[Pw_forum] Fwd: Basic Relax Calculation issues
Apologies this is the error message: Error in routine read_namelists (5010): reading namelist cell Thank you for your response. Kind Regards Zarah On Fri, Mar 7, 2014 at 3:56 PM, Paolo Giannozzi wrote: > On Fri, 2014-03-07 at 14:49 +0800, Zarah Baiyee wrote: > > > I am currently having a few issues with VC-Relax input > > files and cannot seem to get them to work, please find > > attached. I consistently get an error: > > > > Error in routine dos (1): > > reading dos namelist > > this happens during the calculation of the density of > states (code dos.x), not during the variable-cell > optimization (code pw.x) > > P. > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140307/72aaba97/attachment.html
[Pw_forum] Fwd: Basic Relax Calculation issues
Thanks Fillipe,
I am currently having a few issues with VC-Relax input files and cannot
seem to get them to work, please find attached. I consistently get an
error:
Error in routine dos (1):
reading dos namelist
Any suggestions would be greatly appreciated.
Thanks
Zarah
On Fri, Mar 7, 2014 at 11:35 AM, Filipe Camargo Dalmatti Alves Lima <
flima at if.usp.br> wrote:
> Dear Zarah,
>
> Have you ever considered that you may want the cell relaxation in this
> case? (vc-relax)
> It will optimize the cell parameter in order to minimize the total energy.
> You'll see that the system might have lots of interactions.
>
> If you want to explore defects in crystals or surfaces, relaxing the
> internal coordinates are essential since you are breaking the symmetry in
> some way: by having impurities; surface interaction; vacancy defects and
> etc. If it is the case you want to explore, you will need to use a
> supercell approach. Remember: crystals are built based on symmetry rules.
>
> If you are really curious, you might try to change the cell symmetry just
> to observe how the internal coordinations behave (just increase z by 0.2).
> It may not converge, but you will see a lot interactions.
>
> Best regards,
>
> Filipe
>
> On Friday, February 28, 2014, Zarah Baiyee wrote:
>
>> Hi All,
>>
>> I am a new user to Quantum Espresso, therefore this may be a bit trivial
>> but I any help would be very welcome.
>>
>> I am attempting a relax calculation using espresso version 5.0.2, for the
>> geometry optimisation of a perovskite structure. For the input below, the
>> calculation runs, however does not compute any forces and convergence
>> without geometry optimisation to the original structure, with 0 bfgs steps.
>> I am able to perform an expected relaxation if alter the initial atomic
>> positions to asymmetric: (i.e.) an oxygen molecule from: O (0.500 0.5
>> 0.0) to O(0.499 0.5 0.0).
>>
>> Please may someone shed some light on to why this is the case, and if
>> there is anything wrong with my input.
>>
>> Thanks
>>
>> Zarah
>> Zbaiyee at gmail.com
>>
>> &CONTROL
>> calculation = "relax",
>> prefix = "CO",
>> pseudo_dir = "/Users/zarahbaiyee/espresso-5.0.2/pseudo",
>> outdir = "/Users/zarahbaiyee/tmp",
>> forc_conv_thr = 1.0D-5
>> /
>> &SYSTEM
>> ibrav = 0,
>> nat = 5,
>> ntyp = 3,
>> ecutwfc = 60,
>> ecutrho = 420,
>> /
>> &ELECTRONS
>> conv_thr= 1.D-7,
>> mixing_beta = 0.7D0,
>> electron_maxstep = 400
>> /
>> &IONS
>> /
>> CELL_PARAMETERS bohr
>> 7.60 0.0 0.0
>> 0.0 7.60 0.0
>> 0.0 0.0 7.60
>> ATOMIC_SPECIES
>> Ba 137.32 Ba.pbe-mt_fhi.UPF
>> Fe 55.84 Fe.pbe-mt_fhi.UPF
>> O 15.99 O.pbe-kjpaw.UPF
>> ATOMIC_POSITIONS {crystal}
>> Ba 0.000 0.0 0.0 0 0 0
>> Fe 0.500 0.5 0.5
>> O 0.000 0.5 0.5
>> O 0.500 0.0 0.5
>> O 0.500 0.5 0.0
>> K_POINTS {automatic}
>> 9 9 9 0 0 0
>>
>>
>
> --
> _
> Filipe Camargo Dalmatti Alves Lima
> PhD Student
> University of S?o Paulo, Physics Institute, Materials Physics Department,
> Nanomol Group, Brazil.
