[Pw_forum] reconstruction
Dear Ali You can start with (lateral) surface reconstruction of your bulk system. Afterwards I would try different supercells with different starting points, like number of atoms or "surface molecules". Don't forget to saturate dangling bonds (even there you can check different types). I think in Si NWs even a SiH3 group is outermost for some NWs After relaxing your structures you can check the most favorable ones by comparing energies (have a look at surface calculations for details). Good luck Marcel Mohr -- Institut f?r Festk?rperphysik TU Berlin On Tue, 21 Apr 2009, Prasenjit Ghosh wrote: > Dear Ali, > > It depends on the type of reconstruction the surface of the nanowire > undergoes.? May be if you tell a bit more about the type of reconstruction, I > can tell you more. > > Prasenjit. > > 2009/4/21 ali kazempoor > Dear Prasenjit > Thank you for your reply, but I mean what I do to see the surface > reconstruction at lateral nanowire surface. For simulation of a nanowire > in z direction we add vaccum around nanowire in x and y and for z we use > periodic boundary condition . So if we only suppose one unit > repetation in z , we can not observe the surface reconstruction . Therefor > for observing reconstruction , I think we have to make for > example twice unit repetation in z or more. > thanks > > --- On Tue, 4/21/09, Prasenjit Ghosh wrote: > > From: Prasenjit Ghosh > Subject: Re: [Pw_forum] reconstruction > To: "PWSCF Forum" > Date: Tuesday, April 21, 2009, 10:38 AM > > > Dear Ali, > > Usually when you speak of simulating a nanowire, because of the periodic > boundary conditions, you simulate an infinite one. If the > nanowire is aligned along Z axis, which seems to be your case,? then you have > periodicity along the Z-direction. Therefore you need > to? have enough vacuum along the x & y direction so that the periodic images > should not interact. > > Prasenjit. > > 2009/4/20 ali kazempoor > > Dear all > I want to study the fingerprint of reconstruction in nanowire facets. > How can ?I find that wheater I have surface > reconstruction or not? Should I make a bigger supercell in Z direction( > Z is the lenght of nanowire)? > thanks > Ali Kazempour.Isfahan University of Technology,Iran > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > ? ? ? ? ? ? ?+39 3807528672 (M) > > -Inline Attachment Follows- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > -- > PRASENJIT GHOSH, > POST-DOC, > ROOM NO: 265, MAIN BUILDING, > CM SECTION, ICTP, > STRADA COSTERIA 11, > TRIESTE, 34104, > ITALY > PHONE: +39 040 2240 369 (O) > ? ? ? ? ? ? ?+39 3807528672 (M) > >
[Pw_forum] utilization of different Ultrasoft pseudopotentials
On Fri, 27 Mar 2009, saqib.javaid at ipcms.u-strasbg.fr wrote: > > Dear PWSCF users, > I have question regarding utilization of different type of Ultrasoft > pseudopotentials. Is it correct to use different type of ultrasoft PS ( like > rrkjus and Vanderbilt) for different atoms in a given system??? (e.g. one can > use rrkjus PS of Cobalt and Vanderbilt PS of Mn with same XC functionals in a > given system) There is a similar question from beginning of this month, and the answer I remember is yes, as long as they use the same XC functional (as you stated) However I got a question arising from this, too. Why are rrkj pseudos sometimes called ultrasoft? In the book by Richard Martin the terms "ultra-soft" and "norm-conserving" are opposites, so only Vanderbuilt pseudos or (PAW) are "ultrasoft". However Troullier-Martins and rrkj are norm-conserving and thus I conclude "not" ultrasoft ?! I would greatly acknowledge any comment. Cheers Marcel
[Pw_forum] strange bandstructure
Everything fine the crossing comes from your viewer program, it does not know, which points should be connected. Cheers Marcel Marcel Mohr Institut f?r Festk?rperphysik, TU Berlin marcel(at)physik.tu-berlin.de Sekr. EW 5-4 TEL: +49-30-314 24442 Hardenbergstr. 36 FAX: +49-30-314 27705 10623 Berlin On Thu, 5 Mar 2009, idoldog wrote: > Dear PWSCF user, > > I just finished a bandstructure calculation about semiconductor SrTiO3. I get > a strange bandstructure. > > In order to see clearly, I redraw the graph and mark same bands, which may be > wrong, with different colors. > > Some friends tell me it would be better without lines. Another friends tell > me to change the path of markde lines. > > I want to know that whether these bands are correct and if they are wrong, > where my mistakes are and how to solve them. > > The server blocked my files attched, so please visit > graph with colorful > lines:http://pic.emuch.net/200903/04/33e7b7b230bfd248104b8ba1ada65361.jpg > graph without > line:http://pic.emuch.net/200903/04/4a2fdd6cbf9f7d0ce2df725c579e57ea.jpg > > If you couldn't visit them successfully, mail me. > > I need your help. > > all the best. > > Li Fei > 2009-03-04 > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > >
