Re: [Pw_forum] How to get band structure with hse correction in pwscf?
Dear Clarence
Of course something went wrong, but It is not possible to say what without a
careful debugging of all the input and output files that you are fully
entitled to perform!
Somebody is maybe more expert than me in the usage of plotband.x (Have you used
it to draw the attached band plot or is it hand-made?) and He/She can
likely give you better advice.
HTH
Giuseppe
On Wednesday, May 31, 2017 04:05:40 AM LEUNG Clarence wrote:
> Dear Giuseppe,
>
>
> Thanks for you very help suggestion. I follow your method. I use 20 automatic
> mesh and 10 additional point with wk = 0, which is obtained from
> Xcrysden.
>
> However, the resulting band structure is not good. It is noted that there are
> two part in the figure. Which part is the band structure?
>
> [cid:1e216ae8-158c-4c6d-97af-880d3d5a573e]
>
>
> Many thanks
>
> LIANG Xiongyi
>
> City University of Hong Kong
>
>
> 发件人: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> 代表 Giuseppe
> Mattioli <giuseppe.matti...@ism.cnr.it>
> 发送时间: 2017年5月12日 17:24:47
> 收件人: PWSCF Forum
> 主题: Re: [Pw_forum] 答复: How to get band structure with hse correction in pwscf?
>
>
> Yes, it is, if you want to use many k-points.
> Best
> Giuseppe
>
> On Friday, May 12, 2017 09:18:08 AM LEUNG Clarence wrote:
>
> > Dear Giuseppe,
> >
> >
> >
> >
> > Thank you very much for your kindly suggestion.
> >
> >
> >
> > Does HSE band structure calculation take a very long time?
> >
> >
> >
> >
> > Thanks.
> >
> >
> >
> >
> > Clarence
> >
> >
> >
> >
> > å‘件人: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> 代表
> > Giuseppe Mattioli <giuseppe.matti...@ism.cnr.it>
> > å‘é€æ—¶é—´: 2017å¹´5月12æ—¥ 16:57:38
> > 收件人: pw_forum@pwscf.org
> > 主题: Re: [Pw_forum] How to get band structure with hse correction in
> > pwscf?
> >
> >
> >
> >
> > Dear Clarence
> > You can only perform scf calculations with EXX, so you must find a
> > workaround. Let us suppose that your calculation is converged with this mesh
> >
> >
> >
> > K_POINTS {automatic}
> > 8, 8, 8, 0, 0, 0
> >
> >
> >
> > In the pw output you find the K_POINTS {tpiba} trasformation of your
> > automatic mesh, that is
> >
> >
> >
> > number of k points=29 gaussian smearing, width (Ry)= 0.0100
> >
> >cart. coord. in units 2pi/alat
> >
> > k(1) = ( 0.000 0.000 0.000), wk = 0.0039062
> > k(2) = ( -0.125 0.125 -0.125), wk = 0.0312500
> > k(3) = ( -0.250 0.250 -0.250), wk = 0.0312500
> > k(4) = ( -0.375 0.375 -0.375), wk = 0.0312500
> > k(5) = ( 0.500 -0.500 0.500), wk = 0.0156250
> > k(6) = ( 0.000 0.250 0.000), wk = 0.0234375
> > k(7) = ( -0.125 0.375 -0.125), wk = 0.0937500
> > k(8) = ( -0.250 0.500 -0.250), wk = 0.0937500
> > k(9) = ( 0.625 -0.375 0.625), wk = 0.0937500
> > k( 10) = ( 0.500 -0.250 0.500), wk = 0.0937500
> > k( 11) = ( 0.375 -0.125 0.375), wk = 0.0937500
> > k( 12) = ( 0.250 0.000 0.250), wk = 0.0468750
> > k( 13) = ( 0.000 0.500 0.000), wk = 0.0234375
> > k( 14) = ( -0.125 0.625 -0.125), wk = 0.0937500
> > k( 15) = ( 0.750 -0.250 0.750), wk = 0.0937500
> > k( 16) = ( 0.625 -0.125 0.625), wk = 0.0937500
> > k( 17) = ( 0.500 0.000 0.500), wk = 0.0468750
> > k( 18) = ( 0.000 0.750 0.000), wk = 0.0234375
> > k( 19) = ( 0.875 -0.125 0.875), wk = 0.0937500
> > k( 20) = ( 0.750 0.000 0.750), wk = 0.0468750
> > k( 21) = ( 0.000 -1.000 0.000), wk = 0.0117188
> > k( 22) = ( -0.250 0.500 0.000), wk = 0.0937500
> > k( 23) = ( 0.625 -0.375 0.875), wk = 0.1875000
> > k( 24) = ( 0.500 -0.250 0.750), wk = 0.0937500
> > k( 25) = ( 0.750 -0.25000
Re: [Pw_forum] DOS
Dear User Look into the post-processing examples... /path-to-espresso/Examples/PP/README HTH Giuseppe P.S. Please sign the posts to this forum with name and scientific affiliation. On Friday, May 12, 2017 04:24:11 PM Shishir Timilsena wrote: > i am new to Quantum Espresso. > can anyone help to find DOS, i have scf.in file for graphene - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] How to get band structure with hse correction in pwscf?
- Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] QE for aqueous solution?
Dear Ashkan I'm afraid I do not agree with you. Among many examples, I remember this now classical paper written by *very* skilled colleagues ;-) The influence of temperature and density functional models in ab initio molecular dynamics simulation of liquid water. J VandeVondele, F Mohamed, M Krack, J Hutter, M Sprik, M Parrinello The Journal of chemical physics 2005, 122, 014515. That was performed by using the CPMD (periodic+plane waves+pseudopotentials) suite of programs, if I remember well (by heart, because I'm abroad and I cannot access literature now), O-O g(R) was converged and in agreement with measurements by using a not so big periodic box and a not so long (initial equilibration + ~10 ps) simulation time. Maybe there are choices better than QE for this kind of ab initio simulation (CP2K? CPMD?), but I would not give it for granted... Best Giuseppe Quoting ashkan shekaari <sheka...@gmail.com>: > Dear Mattioli, > > Water is not a crystal and therefore it cannot be treated as a > periodic structure. > The aforementioned example provides only a naive picture of water as an > aqueous compartment leading to a crude approximation of the given system as > well. Moreover, QE is not best suited for DFMD simulations of large, > nonperiodic, liquid systems. > > Regards, > Ashkan > > *Ashkan Shekaari* > Plasma Physics Research Center > Science and Research Branch > I A U, 14778-93855 Tehran, Iran. > > On Sat, May 6, 2017 at 12:21 PM, Giuseppe Mattioli < > giuseppe.matti...@ism.cnr.it> wrote: > >> >> Dear David and Ashkan >> >> > You cannot simulate the system as periodic. You have to use a large super >> > cell with vacuum spaces along the three spatial directions. Moreover, you >> > can simulate the solution only via importing a large number of atomic >> > positions of the order of 25000 at least, which does not seem to be >> > feasible by QE even in case of using random generators unless you have a >> > supercomputer facility. >> >> This comments are misleading, if not wrong in some cases. >> First of all you can for sure perform ab initio molecular dynamics >> (aimd) simulations of a water solution in a periodic box, and you do >> not need a huge number of atoms. One of the cp.x examples provides >> starting points, see here >> /Your_Path_To_Espresso_6.1/Examples/CPV/example04 >> >> >> Does anyone know of examples, benchmarks, or recommendations? Would the >> >> X.blyp-van.ak pseudopotentials be appropriate? Any guidance or advice >> >> about parameter settings for this application would be much appreciated >> >> Yes, you can use ultrasoft pseudopotentials such as X.blyp-van.ak. >> They used to be old and well-tested vanderbilt ultrasoft >> pseudopotentials generated many years ago by Axel Kohlmeyer (ak). But >> if you are not familiar with this terminology (ultrasoft, >> norm-conserving, van, mt, rrkj, paw, ...) you should start with some >> tutorial on pseudopotentials, because you must be sure to use >> converged plane-wave and density cutoffs for a given set of >> pseudopotentials. >> >> There is a very large number of options that must be set in the cp.x >> input. I cannot review them here. But there are also tons of >> literature on aimd simulations of water solutions, and you will easily >> find something that will help to choice a lot of parameters (box >> dimensions, NVT, NVP, NVE dynamics, thermostats, ...) >> >> > Indeed, QE is not best suited for MD simulations and I strongly recommend >> > the gromacs package. >> >> Of course Ashkan might be right on a couple of points: if you have >> very big molecules weakly interacting with the solvent, and you are >> interested in the morphology of the solute only, then you have to >> perform very long md simulations and to use a large number of water >> molecules, and this might be costly and time-consuming if performed at >> an aimd level. If you want to study proton exchanges, reactions, >> dipole dynamics, ... you need aimd. You surely know whether your >> scientific task strictly requires aimd rather than model-potential md. >> >> HTH >> Giuseppe >> >> Quoting ashkan shekaari <sheka...@gmail.com>: >> >> > Indeed, QE is not best suited for MD simulations and I strongly recommend >> > the gromacs package. >> >> > You cannot simulate the system as periodic. You have to use a large super >> > cell with vacuum spaces along the three spatial directions. Moreover, you >> > can simulate the solution only via importing a large number of atomic &g
Re: [Pw_forum] QE for aqueous solution?
Dear David and Ashkan > You cannot simulate the system as periodic. You have to use a large super > cell with vacuum spaces along the three spatial directions. Moreover, you > can simulate the solution only via importing a large number of atomic > positions of the order of 25000 at least, which does not seem to be > feasible by QE even in case of using random generators unless you have a > supercomputer facility. This comments are misleading, if not wrong in some cases. First of all you can for sure perform ab initio molecular dynamics (aimd) simulations of a water solution in a periodic box, and you do not need a huge number of atoms. One of the cp.x examples provides starting points, see here /Your_Path_To_Espresso_6.1/Examples/CPV/example04 >> Does anyone know of examples, benchmarks, or recommendations? Would the >> X.blyp-van.ak pseudopotentials be appropriate? Any guidance or advice >> about parameter settings for this application would be much appreciated Yes, you can use ultrasoft pseudopotentials such as X.blyp-van.ak. They used to be old and well-tested vanderbilt ultrasoft pseudopotentials generated many years ago by Axel Kohlmeyer (ak). But if you are not familiar with this terminology (ultrasoft, norm-conserving, van, mt, rrkj, paw, ...) you should start with some tutorial on pseudopotentials, because you must be sure to use converged plane-wave and density cutoffs for a given set of pseudopotentials. There is a very large number of options that must be set in the cp.x input. I cannot review them here. But there are also tons of literature on aimd simulations of water solutions, and you will easily find something that will help to choice a lot of parameters (box dimensions, NVT, NVP, NVE dynamics, thermostats, ...) > Indeed, QE is not best suited for MD simulations and I strongly recommend > the gromacs package. Of course Ashkan might be right on a couple of points: if you have very big molecules weakly interacting with the solvent, and you are interested in the morphology of the solute only, then you have to perform very long md simulations and to use a large number of water molecules, and this might be costly and time-consuming if performed at an aimd level. If you want to study proton exchanges, reactions, dipole dynamics, ... you need aimd. You surely know whether your scientific task strictly requires aimd rather than model-potential md. HTH Giuseppe Quoting ashkan shekaari <sheka...@gmail.com>: > Indeed, QE is not best suited for MD simulations and I strongly recommend > the gromacs package. > You cannot simulate the system as periodic. You have to use a large super > cell with vacuum spaces along the three spatial directions. Moreover, you > can simulate the solution only via importing a large number of atomic > positions of the order of 25000 at least, which does not seem to be > feasible by QE even in case of using random generators unless you have a > supercomputer facility. > > On May 6, 2017 9:09 AM, "D J Anick" <david.an...@rcn.com> wrote: > >> Hello plane wavers, >> >> I am interested in using QE for a molecular dynamics simulation of an >> aqueous solution containing a solute, modeling it as a 3-D periodic cell. >> Principal questions would be about solvation shell geometries, distribution >> of configurations adopted by the solute, and H-bond duration / stability. >> >> Does anyone know of examples, benchmarks, or recommendations? Would the >> X.blyp-van.ak pseudopotentials be appropriate? Any guidance or advice >> about parameter settings for this application would be much appreciated. >> >> Thank you in advance, >> David Anick >> david.anick###rcn.com >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] semiempirical dispersion correction
Dear Tone Thank you for pointing out this! When I messed up D2 years ago, hardcoding was the only way. Best Giuseppe Tone Kokalj <tone.kok...@ijs.si> ha scritto: > On Thu, 2017-04-27 at 17:32 +0200, Giuseppe Mattioli wrote: >> Anyway, with D2 you can reconfigure the C6 >> coefficient of every species to exclude (maybe using dummy names for >> involved atoms) >> whatever atom you want. Look into mm_dispersion.f90, change the >> values and recompile the code. > > There is a much more elegant way to do this: you can change the > C6 coefficient of any atomic-type using the london_c6 variable in the > namelist, i.e.: > > http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm140629872257200 > > Best regards, Tone > -- > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax: +386-1-251-9385) > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] semiempirical dispersion correction
Dear Alexandra AFAIK, D3 is not implemented in QE If you want something better than D2 (not the best for metal surfaces, admittedly) you should use one of the (many) ab initio vdwdf approaches available in the code. Anyway, with D2 you can reconfigure the C6 coefficient of every species to exclude (maybe using dummy names for involved atoms) whatever atom you want. Look into mm_dispersion.f90, change the values and recompile the code. HTH Giuseppe On Thursday, April 27, 2017 05:16:24 PM Alexandra Davila wrote: > Dear QE-user, > > I would like to know if the semiempirical D3 dispersion correction > scheme of Grimme is in QE implemented. > And is it possible to exclude the dispersion correction from some metal > layers of my system? If yes, how? > > thanks a lot, - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Omit Atoms from Vibrational Energy Calculation
-0.129570.55411 > H 7.200991.90429 -0.77089 > H 5.086063.13466 -0.38544 > H 3.493212.351911.31441 > H 5.442031.16504 19.74289 > H 6.733570.52300 17.74347 > H 1.812221.05293 17.45492 > H 2.982751.43849 19.60480 > H 3.074220.42139 15.45283 > > K_POINTS automatic > 2 2 1 0 0 0 > > EOF > > module load espresso/5.4.0 > > ibrun pw.x < $INFILE > $OUTFILE # Run the executable named pw.x > > $INFILE = "$PREFIX.ph.in" > $OUTFILE = "$PREFIX.ph.out" > > cat > $INFILE << EOF > title_line > > > tr2_ph=1.0d-12, > amass(1)=47.88, > amass(2)=12.010, > amass(3)=16.00, > amass(4)=1.0, > epsil=.false., > !lraman=.true., > asr=.true., > prefix='$PREFIX', > fildyn='ANA.dyn', > / > 2 2 1 > EOF > > > module load espresso/5.4.0 > ibrun ph.x < $INFILE > $OUTFILE > > rm *.igk *.wfc* > rm -r *.save - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Convergence problem with Pb180Se180 Cluster optimization
> Use more intense kpoint mesh.
No, this is useless. 0D systems have molecular-like flat rather than dispersed
energy levels in the reciprocal space. There is no reason to sample the
Brillouin zone with more k-points.
HTH
Giuseppe
On Friday, April 21, 2017 05:06:42 PM ashkan shekaari wrote:
> Dear Naren,
> Increase ecut. Use more intense kpoint mesh.
>
> On Apr 21, 2017 4:50 PM, "Giuseppe Mattioli" <giuseppe.matti...@ism.cnr.it>
>
> wrote:
> > Dear Naren
> > Your calculation is very expensive, and calculations of 0D objects in a
> > plane-wave/PBC framework are often prone to convergence issues. This said,
> > you
> > can try to
> >
> > 1) perform a simple calculation of the PbSe unit cell with the same
> > pseudopotentials. Are there similar convergence problems? You are using hgh
> > that
> > are norm-conserving pseudopotentials (NCPP) and they could require a
> > richer pw basis set. I would not be surprised if, after proper convergence
> > tests
> > performed on the unit cell, you ended up with ecutwfc=70~80 Ry. There is
> > no need to specify ecutrho, anyway. It is fixed to a default ecutwfc*4 value
> > in the case of NCPP.
> >
> > 2) lower mixing_beta, even down to very small values such as 0.05~0.01.
> > Sometimes it helps to reach convergence (slowly but steady).
> >
> > It is impossible to say more without looking at you cluster, but if it is
> > simply cut out from the bulk along low-index directions (e.g., a cube) you
> > have to deal with a mess of surface dangling bonds that want to play nasty
> > charge displacements between occupied and unoccupied electronic levels,
> > even inducing a metallic character in your cluster. People used to
> > saturate such dangling bonds with pseudo-H atoms (H atoms having formal
> > charge
> > lower or higher than 1.0, depending on the formal valence of the saturated
> > atom). If you don't want to saturate the surface you must keep into account
> > the possibility that the cluster surface reconstruct, and you should
> > anticipate reconstruction trends by lplacing the atoms nearer to the
> > expected
> > final positions. It could be a very difficult task, look at the
> > instructive story of the Si 7x7 reconstruction in this movie!
> >
> > https://www.youtube.com/watch?v=BXdC0NhAMBY
> >
> > HTH
> > Giuseppe
> >
> > On Friday, April 21, 2017 04:06:06 AM Narendranath Ghosh wrote:
> > > Dear all!
> > >
> > >
> > >
> > > I am currently trying to optimizing a Pb180Se180 cluster using QE.
> > >
> > > But after 83 iterations it didnââ¬â¢t get converged.
> > >
> > > *Input *
> > >
> > > calculation='relax',
> > >
> > > outdir='/staging/op/NAREN_USC/PbSe_360_FINAL_based_Pb68Se68/OUTPUT',
> > >
> > > prefix='PbSe-360',
> > >
> > > pseudo_dir='/staging/op/NAREN_USC/PbSe_360_FINAL_based_
> >
> > Pb68Se68/pseudo',
> >
> > > verbosity='low',
> > >
> > > /
> > >
> > >
> > >
> > >
> > >
> > > ibrav=0,
> > >
> > > celldm(1)=90.7068539791d0,
> > >
> > > nat=360,
> > >
> > > ntyp=2,
> > >
> > > ecutwfc=30.0d0,
> > >
> > > ecutrho=120.0d0,
> > >
> > > input_dft='PBE',
> > >
> > > occupations='smearing',
> > >
> > > smearing='gaussian',
> > >
> > > degauss=0.002000d0,
> > >
> > > /
> > >
> > >
> > >
> > > diagonalization='david',
> > >
> > > mixing_mode='plain',
> > >
> > > mixing_beta=0.700d0,
> > >
> > > /
> > >
> > >
> > >
> > > /
> > >
> > > ATOMIC_SPECIES
> > >
> > > Pb 207.20d0 Pb.pbe-hgh.UPF
> > >
> > > Se 78.96d0 Se.pbe-hgh.UPF
> > >
> > > ATOMIC_POSITIONS {alat}
> > >
> > > Pb 0.483110d0 0.474050d0 0.499930d0
> > >
> > > Se 0.519080d0 0.527870d0 0.598110d0
> > >
> > > Se 0.590190d0 0.471260d0 0.215480d0
> > >
> > > ââ¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦
> >
> > ââ¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦Ã¢â¬Â¦.
> &
Re: [Pw_forum] Convergence problem with Pb180Se180 Cluster optimization
; > > > total energy =1659.36438352 Ry > > Harris-Foulkes estimate = -15989.48139862 Ry > > estimated scf accuracy< 138246.99363207 Ry > > > > Any comment to help me getting started is very much appreciated! > > > > Best regards, > > Naren > > > > > > > > *Dr. Narendra Nath Ghosh* > > *Research Associate* > > *University of Gour Banga* > > *Department of Chemistry* > > *Malda-732102* > > *India* > > *Phone: +919126667601* - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] one Question
Dear Altaf scf.out shows a fast on-the-fly estimate of atomic magnetization. It is not very accurate and its purpose is to check that your system is approximately converging to the desired/expected magnetic state. pdos.out contains the Lowdin partitioning of (valence) charge density projected on the pseudopotential atomic wavefunctions, instead. It is reliable in the limit of reliability of Lowdin charges. HTH Giuseppe On Monday, April 03, 2017 11:37:02 AM Altaf Ur Rahman wrote: > Dear Experts > I have 64 atom super cell of an a and b atom. I doped 4*4*1 supercell with > N atom then *scf.out* shows that local magnetic moment of *N-atom as > MM=2.51* but when i calculated* pdos.out* it shows MM of *N atom as MM=2.79 > *so my question as which one is reliable? > > Thanks in advance > > Altaf Ur Rahman > PhD Student > Department of Physics > Quaid-i-Azam University Islamabad Pakistan - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] NEB first_last_opt
Sorry, the only one *who* can think through it...:-)
G.
Quoting Aleksandra Oranskaia <aleksandra.oransk...@kaust.edu.sa>:
> Hello dear QE users,
>
> I have a question regarding pre-optimization of starting and ending
> points of NEB.
>
> Dealing with multi-scale simulation of a vacancy migration in a huge
> supercell (say, 350-400 atoms), should one make a pre-optimization
> of starting and ending points of a path?
>
> I tried both ways and came to the conclusion that pre-optimization
> pushes the system away from the minimum energy path (leading to the
> increased barriers), because pre-optimization implies too deep
> restructuring towards deeper minimums rather than the local minimums
> closest to the minimum energy pathway.
> In my opinion it is more physical if a migration corresponds to a
> minimum energy pathway AND minimum restructuring.
>
> If you would simulate vacancy migration in a huge supercell with NEB
> optimization, would you optimize starting and ending points? Why?
>
>
> Thanks in advance and hope to hear your opinions and reasonings,
>
> Regards,
> Alex.
> --
>
> --
> This message and its contents, including attachments are intended solely
> for the original recipient. If you are not the intended recipient or have
> received this message in error, please notify me immediately and delete
> this message from your computer system. Any unauthorized use or
> distribution is prohibited. Please consider the environment before printing
> this email.
>
> ___
> Pw_forum mailing list
> Pw_forum@pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
--
- Article premier - Les hommes naissent et demeurent
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ne peuvent être fondées que sur l'utilité commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la liberté,
la propriété, la sûreté et la résistance à l'oppression.
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
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Re: [Pw_forum] NEB first_last_opt
Dear Aleksandra > I tried both ways and came to the conclusion that pre-optimization > pushes the system away from the minimum energy path (leading to the > increased barriers) This is indeed the expected behavior. If your first and last images were potential energy minimum configurations, even if local ones, the pre-optimization 'relax' calculations would let them unchanged, or almost unchanged because only in the case of high symmetry systems input coordinates are "exactly" in a local minimum. This implies that your first and last images are not potential energy minimum configurations, and the code correctly optimizes them, and this of course lowers the potential energy and raises the potential energy barrier connecting the two configurations. > In my opinion it is more physical if a migration corresponds to a > minimum energy pathway AND minimum restructuring. I'm not sure I understand this sentence. If you don't start from/end to a local minimum why do you gain more physical insight into your NEB simulation? If you want to drive your system through some intermediate local minimum which permits the lowering of the global barriers across the PES, you can use the intermediate_image feature. If in the end you find the same high barriers then three interpretations can be given: 1) your initial physical guess is wrong and in the "real" system vacancies do not exist/do not migrate; 2) The DFT level of theory used to perform the NEB calculation is not accurate and does not provide reliable numbers for transition states/barriers; 3) the migration occur through some redox process in which there is a change in the charge state of the defect which lowers the barrier. You are the only one that can think through this... HTH Giuseppe Quoting Aleksandra Oranskaia <aleksandra.oransk...@kaust.edu.sa>: > Hello dear QE users, > > I have a question regarding pre-optimization of starting and ending > points of NEB. > > Dealing with multi-scale simulation of a vacancy migration in a huge > supercell (say, 350-400 atoms), should one make a pre-optimization > of starting and ending points of a path? > > I tried both ways and came to the conclusion that pre-optimization > pushes the system away from the minimum energy path (leading to the > increased barriers), because pre-optimization implies too deep > restructuring towards deeper minimums rather than the local minimums > closest to the minimum energy pathway. > In my opinion it is more physical if a migration corresponds to a > minimum energy pathway AND minimum restructuring. > > If you would simulate vacancy migration in a huge supercell with NEB > optimization, would you optimize starting and ending points? Why? > > > Thanks in advance and hope to hear your opinions and reasonings, > > Regards, > Alex. > -- > > -- > This message and its contents, including attachments are intended solely > for the original recipient. If you are not the intended recipient or have > received this message in error, please notify me immediately and delete > this message from your computer system. Any unauthorized use or > distribution is prohibited. Please consider the environment before printing > this email. > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Dissociation on metallic surface
Dear Vincenzo Sorry for the late answer. The question is so open that I would say "do it as you wrote it". I'm not an expert of applied electric fields, so I can only suggest you try to perform NEB by using the new esm implementation of open boundary conditions. With esm_bc='bc3' you sandwich your slab in a metal-slab-vacuum system and you can indicate a target for the Fermi level of the system. The chemical potential of electrons and the DOS will define the total charge of the system, and you can simulate charge accumulation or charge depletion at the electrode surface. With esm_bc='bc2' you apply a given external field between two metal electrodes and polarize your slab. I've found this recent interesting paper in which the authors use esm to model surface chemistry processes J. Phys. Chem. C 2016, 120, 13485 HTH Giuseppe On Sunday, February 26, 2017 07:58:41 PM Vincenzo Verdolino wrote: > Dear community, > > I would like to study the molecular dissociation of a biatomic system on a > metallic surface through NEB theory under the effect of external electric > field > > What would be your best approach? > > Sorry for the very open question but we could go in details while discussing > > Thank you all and best regards > > Vincenzo Verdolino > > > > > Vincenzo Verdolino, PhD > Computer Science Department, > Università della Svizzera italiana - ETH > Via Giuseppe Buffi 13, Lugano 6900 > Switzerland > Phone: +41 58 666 48 11 > Skype: vincenzo.verdolino > e-mail: verdo...@chem.phys.ethz.ch <mailto:verdo...@chem.phys.ethz.ch> > vincenzo.verdol...@gmail.com <mailto:vincenzo.verdol...@gmail.com> > website: www.gpv-ar.com <http://www.gpv-ar.com/> - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Alignment of total energy?
