[Pw_forum] xcrysden error:***.rx.in is not pwscf input file
about the format in my inputfile,you see a whitespace,it is just
effect here ,in my compute,it is rather in order .i can enclose it if you
could accept it .
2007/11/27, Tone Kokalj :
>
>
> On Tue, 2007-11-27 at 21:19 +0800, xu yuehua wrote:
> > ok .i will put my ***.rx.in here :i put it into XCRYSDEN.BUT
> > THE ERROR SAYS::**,rx.in is not pwscf input file !
>
> On my computer xcrysden says:
>
> invalid number: incomprehensible list input
> apparent state: internal I/O
> lately reading sequential formatted internal IO
>
> Luckily xcrysden is picky enough to complain against your input file,
> because there is typo therein. In particular:
>
> > ATOMIC_POSITIONS { crystal }
> > H0.1102739014 -0.07742902990.6115517241
> > H0.1389927901 -0.04350134551.0285862069
> > H -0.10546646010.02154511120.6018620690
> > H -0.1078330245 -0.04130626000.2584827586
> > H -0.1324180.12410553951.0127586207
> > H - 0.07190011570.10953916680.5982068966
>
> Notice the whitespace after minus sign for last x-coordinate:
> - 0.0719001157
>
> Regards, Tone
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Xu Yuehua
physics Department of Nanjing university
China
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[Pw_forum] xcrysden error:***.rx.in is not pwscf input file
this part is so strange to me !!
CELL_PARAMETERS
33.0694,19.0926 0
0.0 38.1852 0.0
0.0 0.0 5.4820
On Nov 27, 2007 9:19 PM, xu yuehua wrote:
> ok .i will put my ***.rx.in here :i put it into XCRYSDEN.BUT
> THE ERROR SAYS::**,rx.in is not pwscf input file !
>
> calculation = "relax",
> prefix = "h2o",
> pseudo_dir = "/home/xyh/intel_espresso-3.2/pseudo",
> outdir = "/home/xyh/intel_espresso-3.2/tmp",
> /
>
> ibrav = 0,
> nat = 15,
> ntyp = 2,
> ecutwfc = 29.98744D0,
> ecutrho =200
> occupations = "smearing",
> smearing= "gauss",
> degauss = 0.003D0,
> /
>
> conv_thr= 1.D-9,
> mixing_beta = 0.2D0,
> /
>
> pot_extrapolation = "second_order",
> wfc_extrapolation = "second_order",
> /
> CELL_PARAMETERS
> 33.0694,19.0926 0
> 0.0 38.1852 0.0
> 0.0 0.0 5.4820
> ATOMIC_SPECIES
> H 1.0 H.pbe-van_bm.UPF
> O 15.999 O.pbe-van_bm.UPF
> ATOMIC_POSITIONS { crystal }
> H0.1102739014 -0.07742902990.6115517241
> H0.1389927901 -0.04350134551.0285862069
> H -0.10546646010.02154511120.6018620690
> H -0.1078330245 -0.04130626000.2584827586
> H -0.1324180.12410553951.0127586207
> H - 0.07190011570.10953916680.5982068966
> H0.0005944993 -0.09475764570.7058965517
> H0.0681044664 -0.14812649061.07
> H0.01635444670.12481782610.2592758621
> H0.0639829858 0.05074118040.5938965517
> O0.1321617646 -0.04395216940.6873103448
> O -0.0925246679 -0.03294558680.5714137931
> O -0.12000311090.10963521880.6811034483
> O0.0571462440 -0.1256424289 0.753000
> O0.01422796850.09913354050.5491724138
> K_POINTS {automatic}
> 1 1 6 0 0 0
>
>
>
> 2007/11/27, Tone Kokalj :
>
> >
> > On Tue, 2007-11-27 at 17:00 +0800, xu yuehua wrote:
> > > hi everyone:
> > > I have complete the relaxed work ,and want to see the details ,but
> > > when i put my input file **.rx.in into crysden ,and the error message
> > > says:**,rx.in is not pwscf infut file !
> >
> > How can anybody say?
> > It is impossible to say anything without the input file that produces
> > the error !
