[Pw_forum] from cp_read_cell : error # 2
On Sep 22, 2011, at 19:32 , Luis Antonio Leon Martinez wrote: > Hi, no then you are trying to restart from a nonexistent restart file. You need to understand how a Car-Parrinello simulation works before starting to run anything. P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] LDA norm-conserving pseudopotential for Fe
On Sep 22, 2011, at 16:53 , helen at fh.huji.ac.il wrote: > My problem is the fhi2upf code doesn't include values for principle > number and assumes a s-p-d-f ordering, which doesn't make sense > for Fe which doesn't have any occupied f orbitals. I wouldn't be so sure that it doesn't make sense. A PP for Fe could have been generated using 4s2 4p0 3d6 4f0 states. > Could they have used 3s3p3d3f and ignored 4s completely in the fhi > file? 3f, unlikely, but another possibility is 3s2 3p6 3d6 4f0, with no 4s and 4p states > Is this the way the fhi2upf code is written because that is how > fhi files are organized (only s-p-d-f ordering)? he who originally wrote the fhi2upf converter (not myself) had to dig into the format of the fhi file and to make some educated guess. I have no evidence until now that those guesses were not good. > Fritz-Haber so YOU are from FHI, you should know what is inside those files... P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] charge density plot in xcrysden
On Wed, 2011-09-21 at 15:37 -0600, Tram Bui wrote: > Dear Everyone, > I have an output file of the SiC bulk charge density (bulk.xsf). I > open it using xcrysden and do data grid to get the display of > color-plane and isoline, etc. I'd also like to make the isoline with > different color other than just the gray scale, how can I do so in > xcrysden? Dear Tram, Here you will find the information you need: http://www.xcrysden.org/doc/plane1control.html Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html
[Pw_forum] from cp_read_cell : error # 2
On Sep 22, 2011, at 19:13 , Luis Antonio Leon Martinez wrote: > cannot open restart file for reading: .//si_52.save/data-file.xml did you run with "restart_mode='from_scratch" first? P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] NEB procedure
Dear Ettore, putting intermediate images will not help to locate the presumable maximum in your case. (increasing the num_of_images may help though, but even that can be insufficient if transition state is very close to final state) Intermediate images are used to do a better initial guess of the reaction path. Intermediate images are not really used, but all the input images (initial+intermediates+final) are connected so as to produce a piecewise-linear path and then the EQUIDISTANT linear interpolation is performed on this piecewise-linear path. In your case you should set the CI_scheme = 'manual' and specify as the climbing image the last image before the final image in the CLIMBING_IMAGES card, i.e.: num_of_images = N CI_scheme = 'manual' ... / CLIMBING_IMAGES N-1 By doing that the N-1'th image will climb up to the transition state (TS) by the CI-NEB scheme, provided the TS is indeed there before the top site. Best regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html
[Pw_forum] LDA norm-conserving pseudopotential for Fe
Thank you for your help. My problem is the fhi2upf code doesn't
include values for principle number and assumes a s-p-d-f ordering,
which doesn't make sense for Fe which doesn't have any occupied f
orbitals.
DO i=1, nwfs
PRINT '("Wavefunction # ",i1,": label, occupancy > ",$)', i
READ (5,*) els(i), oc(i)
nns (i) = 0
lchi(i) = i-1
rcut(i) = 0.0d0
rcutus(i)= 0.0d0
epseu(i) = 0.0d0
ENDDO
Could they have used 3s3p3d3f and ignored 4s completely in the fhi
file? Is this the way the fhi2upf code is written because that is how
fhi files are organized (only s-p-d-f ordering)? Or should I manually
change the UPF file afterwards to have a more likely 3s3p3d4s ordering?
Thank you again,
Helen
Dr. Helen Eisenberg
Fritz-Haber, Hebrew University, Israel
On Thu, 2011-09-22 at 11:29 +0300, helen at fh.huji.ac.il wrote:
My problem is that it asks me for the label and occupancy of the
wavefunctions, and I don't know what was used to generate the
fhi file on the abinit site.
guess something sensible, then verify if it works. The wavefunction
label is used only for the printout of projected dos. The l value
is used, but I think that the code always assume s-p-d-f ordering.
P.
