Re: [SIESTA-L] Symmetries
Dear all, Siesta is designed for very large systems where, usually, the number of symmetries is very small, so it can't use them This is not entirely true! Using constraints you can force to have symmetrical relaxations. This issue was discussed in this e-mail list some weeks ago. I think Emilio Artacho suggested to look at Lev Kantorovich's SIESTA tool which is indeed very useful. Please, search on the SIESTA-list. Yours, Adam On 13/06/2007, at 9:05, Zoya Shah wrote: Dear everyone I just have a question regarding symmetries. Is it possible to use the advantage of symmetries of molecules and particles in order to reduce the number of particles in SIESTA? If so, have any of you done this before? Best regards Zoya --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
[SIESTA-L] Matrix diagonalization: an 8x speed-up of the exact DFT-calculation
Dear Siesta developers, is there anybody who is working on the implementation of the Chebysev-filtered subpace acceleration to diagonalize the matrices in SIESTA (Phys. Rev. E, vol. 74, 066704 (2006))? Usually, it speeds up the exact DFT-calculations by about 8x making possible to access 1 atoms directly by exact DFT (with supercomputers). Yours, Adam --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] SCF convergence problem on large system
Dear Kevin, I am trying to run a relaxation calculation on a 512 atoms system made up of crystalline Si with one Ga substitutional. The problem I encounter is that the SCF cycle never converges. dDmax acutally rises to ridiculously high values after only a couple of iterations. This seems particularly odd as 512 atoms calculations for pure crystalline Si work perfectly. Ga atom can be tricky. It requires much higher meshcut-off than the pure Si supercell. Beside that there are many possible reason for errors: partially filled, degenerate single electron levels, etc. Yours, Adam --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] A question about local magnetic moment
Dear Marcos, I guess so. I remember one of the e-mails of the list, in which Emilio talks about the calculation of PDOS in siesta. Since it is mulliken-like in nature, it would depend on the basis set as well. However, the integration over atomic spheres is what makes me a bit worried on practical aspects: how to choose the sphere radius? Although it would have the advantage of being effectively independent of the basis set, as you say, I don't see, in principle, a reasonable way of choosing the radii. Maybe there is, but I really can't think, at the moment, of any reasonable way. Any tips? Look at the definition of Bader-charge as I already suggested before. Yours, Adam --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] net charge calculation
Dear Yurko Natanzon, take care! Mulliken-charges could be meaningless by using diffusing orbitals. Draw the net charge density around the atoms (you can do it by SIESTA and utility programs provided with) and you can see that O is negatively polarized while Si is positively polarized opposite what Mulliken-charges would indicate. I suggest to implement and use Bader-charges for analyses which DOES NOT depend on the basis set. Yours, Adam Gali Species: Si Atom Qatom Qorb 3s 3s 3py 3pz 3px 3py 3pz 3px 3Pdxy 3Pdyz 3Pdz2 3Pdxz 3Pdx2-y2 1 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 4 4.026 0.404 0.474 0.308 0.152 0.308 0.254 0.394 0.254 0.338 0.330 0.259 0.330 0.219 Species: O Atom Qatom Qorb 2s 2s 2py 2pz 2px 2py 2pz 2px 2Pdxy 2Pdyz 2Pdz2 2Pdxz 2Pdx2-y2 2 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 3 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 5 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 6 5.987 1.136 0.383 1.391 1.164 1.391 0.139 0.226 0.139 0.003 0.005 0.003 0.005 0.003 mulliken: Qtot = 32.000 then oxygen has positive ionic charge (6-5.987), and silicon has negative (4-4.026). Does it make any sense?? On 19/04/07, Vasilii Artyukhov [EMAIL PROTECTED] wrote: Just subtract the ionic charge from the Mulliken population, you will get -.514 for O and +1.028 for Ti. 2007/4/19, Yurko Natanzon [EMAIL PROTECTED] : Dear SIESTers, I wonder how to calculate net ionic charge with SIESTA. For example, I have TiO2 anatase supercell with 12 atoms. Pseudopotential for Ti has valence electrons in 3s2 3p6 3d2 4s2 (12 electrons), O has 2s2 2p4 (6 electrons). Then i set WriteMullikenPop 2 and obtain 10.972 for each Ti 6.514 fo O Total charge is 10.972*4+6.514*8 = 96 which equals the total number of valence electrons. Then how to obtain net electric charges of Ti and O atoms? If it is the difference between number of valence electrons and a charge obtained by SIESTA, than it is much lower, than is reported in other calculations. Net charge should be around +2 for Ti and -1 for O. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] optimization of the lattice constant of GaN:Wurtzitestructure