[Pw_forum] Two binaries for serial and parallel use needed
> MM> Dear linux experts > MM> > MM> I have newly set up our computer cluster with new mpich2 (1.07) > MM> and ifort. > MM> In the last cluster the binary pw.x (compiled with mpich2 1.04) could be > MM> executed directly or with mpiexec for serial or parallel use, > MM> respectively. > MM> Now, this is not possible anymore, I always have to start an smpd > MM> and run pw.x with mpiexec, even for serial usage. > MM> It is a bit uncomfortable, so if anyone knows a switch for the compiler, > MM> or could comment I would greatly appreciate it. It was a bug in mpich2-1.0.7, with pre release 1.1... it works both ways. > > this has to be a "feature" of MPICH, or the way > you compiled it. > > i'm using OpenMPI and don't have that problem. > if you are after convenience, you should seriously > consider switching to OpenMPI. particularly on PBS/Torque > managed clusters, it is _extremely_ convenient > (job launch through torque, flexible choice of node > assignment, high efficiency, independence of the > executable from the underlying communication layer > (i can compile executable on my desktop with no network > and run them on myrinet, or infiniband machines directly)). we are using SGE, but it was a bit tricky to get parallel environments working. On the next cluster I will give it a try. Cheers Marcel > > cheers, > axel. > > > -- > === > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > ===
[Pw_forum] About band structure.
python
Marcel Mohr Institut f?r Festk?rperphysik, TU Berlin
marcel(at)physik.tu-berlin.de Sekr. EW 5-4
TEL: +49-30-314 24442 Hardenbergstr. 36
FAX: +49-30-314 27705 10623 Berlin
On Thu, 7 Aug 2008, Bipul Rakshit wrote:
> Hello Marcel,
> Thanks for the help. But can you tell me how it works?
>
> On Thu, Aug 7, 2008 at 11:02 AM, Marcel Mohr
> wrote:
> On Thu, 7 Aug 2008, Bipul Rakshit wrote:
>
> And what is /awk/java/whathever_you_are_familiar_with ?
>
>
> I am afraid I can't help you there.
> I do also not know what /awk/java/whatever_I_am_familar_with is,
> but do know a little python,
> In the attachment is a skript, that calculates the k-points along several
> endpoints ("points"), with "fineness", the
> number of k-points in between.
>
> Cheers Marcel
>
>
>
>
>
> thanks
>
>
> On Thu, Aug 7, 2008 at 9:45 AM, Stefano de Gironcoli sissa.it> wrote:
> ? ? ?1.) change the plotting range given in input to your plotting
> routine
> ? ? ?2.) write a 5-10 line fortran_code/bash_script
> ? ? ?/awk/java/whathever_you_are_familiar_with that makes this trivial
> task
> ? ? ?for you and feed the resulting data to pw.x
> ? ? ?best regards,
> ? ? ??Stefano
>
>
> Bipul Rakshit wrote:
> > Hello PWscf users,
> > I have a question about the band structure.
> > 1. ?I have plotted the band structure of ScSb. There i found that in
> > that post script file it draw the band very near the fermi level
> > (-12.0:3.0) only. But if I want the bands range say -20:20, what and
> > where I have to change?
> >
> > 2. I have given the K-points as used in Si calculation in examples, in
> > my ScSb file. It works well. But I am also using SIESTA, where we
> > mention the k-points as below
> >
> > ? ? BandLinesScale ?pi/a
> > ? ? ?%block BandLines ? ? ? ? ? ? ? ? ?# These are comments
> > ? ? ? 1 ?0.000 ?0.000 ?0.000 ?\Gamma ? # Begin at Gamma
> > ? ? ?25 ?2.000 ?0.000 ?0.000 ? ? X ? ? # 25 points from Gamma to X
> > ? ? ?10 ?2.000 ?1.000 ?0.000 ? ? W ? ? # 10 points from X to W
> > ? ? ?15 ?1.000 ?1.000 ?1.000 ? ? L ? ? # 15 points from W to L
> > ? ? ?20 ?0.000 ?0.000 ?0.000 ?\Gamma ? # 20 points from L to Gamma
> > ? ? ?25 ?1.500 ?1.500 ?1.500 ? ? K ? ? # 25 points from Gamma to K
> > ? ? ?%endblock BandLines
> >
> > the first column after* %block BandLines* shows the number of points
> > between the given k-points (like 25 points between Gamma and X). In
> > this way we dont have to mention all the k-points and we get a smooth
> > graph. But in pwscf I have to mention all the k-points in order to get
> > a smooth graph as in the example of Si.