Dear Ari If you have a charged slab and/or a strong dipole along z, the esm pbc in a vacuum-slab-vacuum (i.e. esm='bc1') fashion might help a lot to have a flat asymptotic value of the potential outside the slab. Moreover, pw.x automatically calculates the z average of V_xc and v_H and store them into a prefix.esm1 file. Best Giuseppe On Monday, February 27, 2017 10:05:12 PM Nicola Marzari wrote: > Hi Ari, > > > yes, you can plot Vhartree or Vhartree_xc as they flattens out in the > vacuum - > first should be shorter ranged (see Caspar Fall PhD thesis). > > If you have a slab geometry, you can do a planar average in the directions > parallel to the slab. > > Indeed, make sure it is flat - trickier if you have a charged system (for > a charged slab, it's a simple correction - see Dabo prb 2008). > > nicola > > On 27/02/2017 13:00, Ari P Seitsonen wrote: > > Dear Colleagues, > > > > I tried to search the FAQ and archives but was not successful - sorry > > > > if this is already answered somewhere. > > > > I am trying to calculate core level binding energies of atoms, and for > > > > this I need to align the total energies of the two calculations, with > > and without the core hole; the calculations are on surfaces/slabs, so I > > could use either the Fermi energies or the value of (dipole-corrected) > > potential in the vacuum. But I have forgotten which term is needed > > still... (Sorry, it is some 25 years when I was doing similar things.) > > Was it something like the average potential in the cell times some > > factor...? > > > > Thank you in advance for any answer. :) > > > > Greetings from Paris, > > > >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 > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] GGA+U
Dear Sohail Ahmad Before all why 5.0.1? It is not only an outdated version (10/05/2012!) which nobody has anymore interest in debugging/improving, but it is also the first version of the 5.x release, and it is therefore probably full of bugs that have been corrected later. If you want to stick to 5.x, then use at least the latest 5.4.0 version, or switch to 6.0. > Dear All QE usersI wish to study ScN using GGA+U.I am using QE-5.0.1,If I > understood correctly , I need to modifyPW/set_hubbard_l.f90 and > PW/tabd.f90 Yes, you should add data for Sc PW/src/tabd.f90 add CASE( 'Sc' ) hubbard_occ = 1.d0 just before CASE( 'Ti', 'Zr', 'Hf' ) hubbard_occ = 2.d0 /Espresso/5.4.0/Modules/set_hubbard_l.f90 CASE( 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', & 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', & 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg' ) add 'Sc' to the list --> CASE( 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', & 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', & 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', & 'Sc' ) > exact value of U for ScN ? Of course nobody knows! You should estimate it, there are several (semiempirical or self-consistent) ways. Read this to start: Himmetoglu, B.; Floris, A.; de Gironcoli, S.; Cococcioni, M. Int. J. Quantum Chem. 2014, 114, 14-49 HTH Giuseppe On Saturday, February 25, 2017 07:08:19 PM Sohail Ahmad wrote: > Dear All QE usersI wish to study ScN using GGA+U.I am using QE-5.0.1,If I > understood correctly , I need to modifyPW/set_hubbard_l.f90 and > PW/tabd.f90 I found the file PW/src/tabd.f90 but don't see set_hubbard_l.f90 > in PW/src 1. Can any one explain where can I find this ?2.What > exact line/values need to be modified ?3. exact value of U for ScN ? Any > further guideline regarding input file is appreciated > Best WishesSohail AhmadKing Khalid UniversitySaudi Arabia - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] "vague question" (renamed --> Re: Pw_forum Digest, Vol 115, Issue 25)
Dear unknown user It would be nice if you read the forum rules before posting... 1) Please always provide name and scientific affiliation in your messages 2) Please don't hit "Reply" to the Digest. Start a new thread and use a meaningful subject 3) Don't ask vague questions whose answers you can anyway find by using google... HTH Giuseppe On Saturday, February 25, 2017 04:14:57 PM hamid elbushra wrote: > Hello for all > so l need the in put of TiO2 ( bluk) > Thanks > - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] All Lowdin charges are zero
Dear Semen Flicking through the QE pseudopotential page http://www.quantum-espresso.org/pseudopotentials/ among many other, I've found these ones that should suitable for your purpose (but you should always check with the appropriate convergence tests...). Ultrasoft PPs (suggested cutoffs: ecutwfc=40.0, ecutrho=320.0~400.0) Mo.pbe-spn-rrkjus_psl.0.2.UPF S.pbe-n-rrkjus_psl.0.1.UPF C.pbe-n-rrkjus_psl.0.1.UPF H.pbe-rrkjus_psl.0.1.UPF Cl.pbe-n-rrkjus_psl.0.1.UPF HTH Giuseppe On Friday, February 24, 2017 08:12:20 PM Semen Yesylevskyy wrote: > Dear Giuseppe, > Thank you very much, now it is finally clear for me! > Indeed I used PPs from "official" site. I had no idea that they may not > contain some crucial pieces of information like wavefucntions. > I really don't want to regenerate them at this stage because this work is a > small side project which does not justify going so deep into the field. > Are there any databases of pre-computed PPs with pseudowavefunctions included > for H,C,Cl,S,Mo atoms? > > Sincerely, > Semen > > >ÐÑÑниÑа, 24 ÑевÑÐ°Ð»Ñ 2017, 18:40 +02:00 Ð¾Ñ Giuseppe Mattioli > ><giuseppe.matti...@ism.cnr.it>: > > > > > >Dear Semen > >I suppose that you know what a pseudopotential is and how does it work... If > >you don't, I recommend first that you read this guide > >your-path-to Espresso-6.0/atomic/Doc/pseudo-gen.pdf > >and some of the references contained therein. > >Pseudopotentials can be generated by using the ld1.x (aka atomic) code > >embedded in the QE distributuin, but they are more often imported from > >various databases that are NOT part of the distribution, and are in such > >case used "at your own risk", even if there is a diffuse knowledge > >between QE users regarding the generation and usage of several kinds of > >pseudopotential. > > > >In your case, the optimized norm-conserving Vanderbilt's pseudopotentials > >(ONCV PPs) downloaded from this database > >http://www.quantum-simulation.org/potentials/sg15_oncv/ > >do not contain the pseudowavefunctions, so projwfc.x does not find a > >suitable set of atomic orbitals to calculate the atomic projection of > >Kohn-Sham orbitals and the Lowdin partition of valence charge. > > > >If you want to use such PPs you should > > > >a) download and install the Hamann's code > > > >b) re-generate the same PPs by yourself with the input you find in the > >header at the beginning of the PP file > > > >And this was explained by Lorenzo Paulatto in the old thread mentioned in my > >previous mail. > > > >I suppose that it is not exactly easy for a newbie of PP generation, so for > >the time being I can only suggest you to use different > >pseudopotentials, or to try to find whether there is anybody who can do this > >work for you...:-) > >HTH > >Giuseppe > > > >On Friday, February 24, 2017 06:58:34 PM Semen Yesylevskyy wrote: > >> Dear Giuseppe, > >> Thank you for quick reply, but I hardly understand the terms and local > >> moonspeak because I'm using Quantum Espresso for few days only. > >> I understand that some information for projwfc is missed but the topic you > >> mentioned does not give me any clue of what should I do with my input > >> to > >> have it. Could you please point me to some step-by-step instruction of > >> what should I do to get correct Lowdin charges? I googled for this > >> extensively and the only thing which I've found is the following: 1) do > >> optimization with pw.x > >> 2) do scf with pw.x > >> 3) run projwfc.x > >> > >> That is what I did without success... > >> > >> Sincerely, > >> Dr. Semen Yesylevskyy > >> > >> Department of Physics of Biological Systems > >> Institute of Physics of NAS of Ukraine > >> > >> >ÃÂÃÂÃÂýøÃÂð, 24 ÃÂõòÃÂðûà2017, 17:44 > >> >+02:00 þàGiuseppe Mattioli < giuseppe.matti...@ism.cnr.it >: > >> > > >> > > >> > > >> >Dear Colleague (please sign always the posts with name and affiliation) > >> > > >> >ONCV PPs do not contain pseudowavefunctions, if you do not say to the > >> >Hamann's code to include them. > >> >Look for this old thread in the QE forum > >> > > >> >[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc > >> > > >> >That should contain all you need to rebuild a PP with wfcs and to obtain > >> >Lowdin charges w
Re: [Pw_forum] All Lowdin charges are zero
Dear Semen I suppose that you know what a pseudopotential is and how does it work... If you don't, I recommend first that you read this guide your-path-to Espresso-6.0/atomic/Doc/pseudo-gen.pdf and some of the references contained therein. Pseudopotentials can be generated by using the ld1.x (aka atomic) code embedded in the QE distributuin, but they are more often imported from various databases that are NOT part of the distribution, and are in such case used "at your own risk", even if there is a diffuse knowledge between QE users regarding the generation and usage of several kinds of pseudopotential. In your case, the optimized norm-conserving Vanderbilt's pseudopotentials (ONCV PPs) downloaded from this database http://www.quantum-simulation.org/potentials/sg15_oncv/ do not contain the pseudowavefunctions, so projwfc.x does not find a suitable set of atomic orbitals to calculate the atomic projection of Kohn-Sham orbitals and the Lowdin partition of valence charge. If you want to use such PPs you should a) download and install the Hamann's code b) re-generate the same PPs by yourself with the input you find in the header at the beginning of the PP file And this was explained by Lorenzo Paulatto in the old thread mentioned in my previous mail. I suppose that it is not exactly easy for a newbie of PP generation, so for the time being I can only suggest you to use different pseudopotentials, or to try to find whether there is anybody who can do this work for you...:-) HTH Giuseppe On Friday, February 24, 2017 06:58:34 PM Semen Yesylevskyy wrote: > Dear Giuseppe, > Thank you for quick reply, but I hardly understand the terms and local > moonspeak because I'm using Quantum Espresso for few days only. > I understand that some information for projwfc is missed but the topic you > mentioned does not give me any clue of what should I do with my input to > have it. Could you please point me to some step-by-step instruction of what > should I do to get correct Lowdin charges? I googled for this > extensively and the only thing which I've found is the following: 1) do > optimization with pw.x > 2) do scf with pw.x > 3) run projwfc.x > > That is what I did without success... > > Sincerely, > Dr. Semen Yesylevskyy > > Department of Physics of Biological Systems > Institute of Physics of NAS of Ukraine > > >ÐÑÑниÑа, 24 ÑевÑÐ°Ð»Ñ 2017, 17:44 +02:00 Ð¾Ñ Giuseppe Mattioli > ><giuseppe.matti...@ism.cnr.it>: > > > > > > > >Dear Colleague (please sign always the posts with name and affiliation) > > > >ONCV PPs do not contain pseudowavefunctions, if you do not say to the > >Hamann's code to include them. > >Look for this old thread in the QE forum > > > >[Pw_forum] rebuilding ONCV PPs with PP PSWFC for projwfc > > > >That should contain all you need to rebuild a PP with wfcs and to obtain > >Lowdin charges with projwfc.x > > > >HTH > >Giuseppe > > > >On Friday, February 24, 2017 06:30:47 PM Semen Yesylevskyy wrote: > >> Dear All, > >> I'm new to QE so please forgive if I'm missing something very obvious. I'm > >> trying to study the charge transfer between organic molecules and MoS2 > >> monolayer. I optimized the system, did an scf and then tried to get Lowdin > >> charges with projwcf. However, all charges are almost zero which is > >> not > >> what I can expect: > >> > >> Lowdin Charges: > >> Atom # 1: total charge = 0., s = 0., > >> Atom # 1: total charge = 0., p = 0., pz= 0., px= > >> 0., py= 0., > >> Atom # 2: total charge = 0.0001, s = 0., > >> Atom # 2: total charge = 0.0001, p = 0.0001, pz= 0., px= > >> 0., py= 0., > >> Atom # 3: total charge = 0.0001, s = 0., > >> Atom # 3: total charge = 0.0001, p = 0.0001, pz= 0., px= > >> 0., py= 0., > >> Atom # 4: total charge = 0., s = 0., > >> Atom # 4: total charge = 0., p = 0., pz= 0., px= > >> 0., py= 0., > >> Atom # 5: total charge = 0.0001, s = 0., > >> Atom # 5: total charge = 0.0001, p = 0.0001, pz= 0., px= > >> 0., py= 0., > >> Atom # 6: total charge = 0.0001, s = 0., > >> > >> > >> > >> Could you please give me some advice of what I'm doing wrong? > >> > >> > >> > >> The projwcf input: > >> > >&g
Re: [Pw_forum] All Lowdin charges are zero
S 10.903829602 8.974680010 7.500128022 > C5.700416780 4.960942076 11.705590151 > C5.786661978 6.354516349 11.705273773 > C7.046391983 6.956535202 11.705217371 > C8.203237318 6.173116561 11.705190411 > C8.099168585 4.780492709 11.705023203 > C6.846678887 4.164104064 11.704869934 > Cl 4.129012811 4.204270654 11.705957792 > H4.877613854 6.955359406 11.704377918 > H7.118320846 8.046628444 11.704165169 > H9.184749419 6.647034640 11.704328004 > H8.998646725 4.161998637 11.704137157 > H6.757143341 3.077849963 11.704290956 > K_POINTS automatic > 1 1 1 1 1 1 - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] About output of PDOS calculations of CeO2
Dear Phanikumar
PDOS is not affected by orbital occupation. Occupied orbitals in your plot are
those below the Fermi level of your system, which is printed in the pw.x
output.
HTH
Giuseppe
On Thursday, February 23, 2017 11:52:01 AM Phanikumar Pentyala wrote:
> Thank you Giuseppe Mattioli and Paolo Giannozzi
>
> The order of orbitals it calculates energy values already discussed by
> Paolo Giannozzi. But, in my system it contains *4f* have 7 orbitals in it.
> but all will not fill during electron localizations (only first two
> orbitals). so my doubt was what is the use of remaining line of values in
> above attached document and which orbital values I have to choose in my
> graph?
>
> Please bare with my technical knowledge because I am not a background from
> science
>
> Thank you once again
>
>
> Regards
> Phanikumar
>
>
> On Wed, Feb 22, 2017 at 7:14 PM, Paolo Giannozzi <p.gianno...@gmail.com>
>
> wrote:
> > The order of Y_{lm}(\theta,\phi) is described here:
> > http://www.quantum-espresso.org/wp-content/uploads/Doc/pp_
> > user_guide/node8.html
> > For l=3 the sequence continues with: P_{3,0}, P_{3,1}cos(\phi),
> > P_{3,1}sin(\phi), P_{3,2}cos(2\phi), P_{3,2}sin(2\phi),
> > P_{3,3}cos(3\phi), P_{3,3}sin(3\phi)
> >
> > Paolo
> >
> > On Wed, Feb 22, 2017 at 2:16 PM, Giuseppe Mattioli
> >
> > <giuseppe.matti...@ism.cnr.it> wrote:
> > > Dear Phanikumar
> > > If I understand well your question, the pdos file attached to your
> >
> > previous message should contain 9 columns: the energy scale of PDOS, the
> > total 4f
> >
> > > PDOS and the PDOS of the seven 4f orbitals (if you sum column 3-9 you
> >
> > obtain column 2). As opposed to the l=1 and l=2 cases, the symmetry order of
> >
> > > orbitals in the l=3 case is not reported in the projwfc manual, but
> >
> > maybe there is someone more skilled than me that know the right order...
> >
> > > HTH
> > > Giuseppe
> > >
> > > On Wednesday, February 22, 2017 05:18:40 PM Phanikumar Pentyala wrote:
> > >> Thnk you Lorenzo Paulatto for quick reply
> > >>
> > >> Yes I am doing DFT+U calculations. 4f will be in the valance bands of Ce
> > >> atom. Because of redox property of *Ce*, electron localization take
> >
> > place.
> >
> > >> Here I am attaching my out put file of PDOS. Also I am using GGA (PBE)
> > >> functional, NORM-CONSERVING potentials for my calculation.
> > >>
> > >>
> > >> On Wed, Feb 22, 2017 at 5:02 PM, Lorenzo Paulatto <
> > >>
> > >> lorenzo.paula...@impmc.upmc.fr> wrote:
> > >> > On Wednesday, February 22, 2017 12:18:31 PM CET Phanikumar Pentyala
> >
> > wrote:
> > >> > > My doubt was, cerium electronic structure have only single or double
> > >> > > electron in *f* shell, so can I choose third or fourth line of PDOS
> > >> >
> > >> > output
> > >> >
> > >> > > file or last line (first line belongs to LDOS)?
> > >> >
> > >> > Dear Phanikumar,
> > >> > the pseudopotential you are using for Cerium may or may not have the f
> > >> > electron in valence.
> > >> >
> > >> > If the electron is in valence you will have a corresponding file
> >
> > after the
> >
> > >> > projwfc calculation. But your system will probably be metallica and
> >
> > have
> >
> > >> > all
> > >> > sort of problems, unless you use DFT+U and know what you are doing.
> > >> >
> > >> > If it is in the core, you won't be able to compute its pdos (which
> >
> > anyway,
> >
> > >> > is
> > >> > a delta function at the atomic state energy). Also your valence bands
> >
> > will
> >
> > >> > miss some feature and probably be not completely correct.
> > >> > On the other hand, you will be able to get the calculation working
> >
> > without
> >
> > >> > too
> > >> > much fiddling.
> > >> >
> > >> >
> > >> > hth
> > >> >
> > >> > --
> > >> > Dr. Lorenzo Paulatto
> > >> > IdR @ IMPMC -- CNRS & Université Paris 6
> > >> > phone: +33 (0)1 442 79822 / skype: paulatz
> > >> > www: http://www-int.impmc.upmc.
Re: [Pw_forum] About output of PDOS calculations of CeO2
Dear Phanikumar If I understand well your question, the pdos file attached to your previous message should contain 9 columns: the energy scale of PDOS, the total 4f PDOS and the PDOS of the seven 4f orbitals (if you sum column 3-9 you obtain column 2). As opposed to the l=1 and l=2 cases, the symmetry order of orbitals in the l=3 case is not reported in the projwfc manual, but maybe there is someone more skilled than me that know the right order... HTH Giuseppe On Wednesday, February 22, 2017 05:18:40 PM Phanikumar Pentyala wrote: > Thnk you Lorenzo Paulatto for quick reply > > Yes I am doing DFT+U calculations. 4f will be in the valance bands of Ce > atom. Because of redox property of *Ce*, electron localization take place. > Here I am attaching my out put file of PDOS. Also I am using GGA (PBE) > functional, NORM-CONSERVING potentials for my calculation. > > > On Wed, Feb 22, 2017 at 5:02 PM, Lorenzo Paulatto < > > lorenzo.paula...@impmc.upmc.fr> wrote: > > On Wednesday, February 22, 2017 12:18:31 PM CET Phanikumar Pentyala wrote: > > > My doubt was, cerium electronic structure have only single or double > > > electron in *f* shell, so can I choose third or fourth line of PDOS > > > > output > > > > > file or last line (first line belongs to LDOS)? > > > > Dear Phanikumar, > > the pseudopotential you are using for Cerium may or may not have the f > > electron in valence. > > > > If the electron is in valence you will have a corresponding file after the > > projwfc calculation. But your system will probably be metallica and have > > all > > sort of problems, unless you use DFT+U and know what you are doing. > > > > If it is in the core, you won't be able to compute its pdos (which anyway, > > is > > a delta function at the atomic state energy). Also your valence bands will > > miss some feature and probably be not completely correct. > > On the other hand, you will be able to get the calculation working without > > too > > much fiddling. > > > > > > hth > > > > -- > > Dr. Lorenzo Paulatto > > IdR @ IMPMC -- CNRS & Université Paris 6 > > phone: +33 (0)1 442 79822 / skype: paulatz > > www: http://www-int.impmc.upmc.fr/~paulatto/ > > mail: 23-24/423 Boîte courrier 115, 4 place Jussieu 75252 Paris Cédex 05 > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] GGA+U
Dear F. Marsusi > Is this what one expected always from +U calculations, As I told you before nothing can be considered as "expected" when you apply the U correction to a strongly hybridized sp2 system such as a pi- conjugated molecule or graphene. In my experience this is not a good idea, because you obtain, for example, a higher ionization energy (and this is right when you correct LDA/GGA delocalization errors, and in agreement with a correction with exact exchange like B3LYP or HSE) but also a lower electron affinity (and this is wrong, and the opposite behavior of a correction with exact exchange). So you are walking in "terra incognita" where nothing can be given for granted. HTH Giuseppe On Friday, February 10, 2017 08:38:37 PM FARAH MARSUSI wrote: > Dear Giuseppe, > > Many thanks for your quick response. As you have correctly guessed, the > system is an organic material (fluorinated graphene). From U=0 to 3.4, M is > increasing gradually up to the expected value, M remains constant till U=3.6 > eV, then by increasing U, again M is reduced very soon to zero. Is > this what one expected always from +U calculations, when goes up further from > the optimum U value? From your answer, it is concluded to be a > strange behavior due to the organic nature of this material. > > Best regards, > F. Marsusi, > > Amirkabir University of Technology.â > > On Fri, 02/10/2017 08:09 PM, Giuseppe Mattioli <giuseppe.matti...@ism.cnr.it> > wrote: > > Dear F. Marsusi > > First of all you are not providing any detail of your system, so we cannot > > even guess what is "natural" for it. > > However, you are using the Hubbard U correction in a semiempirical way, and > > there is therefore no way to choose the U value but that reproducing > > some measured parameter, and not very much to do if unexpected or strange > > results appear at a given (unphysical?, problematic?) U value. > > In my experience the application of U to organic molecules has been always > > problematic due to the strong hybridization between C 2s and C 2p > > orbitals, and to the application of the correction to 2p orbitals only. > > HTH > > Giuseppe > > > > On Friday, February 10, 2017 07:25:10 PM FARAH MARSUSI wrote: > > > Dear all, > > > > > > By GGA+U as implemented in QE, the correct magnetization (M) and band gap > > > was obtained. The correct U value for each atom was obtained by > > > intensive > > > step by step runs to reach gradually the experimental M value, and > > > therefore band gap. All results are OK till now (the U value itself also= > > > 3.4 > > > eV > > > for carbon and fluorine is acceptable ). However, by enlarging the > > > obtained U value a bit (to 3.7 eV), the predicted M come back to that of > > > pure > > > GGA. Is it natural, or a problem exist? > > > > > > > > > Best regards, > > > F. Marsusi, > > > > > > - Article premier - Les hommes naissent et demeurent > > libres et égaux en droits. Les distinctions sociales > > ne peuvent être fondées que sur l'utilité commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la liberté, > > la propriété, la sûreté et la résistance à l'oppression. > > **** > > > >Giuseppe Mattioli > >CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > >v. Salaria Km 29,300 - C.P. 10 > >I 00015 - Monterotondo Stazione (RM), Italy > >Tel + 39 06 90672342 - Fax +39 06 90672316 > >E-mail: " target="_blank"><giuseppe.matti...@ism.cnr.it> > >http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ > >ResearcherID: F-6308-2012 > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > > This email was Anti Virus checked by Astaro Security Gateway. > > http://www.sophos.com - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. *
Re: [Pw_forum] GGA+U
Dear F. Marsusi First of all you are not providing any detail of your system, so we cannot even guess what is "natural" for it. However, you are using the Hubbard U correction in a semiempirical way, and there is therefore no way to choose the U value but that reproducing some measured parameter, and not very much to do if unexpected or strange results appear at a given (unphysical?, problematic?) U value. In my experience the application of U to organic molecules has been always problematic due to the strong hybridization between C 2s and C 2p orbitals, and to the application of the correction to 2p orbitals only. HTH Giuseppe On Friday, February 10, 2017 07:25:10 PM FARAH MARSUSI wrote: > Dear all, > > By GGA+U as implemented in QE, the correct magnetization (M) and band gap was > obtained. The correct U value for each atom was obtained by intensive > step by step runs to reach gradually the experimental M value, and therefore > band gap. All results are OK till now (the U value itself also= 3.4 eV > for carbon and fluorine is acceptable ). However, by enlarging the obtained U > value a bit (to 3.7 eV), the predicted M come back to that of pure > GGA. Is it natural, or a problem exist? > > > Best regards, > F. Marsusi, - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Regarding installation of Quantum Espresso
Dear Nipesh Dulal This mailing list does not work the way you seem to expect... Please follow the instructions reported in the user guide and report exactly what you have done and where it went wrong. It is assumed that you already have a decent minimal knowledge of compilers, libraries, etc. HTH Giuseppe nipesh dulal <nipeshdula...@gmail.com> ha scritto: > Hi there, > > I am new user to MacBook Air. Therefore, I am finding it difficult > to install Quantum Espresso. I am writing this email seeking help > for the installation procedure. Looking forward to your response. > > Regards, > Nipesh Dulal, > St. Xavier’s College, Physics Council. > Kathmandu, Nepal > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] gga+u CALCULATION
