[Pw_forum] problem in vc-relax
On Oct 4, 2011, at 22:23 , Alexander G. Kvashnin wrote: > I'm using QE 4.2.1. > 4.1.3 and 4.3 also didn't work go into tests/ and run "./check-pw.x.j lattice-ibrav*in". Does it work? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] problem in vc-relax
On Oct 4, 2011, at 21:34 , Alexander G. Kvashnin wrote: > from calbec : error # 1 > size mismatch > Has anyone known what's problem? input file attached. it works for me. What version of QE are you using? P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] problem with ibrav = -12
On Tue, 2011-10-04 at 12:01 +0200, jose manuel menendez montes wrote: > According to the manual: "Alternate choice (ibrav=-12) uses b as unique > axis: v1 = (a,0,0), v2 = (0,b,0), v3 = (a*sin(beta),0,c*cos(beta)) > where beta is the angle between axis a and c". That is, a and b are > correct but c is not. Instead of (a*sin(beta),0,c*cos(beta)), we are > getting (c*cos(beta),0,c*sin(beta)). Am I doing anything wrong? you did nothing wrong. I think that the manual is wrong: v3 = (c*sin(beta),0,c*cos(beta)) Thank you for remarking this P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] problem in vc-relax
Hello to all,
I have tried for the vc-relax of Mo2C hexagonal system, job is not done
properly it come out in between and the atomic positions
what I have given in the input file and what I am getting in the out file is
different.
(i) Why the crystal positions changes. what I think that the nature of the
atomic postions must be retained.
In Input file
ATOMIC_POSITIONS (alat)
C0.00 0.00 0.00
Mo 0.333 0.66 0.25
Mo 0.666 0.33 0.75
In out file we get
CELL_PARAMETERS (alat= 5.67296009)
0.946518633 0.001215132 -0.004855406
-0.474470641 0.819090796 -0.000958606
0.009278926 0.007480907 1.741942673
ATOMIC_POSITIONS (alat)
C0.156590059 0.041446237 -0.212516996
Mo 0.157761886 0.589915381 0.269109338
Mo 0.636664528 0.321113609 1.041609035
(ii) why cell_parameter changes in the out file . (I think that for
hexagonal system it must be what given in the input file)
my input file
&control
calculation='vc-relax'
restart_mode='from_scratch',
pseudo_dir = '/home/ashish/softwares/espresso/pseudo/',
outdir='/home/ashish/dft/espresso_mo2c/test1/tmp_espresso/'
prefix='mo2c'
tprnfor = .true.,
tstress = .true.
/
&system
ibrav=4, celldm(1) =5.672960087 , celldm(3)=1.573617588 , nat=3, ntyp=2,
nspin = 1, starting_magnetization(1)=0.7,
ecutwfc = 24.0, ecutrho = 288.0,
occupations='smearing', smearing='methfessel-paxton', degauss=0.02
/
&electrons
diagonalization='cg'
conv_thr = 1.0e-8
mixing_beta = 0.7
/
&ions
ion_dynamics='bfgs'
/
&cell
cell_dynamics='bfgs'
/
ATOMIC_SPECIES {crystal}
C 12.01 C.pw91-van_ak.UPF
Mo 95.94 Mo.pw91-n-van.UPF
ATOMIC_POSITIONS
C 0.0 0.0 0.0
Mo 1/3 2/3 1/4
Mo 2/3 1/3 3/4
K_POINTS automatic
4 4 4 0 0 0
can any one help me. What is the mistake (in my input file or else)
with best wishes
Ashish
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[Pw_forum] problem in vc-relax
If you know where the atoms and the cell should be, then you do not need
vc-relax (not even relax)...
but the code apparently disagrees with your thoughts.
trying to figure out why is probably going to increase your understanding.
have you visualized the initial and final configuration by XCrysDen or
other visualization tool?
is it what you think ?
stefano
On 10/04/2011 11:43 AM, Ashish Kumar wrote:
> Hello to all,
>
> I have tried for the vc-relax of Mo2C hexagonal system, job is not done
> properly it come out in between and the atomic positions
>
> what I have given in the input file and what I am getting in the out file is
> different.
> (i) Why the crystal positions changes. what I think that the nature of the
> atomic postions must be retained.