Dear Mu J. Helien, The possible use of Z-matrix or constr.f file (use constraints) was discussed in the SIESTA list about one week ago. You should look at those messages how you can set symmetry for a particular input in SIESTA. Nevertheless, by using i) well-tested pseudopotentials ii) good basis compatible with the psuedopotentials iii) other well-converged parameters (Eshift, MeshCutoff, K-points, force criteria, stress criteria) the calculations should give automatically 'almost' symmetric structure after optimization since that should be the most stable configuration. If it is not the case then one of the afore-mentioned condition is not fulfilled. GaN is very tricky due to Ga 3d orbitals. I suggest first to check the convergence of some parameters on cubic GaN (it is a simpler structure and you can easily impose the symmetry by fixing the fractional coordinates), and look at what is happening during optimization without any constraints. If everything seems to be fine then you can switch to wurtzite GaN and re-check everything. Yours, Adam Gali I want to optimize the lattice constant of GaN of Wurtzite structure.Since the u fractional coordinate of N atom has to be optimized, so I choose MD.Variable-Cell:T and didn't fix the fractional coordinates of all atoms. But when SCF calculations are converged, the fractional coordinates are changed significantly and the symmetry of the cell are broken. I wonder if there is someone who met similar problem and would you like to tell me how to solve this problem? Thank you very much. Before: Ga 0. 0.6667 0. Ga 0.6667 0. 0.5000 N 0. 0.6667 0.3748 N 0.6667 0. -0.1252 outcell: Cell vector modules (Ang) :3.0999323.0999325.130500 outcell: Cell angles (23,13,12) (deg): 90. 90.119.9985 After: 0.284243760.60773737 -0.15293678 1 Ga 1 0.77520.342650060.48122587 1 Ga 2 0.270943530.627445310.50909357 2 N 3 0.786042940.32298514 -0.17115702 2 N 4 outcell: Cell vector modules (Ang) :3.0996403.1048344.925811 outcell: Cell angles (23,13,12) (deg): 90.5244 88.9666119.7208 --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] Restrict geometry optimization
Dear Yong Liu,
I also found the 'routine' of 'GeometryConstraints' in the manual. But
it's too brief for me to use it. Would you mind send me some detail
information about this trick?
Z-matrix was also suggested but if does not work then you can use the
GeometryConstraints block with 'routine'. It means that SIESTA will use
the constraints defined in constr.f file. Unfortunately, I do not find my
original files as example but I give you some hints.
By default, constr.f file does not effect the calculation, it is a
template file. You should edit this file and program your constraints for
your particular input.
Your input:
which has a=b!=c, Pb(0,0,x1),
Ti(0.5,0.5,x2),O1(0,0.5,x3),O2(0.5,0,x3),O3(0.5,0.5,x4)
Then you should program that:
cell(1,1)=cell(2,2)
cell(1,2)=0.0
cell(1,3)=0.0
cell(2,1)=0.0
cell(2,3)=0.0
cell(3,1)=0.0
cell(3,2)=0.0
With this you define a=b!=c system. More important you should define the
constraints for stress matrix:
stress(1,1)=stress(2,2) ,etc.
if the order of your atoms is set as you listed above:
! the third coordinate of the given atom should be the multiplication of
! the third coordinate of the first atom
xa(3,2)= xa(3,1)*2
xa(3,3)= xa(3,1)*3
xa(3,4)= xa(3,1)*3
xa(3,5)= xa(3,1)*4
and you can fix the other coordinates as well. It is important to
symmetrize your atomic forces as well ('fa' array). This will ensure that
you will keep the symmetry during the optimization. You have to look at
the source code for the meaning of 'ntcon' and how to set it. Maybe, it is
needed for normalization of the forces but I do not remember for that any
more.
After you programmed it you should compile the code and run it. I advise
you to first to try it on very simple examples (like small symmetric
molecules), then for very simple lattice (to compute the symmetric stress
tensor) and, then to apply for your problem.
