[Pw_forum] Whether alpha_mix influence the final results in phonon calculation?
Dear all, I have found alpha_mix can help to converge in phonon calculation, but Whether it have an effect on the final results of phonon calculation? For example, whether it get different phonon spectrum when using different alpha_mix? Regards! -- Yue-Wen FANG, PhD candidate Key Laboratory of Polar Materials and Devices, Ministry of Education<http://clpm.ecnu.edu.cn/> East China Normal University <http://www.ecnu.edu.cn/english/> Phone: +86-18321726131 I will persist until I succeed! -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130405/17512b8e/attachment.html
[Pw_forum] using pp.x to calculate psi^2
mesh-grid, does it have the same sequence as the one in that input file? the index "kpoint" refers to the sequence of k-points as it appears in the output 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/20130405/16b4397d/attachment.html
[Pw_forum] Fermi energy reference point shift from 0 to -2
r = '/home//???/???/espresso-4.1.2/upf_files/' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 4, celldm(1) = 18.59490373, celldm(3) = 1.80, nat = 32, ntyp = 1, ecutwfc = 34.D0 , tot_charge = 0.00, occupations = 'smearing' , degauss = 0.02 , smearing = 'fermi-dirac' , / &ELECTRONS conv_thr = 1.D-8 , mixing_beta = 0.7D0 , / ATOMIC_SPECIES C 12.0 C.pw91-van_ak.UPF ATOMIC_POSITIONS (angstrom) C1.22657 0.709326753 1.99753 C2.45165 1.419486000 1.99874 C3.68208 0.709327391 1.99822 C4.92000 1.419486496 1.99944 C4.92000 2.839880146 2.00125 C6.14990 3.549976521 1.99907 C3.69010 3.549976521 1.99907 C2.45764 2.839879152 2.00067 C6.15792 0.709327391 1.99822 C7.38835 1.419486000 1.99874 C7.38236 2.839879152 2.00067 C8.61005 3.549975943 1.99891 C8.60654 4.970023341 2.00208 C9.84000 5.680120078 2.00200 C7.37382 5.680120770 2.00152 C6.14800 4.970024086 2.00150 C4.92000 5.680121474 2.00132 C3.69200 4.970024086 2.00150 C8.61343 0.709326753 1.99753 C9.84000 1.419485253 1.99874 C9.84000 2.839878353 2.00070 C 11.06995 3.549975943 1.99891 C 11.07346 4.970023341 2.00208 C 12.30618 5.680120770 2.00152 C 12.31137 7.100514050 2.00166 C 13.53464 7.810673002 1.99744 C 11.07830 7.810672948 1.99928 C9.84000 7.100514025 2.00287 C8.60170 7.810672948 1.99928 C7.379998863 7.100514050 2.00166 C6.14536 7.810673002 1.99744 C4.92000 7.100514261 2.00041 K_POINTS automatic 6 6 1 0 0 0 Thank you for your kind response. Shamsu Abubakar Postgraduate student Department of Physics University Putra Malaysia ___ 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/20130405/005cdf40/attachment.html
[Pw_forum] problem with bands.x
Dear Dr. Paolo Giannozzi The following lines are found in config.log file. *configure:3970: WARNING: parallel compiler mpif90 uses gfortran, but serial compiler ifort was detected* *configure:3972: WARNING: assuming F90=gfortran, discarding ifort* In my earlier post I have mentioned about ifort only for the basic information about compilers environment which I have. I could able to run pp.x for charge density calculation for the same example (silicon). On Fri, Apr 5, 2013 at 1:57 PM, Paolo Giannozzi wrote: > On Thu, 2013-04-04 at 15:02 +0530, Krishna chaitanya wrote: > > > > PWSCF version 5.0 compiled with intel fortran 12.1.6 version, > > gfortran 4.7.2 > > compiled with two different compilers at the same time? > Anyway: there is nothing wrong in the example, I cannot > reproduce the behavior you describe > > 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 > -- With Best Regards Dr. G. Krishna Chaitanya Assistant Professor School of Chemical Sciences SRTM University Nanded-431 606 India. -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130405/17ec3563/attachment.html
[Pw_forum] compatibility between pseudopotential choice and input_dft token
Dear Cristian
> Any combination is possible? Meaningful?