Dear Kajal Jindal It is only a matter of labels... The first implementation was an LDA+U one, and the input key was named lda_plus_U after that. But if your underlying functional is a GGA one, e.g., PBE, you are performing GGA+U (or DFT+U, that is a generalization) even if the input key is still called (for laziness or compatibility, I don't know... :-) ) lda_plus_U. HTH Giuseppe On Tuesday, January 17, 2017 10:29:36 AM Kajal Jindal wrote: > Dear all, > > I want to perform GGA+U calculation on quantum espresso. The input_PW.html > file shows that for DFT+U calculations i have to set lda_plus_U=.true. But > nothing is given about GGA+U. > > KIndly help. > What are the parameters i need to introduce for GGA+U calculation? > > Thanking You, > Kajal Jindal > University of Delhi > Delhi, INDIA - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] problem
Dear Nasim the message says that you cannot run turbo_lanczos.x after a pw.x run with occupations='smearing'. Use occupations='fixed' instead. HTH Giuseppe On Sunday, January 15, 2017 08:19:19 PM Nasim Ha wrote: > Dear all > > i tried running turbo_lanczos.x ,but there is this error " > turboTDDFT is not extended to metals" > thanks - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] aligning eigenvalues for isolated molecules/atoms
Dear Davide Yes, the procedure is correct, and you can easily compare the results with those obtained in a GTO framework. If you neglect/minimize basis sets issues, pseudopotentials issues, numerical noise, etc., you generally obtain close eigenvalues in PW/GTO frameworks, using the same xc functional. > Then I should have something more or less comparable amongst > different isolated system and in which the HOMO is always negative > and the LUMO is either very close to 0 or positive. This depend on the functional, of course... There are tons of papers on ionization energy, electron affinity and related DFT errors. Best Giuseppe Quoting Tiana Davide <davide.ti...@epfl.ch>: > Dear all > > > I would like to check I am doing the correct things. > > > I need to compare the eigenvalues of some atoms and molecules. > > I am following this procedure: > > > 1) pw in a cube cell bigger enough to exclude any interaction with > its neighbours. > > 2) adding the "assume_isolated='makov-payne'" option in the input > > 3) add the "Corrected vacuum level" found at the bottom of the > output to each eigenvalue. > > > Then I should have something more or less comparable amongst > different isolated system and in which the HOMO is always negative > and the LUMO is either very close to 0 or positive. > > This is what I would expect using LCAO programs like Gamess or > Gaussian, can I expect something similar using pw and mp correction? > > > Best Regards > > ?Davide -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] HSE calculation
28523510696737 > S0.373121190301768 0.871857201740837 0.628100325702825 > S0.122595407121820 0.631661221636976 0.623457680920035 > S0.378401629960358 0.880931755370115 0.128007691557354 > S0.370516759927977 0.627650572115622 0.371503234800683 > S0.120676019249323 0.877880018784136 0.871080486353522 > S0.127877053082689 0.87465737074 0.372628362873367 > S0.381665109983142 0.627410813576234 0.876573570642188 > S0.65243791753 0.622126275574244 0.127398395493092 > S0.872872581014923 0.871637376796884 0.627316989829439 > S0.627882496273248 0.629329558823215 0.628949791420298 > S0.877028056968618 0.878769311284339 0.128059546753167 > S0.869072985188352 0.628398420306380 0.372023399476006 > S0.621642750204393 0.877133981256401 0.87275745701 > S0.628774116539949 0.872978079000506 0.371969741830591 > S0.878145790717181 0.623118862812509 0.871926456963634 > Sn -7.608358306536000E-004 3.222581925182000E-004 0.499443342221132 > Sn 0.256283989515477 0.242473334236634 7.086312024705200E-003 > Sn 0.25147719144 0.48628230229 0.750015148413511 > Sn 0.500756332281728 -3.22864923089E-004 0.499443668263479 > Sn 0.749674703021384 0.249241762433395 5.853144321951000E-004 > Sn -7.528252332882800E-003 0.493714016457111 0.492943834309768 > Sn 0.243712085123441 0.757526932064565 7.088098855306700E-003 > Sn 0.507524071793615 0.506285644594180 0.492942589729261 > Sn 0.750319939734500 0.750758314128771 5.864075895717000E-004 > Zn -8.444909379011000E-004 0.248644383328342 0.249824392514012 > Zn 0.501355703397740 0.249153332059540 0.250202955214345 > Zn 0.75814591615 0.48819958268 0.751230280703815 > Zn -1.354273739554800E-003 0.750845148370982 0.250202011729470 > Zn 0.250001030302999 0.99919970564 0.748797640094973 > Zn 0.500847542910512 0.751353999698878 0.249827089512433 > Zn 0.75701673651 6.63385379001E-008 0.750013712421637 -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] HSE calculation
8309942 0.752294883959966 > Cu 0.75142082280 -5.26130524400E-007 0.250013471551898 > Cu 0.504110794881591 0.497130019670560 2.38719965944E-003 > Cu 0.252864021824887 0.754114287465916 0.497641282622189 > Cu -3.704195077655900E-003 0.753301366753437 0.752296142763722 > Cu 0.24236820237 0.4891942 0.250013182582039 > Cu 0.995875748692389 0.502868653338768 2.390474663852800E-003 > Cu 0.749173286025747 0.751824906786787 0.500389207464035 > Cu 0.503301976072833 0.753704886063385 0.747732698188728 > Cu 0.75264340525 0.49872289094 0.247953552793443 > S0.121607711130560 0.119066726107911 0.128004116420937 > S0.377410970694754 0.368337305224885 0.623452478431281 > S0.126885481660098 0.128142136277065 0.628104013094463 > S0.377653504065843 0.379487027813697 0.128526410123051 > S0.372131518633960 0.127780399961450 0.37262964601 > S0.118342036620952 0.372594923808515 0.876575437772911 > S0.129491327114066 0.372352660069188 0.371503083918088 > S0.379334214207609 0.122123268492755 0.871079119116580 > S0.622980711218032 0.121230496230355 0.128057562219561 > S0.872125990350811 0.370669474457333 0.628947185465573 > S0.627135346433278 0.128362738539397 0.627319397985374 > S0.877782158592530 0.377872619579312 0.127400953525378 > S0.871236086814705 0.127025188823458 0.371968945581645 > S0.621861966674097 0.376885089946700 0.871927004252818 > S0.630936881905509 0.371604494475657 0.372021999310852 > S0.878366210795192 0.122870165561448 0.872709760521635 > S0.122354911128635 0.620512219317389 0.128523510696737 > S0.373121190301768 0.871857201740837 0.628100325702825 > S0.122595407121820 0.631661221636976 0.623457680920035 > S0.378401629960358 0.880931755370115 0.128007691557354 > S0.370516759927977 0.627650572115622 0.371503234800683 > S0.120676019249323 0.877880018784136 0.871080486353522 > S0.127877053082689 0.87465737074 0.372628362873367 > S0.381665109983142 0.627410813576234 0.876573570642188 > S0.65243791753 0.622126275574244 0.127398395493092 > S0.872872581014923 0.871637376796884 0.627316989829439 > S0.627882496273248 0.629329558823215 0.628949791420298 > S0.877028056968618 0.878769311284339 0.128059546753167 > S0.869072985188352 0.628398420306380 0.372023399476006 > S0.621642750204393 0.877133981256401 0.87275745701 > S0.628774116539949 0.872978079000506 0.371969741830591 > S0.878145790717181 0.623118862812509 0.871926456963634 > Sn -7.608358306536000E-004 3.222581925182000E-004 0.499443342221132 > Sn 0.256283989515477 0.242473334236634 7.086312024705200E-003 > Sn 0.25147719144 0.48628230229 0.750015148413511 > Sn 0.500756332281728 -3.22864923089E-004 0.499443668263479 > Sn 0.749674703021384 0.249241762433395 5.853144321951000E-004 > Sn -7.528252332882800E-003 0.493714016457111 0.492943834309768 > Sn 0.243712085123441 0.757526932064565 7.088098855306700E-003 > Sn 0.507524071793615 0.506285644594180 0.492942589729261 > Sn 0.750319939734500 0.750758314128771 5.864075895717000E-004 > Zn -8.444909379011000E-004 0.248644383328342 0.249824392514012 > Zn 0.501355703397740 0.249153332059540 0.250202955214345 > Zn 0.75814591615 0.48819958268 0.751230280703815 > Zn -1.354273739554800E-003 0.750845148370982 0.250202011729470 > Zn 0.250001030302999 0.99919970564 0.748797640094973 > Zn 0.500847542910512 0.751353999698878 0.249827089512433 > Zn 0.75701673651 6.63385379001E-008 0.750013712421637 -- **** - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] problem with tddfpt: This type of the supercell is not supported
Dear Davide I'm working on a large MOF too. There are 8 "molecular" units in my cristallographic unit cell, 180 atoms for each molecule, so *no way* to simulate the whole crystal cell. But learning from quantum chemists (;-)) I've embedded a single unit in a cubic cell and I've used the ENVIRON plugin to surround the molecule with an implicit dielectric medium (generally epsilon=4~8 yield a reasonable "organic" environment). I've calculated accurate interatomic distances by using pslibrary PAW PPs and the XDM dispersion contribution. ENVIRON is also compatible with tddfpt, so you should be able to calculate absorption spectra with the correct "solvent shift". HTH Giuseppe Tiana Davide <davide.ti...@epfl.ch> ha scritto: > Dear Iurii > > Thanks for answering > > 1) MOF is a metal organic framework, namely an hybrid crystalline > material alternating inorganic node with organic ligand > > 2) as you can imagine no it is not a molecule. If the problem is due > to the cell parameters being not orthorhombic I might consider to > run on a cluster. > On the other hand I am genuinely too busy for coding so just in case > do you think comment that error and try to run the calculation could > it be worthy? > > 3) Sure > > Dr Davide Tiana > Scientist > Swiss Federal Institute of Technology Lausanne (EPFL) > Laboratory of Molecular Simulation (LSMO) > CH-1015 Lausanne, Switzerland > -- > > Message: 5 > Date: Fri, 16 Dec 2016 17:11:02 + > From: Timrov Iurii <iurii.tim...@epfl.ch> > Subject: Re: [Pw_forum] problem with tddfpt: This type of the > supercell isnot supported > To: "pw_forum@pwscf.org" <pw_forum@pwscf.org> > Message-ID: <1481908309249.24...@epfl.ch> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Davide, > > > >> Dear all > >> When I try to calculate the charge response using turbo_lanczos.x. >> I obtain this error: > > > Error in routine lr_read_wfc (1): This type of the supercell > is not supported > > > Actually this message comes from the routine "shift_d0psi" in > TDDFPT/src, and not from the routine "lr_read_wfc". The name of the > routine in the errore message is going to be fixed. > > >> The system I am studying is a MOF with 120 atoms and 5 atom types: >> Y,C,N,O,H. > > > What is MOF? (sorry for my ignorance) > > >> The wavefunction is hybrid HSE and the cell parameters (optimised >> using pbesol) are: > >> CELL_PARAMETERS (angstrom) >> 13.942330435 -0.002163729 0.276449127 >> -0.000947780 6.429695941 0.000316833 >> -2.188037024 0.001050297 14.196933852 > > > The cell is not orthorombic, this is why the routine "shift_d0psi" > complains (because this routine was not generalized/tested for cells > with lattice vectors which are not orthogonal to each other). > > > Is your system a molecule? If yes, then you may try to solve your > problem in two ways: > > > 1. Easy way: shift your molecule to the center of the supercell and > set lshift_d0psi=.false. > > 2. More complicated way: Generalize the routine "shift_d0psi" to > deal with cells with non-orthogonal lattice vectors. > > >> Can you help me in finding what is wrong? and more important is >> this problem fixable? > > >> Cheers > >> Davide > > > Please provide your affiliation. > > > Best regards, > > Iurii > > > -- > Dr. Iurii Timrov > Postdoctoral Researcher > Swiss Federal Institute of Technology Lausanne (EPFL) > Laboratory of Theory and Simulation of Materials (THEOS) > CH-1015 Lausanne, Switzerland > +41 21 69 34 881 > http://people.epfl.ch/265334 > > -- > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Projections of quantum number
Dear Jiantuo Gan Please try to post a more specific question. What do you need to project? Kohn-Sham orbitals on some atom-centered basis set (e.g., Lowdin)? Kohn-Sham orbitals in real space (|psi|^2)? At a given k-point (gamma, ...)? > I am programming for Perovskite materials, which has usually a CH3NH3PbCl3 > chemical structure. This is barely relevant. When you ask questions to this forum you are generally expected to know the chemical and/or physical properties of the system you investigate better than all the other fellows. You may find here practical solutions to delimited problems (I've done this, how can I calculate/extract/improve/correct that?), but you should provide a larger amount of details (input files, relevant parts of output files, ...) It is impossible to help you if your questions are so vague. HTH Giuseppe Quoting Jiantuo Gan <jiantuo.gan@gmail.com>: > Hi, > > I am programming for Perovskite materials, which has usually a CH3NH3PbCl3 > chemical structure. > I am having a problem with projection of orbitals. > > Can anyone please tell how I should prepare programme for projection for > this complicated structure. Or please anyone put projection of orbitals in > a simple way. What is the essence here? Thanks a lot! > -- > Yours sincerely, > J. Gan > > PhD Thin Film Solar Cells, University of Oslo 2012-2015 > MSc Nanoscience, Lund University 2010-2012 > BSc Materials Physics Hebei University of Technology 2006-2010 > Tel: +47 96855568 > Linked in:http://se.linkedin.com/pub/jiantuo-gan/31/960/454 -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Interpret Band structure graph
Dear unknown user Please sign always your posts with name and scientific affiliation You may either ask your supervisor or have a look into some textbook... If you are looking for useful answers instead you should post more defined questions (input files, code errors, weird outputs...) HTH Giuseppe Quoting systec...@yahoo.com: > Dear users, > I am beginner on QE I am asking please how to interpret band > structure graph for inorganic compounds.thank you in advance > > Envoyé depuis Yahoo Mail pour Android -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] #error: can't find include file: fftw3.f in QE 6.0
Dear Federico Did you try with the internal FFTW? They should provide something running, and it might turn out that they are not slower than fftw3... HTH Giuseppe On Thursday, November 17, 2016 01:05:42 PM Federico Iori wrote: > Dear QE community > > I am trying to compile QE 6.0 and probably I am the only one who still gets > this error on FFTXlib > > test -d bin || mkdir bin > ( cd FFTXlib ; make TLDEPS= all || exit 1 ) > make[1]: Entering directory `/home/fiori/CODES/QE/qe-6.0/FFTXlib' > mpif90 -O2 -assume byterecl -g -traceback -nomodule -fpp -D__INTEL -D__FFTW3 > -D__MPI -D__SCALAPACK -I/home/fiori/CODES/QE/qe-6.0//include > -I../include/ -c fft_scalar.f90 fft_scalar.FFTW3.f90(40): #error: can't find > include file: fftw3.f > make[1]: *** [fft_scalar.o] Error 1 > make[1]: Leaving directory `/home/fiori/CODES/QE/qe-6.0/FFTXlib' > make: *** [libfft] Error 1 > > > I am using Intel fortran 15 and opempi 1.8.4 and mkl from intel studio > version 15 again. > > I attach my config.log...since I cannot find the error neither the solution. > > Any suggestion? (except hands imposition, of course..) > > Have a nice day and thanks. > > Federico > > > > Federico IORI > Marie Curie Fellow > Laboratoire de Physique des Solides > Bâtiment 510 - Rue André Rivière > 91400 Orsay - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Hot can I calculate band structure using PBE0
Dear Abdullah Well, actually you can't, as stated by the error message... Please read your-path-to-QE/Examples/PW/EXX_example/README HTH Giuseppe On Tuesday, November 08, 2016 10:51:26 AM Abdullah N. Albarakati wrote: > Dear Expert, > > I want to calculate band structure using PBE0, I have run scf calculation > with uniform k-point generation, then I have run pw.x with > "calculation=bands" , but I got the following response > > *** > Atomic positions and unit cell read from directory: > ./ZovZu.save/ > > > > %% > Error in routine setup (1): > HYBRID XC not allowed in non-scf calculations > > %% > > stopping ... > > > > Thank you in advance, > > Abdullah > > > > This email and any files transmitted with it are confidential and intended > solely for the use of the individual or entity to whom they are > addressed. If you have received this email in error please notify Email > System Administrator (e_ad...@uqu.edu.sa ) . Please note that any views or > opinions presented in this email are solely those of the author and do not > necessarily represent those of the Umm Al-Qura University. Finally, the > recipient should check this email and any attachments for the presence of > viruses. The Information Technology and Technical Support Center of Umm > Al-Qura University accepts no liability for any damage caused by any virus > transmitted by this email. - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] 6.0 + environ
Dear Oliviero Thanks! I'll report if something goes wrong Best Wishes G. On Monday, November 07, 2016 03:03:25 PM Oliviero Andreussi wrote: > Dear Giuseppe, > > I am not aware of any problem in running QE-6.0 with environ 0.2, I would > expect everything to run smoothly, but I have only performed basic tests, > so I cannot rule out more subtle incompatibilities. Please let me know if you > find any problem. > > Best regards, > > Oliviero Andreussi > -- > Senior Postdoctoral Researcher > École Polytechnique Fédérale de Lausanne (EPFL) and > Università della Svizzera Italiana (USI) of Lugano > USI Campus, Via G. Buffi 17, 6904 Lugano, Switzerland > Emails: oliviero.andreussi @ epfl.ch -or- usi.ch > Tel: +41-(0)58-666-4810 / Skype: olivieroandreussi > Web: https://sites.google.com/site/olivieroandreussi > > > From: pw_forum-boun...@pwscf.org [pw_forum-boun...@pwscf.org] on behalf of > Giuseppe Mattioli [giuseppe.matti...@ism.cnr.it] > Sent: Wednesday, November 02, 2016 2:21 PM > To: pw_forum@pwscf.org > Subject: [Pw_forum] 6.0 + environ > > Dear all > Do you know if the latest 6.0 version can work with the environ 0.2 plugin? > Thanks in advance > Giuseppe > > > - Article premier - Les hommes naissent et demeurent > libres et égaux en droits. Les distinctions sociales > ne peuvent être fondées que sur l'utilité commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la liberté, > la propriété, la sûreté et la résistance à l'oppression. > > >Giuseppe Mattioli >CNR - ISTITUTO DI STRUTTURA DELLA MATERIA >v. Salaria Km 29,300 - C.P. 10 >I 00015 - Monterotondo Stazione (RM), Italy >Tel + 39 06 90672342 - Fax +39 06 90672316 >E-mail: <giuseppe.matti...@ism.cnr.it> >http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ >ResearcherID: F-6308-2012 > > ___ > 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 - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] 6.0 + environ
Dear all Do you know if the latest 6.0 version can work with the environ 0.2 plugin? Thanks in advance Giuseppe - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Charge on individual atom
Dear Amita Use the projwfc.x postprocessing tool. At the end of its output you'll find Lowdin charges and a spilling parameter indicating how much of the total charge density does not fit into the Lowdin partitioning. N.B.: the "on-the-fly" estimates of atomic charge you see in pw.x output when you perform nspin=2 calculations are not accurate! Use always projwfc.x, or other external tools like, e.g., Bader analysis, see http://theory.cm.utexas.edu/henkelman/code/bader/ HTH Giuseppe On Friday, October 28, 2016 02:32:34 PM Amita Sihag wrote: > Dear all > How can i find charge value on individual atom in Quantum Espresso with > nonmagnetic calculations i.e. taking nspin=1 .Please suggest the necessary. > > > Thank you > Amita > Dept of Chemistry > Indian Institute of Technology Gandhinagar - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] HSE+MD in QE
Dear Jiayu Sorry for the late answer. There has been some effort years ago in the implementation of EXX in cp through the transformation of the plane wave basis set into a maximally localized Wannier functions set. As you can see below, you should be able to perform PBE0 calculations that are better suited for isolated, non-metallic systems than HSE ones. But I do not know if such a setup has been used for real MD simulations or for wavefunction/geometry optimization only. + Variable: input_dft Type: CHARACTER Default:read from pseudopotential files Description:Exchange-correlation functional: eg 'PBE', 'BLYP' etc See Modules/funct.f90 for allowed values. Overrides the value read from pseudopotential files. Use with care and if you know what you are doing! Use 'PBE0' to perform hybrid functional calculation using Wannier functions. Allowed calculation: 'cp-wf' and 'vc-cp-wf' See CP specific user manual for further guidance (or in CPV/Doc/user_guide.tex) and examples in CPV/examples/EXX-wf-example. Also see related keywords starting with exx_. + + Variable: exx_fraction Type: REAL Default:it depends on the specified functional Description:Fraction of EXX for hybrid functional calculations. In the case of input_dft='PBE0', the default value is 0.25. + You might also try to perform a (not-so-slow) Born-Oppenheimer HSE+MD with pw.x by using the new adaptively compressed exchange algorithm implemented in the unstable version of qe. HTH Giuseppe On Thursday, September 29, 2016 06:17:15 PM jiayu dai wrote: > Hello everybody. I am inquiring that if it is possible to do calculations of > MD with HSE functional, although it is expensive. That is to say, if > the forces from HSE energies have been added at the present stage? > > Thanks a lot. > > > > > jiayu > > -- > > > -- > > Jiayu Dai (æ´ä½³é°) > > Associate Professor, > > Department of Physics, > > National University of Defense Technology > > Changsha, 410073, P. R. China > > --- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] mixed supercells
And if you have no experimental hint of the behavior of cell parameters at the interface you can start by averaging the parameters, with a (hopefully little) strain of both materials. HTH Giuseppe On Wednesday, September 21, 2016 03:09:49 PM Jess Wellendorff wrote: > The VNL "Interface Builder" would make it very easy for you to build a > minimum-strain interface: > > http://docs.quantumwise.com/tutorials/ag_au_interface/ag_au_interface.html > > On 09/21/2016 03:04 PM, Lorenzo Paulatto wrote: > > Dear Lorenzo, > > you cannot specify different periodicity, you have to build a > > super-cell, as big as the 3x3 cell of the first material, or the 2x2 > > cell of the second, then you fill it with 9 units of the first > > material and 4 of the other. This can be done by hand (the first time > > it'll take you an hour or two), or there are some softwares that can > > help you I have never used one, as hence I cannot recommend any. > > > > > > On 21 September 2016 at 14:46, Lorenzo Pedrazzetti > > <lorenzo.pedrazze...@polimi.it <mailto:lorenzo.pedrazze...@polimi.it>> > > > > wrote: > > Good afternoon, > > > > I am trying to model the interface between two solid with > > different cella parameter. By looking at their experimental cell > > value I am supposed to stack a 3x3 slab onto a 2x2 slab made of > > different material. > > > > My problemi s the âCELL_PARAMETERSâ card; i found some > > difficulties to understand how to specify the different > > periodicity of the two materials. > > > > Thanks a lot, > > > > Lorenzo. > > > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org <mailto:Pw_forum@pwscf.org> > > http://pwscf.org/mailman/listinfo/pw_forum > > <http://pwscf.org/mailman/listinfo/pw_forum> > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Fwd: Error in Hybrid Exc calculations
Dear user (please sign always the posts with name and scientific affiliation) There is generally no strict reason in using an US pseudopotential for Ge, and in this case US is detrimental because 1) the EXX calculation is still less stable for US and 2) ecutfock is forced to assume the ecutrho value and you don't gain any speedup. I suggest you to try with a NC pseudopotential. HTH Giuseppe Quoting Debnath Talukdar <debnath.taluk...@students.iiserpune.ac.in>: > -- Forwarded message -- > From: Debnath Talukdar <debnath.taluk...@students.iiserpune.ac.in> > Date: Tue, Sep 13, 2016 at 4:25 PM > Subject: Error in Hybrid Exc calculations > To: PWSCF Forum <pw_forum@pwscf.org> > > > Hi, >I was trying to do hybrid calculations in quantum espresso. The > calculation stopped by printing the following message > > Error in routine electrons (1): > dexx is negative! Check that exxdiv_treatment is appropriate for the > system > > As I know that in hybrid Exc calculation to solve the poisson equation in > reciprocal space their is > fourier transform of density from real to q space. That colomb potential in > poisson equation is diverge at q=0. To remove this divergencies in coulomb > potential in q space is adds a small G to > denomenetor(q+G); known as gygi-baldereschi method, but it is > appropriate for cubic and quasi cubic supercell (Gygi-Baldereschi PRB 34, > 4405 (1986)). > > At first I have used gygi-baldereschi method for my system that is > hexagonal metallic but I have found above error then I have changed this > method from 'gygi-baldereschi' to 'vcut_ws' that is appropriate for > anisotropic supercell but I still got that same error message. > > After that I have changed Hybrid functional from HSE to gau-PBE which used > exxdiv_treatment='none' and x_gamma_extrapolation=.false. but I still got > that same error > message again. > > > Can anybody give any suggestion that how can I solve this problem ? > > I have also doubt about following... > > 1)As we all know that hybrid calculation is very expansive so how can I > reduce different parameter in Hybrid calculation as compared to normal > scf calculations. > >Such that in my normal scf with DFT Exc I have used k -mesh 21x21x1, scf > threshold 10-8Ry, >then how can I reduce these parameters in Hybrid calculations; is it > arbitrary? > > 2)How can I reduce ecutfock to speed up the calculation. Currently I have > used ecutfock=ecutrho (for my system ecutrho=10*ecutwfc), is their is any > way to reduce this kinetic energy cutoff for fock (exchange) operator at > the cost of loss in accuracy in my calculations. > > 3) In our pwscf input file we give explicitly effect of > exchange-correlation functional through card > input_dft, I am doubt that how can I gave both vdW(rev-vdw-b86r) functional > with hybrid calculations(where input_dft='HSE'). > > I have read papers but I am unable to solve these issues can anyone will > give any other papers that how can I solve this. > > Below I have attached input, output files of my calculations. > 1)PRB 34, 4405 (1986) > 2)PHYSICAL REVIEW B 80, 115205 ͑2009͒ > 3)PHYSICAL REVIEW B 74, 121102͑R͒ ͑2006͒ > 4)JCP 118, 8207 (2003) > 5)THE JOURNAL OF CHEMICAL PHYSICS 134, 024116 (2011) > > > > > Thanks -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Image charge interaction
