[Pw_forum] single atom calculations
Dear Adib
please try to learn the following example about atomic oxygen and not bad
to apply it to other atoms and compare the result with your
general chemistry comprehension.
calculation='scf',
restart_mode='restart',
prefix='O',
pseudo_dir = '../../pseudo/',
outdir='../tmp/',
/
ibrav= 0, celldm(1)=2.7585, nat= 1, ntyp= 1,
ecutwfc = 40, ecutrho = 400, nspin=2, starting_magnetization=1,
occupations='smearing', smearing='marzari-vanderbilt', degauss=0.001,
/
conv_thr = 1.0d-8,
mixing_beta=0.3,
electron_maxstep=200
/
CELL_PARAMETERS
10. 0. 0.
0.0 10.000 0.
0. 0. 10.000
ATOMIC_SPECIES
O 15.9994 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS {alat}
O0.0 0.0 0.0
K_POINTS {gamma}
Best Wishes, m
Masoud Nahali
SUT
masoud.nahali at gmail.com
alum.sharif.edu/~m_nahali
On Tue, Jul 15, 2014 at 2:31 AM, Samin, Adib J. wrote:
> Dear Quantum Espresso users,
>
>
> Is it possible to use Quantum Espresso to calculate the properties of a
> single atom from a certain element?
>
> It is my understanding that periodic boundary conditions need to be
> imposed.
>
> Would it be possible to create a sufficiently large unit cell containing a
> single atom of the desired element?
>
> Any clarifications on this issue would be greatly appreciated.
>
>
> Thanks,
>
> Adib Samin
>
>
> Adib Samin
>
> Graduate Fellow
>
> The Department of Aerospace and Mechanical Engineering
>
> The Ohio State University
>
>
>
>
>
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> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
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[Pw_forum] Fwd: au111 surface
Dear Khadije
1. For ibrav=0 you should specify the lattice parameter celldm(1) or "a"
and not all celldms.
2. If you study a surface why you have used the smallest vector for the
z-direction ? in this way you have made a cage not a surface.
Use larger vector in the direction that you expect to make a surface
and do more exercises about surfaces before solving this problem.
I hope it helps.
Best Wishes, m
--------
Masoud Nahali
SUT
masoud.nahali at gmail.com
alum.sharif.edu/~m_nahali
On Sat, Apr 19, 2014 at 12:45 PM, raha khalili wrote:
> Dear QE users
>
> I want to construct Au111 surfaces. But my output file seems to be
> incorrect. Could you help me for it?
>
> Input:
>
> calculation = 'relax'
> restart_mode='from_scratch',
> prefix='au',
> tprnfor = .true.
> pseudo_dir = '/home/khalili/espresso-5.0.2/pseudo',
> outdir='./'
> /
>
> ibrav= 0, celldm(1)=6.0, celldm(2)=1, celldm(3)=0.222460766,
> nat= 13, ntyp= 1,
> noncolin=.true.,
> lspinorb=.true.,
> starting_magnetization(1)=0.0,
> ecutwfc = 27.0,
> ecutrho = 391.0,
> occupations='smearing',
> smearing='fd',
> degauss=0.001
> /
>
> diagonalization='david'
> electron_maxstep = 500,
> mixing_mode = 'plain'
> mixing_beta = 0.7
> conv_thr = 1.0d-6
> /
>
> ion_dynamics = 'bfgs'
> /
> ATOMIC_SPECIES
> Au 196.966 Au.rel-pz-dn-rrkjus_psl.0.1.UPF
> ATOMIC_POSITIONS
> Au 2.949785413 3.672551581 0.719332431
> Au 2.742687251 2.86557 0.719332431
> Au 3.563230179 3.098796549 0.719332431
> Au 3.356132017 2.291817190 0.719332431
> Au 3.534436578 1.470557957 0.051950134
> Au 3.732270300 2.268356755 0.051950134
> Au 3.928237209 3.069472551 0.051950134
> Au 2.912648680 2.043258658 0.051950134
> Au 3.119592323 2.850332820 0.051950134
> Au 3.343806277 3.659523280 0.051950134
> Au 2.299120168 2.617060049 0.051950134
> Au 2.523263349 3.426298953 0.051950134
> Au 2.730361511 4.233278312 0.051950134
> CELL_PARAMETERS
> 6.0 0.0 0.0
> 0.0 6.0 0.0
> 0.0 0.0 1.334764594
> K_POINTS {Automatic}
> 1 1 4 1 1 1
>
> output:
> ATOMIC_POSITIONS (alat)
> Au 2.937386209 3.582923161 0.719330203
> Au 2.593545725 2.740963547 0.719333040
> Au 3.670168686 3.044796914 0.719331555
> Au 3.326200204 2.202685361 0.719334648
> Au 3.478788201 1.670372948 0.051951374
> Au 3.865644556 2.412608619 0.051953914
> Au 4.175978091 3.185452798 0.051947555
> Au 2.759515725 2.097309245 0.051954205
> Au 3.133871517 2.883011335 0.051949504
> Au 3.504225226 3.675472063 0.051948273
> Au 2.091449270 2.593809644 0.051950705
> Au 2.407897276 3.365285757 0.051948060
> Au 2.790900569 4.112185484 0.051947893
> End final coordinates
>
> Any help will be appreciated.
> --
> Khadije Khalili
> Ph.D Student of Solid-State Physics
> Department of Physics
> University of Mazandaran
> Babolsar, Iran
> kh.khalili at stu.umz.ac.ir
>
>
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>
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[Pw_forum] band calculation
Dear Ehsan
You should have used a k_point mesh (say k_point {automatic} 4 4 4 0 0 0)
for the first self consistent field calculation and so on. Probably You did
the computation at Gamma point. It depends on the system that you study how
to choose the proper k_points. For the next nscf step you should increase
the mesh grid to get a better band. I hope it helps.
Best Wishes, m
Masoud Nahali
SUT
masoud.nahali at gmail.com
alum.sharif.edu/~m_nahali
On Mon, Feb 3, 2014 at 9:50 PM, ehsan targholi wrote:
> hi
> i want to obtain band structure. i use of this method:
> scf->nscf->bands
> is right my method?
> when i do this way the bands calculation give this error:
>
>
>
> %%
> Error in routine bands (1):
> gamma_only case not implemented
>
>
> %%
>
> stopping ...
> please help me to solve this problem.
>
> best regard
> ehsan
> graduate student of iust
>
>
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[Pw_forum] Running jobs with Script on a cluster
Elliot wrote: Hello, > Can someone please help me incorporate my prepared job to be ran on a > cluster into the script(run_example) that is used to ran Quantum > Espresso calculations on a cluster. I'm working with a 128 core cluster > and I would like to use 8 cores. a short reply: your input: outdir = '/path/to/your/folder/tmp/' pseudo_dir = '/path/to/pseudo/' a command to run pw.x in parallel (without the script): /path/to/openmpi/bin/mpirun -np 8 /path/to/Quantum-Espresso/bin/pw.x < your-input.in > your-output.out Also you can set your environment_variables to run the examples using the script. In this case you should revise the following line to run the examples in parallel. PARA_PREFIX="/path/to/openmpi/bin/mpirun -np 8" ps* if you have already defined your paths in the .bashrc you won't need to write "/path/to/..." in above lines. Best Wishes, m -------- Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20131228/c8147c8a/attachment.html
[Pw_forum] no subject
Pallavi wrote: > So, here in the last iteration it is found that image 4, 5 and 6 are lower > in energy than the initial one. > But how is it possible? > What is the wrong in the procedure? > Thank you very much > Regards > Pallavi Bothra > Graduate student > JNCASR, Bangalore > India Dear Pallavi As you can see the error (eV/A) values your calculation has not converged yet ! so we can not speak about the physics of your system. You should increase the steps using nstep_path to make it converged. Also I think that conv_thr = 1.0d-10 is too much for such calculation. I hope it helps. Best Wishes, m -------- Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20131227/6cfdc7ce/attachment.html
[Pw_forum] vdW+PBE0
Dear Valentina In case you would like to consider the van der Waals interaction in the system that you study you can try the Grimme's DFT-D2 method which was implemented in q/e. In this method a semi-empirical dispersion potential is added to the conventional Kohn-Sham DFT energy. In practice you can add london=.true. to system name-list to cause it work. Best Wishes, m Valentina wrote on *Thu Dec 12 16:22:15 CET 2013 :* > Dear Quantum Espresso users, > We are modeling a system which needs the hybrid functional approach to be > correctly simulated. Next, we need to compute the Oxygen chemical > potential, and it has to be compared with the energy of the system. It is a > fact that van der Waals interactions are not negligible when modeling > molecular Oxygen. In order to have comparable quantities, we are wondering > if it is possible to use in Quantum Espresso a mixture of van der Waals and > PBE0 to model the Oxygen molecule. > Thanks, > Valentina > Valentina Dellac? > Group Materials Labs > PA - Virtual Analysis & Materials Modelling > Centro Ricerche Fiat S.C.p.A. > Sede legale e amministrativa: Strada Torino, 50 > 10043 Orbassano (TO), Italia > Tel +39 011 9083138 > Fax +39 011 9083666 Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20131212/14d6822b/attachment.html
[Pw_forum] QE 5.0.2 compile problem and MKL problem
Yue-Wen wrote *Mon Dec 9 09:58:40 CET 2013* In recent days, I'have compiled QE 5.0.2 for many times using different ways in several computing centers. Surprisingly, all gave me errors. The main problem is the MKL. ld: *cannot find -libmkl_scalapack_lp64.a* try configuring the q/e using "--with-scalalapack=no" ! it should work for your case. Best Wishes, m -------- Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20131209/d70a9fc5/attachment.html
[Pw_forum] How to relax heterojunction (supercell) structure in a appropriate way?
