[Pw_forum] Lowdin charge problem
Hi,I don't think you can get 17e for not only Lowdin charge but also others. This estimated charge does not follow the sum rule. I believe the "error" comes from the delocolized charge which can not be well estimated or taken in to account. D. On Fri, Sep 4, 2009 at 9:59 PM, loc duong ding wrote: > Dear QE users, > > I try to analysis the atomic charge. I found that Lowdin charge analysis > can be implemeted by QE. I dod a test with NO2. I get the the result as > following: > > Lowdin Charges: > Atom # 1: total charge = 4.5377, s = 1.2595, p = 3.2782, > spin up = 2.4718, s = 0.7016, p = 1.7701, > spin down= 2.0659, s = 0.5578, p = 1.5081, > polarization = 0.4058, s = 0.1438, p = 0.2620, > Atom # 2: total charge = 6.1075, s = 1.7256, p = 4.3818, > spin up = 3.1926, s = 0.8642, p = 2.3284, > spin down= 2.9149, s = 0.8614, p = 2.0534, > polarization = 0.2777, s = 0.0027, p = 0.2749, > Atom # 3: total charge = 6.1113, s = 1.7254, p = 4.3859, > spin up = 3.1939, s = 0.8641, p = 2.3298, > spin down= 2.9174, s = 0.8613, p = 2.0561, > polarization = 0.2765, s = 0.0028, p = 0.2737, > > The strange thing is that the total charge of all atom is ~16.7 instead of > 17 in NO2 molecules. > > Can you give me some instructions or explanation to fix this problem? > > I great appreciate your help. > > Sincerely, --- > Loc Duong Dinh > Ms-Ph.D Student > Sungkyunkwan Advanced Institute of Nanotechnology, > Sungkyunkwan University, > Suwon, 440-746, Korea > Email: mambom1902 at yahoo.com, ddloc at skku.edu > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- -- Duy Le PhD Student Department of Physics University of Central Florida. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090904/48e51ed7/attachment.htm
[Pw_forum] Help in using xcrysden for making structures
hi,
I need some help in drawing crystal using xcrysden. Sir/Madam, let us take the
case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i know that i have
18 atoms in my unit cell and i know the Cartesian co-ordinates{x,y,z} of each
atom in angstrom/bhor. I want to know that how can i draw my unit cell with
giving positions of all the atoms without using the symmetries by xcrysden??.
Means like if i specifiy,
& system
ibrav=2, celldm(1)=9.00, nat=1,..
ATOMIC POSITIONS{angstrom}
A? 0? 4.5 0
now if we visualise this type of structure with Xcrysden, we found a number of
atoms genrated due to symmetry. If i make a file like
?& system
ibrav=2, celldm(1)=9.00, nat=18,..
ATOMIC POSITIONS{angstrom}
A? 0? 4.5 0
/
18 times we have specified the co-ordinates
/
/
A? 4.5 0 0
Xcrysden will give warning like atom 10 and 90 are very close like that.
Sir i want to know is there any way so that i can make my PWSCF input file with
angstrom/bohr postions such that with one atomic postion Xcrysden will show
only one atom??
Means i will give 18 atomic postions and xcrysden will produce 18 atom unit
cell without using symmatries.