> Phones:(11) 3091-6881 (USP)
> (11) 97408-2755 (Vivo)
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] Fwd: Basic Relax Calculation issues
On Fri, 2014-03-07 at 17:25 +0800, Zarah Baiyee wrote: > Apologies this is the error message: > Error in routine read_namelists (5010): > reading namelist cell there is an error in namelist cell (hint: namelist cell starts with "&cell", ends with "/") P. > Thank you for your response. > > > Kind Regards > > > Zarah > > > On Fri, Mar 7, 2014 at 3:56 PM, Paolo Giannozzi > wrote: > On Fri, 2014-03-07 at 14:49 +0800, Zarah Baiyee wrote: > > > I am currently having a few issues with VC-Relax input > > files and cannot seem to get them to work, please find > > attached. I consistently get an error: > > > > Error in routine dos (1): > > reading dos namelist > > > this happens during the calculation of the density of > states (code dos.x), not during the variable-cell > optimization (code pw.x) > > P. > > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Fwd: Basic Relax Calculation issues
On Fri, 2014-03-07 at 14:49 +0800, Zarah Baiyee wrote: > I am currently having a few issues with VC-Relax input > files and cannot seem to get them to work, please find > attached. I consistently get an error: > > Error in routine dos (1): > reading dos namelist this happens during the calculation of the density of states (code dos.x), not during the variable-cell optimization (code pw.x) P. -- Paolo Giannozzi, Dept. Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Fwd: Basic Relax Calculation issues
Dear Zarah,
Have you ever considered that you may want the cell relaxation in this
case? (vc-relax)
It will optimize the cell parameter in order to minimize the total energy.
You'll see that the system might have lots of interactions.
If you want to explore defects in crystals or surfaces, relaxing the
internal coordinates are essential since you are breaking the symmetry in
some way: by having impurities; surface interaction; vacancy defects and
etc. If it is the case you want to explore, you will need to use a
supercell approach. Remember: crystals are built based on symmetry rules.
If you are really curious, you might try to change the cell symmetry just
to observe how the internal coordinations behave (just increase z by 0.2).
It may not converge, but you will see a lot interactions.
Best regards,
Filipe
On Friday, February 28, 2014, Zarah Baiyee wrote:
> Hi All,
>
> I am a new user to Quantum Espresso, therefore this may be a bit trivial
> but I any help would be very welcome.
>
> I am attempting a relax calculation using espresso version 5.0.2, for the
> geometry optimisation of a perovskite structure. For the input below, the
> calculation runs, however does not compute any forces and convergence
> without geometry optimisation to the original structure, with 0 bfgs steps.
> I am able to perform an expected relaxation if alter the initial atomic
> positions to asymmetric: (i.e.) an oxygen molecule from: O (0.500 0.5
> 0.0) to O(0.499 0.5 0.0).
>
> Please may someone shed some light on to why this is the case, and if
> there is anything wrong with my input.
>
> Thanks
>
> Zarah
> Zbaiyee at gmail.com
>
> &CONTROL
> calculation = "relax",
> prefix = "CO",
> pseudo_dir = "/Users/zarahbaiyee/espresso-5.0.2/pseudo",
> outdir = "/Users/zarahbaiyee/tmp",
> forc_conv_thr = 1.0D-5
> /
> &SYSTEM
> ibrav = 0,
> nat = 5,
> ntyp = 3,
> ecutwfc = 60,
> ecutrho = 420,
> /
> &ELECTRONS
> conv_thr= 1.D-7,
> mixing_beta = 0.7D0,
> electron_maxstep = 400
> /
> &IONS
> /
> CELL_PARAMETERS bohr
> 7.60 0.0 0.0
> 0.0 7.60 0.0
> 0.0 0.0 7.60
> ATOMIC_SPECIES
> Ba 137.32 Ba.pbe-mt_fhi.UPF
> Fe 55.84 Fe.pbe-mt_fhi.UPF
> O 15.99 O.pbe-kjpaw.UPF
> ATOMIC_POSITIONS {crystal}
> Ba 0.000 0.0 0.0 0 0 0
> Fe 0.500 0.5 0.5
> O 0.000 0.5 0.5
> O 0.500 0.0 0.5
> O 0.500 0.5 0.0
> K_POINTS {automatic}
> 9 9 9 0 0 0
>
>
--
_
Filipe Camargo Dalmatti Alves Lima
PhD Student
University of S?o Paulo, Physics Institute, Materials Physics Department,
Nanomol Group, Brazil.
Phones:(11) 3091-6881 (USP)
(11) 97408-2755 (Vivo)
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[Pw_forum] Fwd: Basic Relax Calculation issues
Thank you both for your responses.
Paolo to clarify, only non-symmetric systems can be relaxed?
Regards
Zarah
On Fri, Feb 28, 2014 at 3:07 PM, Paolo Giannozzi
wrote:
> If forces are zero by symmetry, there is nothing to relax
>
> P.
>
> On Fri, 2014-02-28 at 13:06 +0800, Zarah Baiyee wrote:
> > Hi All,
> >
> >
> > I am a new user to Quantum Espresso, therefore this may be a bit
> > trivial but I any help would be very welcome.