In my experience QE is (moderately) designed to let every user try his/her own
DFT-like cake... Focusing on long range correlation, van der Waals et
similia, there is some "wrong" physics you can avoid. For instance
> For example, can I safely set input_dft="vdw-df"
> and choose a LDA pseudo (say C.pz-vbc.UPF)?
LDA is known to overbind, and has been sometimes used as a "poor replacement"
of vdW correlation (a horrible thing, in my opinion). Add a more correct
scheme like VDWDF to such tendency could lead to... cold fusion? :-)
> Or a GGA (say C.pbe-mt_fhi.UPF in my case)
All the vdW corrections (semiempirical DFTD2 included, london=.true., in
&system) are well tested with a given kind of xc functional. This is often
discussed in the related papers. If you are not certain of the functional
recipes, look into the funct.f90 file. But this is not a hard limit. You may
build your own functional, including vdW. I've tested, with PBE
pseudopotentials, an hybrid+vdW functional time ago ('sla+pw+hse+vdw1'), with
good
results on molecule-surface interactions.
HTH
Giuseppe
On Friday 05 April 2013 13:08:39 Cristian Degli Esposti Boschi wrote:
> Dear all,
>
> in these days I am doing some basic attempts using
> the implementation of van der Waals interactions within QE,
> taking for example carbon-based systems.
>
> My question is about the compatibility (both at the code
> level and even at the physical level, if the question is
> addressable in this forum) of the form chosen
> through the input_dft token on the one hand
> and of the actual pseudopotential file on the other hand.
>
> Any combination is possible? Meaningful?
>
> For example, can I safely set input_dft="vdw-df"
> and choose a LDA pseudo (say C.pz-vbc.UPF)?
>
> Or a GGA (say C.pbe-mt_fhi.UPF in my case)?
>
> The same with input_dft="vdw-df-c09" or
> "vdw-df2-c09" ?
>
> Thanks in advance for any help. Have a nice weekend.
>
> Cristian
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[Pw_forum] fix ions during relaxation / compile as a library?
On Fri, Apr 5, 2013 at 1:09 PM, Denis Davydov wrote:
> Dear Prof. Giannozzi, Dr. Paulatto
>
> thanks for your replies.
>
[...]
> my intention is to understand if it can be (from MPI point of view)
> sequentially combined with another parallel code (e.g. Lammps MD code).
> That is why I mentioned those C++ lines of MPI usage which
> take part of the given current communicator and (hypothetically)
> use them to create an instance of QE object.
>
> I know that QE is written in Fortran, but i read somewhere that
> at the very top level (say the main file) it's wrapped in C/C++,
> however, i can't find a confirmation to this in the sources.
it should not be that much of a stretch to do one by yourself. what
you'd need to do are roughly the following things:
- define a "world" module variable in the mp module that is
initialized by default to MPI_COMM_WORLD
- look for all places that use MPI_COMM_WORLD (or mpi_comm_world) and
replace it with that variable
- write a fortran 77 style mp_library_init function that is callable
from a C wrapper so it can initialize your "world" variable in the mp
module to the custom communicator that you have split off the world
communicator
- in the c wrapper you split the communicator and then translate it
into a fortran communicator using MPI_Comm_c2f()
at this point, you should be mostly set and only need to write a
suitable replacement for pwscf.f90
as you can see, it does things in a very similar matter than LAMMPS.
if you need more help with this, i am happy to collaborate. it would
probably only take me a few hours on a rainy sunday afternoon to get a
working prototype done. i've done similar things before and know a
little bit of both codes. ;-)
axel.
PROGRAM pwscf
!
!
! ... Main program calling one instance of Plane Wave
Self-Consistent Field code
!
