[Wien] (no subject)
Dear All I need your help regarding the super cell, I have the structure with two atoms, one atom have 2 positions and the other atoms have five positions. I make the super cell with 1*1*1, and the first atom got four positions while the 2nd atom got 10 positions but i need three positions for the first atom and 8 positions for the second atom. So please help me what should I do. with regrads Kalsoom ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] (no subject)
You should post - your input structure - the exact input you gave after typing x supercell - the output structure (1*1*1 means you're just replicating your original structure ... possibly converting the lattice type -- right?) Cheers, Kevin On Tue, Sep 23, 2014 at 1:39 PM, kalsoom Khan kkkhan.qu...@yahoo.com wrote: Dear All I need your help regarding the super cell, I have the structure with two atoms, one atom have 2 positions and the other atoms have five positions. I make the super cell with 1*1*1, and the first atom got four positions while the 2nd atom got 10 positions but i need three positions for the first atom and 8 positions for the second atom. So please help me what should I do. with regrads Kalsoom ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] why the extremely small RMT occurs in the unit cell?
Dear Peter, Many thanks! Best wishes, Bing On Tue, 9/23/14, Peter Blaha pbl...@theochem.tuwien.ac.at wrote: Subject: Re: [Wien] why the extremely small RMT occurs in the unit cell? To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at Received: Tuesday, September 23, 2014, 1:42 PM This is a rhombohedral structure !!! The most common problems are: For Lattice parameters you need to specify the HEXAGONAL a,a,c atomic coordinates you need to put them in RHOMBOHEDRAL coordinates You won't find this information in a single exp. paper, because nobody mixes the information like that. Read the UG how to convert from H to R coordinates. Just count the number of atoms in your cell. For instance I see 6 Zn atoms 6 Cl atoms, ... so this can hardly make Zn3 B7O13 Cl1 and similar for B and O Am 22.09.2014 18:17, schrieb Bing Zhou: Dear all, I am puzzled by the extremely small RMT in the following unit cell, did I do something wrong? could you please check the case.struct and help me out? Thanks! Bing Mi et al, Zn3B7O13Cl R LATTICE,NONEQUIV.ATOMS: 10161_R3c MODE OF CALC=RELA unit=bohr 16.133071 16.133071 39.624719 90.00 90.00120.00 ATOM -1: X=0.14634999 Y=0.29415000 Z=0.3270 MULT= 6 ISPLIT= 8 ATOM -1:X= 0.29415000 Y=0.3270 Z=0.14634999 ATOM -1:X= 0.64634999 Y=0.8270 Z=0.79415000 ATOM -1:X= 0.3270 Y=0.14634999 Z=0.29415000 ATOM -1:X= 0.8270 Y=0.79415000 Z=0.64634999 ATOM -1:X= 0.79415000 Y=0.64634999 Z=0.8270 Zn NPT= 781 R0=0.5000 RMT= 1.3400 Z: 30.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -2: X=0. Y=0. Z=0.2667 MULT= 6 ISPLIT= 8 ATOM -2:X= 0. Y=0.2667 Z=0. ATOM -2:X= 0.5000 Y=0.7667 Z=0.5000 ATOM -2:X= 0.2667 Y=0. Z=0. ATOM -2:X= 0.7667 Y=0.5000 Z=0.5000 ATOM -2:X= 0.5000 Y=0.5000 Z=0.7667 Cl NPT= 781 R0=0.0001 RMT= 1.2200 Z: 17.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -3: X=0.16450001 Y=0.8347 Z=0.0831 MULT= 6 ISPLIT= 8 ATOM -3:X= 0.8347 Y=0.0831 Z=0.16450001 ATOM -3:X= 0.66450001 Y=0.5831 Z=0.3347 ATOM -3:X= 0.0831 Y=0.16450001 Z=0.8347 ATOM -3:X= 0.5831 Y=0.3347 Z=0.66450001 ATOM -3:X= 0.3347 Y=0.66450001 Z=0.5831 B NPT= 781 R0=0.0001 RMT= 0.3700 Z: 5.