This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] semi conducting / metallic
Dear users, The question I have is not very technical. I just wanted put a doubt ahead. I submitted a metallic structure ( what I analyzed using bandstructures from other software) into espresso. and I did not define smearing and degauss, but I did not receive and warning or error of system is metallic. definer smearing etc. Does this mean I have analyzed the bandstructure in a wrong way when I visualized it , or it happens. Can anyone comment -- Regards, Swapnil Chandratre Graduate Student Dept. of Mechanical Engineering, University of Houston, Houston, TX (M)-713-294-9546 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/41cd590f/attachment.htm
[Pw_forum] band structure calculation
Dear Everyone, I have run DOS calculation on my bulk SiC and I also wonder how to do the band structure and plot the band structure. Would you give me some information or some examples regarding generating the band structure? Thank you very much, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/f9ff7ce8/attachment.htm
[Pw_forum] charge density map
Dear Everyone, I have done my charge density calculation and the contour maps for my bulk SiC. I also see the scale based on the thermometer around each atom (Si, C). But my questions is what should I focus on in order to help me understand the charge density map ? what information can I get out of the charge density contour maps? Regards, Tram Bui M.S. Materials Science & Engineering trambui at u.boisestate.edu -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/81987074/attachment.htm
[Pw_forum] NEB procedure
Dear Ettore, you can put more intermediate images by hand and the NEB algorythm will "relax" then for you. I put relax within "" because neb relaxes along the perpendicular directions of the chain. best regards Layla 2011/9/22 Ettore Baldini-Neto > Dear users, > > I have some questions regarding a NEB calculation. > > As input to a neb file I should use, at least, the initial and final > positions (both well previously relaxed). > What I want is to calculated the energy barrier for the transition of a > metal from one stable position (let's say a hollow position on a C ring) to > another one (also stable but with slightly higher total energy than first, > let's say the Top position). > > When I use just the initial and final positions and perform the > calculations, asking the code to automatically divide the grid, I get an > ascendent curve form the first to the last as expected. > But at a position just before the Top position I also expect the energy > barrier to be a little higher than the energy at this final site (Top) > because the metal is at a unstable position. > > So here are is my question, a very basic one since I have no previous > experience with this kind of calculation. > > I can put more intermediate images, automatically or by hand, in order to > better mapping the region around this position (Top). > In the second case, should these intermediate images be previously > optimized or the neb does it for me?? > > Thanks in advance, > > > > *** > Ettore Baldini-Neto > Researcher at W. von Braun Center for Advanced Research, Campinas, Brazil > > *** > ___ > 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/20110922/e7bf1c0d/attachment.htm
[Pw_forum] epsilon.x and scissor shift renormalization of momentum operator
Hi all, Recently a reviewer has warned me about a problem of the dielectric function calculation that I performed using the epsilon code, where I applied the scissor shift (option shift in the input) to correct the infamous gap problem. Following the referee's criticism I got to an article by Rodolfo del Sole and Rafaello Girlanda, PRB 48, 11780 (1993), when a scissor shift is applied to correct the LDA underestimation of the transition energies, the momentum matrix elements <c|e.p|v> must be multiplied by (Ec-Ev)/(Ec0-Ev0), (see unnumbered equation after Eq. (15) in the cited paper) , where Ec0-Ev0 is the LDA transition energy and Ec-Ev=Ec0-Ev0 +\Delta ( \Delta is the scissor shift). Equivalently, one can replace the \omega^2 in the denominator by (\omega-\Delta/\hbar)^2 (Eq. 17 and 19 of the above article) . As shown by del Sole and Girlanda (and repeated many times in the