USE environment, ONLY : environment_start, environment_end
USE io_global, ONLY : ionode, ionode_id, stdout
USE mp_global, ONLY : mp_startup
USE read_input,ONLY : read_input_file
USE command_line_options, ONLY: input_file_
!
IMPLICIT NONE
LOGICAL :: conv
!
!
CALL mp_startup ( )
CALL environment_start ( 'PWSCF' )
!
CALL read_input_file ('PW', input_file_ )
!
! ... Perform actual calculation
!
CALL run_pwscf ( conv )
!
CALL stop_run( conv )
!
STOP
!
END PROGRAM pwscf
>
>
> Kind regards,
> Denis
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
Dr. Axel Kohlmeyer akohlmey at gmail.com http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.
[Pw_forum] fix ions during relaxation / compile as a library?
Dear Prof. Giannozzi, Dr. Paulatto
thanks for your replies.
On 05.04.2013, at 12:00, pw_forum-request at pwscf.org wrote:
>
>> 2) is it possible to compile QE as a library (preferably C++) and
>> then provide an MPI communicator to be used, something like:
>>
>>MPI_Comm_split(MPI_COMM_WORLD,my_color,0,&comm_qe);
>>qe = new QE_NS::QE(0,NULL,comm_qe);
>>qe.run("my_input.txt");
> No... not yet at least. It's not that easy to do. I know that some work
> in this direction has been done, and IS being done right now. i.e. PW
> can be used as a plugin for PLUMED (or PLUMED as a plugin for PW,
> depending on the website you're on); so maybe you can study and reuse
> this interface mechanism.
i will have a look.
>> 2) is it possible to compile QE as a library (preferably C++) and
>> then provide an MPI communicator to be used, something like:
>>
>> MPI_Comm_split(MPI_COMM_WORLD,my_color,0,&comm_qe);
>> qe = new QE_NS::QE(0,NULL,comm_qe);
>> qe.run("my_input.txt");
>
> the above syntax is completely obscure to me, but it is definitely
> possible to call QE from a C++ code: it has been done in the past.
> QE is actually already a library, with a few small main codes that
> call all the rest, but it is not yet in a very usable form as a
> library.
my intention is to understand if it can be (from MPI point of view)
sequentially combined with another parallel code (e.g. Lammps MD code).
That is why I mentioned those C++ lines of MPI usage which
take part of the given current communicator and (hypothetically)
use them to create an instance of QE object.
I know that QE is written in Fortran, but i read somewhere that
at the very top level (say the main file) it's wrapped in C/C++,
however, i can't find a confirmation to this in the sources.
Kind regards,
Denis
[Pw_forum] compatibility between pseudopotential choice and input_dft token
Dear all, in these days I am doing some basic attempts using the implementation of van der Waals interactions within QE, taking for example carbon-based systems. My question is about the compatibility (both at the code level and even at the physical level, if the question is addressable in this forum) of the form chosen through the input_dft token on the one hand and of the actual pseudopotential file on the other hand. Any combination is possible? Meaningful? For example, can I safely set input_dft="vdw-df" and choose a LDA pseudo (say C.pz-vbc.UPF)? Or a GGA (say C.pbe-mt_fhi.UPF in my case)? The same with input_dft="vdw-df-c09" or "vdw-df2-c09" ? Thanks in advance for any help. Have a nice weekend. Cristian -- Cristian Degli Esposti Boschi CNR-IMM, Sezione di Bologna, via Gobetti, 101, 40129, Bologna, Italia tel. ++39 051 6399152, fax ++39 051 6399216 email: degliesposti -AT- bo.imm.cnr.it web: www.bo.imm.cnr.it/site/staff/personal_pages/degliesposti/
[Pw_forum] parallel execution