Yue-Wen Fang wrote on *Thu May 9 15:40:00 CEST 2013* > Dear all, > > when we need to make a relaxation of heterojunction (supercell, such as a > system contains 40 atoms), *which one in the following choices is the best > way?* > *A:* full relaxation (volume shape, lattice constant and atomic positions > vary) > *B: * fix the lattice constant > when you don't know the details of your system or it is not a common solid state system you should relax all the parameters. But if you know some little details of your system you can decrease the cost of variable-cell calculations. For instance if your system is a simple cubic with orthogonal vectors you can simply do some SCF calculation and plot E versus lattice constant to have an estimate of your cell parameter. Also it is not bad to use this cell constant as an input in a relaxation (not variable-cell one) process to find the optimized position of atoms. In this way you may be known more about your system and it is easier to start a vc-relax calculation. > any other better relaxation manners is welcome > thank you very much! > You can directly go to doing "vc-relax" and see whether the above procedure is less expensive or the current one ! let us know :) > > -- > > > Yue-Wen FANG, PhD candidate > Key Laboratory of Polar Materials and Devices, Ministry of > Education<http://clpm.ecnu.edu.cn/> > East China Normal University <http://www.ecnu.edu.cn/english/> > I will persist until I succeed! > -- next part -- > An HTML attachment was scrubbed... > URL: > http://pwscf.org/pipermail/pw_forum/attachments/20130509/6d87d04d/attachment-0001.html > Best Wishes, m Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali <http://alum.sharif.edu/%7Em_nahali> -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130510/5d0e0b9c/attachment.html
[Pw_forum] neb input using runjob
On Thu, Apr 25, 2013 at 12:00 PM, Alberto wrote: > > > I've had problems letting neb.x read the input. I need to use load leveler > and runjob. The command in the script I used looks like this: > > runjob --np 16 --ranks-per-node 8 --envs OMP_NUM_THREADS=4 --exe neb.x > -inp input_neb.in >> out_scf > > The neb.x program is unable to find any input, and gives me the following > error: > > > > %% > Error in routine string_methods (1): > Neither a file to parse nor input files for each image found > > > %% > > Anyone knows how to let the program read the input? > Thank you, > Alberto > > > Dear Alberto A simple script like the following line always function on Linux machines: mpirun -np 16 /PATH/To/QE/neb.x -inp A.in > A.out try this simple on or do it once with one CPU to check out your neb.x binary file. I hope it helps. Best Wishes, m Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130425/3253a469/attachment.html
[Pw_forum] Difficulties with scf convergence
Dear *?? ?? * Have you tried the calculation considering spin polarization, nspin=2 and checking the convergence ? you can try a smaller degauss value using marzari-vanderbilt or gaussian too. Please check the smearing energy contribution to your total energy. Are the interface atoms in close distances from each other ? I mean 1.2-2.0 angstrom for instance. If not and you put them at far distances from each other you may relax a van der Waals interaction in which the pure DFT is weak. Do you really need such high amount of cutoff for energy and density ? I hope it helps. Best Wishes, m Masoud Nahali SUT masoud.nahali at gmail.com alum.sharif.edu/~m_nahali On Mon, Apr 8, 2013 at 12:00 PM, *?? ??* wrote: > > Hi everybody, > > I am trying to optimize the structure of an interface between metal and > insulator but have difficulties with scf convergence. Here are the changes > in energies during scf cycle: > estimated scf accuracy < 17.58555120 Ry > estimated scf accuracy < 14.17435383 Ry > estimated scf accuracy < 2.05765892 Ry > estimated scf accuracy < 2.09375911 Ry > estimated scf accuracy < 1.37675281 Ry > estimated scf accuracy < 0.42594758 Ry > estimated scf accuracy < 0.29104539 Ry > estimated scf accuracy < 0.51143695 Ry > estimated scf accuracy < 0.18765814 Ry > estimated scf accuracy < 0.92590998 Ry > estimated scf accuracy < 0.93126088 Ry > estimated scf accuracy < 0.44023978 Ry > estimated scf accuracy < 0.33756785 Ry > estimated scf accuracy < 0.34216551 Ry > estimated scf accuracy < 0.36573444 Ry > estimated scf accuracy < 0.29089342 Ry > estimated scf accuracy < 0.29287805 Ry > estimated scf accuracy < 0.16940331 Ry > estimated scf accuracy < 0.17503222 Ry > estimated scf accuracy < 0.09708451 Ry > estimated scf accuracy < 0.07751341 Ry > estimated scf accuracy < 0.06774554 Ry > estimated scf accuracy < 0.15834930 Ry > estimated scf accuracy < 0.12269823 Ry > estimated scf accuracy < 0.12679734 Ry > estimated scf accuracy < 0.08558475 Ry > estimated scf accuracy < 0.04411767 Ry > estimated scf accuracy < 0.04754042 Ry > > I found similar posts on the forum ?but it didn't solve the problem. I > checked my structure with xcrysen...it seems to be ok. I am using USPP. > Any help and suggestions would be greatly appreciated. > > Thanks > > Here is my input: > > title = interface , > calculation = 'relax' , > restart_mode = 'from_scratch' , > wf_collect = .true. , > outdir = 'interface/' , > pseudo_dir = './' , > prefix = 'interface' , > lkpoint_dir = .true. , > disk_io = 'high' , > verbosity = 'high' , > nstep = 100 , > tstress = .false. , > tprnfor = .true. , > / > > ibrav = 8, > celldm(1) = 9.3957, > celldm(2) = 1.7321, > celldm(3) = 6., > nat = 72, > ntyp = 3, > ecutwfc = 50 , > ecutrho = 500 , > nbnd = 500, > occupations = 'smearing' , > degauss = 0.025 , > smearing = 'methfessel-paxton' , > nspin = 1 , > / > > electron_maxstep = 200, > conv_thr = 1.0d-6 , > mixing_mode = 'local-TF' , > mixing_beta = 0.1 , > mixing_ndim = 8 , > / > > ion_dynamics = 'bfgs' , > / > ATOMIC_SPECIES > ? BR, > > N V > -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20130408/a5191cad/attachment.html
[Pw_forum] Using a big box model to calculating the energy of isolated atom
Dear Hongsheng In this case I think that the more important issue to be noticed is considering spin polarization for most of atoms. Many mistakes in this issue arise from not considering spin polarization. I guess Considering "Symmetry" may symmetrize the charge density and causes some changes in electronic structure of atom (population of orbitals) or may do reversely with nosym='true'. Also, it is impossible for me to describe this issue based on DFT and the exchange-correlation parts in details. In quantum chemistry software based on Gaussian type orbitals basis set (not plane wave basis set) we compare energy of an atom with considering different spin multiplicities then find the lowest energy and call it "ground state". I can do it for some atoms (whatever you select) by Firefly software (former PC-GAMESS) and then you can compare it with the corresponding calculation by QE. These days I am very busy and going on a journey so let me do it in a due course; contact me :) Best Wishes Masoud ------ Masoud Nahali, Sharif University of Technology masoud.nahali at gmail.com; a <http://alum.sharif.edu/%7Em_nahali> lum.sharif.edu/~m_nahali P Save a Tree . . . Please don't print this e-mail unless you really need to. Hongsheng Zhao Wrote : Thanks a lot for all of the helps on this topic. I've checked and read > most the topics on this ML which are related to "calculating the energy > of isolated atom". It seems this is a tricky thing based on most of > the replies on this similar topics on this ML. > > Based on my understanding, till now, there are still some issues > puzzling me on this topic: > > 1- On the manual of pwscf (p37), we can find the following descriptions: > > > ... > Specify nosym=.true. to avoid generation of additional k-points in low > symmetry > ... > --- > > I want to know, by using nosym=.true., what's the different on the > k-points set obtained with the ones without using this option? For > example, when using a bcc box with a atom at its center, what's the > corresponding k-points set when using nosym=.true.? > > Furthermore, when we say a isolated atom, we mean a zero dimension > system. So the corresponding BZ sampling by using gamma only should be > OK. If so, there is no k-points issues at all - there only one k point > should be considered. Hence I'm confused on the description given by > the manual *avoid generation of additional k-points in low symmetry*. > Any hints? > > 2- From this ML, I found the following notes: > > - > while doing calculations for any zero dimensions you should always set > nosym =.true. > --- > > Does this mean: when I do the calculations for isolated > atom/molecule/nanocluster and so on, I should always set nosym =.true.? > > 3- Prof. Paolo Giannozzi given the following descriptions on some > similar topic in this ML: > > - > calculations on isolated atoms with plane waves are tricky. > Compare your results with what you get with the atomic code, > in which you can fix occupancies at will > > > My issue: how to fix the occupancies based on the results? Any examples? > > What do you mean by saying *at will*? If really is a thing *at will*, > why should we do it? > > Regards > > > > > On Thu, Jul 28, 2011 at 10:12 AM, Gabriele Sclauzero > > mailto:gabriele.sclauzero at epfl.ch>> > > wrote: > > > > > > Il giorno 28/lug/2011, alle ore 01.55, Hongsheng Zhao ha scritto: > > > >> Hi all, > >> > >> I've learned that when using the a large-cell ( i.e., a big box ) to > >> calculate the energy of isolated atom, it should be done without > >> symmetry. But I'm not sure what's the meaning of the "without > >> symmetry" here and how to ensure this when we using a a big box > >> model > >> for this purpose. Any hints on this issue? > > > > This is a FAQ on this forum: have you spent some time browsing the > > archives? > > > > OK, I'll give you a hint: "nosym"... but use it with care! > > > > HTH > > > > GS > > > >> > >> Regards > >> -- > >> Hongsheng Zhao >> <mailto:zhaohscas at yahoo.com.cn>> > >> School of Physics and Electrical Information Science, > >> Ningxia University, Yinchuan 750021, China > >> ___ > >> Pw_forum mailing list > >> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org> > >> http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > > / PH H2 462, Station 3, CH-1015 Lausanne/ > > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110730/73b581d9/attachment.htm
[Pw_forum] "relax" vs. "vc-relax" calculation
Dear Tram I think that vc-relax calculation is more convenient for your case; in addition you should glance over the below tutorial about defects : http://www.fisica.uniud.it/~giannozz/QE-Tutorial/tutorial_defects.pdf I hope it is useful. Best Wishes Masoud -- Masoud Nahali, Sharif University of Technology masoud.nahali at gmail.com; alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali> P Please don't print this e-mail unless you really need to. *Tram wrote on Thu Jul 7 06:47:35 CEST 2011* > Dear Everyone, I have a quick question regarding the "relax" vs. "vc-relax" calculation for my SiC structure. As I run the " scf" calculation with a single defect, e.g. interstitial or sustitutional, the lattice parameter of the unit cell is expected to be stretched. And as I checked, the lattice constant got larger when introduced defect. Now, I'm just wondering between the "relax" calculation (which will only relax the atomic position ) and the "vc-relax" one (which will relax both atomic position and the lattice of the unit cell), which one would you recommend to use? Thank you very much, Tram Bui M.S. Materials Science & Engineeringtrambui at u.boisestate.edu <http://www.democritos.it/mailman/listinfo/pw_forum> -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110707/e82540c7/attachment.htm
[Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
Dear Paolo and QE Users I am writing since maybe it is useful for others; I replaced the MKL (10.2.3.029) by MKL (10.3.4.191, version of 2011.4.19) and got rid of the error. Now, all examples run well. Best Wishes Masoud -- Masoud Nahali, Sharif University of Technology masoud.nahali at gmail.com; alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali> P Please don't print this e-mail unless you really need to. > On Fri, 2011-07-01 at 13:56 +0430, Masoud Nahali wrote: > > > > In all tries both QE (4.2) and QE(4.3.1) compiles well but QE (4.3.1) > > could not find shared libraries such as libmkl_intel_lp64.so and stopped > > once again: it is a problem of your software setup, not of QE. > You should put in your .basrch, .profile, .cshrc, .whatever, > the correct initialization for MKL libraries. What you have > is either not correct or not executed when it is needed. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110702/a62b038d/attachment.htm
[Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
Dear Paolo Thanks for your reply; it is the results of list dynamic dependencies command for pw.x binary of QE (4.2) and QE (4.3.1) : *looki at looki:~$ ldd /home/looki/QE4.3.1/QE/bin/pw.x* linux-vdso.so.1 => (0x7fff489e2000) libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x7fe662b13000) libmkl_intel_lp64.so => not found libmkl_sequential.so => not found libmkl_core.so => not found libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x7fe66290e000) libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x7fe6626d5000) libmpi.so.0 => /usr/lib/libmpi.so.0 (0x7fe662425000) libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x7fe6621d9000) libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x7fe661f64000) libdl.so.2 => /lib/libdl.so.2 (0x7fe661d6) libnsl.so.1 => /lib/libnsl.so.1 (0x7fe661b46000) libutil.so.1 => /lib/libutil.so.1 (0x7fe661942000) libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x7fe661655000) libm.so.6 => /lib/libm.so.6 (0x7fe6613d2000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x7fe6611ba000) libpthread.so.0 => /lib/libpthread.so.0 (0x7fe660f9d000) libc.so.6 => /lib/libc.so.6 (0x7fe660c1a000) /lib64/ld-linux-x86-64.so.2 (0x7fe662e3) *looki at looki:~$ ldd /home/looki/QE4.2/QE/bin/pw.x * linux-vdso.so.1 => (0x7fff61dff000) libfftw3.so.3 => /usr/lib/libfftw3.so.3 (0x7f4ae2c3f000) libblas.so.3gf => /usr/lib/atlas/libblas.so.3gf (0x7f4ae22a4000) libmpi_f90.so.0 => /usr/lib/libmpi_f90.so.0 (0x7f4ae209f000) libmpi_f77.so.0 => /usr/lib/libmpi_f77.so.0 (0x7f4ae1e67000) libmpi.so.0 => /usr/lib/libmpi.so.0 (0x7f4ae1bb7000) libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0x7f4ae196a000) libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0x7f4ae16f6000) libdl.so.2 => /lib/libdl.so.2 (0x7f4ae14f2000) libnsl.so.1 => /lib/libnsl.so.1 (0x7f4ae12d7000) libutil.so.1 => /lib/libutil.so.1 (0x7f4ae10d4000) libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x7f4ae0de7000) libm.so.6 => /lib/libm.so.6 (0x7f4ae0b63000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x7f4ae094c000) libpthread.so.0 => /lib/libpthread.so.0 (0x7f4ae072f000) libc.so.6 => /lib/libc.so.6 (0x7f4ae03ab000) /lib64/ld-linux-x86-64.so.2 (0x7f4ae2f5c000) Although the exact path of MKL libraries was included in .bashrc file, as it is shown "libmkl_intel_lp64.so" and some other *.so files were not found by QE (4.3.1). In addition, I have copied the library files to /usr/lib and for a test the code was configured with including the path of library directory by LIBDIR. In all tries both QE (4.2) and QE(4.3.1) compiles well but QE (4.3.1) could not find shared libraries such as libmkl_intel_lp64.so and stopped. I appreciate your help in advance. Best Wishes Masoud -- Masoud Nahali, Sharif University of Technology masoud.nahali at gmail.com; alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali> P Please don't print this e-mail unless you really need to. > On Fri, 2011-07-01 at 03:08 +0430, Masoud Nahali wrote: > > > The MKL libraries path was exactly included in the .bashrc file, > > ...] I can run all examples of QE (version 4.2) successfully and for > > the 4.3 and 4.3.1 ones I get the error while loading shared libraries: > > libmkl_intel_lp64.so: cannot open shared object file: No such file or > > directory. It is strange for me what makes such difference. > On Fri, Jul 1, 2011 at 11:48 AM, Paolo Giannozzi wrote: if I remember correctly, v.4.2 was linking *.a (static) mkl libraries, > while v 4.3 links *.so (shared) libraries, by default. You can verify > this using "ldd executable-file-name". If a compiled code doesn't > find shared libraries, there is something incorrect in your init files. > > P. > -- > Paolo Giannozzi, IOM-Democritos and University of Udine, Italy > > > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110701/9b6fd569/attachment.htm