literature) this is a simple approximation for the fact that "exact" transition energies Ec-Ev arise from non-local self-energy (e.g. from GW) and for non-local one electron hamiltonians the interaction with an electromagnetivc wabe is not longer A.p. It is very easy to set this correction in the code epsilon.x, for example , in subroutine eps_calc one can change etrans = ( et(iband2,ik) -et(iband1,ik) ) * RYTOEV + shift ... epsi(:,iw) = epsi(:,iw) + dipole(:,iband1,iband2) * intersmear * w* & RYTOEV**3 * (focc(iband1,ik))/ & (( (etrans**2 -w**2 )**2 + intersmear**2 * w**2 )* etrans ) epsr(:,iw) = epsr(:,iw) + dipole(:,iband1,iband2) * RYTOEV**3 * & (focc(iband1,ik)) * & (etrans**2 - w**2 ) / & (( (etrans**2 -w**2 )**2 + intersmear**2 * w**2 )* etrans ) by the following etrans = ( et(iband2,ik) -et(iband1,ik) ) * RYTOEV + shift shift_renorm = ( etrans/(etrans-shift) )**2 epsi(:,iw) = epsi(:,iw) + dipole(:,iband1,iband2) *shift_renorm* intersmear * w* & RYTOEV**3 * (focc(iband1,ik))/ & (( (etrans**2 -w**2 )**2 + intersmear**2 * w**2 )* etrans ) epsr(:,iw) = epsr(:,iw) + dipole(:,iband1,iband2) *shift_renorm* RYTOEV**3 * & (focc(iband1,ik)) * & (etrans**2 - w**2 ) / & (( (etrans**2 -w**2 )**2 + intersmear**2 * w**2 )* etrans ) and similarly in a few other parts of the code. This is equivalent to replace epsilon_2(omega) by epsilon2(omega- shift/hbar) , at least for small broadening parameter so that the "delta function" is sharp , and it corrects automatically the real part of the dielectric function. This is valid for LDA, and in principle not valid for GGA, although I suspect that in practice gives the same results. In fact I would appreciate a feedback to this comment. Best regards -- Eduardo Menendez Proupin Departamento de Qu?mica Fisica Aplicada Facultad de Ciencias Universidad Aut?noma de Madrid 28049 Madrid, Spain Phone: +34 91 497 6706 On leave from: Departamento de Fisica, Facultad de Ciencias, Universidad de Chile URL: http://fisica.ciencias.uchile.cl/~emenendez "*Padece, espera y trabaja para gentes que nunca conocer? y que a su vez padecer?n, esperar?n y trabajar?n para otros, que tampoco ser?n felices, pues el hombre ans?a siempre una felicidad situada m?s all? de la porci?n que le es otorgada. Pero la grandeza del hombre est? precisamente en querer mejorar lo que es. En imponerse Tareas. En el Reino de los Cielos no hay grandeza que conquistar, puesto que all? todo es jerarqu?a establecida, inc?gnita despejada, existir sin t?rmino, imposibilidad de sacrificio, reposo y deleite. Por ello, agobiado de penas y de Tareas, hermoso dentro de su miseria, capaz de amar en medio de las plagas, el hombre puede hallar su grandeza, su m?xima medida en el Reino de este Mundo*". Alejo Carpentier, El reino de este mundo, (1949). Translate from spanish here http://translate.google.com/?hl==UTF-8==es=en -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/1201fad8/attachment.htm
[Pw_forum] NEB procedure
Thanks a lot Anton, Best regards, Ettore On Sep 22, 2011, at 2:16 PM, Tone Kokalj wrote: > Dear Ettore, > > putting intermediate images will not help to locate the presumable > maximum in your case. > > (increasing the num_of_images may help though, but even that can be > insufficient if transition state is very close to final state) > > > Intermediate images are used to do a better initial guess of the > reaction path. Intermediate images are not really used, but all the > input images (initial+intermediates+final) are connected so as to > produce a piecewise-linear path and then the EQUIDISTANT linear > interpolation is performed on this piecewise-linear path. > > In your case you should set the CI_scheme = 'manual' > and specify as the climbing image the last image before the final image > in the CLIMBING_IMAGES card, i.e.: > > >num_of_images = N >CI_scheme = 'manual' >... > / > > CLIMBING_IMAGES > N-1 > > By doing that the N-1'th image will climb up to the transition state > (TS) by the CI-NEB scheme, provided the TS is indeed there before the > top site. > > Best regards, > -- > Anton Kokalj > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax:+386-1-477-3822) > > Please, if possible, avoid sending me Word or PowerPoint attachments. > See: http://www.gnu.org/philosophy/no-word-attachments.html > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum
