[Pw_forum] Conversion
taking a basic undergrad textbook and studying till ca pag 10-12? > > 2014-09-13 13:20 GMT-03:00 zahra vatankhah : > >> Dear All >> How can i convert angstrom to crystal coordinate? >> >> Thanks >> >> ___
[Pw_forum] tpss: too many bands are not converged
Dear all, I've been trying to calculate a polymer using tpss. I already fully optimised it with different functional (pbesol, pw91, hse) and pseudopotential (nc, paw). For some reason (apologise my ignorance if it should be well known) when I try to calculate using tpss nc the system simply does not converge crashing with this error: Error in routine c_bands (1): too many bands are not converged After some reaserch in old pw-forum mails, I tried decreasing mixing_beta=0.2, increasing mixing_ndim=12, as well as mixing mode TF and local-TF. everythings failed. Does anyone have any tips or idea of why the system can't converge? Thanks a lot, Davide
[Pw_forum] how to expolit the parallelism
Dear all, I'm testing how to have the best parallelism of pw.x on archer (the new uk supercomp). I'm a bit confused on 1) task parallelisation: how choose the ntg. If I understood correctly it should be to the 3 dimension of the smooth FFT grid. Looking on the output I can only have the dense one: Dense grid: 1142409 G-vectors FFT dimensions: ( 108, 108, 192) how can I know the smooth dimensions? 2) band parallelisation: is it worthy? I think here the number I've to look is, for instance, 56 Kohn-Sham Wavefunctions 1.03 Mb ( 1201, 56) am I right? if yes, what could be a good splitting vs npool? probably more important is it alternative and better to ntg or it can be combine with it? Happy Easter to everyone Davide
[Pw_forum] postprocess pp require wfc_collect although that was set
hello, I've got a very weird problem. I optimised some structure and I would like to plot now the frontier orbitals. When I try to run pp it complains cause: %% Error in routine postproc (1): pw.x run with a different number of procs/pools. Use wf_collect=.true. %% but [davide at wmd-master lda]$ head opta.in &control calculation='vc-relax', title='up-down', disk_io='low', wf_collect=.true. prefix='up-down' etot_conv_thr=5.0d-4, forc_conv_thr=5.0d-3, / so I am a bit lost now :-S any suggestion? Thanks you, Davide
[Pw_forum] plotting of the wfn with phases
Dear all, I would like to compare the crystalline orbitals of periodic calc made with pw.x with molecular made with gamess on a single molecule. using pw.x is it possible have the full information of the wfn (so including the phases) at the gamma point? Cheers, Davide
[Pw_forum] hybrid band structure calculation
Dear Paolo, thanks a lot for answering. The last question. my system is a linear 1D polymer. what about make a scf calc using a uniform grid like kpoint(crystal) 1 1 8 which produces this grid k(1) = ( 0.000 0.000 0.000), wk = 0.250 k(2) = ( 0.000 0.000 0.2238490), wk = 0.500 k(3) = ( 0.000 0.000 0.4476981), wk = 0.500 k(4) = ( 0.000 0.000 0.6715471), wk = 0.500 k(5) = ( 0.000 0.000 -0.8953961), wk = 0.250 From my point of view it should be fine but my background is single molecule and LCAO approximation so I'm not 100% confident on the weight of the different k point. how can that affect th BS? Thanks a lot, Davide > > On Mon, 2013-06-17 at 16:16 +0100, Davide Tiana wrote: > >> thanks for answering. So, if I correctly understood >> I can't run a hybrid band structure from Gamma to X? > > I don't think you can, unless you happen to have a uniform > grid along Gamma-X > >> is there a particular reason for this limitation or is just cause >> hybrid functional has just been implemented inside of QE? > > the latter you say, I think > > P. > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] hybrid band structure calculation
Dear Paolo, thanks for answering. So, if I correctly understood I can't run a hybrid band structure from Gamma to X? is there a particular reason for this limitation or is just cause hybrid functional has just been implemented inside of QE? Regards, Davide > > > -- > > Message: 4 > Date: Mon, 17 Jun 2013 11:08:56 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] hybrid band structure calculation > To: PWSCF Forum > Message-ID: <1371460136.20654.29.camel at fe12lx.fisica.uniud.it> > Content-Type: text/plain; charset="UTF-8" > > On Sun, 2013-06-16 at 13:21 +0100, Davide Tiana wrote: > >> I've tried to calc a band structure using hybrid as suggested >> [...] the problem is that pw complain and stop to run since: > >> Error in routine exx_grid_init (2): >>k + q is not an S*k > > I think that the hybrid code works only with a uniform grid > of k-points, so all you can do is to calclaute a band > structure for those points only > > P. > -- > Paolo Giannozzi, Dept. Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > >
[Pw_forum] hybrid band structure calculation
Hello,
I've tried to calc a band structure using hybrid as suggested
"
Message: 5
Date: Sat, 8 Jun 2013 17:09:31 +0800
From: xirainbow
Subject: Re: [Pw_forum] band structure, can't I use hybrid functional?
To: PWSCF Forum
Message-ID:
Content-Type: text/plain; charset=ISO-8859-1
Dear Davide:
I have a tip to do band calculation for band with HSE
hybrid functional.