> > So my question is, is there any way so that we have to mention only
> > the points at the zone boundary, and rest of the points it will take
> > automatically?
> >
> > --
> > Bipul Rakshit
> > PhD Student,
> > Barkatullah University,
> > Bhopal 462026,
> > MP, India
> >
>
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
> Bipul Rakshit
> PhD Student,
> Barkatullah University,
> Bhopal 462026,
> MP, India
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
> Bipul Rakshit
> PhD Student,
> Barkatullah University,
> Bhopal 462026,
> MP, India
>
>
[Pw_forum] About band structure.
On Thu, 7 Aug 2008, Bipul Rakshit wrote:
> And what is /awk/java/whathever_you_are_familiar_with ?
I am afraid I can't help you there.
I do also not know what /awk/java/whatever_I_am_familar_with is,
but do know a little python,
In the attachment is a skript, that calculates the k-points along
several endpoints ("points"), with "fineness", the number of k-points in
between.
Cheers Marcel
>
> thanks
>
>
> On Thu, Aug 7, 2008 at 9:45 AM, Stefano de Gironcoli
> wrote:
> 1.) change the plotting range given in input to your plotting routine
> 2.) write a 5-10 line fortran_code/bash_script
> /awk/java/whathever_you_are_familiar_with that makes this trivial task
> for you and feed the resulting data to pw.x
> best regards,
> ?Stefano
>
>
> Bipul Rakshit wrote:
> > Hello PWscf users,
> > I have a question about the band structure.
> > 1. ?I have plotted the band structure of ScSb. There i found that in
> > that post script file it draw the band very near the fermi level
> > (-12.0:3.0) only. But if I want the bands range say -20:20, what and
> > where I have to change?
> >
> > 2. I have given the K-points as used in Si calculation in examples, in
> > my ScSb file. It works well. But I am also using SIESTA, where we
> > mention the k-points as below
> >
> > ? ? BandLinesScale ?pi/a
> > ? ? ?%block BandLines ? ? ? ? ? ? ? ? ?# These are comments
> > ? ? ? 1 ?0.000 ?0.000 ?0.000 ?\Gamma ? # Begin at Gamma
> > ? ? ?25 ?2.000 ?0.000 ?0.000 ? ? X ? ? # 25 points from Gamma to X
> > ? ? ?10 ?2.000 ?1.000 ?0.000 ? ? W ? ? # 10 points from X to W
> > ? ? ?15 ?1.000 ?1.000 ?1.000 ? ? L ? ? # 15 points from W to L
> > ? ? ?20 ?0.000 ?0.000 ?0.000 ?\Gamma ? # 20 points from L to Gamma
> > ? ? ?25 ?1.500 ?1.500 ?1.500 ? ? K ? ? # 25 points from Gamma to K
> > ? ? ?%endblock BandLines
> >
> > the first column after* %block BandLines* shows the number of points
> > between the given k-points (like 25 points between Gamma and X). In
> > this way we dont have to mention all the k-points and we get a smooth
> > graph. But in pwscf I have to mention all the k-points in order to get
> > a smooth graph as in the example of Si.
> > So my question is, is there any way so that we have to mention only
> > the points at the zone boundary, and rest of the points it will take
> > automatically?
> >
> > --
> > Bipul Rakshit
> > PhD Student,
> > Barkatullah University,
> > Bhopal 462026,
> > MP, India
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
>
>
> --
> Bipul Rakshit
> PhD Student,
> Barkatullah University,
> Bhopal 462026,
> MP, India
>
>
-- next part --
# This program produces a list of q-points needed for anadbb. The total amount
of q-points is written.