[Pw_forum] LDA norm-conserving pseudopotential for Fe: to Pengju Ren
On Thu, 2011-09-22 at 11:29 +0300, helen at fh.huji.ac.il wrote: > My problem is that it asks me for the label and occupancy of the > wavefunctions, and I don't know what was used to generate the > fhi file on the abinit site. guess something sensible, then verify if it works. The wavefunction label is used only for the printout of projected dos. The l value is used, but I think that the code always assume s-p-d-f ordering. P. -- Paolo Giannozzi, IOM-Democritos and University of Udine, Italy
[Pw_forum] stable phase
If you found a phonon with an imaginary frequency, then you can find a supercell of the L10 structure, displace the atoms in it according to the symmetry of the phonon, and relax the structure to obtain another structure with lower energy (enthalpy if you are working at fixed pressure). Here's how I did it: Michael J. Mehl, Gus L. W. Hart and Stefano Curtarolo Density functional study of the L10??IrV transition in IrV and RhV Journal of Alloys and Compounds Volume 509, Issue 3, 21 January 2011, Pages 560-567 http://dx.doi.org/10.1016/j.jallcom.2010.08.102 Note that the instabilities we found in the IrV L10 structure will not necessarily be the same as you find in L10 M-C. On 09/22/2011 01:30 PM, bhabya sahoo wrote: > i am calulated b1 to b2 transition of some metal carbide > i found b1 to b2 transition at 140 gpa > from phonon dispersion i found dyanamical unstabilty at 140 gpa b1 phase > but i am also > found b2 is dyanamical unstable(in X and M) directions so i thought > there must be other phase which may be stable at 140 gpa > for this calculated L10 phase which will less enthalpy than b2 at 140 > gpa but also this shows imaginary frequency in X direction > so what is the stable phase? > > b d sahoo barc > mumbai > -- Michael J. Mehl Head, Center for Computational Materials Science Naval Research Laboratory Code 6390 Washington DC
[Pw_forum] Other example with cpx problem on qe-43
0.000 the requested type of NH chains is 0 total number of thermostats used 1 0 0 ionic degrees of freedom for each chain9 nose` mass(es) for chain1 = 14.437 atom i (in sorted order) is assigned to this thermostat : 1 1 1 Cell Dynamics Parameters (from STDIN) - internal stress tensor calculated Starting cell generated from CELLDM Cell parameters will be re-read from restart file Constant VOLUME Molecular dynamics cell parameters are not allowed to move Verbosity: iprsta = 1 Simulation dimensions initialization unit vectors of full simulation cell in real space: in reciprocal space (units 2pi/alat): 110.0.0. 1.0.0. 2 0. 10.0. 0.1.0. 3 0.0. 10. 0.0.1. Stick Mesh -- nst = 1117, nstw = 277, nsts = 1117 n.st n.stw n.stsn.gn.gw n.gs min2233 5532233 791179843 79117 max2233 5532233 791179843 79117 2233 5532233 791179843 79117 Real Mesh - Global Dimensions Local Dimensions Processor Grid .X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z. 545454 545454 1 1 1 Array leading dimensions ( nr1x, nr2x, nr3x ) = 545454 Local number of cell to store the grid ( nrxx ) = 157464 Number of x-y planes for each processors: nr3l =54 Smooth Real Mesh Global Dimensions Local Dimensions Processor Grid .X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z. 545454 545454 1 1 1 Array leading dimensions ( nr1x, nr2x, nr3x ) = 545454 Local number of cell to store the grid ( nrxx ) = 157464 Number of x-y planes for each processors: nr3sl =54 Reciprocal Space Mesh - Large Mesh Global(ngm_g)MinLocal MaxLocal Average 39559 39559 39559 39559.00 Smooth Mesh Global(ngms_g) MinLocal MaxLocal Average 39559 39559 39559 39559.00 Wave function Mesh Global(ngw_g)MinLocal MaxLocal Average 4922 4922 49224922.00 System geometry initialization -- Scaled positions from standard input O0.500990E+00 0.500990E+00 0.50E+00 H0.683250E+00 0.477570E+00 0.40E+00 H0.477570E+00 0.683250E+00 0.499980E+00 Position components with 0 are kept fixed ia x y z 1 0 0 0 2 1 1 1 3 1 1 1 %% from cp_read_cell : error # 1 cannot open restart file for reading: .//h2o_mol_52.save/data-file.xml %% stopping ... STOP 2 Thanks for your attention. Luis A. Leon. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/24a86cfb/attachment-0001.htm
[Pw_forum] from cp_read_cell : error # 2