[Pw_forum] libmkl_intel_lp64 (QE 4.2 vs 4.3)
Dear Quantum Espresso Users In QE (version 4.2) the code read and open shared objects without any error but in QE (version 4.3 and 4.3.1) the code cannot open libmkl_intel_lp64.so file and so I cannot run the examples of QE successfully. The MKL libraries path was exactly included in the .bashrc file, mpif90 works well, and all versions were compiled without any error. The versions were configured by "./configure MPIF90=mpif90 F77=gfortran" and then made. But, only I can run all examples of QE (version 4.2) successfully and for the 4.3 and 4.3.1 ones I get the error while loading shared libraries: libmkl_intel_lp64.so: cannot open shared object file: No such file or directory. It is strange for me what makes such difference. Thank you for your help in advance. I appreciate the answers. Best Wishes Masoud ------ Masoud Nahali, Sharif University of Technology masoud.nahali at gmail.com; alum.sharif.edu/~m_nahali<http://alum.sharif.edu/%7Em_nahali> P Please don't print this e-mail unless you really need to. -- next part -- An HTML attachment was scrubbed... URL: http://pwscf.org/pipermail/pw_forum/attachments/20110701/b4e548a7/attachment-0002.html
[Pw_forum] charge density
Dear Vicky As I know, a new structure should be relaxed so then you can use the relaxed structure as input for post-processing process like calculating charge density. I hope it helps. Best Wishes Masoud -- Masoud Nahali, Sharif University of Technology On Sun, May 15, 2011 at 12:10 PM, vicky singh wrote: > > > Hi > > can anybody please suggest me. I am studying a system of Ni with 40 atoms > and then i am replacing one Ni with any other alloying elements. I want to > the charge density plot. I have got the charge density by two methods. > 1) substituted the alloying element and performed scf through pw.x, and > pp.x > 2) relax the structure and then performed scf through pw.x, and pp.x. > > what difference should i try to figure out which will suggest the right > method. > > Thanks in advance > vicky singh > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110515/3bdf970b/attachment.htm
[Pw_forum] charge density
On Mon, May 9, 2011 at 12:29 PM, vicky singh wrote: > > > Hi > > I am studying the effect of alloying on a supercell with 40 atoms. I am > replacing one Ni with different alloying elements. To get the charge > density > should i relax the system and the perform the scf or simple scf will give > the effect of alloying. > > Thanks in advance. > > vicky singh > research student > Bangalore > Dear Vicky Atoms with different sizes have different strain effects in your system and certainly their electronic states aren't same. So if I were you I do a relax calculation. Also, if you want to decrease the cost of your calculations, sometimes it may be good to fix the positions of some side atoms. I hope it helps. Best Wishes Masoud -- Masoud Nahali, Sharif University of Technology -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110509/8923e111/attachment.htm
[Pw_forum] Cohesive Energy of N2 molecule
> > Izaak Williamson wrote on Tue, 3 May 2011 09:54:14 -0700 > > I am trying to calculate the cohesive energy of the N2 molecule using the > attached input file (relax.in) and am getting a value of -16.57 eV. I use > DFT > with GGA and the pseudo-potential N.pbe-rrkjus.UPF. Other work [Fuchs et. > al., > Phys. Rev. B 65, (2002)245212] has performed similar calculations and > obtained > values ~10.5 eV. They even list an experimental value of 9.76 eV. Why is my > value so much higher? Is there anything in my input file that could be > giving > inaccurate results? Is it my pseudo-potential that is causing this problem? > > Thanks for any help. > > -- > Izaak Williamson > Research Assistant > Physics Department > Boise State University > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110503/9e728584/attachment.htm > -- next part -- > A non-text attachment was scrubbed... > Name: relax.in > Type: application/octet-stream > Size: 662 bytes > Desc: not available > Url : > http://www.democritos.it/pipermail/pw_forum/attachments/20110503/9e728584/attachment.obj > Dear Izaak Did you considered symmetry for energy calculation of atomic nitrogen or not ? As you know the electronic configuration of atomic nitrogen is 1s[2] 2s[2] 2px[1] 2py[1] 2pz[1] and seems symmetric. In some quantum mechanical codes when one calculates the energy of this system without considering symmetry may get wrong answer since the system may go to a non-symmetric status like 1s[2] 2s[2] 2px[2] 2py[1]. Please calculate the energy with and without symmetry and compare them. Another important issue is that did you considered polarization of spin (with defining a proper starting magnetization value for nitrogen) in your calculations ? It can cause a significant change in the energy since your system includes unpaired electrons. Let us know the changes after considering the above issues. I hope it helps. Best Wishes Masoud -- Masoud Nahali, Sharif University of Technology > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110503/aa8d1a4d/attachment.htm
[Pw_forum] dos vs. pdos.tot
*Dear Mehrnoosh I think that a**tomic states on different atoms are not orthonormal which makes PDOS-tot different from DOS. I hope it helps. * Best Wishes Masoud -- Masoud Nahali, Ph.D Student at Sharif University of Technology *>Mehrnoosh Hazrati* Wrote on W*ed Apr 27 08:35:51 CEST 2011* >Hi dear QE users, >I have a question about DOS diagram : what is the difference between DOS >gained of the dos.x code and PDOS_tot gained of projwfc.x code output ?! >Regards -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110427/ea272a3d/attachment.htm
[Pw_forum] Fortan compiler cannot create executables
Dear Elie Using csh/tcsh you should try "setenv" instead of "export". Elie on Sun, 17 Apr 2011 00:31:35 wrote: > > Unfortunately, my CSH shell does not support the EXPORT command. > > Best Wishes Masoud -- Masoud Nahali, Ph. D Student Sharif University of Technology -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110417/56082aa6/attachment.htm
[Pw_forum] Fortan compiler cannot create executables
Dear Elie Try "export PATH=$PATH:/path/to/your/directory/where/g95/installed" then update your database (updatedb command) and restart your computer. Also, you can copy g95 binary files from where you have installed the g95 to /bin.You should examine "g95" or "gfortran" commands in your linux console before trying to compile the QE. I hope it helps. Best Wishes Masoud -- Masoud Nahali, Ph. D Student Sharif University of Technology On Sat, Apr 16, 2011 at 11:57 AM, Elie Moujaes wrote : > > Hello everyone, > > > > I am trying to re-install quantum espresso-4.3 on the University's LINUX > interface (because of a recent crash and I lost most of my files). > > when I "sudo ./configure ", It is giving an error stating that : > > checking building system type... x86_64-unknown-linux-gnu > > checking architecture... x86_64 > > checking for ifort.. no > > checking for pgf90... no > > checking for pathf95.. no > > checking for sunf95.. no > > checking for openf95... no > > checking for gfortran... no > > checking for g95... no > > checking for f90... no > > checking for Fortran compiler default output... configure: error: Fortran > compiler cannot create executables > > See `config.log' for more details. > > > > I have already installed g95. I really don't know why > this error is coming. > Please can anyone help. > > Thanks > > Elie Moujaes > University of Nottingham > Nottingham > NG7 2RD > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110416/501c2f16/attachment.htm
[Pw_forum] Re : graphite cell optimization failed
Dear Eric Try london="true" to get improved answer; as you should know DFT is weak to calculate dispersion forces and by using the keyword one can include these forces semi-empirically. I hope it helps. Best Wishes Masoud ------ Masoud Nahali, Sharif University of Technology Eric Wrote: Dear all, I'm trying to optimize unit cell parameter of graphite. The problem is the c axis gets too long. Starting from published data my initial parameters are a=4.59203 Bohr and c=12.513 Bohr. The final values are 4.664 and 15.829 respectively. I need someone to explain to me what I did wrong, I've attached my input file. That's a basic calculation so it's very frustrating to not make it done. I thank you in advance, Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau <mailto:germaneau at gucas.ac.cn <http://www.democritos.it/mailman/listinfo/pw_forum>> College of Physical Sciences Graduate University of Chinese Academy of Sciences Yuquan Road 19A Beijing 100049 China -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110323/dd7527a4/attachment.htm
[Pw_forum] van der waals
Dear Mahdi Try "london=.true." in your input file and then check your result carefully to find the changes compared to the input file which does not have the "london=.true.'. Best Wishes Masoud ------ Masoud Nahali, Sharif University of Technology Mahdi Mirnezhad wrote: > > Dear,all > How can I calculate van der waals interaction between to layer in nanotube > ? > or > related between van der waals and energy? > thanks for your attention > mahdi mirnezhad,iran,guilan > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20110116/e8e0e5da/attachment.htm
[Pw_forum] electron configuration of Ni
Dear Heather and QE Users Many thanks for your attention and answer. The case of study is a Ni atom which is connected to 4 carbon atoms in a graphite-like structure. The projected DOS calculation by projwfc.x (lowdin charge analysis) after relaxation procedure shows that the Ni electronic configuration is : 4s[0.4023] + 3d[8.8971]. As I know the initial guess of this pseudo-potential is 3d[9] 4s[1] for Ni and I wanna to know that if the initial guess was 3d[8] 4s[2], would I get 4s[0.4023] + 3d[8.8971] again after the relaxation procedure or not ? I appreciate any suggestion in advance. Best Wishes * - Masoud Nahali PhD Student of Physical Chemistry Sharif University of Technology * Heather Kulik wrote : > > Dear Masoud, > > You are correct in that the pseudopotential was generated in the state 3d9 > 4s1. > > One minor point is that according to NIST ( > http://physics.nist.gov/PhysRefData/ASD/levels_form.html), the low-lying > experimental atomic energy levels of Ni are: > > ^3F(3d84s2) ~0 and ^3D(3d94s1) ~ <0.1 eV, ^1D(3d94s1) ~ <0.5 eV. > > However, the good news is that, the state in which the pseudopotential was > generated should not prevent you from accurately describing states that > have > 3d84s2 character since the core electrons from a 3d94s1 and 3d84s2 Ni > should > be described fairly similarly. > > You can also verify the character of your electronic states using any of > the > postprocessing codes (e.g. projected density of states from projwfc.x) > > Note: A more serious problem is that if your extended system (i.e. more > than > one atom) has numerous solutions close in energy comparable to the > character > of the atomic system, most x-c functionals will likely fail to predict the > correct ordering. > > You should try comparing the relative energies you get for a few > representative systems to experimental data where possible to identify if > the GGA (or LDA) suffers from any particular bias in the relative ordering > of these states. > > Hope that helps! > -- > Heather K > Postdoc at Stanford University > > > On Wed, Dec 15, 2010 at 12:31 AM, Masoud Nahali live.com<http://www.democritos.it/mailman/listinfo/pw_forum> > >wrote: > >* Dear Quantum Espresso Users *>* *>* I have used Ni.pbe-nd-rrkjus.UPF pseudo-potential for nickel in my project. *>* In the info part of this pseudopotential has been written : *>* *>* Info: Ni PBE 3d9 4s1 RRKJ3 US *>* *>* But I know that the well established electron configuration for nickel is *>* "3d8 4s2" and now I am too worry that it may cause an error in my work. May *>* it ? *>* I appreciate your help to understand the point in advance. Many Thanks *>* *>* *>* *>* Best Wishes *>* * *>* *>* - *>* *>* Masoud Nahali *>* *>* PhD Student of Physical Chemistry *>* Sharif University of Technology *>* * *>* * ** ** -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101216/6adaa95d/attachment.htm
[Pw_forum] electron configuration of Ni
Dear Quantum Espresso Users I have used Ni.pbe-nd-rrkjus.UPF pseudo-potential for nickel in my project. In the info part of this pseudopotential has been written : Info: Ni PBE 3d9 4s1 RRKJ3 US But I know that the well established electron configuration for nickel is "3d8 4s2" and now I am too worry that it may cause an error in my work. May it ? I appreciate your help to understand the point in advance. Many Thanks Best Wishes * ----- Masoud Nahali PhD Student of Physical Chemistry Sharif University of Technology * -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20101215/1f51f2bf/attachment.htm
[Pw_forum] relaxation and TS
Dear Prof. Stefano Baroni and Vega Lew
Many many thanks for your detailed answers and helpful comments. This is
scf energy of each relaxation steps :
-411.0652023864
-411.1576447124
-411.1877929276
-411.1989785058
-411.1027361193**
-411.2006610355
-411.2078087316
-411.2087637085
-411.2094335080
-411.2112728535
-411.2137042660
-411.2145098860
-411.2163180058
-411.2200044391
-411.2186337506**
-411.2238781353
-411.2272606876
-411.233547
-411.2410057850
-411.248714
-411.2432716037**
-411.2545344840
-411.2632404207
-411.2686094326
-411.2697596541
-411.2688830229**
-411.2723156669
-411.2728025269
-411.2731592912
-411.2735337540
-411.2741229900
-411.2749931725
-411.2755105410
-411.2761617487
-411.2768678588
-411.2772028256
-411.2775503379
-411.2785154793
-411.2823072885
-411.2298751795**
-411.2825004743
-411.2845206434
-411.2875009929
-411.2801470356**
-411.2954982819
-411.3096061836
-411.3466223605
-411.367570164
-411.3724319076
-411.3795692495
-411.3812435563
-411.3823959522
-411.3829995766
-411.3833540501
-411.3835954004
-411.3839027669
-411.3841960285
-411.3843908495
-411.3844986818
-411.3845647753
-411.3846244537
-411.3846644112
-411.3846945470
-411.3847346519
-411.3848191008
-411.3848652595
-411.3849367730
-411.3849811533
-411.3851262954
-411.3534987061**
-411.3850020755
-411.3851753523
-411.3852665074
-411.3853358233
-411.3855056618
-411.3858383834
-411.3860833880
-411.3866016967
-411.3874393558
-411.3878819548
-411.3881741927
-411.3884732905
-411.3886017423
-411.3886998952
-411.3887918295
-411.3888586159
-411.3888992755
-411.3889304888
-411.3889622530
-411.3889906826
-411.3890146960
-411.3890447538
-411.3890806506
-411.3891138607
-411.3891306978
-411.3891510321
-411.3891853920
-411.3892253795
-411.3892680354
-411.3893152439
-411.3893766070
-411.3894890010
-411.3895516220
-411.3896539375
-411.3896995617
-411.3897936720
-411.3898406152
-411.3898796419
-411.3899004418
** shows the step in which the energy rises. I don't think that these
points indicate a TS or something like that since one may see such points
through any optimization procedure; am I correct ?
Also, here is the input :
calculation = "relax",
pseudo_dir = "/home/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/AB/tmp",
restart_mode = 'from_scratch'
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
nstep=120
/
ibrav = 4,
a = 4.864990484,
b = 4.864990484,
c = 16.418933296,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 26,
ntyp = 3,
ecutwfc = 40.D0,
ecutrho = 480.D0,
occupations = 'smearing'
smearing ='mp',
degauss = 0.03,
nspin = 2,
starting_magnetization(1)= 0.01,
starting_magnetization(2)= 0.01,
starting_magnetization(3)= 0.01,
london=.true.,
nosym=.true.