1:do scf calculation on a regular k-mesh (for example
4*4*4) and save charge density and wavefunction.
2: write the k mesh by hand: Add additional k points to
the regular k-mesh and set the weight of these k point to zero.
3: do scf calculation again.
"
so after a 1st scf calc I modyfied the input adding:
startingpot='file',
startingwfc='file',
and two kpoints with weight 0:
K_POINTS {crystal}
10
0.250 0.2361501 0.0559623 0.250
0.250 0.2361501 0.1678868 0.250
0.250 0.2361501 0.2798113 0.250
0.250 0.2361501 0.3917358 0.250
0.250 0.2361501 0.5036603 0.250
0.250 0.2361501 0.6155848 0.250
0.250 0.2361501 0.7275093 0.250
0.250 0.2361501 0.8394339 0.250
0. 0. 0. 0.
0. 0. .5 0.
the problem is that pw complain and stop to run since:
%%
Error in routine exx_grid_init (2):
k + q is not an S*k
%%
what have I exactly to do?
Thanks a lot,
Davide
[Pw_forum] band structure, can't I use hybrid functional?
Dear Hui Wang thanks for answering. I know how to it with vasp, so in QE I had to do exactly the same procedure as in vasp? Cheers, Davide > > -- > > Message: 5 > Date: Sat, 8 Jun 2013 17:09:31 +0800 > From: xirainbow > Subject: Re: [Pw_forum] band structure, can't I use hybrid functional? > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Dear Davide: > I have a tip to do band calculation for band with HSE > hybrid functional. > 1:do scf calculation on a regular k-mesh (for example > 4*4*4) and save charge density and wavefunction. > 2: write the k mesh by hand: Add additional k points to > the regular k-mesh and set the weight of these k point to zero. > 3: do scf calculation again. > > You can find more information at here: > http://blog.sina.com.cn/s/blog_5f15ead20100wpqr.html > It is HSE band calculation procedure using VASP. > > > > -- > > Hui Wang > School of physics, Fudan University, Shanghai, China > >
[Pw_forum] band structure, can't I use hybrid functional?
Hello, I need to perform an hybrid calculation on a 1D polymer. I managed to make an optimisation but when I run the bands calc, pw complains saying it can't perform a non-scf calc using hybrid. is there any way to avoid this? I mean, is there a chance to have an hybrid band strucutre? Cheers, Davide
[Pw_forum] scf_must_converge
why are you using such tight threshold? setting such small value and don't care about the convergence (if you can obtain one) makes no sense. Try with a loose conv_thr such as 1D-4 > &electrons > electron_maxstep=100, > conv_thr=7.35D-8, > scf_must_converge=.false. > /
[Pw_forum] Frozen atomic coordinates on phonon calculations:references
google scholar http://scholar.google.co.uk (free) scifinder http://www.cas.org/products/scifinder web of science http://thomsonreuters.com/products_services/science/science_products/a-z/web_of_science/ > > Dear all, > > Could anyone indicate me a published paper using/testing frozen atomic > coordinates on phonon calculations (nat_todo option in QE)? > > Thanks in advance. > > -- > Ant?nio M. Da Silva Jr. (PhD student) > Nucleus of studies in computational chemistry (NEQC) > Department of Chemistry > Federal *University of Juiz de Fora* (UFJF) - Brazil > http://lattes.cnpq.br/0895213089855328
[Pw_forum] doubts (problems?) in DOS calculation
does scf is not included in optimisation? > > -- > > Message: 2 > Date: Wed, 19 Sep 2012 20:57:55 +0800 > From: Yue-Wen Fang > Subject: Re: [Pw_forum] doubts (problems?) in DOS calculation > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > When calculate DOS, you should make a scf calculation first, then nscf, > last is bands and dos. > > 2012/9/19 Davide Tiana > >> Dear all, >> I am trying to calculate DOS and projected DOS for a semiconducting 1D >> hybrid (i.e. metal-organic) polymer. The band gap I found is about >> 0.4. However when I try to calculate DOS I don't find 0 contribution >> at the Fermi level nor a band gap around it. I am in doubt and I think >> something wrong happened (namely I made some errors). How can I check >> that everything is fine and-or explain this behaviour? >> >> By the way here what I've done: >> >> pw optimisation >> pw band calculation >> pw nscf calculation >> dos dos calculation (at first instance I did't make but finding >> something "weird" in the total projwfc I run it to check) >> projwfc projected dos calc >> >> thanks a lot >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > > Yue-Wen Fang > -- next part -- > An HTML attachment was scrubbed... > URL:
[Pw_forum] doubts (problems?) in DOS calculation
Dear all, I am trying to calculate DOS and projected DOS for a semiconducting 1D hybrid (i.e. metal-organic) polymer. The band gap I found is about 0.4. However when I try to calculate DOS I don't find 0 contribution at the Fermi level nor a band gap around it. I am in doubt and I think something wrong happened (namely I made some errors). How can I check that everything is fine and-or explain this behaviour? By the way here what I've done: pw optimisation pw band calculation pw nscf calculation dos dos calculation (at first instance I did't make but finding something "weird" in the total projwfc I run it to check) projwfc projected dos calc thanks a lot
[Pw_forum] band vs plotband output.