>
> In Input file
> ATOMIC_POSITIONS (alat)
> C0.00 0.00 0.00
> Mo 0.333 0.66 0.25
> Mo 0.666 0.33 0.75
>
>
>
> In out file we get
>
> CELL_PARAMETERS (alat= 5.67296009)
> 0.946518633 0.001215132 -0.004855406
>-0.474470641 0.819090796 -0.000958606
> 0.009278926 0.007480907 1.741942673
>
> ATOMIC_POSITIONS (alat)
> C0.156590059 0.041446237 -0.212516996
> Mo 0.157761886 0.589915381 0.269109338
> Mo 0.636664528 0.321113609 1.041609035
>
>
>
>
> (ii) why cell_parameter changes in the out file . (I think that for
> hexagonal system it must be what given in the input file)
>
>
> my input file
>
> &control
> calculation='vc-relax'
> restart_mode='from_scratch',
> pseudo_dir = '/home/ashish/softwares/espresso/pseudo/',
> outdir='/home/ashish/dft/espresso_mo2c/test1/tmp_espresso/'
> prefix='mo2c'
> tprnfor = .true.,
> tstress = .true.
> /
> &system
> ibrav=4, celldm(1) =5.672960087 , celldm(3)=1.573617588 , nat=3, ntyp=2,
> nspin = 1, starting_magnetization(1)=0.7,
> ecutwfc = 24.0, ecutrho = 288.0,
> occupations='smearing', smearing='methfessel-paxton', degauss=0.02
> /
> &electrons
> diagonalization='cg'
> conv_thr = 1.0e-8
> mixing_beta = 0.7
> /
> &ions
>ion_dynamics='bfgs'
> /
> &cell
> cell_dynamics='bfgs'
> /
> ATOMIC_SPECIES {crystal}
> C 12.01 C.pw91-van_ak.UPF
> Mo 95.94 Mo.pw91-n-van.UPF
> ATOMIC_POSITIONS
> C 0.0 0.0 0.0
> Mo 1/3 2/3 1/4
> Mo 2/3 1/3 3/4
>
> K_POINTS automatic
> 4 4 4 0 0 0
>
>
> can any one help me. What is the mistake (in my input file or else)
>
>
> with best wishes
> Ashish
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
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[Pw_forum] problem in vc-relax
Yes, I check that, it works On 4 October 2011 13:27, Paolo Giannozzi wrote: > > On Oct 4, 2011, at 22:23 , Alexander G. Kvashnin wrote: > > > I'm using QE 4.2.1. > > 4.1.3 and 4.3 also didn't work > > go into tests/ and run "./check-pw.x.j lattice-ibrav*in". > Does it work? > > P. > --- > Paolo Giannozzi, Dept of 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://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely yours *Alexander G. Kvashnin* Second year of master degree study Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111004/ede7dfcb/attachment-0001.htm
[Pw_forum] problem in vc-relax
I'm using QE 4.2.1. 4.1.3 and 4.3 also didn't work On 4 October 2011 13:21, Paolo Giannozzi wrote: > > On Oct 4, 2011, at 21:34 , Alexander G. Kvashnin wrote: > > > from calbec : error # 1 > > size mismatch > > > Has anyone known what's problem? input file attached. > > it works for me. What version of QE are you using? > > P. > --- > Paolo Giannozzi, Dept of 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://www.democritos.it/mailman/listinfo/pw_forum > -- Sincerely yours *Alexander G. Kvashnin* Second year of master degree study Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia -- next part ------ An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111004/86afdf8b/attachment.htm
[Pw_forum] problem in vc-relax
Dear QE users, I have some trouble with obtaining energy of atomic hydrogen using LDA pseudopotentials. When I ran my calculations I have the following error: from calbec : error # 1 size mismatch But when I try to use GGA pseudos I haven't got this error, and calculation done successfully Has anyone known what's problem? input file attached. Thanks for any advice -- Sincerely yours *Alexander G. Kvashnin* Second year of master degree study Moscow Institute of Physics and Technology http://mipt.ru/ 141700, Institutsky lane 9, Dolgoprudny, Moscow Region, Russia Junior research scientist Technological Institute for Superhard and Novel Carbon Materials http://www.ntcstm.troitsk.ru/ 142190, Central'naya St. 7a, Troitsk, Moscow Region, Russia -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111004/a641cd36/attachment.htm -- next part -- A non-text attachment was scrubbed... Name: input_H.opt Type: application/octet-stream Size: 890 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20111004/a641cd36/attachment.obj
[Pw_forum] problem in vc-relax
ATOMIC_POSITIONS {crystal}
C0.00 0.00 0.00
Mo 0.333 0.66 0.25
Mo 0.666 0.33 0.75
This will work for hexagonal system.
Quoting "Arles V. Gil Rebaza" :
> Hi Ashish Kumar, if you don't know: vc-relax means variable-cell relax. So,
> you're doing this kind of calculation, where the default is relax all cell
> parameters ( axis, angles, position). You can choose which parameters are
> fixed or which parameters are relaxed, please read the QE manual, the
> section &CELL , the variable "cell_dofree"
>
> Best.