# It connects the points with steps between. The first
entry of fineness governs the steps between the 1st
# and 2nd entry of points.
from Numeric import array, Float
import sys
points=array([ [0,0,0] , [0.5,0.5,0.0] , [1 , 0 ,0]])
fineness=array([99,57])#,15,29,15,29,29,29])
counter=0
# check of fineness contains points-1 entries
if fineness.shape[0] != (points.shape[0]-1):
print ("Die Anzahl der Schritte und K-Punte stimmt nicht ueberein")
sys.exit()
#produce q-points
for i in range(points.shape[0]-1):
divisor=float(fineness[i])
for j in range(int(divisor)):
jfloat=float(j)
punkt=points[i]+jfloat/divisor*(points[i+1]-points[i])
print "\t %5.5f \t %5.5f \t %5.5f \t 1.0" %
(punkt[0],punkt[1],punkt[2])
counter=counter+1
#last point
print "\t %5.5f \t %5.5f \t %5.5f \t 1.0" %
(points[i+1][0],points[i+1][1],points[i+1][2])
#print number of qpoints
print counter+1
[Pw_forum] multi core Vs Single core
There are some posts about this topic some time ago. Planewave codes use a lot of memory bandwith, so an Intel quadcore is not much faster than a dual core on the same mainboard, because the memory bus becomes the bottleneck of the system, and all core share the same bus. Cheers Marcel On Fri, 8 Feb 2008, Axel Kohlmeyer wrote: > On Fri, 8 Feb 2008, ambavale sagar wrote: > > > sagar, > > AS> Is multi (quad) core processor more efficient than single core for our > > please clarify what you mean by "efficient". > more throughput for the same money, faster execution, > better utilization of the cpu, less room needed for > a given computational capability? > > AS> abinitio calculations? How efficiently multi-threading is done while > AS> working with serial version of code on multicore machine? > > it is a common misconceptions that you need to use multi-threading > to take advantage of multicore cpus. the vendors of those cpus > are somewhat promoting it, because it is simpler to add multi-threading > to a code than to parallelize it completely, and also because > their new cpus don't have any advantage over the older ones without > paralleization. fortunately, the methods used in quantum espresso > are well parallelizable and the code offers multiple levels of MPI > parallelism which i found to be almost always more efficient than > using OpenMP (and thus multi-threading). even more so, QE does not > support OpenMP (only indirectly via threaded BLAS/LAPACK libraries). > > depending on your hardware, problem set size and compiler/library > combination, you can get a speedup of roughly 2.5x to 3.5x from > a quad core cpu over a corresponding single core. when using multiple > nodes via a network, however, the speed and the latency of the > network (and the options of parallization, i.e. if you can parallelize > over k-points or not) start to matter and can make it all very > confusing. > > in the end, apart from a few general observations, there is no other > way to get a definite answer than running tests with representative > input files. > > cheers, > axel. > > p.s.: this brings up the question again, that we should compile a > list of such typical inputs and run them on mutually available > machines so people can see what to expect > > AS> > AS> Thanx. > AS> > AS> ? > AS> > AS> Sagar K. Ambavale > AS> > AS> PhD student, > AS> > AS> The M.S. University of Baroda, > AS> > AS> India > AS> > AS> > AS> > > AS> 5, 50, 500, 5000 - Store N number of mails in your inbox. Click here. > AS> > > -- > === > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu > Center for Molecular Modeling -- University of Pennsylvania > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 > === > If you make something idiot-proof, the universe creates a better idiot.
[Pw_forum] wurtzite AlN
Hi, wurtzite has 4 atoms in the unit cell. Cheers Marcel On Tue, 15 Jan 2008, Helen wrote: > Hi, > I've successfully calculated the bandstructure for zinc-blende AlN, and I > wanted to do the same for wurtzite AlN but am running into problems. I > started off with a=5.88 a.u. c/a=1.600 and u=0.382 , I then kept a and c > constant and altered u. The results showed that u needed to be smaller but > when I reached u=0.369 my scf calculations stopped converging. I tried using > both cg and davidson diagonalization. I then tried keeping u constant and > altering c, I don't get convergence problems but I get unrealistically small > values of c. Also the bandgap data I'm getting is nonsense (no band gap at > all). Perhaps I have a mistake in my input file? > Thank you for your help and advice, > Dr. Helen Eisenberg (Fritz Haber Center, Hebrew University) > > &control >calculation='scf' >restart_mode='from_scratch', >tstress = .true. >tprnfor = .true. >prefix='alas', >pseudo_dir = '$PSEUDO_DIR/', >outdir='$TMP_DIR/' > / > &system >ibrav= 4, celldm(1) =5.88, celldm(3)=1.600, nat= 2, ntyp= 2, >ecutwfc =80.0, nbnd = 8, >nr1=32, >nr2=32, >nr3=32, >ecutrho = 240.0 > / > &electrons >conv_thr = 1.0d-6 >mixing_beta = 0.7 > / > ATOMIC_SPECIES > Al 26.98 Al.vbc.UPF > N 14.007 N.pz-vbc.UPF > ATOMIC_POSITIONS > Al 0.00 0.00 0.00 > N 0.00 0.00 0.611 > K_POINTS (automatic) > 4 4 4 0 0 0 > EOF
[Pw_forum] raman cross section
Hello the problem is that the calculation does not work for metals. It was discussed a few month ago here. Best Marcel On Sun, 13 Jan 2008, zahra sadat naghavi wrote: > dear everybody! > i wanted to calculate raman tensor in ph.x for a metal(at gamma point) and > then run dynmat.x to find raman cross section but ph.x can not be run if ' > lraman' is added in input file . > what is wrong ? > is there any other way? > > > - > Never miss a thing. Make Yahoo your homepage.