Dear all, I found some cases where after reorganise the bands output with plot bands, the homo - lumo are swapped. Why does his happen? More important to calculate the Band Gap what values should I used? here an example: electron = 94, homo band numb 47. band.out k = 0. 0. 0. band energies (ev): -55.9850 -55.9850 -27.9953 -27.9953 -27.9793 -27.9793 -27.9357 -27.9357 -20.6223 -20.5647 -19.6426 -17.8930 -17.1262 -15.8489 -15.6076 -14.4238 -13.4669 -12.7303 -11.1590 -10.9066 -10.8380 -10.8160 -10.7731 -9.7812 -9.6601 -8.6932 -7.8692 -7.7732 -7.7280 -7.1303 -6.6701 -6.6130 -6.1019 -6.0213 -5.5373 -5.2958 -5.0030 -4.4158 -4.2662 -4.0390 -3.8182 -3.7469 -3.6889 -3.6568 -2.7622 -2.1193 -1.5121 -1.4329 -1.0247 -0.6744 0.1096 0.2954 0.4064 0.7536 0.8100 1.0277 ... k = 0. 0. 0.8327 band energies (ev): -55.9850 -55.9850 -27.9953 -27.9953 -27.9793 -27.9793 -27.9357 -27.9357 -20.6203 -20.5647 -19.6429 -17.9201 -17.1113 -15.9214 -15.4652 -14.2886 -13.7199 -12.6999 -11.5050 -10.9082 -10.8380 -10.8359 -10.6059 -9.7363 -9.1694 -8.6237 -8.2259 -7.6547 -7.4356 -7.3467 -6.8330 -6.5799 -6.3278 -5.8338 -5.4976 -5.2352 -4.9676 -4.7183 -4.5833 -4.1295 -4.0561 -3.6146 -3.2923 -2.9937 -2.9251 -2.6585 -1.5326 -1.4329 -0.9754 -0.6156 0.3641 0.4861 0.5199 0.5499 0.5910 1.0285 bands.dat 0.00 0.00 0.00 -55.985 -55.985 -27.995 -27.995 -27.979 -27.979 -27.936 -27.936 -20.622 -20.565 -19.643 -17.893 -17.126 -15.849 -15.608 -14.424 -13.467 -12.730 -11.159 -10.907 -10.838 -10.816 -10.773 -9.781 -9.660 -8.693 -7.869 -7.773 -7.728 -7.130 -6.670 -6.613 -6.102 -6.021 -5.537 -5.296 -5.003 -4.416 -4.266 -4.039 -3.818 -3.747 -3.689 -3.657 -2.762 -2.119 -1.512 -1.433 -1.025 -0.674 0.110 0.295 0.406 0.754 0.810 1.028 ..0.00 0.00 0.832734 -55.985 -55.985 -27.995 -27.995 -27.979 -27.979 -27.936 -27.936 -20.620 -20.565 -19.643 -17.920 -17.111 -15.921 -15.465 -14.289 -13.720 -12.700 -11.505 -10.908 -10.838 -10.836 -10.606 -9.736 -9.169 -8.624 -7.436 -8.226 -7.655 -7.347 -6.328 -6.833 -6.580 -5.834 -5.498 -5.235 -4.968 -4.718 -4.583 -4.056 -3.292 -4.129 -2.925 -3.615 -2.994 -2.658 -1.433 -1.533 -0.975 -0.616 0.550 0.364 0.520 0.486 0.591 1.028 band.out HOMO -1.5121 LUMO -1.4329 HOMO -1.5326 LUMO -1.4329 bands.dat HOMO -1.512 LUMO -1.433 HOMO -1.433 LUMO -1.533 Thank you for helping me
[Pw_forum] k points weights
As remembered in many QE tutorials, weights are meaningless in NSCF calculations such as band ones. by the way when required (for instance during optimisation) weights are simply related to the multiplicity of the points and can be obtained looking International Cryst tables or Bilbao Cryst server. Regards Davide > > Message: 1 > Date: Thu, 26 Jul 2012 19:10:07 +0800 (SGT) > From: Sohail Ahmad > Subject: [Pw_forum] k points weights > To: Plane Wave > Message-ID: > <1343301007.14468.YahooMailClassic at web190902.mail.sg3.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Pw users > > In example 01 of version QE-4.2.3 > In band.in file k points are given as > ?K_POINTS > ?28 > ?? 0.0 0.0 0.0 1.0 > ?? 0.0 0.0 0.1 1.0 > ?? 0.0 0.0 0.2 1.0 > > while > in lab exercise2 > day1 (given by Prof Shobhana Narasimhan on july 20, 2009) tutorial held > in Santa Barbara > http://media.quantum-espresso.org/santa_barbara_2009_07/ > 36 > ?? 0.5 0.5 0.5? 1 > ?? 0.4 0.4 0.4? 2 > ?? 0.3 0.3 0.3? 3 > ?? 0.2 0.2 0.2? 4 > ?? 0.1 0.1 0.1? 5 > > Now my question is whether i should write weights or the simply serial no. > in band.in file > i believe it should be its weitghs then the question is how to claculate > > Sohail Ahmad > King Khalid University > Saudi Arbia
[Pw_forum] I can't find the error (SOLVED!)