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
Ni 58.69Ni.pbe-nd-rrkjus.UPF
O 15.9994 O.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C0.0 0.0 0.00 0 0
C2.461165257 -0.001796837 0.002770193
C -1.232804188 2.130698110 0.002678921
C1.230011567 2.131364695 0.003376901
C -0.00507 1.422214727 0.001510708
C -1.234100323 3.553382228 0.001755289
C2.458567713 1.421054385 0.003703007
C1.228614904 3.554143930 0.002513562
C -0.235163108 0.160826352 3.247131267
C2.244119337 0.161060766 3.248352597
C -1.457317029 2.298122349 3.233987380
C1.004488573 2.308122685 3.246477338
C1.003490453 0.877294779 3.260744638
C -0.228726740 3.007907781 3.234369538
C3.466400555 0.879138405 3.235278922
C2.237111888 3.008093688 3.233133671
C1.014869884 -0.620629524 6.400327421
C3.476740887 -0.544001537 6.494151711
C -0.280354238 1.625208172 6.378065136
C2.312052832 1.626645989 6.400900301
Ni 1.023326058 0.872911705 5.337347244
O1.023326000 0.872911000 8.7
O2.012052000 1.326645000 8.7
C -0.206008752 3.013580161 6.506783380
C3.478548719 0.866737695 6.505990211
C2.235793764 3.015530163 6.513155404
K_POINTS {automatic}
4 4 1 1 1 1
*-*
*Masoud Nahali*
*PhD Student of Physical Chemistry
Sharif University of Technology
*
Stefano Baroni wrote :
>
> On Sep 29, 2010, at 5:32 PM, vega lew wrote:
>
> > Through the relaxation of a oxygen molecule on a surface by QE4.2, it
> dissociated and adsorbed on the surface. The scf energy of each step has
> decreased in compared with the previous step until the relaxation completed.
> Now, can one say that there is not any TS for O2 dissociation here ?
> >
> >> Probably not. The potential energy
[Pw_forum] relaxation and TS
Dear PWscf Users Through the relaxation of a oxygen molecule on a surface by QE4.2, it dissociated and adsorbed on the surface. The scf energy of each step has decreased in compared with the previous step until the relaxation completed. Now, can one say that there is not any TS for O2 dissociation here ? Or is the reaction spontaneous ? If there was a TS in this procedure (dissociation and adsorption of O2) would the optimization algorithm of QE4.2 stop the work or continue ? Any help would be *appreciate*. Many Thanks ** ** *-* *Masoud Nahali* *PhD Student of Physical Chemistry Sharif University of Technology * -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100929/431b9443/attachment.htm
[Pw_forum] plotband.x and displaying style
Dear Gabriele Sclauzero I need to eliminated the lines not the dots since the line style causes the noisy display. Replacing the dot by line in the grep command dose not eliminate the lines. would you please help me to eliminate the lines. Many thanks for your helps. Sincerely Yours Masoud Nahali SUT > You can modify the postscript file using this bash onliner. Suppose your PS > file is named file1.ps, then simply do > > grep -v dot file1.ps > file2.ps > > and you will get the same graph without dots in file2.ps > > > HTH > > GS > > > Il giorno 27/ago/2010, alle ore 09.53, Masoud Nahali ha scritto: > > > Dear QE Users > > > > When I use plotband.x to produce the band structure, the output PS file > is a mixed of points and lines. > > Is there a way that the plotband.x produces only points in the PS file > and neglect the lines ? > > Since, sometimes the bands are too close to each other and using line and > point style will cause some noisy display and so I need displaying the > points only. > > > > I would appreciate your help and thank you in advance. > > > > > > Best Wishes > > Masoud Nahali > > SUT > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100828/7138e707/attachment-0001.htm
[Pw_forum] plotband.x and displaying style
Dear QE Users When I use plotband.x to produce the band structure, the output PS file is a mixed of points and lines. Is there a way that the plotband.x produces only points in the PS file and neglect the lines ? Since, sometimes the bands are too close to each other and using line and point style will cause some noisy display and so I need displaying the points only. I would appreciate your help and thank you in advance. Best Wishes Masoud Nahali SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100827/a45019a8/attachment.htm
[Pw_forum] vc-relax, GGA
> > Dear Santos Using vc-relax variable, all cell parameters ( distances and angles) are optimized so one may obtain some parameters lower than expected. Did you consider symmetry in your job or not? this would affect the resuls. I think that your obtained value is plausible. vc-relaxed calculation in quantum espresso works very well and effective. Best Wishes Masoud Nahali SUT > Hello PWscf users. I optimize a triclinic cell using the vc-relax, GGA > functional. My expectation was that all values of the calculated parameters > were > slightly higher than the respective experimental values. But, the angle > alpha > showed a value slightly lower. The experimental value is in degree, 103.32, > the > calculated value is 102.6. There is some inconsistency in this result? > > Sincerely, > A. S. Santos > > Univesidade Federal Fluminense > Niter?i-Rio de Janeiro-Brasil > > > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100824/19c8ccef/attachment.htm
[Pw_forum] Band Structure of Graphite
999 0.50 1.00
0.12 0.12 0.50 1.00
0.11 0.11 0.50 1.00
0.09 0.09 0.50 1.00
0.083332 0.083332 0.50 1.00
0.06 0.06 0.50 1.00
0.04 0.04 0.50 1.00
0.03 0.03 0.50 1.00
0.01 0.01 0.50 1.00
0.00 0.00 0.50 1.00
0.025000 0.00 0.50 1.00
0.05 0.00 0.50 1.00
0.075000 0.00 0.50 1.00
0.10 0.00 0.50 1.00
0.125000 0.00 0.50 1.00
0.15 0.00 0.50 1.00
0.175000 0.00 0.50 1.00
0.20 0.00 0.50 1.00
0.225000 0.00 0.50 1.00
0.25 0.00 0.50 1.00
0.275000 0.00 0.50 1.00
0.30 0.00 0.50 1.00
0.325000 0.00 0.50 1.00
0.35 0.00 0.50 1.00
0.375000 0.00 0.50 1.00
0.40 0.00 0.50 1.00
0.425000 0.00 0.50 1.00
0.45 0.00 0.50 1.00
0.475000 0.00 0.50 1.00
0.50 0.00 0.50 1.00
0.491667 0.016667 0.50 1.00
0.48 0.03 0.50 1.00
0.475000 0.05 0.50 1.00
0.46 0.06 0.50 1.00
0.458333 0.08 0.50 1.00
0.44 0.09 0.50 1.00
0.441666 0.11 0.50 1.00
0.42 0.12 0.50 1.00
0.424999 0.14 0.50 1.00
0.416665 0.15 0.50 1.00
0.408332 0.183332 0.50 1.00
0.38 0.18 0.50 1.00
0.391665 0.216665 0.50 1.00
0.383331 0.21 0.50 1.00
0.374998 0.249998 0.50 1.00
0.34 0.24 0.50 1.00
0.358331 0.283331 0.50 1.00
0.349997 0.27 0.50 1.00
0.341664 0.316664 0.50 1.00
0.30 0.30 0.50 1.00
*SCF input:*
calculation = "scf",
pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/koa/Graphite(2010-08-16)-A/Bulk/Band-DOS/tmp",
prefix='bulk'
/
ibrav = 4,
a = 2.457917036,
b = 2.457917036,
c = 6.302440996,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 4,
ntyp = 1,
ecutwfc = 40.D0,
ecutrho = 480.D0,
occupations = 'smearing'
smearing ='mp',
degauss = 0.03,
nspin = 2,
starting_magnetization(1)= 0.01,
london=.true.,
/
conv_thr = 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C 0.0 0.0 0.0
C 0.0 1.419079061 0.0
C 0.0 0.0 3.151220498
C 1.228958518 0.709539531 3.151220498
K_POINTS {automatic}
10 10 5 1 1 1
Truly Yours
Masoud Nahali
SUT
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[Pw_forum] Band Structure of Graphite
Dear Phillip and PWscf Users
As I said below, the calculated band structure for graphite is wrong and
I could not find the reason to solve the problem.
Would you please help me to find the correct band structure. The input
files are below. Many Thanks
> You have not asked any question. Could you please ask the question.
>
> On Thu, Aug 19, 2010 at 2:19 PM, Masoud Nahali >wrote:
>
> > Dear Quantum Espresso Users
> >
> > I take a wrong band from the input which is placed below.
> > I have selected 4 essential points in the K_POINTS {crystal} section,
> which
> > are P (0.3,0.3,0.0) , Q(0.0,0.5,0.0) , Gamma (0.0,0.0,0.0) , and
> > again
> > P (0.3,0.3,0.0) to plot the band-structure and compare it with
> > PRB,4,8,2441,1971. The distance between every two essential points is
> > divided to 50 parts
> > I would appreciate your help.
> >
> > Band input:
> >
> >
> > calculation = "bands",
> > pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
> > outdir = "/home/koa/Graphite(2010-08-16)-A/Bulk/Band-DOS/tmp",
> > prefix='bulk'
> > /
> >
> > ibrav = 4,
> > a = 2.457917036,
> > b = 2.457917036,
> > c = 6.302440996,
> > cosab = -0.5,
> > cosac = 1.0,
> > cosbc = 1.0,
> > nat = 4,
> > ntyp = 1,
> > ecutwfc = 40.D0,
> > ecutrho = 480.D0,
> > occupations = 'smearing'
> > smearing ='mp',
> > degauss = 0.03,
> > nspin = 2,
> > starting_magnetization(1)= 0.01,
> > london=.true.,
> > /
> >
> > conv_thr= 1.D-6,
> > mixing_beta = 0.7D0,
> > diagonalization = "david",
> > /
> > ATOMIC_SPECIES
> > C 12.0107 C.pbe-rrkjus.UPF
> > ATOMIC_POSITIONS {angstrom}
> > C0.0 0.0 0.0
> > C0.0 1.419079061 0.0
> > C0.0 0.0 3.151220498
> > C1.228958518 0.709539531 3.151220498
> > K_POINTS {crystal}
> > 151
> > 0.300.300.001
> > 0.3266630.3266630.002
> > 0.3199970.3199970.003
> > 0.3133300.3133300.004
> > 0.3066640.3066640.005
> > 0.270.270.006
> > 0.2933300.2933300.007
> > 0.2866640.2866640.008
> > 0.2799970.2799970.009
> > 0.2733310.2733310.0010
> > 0.240.240.0011
> > 0.2599970.2599970.0012
> > 0.2533310.2533310.0013
> > 0.2466640.2466640.0014
> > 0.2399980.2399980.0015
> > 0.210.210.0016
> > 0.2266640.2266640.0017
> > 0.2199980.2199980.0018
> > 0.2133310.2133310.0019
> > 0.2066650.2066650.0020
> > 0.180.180.0021
> > 0.1933310.1933310.0022
> > 0.1866650.1866650.0023
> > 0.1799980.1799980.0024
> > 0.1733320.1733320.0025
> > 0.150.150.0026
> > 0.1599980.1599980.0027
> > 0.1533320.1533320.0028
> > 0.1466650.1466650.0029
> > 0.130.130.0030
> > 0.120.120.0031
> > 0.1266650.1266650.0032
> > 0.110.110.0033
> > 0.1133320.1133320.0034
> > 0.100.100.0035
> > 0.090.090.0036
> > 0.0933320.0933320.0037
> > 0.080.080.0038
> > 0.070.070.0039
> > 0.070.070.0040
> > 0.060.060.0041
> > 0.050.050.0042
> > 0.050.050.0043
> > 0.040.040.0044
> > 0.040.040.0045
> > 0.030.030.0046
> > 0.020.020.0047
> > 0.020.020.0048
> > 0.010.010.0049
> > 0.0066670.0066670.0050
> > 0.000.000.0051
> > 0.000.010.0052
> > 0.000.020.0053
> > 0.000.030.0054
> > 0.00
[Pw_forum] OpenMPI / QE INSTALLATION ISSUES
Dear Edmund Formerly I had installed PWscf on CentOS and there was not any main problem. Please be sure that your gfortran works well and note that "--with-tm" option is generally only necessary if the TM headers and libraries are not in default compiler/linker search paths. I have installed the Openmpi without "--with-tm". Did you install proper libraries on your system ? Best Wishes Masoud Nahali SUT > > Hi, > I am in the process of installing Quantum espresso but, am > experiencing issues compiling my OpenMPI. I get the error "configure: > error: could not run a simple Fortran 77 program. Aborting." > > Am using gcc-4.2.2 and OpenMPI-1.4.2 on CentOS-5.4. The configure > instruction isssued appears as below: > ./configure --prefix=/opt/openmpi/1.4.2 --with-tm=/opt/torque/2.5.1 > CC=gcc CXX=g++ F77=gfortran FC=gfortran > > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100819/94509e82/attachment.htm
[Pw_forum] Band Structure of Graphite
00.420.0093
0.000.430.0094
0.000.440.0095
0.000.450.0096
0.000.460.0097
0.000.470.0098
0.000.480.0099
0.000.490.00100
0.000.500.00101
0.0066670.4966670.00102
0.010.490.00103
0.020.490.00104
0.020.480.00105
0.030.480.00106
0.040.480.00107
0.040.470.00108
0.050.470.00109
0.050.460.00110
0.060.460.00111
0.070.460.00112
0.070.450.00113
0.080.450.00114
0.0933320.4533320.00115
0.090.440.00116
0.100.440.00117
0.1133320.4433320.00118
0.110.430.00119
0.1266650.4366650.00120
0.120.420.00121
0.130.420.00122
0.1466650.4266650.00123
0.1533320.4233320.00124
0.1599980.4199980.00125
0.150.4166650.00126
0.1733320.4133320.00127
0.1799980.4099980.00128
0.1866650.4066650.00129
0.1933310.4033310.00130
0.180.380.00131
0.2066650.3966650.00132
0.2133310.3933310.00133
0.2199980.3899980.00134
0.2266640.3866640.00135
0.210.3833310.00136
0.2399980.3799980.00137
0.2466640.3766640.00138
0.2533310.3733310.00139
0.2599970.3699970.00140
0.240.340.00141
0.2733310.3633310.00142
0.2799970.3599970.00143
0.2866640.3566640.00144
0.2933300.3533300.00145
0.270.3499970.00146
0.3066640.3466640.00147
0.3133300.3433300.00148
0.3199970.3399970.00149
0.3266630.3366630.00150
0.300.300.00151
scf input:
calculation = "scf",
pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/koa/Graphite(2010-08-16)-A/Bulk/Band-DOS/tmp",
prefix='bulk'
/
ibrav = 4,
a = 2.457917036,
b = 2.457917036,
c = 6.302440996,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 4,
ntyp = 1,
ecutwfc = 40.D0,
ecutrho = 480.D0,
occupations = 'smearing'
smearing ='mp',
degauss = 0.03,
nspin = 2,
starting_magnetization(1)= 0.01,
london=.true.,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C0.0 0.0 0.0
C0.0 1.419079061 0.0
C0.0 0.0 3.151220498
C1.228958518 0.709539531 3.151220498
K_POINTS {automatic}
10 10 5 1 1 1
Many Thanks
Masoud Nahali
SUT
