[Pw_forum] Error computing Cholesky
On Apr 25, 2011, at 2:14 , swapnil chandratre wrote: > I get the following error for Graphene Ribbon with porosity, can > anyone help. > > from cdiaghg : error # 426 > problems computing cholesky what about searching the mailing list for "cholesky" ? http://www.quantum-espresso.org/user_guide/ node52.html#SECTION000121070 > 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] fft error in XSPECTRA of 4.3 version
On Apr 25, 2011, at 14:29 , jiayudai wrote: > I met a error message when i used xspectra code, which is > ...the same as this: http://www.democritos.it/pipermail/pw_forum/2011-April/01.html > from fft_dlay_set : error # 2 wrong fft dimensions > 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] why are there two Fermi energies?
On Apr 25, 2011, at 15:10 , Eduardo Ariel Menendez Proupin wrote: > > >The "two Fermi energies" of the constrained > >case need not to be exactly the same as the (single) > >Fermi energy of the unconstrained case, as long as the > >occupancies for spin-up and spin-down are the same in the > >two cases. > > Why not? Aren't the the energies and occupations related by > the Fermi-Dirac function? they are (Fermi-Dirac or whatever function applies), but if you have a gap and a small broadening, the occupancies will do not (visibly) depend upon Ef for some interval of values > 2) tot_magnetization=1 > the spin up/dw Fermi energies are 6.38536.1614 ev > up: 4.8593 4.8594 5.2221 5.2221 5.2221 6.1335 6.1337 > 6.1338 > 1. 1. 1. 1. 1. 1. > 1. 1. Ef=6.3853eV is perfectly consistent with these occupations, as long as there are no states between 6.14eV and 6.40eV or so > > dw: 4.8796 4.8796 5.2528 5.2530 5.2531 6.1595 6.1596 > 6.1596 > 1. 1. 1. 1. 1. 0.6715 > 0.6660 0.6625 this is quite the same as case with spin magnetization not set 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] fft error in XSPECTRA of 4.3 version
Dear developers, I met a error message when i used xspectra code, which is %% from fft_dlay_set : error # 2 wrong fft dimensions %% I knew it from the reason of nr1http://www.democritos.it/pipermail/pw_forum/attachments/20110425/a4a84c76/attachment.htm
[Pw_forum] k-point
Abolore,I do not know any standard set of k-points for monoclinic system. Chose the points that you think are representative, e.g, half of every reciprocal lattice vectors, and path between them. I suggest you first calculate the DOS, locate the points of the valence band maximum and conduction band minimum, and be sure that they are in included in the k-points path of the band diagram. Some maxima of the DOS are related to lines were some bands are flat. Assure that these lines are included in the path. A good method is to explain the DOS features with the band diagram. If some feature cannot be explained with the band diagram, investigate the reason. It is like choosing 4 or 5 cities to visit in a tour by Italy, with a good choice you will get some idea about the country and you can explain some of the history from the monuments and museum, or the cafes that you visited. As there is no convention for the letters that design the k-points in a monoclinic crystal, PLEASE, indicate the coordinates of the points in the figure caption or in the text. [Pw_forum] k-point *Abolore Musari* abmus007 at gmail.com *Mon Apr 25 23:57:21 CEST 2011* - Previous message: [Pw_forum] why are there two Fermi energies? <http://www.democritos.it/pipermail/pw_forum/2011-April/020228.html> - *Messages sorted by:* [ date ]<http://www.democritos.it/pipermail/pw_forum/2011-April/date.html#20233> [ thread ]<http://www.democritos.it/pipermail/pw_forum/2011-April/thread.html#20233> [ subject ]<http://www.democritos.it/pipermail/pw_forum/2011-April/subject.html#20233> [ author ]<http://www.democritos.it/pipermail/pw_forum/2011-April/author.html#20233> -- Dear QE User, I am having a problem as regard (k-point) I am working on monoclinic system, and am using xcrysden to get my k-point and my question is how do I know the special points (k-points) to select from the Brillion zone in the xcrysden k path selection? Thanks in anticipation of your favourable assistance Musari Abolore Dept Of Physics University of Agriculture, Abeokuta Nigeria -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110425/58c1cbb1/attachment.htm -- Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110425/c7881942/attachment.htm
[Pw_forum] k-point
Dear QE User, I am having a problem as regard (k-point) I am working on monoclinic system, and am using xcrysden to get my k-point and my question is how do I know the special points (k-points) to select from the Brillion zone in the xcrysden k path selection? Thanks in anticipation of your favourable assistance Musari Abolore Dept Of Physics University of Agriculture, Abeokuta Nigeria -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110425/58c1cbb1/attachment.htm
[Pw_forum] cell(dm)
Dear Sir, I am really glad for the assistance u have rendered so far in fact i has been really helpful, Thanks a lot I am having another problem as regard (k-point) I am working on monoclinic system, and am using xcrysden to get my k-point and my question is how do I know the special points (k-points) to select from the Brillion zone in the xcrysden k path selection? Thanks in anticipation of your favourable assistance Musari Abolore Dept Of Physics University of Agriculture, Abeokuta Nigeria On Mon, Apr 25, 2011 at 3:58 AM, Emine Kucukbenli wrote: > Dear Abolore, > Sorry I couldnt understand your first question.Please rephrase it. > For the second one: > During the vc-relax run, at each step towards convergence, new cell > parameters are written on the output. Look for CELL_PARAMETERS (a 3x3 > matrix) values.The final one should be the relaxed one. (Please verify > this before progressing further, check stress, pressure ) > > You may want to examine the VCSexample directory and examples therein, > before dong anything , actually. (It is different than example03, > which you have been dong similar calculations till now, in which only > the atomic positions are relaxed) > best, > emine kucukbenli, phd student, sissa, it > > Quoting Abolore Musari : > > > Dear sir, am glad for the info thanks, but first if my celldm(4) = > > -0.7724 Sir is d -ve sign allowed note that i got this from cos(ab) > > where a and b r in bohr, secondly hw do l locate my answer? afta d vc > > relax cos ve done it using example03 of the expresso. THANKS > > > > > > SISSA Webmail https://webmail.sissa.it/ > Powered by Horde http://www.horde.org/ > > > ___ > 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/20110425/13259bb1/attachment.htm
[Pw_forum] Should we use a double bond or 2 H atoms to saturate the system?
Dear All, This issues is somehow not so pertained to the PWSCF, but a gerneral DFT modelling problem, sorry for this request on this list. We all know that the H atoms is often used to saturate the dangling bonds in the system's edge, say, for graphene nanoribbon. My issue is: as far as the passivation results is concerned, adding 2 atoms is equivalent to introduce a double bond between the two adjacent ions in the system, am I right? If so, Should we use a double bond or 2 H atoms to saturate the system? Regards. -- Hongsheng Zhao School of Physics and Electrical Information Science, Ningxia University, Yinchuan 750021, China GnuPG DSA: 0xD108493 2011-4-25
[Pw_forum] Should we use a double bond or 2 H atoms to saturate the system?