[Pw_forum] bands_FS.x and spin polarized metals
On Thu, 13 Dec 2007, Huiqun Zhou wrote: > Wow, what a "home computer"! Moor's law hadn't been invented > at that time, right? :-) > Are there any copyright issue to prevent me from using it in my > presentation about "concise history of personal computer"? Although I liked it very much, too. I showed it to a colleague and he told me it is fake. It is a picture of a sumbarine control station see http://www.snopes.com/inboxer/hoaxes/computer.asp Sorry for being the spoiler Marcel > > > Thanks for sharing the precious picture with us! > > Huiqun Zhou > @Earth Sciences, Nanjing University, China > > - Original Message - > From: "Paolo Giannozzi" > To: "PWSCF Forum" > Sent: Thursday, December 13, 2007 5:12 AM > Subject: Re: [Pw_forum] bands_FS.x and spin polarized metals > > >> >> On Dec 12, 2007, at 21:58 , Nicola Marzari wrote: >> I am old enough to have seen card punchers in action, so the term "abend" is not unknown to me, but I guess younger people don't know that it is a shorthand for "abnormal end", on IBM mainframes... >>> >>> What's a mainframe ? Is it like a really, really big ipod ? >> >> do you remember the picture of the "home computer >> in 2004" you sent me some time ago ? >> http://www.fisica.uniud.it/~giannozz/public/pc2004.jpg >> :-) >> >> P. >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > >
[Pw_forum] Strange phonon branches appear in phonon dispersion
595 10.1665 21.2176 228.1041 353.2106 >0.00 0.00 1.00 > -83.4878 -36.1149 10.5785 21.4924 233.0809 349.4591 >0.00 0.00 1.10 > -83.9637 -39.93806.4409 21.5912 237.7521 345.4939 >0.00 0.00 1.20 > -83.3549 -43.0700 -11.8614 21.8643 242.0400 341.2345 >0.00 0.00 1.30 > -81.7148 -45.5109 -19.5363 22.1233 245.9755 336.7214 >0.00 0.00 1.40 > -79.2450 -47.4002 -24.2602 21.7049 249.6731 332.1110 >0.00 0.00 1.50 > -76.4698 -48.7989 -26.8527 20.1426 253.2412 327.5276 >0.00 0.00 1.60 > -74.0708 -49.5494 -28.8342 17.6459 256.7020 322.9460 >0.00 0.00 1.70 > -72.4259 -49.4368 -31.6947 14.8469 259.9856 318.2672 >0.00 0.00 1.80 > -71.2114 -48.4948 -35.6608 11.6256 263.0044 313.5063 >0.00 0.00 1.90 > -69.6799 -47.0750 -39.79634.2536 265.7429 308.8670 >0.00 0.00 2.00 > -67.4586 -45.5010 -43.2503 -12.7026 268.2849 304.5960 >0.00 0.00 2.10 > -64.9647 -46.1360 -43.6300 -19.3793 270.7903 300.7406 >0.00 0.00 2.20 > -63.0506 -49.2247 -40.9136 -23.4729 273.4711 297.0578 >0.00 0.00 2.30 > -62.1609 -52.8376 -37.0315 -25.3558 276.5514 293.2015 >0.00 0.00 2.40 > -61.8563 -56.2311 -32.5370 -26.2996 280.1674 289.0264 >0.00 0.00 2.50 > -61.6387 -57.8617 -29.3445 -27.6304 283.8161 285.1565 >0.00 0.00 2.503000 > -61.6384 -57.8633 -29.3391 -27.6341 283.8284 285.1440 > > > Bac, > > -- > Phung Viet Bac > Division of Mathematical and Physical Science, > Graduate School of Natural Science and Technology, > Kanazawa University, > Kakuma, Kanazawa 920-1192, JAPAN > > > > > > > > >> >> your phonon branches are really strange... >> with two atoms I would expect 6 modes per each q-point >> >> stefano >> >> >> >> 6 branches for 2 atom are what one expects (in general 3n branches and 3 >> acoustical and 3n-3 optical ones). >> >> However negative values indicate some error in your calculation, dependent >> on the magnitude and system. >> You can impose some sum-rules for the acoustic ones, to force them to be >> 0 at the Gamma point. >> >> Acoustic forces are harder to calculate (smaller forces). In your case I >> would guess up to 15 cm^1 should be ok for the acoustic ones. >> Negative optical ones should not occur. >> >> Best >> Marcel Mohr >> >> >> >
[Pw_forum] Strange phonon branches appear in phonon dispersion