Hi, no. I have tried the examples that comes with the program, and I get the same error. I have changed this order, and I get the same error. I do not know. Thanks for your collaboration. On Thu, Sep 22, 2011 at 12:25 PM, Paolo Giannozzi wrote: > > On Sep 22, 2011, at 19:13 , Luis Antonio Leon Martinez wrote: > > > cannot open restart file for reading: .//si_52.save/data-file.xml > > did you run with "restart_mode='from_scratch" first? > > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/a9eebc18/attachment.htm
[Pw_forum] from cp_read_cell : error # 2
5 7.65 2.55 7.65 Ionic position will be re-read from restart file All atoms are allowed to move Ionic temperature is not controlled Cell Dynamics Parameters (from STDIN) - internal stress tensor calculated Starting cell generated from CELLDM Cell parameters will be re-read from restart file Volume dynamics with newton equations Volume dynamics: the temperature is not controlled Constant PRESSURE Molecular dynamics: External pressure (GPa) =0.00 Volume mass =7.00 Verbosity: iprsta = 1 Simulation dimensions initialization unit vectors of full simulation cell in real space: in reciprocal space (units 2pi/alat): 110.20000.0. 1.0.0. 2 0. 10.20000. 0.1.0. 3 0.0. 10.2000 0.0.1. Stick Mesh -- nst = 259, nstw =69, nsts = 259 n.st n.stw n.stsn.gn.gw n.gs min 517 137 517909311899093 max 517 137 517909311899093 517 137 517909311899093 Real Mesh - Global Dimensions Local Dimensions Processor Grid .X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z. 252525 252525 1 1 1 Array leading dimensions ( nr1x, nr2x, nr3x ) = 252525 Local number of cell to store the grid ( nrxx ) = 15625 Number of x-y planes for each processors: nr3l =25 Smooth Real Mesh Global Dimensions Local Dimensions Processor Grid .X. .Y. .Z. .X. .Y. .Z. .X. .Y. .Z. 252525 252525 1 1 1 Array leading dimensions ( nr1x, nr2x, nr3x ) = 252525 Local number of cell to store the grid ( nrxx ) = 15625 Number of x-y planes for each processors: nr3sl =25 Reciprocal Space Mesh - Large Mesh Global(ngm_g)MinLocal MaxLocal Average 4547 4547 45474547.00 Smooth Mesh Global(ngms_g) MinLocal MaxLocal Average 4547 4547 45474547.00 Wave function Mesh Global(ngw_g)MinLocal MaxLocal Average 595595595 595.00 System geometry initialization -- Scaled positions from standard input Si 0.00E+00 0.00E+00 0.00E+00 Si 0.50E+00 0.50E+00 0.00E+00 Si 0.00E+00 0.50E+00 0.50E+00 Si 0.50E+00 0.00E+00 0.50E+00 Si 0.25E+00 0.25E+00 0.25E+00 Si 0.75E+00 0.75E+00 0.25E+00 Si 0.25E+00 0.75E+00 0.75E+00 Si 0.75E+00 0.25E+00 0.75E+00 %% from cp_read_cell : error # 2 cannot open restart file for reading: .//si_52.save/data-file.xml %% stopping ... STOP 2 Now, I want to know if you you have a list of errors showed in this program, for instance, error # 1, error # 2, and so on. This is an example proposed in a tutorial. What can I do? Thanks for your colaboration. Luis A. Leon. -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/b40d02cf/attachment-0001.htm
[Pw_forum] LDA norm-conserving pseudopotential for Fe: to Pengju Ren
Dear Pengju Ren, Thank you very much for your reply. I've tried using fhi2upf.f90 in the upftools directory to covert the .fhi file I downloaded from the abinit site. My problem is that it asks me for the label and occupancy of the wavefunctions, and I don't know what was used to generate the fhi file on the abinit site. There appear to be 4 wavefunctions in this file so I tried guessing that they were 3s,3p,3d and 4s, as these are the obvious choices. However the generated UPF file then lists: Generated using Fritz-Haber code Author: unknownGeneration date: as well iron, fhi98PP : Trouiller-Martins-type, LDA Ceperley/Alder Perdew/Wang (1992), l 1The Pseudo was generated with a Scalar-Relativistic Calculation nl pn l occ RcutRcut US E pseu 3s 0 0 2.00 0.000 0.000 0.000 3p 0 1 6.00 0.000 0.000 0.000 3d 0 2 6.00 0.000 0.000 0.000 4s 0 3 2.00 0.000 0.000 0.000 and the angular momentum values do not make sense This is the info given in the fhi file: iron, fhi98PP : Trouiller-Martins-type, LDA Ceperley/Alder Perdew/Wang (1992), l= 1 local 26.000 8.000011001 zatom,zion,pspdat 6 73 1521 0 pspcod,pspxc,lmax,lloc,mmax,r2well 0.000 0.000 0.000 rchrg, fchrg, qchrg 5--- These two lines are available for giving more information, later 6 7-Here follows the cpi file from the fhi98pp code- 8.0E+004 I would be very grateful for any help with this, Dr.Helen Eisenberg, Post-doc, Fritz-Haber Research Center, Hebrew University, Jerusalem Dear Helen If you have a abinit format PP, you can convert it to pwscf format by the tools fhi2upf in upftools/ directory. I suggest you read http://www.quantum-espresso.org/pseudo-notes.php for more information. Good luck! Pengju Ren This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] NEB procedure