Dear Hongsheng Zhao, Unless you are asking if someone ever tried forcing a particular "bond" or aromaticity in PW explicitly (one can try to constrain some number of KS states trying to estimate a particular bond, but I don't think this is a good idea to do in a pw DFT code), I think you might be a little confused by the concepts. Beware that in literature they tend to do assume hydrogens implicitly in order not to complicate figure presentation. Also, please notice that you add hydrogens not just to saturate, but to put the atom in a particular "bonding state" (i.e. sp3 or sp2 hybridization etc.). That "bonding state" is handled by PW with no additional constraints (i.e. when you input the coordinates of Carbon and Hydrogen atoms in Benzene, with a suitable XC kernel, the electronic structure will assume aromaticity without you explicitly mentioning it, and if you want to see explicit proof of aromaticity using the nomenclature of theoretical chemistry, you can, for example, project the ks states in terms of atom centered pi levels) Best, Baris -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. O. Baris Malcioglu, University of Liege, B?t. B5 Physique de la mati?re condens?e all?e du 6 Ao?t 17 4000 Li?ge 1 Belgique Tel:+32 4366 3612 Fax: +32 4366 3629 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= 2011/4/25 Hongsheng Zhao : > Dear All, > > This issues is somehow not so pertained to the PWSCF, but a gerneral DFT > modelling problem, sorry for this request on this list. > > We all know that the H atoms is often used to saturate the dangling bonds in > the system's edge, say, for graphene nanoribbon. ?My issue is: as far as the > passivation results is concerned, adding 2 atoms is equivalent to introduce a > double bond between the two adjacent ions in the system, am I right? ?If so, > Should we use a double bond or 2 H atoms to saturate the system? > > Regards. > -- > Hongsheng Zhao > School of Physics and Electrical Information Science, > Ningxia University, Yinchuan 750021, China > GnuPG DSA: 0xD108493 > 2011-4-25 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] TDDFT approach for periodic system
I completely agree, one should focus on excitonic characters in these kind of discussions For archival purposes and for not risking being esoteric to the newcomers to the field, I would like to mention some commonly used references regarding the tests performed in the theoretical chemistry literature comparing TDDFT with other methods. The summary is that: When you are sure the type of excitons in your system is covered by the "kernel" at hand, TDDFT results are on par with some higher level wavefunction based methods at a fraction of the computational cost. The current implementation in QE 4.3 is ALDA only, thus it is good for systems with -no- charge transfer or -no- zwitterionic character. (if I may risk a adumbrate use of nomenclature, I would say it works better for excitons with more Frenkel-like character, and that seems to be the usual argument used to discuss why quantum confinement tends to work in favor of the accuracy of TDDFT-ALDA in size constrained isolated systems, for example in quantum dots etc. ). The problem resides in the locality of the kernel, which is being worked on for the next version. and here are the references: M Parac et al. Chem. Phys. 292, 11 (2003); A. Rosa et al. Structure and Bonding, 112, 49 (2004) I. Tavernelli et al. Molecular Physics 103, 963 (2005) 2011/4/21 Stefano Baroni : > Just a couple of further comments. > 1) The ability (or lack thereof) of (adiabatic) tddft to properly describe > optical excitations in extended systems does not depend on the code's > ability to sample the whole BZ using special k-points. The current version > of the tddfpt code distributed with QE is only apt to sample k=0 Bloch > state, but periodic systems can nevertheless be treated (admittedly not very > efficiently) to arbitrary numerical accuracy, by using suitable supercells. > 2) adiabatic XC functionals miss excitonic effects in periodic systems > (irrespective of the number of k-points used to sample the BZ) for the same > reason why they miss Rydberg series in molecular systems. Always be > suspicious of statements such as "TDDFT works for molecules, but it fails > for crystals". This is nonsense: any crystal is nothing but a "big > molecule". TDDFT works for both, and it fails for both. Only the failures > manifest themselves in different ways, according to the size of the system. > Cheers - SB > > On Apr 20, 2011, at 11:21 AM, Giuseppe Mattioli wrote: > > Dear all > I did not say that TDDFPT does not work with periodic system, but you cannot > have a realistic absorption spectra of a slab (or bulk crystal) if you > sample > the Brillouin zone by using Gamma only... TDDFPT works fine with finite > systems, i.e., which