Thanks for your help,
Neel Singh,
Univeristy of Delhi,
India
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[Pw_forum] Lowdin charge problem
Dear QE users, I try to analysis the atomic charge. I found that Lowdin charge analysis can be implemeted by QE. I dod a test with NO2. I get the the result as following: Lowdin Charges: Atom #?? 1: total charge =?? 4.5377, s =? 1.2595, p =? 3.2782, spin up? =?? 2.4718, s =? 0.7016, p =? 1.7701, spin down??? =?? 2.0659, s =? 0.5578, p =? 1.5081, polarization =?? 0.4058, s =? 0.1438, p =? 0.2620, Atom #?? 2: total charge =?? 6.1075, s =? 1.7256, p =? 4.3818, spin up? =?? 3.1926, s =? 0.8642, p =? 2.3284, spin down??? =?? 2.9149, s =? 0.8614, p =? 2.0534, polarization =?? 0.2777, s =? 0.0027, p =? 0.2749, Atom #?? 3: total charge =?? 6.1113, s =? 1.7254, p =? 4.3859, spin up? =?? 3.1939, s =? 0.8641, p =? 2.3298, spin down??? =?? 2.9174, s =? 0.8613, p =? 2.0561, polarization =?? 0.2765, s =? 0.0028, p =? 0.2737, The strange thing is that the total charge of all atom is ~16.7 instead of 17 in NO2 molecules. Can you give me some instructions or explanation to fix this problem? I great appreciate your help. Sincerely,?--- Loc Duong Dinh Ms-Ph.D Student Sungkyunkwan Advanced Institute of Nanotechnology, Sungkyunkwan University, Suwon, 440-746, Korea Email: mambom1902 at yahoo.com, ddloc at skku.edu
[Pw_forum] How to figure out machine accuracy
In data 04 settembre 2009 alle ore 15:54:38, Manoj Srivastava ha scritto: > The input is CMACH, I can specify various input variables for 'CMACH' to > get output, but what variable is returned as output, as there is only one > in this subroutine? Would you mind having a look at this- its in > espresso4.0.4/flib/dlamch.f Dear Manoj, QE does not use simple LAPACK routines for most of its algebra. Hamiltonian diagonalization is computed using a custom implementation of the iterative Davidson (or conjugate-gradient) algorithm that only uses LAPACK to diagonalize a reduced hamiltonian during each iteration. Said that, you can control the accuracy to which eigenvalues are computed cannot be controlled directly by the user (without modifying the code) and is decreased automatically as the self-consistency approaches convergence. The formula used is the following: ethr = MIN( ethr, 0.1D0*dr2 / MAX( 1.D0, nelec ) ) where dr2 is the estimated scf accuracy. As you can see you can increase the accuracy (at convergence) of eigenvalues and eigenvectors by increasing the convergence threshold. In a more general frame, I think you could disclose some more information on your "symmetry problem"; personally I doubt it is caused by insufficient diagonalization accuracy. best regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/
[Pw_forum] Help in using xcrysden for making structures
If
1. you know there are 18 atoms in a unit cell
2. AND if you know their Cartesian coordinates
3. AND if you don't want to use the Bravais-lattice index,
you could use
1. ibrav=0
2. AND define your unit cell (using CELL_PARAMETERS): nothing more than the
3 "primitive" lattice vectors
3. AND ATOMIC_POSITIONS: I suggest that you should use crystal coordinates
instead of using Cartesian coordinates.
You can find description in
http://www.quantum-espresso.org/input-syntax/INPUT_PW.html
:)
On Fri, Sep 4, 2009 at 12:14 PM, Neel Singh wrote:
> hi,
> I need some help in drawing crystal using xcrysden. Sir/Madam, let us take
> the case of FCC for which ibrav=2, and celldm(1)=9.000. Now if i know that i
> have 18 atoms in my unit cell and i know the Cartesian co-ordinates{x,y,z}
> of each atom in angstrom/bhor. I want to know that how can i draw my unit
> cell with giving positions of all the atoms without using the symmetries by
> xcrysden??. Means like if i specifiy,
> & system
> ibrav=2, celldm(1)=9.00, nat=1,..
> ATOMIC POSITIONS{angstrom}
> A 0 4.5 0
>
> now if we visualise this type of structure with Xcrysden, we found a number
> of atoms genrated due to symmetry. If i make a file like
> & system
> ibrav=2, celldm(1)=9.00, nat=18,..
> ATOMIC POSITIONS{angstrom}
> A 0 4.5 0
> /
> 18 times we have specified the co-ordinates
> /
> /
> A 4.5 0 0
> Xcrysden will give warning like atom 10 and 90 are very close like that.
> Sir i want to know is there any way so that i can make my PWSCF input file
> with angstrom/bohr postions such that with one atomic postion Xcrysden will
> show only one atom??
> Means i will give 18 atomic postions and xcrysden will produce 18 atom unit
> cell without using symmatries.