> >
> > Regards, Tone
> >
> >
> > ___
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
> --
> Xu Yuehua
> physics Department of Nanjing university
> China
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
--
Hai-Ping Lan
Department of Electronics ,
Peking University , Bejing, 100871
lanhaiping at gmail.com, hplan at pku.edu.cn
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[Pw_forum] xcrysden error:***.rx.in is not pwscf input file
ok .i will put my ***.rx.in here :i put it into XCRYSDEN.BUT
THE ERROR SAYS::**,rx.in is not pwscf input file !
calculation = "relax",
prefix = "h2o",
pseudo_dir = "/home/xyh/intel_espresso-3.2/pseudo",
outdir = "/home/xyh/intel_espresso-3.2/tmp",
/
ibrav = 0,
nat = 15,
ntyp = 2,
ecutwfc = 29.98744D0,
ecutrho =200
occupations = "smearing",
smearing= "gauss",
degauss = 0.003D0,
/
conv_thr= 1.D-9,
mixing_beta = 0.2D0,
/
pot_extrapolation = "second_order",
wfc_extrapolation = "second_order",
/
CELL_PARAMETERS
33.0694,19.0926 0
0.0 38.1852 0.0
0.0 0.0 5.4820
ATOMIC_SPECIES
H 1.0 H.pbe-van_bm.UPF
O 15.999 O.pbe-van_bm.UPF
ATOMIC_POSITIONS { crystal }
H0.1102739014 -0.07742902990.6115517241
H0.1389927901 -0.04350134551.0285862069
H -0.10546646010.02154511120.6018620690
H -0.1078330245 -0.04130626000.2584827586
H -0.1324180.12410553951.0127586207
H -0.07190011570.10953916680.5982068966
H0.0005944993 -0.09475764570.7058965517
H0.0681044664 -0.14812649061.07
H0.01635444670.12481782610.2592758621
H0.06398298580.05074118040.5938965517
O0.1321617646 -0.04395216940.6873103448
O -0.0925246679 -0.03294558680.5714137931
O -0.12000311090.10963521880.6811034483
O0.0571462440 -0.12564242890.753000
O0.01422796850.09913354050.5491724138
K_POINTS {automatic}
1 1 6 0 0 0
2007/11/27, Tone Kokalj :
>
>
> On Tue, 2007-11-27 at 17:00 +0800, xu yuehua wrote:
> > hi everyone:
> > I have complete the relaxed work ,and want to see the details ,but
> > when i put my input file **.rx.in into crysden ,and the error message
> > says:**,rx.in is not pwscf infut file !
>
> How can anybody say?
> It is impossible to say anything without the input file that produces
> the error !
>
> Regards, Tone
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
--
Xu Yuehua
physics Department of Nanjing university
China
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[Pw_forum] Units of conv_thr and tr2_ph
On Nov 27, 2007, at 19:00 , Katalin Gaal-Nagy wrote: > Are the units of conv_thr and tr2_ph Ry yes > meaning that the self consistency is checked agains the energy > of the system or are they different? this is a more complicated issue. conv_thr is an estimate of the error on the energy due to self-consistency. tr2_ph is an estimate of...I don't remember exactly what, but it is NOT (unfortunately) related to an error on any energy, but to the difference of input and output potentials Paolo --- 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] Installation problem on Intel i32 ubuntu
On Nov 27, 2007, at 20:36 , Jeongnim Kim wrote: > Adding "-lmkl_sequential" may work. > > libmkl_sequential.so:00145340 T mkl_serv_load_fun have fun loading mkl :-( --- 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] Using make clean
On Nov 27, 2007, at 18:56 , ramesh kumar wrote: > checking for Fortran name-mangling scheme... lower case, > underscore, extra underscore go to include/c_defs.h . There should be two lines: #define F77_FUNC(name,NAME) name ## _ #define F77_FUNC_(name,NAME) name ## __ remove the second underscore. Not sure why, it looks like configure doesn't get the correct number of underscores to add (note that all missing symbols have one underscore in the name; some genius has decided that they deserve one more at the end, go figure why) --- 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] Installation problem on Intel i32 ubuntu
On Nov 27, 2007, at 19:05 , ZEYAD ALAHMED wrote: > Both methods suggested below did not help. The problem has not been > solved yet. >>> You might try Axel's advice for newer MKL: ...this was the first suggestion... >>> If this doesn't work, please read the instructions on how to use >>> your >>> specific version of MKL (they should be included in the MKL library) >>> and let us know what must be done so that we may try to update >>> "configure" ...and this was the second. Apparently your software installation has some weirdness that prevents linking of MKL libraries, using the syntax that is known to work in many other cases. If you do not find out how to link YOUR specific version of MKL on YOUR machine, it is very unlikely that anybody else can. --- 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] honeycomb lattices and shift in gamma point?