Yours,
Adam
---
Dr. Gali ÁdámAdam Gali, PhD
Budapesti Műszaki és Department of Atomic Physics,
Gazdaságtudományi Egyetem, Budapest University of Technology and
Atomfizika Tanszék Economics
Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest,
Hungary
telefon: 463-1580telephone: [36]-(1)-463-1580
fax: 463-4357fax: [36]-(1)-463-4357
e-mail: [EMAIL PROTECTED]
http://www.fat.bme.hu/homepages/galia/index.en.html
---
Re: [SIESTA-L] Restrict geometry optimization
Dear Yong Liu, The symmetry is NOT included basically in SIESTA. In some simple cases you can use some tricks in which you can still conserve the symmetry during relaxation (using fixed fractional coordinates, etc). In your case these tricks may not work. What you can still do is to use the constraints.f file in SIESTA which can be activated within GeometryConstraints block. By default, constraints.f file is a template source and your calculation would not be affected. However, you can write your specific constraints into this file using your specified atoms, etc, which will conserve the symmetry what you want to achieve. You have to compile the code again, and you will have such a code which will conserve the symmetry for your particular(!) input. This indeed works (with 1.3f version, for sure); for instance I could use for studying the migration of a defect in a crystal constrained in a chosen plane. Yours, Adam I'd like to apply a restrict geometry optimization considering the symmetry of the system, but from the manual I do not find the useful parameters. For instance, How can I fully optimize tetragonal PbTiO3 (P4mm, No.99) which has a=b!=c, Pb(0,0,x1), Ti(0.5,0.5,x2),O1(0,0.5,x3),O2(0.5,0,x3),O3(0.5,0.5,x4). I'm afraid that 'GeometryConstraints' is not good enough to deal with this work since the constrainsts of this parameter are not implemented, as mentioned in the manual. Is there any parameters provide a mode of structural relaxtion taking into account the symmetry of the system and how to use them? Thanks a lot in advance. --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] Qtot SWCNT+F
Dear Pablo, if you have delocalized state then usually the spin polarization energy will be small. Check the ElectronicTemperature option. Most probably you smeared the electrons between the spin up and spin down levels which halfly occupies both states. Lowering the smearing can result in other occupation but if the delocalization is strong then you will have this smearing effect even at 10 K. If you set T= 0K, however, can lead to convergency problems because your system is metallic. Yours, Adam Gali --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] Gold band structure
Dear Salvador Barraza Lopez, I think that the problem is with the K-point set: %block kgrid_Monkhorst_Pack 4 0 0 0.0 0 4 0 0.0 0 0 4 0.0 %endblock kgrid_Monkhorst_Pack For metals usually much more dense K-point sampling is needed. Have you tried to increase the number of K-points? (Let's say 30x30x30?) Yours, Adam Gali --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] E_tot E_KS ?!
Dear Oleksandr, Did you obtain it by siesta-2.0? If yes, you may check it by siesta-1.3. Yours, Adam After some steps I obtain strange results, total energy becomes lower than Kohn-Sham energy: # Step T (K) E_KS (eV)E_tot (eV) Vol (A^3)P (kBar) 1335.00 -12986.05776 -12982.333933328.182 -2.090 2324.32 -12985.93131 -12982.326223328.182 -1.660 3301.07 -12985.65682 -12982.311263328.182 -1.255 ... 172378.58 -12981.36638 -12982.307113328.182 2.821 173374.43 -12981.34941 -12982.304393328.182 2.528 174369.96 -12981.33431 -12982.302273328.182 2.346 What is the physical meaning of that??? Sincerely, Alexander --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
Re: [SIESTA-L] Mulliken population
Dear Siesta users, I have performed calculations for a silicon carbide (SiC) material. Analysis of Mulliken population revealed a charge transfer from C to Si of about 0.45|e| (well, I believe so). For instance: But, of course, I was expecting a charge transfer from Si to C. What may be wrong? I have the same experience. I assume you used DZP basis. The Mulliken-charge is very dependent on the applied basis set. I think that the simple Mulliken-population analysis should not be used for basis sets which involve diffuse orbitals. The reason could be in the definition of the Mulliken charge which divides the overlap part equally between the atoms in the bond. I think if it is possible to plot the charge density around the atoms then you should see higher density around C-atoms and lower density around Si-atoms as you expected. Try to use smaller basis set and look at the trend. Yours, Adam Gali --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Mûszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] ---
Re: [SIESTA-L] Ga pseudopotential
Dear Siesta users/developers, has anybody a well-tested Ga-pseudopotential for me? Ga with 4s^2 4p^1 with nlcc or Ga with d-semicore states with the corresponding basis for 3d are also appreciated. Yours, Adam Gali --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] --- --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] ---
[SIESTA-L] fractional valence for H
Dear Users/Developers of SIESTA, I would like to ask whether is it possible to use fractional valence charge for H (Zval=0.75 instead of 1.0, for instance)? It would be neccesary to saturate the dangling bonds at partially ionic surface. Yours, Adam Gali --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] ---