Thanks Layla, Bests Ettore On Sep 22, 2011, at 9:46 AM, Layla Martin-Samos wrote: > Dear Ettore, you can put more intermediate images by hand and the NEB > algorythm will "relax" then for you. I put relax within "" because neb > relaxes along the perpendicular directions of the chain. > > best regards > > Layla > > 2011/9/22 Ettore Baldini-Neto > Dear users, > > I have some questions regarding a NEB calculation. > > As input to a neb file I should use, at least, the initial and final > positions (both well previously relaxed). > What I want is to calculated the energy barrier for the transition of a metal > from one stable position (let's say a hollow position on a C ring) to another > one (also stable but with slightly higher total energy than first, let's say > the Top position). > > When I use just the initial and final positions and perform the calculations, > asking the code to automatically divide the grid, I get an ascendent curve > form the first to the last as expected. > But at a position just before the Top position I also expect the energy > barrier to be a little higher than the energy at this final site (Top) > because the metal is at a unstable position. > > So here are is my question, a very basic one since I have no previous > experience with this kind of calculation. > > I can put more intermediate images, automatically or by hand, in order to > better mapping the region around this position (Top). > In the second case, should these intermediate images be previously optimized > or the neb does it for me?? > > Thanks in advance, > > > *** > Ettore Baldini-Neto > Researcher at W. von Braun Center for Advanced Research, Campinas, Brazil > *** > ___ > 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 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/672c2137/attachment.htm
[Pw_forum] NEB procedure
Dear users, I have some questions regarding a NEB calculation. As input to a neb file I should use, at least, the initial and final positions (both well previously relaxed). What I want is to calculated the energy barrier for the transition of a metal from one stable position (let's say a hollow position on a C ring) to another one (also stable but with slightly higher total energy than first, let's say the Top position). When I use just the initial and final positions and perform the calculations, asking the code to automatically divide the grid, I get an ascendent curve form the first to the last as expected. But at a position just before the Top position I also expect the energy barrier to be a little higher than the energy at this final site (Top) because the metal is at a unstable position. So here are is my question, a very basic one since I have no previous experience with this kind of calculation. I can put more intermediate images, automatically or by hand, in order to better mapping the region around this position (Top). In the second case, should these intermediate images be previously optimized or the neb does it for me?? Thanks in advance, *** Ettore Baldini-Neto Researcher at W. von Braun Center for Advanced Research, Campinas, Brazil ***
[Pw_forum] cluster timing & delay -v.lousy way-
Dear Changru, Since there are other programs included such as Yambo which are not compatible with the recent version of Q.E. , this version is used -- Your sincerely, Mona Elfadil SudREN - Network Engineer www.suin.edu.sd +249911319113 > Dear Mona Elfadil, > > Q.E.3.0 was released on 2005. I would suggest you to try the newest > version 4.3.2 first. You can find it here: > > http://www.quantum-espresso.org/download.php > > HTH, > Changru > > On 21 Sep, 2011, at 17:19, Mona M.O. Elfadil wrote: > >> Dear all, >>We had run an example -Q.E.3.0.1- from your package few days ago >> on a linux cluster- CentOS 5-, and it worked although we had no >> BLAS, LAPACK nor an FFTW packages previously