>
> PhD stud Arles V. Gil Rebaza
> IFLP - Argentina
>
> 2011/10/4 Ashish Kumar
>
>> Hello to all,
>>
>> I have tried for the vc-relax of Mo2C hexagonal system, job is not done
>> properly it come out in between and the atomic positions
>>
>> what I have given in the input file and what I am getting in the out file
>> is different.
>> (i) Why the crystal positions changes. what I think that the nature of the
>> atomic postions must be retained.
>>
>> In Input file
>> ATOMIC_POSITIONS (alat)
>> C0.00 0.00 0.00
>> Mo 0.333 0.66 0.25
>> Mo 0.666 0.33 0.75
>>
>>
>>
>> In out file we get
>>
>> CELL_PARAMETERS (alat= 5.67296009)
>>0.946518633 0.001215132 -0.004855406
>> -0.474470641 0.819090796 -0.000958606
>>0.009278926 0.007480907 1.741942673
>>
>> ATOMIC_POSITIONS (alat)
>> C0.156590059 0.041446237 -0.212516996
>> Mo 0.157761886 0.589915381 0.269109338
>> Mo 0.636664528 0.321113609 1.041609035
>>
>>
>>
>>
>> (ii) why cell_parameter changes in the out file . (I think that for
>> hexagonal system it must be what given in the input file)
>>
>>
>> my input file
>>
>> &control
>> calculation='vc-relax'
>> restart_mode='from_scratch',
>> pseudo_dir = '/home/ashish/softwares/espresso/pseudo/',
>> outdir='/home/ashish/dft/espresso_mo2c/test1/tmp_espresso/'
>> prefix='mo2c'
>> tprnfor = .true.,
>> tstress = .true.
>> /
>> &system
>> ibrav=4, celldm(1) =5.672960087 , celldm(3)=1.573617588 , nat=3,
>> ntyp=2,
>> nspin = 1, starting_magnetization(1)=0.7,
>> ecutwfc = 24.0, ecutrho = 288.0,
>> occupations='smearing', smearing='methfessel-paxton', degauss=0.02
>> /
>> &electrons
>> diagonalization='cg'
>> conv_thr = 1.0e-8
>> mixing_beta = 0.7
>> /
>> &ions
>> ion_dynamics='bfgs'
>> /
>> &cell
>> cell_dynamics='bfgs'
>> /
>> ATOMIC_SPECIES {crystal}
>> C 12.01 C.pw91-van_ak.UPF
>> Mo 95.94 Mo.pw91-n-van.UPF
>> ATOMIC_POSITIONS
>> C 0.0 0.0 0.0
>> Mo 1/3 2/3 1/4
>> Mo 2/3 1/3 3/4
>>
>> K_POINTS automatic
>> 4 4 4 0 0 0
>>
>>
>> can any one help me. What is the mistake (in my input file or else)
>>
>>
>> with best wishes
>> Ashish
>>
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
>
> --
> ###-> Arles V. <-###
>
[Pw_forum] problem with ibrav = -12
Dear All, Has anyone used the new setting for the P monoclinic Bravais lattice (ibrav=-12)? Using 4.3.2 version or the svn latest one everything goes smooth but when it comes to analyse the crystal vectors, it turns out to work out a completely different thing from what it is said in the manual (INPUT_PW.html). The relevant part of the output is pasted below: celldm(1)= 7.982458 celldm(2)= 1.638821 celldm(3)= 1.861446 celldm(4)= 0.00 celldm(5)= -0.167251 celldm(6)= 0.00 crystal axes: (cart. coord. in units of alat) a(1) = ( 1.00 0.00 0.00 ) a(2) = ( 0.00 1.638821 0.00 ) a(3) = ( -0.311328 0.00 1.835226 ) According to the manual: "Alternate choice (ibrav=-12) uses b as unique axis: v1 = (a,0,0), v2 = (0,b,0), v3 = (a*sin(beta),0,c*cos(beta)) where beta is the angle between axis a and c". That is, a and b are correct but c is not. Instead of (a*sin(beta),0,c*cos(beta)), we are geting (c*cos(beta),0,c*sin(beta)). Am I doing anything wrong? Any help would be very much appreciated. J.M. Menendez Universidad de Oviedo (Spain) Departamento de Quimica Fisica y Analitica http://www.malta-consolider.com
[Pw_forum] projwfc.x error
Sorry that I was using espresso-4.2. When I use a newer version, it works now. From: pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] On Behalf Of Paolo Giannozzi [giann...@democritos.it] Sent: Tuesday, October 04, 2011 3:11 AM To: PWSCF Forum Subject: Re: [Pw_forum] projwfc.x error On Wed, 2011-09-28 at 23:04 -0400, Zhiting Tian wrote: > from d_matrix_so : error #19 > D_S (j=1/2) for this symmetry operation is not unitary please provide an example with all needed data to be reproduced, or file a bug report on qe-forge.org P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy ___ Pw_forum mailing list Pw_forum at pwscf.org http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] problem in vc-relax
On 10/04/2011 05:43 AM, Ashish Kumar wrote: > Hello to all, > > I have tried for the vc-relax of Mo2C hexagonal system, job is not done > properly it come out in between and the atomic positions > > what I have given in the input file and what I am getting in the out > file is different. > (i) Why the crystal positions changes. what I think that the nature of > the atomic postions must be retained. > > In Input file > ATOMIC_POSITIONS (alat) > C0.00 0.00 0.00 > Mo 0.333 0.66 0.25 > Mo 0.666 0.33 0.75 > alat tells the program that the coordinates are Cartesian positions. You want "crystal" here. -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC
[Pw_forum] problem in vc-relax
Hi Ashish Kumar, if you don't know: vc-relax means variable-cell relax. So,
you're doing this kind of calculation, where the default is relax all cell
parameters ( axis, angles, position). You can choose which parameters are
fixed or which parameters are relaxed, please read the QE manual, the
section &CELL , the variable "cell_dofree"
Best.
