf.br > Cell# +55 32 9110-7851 > https://www.researchgate.net/profile/Saif_Ullah41 > > On Tue, Dec 19, 2017 at 11:43 AM, B S Bhushan > wrote: > >> Dear Dr. Saif, >> >> I have through this link before posting the error. However, I could not >> find a solution to my problem there. >> >> >> On Tue, Dec 19, 2017 at 6:07 PM, Saif Ullah >> wrote: >> >>> It is a well-known error. >>> >>> The following links may be helpful. >>> http://qe-forge.org/pipermail/pw_forum/2014-September/105225.html >>> https://www.mail-archive.com/pw_forum@pwscf.org/msg29759.html >>> >>> Regards >>> Saif >>> >>> >>> On Tue, Dec 19, 2017 at 7:38 AM, B S Bhushan >>> wrote: >>> Dear experts... I have received this following error when I was trying to optimize a doped graphene sheet. %% Error in routine bfgs (1): dE0s is positive which should never happen %%% %%% Please suggest me how to avoid this error. Thank you very much for your precious time and knowledge. Sincerely, B S Bhushan, Ph.D Scholar, ABV-IIITM Gwalior, India. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] Example matdyn.in file for bcc iron ferrite
Dear experts, Is it possible to have an example matdyn.in file for bcc iron ferrite. I am interested in calculating phonon dispersion for the same as was reported in the paper: Dal Corso, A., and S. de Gironcoli, 2000, Phys. Rev. B 62, 273. Thanking you, Yours sincerely, Krishnendu -- Dr. Krishnendu Mukherjee, Principal Scientist, CSIR-NML, Jamshedpur. ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Converged SCF total energies different in 6.0/6.1/6.2
From Doc/release-notes
Fixed in 6.2 version
...
* Some constants in the definition of PBE functionals were truncated to
6 significant digits. While not a bug, this could lead to tiny
differences with respect to previous results and other XC
implementations (r13592)
kind regards
On 21/12/17 03:11, WF wrote:
> Dear all,
>
> In tests a normal DFT calculations with Si, I noticed that QE 6.0 and
> 6.1 gives exactly same total energy with 6.0 and 6.1 (-15.75190880 Ry),
> but with QE 6.2.1, the total energy is -15.75191309Ry. I tested this on
> two different machines with different compilers, the results are the
> same across all of them (at least to last digit). I did some tests on
> larger systems also and found even larger difference. This 1e-5 Ry order
> of difference is not negligible. Is there anything introduced in 6.2
> leads to this difference? Thanks very much.
>
> Best regards,
>
> Feng
>
> The input file is attached:
>
>
>
> &control
>
> calculation='scf'
>
> outdir='./tmp'
>
> prefix='si'
>
> wf_collect = .true.,
>
> /
>
> &system
>
> ibrav=2,
>
> celldm(1) = 10.263,
>
> nat=2,
>
> ntyp= 1,
>
> ecutwfc = 40,
>
> /
>
> &electrons
>
> mixing_mode='plain'
>
> mixing_beta = 0.7,
>
> conv_thr = 1.0d-10,
>
> /
>
> ATOMIC_SPECIES
>
> Si 1.0 Si_ONCV_PBE-1.1.upf
>
> ATOMIC_POSITIONS {alat}
>
> Si 0.00 0.00 0.00
>
> Si 0.25 0.25 0.25
>
> K_POINTS (automatic)
>
> 4 4 4 0 0 0
>
> ==
>
> --
>
> Dr. Feng Wu
>
> Postdoctoral researcher
>
> Department of Chemistry and Biochemistry
>
> University of California, Santa Cruz
>
> Phone: 831-459-2874
>
>
>
> ___
> Pw_forum mailing list
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> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Lorenzo Paulatto - Paris
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Re: [Pw_forum] Converged SCF total energies different in 6.0/6.1/6.2
See this note in file Doc/release-notes:
* Some constants in the definition of PBE functionals were truncated to
6 significant digits. While not a bug, this could lead to tiny
differences
with respect to previous results and other XC implementations (r13592)
More explicitly: some constants that previously were truncated to 6 digits,
are now defined with full precision. This removes minor numerical
discrepancies with the results obtained using libxc.
Paolo
On Thu, Dec 21, 2017 at 3:11 AM, WF wrote:
> Dear all,
>
> In tests a normal DFT calculations with Si, I noticed that QE 6.0 and 6.1
> gives exactly same total energy with 6.0 and 6.1 (-15.75190880 Ry), but
> with QE 6.2.1, the total energy is -15.75191309Ry. I tested this on two
> different machines with different compilers, the results are the same
> across all of them (at least to last digit). I did some tests on larger
> systems also and found even larger difference. This 1e-5 Ry order of
> difference is not negligible. Is there anything introduced in 6.2 leads to
> this difference? Thanks very much.
>
>
>
> Best regards,
>
> Feng
>
>
>
> The input file is attached:
>
>
>
> &control
>
> calculation='scf'
>
> outdir='./tmp'
>
> prefix='si'
>
> wf_collect = .true.,
>
> /
>
> &system
>
> ibrav=2,
>
> celldm(1) = 10.263,
>
> nat=2,
>
> ntyp= 1,
>
> ecutwfc = 40,
>
> /
>
> &electrons
>
> mixing_mode='plain'
>
> mixing_beta = 0.7,
>
> conv_thr = 1.0d-10,
>
> /
>
> ATOMIC_SPECIES
>
> Si 1.0 Si_ONCV_PBE-1.1.upf
>
> ATOMIC_POSITIONS {alat}
>
> Si 0.00 0.00 0.00
>
> Si 0.25 0.25 0.25
>
> K_POINTS (automatic)
>
> 4 4 4 0 0 0
>
> ==
>
>
>
>
>
> --
>
> Dr. Feng Wu
>
> Postdoctoral researcher
>
> Department of Chemistry and Biochemistry
>
> University of California, Santa Cruz
>
> Phone: 831-459-2874 <(831)%20459-2874>
>
>
>
>
>
> ___
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>
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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