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[Pw_forum] problem with vc-relax
Dear Olga Sedelnikova At first please use the C.pbe-rrkjus.UPF as the pseudopotential. This is well tested by Nicola Marzari , Phys. Rev. B 71, 205214 (2005), and also I have tested it. The paper of Nicola is very useful. please be careful that it is an ultra soft pseudopotential and you should select ecutrho 10X greater than ecutwfc. Don't be worry about the cell size in the Z-direction since it is due to london interactions and may not be predicted well by DFT. But you can use ?london=.true.? to improve the results. For both ion_dynamics and cell_dynamics I have used ?bfgs?. I am sure that you will get better results. Please examine and don't hesitates to inform me about the problem. Best wishes Masoud Nahali SUT > The problem is not with wrong charge. The error "charge is wrong" appeared > only for current options (smearing='mv', dynamics='damp', cg > diagonalization). If I use other physically appropriate options I will > obtain other errors: problem with davidson diagonalization, too small > trust_radius for bfgs method and sometimes error from efirmig.f90 "internal > error, cannot braket Ef". I have checked the dynamics of unit cell during > vc-relaxation by XCrySDen and found that interlayer distance and bond > length > in graphite decreased to ~ 2 and 1.2 Angstroms correspondingly. For > graphene calculations the unit cell was compressed along the z-axis and C-C > bond length decreased. However the "relax" calculation is fine. > > Can anybody recommend the right options for "vc-relax" calculation of > graphite? > > Thank you, > > Olga Sedelnikova > Nikolaev Institute of Inorganic Chemistry of SB RAS > > > > > Please visit this achieve > > http://www.democritos.it/pipermail/pw_forum/2006-August/004713.html, and > > http://www.democritos.it/pipermail/pw_forum/2008-December/010853.html, > > you may find the solution. > > Best Regards > > Sanjeev > > > > Dept. of Physics > > Bhavnagar University > > Gujarat > > > > > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100728/5efc99a5/attachment-0001.htm > > -- > > Message: 2 > Date: Wed, 28 Jul 2010 11:44:27 +0200 > From: Merlin Meheut > Subject: [Pw_forum] Ni.pbe-sp-mt_gipaw.UPF > To: pw_forum at pwscf.org > Message-ID: <4C4FFBFB.6030206 at lmtg.obs-mip.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Dear PWSCF users, > > I would like to compute fcc Nickel metal using the pseudopotential > Ni.pbe-sp-mt_gipaw.UPF, available on your website. > I do not need the GIPAW part, but I have been said that this should not > be an issue. However, using an input very > similar to example02, the calculation fails by "not recognizing the > pseudo": > > --- > > %% > > from read_pseudo_gipaw : error # 1 > UPF/GIPAW in unknown format > > > %% > > stopping ... > > > I use Quantum Espresso version 4.1.2. > > Below is my input file (which works with pseudo Ni.pbe-nd-rrkjus.UPF > <http://www.quantum-espresso.org/pseudo/1.3/UPF/Ni.pbe-nd-rrkjus.UPF>) : > > >disk_io = 'default' , > pseudo_dir = '$PBS_O_WORKDIR', > outdir = '/tmpdir/$PBS_O_LOGNAME/', > tprnfor= .true., > tstress= .true., > calculation= 'scf' > prefix = 'ni', > verbosity = 'high', > / > > ibrav=2, celldm(1) =6.65, nat= 1, ntyp= 1, > nspin=2, > starting_magnetization(1)=0.5, > degauss=0.02, > smearing='mp', > occupations='smearing', > ecutwfc =27.0 > ecutrho =300.0 > / > > conv_thr = 1.0d-8 > mixing_beta = 0.7 > / > ATOMIC_SPECIES > Ni 58.6934 Ni.pbe-sp-mt_gipaw.UPF > ATOMIC_POSITIONS > Ni 0.00 0.00 0.00 > K_POINTS AUTOMATIC > 8 8 8 1 1 1 > > Thanks for any help, > > Merlin Meheut > > -- > Merlin M?heut > Maitre de conf?rences > LMTG- Universit? Paul Sabatier Toulouse 3 > 14 avenue Edoaurd Belin > 31400 Toulouse > tel: (+33)5 61 33 26 21 > Fax: (+33) 5 61 33 25 60 > Mobile: (+33) 6 34 67 57 02 > > > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20100728/a31abd1f/attachment-0001.htm
[Pw_forum] Sym.Ops
Dear PWscf Users For the graphite bulk, in the output file I see "24 Sym.Ops." but for the graphite surface (a slab with 10 angstrom vacuum) I see "6 Sym.Ops." . Is this plausible and correct ? I appreciate your help. Many Thanks Masoud Nahali SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100721/8d967297/attachment.htm
[Pw_forum] c_bands: 4 eigenvalues not converged
Dear Paolo Giannozzi
Many thanks for your help. I had a mistake and thought that it is a
significant error of vc-relax.
> > I get the below lines in the first iterations but after the
> > iteration # 4 or 5 disappears and again in the next steps the
> > story repeats.
> >
> > Davidson diagonalization with overlap
> > c_bands: 1 eigenvalues not converged
> > c_bands: 4 eigenvalues not converged
> >
> > As proposed in the manual and forum I tried to ran the Job without
> > considering symmetry
>
> where did you read that?
>
> \paragraph{{\em Warning : N eigenvectors not converged}}
> This is a warning message that can be safely ignored if it is not
> present in the last steps of self-consistency. If it is still present
> in the last steps of self-consistency, and if the number of
> unconverged eigenvector is a significant part of the total, it may
> signal serious trouble in self-consistency (see next point) or
> something badly wrong in input data.
>
> > I do not know that I must be worry of encountering such lines or not?
>
> as explained above, you shouldn't.
>
> > Also, May you please say me the "c_band" is related to my Carbon
> > atoms or not?
>
> no: "c_bands" is the routine that issues the message
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
> Best Wishes
Masoud Nahali
SUT
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[Pw_forum] c_bands: 4 eigenvalues not converged
Dear PWscf Users I get the below lines in the first iterations but after the iteration # 4 or 5 disappears and again in the next steps the story repeats. Davidson diagonalization with overlap c_bands: 1 eigenvalues not converged c_bands: 4 eigenvalues not converged As proposed in the manual and forum I tried to ran the Job without considering symmetry and the number of such lines reduced but did not disappear completely and the vc-relax calculation in such way is too time consuming and not completed yet. My system is a 3 layers graphite with palladium impurity. I do not know that I must be worry of encountering such lines or not? Also, May you please say me the "c_band" is related to my Carbon atoms or not? I appreciate your help. calculation = "vc-relax", etot_conv_thr= 1.0D-4, forc_conv_thr= 1.0D-3, / ibrav = 4, a = 4.9178, b = 4.9178, c = 22.8224, cosab = -0.5, cosac = 1.0, cosbc = 1.0, nat = 25, ntyp = 2, ecutwfc = 40.D0, ecutrho = 480.D0, occupations = 'smearing' smearing ='mp', degauss = 0.03, nspin = 2, starting_magnetization(1)= 0.01, starting_magnetization(2)= 0.5, london=.true., / conv_thr= 1.D-6, mixing_beta = 0.7D0, diagonalization = "david", / ion_dynamics="bfgs" / cell_dynamics = 'bfgs', press = 0.0, / Many Thanks Masoud Nahali SUT -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100718/99ef352e/attachment.htm
[Pw_forum] vc-relax and dt
Dear PWscf Users Is using and setting the variable "dt" in the vc-relax calculation necessary or not ? In the forum are many different suggestions. Also, how can one determine which value of the variable "max_seconds" is sufficient and safe. when one does not use the "max_seconds" the vc-relax calculation may takes huge time without changing the cell after a specific time. A comprehensive example for vc-relax calculation should be very useful. Many Thanks Masoud -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100715/dbe6cfb3/attachment.htm
[Pw_forum] vc-relax time
Dear Gabriele and pwscf users Perfectly I am sure that the positions of atoms is exactly correct. Note that the input is belong to a (1*1) slab and indeed you could not see a honeycomb ! but It is easy to see a honeycomb when you have a (2*2) slab like this: C0.000352513 0.001055549 0.0 C2.459305478 0.000933657 -0.008798962 C -1.229191611 2.130502759 -0.008802160 C1.229819481 2.130516670 -0.008801637 C0.000327447 1.420695799 -0.007291549 C -1.229173562 3.550193436 -0.007292113 C2.459296954 1.420621766 -0.009715082 C1.229852979 3.550208684 -0.007292392 C0.000507119 0.000488868 3.187515573 C2.459486429 0.000491165 3.187352189 C -1.228985445 2.130026298 3.187352283 C1.229997454 2.130026366 3.187352273 C1.229970852 0.710263879 3.187439366 C0.000476982 2.839800509 3.187332530 C3.688943914 0.710263968 3.187439418 C2.459456202 2.839797012 3.187439363 C0.000212609 0.000545761 6.403453823 C2.459191836 0.000545600 6.403451859 C -1.229278051 2.130084159 6.403451942 C1.229700861 2.130084205 6.403451921 C0.000121431 1.420208410 6.403892505 C -1.229369239 3.549746424 6.403892711 C2.459100653 1.420208253 6.403888354 C1.229609673 3.549746469 6.403892772 a = 4.9178, b = 4.9178, c = 16.4112, 10 angstrom vacuum Also, see the "As.vcs00.in" example in the "VCSexample" folder of quantum espresso 4.2. In this example a vc-relax calculation has been performed using the max_seconds and dt keyboard. Many Thanks I hope one helps these problems mentioned below. >Are you completely sure? You can find as an attachment a picture (from >xcrysden) of the central graphene layer according to the positions given >in your input. You can now judge if it looks like a honeycomb lattice. > Yes, indeed the high ecutrho is important for ultrasoft > pseudopotentials. About the rippling : It was my mistake in selecting > a wrong pseudopotential which has a hole. Nicola had explained it > before and accordingly I solved it. The graphite surface is not > ripple. When I use the "max_second=6000 and dt=150" the job completes > very fast as the example of pwscf. Is the using of such keyboards > plausible? >Please spend some time reading Doc/INPUT_PW to understand the meaning of >the _keywords_. dt is used only for molecular dynamics runs, not >relaxations, while max_seconds has nothing to do with how fast your job >is completed. > > Dear Gabriele Sclauzero and pwscf Users > > > Many thanks for your attentions. The cell dimension and the positions of > >the atoms are exactly correct. Yes, indeed the high ecutrho is important > for > >ultrasoft pseudopotentials. About the rippling : It was my mistake in > >selecting a wrong pseudopotential which has a hole. Nicola had explained > it > >before and accordingly I solved it. The graphite surface is not ripple. > When > >I use the "max_second=6000 and dt=150" the job completes very fast as the > >example of pwscf. Is the using of such keyboards plausible? > >As I mentioned before I had used the optimized cell parameters of (1*1 > >slab) for vc-relaxing the (2*2 slab) and I expected to see the results > very > >soon but the calculation was time consuming while there was only a very > very > >bit change of the cell dimensions during this 16 hours. There is only 1-3 > >iterations per each step in the output file and each of them was time > >consuming. The job was completed after about 50 steps. > > - > > > Dear Masoud, > > > > first I would suggest you to use bfgs as the algorithm for both ions > and > > cell dynamics. Excepted particular cases, it should reach the minimum > much > > faster. > > > > Also, why do you specify the cell with such an unusual way. You simply > need > > celldm(1) and celldm(3) with ibrav=4 if you want to describe an hexagonal > > lattice. Other suggestions: your ecutrho looks really large to me, do you > > really need it. On the other hand, degauss might be too large to describe > a > > spin-polarized system. > > > > Then, are you sure that you have built correctly your supercell? It looks > > like there are some C-C bonds much shorter that others in the central > > graphene plane (1.2 instead of 1.4 angs). Please check again your > structure. > > In general, you can expect that if you relax the atoms in the supercell > > some kind of surface-reconstruction may appear, since you leave more > freedom > > to atoms to rearrange in structures with larger periodicity. I don't > think > > this is the case for graphite, but you may find some ripples (as you > > mentioned in your earlier emails, if I am not wrong) if the C-C bonds are > at > > a distance shorter than the theoretical equilibrium
[Pw_forum] vc-relax time
Dear Gabriele Sclauzero and pwscf Users
Many thanks for your attentions. The cell dimension and the positions of
the atoms are exactly correct. Yes, indeed the high ecutrho is important for
ultrasoft pseudopotentials. About the rippling : It was my mistake in
selecting a wrong pseudopotential which has a hole. Nicola had explained it
before and accordingly I solved it. The graphite surface is not ripple. When
I use the "max_second=6000 and dt=150" the job completes very fast as the
example of pwscf. Is the using of such keyboards plausible?