> so maybe there is some horrible non-printable characters in your input... > > why don't you create a new input file taking a working one and typing in > the data using a simple editor and try again ? > > stefano > > > cat -vte > > works well for finding bad characters. > > Eric > Here we are. That was the problem. cat -vte opt.in cosBC=M-bM-^HM-^R0.073568915,$ cosAC=M-bM-^HM-^R0.163584241,$ cosAB=M-bM-^HM-^R0.046461386,$ Originated copy and paste from calculator. Thanks all of you Davide
[Pw_forum] I can't find the error
Dear again, thanks for helping. @Duy > It is usually easier for pwscfers to help you if you post error messages as > well. sorry about that, I did not post it since I guess the error is a wrong digit somewhere. However: %% from read_namelists : error # 5010 reading namelist system %% > > BTW, what are the question marks (?) in cosAB... standing for? well in the original input they are -. Something horrible happened open the file with abiword (to copy and paste here). so nothing to worry about that. @Paolo > > > On Jul 5, 2012, at 21:17 , Davide Tiana wrote: > >> I can't figure out why this input is wrong > > I can't figure out why you do not specify "what" is wrong > > P. > --- Sorry if I was too cryptic. That is the problem. From my side the input should be fine but it push out the error I post above in the message. i.e. there is something wrong inside but I am not able to find where it is wrong.
[Pw_forum] I can't find the error :-(
Dear all,
sorry if I bother you with a silly pw input. I can't figure out why
this input is wrong. Comparing with similar ones everything seems to
be fine.
(I don't know if it is another clue but it can be open with no problem
with PWgui).
Thanks in advanced for any helps you can give me.
where is the error in this input file?
&control
calculation='relax',
title='zigzag',
wf_collect=.true.,
outdir='./',
prefix='zigzag',
etot_conv_thr=5.0d-4,
forc_conv_thr=1.0d-3,
/
&system
ibrav=14,
A=7.0008,
B=9.7164,
C=16.693,
cosBC=?0.073568915,
cosAC=?0.163584241,
cosAB=?0.046461386,
nat=53,
ntyp=6,
tot_charge=0.0,
ecutwfc=45.0,
ecutrho=450.0,
nosym=.false.,
nosym_evc=.false.,
london=.true.,
london_s6=0.75,
london_rcut=200,
occupations='smearing',
smearing='marzari-vanderbilt'
degauss=0.04
/
&electrons
electron_maxstep=80,
conv_thr=1.0d-6,
mixing_mode='plain',
mixing_beta=0.7,
mixing_ndim=8,
mixing_fixed_ns=0,
diagonalization='david',
/
&ions
ion_dynamics='bfgs',
ion_positions='default',
phase_space='full',
pot_extrapolation='atomic',
wfc_extrapolation='none',
remove_rigid_rot=.false.,
upscale=100.d0,
bfgs_ndim=1,
trust_radius_max=0.8D0,
trust_radius_min=1.D-3,
trust_radius_ini=0.5D0,
w_1=0.01D0
w_2=0.5D0
/
ATOMIC_SPECIES
H 1.007 H.pw91-rrkjus.UPF
C 12.011 C.pw91-n-rrkjus.UPF
N 14.007 N.pw91-n-rrkjus.UPF
O 15.999 O.pw91-n-rrkjus.UPF
S 32.066 S.pw91-n-rrkjus.UPF
Zn 65.409 Zn.pw91-dn-rrkjus.UPF
ATOMIC_POSITIONS (crystal)
Zn 0.578420 0.797930 0.245020
S 0.892900 0.754800 0.321720
S 0.532400 0.630140 0.359300
C 0.775600 0.651200 0.377600
C 0.893100 0.574400 0.441400
C 0.802500 0.499300 0.494300
C 1.092900 0.573600 0.448400
H 0.658484 0.497791 0.491135
H 1.162620 0.626518 0.411599
S 0.232700 0.793820 0.174940
S 0.513200 0.591440 0.145020
C 0.286200 0.648800 0.123000
C 0.138700 0.573400 0.060200
C 0.053700 0.395600 -0.051300
C 0.191700 0.466400 0.008600
H 0.093523 0.320982 -0.088598
H 0.329520 0.440313 0.014493
O 0.543300 0.972400 0.325600
C 0.401000 0.972900 0.360600
C 0.495200 1.200600 0.427500
C 0.202400 1.072700 0.453100
N 0.365000 1.076500 0.411100
H 0.312744 0.887449 0.347623
H 0.632077 1.173674 0.441456
H 0.461004 1.259340 0.474237
H 0.481812 1.253835 0.378051
H 0.200577 1.162451 0.486274
H 0.079775 1.057289 0.412588
H 0.213205 0.995558 0.489830
O 0.687700 0.922400 0.166600
C 0.597200 1.022500 0.140400
C 0.540300 1.212500 0.055600
C 0.818000 1.065600 0.046900
N 0.647900 1.095500 0.082600
H 0.481877 1.044650 0.166216
H 0.630783 1.296591 0.061083
H 0.437698 1.228952 0.089877
H 0.478294 1.192415 -0.002688
H 0.918244 1.143828 0.062698
H 0.781594 1.053830 -0.013740
H 0.871518 0.978618 0.067224
O 1.235300 0.156000 0.202600
C 1.085900 0.157600 0.233400
C 1.063400 0.403000 0.231000
C 0.820300 0.263900 0.285800
N 0.993400 0.269100 0.249500
H 1.037676 0.064331 0.245752