Dear Ilya I'm afraid there is not too much to add. You can test yourself the effect of sa emiempirical application of U by monitorizing the occupation of 3s and 3p Cl orbitals in some simple system like a Na and a Cl atom far from bond distance or a Cl[H2O]6(-) cluster to see when you get Cl(-). A polar solvent/medium stabilizes the excess charge and screen the interaction with images (see the role of dielectric constant in the old Makov-Payne paper) so that you should be able to use lower U values. I've still not published the psII calculations and I'm not sure that I will, because it turned out that structural results are in a closer agreement with experiment by using a GTO framework and COSMO as implicit dielectric environment. HTH Giuseppe Quoting Ilya Ryabinkin <igryabin...@gmail.com>: > 2 Thomas: > >> Or you can also use the simple dipole correction which was actually >> developed for charged (particles on) surfaces, see, e.g., > > No, I think I wish the opposite: currently my pseudo-anion is neutral, > but the *real* one should not be -- and, hence, image charge > interaction is missing... I'd like to get it back. > > Of course, I it is possible and straightforward to keep an extra > electron on chlorine and simulate the system with real -1 charge, that > all what you've said are relevant and good. > > So, Giuseppe > >> I've used a semiempirical U value of 4 eV on the Cl 3p electrons to >> keep together the electrons of Cl- in photosystem II. > > Could you elaborate more on that? Or may be you've published the > results -- I could read and reference them. > > Thanks to all of you, colleagues! > > -- > I. > > On Tue, Sep 13, 2016 at 11:34 AM, Thomas Brumme > <thomas.bru...@mpsd.mpg.de> wrote: >> Or you can also use the simple dipole correction which was actually >> developed for charged (particles on) surfaces, see, e.g., >> >> Phys. Rev. B 59, 12301 (1999) >> >> Phys. Rev. B 63, 205426 (2001) >> >> >> On 09/13/2016 05:22 PM, Giuseppe Mattioli wrote: >>> P.S. >>> If your main concern is the vertical interaction between charges you >>> can discard the interaction by using the ESM boundary conditions in a >>> vacuum-slab-vacuum geometry (see the manual, the implementation is >>> very simple and the calculation is stable in my hands). >>> HTH >>> Giuseppe >>> >>> Quoting Ilya Ryabinkin <igryabin...@gmail.com>: >>> >>>> Hi Thomas: >>>> SIC is definitely one of the ways to address this problem, but we also >>>> thinking about tconstrained DFT approach. Unfortunately, this is more >>>> i) long-term investment, ii) this doesn't rule out the problem of >>>> image charge completely if a slab is too thin. >>>> >>>> BTW: it is written in a manual >>>> >>>>> This approach has known problems for dissociation mechanism driven >>>>> by excess electrons. >>>> >>>> I wonder, what are these problems? >>>> >>>> >>>> -- >>>> I. >>>> >>>> On Tue, Sep 13, 2016 at 10:01 AM, Thomas Brumme >>>> <thomas.bru...@mpsd.mpg.de> wrote: >>>>> Hi Ilya, >>>>> >>>>> I wonder if the SIC implementation in CP can help: >>>>> >>>>> http://www.quantum-espresso.org/wp-content/uploads/Doc/cp_user_guide/node11.html >>>>> >>>>> Unfortunately, I'm not familiar with CP... >>>>> >>>>> Regards >>>>> >>>>> Thomas >>>>> >>>>> >>>>> On 09/13/2016 03:44 PM, Ilya Ryabinkin wrote: >>>>>> 2NIcola: >>>>>> >>>>>>> If I understand this correctly, it seems a less satisfactory >>>>>>> answer that >>>>>> just having the uniform jellium background? >>>>>> >>>>>> No. In particular, I have Cl- species in my system, but there is no >>>>>> way in common GGAs to keep an electron on chlorine -- due to self >>>>>> interaction the electron is too weakly bound (if any) to Cl and DFT >>>>>> gives a completely wrong, de-localized solution for an extra electron. >>>>>> Neutralizing background will simply eat up the field of this >>>>>> delocalized electron and I'll be simulating a system which resembles >>>>>> more a *neutral* Cl atom on a slab rather than an anion. >>>>>> One of the
Re: [Pw_forum] Image charge interaction
/ >>>> 23-24/4é16 Boîte courrier 115, >>>> 4 place Jussieu 75252 Paris Cédex 05 >>>> >>>> ___ >>>> Pw_forum mailing list >>>> Pw_forum@pwscf.org >>>> http://pwscf.org/mailman/listinfo/pw_forum >>> >>> >> >> -- >> Dr. rer. nat. Thomas Brumme >> Max Planck Institute for the Structure and Dynamics of Matter >> Luruper Chaussee 149 >> 22761 Hamburg >> >> Tel: +49 (0)40 8998 6557 >> >> email: thomas.bru...@mpsd.mpg.de >> >> ___ >> Pw_forum mailing list >> Pw_forum@pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum > > > > -- > *** > Ilya Ryabinkin > Postdoctoral Scholar > Physical and Environmental Sciences >University of Toronto Scarborough > http://www.utsc.utoronto.ca/~aizmaylov/Members.html > *** > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Image charge interaction
Dear Ilya I've used a semiempirical U value of 4 eV on the Cl 3p electrons to keep together the electrons of Cl- in photosystem II. However the ion was also screened by a few ligands and by the ENVIRON dielectric medium. Notwithstanding DFT+U and a well-shaped ENVIRON dielectric can be both of help in your system. HTH Giuseppe Quoting Thomas Brumme <thomas.bru...@mpsd.mpg.de>: > Hi Ilya, > > I wonder if the SIC implementation in CP can help: > > http://www.quantum-espresso.org/wp-content/uploads/Doc/cp_user_guide/node11.html > > Unfortunately, I'm not familiar with CP... > > Regards > > Thomas > > > On 09/13/2016 03:44 PM, Ilya Ryabinkin wrote: >> 2NIcola: >> >>> If I understand this correctly, it seems a less satisfactory answer that >> just having the uniform jellium background? >> >> No. In particular, I have Cl- species in my system, but there is no >> way in common GGAs to keep an electron on chlorine -- due to self >> interaction the electron is too weakly bound (if any) to Cl and DFT >> gives a completely wrong, de-localized solution for an extra electron. >> Neutralizing background will simply eat up the field of this >> delocalized electron and I'll be simulating a system which resembles >> more a *neutral* Cl atom on a slab rather than an anion. >> One of the possible ways to work around -- is to devise a >> pseudopotential for Cl with the configuration [He] 2s^2 2p^5 3s^2 >> 3p^6, which has a hole in 2p and an extra electron in 3p, then "bury" >> the hole inside a pseudopotential... This solution, however, leads to >> the apparent lack of charge-image interaction since the resulting >> pseudoatom is neutral (in fact, it looks like Ar). >> >>> the state of charge of your particle >>> will be determined by the physics - i.e. the xc functional will decide >>> how much charge should sit on the particle >> I wish it could be true... but not for the common DFA-s >> >>> Which capability? Adding an empirical extra term in the forces for >>> the charge? >> Yes. I'm wondering if some one already did this. I can do it myself, >> but for the sake of not re-inventing the wheel... >> >> I. >> >> On Tue, Sep 13, 2016 at 6:26 AM, Lorenzo Paulatto >> <lorenzo.paula...@impmc.upmc.fr> wrote: >>> Hello, >>> it is not too clear to me what you need, but is something like >>> this: http:// >>> journals.aps.org/prb/abstract/10.1103/PhysRevB.89.245406 ? >>> >>> It is implemented in the upcoming version 6.0 of QE, >>> The feature is still disabled in the downloadable beta versione, but it is >>> enabled in the last daily snapshots at http://qe-forge.org/snapshots/ (no >>> guarantee anything works). >>> >>> hth >>> >>> On Monday, 12 September 2016 18:13:25 CEST Ilya Ryabinkin wrote: >>>> Dear colleagues: >>>> I am simulating dynamics of a charged particle on a metallic slab. To >>>> avoid difficulties with Coulomb energy of a charged cell, we use a >>>> core-hole trick to introduce a compensatory positive charge directly >>>> into a particle. However, the image-charge interaction is clearly >>>> absent and we would like to bring it back. >>>> >>>> Did anyone bother him/herslef to implement is in QE? I know VASP has >>>> this capability, but it is out of scope. >>>> >>>> Thanks in advance, >>>> I. >>> >>> -- >>> Dr. Lorenzo Paulatto >>> IdR @ IMPMC -- CNRS & Université Paris 6 >>> +33 (0)1 44 275 084 / skype: paulatz >>> http://www.impmc.upmc.fr/~paulatto/ >>> 23-24/4é16 Boîte courrier 115, >>> 4 place Jussieu 75252 Paris Cédex 05 >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum@pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >> >> > > -- > Dr. rer. nat. Thomas Brumme > Max Planck Institute for the Structure and Dynamics of Matter > Luruper Chaussee 149 > 22761 Hamburg > > Tel: +49 (0)40 8998 6557 > > email: thomas.bru...@mpsd.mpg.de > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum -- **** - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] testing HSE for BCC Fe
gt; > charge: 14.4350 magn: 2.6346 constr: 0. > > >> atom: 2 charge: 14.4351 > > magn: 2.6343 constr: 0. > > >> total cpu time spent up to now is 7.2 > > secs > > >> End of self-consistent calculation > >> > >> convergence has > > been achieved in 9 iterations > > >> EXX: now go back to refine exchange > > calculation > > >> total cpu time spent up to now is 4239.4 secs > > Self-consistent Calculation > > >> iteration # 1 ecut= 33.00 Ry > > beta=0.70 > > >> Davidson diagonalization with overlap > >> ethr = 5.49E-08, > > avg # of iterations = 4.9 > > >> total cpu time spent up to now is > > 52490.2 secs > > >> iteration # 2 ecut= 33.00 Ry beta=0.70 > >> Davidson > > diagonalization with overlap > > >> === > >> > >> > >> So, the calculation takes 7 seconds for converging with PBE, 1h10min > > for calculating the EXX term and 14h35min for the first HSE iteration. > Is this correct ? And if so, please, could you try to explain me how to > reduce the computation time. Thanks in advance. > > >> Best wishes, > >> > >> > >> Daniel > >> > >> ___ > > Pw_forum mailing list > > >> Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum [1] > > > ___ > > > Pw_forum mailing > > list > > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > [1] > > > Links: > -- > [1] http://pwscf.org/mailman/listinfo/pw_forum - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] H-bonding in DFT
Dear user Please remember always to sign your post to this forum with name and scientific affiliation. Your question is very general and very difficult, so that a general answer is impossible, and a detailed answer depends strongly on your system features and on your purposes. I can therefore only suggest you that unless you are interested in very fine details a standard GGA functional should behave decently in describing H-bonds, provided that you combine the electrostatic interactions inscribed in the GGA description with one of the (semiempirical or ab initio) models that add long-range dispersion forces. HTH Giuseppe Quoting ZARA NBSH <z.nr...@gmail.com>: > Dear all > > I would like to study the interaction between two organic molecules > (contains C, H and O atoms). > It seems that hydrogen-bonding between H and O atoms of different molecules > play an important role. > > My question is that what is the best method to study this system? > Could usual DFT (GGA for example blyp PP) have a correct prediction of this > system? > > I really appreciate your help in advance. > > WBR > -NN -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Question on Estimated SCF Accuracy
Dear user Please sign always your posts to the forum with name and scientific affiliation. Yes, you are wasting your time and your calculation is likely never going to converge. Impossible to say more without seeing more details of your input file. HTH Giuseppe Quoting Jon G <mike27...@gmail.com>: > I have a rather large unit cell(160 atoms that take up the entirety of the > space - symmetry doesn't let me shrink the cell as far as I know)... > > My question is: Should scf accuracy be going down with each iteration? I > don't have much experience on large systems and I'm wondering if I'm > wasting my time on this calculation(which is still ongoing). I've cherry > picked a few data points below to show you my dilemma. > > IterationSCF accuracy: > 10th< 10.8 Ry > 20th< 14 Ry > 21st< 618 Ry > 50th< 644 Ry > 64th< 207Ry > 65th< 469 Ry -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Problem in SCF convergence with larger unit cells
Dear Reza You can try to use ultrasoft pseudopotentials you may try these ones you find in the online library Ga.pbe-dn-rrkjus_psl.0.2.UPF P.pbe-n-rrkjus_psl.0.1.UPF But you should check the convergence, and I expect something like ecutwfc=40.0 ecutrho=320.0~480.0 Best Regards Giuseppe Quoting reza vatan <rezavata...@gmail.com>: > Dear Giuseppe, > > I had tried the calculations with higher ecutwfc before and as you said it > perfectly worked. But the problem is that the calculations take much > longer. Is there any way to keep the ecutwfc as small as possible and use > different pseudopotentials and still get convergence? Please advise. > > Many thanks in advance. > > Regards, > Reza > > On Sat, Jun 11, 2016 at 2:21 PM, Giuseppe Mattioli < > giuseppe.matti...@ism.cnr.it> wrote: > >> >> Dear Reza Vatan >> >> > ecutwfc = 12.0, >> >> > Ga 69.72 Ga.blyp-d-hgh.UPF >> > P 30.97 P.blyp-hgh.UPF >> >> It is very strange that you converge at all with a so minimal cutoff >> and so hard hgh norm-conserving pseudopotentials. I would bet that >> ecutwfc = 100.0 is barely sufficient for Ga with semicore d shell in >> valence. I suggest that you raise ecutwfc and find convergence for GaP >> in the 2 atoms cell. >> HTH >> Giuseppe >> >> Quoting reza vatan <rezavata...@gmail.com>: >> >> > Dear all, >> > >> > I'm trying to optimize the atomic structure of GaP using QE. When I use a >> > unit cell only containing two atoms, I have no problem in SCF convergence >> > and the structure get optimized in the first step. But when I make my >> unit >> > cell bigger (let's say a unit cell with 64 atoms) just by repeating my >> > smaller optimized unit cell in real space and run relax calculation, the >> > SCF calculation never get converged. Does anyone know where the problem >> is? >> > >> > Following is my input: >> > >> > >> > >> > calculation = "relax", >> > dt = 30.D0, >> > prefix = 'gap', >> > pseudo_dir = './', >> > outdir='./', >> > / >> > >> > ibrav= 6, celldm(1) =20.52, celldm(3) =1, nat= 64, ntyp= 2, >> > ecutwfc = 12.0, >> > degauss = 0.05D0, >> > occupations = "fixed", >> > smearing= "methfessel-paxton", >> > / >> > >> > conv_thr= 1.D-7, >> > mixing_beta = 0.3D0, >> > electron_maxstep= 200, >> > / >> > >> > pot_extrapolation = "second_order", >> > wfc_extrapolation = "second_order", >> > / >> > ATOMIC_SPECIES >> > Ga 69.72 Ga.blyp-d-hgh.UPF >> > P 30.97 P.blyp-hgh.UPF >> > ATOMIC_POSITIONS (angstrom) >> > Ga 2.714678 2.714678 0.00 >> > Ga 0.00 0.00 0.00 >> > Ga 2.714678 0.00 2.714678 >> > Ga 0.00 2.714678 2.714678 >> > P 4.072017 4.072017 1.357339 >> > P 1.357339 1.357339 1.357339 >> > P 4.072017 1.357339 4.072017 >> > P 1.357339 4.072017 4.072017 >> > Ga 2.714678 2.714678 5.429356 >> > Ga 0.00 0.00 5.429356 >> > Ga 2.714678 0.00 8.144034 >> > Ga 0.00 2.714678 8.144034 >> > P 4.072017 4.072017 6.786695 >> > P 1.357339 1.357339 6.786695 >> > P 4.072017 1.357339 9.501373 >> > P 1.357339 4.072017 9.501373 >> > Ga 2.714678 8.144034 0.00 >> > Ga 0.00 5.429356 0.00 >> > Ga 2.714678 5.429356 2.714678 >> > Ga 0.00 8.144034 2.714678 >> > P 4.072017 9.501373 1.357339 >> > P 1.357339 6.786695 1.357339 >> > P
Re: [Pw_forum] Problem in SCF convergence with larger unit cells
678 8.144034
> P 9.501373 4.072017 6.786695
> P 6.786695 1.357339 6.786695
> P 9.501373 1.357339 9.501373
> P 6.786695 4.072017 9.501373
> Ga 8.144034 8.144034 0.00
> Ga 5.429356 5.429356 0.00
> Ga 8.144034 5.429356 2.714678
> Ga 5.429356 8.144034 2.714678
> P 9.501373 9.501373 1.357339
> P 6.786695 6.786695 1.357339
> P 9.501373 6.786695 4.072017
> P 6.786695 9.501373 4.072017
> Ga 8.144034 8.144034 5.429356
> Ga 5.429356 5.429356 5.429356
> Ga 8.144034 5.429356 8.144034
> Ga 5.429356 8.144034 8.144034
> P 9.501373 9.501373 6.786695
> P 6.786695 6.786695 6.786695
> P 9.501373 6.786695 9.501373
> P 6.786695 9.501373 9.501373
> K_POINTS {automatic}
> 2 2 2 0 0 0
> ~
>
>
> Thanks in advance.
>
> Regards,
> Reza Vatan
> School of Electrical, Computer and Energy Engineering
> Arizona State University
--
- Article premier - Les hommes naissent et demeurent
libres et égaux en droits. Les distinctions sociales
ne peuvent être fondées que sur l'utilité commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la liberté,
la propriété, la sûreté et la résistance à l'oppression.
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM)
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail: <giuseppe.matti...@ism.cnr.it>
http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
ResearcherID: F-6308-2012
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Re: [Pw_forum] Spin orbit coupling
Dear user
First of all sign your posts with name and scientific affiliation, please.
When you start using a new code you should read the documentation
before computing.
Apart from the general documentation, there are several examples
embedded in the QE distribution. Look into
your-path-to-QE/PW/examples/README
and you will find
example07:
This example shows how to use pw.x to calculate the total energy
and the band structure of fcc-Pt with a fully relativistic US-PP
which includes spin-orbit effects.
Then look into the example directory
your-path-to-QE/PW/examples/example07/README
REFERENCES:
A. Dal Corso and A. Mosca Conte,
Spin-orbit coupling with ultrasoft pseudopotentials: application to Au and Pt,
Phys. Rev. B 71, 115106 (2005)
A. Dal Corso,
Projector augmented-wave method with spin-orbit coupling: applications to
simple solids and zincblende-type semiconductors,
Phys. Rev. B 86, 085135 (2012)
A. Dal Corso,
Projector augmented-wave method: application to relativistic
spin-density functional theory,
Phys. Rev. B 82, 075116 (2010).
Pseudopotentials with spin-orbit and other tests:
A. Dal Corso,
Pseudopotentials periodic table: from H to Pu,
Comp. Material Science 95, 337 (2014).
and you will find the references to this kind of calculation
If you want to know the meaning of the variables in the input files,
then look here
your-path-to-QE/Doc/INPUT_PW.txt
HTH
Giuseppe
Quoting tanmay chaki <tanmaych...@gmail.com>:
> I am new in quantum espresso.pls help me how to calculate scf with spin
> orbit coupling
--
- Article premier - Les hommes naissent et demeurent
libres et égaux en droits. Les distinctions sociales
ne peuvent être fondées que sur l'utilité commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la liberté,
la propriété, la sûreté et la résistance à l'oppression.
****
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM)
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail: <giuseppe.matti...@ism.cnr.it>
http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
ResearcherID: F-6308-2012
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Re: [Pw_forum] charge is wrong: smearing is needed
Dear Evan (sign always with full name, please) You are not simulating an insulator LiF, you are simulating a LiF with an interstitial H that add one electron to the system, so that you have an even number of electrons. But you required a closed shell calculation. The code is not able to fit the excess electron in a closed shell orbital if you do not permit the treatment of the system as a "metal" by using one of the flavours of occupations='smearing'. You might also want to consider if nspin=2 is more suitable in your case. HTH Giuseppe On Friday, June 10, 2016 04:20:55 PM evan wrote: > Dear all, > > I am performing geometry optimization calculations on insulator LiF. For > insulators with a gap, I read from the variable document and set > âoccupations = fixedâ in the input file (attached). However, at the end > of one BFGS optimization step (contains 15 scf iterations), the error is > followed (also attached): > > > > %% > > Error in routine electrons (1): > > charge is wrong: smearing is needed > > %% > > > > The error is self-explained, and it can be fixed by âoccupations = > smearingâ, but it is conflict with what is said in the document. > > So, how to fix the problem. Your comments or suggestions are much > appreciated. > > Regards > > Evan > > University of South China, China - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] CPO-27-Zn scf not converge
Dear Lorenzo
Sorry, I'm not familiar with the new crystal_sg coordinates, but it seems to me
that there is something strange in the structure. I suggest that you
"fill the unit cell" with all the equivalent atoms (Avogadro or Vesta can do it
for you) and check the results to be sure that you are calculating
exactly what you want. If pw.x fills the unit cell and write the resulting alat
coordinates of all atoms (as usual), then you may directly check them
with xcrysden. You might try to run the job with the full structure and simple
"crystal" coordinates. Maybe something goes wrong when the code try to
fill the unit cell in the crystal_sg case. Anyway I suppose that there is no
computational gain in using the crystal_sg coordinates ("no free lunch"
:-)).
HTH
Giuseppe
On Sunday, May 29, 2016 09:11:49 PM Lorenzo Donà wrote:
> Dear all can you help me or give me some tips to make scf convergence on this
> calculation:
>
>
> pseudo_dir='/home/utente/Scaricati/espresso-5.4.0/pseudo/'
> outdir = './',
> wf_collect = .true.,
> verbosity= high,
> /
>
> ibrav= 5,
> a= 25.226, cosab= 0.5, space_group = 148,
> nat= 9, ntyp= 4,
> ecutwfc =15.0,
> occupations='fixed', smearing='gauss',
> input_dft= PBE,
> /
>
> mixing_mode='plain'
> diagonalization='david'
> mixing_beta = 0.01
> conv_thr= 1.0e-4
> electron_maxstep=500,
> /
> ATOMIC_SPECIES
> Zn 65.409 Zn.pbe-van.UPF
> C 12.010 C.pbe-van_ak.UPF
> O 16.00 O.pbe-van_ak.UPF
> H 1.00H.pbe-van_ak.UPF
> ATOMIC_POSITIONS crystal_sg
> C 7.127430447398E-02 -2.455696438145E-01 7.991093030472E-02
> C 1.197468901477E-01 -2.066445045066E-01 2.152449225957E-01
> C 2.117353032357E-01 -1.117780631842E-01 2.553368090727E-01
> C 1.646071563067E-01 -1.528403540257E-01 1.440875844425E-01
> H 1.629458066146E-01 -1.419696182443E-01 -4.760745519579E-03
> Zn -1.943259345214E-02 2.834354147594E-01 3.060064447988E-01
> O 7.229455751443E-02 -2.290060932141E-01 -9.085450716092E-02
> O 3.018234203718E-02 -2.947952345384E-01 1.422041978763E-01
> O 2.519030126218E-01 -6.097111538485E-02 1.721974260943E-01
> K_POINTS gamma
>
> Thanks a lot to help me
>
> dearly
>
> lorenzo
- Article premier - Les hommes naissent et demeurent
libres et égaux en droits. Les distinctions sociales
ne peuvent être fondées que sur l'utilité commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la liberté,
la propriété, la sûreté et la résistance à l'oppression.
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM), Italy
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: <giuseppe.matti...@ism.cnr.it>
http://www.ism.cnr.it/en/staff/giuseppe-mattioli/
ResearcherID: F-6308-2012
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Re: [Pw_forum] Hybrid XC Functional
Dear Amir M. Mofrad Look into your-path-to-quamtum-espresso/PW/examples/EXX_example before all read carefully the README file HTH Giuseppe On Wednesday, May 18, 2016 09:24:08 PM Mofrad, Amir Mehdi wrote: > Dear all QE users and developers, > > I want to run my simulations using hybrid functional however, I don't know > how to specify it in my input file. Any help would be thoroughly > appreciated. > > > Best, > > > Amir M. Mofrad > > University of Missouri - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Phonon calculations for functionalized frequencies.
Dear Gangotri Dey > "Error in routine phq_readin (1): > no elec. field with metals" You are probably using occupations=smearing in your pw.x calculations. If I remember well, the ph.x code stops and complains because it is not able to perform IR and Raman calculations on what could be a "metal", even it is not necessarily a real metal. Use occupations=fixed, instead. HTH Giuseppe Quoting gangotri dey <holyriv...@gmail.com>: > Hello! > > I am trying to extract the IR and Raman frequencies of my functionalized > frequencies. I have successfully done my geometry relaxation. However, when > I am doing the Phonon calculations it shows me this problem, > > "Error in routine phq_readin (1): > no elec. field with metals" > > I do not understand the reason for this problem. If anyone has some idea, > it will be highly appreciated. > > > *Thank you* > > *Gangotri Dey* -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] error in producing ultra soft pseudo potential.
