[Pw_forum] Wave function file visualising
You have to use the post processing tool to convert it to readable format. Read the documentation for pp.x. On Fri, Feb 7, 2014 at 10:30 AM, Suresh A wrote: > Hi, > how to visualise wave function file stored at temporary(tmp) folder . > I just tried to open it with gedit and it is in unreadable format. Can any > one suggest binary (octet-stream) to text file converter or how to open it. > Thanks > With Regards, > A.Suresh, > Research Scholar, > Madurai Kamaraj University, > Madurai. > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, --------- Mohnish Pandey, PhD Student, Center for Atomic-scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140207/50bd773f/attachment.html
[Pw_forum] hybrid calculation with dexx negative
Hi Valentina,
May be it will help:
http://qe-forge.org/pipermail/pw_forum/2013-November/102690.html
On Thu, Jan 30, 2014 at 10:52 AM, DELLACA' Valentina (CRF) <
valentina.dellaca at crf.it> wrote:
> Dear all,
>
> We are performing surface calculations with hybrid functional, and for the
> following surface structure at the moment the error saying: 'dexx is
> negative, error # 1 , check that exxdiv_treatment is appropriate for the
> system' is giving us some troubles. We already tried to change the distance
> between surfaces, changing celldm(3), around its optimized value 2.39, we
> changed also mixing_beta to 0.3, and we tried with few different k point
> grids. None of this attempt was successful in solving the error. We also
> changed the occupations to smearing, and we gave a small degauss (1d-20),
> but then (with many celldm(3)) it was not even converging the first scf.
>
> Any suggestion on how to fix this error?
>
> Thank you,
>
> Regards,
>
> Valentina
>
>
>
>
>
> calculation = 'scf',
>
> restart_mode = 'from_scratch',
>
>outdir = '',
>
> pseudo_dir = '',
>
> prefix = 'ta2o5' ,
>
> disk_io = 'default',
>
> /
>
>
>
> ibrav = 8,
>
> celldm(1) = 14.241893092,
>
> celldm(2) = 0.822831603,
>
> celldm(3) = 2.39,
>
> nat = 38,
>
> ntyp = 2,
>
>ecutwfc=70, nbnd=700, occupations='fixed',
>
> input_dft = 'PBE0',
>
> exxdiv_treatment = 'gygi-baldereschi'
>
> x_gamma_extrapolation=.true.
>
> nqx1 = 1 , nqx2 = 1, nqx3 = 1
>
> /
>
>
>
> conv_thr=1.0d-9, mixing_beta=0.5
>
> /
>
> ATOMIC_SPECIES
>
> Ta 180.95 Ta.pbe-mt-fhi.UPF
>
> O 15.999 O.pbe-mt-fhi.UPF
>
>
>
>
>
>
>
> ATOMIC_POSITIONS (angstrom)
>
> O0.813278477 4.617988459 8.007774872
>
> O2.023476210 0.776972843 8.441046448
>
> Ta 1.546871435 2.767467670 7.799599600
>
> O3.366054079 3.877523758 8.440539307
>
> Ta 3.843027211 5.867856582 7.799473875
>
> O5.792152399 5.359043398 8.438587876
>
> Ta 5.314346183 3.366897623 7.799507537
>
> O4.577766398 1.516932685 8.008262086
>
> O7.134074123 2.258690100 8.438344309
>
> Ta 7.612245398 0.266340494 7.800172819
>
> O3.496914324 5.857316984 5.883545751
>
> O5.660946844 3.375012981 5.883534436
>
> O1.890303432 2.756178342 5.883603671
>
> O7.271488124 0.274248516 5.883520878
>
> O5.637305636 5.330921586 3.862497327
>
> O3.523414777 3.905957403 3.865060769
>
> O0.813798912 4.618557268 3.867613313
>
> O1.868771197 0.805909423 3.864412229
>
> O4.578829938 1.517577526 3.866842485
>
> O7.290961638 2.230024951 3.864847639
>
> O3.497903745 5.858106076 1.841803379
>
> O1.888736406 2.757775274 1.841813170
>
> O5.659923444 3.372905841 1.841275566
>
> O7.273010266 0.273369852 1.841504469
>
> O5.792500075 5.359007930 -0.713580871
>
> O3.366000630 3.876131545 -0.715282591
>
> O0.813543928 4.618155682 -0.280250553
>
> O2.025151305 0.776423231 -0.714789822
>
> O4.578389288 1.516157053 -0.281620473
>
> O7.134187444 2.259560146 -0.714019402
>
> Ta 3.631274701 5.991239815 3.862567887
>
> Ta 1.760248756 2.890622602 3.862584360
>
> Ta 5.528096689 3.245167855 3.862383012
>
> Ta 7.400881489 0.144629430 3.862458735
>
> Ta 7.613260471 0.266812681 -0.075602588
>
> Ta 5.314089138 3.366439123 -0.075243654
>
> Ta 3.843827877 5.867144678 -0.074583652
>
> Ta 1.546399836 2.767291744 -0.074953513
>
>
>
>
>
>
>
> K_POINTS {automatic}
>
> 2 2 1 0 0 0
>
>
>
> Valentina Dellac?
> Group Materials Labs
> PA - Virtual Analysis & Materials Modelling
>
>
> Centro Ricerche Fiat S.C.p.A.
> Sede legale e amministrativa: Strada Torino, 50
> 10043 Orbassano (TO), Italia
> Tel +39 011 9083138
> Fax +39 011 9083666
>
> www.crf.it
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Regards,
MOHNISH,
-
Mohnish Pandey,
PhD Student,
Center for Atomic-scale Materials Design,
Department of Physics,
Technical University of Denmark
-
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[Pw_forum] Having problem with Total energy in Band structure calculation
3.7E-09 Ry > > The total energy is the sum of the following terms: > > one-electron contribution =-373.71256696 Ry > hartree contribution = 195.30418819 Ry > xc contribution = -26.64451511 Ry > ewald contribution= 513.04826235 Ry > > convergence has been achieved in 30 iterations > > Forces acting on atoms (Ry/au): > > atom1 type 1 force =65.43446471 65.42533969 65.42845937 > atom2 type 1 force = -39.98837920 -39.97896189 -39.94906074 > atom3 type 2 force = 148.86971851 148.86160168 148.92941675 > atom4 type 2 force = -69.52414233 -69.51568720 -69.58409401 > atom5 type 3 force = -104.79166169 -104.79229228 -104.82472138 > > Total force = 362.763292 Total SCF correction = 0.000163 > > > entering subroutine stress ... > > total stress (Ry/bohr**3) (kbar) > P=24248.94 >0.16474447 0.16704983 0.16696437 24234.74 24573.87 24561.30 >0.16704983 0.16464995 0.16695682 24573.87 24220.84 24560.19 >0.16696437 0.16695682 0.16512844 24561.30 24560.19 24291.23 > > > Writing output data file Bi2Te2SRH_exc1.save > > init_run : 31.46s CPU 31.66s WALL ( 1 calls) > electrons:966.22s CPU973.94s WALL ( 1 calls) > forces : 1.27s CPU 1.28s WALL ( 1 calls) > stress : 2.90s CPU 3.01s WALL ( 1 calls) > > Called by init_run: > wfcinit : 30.47s CPU 30.64s WALL ( 1 calls) > potinit : 0.36s CPU 0.37s WALL ( 1 calls) > > Called by electrons: > c_bands :825.93s CPU832.30s WALL ( 30 calls) > sum_band :133.86s CPU134.56s WALL ( 30 calls) > v_of_rho : 5.86s CPU 6.15s WALL ( 31 calls) > mix_rho : 0.34s CPU 0.34s WALL ( 30 calls) > > Called by c_bands: > init_us_2: 5.90s CPU 6.48s WALL (4032 calls) > cegterg :811.64s CPU816.39s WALL (1920 calls) > > Called by *egterg: > h_psi:799.79s CPU803.81s WALL ( 10590 calls) > g_psi: 1.70s CPU 1.74s WALL (8606 calls) > cdiaghg : 6.48s CPU 6.70s WALL ( 10526 calls) > > Called by h_psi: > add_vuspsi : 17.46s CPU 17.33s WALL ( 10590 calls) > > General routines > calbec : 20.34s CPU 20.37s WALL ( 10718 calls) > fft : 2.31s CPU 2.39s WALL ( 348 calls) > fftw :807.28s CPU812.56s WALL ( 184596 calls) > davcio : 0.52s CPU 1.30s WALL (5952 calls) > > > PWSCF: 16m42.21s CPU16m50.46s WALL > > >This run was terminated on: 12: 1:18 12Jan2014 > > > =--= >JOB DONE. > Thanks ALLASSAN SHUAIBU > PhD Theoretical Physics > UPM Malaysia > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic-scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20140112/9217d1d7/attachment.html
[Pw_forum] Binding energy of an interface
S.Q. Wang, H.Q. Ye, Curr. Opin. Solid State Mater. Sci. 10, 26 (2006)
This article is also available on the author's website I think. Below is
the link, I hope it works for you.
http://www.synl.ac.cn/upPdf/COSSMS_sqw_print.pdf.pdf
On Tue, Jul 2, 2013 at 6:08 AM, Tram Bui wrote:
> Dear Mohnish,
> Thank you so much for your information. By any chance, if you have
> any reference works that mention about this. Would you please direct me to
> them?
>
> Regards,
> Tram
>
>
> On Tue, Jun 18, 2013 at 11:56 PM, mohnish pandey gmail.com>wrote:
>
>> The interfacial energy of the system will be E_{interfacial} = E_{
>> fcc-ZrH [111] + Zr [0001] } - E_{ fcc-ZrH [111] } - E_{ Zr [0001] }. So it
>> will be the difference in total energy of your combined system(the slab
>> containing both ZrH and Zr here) minus sum of total energy of the
>> individual systemv(individual slab).
>>
>>
>> On Wed, Jun 19, 2013 at 12:13 AM, Tram Bui > u.boisestate.edu>wrote:
>>
>>> Dear All Users,
>>> Would you please give me some suggestion on how to obtain a correct
>>> formula to determine the binding energy of an interface between two
>>> materials? I have a system including the interface of fcc-ZrH [111] and
>>> hcp Zr [0001]. I have obtained the total energy of this system as well as
>>> the energy of individual material. Based on a previous work on the similar
>>> matter (
>>> http://mpdc.mae.cornell.edu/Courses/MAE715/Symposium12/NiniMunoz-Paper.pdf),
>>> I try to obtain the binding energy by subtracting the total energy of the
>>> big system (including both ZrH and Zr with their interface) with energies
>>> of isolated material (like the bulk), but the result is odd. I have check
>>> all my calculations and find nothing wrong, so I think it might be because
>>> of the formula I use. It might be missing something. So if anyone can
>>> please give me some guidance on this, I really appreciate that.
>>>
>>> Regards,
>>>
>>> Tram Bui
>>>
>>> M.S. Materials Science & Engineering
>>> trambui at u.boisestate.edu
>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>
>>
>>
>> --
>> Regards,
>> MOHNISH,
>> -
>> Mohnish Pandey,
>> PhD Student,
>> Center for Atomic-scale Materials Design,
>> Department of Physics,
>> Technical University of Denmark
>> -
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Regards,
MOHNISH,
-
Mohnish Pandey,
PhD Student,
Center for Atomic-scale Materials Design,
Department of Physics,
Technical University of Denmark
-
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[Pw_forum] Binding energy of an interface
The interfacial energy of the system will be E_{interfacial} = E_{ fcc-ZrH
[111] + Zr [0001] } - E_{ fcc-ZrH [111] } - E_{ Zr [0001] }. So it will be
the difference in total energy of your combined system(the slab containing
both ZrH and Zr here) minus sum of total energy of the individual
systemv(individual slab).
On Wed, Jun 19, 2013 at 12:13 AM, Tram Bui wrote:
> Dear All Users,
> Would you please give me some suggestion on how to obtain a correct
> formula to determine the binding energy of an interface between two
> materials? I have a system including the interface of fcc-ZrH [111] and
> hcp Zr [0001]. I have obtained the total energy of this system as well as
> the energy of individual material. Based on a previous work on the similar
> matter (
> http://mpdc.mae.cornell.edu/Courses/MAE715/Symposium12/NiniMunoz-Paper.pdf),
> I try to obtain the binding energy by subtracting the total energy of the
> big system (including both ZrH and Zr with their interface) with energies
> of isolated material (like the bulk), but the result is odd. I have check
> all my calculations and find nothing wrong, so I think it might be because
> of the formula I use. It might be missing something. So if anyone can
> please give me some guidance on this, I really appreciate that.
>
> Regards,
>
> Tram Bui
>
> M.S. Materials Science & Engineering
> trambui at u.boisestate.edu
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Regards,
MOHNISH,
-
Mohnish Pandey,
PhD Student,
Center for Atomic-scale Materials Design,
Department of Physics,
Technical University of Denmark
-
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[Pw_forum] change of crystal symmetry during vc-relax calculations with pressure
Dear Saqib, The number of symmetry operations may be the same but the 'kind' of symmetry may be different. The way to study the pressure induced phase transition is to plot the enthalpy as a function of pressure both the systems and look for the crossover. Geometry optimization doesn't convert the one type of crystal to the other. So you have to do the calculations for both of your system. At the transition pressure the enthalpy of the dominant phase will be lower. I hope it helps. On Fri, Jun 14, 2013 at 3:09 PM, saqib javed wrote: > Dear Paolo, > > Actually lattice parameters obtained for high pressures ( 25, 30, 35 GPa) > are the same if initial structure is either tetragonal or orthorhombic. > Furthermore the initial symmetry for both cases as written at start of > output reads the same > > *2 Sym. Op. (with inversion)* > > Thus perhaps change from tetragonal to orthorhombic structures at high > pressure may not represent symmetry breaking ?? And results obtained are > physicall meaningful i.e., tetragonal phase is unstable at high pressures > in favor of orthorhombic phase. Plz correct me if you see anything wrong in > my reasoning. > > cheers > Saqib > NCP, Pakistan > > > > From: paolo.giannozzi at uniud.it > > To: pw_forum at pwscf.org > > Date: Fri, 14 Jun 2013 12:34:57 +0200 > > > Subject: Re: [Pw_forum] change of crystal symmetry during vc-relax > calculations with pressure > > > > On Fri, 2013-06-14 at 09:13 +, saqib javed wrote: > > > > > i started with tetragonal structure (ibrav=6) so i would have imagined > > > that a=b would have been enforced by the code in case symmetry is > > > conserved during optimization ... > > > > symmetry IS conserved during optimization, apart from unfortunate cases, > > but only the symmetry of the starting configuration, as found by the > > code. Look at which symmetries are found by the code in the starting > > configuration. > > > > > you are saying that these results don't represent physical > > > pressure-induced tetragonal to orthorhombic transition but just a > > > numerical artificat ? > > > > I don't know. Likely: it is a 0.3% difference. Do you trust it? > > I wouldn't. At least, not without some additional evidence. > > > > P. > > -- > > Paolo Giannozzi, Dept. Chemistry, > > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic-scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130614/def7da1f/attachment.html
[Pw_forum] vc-relax gives good result of lattice constant, but not good in cohesive energy
You have to do the spin-polarized calculation for isolated atom. Zr has two unpaired electron in outer d-shell. On Tue, Jun 4, 2013 at 1:02 PM, Dongsheng Zhang wrote: > Hi, > > I am calculating the optimum lattice constant nd cohesive energy of Zr hcp > crystal. The total energy of a sinle Zr atom I got from input file Zr.in is > -5.53133015 Ry, the total energy of Zr hcp crystal I got from input file > Zr.hcp.in is -12.13562915 Ry, so the cohesive energy is -0.536 Ry, > converted to -7.30 eV. From a reference paper, the cohesive energy should > be -6.2eV. Attached below are Zr.in and Zr.hcp.in. Could anyone tell me > if I had made any mistake in those input files? Thanks. > > Zr.in: > > > prefix='Zr', > pseudo_dir = '/home/zhang/Software/espresso_PP/', > outdir='/share/scratch/tmpZr/eCut120SM0.01/', > / > > ibrav= 1, celldm(1) =50, nat= 1, ntyp= 1, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01, > ecutwfc =120, > > / > > / > ATOMIC_SPECIES > Zr 91.224 Zr.pbe-mt_fhi.UPF > ATOMIC_POSITIONS > Zr 0. 0. 0. > K_POINTS gamma > > > Zr.hcp.in > > > prefix='Zr', > pseudo_dir = '/home/zhang/Software/espresso_PP/', > outdir='/share/scratch/tmpZr/eCut120K18hcpSM0.01/', > calculation='vc-relax' > / > > ibrav= 4, celldm(1) =6, celldm(3) =1.633, nat= 2, ntyp= 1, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.01, > ecutwfc =120, > / > > / > > / > > / > ATOMIC_SPECIES > Zr 91.224 Zr.pbe-mt_fhi.UPF > ATOMIC_POSITIONS crystal > Zr 0. 0. 0. > Zr 0. 0. 0.500 > K_POINTS automatic > 18 18 36 1 1 1 > > PS The optimum lattice constant got from Zr.hcp.in is very close to the > data in literature. > > > I have tried different value of the smearing parameter ranged from 0.001 > to 0.05, none of their cohesive energy is good. > > If the smearing value is 0.1, simulation by zr.in (single atom) will stop > at iteration # 10 without any error message. Why does it happen? > > Thank you for your help, > > Dongsheng > > _______ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic-scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130604/faf91c7f/attachment.html
[Pw_forum] (no subject)
Hi, You have to do slab calculation to simulate a thin film. There are many examples involving slabs in QE. But you have to create the slab by yourself using the optimized bulk structure. First you have to decide the direction in which you want to cleave the bulk then with the help of visualization tool like XCrysden, you can create the slab. On Mon, Jun 3, 2013 at 8:07 AM, samad zare wrote: > Dear all, > > > Now, i am trying to calculate same properties sio2 for thin films. As a > first step, we need to generate case.struct for the thin film. > For this, i have searched in pwscf forum to do these kind of > calculations, i didn't find any tutorial type input for thin film > structure file. > As a beginners,i need some basic guidelines to build the thin film > structure file. So, i am requesting some one to provide the > preliminary > details to do so. What are all the changes in structure file from bulk > to thin films ???* > * > Thanks in advance > > > > -- > With Best Regards > SAMAD ZARE, phD Student UTM university > Nanotechnology Research Alliance > APSI, UTM 81310, Skudai,Johor Bahru, Malaysia > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic-scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130603/bed12782/attachment.html
[Pw_forum] Questions on ibrav in pw.x
Hi Yantao,
A crystal is defined as lattice + basis. A bulk crystal has an infinite
size (infinite is a good approximation for the bulk description) and made
of identical units (which is one unitcell). So you need to know the
geometry of the unitcell (which is lattice) and what is it composed of
(which is basis), which in the input description is atomic positions. So
you need both the lattice type and atomic positions. This link will be
useful for you, you need to understand a bit of crystallography, that will
help you to get rid of the error you are getting.
http://www.vlab.msi.umn.edu/events/download/tutorial_wyckoff.pdf
On Tue, May 28, 2013 at 9:57 AM, Yantao Wu wrote:
> Dear QE,
>
> I'm wondering what ibrav means in pw.x. My confusion is that if you can
> specify atomic positions freely, isn't the structure of the solid already
> implied by the positions? So why do we need the extra variable of ibrav. Or
> does ibrav carries more meaning than just the initial lattice structure of
> the solid?