H 0.950768 0.458791 0.212031
H 1.143621 0.451642 0.281051
H 1.11 0.391320 0.187189
H 0.711560 0.301097 0.248624
H 0.785186 0.165940 0.294816
H 0.844111 0.320974 0.339219
K_POINTS {automatic}
4 3 7 0 0 0
[Pw_forum] postdoc available
Hi all, it seems we've got a postdoc available but no so many (good) candidates. At present the position is not going to be covered (and so we will lost money) If you know someone (good scientist please) that could be interested. Postdoctoral Research Associate in Computational Materials Science "Transparent Conducting Oxides for Solar Cells" The project will involve solid-state simulations of the bulk, surface and defect properties of metal oxide materials, primarily based on density functional theory. Critical material properties include optical absorption, conductivity and energy band alignments. Close interaction with leading experimental groups will allow for rapid validation of predictions and the development of novel solar cell architectures. http://www.bath.ac.uk/jobs/Vacancy.aspx?ref=JK1137
[Pw_forum] CRYSTAL OPTIMISATION
Dear Marta,
I am not really expert in solid state and plane-wave calc (I've
started making plane wave calc few months ago), anyway here some
comments that I hope could help you.
you are optimising the cell parameters. Did you previously optimise
the atomic position?
Anyway, checking your output it seems that the 1st system, could
probably converge in few steps (so run it again starting from the last
point)
"
chpc-aw7:Downloads davidetiana$ grep "enthalpy old"
CristalXX.vcrelax.pbe_6-60-500.out
enthalpy old= -2073.6107364912 Ry
enthalpy old= -2075.4476327812 Ry
enthalpy old= -2075.8476883991 Ry
enthalpy old= -2075.9872095194 Ry
enthalpy old= -2076.0338351603 Ry
enthalpy old= -2076.0481135064 Ry
enthalpy old= -2076.0609253277 Ry
enthalpy old= -2076.0737452991 Ry
enthalpy old= -2076.0836740723 Ry
enthalpy old= -2076.0866052168 Ry
enthalpy old= -2076.0888066767 Ry
enthalpy old= -2076.0912973209 Ry
chpc-aw7:Downloads davidetiana$ grep volume CristalXX.vcrelax.pbe_6-60-500.out
unit-cell volume = 15197.3430 (a.u.)^3
new unit-cell volume = 15854.52474 a.u.^3 ( 2349.39814 Ang^3 )
new unit-cell volume = 16243.99458 a.u.^3 ( 2407.11162 Ang^3 )
new unit-cell volume = 16142.99843 a.u.^3 ( 2392.14553 Ang^3 )
new unit-cell volume = 15959.34517 a.u.^3 ( 2364.93093 Ang^3 )
new unit-cell volume = 15912.47810 a.u.^3 ( 2357.98594 Ang^3 )
new unit-cell volume = 15875.48556 a.u.^3 ( 2352.50422 Ang^3 )
new unit-cell volume = 15780.27042 a.u.^3 ( 2338.39479 Ang^3 )
new unit-cell volume = 15598.61538 a.u.^3 ( 2311.47629 Ang^3 )
new unit-cell volume = 15524.64761 a.u.^3 ( 2300.51540 Ang^3 )
new unit-cell volume = 15493.58732 a.u.^3 ( 2295.91274 Ang^3 )
new unit-cell volume = 15439.91245 a.u.^3 ( 2287.95894 Ang^3 )
new unit-cell volume = 15387.53554 a.u.^3 ( 2280.19748 Ang^3 )
new unit-cell volume = 15346.52555 a.u.^3 ( 2274.12043 Ang^3 )
chpc-aw7:Downloads davidetiana$
"
I am a bit less confident with the second one since if the volume as
in the previous case decrease rapidly, the enthalpy is not (however I
usually relax the atomic position working with total energy so it can
be different in this case). However, looking with Xcrysden it seems
nothing weird happen:
"
chpc-aw7:Downloads davidetiana$ grep "enthalpy old"
CristalXX.vcrelax.second.pbe_6-60-500.out
enthalpy old= -2076.0940909869 Ry
enthalpy old= -2076.094783 Ry
enthalpy old= -2076.0958973172 Ry
enthalpy old= -2076.0966745403 Ry
enthalpy old= -2076.0974062802 Ry
enthalpy old= -2076.0982401038 Ry
enthalpy old= -2076.0993096777 Ry
enthalpy old= -2076.1007114162 Ry
enthalpy old= -2076.1024392593 Ry
enthalpy old= -2076.1042708808 Ry
enthalpy old= -2076.1055118520 Ry
enthalpy old= -2076.1068005511 Ry
enthalpy old= -2076.1081007153 Ry
chpc-aw7:Downloads davidetiana$ grep volume
CristalXX.vcrelax.second.pbe_6-60-500.out
unit-cell volume = 15346.5256 (a.u.)^3
new unit-cell volume = 15347.63578 a.u.^3 ( 2274.28495 Ang^3 )
new unit-cell volume = 15344.50987 a.u.^3 ( 2273.82174 Ang^3 )
new unit-cell volume = 15338.58618 a.u.^3 ( 2272.94394 Ang^3 )
new unit-cell volume = 15326.37995 a.u.^3 ( 2271.13516 Ang^3 )
new unit-cell volume = 15307.15200 a.u.^3 ( 2268.28587 Ang^3 )
new unit-cell volume = 15275.28713 a.u.^3 ( 2263.56399 Ang^3 )