>> I am trying to do calculation phonon dispersion and EPC for 1D >> Aluminum chain. I got the results which are strange phonon branches >> appearing. In the case of 2 atom-cell, I got 4 phonon branches, two of >> them are Optical and Acoustical phonon branches and two others, which >> have zero and negative values, are unknown for me. In the case if I >> have 1 atom-cell, that strange branch also appears. Could any body >> explain for me what kind of frequencies here? 6 branches for 2 atom are what one expects (in general 3n branches and 3 acoustical and 3n-3 optical ones). However negative values indicate some error in your calculation, dependent on the magnitude and system. You can impose some sum-rules for the acoustic ones, to force them to be 0 at the Gamma point. Acoustic forces are harder to calculate (smaller forces). In your case I would guess up to 15 cm^1 should be ok for the acoustic ones. Negative optical ones should not occur. Best Marcel Mohr >> >> I was surfing this forum and FAQ and I found many discussion about >> negative frequencies, but I still cannot find the answers for me. >> >> Bac >> > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > >
[Pw_forum] Plot phonon dispersion
Dear list members,
i have written a small python /script-program to convert the matdyn output
matdyn.freq into a two-column format that I want to share with you.
This can easily be plotted by xmgrace, gnuplot etc.
For simplicity I took the absolute value of the k-vector, so one has to
modify the 1st column for non-cubic systems.
Best
Marcel
I just see, my email program is wrapping lines, so below has to be
modified, the attachment works.
--> program starts here
# small program to convert freq-Output into two-column dat
# written by Marcel Mohr
# usage: python mat2agr.py freqfile > phonons.dat
# Caution:# in the output, the absolute value of k-vector is taken -> 1,1,1
#->sqrt(3)
#
import sys,string
import os
import math
import re
#
def flatten(lst):
for elem in lst:
if type(elem) in (tuple, list):
for i in flatten(elem):
yield i
else:
yield elem
atom=[]
steps= 0
kk=0
input = open(sys.argv[1],'r')
line=input.readline()
#print line
bla=line.split()
if bla==[]:
pass
elif bla[1]=="nbnd=":
# komma muss weg
bla[2]=re.compile( "," ).sub( '', bla[2] )
nbnd=string.atoi(bla[2])
# print nbnd
nkpt=string.atoi(bla[4])
# print nkpt
# Anzahl der Lines sind jetzt nktp + nkpt *(nbnd/6)
lines=input.readlines()
for n, bla in enumerate(lines):
dummy=0
# bloedes \n am Ende weg
for i in range(n+1):
lines[i]=re.compile( "\n" ).sub( '' , lines[i] )
# Wir haben jetzt die Anzahl der Linien, Jetzt die Anzahl pro k-punkt
#(nprok)
# 6 pro Spalte (also nbnd/6), falls nicht durch 6 teilbar, muss man plus 1
#zahlen
if (nbnd%6)==0:
nprok=nbnd/6
else:
nprok=nbnd/6 + 1
kabslist=[]
freqlist=[]
for j in range(nkpt):
klist=[]
#linnum: only lines in which k-point info is stored
linnum=j*(nprok+1)
kptstr=lines[linnum].split()
klist=[]
for i in range(3):
k=string.atof(kptstr[i])
klist.append(k)
kabslist.append( math.sqrt( klist[0]**2 + klist[1]**2 +
klist[2]**2 ))
freqK=[]
for i in range(nprok):
freqK.append( lines[linnum+1+i].split())
dummy=list(flatten(freqK))
freqlist.append(dummy)
#output
for i in range(nbnd):
for j in range(nkpt):
print ("%9.9f%9.9f") %(kabslist[j],string.atof(
freqlist[j][i]) )
print " "
print " "
-- next part --
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[Pw_forum] zigzag nanotube input error