>
> Another related question: When I ran vc-relax, I specified ibrav = 2 (fcc)
> and the atomic positions as follows:
>
> ATOMIC_POSITIONS {alat}
> Al 0.0 0.5 0.5
> Al 0.5 0.0 0.0
> Al 0.25 0.250.25
> Al 0.0 0.5 0.0
> Ti 0.75 0.750.75
> Ti 0.5 0.0 0.5
> Cr 0.0 0.0 0.0
> Cr 0.75 0.750.25
> Fe 0.5 0.5 0.0
> Fe 0.75 0.250.25
> Co 0.0 0.0 0.5
> Co 0.25 0.750.25
> Co 0.75 0.250.75
> Ni 0.25 0.750.75
> Ni 0.25 0.250.75
> Ni 0.5 0.5 0.5
>
> QE erred and complained that atom #1 and atom #6 overlap, which they
> apparently don't from the first sight. When I set ibrav = 1 (sc) and kept
> the same atomic positions, the complaint disappeared. So does anyone know
> why did the error occur?
>
> I appreciate your replies with all my gratitude.
>
> Yantao "ignorant student" Wu
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Regards,
MOHNISH,
-
Mohnish Pandey,
PhD Student,
Center for Atomic Scale Materials Design,
Department of Physics,
Technical University of Denmark
-
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[Pw_forum] scf calculation stops at starting wfc ...
Dear Xue, Do you really need this high cutoff as pointed out by Jia? Just a side note: I think starting with 'atomic + random' is a better choice rather than just 'atomic'. On Thu, May 16, 2013 at 2:34 AM, Jia Chen wrote: > Hello, > > 1000 states with 100Ry as cutoff. I guess you really need to wait for a > while... > > > On Wed, May 15, 2013 at 7:28 PM, Yong Xue wrote: > >> Dear All >> I am doing a relax calculation for a system composed of Na, Si, and O. >> However, the calculations stops printing any results though it is still in >> running. >> >> The last line in the output file: >> >> starting charge 886.76971, renormalised to 1024.0 >> Starting wfc are 1232 atomic wfcs >> >> here is my input: >> >> >> >> calculation = 'relax' >> >> restart_mode = 'from_scratch' >> >> pseudo_dir = './' >> >> outdir = './scratch/' >> >> prefix = 'Na4SiO4-300k_glass' >> >> etot_conv_thr = 1e-5 >> >> forc_conv_thr = 1e-3 >> >> tstress = .true. >> >> tprnfor = .true. >> >> / >> >> >> >> ibrav = 0 >> >> celldm(1) = 1.889 >> >> nat = 144 >> >> ntyp = 3 >> >> ecutwfc = 100 >> >> nosym = .false. >> >> / >> >> >> >> electron_maxstep = 200 >> >> diagonalization='david' >> >> startingpot = 'atomic' >> >> startingwfc = 'atomic' >> >> mixing_mode = 'plain' >> >> conv_thr = 1.0d-8 >> >> / >> >> >> >> ion_dynamics = 'bfgs' >> >> pot_extrapolation = 'atomic' >> >> wfc_extrapolation = 'none' >> >> / >> >> ATOMIC_SPECIES >> >> O 15.9994 O.pbe-tm-gipaw.UPF >> >> Na 28.086 Na_hard_pbe-20090916.UPF >> >> Si 28.086 Si.pbe-tm-gipaw.UPF >> >> CELL_PARAMETERS (alat) >> >> 8.997127919581955 -6.324877651395790 -0.850851588232427 >> >> 0.000 12.030047148094420 -3.025645546360610 >> >> 0.000 0.000 16.843099594116211 >> >> ATOMIC_POSITIONS (crystal) >> thanks >> >> Xue >> -- >> Ms. Xue Yong(??) >> Department of Physics and Engineering Physics >> University of Saskatchewan >> 116 Science Place >> Saskatoon, SK S7N 5E2 >> Canada >> Tel: +1 306 261 2369 >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > Jia Chen > Graduate student of Department of Chemistry, Princeton University > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130516/afd1f264/attachment.html
[Pw_forum] A quick question about the derivative of enhancement factor in HSE
Dear All, In the calculation of HSE enhancement factor and its derivative, the derivative of the enhancement factor with respect to the reduced density gradient (s) is with respect to the 's' itself or its square (s2)? Thanks a lot in advance :) -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130506/219fb834/attachment.html
[Pw_forum] "not orthogonal operation" during vc-relax when optimizing graphene
Dear Peng, The cell you might be using is 'hexagonal' and the 'vc-relax' that you are doing has two degrees of freedom in x and y direction which are orthogonal due the flag 'cell_dofree = xy' you set. Since the symmetry is breaking in the second step due to relaxation in x and y direction it is changing the number of k-points. That's why you are getting that error. A simple work-around for this is you use a bit bigger cell with orthorhombic symmetry (in which you have orthogonal 'a' and 'b' vectors). In orthorhombic cell symmetry won't break due to 'cell_dofree = xy'. On Fri, May 3, 2013 at 4:13 AM, Peng Tao wrote: > Dear all, > > Recently, I just want to putting 'vc-relax' to optimize the graphene > structure, > but it repots an error: > > %% > from checkallsym : error # 2 > not orthogonal operation > > %% > > And I set 'cell_dofree = xy' in the vc-relax run. > > I know, it is no need to apply vc-relax to graphene, and only relax can > aquire > my result. But if I want to relax bi-layer and mutilayer graphene and my > ultimate > goal is to get their phonon dispersion curves(so the symmetry should not > be broken), > how could I do? Is there any convienient method to relax them? > > Thanks a lot. > > Yours, > Peng Tao > > -- > --- > PH.D. candidate Peng Tao > Magnetism and Magnetic Materials Division > National Laboratory for Material Science > Institute of Metal Research, Chinese Academy of Sciences > Phone +86-024-83978751 > --- > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130503/02743303/attachment.html
[Pw_forum] Is the results of structural relaxiation by pwscf accurate?
Try calculating it and report it here. That will be a nice exercise for you. On Tue, Apr 30, 2013 at 1:42 PM, ??? <18733462676 at 163.com> wrote: > yes. > except this,i want to know how much the difference of Tc calculated with > different pseudopotential is . > > > > > > > Yun Wang ??? > > > The validity of the optimization results using PWscf can be verified > through the comparison with the available experimental data. > > > On Tue, Apr 30, 2013 at 3:19 PM, GAO Zhe wrote: > >> According to the pointview of methods/theories implemented in DFT codes, >> all of the relaxed structures from QE, VASP and CASTEP are definitely >> reliable. >> But, these codes use different pseudo-potentials, which induce slight >> fluctuation to the final structure. >> Most important, all the structures should be obtained from the converged >> computational parameters. Otherwise, there is no code being able to provide >> "reliable" structure. >> >> -- >> GAO Zhe, Dr., >> Research Engineer, Quartz, >> Saint-Gobain Research (Shanghai), >> No. 55, Wenjing-road, Minhang-district, Shanghai, China >> >> At 2013-04-30 00:42:32,"???" <18733462676 at 163.com> wrote: >> >> dear all >>According to my trying with different software,i found that there >> is a large difference between relaxiation with pwscf and other >> software(e.g.vasp and castep),So i want to know wh ether the relaxiation of >> pwscf is reliable? And can you provide some suggestions? >> >> >> ?? <http://shouji.163.com> >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://pwscf.org/mailman/listinfo/pw_forum >> > > > > -- > > Dr. Yun Wang > Research Fellow > Centre for Clean Environment and Energy > Griffith School of Environment > Gold Coast Campus, Griffith University > QLD 4222, Australia > Tel:(61-7) 5552 8456 > Fax:(61-7) 5552 8067 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130430/0d1f56cf/attachment.html
[Pw_forum] optical properties
Dear Shiva, Please devote sometime in framing the question, try to avoid posting anything whatever comes to your mind without giving a second thought about it. By the description of your problem I am sure nobody will be able to help you. You have to post very specific questions, please don't be to naive. I hope you understand. On Fri, Apr 19, 2013 at 9:17 AM, shiva mokhavat wrote: > dear all > I am trying to calculate optical properties of HgTe, but the results are > not correct.can anyone help me in this? > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, --------- Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130419/5f589e6a/attachment.html
[Pw_forum] Relaxation says max steps reached despite changing nsteps
Dear Alejandro,
Changing ionic relaxation steps of scf steps won't help if you are far from
convergence. Your system has convergence problem. So you need to change the
parameters which have effect on convergence. You can decrease the mixing
parameter beta, or play with smearing. They may help you to reach
convergence.
On Wed, Apr 10, 2013 at 3:55 PM, Alejandro Suarez <
al.suarez.ctr at nrl.navy.mil> wrote:
> Hello,
>
> In my relaxation calculation, my job always finishes with the following
> lines:
>
> The maximum number of steps has been reached.
>
> End of BFGS Geometry Optimization
> Begin final coordinates
> ...
> --
> To remedy this, I changed nstep to and electron_maxstep to 999 in my
> input file, however the failure continues.
> This happens both in a restarted calculation or when the calculation is
> redone from scratch (and the save files are deleted).
>
> Here is a copy of my input file:
> --
>
> calculation='relax',
> restart_mode='from_scratch',
> prefix='4-BN-Gr',
> pseudo_dir = '../pseudos',
> outdir='../save',
> etot_conv_thr = 1.0D-5
> forc_conv_thr = 1.0D-4
> tefield=.true.
> dipfield=.true.
> nstep = 999,
> /
>
> ibrav= 4,
> A=2.44624, C=33.0,
> nat= 10, ntyp= 3,
> ecutwfc = 45.0,
> ecutrho = 300.0,
> occupations='smearing',
> degauss = 0.005
>
>
> edir=3,
> emaxpos=0.696
> eopreg=0.045
> eamp=0
> /
>
>conv_thr = 1.0D-8,
>electron_maxstep = 999
> /
>
> /
> ATOMIC_SPECIES
> B 10.81 B.pz-n-kjpaw_psl.0.1.UPF
> C 12.01 C.pz-n-kjpaw_psl.0.1.UPF
> N 14.007 N.pz-n-kjpaw_psl.0.1.UPF
>
> ATOMIC_POSITIONS crystal
> B 0.7 0.3 0.0 0 0 0
> N 0.3 0.7 0.0 0 0 0
> N 0.7 0.3 0.098182000
> B 0.3 0.7 0.098182000
> B 0.7 0.3 0.196364000
> N 0.3 0.7 0.196364000
> N 0.7 0.3 0.294545000
> B 0.3 0.7 0.294545000
> C 0.3 0.7 0.391818000
> C 0.7 0.3 0.391818000
> K_POINTS {automatic}
> 10 10 1 0 0 0
>
>
> Any help would be greatly appreciated.
>
> Thank you,
>
> --
>
> Alejandro Suarez
> NRC Research Associate
> Naval Research Laboratory, Code 6877
> 4555 Overlook Ave., SW
> Washington, DC 20375
> Phone: (202) 404-4635
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Regards,
MOHNISH,
-
Mohnish Pandey,
PhD Student,
Center for Atomic Scale Materials Design,
Department of Physics,
Technical University of Denmark
-
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[Pw_forum] S matrix not positive definite
May be this will be of help http://qe-forge.org/pipermail/pw_forum/2013-January/100744.html On Tue, Apr 9, 2013 at 6:02 PM, farouk boutaiba wrote: > Dear all; > > I am trying to calculate band gap of ZnSe in hexagonal phases including spin > orbite interaction, using the approximation LDA-1/2. > > I started with a pseudo-relativistic: Zn.rel-pz-dn-rrkjus_psl.0.2.2.UPF > and Se.rel-pz-n-rrkjus_psl.0.2.UPF. > the scf calculation stop with following error: > > iteration # 1 ecut=80.00 Ry beta=0.70 > Davidson diagonalization with overlap > > %% > Error in routine cdiaghg (263): > S matrix not positive definite > %% > > stopping ... > > the input file is: > > > calculation='scf' > > restart_mode='from_scratch', > tstress = .true. > tprnfor = .true. > prefix='znse-2h', > pseudo_dir = '/home/espresso-5.0.1/pseudo/', > outdir='/home/tmp/' > nstep= 3 > / > > ibrav= 4, celldm(1) =7.437,celldm(3) =1.642, nat= 4, ntyp= 2, > ecutwfc =80.0, > lspinorb=.true., > noncolin=.true., > starting_magnetization=0.0, > occupations='smearing', > degauss=0.02, > smearing='mp', > ecutrho =600.0, > / > > diagonalization='david' > conv_thr =1.0e-7 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Zn 65.38 Zn.LDA.1.665.UPF > Se 78.96 Se.LDA.3.42.UPF > ATOMIC_POSITIONS crystal > Zn 0. 0. 0. > Zn 0. 0.6667 0.5000 > Se 0. 0. 0.3750 > Se 0. 0.6667 0.8750 > K_POINTS (automatic) > 8 8 6 1 1 1 > > > Thanks in > advance. > > > BOUTAIBA Farouk > Department of Physics > Faculty of Science > University of Science and Technology of Oran > Oran Algeria > > _______ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130409/b013b92a/attachment.html
[Pw_forum] hybrid functional
Dear Valentina, You can do the calculations with the SCF run in HSE/PBE0, that shouldn't be a problem. And why do you need nscf calculation anyway to do the DOS calculation. 'nscf' calculation is needed when you are interested in band-structure where you use the ground state charge density for interpolation along certain directions. Your scf calculations will won't have any problem in calculation the DOS. Hope it helps :) On Tue, Apr 9, 2013 at 3:10 PM, "Valentina Dellac? C.R.F. S.C.p.A." < valentina.dellaca at tirocinanti.crf.it> wrote: > Dear Arles, > thanks for your answer. My doubts are about the employment of the > projwfc.x, post processing tool, when using hybrid functional, since the > README of the hybrid functional tutorial says that one gets into troubles > when performing non-scf calculations. At the moment I see the way to > proceed if I wish to plot the band structure from the log file of the scf > run, but i do not know how to get informations about the dos from such > file, since it (as far as I understand) seems to be the only run i can > perform when employing hybrid functionals. Do you know how to get > informations about the dos from the .log of a scf run? > Thank you!!! > Valentina > > Il 04/09/2013 02:24 PM, Arles V. Gil Rebaza ha scritto: > >Dear Valentina, > Yes, projwfc.x is a postprocessing tool like dos.x, whether you want to > get only the density of state, "dos.x" is enough, whereas "projwfc.x" you > can obtain DOS, projected DOS (PDOS) and the magnetic moment per atom too. > http://www.quantum-espresso.org/?page_id=876 > > Best > > PhD Arles V. Gil Rebaza > Instituto de F?sica de La Plata > Argentina > > > 2013/4/9 "Valentina Dellac? C.R.F. S.C.p.A." < > valentina.dellaca at tirocinanti.crf.it> > >> Dear Mohnish, >> thanks for you answer. I will follow your suggestion and try also HSE, >> with a coarser k-point mesh, (indeed with PBE0 the computation time is >> quiet large), and I did not know about projwfc.x. >> I have a further question concerning the DOS. If I wish to know about the >> DOS of my system, which uses the hybrid functional implementation, am I >> able to use the projwfc.x? Is'n it a postprocessing tool? >> Thanks, >> regards, >> Valentina >> >> Il 04/09/2013 11:18 AM, mohnish pandey ha scritto: >> >> Hi, >> >> As far as I can understand there is no rule. It depends how fine you >> want to represent your Fock operator. Normally calculations of the Fock >> exchange in expensive, so its not affordable to do very fine grid >> calculations So I suggest you start with low nqx(1, 2, 3) and increase it >> systematically. Increasing it will give you better results( I mean >> converged results, not necessarily close to experiments). >> >> Just an advice, PBE0 needs much more high density k-point mesh for the >> convergence of Fock exchange since it's a long range interaction. So you >> have to do calculations with high density of k-points. But if you use HSE >> instead of PBE0 you get away with coarser k-point mesh since it involves >> screened exchange interaction which converges much faster than bare Coulomb >> exchange as in PBE0. Regarding to the DOS plot you will find a nice >> tutorial on Heither's website, I am pasting the link >> http://www.stanford.edu/~hkulik/www/Tutorials/Entries/2012/1/24_Population_analysis_and_PDOS.html >> >> >> On Tue, Apr 9, 2013 at 10:05 AM, "Valentina Dellac? C.R.F. S.C.p.A." < >> valentina.dellaca at tirocinanti.crf.it> wrote: >> >>> Hi, >>> I am a Quantum Espresso beginner user, and I am simulating the Ta2O5 >>> structure, with the employment of the hybrid functional PBE0. I have some >>> questions : >>> >>> - if I choose a k-point grid not in automatic, how should I pick the >>> nqx1,2,3? Is there a rule? >>> - when one wishes to have informations (ex. plot) about the density of >>> states from the scf run, how should I proceed? >>> >>> Thank you, >>> regards >>> Valentina >>> >>> >>> -- >>> >>> >>> >>> -- >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://pwscf.org/mailman/listinfo/pw_forum >>> >> >> >> >> -- >> Regards, >> MOHNISH, >> - >> Mohnish Pandey, >> PhD Student, >> Center for Atomic Scale Materials Design, >>
[Pw_forum] Mn PAW PP
Dear Pietro, Thanks a lot :) On Thu, Apr 4, 2013 at 12:22 PM, Pietro Bonfa' wrote: > Dear Mohnish, > > there's a Mn pseudopotential in the pslibrary: > > http://qe-forge.org/gf/project/pslibrary/ > > It's inside: paw_ps_collection_tot.job > > >From the code's comments: > # > # Be careful these PPs might have problems. > # > > Kind regards, > Pietro Bonfa' > > > > > On 04/04/13 10:13, mohnish pandey wrote: > > Dear QE users, > > > > Does anybody have Mn PAW PP. I checked on QE PP database but its not > > available. If anybody of you have it, can you please provide me? Thanks > > a lot in advance. > > > > -- > > Regards, > > MOHNISH, > > - > > Mohnish Pandey, > > PhD Student, > > Center for Atomic Scale Materials Design, > > Department of Physics, > > Technical University of Denmark > > - > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://pwscf.org/mailman/listinfo/pw_forum > > > > > -- > Pietro Bonfa' - PhD student > Dipartimento di Fisica e Scienze della Terra "Macedonio Melloni" > Viale delle Scienze 7A > 43124 Parma - Italy > _______ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130405/50990b3d/attachment.html
[Pw_forum] Mn PAW PP
Dear QE users, Does anybody have Mn PAW PP. I checked on QE PP database but its not available. If anybody of you have it, can you please provide me? Thanks a lot in advance. -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130404/bab01bad/attachment.html
[Pw_forum] (no subject)
There have been lot of studies on this system. I guess the structure is stable in certain range of strain. I suggest you do the calculations for a range of lattice constant, may be you will get the optimum one at which your structure will be stable. Below are the few references if you want to take a look. Phys. Rev. B 76, 020102(R) (2007)Appl. Phys. Lett. 87, 052903 (2005); http://dx.doi.org/10.1063/1.2006216<http://link.aip.org/link/doi/10.1063/1.2006216>Appl. Phys. Lett. 91, 112914 (2007); http://dx.doi.org/10.1063/1.2785121<http://link.aip.org/link/doi/10.1063/1.2785121> On Mon, Mar 18, 2013 at 8:42 AM, shruti shukla wrote: > Dear users, > > I am making an artificial superlattice (BaTiO3/SrTiO3). The total energy > of superlattice is greater than the sum of the total energies of its two > component lattices. Should I proceed with my calculations or not? > > Shruti > > <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm > at Middle?> > Get your own *FREE* website and domain with business email solutions, click > here<http://track.rediff.com/click?url=___http://hosting.rediff.com/rediffmailpro/business-email?sc_cid=sig___=sig=sig=host> > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, ----- Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130318/303ac3ba/attachment.html
[Pw_forum] big difference between "total magnetization" and "absolute magnetization" for 4f elements
Did you try using different initial spin configurations? If your interested
in FM ground state then may be you should try initial magnetic
configuration as FM. e.g. +1, +1 for both.