Dear Pranay Biswas Version 4.1.2 is outdated since six or seven years. I'm not even going to try to understand your problem if you use such an old version of the code. HTH Giuseppe On Tuesday, May 17, 2016 04:25:42 PM pranay biswas wrote: > dear quantum espresso users, > I'm new in this world.please help me > I'm trying to produce ultra soft pseudo potential for Titanium using QE > 4.1.2. > given input is > > > > title='Ti', > > zed=22, > > rel=0, > > beta=0.5, > > rlderiv=2.4, > > eminld=-4.0, > > emaxld=4.0, > > deld=0.02d0, > > nld=3, > > config='[Ar] 3d2 4s2 ', > iswitch=3, > > dft='PBE', > > / > > > > pseudotype=3, > > lloc=0, > > rcloc=2.90, > > file_pseudopw='Ti.pbe.nrUS', > > / > > 6 > > 3D 3 2 1.00 0.00 2.00 2.60 > > 3D 3 2 0.00 0.05 2.00 2.60 > > 3D 3 2 1.00 0.00 2.00 2.60 > > 3D 3 2 0.00 -0.00 2.00 2.60 > > 4S 1 0 2.00 0.00 2.20 2.90 > > 4S 1 0 0.00 -0.00 2.20 2.90 > > > and when run the error appear as follow > > > Program LD1 v.4.1.2 starts ... > > Today is 17May2016 at 15:38:57 > > > %% > > from ld1_readin : error # 1 > > only one local channel > > %% > > > stopping ... > > > how can I recover this problem. anybody help ,thanks by advanced... - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] one strange result about the phenazine molecule
Dear Dai Zhenxiang You may be aware that DFT eigenvalues depend on the exchange-correlation functional employed in the calculation. Chemists usually use B3LYP for database purpose (it is not indicated in the link you provided, so I assume that it is B3LYP). Which xc functional have you used in your calculation? You might enjoy this paper if you are puzzled by my considerations... Cohen, A. J.; Mori-Sànchez, P.; Yang, W. Insights into Current Limitations of Density Functional Theory. Science 2008, 321, 792−794. HTH Giuseppe Quoting Dai Zhenxiang <phys...@qq.com>: > Dear all: > These days I have performed one test calculation about the > phenazine molecule. > From the website Nanoniele, it can be found that its HOMO-LUMO gap > should be 3.654eV. > http://www.nanoniele.jp/cgi-bin/nanoniele.cgi?inputsite=ranking_HOMO_China%20Telecom=homolumo=174679811422510=phz > However, my QE calculation suggests HOMO-LUMO gap is only about > 2.20 eV. So, the difference is very, very big ! > > These corresponding files are attached. Would you like to give me > some advice? > > Best wishes! > > DAI -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] crmno4 structure is not converging
Dear Rajkamal.A. You will hardly perform a calculation such as yours with NC PPs (mt=Martins-Troullier norm-conserving pseudopotentials) and with a 30Ry cutoff on wavefunctions. Check *always* convergence wrt the basis set *before* starting production runs. HTH Giuseppe On Thursday, May 12, 2016 07:51:56 AM Raj kamal wrote: > dear QE experts below my input file is attached which is not > convergingplease suggest me how to converge this file.thanks in advance > > > > calculation = 'vc-relax' , >outdir = '/home/ > pseudo_dir = '/home/ > prefix = 'crmno112', >etot_conv_thr = 1.0D-5, >forc_conv_thr = 1.0D-4, > tprnfor=.TRUE. > / > > ibrav = 0, > nat = 112, >ntyp = 3, > ecutwfc =30.0 , > ecutrho =120, > occupations='smearing', > smearing='gauss', > degauss=0.02, > nspin = 2, > starting_magnetization(1)= 0.5, > starting_magnetization(2)= 0.5, > / > > electron_maxstep = 500 > mixing_mode = 'plain' , > mixing_beta = 0.4, > diagonalization = 'cg' , > conv_thr = 1.0e-6, > > / > > ion_dynamics = 'bfgs' , > / > > cell_dynamics = 'bfgs', > cell_dofree = 'all' > / > ATOMIC_SPECIES > Cr 51.9961 Cr.pbe-mt_fhi.UPF > Mn 54.938049 Mn.pbe-mt_fhi.UPF > O15.9997 O.pbe-mt_fhi.UPF > CELL_PARAMETERS angstrom > 16.87400 0.0 0.0 > -0.0 8.43700 0.0 > -0.0 -0.0 8.43700 > ATOMIC_POSITIONS angstrom > Mn 0.0 0.0 0.0 > Mn -0.0 4.21850 4.21850 > Mn 4.21850 -0.0 4.21850 > Mn 4.21850 4.21850 0.0 > Mn 6.32775 2.10925 6.32775 > Mn 2.10925 2.10925 2.10925 > Mn 2.10925 6.32775 6.32775 > Mn 6.32775 6.32775 2.10925 > Cr 5.27312 5.27312 5.27313 > Cr 5.27313 1.05462 1.05463 > Cr 1.05462 5.27313 1.05463 > Cr 1.05462 1.05462 5.27313 - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] PDOS error
I used to perform projwfc.x calculations after EXX without (particular) problems. My last attempt has been done with v.5.2.0 anyway. HTH Giuseppe On Wednesday, May 11, 2016 12:23:42 PM Paolo Giannozzi wrote: > If this happens in a large memory run, typically it means "out of memory". > If not: I am not sure projected DOS is implemented for hybrid and > Hartree-Fock calculations > > On Wed, May 11, 2016 at 12:17 PM, stefano < > > stefano.di-sabat...@polytechnique.edu> wrote: > > Dear all, > > > > I'm trying to plot the projected DOS of a Hartree-Fock calculation. But > > I get the following error: > > > > *** Error in `projwfc.x': malloc(): smallbin double linked list > > corrupted: 0x02fb7590 *** > > Program received signal SIGABRT: Process abort signal. > > Backtrace for this error: > > > > or > > > > Program received signal SIGSEGV: Segmentation fault - invalid memory > > reference. > > > > What does it mean? In the case of the total dos instead I have no problem. > > I tried to change some of the parameters but I always get an error from > > projwfc.x. > > > > > > Here follows the input files: > > > > #!/bin/sh > > > > # > > # output in results_NiO_nm/ > > # > > if [ ! -d results_NiO_nm ]; then > > > > mkdir results_NiO_nm > > > > fi > > > > # self-consistent calculation > > cat > nio_nm.scf.in << EOF > > > > > > > > prefix='nio', > > > > / > > > > > > ibrav= 0, celldm(1)=3.9468, nat= 2, ntyp= 2, > > ecutwfc = 30.0, ecutrho = 120.0, > > input_dft='hf', nqx1 = 1, nqx2 = 1, nqx3 = 1, > > x_gamma_extrapolation = .TRUE., > > ecutvcut=0.7, > > occupations='smearing', smearing='mp', degauss=0.02, > > nspin=1, > > > > / > > > > > > mixing_beta = 0.3 > > > > / > > > > CELL_PARAMETERS > > 1 1 0 > > 1 0 1 > > 0 1 1 > > ATOMIC_SPECIES > > > > O1. O.pbe-mt.UPF > > Ni 1. Ni.pbe-mt_fhi.UPF > > > > ATOMIC_POSITIONS crystal > > > > O 0.5 0.5 0.5 > > Ni 0.0 0.0 0.0 > > > > K_POINTS automatic > > 4 4 4 0 0 0 > > EOF > > pw.x < nio_nm.scf.in > results_NiO_nm/nio.scfHF.out > > > > > > # non self-consistent calculation > > cat > nio_nm.nscf.in << EOF > > > > > > > > calculation='nscf' > > prefix='nio', > > > > / > > > > > > ibrav= 0, celldm(1)=3.9468, nat= 2, ntyp= 2, > > ecutwfc = 30.0, ecutrho = 120.0, > > occupations='smearing', smearing='mp', degauss=0.02, > > nspin=1, > > > > / > > > > > > mixing_beta = 0.3 > > > > / > > > > CELL_PARAMETERS > > 1 1 0 > > 1 0 1 > > 0 1 1 > > ATOMIC_SPECIES > > > > O1. O.pbe-rrkjus.UPF > > Ni 1. Ni.pbe-nd-rrkjus.UPF > > > > ATOMIC_POSITIONS crystal > > > > O 0.5 0.5 0.5 > > Ni 0.0 0.0 0.0 > > > > K_POINTS automatic > > 8 8 8 0 0 0 > > EOF > > pw.x < nio_nm.nscf.in > results_NiO_nm/nio.nscf.out > > > > cat > nio.dos.in << EOF > > > > > > > > prefix='nio' > > fildos='nio.dos' > > degauss = 0.007d0, > > ngauss = 0 > > DeltaE=0.1 > > Emin=-10 > > Emax=40 > > > > / > > > > EOF > > dos.x < nio.dos.in > results_NiO_nm/nio.dos.out > > > > > > cat > nio.pdos.in << EOF > > > > > > > > prefix='nio' > > degauss = 0.007d0, > > ngauss = 0 > > DeltaE=0.1 > > Emin=-10 > > Emax=40 > > > > / > > > > EOF > > projwfc.x < nio.pdos.in > results_NiO_nm/nio.pdos.out > > > > mv nio.dos nio.pdos_* results_NiO_nm/ > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] B3LYP+D
Dear Anna What is B3LYP+D? Best Giuseppe Anna Maria Ferrari <anna.ferr...@unito.it> ha scritto: > dear all > i need to calculate TiO2 with B3lYP+D > where it is possible to find and example of input for this or any system? > > thanks in advance > anna > > <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail> > Mail > priva di virus. www.avast.com > <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail> > <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2> -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] London Dispersion force: DFT-D2
Dear Elliot I do not know if I understand well your questions, but I try to answer: > Could someone please assist me as to how to account for London > dispersion forces with QE or essentially how to do a DFT-D2 calculation > with the the aim of accounting for the energy contribution of dispersion > forces. Use vdw_corr='grimme-d2' You will find in the output the dispersion force contribution to the total energy: !total energy = -2369.89004091 Ry Harris-Foulkes estimate = -2369.89004090 Ry estimated scf accuracy< 0.0001 Ry The total energy is the sum of the following terms: one-electron contribution = -22567.16723495 Ry hartree contribution = 11423.49753189 Ry xc contribution =-757.0298 Ry ewald contribution=9530.66102736 Ry Dispersion Correction = -0.98373910 Ry Hubbard energy= 1.13399751 Ry smearing contrib. (-TS) = -0.00195694 Ry > I'm trying to account for the energy contribution of London dispersion > forces on the total energy of a hydrazine-nickel system. Remember that DFT-D2 badly overestimate the interaction of molecules with metal surfaces, see Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J. Chem. Phys. 2010, 132, 154104. In cases such as N2H2 on Ni I would rather use vdwdf or vdwdf-c09 (see usage and related papers in QE documentation). > -- > > tefield = .TRUE., >dipfield = .TRUE., >disk_io = 'low', > > >edir=3, >emaxpos=0.65, >eopreg=0.06, >eamp=0, > -- > This is a well tested but old and complex machine to correct the interaction of a dipole with its periodic replicas along z. I do not know if it is possible to estimate its impact on dispersion forces in a different way than by using/not using the dipole correction and check the difference between the above "Dispersion Correction" contribution to the total energy. However, I've satisfactorily used for a system similar to yours (thiol SAM on Au surface) this new setup (again, read the documentation and related papers), which decouple in a simpler way the dipole along z. input_dft='vdw-df-c09' assume_isolated = 'esm', esm_bc='bc1', / HTH Giuseppe On Tuesday, May 03, 2016 12:41:49 AM Elliot Menkah wrote: > Hi all, > I'm trying to account for the energy contribution of London dispersion > forces on the total energy of a hydrazine-nickel system. > > Could someone please assist me as to how to account for London > dispersion forces with QE or essentially how to do a DFT-D2 calculation > with the the aim of accounting for the energy contribution of dispersion > forces. > > When I correct the net-surface dipole on a system by using the variables > and values below, does it affect the energy from dispersion forces, if > so, how? > How does correcting the net-surface dipole relate to accounting for > dispersion forces? > > -- > > tefield = .TRUE., >dipfield = .TRUE., >disk_io = 'low', > > >edir=3, >emaxpos=0.65, >eopreg=0.06, >eamp=0, > -- > > > I'm basically trying to account for London dispersion forces on a > hydrazine-nickel system. > Any info to help my computation would be gladly appreciated. > Thank you > > Kind Regards, > Elliot - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] relaxation of doped system
Dear Yao-Hong it is difficult to say much without seeing any detail of your calculation (version of the code, method, functional, pseudopotentials, ...) > My question is should I do the vc-relax again after doping? Yes, you should do it. And sometimes you should also check the stress tensor to verify that doping does not tend to alter too much the lattice parameter. It is not strictly mandatory, but sometimes you find interesting physics/chemistry (isoelectronic N in GaAs, H in InN only to provide a couple of examples). > After relaxation, I built a 1*2*2 supercell (32 atoms), > then I changed one Sn atom into Cu and do the vc-relax again, This is > 6% doping. Are you sure that it is correct for your system? > The program have been working for 3 days but it seems that it won't be done What is it doing? Where is it running? Are you using LDA/GGA or EXX? HTH Giuseppe On Sunday, May 01, 2016 01:00:58 PM n16031320 wrote: > Dear users and developers: > > I'm studying SnSe doped with Cu, first I do the vc-relax for SnSe of > unitcell. > > After relaxation, I built a 1*2*2 supercell (32 atoms), > > then I changed one Sn atom into Cu and do the vc-relax again, > > My question is should I do the vc-relax again after doping? > > The program have been working for 3 days but it seems that it won't be > done... > > Thank you in advance ! > > Regards > > > Yao-Hong Huang - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Hubbard Correction demo files
Dear Vijay Khanal Many pages should be written to explain why the simplified linear-response DFT+U formulation is not quite suitable for strongly hybridized sp3 materials like silicon or diamond... If you only want to practice around with the U correction you can (carefully) make your way through this tutorial (download the "correlated materials" files) http://www.fisica.uniud.it/~giannozz/QE-Tutorial/ Read also Himmetoglu, B.; Floris, A.; de Gironcoli, S.; Cococcioni, M. Hubbard-Corrected DFT Energy Functionals: The LDA+U Description of Correlated Systems. Int. J. Quantum Chem. 2014, 114, 14. If you also want to try to understand why DFT+U is not suitable for Si, then you should start (for example) with these papers: Leiria Campo Jr, V. and Cococcioni, M. Extended DFT + U + V method with on-site and inter-site electronic interactions. J. Phys.: Condens. Matter 22 (2010) 055602 Cohen, A. J.; Mori-Sànchez, P.; Yang, W. Insights into Current Limitations of Density Functional Theory. Science 2008, 321, 792-794. Luis A. Agapito, Stefano Curtarolo, and Marco Buongiorno Nardelli Reformulation of DFT+U as a Pseudohybrid Hubbard Density Functional for Accelerated Materials Discovery. PHYSICAL REVIEW X 5, 011006 (2015) HTH Giuseppe On Wednesday, April 27, 2016 11:30:06 PM Vijay Khanal wrote: > Dear Everyone, > > I am new to Quantum Espresso. I am trying to see how hybrid functionals > better estimate the bandgap of a semiconductor like Silicon. I was > wondering, therefore, if somebody could provide me with demo input/output > files that involve Hubbard's Correction. > > Any response would be highly appreciated. > > > Thank you. > > Respectfully, > Vijay Khanal > *Vijay Khanal* > Department of Physics > University of Nevada, Reno > Phone:(1-*775-440-7036)* - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Work function issues
Dear all If you do not want to bother with potential realignment in slab calcuations of WF you can use the (very nice) new implementation of the ESM method in a vacuum-slab-vacuum framework. The usage is very simple assume_isolated = 'esm', esm_bc='bc1', and you find in the outdir some prefix.esm1 file containing all the desired quantities (charge density, a variety of potentials) averaged along the z axis of the cell. #z (A) Tot chg (e/A) Avg v_hartree (eV) Avg v_local (eV) Avg v_hart+v_loc (eV) As the method decouple the slab along z you can also treat polar interfaces (e.g. gold electrode + polar SAM) and obtain two nice, different, flat asymptotic values of the potential on the two sides of the slab, without using any dipole correction. HTH Giuseppe On Friday, April 22, 2016 04:51:18 PM Giovanni Cantele wrote: > Maybe it is neither a poor pseudo potential choice nor a bug or user error. > > Using for example Au.pbe-mt_fhi.UPF I get > > Fermi level ~ 3.30 eV > vacuum level ~ 8.48eV > > with a plot similar to what you attach in a follow-up e-mail. > That corresponds to a ~ 5.17 gold work function, not that far from literature > results, see, e.g., PHYSICAL REVIEW B 80, 235407 2009 . > > Take care of slab thickness convergence issues as well as of the fact that a > more accurate calculation might require a bulk crystal calculation, > see details in the above reported reference. > > Giovanni > > > On 21 Apr 2016, at 17:57, Hepplestone, Steven > > <s.p.hepplest...@exeter.ac.uk> wrote: > > > > Dear all, > > > > I am having difficulties with calculating the work function of various > > metals (Au and Pt in particular) using the X.pbe-mt_fhi.UPF and > > X.pbe-n-nc.UPF pseudo potentials. Unlike in the example in WorkFct_example > > in PP I am regularly getting a positive Fermi energy and a vacuum > > level which is lower than the average level for the potential of the atoms. > > Is this a case of poor pseudo potential choice, a bug or user error? > > > > Any advice would be appreciated, > > > > Kind regards > > > > Steven > > > > > > Dr. Steven Hepplestone > > Physics > > University of Exeter > > Stocker Road > > Exeter > > EX4 4QL > > Ext.: +44 (0)1392 723048 > > Int.: 3048 > > > > ___ > > Pw_forum mailing list > > Pw_forum@pwscf.org <mailto:Pw_forum@pwscf.org> > > http://pwscf.org/mailman/listinfo/pw_forum > > <http://pwscf.org/mailman/listinfo/pw_forum> - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] vdW-DF + starting_magnetization
Dear Mohammad If I remember well the new formulation of open-shell vdwdf has been implemented in the 5.2.1.or 5.3.0 version. I've performed satisfactory calculations with vdw-df-c09 (but I've not tested vdw-df2-c09) on an open shell molecule. It seems that you are using the 5.2.0 version. You may try to switch to a newer version. HTH Giuseppe On Friday, April 22, 2016 06:08:23 PM Mohamad Moadeli wrote: > Dear all, > > I am trying to use input_dft='vdw-df2-c09' for an antiferromagnetic system. > > > > > calculation= 'relax', > restart_mode= 'from_scratch' , > pseudo_dir = '~/pseudo/' , > outdir= 'tmp' , > prefix= 'vdW-afm-NiCu' > verbosity='high' , > tstress= .TRUE. > tprnfor= .TRUE. > nstep=200 , > / > > ibrav = 4, > celldm(1)= 4.639055, celldm(3)= 12.0, > nat =9 , ntyp =3, > nspin =2, starting_magnetization(1)=0.7, starting_magnetization(2)=-0.7, > ecutwfc = 65, ecutrho = 450, > occupations = 'smearing',smearing='mp',degauss=0.01, > input_dft='vdw-df2-c09' , > / > > conv_thr = 1.0d-6, > mixing_mode = 'plain', > mixing_beta = 0.3 , > diagonalization = 'david', > electron_maxstep =400, > / > > ion_dynamics= 'bfgs', > / > ATOMIC_SPECIES > Ni 58.6934 Ni.pbe-n-rrkjus_psl.0.1.UPF > Cu 63.546Cu.pbe-dn-rrkjus_psl.0.2.UPF > C12.0107 C.pbe-n-rrkjus_psl.0.1.UPF > > ATOMIC_POSITIONS (crystal) > Ni *0 0 0 > Ni * > Ni * > Ni * > Ni * > Ni * > Cu * > C * > C* > > K_POINTS automatic > 24 24 1 0 0 0 > == > > I got the following error: > > === > > Program PWSCF v.5.2.0 starts on 24Sep2015 at 12:35: 4 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > URL http://www.quantum-espresso.org;, > in publications or presentations arising from this work. More details > at > http://www.quantum-espresso.org/quote > > Parallel version (MPI), running on16 processors > R & G space division: proc/nbgrp/npool/nimage = 16 > Waiting for input... > Reading input from standard input > ... > ... > ... > ... > Check: negative/imaginary core charge= -0.060.00 > > Initial potential from superposition of free atoms > > starting charge 78.99818, renormalised to 79.0 > > negative rho (up, down): 2.400E-05 8.455E-06 > > > %% > Error in routine gcx_spin (16): > not implemented > > %% > > stopping ... > > > %% > Error in routine gcx_spin (16): > not implemented > > %% > > stopping ... > > == > > It seems that running such an input is not implemented. I was wondering if > there is a solution to this problem. > > Any help will be greatly appreciated. > > Mohammad Moaddeli, > > Shahid Chamran University of Ahvaz - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] TiO2, ZO2 and BaTiO3 nanoclusters
Dear Andrey Sorry for the late reply. > I read the manual. So, need I take the parameters assume_isolated? Yes, the Makov-Payne implementation of assume_isolated, e.g., provides decoupling of long-range electrostatic interaction between periodically replicated images of your clusters, as well as an estimate of the vacuum level, useful to the "absolute" alignment of band edges of different materials. It also works fine with the ENVIRON plug-in; if you are planning to perform calculations of charged clusters you may want to flick through the environ homepage here: http://www.quantum-environment.org/ > I read the manual. So, need I take the parameters lda_plus_u? Yes, but you should know what you are doing... Read carefully the DFT+U review papers, specially this one: Himmetoglu et al International Journal of Quantum Chemistry 2014, 114, 14 For an interesting discussion about some limits of the simplified DFT+U approach in the case of TiO2 and ZnO you may flick through this paper: Agapito et al Phys. Rev. X 5, 011006 2015 and for a "semiempirical" estimate of U in the cases of TiO2 and ZnO you may read my papers (for ZnO also the SuppInfo): J. Phys. Chem. C 2012, 116, 15439 J. Phys. Chem. C 2014, 118, 29928 HTH Giuseppe On Wednesday, March 23, 2016 12:23:22 PM Andrey Chibisov wrote: > Dear Colleagues! > I have some questions. > I want to calculate the electronic structure of the TiO2, ZO2 and BaTiO3 > nanoclusters and get good value of bandgap. > I read the manual. So, need I take the parameters assume_isolated and > lda_plus_u? > > -- > Best regards, > Andrey Chibisov. Ph.D. > Numerical method of mathematical physics Laboratory, > Computational Center, Russian Academy of Sciences. > Khabarovsk, Russia > Web page: https://www.researchgate.net/profile/A_Chibisov > http://ru.linkedin.com/pub/andrey-chibisov/55/253/986/en - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] citing PSLibrary
Dear Merlin Dal Corso, A. Comput. Mater. Sci. 2014, 95, 337−350. HTH Giuseppe On Tuesday, March 22, 2016 12:23:34 PM Merlin Meheut wrote: > Dear PWSCF users, > > I have made important use of some pseudopotentials present in the > PSLibrary, and I would like to describe them in a publication. More > precisely, I used the pseudopotentials Mg.blyp-spn-rrkjus_psl.1.0.0.UPF, > K.blyp-spn-rrkjus_psl.1.0.0.UPF, and Li.blyp-sl-rrkjus_psl.1.0.0.UPF. > > Do you have any advice on how to describe them, and/or on how to cite the > PSLIbrary (version 1.0.0)? > > Thank you very much for any advice, > > Best regards, > > Merlin Meheut - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Mailing issue
dear Vijay Khanal This is the best (and only) way. Use a meaningful subject and write another e-mail to this address... HTH Giuseppe On Monday, March 21, 2016 09:03:47 AM Vijay Khanal wrote: > Hello there, > > I would like to ask a question in the pw forum. Could you please suggest me > what is the best way to do that? > > > Thanks. > > > Sincerely, > Vijay Khanal. > *Vijay Khanal* > Department of Physics > University of Nevada, Reno > Phone:(1-*775-440-7036)* - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] ENVIRON vs COSMO solvation models
Dear Oliviero Thank you for your prompt and detailed answer! I will surely contact you in private for further discussions. Best Wishes Giuseppe On Wednesday, March 09, 2016 10:49:52 AM Oliviero Andreussi wrote: > Hi Giuseppe, > > You can play with the same two parameters in Environ as well, you just > need to set env_static_permittivity (and env_optical_permittivity for > TDDFT) to the ones of the medium you want to simulate. This is assuming > that you are only interested in the electrostatic interaction with the > solvent and that the shape of the cavity, i.e. how close to the solute > you get the continuum solvent, does not depend on the kind of solvent. > Both these assumptions are implicit in your analogy with COSMO (which by > the way is a less refined continuum model than the standard PCM or than > the SCCS model of Environ), but they may be crude depending in the > system/property you want to study. In particular, I am quite sure that > standard PCM uses a different scaling of the size of the cavity for > different solvents. > > Clearly, if you are only interested in studying the effects of a > different dielectric constant of the environment on your embedded > quantum-mechanical system (e.g. as was done in Fortunelli et al. Angew. > Chem. Int. Ed. 126, 6787 (2014) doi:10.1002/ange.201403264) you can do > it very easily with the parameters above. Instead of using one of the > preset solvent setups (environ_type = > vacuum/water/water-cation/water-anion), you specify in input only the > dielectric constant that you want to use, env_static_permittivity = XXX, > and use the defaults for all the other parameters (which corresponds to > no contribution from non-electrostatic terms, env_pressure = 0.D0, > env_surface_tension = 0.D0, and to a shape of the cavity equal to the > one optimized for water, rhomax = 0.005, rhomin = 0.0001). > > Otherwise, if you have to study a well defined solvent and want to be > more accurate, you would need to redo the parametrization of the model > for the new solvent, which for Environ only requires to tune 3 (or 4) > parameters (rhomax and rhomin, which controls the shape of the cavity, > env_static_permittivity and env_pressure, which are used to model non > electrostatic effects in a simplified way). Ideally you want to tune > these parameters to reproduce experimental solvation free energies of a > reasonable range of solutes in the new solvent (a good database of > experimental data is from the group of Truhlar > http://comp.chem.umn.edu/mnsol/ ). > > Since I am trying to improve on the documentation of the module, which > probably is not clear enough, can I ask you which documentation have you > been studying? The website (www.quantum-environ.org), the input keywords > (as in the Environ/Doc/ directory or from the website > http://nebula.wsimg.com/c3d04ee804fb1a1ddb5402d80b7c8194?AccessKeyId=ECF106C2B7F0B5C40F7B=0=1 > ), the references? If you have more doubts on setting up the input or on > the implemented models, please don't hesitate to write to the forum or > to contact me directly. > > Regards, > > Oliviero Andreussi > > > Dear All > > I was studying the documentation of the ENVIRON 0.2 plugin and it seems > > that water only is coded as solvent for isolated molecules. I was > > wondering > > whether there is somewhere a subset of variables (which I was not able to > > found...) that setup alternative dielectric media as in the case of the > > COSMO model (cited in the ENVIRON documentation), which basically requires > > the solvent dielectric constant (ground state DFT) or dielectric > > constant+refractive index (TDDFT) only. > > Thank you in advance > > Giuseppe > > > > > > - Article premier - Les hommes naissent et demeurent > > libres et égaux en droits. Les distinctions sociales > > ne peuvent être fondées que sur l'utilité commune > > - Article 2 - Le but de toute association politique > > est la conservation des droits naturels et > > imprescriptibles de l'homme. Ces droits sont la liberté, > > la propriété, la sûreté et la résistance à l'oppression. > > > > > > Giuseppe Mattioli > > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > > v. Salaria Km 29,300 - C.P. 10 > > I 00015 - Monterotondo Stazione (RM), Italy > > Tel + 39 06 90672836 - Fax +39 06 90672316 > > E-mail: <giuseppe.matti...@ism.cnr.it> > > http://www.ism.cnr.it/english/staff/mattiolig > > ResearcherID: F-6308-2012 > > > > ___ > > Pw_f