new unit-cell volume = 15226.01665 a.u.^3 ( 2256.26285 Ang^3 )
new unit-cell volume = 15151.73791 a.u.^3 ( 2245.25588 Ang^3 )
new unit-cell volume = 15040.70206 a.u.^3 ( 2228.80207 Ang^3 )
new unit-cell volume = 14958.62861 a.u.^3 ( 2216.64003 Ang^3 )
new unit-cell volume = 14914.57199 a.u.^3 ( 2210.11152 Ang^3 )
new unit-cell volume = 14876.72700 a.u.^3 ( 2204.50347 Ang^3 )
new unit-cell volume = 14843.89863 a.u.^3 ( 2199.63881 Ang^3 )
new unit-cell volume = 14767.53018 a.u.^3 ( 2188.32217 Ang^3 )
chpc-aw7:Downloads davidetiana$
"
The last suggestion is to reduce, at least at first instance, your cut-off.
Concerning this:
>
> 3- do you know if there is a limit on the number of atoms in teh
> conventional cell?
>
This is not strictly related with your problem. You can run it.
I am not a developer but, checking PW routines, I don't think so:
"
read_file.f90: IF (nat > 0) CALL checkallsym( nat, tau, ityp, nr1, nr2, nr3 )
setup.f90: IF (nat==0) CALL errore('setup','free electrons: n
[Pw_forum] wanT download
Dear all, Although not strictly related to QE forum there are probably other people like me that wonder why the link of wanT does not work.It seems that http://www.wannier-transport.org/ has some restricted acces (or maybe it doesn't exhist anymore). I don't really need that program but I was curious to try it. Bye
[Pw_forum] Pw_forum Digest, Vol 60, Issue 19. Re:Cystal optimisation
Thinking you are using QE, it could be because 200 atoms is quite big system and you are using a small machine. how many optimisation step do your calculation perform? In what machine are you running the calculation? have you optimise the parallelisation? Quoting pw_forum-request at pwscf.org: > 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. CRYSTAl optimization (MARTA FERRARO) >2. Re: CRYSTAl optimization (Paolo Giannozzi) > > > -- > > Message: 1 > Date: Tue, 12 Jun 2012 14:04:36 -0300 > From: MARTA FERRARO > Subject: [Pw_forum] CRYSTAl optimization > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear all > I have problems to optimise a CRYSTAl Structure with 220 atoms in the > conventional cell. The job never ends employing the default values for the > convergence parameter in energy and force. We couldnt find the stationary > point with 220 atoms, > We reached the stationary point for systems with a lower number of atoms > in the conventional cell. > > We tried to change the default values for the energy convergence and force > parameters. The output file showed that the new parameters were read, but > the calculation was not afected at all. > > Is there a receipt not included in the guide, to change the default values > efficientely, > > Thanks a lot > MARTA > > -- > Professor > Marta Ferraro > Physics Department > FCE. y N, Universidad de Buenos Aires > (1428)Ciudad Universitaria-Pab. I > www.df.uba.ar/users/ferraro > e-mail:ferraro at df.uba.ar > subscribe ATMOL (LISTA DE LA DIVISION FISICA ATOMICA Y MOLECULAR) > http://www.df.uba.ar/mailman/listinfo/atmol > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120612/f939de73/attachment.html > > -- > > Message: 2 > Date: Tue, 12 Jun 2012 21:43:25 +0200 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] CRYSTAl optimization > To: PWSCF Forum > Message-ID: <96EED408-0D27-436B-AE33-3BEF8821B094 at democritos.it> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > On Jun 12, 2012, at 19:04 , MARTA FERRARO wrote: > >> I have problems to optimise a CRYSTAL Structure with 220 atoms > > optimise with what code? CRYSTAL? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > -- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 60, Issue 19 >
[Pw_forum] pw bands calculation crash
Dear all,
After optimised a molecule I tried to calculate the band structure but
pw crashes and I can't figure out why.
The optimisation step should be fine(here it converge immediately
since I rerun my previous calculation):
BFGS Geometry Optimization
bfgs converged in 1 scf cycles and 0 bfgs steps
(criteria: energy < 0.10E-03, force < 0.10E-02)
Final energy =-646.2249695321 Ry
Begin final coordinates
ATOMIC_POSITIONS (crystal)
C0.953315090 0.000413805 0.235484404
..
..
H1.009939685 0.169442779 0.056058275
H1.044496546 0.158711398 -0.056214459
End final coordinates
Writing output data file mol_a.save
..