On Wed, Mar 13, 2013 at 9:03 PM, ?? wrote:
> Thank you for your suggestions. When I set two atoms in the unit cell
> to be antiferromagnetic, the "total magnetization" is nearly zero, and
> the "absolute magnetization" is about 14.67. And the magnetic moment
> for two atoms are about 7.16 and -7.18, which is more or less
> acceptable.
>
> Now, the question is that why "total magnetization" and "absolute
> magnetization" differs so much if I want to force two atoms into a
> ferromagnetic configuration.
>
> Any suggestions? Thanks!
>
> With regards,
> Kun Tao
>
>
> On 13 March 2013 11:14, Andrei Malashevich
> wrote:
> > If you want to model antiferromagnetic structure, you should define two
> > types of atoms, Gd1 and Gd2.
> > Change ntyp to 2. Use, e.g.,
> > starting_magnetization(1)=1.0
> > starting_magnetization(2)=-1.0
> >
> > ATOMIC_SPECIES
> > Gd1 1.0 Gd.GGA-PBE-paw.UPF
> > Gd2 1.0 Gd.GGA-PBE-paw.UPF
> > ATOMIC_POSITIONS {crystal}
> > Gd1 0. 0.6667 0.25
> > Gd2 0.6667 0. 0.75
> >
> >
> > On Wed, Mar 13, 2013 at 11:05 AM, ?? wrote:
> >>
> >> Hi,
> >>
> >> Yes, the bulk Gd without Hubbard U is antiferromagnetic. If I set the
> >> two atoms in the unit cell to be antiferromagnetic, the "total
> >> magnetization" should be equal to zero, and the "absolute
> >> magnetization" is what I have gotten. Now, however, the "total
> >> magnetization" is not zero. Could you give me some suggestions?
> >> Thanks!
> >>
> >> With regards,
> >> Kun Tao
> >>
> >> On 13 March 2013 10:48, Stefano de Gironcoli wrote:
> >> > are you sure you are defining the correct magnetic structure ?
> >> > is Gd maybe antiferromagnetic ?
> >> > stefano
> >> >
> >> > On 03/13/2013 03:19 PM, ?? wrote:
> >> >> Dear everyone,
> >> >>
> >> >> I want to calculate the magnetic properties of bulk Gd whose magnetic
> >> >> moment is about 8 Bohr magneto/atom. Usually, in the output file
> >> >> values of "total magnetization" and "absolute magnetization" should
> be
> >> >> nearly the same. However, in my output file, I found a big difference
> >> >> between them as following:
> >> >>
> >> >> total magnetization = 8.00 Bohr mag/cell
> >> >> absolute magnetization=15.72 Bohr mag/cell
> >> >>
> >> >> The good news is that the "absolute magnetization" is close to the
> >> >> experimental results (7.86 Bohr mag/atom), the bad news is that the
> >> >> "total magnetization" is wrong. Moreover, when I try to calculate the
> >> >> magnetic moment on each atom with projwfc.x program, I got about 4.1
> >> >> Bohr mag/atom.
> >> >>
> >> >> Could you give me some suggestions? Any advice are appreciated,
> thanks!
> >> >>
> >> >> Regards,
> >> >> Kun Tao
> >> >>
> >> >>
> >> >> Attached below is the input file:
> >> >>
> >> >>
> >> >> calculation='scf'
> >> >> restart_mode='from_scratch',
> >> >> prefix='Gd',
> >> >> pseudo_dir = './'
> >> >> outdir='./',
> >> >> /
> >> >>
> >> >> ibrav= 4, celldm(1)= 6.96, celldm(3)= 1.59,
> >> >> nat= 2, ntyp=1,
> >> >> nspin = 2,
> >> >> starting_magnetization(1)=1.0,
> >> >> ecutwfc=55.0,
> >> >> ecutrho=220.0,
> >> >> occupations ='smearing',
> >> >> smearing ='gauss',
> >> >> degauss = 0.01,
> >> >> /
> >> >>
> >> >> diagonalization='david',
> >> >> mixing_beta = 0.3,
> >> >> conv_thr = 1.0d-8,
> >> >> /
> >> >> ATOMIC_SPECIES
> >> >> Gd 1.0 Gd.GGA-PBE-paw.UPF
> >> >> ATOMIC_POSITIONS {crystal}
> >> >> Gd 0. 0.6667 0.25
> >> >> Gd
[Pw_forum] Error in Execution while linked with Intel MKL - 11.0 64-bit : QE-5.0.2
It seems you are messing up with the symmetry by the way you are defining the cell. I ran your input file wit nosym = .true and it works. Though your original input file is giving me a symmetry error, so I tried without symmetry, may be you can do the same. On Wed, Mar 6, 2013 at 6:48 AM, Nisha Agrawal wrote: > Hi > > I am using the below configuration while installing the Parallel > version of Quantum Espresso-5.0.2 > > 1. Intel MPI > 2. Intel compose xe_2013 ( Intel MKL-11.0, ifort 13.0, Intel MKL LAPACK & > FFTW3) > > I) Below are the steps I am using to configure and install quantum > espresso-5.0.2 ( attached make.sys file) > > Step 1: below is the configure command > > ./configure --prefix=~/espresso_5.0.2 MPIF90=mpiifort FC=ifort > F77=ifort F90=ifort CXX=icpc CC=icc > BLAS_LIBS="-L/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64 > -lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread -lm" > LAPACK_LIBS="-L/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/" > > FFT_LIBS="/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/libfftw3x_cdft_ilp64.a" > SCALAPACK_LIBS="-L/opt/intel/composer_xe_2013.1.117/mkl/lib/intel64/ > -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64" > > Step 2: make all > > II) Command for execution > > mpirun -np 2 ./bin/pw.x -in BN.in > > III) While running I am getting the following error message ( > attached input file) > > > > --- > Program PWSCF v.5.0.2 (svn rev. 9392) starts on 4Mar2013 at 16:50:15 > > 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.php > > Parallel version (MPI), running on 2 processors > R & G space division: proc/nbgrp/npool/nimage = 2 > > Current dimensions of program PWSCF are: > Max number of different atomic species (ntypx) = 10 > Max number of k-points (npk) = 4 > Max angular momentum in pseudopotentials (lmaxx) = 3 > Reading input from ./only-BN.in > Warning: card ignored > Warning: card / ignored > [eval_infix.c] A parsing error occurred > helper string: > - > error code: > Error: missing operand > > [eval_infix.c] A parsing error occurred > helper string: > - > > %% > Error in routine card_atomic_positions (1): > Error while parsing atomic position card. > error code: > Error: missing operand > > > > stopping ... > > % > Error in routine card_atomic_positions (1): > Error while parsing atomic position card. > > > stopping ... > > > > > Kindly help to resolve this issue. > > > > With Thanks & Regards > Nis > > > > > "Apologizing does not mean that you are wrong and the other one is right... > It simply means that you value the relationship much more than your ego.." > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130306/ec708290/attachment.html
[Pw_forum] Zero point energy correction for energy barrier calculation
Dear Pallavi, I think you need to calculate the vibrational frequencies of the reactant and transition state which is explained in the link below * http://www.stanford.edu/~hkulik/www/Tutorials/Entries/2011/12/27_Vibrational_properties_of_molecules.html * Then you can calculate the zero point correction in your barriers using a small piece of code the link of which is given below :) * http://www.stanford.edu/~hkulik/www/Tutorials/Entries/2011/12/27_Vibrational_properties_of_molecules.html * On Wed, Feb 6, 2013 at 8:31 AM, Pallavi Bothra wrote: > Dear Sir, > I have calculated reaction pathway using NEB method. I read in > one paper to reduce the energy barrier 'zero point energy corrections' need > to be done. But may I know how this is implemented in Quantum espresso and > how to calculate it. > > Thanks in advance > > Pallavi Bothra > Ph.D student > JNCASR, Bangalore > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, --------- Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130206/5407fa9f/attachment.html
[Pw_forum] (no subject)
Yea you can mix USPP with NC. See the FAQ http://www.quantum-espresso.org/?page_id=356#2.3 On Sun, Jan 27, 2013 at 12:56 PM, Banafshe Noori wrote: > Hi > > I am using with LDA approximation . the pesduopotential of normconserving > for carbon is applied. > > can i use a potential of type ultrasoft for a doped element for example > (Cd). > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://pwscf.org/mailman/listinfo/pw_forum > -- Regards, MOHNISH, --------- Mohnish Pandey, PhD Student, Center for Atomic Scale Materials Design, Department of Physics, Technical University of Denmark - -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130127/c9f8e442/attachment-0001.html
[Pw_forum] troubleshooting cdiaghg-have checked faq
Dear Vijaya,
Your 'mixing_beta' is to high. Try reducing it. Generally the default value
which is 0.7 is good. I see no reason to use 0.9 as you are using. 'cg' is
quite robust but its slower than 'david' so you can use 'david' as
diagonalization scheme for faster calculations. But try the first
suggestion for mixing parameter (May be 0.5 will be good)
On Tue, Jan 8, 2013 at 1:57 AM, vijaya subramanian wrote:
> Hi
> I am trying to run a simple scf calculation on a polymer crystal.
> The system has already been studied in a paper in PRL. I am using the
> input parameters (not all input parameters are specified in the paper)
> as closely as possible as well as atomic coordinates from the paper.
> I have looked at the structure and its periodic images using Xcrysden and
> dont see any problems with my pwscf input file. I am using pbe-Vanderbilt
> ultrasoft pseudopotential provided in the QE website for C, F and H.
>
> I am using QE version 5.0.1 on cygwin and inbuilt libraries, ie. I am
> using the algebra packages provided by
> QE. I get the cdiaghg error and have eliminated the following causes for
> the error:
> 1) Atomic coordinates are correct-I dont see any contacts that are too
> close.
> 2) Vanderbilt pseudo potential is used in the paper (though they dont
> specify where they got it) -I am assuming
> the versions provided on the QE website are equally reliable.
> 3) I have used diagonalization=cg and still have the problem.
>
>
> So is there any other reason I am getting this error?
>
> My input parameters are as follows:
> calculation = "scf",
> prefix = "pvf2",
> pseudo_dir = "/home/vijaya/espresso-5.0.1/pseudo",
> outdir = "/home/vijaya/tmp",
> /
>
> ibrav = 0,
> nat =24,
> ntyp = 3,
> ecutwfc = 35.D0,
> ecutrho = 340.D0,
> /
>
>diagonalization = 'cg'
> conv_thr= 1.D-5,
> mixing_beta = 0.9D0,
> /
>
> /
> CELL_PARAMETERS bohr
> 16.2138 0. 0.
> 0. 9.2785 0.
> 0. 0. 4.8376
> ATOMIC_SPECIES
> C 12.011 C.pbe-van_bm.UPF
> F 18.998 F.pbe-n-van.UPF
> H 1.00794 H.pbe-van_bm.UPF
> ATOMIC_POSITIONS {angstrom}
> C0.0 0.0 0.0
> C0.0 0.85434 1.28000
> C0.0 0.0 2.55997
> C0.0 0.85434 3.83997
> F1.08108 1.74305 1.28000
> F -1.08108 1.74305 1.28000
> F1.08108 1.74305 3.83997
> F -1.08108 1.74305 3.83997
> H0.90090 -0.60884 0.0
> H -0.90090 -0.60884 0.0
> H0.90090 -0.60884 2.55997
> H -0.90090 -0.60884 2.55997
> C4.29000 2.45500 0.0
> C4.29000 3.30934 1.28000
> C4.29000 2.45500 2.55997
> C4.29000 3.30934 3.83997
> F5.37108 4.19805 1.28000
> F3.20892 4.19805 1.28000
> F5.37108 4.19805 3.83997
> F3.20892 4.19805 3.83997
> H5.19090 1.84616 0.0
> H3.38910 1.84616 0.0
> H5.19090 1.84616 2.55997
> H3.38910 1.84616 2.55997
>
>
> K_POINTS {automatic}
> 1 2 2 0 0 0
>
> Thanks in Advance
> Vijaya
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
Regards,
MOHNISH,
-
Mohnish Pandey,
PhD Student,
Center for Atomic Scale Materials Design,
Department of Physics,
Technical University of Denmark
-
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[Pw_forum] reg: pseudopotential
Did you try browsing the QE website? Any below is the link: http://www.quantum-espresso.org/?page_id=887_id=22_id=_id=_k= Or you can also download the pslibrary which contain the inputs for ld1 code to generate PPs for different atoms. http://qe-forge.org/projects/pslibrary PS: Putting the affiliation is very much appreciated. On Thu, Jul 26, 2012 at 10:11 AM, Swetarekha Ram wrote: > Dear users, > > I need Tl pseudopotential, either PBE UPF or pw91 UPF. > > Can any one help me to get this potential. > > > > -- > Swetarekha Ram, > Research Scholar, > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, --------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120726/b9731e28/attachment.htm
[Pw_forum] Calculation of lattic constants and bulk modulus od w-ZnO
Dear Muhammad, Their is an easier way to calculate the optimized the lattice constant which is based on calculation of stress and forces on the system. In the flag "calculation" put "vc-relax" and in "ion_dynamics" put "bfgs" (there are other options too) and in the "cell_dynamics" put "bfgs" (again there are other options also) and run the job. When the calculation is over the code will print the final lattice vectors by which you can calculate the optimized lattice constant. For further details look into /quantum-espresso-folder/Doc/INPUT_PW.html On Sun, May 13, 2012 at 2:52 AM, zafar rasheed wrote: > Dear All > > I want to calculate lattice constants a, and c and bulk modulus of w-ZnO. > For this purpose: > >1. > >I take experimental lattice constants (a= 3.25 Ang. and c = 5.206 Ang. >and by changing these values into bohr.) and first take different values >above and below a and do scf calculations to optimize a. As in case of W >ZnO (Hexagonal and Trigonal P) ibrav= 4 and celldm(3) =c/a is used. So when >I change a (celldm (1))I have to change celldm (3). In this way I get >lattice constant a which is nearly same as experimental with 2 percent >error. >2. > >Then I fix this lattice constant a (celldm (1)) and change lattice >constant c (By taking different values above and below experimental value >of c). As c changes celldm (3) also changes. In this way I get lattice >constant c which is very close to experimental lattice constant with a >little error of 2 percent. >3. > >The output data for the calculation of c by fixing a I use to >calculate BULK modulus for ZnO. Again these results are comparable with >experimental and already calculated results by different techniques . >4. > >Now I want to know that, Is my calculation procedure is right? > > Best Regards > > Muhammad Zafar > PhD Scholar > Department of Physics > The Islamia University of Bahawalpur,Pakistan > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120513/b914f805/attachment.htm
[Pw_forum] benzoic acid structure optimization
30 Rydberg at least for wavefunction cutoff and 240 for charge density. On Wed, May 2, 2012 at 9:03 AM, matt reish wrote: > Thanks for the reply, seemed to be going way too fast for what I had read I > that I should expect. Any thoughts on what would be more reasonable cutoffs > for wavefunction and density? Would it be reasonable to try to attain a > useable result on a "cluster" using 8 processors? > > Cheers, > > Matt > > > On Wed, May 2, 2012 at 3:02 PM, Axel Kohlmeyer wrote: >> >> On Tue, May 1, 2012 at 10:53 PM, matt reish wrote: >> > Hi PW list, >> > >> > I am working with Quantum Espresso (v4.3.2.1) in the hopes of attaining >> > Raman phonon frequencies of a benzoic acid crystal. I attained the >> > optimized >> > output geometry from a CASTEP calculation in the supplemental material >> > of a >> > paper. This geometry was used by the authors to calculate accurate IR >> > phonon >> > frequencies. I used a 'relax' calculation in Quantum Espresso on the >> > optimized geometry but this led to large shifts in the atomic positions >> > in >> > the lattice and unreasonable structures for the molecules in the lattice >> > after finding the optimized structure. My question is does anyone have a >> > some experience calculating organic crystals in Quantum Espresso that >> > could >> > give me some tips? >> >> >> matt, >> >> you are using a *ridiculously* low wavefunction >> and density cutoff, that means your basis set >> is *far* too small. unphysical results are the >> logical consequence. >> >> axel. >> >> >> > >> > Here is my input file minus the atomic posititions: >> > >> > >> > ?? title = 'benzacidscftest' , >> > calculation = 'relax' , >> > ??? restart_mode = 'from_scratch' , >> > ? outdir = '/home/mreish/tmp/' , >> > ? pseudo_dir = '/usr/share/espresso/pseudo/' , >> > ? prefix = 'batest5' , >> > disk_io = 'default' , >> > ?? nstep = 600 , >> > ?/ >> > ? >> > ?? ibrav = 12, >> > ?? A = 5.4996 , >> > ?? B = 5.1283 , >> > ?? C = 21.950 , >> > ?? cosAB = 0 , >> > ?? cosAC = -.128276341 , >> > ?? cosBC = 0 , >> > nat = 60, >> > ??? ntyp = 3, >> > ecutwfc = 5 , >> > ecutrho = 40 , >> > ?/ >> > ? >> > ??? electron_maxstep = 200, >> > ??? conv_thr = 1.0d-11 , >> > ?/ >> > ? >> > ?/ >> > ATOMIC_SPECIES >> > ??? C?? 12.01000? C.pbe-rrkjus.UPF >> > ??? O?? 16.0? O.pbe-rrkjus.UPF >> > ??? H??? 1.0? H.pbe-rrkjus.UPF >> > ATOMIC_POSITIONS angstrom >> > >> > K_POINTS automatic >> > ? 1 1 1?? 1 1 1 >> > >> > >> > Cheers, >> > >> > Matthew Reish >> > University of Otago >> > Dunedin >> > New Zealand >> > >> > ___ >> > Pw_forum mailing list >> > Pw_forum at pwscf.org >> > http://www.democritos.it/mailman/listinfo/pw_forum >> > >> >> >> >> -- >> Dr. Axel Kohlmeyer >> akohlmey at gmail.com ?http://goo.gl/1wk0 >> >> College of Science and Technology >> Temple University, Philadelphia PA, USA. > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA -
[Pw_forum] volume optimization
On Fri, Feb 3, 2012 at 2:59 AM, berber mo wrote: > I work on wien2k 8 and i have problem with volume optimization . > I would like to know in detail how to optimize the volume > a =15.95 u.a b = 19.53 u.ac =15.95 > u.a > alpha=90 ? beta =90 ? gamma > =144.73 ? > The information you provided is very less. As far as I can understand this is the input that you want to give and then see the optimized structure with optimized volume and atomic coordinates. since your alpha and beta are equal as well "a" and "c" so I will suggest you to reorient (rotate the unit cell around x-axis by Pi/2 ) the cell such that your "b" becomes "c" and "gamma" will become "alpha." So in the new unit cell you will have (just check it carefully, I may be slightly wrong) a =15.95 A? b =15.95 A? c =19.53 A? alpha=144.73 ? beta =90 ? gamma =90 ? With this cell you can use the option ibrav = 5 ( celldm4 = cos(alpha) ). And next time you post on this forum please sign in your affiliation. > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120203/1b3c62f5/attachment.htm