> >
> >
> > I am attempting a relax calculation using espresso version 5.0.2, for
> > the geometry optimisation of a perovskite structure. For the input
> > below, the calculation runs, however does not compute any forces and
> > convergence without geometry optimisation to the original structure,
> > with 0 bfgs steps. I am able to perform an expected relaxation if
> > alter the initial atomic positions to asymmetric: (i.e.) an oxygen
> > molecule from: O (0.500 0.5 0.0) to O(0.499 0.5 0.0).
> >
> >
> > Please may someone shed some light on to why this is the case, and if
> > there is anything wrong with my input.
> >
> >
> > Thanks
> >
> >
> > Zarah
> > Zbaiyee at gmail.com
> >
> >
> > &CONTROL
> > calculation = "relax",
> > prefix = "CO",
> > pseudo_dir = "/Users/zarahbaiyee/espresso-5.0.2/pseudo",
> > outdir = "/Users/zarahbaiyee/tmp",
> > forc_conv_thr = 1.0D-5
> > /
> > &SYSTEM
> > ibrav = 0,
> > nat = 5,
> > ntyp = 3,
> > ecutwfc = 60,
> > ecutrho = 420,
> > /
> > &ELECTRONS
> > conv_thr= 1.D-7,
> > mixing_beta = 0.7D0,
> > electron_maxstep = 400
> > /
> > &IONS
> > /
> > CELL_PARAMETERS bohr
> > 7.60 0.0 0.0
> > 0.0 7.60 0.0
> > 0.0 0.0 7.60
> > ATOMIC_SPECIES
> > Ba 137.32 Ba.pbe-mt_fhi.UPF
> > Fe 55.84 Fe.pbe-mt_fhi.UPF
> > O 15.99 O.pbe-kjpaw.UPF
> > ATOMIC_POSITIONS {crystal}
> > Ba 0.000 0.0 0.0 0 0 0
> > Fe 0.500 0.5 0.5
> > O 0.000 0.5 0.5
> > O 0.500 0.0 0.5
> > O 0.500 0.5 0.0
> >
> > K_POINTS {automatic}
> > 9 9 9 0 0 0
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://pwscf.org/mailman/listinfo/pw_forum
>
> --
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] Fwd: Basic Relax Calculation issues
Hi All,
I am a new user to Quantum Espresso, therefore this may be a bit trivial
but I any help would be very welcome.
I am attempting a relax calculation using espresso version 5.0.2, for the
geometry optimisation of a perovskite structure. For the input below, the
calculation runs, however does not compute any forces and convergence
without geometry optimisation to the original structure, with 0 bfgs steps.
I am able to perform an expected relaxation if alter the initial atomic
positions to asymmetric: (i.e.) an oxygen molecule from: O (0.500 0.5
0.0) to O(0.499 0.5 0.0).
Please may someone shed some light on to why this is the case, and if there
is anything wrong with my input.
Thanks
Zarah
Zbaiyee at gmail.com
&CONTROL
calculation = "relax",
prefix = "CO",
pseudo_dir = "/Users/zarahbaiyee/espresso-5.0.2/pseudo",
outdir = "/Users/zarahbaiyee/tmp",
forc_conv_thr = 1.0D-5
/
&SYSTEM
ibrav = 0,
nat = 5,
ntyp = 3,
ecutwfc = 60,
ecutrho = 420,
/
&ELECTRONS
conv_thr= 1.D-7,
mixing_beta = 0.7D0,
electron_maxstep = 400
/
&IONS
/
CELL_PARAMETERS bohr
7.60 0.0 0.0
0.0 7.60 0.0
0.0 0.0 7.60
ATOMIC_SPECIES
Ba 137.32 Ba.pbe-mt_fhi.UPF
Fe 55.84 Fe.pbe-mt_fhi.UPF
O 15.99 O.pbe-kjpaw.UPF
ATOMIC_POSITIONS {crystal}
Ba 0.000 0.0 0.0 0 0 0
Fe 0.500 0.5 0.5
O 0.000 0.5 0.5
O 0.500 0.0 0.5
O 0.500 0.5 0.0
K_POINTS {automatic}
9 9 9 0 0 0
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[Pw_forum] Fwd: Basic Relax Calculation issues
If forces are zero by symmetry, there is nothing to relax
P.
On Fri, 2014-02-28 at 13:06 +0800, Zarah Baiyee wrote:
> Hi All,
>
>
> I am a new user to Quantum Espresso, therefore this may be a bit
> trivial but I any help would be very welcome.