>
> Thanks for your help,
> Neel Singh,
> Univeristy of Delhi,
> India
>
> --
> See the Web's breaking stories, chosen by people like you. Check out Yahoo!
> Buzz <http://in.rd.yahoo.com/tagline_buzz_1/*http://in.buzz.yahoo.com/>.
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
--
Duy Le
PhD Student
Department of Physics
University of Central Florida.
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[Pw_forum] GWW-band (P. Umari)
Dear Ali, First of all, note that the GWW is implemented only at the gamma point, so it requires large supercells, (or better it is appropriate for non-crystalline systems). However the long-range parts of the symmetric dielectric matrix and of the screened-interaction can be calculated using k-points. With the code ph.x you are calculating the head and the wings of the symmetric dielectric matrix. E_HEAD are the head terms of the symmetric dielectric matrix calculated on the imaginary frequency axis (e.g. "E_HEAD : 58" is relative to the 58th frequency step). These terms together with the wings are calculated using linear response. Then, also the long range part (element G=0,G=0) of the screened interaction can also be calculated using a k-points grid. The calculated elements are <\Psi_i|G(i \tau)v|\Psi_i>, where \Psi_i are the KS states G(i\tau) is the KS Green function in imaginary time and v is the bare Coulomb interaction. The term "X energy 1" is the exchange energy relative to the 1st KS state. > I am trying to use implemented approach GWW in espresso to obtain > quasiparticle state for bulk TiO2 ,but I didn,t succeed to get true band > gap by GW density of state. > I used 10 10 12 kmesh for k sampling but I don't know which file and which > rows contains dielectric constant. when I grep E_HEAD ,the last lines is > E_HEAD : 58 (-0.288322417972075195E-19,-0.347622164532722579E-06) > E_HEAD : 59 (0.136048521030191330E-19,-0.268035068560476896E-06) . . > what is these two columns? where do I look for dielectric constant? > also when I grep the energy in exchange file I see > X energy 1 -3.13056306094735648 > X energy 2 -3.13125888267243768 Best regards, P. Umari (Democritos) This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] How to figure out machine accuracy
Dear Lorenzo, Thank you for your reply. I figured out my problem. You are right, it is not coming from lapack routine. Regards, Manoj On Fri, 4 Sep 2009, Lorenzo Paulatto wrote: > In data 04 settembre 2009 alle ore 15:54:38, Manoj Srivastava > ha scritto: > > The input is CMACH, I can specify various input variables for 'CMACH' to > > get output, but what variable is returned as output, as there is only one > > in this subroutine? Would you mind having a look at this- its in > > espresso4.0.4/flib/dlamch.f > > > Dear Manoj, > QE does not use simple LAPACK routines for most of its algebra. > Hamiltonian diagonalization is computed using a custom implementation of > the iterative Davidson (or conjugate-gradient) algorithm that only uses > LAPACK to diagonalize a reduced hamiltonian during each iteration. > > Said that, you can control the accuracy to which eigenvalues are computed > cannot be controlled directly by the user (without modifying the code) and > is decreased automatically as the self-consistency approaches convergence. > > The formula used is the following: > ethr = MIN( ethr, 0.1D0*dr2 / MAX( 1.D0, nelec ) ) > where dr2 is the estimated scf accuracy. > As you can see you can increase the accuracy (at convergence) of > eigenvalues and eigenvectors by increasing the convergence threshold. > > > In a more general frame, I think you could disclose some more information > on your "symmetry problem"; personally I doubt it is caused by > insufficient diagonalization accuracy. > > best regards > > -- > Lorenzo Paulatto > SISSA & DEMOCRITOS (Trieste) > phone: +39 040 3787 511 > skype: paulatz > www: http://people.sissa.it/~paulatto/ > > *** save italian brains *** > http://saveitalianbrains.wordpress.com/ > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] How to figure out machine accuracy
Dear PWSCF users and developers,
I am wondering how can one find machine accuracy? I am having
some symmetry problem, and for that I want to solve eigen value
problem with the best accuracy. In the lapack library it says-
ABSTOL (input) DOUBLE PRECISION
* The absolute error tolerance for the eigenvalues.