[Pw_forum] Thanks a lot to QE forum for immense help in my first paper
Dear QE users, I thank you all for being so helpful in guiding me in learning QE. I especially thank Prof. Giannozzi, Prof. Baroni, Prof. Marzari, Dr. Paulatto for immense help in the beginning. With guidance of you people I got my first paper accepted in The Journal of Chemical Physics. Below is the title and link to the paper. "Stabilization and growth of non-native nanocrystals at low and atmospheric pressures" J. Chem. Phys. *136*, 044703 (2012); doi:10.1063/1.3678181 I thank you all once again for your cooperation. -- Regards, MOHNISH, ----- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120125/ef8b16a7/attachment.htm
[Pw_forum] distinguish between the isotopes of an element
Sorry I mistook isotopes as allotropes. On Mon, Jan 16, 2012 at 6:34 PM, Stefano de Gironcoli wrote: > ** > from the electronic point of view, all isotopes are the same. > what is different for different isotopes is their mass, which enters in > the vibrational contribution to the free energy. > > stefano > > > On 01/16/2012 06:08 AM, Mahdi Faghih nasiri wrote: > > Dear all, > How can we distinguish between the isotopes of an elementin pwscf? > > Mahdi Faghih nasiri > MSC, > Guilan University, > Rasht, Iran. > > > ___ > Pw_forum mailing listPw_forum at > pwscf.orghttp://www.democritos.it/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20120116/b4874c06/attachment.htm
[Pw_forum] help regarding phonon life time calculation
You can download that from net. They will give you are license number. Its free for academic purposes. On Wed, Dec 28, 2011 at 3:51 PM, bramha pandey wrote: > Dear All QE users:-- > I wanted to use the QHA pakage given in espresso-4.3.2,..but there is > a need of IFORT compiler which was not found and recognized by > me.currently i am using gfortaran compiler in ubantu 11.2 unix > version > > Thanks in advance for your kind cooperation...to get (ifort). > > On 12/27/11, Tribhuwan Pandey wrote: > > Hi all , > > Quatum espresso users.I am using Quantum espresso for phonon > > life time calculation.I have some problem in understanding the output > file > > *file.anh_G*. If anyone of you have done those calculation before > please > > help me. > > > > > > any suggestion in this matter will be appreciated > > > > Thanking you > > tribhuwan > > > > -- > > * > > With Regards > > Tribhuwan Pandey > > Indian Institute of Science, Bangalore, India > > > > > > > > * > > > > > -- > Thanks and Regards > Bramha Prasad Pandey > Assistant Professor (Electronics and Communication Engg) > GLA Group of Institutions, Mathura. > Ph. No. 08954143009 > email id pandey.bramha at gmail.com >bpglaitm at yahoo.co.in > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111228/c01420f6/attachment.htm
[Pw_forum] Electric field calculation
Inclusion of van der Waals forces in electric field should not make a difference. But it should mimic the physical system which you are trying to simulate. On Tue, Dec 27, 2011 at 3:46 PM, Niharika Joshi wrote: > Hello, > Is it fine to include van der Waal forces in a electric field (sawtooth > potential) calculation? > > -Niharika Joshi > (project student, Indian Institute of Science Education and Research, Pune) > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, --------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111228/504d3380/attachment.htm
[Pw_forum] Re : how to construct supercell for an fcc crystal compound
The best way is to sit for sometime and write your own code implementing periodic boundary condition. Writing the code may enhance you understanding of the periodicity in the crystal. On Thu, Dec 15, 2011 at 3:51 PM, Giovanni La Penna wrote: > > In the past I used an utility of DL_POLY (a package widely used for > simulations of empirical models of liquids, solids and partially > ordered systems, membranes, liquid crystals, etc.): > > http://www.cse.scitech.ac.uk/ccg/software/DL_POLY/ > > The utility was genlat.f (hopefully still contained in > the open-source distributed version DL_POLY_CLASSIC). > Any reminiscence in the latgen subroutine of QE? > > I see latgen.f is still used. > As for an application, see for instance: > http://arxiv.org/abs/1108.3396 > > However, I agree that if the things are not too complicated, > the best is typing coordinates into an XYZ file, after > a bit of manual drawing. Finally, watching at the result with > some 3d-rendering graphic package. > >Giovanni La Penna (Cnr-ICCOM) > > > Giovanni La Penna - National research council (Cnr) > Institute for chemistry of organo-metallic compounds (Iccom) > via Madonna del Piano 10, > I-50019 Sesto Fiorentino, Firenze, Italy > tel.: +39 055 522-5264, fax: +39 055 522-5203 > e-mail: glapenna at iccom.cnr.it - http://www.iccom.cnr.it/lapenna > skype: giovannilapenna > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111215/02b570af/attachment-0001.htm
[Pw_forum] Fixing magnetization in a given direction for "vc-relax" or relax calculations
Dear QE users, I am trying to optimize the structure of MnSe which in ground state has magnetization in (111) direction. I am considering three type of unit cells for the calculation (1) The cubic unit cell(8 atoms) (2) Rhobohedral(4 atoms) (3) Hexagonal(12 atoms). But as in cubic unit cell and rhombohedral unit cell the default value of the magnetization direction is along the z-axis which is not same as (111) whereas in hexagonal unit cell with magnetization along z-axis is same as (111). My question is can we fix the magnetization direction for example in rhombohedral unit cell along (111) for "vc-relax" or "relax" calculation? I tried the non-collinear option with giving the direction but after a scf cycle it shows that "stress not implemented in non-collinear option" for vc-relax calculation. And when I do the calculation for cubic and rhombohedral unit cell the individual magnetization that I am getting is around ~0.4 (which is very small) and for the hexagonal unit cell its about ~4. So there is lot of difference I am getting in changing the type of unit cell. Somebody please give a suggestion for overcoming the problem. Thanks a lot in advance. -- Regards, MOHNISH, --------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2023/1da7d199/attachment-0001.htm
[Pw_forum] SCF calculations do not converge
Dear Aiyad ! Try reducing "mixing_beta"(make it ~ 0.2 to 0.5) and your "ecutwfc" is too large.. I think 40-50 Ryd will suffice. Since you are using ultrasoft pseudopotential your ecutrho should be atleast 8 times the ecutwfc. And the value of the convergence threshold that you have set is too low. Make it to ~1.E-08..Try the suggestions, may be you will get rid of the convergence problem. On Mon, Nov 21, 2011 at 11:27 PM, IYAD AL-QASIR wrote: > Hello All, > I am trying to calculate the phonon dispersion relations and phonon > density of states of UO2. > Please find the attached files UO2.scf.in and UO2.ph.in > > The calculations assume GGA and include spin-polarized effects. > > There are 6 representations and nine modes. The problem I have is: When I > run the input file UO2.ph.in, the second representation of the second > mode for q (-0.167 0.167 -0.167), the *scf **calculations > do not converge.* > > Notes: > 1- My runs assume UO2 is metallic, in fact UO2 is insulator with band gap > of 2eV.( However, when I do the calculations using the VASP code I got very > good result only by including the polarization effects) > 2- In order to account for the band gap, one should implement the Hubbard > term (LDA/GGA+U) > 3- I tried different occupations (smearing, tetrahedra) > 4- I tried different starting_magnetization= 0.5, 1.0 > 5- the lattice parameter a= 10.285, is based on optimizing the structure > and including spin-polarization effects. > > > Any adivce to overcome this problem is highly welcomed. > > Kindest Regards, > __ > aIYAD I. AL-QASIR, PhD > Research Associate > > Department of Nuclear Engineering > North Carolina State University > Campus Box 7909 > 2500 Stinson Dr. > Raleigh, NC 27695-7909 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2022/585531c3/attachment.htm
[Pw_forum] k point value
Dear Padmaja, These k-values are the k-points in high symmetry direction which you choose to plot the band structure. Automatic grid generated for "scf" calculation if often not suitable for band-structure plot so we choose a high symmetry direction and discretize the reciprocal space in that direction. These are called special k-points for band structure plot. You can write a small code to generate a mesh with given high symmetry special k-points. And regarding the answer to your second question the unit of the total energy is always in Ryd. Its not a very big issue to figure out. Generally the fermi energy and in few more cases the energy could be in eV. Hope this helps. On Thu, Nov 17, 2011 at 11:17 PM, Padmaja Patnaik < padmaja_patnaik at yahoo.co.uk> wrote: > Dear all > I am using QE since last few yeras but still could not answer few > questions a new student in my lab asked me. When we are doing band plot its > a curve between k~E. In the input file we give ka values as, > >0.0 0.0 0.0 >0.0 0.0 0.1 >0.0 0.0 0.2 >0.0 0.0 0.3 >0.0 0.0 0.4 > > then what how are we getting the k values to plot the band structure. The > values in the data file looks different from these values. > > Another question is, which unit is followed in QE? > a.u. (hbar = e^2 = m_e = 1, energy in Hartree) or Rydberg unit ( hbar=1, > e^2=2, m_e=1/2, energy in rydberg). > > Sometimes the output energy is given in eV and sometimes in Rydberg. This > is confusing that which unit is followed in QE. > > please suggest on these two points. > Regards > > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2018/b0364ed6/attachment-0001.htm
[Pw_forum] Elastic Constants
Search archives. And provide your affiliation in future. On Sat, Nov 5, 2011 at 1:11 PM, henry odhiambo wrote: > Hello everyone! > > This may be trivial but just try, please. > > Can anyone give me direction on how to calculate elastic constants using > Quantum ESPRESSO codes. > > Thank you. > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, --------- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/2005/1e99d5de/attachment.htm
[Pw_forum] Tr : Pw_forum Digest, Vol 52, Issue 61
Dear Debbichi, The k-point grid for the phonon calculation depends upon the symmetry direction in which you want to plot the band structure. Please see some basic solid state physics book for the same. You will get the better idea. And use fine mesh for better calculation. Information will be available in Marder's solid state physics book, and some basic crystallography books... On Fri, Oct 21, 2011 at 2:04 PM, debbichi mourad wrote: > Hi, > thanks for hepl > what are the values k-points ??that can I use in this case > thanks > > DEBBICHI Mourad > Unit? de Recherche Physique des Solides,99/UR/13-19, > D?partement de Physique, Facult? des Science de Monastir, > Avenue de l'Environnement 5019, Monastir Tunisie. > t?l:+21697487042 > mourad_fsm at yahoo.fr > - Mail transf?r? - > *De :* "pw_forum-request at pwscf.org" > *? :* pw_forum at pwscf.org > *Envoy? le :* Vendredi 21 Octobre 2011 8h50 > *Objet :* Pw_forum Digest, Vol 52, Issue 61 > > Send Pw_forum mailing list submissions to > pw_forum at pwscf.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/pw_forum > or, via email, send a message with subject or body 'help' to > pw_forum-request at pwscf.org > > You can reach the person managing the list at > pw_forum-owner at pwscf.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Pw_forum digest..." > > > Today's Topics: > > 1. Re: error band structure of ZnO (Paolo Giannozzi) > 2. Re: error band structure of ZnO (Lorenzo Paulatto) > > > -- > > Message: 1 > Date: Fri, 21 Oct 2011 09:10:39 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] error band structure of ZnO > To: PWSCF Forum > Message-ID: <1319181039.31930.6.camel at fe12lx.fisica.uniud.it> > Content-Type: text/plain > > On Fri, 2011-10-21 at 11:20 +0530, mohnish pandey wrote: > > > > The automatically generated k-points may not be in the > > high symmetry direction in which one may want to plot > > the band structure > > autimatically generated k-points form a uniform grid > in the Brillouin Zone. Typically they aren't suitable > for a band structure plot > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > > -- > > Message: 2 > Date: Fri, 21 Oct 2011 09:16:37 +0200 > From: "Lorenzo Paulatto" > Subject: Re: [Pw_forum] error band structure of ZnO > To: "PWSCF Forum" > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes > > In data 21 ottobre 2011 alle ore 07:50:39, mohnish pandey > ha scritto: > > The automatically generated k-points may not be in the high symmetry > > direction in which one may want to plot the band structure. Am I right? > > > Indeed, i did not notice it was a band calculation.. yet the points chosen > > by Debbichi are not forming a typical BZ path either; I guess everybody is > > free to put his k-points wherever he wishes :-) > > > > -- > Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 > phone: +33 (0)1 44275 084 / skype: paulatz > www: http://www.impmc.upmc.fr/~paulatto/ > mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 > > > -- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 52, Issue 61 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111021/bec384ce/attachment.htm
[Pw_forum] Running an input file
Before running the calculation visualizing the structure is extremely important. Try using XCrysden to visualize the structure which you made. And some basic info you will find on MIT-OCW Atomistic material modelling lectures to prepare a QE input file. Below is the link. http://ocw.mit.edu/courses/materials-science-and-engineering/3-320-atomistic-computer-modeling-of-materials-sma-5107-spring-2005/ And please sign your affiliation while writing to this forum so that we know whom we are interacting with. On Thu, Oct 20, 2011 at 8:51 AM, Gulcin Kucukdalyan wrote: > Dear Mohnish, > > Thanks a lot for your response. I am trying to prepare an input file for > graphene. I just prepared a text file and tried to run it and did not work. > I really cannot find detailed explanation about how to prepare an input > file. Can you please suggest me any if exist? > > Gulcin > > On Oct 19, 2011, at 10:53 PM, mohnish pandey > wrote: > > Dear Gulcin ! > > To run an an input file for example an input file of pw.x you should invoke > the command for pw.x. /espresso directory/bin/pw.x > abc.scf.out. In this /espresso directory/ is the address to espresso > directory, "abc.scf.in" is the name of the QE input file and "abc.scf.out" > is the the QE output file. This is the crudest way to run an input file. And > next time please mention your affiliation. Hope it helps. > > On Thu, Oct 20, 2011 at 2:22 AM, Gulcin Kucukdalyan < gmail.com> > gkucukdalyan at gmail.com> wrote: > >> HI All, >> >> Could you please tell me how can i run an input file. It is the second >> time i am asking this question. Last time i was asked to read tutorials. It >> is not specified there if i have to prepare a text file or an executable >> file (run_example) like the ones in the examples. If i have to prepare a >> text file how can i run it. >> >> Thanks, >> >> Gulcin >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> <http://www.democritos.it/mailman/listinfo/pw_forum> >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > > -- > Regards, > MOHNISH, > - > Mohnish Pandey > BTech-Mtech, IIT Kanpur > Senior Project Associate, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > - > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111020/b057977d/attachment-0001.htm
[Pw_forum] Running an input file
Dear Gulcin ! To run an an input file for example an input file of pw.x you should invoke the command for pw.x. /espresso directory/bin/pw.x abc.scf.out. In this /espresso directory/ is the address to espresso directory, " abc.scf.in" is the name of the QE input file and "abc.scf.out" is the the QE output file. This is the crudest way to run an input file. And next time please mention your affiliation. Hope it helps. On Thu, Oct 20, 2011 at 2:22 AM, Gulcin Kucukdalyan wrote: > HI All, > > Could you please tell me how can i run an input file. It is the second time > i am asking this question. Last time i was asked to read tutorials. It is > not specified there if i have to prepare a text file or an executable file > (run_example) like the ones in the examples. If i have to prepare a text > file how can i run it. > > Thanks, > > Gulcin > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111020/757c12bf/attachment.htm
[Pw_forum] Structure Optimization under Sawtooth potential
Dear Swapnil ! In the /espresso/doc.pw.html or text file the details of implementation of sawtooth potential are given. Please take a look at that, On Thu, Oct 20, 2011 at 3:13 AM, swapnil chandratre < swapnil.chandratre at gmail.com> wrote: > Hi, > > I am trying to observe in plane piezoelectric response of a system. As I > understand I should apply sawtoooth potential and observe the change in > positions of atoms. Are there any examples or tutorials on this ? And is > what I am thinking the actual way of approaching the problem ? > > -- > Regards, > Swapnil Chandratre > Graduate Student > Dept. of Mechanical Engineering, > University of Houston, > Houston, TX > (M)-713-294-9546 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20111020/54d84c23/attachment.htm
[Pw_forum] from check_atoms : error #