>
>
> I am attempting a relax calculation using espresso version 5.0.2, for
> the geometry optimisation of a perovskite structure. For the input
> below, the calculation runs, however does not compute any forces and
> convergence without geometry optimisation to the original structure,
> with 0 bfgs steps. I am able to perform an expected relaxation if
> alter the initial atomic positions to asymmetric: (i.e.) an oxygen
> molecule from: O (0.500 0.5 0.0) to O(0.499 0.5 0.0).
>
>
> Please may someone shed some light on to why this is the case, and if
> there is anything wrong with my input.
>
>
> Thanks
>
>
> Zarah
> Zbaiyee at gmail.com
>
>
> &CONTROL
> calculation = "relax",
> prefix = "CO",
> pseudo_dir = "/Users/zarahbaiyee/espresso-5.0.2/pseudo",
> outdir = "/Users/zarahbaiyee/tmp",
> forc_conv_thr = 1.0D-5
> /
> &SYSTEM
> ibrav = 0,
> nat = 5,
> ntyp = 3,
> ecutwfc = 60,
> ecutrho = 420,
> /
> &ELECTRONS
> conv_thr= 1.D-7,
> mixing_beta = 0.7D0,
> electron_maxstep = 400
> /
> &IONS
> /
> CELL_PARAMETERS bohr
> 7.60 0.0 0.0
> 0.0 7.60 0.0
> 0.0 0.0 7.60
> ATOMIC_SPECIES
> Ba 137.32 Ba.pbe-mt_fhi.UPF
> Fe 55.84 Fe.pbe-mt_fhi.UPF
> O 15.99 O.pbe-kjpaw.UPF
> ATOMIC_POSITIONS {crystal}
> Ba 0.000 0.0 0.0 0 0 0
> Fe 0.500 0.5 0.5
> O 0.000 0.5 0.5
> O 0.500 0.0 0.5
> O 0.500 0.5 0.0
>
> K_POINTS {automatic}
> 9 9 9 0 0 0
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Fwd: Basic Relax Calculation issues
Hi,
You need to tell the code to print the force and the stress by setting
tstress=.true. tprnfor=.true. , under the control block.
Regards,
---
Present Address
Condensed Matter Sector,
International School for Advanced Studies(SISSA)
Via Bonomea, 265, 34136 Trieste,
Italy.
e-mail:badetunj at sissa.it
---
Permanent Address
Adetunji Bamidele Ibrahim(PhD Student)
Department of physics,University of Agriculture,
Abeokuta, Ogun State,Nigeria.
Tel: +2348060270603
---
"Lord give me a place to stand, and i will move the earth"
On Friday, February 28, 2014 6:08 AM, Zarah Baiyee
wrote:
Hi All,?
I am a new user to Quantum Espresso, therefore this may be a bit trivial but I
any help would be very welcome.?
I am attempting a relax calculation using espresso version 5.0.2, for the
geometry optimisation of a perovskite structure. For the input below, the
calculation runs, however does not compute any forces and convergence without
geometry optimisation to the original structure, with 0 bfgs steps. I am able
to perform an expected relaxation if alter the initial atomic positions to
asymmetric: (i.e.) ?an oxygen molecule from: ?O (0.500 ?0.5 ?0.0) to O(0.499
0.5 0.0).?
Please may someone shed some light on to why this is the case, and if there is
anything wrong with my input. ?
Thanks
Zarah
Zbaiyee at gmail.com
&CONTROL
? calculation ?= "relax",
? prefix ? ? ? = "CO",
? pseudo_dir ? = "/Users/zarahbaiyee/espresso-5.0.2/pseudo",
? outdir ? ? ? = "/Users/zarahbaiyee/tmp",
? forc_conv_thr = 1.0D-5
/
&SYSTEM
? ibrav ? ? = 0,
? nat ? ? ? = 5,
? ntyp ? ? ?= 3,
? ecutwfc ? = 60,
? ecutrho ? = 420,
/
&ELECTRONS
? conv_thr ? ?= 1.D-7,
? mixing_beta = 0.7D0,
? electron_maxstep = 400
/
&IONS
/
CELL_PARAMETERS bohr
?7.60 ?0.0 ?0.0
?0.0 ?7.60 ?0.0
?0.0 ?0.0 ?7.60
ATOMIC_SPECIES
?Ba ?137.32 Ba.pbe-mt_fhi.UPF
?Fe ?55.84 Fe.pbe-mt_fhi.UPF
?O ? 15.99 O.pbe-kjpaw.UPF
ATOMIC_POSITIONS {crystal}
Ba ?0.000 ?0.0 ?0.0 ?0 0 0?
Fe ?0.500 ?0.5 ?0.5
O ? 0.000 ?0.5 ?0.5
O ? 0.500 ?0.0 ?0.5
O ? 0.500 ?0.5 ?0.0
K_POINTS {automatic}
9 9 9 0 0 0
___
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