Dev, I believe that if you look closely at the published band structures of graphene you'll find that many graphs are centered on the K point. This doesn't mean that the K point is now the origin, it just means that the K point is the center of the published graph. That's because K is the interesting part of the band structure. A quick Google (TM) of the web reveals more about graphene than I really wanted to know tonight. Here's a useful tutorial: http://www.ph.utexas.edu/~macdgrp/meetings/hongki-graphene(partial).pdf Note particularly the band structure on page 8, and compare it to the band structure on page 19. harman dev wrote: > Dear all, > > This is short extension with reference to my previous message. I > was wondering if this shift in the origin of the Brillouin Zone for > graphene is associated with the honeycomb symmetry. As mentioned, a > hcp cell such as that of Mg has the gamma point as the origin of its > Brillouin Zone whilst the point K seems to be the origin of the > Brillouin Zone for honeycomb lattices such as graphene and boron > nitride. Any comments on this would be great appreciated. Thank you. > > Cheers, > Dev > -- Mike Mehl Naval Research Laboratory Washington DC USA
[Pw_forum] Installation problem on Intel i32 ubuntu
Dear all, Both methods suggested below did not help. The problem has not been solved yet. Any idea! Zeyad Alahmed, PhD > Date: Tue, 27 Nov 2007 14:38:14 + > From: nazari at iasbs.ac.ir > To: pw_forum at pwscf.org > Subject: Re: [Pw_forum] Installation problem on Intel i32 ubuntu > >> On Nov 26, 2007, at 21:47 , ZEYAD ALAHMED wrote: >> >>> [...] -lmkl_lapack -L/opt/intel/mkl/10.0.011/lib/32 -lmkl_ia32 - >>> lguide -lpthread -lfftw >>> /opt/intel/mkl/10.0.011/lib/32/libmkl_lapack.so: undefined >>> reference to `mkl_serv_load_fun' >>> /opt/intel/mkl/10.0.011/lib/32/libmkl_lapack.so: undefined >>> reference to `mkl_serv_load_dll' >> >> like states in the Lanczos chain, each new version of Intel software >> is orthogonal >> to all preceding versions. You might try Axel's advice for newer MKL: >> >> LDFLAGS=-i-static -openmp >> BLAS_LIBS= -L/opt/intel/mkl/10.0.011/lib/32 -lmkl_ia32 >> (without -lguide -lpthread) >> >> If this doesn't work, please read the instructions on how to use your >> specific >> version of MKL (they should be included in the MKL library) and let >> us know >> what must be done so that we may try to update "configure" >> >> Paolo >> --- >> Paolo Giannozzi, Dept of Physics, University of Udine >> via delle Scienze 208, 33100 Udine, Italy >> Phone +39-0432-558216, fax +39-0432-558222 >> >> I just add the follwing lines in .bashrc and the problem lik this > > is solved. > source /opt/intel/cc/10.0.026/bin/iccvars.sh > source /opt/intel/fc/10.0.026/bin/ifortvars.sh > source /opt/intel/idb/10.0.026/bin/idbvars.sh > LD_LIBRARY_PATH=/opt/intel/mkl/9.1.023/lib/32 > > > Regards > Fariba Nazari > >> >> ___ >> 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 _ Connect and share in new ways with Windows Live. http://www.windowslive.com/connect.html?ocid=TXT_TAGLM_Wave2_newways_112007
[Pw_forum] Using make clean
regards K. Ramesh Kumar On Tue, 27 Nov 2007 Stefano de Gironcoli wrote : >ramesh kumar wrote: >> >> >>Dear users >> >>i am new to pwscf when i try to configure it says success and it recognized >>all the lib files and compliers. >> >>but when i give the command make all >> >>it says >> >> erry_phase.f90:(.text+0x33): undefined reference to `ln_alloc_' >>berry_phase.f90:(.text+0x8f): undefined refer >> >have you tried make clean; ./configure ; make all ? >stefano > -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071127/dbe93b55/attachment.htm
[Pw_forum] xcrysden error:***.rx.in is not pwscf input file
hi everyone: I have complete the relaxed work ,and want to see the details ,but when i put my input file **.rx.in into crysden ,and the error message says:**, rx.in is not pwscf infut file ! and i want to ask what is input file in pwscf? why **.rx.in is not ? i need your help bests -- Xu Yuehua physics Department of Nanjing university China -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071127/1cc483c1/attachment.htm
[Pw_forum] Still problems on my intel mac .... again HELP !!!!