As I mentioned before I had used the optimized cell parameters of (1*1
slab) for vc-relaxing the (2*2 slab) and I expected to see the results very
soon but the calculation was time consuming while there was only a very very
bit change of the cell dimensions during this 16 hours. There is only 1-3
iterations per each step in the output file and each of them was time
consuming. The job was completed after about 50 steps.
-
> Dear Masoud,
>
> first I would suggest you to use bfgs as the algorithm for both ions and
> cell dynamics. Excepted particular cases, it should reach the minimum much
> faster.
>
> Also, why do you specify the cell with such an unusual way. You simply need
> celldm(1) and celldm(3) with ibrav=4 if you want to describe an hexagonal
> lattice. Other suggestions: your ecutrho looks really large to me, do you
> really need it. On the other hand, degauss might be too large to describe a
> spin-polarized system.
>
> Then, are you sure that you have built correctly your supercell? It looks
> like there are some C-C bonds much shorter that others in the central
> graphene plane (1.2 instead of 1.4 angs). Please check again your structure.
> In general, you can expect that if you relax the atoms in the supercell
> some kind of surface-reconstruction may appear, since you leave more freedom
> to atoms to rearrange in structures with larger periodicity. I don't think
> this is the case for graphite, but you may find some ripples (as you
> mentioned in your earlier emails, if I am not wrong) if the C-C bonds are at
> a distance shorter than the theoretical equilibrium distance (I guess).
>
> HTH
>
Dear Quantum Espresso Users
>
> I vc-relaxed a (1*1) slab of graphite surface with 3 layers; It takes 20
minutes with parallel running by 4 CPUs. Then I used the exact optimized
cell parameters (obtained from vc-relaxed calculation) to make a (2*2) slab
of graphite with 3 layers and I expected to see the results in a few
minutes. But amazingly it took 17 hours to complete. 48 steps were done in
the calculation for vc-relaxing the cell which have the parameters that had
been optimized before. The cell parameters only change a very bit in the
current vc-relaxing the (2*2) slab. I appreciate if one explain the physical
procedure of vc-relaxing and the reason of the time needed for the
computation.
>
> input file:
>
> CONTROL
> calculation = "vc-relax",
> pseudo_dir = "/home/koa/soft/qe4.2/
> espresso-4.2/pseudo",
> outdir = "/home/koa/tmp",
> etot_conv_thr= 1.0D-4,
> forc_conv_thr= 1.0D-3,
> dt=80,
> /
>
> ibrav = 4,
> a = 2.4579,
> b = 2.4579,
> c = 16.3069,
> cosab = -0.5,
> cosac = 1.0,
> cosbc = 1.0,
> nat = 6,
> ntyp = 1,
> ecutwfc = 40.D0,
> ecutrho = 480.D0,
> occupations = 'smearing'
> smearing ='mp',
> degauss = 0.03,
> nspin = 2,
> starting_magnetization(1)= 0.003,
> london=.true.,
> /
>
> conv_thr= 1.D-6,
> mixing_beta = 0.7D0,
> diagonalization = "david",
> /
>
> ion_dynamics="cg"
> /
>
> cell_dynamics = 'damp-w',
> press = 0.0,
> /
> ATOMIC_SPECIES
> C 12.0107 C.pbe-rrkjus.UPF
> ATOMIC_POSITIONS {angstrom}
> C 0.0.0. 1 1 0
> C 0.1.419084720.
> C 0.00000.3.15347111
> C 11.228963420.709542363.15347111
> C 0.0.6.30694222
> C 0.1.419084726.30694222
> K_POINTS {automatic}
> 4 4 1 1 1 1
>
Sincerely Yours
Masoud Nahali
SUT
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[Pw_forum] vc-relax time
Dear Quantum Espresso Users
I vc-relaxed a (1*1) slab of graphite surface with 3 layers; It takes 20
minutes with parallel running by 4 CPUs. Then I used the exact optimized
cell parameters (obtained from vc-relaxed calculation) to make a (2*2) slab
of graphite with 3 layers and I expected to see the results in a few
minutes. But amazingly it took 17 hours to complete. 48 steps were done in
the calculation for vc-relaxing the cell which have the parameters that had
been optimized before. The cell parameters only change a very bit in the
current vc-relaxing the (2*2) slab. I appreciate if one explain the physical
procedure of vc-relaxing and the reason of the time needed for the
computation.
input file:
CONTROL
calculation = "vc-relax",
pseudo_dir = "/home/koa/soft/qe4.2/
espresso-4.2/pseudo",
outdir = "/home/koa/tmp",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
dt=80,
/
ibrav = 4,
a = 2.4579,
b = 2.4579,
c = 16.3069,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 6,
ntyp = 1,
ecutwfc = 40.D0,
ecutrho = 480.D0,
occupations = 'smearing'
smearing ='mp',
degauss = 0.03,
nspin = 2,
starting_magnetization(1)= 0.003,
london=.true.,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="cg"
/
cell_dynamics = 'damp-w',
press = 0.0,
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C 0.0.0. 1 1 0
C 0.1.419084720.
C 0.0.3.15347111
C 11.228963420.709542363.15347111
C 0.0.6.30694222
C 0.1.419084726.30694222
K_POINTS {automatic}
4 4 1 1 1 1
Sincerely Yours
Masoud Nahali
SUT
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[Pw_forum] vc-relax time and physical procedure
Dear Quantum Espresso Users
I vc-relaxed a (1*1) slab of graphite surface with 3 layers; It takes 20
minutes with parallel running by 4 CPUs. Then I used the exact optimized
cell parameters (obtained from vc-relaxed calculation) to make a (2*2) slab
of graphite with 3 layers and I expected to see the results in a few
minutes. But amazingly it took 17 hours to complete. 48 steps were done in
the calculation for vc-relaxing the cell which have the parameters that had
been optimized before. The cell parameters only change a very bit in the
current vc-relaxing the (2*2) slab. I appreciate if one explain the physical
procedure of vc-relaxing and the reason of the time needed for the
computation.
input file:
CONTROL
calculation = "vc-relax",
pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/koa/tmp",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
dt=80,
/
ibrav = 4,
a = 2.4579,
b = 2.4579,
c = 16.3069,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 6,
ntyp = 1,
ecutwfc = 40.D0,
ecutrho = 480.D0,
occupations = 'smearing'
smearing ='mp',
degauss = 0.03,
nspin = 2,
starting_magnetization(1)= 0.003,
london=.true.,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="cg"
/
cell_dynamics = 'damp-w',
press = 0.0,
/
ATOMIC_SPECIES
C 12.0107 C.pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C 0.0.0. 1 1 0
C 0.1.419084720.
C 0.0.3.15347111
C 11.228963420.709542363.15347111
C 0.0.6.30694222
C 0.1.419084726.30694222
K_POINTS {automatic}
4 4 1 1 1 1 Nahali
SUT
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[Pw_forum] Re : Is the Graphite surface flat ?
Dear Quantum Espresso Users I thank Prof. Nicola Marzari and Giuseppe Mattioli for their kind attentions and helps. I read the paper; it was too useful for me. Yes, I had a bad mistake in selecting a wrong pseudopotential, Sincerely Yours Masoud Nahali Sharif University of Technology -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100708/17fd6888/attachment.htm
[Pw_forum] Is the Graphite surface flat ?
Dear pwscf users
answer to the comments:
(many thanks for your kind attention and help but I could not solve the problem)
to G. Scluuzero: I have used the experimental C-C distance but then I have
vc-relaxed the bulk cell and found the new positions. After vc-relax I have
used
these coordinates to "relax" the atoms in the cell with vacuum. Also the
innermost layer is not graphite-like and is rippled.
to D. C. Andera: this pseudopotential reproduces the experimental cell
parameter of the bulk correctly and exactly. the predicted cell parameter in
z-direction (c) by the other pseudopotentials is not so exact and sometimes, a
difference about 1 angstrom compared to experimental value appears.
to G. Mattioli:
london=.true. closes the atoms in the different layers to each other in the
relax calculation and did not solve the problem.
Now I am trying to relax a 5-layer sample and see the result. but it has not
completed yet. really I do not know the surface of graphite is "ripple" in the
nature (experimentally) or not? I appreciate your help.
> On 07/05/2010 08:19 PM, Masoud Nahali wrote:
> > Dear Quantum Espresso users
> >
> > I optimized the graphite bulk and the layers were completely flat. But
> > when I try to "relax" the graphite surface (slab 2*2 with 3 monolayer)
> > with 10 angstrom vacuum all the layers become extremely ripple!!! I
> > can not find the problem. May it related to the number of layers?
> > anyhow the number of layers is like the bulk. Your help would be a
> > great gift.
G. Scluuzero:
> > __
> Are you using the experimental or the theoretical value for the in-plane
> (graphene) C-C distance? I guess that the PBE value is larger than the
> experimental one, so that if you start from the experimental C-C
> distance in the graphene layer and let everything relax, then the atoms
> would like to go towards the theoretical equilibrium distance and this
> may cause the rippled structure.
> Secondly, I don't know if you can pretend that the innermost layer is
> graphite bulk-like, having only three layers in total.
Dal Corso Andrea :
> Check the pseudopotential. This is a PP with a core hole for special
> purposes not for standard simulations.
Giuseppe Mattioli :
> Dear Masoud
> apart from the pseudo problem issued by Andrea, you could try the keyword
> london=.true.
> It adds a Van der Waals contribution to total energy and it is likely to
> improve the interlayer interactions in your system.
> Hope this helps
> Giuseppe
input file:
calculation = "relax",
pseudo_dir =
"/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir =
"/home/koa/tmp",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
nstep=150,
/
ibrav = 4,
a =
4.9318,
b = 4.9318,
c = 16.7029,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 24,
ntyp = 1,
ecutwfc = 40.D0,
ecutrho = 400.D0,
occupations = 'smearing'
smearing ='mp',
degauss = 0.01,
nspin = 2,
starting_magnetization(1)= 1.0,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C
12.0107 C.star1s-pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C
0.000.000.00
C2.4659000.00
0.00
C-1.2329502.1355320.00
C1.232950
2.1355320.00
C0.001.4236880.00
C
-1.2329503.5592200.00
C2.4659001.423688
0.00
C1.2329503.5592200.00
C0.00
0.003.351450
C2.4659000.003.351450
C
-1.2329502.1355323.351450
C1.2329502.135532
3.351450
C1.2329500.7118443.351450
C0.00
2.8473763.351450
C3.6988500.7118443.351450
C
2.4659002.8473763.351450
C0.000.00
6.702900
C2.4659000.006.702900
C-1.232950
2.1355326.702900
C1.2329502.1355326.702900
C
0.001.4236886.702900
C-1.2329503.559220
6.702900
C2.4659001.4236886.702900
C1.232950
3.5592206.702900
K_POINTS {automatic}
4 4 1 1 1 1
out
put (optimized positions):
C0.0
-0.0 -0.686394528
C2.46590 -0.003714144
-0.758610095
C -1.229733457 2.137389072 -0.758610095
C
1.229733457 2.137389072 -0.758610095
C0.0
1.427474855 -0.213813075
C -1.229670488 3.557326573
-0.213813075
C2.46590 1.423688000 -0.285079086
C
1.229670488 3.557326573 -0.213813075
C -0.0
0.0 3.630366631
C2.46590 -0.014904710
3.544792504
C -1.220042143 2.142984355 3.544792504
C
1.
[Pw_forum] Is the Graphite surface flate?