Dear Ramesh! Visualize the structure with Xcrysden. You may be figure out the problem by yourself. On Sat, Sep 17, 2011 at 5:27 PM, ramesh kumar wrote: > Dear All > > I am trying to make a tetragonal supercell with 32 atoms but got this error > > > from check_atoms : error # 1 > atoms # 1 and # 2 overlap! > > I tried searching forum got the answer like because of the equivalent atom > positions it shows the > error. So i tried to use p1 space group (triclinic cell) but i am unable to > get rid of the error. > Anyboday faced this problem earlier please help me in this regard... > > Thankyou > > With regards > > K. Ramesh Kumar > Research Scholar > Department of Physics > IIT-Madras > Chennai-600 036 > > <http://sigads.rediff.com/RealMedia/ads/click_nx.ads/www.rediffmail.com/signatureline.htm > at Middle?> > Treat yourself at a restaurant, spa, resort and much more with *Rediff > Deal ho > jaye!<http://track.rediff.com/click?url=___http://dealhojaye.rediff.com?sc_cid=mailsignature___=signature=rediffmailsignature=deals> > * > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110917/dd93d07e/attachment.htm
[Pw_forum] relaxation of the 60 C atom supercell
Dear Ellie, For phonon calculation you definitely need to converge forces and energy to much accuracy. First check the convergence for these two for relax calculation then do phonon calculation. On Mon, Sep 12, 2011 at 2:50 AM, Elie Moujaes wrote: > Dear all, > I am still "fighting" with the 60 carbon atom system that I am trying to > relax. I did a relaxation using 4 k-points and I got the system relaxed then > I did an scf calculation with 25 points (for phonon calculations) and the > total force is 0.099839. Does this mean that using 4 points is not enough? > how many points do I have to consider as 25 points would really take a lot > of time? Shall I relax for 10 k-points, the same as I was doing for an scf > calculation? Can anyone advise me on that? > Thanks again and sorry to disturb you with that many times. I am trying to > avoid the negative frequencies that I obtained before totally relaxing the > crystal. > > Elie M > University of Nott > ng7 2rd > uk > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA -
[Pw_forum] Problem with Bi2Se3 SCF converge
Dear Wu ! Can you please paste your complete input file so that we can take a look and may be able to tell where is the problem. On Sat, Sep 3, 2011 at 6:36 AM, WF wrote: > Dear Mohnish: >Thanks for our advices. I tried beta = 0.1 and 0.2, and those > message is postponed to 100+ iteration, but the convergence still cannot be > achieved. > > > On Fri, Sep 2, 2011 at 11:45 AM, mohnish pandey > wrote: > > Try reducing "beta" > > >On Wed, Aug 31, 2011 at 8:07 AM, WF wrote: > > > Hello everyone, > > > > I am doing calculation of Bi2Se3 with vdW-DF functional, but > > it really hard to converge. After several iterations it keeps to > > prompt things > > like: > > > > ** ** > > > > iteration # 58 ecut=60.00 Ry beta=0.70 > > > > CG style diagonalization > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 2 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 2 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 1 eigenvalues not converged > > > > c_bands: 2 eigenvalues not converged > > > > c_bands: 2 eigenvalues not converged > > > > c_bands: 2 eigenvalues not converged > > > > c_bands: 2 eigenvalues not converged > > > > > > > > and will not converge in 1000 iteration. > > > > ** ** > > > > But the calculation of LDA and PBE can converge, however. All > > pseudo-potential is generated by ld1.x with same parameters except > > functional. > > > > ** ** > > > > I have tried to change some parameter in SCF but it doesn?t > > seem to be helpful. Is there any suggestion for this problem? > > > > ** ** > > > > Thanks. > > > > ** ** > > > > F,Wu > > > > ** ** > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > - > Regards > > --- > F, Wu > College of Chemistry and Molecular Engineering > Peking University > -- > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110903/6894c488/attachment.htm
[Pw_forum] Problem with Bi2Se3 SCF converge
Try reducing "beta" On Wed, Aug 31, 2011 at 8:07 AM, WF wrote: > Hello everyone, > > I am doing calculation of Bi2Se3 with vdW-DF functional, but it > really hard to converge. After several iterations it keeps to prompt things > like: > > ** ** > > iteration # 58 ecut=60.00 Ry beta=0.70 > > CG style diagonalization > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 1 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > c_bands: 2 eigenvalues not converged > > > > and will not converge in 1000 iteration. > > ** ** > > But the calculation of LDA and PBE can converge, however. All > pseudo-potential is generated by ld1.x with same parameters except > functional. > > ** ** > > I have tried to change some parameter in SCF but it doesn?t seem > to be helpful. Is there any suggestion for this problem? > > ** ** > > Thanks. > > ** ** > > F,Wu > > ** ** > > --- > > F, Wu > > College of Chemistry and Molecular Engineering > > Peking University > > --**** > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110902/6b7cdcf5/attachment.htm
[Pw_forum] convergence w.r.t ecutwfc
Dear Amin! Are you trying to calculate the energy of BH3 dimer? If it so then the vacuum space you have used is very less, there will be lot of spurious interaction. Increase the vacuum space such that the minimum distance between the images is greater than 15 angstrom. Please try it. On Mon, Aug 29, 2011 at 4:04 AM, Amin Torabi wrote: > Dear QE-users, > > > Will you please take a look at my input file and convergence table below: > > I am using PBE USPP for both hydrogen and boron, but calculating energies > using PBEsol. (ecutrho is set to 12* ecutwfc.) > > My question is: > 1. Does it look normal? I was expecting to see 1mRy accuracy at lower > ecutwfc values. > 2. I didn't use "occupations" or "smearing" and I didn't get any error in > output files. Do they affect the convergence? > 3. I want to do vc-relax calculation at high pressure. Based on my table, > what ecutwfc do you suggest? > > Thanks in advance. > > > > ecutwfc energy > 30 -38.28149597 > 35 -38.28437812 > 40 -38.28554856 > 45 -38.28658930 > 50 -38.28772083 > 55 -38.28883141 > 60 -38.28989311 > 65 -38.29086868 > 70 -38.29167889 > 75 -38.29227767 > 80 -38.29267847 > 85 -38.29291696 > 90 -38.29302834 > 95 -38.29305836 > 100 -38.29305908 > 105 -38.29307545 > 110 -38.29313486 > 115 -38.29324982 > > > pseudo_dir = ** > outdir = ** > prefix = '$a' > tstress = .true > tprnfor = .true > verbosity = 'low' > / > > ibrav = 12 > celldm(1) = 8.31479435 > celldm(2) = 1.3 > celldm(3) = 1.4772727273 > celldm(4) = -0.260504508642648 > nat= 16 > ntyp = 2 > ecutwfc = $a > ecutrho = `expr 12 \* $a` > input_dft= 'pbesol' > / > > / > ATOMIC_SPECIES > B 10.811B.pbe-n-van_ak.UPF > H 1.00794 H.pbe-van_ak.UPF > ATOMIC_POSITIONS crystal > B0.002 0.146 0.042 > H -0.194 0.166 0.140 > H0.196 0.294 -0.005 > H0.104 -0.019 0.112 > B -0.002 -0.146 -0.042 > H0.194 -0.166 -0.140 > H -0.196 -0.294 0.005 > H -0.104 0.019 -0.112 > B0.498 0.354 0.542 > H0.694 0.334 0.640 > H0.304 0.206 0.495 > H0.396 0.519 0.612 > B0.502 0.646 0.458 > H0.306 0.666 0.360 > H0.696 0.794 0.505 > H0.604 0.481 0.388 > K_POINTS automatic > 8 8 8 0 0 0 > > -- > Amin Torabi > Ph.D. Student > Chemistry Department > The University *of* Western Ontario > London, On Canada, N6A 5B7 > Phone: 519-661-2111 Ext: 87871 > > > > > -- > Amin Torabi > Ph.D. Student > Chemistry Department > The University *of* Western Ontario > London, On Canada, N6A 5B7 > Phone: 519-661-2111 Ext: 87871 > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110829/5e4ecca6/attachment.htm
[Pw_forum] Problem in Xspectra calculation
Dear Niharika! Its very hard to answer without taking a look a look at your input file. And please mention your affiliation so that we know that whom we are interacting with.. On Wed, Aug 10, 2011 at 1:23 PM, Niharika Joshi wrote: > Hi, > I was trying the tutorial examples for the X-ray absorption spectra > calculation for diamond. > The examples were downloaded from the following site: > http://www.ictp.it/~rgebauer/Matteo_XAS.tar.gz > when I execute the Xspectra input file the execution terminates with the > error message: wrong fft dimensions. > The Quantum esspresso version that i am using is esspresso 4.3 and > executing as stated below, > /opt/MPI/lam-7.1.4/lam/bin/mpirun -np 12 > /home/Desktop/espresso-4.3/bin/xspectra.x < input file >output file & > Any idea what could be wrong? > -Niharika > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----- Mohnish Pandey BTech-Mtech, IIT Kanpur Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110810/6e1cd469/attachment-0001.htm
[Pw_forum] large error in RuO2 lattice parameter
Dear QE users, 2.7438 I want to study RuO2 surfaces. I did calculation of ruthenium metal and found the lattice constant right(experimental = 2.70 and 1.584, I got 2.7438 and 1.582) But after doing calculation of bulk ruthenium oxide I am getting very different lattice parameter as compared to the experimental value. Experimental value is 4.494 and 3.107 and I am getting the value of 4.6421 and 3.1888. Can anybody please tell from where the discrepancy is coming? Thanks a lot in advance *input file* calculation = 'vc-relax', restart_mode='restart', nstep=100 outdir='/home/mohnish/Desktop/Ruo2-bulk', pseudo_dir='/home/mohnish/Desktop/Ruo2-bulk', prefix='Ruo2', tstress = .true., tprnfor = .true., / ibrav= 6, a = 4.6379, c = 3.1844,nat= 6, ntyp= 2, ecutwfc = 40,ecutrho=400,occupations='smearing',degauss=0.01,smearing='gaussian' / diagonalization='david' mixing_mode = 'plain' mixing_beta = 0.7 conv_thr = 1.0d-8 startingpot = 'file' startingwfc = 'file' / ion_dynamics='bfgs' / cell_dynamics = 'bfgs' / ATOMIC_SPECIES Ru 101.07 Ru.pbe-n-van.UPF O 15.099 O.pbe-rrkjus.UPF ATOMIC_POSITIONS (crystal) Ru 0. 0. 0. Ru 0.5000 0.5000 0.5000 O 0.3060 0.3060 0. O 0.6940 0.6940 0. O 0.1940 0.8060 0.5000 O 0.8060 0.1940 0.5000 K_POINTS (automatic) 10 10 12 0 0 0 *Section of output file,* bfgs converged in 8 scf cycles and 4 bfgs steps (criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00) End of BFGS Geometry Optimization Final enthalpy =-227.8256404205 Ry Begin final coordinates new unit-cell volume =463.72196 a.u.^3 (68.71650 Ang^3 ) CELL_PARAMETERS (alat= 8.76436083) 1.000910330 0.0 0.0 0.0 1.000910330 0.0 0.0 0.0 0.687553615 ATOMIC_POSITIONS (crystal) Ru 0.0 0.0 0.0 Ru 0.5 0.5 0.5 O0.306258404 0.306258404 0.0 O0.693741596 0.693741596 0.0 O0.193741596 0.806258404 0.5 O0.806258404 0.193741596 0.5 End final coordinates -- Regards, MOHNISH, ----- Mohnish Pandey Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110804/ada00234/attachment-0001.htm
[Pw_forum] Regarding supercell dimensions
Dear Deepak!
There no cell parameter in your input. You have to take the experimental
value of the lattice constant available or dig out some paper in which the
relevant calculations are done. See the INPUT_PW.txt in DOC folder of
espresso distribution. The meaning of parameters are very clearly mentioned
there. And next time please mention your affiliation so that we should know
whom we are interacting with.
On Wed, Aug 3, 2011 at 11:19 PM, dipak thakur wrote:
> I am nobe to quantum espresso and using supercell for first time.
> Can any one help me in understanding few things regarding the supecell
> determination?
>
> The following is a typical input file I am using (copied from one of the
> earlier post).
>
> CONTROL
> title = 'Graphene mono layer'
> calculation = "relax" ,
> restart_mode = 'from_scratch' ,
> outdir='/home/usuarios/baldini/espresso-4.2.1/tmp/' ,
> pseudo_dir = '/home/usuarios/baldini/espresso-4.2.1/pseudo' ,
>
> etot_conv_thr = 1.0E-4 ,
> forc_conv_thr = 1.0D-3 ,
> nstep=50,
> dt=40,
> prefix='1MLG_Ti_H2',
> /
>
> ibrav = 0.,
>
> ntyp = 2 ,
> nat = 33 ,
> ecutwfc = 50.0 ,
> ecutrho = 400.0,
> /
>
> electron_maxstep = 300.,
> conv_thr = 1.0d-8 ,
>
> mixing_mode = 'plain',
> mixing_beta = 0.5,
> diagonalization = 'cg' ,
> diago_cg_maxiter = 50,
> /
>
> /
> CELL_PARAMETERS
> 16.12131954 9.383047808 0.000
>
> 0. 18.658162370 0.000
> 0.0000.00056.6893424
> ATOMIC_SPECIES
> C 12.0107 C.pbe-van_ak.UPF
> Ti 47.8670 Ti.pbe-sp-van_ak.UPF
> ATOMIC_POSITIONS angstrom
> C 2.891637.402191.8862
>
> C 3.592928.638321.8826
> C 3.603496.167021.8884
> C 5.0186 8.645011.8612
> C 5.0215 6.165981.8904
> C 5.733027.405221.8718
>
> C 1.471847.396161.891
> C 2.891129.870661.886
> C 2.894714.932641.8916
> C 5.733199.8885 1.8612
> C 5.736434.9413 1.8924
>
> C 7.163487.412031.882
> C 1.474744.9269 1.8924
> C 0.762281 8.627831.8946
> C 0.763134 6.161721.8914
> C 1.4715 9.863351.8934
>
> C 3.6034111.10951.8868
> C 5.0212411.12391.882
> C 3.605123.701561.8932
> C 5.026453.707891.891
> C 7.878078.655321.8816
>
> C 7.163739.894971.872
> C 7.162034.948141.8954
> C 7.876196.176771.8996
> C 5.7363412.35221.8872
> C 0.772689 3.691021.898
>
> C 0.762793 1.220031.8968
> C 7.8764511.13371.8894
> C 7.1620312.35871.889
> C 7.8720113.59221.8942
> C 2.894792.466191.8922
>
> C 1.474822.458781.8952
> Ti 6.416048.659743.74
> K_POINTS {automatic}
> 6.0 6.0 1.0 1.0 1.0 1.0
>
> Can anyone help me understanding how are these Cell parameters calculated?
>
> Also in some cases celld(m) are used. Can anyone comment on these also?
> How are the cell parameters and lattice constant or atomic spacing related?
>
> Any clue would be of great help.
>
> Thanks in advance.
>
>
> Rgds
> Deepak
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
Regards,
MOHNISH,
-
Mohnish Pandey
Senior Project Associate,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
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[Pw_forum] antiferromagnetism in thin films
Dear Dr. Mattioli, I will do the calculation for different spin configurations and will let you know as soon as I have the results. And regarding the "subject" I am sorry to change that, I did that by mistake and did not realize. On Tue, Jul 26, 2011 at 7:01 PM, Giuseppe Mattioli < giuseppe.mattioli at mlib.ism.cnr.it> wrote: > > Dear Mohnish > changing the subject will not produce automatically an answer... I suspect > that you are asking something that deserves itself a full investigation. > Let > us know the results. > Yours > Giuseppe > > On Tuesday 26 July 2011 12:03:57 mohnish pandey wrote: > > Dear QE users, > > > > I want to do calculations of thin films of antiferromagnetic oxide like > > CoO. The CoO has rocksalt structure and magnetization along (111) > > direction. Suppose we take 3 layers and 4 layers for of CoO along (111), > > then my doubt is that will the magnetization oscillate i.e. in even > number > > of layers it will be zero and odd number of layers will have some finite > > value? Or wil the film will show antiferrromagnetism in plane i.e. every > > layers of CoO will be antiferromagnetic? And what about other directions > > like (001) or (10-10) in wurtzite structure. > > > > Thanks a lot in advance for help.. > > > > -- > > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits. Les distinctions sociales > ne peuvent ?tre fond?es que sur l'utilit? commune > - Article 2 - Le but de toute association politique > est la conservation des droits naturels et > imprescriptibles de l'homme. Ces droits sont la libert?, > la propri?t?, la s?ret? et la r?sistance ? 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: > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110727/92e7eb71/attachment.htm
[Pw_forum] antiferromagnetism in thin films
Dear QE users, I want to do calculations of thin films of antiferromagnetic oxide like CoO. The CoO has rocksalt structure and magnetization along (111) direction. Suppose we take 3 layers and 4 layers for of CoO along (111), then my doubt is that will the magnetization oscillate i.e. in even number of layers it will be zero and odd number of layers will have some finite value? Or wil the film will show antiferrromagnetism in plane i.e. every layers of CoO will be antiferromagnetic? And what about other directions like (001) or (10-10) in wurtzite structure. Thanks a lot in advance for help.. -- Regards, MOHNISH, - Mohnish Pandey Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110726/4ce189fe/attachment.htm
[Pw_forum] Nature of antiferomagnetism in thin films
Dear QE users, I want to do calculations of thin films of antiferromagnetic oxide like CoO. The CoO has rocksalt structure and magnetization along (111) direction. Suppose we take 3 layers and 4 layers for of CoO along (111), then my doubt is that will the magnetization oscillate i.e. in even number of layers it will be zero and odd number of layers will have some finite value? Or wil the film will show antiferrromagnetism in plane i.e. every layers of CoO will be antiferromagnetic? And what about other directions like (001) or (10-10) in wurtzite structure. Thanks a lot in advance for help.. -- Regards, MOHNISH, - Mohnish Pandey Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110725/04edc51c/attachment.htm
[Pw_forum] How to use the wave functions
What type of data you want? If you want to get the charge density then you can use post-processing tools to extract the charge density from prefix.save folder written in chargedensity.dat file.. On Thu, Jun 30, 2011 at 4:41 AM, yaohua tan wrote: > How to use the wave functions generated by Quantum espresso? > when I set the option in the > wf_collect = .true. > QE generate the wave functions in the output dir. > Can anyone tell me how to read and use the data file in prefix.save? > It seems that they are binary files containing both text and data. > Is there any easy way to get the data from those files? > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, --------- Mohnish Pandey Senior Project Associate, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110630/e72833e9/attachment.htm
[Pw_forum] surface relaxation and non-zero parallel forces.