Dear all, I actually did some calculations with my pc and i passed another group that they are creating an account for me on a machine (Parallel calculation). I saw an example of a script they use, rely on input (using the code VASP). My question is how can i write a script that i can "call" the pseudopotentials, input ...? the script contains loops. thankx == sakhraoui taoufik laboratoire de la mati?re condens?e et des nanosciences Facult? des sciences de Monastir === -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130405/ae26a22d/attachment.html
[Pw_forum] problem with bands.x
On Fri, 2013-04-05 at 14:31 +0530, Krishna chaitanya wrote: > configure:3970: WARNING: parallel compiler mpif90 uses gfortran, but > serial compiler ifort was detected > configure:3972: WARNING: assuming F90=gfortran, discarding ifort so it's compiled with gfortran, not intel. Recently I have heard about a potential problem with gfortran+MKL that might explain your error. Go into the make.sys file, locate line starting with "BLAS_LIBS". If it looks like this: BLAS_LIBS = -lmkl_intel_lp64 -lmkl_sequential -lmkl_core change it as follows BLAS_LIBS = -lmkl_gf_lp64 -lmkl_sequential -lmkl_core remove all executable (*.x) files, recompile 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] problem with bands.x
Dear Pandey Thank you for your post. I even tried to increase ecutwfc upto 50Ry and nbnd=16 but failed and got the same error. On Thu, Apr 4, 2013 at 9:36 PM, Bramha Pandey wrote: > You may be try with incresing the ecut cuoff value in your input file, it > may be around 18Ry and incresed it upto approx 35 Ry, if it works then see > the reason for that increased value of this ecut cutoff. > > > On Thu, Apr 4, 2013 at 3:49 PM, Krishna chaitanya < > krishnachaitanya.gunturu at gmail.com> wrote: > >> Dear Prof. Paolo Giannozzi >> >> My sincere apologies for the incomplete details about my issue. I am >> using PWSCF version 5.0 compiled with intel fortran 12.1.6 version, >> gfortran 4.7.2 and mpich 3.0.2 environment. >> >> When I am trying to do band structure calculation according to webpage * >> http://people.sissa.it/~degironc/QE-Tutorial/examples_pwscf_ex.tgz *I am >> getting the following error for silicon case. >> >> *Program received signal SIGSEGV: Segmentation fault - invalid memory >> reference.* >> * >> * >> *Backtrace for this error:* >> *#0 0x2B8949244F27* >> *#1 0x2B89492454F4* >> *#2 0x3D036302CF* >> *#3 0x2B894A53B270* >> *#4 0x2B894825748C* >> *#5 0x2B89473DC47D* >> *#6 0x411782 in cgracsc_ at cgracsc.f90:67* >> *#7 0x4084D8 in punch_band_ at bands.f90:331* >> *#8 0x40951E in do_bands at bands.f90:112* >> * >> * >> *[1]+ Segmentation fault ../bin/bands.x < bands.in > bands.out* >> >> Moreover nothing is written in bands.out and bands.dat files. I hope with >> this information I will get solution for the above error. >> >> >> >> On Wed, Apr 3, 2013 at 6:49 PM, Paolo Giannozzi > > wrote: >> >>> On Wed, 2013-04-03 at 11:22 +0530, Krishna chaitanya wrote: >>> >>> > Please suggest me how to solve this problem. >>> >>> please see page http://www.quantum-espresso.org/?page_id=26 >>> section "Reporting Bugs". There is no way anybody can suggest >>> anything without a clear explanation of which exact operations >>> have been done, on which version of the code, etc. etc. >>> >>> 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 >>> >> >> >> >> -- >> With Best Regards >> >> Dr. G. Krishna Chaitanya >> Assistant Professor >> School of Chemical Sciences >> SRTM University >> Nanded-431 606 >> India. >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > Thanks and Regards > Bramha Prasad Pandey > Indian School of Mines(ISM) > Dhanbad, INDIA. > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- With Best Regards Dr. G. Krishna Chaitanya Assistant Professor School of Chemical Sciences SRTM University Nanded-431 606 India. -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130405/c35af91c/attachment.html
[Pw_forum] problem with bands.x