Hi I think your z coordinates are wrong, they are in units of lattice constants. Try to use angstrom as input coordinates - you will see errors much easier. BTW, you only need 1 k-point in the non-repeating directions, as long yuo are not interested in bundling effects. The ectuwfc looks also very small for C, did you check convergence ? Cheers Marcel Marcel Mohr Institut f?r Festk?rperphysik, TU Berlin marcel(at)physik.tu-berlin.de Sekr. EW 5-4 TEL: +49-30-314 24442 Hardenbergstr. 36 FAX: +49-30-314 27705 10623 Berlin On Tue, 27 Nov 2007, meisam aghtar wrote: > hi > I had a problem during runing the pw input of (5,0) nanotube . the input and > the error is in following. another problem is that I dont know wich > parameters should be in a pw input for a nanotube. > &CONTROL > calculation = 'scf' , >restart_mode = 'restart', > outdir = '/home/meisam/projhe/5-0/band/ scratch/' > pseudo_dir = '/home/meisam/espresso-3.1.1/pseudo/', > prefix = 'cnt-scf' , > / > &SYSTEM > ibrav = 4, > celldm(1) = 19, > celldm(3) = 0.282460, > nat = 20, >ntyp = 1, > ecutwfc = 30, > / > > &ELECTRONS > / > ATOMIC_SPECIES >C 12.0 C.pz-vbc.UPF > ATOMIC_POSITIONS alat >C 0.194660.00.0 > >C 0.157490.114420.07062 >C 0.060150.185130.0 >C -0.060150.185130.07062 >C -0.157490.114420.0 >C -0.194660.00.07062 >C -0.15749 -0.114420.0 >C -0.06015 -0.185130.07062 >C 0.06015 -0.185130.0 >C 0.15749 -0.114420.07062 >C 0.157490.114420.21185 >C 0.060150.185130.28246 >C -0.060150.185130.21185 >C -0.157490.114420.28246 >C -0.194660.00.21185 >C -0.15749 -0.114420.28246 >C -0.06015 -0.185130.21185 >C 0.06015 -0.185130.28246 >C 0.15749 -0.114420.21185 >C 0.194660.00.28246 > K_POINTS automatic > 2 2 14 1 1 1 > erro : >Starting configuration read from file cnt-scf.save > Failed to open file >cnt-scf.save > Using input configuration > > %% > from setup : error # 1 > Wrong atomic coordinates > %% > stopping ... > > > > > Be a better pen pal. > Text or chat with friends inside Yahoo! Mail. See how. > http://overview.mail.yahoo.com/
[Pw_forum] still can not get the modes with the dynmat.x
Hi Yuehua Try to run dynmat interactively without using the queue manager ! There should be a files called dynmat.out, dynmat.mold, dynmat.x... See in example09. Nobody can guess, where your computer puts them ;) Cheers Marcel Marcel Mohr Institut f?r Festk?rperphysik, TU Berlin marcel(at)physik.tu-berlin.de Sekr. EW 5-4 TEL: +49-30-314 24442 Hardenbergstr. 36 FAX: +49-30-314 27705 10623 Berlin On Tue, 20 Nov 2007, xu yuehua wrote: > i use dynmat.x to add lo-to split ,and want to get the new frequencies and > modes, and only the frequencies is present . > my infile now: > > &input > fildyn='/raid/xyh/pwscf/fourringwater/pho_scf_relax_fromlqf_via_vaspz/*.dynG', > asr='one-dim', > q(1)=0,q(2)=0,q(3)=12, > filout= 'dynmat.out'/ > > > > but there is not dynmat.out .only the file like pwscf.sh.o8645 > and in pwscf.sh.o8645 > > there is : > > ue Nov 20 17:29:58 CST 2007 > > Reading Dynamical Matrix from file > /raid/xyh/pwscf/fourringwater/pho_scf_relax_fromlqf_via_vaspz/fourringwater.dynG > asr rotation axis in 1D system=3 > Acoustic Sum Rule: || Z*(ASR) - Z*(orig)|| =0.815659E-01 > Acoustic Sum Rule: ||dyn(ASR) - dyn(orig)||=0.697493E-01 > > Polarizability (A^3 units) > multiply by 0.971817 for Clausius-Mossotti correction > 5.6254140.0006580.000133 > 0.0006585.6241280.000114 > 0.0001330.0001148.860593 > > IR cross sections are in (D/A)^2/amu units > # mode [cm-1] [THz] IR >1 0.000.0. >2 0.000.0. >3 0.000.0. >4 0.000.0. >5 49.161.47380.0064 >6 63.881.91510.0043 >7 68.562.05540.0016 >8106.293.18650.0002 >9156.914.70400.0002 > 10252.937.58260.2436 > 11254.667.63440.4708 > 12257.937.73240.6958 > 13564.27 16.91630.4540 > 14631.40 18.92870.1605 > 15632.64 18.96591.7223 > 16633.03 18.97771.8109 > 17705.34 21.14551.3172 > 18750.19 22.49003.3584 > 19750.80 22.50843.3466 > 20793.99 23.80300.0001 > 21854.32 25.61173.6181 > > ... > > > > > no mode ! .i am puzzled .and where is my error ? > > > -- > Xu Yuehua > physics Department of Nanjing university > China >
[Pw_forum] Plot phonon dispersion