On Nov 27, 2007, at 16:40 , Riccardo Sabatini wrote: > ranlib: file: libpw.a(a2fmod.o) has no symbols ls -l a2fmod.o nm a2fmod.o > i'm starting to think something spooky is going on in my mac not impossible. I have a Mac and Q-E compiles perfectly on it with g95, gfortran, ifort, but I have to say that the reliability of its software is wy below my expectations. 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] how to get the *.xyz OR *XSF file which can be used in XCrySDen
hi : thank for lan haiping , and there is another problem present when i put *.o (a out file produced by machine)to xcrysden ,the software ask me which to see,i choose the initial structure ,and it is OK ,but when i choose to havea look at the optimized and latest structure ,it gives error message :an error occurred while trying to update a structure;error reading /home/xyh/xcry_tmp/xc_8016/xc_structure8016 so i do not know the reason and how to resolve it .if you could give me a piece of advice .i will be thankful. bests 2007/11/27, lan haiping : > > Dear Yuehua, > > xcrysden can read input/output of pwscf . you can achieve just by > 'xcrysden --pwi (or -pwo) pwscf.in(pwscf.out)' . > good luck > > Regards. > > > On Nov 27, 2007 2:39 PM, xu yuehua < njuxuyuehua at gmail.com> wrote: > > > > > hi all: > > i relaxed a structure ,and want to see the details,and the XCrySDen can > > read the *xyz AND *XSF .SO HOW TO get the above file .my out file does not > > including the above . > > thanks for your help. > > bests > > -- > > Xu Yuehua > > physics Department of Nanjing university > > China > > > > ___ > > Pw_forum mailing list > > Pw_forum at pwscf.org > > http://www.democritos.it/mailman/listinfo/pw_forum > > > > > > > -- > Hai-Ping Lan > Department of Electronics , > Peking University , Bejing, 100871 > lanhaiping at gmail.com, hplan at pku.edu.cn > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Xu Yuehua physics Department of Nanjing university China -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071127/0a8887ca/attachment.htm
[Pw_forum] Still problems on my intel mac .... again HELP !!!!
Hi everyone,
first of all many many thanks for the help you gave me, but still
something id wrong :(((
I tried all the suggestions you gave me. I cleaned with make clean,
i even deleted the directory and started from scratch several times but
nothing different, still the problem at the library.
I used the make.sys-mac-intel suggestions, i mixed them and my
configuration (i don't have intel mkl). Still everything works great but
when is the time of compiling pw.x
--
ifort -o pw.x \
pwscf.o ../Modules/at{***CUTTED***}ml_io_base.o libpw.a
../flib/ptools.a ../flib/flib.a ../clib/clib.a ../iotk/src/libiotk.a
-llapack -latlas
ipo: warning #11023: file format not recognized for ../flib/flib.a
ipo: warning #11023: file format not recognized for ../iotk/src/libiotk.a
ld: warning empty table of contents: ../flib/flib.a (can't load from it)
ld: warning empty table of contents: ../iotk/src/libiotk.a (can't load
from it)
ld: Undefined symbols:
_MAIN__
make[1]: *** [pw.x] Error 1
make: *** [pw] Error 2
--
What i understood id that there is a problem either with ranlib or
ar. I tried different solutions and configurations in make.sys. I tried
AR = ar
ARFLAGS= ruv
RANLIB = ranlib
No luck, same error. Then i tried (as in the make.sys-mac-intel)
AR = ar
ARFLAGS= ruv
RANLIB = echo
With this i recive a strange error, something about "ar error, cannot
use the argument k". I found that that configuration doesn't work
because no arguments are passed to ar, expect if i add
ARFLAGS_DYNAMIC= ruv
In this case the ar works fine but then again the same error !!