installed - not >> surprising,since you have said so in your user guide-. >> Then we had tried an experimental data. It took a single CPU 10 min to >> get >> the results. While, unfortunately, it took a 16 CPUs more than 40 min to >> process the same data. >> We had tried the following: >> - Referring to your user guide: It needs a detailed physics background >> which is unavailable at the moment. >> - Downloading these mathematical packages: >> FFTW 3.1.2-3 & FFTW 2.1.5-2 >> LAPACK 3_0-2 >> BLAS 3_0-2 >> (RPM versions) >> In the configuration phase of Q.E. it said that both LAPACK and FFTW are >> not found although BLASS was successfully configured. >> >> We could not find FFTWND in our internet search(As a packet). But in >> your >> archive you have said it is not an error. >> >> Assuming that all other factors are well, what could be the cause?? >> >> (P.S.: we are the system administrators) >> >> -- >> Your sincerely, >> Mona Elfadil >> SudREN - Network Engineer >> www.suin.edu.sd >> +249911319113 >> >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Changru Ma > SISSA & Theory at Elettra group > email: crma at sissa.it > tel: +39 040 378 7870 > http://www.sissa.it/~crma > --- > > ___ > 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/20110922/3a38642e/attachment.htm
[Pw_forum] charge density plot in xcrysden
Hi! I do not know how to help you. If you do not assistance on this mailing list, you may want to try with a specific mailing list for xcrysden users, which, I am sure, must exist. Good luck - SB On Sep 21, 2011, at 11:37 PM, Tram Bui wrote: > Dear Everyone, > I have an output file of the SiC bulk charge density (bulk.xsf). I open > it using xcrysden and do data grid to get the display of color-plane and > isoline, etc. I'd also like to make the isoline with different color other > than just the gray scale, how can I do so in xcrysden? > > Regards, > Tram Bui > > M.S. Materials Science & Engineering > trambui at u.boisestate.edu > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum --- Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste http://stefano.baroni.me [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype) La morale est une logique de l'action comme la logique est une morale de la pens?e - Jean Piaget -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110922/6aecad08/attachment.htm
[Pw_forum] FFT on a small mesh
On Sep 22, 2011, at 2:13 , dario rocca wrote: > Dear Developers (reminder: the proper place where to contact developers is the q-e- developers mailing list on qe-forge.org) > I would be interested in calculating the FFT with a small > reciprocal space cutoff. > Namely beyond the FFT for wavefunctions and density I would like to > use an > additional FFT on an "object" that requires a cutoff smaller than > the wavefunctions > (but of course the real space mesh would still be the same). All > the standard > FFT machinery seems very specialized to the wavefunction/density case it is, by construction. In the most recent versions, however, the FFT stuff is encapsulated into a few "descriptors" that are initialized in a few specific routines. Note that the CP code has a third grid, the "small box" grid, a subset of the dense grid in real space.This is used to deal with augmentation charges in the USPP framework. You may want to have a look at it. I have heard of work done to speed up exact exchange and GW calculations, consisting in performing the needed FFT with a lower cutoff. Nothing has yet percolated to the current development version, though. P. --- Paolo Giannozzi, Dept of Chemistry, Univ. Udine, via delle Scienze 208, 33100 Udine, Italy Phone +39-0432-558216, fax +39-0432-558222
[Pw_forum] Questions about pseudopotential generation.
Dear Daniel, I think you can find the answers to your questions in the guide inside the QE distribution (new address in svn version is atomic/Doc) plus these: http://people.sissa.it/~dalcorso/lectures/lecture_pseudo_sb_2009.pdf http://www.impmc.upmc.fr/~paulatto/shanghai.pdf I am linking the PAW one (the second) in case you want to do GIPAW calculations. It is important to understand the PAW formalism before doing so. cheers, emine kucukbenli, phd student, sissa, italy SISSA Webmail https://webmail.sissa.it/ Powered by Horde http://www.horde.org/