Dear Quantum Espresso users
I optimized the graphite bulk and the
layers were completely flat. But when I try to "relax" the graphite
surface (slab 2*2 with 3 monolayer) with 10 angstrom vacuum all the layers
become extremely ripple!!! I can not find the problem. May it related to the
number of layers? anyhow the number of layers is like the bulk. Your help would
be a great gift.
input file:
calculation = "relax",
pseudo_dir =
"/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir =
"/home/koa/tmp",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
nstep=150,
/
ibrav = 4,
a =
4.9318,
b = 4.9318,
c = 16.7029,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 24,
ntyp = 1,
ecutwfc = 40.D0,
ecutrho = 400.D0,
occupations = 'smearing'
smearing ='mp',
degauss = 0.01,
nspin = 2,
starting_magnetization(1)= 1.0,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C
12.0107 C.star1s-pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C
0.000.000.00
C2.4659000.00
0.00
C-1.2329502.1355320.00
C1.232950
2.1355320.00
C0.001.4236880.00
C
-1.2329503.5592200.00
C2.4659001.423688
0.00
C1.2329503.5592200.00
C0.00
0.003.351450
C2.4659000.003.351450
C
-1.2329502.1355323.351450
C1.2329502.135532
3.351450
C1.2329500.7118443.351450
C0.00
2.8473763.351450
C3.6988500.7118443.351450
C
2.4659002.8473763.351450
C0.000.00
6.702900
C2.4659000.006.702900
C-1.232950
2.1355326.702900
C1.2329502.1355326.702900
C
0.001.4236886.702900
C-1.2329503.559220
6.702900
C2.4659001.4236886.702900
C1.232950
3.5592206.702900
K_POINTS {automatic}
4 4 1 1 1 1
out
put (optimized positions):
C0.0
-0.0 -0.686394528
C2.46590 -0.003714144
-0.758610095
C -1.229733457 2.137389072 -0.758610095
C
1.229733457 2.137389072 -0.758610095
C0.0
1.427474855 -0.213813075
C -1.229670488 3.557326573
-0.213813075
C2.46590 1.423688000 -0.285079086
C
1.229670488 3.557326573 -0.213813075
C -0.0
0.0 3.630366631
C2.46590 -0.014904710
3.544792504
C -1.220042143 2.142984355 3.544792504
C
1.220042143 2.142984355 3.544792504
C1.220249305
0.704511250 3.106073641
C0.0 2.847376000
3.022325711
C3.711550695 0.704511250 3.106073641
C
2.46590 2.862041499 3.106073641
C0.0
0.0 7.468882932
C2.46590 0.008344370
7.466151214
C -1.240176436 2.131359815 7.466151214
C
1.240176436 2.131359815 7.466151214
C0.0
1.414904155 6.963129179
C -1.240557033 3.563611923
6.963129179
C2.46590 1.423688000 6.961528237
C
1.240557033 3.563611923 6.963129179
Many Thanks
Masoud Nahali
Sharif
University of Technology
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[Pw_forum] graphite surface optimizing problem
Dear Quantum Espresso users
I optimized the graphite bulk and
the layers were completely flat. But when I try to "relax" the graphite
surface (slab 2*2 with 3 monolayer) with 10 angstrom vacuum the layers
become extremely ripple!!! I can not find the problem. Your help would
be a great gift.
input file:
calculation = "relax",
pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/koa/tmp",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
nstep=150,
/
ibrav = 4,
a = 4.9318,
b = 4.9318,
c = 16.7029,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 24,
ntyp = 1,
ecutwfc = 40.D0,
ecutrho = 400.D0,
occupations = 'smearing'
smearing ='mp',
degauss = 0.01,
nspin = 2,
starting_magnetization(1)= 1.0,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C 12.0107 C.star1s-pbe-rrkjus.UPF
ATOMIC_POSITIONS {angstrom}
C0.000.000.00
C2.4659000.000.00
C-1.2329502.1355320.00
C1.2329502.1355320.00
C0.001.4236880.00
C-1.2329503.5592200.00
C2.4659001.4236880.00
C1.2329503.5592200.00
C0.000.003.351450
C2.4659000.003.351450
C-1.2329502.1355323.351450
C1.2329502.1355323.351450
C1.2329500.7118443.351450
C0.002.8473763.351450
C3.6988500.7118443.351450
C2.4659002.8473763.351450
C0.000.006.702900
C2.4659000.006.702900
C-1.2329502.1355326.702900
C1.2329502.1355326.702900
C0.001.4236886.702900
C-1.2329503.5592206.702900
C2.4659001.4236886.702900
C1.2329503.5592206.702900
K_POINTS {automatic}
4 4 1 1 1 1
out put (optimized positions):
C0.0 -0.0 -0.686394528
C2.46590 -0.003714144 -0.758610095
C -1.229733457 2.137389072 -0.758610095
C1.229733457 2.137389072 -0.758610095
C0.0 1.427474855 -0.213813075
C -1.229670488 3.557326573 -0.213813075
C2.46590 1.423688000 -0.285079086
C1.229670488 3.557326573 -0.213813075
C -0.0 0.0 3.630366631
C2.46590 -0.014904710 3.544792504
C -1.220042143 2.142984355 3.544792504
C1.220042143 2.142984355 3.544792504
C1.220249305 0.704511250 3.106073641
C0.0 2.847376000 3.022325711
C3.711550695 0.704511250 3.106073641
C2.46590 2.862041499 3.106073641
C0.0 0.0 7.468882932
C2.46590 0.008344370 7.466151214
C -1.240176436 2.131359815 7.466151214
C1.240176436 2.131359815 7.466151214
C0.0 1.414904155 6.963129179
C -1.240557033 3.563611923 6.963129179
C2.46590 1.423688000 6.961528237
C 1.240557033 3.563611923 6.963129179
Many Thanks
Masoud Nahali
Sharif University of Technology
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[Pw_forum] optimizing cell parameters and choosing k-points of graphite
One of the origins of this bad convergence is the selection of ecurho. For
ultra-soft pseudo-potentials,the ecurho should be 10X of ecutwfc
and I had not considered it well.
very best wishes
Masoud Nahali
SUT
Dear Quantum Espresso users
I have done a 'vc-relax' calculation to find the cell parameters of graphite.
The selected k-points are (4*4*4) and automatic.
obtained cell parameters:
a = 2.469,
b = 2.469,
c = 7.069,
then I used these values to 'relax' the atoms in cell (k-points were 4*4*4 too)
. Finally I used the obtained cell parameters to find the proper k-points for
graphite.
I performed some 'scf' calculations with different k-points and in whole of
them the cell parameters and positions were what is obtained from the relax
part with 4*4*4 k-points.
'scf' energy with different k-points:
k-points energy
(4*4*4): -45.5732791969 Ry
(5*5*5): -45.57637408 Ry
(6*6*6): -45.57592043 Ry
(7*7*7): -45.57420434 Ry
(8*8*8): -45.57474553 Ry
(9*9*9): -45.57500776 Ry
(10*10*10): -45.57454272 Ry
(11*11*11): -45.57464463 Ry
(12*12*12): -45.57480118 Ry
(13*13*13): -45.57462800 Ry
(14*14*14): -45.57463705 Ry
(15*15*15): -45.57473135 Ry
(16*16*16): -45.57465384 Ry
I appreciate if one help me to find the answers to these questions:
1. Is the whole procedure plausible ?2. why a energy convergence is not
occurred after selecting these high values of k-points?3. How can I find the
proper k-points safely?
the input file for 'scf' calculation:
calculation = "scf",
pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/koa/tmp",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
nstep=150,
/
ibrav = 4,
a = 2.469,
b = 2.469,
c = 7.069,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 4,
ntyp = 1,
ecutwfc = 30.D0,
ecutrho = 200.D0
occupations = 'smearing'
smearing ='mp',
degauss = 0.01,
nspin = 2,
starting_magnetization(1)= 1.0,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C 12.0107 C.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
C0.0 0.0 0.0
C0.0 1.425534302 0.0
C0.0 0.0 3.534553118
C1.234548920 0.712767151 3.534553118
K_POINTS {automatic}
16 16 16 1 1 1
the vc-relax input:
calculation = "vc-relax",
pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/koa/tmp",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
dt=70,
nstep=150,
/
ibrav = 4,
a = 2.456,
b = 2.456,
c = 6.696,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 4,
ntyp = 1,
ecutwfc = 30.D0,
ecutrho = 200.D0
occupations = 'smearing'
smearing ='mp',
degauss = 0.01,
nspin = 2,
starting_magnetization(1)= 1.0,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="bfgs"
/
cell_dynamics = 'damp-w',
press = 0.0 ,
/
ATOMIC_SPECIES
C 12.0107 C.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
C 0.0.0.
C 0.1.417972260.
C 0.0.3.3480
C 1.22800.708986133.3480
K_POINTS {automatic}
4 4 4 1 1 1
very best wishes
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[Pw_forum] optimizing cell parameters and choosing k-points of graphite
Dear Quantum Espresso users
I have done a 'vc-relax' calculation to find the cell parameters of graphite.
The selected k-points are (4*4*4) and automatic.
obtained cell parameters:
a = 2.469,
b = 2.469,
c = 7.069,
then I used these values to 'relax' the atoms in cell (k-points were 4*4*4 too)
. Finally I used the obtained cell parameters to find the proper k-points for
graphite.
I performed some 'scf' calculations with different k-points and in whole of
them the cell parameters and positions were what is obtained from the relax
part with 4*4*4 k-points.
'scf' energy with different k-points:
k-points energy
(4*4*4): -45.5732791969 Ry
(5*5*5): -45.57637408 Ry
(6*6*6): -45.57592043 Ry
(7*7*7): -45.57420434 Ry
(8*8*8): -45.57474553 Ry
(9*9*9): -45.57500776 Ry
(10*10*10): -45.57454272 Ry
(11*11*11): -45.57464463 Ry
(12*12*12): -45.57480118 Ry
(13*13*13): -45.57462800 Ry
(14*14*14): -45.57463705 Ry
(15*15*15): -45.57473135 Ry
(16*16*16): -45.57465384 Ry
I appreciate if one help me to find the answers to these questions:
1. Is the whole procedure plausible ?2. why a energy convergence is not
occurred after selecting these high values of k-points?3. How can I find the
proper k-points safely?
the input file for 'scf' calculation:
calculation = "scf",
pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/koa/tmp",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
nstep=150,
/
ibrav = 4,
a = 2.469,
b = 2.469,
c = 7.069,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 4,
ntyp = 1,
ecutwfc = 30.D0,
ecutrho = 200.D0
occupations = 'smearing'
smearing ='mp',
degauss = 0.01,
nspin = 2,
starting_magnetization(1)= 1.0,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="bfgs"
/
ATOMIC_SPECIES
C 12.0107 C.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
C0.0 0.0 0.0
C0.0 1.425534302 0.0
C0.0 0.0 3.534553118
C1.234548920 0.712767151 3.534553118
K_POINTS {automatic}
16 16 16 1 1 1
the vc-relax input:
calculation = "vc-relax",
pseudo_dir = "/home/koa/soft/qe4.2/espresso-4.2/pseudo",
outdir = "/home/koa/tmp",
etot_conv_thr= 1.0D-4,
forc_conv_thr= 1.0D-3,
dt=70,
nstep=150,
/
ibrav = 4,
a = 2.456,
b = 2.456,
c = 6.696,
cosab = -0.5,
cosac = 1.0,
cosbc = 1.0,
nat = 4,
ntyp = 1,
ecutwfc = 30.D0,
ecutrho = 200.D0
occupations = 'smearing'
smearing ='mp',
degauss = 0.01,
nspin = 2,
starting_magnetization(1)= 1.0,
/
conv_thr= 1.D-6,
mixing_beta = 0.7D0,
diagonalization = "david",
/
ion_dynamics="bfgs"
/
cell_dynamics = 'damp-w',
press = 0.0 ,
/
ATOMIC_SPECIES
C 12.0107 C.pbe-van_ak.UPF
ATOMIC_POSITIONS {angstrom}
C 0.0.0.
C 0.1.417972260.