Sorry but i'm getting crazy...any help is very appreciated ! By
the way, thanks again for the help, i rellay appreciate.
Riccardo
P.S.: I give you here somethig that can help. The error comes out right
after ar creates the libraries at the first time. When ar runs both in
iotk, libpw or any other one i have the same strange message. I write
down the case for iotk (the main behaviour happens everytime ar runs)
---
ar ruv libpw.a a2fmo***CUT***wsweight.o
ar: creating archive libpw.a
***CUT***
a - a2fmod.o
a - wsweight.o
ranlib: file: libpw.a(a2fmod.o) has no symbols
ranlib: file: libpw.a(add_bfield.o) has no symbols
***CUT***
ranlib: file: libpw.a(write_ns.o) has no symbols
ranlib: file: libpw.a(wsweight.o) has no symbols
echo libpw.a
libpw.a
---
in this case i used RANLIB = echo but seems ranlib runs anyway.i'm
starting to think something spooky is going on in my mac
[Pw_forum] Error msg while configure
/xml_io_base.o: In function `__xml_io_base__create_directory': xml_io_base.f90:(.text+0x20a): undefined reference to `c_mkdir_' libpw.a(input.o): In function `verify_tmpdir_': input.f90:(.text+0x756): undefined reference to `c_mkdir_' libpw.a(bp_c_phase.o): In function `c_phase_': bp_c_phase.f90:(.text+0x107a): undefined reference to `ylm_q_' libpw.a(c_phase_field.o): In function `c_phase_field_': c_phase_field.f90:(.text+0x20cf): undefined reference to `ylm_q_' libpw.a(h_epsi_her.o): In function `h_epsi_her_': h_epsi_her.f90:(.text+0xdf5): undefined reference to `ylm_q_' h_epsi_her.f90:(.text+0x1341): undefined reference to `ylm_q_' collect2: ld returned 1 exit status make[1]: *** [pw.x] Error 1 make[1]: Leaving directory `/home/ramesh/espresso-3.2.3/PW' make: *** [pw] Error 2 can anybody help in that thanks in advance with rgds K.Ramesh Kumar Research scholar IIT Madras Chennai-36 India -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071127/d14875a4/attachment-0001.htm
[Pw_forum] how to get the *.xyz OR *XSF file which can be used in XCrySDen
Dear Yuehua, xcrysden can read input/output of pwscf . you can achieve just by 'xcrysden --pwi (or -pwo) pwscf.in(pwscf.out)' . good luck Regards. On Nov 27, 2007 2:39 PM, xu yuehua wrote: > > hi all: > i relaxed a structure ,and want to see the details,and the XCrySDen can > read the *xyz AND *XSF .SO HOW TO get the above file .my out file does not > including the above . > thanks for your help. > bests > -- > Xu Yuehua > physics Department of Nanjing university > China > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071127/90f3aa2f/attachment.htm
[Pw_forum] xcrysden error:***.rx.in is not pwscf input file
On Tue, 2007-11-27 at 21:19 +0800, xu yuehua wrote:
> ok .i will put my ***.rx.in here :i put it into XCRYSDEN.BUT
> THE ERROR SAYS::**,rx.in is not pwscf input file !