Dear Dr. Bocan, AS your input file suggest, you are not relaxing the system, you are doing the calculation for only one electronic cycle. As you have cleaved the bulk the atoms will relax upon cleaving and they wont be in the bulk-like position, so you must relax all of them. Put the flag "calculation" = "relax", it will minimize the forces and finally you will get the systems with atoms having force below the threshold value(you can use the default value in the code). And I think there is not need to use such a dense grid of k- points, I think 12x10x1 will suffice. On Sat, Jun 11, 2011 at 8:05 AM, Gisela Bocan wrote: > Hello, > I assumed surface relaxation for the Ag(110) surface would be an > easy matter. As it happens, I find non-zero forces parallel to the surface > and therefore, upon relaxation, I get a non-neglectable parallel > displacement of the ions. I am working with a 2x2sqrt(2) unit cell. I attach > my file.in and the forces I get. Note that the forces along one direction > (x) are much larger that along the other one (y). Note as well the large > values considered for ecutwfc, ecutrho, kpoints and the small degauss and > conv_thr. Any ideas on how to correct this behaviour? Am I missing > something? Thanks in advance and sorry if this is a stupid question. Small > changes in the input parameters can lower the forces I get but I find > nothing systematic. > > >prefix= 't_G0', >outdir= ' ', >pseudo_dir= '/home/qe/pseudo', >calculation = 'scf', >tprnfor = .true., >lkpoint_dir = .false., >verbosity = 'high', > / > >ibrav = 8, >celldm(1) = 11.1298607358762567, >celldm(2) = 1.4142135623730949, >celldm(3) = 2.25, >nat = 16, >ntyp= 1, >ecutwfc = 45, >ecutrho = 450.00, >occupations = 'smearing', >smearing= 'mv', >degauss = 0.002, > / > >conv_thr = 1.d-12 >diagonalization = 'cg' > / > > / > ATOMIC_SPECIES >Ag 107.8682 Ag.pbe-d-rrkjus.UPF > ATOMIC_POSITIONS crystal >Ag 0. 0. 0. >Ag 0.5000 0. 0. >Ag 0. 0.5000 0. >Ag 0.5000 0.5000 0. >Ag 0.2500 0.2500 0. >Ag 0.7500 0.2500 0. >Ag 0.2500 0.7500 0. >Ag 0.7500 0.7500 0. >Ag 0. 0. 0. >Ag 0.5000 0. 0. >Ag 0. 0.5000 0. >Ag 0.5000 0.5000 0. >Ag 0.2500 0.2500 0. >Ag 0.7500 0.2500 0. >Ag 0.2500 0.7500 0. >Ag 0.7500 0.7500 0. > K_POINTS automatic >33 23 1 0 0 0 > > atom 1 type 1 force = 0.0. -0.01175276 > atom 2 type 1 force = 0.0. -0.01175282 > atom 3 type 1 force = 0.0. -0.01175318 > atom 4 type 1 force = 0.0. -0.01175325 > atom 5 type 1 force =-0.42210.00330.01048323 > atom 6 type 1 force = 0.42210.00330.01048323 > atom 7 type 1 force =-0.4221 -0.00330.01048323 > atom 8 type 1 force = 0.4221 -0.00330.01048323 > atom 9 type 1 force = 0.0. -0.01048309 > atom 10 type 1 force = 0.0. -0.01048306 > atom 11 type 1 force = 0.0. -0.01048272 > atom 12 type 1 force = 0.0. -0.01048269 > atom 13 type 1 force =-0.41480.00030.01175266 > atom 14 type 1 force = 0.41480.00030.01175266 > atom 15 type 1 force =-0.4148 -0.00030.01175266 > atom 16 type 1 force = 0.4148 -0.00030.01175266 > > Dr. G. A. Bocan > Surface Physics Group, > Centro At?mico Bariloche, > > ___ > Pw_forum mail
[Pw_forum] How to obtain the binding energy ( in the unit of eV/Zn-O pair ) for Wurtsite ZnO?
Dear Hongsheng,
All the four bonds in ZnO wurtzite are equivalent. So to calculate the
binding energy you have to use the below formula :
E_{binding-ZnO}=E{calculated-ZnO-wurtzite}-E_{Zn_{crystal-total}}-E_{E(1/2*O2}}.
Remember that you have to do spin-polarised calculation for O2 otherwise it
will give wrong answer. Binding energy definition is same as above. And
cohesive energy is the difference in energy between the energy of crystal
and corresponding species in isolated phases. Below are the some references.
http://arxiv.org/ftp/cond-mat/papers/0610/0610002.pdf
<http://arxiv.org/ftp/cond-mat/papers/0610/0610002.pdf>
http://prb.aps.org/pdf/PRB/v70/i5/e054104
On Fri, May 27, 2011 at 12:19 PM, ?? ? wrote:
> Hi all,
>
> I want to obtain the binding energy ( in the unit of eV/Zn-O pair ) for
> Wurtsite ZnO. Considering that there are two different length of Zn-O bond,
> I cann't figure out how to calculate the binding energy in the unit ev/ZnO.
> Any hints on this issue?
>
> Regards.
> Hongsheng.
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
Regards,
MOHNISH,
---------
Mohnish Pandey
Y6927262,5th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
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[Pw_forum] K point in matdyn.x
Dear Mahdi, Your answer lies here: http://www.democritos.it/pipermail/pw_forum/2011-May/020576.html On Wed, May 25, 2011 at 6:37 PM, Mahdi Mirnezhad wrote: > Dear All, > I want to calculate the phonon dispersion-relation with matdyn.x. What > is the unit of q-points in this code (tpiba, crystal, tpiba-b, > crystal-b)?? > Best Regards, > > Mahdi Mirnezhad, > Guilan University, Rasht, Iran. > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, --------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110525/a860cf95/attachment.htm
[Pw_forum] Single point energy calculation within PWSCF.
Dear Hongsheng! The flag is "calculation" = 'scf' for single point energy calculation. But I will suggest you if you want to test the convergence for structure then you must relax the atomic position as well as cell volume, because the single point energy calculation will not relax the stress and forces. So for bulk structures "calculation = 'vc-relax' is the way to test the convergence with respect to energy, because that will release the stress and forces in the system. I hope it helps. Feel free to ask any doubt further. On Wed, May 25, 2011 at 10:19 PM, Hongsheng Zhao wrote: > Hi all, > > I've learned that the single point energy calculation should be the > most appropriate method for any type of convergence testings (whether > that be k-point, cutoff, fine grid or cell size). I want to know if > there are keywords/flags within PWSCF for single point energy calculation? > > Regards. > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, --------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110525/a0046eb3/attachment.htm
[Pw_forum] "Not orthogonal operation" error in vc-relax optimization
Dear Seyed! The relaxation of cell is breaking the symmetry, this error message shows that. For example, if you use surface unit cell as hexagonal and try to relax the 'x' and 'y' direction of the cell, then it will give the error message because the cell vector is not orthogonal and the direction of relaxation of your cell is is independent in 'x' and 'y' direction. So if you want to get to rid of this error message then the direction of relaxation should be in the direction of unit cell vector. The relaxation process should not break the symmetry of the system. Hope it helps. Feel free to ask further if you have any doubts. On Tue, May 24, 2011 at 11:35 AM, Seyed Mojtaba Rezaei Sani < s.m.rezaeisani at gmail.com> wrote: > Dear all > > My vc-relax opt, although I set cell dynamics='damp-w',ends with this > error : > > > from checkallsym : error # 2 > > not orthogonal operation > > Is there any suggestion for solving that? > (If anyone thinks about using nonsymmetric cell, I will send my input file > and will be grateful to learn how it can be) > > Thanks > -- > == > Seyed Mojtaba Rezaei Sani > Computational Condensed Matter Research Lab > Physics Department, Isfahan University of Technology > 84156-83111 Isfahan, Iran > Tel Lab: +98 311 391 3731 > s.rezaeisani at ph.iut.ac.ir > === > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110524/28694cc7/attachment.htm
[Pw_forum] Negative phonon frequency
Dear Mayank! There is no need to use this much high cutoff. First of all see proper convergence with k-points grids. Then "conv_thr" should be less than 10^-12. Before doing phonon calculation do vc-relax with high accuracy. And if you get very small negative value then you can ignore it.. On Wed, May 11, 2011 at 3:18 PM, mayank gupta wrote: > Hi Dear User's > > > I am trying to calculate the phonon frequency of SrFeO compund, but I > got negative frequancies at gamma also at other Q points, while I have > chossen very high cutoff (ecut=100Ry and ecut_rho=1000), while > experimentally the structure is stable at room temperature even up to > very low temperature. what could be the possible reason for such > negative frequecies. > > -- > Mayank > > BHABHA ATOMIC RESEARCH CENTER > MUMBAI > Office: 022-25595606 > Home: 9920397437/9869834437 > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110512/592fd3f4/attachment.htm
[Pw_forum] Conservation of spin on oxygen adsorption
Dear QE users, I am doing O2 adsorption on metal clusters. I have the question of how to conserve the spin multiplicity of O2 molecule during adsorption. I tried searching in the forum archive but did not find it. Can anybody please help me? Thanks a lot. -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110301/44613d6f/attachment.htm
[Pw_forum] a question about MnSe
Dear Lorenzo ! Can you give me a direction for my question about MnSe. I am really struck in it... On Fri, Jan 21, 2011 at 12:40 PM, Lorenzo Paulatto < lorenzo.paulatto at impmc.upmc.fr> wrote: > In data 20 gennaio 2011 alle ore 19:37:16, jia chen > ha scritto: > > I also have a question about vc-relax. How do you know if your cutoff is > > large enough to overcome Pulay stress, or you can do something else to > > get > > rid of it in you calculations. Thanks. > > The vc-relax algorithm keeps number of plane waves constant (i.e. it > changes ecutwfc as ~ V^3/2) in order to avoid Pulay stress. > > best regards > > > -- > Lorenzo Paulatto > post-doc @ IMPMC/UPMC - Universit? Paris 6 > phone: +33 (0)1 44 27 74 89 > www: http://www-int.impmc.upmc.fr/~paulatto/ > > previously (take note of the change!): > phd student @ SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > www: http://people.sissa.it/~paulatto/ > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110121/b6eb6dcc/attachment.htm
[Pw_forum] a question about MnSe
Dear QE users,
I am trying to do bulk calculations for MnSe in
rocksalt and wurtzite structure. Its has AFM ground state in rocksalt
structure but after checking convergence I am finding "rocksalt" structure
to be energetically higher than wurtzite structure. I am pasting my segments
of input and output files. Can anybody please help me in figuring out the
problem.
*INPUT FOR ROCKSALT*
calculation = 'vc-relax'
restart_mode='restart',
wf_collect = .true.
prefix='mnse',
pseudo_dir = '/home/mohnish/mnse-rocksalt-bulk',
outdir='/home/mohnish/mnse-rocksalt-bulk',
tprnfor = .true.,
tstress=.true.
/
ibrav= 0, celldm(1)= 10.3026, nat= 4, ntyp= 3,
ecutwfc = 40.0, ecutrho = 320.0,
occupations='smearing', smearing='gauss', degauss=0.01,
nspin=2,
starting_magnetization(1)= 0.0,
starting_magnetization(2)= 0.5,
starting_magnetization(3)=-0.5,
/
diagonalization='david'
mixing_mode = 'plain'
mixing_beta = 0.4
conv_thr = 1.0d-8
startingpot = 'file'
startingwfc = 'file'
/
ion_dynamics='bfgs'
trust_radius_max = 0.40
trust_radius_ini = 0.20
/
cell_dynamics='bfgs',
/
ATOMIC_SPECIES
Se 78.960 Se.pbe-van.UPF
Mn1 54.938 Mn.pbe-sp-van_mit.UPF
Mn2 54.938 Mn.pbe-sp-van_mit.UPF
CELL_PARAMETERS
0.50 0.50 1.00
0.50 1.00 0.50
1.00 0.50 0.50
ATOMIC_POSITIONS {crystal}
Se 0.25 0.25 0.25
Se 0.75 0.75 0.75
Mn1 0.0 0.0 0.0
Mn2 0.5 0.5 0.5
K_POINTS {automatic}
6 6 6 0 0 0
*OUTPUT FOR ROCKSALT*
bfgs converged in 8 scf cycles and 4 bfgs steps
(criteria: energy < 0.10E-03, force < 0.10E-02, cell < 0.50E+00)
End of BFGS Geometry Optimization
Final enthalpy =-464.4688263706 Ry
Begin final coordinates
new unit-cell volume =533.55466 a.u.^3 (79.06464 Ang^3 )
CELL_PARAMETERS (alat= 10.3026)
0.494008772 0.494008772 0.990589056
0.494008772 0.990589056 0.494008772
0.990589056 0.494008772 0.494008772
ATOMIC_POSITIONS (crystal)
Se 0.24854 0.24854 0.24854
Se 0.75146 0.75146 0.75146
Mn1 0.0 0.0 0.0
Mn2 0.5 0.5 0.5
End final coordinates
*INPUT FOR WURTZITE*
calculation = 'vc-relax',
restart_mode='restart',
verbosity = 'high'
wf_collect = .true.
outdir='/home/mohnish/mnse-wurtzite-bulk',
pseudo_dir='/home/mohnish/mnse-wurtzite-bulk'
prefix='mnse',
tstress = .true.,
tprnfor = .true.,
/
ibrav= 4, a = 4.178, c = 6.783,nat= 4, ntyp= 3,
ecutwfc =
40,ecutrho=320,occupations='smearing',degauss=0.01,smearing='gaussian',
nspin =2,starting_magnetization(1)=0.5,starting_magnetization(2)= -0.5,
/
diagonalization='david'
mixing_mode = 'plain'
mixing_beta = 0.4
conv_thr = 1.0d-8
startingpot = 'file'
startingwfc = 'file'
/
ion_dynamics='bfgs'
trust_radius_max = 0.40
trust_radius_ini = 0.20
/
cell_dynamics='bfgs',
/
ATOMIC_SPECIES
Mn1 54.938 Mn.pbe-sp-van_mit.UPF
Mn2 54.938 Mn.pbe-sp-van_mit.UPF
Se 78.960 Se.pbe-van.UPF
ATOMIC_POSITIONS (crystal)
Mn1 0.0 0. 0.0
Mn2 0.3 0.6667 0.5
Se 0.0 0. 0.34500
Se 0.3 0.6667 0.84500
K_POINTS (automatic)
6 6 4 0 0 0
*OUTPUT FOR WURTZITE*
End of BFGS Geometry Optimization
Final enthalpy =-464.4799667612 Ry
Begin final coordinates
new unit-cell volume =681.36082 a.u.^3 ( 100.96726 Ang^3 )
CELL_PARAMETERS (alat= 7.89527578)
1.001414763 0.0 0.0
-0.500707382 0.867250625 0.0
0.0 0.0 1.594103933
ATOMIC_POSITIONS (crystal)
Mn1 0.0 0.0 -0.014999731
Mn2 0.3 0.7 0.485592670
Se 0.0 0.0 0.359333481
Se 0.3 0.7 0.860073579
End final coordinates
--
Regards,
MOHNISH,
---------
Mohnish Pandey
Y6927262,5th Year dual degree student,
Department of Chemical Engineering,
IIT KANPUR, UP, INDIA
-
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[Pw_forum] anti-ferromagnetic calculations
Dear Padmaja! As I am using the latest version of QE(i.e 4.2) the 'nelup' and "neldw" variables are no longer there anymore. For magnetic calculations starting with some initial magnetization i.e. starting_magnetization(i). In my experience with AF calculations you should have even number of atoms in the unitcell( unless the system is frustrated or something like that). I did the calculation for NiO which have rocksalt structure so there will be 2 atoms in the unit cell with ibrav = 2. But with this I was not able to hit the ground state because there was only one Ni. So the number mag/unitcell was not zero. But when I did the calculation with ibrav = 1 and 8 atoms the total magnetization~0 and I am able to reach the ground state. And as also Shrubha pointed out that you must do Lowdin analysis to see the magnetization and check the up and down spins. I hope it helps. On Thu, Jan 13, 2011 at 11:25 AM, Padmaja Patnaik < padmaja_patnaik at yahoo.co.uk> wrote: > Dear All > > For an anti-ferromagnetic calculation to run in QE which of the following > way is more correct. > 1. specify different values of starting magnetization for different atoms > in the compound. I mean one positive and one negative value. > > 2. specifying the nelup and neldown. > > Thanks and regards > Padmaja Patnaik > Research Scholar > Dept of Physics > IIT Bombay > Mumbai, India > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110113/c8060957/attachment.htm
[Pw_forum] how does the calculation scales with number of processors
Thanks a lot Dr. Stefano for your reply. On Fri, Dec 24, 2010 at 3:50 PM, Stefano de Gironcoli wrote: > It strongly depends on the particular calculation and on the > parallelization strategy you choose. Linear scaling would be the ideal > scaling which you never get. > The things to keep in mind are load balancing and communication > overhead. This last is affected by your communication network latency > and bandwidth ... As a general rule the bigger the calculation the > easier is to scale. > It may be useful to have a look at the final timing summary of a > calculation to see the fraction of time spent in communication (FFT > scatter/gather and reduce operations) compared with the total wall clock > time for your system and how this changes for different settings. > Another factor to keep in mind is RAM memory as with certain > parallelization strategies you can trade some speed with increased memory. > > stefano > > mohnish pandey wrote: > > Dear QE users, > > I am trying to see how the runtime scales with > > number of processors. I did the same calculation using one node with > eight > > processors on one cluster and 8 nodes with total 56 processors on other > > cluster but the time does not seem to scale linearly with the number of > > processors. Can anybody give me an idea how does the time scale with > number > > of processors. > > Thanks a lot in advance. > > > > > > > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101224/e6654593/attachment.htm
[Pw_forum] how does the calculation scales with number of processors
Dear QE users, I am trying to see how the runtime scales with number of processors. I did the same calculation using one node with eight processors on one cluster and 8 nodes with total 56 processors on other cluster but the time does not seem to scale linearly with the number of processors. Can anybody give me an idea how does the time scale with number of processors. Thanks a lot in advance. -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101224/094c0e6d/attachment.htm
[Pw_forum] calculation for system having number of different species greater than 10
Thanks a lot Dr. Eyvaz. On Wed, Dec 22, 2010 at 6:06 PM, Eyvaz Isaev wrote: > Hi, > > Just go to /Modules/parameters.f90, and change ntypx=10 to that you want > to. > Then make clean and make pw (or whatever you want to re-compile). > > Bests, > Eyvaz. > > --- > Prof. Eyvaz Isaev, > Department of Physics, Chemistry, and Biology (IFM), Linkoping University, > Sweden > Theoretical Physics Department, Moscow State Institute of Steel & Alloys, > Russia, > isaev at ifm.liu.se, eyvaz_isaev at yahoo.com > > > -- > *From:* mohnish pandey > *To:* PWSCF Forum > *Sent:* Wed, December 22, 2010 1:30:07 PM > *Subject:* [Pw_forum] calculation for system having number of different > species greater than 10 > > Dear QE users, > I want to do some calculations having number of > different species greater than 10. I want to know is it possible to increase > the dimension of QE for more than 10 different species. > > -- > Regards, > MOHNISH, > - > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > - > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101222/8b00df99/attachment.htm
[Pw_forum] calculation for system having number of different species greater than 10
Dear QE users, I want to do some calculations having number of different species greater than 10. I want to know is it possible to increase the dimension of QE for more than 10 different species. -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101222/5f7c1d83/attachment.htm
[Pw_forum] speed becomes very slow after some electronic or ionic relaxation cycles
Dear QE users, I am trying to simulate supercell of ZnO zincblende structure with 56 atoms. I have checked the structure with Xcrysden and it is right. But the problem is after performing some electronic cycle the speed becomes very slow and the calculations are stuck. When I reduce the "ecut" value it performs some ionic relaxation step but the same problem come after some ionic relaxation steps. Can anybody please help whats wrong with the calculation? -- Regards, MOHNISH, ----- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101208/3c9cf56d/attachment.htm
[Pw_forum] cohesive energy of tungsten
Dear Vicky! Check the convergence of energy of isolated atoms also. Normally convergence threshold for energy for isolated species is higher than the crystal system. Check for different values of ecut and use the converged value. And next thing is you are doing calculations for bulk system so all the degrees of freedom should be relaxed for geometry optimization so instead of flag "relax" use "vc-relax".. The former one will converge the forces but not the stress and latter one converges the stress also... On Sun, Dec 5, 2010 at 11:53 AM, vicky singh wrote: > Hi > > I am trying to calculate the cohesive energy for tungsten. the code is > attached. I am able to get the lattice parameter of 3.19 ang while > experimental is 3.16 angs. Then i calculated the cohesive energy of w by > calculating the energy of isolated w atom by changing lattice parameter up > to 25. I got the cohesive energy of 11.1 ev/atom while reported value is 8.9 > ev/atom. This is way too high. can anybody help me. I have varied the K > point as well as The E_cut but no advantage. > > vicky singh > research student > Bangalore > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101206/42b627a2/attachment.htm
[Pw_forum] enthalpy of adsorbtion of o2 molecule on a ZnO supercell
Dear Meysam, First you relax the supecell using "relax" calculation, it will make all the atoms to attain an equilibrium position. Then adsorb the atom (make it close enough so that your surface is interacting with the adorbate) and make the "relaax" calculation again. The energy that you get from latter step subtract the "former energy of the supercell+energy of the isolated adsorbate"..This difference should give the adsorption energy. In fact I have not done any adsorption calculations but intuitively what I have said seems correct to me. On Thu, Oct 14, 2010 at 5:08 PM, meysam pazoki wrote: > Dear PWSCF users > > I want to calculte the enthalpy of adsorbtion of o2 molecule on the surface > of a ZnO.Can i use variable cell relaxation for the supercell and use the > enthalpy that printed in output file? > I can also run a series of scf jobs with different cell volumes,and then > calculate the pressure of system from E-V diagram and then calculate > enthalpy by H=E+PV from my data.Is it also true? > > Thanks > Best Regards > Meysam Pazoki > SUT > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101014/880f149b/attachment.htm
[Pw_forum] Way to do calculation using charge density of coarse grid for fine grid...