..
..
This run was terminated on: 13: 4:41 27Apr2012
=--=
JOB DONE.
=--=
"
but when I run pw.x to calculate bands it crashes
"
Atomic positions and unit cell read from directory:
./mol_a.save/
Subspace diagonalization in iterative solution of the eigenvalue problem:
a serial algorithm will be used
Application 1981542 exit codes: 139
Application 1981542 exit signals: Killed
Application 1981542 resources: utime ~2s, stime ~2s
"
My input should not contain any errors. I used it for other systems
similar to this one and it works. just in case:
"
&control
calculation='bands',
title='mol_a',
wf_collect=.true.,
outdir='./',
prefix='mol_a'
etot_conv_thr=1.0d-4,
forc_conv_thr=1.0d-3,
/
&system
ibrav=14,
celldm(1)=28.4693677,
celldm(2)=1.058648879,
celldm(3)=0.600431923,
celldm(4)=0,
celldm(5)=0,
celldm(6)=0,
nat=23,
ntyp=6,
nbnd=70
tot_charge=0.0,
ecutwfc=45.0,
ecutrho=450.0,
nosym=.false.,
nosym_evc=.false.,
london=.true.,
london_s6=0.75,
london_rcut=200,
/
&electrons
electron_maxstep=80,
conv_thr=1.0d-6,
mixing_mode='plain',
mixing_beta=0.7,
mixing_ndim=8,
mixing_fixed_ns=0,
diagonalization='david',
/
ATOMIC_SPECIES
H 1.007 H.pw91-van_ak.UPF
...
Zn 65.409 Zn.pw91-n-van.UPF
ATOMIC_POSITIONS {crystal}
C 0.952835 0.50 0.826917
Zn 0.0.50 0.191590
K_POINTS {crystal}
11
0 0 0 1
0 0 .1 2
0 0 .2 3
0 0 .3 4
0 0 .4 5
0 0 .5 6
0 0 .6 7
0 0 .7 8
0 0 .8 9
0 0 .9 10
0 0 1 11
"
Any suggestion?
thanks a lot
Davide
[Pw_forum] Contents of Pw_forum Digest, Vol 58, Issue 41Re: using Octave or GDIS to make the surface (m)
Agree and, by the way, I always thought this was the Quantum Espresso forum not the Octave or "the how to calculate a surface" one :-) > > Message: 1 > Date: Tue, 24 Apr 2012 12:56:26 +0430 > From: m > Subject: Re: [Pw_forum] using Octave or GDIS to make the surface > To: pw_forum at pwscf.org > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear Meghdad > > Not bad doing it with a pencil, a paper, and may be a simple modal once in > your life ! Best Wishes > > ps. > please sign your letter with your affiliation. many thanks. > > > > :) > > > m > > > > > Masoud Nahali, Ph. D Student > International School for Advanced Studies (SISSA) > Sharif University of Technology > > > > On Tue, Apr 24, 2012 at 12:15 PM, meghdad saeedian wrote: > >> >> >> Dear All >> ? >> I want to make [1010]?the surface from the?ZnO (hegzagonal) unit cell (the >> plane which contain c and b parameters). ?I?have installed the?Octave and >> GDIS softwares,I but can not use them to make this surface. >> can anyone guide me? >> ? >> Thanx in advance >> ? >> Meghdad. Saeedian >> >> > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120424/e3959df9/attachment.html > > -- > > Message: 2 > Date: Tue, 24 Apr 2012 13:27:04 +0200 > From: Layla Martin-Samos > Subject: Re: [Pw_forum] Testing subscription > To: pasianot at cnea.gov.ar > Cc: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="utf-8" > > Dear Roberto, we have controlled the server and apparently there is nothing > strange with your subscription to pw_forum. The server indicates that the > emails are sent to you. Maybe you could control on your side if your server > is considering the emails as spam. > > keep us informed > > best regards > > Layla and Moreno > > 2012/4/23 R.C.Pasianot > >> >> Hello >> >> Please disregard this if you're not the list administrator. >> Since some time ago I stopped receiving posts to the list, should >> I re-subscribe ?. >> Thanks for your attention, >> >> Roberto >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120424/cc0a44bb/attachment-0001.htm > > -- > > Message: 3 > Date: Tue, 24 Apr 2012 06:25:09 -0700 (PDT) > From: meghdad saeedian > Subject: Re: [Pw_forum] using Octave or GDIS to make the surface > To: PWscf > Message-ID: > <1335273909.73617.YahooMailClassic at web161403.mail.bf1.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > > Dear Masoud > Thanks :) > ? > Meghdad Saeedian > MSc graduated from the University Of Tehran Departemant Of Physics > > --- On Tue, 4/24/12, m wrote: > > From: m > Subject: Re: [Pw_forum] using Octave or GDIS to make the surface > To: pw_forum at pwscf.org > Date: Tuesday, April 24, 2012, 12:56 PM > > > Dear?Meghdad > Not bad doing it with a pencil, a paper, and may be a simple modal > once in your life ! Best Wishes > ps.please sign your letter with your?affiliation. many thanks. > > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? > ? ? ? ? :) > > ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? m > ? > > > > > Masoud Nahali, Ph. D Student > International School for Advanced Studies (SISSA) > Sharif University of Technology > > > > > On Tue, Apr 24, 2012 at 12:15 PM,?meghdad saeedian?wrote: > > > ? ?? > > Dear All > > ? > > I want to make [1010]?the surface from the?ZnO (hegzagonal) unit > cell (the plane which contain c and b parameters). ?I?have installed > the?Octave and GDIS softwares,I but can not use them to make this > surface. > > can anyone guide me? > > ? > > Thanx in advance > > ? > > Meghdad. Saeedian > > > > > > -Inline Attachment Follows- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120424/3340a6cc/attachment-0001.htm > > -- > > > > > End of Pw_forum Digest, Vol 58, Issue 41 >