On my computer xcrysden says:
invalid number: incomprehensible list input
apparent state: internal I/O
lately reading sequential formatted internal IO
Luckily xcrysden is picky enough to complain against your input file,
because there is typo therein. In particular:
> ATOMIC_POSITIONS { crystal }
> H0.1102739014 -0.07742902990.6115517241
> H0.1389927901 -0.04350134551.0285862069
> H -0.10546646010.02154511120.6018620690
> H -0.1078330245 -0.04130626000.2584827586
> H -0.1324180.12410553951.0127586207
> H - 0.07190011570.10953916680.5982068966
Notice the whitespace after minus sign for last x-coordinate:
- 0.0719001157
Regards, Tone
[Pw_forum] xcrysden error:***.rx.in is not pwscf input file
On Nov 27, 2007, at 14:34 , lan haiping wrote: > this part is so strange to me !! > CELL_PARAMETERS > 33.0694,19.0926 0 > 0.0 38.1852 0.0 > 0.0 0.0 5.4820 it is a perfectly acceptable syntax --- 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] symmetry problem with Si lattice
On Nov 27, 2007, at 13:43 , Ezad Shojaee wrote: > i have a silly problem about Si lattice. I defined it as an SC > (simple cubic) > with 8 atoms per basis: > > ATOMIC_POSITIONS > Si 0.00 0.00 0.00 > Si 0.50 0.50 0.00 > Si 0.00 0.50 0.50 > Si 0.50 0.00 0.50 > Si 0.25 0.25 0.25 > Si 0.75 0.75 0.25 > Si 0.25 0.75 0.75 > Si 0.75 0.25 0.75 > > K_POINTS > 4 >0.125 0.125 0.125 1.00 >0.375 0.375 0.375 1.00 >0.375 0.125 0.125 3.00 >0.375 0.375 0.125 3.00 > > the Total Energy is 4-times as great as the Fcc structure > total energy (till the 5-th digit), but the code has detected > 24 symmetries, with no inversion for the SC one. What's > the problem(if there is any)? Should'nt be 48 symmetries? there isn't any problem, but there is a subtlety. The 24 symmetries that have no associated fractional translation are found; the remaining 24 have an associated fractional translation (1/4 1/4 1/4) and are also found, but not accepted. The reason is that in a supercell the choice of fractional translations is not unique and you have no (simple) way to be sure that the set of all symmetry operations is actually a group, in the mathematical sense. Paolo --- 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] how to get the *.xyz OR *XSF file which can be used in XCrySDen
hi all: i relaxed a structure ,and want to see the details,and the XCrySDen can read the *xyz AND *XSF .SO HOW TO get the above file .my out file does not including the above . thanks for your help. bests -- Xu Yuehua physics Department of Nanjing university China -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071127/07143545/attachment.htm
[Pw_forum] Installation problem on Intel i32 ubuntu
> On Nov 26, 2007, at 21:47 , ZEYAD ALAHMED wrote: > >> [...] -lmkl_lapack -L/opt/intel/mkl/10.0.011/lib/32 -lmkl_ia32 - >> lguide -lpthread -lfftw >> /opt/intel/mkl/10.0.011/lib/32/libmkl_lapack.so: undefined >> reference to `mkl_serv_load_fun' >> /opt/intel/mkl/10.0.011/lib/32/libmkl_lapack.so: undefined >> reference to `mkl_serv_load_dll' > > like states in the Lanczos chain, each new version of Intel software > is orthogonal > to all preceding versions. You might try Axel's advice for newer MKL: > > LDFLAGS=-i-static -openmp > BLAS_LIBS= -L/opt/intel/mkl/10.0.011/lib/32 -lmkl_ia32 > (without -lguide -lpthread) > > If this doesn't work, please read the instructions on how to use your > specific > version of MKL (they should be included in the MKL library) and let > us know > what must be done so that we may try to update "configure" > > Paolo > --- > Paolo Giannozzi, Dept of Physics, University of Udine > via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > I just add the follwing lines in .bashrc and the problem lik this is solved. source /opt/intel/cc/10.0.026/bin/iccvars.sh source /opt/intel/fc/10.0.026/bin/ifortvars.sh source /opt/intel/idb/10.0.026/bin/idbvars.sh LD_LIBRARY_PATH=/opt/intel/mkl/9.1.023/lib/32 Regards Fariba Nazari > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum >
[Pw_forum] symmetry problem with Si lattice
Hi in order to have the Gamma-point phonon frequencies, if we use the SC lattice schemma for Si, it seems that we have frequencies rather diffrerent from the FCC schemma. What do you expect of the irreps and the symmetries of the modes(and also their number) of SC schemma with 8-atom basis comparing to the FCC one(with 2 atoms per basis)? what should be the same in two shemmas? _ Invite your mail contacts to join your friends list with Windows Live Spaces. It's easy! http://spaces.live.com/spacesapi.aspx?wx_action=create_url=/friends.aspx=en-us -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071127/68fa1c66/attachment.htm
[Pw_forum] Installation problem on Intel i32 ubuntu