[Pw_forum] ENVIRON vs COSMO solvation models
Dear All I was studying the documentation of the ENVIRON 0.2 plugin and it seems that water only is coded as solvent for isolated molecules. I was wondering whether there is somewhere a subset of variables (which I was not able to found...) that setup alternative dielectric media as in the case of the COSMO model (cited in the ENVIRON documentation), which basically requires the solvent dielectric constant (ground state DFT) or dielectric constant+refractive index (TDDFT) only. Thank you in advance Giuseppe - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Charge analysis in QE
Dear Chi-Ta > ".cube" shows a new set of cartesian coordinates based on fileout, > which is different from my original cartesian coordinates. Check whether the refolding of coordinates into your supercell possibly made by pw.x or pp.x yielded a different but equivalent set of cartesian coordinates. > Is it normal to have a new set of cartesian coordinates? In this > case, will it affect bader charge? It is in cube files, and no, it does not affect the results of Bader analysis. HTH Giuseppe Quoting "Yang, Chi-Ta" <chita-y...@uiowa.edu>: > Dear Giuseppe, > > Thanks for your replay. I tried bader charge analysis, but have a > concern about it. > I used cartesian coordinates in my pw.x input file. I noticed that > the coordinate systems in the output files of pp.x (fileout and.cube > ) are different. > > "fileout" shows crystal coordinates > > ".cube" shows a new set of cartesian coordinates based on fileout, > which is different from my original cartesian coordinates. > > Is it normal to have a new set of cartesian coordinates? In this > case, will it affect bader charge? > > Thanks a lot, > Chi-Ta Yang > University of Iowa > > ____ > From: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on > behalf of Giuseppe Mattioli <giuseppe.matti...@ism.cnr.it> > Sent: Monday, February 8, 2016 9:50 AM > To: pw_forum@pwscf.org > Subject: Re: [Pw_forum] Charge analysis in QE > > Dear Chi-Ta Yang > >> For the charge analysis in QE, is it fine to use the charge values >> from the .out files? > > No, it is a fast on-the-fly calculation. You can post-process your > results a) with projwfc.x to obtain Lowdin charges or b) with pp.x > to export the > total charge density as a .cube file and then with an external tool > you find here (http://theory.cm.utexas.edu/henkelman/code/bader) to > calculate the > Bader charges from the cube files. Better results are obtained by > using denser FFT grids than default ones and by using NC or PAW PPs > in the case of > the Bader tool. > > HTH > Giuseppe > > On Monday, February 08, 2016 03:26:32 PM Yang, Chi-Ta wrote: >> Dear All, >> >> >> For the charge analysis in QE, is it fine to use the charge values >> from the .out files? (below) >> >> If yes, do you recommend to use high K point for a better quality >> of these values or other recommendations? What kind of charge is >> this (ex: >> bader...) ? >> >> >> >> Magnetic moment per site: >> atom:1charge:2.1845magn:0.1742constr:0. >> atom:2charge:2.1716magn:0.1740constr:0. >> atom:3charge:2.1820magn:0.1742constr:0. >> atom:4charge:2.1826magn:0.1743constr:0. >> atom:5charge:2.1711magn:0.1739constr:0. >> atom:6charge:2.1841magn:0.1741constr:0. >> atom:7charge:7.3535magn:1.9625constr:0. >> atom:8charge:7.3507magn:2.0039constr:0. >> >> Thanks a lot, >> Chi-Ta Yang >> University of Iowa > > > - Article premier - Les hommes naissent et demeurent > libres et égaux en droits. Les distinctions sociales > ne peuvent être fondées que sur l'utilité commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la liberté, > la propriété, la sûreté et la résistance à l'oppression. > > >Giuseppe Mattioli >CNR - ISTITUTO DI STRUTTURA DELLA MATERIA >v. Salaria Km 29,300 - C.P. 10 >I 00015 - Monterotondo Stazione (RM), Italy >Tel + 39 06 90672836 - Fax +39 06 90672316 >E-mail: <giuseppe.matti...@ism.cnr.it> >http://www.ism.cnr.it/english/staff/mattiolig >ResearcherID: F-6308-2012 > > ___ > 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 -- **** - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Art
Re: [Pw_forum] Charge analysis in QE
Dear Chi-Ta Yang > For the charge analysis in QE, is it fine to use the charge values from the > .out files? No, it is a fast on-the-fly calculation. You can post-process your results a) with projwfc.x to obtain Lowdin charges or b) with pp.x to export the total charge density as a .cube file and then with an external tool you find here (http://theory.cm.utexas.edu/henkelman/code/bader) to calculate the Bader charges from the cube files. Better results are obtained by using denser FFT grids than default ones and by using NC or PAW PPs in the case of the Bader tool. HTH Giuseppe On Monday, February 08, 2016 03:26:32 PM Yang, Chi-Ta wrote: > Dear All, > > > For the charge analysis in QE, is it fine to use the charge values from the > .out files? (below) > > If yes, do you recommend to use high K point for a better quality of these > values or other recommendations? What kind of charge is this (ex: > bader...) ? > > > > Magnetic moment per site: > atom:1charge:2.1845magn:0.1742constr:0. > atom:2charge:2.1716magn:0.1740constr:0. > atom:3charge:2.1820magn:0.1742constr:0. > atom:4charge:2.1826magn:0.1743constr:0. > atom:5charge:2.1711magn:0.1739constr:0. > atom:6charge:2.1841magn:0.1741constr:0. > atom:7charge:7.3535magn:1.9625constr:0. > atom:8charge:7.3507magn:2.0039constr:0. > > Thanks a lot, > Chi-Ta Yang > University of Iowa - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Spin-Polarized NEB
Dear Victor I see two levels at which your question can be answered. At a technical level, the pw.x code (the "engine" of neb.x) starts from scratch the scf cycle of every image. If all your images converge the first scf iteration to a non-magnetic state then a) they will propagate the non-magnetic state to the following neb steps and b) the transition state might really be non-magnetic. You can force a paramagnetic ground state (tot_magnetization =/ 0) to have a paramagnetic transition state. However, note that at a "quantum chemistry" level, if you are right then your system jumps somewhere between a 2S+1=1 to a 2S+1=3 state (and then revert to a 2S+1=1 state in the end? Sounds strange but not unheard of, e.g. the rotation of ethylene around the double bond), and this cannot be mapped along a single PES. You could calculate the fully diamagnetic and fully paramamagnetic paths (i.e., including initial and final configurations, by constraining the tot_magnetization value) and then see if the paramagnetic curve goes below the diamagnetic curve around the transition state. Be aware of the fact that if your transition state is intrinsically a multireference state (e.g., a diradical like twisted ethylene, which cannot be described by a single determinant), then DFT-based numbers could be poor numbers... HTH Giuseppe On Monday, February 08, 2016 06:26:29 AM Vic Bermudez wrote: > Hello, > > I'm doing a NEB calculation for a reaction where I suspect that the > transition state might be paramagnetic. In the "engine_input" section I set > 'nspin=2', and I set a non-zero starting magnetization for one of the atom > types. In the first SCF cycle of the first NEB iteration the absolute > magnetization is initially non-zero and converges to a zero absolute > magnetization. The total magnetization remains zero at all times. This > applies to all 15 of the NEB images. > However, in successive NEB iterations the SCF starts right from the > beginning with zero absolute and total magnetizations and remains at zero > for both quantities right up to SCF convergence. > Here's my question. Given all this, am I really doing a spin-polarized > calculation, or is my calculation actually spin-restricted. If the latter, > what should I be doing to get a spin-unrestricted NEB run ? > > Thank you in advance for your help. > > This is the relevant part of the input. Here I'm restarting a calculation > that was spin-restricted and appeared to be getting somewhat close to NEB > convergence > > BEGIN > BEGIN_PATH_INPUT > > restart_mode='restart', > string_method='neb', > ds=1.D0, > opt_scheme='broyden', > nstep_path=4000, > num_of_images=15, > k_max=0.6D0, > k_min=0.1D0, > first_last_opt=.TRUE., > use_freezing=.TRUE., > CI_scheme='auto' > / > END_PATH_INPUT > > BEGIN_ENGINE_INPUT > > title='NEB Run', > ! restart_mode='from_scratch', > pseudo_dir='/lustre/cmf/scratch/b/bermudez/QE_PP/', > ! outdir='/lustre/cmf/scratch/b/bermudez/NEB-SO2_2/', > etot_conv_thr=1.0D-4, > forc_conv_thr=1.0D-3, > verbosity='default' > / > > > ibrav=8, > a=14.5898, b=14.7815, c=35.00, > nat=138, > ntyp=4, > ecutwfc=40.0, > ecutrho=400.0, > nspin=2, > starting_magnetization(1)=0.0, > starting_magnetization(2)=0.0, > starting_magnetization(3)=0.0, > starting_magnetization(4)=0., > london=.true., > occupations='smearing', > smearing='gaussian', > degauss=0.002, > nosym=.TRUE. > / > > > electron_maxstep=200, > conv_thr=3.0D-9, > mixing_beta=0.7D0, > mixing_ndim=8, > mixing_mode='local-TF' > / > > ATOMIC_SPECIES > Zr 91.22 Zr.pbe-spn-kjpaw_psl.0.2.3.UPF > O 15.9994 O.pbe-n-kjpaw_psl.0.1.UPF > H 1.0079 H.pbe-kjpaw_psl.0.1.UPF > S 32.06S.pbe-n-kjpaw_psl.0.1.UPF > > > Victor M. Bermudez > E-mail: bermu...@alum.mit.edu > > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Enquiry about the Pseudopotential
Dear Kieran You can use and mix different kinds of pseudopotential. But you should know why they are different, and this I'm afraid that you cannot learn by asking to the mailing list... However, non collinear calculations are not the best kind of calculation to start with for a newbie. HTH Giuseppe On Monday, February 08, 2016 09:19:07 AM song kenan wrote: > Dear All, > > I am a new user of Quantum Espresso code. I have carbon, hydrogen and bismuth > atoms in my system and want to do the non-collinear calculation. Can I > use C.pbe-mt_fhi.UPF, H.pbe-kjpaw.UPF and Bi_MT_PBE.UPF as the > pseudopotentials for these three atoms when calculating the band structure? I > check > the pseudopotential files and found the the following information. > > For C.pbe-mt_fhi.UPF > > Generated using FHI98PP, converted with fhi2upf.x v.5.0.2 > Origin: Abinit web site > Date: 08-Sep-2012 (PG) > Pseudopotential type: SL > Element: C > Functional: PBE > > Suggested minimum cutoff for wavefunctions: 0. Ry > Suggested minimum cutoff for charge density: 0. Ry > The Pseudo was generated with a Scalar-Relativistic Calculation > L component and cutoff radius for Local Potential: 2 0. > > > For H.pbe-kjpaw.UPF > > Generated using "atomic" code by A. Dal Corso (espresso distribution) > Author: "Lorenzo Paulatto" /paula...@sissa.it/ > Generation date: 15Apr2008 > Pseudopotential type: PAW > Element: H > Functional: SLA PW PBX PBC > > Suggested minimum cutoff for wavefunctions: 46. Ry > Suggested minimum cutoff for charge density: 201. Ry > The Pseudo was generated with a Non-Relativistic Calculation > L component and cutoff radius for Local Potential: 1 0.7500 > > For Bi_MT_PBE.UPF > > Generated using "atomic" code by A. Dal Corso (espresso distribution) > Author: anonymous > Generation date: 5Mar2010 > Pseudopotential type: NC > Element: Bi > Functional: PBE > > Suggested minimum cutoff for wavefunctions: 27. Ry > Suggested minimum cutoff for charge density: 108. Ry > The Pseudo was generated with a Fully-Relativistic Calculation > L component and cutoff radius for Local Potential: 0 2.2000 > Pseudopotential contains additional information for spin-orbit > calculations. > > > The Bi pseudopotential is fully relativistic and the C one is scalar > relativistic; while H one is non relativistic. If I want to do the > non-collinear calculation of band structure for my system, would anyone > please give some suggestions on what pseudopotentials I should use for > these atoms? Thank you very much in advance. > > Kind regards, > > Kieran Song - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] possible i/o bug in turbo_lanczos.x and turbo_davidson.x 5.3.0
Dear Iurii Thank you. I'm less than a dummy with allocation/parallelization etc. issues. Otherwise I would be glad to help... Best Giuseppe > Really? And there is no problem on Linux? no, not at all...;-) On Friday, February 05, 2016 01:07:22 PM Timrov Iurii wrote: > Dear Giuseppe, > > I am going to check if there is some extra allocations and/or a memory leak, > when I have some time. > > > Indeed!!! Only microsoft windows requires more memory to do the same thing > > in newer versions > > Really? And there is no problem on Linux? > > Best regards, > Iurii > > -- > Dr. Iurii Timrov > Postdoctoral Researcher > École Polytechnique Fédérale de Lausanne, > Theory and Simulation of Materials > CH-1015 Lausanne, Switzerland > +41 21 69 34 881 > http://people.epfl.ch/265334 > > > From: Giuseppe Mattioli <giuseppe.matti...@ism.cnr.it> > Sent: Friday, February 5, 2016 1:55 PM > To: Timrov Iurii > Cc: pw_forum@pwscf.org > Subject: Re: Re: Re: [Pw_forum] possible i/o bug in turbo_lanczos.x and > turbo_davidson.x5.3.0 > > Dear Iurii > > > It seems that this is a RAM issue. > > Maybe something connected with memory allocation which is changed between > 5.1.1 and 5.2.1 > > > I runned your test case with QE-5.2.1 on my local workstation with 8 cores > > and 64 Gb RAM and the Lanczos code crashed. When I changed the input of > > PWscf so that only the occupied states are computed (actually, the empty > > states are not need in the Lanczos calculation), which of course > > decreased > > RAM requirements, the code didn't crash. > > the code didn't crash even on my 8 cores 16 GB RAM cluster with 5.1.1. And it > is not a large benchmark. I used to run larger ones on the same node > and far larger ones on two nodes of the same machine with older versions. The > problem cannot be due to the overall memory requirements, but to some > problematic memory allocation (a leak somewhere?). > > > If this is indeed the reason of the problem, then it seems strange to me > > why the QE-5.1.1 does not have this problem. Maybe some investigation > > would be desired. > > Indeed!!! Only microsoft windows requires more memory to do the same thing in > newer versions > > Best > Giuseppe > > On Friday, February 05, 2016 10:07:14 AM Timrov Iurii wrote: > > Dear Giuseppe, > > > > It seems that this is a RAM issue. > > > > I runned your test case with QE-5.2.1 on my local workstation with 8 cores > > and 64 Gb RAM and the Lanczos code crashed. When I changed the input of > > PWscf so that only the occupied states are computed (actually, the empty > > states are not need in the Lanczos calculation), which of course > > decreased > > RAM requirements, the code didn't crash. > > > > In Bluegene machine you may try to optimize RAM too. Maybe you know, one > > can allocate all cores per node but use only a few of them which would > > allow you to increase RAM per core. Please note that with Davidson the RAM > > requirements are even much larger, so it is not easy to optimize the > > script for submission the jobs for large systems. > > > > In order to verify if you also have a memory issue, you may try to decrease > > the value of celldm(1), cutoffs etc. and see if the code does not > > crash. > > > > If this is indeed the reason of the problem, then it seems strange to me > > why the QE-5.1.1 does not have this problem. Maybe some investigation > > would be desired. > > > > HTH > > > > Best regards, > > Iurii > > > > -- > > Dr. Iurii Timrov > > Postdoctoral Researcher > > École Polytechnique Fédérale de Lausanne, > > Theory and Simulation of Materials > > CH-1015 Lausanne, Switzerland > > +41 21 69 34 881 > > http://people.epfl.ch/265334 > > > > > > From: Giuseppe Mattioli <giuseppe.matti...@ism.cnr.it> > > Sent: Thursday, February 4, 2016 5:59 PM > > To: Timrov Iurii > > Cc: pw_forum@pwscf.org > > Subject: Re: Re: [Pw_forum] possible i/o bug in turbo_lanczos.x and > > turbo_davidson.x5.3.0 > > > > Silent crash on bluegene with 5.2.1 (I have no time to compile 5.3.0 now. I > > may try tomorrow if you think it is important). > > > > Program turboTDDFT v.5.2.1 starts on 4Feb2016 at 17:56:55 > > > > This program is part of the open-source Quantum ESPRESSO suite > > for quantum simulation of materials; please c
Re: [Pw_forum] possible i/o bug in turbo_lanczos.x and turbo_davidson.x 5.3.0
Dear Iurii > It seems that this is a RAM issue. Maybe something connected with memory allocation which is changed between 5.1.1 and 5.2.1 > I runned your test case with QE-5.2.1 on my local workstation with 8 cores > and 64 Gb RAM and the Lanczos code crashed. When I changed the input of > PWscf so that only the occupied states are computed (actually, the empty > states are not need in the Lanczos calculation), which of course decreased > RAM requirements, the code didn't crash. the code didn't crash even on my 8 cores 16 GB RAM cluster with 5.1.1. And it is not a large benchmark. I used to run larger ones on the same node and far larger ones on two nodes of the same machine with older versions. The problem cannot be due to the overall memory requirements, but to some problematic memory allocation (a leak somewhere?). > If this is indeed the reason of the problem, then it seems strange to me why > the QE-5.1.1 does not have this problem. Maybe some investigation would > be desired. Indeed!!! Only microsoft windows requires more memory to do the same thing in newer versions Best Giuseppe On Friday, February 05, 2016 10:07:14 AM Timrov Iurii wrote: > Dear Giuseppe, > > It seems that this is a RAM issue. > > I runned your test case with QE-5.2.1 on my local workstation with 8 cores > and 64 Gb RAM and the Lanczos code crashed. When I changed the input of > PWscf so that only the occupied states are computed (actually, the empty > states are not need in the Lanczos calculation), which of course decreased > RAM requirements, the code didn't crash. > > In Bluegene machine you may try to optimize RAM too. Maybe you know, one can > allocate all cores per node but use only a few of them which would > allow you to increase RAM per core. Please note that with Davidson the RAM > requirements are even much larger, so it is not easy to optimize the > script for submission the jobs for large systems. > > In order to verify if you also have a memory issue, you may try to decrease > the value of celldm(1), cutoffs etc. and see if the code does not crash. > > If this is indeed the reason of the problem, then it seems strange to me why > the QE-5.1.1 does not have this problem. Maybe some investigation would > be desired. > > HTH > > Best regards, > Iurii > > -- > Dr. Iurii Timrov > Postdoctoral Researcher > École Polytechnique Fédérale de Lausanne, > Theory and Simulation of Materials > CH-1015 Lausanne, Switzerland > +41 21 69 34 881 > http://people.epfl.ch/265334 > > > From: Giuseppe Mattioli <giuseppe.matti...@ism.cnr.it> > Sent: Thursday, February 4, 2016 5:59 PM > To: Timrov Iurii > Cc: pw_forum@pwscf.org > Subject: Re: Re: [Pw_forum] possible i/o bug in turbo_lanczos.x and > turbo_davidson.x5.3.0 > > Silent crash on bluegene with 5.2.1 (I have no time to compile 5.3.0 now. I > may try tomorrow if you think it is important). > > > Program turboTDDFT v.5.2.1 starts on 4Feb2016 at 17:56:55 > > This program is part of the open-source Quantum ESPRESSO suite > for quantum simulation of materials; please cite > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); > URL http://www.quantum-espresso.org;, > in publications or presentations arising from this work. More details at > http://www.quantum-espresso.org/quote > > Parallel version (MPI & OpenMP), running on2048 processor cores > Number of MPI processes: 512 > Threads/MPI process: 4 > R & G space division: proc/nbgrp/npool/nimage = 512 > > Reading data from directory: > /gpfs/scratch/userexternal/gmattiol/test/tddft/run/tmp/././l0-5.3.0.save > >Info: using nr1, nr2, nr3 values from input > >Info: using nr1, nr2, nr3 values from input > > IMPORTANT: XC functional enforced from input : > Exchange-correlation = SLA PW PBE PBE ( 1 4 3 4 0 0) > Any further DFT definition will be discarded > Please, verify this is what you really want > > > Parallelization info > > sticks: dense smooth PW G-vecs:dense smooth PW > Min 78 38 812054 4220 492 > Max 80 40 1012104 4300 550 > Sum 40733 20369 5097 6186431 2186841 273425 > Tot 20367 10185 2549 > > > negative rho (up, down): 9.597E-02 0.000E+00 > > Subspace diagonalization in iterative solution of the eigenvalue problem: > scalapack distributed-mem
Re: [Pw_forum] possible i/o bug in turbo_lanczos.x and turbo_davidson.x 5.3.0
Silent crash on bluegene with 5.2.1 (I have no time to compile 5.3.0 now. I may try tomorrow if you think it is important). Program turboTDDFT v.5.2.1 starts on 4Feb2016 at 17:56:55 This program is part of the open-source Quantum ESPRESSO suite for quantum simulation of materials; please cite "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); URL http://www.quantum-espresso.org;, in publications or presentations arising from this work. More details at http://www.quantum-espresso.org/quote Parallel version (MPI & OpenMP), running on2048 processor cores Number of MPI processes: 512 Threads/MPI process: 4 R & G space division: proc/nbgrp/npool/nimage = 512 Reading data from directory: /gpfs/scratch/userexternal/gmattiol/test/tddft/run/tmp/././l0-5.3.0.save Info: using nr1, nr2, nr3 values from input Info: using nr1, nr2, nr3 values from input IMPORTANT: XC functional enforced from input : Exchange-correlation = SLA PW PBE PBE ( 1 4 3 4 0 0) Any further DFT definition will be discarded Please, verify this is what you really want Parallelization info sticks: dense smooth PW G-vecs:dense smooth PW Min 78 38 812054 4220 492 Max 80 40 1012104 4300 550 Sum 40733 20369 5097 6186431 2186841 273425 Tot 20367 10185 2549 negative rho (up, down): 9.597E-02 0.000E+00 Subspace diagonalization in iterative solution of the eigenvalue problem: scalapack distributed-memory algorithm (size of sub-group: 16* 16 procs) Warning: There are virtual states in the input file, trying to disregard in response calculation Ultrasoft (Vanderbilt) Pseudopotentials Normal read Gamma point algorithm 2016-02-04 17:57:18.063 (WARN ) [0x4ee8d50] :7014845:ibm.runjob.client.Job: terminated by signal 6 2016-02-04 17:57:18.065 (WARN ) [0x4ee8d50] :7014845:ibm.runjob.client.Job: abnormal termination by signal 6 from rank 295 On Thursday, February 04, 2016 03:46:10 PM Timrov Iurii wrote: > Dear Giuseppe, > > As far as I understand the code crashes when it tries to write the vectors > "d0psi" to the disc. First thing to do, I think, is to check that you > have enough space on the disc. If this is not the issue, then let's continue > looking for a reason. > > You may want to look in the routine TDDFPT/src/lr_solve_e.f90 at lines > 110-138 where the code writes vectors to the disc in parallel. Please make > sure that the "outdir" is the same in PWscf and in Lanczos/Davidson (and > don't specify wfcdir). If this does not solve the problem, could you > report please also the output of Lanczos/Davidson (better Lanczos)? > > HTH > > Best regards, > Iurii Timrov > Post-doctoral researcher > THEOS - École Polytechnique Fédérale de Lausanne > Lausanne, Switzerland > > > ____ > From: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on behalf of > Giuseppe Mattioli <giuseppe.matti...@ism.cnr.it> > Sent: Thursday, February 4, 2016 11:34 AM > To: pw_forum@pwscf.org > Subject: [Pw_forum] possible i/o bug in turbo_lanczos.x and turbo_davidson.x > 5.3.0 > > Dear All > I'm having problems when performing nontrivial runs of turbo_davidson.x and > turbo_lanczos.x with 5.2.1 and 5.3.0 versions of QE. > Let me say first that "trivial" runs (CH4 molecule with same pseudopotentials > and cutoffs but a smaller 30 a.u.^3 cubic cell) work fine with all the > tested versions. > However, the input files for a nontrivial case that leads to crash should run > on a decent pc in about 1 hr, so they provide a significant but not > huge test. *Note* that if I run the same input files with the 5.1.1 version > (compiled against the very same environment) everything goes (more > slowly but) fine! The 5.3.0 (and 5.2.1) crashes have been reproduced on two > different machines (intel 8 cores 16GB RAM, amd 32 cores 64 GB RAM), so > they should not be considered as erratic. > > here is the pw.x run. The PPs are quite old and can be found in the online > library (or provided by me on demand). > > > calculation = 'scf' > restart_mode='from_scratch', > prefix='l0-5.3.0', > pseudo_dir = '/home/mattioligi/PP_UPF/', > outdir='/home/mattioligi/cocat/test_tddft/5.2.1/l0/5.3.0/run/tmp/', > nstep=300, > max_seconds=8, > disk_io='low', > tprnfor=.true., > / > > ibrav=1, celldm(1)=40.00, > nat=42, ntyp=4, nbnd=75, >
Re: [Pw_forum] possible i/o bug in turbo_lanczos.x and turbo_davidson.x 5.3.0
Dear Iurii
Thanks for your help.
> First thing to do, I think, is to check that you
> have enough space on the disc.
Yes, there is
> You may want to look in the routine TDDFPT/src/lr_solve_e.f90 at lines
> 110-138 where the code writes vectors to the disc in parallel.
I've checked that the lines are very similar (substantially identical?) in
5.3.0 and 5.1.1. So it is very strange that the latter works when the
former does not.
> Please make
> sure that the "outdir" is the same in PWscf and in Lanczos/Davidson (and
> don't specify wfcdir).
Done, I've also tried to place "outdir" in local or distributed filesystem:
always same results
> If this does not solve the problem, could you
> report please also the output of Lanczos/Davidson (better Lanczos)?
Lanczos output attached
I'm sending the same test to the fermi@cineca bluegene machine to see if the
xlf compilers like my scripts more than the intel compilers...
Best Wishes
Giuseppe
On Thursday, February 04, 2016 03:46:10 PM Timrov Iurii wrote:
> Dear Giuseppe,
>
> As far as I understand the code crashes when it tries to write the vectors
> "d0psi" to the disc. First thing to do, I think, is to check that you
> have enough space on the disc. If this is not the issue, then let's continue
> looking for a reason.
>
> You may want to look in the routine TDDFPT/src/lr_solve_e.f90 at lines
> 110-138 where the code writes vectors to the disc in parallel. Please make
> sure that the "outdir" is the same in PWscf and in Lanczos/Davidson (and
> don't specify wfcdir). If this does not solve the problem, could you
> report please also the output of Lanczos/Davidson (better Lanczos)?