PhD stud Arles V. Gil Rebaza
IFLP - Argentina
2011/10/4 Ashish Kumar
> Hello to all,
>
> I have tried for the vc-relax of Mo2C hexagonal system, job is not done
> properly it come out in between and the atomic positions
>
> what I have given in the input file and what I am getting in the out file
> is different.
> (i) Why the crystal positions changes. what I think that the nature of the
> atomic postions must be retained.
>
> In Input file
> ATOMIC_POSITIONS (alat)
> C0.00 0.00 0.00
> Mo 0.333 0.66 0.25
> Mo 0.666 0.33 0.75
>
>
>
> In out file we get
>
> CELL_PARAMETERS (alat= 5.67296009)
>0.946518633 0.001215132 -0.004855406
> -0.474470641 0.819090796 -0.000958606
>0.009278926 0.007480907 1.741942673
>
> ATOMIC_POSITIONS (alat)
> C0.156590059 0.041446237 -0.212516996
> Mo 0.157761886 0.589915381 0.269109338
> Mo 0.636664528 0.321113609 1.041609035
>
>
>
>
> (ii) why cell_parameter changes in the out file . (I think that for
> hexagonal system it must be what given in the input file)
>
>
> my input file
>
> &control
> calculation='vc-relax'
> restart_mode='from_scratch',
> pseudo_dir = '/home/ashish/softwares/espresso/pseudo/',
> outdir='/home/ashish/dft/espresso_mo2c/test1/tmp_espresso/'
> prefix='mo2c'
> tprnfor = .true.,
> tstress = .true.
> /
> &system
> ibrav=4, celldm(1) =5.672960087 , celldm(3)=1.573617588 , nat=3,
> ntyp=2,
> nspin = 1, starting_magnetization(1)=0.7,
> ecutwfc = 24.0, ecutrho = 288.0,
> occupations='smearing', smearing='methfessel-paxton', degauss=0.02
> /
> &electrons
> diagonalization='cg'
> conv_thr = 1.0e-8
> mixing_beta = 0.7
> /
> &ions
> ion_dynamics='bfgs'
> /
> &cell
> cell_dynamics='bfgs'
> /
> ATOMIC_SPECIES {crystal}
> C 12.01 C.pw91-van_ak.UPF
> Mo 95.94 Mo.pw91-n-van.UPF
> ATOMIC_POSITIONS
> C 0.0 0.0 0.0
> Mo 1/3 2/3 1/4
> Mo 2/3 1/3 3/4
>
> K_POINTS automatic
> 4 4 4 0 0 0
>
>
> can any one help me. What is the mistake (in my input file or else)
>
>
> with best wishes
> Ashish
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
###-> Arles V. <-###
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[Pw_forum] projwfc.x error
On Wed, 2011-09-28 at 23:04 -0400, Zhiting Tian wrote: > from d_matrix_so : error #19 > D_S (j=1/2) for this symmetry operation is not unitary please provide an example with all needed data to be reproduced, or file a bug report on qe-forge.org P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] images and pools
On Oct 1, 2011, at 14:37 , Charlie Eppes wrote: > I was wondering, in a system administrating point of view, how far > is varying the number of images and pools can affect the speed, > efficiency, and the results of execution?! I understand the basic > concepts of them, but how dependent on the specific input and > purpose are they?? can we look to them as pure system and network > variables or are they highly dependent on the specific task?? I am not sure I understand your question, but as a rule, the effectiveness of all kinds of parallelization depends quite a bit on both the available hardware/ software and on the specific calculation > do they affect the answer?? the final result? of course they don't (apart from small unavoidable numerical differences) P. --- Paolo Giannozzi, Dept of Chemistry&Physics&Environment, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