C 0.0.3.3480
C 1.22800.708986133.3480
K_POINTS {automatic}
4 4 4 1 1 1
very best wishes
Many ThanksMasoud NahaliSharif University of Technology
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[Pw_forum] electrochemical potential
Dear QE users How can one apply electrochemical potential to a metal in quantum espresso? for example +0.2 or +1.0 that is proper for oxidation and also negative extents like -0.3 and -1.5. I think that it may related to fermi level but I can not apply. I appreciate to your help. very best wishes Masoud Nahali Sharif University of Technology Ph. D student of physical chemistry _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100629/c43316d5/attachment.htm
[Pw_forum] error # 800
Dear Quantum Espresso Users I have a simulation system with 72 Au atoms in a slab form. My OS is Ubuntu and the used compiler is gfortran. The k-points are 2*1*1. Position of Atoms : Cartesian axes site n. atom positions (a_0 units) 1 Au tau( 1) = ( 0.000 0.000 0.000 ) 2 Au tau( 2) = ( 0.1666180 0.1666180 0.000 ) 3 Au tau( 3) = ( 0.000 0.1666180 0.1666180 ) 4 Au tau( 4) = ( 0.1666180 0.000 0.1666180 ) 5 Au tau( 5) = ( 0.3332361 0.000 0.000 ) 6 Au tau( 6) = ( 0.4998541 0.1666180 0.000 ) 7 Au tau( 7) = ( 0.3332361 0.1666180 0.1666180 ) 8 Au tau( 8) = ( 0.4998541 0.000 0.1666180 ) 9 Au tau( 9) = ( 0.6664721 0.000 0.000 ) 10 Au tau( 10) = ( 0.8330901 0.1666180 0.000 ) 11 Au tau( 11) = ( 0.6664721 0.1666180 0.1666180 ) 12 Au tau( 12) = ( 0.8330901 0.000 0.1666180 ) 13 Au tau( 13) = ( 0.000 0.3332361 0.000 ) 14 Au tau( 14) = ( 0.1666180 0.4998541 0.000 ) 15 Au tau( 15) = ( 0.000 0.4998541 0.1666180 ) 16 Au tau( 16) = ( 0.1666180 0.3332361 0.1666180 ) 17 Au tau( 17) = ( 0.3332361 0.3332361 0.000 ) 18 Au tau( 18) = ( 0.4998541 0.4998541 0.000 ) 19 Au tau( 19) = ( 0.3332361 0.4998541 0.1666180 ) 20 Au tau( 20) = ( 0.4998541 0.3332361 0.1666180 ) 21 Au tau( 21) = ( 0.6664721 0.3332361 0.000 ) 22 Au tau( 22) = ( 0.8330901 0.4998541 0.000 ) 23 Au tau( 23) = ( 0.6664721 0.4998541 0.1666180 ) 24 Au tau( 24) = ( 0.8330901 0.3332361 0.1666180 ) 25 Au tau( 25) = ( 0.000 0.6664721 0.000 ) 26 Au tau( 26) = ( 0.1666180 0.8330901 0.000 ) 27 Au tau( 27) = ( 0.000 0.8330901 0.1666180 ) 28 Au tau( 28) = ( 0.1666180 0.6664721 0.1666180 ) 29 Pd tau( 29) = ( 0.3332361 0.6664721 0.000 ) 30 Au tau( 30) = ( 0.4998541 0.8330901 0.000 ) 31 Au tau( 31) = ( 0.3332361 0.8330901 0.1666180 ) 32 Au tau( 32) = ( 0.4998541 0.6664721 0.1666180 ) 33 Pd tau( 33) = ( 0.6664721 0.6664721 0.000 ) 34 Au tau( 34) = ( 0.8330901 0.8330901 0.000 ) 35 Au tau( 35) = ( 0.6664721 0.8330901 0.1666180 ) 36 Au tau( 36) = ( 0.8330901 0.6664721 0.1666180 ) 37 Au tau( 37) = ( 0.000 0.000 0.3332361 ) 38 Au tau( 38) = ( 0.1666180 0.1666180 0.3332361 ) 39 Au tau( 39) = ( 0.000 0.1666180 0.4998541 ) 40 Au tau( 40) = ( 0.1666180 0.000 0.4998541 ) 41 Au tau( 41) = ( 0.3332361 0.000 0.3332361 ) 42 Au tau( 42) = ( 0.4998541 0.1666180 0.3332361 ) 43 Au tau( 43) = ( 0.3332361 0.1666180 0.4998541 ) 44 Au tau( 44) = ( 0.4998541 0.000 0.4998541 ) 45 Au tau( 45) = ( 0.6664721 0.000 0.3332361 ) 46 Au tau( 46) = ( 0.8330901 0.1666180 0.3332361 ) 47 Au tau( 47) = ( 0.6664721 0.1666180 0.4998541 ) 48 Au tau( 48) = ( 0.8330901 0.000 0.4998541 ) 49 Au tau( 49) = ( 0.000 0.3332361 0.3332361 ) 50 Au tau( 50) = ( 0.1666180 0.4998541 0.3332361 ) 51 Au tau( 51) = ( 0.000 0.4998541 0.4998541 ) 52 Au tau( 52) = ( 0.1666180 0.3332361 0.4998541 ) 53 Au tau( 53) = ( 0.3332361 0.3332361 0.3332361 ) 54 Au tau( 54) = ( 0.4998541 0.4998541 0.3332361 ) 55 Au tau( 55) = ( 0.3332361 0.4998541 0.4998541 ) 56 Au tau( 56) = ( 0.4998541 0.3332361 0.4998541 ) 57 Au tau( 57) = ( 0.6664721 0.3332361 0.3332361 ) 58 Au tau( 58) = ( 0.8330901 0.4998541 0.3332361 ) 59 Au tau( 59) = ( 0.6664721 0.4998541 0.4998541 ) 60 Au tau( 60) = ( 0.8330901 0.3332361 0.4998541 ) 61
[Pw_forum] Re : Occupations
Dear QE users Until now I have not found a clear cut explanation about occupations ! the reference that is suggested by Nicola is short. Many Thanks Masoud Nahali SUT >Dear Masoud, >http://media.quantum-espresso.org/santa_barbara_2009_07/index.php#20090719 >but in short, yes, it is necessary for metals. For graphite it is >probably less important, >you could try with and without, and see what happens. nicola >Masoud Nahali wrote: > Dear QE users > > Is "Occupations" variable necessary for Metals? It seems that the > "tetrahedra" along with occupations variable is not suitable for > optimization calculations ! > my studing sample is Graphite and I do not know that the specifying of > the metallicity is needed or not? a simple physical definition of > "occupations" should be useful for me. I could not find a clear one in > the forum. Is this variable related to the how should one select the > K-POINTS !? > > > Masoud Nahali > SUT > _ Hotmail: Free, trusted and rich email service. https://signup.live.com/signup.aspx?id=60969 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100505/ec492fa9/attachment.htm
[Pw_forum] Occupations
Dear QE users Is "Occupations" variable necessary for Metals? It seems that the "tetrahedra" along with occupations variable is not suitable for optimization calculations ! my studing sample is Graphite and I do not know that the specifying of the metallicity is needed or not? a simple physical definition of "occupations" should be useful for me. I could not find a clear one in the forum. Is this variable related to the how should one select the K-POINTS !? Masoud Nahali SUT _ Hotmail: Trusted email with Microsoft?s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100503/a65bab67/attachment.htm
[Pw_forum] AMD Open64 Compiler Suite
> anyone tried to compile PWSCF using the AMD Open64 Compiler Suite (the > last versione -afaik- is v4.2.3), possibly with the AMD Core Math > Library (ACML)? > I know that ACML should work, but how about Open64? > After reading that Intel Compilers deliberately does not take in account > of all math speedup present in non-intel CPUs, I'm considering which > optimized compiler I should use on my old non-Intel based linux... > > Thanks, > Carlo Dear Carlo I have compiled QE using GNU compilers (gfortran, gcc, and g++) on my AMD(3 Cores CPU) . the operating system is SUSE 11.2 (64 bit). Both ACML and MathKernel libraries have been installed on my system before. with these configurations QE works but I am not sure about the efficiency of the work. I had tried intel compilers (ifort, icc, and icpc) before ! but I think that you will have less error in compiling when use the gnu compilers here. Best Wishes Masoud Nahali Sharif University of Technology _ Hotmail: Powerful Free email with security by Microsoft. https://signup.live.com/signup.aspx?id=60969 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100316/1a5006ae/attachment.htm
[Pw_forum] 'Relax' variable
Dear QE users Is there any variable alongside the 'relax' for these usages ?! : 1. fixing or changing the cell symmetry through the calculation. 2. fixing or optimizing the cell size through the calculation. 3. optimizing all positions without considering any restrictions. Many Thanks Masoud Nahali Sharif University of Technology _ Hotmail: Trusted email with Microsoft?s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100310/604c8e19/attachment.htm
[Pw_forum] calculating the cell parameters in crystals
Dear Elie Try the VESTA software ! I am not that this can solve your problem; anyhow is a good graphical software for solids. Best Wishes Masoud Nahali Sharif University of Technology _ Hotmail: Trusted email with Microsoft?s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100310/fcdf6482/attachment.htm
[Pw_forum] Parallel Running the Example 01 (Stop !!!!)
Dear Quantum Espresso Users I have installed parallel Quantum Espresso successfully and tried to run the exapmle 01. at first I tried to run the example 01 from the root but the program did't run and then I went out of the root for running (this is the proposed by the QE). the first problem solved by going out of the root. Once I could run the example 01 but amazingly I cannot now !!. when I run the exaplme 01 the program stopped at this line: running the scf calculation for Si...and did not continue and any CPU's did not work and there is not any results. My system is AMD (3 cores) and LAM-MPI works well. but I think that the problem is related to lam ! since at first time that I tried QE aked me to boot the lam by lamboot and I do to continue. and it is so interesting that I runned once and cleaned the temporary but again I can not !!! this is the lines : koa at linux-xd0f:~/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01> ./run_example /home/koa/QSPRESSO4.1.2/espresso-4.1.1-Example/examples/example01 : starting This example shows how to use pw.x to calculate the total energy and the band structure of four simple systems: Si, Al, Cu, Ni. executables directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin pseudo directory: /home/koa/QSPRESSO4.1.2/espresso-4.1.2/pseudo temporary directory: /home/koa/tmp checking that needed directories and files exist... done running pw.x as: mpirun -np 3 /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/pw.x -npool 1 running bands.x as: mpirun -np 3 /home/koa/QSPRESSO4.1.2/espresso-4.1.2/bin/bands.x -npool 1 cleaning /home/koa/tmp... done running the scf calculation for Si... Your Help is a Good Gift to Me, Many Thanks Masoud Nahali Sharif University of Technology Physical Chemistry _ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. https://signup.live.com/signup.aspx?id=60969 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100227/fee00fc9/attachment.htm
[Pw_forum] error: Fortran 77 compiler cannot create executables
Dear Quantum Espresso Users I had installed Quantum Espresso previously on my AMD (3 core) parallel. but Now I get an error !! I have installed Intel Compilers (version 11) included fort, icc, icpc, and Math Kernel; and parallelized them by lam successfully. my operating system is OpenSUSE 11.2 (64 bit). Also mpif77 and mpicc work well on my 3 core AMD. I have installed ACML also, that is not necessary when we have MKL. but error: Fortran 77 compiler cannot create executables !! linux-4koa:~/Install/QSPRESSO4.1.2/espresso-4.1.2 # ./configure MPIF90=mpif77 F77=mpif77 CC=mpicc --enable-parallel checking build system type... x86_64-unknown-linux-gnu checking architecture... x86_64 checking for ifort... ifort checking for Fortran 77 compiler default output file name... configure: error: Fortran 77 compiler cannot create executables See `config.log' for more details. with and without --enable-parallel I saw the same error. anyhow it is amazing that I had installed parallel Quantum Espresso on this AMD and using CentOS5.4 (64 bit) as the Operating system. This is Ngoc Linh Nguyen's solution : The problem could come from Fortran 77 compiler. You say that the Intel Compilers (version 11) included ifort, icc ... has been installed, so let try compiling without specifying "F77=mpif77 CC=mpicc". but this can not help me, and the error remained. Someone here suggested me below lines but the error remained: linux-76gb:~/LinSoft/QSPRESSO4.1.2/espresso-4.1.2 # ./configure MPIF90=mpif77 F77=ifort CC=icc ?enable-parallel checking build system type... x86_64-unknown-linux-gnu checking architecture... x86_64 checking for ifort... ifort checking for Fortran 77 compiler default output file name... configure: error: Fortran 77 compiler cannot create executables See `config.log' for more details. Is it really necessary to install a F77 compiler? I think that the ifort is sufficient !! No ?!! I appreciate so much if you help me. Many thanks Masoud Nahali SUT Physical Chemistry _ Hotmail: Trusted email with powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100201/faba1cfb/attachment.htm
[Pw_forum] Fortran 77 compiler cannot create executables (Parallel Installation)
Dear Quantum Espresso Users I had installed Quantum Espresso previously on my AMD (3 core) parallel. but Now I get an error !! I have installed Intel Compilers (version 11) included fort, icc, icpc, and Math Kernel; and parallelized them by lam successfully. my operating system is SUSE 11 (64 bit,Enterprise). Also mpif77 and mpicc work well on my 3 core AMD. but error: Fortran 77 compiler cannot create executables !! linux-4koa:~/Install/QSPRESSO4.1.2/espresso-4.1.2 # ./configure MPIF90=mpif77 F77=mpif77 CC=mpicc --enable-parallel checking build system type... x86_64-unknown-linux-gnu checking architecture... x86_64 checking for ifort... ifort checking for Fortran 77 compiler default output file name... configure: error: Fortran 77 compiler cannot create executables See `config.log' for more details. with and without --enable-parallel I saw the same error. anyhow it is amazing that I had installed parallel Quantum Espresso on this AMD and using CentOS5.4 (64 bit) as the Operating system. I appreciate so much if you help me. Many thanks This is Ngoc Linh Nguyen's solution : The problem could come from Fortran 77 compiler. You say that the Intel Compilers (version 11) included ifort, icc ... has been installed, so let try compiling without specifying "F77=mpif77 CC=mpicc". but this can not help me, and the error remained. _ Hotmail: Trusted email with Microsoft?s powerful SPAM protection. https://signup.live.com/signup.aspx?id=60969 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100128/e44d8771/attachment.htm
[Pw_forum] Parallel Installation Error
Dear Quantum Espresso Users I had installed Quantum Espresso previously on my AMD (3 core) parallel. but Now I get an error !! I have installed Intel Compilers (version 11) included fort, icc, icpc, and Math Kernel; and parallelized them by lam successfully. my operating system is SUSE 11 (64 bit,Enterprise). Also mpif77 and mpicc work well on my 3 core AMD. but error: Fortran 77 compiler cannot create executables !! linux-4koa:~/Install/QSPRESSO4.1.2/espresso-4.1.2 # ./configure MPIF90=mpif77 F77=mpif77 CC=mpicc --enable-parallel checking build system type... x86_64-unknown-linux-gnu checking architecture... x86_64 checking for ifort... ifort checking for Fortran 77 compiler default output file name... configure: error: Fortran 77 compiler cannot create executables See `config.log' for more details. with and without --enable-parallel I saw the same error. anyhow it is amazing that I had installed parallel Quantum Espresso on this AMD and using CentOS5.4 (64 bit) as the Operating system. I appreciate so much if you help me. Many thanks Best Wishes Masoud Nahali Physical Chemistry SUT _ Windows Live: Make it easier for your friends to see what you?re up to on Facebook. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_2:092009 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100122/97765b86/attachment.htm
[Pw_forum] Parallel Installation Error (error: Fortran 77 compiler cannot create executables)
Dear Quantum Espresso users I have installed intel compilers such as ifort, icc, icpc (version 11) on my AMD 3 core (64 bit). All installed compilers are 64 bit and the installation was successful. then I installed MKL (version 11) and ACML on my computer. using "lam" I made the parallel compilers such as mpif77, mpicc, mpiCC and and the parallel installation of compilers was successful. also my operating system is CentOS 5.4 (64 bit) . then I tryed many times to compile the Quantum Spresso but I have received an error: [root at localhost espresso-4.1.2]# ./configure MPIF90=/usr/bin/mpif77 CC=/usr/bin/icc CFLAGS=-O3 F90=/usr/bin/mpif77 F77=/usr/bin/mpif77 LIBDIRS=/lib64 checking build system type... x86_64-unknown-linux-gnu checking architecture... x86_64 checking for /usr/bin/mpif77... no checking for Fortran 77 compiler default output file name... configure: error: Fortran 77 compiler cannot create executables See `config.log' for more details. I appreciate so much if you help me. Best Wishes Masoud Nahali Physical Chemistry SUT _ Windows Live: Keep your friends up to date with what you do online. http://www.microsoft.com/middleeast/windows/windowslive/see-it-in-action/social-network-basics.aspx?ocid=PID23461::T:WLMTAGL:ON:WL:en-xm:SI_SB_1:092010 -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20100113/4730d353/attachment.htm