>
> HTH
>
> Best regards,
> Iurii Timrov
> Post-doctoral researcher
> THEOS - École Polytechnique Fédérale de Lausanne
> Lausanne, Switzerland
>
>
> ____
> From: pw_forum-boun...@pwscf.org <pw_forum-boun...@pwscf.org> on behalf of
> Giuseppe Mattioli <giuseppe.matti...@ism.cnr.it>
> Sent: Thursday, February 4, 2016 11:34 AM
> To: pw_forum@pwscf.org
> Subject: [Pw_forum] possible i/o bug in turbo_lanczos.x and turbo_davidson.x
> 5.3.0
>
> Dear All
> I'm having problems when performing nontrivial runs of turbo_davidson.x and
> turbo_lanczos.x with 5.2.1 and 5.3.0 versions of QE.
> Let me say first that "trivial" runs (CH4 molecule with same pseudopotentials
> and cutoffs but a smaller 30 a.u.^3 cubic cell) work fine with all the
> tested versions.
> However, the input files for a nontrivial case that leads to crash should run
> on a decent pc in about 1 hr, so they provide a significant but not
> huge test. *Note* that if I run the same input files with the 5.1.1 version
> (compiled against the very same environment) everything goes (more
> slowly but) fine! The 5.3.0 (and 5.2.1) crashes have been reproduced on two
> different machines (intel 8 cores 16GB RAM, amd 32 cores 64 GB RAM), so
> they should not be considered as erratic.
>
> here is the pw.x run. The PPs are quite old and can be found in the online
> library (or provided by me on demand).
>
>
> calculation = 'scf'
> restart_mode='from_scratch',
> prefix='l0-5.3.0',
> pseudo_dir = '/home/mattioligi/PP_UPF/',
> outdir='/home/mattioligi/cocat/test_tddft/5.2.1/l0/5.3.0/run/tmp/',
> nstep=300,
> max_seconds=8,
> disk_io='low',
> tprnfor=.true.,
> /
>
> ibrav=1, celldm(1)=40.00,
> nat=42, ntyp=4, nbnd=75,
> ecutwfc = 40.0,
> ecutrho = 320.0,
> nspin=1,
> /
>
> diagonalization='david',
> mixing_mode='plain'
> mixing_beta=0.1
> conv_thr=1.0d-8
> electron_maxstep=100
> /
>
> /
> ATOMIC_SPECIES
> O15.999O_pbe.van.UPF
> N14.007N.pbe-van_bm.UPF
> C12.011C_pbe.van.UPF
> H 1.008H_pbe.van.UPF
> ATOMIC_POSITIONS {angstrom}
> C4.815369179 12.355337788 8.111406911
> C5.639537337 12.072210478 7.018248617
> C6.373883049 10.886794669 6.974735758
> H5.707874252 12.778745273 6.179910928
> C4.734413944 11.441350355 9.166316558
> H4.235443595 13.287281698 8.140567718
> C6.304598307 9.97703 8.041477142
> H7.012644682 10.659891408 6.32336
> C5.477180541 10.260422385 9.138835842
> H4.092409998 11.653694694 10.031778418
> H5.418528381 9.546881383 9.971310698
> N7.058612774 8.759574945 8.006208499
> C6.384981399 7.544139013 8.340645249
> C6.997532612 6.588483316 9.168188787
> C5.084708421 7.308024697 7.864810575
>
Re: [Pw_forum] Germanium bulk band structure
Dear Priyank Short answer: use an hybrid functional such as HSE. Bulk Ge is a metal with every flavour of GGA. HTH Giuseppe On Thursday, February 04, 2016 12:12:32 PM Michael Schofield wrote: > Dear sir/madam, > > I am trying to calculate the bulk band structure for Germanium using GGA > exchange-correlation with PAW basis, but the band gap is coming out to be > almost zero. I know DFT underestimates the band gap but it is coming almost > zero (~0.03eV). Is there any means by which I can get more accurate band > gap. > > My input script is here: > > > > calculation = 'nscf', > verbosity = 'high', > restart_mode = 'from_scratch', > prefix = 'Ge_bulk_nscf', > tstress = .false., > tprnfor = .false., > pseudo_dir = '/home/Software/QE/pseudopotentials/upf_files/', > outdir = './output/' > / > > > ibrav=2, > celldm(1) = 10.690937, > nat=2, ntyp=1, > nbnd = 12, > ecutwfc=60, > ecutrho= 600, > / > > > diagonalization='david', > mixing_mode = 'plain', > mixing_beta = 0.7, > conv_thr = 1.0d-6, > electron_maxstep = 500, > / > > ATOMIC_SPECIES > Ge 72.64 Ge.pbe-kjpaw.UPF > > ATOMIC_POSITIONS crystal > Ge 0.00 0.00 0.00 > Ge 0.25 0.25 0.25 > > K_POINTS crystal_b > 6 > 0.0 0.00.0 100 > 0.0 0.50.0 100 > 0.0 0.375 -0.375 100 > -0.25 0.25 -0.5 100 > -0.5 0.0 -0.5 100 > 0.0 0.00.0 1 > - > PFA the band structure I am getting from it. > > Any help/suggestions will be helpful. > > > > > Thanks > Priyank > Dept. of EE > IIT Kanpur, India - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] possible i/o bug in turbo_lanczos.x and turbo_davidson.x 5.3.0
en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] E-field: please any response!
, QiASU -- - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/en/staff/giuseppe-mattioli/ ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
[Pw_forum] question on the lplot_drho variable of turbo_davidson
Dear All What is exactly the "response charge-density at each resonance" which can be calculated with turbo_davidson.x? Let me rephrase the question in another way: I want to calculate the charge displacement between the S0 (ground state) and S1* (first singlet excited state) of a given molecule. So I need the total charge density of S0 (easy to compute with pp.x) and the total charge density of S1*. I do not know how to compute the latter quantity. I was wondering whether lplot_drho=true plots such a quantity, but I believe it does not, because the h2o-plotrho example produces a cube file containing a symmetric positive and negative charge distribution. Or is this lplot_drho result exactly what I'm looking for? Please enlighten me and thank you in advance. Giuseppe - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Atomic positions for Black Phosphorus calculations
32 1.39832 0.58056 > >> P 0.39832 0.60168 0.41944 These two atom positions have the same > >> coordinate. This could be the problem. > >> > >> Duc-Long > >> > >> On 1/12/2016 6:44 AM, Elio Physics wrote: > >>> Dear all, > >>> > >>> I am trying to perform some calculations on Black Phosphorus (BP). > >>> To get the atomic positions I used the Crystal Builder, where I > >>> have chosen the lattice type to be base centered orthorhombic. > >>> The "builder" produced a set of cartesian and fractional (in > >>> terms of the primitive cell vectors) . I have used the fractional > >>> ones and I have also used ibrav=0 with the CELL_PARAMETERS defined > >>> as in the builder (a/2, -b/2, 0), (a/2, b/2,0), (0,0,c). However I > > > >>> have got the following error: > > %% > > > >>> from check_atoms : error # 1 > >>> atoms # 1 and # 4 overlap! > > > > %% > > > >>> Doing the same calculation with ibrav=8 and using the coordinates > >>> produced by the Crystal builder for a simple orthorhombic does not > >>> produce any errors. Can anyone please tell me what is wrong with > >>> atoms (1) and (4). Is BP simple or base centered > >>> orthorhombic..Where can I find the coorect atomic position of bulk > >>> BP? The scf input is below: > >>> > >>> > >>> prefix='bp', > >>> calculation='scf', > >>> restart_mode='from_scratch', > >>> wf_collect=.true., > >>> forc_conv_thr=1.D-4 > >>> etot_conv_thr=1.D-5 > >>> tstress=.true., > >>> tprnfor=.true., > >>> pseudo_dir ='/home_cluster/fis718/elio/espresso-4.1.3/pseudo', > >>> > >>> outdir='/home_cluster/fis718/elio/espresso-4.1.3/BP/OUT' > >>> / > >>> > >>> ibrav=0,celldm(1)=6.26179,nat=8, ntyp= 1, ecutwfc=10, > >>> ecutrho=40, occupations='smearing', london=.true., smearing='mp', > >>> degauss=0.035,nbnd=32 > >>> / > >>> > >>> conv_thr=1.D-8, > >>> mixing_beta=0.1 > >>> / > >>> > >>> ion_dynamics='bfgs' > >>> / > >>> > >>> cell_dynamics='bfgs' > >>> press=0.0 > >>> / > >>> ATOMIC_SPECIES > >>> P 30.97376 P.pbe-n-van.UPF > >>> ATOMIC_POSITIONS crystal > >>> P -0.89832 0.89832 0.91944 > >>> P -0.39832 0.39832 0.58056 > >>> P -0.10168 0.10168 0.08056 > >>> P 0.10168 0.89832 0.91944 > >>> P -0.10168 1.10168 0.08056 > >>> P -0.60168 0.60168 0.41944 > >>> P -0.39832 1.39832 0.58056 > >>> P 0.39832 0.60168 0.41944 > >>> > >>> K_POINTS automatic > >>> 2 2 2 0 0 0 > >>> > >>> CELL_PARAMETERS alat > >>> 0.5000 -1.58106 0.0000 > >>> 0.500 1.58106 0. > >>> 0. 0.0 4.3763 > >>> > >>> thanks > >>> > >>> Elio Arbid > >>> University of Nottingham > >>> UK > >>> > >>> ___ > >>> Pw_forum mailing list > >>> Pw_forum@pwscf.org > >>> http://pwscf.org/mailman/listinfo/pw_forum > >> > >> -- > >> Duc-Long Nguyen > >> Graduate Student, Molecular Science and Technology Program, TIGP > >> Institute of Atomic and Molecular Sciences, > >> Academia Sinica, Taipei 106, Taiwan > >> Phone +886 979279073 > >> > >> ___ > >> 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 - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Hubbard term U in optical properties
Dear Mulwa Winfred Your question is too vague (which optical properties? what system? a doped crystal? a doped nanoparticle?). There is *very abundant literature* on DFT+U & anatase TiO2, so you should first clarify your ideas before asking. However, remember that here you can generally expect to find help on technical details of scientific problems. You should not ask the mailing list for help on scientific problems... HTH Giuseppe On Tuesday, December 15, 2015 10:37:05 AM Winfred Mulwa wrote: > Dear all, > I am calculating the optical properties of Gd doped anatase TiO2. My > question is, > should i include the value of U in my input file. > Thank you in advance > Regards > Mulwa Winfred. > D Phil Student, Computational Material Science Group, > University of the Free State - QwaQwa, > South Africa. - Article premier - Les hommes naissent et demeurent libres et égaux en droits. Les distinctions sociales ne peuvent être fondées que sur l'utilité commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la liberté, la propriété, la sûreté et la résistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Charge accumulation and depletion
Dear Jaret > 1) You said the spilling parameter has to be the same in all systems, Not "the same", only "similar" > in my case this is what I got:system A : spilling > parameter=0.0031system B : spilling parameter=0.0021interface(A+B) : > spilling parameter=0.0027,they are close but not the same, is this > fine? Yes, it is fine in my opinion. You can compare the values. If you want to be very diligent you can add the charge spilt out by adding 0.31%, 0.27%, 0.21% to all the atoms (this is an arbitrary but wise choice) of your three systems, respectively. However, I suppose that this will not change your results very much so you can safely skip. > 2) To get the charge accumulation and depletion, is there a formula > to each on of them or what?I have calculate the charge difference of > each atom like this : > Charge diff.=Lowdin charge (atom in the interface)-Lowdin charge > (atom in the separate system A(B)) > Using this, I've got positive and negative values, does the positive > means accumulation and the negative means depletion? The reply is yes to both questions, with only one further note: three-dimensional deltarho maps help you to see if there is a consistent interfacial charge accumulation, which is not always easy to fit into the Lowdin partitioning. You might like to be inspired by the theoretical results "just accepted" for publication (see also the supporting information). The calculation has been applied to oligothiophenes in contact with a silver surface. http://pubs.acs.org/doi/abs/10.1021/acs.jpcc.5b08733 This information generally completes that contained in the Lowdin analysis of accumulation and depletion of charge in single atoms. HTH Giuseppe Quoting Jaret Qi <jare...@yahoo.com>: > Hello Mattioli,I tried the second case to calculate the charge > accumulation and depletion. Now I have some concerns:1) You said the > spilling parameter has to be the same in all systems, in my case > this is what I got:system A : spilling parameter=0.0031system B : > spilling parameter=0.0021interface(A+B) : spilling > parameter=0.0027,they are close but not the same, is this fine? if > not how one can get same values? > 2) To get the charge accumulation and depletion, is there a formula > to each on of them or what?I have calculate the charge difference of > each atom like this : > Charge diff.=Lowdin charge (atom in the interface)-Lowdin charge > (atom in the separate system A(B)) > Using this, I've got positive and negative values, does the positive > means accumulation and the negative means depletion? > -- > > > On Friday, October 23, 2015 1:36 AM, Giuseppe Mattioli > <giuseppe.matti...@ism.cnr.it> wrote: > > > > Dear Jaret > You may do two (complementary) things: > > 1) a Deltarho map. a) Calculation of your whole system and usage of > pp.x to extract the charge density (plot_num=0). b) two separate scf > calculations > of the insulator slab and metal slab in the same atomic position of > the previous one and usage of pp.x to extract the charge densities. > c) Subtract > the charge densities calculated in b) to the charge densities > calculated in a). If you open the obtained file with xcrysden you > can visualize the > charge displacement at the interface (menu tools --> data grid). > > Something like this, which has been set up for a molecule/surface system... > > export FILEA="molecule+surface" > export INPFILE=$FILEA-cha.inp > export OUTFILE=$FILEA-cha.out > echo " $FILEA" > echo " $INPFILE" > echo " $OUTFILE" > cat > $INPFILE << EOF > > prefix = '$FILEA' > outdir = '$TMP_DIR/' > filplot = '$FILEA-cha.dat' > plot_num= 0 > / > EOF > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE > > export FILEB="molecule" > export INPFILE=$FILEB-cha.inp > export OUTFILE=$FILEB-cha.out > echo " $FILEB" > echo " $INPFILE" > echo " $OUTFILE" > cat > $INPFILE << EOF > > prefix = '$FILEB' > outdir = '$TMP_DIR/' > filplot = '$FILEB-cha.dat' > plot_num= 0 > / > EOF > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE > > > export FILEC="surface" > export INPFILE=$FILEC-cha.inp > export OUTFILE=$FILEC-cha.out > echo " $FILEC" > echo " $INPFILE" > echo " $OUTFILE" > cat > $INPFILE << EOF > > prefix = '$FILEC' > outdir = '$TMP_DIR/' > filplot = '$FILEC-cha.dat' > plot_num= 0 > / > EOF > $PARA_PREFIX $ESPRE
Re: [Pw_forum] Raman
Dear Amir AFAIK Raman intensities can be calculated at the LDA level of theory only. You are using meta-GGA HTH Giuseppe On Tuesday, December 08, 2015 11:25:05 PM Mofrad, Amir Mehdi wrote: > Dear Quantum Espresso users and developers, > > Does anyone know that Quantum Espresso is capable of calculating Raman > intensities? When I want to do the phonon calculations I get the following > error: > > > error: task # 0 > from phq_setup : error # 1 > third order derivatives not implemented with GGA > > > According to what is provided on the Quantum Espresso website, Raman > calculations work only with NC pseudo-potentials and I tried to use that kind > of PP in my scf calculations. Below is my scf and phonon calculations input > files. Any help would be thoroughly appreciated on how to get Raman > intensities. > > > SCF INPUT: > > > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .true. , > outdir = './scratch' , > wfcdir = './scratch' , > pseudo_dir = '/global/espresso/pseudo' , > prefix = 'SOD' , > verbosity = 'high' , > etot_conv_thr = 1e-5 , > forc_conv_thr = 1e-4 , > nstep = 50 , > tstress = .true. , > tprnfor = .true. , > > / > > > ibrav = 0, > nat = 36, > ntyp = 2, > ecutwfc = 50 , > ecutrho = 200 , > > / > > > electron_maxstep = 100, > conv_thr = 3e-8 , > mixing_mode = 'plain' , > mixing_beta = 0.7 , > diagonalization = 'david' , > > / > CELL_PARAMETERS bohr > 16.7202967500.00.0 > 0.0 16.7202967500.0 > 0.00.0 16.720296750 > ATOMIC_SPECIES >Si 28.08600 Si.tpss-mt.UPF > O 15.99940 O.tpss-mt.UPF > ATOMIC_POSITIONS angstrom > Si 2.2114340870.04.42400 >Si 6.6365659130.04.42400 >Si 4.424002.2114340870.0 >Si 4.424006.6365659130.0 >Si 0.04.424002.211434087 >Si 0.04.424006.636565913 >Si 2.2114241384.42400 -0.0 >Si 6.6365758624.42400 -0.0 >Si 0.02.2114241384.42400 >Si 0.06.6365758624.42400 >Si 4.424000.02.211424138 >Si 4.424000.06.636575862 > O 1.2872841424.0775133401.287298380 > O 7.5607158584.7704866601.287298380 > O 7.5607158584.0775133407.560701620 > O 1.2872841424.7704866607.560701620 > O 1.2872983801.2872841424.077513340 > O 1.2872983807.5607158584.770486660 > O 7.5607016207.5607158584.077513340 > O 7.5607016201.2872841424.770486660 > O 4.0775133401.2872983801.287284142 > O 4.7704866601.2872983807.560715858 > O 4.0775133407.5607016207.560715858 > O 4.7704866607.5607016201.287284142 > O 8.5066504985.7138707755.713853509 > O 0.3413495023.1341292255.713853509 > O 8.5066504983.1341292253.134146491 > O 0.3413495025.7138707753.134146491 > O 5.7138707755.7138535098.506650498 > O 3.1341292255.7138535090.341349502 > O 3.1341292253.1341464918.506650498 > O 5.7138707753.1341464910.341349502 > O 5.7138535098.5066504985.713870775 > O 5.7138535090.3413495023.134129225 > O 3.1341464918.5066504983.134129225 > O 3.1341464910.3413495025.713870775 > K_POINTS automatic > 4 4 4 1 1 1 > > > Phonon Input File > > > phonons of Sodalite at Gamma > > tr2_ph= 1e-14, > prefix= 'SOD', > amass(1) = 28.08600, > amass(2) = 15.9940, > outdir= './scratch/', > fildyn= 'SOD.dyn', > recover = .false., > epsil = .true., > lraman= .true., > trans = .true., > max_seconds = 35 > / > 0.0 0.0 0.0 > > > Best regards, > > > Amir M. Mofrad > > University of Missouri - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels e
Re: [Pw_forum] bfgs optimization not going anywhere
> As for the dispersion correction, the discussion is still open :-) And we will not close it soon :-) > to summarize: what would be 'the best' DFT correction on to of > *existing* functionals, e.g. PBE for molecule-metal-interaction? There is likely no best correction, but the best correction for a given system may be found by trial and error. > As far as I understood, vdw-DF must be used with the corresponding > pseudopotential > (BTW, where one can get them?). Look into the corresponding papers. They usually say which GGA flavour should be used to build the PPs. Then build (with pslibrary and ld1.x, for example) and test them! For vdwdf revPBE is suggested to perform better than PBE, but I suppose that it could be interesting to see what happens in the case of systems a bit larger than Ar dimers... I expect to find negligible differences in, e.g., adsorption energies and geometries of large molecules interacting with surfaces if you use old PBE PPs rather than "equivalent" revPBE ones. But I may be wrong... HTH Giuseppe On Thursday, November 26, 2015 07:24:27 AM Matej Huš wrote: > Found the culprit! > When I turned off the dipole correction, the system converged. > Digging deeper, I found the underlying problem. > > I had been reckless and used the 'emaxpos' value unchanged from a different > set of calculation, inadvertently setting it to too close to the edge of > the vacuum. A change from 0.70 to 0.50 solved the problem. > > Thanks for the all contributions! > > As for the dispersion correction, the discussion is still open :-) > > Matej > > -Original Message- > From: pw_forum-boun...@pwscf.org [mailto:pw_forum-boun...@pwscf.org] On > Behalf Of Ilya Ryabinkin > Sent: Tuesday, November 24, 2015 8:03 PM > To: PWSCF Forum <pw_forum@pwscf.org> > Subject: Re: [Pw_forum] bfgs optimization not going anywhere > > Colleagues, > to summarize: what would be 'the best' DFT correction on to of > *existing* functionals, e.g. PBE for molecule-metal-interaction? As far as I > understood, vdw-DF must be used with the corresponding pseudopotential > (BTW, where one can get them?). > > -- > I. > > On Tue, Nov 24, 2015 at 8:30 AM, Giuseppe Mattioli > <giuseppe.matti...@ism.cnr.it> wrote: > > Dear Matej (and all) > > > >> As for DFT-D2, I admit I am a bit in the dark here. How 'wrong' is > >> it? Or to put differently, is it more wrong that not using dispersion > >> correction at all? > > > > Regarding the dispersion correction(s) this is the Stephan Grimme's > > paper which indicates that DFT-D2 doubles the DFT-D3 interaction energy > > between molecules and metal surfaces: > > > > J. Chem. Phys. (2010) 132, 154104 > > > > In my experience of phthalocyanine/metal interactions (but if I > > remember well Ari has also performed calculations on > > porphyrin/phthalocyanine molecules adsorbed on metal surfaces and he > > can add his own knowledge), adsorption geometries and energies are > > very different, so that the results are also quite different. See for > > example this paper (Cu phthalocyanine interacting with Ag (100) with > > DFT-D2) > > > > PRL 105, 115702 (2010) > > > > And my paper (TiO phthalocyanine interacting with Ag (100) with > > vdW-DF) > > > > J. Phys. Chem. C 2014, 118, 5255 > > > > And, yes, of course: if you use no dispersion correction you badly > > underestimate the interaction between the molecule and the surface... > > > > 2 more hints: > > > > 1) In the case of molecule/metal systems, ab initio functionals > > modeling long distance correlation between electrons should be (in my > > opinion) preferred to semiempirical functional with add pairwise > > forces based on tabulations (or partial calculations) of C6 > > coefficients. There is a nice perspective written by J. L. Bredas > > which addresses the issue > > > > Nature Nanotechnology > > 8, > > 230–231 > > (2013) > > > > 2) Regarding lattice parameters, Ari is right in the case of vdwdf. > > But I've tried to simulate gold (bulk and) surfaces in contact with > > molecules by using the reparametrized vdwdf-c09 functional: lattice > > parameter of gold is ok, and also molecule-surface interactions are expected > > to be improved with respect to vdwdf!> > >> Also, if I change/switch off the dispersion correction, then I will > >> have to re-optimize all already converged structures (metal, isolated > >> molecules, adsorbed intermediates), right? Looks rather tedious > > > > Yes, you sho
Re: [Pw_forum] bfgs optimization not going anywhere
ce of the vdW-DF* you take, > but still, I would study a bit the literature first. If any one has a > reference for a good review on the vdW-DF* et co applied to surfaces and > adsorption, I would also be very thankful! :) > > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*= > - >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, 24 Nov 2015, Matej Huš wrote: > > Dear PW community > > > > I have a problem when trying to find optimized geometry of an adsorbed > > intermediate in "benzene" hydrogenation on Ru surface (see input below). > > > > I believe I am fairly close to optimised structure since I'm only > > adding one hydrogen atom to an already optimised reactant and only > > slight displacing the adjacent atoms. > > > > > > > > The problem is that BFGS doesn't seem to go anywhere. Energy only > > fluctuates, which to my understanding is a sign of being close to a > > minimum. > > > However, forces remain large. > > > > > > > > I've switched to the damp algorithm and the problem persists. I've > > searched through the forum and the usual approaches of tackling this > > issue do not seem to work. > > > > > > > > Any ideas? Thank you! > > > > Matej Hus > > > > Laboratory of Catalysis and Chemcial Reaction Engineering > > > > National Institute of Chemistry > > > > Ljubljana, Slovenia > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum **** - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] bfgs optimization not going anywhere
> But have you converged the calculation with respect to ecutwfc > after adding the hydrogen atom? 50 Ry looks quite low to me. Rather high with US pseudopotentials. And you should not check again because H was already present in the system. HTH Giuseppe On Tuesday, November 24, 2015 11:02:05 AM Jure Varlec wrote: > On Tue, 24 Nov 2015 09:43:02 +0100 > > Matej Huš <matej@gmail.com> wrote: > > I believe I am fairly close to optimised structure since I'm only > > adding one hydrogen atom to an already optimised reactant and only > > slight displacing the adjacent atoms. > > But have you converged the calculation with respect to ecutwfc > after adding the hydrogen atom? 50 Ry looks quite low to me. BTW, it's > good to find another QE user here at KI, I got the impression there > aren't (m)any. You're welcome to visit anytime :) > > Regards > Jure Varlec, L09 > > ___ > Pw_forum mailing list > Pw_forum@pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] bfgs optimization not going anywhere
; Ru 8.189451105 6.281486450 0.081381753 > > Ru 8.160703714 6.280573700 4.346822355 > > Ru 9.517621531 5.499394333 2.173047145 > > Ru 9.520829308 5.496568229 6.4500410790 0 0 > > Ru 6.841663951 8.643529802 0.068313157 > > Ru 6.801904020 8.635893952 4.339414209 > > Ru 8.168141305 7.845815871 2.185333857 > > Ru 8.160778897 7.852243693 6.4500410790 0 0 > > Ru 5.433547125 10.992149835 0.049127076 > > Ru 5.442657302 10.995054115 4.340836317 > > Ru 6.815744098 10.204943141 2.198574971 > > Ru 6.800728486 10.207919156 6.4500410790 0 0 > > Ru 4.079480921 13.360641882 0.078153880 > > Ru 4.080494286 13.349362578 4.343090628 > > Ru 5.440940622 12.563860374 2.187844380 > > Ru 5.440678075 12.563594620 6.4500410790 0 0 > > Ru 13.604344342 1.565286819 0.072478575 > > Ru 13.601163563 1.568664789 4.341371157 > > Ru 14.966982409 0.780981459 2.171507067 > > Ru 14.961130130 0.785217302 6.4500410790 0 0 > > Ru 12.241120605 3.924345358 0.072554514 > > Ru 12.241744039 3.923837130 4.343597181 > > Ru 13.606742641 3.142557639 2.175631341 > > Ru 13.601079719 3.140892766 6.4500410790 0 0 > > Ru 10.884351321 6.278690027 0.072299677 > > Ru 10.879668506 6.281316628 4.344298574 > > Ru 12.243274378 5.496483653 2.180453775 > > Ru 12.241029308 5.496568229 6.4500410790 0 0 > > Ru 9.531759423 8.633513554 0.076632767 > > Ru 9.520456632 8.639518177 4.346293156 > > Ru 10.881698865 7.856614979 2.176720077 > > Ru 10.880978897 7.852243693 6.4500410790 0 0 > > Ru 8.195939103 11.007704289 0.083611578 > > Ru 8.161520470 10.993102063 4.345293546 > > Ru 9.520699512 10.210057797 2.178590684 > > Ru 9.520928486 10.207919156 6.4500410790 0 0 > > Ru 6.804866616 13.357686743 0.079162526 > > Ru 6.801935753 13.349151958 4.343390811 > > Ru 8.155982796 12.556965776 2.185900158 > > Ru 8.160878075 12.563594620 6.4500410790 0 0 > > H 3.668277 3.396562 -1.870805 > > K_POINTS automatic > > 2 2 1 1 1 0 - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] [pw-forum]: Celldm(4) Celldm(5) Celldm(6)
Dear Francesco
The answer is quite easy.
ibrav=0, celldm(1)=9.35454172,
...