Adding "-lmkl_sequential" may work. libmkl_sequential.so:00145340 T mkl_serv_load_fun On Nov 27, 2007 8:38 AM, wrote: > > On Nov 26, 2007, at 21:47 , ZEYAD ALAHMED wrote: > > > >> [...] -lmkl_lapack -L/opt/intel/mkl/10.0.011/lib/32 -lmkl_ia32 - > >> lguide -lpthread -lfftw > >> /opt/intel/mkl/10.0.011/lib/32/libmkl_lapack.so: undefined > >> reference to `mkl_serv_load_fun' > >> /opt/intel/mkl/10.0.011/lib/32/libmkl_lapack.so: undefined > >> reference to `mkl_serv_load_dll' > > > > like states in the Lanczos chain, each new version of Intel software > > is orthogonal > > to all preceding versions. You might try Axel's advice for newer MKL: > > > > LDFLAGS=-i-static -openmp > > BLAS_LIBS= -L/opt/intel/mkl/10.0.011/lib/32 -lmkl_ia32 > > (without -lguide -lpthread) > > > > If this doesn't work, please read the instructions on how to use your > > specific > > version of MKL (they should be included in the MKL library) and let > > us know > > what must be done so that we may try to update "configure" > > > > Paolo > > --- > > Paolo Giannozzi, Dept of Physics, University of Udine > > via delle Scienze 208, 33100 Udine, Italy > > Phone +39-0432-558216, fax +39-0432-558222 > > > > I just add the follwing lines in .bashrc and the problem lik this > > is solved. > source /opt/intel/cc/10.0.026/bin/iccvars.sh > source /opt/intel/fc/10.0.026/bin/ifortvars.sh > source /opt/intel/idb/10.0.026/bin/idbvars.sh > LD_LIBRARY_PATH=/opt/intel/mkl/9.1.023/lib/32 > > > Regards > Fariba Nazari > > > > > > ___ > > 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 > -- Dr. Jeongnim Kim NCSA and MCC, University of Illinois at Urbana-Champaign (Tel) 217-244-4971
[Pw_forum] zigzag nanotube input error
Hi, If you really have the balnk line between the first and the second atomic coordinates that could be your problem. A more severe problem is that the code failed to read the configuration you meant to restart from. This could be due to the space in the name of your outdir, again of course if you really have it there in your input. As for the parameters, first off, there's a single k point should be enough in the plane perp to the NT axis. To determine the no of kpoints along the axis, you should do a convergence study, increasing the number until you are satisfied with the difference of energy values (or whichever value you are interested in). Same goes for Ecut. You are lucky in that a (5,0) has a substantial gap so you don't have to worry about smearing. Your vacuum value seems a little small to me. I usually leave about 10 A between the closest atoms belonging to neigboring images. But then again you should increase this value a little bit and see if it has any effects. These are all the parameters I can think of. Best wishes, Hande Ustunel 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. > > 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' , > / > >ibrav = 4, >celldm(1) = 19, >celldm(3) = 0.282460, > nat = 20, > ntyp = 1, > ecutwfc = 30, > / > > > / > 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/ -- Hande Ustunel Department of Physics Office 439 Middle East Technical University Ankara 06531, Turkey Tel : +90 312 210 3264 http://www.physics.metu.edu.tr/~hande
[Pw_forum] symmetry problem with Si lattice
Hi i have a silly problem about Si lattice. I defined it as an SC(simple cubic) with 8 atoms per basis: ATOMIC_POSITIONS Si 0.00 0.00 0.00 Si 0.50 0.50 0.00 Si 0.00 0.50 0.50 Si 0.50 0.00 0.50 Si 0.25 0.25 0.25 Si 0.75 0.75 0.25 Si 0.25 0.75 0.75 Si 0.75 0.25 0.75K_POINTS 4 0.125 0.125 0.125 1.00 0.375 0.375 0.375 1.00 0.375 0.125 0.125 3.00 0.375 0.375 0.125 3.00 the Total Energy is 4-times as great as the Fcc structure total energy (till the 5-th digit), but the code has detected 24 symmetries, with no inversion for the SC one. What's the problem(if there is any)? Should'nt be 48 symmetries? _ News, entertainment and everything you care about at Live.com. Get it now! http://www.live.com/getstarted.aspx -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071127/b9bde83a/attachment.htm
[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. > > 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' , > / > > ibrav = 4, > celldm(1) = 19, > celldm(3) = 0.282460, > nat = 20, >ntyp = 1, > ecutwfc = 30, > / > > > / > 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] Installation problem on Intel i32 ubuntu
On Nov 26, 2007, at 21:47 , ZEYAD ALAHMED wrote: > [...] -lmkl_lapack -L/opt/intel/mkl/10.0.011/lib/32 -lmkl_ia32 - > lguide -lpthread -lfftw > /opt/intel/mkl/10.0.011/lib/32/libmkl_lapack.so: undefined > reference to `mkl_serv_load_fun' > /opt/intel/mkl/10.0.011/lib/32/libmkl_lapack.so: undefined > reference to `mkl_serv_load_dll' like states in the Lanczos chain, each new version of Intel software is orthogonal to all preceding versions. You might try Axel's advice for newer MKL: LDFLAGS=-i-static -openmp BLAS_LIBS= -L/opt/intel/mkl/10.0.011/lib/32 -lmkl_ia32 (without -lguide -lpthread) If this doesn't work, please read the instructions on how to use your specific version of MKL (they should be included in the MKL library) and let us know what must be done so that we may try to update "configure" Paolo --- 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] honeycomb lattices and shift in gamma point?