Hi, what do you usually do to convert the *.freq file, that comes from matdyn.x ? I found an old post from Eyvaz Isaev from (Feb 4 2007), but couldn't fetch the attachments from the archive. Cheers Marcel Marcel Mohr Institut f?r Festk?rperphysik, TU Berlin marcel(at)physik.tu-berlin.de Sekr. EW 5-4 TEL: +49-30-314 24442 Hardenbergstr. 36 FAX: +49-30-314 27705 10623 Berlin
[Pw_forum] 3.2 executables
Hi The intel fortran and c compiler are free for non-commercial. You can download them. Here, the compilation of pw was 1.) really easy (the configure script does everything) 2.) not portable, due to some linked libraries (somebody who has statically linked, can probably overcome this) In the current version the graphical user interface (pwgui) is missing, so maybe try espresso-3.1.1 (for pwgui) and espresso-3.2.1 for newest version. Kind Regards Marcel Marcel Mohr Institut f?r Festk?rperphysik, TU Berlin marcel at physik.tu-berlin.de Sekr. PN 5-4 TEL: +49-30-314 24442 Hardenbergstr. 36 FAX: +49-30-314 27705 10623 Berlin On Tue, 20 Feb 2007, Amall Ramanathan wrote: > Hi, > Thanks for your email. I do not have a Fortran compiler thats why I was > interested if somebody who has compiled and has the executables in the bin > directory of pwscf on his comuter for version 3.2 could send me > the executables as a zipped attachment to my email. Thanks, keep in touch. > Amall*,* > amallahmad at gmail.com > > On 2/19/07, halim said wrote: >> >> Hi, >> >> I would like please to ask you, do you have compiler 90 fortran in your >> machine, could you please give me informations which compiler do you have >> in >> your machine, also do you have packages for algebra optimizations. >> >> Could you give me these informations, may be I could help. >> >> If you have compiler intel fortran and mkl libraries are in your pc, every >> thing is fine. >> >> just what you need to get the excecutable, type: >> >> ./configure (first step) >> >> make pw (second step) >> >> if you want to compile just pw code otherwise for comipling every thing >> you should type make all. >> >> I am looking forward your email. >> >> Regards, >> >> Halim >> >> >> >> *Amall Ramanathan * a ?crit : >> >> Hi, >> I am a new user and would appreciate it if aybody who has complied pwscf >> version 3.2 for a sequential pentium 4 machine under linux can send me >> only the executables bin folder in zip or tar format as a attachment to my >> email or please put it in the pwscf.org home so that I and anybody else in >> need of it can download it. >> Thanks, >> Amall >> amallahmad at gmail.com >> >> >> -- >> D?couvrez une nouvelle fa?on d'obtenir des r?ponses ? toutes vos questions >> ! Profitez des connaissances, des opinions et des exp?riences des >> internautes sur Yahoo! >> Questions/R?ponses<http://fr.rd.yahoo.com/evt=42054/*http://fr.answers.yahoo.com>. >> >> >> >
[Pw_forum] memory usage
Dear list-members I have the suspicion that all of you have supercomputers where memory usage is incidental. OK, not really, but how can i print or estimate the memory a calculation would need? (In older versions there was memory.x, and later the routine show_memory). Kind regards Marcel
[Pw_forum] phonon calculation with ultrasoft potentials
Dear espresso-users, I am calculating wurtzite CdSe with the PBE Vanderbilt pseudos provided by the pwscf page. Lattice constant is very good. I am using a cutoff of 50 Ry, (that is even far beyond convergence). When I try to calculate phonon frequencies, I obtain acoustic phonon at 30 and 90 cm^-1. And the higehst optical phonon is twice as it should be. This is my ph.x input file &inputph tr2_ph=1.0d-14, prefix='cdse', epsil=.true., amass(1)=112.4, amass(2)=78.96, fildyn='cdse.dynG', / 0.0 0.0 0.0 Maybe the electric field has to be included in the calculation, but I do not know how. Best Regards Marcel Mohr