On Thu, 2013-04-04 at 15:02 +0530, Krishna chaitanya wrote: > PWSCF version 5.0 compiled with intel fortran 12.1.6 version, > gfortran 4.7.2 compiled with two different compilers at the same time? Anyway: there is nothing wrong in the example, I cannot reproduce the behavior you describe 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] Mn PAW PP
Dear Pietro, Thanks a lot :) On Thu, Apr 4, 2013 at 12:22 PM, Pietro Bonfa' wrote: > Dear Mohnish, > > there's a Mn pseudopotential in the pslibrary: > > http://qe-forge.org/gf/project/pslibrary/ > > It's inside: paw_ps_collection_tot.job > > >From the code's comments: > # > # Be careful these PPs might have problems. > # > > Kind regards, > Pietro Bonfa' > > > > > On 04/04/13 10:13, mohnish pandey wrote: > > Dear QE users, > > > > Does anybody have Mn PAW PP. I checked on QE PP database but its not > > available. If anybody of you have it, can you please provide me? Thanks > > a lot in advance. > > > > -- > > Regards, > > MOHNISH, > > - > > Mohnish Pandey, > > PhD Student, > > Center for Atomic Scale Materials Design, > > Department of Physics, > > Technical University of Denmark > > - > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > Pietro Bonfa' - PhD student > Dipartimento di Fisica e Scienze della Terra "Macedonio Melloni" > Viale delle Scienze 7A > 43124 Parma - Italy > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130405/50990b3d/attachment.html
[Pw_forum] problems with pressure calculation
Dear Paolo, Thanks for your advice. The wild pressure oscillations dissapear using a smaller value of con_thr. >it looks like a nonlinear interaction between symmetry and insufficient >convergence of self-consistency. If you reduce the convergence >threshold >to conv_thr=1.0e-8 or so (default is 10e-6) the jumps disappear; same if >you use all symmetries, whether their fractional translation is >commensurate or not with the FFT grid (option use_all_frac). I guess >that the discrepancy wrt previous versions has a similar origin. >The default value for the convergence threshold is good if you are >interested in energies, reasonable if you are interested in forces, >not so good for stress and pressure Best regards -- Eduardo Menendez Proupin Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez *"Lograremos el anhelado desarrollo cuando sea la ciudadan?a, y no los cient?ficos, la que pida m?s ciencia para Chile." J. Babul* -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130405/6617e195/attachment.html
[Pw_forum] Fermi energy reference point shift from 0 to -2
10?? 3.549976521?? 1.99907 C??? 2.45764?? 2.839879152?? 2.00067 C??? 6.15792?? 0.709327391?? 1.99822 C??? 7.38835?? 1.419486000?? 1.99874 C??? 7.38236?? 2.839879152?? 2.00067 C??? 8.61005?? 3.549975943?? 1.99891 C??? 8.60654?? 4.970023341?? 2.00208 C??? 9.84000?? 5.680120078?? 2.00200 C??? 7.37382?? 5.680120770?? 2.00152 C??? 6.14800?? 4.970024086?? 2.00150 C??? 4.92000?? 5.680121474?? 2.00132 C??? 3.69200?? 4.970024086?? 2.00150 C??? 8.61343?? 0.709326753?? 1.99753 C??? 9.84000?? 1.419485253?? 1.99874 C??? 9.84000?? 2.839878353?? 2.00070 C?? 11.06995?? 3.549975943?? 1.99891 C?? 11.07346?? 4.970023341?? 2.00208 C?? 12.30618?? 5.680120770?? 2.00152 C?? 12.31137?? 7.100514050?? 2.00166 C?? 13.53464?? 7.810673002?? 1.99744 C?? 11.07830?? 7.810672948?? 1.99928 C??? 9.84000?? 7.100514025?? 2.00287 C??? 8.60170?? 7.810672948?? 1.99928 C??? 7.379998863?? 7.100514050?? 2.00166 C??? 6.14536?? 7.810673002?? 1.99744 C??? 4.92000?? 7.100514261?? 2.00041 ? K_POINTS automatic ? 6 6 1?? 0 0 0? ? Thank you for your kind response. ? Shamsu Abubakar Postgraduate student Department of Physics University Putra Malaysia -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130405/8e77a677/attachment.html