* An approximate eigenvalue is accepted as converged
* when it is determined to lie in an interval [a,b]
* of width less than or equal to
*
* ABSTOL + EPS * max( |a|,|b| ) ,
*
* where EPS is the machine precision. If ABSTOL is less than
* or equal to zero, then EPS*|T| will be used in its place,
* where |T| is the 1-norm of the tridiagonal matrix obtained
* by reducing A to tridiagonal form.
*
* Eigenvalues will be computed most accurately when ABSTOL is
* set to twice the underflow threshold 2*DLAMCH('S'), not zero.
* If this routine returns with INFO>0, indicating that some
* eigenvectors did not converge, try setting ABSTOL to
* 2*DLAMCH('S').
the last paragraph is useful. so i looked up DLAMCH-
DOUBLE PRECISION FUNCTION DLAMCH( CMACH )
The input is CMACH, I can specify various input variables for 'CMACH' to
get output, but what variable is returned as output, as there is only one
in this subroutine? Would you mind having a look at this- its in
espresso4.0.4/flib/dlamch.f
espresso4.0.4 can be replaced by whatever version you are using.
Regards,
Manoj Srivastava
University of Florida
Gainesville, USA
[Pw_forum] references for philosophy of parallel execution
Dear Sreekar Guddeti, in addition to reading the documentation you have been pointed to, please take into account the hardware (cpu and communication network) you have at hand. R and G parallelization is memory efficient but involves large and frequent communications hence it will not be efficient unless your communication network is very good. For massively parallel machines (such as blue gene etc) one needs to introduce further divide and conquer tricks (see the discussion in our recently appeared "reference paper") Other types of parallelization (k-point, neb-images) involve much less communication and can be of help even if the network is not very good. In any case at the end of PWscf output there is some timing report that should tell you how much are you spending in computing and how much in communicating ... this should give you an idea whether increasing the number of cpus can help or actually worsen the performance Hope this helps, stefano de Gironcoli sreekar guddeti wrote: > hello QE users, > i would be grateful if u could provide me with any references for the > principles involved in parallel execution like how the grids are > divided among processors which, should supposedly enhance perfomance, > etc. because i performed a parallel execution and the CPU time taken > is more than that in the serial case > > thnks in advance > > > -- > Sreekar Guddeti > Physics Department > IIT Bombay > India > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] parallel matrix problem
On Sep 4, 2009, at 1:22 , Marc Segovia wrote: > from cyc2blk_redist : error # 1 > inconsistent block dim nb please provide a test job (or, better, file a bug report on qe-forge) 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] Use of wannier90.x for the calculation of Born Effective Charge
Dear Yukihiro, not sure if you got an answer (btw, this question might be more suited to the wannier mailing list) - but wouldn't it just require the calculation with the undisplaced Ti to be done with the exact same mesh of the displaced Ti ? A quick and dirty approach would be moving the Ti by a tiny amount, that essentially does not change the results for the cubic system, but is recognized by the code as off axis. Try 0.50001 and 0.51. Note that BaTiO3 cubic has zero polarization, although that is not always the case (there is a 2007 review paper by Resta and Vanderbilt on this - e.g. from Vanderbilt's web site). nicola > If we set nosym in the input file of non-SCF calculation with k-points is > same as > > BaTiO3.win file., the symmetry of the results of wannier center > > broken, so the calculated Born Effective Charges are wrong. > > How should treat the k-points inconsistent when we calculate the Born > effective > > charge in displacing the atom. > > Here is my input file for BaTiO3.win. > -- - Prof Nicola Marzari Department of Materials Science and Engineering 13-5066 MIT 77 Massachusetts Avenue Cambridge MA 02139-4307 USA tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu
[Pw_forum] references for philosophy of parallel execution
hello QE users, i would be grateful if u could provide me with any references for the principles involved in parallel execution like how the grids are divided among processors which, should supposedly enhance perfomance, etc. because i performed a parallel execution and the CPU time taken is more than that in the serial case thnks in advance -- Sreekar Guddeti Physics Department IIT Bombay India -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20090904/03b37fcb/attachment.htm