do not show a (strong) k dependence of the psi_n,k > eigenvalues. > > Giuseppe > > On Wednesday 20 April 2011 03:00:41 Johari, Priya Sudhir wrote: > > Thanks Marton, its working. > > On Tue, Apr 19, 2011 at 5:40 PM, Marci wrote: > > Dear Priya, > > Though I have never tried, it should work with periodic systems if you > > sample the Brillouin zone only with the gamma point. Keep in mind that > > the usual adiabatic approximations with (semi)local functionals might > > not work very well for calculating the absorption of periodic systems. > > Marton > > -- > > Marton Voros > > PhD student > > Department of Atomic Physics > > Budapest University of Technology and Economics > > Budafoki ?t 8., H-, Budapest, Hungary > > www.fat.bme.hu/MartonVoros > > On Tue, Apr 19, 2011 at 11:02 PM, Johari, Priya Sudhir > > wrote: > > Thanks Duy, but the link does not give sufficient information. However, > > I found a discussion on forum's archive itself where Giuseppe Mattioli > > has mentioned that TDDPFT does not work for periodic systems :-( > > Dr Priya Johari. > > Brown University, > > Providence, RI - 02906. USA > > On Tue, Apr 19, 2011 at 3:59 PM, Duy Le wrote: > > If you do a little homework (such as googling keyword TD-DFPT), you'll > > find this link > > http://qe-forge.org/projects/tddfpt/ > > I have not read it carefully but I guess it contains some useful > > information. > > -- > > Duy Le > > PhD Student > > Department of Physics > > University of Central Florida. > > "Men don't need hand to do things" > > > > On Tue, Apr 19, 2011 at 3:26 PM, Johari, Priya Sudhir > > wrote: > > TD-DFPT > > ___ > > 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 > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > -- > > - Article premier - Les hommes naissent et demeurent > libres et ?gaux en droits.
[Pw_forum] cell(dm)
Dear Abolore, Sorry I couldnt understand your first question.Please rephrase it. For the second one: During the vc-relax run, at each step towards convergence, new cell parameters are written on the output. Look for CELL_PARAMETERS (a 3x3 matrix) values.The final one should be the relaxed one. (Please verify this before progressing further, check stress, pressure ) You may want to examine the VCSexample directory and examples therein, before dong anything , actually. (It is different than example03, which you have been dong similar calculations till now, in which only the atomic positions are relaxed) best, emine kucukbenli, phd student, sissa, it Quoting Abolore Musari : > Dear sir, am glad for the info thanks, but first if my celldm(4) = > -0.7724 Sir is d -ve sign allowed note that i got this from cos(ab) > where a and b r in bohr, secondly hw do l locate my answer? afta d vc > relax cos ve done it using example03 of the expresso. THANKS > SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/
[Pw_forum] cell(dm)
Dear Abolore Musari , I'm not sure I understood your question... it would help if you would write in English. stefano Quoting Abolore Musari : > Dear sir, am glad for the info thanks, but first if my celldm(4) = > -0.7724 Sir is d -ve sign allowed note that i got this from cos(ab) > where a and b r in bohr, secondly hw do l locate my answer? afta d vc > relax cos ve done it using example03 of the expresso. THANKS > > On 4/24/11, Stefano de Gironcoli wrote: >> the simplest way to optimize the cell of your system would be to use >> vc-relax choosing bfgs or damp dynamics. as a default I would begin >> with bfgs >> >> stefano >> >> Quoting Abolore Musari : >> >>> Dear QE User, l want to ask if for instance am workn on orthorhombic >>> sys r we going to perform lattice constant optimization for b and c >>> also afer performing for a. THANKS MUSARI, A. A DEPT OF PHY UNAAB >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >> >> >> >> >>SISSA Webmail https://webmail.sissa.it/ >>Powered by Horde http://www.horde.org/ >> >> >> ___ >> 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 > SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/
[Pw_forum] why are there two Fermi energies?
I am sorry, Murphy's law has just acted. Find the figures here http://www.gnm.cl/emenendez/uploads/Temp/impurity-energy.eps http://www.gnm.cl/emenendez/uploads/Temp/impurity-fermi.eps Finally, I plotted Energy vs magnetization. Indeed, I have a minimum at total magnetization equal 1. However, the behavior is strange. The plot of E vs M is linear at each side of the minimum, with a kink at M=1. Should'n it be rather like a parable ? Please, see the plots here (above) Eduardo Menendez Departamento de Fisica Facultad de Ciencias Universidad de Chile Phone: (56)(2)9787439 URL: http://fisica.ciencias.uchile.cl/~emenendez -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110425/9473060a/attachment.htm
[Pw_forum] why are there two Fermi energies?