/
and, at the bottom of the input file
CELL_PARAMETERS {alat}
1.031703302 -0.002607611 0.034483284
-0.004621093 2.150980697 0.080635052
-0.031624028 0.077886584 1.892891072
HTH
Giuseppe
On Friday, November 20, 2015 10:19:56 AM Francesco Pelizza wrote:
> Hi dear Users and Developers,
>
> I really need a full explanation on how to get Celldm(4) Celldm(5)
> Celldm(6) from a VC-relaxation.
>
> The optimized structure of a system with angles between a-lat b-lat a
> c-lat not equals to 90° is given to me in some systems I am studying,
>
> But I can not find a way of putting this in a new input file.
>
> If I masure with xcrysden the inclination between periodic images, I got
> an angle that if i translate in the cosine value and put it into the
> input file, it does not give me the right angle when I open again the
> input file with xcrysden.
> Also a SCF calculation does not give a value identical or not even
> slightly different from the VC-rel calculation itself.
>
> So, How can I find out exactly Celldm(4) Celldm(5) Celldm(6) from this
> piece of output file?
>
> How do I put this in an input file being sure that quantum espresso will
> consider this value for building the lattice and doing the calculation
> properly ??
>
> Thank you very much for your time and patience
>
> Francesco Pelizza - PhD
> Strathclyde University (Glasgow)
>
> HERE you can find an output file as example
>
>
> Begin final coordinates
> new unit-cell volume = 3435.21521 a.u.^3 ( 509.04637 Ang^3 )
>
> CELL_PARAMETERS (alat= 9.35454172)
> 1.031703302 -0.002607611 0.034483284
>-0.004621093 2.150980697 0.080635052
>-0.031624028 0.077886584 1.892891072
>
> ATOMIC_POSITIONS (angstrom)
> H2.323443642 3.458500775 8.048639166
> H2.246157109 6.259499847 5.493082766
> H2.238584163 4.257844190 0.859706518
> H3.682576551 4.461248011 7.513953456
> H3.660946840 5.289309420 5.076217107
> H2.349858362 7.288089944 3.177035899
> H3.698019711 6.240499825 2.728594264
> H3.699705365 5.164845115 0.461710112
> F2.578959296 7.555136884 0.769673740
> F0.723629375 6.423372715 1.255939854
> F2.384732674 3.966152941 3.106747236
> F0.653462109 5.273905894 3.651911386
> F2.644696706 2.964473519 5.656123191
> F0.735387849 4.041727492 6.056045010
> F0.629819356 5.581707632 8.226678603
> F2.449175259 6.758487891 7.688004312
> F4.791542403 2.350295723 2.918699000
> F5.145230100 1.372558160 5.464114891
> H3.794899005 0.874565766 1.033564982
> H3.767987315 0.169480940 8.124815255
> F1.620809549 1.343881537 2.353960638
> H0.055376396 1.880995718 0.351068538
> F1.746935882 0.059135078 4.717276882
> H0.118749183 1.089942064 7.543474278
> H0.038360119 8.721213695 5.604899727
> H0.156416543 9.733931543 3.301761239
> F1.606381831 9.555176644 7.542110410
> F1.724803088 10.423382736 0.580085061
> H3.762597275 9.742742557 6.180086748
> H3.818806059 10.647160213 3.895291475
> F4.834332727 8.431554403 8.190079715
> F5.022683471 9.219462377 1.286641665
> C4.861902815 0.149655116 8.161361938
> C4.884761682 0.947642455 1.045408665
> C0.337188869 0.143176054 4.742567438
> C0.232687916 1.146022481 2.332101032
> C2.593624135 4.380706568 7.522390456
> C2.129082034 4.198114186 6.068998645
> C2.035262317 5.577048626 8.307268734
> C2.567916441 5.297168460 5.092510941
> C2.062790705 5.205690370 3.651450062
> C2.607997073 5.181809062 0.410338732
> C2.124256003 6.343778231 1.286849130
> C2.609613700 6.314467444 2.746950137
> C0.204140831 9.649137133 7.505914552
> C0.317897336 10.413912382 0.493174549
> C4.910634377 10.672243764 3.875929892
> C4.854146045 9.672373698 6.207264609
> End final coordinates
>
> ___
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- Article premier - Les hommes naissent et demeurent
libres et ègaux en droits. Les distinctions sociales
ne peuvent être fondèes que sur l'utilitè commune
- Article 2 - Le but de toute associat
Re: [Pw_forum] Problems with high ecutwfc for a C H As F S containing compound
85431 7.44995 10.96286 > H 10.46280 3.45270 10.96286 > H 28.18126 7.63147 6.56310 > H 11.78976 3.63422 6.56310 > H 28.92184 0.36303 1.02742 > H 12.53034 4.36028 1.02742 > C 27.26323 6.60922 5.13933 > C 10.87173 2.61197 5.13933 > C 26.52265 1.38528 10.67501 > C 10.13115 5.38253 10.67501 > H 27.61795 5.83339 5.59879 > H 11.22645 1.83614 5.59879 > H 28.35854 2.16111 0.06311 > H 11.96704 6.15836 0.06311 > H 27.78169 6.73853 4.33001 > H 11.39019 2.74128 4.33001 > H 27.04111 1.25597 9.86569 > H 10.64961 5.25322 9.86569 > C 13.44202 0.18298 1.85556 > C 29.83352 4.18023 1.85556 > C 12.70144 7.81152 7.39124 > C 29.09294 3.81427 7.39124 > H 13.72839 7.55876 1.16581 > H 30.11989 3.56151 1.16581 > H 12.98780 0.43574 6.70150 > H 29.37930 4.43299 6.70150 > H 14.02273 0.95930 1.82235 > H 30.41423 4.95655 1.82235 > H 13.28214 7.03520 7.35803 > H 29.67364 3.03795 7.35803 > C 13.55775 7.53144 3.17416 > C 29.94925 3.53419 3.17416 > C 12.81716 0.46306 8.70984 > C 29.20866 4.46031 8.70984 > H 13.68661 0.21518 3.85616 > H 30.07811 4.21243 3.85616 > H 12.94602 7.77932 9.39184 > H 29.33752 3.78207 9.39184 > H 14.33307 6.94883 3.18191 > H 30.72457 2.95158 3.18191 > H 13.59248 1.04567 8.71759 > H 29.98398 5.04292 8.71759 > K_POINTS automatic > 1 2 2 0 0 0 > > > > > - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Dielectric constant
Dear Sohail Ahmad
The error message is quite clear: epsilon.x works only with
norm-conserving pseudopotentials (NCPP), while you are using
Vanderbilt's ultrasoft pseudopotentials (USPP).
HTH
Giuseppe
Giuseppe Mattioli
ISM-CNR
Italy
Quoting Sohail Ahmad <sohailphys...@yahoo.co.in>:
> Dear QE users,
>
> I wish to calculate dielectric constants and some other related properties.
> I am getting following errors. My input file (scf and eps) are attached.
> I am using QE-5.0.1
>
> Fermi energy [eV] is: 12.49326
> The system is a metal...
>
> Performing eps calculation...
>
>
> %%
> Error in routine grid_build (1):
> USPP are not implemented
>
> %%
>
>
> prefix = 'ScN',
> outdir = './OUT',
> calculation = 'eps',
> /
> _GRID
> smeartype = 'gaussian',
> intersmear = 0.1,
> wmin = 0.00
> wmax = 10.00
> nw = 5000
> /
>
>
> calculation = 'scf',
> restart_mode = 'from_scratch',
> prefix = 'ScN',
> pseudo_dir = '/home/sohail/Espresso/espresso-5.0.1/pseudo',
> outdir = './OUT',
> /
>
> ibrav = 2, a = 4.501,
> nat = 2, ntyp = 2,
> ecutwfc = 250,
> ecutrho = 1000,
> nbnd = 20,
> occupations = 'smearing', smearing = 'gaussian', degauss = 0.001,
> nspin = 2,
> starting_magnetization(1) = 0.1d0,
> /
>
> mixing_beta = 0.3,
> conv_thr = 1.0d-9,
> /
> ATOMIC_SPECIES
> Sc 44.956 Sc.pw91-nsp-van.UPF
> N 14.007 N.pw91-van_ak.UPF
> ATOMIC_POSITIONS {angstrom}
> Sc 0.00 0.00 0.00
> N 2.250500 2.250500 2.250500
> K_POINTS AUTOMATIC
> 12 12 12 1 1 1
>
> -
> SOHAIL AHMAD
> KING KHALID UNIVERSITY
> SAUDI ARABIA
> ___
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--
- Article premier - Les hommes naissent et demeurent
libres et ègaux en droits. Les distinctions sociales
ne peuvent être fondèes que sur l'utilitè commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la libertè,
la propriètè, la sùretè et la rèsistance à l'oppression.
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM)
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail: <giuseppe.matti...@ism.cnr.it>
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Re: [Pw_forum] Band gap hybrid functionals
Dear Phil > But I mentioned a problem with using a very dense k - point grid and an 8 > atom Si cell, the program exits before it can output the forces, stresses, > and the individual contributions to the total energy Sorry, but this was not mentioned in the current thread in which you asked how to calculate the band gap... > Nobody was able to point me in the right direction with that. Also, another > user has previously reported that using a 2 atom si cell results in an > oscillation in the total energy as you increase ecutwfc (something I have > also verified) Have you checked if the Gamma gap or the "best" gap (at fixed occupations) jumps like the total energy or if it is already converged? However, both Stefano's and Mostafa's suggestions deserve to be considered. Have a nice computation and don't forget to add your affiliation to the posts to this forum. Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting Ref Fymz <reff...@gmail.com>: > But I mentioned a problem with using a very dense k - point grid and an 8 > atom Si cell, the program exits before it can output the forces, stresses, > and the individual contributions to the total energy (hence why regardless > of what screening parameter I used I got the same band gap, as the fock). > Nobody was able to point me in the right direction with that. Also, another > user has previously reported that using a 2 atom si cell results in an > oscillation in the total energy as you increase ecutwfc (something I have > also verified), so I'm not sure I can accurately calculate the band gap > using a 2 atom cell either. > > Phil > > On 11 November 2015 at 12:18, Ref Fymz <reff...@gmail.com> wrote: > >> Hey, >> >> Thanks for the reply. So if I use an 8 atom Si cell, and use fixed >> occupations with 32 bands, the difference between the highest occupied and >> lowest unoccupied is my actual band gap? (i.e the one I can compare to PBE >> and experiment) >> >> >> Phil >> >> On 11 November 2015 at 10:13, Ref Fymz <reff...@gmail.com> wrote: >> >>> Hey, >>> >>> I've tried searching the forum, and I haven't come across a way to >>> calculate the band gap in a material using the hybrid functionals. I know >>> you can't do nscf calculations, but is there any simple way to calculate >>> the band gap for a material using scf simulations? >>> >>> Thanks, >>> >>> Phil >>> >> >> -- - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Band gap hybrid functionals
Dear all > So if I use an 8 atom Si cell, and use fixed > occupations with 32 bands, the difference between the highest occupied and > lowest unoccupied is my actual band gap? This is true for direct band gap semiconductors, where both VBM and CBM can be found at Gamma, which must be included in the list. This is easy because every N, N, N, 0, 0, 0 automatically generated grid includes Gamma. However, in the case of bulk Si the CBM falls somewhere along the Gamma-X direction, close to X. If your k-point mesh is *very* dense, then the CBM found by the code at a given k-point will be negligibly shifted wrt the proper CBM. Otherwise you should perform the calculation by using the proper 2-atom Si cell (faster calculation with EXX functionals...) and you should be sure to include one k-point close to the CBM in the mesh. You can still work with the sc 8-atom cell, if you prefer. But you must *fold* the 8-atom sc cell into the 2-atom fcc cell. HTH Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting Ref Fymz <reff...@gmail.com>: > Hey, > > Thanks for the reply. So if I use an 8 atom Si cell, and use fixed > occupations with 32 bands, the difference between the highest occupied and > lowest unoccupied is my actual band gap? (i.e the one I can compare to PBE > and experiment) > > > Phil > > On 11 November 2015 at 10:13, Ref Fymz <reff...@gmail.com> wrote: > >> Hey, >> >> I've tried searching the forum, and I haven't come across a way to >> calculate the band gap in a material using the hybrid functionals. I know >> you can't do nscf calculations, but is there any simple way to calculate >> the band gap for a material using scf simulations? >> >> Thanks, >> >> Phil >> -- - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM) Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Silicon HSE - Valence band level
Dear Dhirendra > HSE06 should improve conduction band levels, why is > it changing the valence band too? Why do you think so? Your ideas on DFT approximation levels seem a bit confused... You may want to read these enlightening articles: Cohen, A. J.; Mori-Sànchez, P.; Yang, W. Science 2008, 321, 792. Mori-Sànchez, P.; Cohen, A. J.; Yang, W. Phys. Rev. Lett. 2008, 100, 146401. HTH Giuseppe On Friday, October 30, 2015 02:18:09 PM DHIRENDRA VAIDYA wrote: > Hi, > > I am doing Silicon bulk calculations to determine the valence band level > w.r.t average electrostatic potential. When HSE is used I am getting > valence band maximum closer to the average electrostatic potential by 0.3eV > which is significant. HSE06 should improve conduction band levels, why is > it changing the valence band too? I am using occupations as fixed to > determined the valence band level. > > -- > Dhirendra > IIT Bombay - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Charge accumulation and depletion
Dear Jaret Yes, I suppose you understood me well...:-) In the case of US PPs the Bader post-processing does not work well because, in my experience at least, the Bader minima may fall into the US augmentation charge sphere, so that the values of atomic charge become erratic. Have a nice computation! Giuseppe Giuseppe Mattioli ISM-CNR Italy Quoting Jaret Qi <jare...@yahoo.com>: > To make sure I understood you:-case one gives a charge density > plot-case two gives a numerical charges difference, right?>>You may > also use the external Bader post processing to estimate atomic > charges, but it requires (to be reliable) PAW or NC pseudopotentials > and hand-adjusted very dense FFT gridsI'm using Ultrasoft PP which > means it won't work in my case? > best-jaretASU > > > On Friday, October 23, 2015 2:36 AM, Giuseppe Mattioli > <giuseppe.matti...@ism.cnr.it> wrote: > > > > Dear Jaret > You may do two (complementary) things: > > 1) a Deltarho map. a) Calculation of your whole system and usage of > pp.x to extract the charge density (plot_num=0). b) two separate scf > calculations > of the insulator slab and metal slab in the same atomic position of > the previous one and usage of pp.x to extract the charge densities. > c) Subtract > the charge densities calculated in b) to the charge densities > calculated in a). If you open the obtained file with xcrysden you > can visualize the > charge displacement at the interface (menu tools --> data grid). > > Something like this, which has been set up for a molecule/surface system... > > export FILEA="molecule+surface" > export INPFILE=$FILEA-cha.inp > export OUTFILE=$FILEA-cha.out > echo " $FILEA" > echo " $INPFILE" > echo " $OUTFILE" > cat > $INPFILE << EOF > > prefix = '$FILEA' > outdir = '$TMP_DIR/' > filplot = '$FILEA-cha.dat' > plot_num= 0 > / > EOF > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE > > export FILEB="molecule" > export INPFILE=$FILEB-cha.inp > export OUTFILE=$FILEB-cha.out > echo " $FILEB" > echo " $INPFILE" > echo " $OUTFILE" > cat > $INPFILE << EOF > > prefix = '$FILEB' > outdir = '$TMP_DIR/' > filplot = '$FILEB-cha.dat' > plot_num= 0 > / > EOF > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE > > > export FILEC="surface" > export INPFILE=$FILEC-cha.inp > export OUTFILE=$FILEC-cha.out > echo " $FILEC" > echo " $INPFILE" > echo " $OUTFILE" > cat > $INPFILE << EOF > > prefix = '$FILEC' > outdir = '$TMP_DIR/' > filplot = '$FILEC-cha.dat' > plot_num= 0 > / > EOF > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE > > export FILE="rho-int-$FILEA" > export INPFILE=$FILE.inp > export OUTFILE=$FILE.out > echo " $FILE" > echo " $INPFILE" > echo " $OUTFILE" > cat > $INPFILE << EOF > > / > > nfile = 3 > filepp(1) = '$FILEA-cha.dat' > weight(1) = 1.0 > filepp(2) = '$FILEB-cha.dat' > weight(2) = -1.0 > filepp(3) = '$FILEC-cha.dat' > weight(3) = -1.0 > iflag = 3 > output_format = 5 > fileout = '$FILE.plot' > e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0, > e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, > nx=56, ny=40 > / > EOF > $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE > > 2) Use projwfc.x to obtain (Lowdin) atomic charges of your whole > system and of the separate slabs (you may also relax the slabs, in > this case, to > account for surface effects). Then you compare the atomic charges to > look for charge displacement. Be aware that there is a spilling > parameter at the > end of the projwfc output which indicates how much of your charge > density does not fit into the Lowding atomic partitioning. Your > results are > reasonably meaningful only if the spilling parameter is similar for > all your calculations... You may also use the external Bader post > processing to > estimate atomic charges, but it requires (to be reliable) PAW or NC > pseudopotentials and hand-adjusted very dense FFT grids. You may > like to have a > look here if you want to try > > http://theory.cm.utexas.edu/henkelman/code/bader/ > > HTH > Giuseppe > > On Friday, October 23, 2015 06:12:17 AM you wrote: >> Dear Giuseppe,My system is an interface between an insulator and half-metal. >> -Jaret >> AST, USA>Dear mahmo
Re: [Pw_forum] Ionization in QE
Dear Vipul You can do it by using, e.g., tot_charge=+1.0. Remember that you are not performing all-electron calculations in a GTO framework: a background charge density is added to your supercell in order to calculate Ewald's sums. This is going to shift the potential energy (and eigenvalues) of your charged cell wrt the neutral one. HTH Giuseppe On Friday, October 23, 2015 03:22:32 PM Vipul Shivaji Ghemud wrote: > I want to ionize my cluster i.e. I want to remove an electron from overall > structure and not a specific atom, so that the charge distribution is > uniform and overall charge is less by the charge of 1 electron. Similarly, > I want to do it for cation - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Charge accumulation and depletion
Dear Jaret You may do two (complementary) things: 1) a Deltarho map. a) Calculation of your whole system and usage of pp.x to extract the charge density (plot_num=0). b) two separate scf calculations of the insulator slab and metal slab in the same atomic position of the previous one and usage of pp.x to extract the charge densities. c) Subtract the charge densities calculated in b) to the charge densities calculated in a). If you open the obtained file with xcrysden you can visualize the charge displacement at the interface (menu tools --> data grid). Something like this, which has been set up for a molecule/surface system... export FILEA="molecule+surface" export INPFILE=$FILEA-cha.inp export OUTFILE=$FILEA-cha.out echo " $FILEA" echo " $INPFILE" echo " $OUTFILE" cat > $INPFILE << EOF prefix = '$FILEA' outdir = '$TMP_DIR/' filplot = '$FILEA-cha.dat' plot_num= 0 / EOF $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE export FILEB="molecule" export INPFILE=$FILEB-cha.inp export OUTFILE=$FILEB-cha.out echo " $FILEB" echo " $INPFILE" echo " $OUTFILE" cat > $INPFILE << EOF prefix = '$FILEB' outdir = '$TMP_DIR/' filplot = '$FILEB-cha.dat' plot_num= 0 / EOF $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE export FILEC="surface" export INPFILE=$FILEC-cha.inp export OUTFILE=$FILEC-cha.out echo " $FILEC" echo " $INPFILE" echo " $OUTFILE" cat > $INPFILE << EOF prefix = '$FILEC' outdir = '$TMP_DIR/' filplot = '$FILEC-cha.dat' plot_num= 0 / EOF $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE export FILE="rho-int-$FILEA" export INPFILE=$FILE.inp export OUTFILE=$FILE.out echo " $FILE" echo " $INPFILE" echo " $OUTFILE" cat > $INPFILE << EOF / nfile = 3 filepp(1) = '$FILEA-cha.dat' weight(1) = 1.0 filepp(2) = '$FILEB-cha.dat' weight(2) = -1.0 filepp(3) = '$FILEC-cha.dat' weight(3) = -1.0 iflag = 3 output_format = 5 fileout = '$FILE.plot' e1(1) =1.0, e1(2)=1.0, e1(3) = 0.0, e2(1) =0.0, e2(2)=0.0, e2(3) = 1.0, nx=56, ny=40 / EOF $PARA_PREFIX $ESPRESSO/pp.x $PARA_POSTFIX < $INPFILE >> $OUTFILE 2) Use projwfc.x to obtain (Lowdin) atomic charges of your whole system and of the separate slabs (you may also relax the slabs, in this case, to account for surface effects). Then you compare the atomic charges to look for charge displacement. Be aware that there is a spilling parameter at the end of the projwfc output which indicates how much of your charge density does not fit into the Lowding atomic partitioning. Your results are reasonably meaningful only if the spilling parameter is similar for all your calculations... You may also use the external Bader post processing to estimate atomic charges, but it requires (to be reliable) PAW or NC pseudopotentials and hand-adjusted very dense FFT grids. You may like to have a look here if you want to try http://theory.cm.utexas.edu/henkelman/code/bader/ HTH Giuseppe On Friday, October 23, 2015 06:12:17 AM you wrote: > Dear Giuseppe,My system is an interface between an insulator and half-metal. > -Jaret > AST, USA>Dear mahmoudASU > > >First of all sign always your posts to this Forum with name and affiliation, > >please. > > > >There are many ways to calculate charge displacements (Deltarho plots, > >atomic charge calculations, ...), but their best usage depends on >the kind > >of charge displacement occurring in your system (molecule-surface > >interaction, charge transfer affecting dopants or defects in a >semiconductor > >matrix, ...). Impossible to say more without knowing more... > > > >HTH > > > >Giuseppe > > > >On Wednesday, October 21, 2015 11:42:37 PM Jaret Qi wrote: > >> Hello QE users,Is there a way to calculate Charge accumulation and > >> depletion in quantum espresso, if so then how? > >> -mahmoudASU - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] Charge accumulation and depletion
Dear mahmoudASU First of all sign always your posts to this Forum with name and affiliation, please. There are many ways to calculate charge displacements (Deltarho plots, atomic charge calculations, ...), but their best usage depends on the kind of charge displacement occurring in your system (molecule-surface interaction, charge transfer affecting dopants or defects in a semiconductor matrix, ...). Impossible to say more without knowing more... HTH Giuseppe On Wednesday, October 21, 2015 11:42:37 PM Jaret Qi wrote: > Hello QE users,Is there a way to calculate Charge accumulation and depletion > in quantum espresso, if so then how? > -mahmoudASU - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
Re: [Pw_forum] starting magnetization in DFT+U calculation
Dear K. Krishna + Variable: starting_magnetization(i), i=1,ntyp Type: REAL Description:starting spin polarization on atomic type 'i' in a spin polarized calculation. Values range between -1 (all spins down for the valence electrons of atom type 'i') to 1 (all spins up). Breaks the symmetry and provides a starting point for self-consistency. The default value is zero, BUT a value MUST be specified for AT LEAST one atomic type in spin polarized calculations, unless you constrain the magnetization (see "tot_magnetization" and "constrained_magnetization"). Note that if you start from zero initial magnetization, you will invariably end up in a nonmagnetic (zero magnetization) state. If you want to start from an antiferromagnetic state, you may need to define two different atomic species corresponding to sublattices of the same atomic type. starting_magnetization is ignored if you are performing a non-scf calculation, if you are restarting from a previous run, or restarting from an interrupted run. If you fix the magnetization with "tot_magnetization", you should not specify starting_magnetization. In the spin-orbit case starting with zero starting_magnetization on all atoms imposes time reversal symmetry. The magnetization is never calculated and kept zero (the internal variable domag is .FALSE.). + HTH Giuseppe On Monday, October 12, 2015 06:32:06 PM you wrote: > what value can i give as starting magnetization for Fe2O3 in DFT+U > calculations. can i give any random value? > > > > > > Thanks and Regards, > K.Krishna > JRF, CSIR-SERC > India - Article premier - Les hommes naissent et demeurent libres et ègaux en droits. Les distinctions sociales ne peuvent être fondèes que sur l'utilitè commune - Article 2 - Le but de toute association politique est la conservation des droits naturels et imprescriptibles de l'homme. Ces droits sont la libertè, la propriètè, la sùretè et la rèsistance à l'oppression. **** Giuseppe Mattioli CNR - ISTITUTO DI STRUTTURA DELLA MATERIA v. Salaria Km 29,300 - C.P. 10 I 00015 - Monterotondo Stazione (RM), Italy Tel + 39 06 90672836 - Fax +39 06 90672316 E-mail: <giuseppe.matti...@ism.cnr.it> http://www.ism.cnr.it/english/staff/mattiolig ResearcherID: F-6308-2012 ___ Pw_forum mailing list Pw_forum@pwscf.org http://pwscf.org/mailman/listinfo/pw_forum