Dear all, This is short extension with reference to my previous message. I was wondering if this shift in the origin of the Brillouin Zone for graphene is associated with the honeycomb symmetry. As mentioned, a hcp cell such as that of Mg has the gamma point as the origin of its Brillouin Zone whilst the point K seems to be the origin of the Brillouin Zone for honeycomb lattices such as graphene and boron nitride. Any comments on this would be great appreciated. Thank you. Cheers, Dev Dear all, I am a little perplexed by the definition of some high symmetry k-points in the hexagonal Brillouin Zone (BZ) of say something like graphene and Magnesium (Mg). I've carried out a number of nscf type calculations (to obtain the band structure) for graphene and magnesium. Typically, one defines the gamma-point as (0,0,0) and the K point as say something like (0,0.577,0), given a set of b-vectors, both in units of 2pi/a0. However, I found that whilst this does apply to bulk Mg, which has a hcp unit cell, the same isn't true for graphene. In the case of graphene, it appears that in order to reproduce the bandstructure that we nominally see in literature, the high-symmetry K point has the coordinates (0,0,0) and the gamma point as (0,0.577,0)! It "appears" as if the origin has shifted in that regard and I'm really quite puzzled by this. If I do follow this and be careful with my selection of k-points in the BZ (using the b-vectors to define its boundaries and so on and so forth), I do in fact get the usual band structure of graphene. Whilst this is ok, I'm not quite contented since I'm not sure as to the actual mechanics of how the program works. Is there any explanation as to why this is the case? Note that I am not using a Monkhorst-Pack grid but am actually specifying the exact k-vectors to be used in the nscf type calculation. I would really appreciate any feedback on this and any suggestions.The following is the list of k-points that I used for graphene, which I should say again, actually generates the correct band structure: 0.000 0.000 0.000 1.0!K 0.000 0.192 0.000 1.0 0.000 0.385 0.000 1.0 0.000 0.577 0.000 1.0!GAMMA 0.083 0.433 0.000 1.0 0.167 0.288 0.000 1.0 0.250 0.144 0.000 1.0!M 0.167 0.096 0.000 1.0 0.083 0.048 0.000 1.0 0.000 0.000 0.000 1.0!K My apologies for the extremely lengthy description of the problem. Thank you very much for your time and happy computing. Cheers, Dev
[Pw_forum] xcrysden error:***.rx.in is not pwscf input file
On Tue, 2007-11-27 at 17:00 +0800, xu yuehua wrote: > hi everyone: > I have complete the relaxed work ,and want to see the details ,but > when i put my input file **.rx.in into crysden ,and the error message > says:**,rx.in is not pwscf infut file ! How can anybody say? It is impossible to say anything without the input file that produces the error ! Regards, Tone
[Pw_forum] zigzag nanotube input error
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. 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' , / ibrav = 4, celldm(1) = 19, celldm(3) = 0.282460, nat = 20, ntyp = 1, ecutwfc = 30, / / 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/ -- next part -- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/pw_forum/attachments/20071127/6d4b7f43/attachment-0001.htm