Hi Paolo,
>>* the restriction is in this code
*>>* if ( ((MOD(NINT(tot_magnetization_),2) == 0) .and. (MOD
*>>* (NINT(nelec_),2)==1)) .or. &
*>>* ((MOD(NINT(tot_magnetization_),2) == 1) .and. (MOD
*>>* (NINT(nelec_),2)==0)) ) &
*>>* CALL errore(' set_nelup_neldw
*>>* ', &
*>>* 'tot_magnetization is inconsistent with total number
*>>* of electrons ', 2 )
*
>in the new version, this restriction (now a warning, no longer an
>error) applies only if the
>number of electrons is integer and if the magnetization is integer.
>For noninteger charge
>or magnetization, it doesn't make sense.
In fact, increasing the k-point sampling, the unrestricted calculation
converges towards
0 total magnetization, with a lower energy than magnetization =1, but
setting tot_magnetization=0, or 0.1, 0.2, etc, stops due to the above
instruction in versiom 4.2.1.
This is one more reason to change to the newest version.
*You stated something in a previous post*
>The "two Fermi energies" of the constrained
>case need not to be exactly the same as the (single)
>Fermi energy of the unconstrained case, as long as the
>occupancies for spin-up and spin-down are the same in the
>two cases.
Why not? Aren't the the energies and occupations related by
the Fermi-Dirac function? I verified that the occupations are the
same, then I do not understand
why it is possible with different Fermi energies.
These are my KS energies and the occupations, using degauss=0.00019. I
think the differences are just numerical noise.
1) tot_magnetization unset
the Fermi energy is 6.1614 ev
!total energy =-502.92571441 Ry total
magnetization = 1.00 Bohr mag/cell
up: 4.8593 4.8594 5.2221 5.2221 5. 6.1335 6.1336 6.1338
1. 1. 1. 1. 1. 1. 1. 1.
dw: 4.8796 4.8796 5.2528 5.2530 5.2531 6.1595 6.1596 6.1596
1. 1. 1. 1. 1. 0.6709 0.6661 0.6631
2) tot_magnetization=1
the spin up/dw Fermi energies are 6.38536.1614 ev
!total energy =-502.92571439 Ry total
magnetization = 1.00 Bohr mag/cell
up: 4.8593 4.8594 5.2221 5.2221 5.2221 6.1335 6.1337 6.1338
1. 1. 1. 1. 1. 1. 1. 1.
dw: 4.8796 4.8796 5.2528 5.2530 5.2531 6.1595 6.1596 6.1596
1. 1. 1. 1. 1. 0.6715 0.6660 0.6625
Finally, I plotted Energy vs magnetization. Indeed, I have a minimum
at total magnetization equal 1. However, the
behavior is strange. The plot of E vs M is linear at each side of the
minimum, with a kink at M=1. Should'n it be rather like a parable ?
Please, see the plots here
http://www.gnm.cl/emenendez/pmwiki.php/Temp/Plots?action=upload&upname=impurity-energy.eps
http://www.gnm.cl/emenendez/pmwiki.php/Temp/Plots?action=upload&upname=impurity-fermi.eps
This was using gamma point fo sample the Brillouin zone. That is not
converged, using a 3x3x3 grid the lowest energy seems to be
for null magnetization (I am doing more calculations). Maybe the kinks
are due to insufficient Brillouin zone sampling.
Best regards
--
Eduardo Menendez
Departamento de Fisica
Facultad de Ciencias
Universidad de Chile
Phone: (56)(2)9787439
URL: http://fisica.ciencias.uchile.cl/~emenendez
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