[Pw_forum] pp.x problem and doubts related to the point keyword
I am trying to write a xsf file with the LUMO electron charge density using pp.x. I am in doubt with the meaning of kpoint option. Indeed if I don't put that keyword (or if I chose gamma point) the program crash. " Calling punch_plot, plot_num = 7 Plotting k_point = 0 band = 49 %% from local_dos : error # 1 wrong kpoint specified %% stopping ... " Everything works fine if I put kpoint=1 or 2 what is the correct meaning of this keyword? What I think is that, using kpoint=X, the properties is calculated at a specific point instead of in all the reciprocal space (i.e. all the point used during pw.x calc). Is this correct? if yes, how Can I calculate a properties over all the reciprocal space? Thanks a lot
[Pw_forum] bands calculation crash
I run all the examples and tried on other systems. I can conclude it crashes always. Thus, Although during the compilation I didn't have any problems, warnings or errors, I guess it is a compilation problem. My workstation is a MacOS Lion, I compiled with mpi and mkl. Quoting Paolo Giannozzi : > > in all cases? only for a specific set of data? also for the > provided examples? > > P. > --- > Paolo Giannozzi, Dept of Chemistry&Physics&Environment, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] bands calculation crash
>> I am running some calculations on coordination polymers. I made >> calculations on other 8 molecules and everything was ok. Making >> calculation on this new molecule bands crash pushing out this error: > > the error is for the bands.x executable. You should first of all understand > under which circumstances it crashes (serial, parallel, always, random...) > > P. > --- It crashes always both running serial and parallel Davide
[Pw_forum] bands calculation crash
Dear all, I am running some calculations on coordination polymers. I made calculations on other 8 molecules and everything was ok. Making calculation on this new molecule bands crash pushing out this error: " chpc-aw7:mol_i davidetiana$ [chpc-aw7:00467] *** Process received signal *** [chpc-aw7:00467] Signal: Segmentation fault: 11 (11) [chpc-aw7:00467] Signal code: Address not mapped (1) [chpc-aw7:00467] Failing at address: 0x26ddb6df8 [chpc-aw7:00467] [ 0] 2 libsystem_c.dylib 0x7fff904b4cfa _sigtramp + 26 [chpc-aw7:00467] [ 1] 3 libsystem_c.dylib 0x7fff904501f0 gettimeofday + 43 [chpc-aw7:00467] [ 2] 4 bands.x 0x000107d453c9 cgracsc_ + 121 [chpc-aw7:00467] *** End of error message *** " I can't see any problem in the pw.x band output file : " Writing output data file mol_g.save init_run : 39.73s CPU 41.63s WALL ( 1 calls) electrons:684.36s CPU699.78s WALL ( 1 calls) Called by init_run: wfcinit : 0.00s CPU 0.00s WALL ( 1 calls) potinit : 3.10s CPU 3.30s WALL ( 1 calls) Called by electrons: c_bands :684.36s CPU699.78s WALL ( 1 calls) v_of_rho : 2.44s CPU 2.57s WALL ( 1 calls) newd : 13.11s CPU 14.51s WALL ( 1 calls) Called by c_bands: init_us_2: 0.43s CPU 0.50s WALL ( 11 calls) cegterg :608.19s CPU621.12s WALL ( 22 calls) Called by *egterg: h_psi:546.45s CPU562.23s WALL ( 385 calls) s_psi: 23.37s CPU 22.46s WALL ( 385 calls) g_psi: 1.05s CPU 1.33s WALL ( 352 calls) cdiaghg : 6.79s CPU 6.93s WALL ( 363 calls) Called by h_psi: add_vuspsi : 23.84s CPU 27.38s WALL ( 385 calls) General routines calbec : 25.01s CPU 25.23s WALL ( 385 calls) fft : 2.26s CPU 2.36s WALL ( 13 calls) ffts : 0.04s CPU 0.04s WALL ( 1 calls) fftw :381.94s CPU390.76s WALL ( 17028 calls) interpolate : 0.22s CPU 0.24s WALL ( 1 calls) davcio : 0.00s CPU 0.17s WALL ( 22 calls) Parallel routines fft_scatter : 86.85s CPU 89.38s WALL ( 17042 calls) PWSCF: 12m 9.06s CPU12m29.92s WALL This run was terminated on: 21:26:28 15Mar2012 =--= JOB DONE. =--= " So I am lost and I am not able to manage such error. Any help, tips or suggestion? Thank a lot