Dear QE users, I am doing calculations for large supercells. The way I am trying to do is first I do calculation for gamma point(which will be quit less time consuming), then what I want to do is use the charge density obtained form gamma point to do the calculation for 2x2x1 and then 2x2x1 to do 3x3x1 k-point grid. I there anyway to do this because when I am using the charge density of coarser grid to the calculation for finer grid I am getting the error "davcio error". I am also using the wave-function of the coarser grid for fine grid calculation. Thanks in advance -- Regards, MOHNISH, ----- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101011/cf143f4f/attachment.htm
[Pw_forum] Si diamond-cubic to beta-Sn transformation
Dear Prof Daryl ! Can you please attach your VASP file also so that I can have a closer look at your VASP file. In fact I did the calculation with your input file and after optimizing the structure I was getting the energy difference of 0.69 ev/atom. I just wanted to see the structures. On Wed, Oct 6, 2010 at 4:09 AM, Daryl Chrzan wrote: > Input files were stripped on the previous message. Here they are as part > of the message: > > Diamond Cubic: > > > calculation='scf' > restart_mode='from_scratch', > prefix='silicon', > tstress= .true. > tprnfor= .true. > pseudo_dir='/Users/darylchrzan/ResearchProjects/PSEUDOS/', > > outdir='/Users/darylchrzan/Desktop/MSE215Fall2010/Assignments/One/BetaSn/tmp/' > / > > ibrav=0, > celldm(1)=7.29052, > nat=2, > ntyp=1, > ecutwfc=29.3991, > ecutrho=352.789, > nbnd=8, > smearing = 'gaussian', > degauss = 0.02, > / > > diagonalization='cg' > mixing_mode='plain' > mixing_beta=0.7, > conv_thr=3.0d-7, > / > ATOMIC_SPECIES > Si 28.086 Si.pw91-n-van.UPF > ATOMIC_POSITIONS crystal > Si -0.125 0.125 -0.250 0 0 0 > Si 0.125 -0.125 0.250 0 0 0 > K_POINTS automatic > 12 12 12 0 0 0 > CELL_PARAMETERS > -0.5 0.5 0.707107 > 0.5 -0.5 0.707107 > 0.5 0.5 -0.707107 > > > Beta-Sn: > > > calculation='scf' > restart_mode='from_scratch', > prefix='silicon', > tstress= .true. > tprnfor= .true. > pseudo_dir='/Users/darylchrzan/ResearchProjects/PSEUDOS/', > > outdir='/Users/darylchrzan/Desktop/MSE215Fall2010/Assignments/One/BetaSn/tmp/' > / > > ibrav=0, > celldm(1)=9.13116, > nat=2, > ntyp=1, > ecutwfc=29.3991, > ecutrho=352.789, > nbnd=8, > smearing = 'gaussian', > degauss = 0.02, > / > > diagonalization='cg' > mixing_mode='plain' > mixing_beta=0.7, > conv_thr=3.0d-7, > / > ATOMIC_SPECIES > Si 28.086 Si.pw91-n-van.UPF > ATOMIC_POSITIONS crystal > Si -0.125 0.125 -0.250 0 0 0 > Si 0.125 -0.125 0.250 0 0 0 > K_POINTS automatic > 12 12 12 0 0 0 > CELL_PARAMETERS > -0.5 0.5 0.2735 > 0.5 -0.5 0.2735 > 0.5 0.5 -0.2735 > > > > Daryl C. Chrzan > Professor, Materials Science and Engineering > University of California > Berkeley, CA 94720 > > and > > Materials Sciences Division > Lawrence Berkeley National Laboratory > Berkeley, CA 94720 > > ph./fax: 510 643 1624 > > > > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101007/b758d7c3/attachment.htm
[Pw_forum] energy cutoff for oxides
Dear Mayank! Are you sure you are relaxing the bulk system for convergence test? For convergence test you have to vc-relax calculation not 'scf'. 'SCF' calculation will not convergence stress and forces in the system so your energy will show the behavior that you are getting and by the way as Dr. Lorenzo said you should specify the type of pseudopotential you are using. And mention you affiliation also not only phone numbers ;) On Mon, Sep 27, 2010 at 1:03 PM, mayank gupta wrote: > Dear all pwscf users > > I have some problem regarding ecutoff in scf run. I did a series of > calculation for oxides like lithium oxide silver oxide and copper > oxide. To get the energy convergence of the order of meV, the ecuttoff > parameters is beyond 100Ry in all the above cases even with upps. Is > it ok? > > > Mayank kumar gupta > Contact No- 9869834437 > 8097400037 > 8080458227 > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, --------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100927/31b4322f/attachment.htm
[Pw_forum] question about the stress in relax process
Dear Wang, Are you sure that this is your input file? Because the calculation flag says it is "scf" ..Which will not definitely do the relax calculation On Mon, Sep 20, 2010 at 3:32 PM, Wang Di wrote: > Dear Mohnish: > I have used the 'vc-relax' process optimized the cell parameter, however, > the result were seem to deviate from the initial value (experimental value) > too much.The aim of the structure optimizes is for calculating the Raman > spectra of the structure, I think the bad structure ( not coincide to the > experiment) is hard to got the true spectra. So I don't how to deal with the > case. According to your experience, what should I do for the next step? > > Thank you, dear Mohnish, for your kind help. > > > > 2010/9/20 mohnish pandey > > Dear Wang, >> The 'relax' process optimizes the structure within >> given geometric constraint. It does'nt care for stress. It minimizes force >> only in the given constraint. If you want to minimize the stress also you >> have to do 'vc-relax' calculation, It will give you what you want. >> >> On Mon, Sep 20, 2010 at 11:37 AM, Wang Di wrote: >> >>> Dear all >>> >>> I perform the relax calculate to the crystal structure. After 11 step >>> bfgs, the total force and total scf correction had reach to the criterion, >>> however, the total stress was so big P=-3443.87. I have no idea about deal >>> with the case, could anyone give some advices? Thanks in advance. >>> >>> the input file >>> : >>> calculation = 'scf' , >>> restart_mode = 'from_scratch' , >>> wf_collect = .true. , >>> outdir = '/lustre/AIOFM/gxgu/workLCAF/5/temp/' , >>> wfcdir = '/lustre/AIOFM/gxgu/workLCAF/5/wftemp/' , >>> pseudo_dir = '/home/AIOFM/gxgu/work/NCPP/' , >>> prefix = 'LCAF' , >>>etot_conv_thr = 1.0D-7 , >>>forc_conv_thr = 1.0D-6 , >>>nstep = 100 , >>> tstress = .true. , >>> tprnfor = .true. , >>> dipfield = .true. , >>> / >>> >>>ibrav = 4, >>>celldm(1) = 9.42432151, >>>celldm(3) = 1.94804220, >>> nat = 18, >>> ntyp = 4, >>> ecutwfc = 30 , >>> ecutrho = 120 , >>>nosym = .false. , >>> / >>> >>> electron_maxstep = 100, >>> conv_thr = 1.0D-10 , >>> / >>> ATOMIC_SPECIES >>>Li6.94100 03-Li.LDA.fhi.UPF >>>Al 26.98154 13-Al.LDA.fhi.UPF >>>Ca 40.07800 20-Ca.LDA.fhi.UPF >>> F 18.99840 09-F.LDA.fhi.UPF >>> ATOMIC_POSITIONS crystal >>>Li 0.30.70.25000 >>>Li -0.3 -0.7 -0.25000 >>> F 0.389997 0.045970 0.148326 >>> F -0.045970 0.344027 0.148326 >>> F -0.344027 -0.389997 0.148326 >>> F -0.045970 -0.389997 0.351674 >>> F -0.344027 0.045970 0.351674 >>> F 0.389997 0.344027 0.351674 >>> F -0.389997 -0.045970 -0.148326 >>> F 0.045970 -0.344027 -0.148326 >>> F 0.344027 0.389997 -0.148326 >>> F 0.045970 0.389997 0.648326 >>> F 0.344027 -0.045970 0.648326 >>> F -0.389997 -0.344027 0.648326 >>>Al 0.70.30.25000 >>>Al -0.7 -0.3 -0.25000 >>>Ca 0.00.00.0 >>>Ca 0.00.00.5 >>> K_POINTS automatic >>> 16 16 16 0 0 0 >>> >>> best regart >>> >>> Wang Di >>> >>> -- >>> - >>> *Wang Di** >>> The Crystal Lab,* >>> *AnHui Institute of Optics and Fine Mechanics, *** >>> *Chinese Academy of Sciences,** >>> No350. , Shushanhu Road, He
[Pw_forum] question about the stress in relax process
Dear Wang, The 'relax' process optimizes the structure within given geometric constraint. It does'nt care for stress. It minimizes force only in the given constraint. If you want to minimize the stress also you have to do 'vc-relax' calculation, It will give you what you want. On Mon, Sep 20, 2010 at 11:37 AM, Wang Di wrote: > Dear all > > I perform the relax calculate to the crystal structure. After 11 step > bfgs, the total force and total scf correction had reach to the criterion, > however, the total stress was so big P=-3443.87. I have no idea about deal > with the case, could anyone give some advices? Thanks in advance. > > the input file > : > calculation = 'scf' , > restart_mode = 'from_scratch' , > wf_collect = .true. , > outdir = '/lustre/AIOFM/gxgu/workLCAF/5/temp/' , > wfcdir = '/lustre/AIOFM/gxgu/workLCAF/5/wftemp/' , > pseudo_dir = '/home/AIOFM/gxgu/work/NCPP/' , > prefix = 'LCAF' , >etot_conv_thr = 1.0D-7 , >forc_conv_thr = 1.0D-6 , >nstep = 100 , > tstress = .true. , > tprnfor = .true. , > dipfield = .true. , > / > >ibrav = 4, >celldm(1) = 9.42432151, >celldm(3) = 1.94804220, > nat = 18, > ntyp = 4, > ecutwfc = 30 , > ecutrho = 120 , >nosym = .false. , > / > > electron_maxstep = 100, > conv_thr = 1.0D-10 , > / > ATOMIC_SPECIES >Li6.94100 03-Li.LDA.fhi.UPF >Al 26.98154 13-Al.LDA.fhi.UPF >Ca 40.07800 20-Ca.LDA.fhi.UPF > F 18.99840 09-F.LDA.fhi.UPF > ATOMIC_POSITIONS crystal >Li 0.30.70.25000 >Li -0.3 -0.7 -0.25000 > F 0.389997 0.045970 0.148326 > F -0.045970 0.344027 0.148326 > F -0.344027 -0.389997 0.148326 > F -0.045970 -0.389997 0.351674 > F -0.344027 0.045970 0.351674 > F 0.389997 0.344027 0.351674 > F -0.389997 -0.045970 -0.148326 > F 0.045970 -0.344027 -0.148326 > F 0.344027 0.389997 -0.148326 > F 0.045970 0.389997 0.648326 > F 0.344027 -0.045970 0.648326 > F -0.389997 -0.344027 0.648326 >Al 0.70.30.25000 >Al -0.7 -0.3 -0.25000 >Ca 0.00.00.0 >Ca 0.00.00.5 > K_POINTS automatic > 16 16 16 0 0 0 > > best regart > > Wang Di > > -- > - > *Wang Di** > The Crystal Lab,* > *AnHui Institute of Optics and Fine Mechanics, *** > *Chinese Academy of Sciences,** > No350. , Shushanhu Road, Hefei, 230031, China**, > E-mail: didi5158 @gmail.ocm** ,* > - > > ___________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100920/4257ed30/attachment.htm
[Pw_forum] vc-relax problem when calculate lattice parameters
Dear Wang, To the best of my knowledge there is not any other way..But you can try increasing the smearing parameter.. This will help in convergence but I dont know whether it will solve your problem or not... On Thu, Sep 16, 2010 at 8:12 AM, Wang Di wrote: > Dear MOHNISH > > First, thank you very much for your advices. The initial crystal structure > were referenced to the experimental value. Using the vc-relax calculation is > to find the structure with minimum energy for Raman frequencies calculation. > Beside the change of the initial lattice parameter and atom position, is > there another means to solve the case such as changing some threshold value? > > Best regards > Wang > > > - > *Wang Di** > The Crystal Lab,* > *AnHui Institute of Optics and Fine Mechanics, *** > *Chinese Academy of Sciences,** > No350. , Shushanhu Road, Hefei, 230031, China**, > E-mail: didi5158 @gmail.ocm** ,* > - > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100916/56937243/attachment.htm
[Pw_forum] vc-relax problem when calculate lattice parameters
ynamics = 'bfgs' , > / > ATOMIC_SPECIES >Li6.94100 03-Li.LDA.fhi.UPF >Al 26.98154 13-Al.LDA.fhi.UPF >Ca 40.07800 20-Ca.LDA.fhi.UPF > F 18.99840 09-F.LDA.fhi.UPF > ATOMIC_POSITIONS crystal >Li 0.30.70.25000 >Li 0.70.30.75000 > F 0.3755956710.0084557460.142528376 > F 0.9915442540.3671399250.142528376 > F 0.6328600750.6244043290.142528376 > F 0.9915442540.6244043290.357471624 > F 0.6328600750.0084557460.357471624 > F 0.3755956710.3671399250.357471624 > F 0.6244043290.9915442540.857471624 > F 0.0084557460.6328600750.857471624 > F 0.3671399250.3755956710.857471624 > F 0.0084557460.3755956710.642528376 > F 0.3671399250.9915442540.642528376 > F 0.6244043290.6328600750.642528376 >Al 0.70.30.25000 >Al 0.30.70.75000 >Ca 0.00.00.0 >Ca 0.00.00.5 > K_POINTS automatic > 16 16 16 0 0 0 > > - > > Do you have some advises for the solution the case or elimination the Raman > negative frequencies, any help is greatly appreciated. > > Thanks in advance > Wang Di > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100915/02958e6c/attachment.htm
[Pw_forum] "segmentation fault" in new version of ubuntu
Dear QE users! Previously I was using QE on UBUNTU-9.04, it was working fine with that. But now I am using UBUNTU -10.04 . I started doing vc-relax calculation but it is 'segmentation fault'. Can anybody please help me. Thanks alot in advance -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100914/3cf79e7c/attachment.htm
[Pw_forum] calculation of lattice parameters[ i.e. 'a' and 'c/a' ratio] for HCP metals say Mg.
Dear Biswaranjan! First try to get the experimental (or theoretical value done by somebody else) value of the lattice parameter of your system. If you are using ultrasoft pseudopotential then ecutrho between 8-10 times of ecut will suffice. For fixing 'ecutwfc' you have to do "vc-relax" calculation (see doc-input-pw for more detail) at different 'ecutwfc' then see the convergence with respect to ecut. When the difference between energies for two consecutive ecutwfc is below the minimum limit of accuracy you want then choose lower value(difference of 5 Ry. between two consecutive ecut will suffice). The same procedure you have to repeat for convergence with respect to k-points. You can write a script for doing all the calculations in one shot. On Wed, Sep 8, 2010 at 1:24 PM, wrote: > Dear all, > Can someone tell me the correct methodology to start with > lattice parameters estimation for HCP metals. I shall tell > what I did for my earlier simulations involving Magnesium. > > First, I fixed the ecut value and then used the same ecut value to fix the > ecutrho value. Then using the fixed ecut and ecutrho, I varied the > k-points to obtain the K-points. in my case I obtained [12 12 9]. Then > for lattice parameter calculation, [ having fixed ecut, ecutrho, k-points > of course] I fixed 'c/a' ratio initially[ c/a= sqrt(8/3)] and varied the > 'a' across the ideal value of 'a'[ a=3.21 Angstroms =6.06602 at. units] > and obtained the value for 'a' corresponding for the minimum energy > configuration. Then using the obtained 'a' in the previous step, I varied > the 'c/a' ratio across the ideal value to obtain c/a=1.58, corresponding > to the minimum energy configuration. However this estimate involves > significant error since the ideal value for c/a( for Mg=sqrt(8/3)=1.624). > Then I used the value for 'c/a' in the previous step[ i.e 1.58] and varied > 'a' to find the value of 'a'. > > Finally, I obtained a=6.1 a.u=3.23 angstroms, c/a=1.58. The > psuedopotential I used for Mg is Mg.pw91-np-van.UPF . > > Thanks all, > > regards, > Biswaranjan Dash > Research Scholar, > Deformation Mechanisms Modeling Group, > C/0- Asst Prof S.Karthikeyan > Indian Institute of Science,Bangalore > India > > > > > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100908/f0d8475b/attachment.htm
[Pw_forum] Mg pseudopotential without semi-core state
Dear QE users, Does anybody have Mg Pseudopotential without semi-core state? If somebody has then please give me. Thanks a lot in advance -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100906/ce288755/attachment.htm
[Pw_forum] PBE functional for Mg
Dear QE users, Does anybody has PBE exchange functional for Mg? Please give me if you have it. Thanks in advance. -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100905/6c2765d1/attachment.htm
[Pw_forum] Total energy value in QE, strange value.
Dear Joaquin !
First off all I will suggest you to decrease the
charge density cutoff. Normally for Ultrasoft Pseudopotential charge density
cutoff equal to 8-10 times of energy cutoff will suffice. Now check the
stress in and forces in you system. And of course before submitting the
calculation I hope you have visualized the structure. The better thing will
be to do relax or vc-relax calculation to get well converged results instead
of doing scf calculation only, because as you know scf is just one
electronic cycle calculation, it does not care for stress or forces.
On Mon, Aug 23, 2010 at 9:10 PM, joaquin peralta wrote:
> Dear Forum,
>
> I calculated the energy of a aluminium surface, but the value that i
> obtained using this is 'extremely high' energy, i obtain the same using
> 4.2.1 and 4.1 version of QE.
>
> My input file is :
> =
>
>calculation = 'scf'
>prefix= 'al-111-43.5'
>tprnfor = .true.
>wfcdir= './restore/'
>pseudo_dir= '/home/jperalta/pseudo/'
>outdir= './restore'
> /
>
>ibrav = 0
>celldm(1) = 1.0
>nat = 21
>ntyp = 1
>ecutwfc = 30
>ecutrho = 500
>degauss = 0.03
>occupations = 'smearing'
>smearing = 'mv'
>nspin = 2
>starting_magnetization= 0.1
>nbnd = 300
> /
>
>electron_maxstep = 300
>mixing_mode = 'local-TF'
>mixing_beta = 0.3
>mixing_ndim = 10
> /
>
> ! ion_dynamics = 'bfgs'
> /
>
> ! cell_dynamics = 'bfgs'
> ! press = 0.0D0
> ! press_conv_thr= 0.1D0
> /
> ATOMIC_SPECIES
> Al 26.982 Al.pbe-sp-van.UPF
> ATOMIC_POSITIONS (angstrom)
> Al 4.295143 -2.479802 43.5
> Al 5.726858 -3.306403 41.689899
> Al 1.431714 -0.826601 41.689899
> Al 2.863429 -3.306403 41.689899
> Al 4.295143 -0.826601 41.689899
> Al 2.863429 -1.653201 39.351919
> Al 7.158572 -4.133004 39.351919
> Al 5.726858 -1.653201 39.351919
> Al 4.295143 -4.133004 39.351919
> Al 8.590287 -4.959604 37.013940
> Al 4.295143 -2.479802 37.013940
> Al 5.726858 -4.959604 37.013940
> Al 7.158572 -2.479802 37.013940
> Al 5.726858 -3.306403 34.675960
> Al 1.431714 -0.826601 34.675960
> Al 2.863429 -3.306403 34.675960
> Al 4.295143 -0.826601 34.675960
> Al 2.863429 -1.653201 32.337980
> Al 7.158572 -4.133004 32.337980
> Al 5.726858 -1.653201 32.337980
> Al 4.295143 -4.133004 32.337980
> K_POINTS (automatic)
> 6 6 6 0 0 0
> CELL_PARAMETERS {cubic}
> 10.8221920.000.00
> 5.411096 -9.372293 0.00
> 0.00 0.00139.892407
>
>
> i change some electrons parameters in order to improve the convergence. I
> don't know if the enery problem is caused for some special parameter or some
> like that. but in a paper of Sanchez et al (Molecular Physics, 2004, vol
> 102, 1045-1055), the energies are aroung 2 to 20 eV.
>
> And the ouput in my case say :
>
> the Fermi energy is-1.8658 ev
>
> !total energy = -3357.65873780 Ry ---> 2K
> eV by atom.
> Harris-Foulkes estimate = -3357.65873669 Ry
> estimated scf accuracy< 0.0057 Ry
>
> The total energy is the sum of the following terms:
>
> one-electron contribution = -110140.98098627 Ry
> hartree contribution = 54852.05508820 Ry
> xc contribution =-409.97773145 Ry
> ewald contribution= 52341.24991020 Ry
> smearing contrib. (-TS) = -0.00501849 Ry
>
> total magnetization = 0.00 Bohr mag/cell
> absolute magnetization= 0.00 Bohr mag/cell
>
> convergence has been achieved in 34 iterations
>
>
> Any help i really appreciate it.
>
> Best Regards
> Joaquin Peralta
> Iowa State University.
>
> --
>
> Group of NanoMaterials
>
> http://www.gnm.cl
>
> Joaqu?n Andr?s Peralta Camposano
> ------------
> http://www.lpmd.cl/jperalta
>
> In a world without frontiers,
> who needs Gates and Win.
[Pw_forum] calculation for antiferromagnetic MnO
Thank you so much Prof. Matteo, in fact I also wanted to do that myself but I was not able to get the starting point but know I believe I can do that... On Fri, Jul 30, 2010 at 1:59 PM, Matteo Cococcioni wrote: > Dear Mohnish > > I would recommend you to figure this out yourself first. > Then, if you want to verify your results you can go on > quantum-espresso.org and look for the tutorials > for the school held in Santa Barbara in 2009. you will find an example > about NiO (and maybe FeO, I don't remember) > that are materials with the same structure and AF order of MnO. > > Matteo > > > On Fri, Jul 30, 2010 at 1:59 AM, mohnish pandey gmail.com>wrote: > >> Dear users, >> I want to do calculation for MnO antiferromagnetic >> system. I want to know how to start the calculation for this >> antiferromagnetic system, i.e. should the magnetization be conserved to be >> in antiferromagnetic state? And how to build the cell for this rocksalt >> structure so that structure is antiferromagnetic. >> >> -- >> Regards, >> MOHNISH, >> - >> Mohnish Pandey >> Y6927262,5th Year dual degree student, >> Department of Chemical Engineering, >> IIT KANPUR, UP, INDIA >> +919235721300 >> - >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> >> > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100730/3baa2bb4/attachment.htm
[Pw_forum] calculation for antiferromagnetic MnO
Dear users, I want to do calculation for MnO antiferromagnetic system. I want to know how to start the calculation for this antiferromagnetic system, i.e. should the magnetization be conserved to be in antiferromagnetic state? And how to build the cell for this rocksalt structure so that structure is antiferromagnetic. -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100730/a30b49c9/attachment.htm
[Pw_forum] Slab calculation in pwscf
Dear Karthik, To my knowledge most of the DFT codes use *periodic boundary condition*, the same case is with PWSCF. For supercell calculation you have to take the size of the supercell large enough so that there is no interaction between slabs. And will be glad if you mention your affiliation so that we can know whom are interacting with. On Sat, Jul 24, 2010 at 12:50 AM, Guda Karthik wrote: > > > Hi all, >> > > >I am trying to do some slab calculations using pw.x . I made a supercell > in the direction normal to the surface I am interested in, and made the > lattice vector much larger than the actual supercell length to avoid > interaction between two periodic images. Is this the way to do in pwscf? or > is there an option where one could do a non periodic calculation by > specifying the dimension and setting the k-points in the direction normal to > the surface to zero (this information I could not find in the manual)? > Please reply. > > regards, > Karthik > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100724/5c2ac3aa/attachment.htm
[Pw_forum] Is there a way to fix the c of supercell and vary only a and b
Dear Prof. Paolo, Sorry to bug you again but I am using 'cell_dofree" as 'xy' in the supercell calculation but even after using this flag the 'c' is varying at every step. I am attaching my input and output file(output file is not complete but it contains 3 iterations). On Sat, Jun 26, 2010 at 9:21 PM, Paolo Giannozzi wrote: > > On Jun 26, 2010, at 7:10 , mohnish pandey wrote: > > > many times its given error " Enough space not allocated to fft grid" > > this means that you are starting from an initial cell that is too > different > from the final one. > > > I was thinking of the way to vary a and b and fix the c. > > look at "cell_dofree" variables and how they are used. > > P. > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100627/2ff559e4/attachment-0001.htm -- next part -- A non-text attachment was scrubbed... Name: mnse.scf.in Type: application/octet-stream Size: 864 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100627/2ff559e4/attachment-0002.obj -- next part -- A non-text attachment was scrubbed... Name: mnse.scf.out Type: application/octet-stream Size: 93714 bytes Desc: not available Url : http://www.democritos.it/pipermail/pw_forum/attachments/20100627/2ff559e4/attachment-0003.obj
[Pw_forum] Is there a way to fix the c of supercell and vary only a and b
Dear QE users, I am doing supercell calculation for some systems. But I want to change the a and b parameter for the supercell but want to fix the c for that because the in plane lattice parameter(xy plane) should change on relaxation process. Right now I am using 'vc-relax' calculation for the same. But many times its given error " Enough space not allocated to fft grid". I am increasing the cell_factor to 1.8 which I think is very large value and this also makes the relaxation computationally expensive. Can anybody suggest a way to resolve it, I was thinking of the way to vary a and b and fix the c. Thanks a lot in advance. -- Regards, MOHNISH, ----- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100626/581e8325/attachment.htm
[Pw_forum] how to do fixed volume optimization
Dear Yin 'vc-relax' calculation optimizes the structures by the lattice parameters also but if you set the calculation 'relax' then it optimizes the geometry within the given fixed volume constraints. This calculation moves the atom keeping the volume constant within the given symmetry constraint. hope this helps :) On Sun, May 30, 2010 at 6:12 PM, Kun Yin wrote: > Dear All, > > Does anyone have the experience to do volume fixed optimization with QE, > which means the structure is optimized allowing all cell parameters and > atomic positions to vary while keeping the volume fixed? > > Kun Yin > Najing University, China > 2010-05-30 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, --------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100530/7e7a28aa/attachment.htm
[Pw_forum] dipole moment of thin polar films
Thanks a lot Dr. Paolo and dear Linh. On Fri, May 21, 2010 at 10:11 PM, Paolo Giannozzi wrote: > mohnish pandey wrote: > > > I want to calculate the dipole moment of some thin polar films. > > for a thin polar film, you can try to make a planar average > of the charge density (code average.x, doc in the header of > PP/average.f90) and then calculate the dipole by integrating > along z. > > P > -- > Paolo Giannozzi, Democritos and University of Udine, Italy > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, --------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/bf3d441a/attachment.htm
[Pw_forum] dipole moment of thin polar films
Dear users, I want to calculate the dipole moment of some thin polar films. Does QE has any module for doing the same? And if it does have then that dipole moment is per unit volume (volume of the supercell ) or it is total dipole moment? I am really stuck in this. Thanks a lot in advance, -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/f08e46a3/attachment-0001.htm
[Pw_forum] dipole moment of thin film
Dear users, I want to calculate the dipole moment of some thin polar films. Does QE has any module for doing the same? And if it does have then that dipole moment is per unit volume (volume of the supercell ) or it is total dipole moment? I am really stuck in this. Thanks a lot in advance, -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100521/cc13f6f2/attachment.htm
[Pw_forum] Lowdin and Bader analysis
Dear QE users, I want to do Bader and Lowdin analysis for thin films of some materials. I was searching for some module in QE for the same but I did'nt get it. Can somebody please tell me how can I do that analysis using QE. Thanks a lot in advance, -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100511/f2249a93/attachment.htm
[Pw_forum] Bader and LOwdin analysis
Dear QE users, I want to do Bader and Lowdin analysis for thin films of some materials. I was searching for some module in QE for the same but I did'nt get it. Can somebody please tell me how can I do that analysis using QE. Thanks a lot in advance, -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100511/85f9ba0c/attachment.htm
[Pw_forum] Wyckoff sites
Dear Bahareh ! You must use Xcrysden to visualize the structure first before submitting job for running. It will help you to make correct structure. Its available free at Xcrysden website. And please provide your affiliation next time. On Thu, Apr 29, 2010 at 6:55 AM, bahareh rahmani wrote: > Dear All > > I have converted Wyckoff positions to x,y,x coordinates for a Clathrate > type VIII . As an example I converted 2a site to 0,0,0 and 1/2,1/2,1/2 > based on literature but quantum-espresso produces an error message and says > the above mentioned atoms have overlap. This happens for many other sites > too. Deos anyone any idea how to solve this problem? > > Best regards,Bahareh Rahmani > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, --------- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100429/5b5c43bf/attachment-0001.htm
[Pw_forum] recovering interrupted jobs
For pw.x calculation you can use "restart_mode" = "restart" flag in to recover your jobs. On Sat, Apr 24, 2010 at 9:26 AM, Payam Norouzzadeh < payam.norouzzadeh at gmail.com> wrote: > Hello All > I have time limitation in running jobs on cluster (48 hours at most) . > After that time the job is not processed more and I need to learn how to > recover interrupted jobs. > I created prefix.EXIT in working directory to recover job for ph.x later > but it does not reply at all. > The version of quantum-espresso I am using is 4-0-5. > Could anyone do me a favor and teach me how to recover my interrupted jobs? > Breg, Payam Norouzzadeh > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Regards, MOHNISH, ----- Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100424/893de6e5/attachment.htm
[Pw_forum] phonon calculation for optimized geometry -one subtle confusion
Yea dear Linh, I have used the converged cell parameter from vc-relax calculation for scf run, Thnaks, mohnish On Sun, Apr 18, 2010 at 8:33 PM, Ngoc Linh Nguyen wrote: > > > Dear Hanyu ! > > Thanks for your reply. As you now the default value > > for > > the pressure in PWSCF is 0.5. > > This value should be 0.0 as the default value (see in input PW website) > > > I am using that value as convergence > > threshold > > but when I am doing scf calculation with the geometrical parameters value > > obtained from the vc-relax calculation the pressure value is different > > from > > vc-relax final run. And as you know pressure will effect the phonon > > dispresion relation..Can you please give me any suggestion, > > Before doing scf calculations, have you changed the cell-parameters in scf > input file as same as the converged cell-parameters from vc-relax? > > Best regards, > > Linh > > > > > > > Thanks alot, > > MOHNISH > > > > On Sun, Apr 18, 2010 at 3:00 PM, Hanyu wrote: > > > >> dear mohnish : > >> I think you should check it carefully again. I don't think it should > >> be happen. In fact, the stress of scf and vc-relax should be the same. > >> but if the stress is not the hydrostatic pressure, the result is not > >> be believed. you have to relax the structure until the stress of the > >> phase is what you want. > >> > >> best regards. > >> > >> Hanyu > >> > >> On Sun, Apr 18, 2010 at 11:16 AM, mohnish pandey > >> > >> wrote: > >> > Dear users, > >> > I want to do phonon calculation for some structures, > >> but > >> > after geometry optimization when I am using optimized geometry > >> parameters > >> > for scf calculation there is difference in stress of scf calculation > >> and > >> > vc-relax calculation which is changing phonon dispersion. Can anybody > >> please > >> > tell me if there is any option to use the data of relax or vc-relax > >> > calculation for phonon dispersion.. Or can I doing phonon calculation > >> along > >> > with relax or vc-relax calculation.? > >> > Thanks a lot in advance, > >> > > >> > -- > >> > Regards, > >> > MOHNISH, > >> > - > >> > Mohnish Pandey > >> > Y6927262,4th Year dual degree student, > >> > Department of Chemical Engineering, > >> > IIT KANPUR > >> > 09235721300 > >> > - > >> > > >> > ___ > >> > Pw_forum mailing list > >> > Pw_forum at pwscf.org > >> > http://www.democritos.it/mailman/listinfo/pw_forum > >> > > >> > > >> > >> > >> > >> -- > >> -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- > >> Hanyu Liu(?), > >> MS. > >> State key Laboratory of Superhard Materials, Jilin University, China > >> Email: liuhanyu08 at mails.jlu.edu.cnouuing at gmail.com > >> ___ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org > >> http://www.democritos.it/mailman/listinfo/pw_forum > >> > > > > > > > > -- > > Regards, > > MOHNISH, > > - > > Mohnish Pandey > > Y6927262,4th Year dual degree student, > > Department of Chemical Engineering, > > IIT KANPUR > > 09235721300 > > - > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > - > Nguyen Ngoc Linh, PhD Student > c/o: SISSA & CNR-INFM Democritos, >via Beirut 2-4, 34014 Trieste (Italy) > email: nnlinh at sissa.it > phone: +39 04 03787 319 > skype: ngoclinh84phys > - > "The physics is theoretical but the fun is real" > > > > SISSA Webmail https://webmail.sissa.it/ > Powered by SquirrelMail http://www.squirrelmail.org/ > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100419/69117321/attachment.htm
[Pw_forum] phonon calculation for optimized geometry -one subtle confusion
Dear Hanyu ! Thanks for your reply. As you now the default value for the pressure in PWSCF is 0.5. I am using that value as convergence threshold but when I am doing scf calculation with the geometrical parameters value obtained from the vc-relax calculation the pressure value is different from vc-relax final run. And as you know pressure will effect the phonon dispresion relation..Can you please give me any suggestion, Thanks alot, MOHNISH On Sun, Apr 18, 2010 at 3:00 PM, Hanyu wrote: > dear mohnish : > I think you should check it carefully again. I don't think it should > be happen. In fact, the stress of scf and vc-relax should be the same. > but if the stress is not the hydrostatic pressure, the result is not > be believed. you have to relax the structure until the stress of the > phase is what you want. > > best regards. > > Hanyu > > On Sun, Apr 18, 2010 at 11:16 AM, mohnish pandey > wrote: > > Dear users, > > I want to do phonon calculation for some structures, > but > > after geometry optimization when I am using optimized geometry parameters > > for scf calculation there is difference in stress of scf calculation and > > vc-relax calculation which is changing phonon dispersion. Can anybody > please > > tell me if there is any option to use the data of relax or vc-relax > > calculation for phonon dispersion.. Or can I doing phonon calculation > along > > with relax or vc-relax calculation.? > > Thanks a lot in advance, > > > > -- > > Regards, > > MOHNISH, > > - > > Mohnish Pandey > > Y6927262,4th Year dual degree student, > > Department of Chemical Engineering, > > IIT KANPUR > > 09235721300 > > - > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > > -- > -=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=**=-=**=-=**=-=*=-=*=-=*=-=*=-=*=- > Hanyu Liu(???), > MS. > State key Laboratory of Superhard Materials, Jilin University, China > Email: liuhanyu08 at mails.jlu.edu.cnouuing at gmail.com > ___________ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100418/33c1d112/attachment.htm
[Pw_forum] phonon calculation for optimized geometry
Dear users, I want to do phonon calculation for some structures, but after geometry optimization when I am using optimized geometry parameters for scf calculation there is difference in stress of scf calculation and vc-relax calculation which is changing phonon dispersion. Can anybody please tell me if there is any option to use the data of relax or vc-relax calculation for phonon dispersion.. Or can I doing phonon calculation along with relax or vc-relax calculation.? Thanks a lot in advance, -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100418/d814100a/attachment.htm
[Pw_forum] phonon calculation of optimized structure
Dear users, I want to do phonon calculation for some structures, but after geometry optimization when I am using optimized geometry parameters for scf calculation there is difference in stress of scf calculation and vc-relax calculation which is changing phonon dispersion. Can anybody please tell me if there is any option to use the data of relax or vc-relax calculation for phonon dispersion.. Or can I doing phonon calculation along with relax or vc-relax calculation.? Thanks a lot in advance, -- Regards, MOHNISH, - Mohnish Pandey Y6927262,4th Year dual degree student, Department of Chemical Engineering, IIT KANPUR 09235721300 - -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100417/98f93058/attachment.htm