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -4: X=0.10220001 Y=0.8975 Z=0.9712 MULT= 6 ISPLIT= 8 ATOM -4:X= 0.8975 Y=0.9712 Z=0.10220001 ATOM -4:X= 0.60220001 Y=0.4712 Z=0.3975 ATOM -4:X= 0.9712 Y=0.10220001 Z=0.8975 ATOM -4:X= 0.4712 Y=0.3975 Z=0.60220001 ATOM -4:X= 0.3975 Y=0.60220001 Z=0.4712 B NPT= 781 R0=0.0001 RMT= 0.3700 Z: 5.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -5: X=0. Y=0. Z=0.1017 MULT= 6 ISPLIT= 8 ATOM -5:X= 0. Y=0.1017 Z=0. ATOM -5:X= 0.5000 Y=0.6017 Z=0.5000 ATOM -5:X= 0.1017 Y=0. Z=0. ATOM -5:X= 0.6017 Y=0.5000 Z=0.5000 ATOM -5:X= 0.5000 Y=0.5000 Z=0.6017 B NPT= 781 R0=0.0001 RMT= 0.3700 Z: 5.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -6: X=0. Y=0. Z=0.9891 MULT= 6 ISPLIT= 8 ATOM -6:X= 0. Y=0.9891 Z=0. ATOM -6:X= 0.5000 Y=0.4891 Z=0.5000 ATOM -6:X= 0.9891 Y=0. Z=0. ATOM -6:X= 0.4891 Y=0.5000 Z=0.5000 ATOM -6:X= 0.5000 Y=0.5000 Z=0.4891 O NPT= 781 R0=0.0001 RMT= 0.0900 Z: 8.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -7: X=0.8396 Y=0.9997 Z=0.1050 MULT= 6 ISPLIT= 8 ATOM -7:X= 0.9997 Y=0.1050 Z=0.8396 ATOM -7:X= 0.3396 Y=0.6050 Z=0.4997 ATOM -7:X= 0.1050
[Wien] the current integration for NMR calculation failed
Dear all, The current integration for NMR calculation of boric acid kept failed with the following information, how can I fix it? Thank you in advance! Bing EXECUTING: /global/software/wien2k-13-2/bin/nmrc -case boric-acid -mode current-green -scratch /scratch/ -noco *** glibc detected *** /global/software/wien2k-13-2/bin/nmrc: realloc(): invalid pointer: 0x0124e7b0 *** === Backtrace: = /lib64/libc.so.6[0x36e9076166] /lib64/libc.so.6(realloc+0x2e2)[0x36e907bfd2] /global/software/wien2k-13-2/bin/nmrc[0x4d3406] /global/software/wien2k-13-2/bin/nmrc[0x4ad6ff] /global/software/wien2k-13-2/bin/nmrc[0x4c5bc4] /global/software/wien2k-13-2/bin/nmrc[0x42ae0a] /global/software/wien2k-13-2/bin/nmrc[0x446625] /global/software/wien2k-13-2/bin/nmrc[0x40ff92] /global/software/wien2k-13-2/bin/nmrc[0x402cac] /lib64/libc.so.6(__libc_start_main+0xfd)[0x36e901ed1d] /global/software/wien2k-13-2/bin/nmrc[0x402ba9] === Memory map: 0040-005ae000 r-xp 00:15 33556202 /global/software/wien2k-13-2/bin/nmrc 007ae000-007c7000 rw-p 001ae000 00:15 33556202 /global/software/wien2k-13-2/bin/nmrc 007c7000-007fe000 rw-p 00:00 0 01204000-01268000 rw-p 00:00 0 [heap] 36e880-36e882 r-xp 08:03 523695 /lib64/ld-2.12.so 36e8a1f000-36e8a2 r--p 0001f000 08:03 523695 /lib64/ld-2.12.so 36e8a2-36e8a21000 rw-p 0002 08:03 523695 /lib64/ld-2.12.so 36e8a21000-36e8a22000 rw-p 00:00 0 36e8c0-36e8c83000 r-xp 08:03 523713 /lib64/libm-2.12.so 36e8c83000-36e8e82000 ---p 00083000 08:03 523713 /lib64/libm-2.12.so 36e8e82000-36e8e83000 r--p 00082000 08:03 523713 /lib64/libm-2.12.so 36e8e83000-36e8e84000 rw-p 00083000 08:03 523713 /lib64/libm-2.12.so 36e900-36e918b000 r-xp 08:03 523696 /lib64/libc-2.12.so 36e918b000-36e938a000 ---p 0018b000 08:03 523696 /lib64/libc-2.12.so 36e938a000-36e938e000 r--p 0018a000 08:03 523696 /lib64/libc-2.12.so 36e938e000-36e938f000 rw-p 0018e000 08:03 523696 /lib64/libc-2.12.so 36e938f000-36e9394000 rw-p 00:00 0 36e940-36e9402000 r-xp 08:03 523702 /lib64/libdl-2.12.so 36e9402000-36e9602000 ---p 2000 08:03 523702 /lib64/libdl-2.12.so 36e9602000-36e9603000 r--p 2000 08:03 523702 /lib64/libdl-2.12.so 36e9603000-36e9604000 rw-p 3000 08:03 523702 /lib64/libdl-2.12.so 36e980-36e9817000 r-xp 08:03 523697 /lib64/libpthread-2.12.so 36e9817000-36e9a17000 ---p 00017000 08:03 523697 /lib64/libpthread-2.12.so 36e9a17000-36e9a18000 r--p 00017000 08:03 523697 /lib64/libpthread-2.12.so 36e9a18000-36e9a19000 rw-p 00018000 08:03 523697 /lib64/libpthread-2.12.so 36e9a19000-36e9a1d000 rw-p 00:00 0 36ea80-36ea816000 r-xp 08:03 523726 /lib64/libgcc_s-4.4.7-20120601.so.1 36ea816000-36eaa15000 ---p 00016000 08:03 523726 /lib64/libgcc_s-4.4.7-20120601.so.1 36eaa15000-36eaa16000 rw-p 00015000 08:03 523726 /lib64/libgcc_s-4.4.7-20120601.so.1 2b1aaeb9f000-2b1aaeba1000 rw-p 00:00 0 2b1aaeba1000-2b1aaed36000 r-xp 00:15 23068700 /global/software/fftw-3.3.3-intel12-mpi/lib/libfftw3.so.3.3.2 2b1aaed36000-2b1aaef36000 ---p 00195000 00:15 23068700 /global/software/fftw-3.3.3-intel12-mpi/lib/libfftw3.so.3.3.2 2b1aaef36000-2b1aaef42000 rw-p 00195000 00:15 23068700 /global/software/fftw-3.3.3-intel12-mpi/lib/libfftw3.so.3.3.2 2b1aaef42000-2b1aaf514000 r-xp 00:15 20979783 /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so 2b1aaf514000-2b1aaf714000 ---p 005d2000 00:15 20979783 /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so 2b1aaf714000-2b1aaf723000 rw-p 005d2000 00:15 20979783 /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so 2b1aaf723000-2b1aaf728000 rw-p 00:00 0 2b1aaf728000-2b1ab044c000 r-xp 00:15 20979787 /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_thread.so 2b1ab044c000-2b1ab064c000 ---p 00d24000 00:15 20979787 /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_thread.so 2b1ab064c000-2b1ab07a4000 rw-p 00d24000 00:15 20979787
Re: [Wien] the current integration for NMR calculation failed
Hi, it says it is crashing in mode current. It is hard to say anything, I would check memory consumption, what is in output_current_??, eventually recompile with -check and run again. regards Robert On 23 September 2014 PM 5:05:10 Bing Zhou wrote: Dear all, The current integration for NMR calculation of boric acid kept failed with the following information, how can I fix it? Thank you in advance! Bing EXECUTING: /global/software/wien2k-13-2/bin/nmrc -case boric-acid -mode current-green -scratch /scratch/ -noco *** glibc detected *** /global/software/wien2k-13-2/bin/nmrc: realloc(): invalid pointer: 0x0124e7b0 *** === Backtrace: = /lib64/libc.so.6[0x36e9076166] /lib64/libc.so.6(realloc+0x2e2)[0x36e907bfd2] /global/software/wien2k-13-2/bin/nmrc[0x4d3406] /global/software/wien2k-13-2/bin/nmrc[0x4ad6ff] /global/software/wien2k-13-2/bin/nmrc[0x4c5bc4] /global/software/wien2k-13-2/bin/nmrc[0x42ae0a] /global/software/wien2k-13-2/bin/nmrc[0x446625] /global/software/wien2k-13-2/bin/nmrc[0x40ff92] /global/software/wien2k-13-2/bin/nmrc[0x402cac] /lib64/libc.so.6(__libc_start_main+0xfd)[0x36e901ed1d] /global/software/wien2k-13-2/bin/nmrc[0x402ba9] === Memory map: 0040-005ae000 r-xp 00:15 33556202 /global/software/wien2k-13-2/bin/nmrc 007ae000-007c7000 rw-p 001ae000 00:15 33556202 /global/software/wien2k-13-2/bin/nmrc 007c7000-007fe000 rw-p 00:00 0 01204000-01268000 rw-p 00:00 0 [heap] 36e880-36e882 r-xp 08:03 523695 /lib64/ld-2.12.so 36e8a1f000-36e8a2 r--p 0001f000 08:03 523695 /lib64/ld-2.12.so 36e8a2-36e8a21000 rw-p 0002 08:03 523695 /lib64/ld-2.12.so 36e8a21000-36e8a22000 rw-p 00:00 0 36e8c0-36e8c83000 r-xp 08:03 523713 /lib64/libm-2.12.so 36e8c83000-36e8e82000 ---p 00083000 08:03 523713 /lib64/libm-2.12.so 36e8e82000-36e8e83000 r--p 00082000 08:03 523713 /lib64/libm-2.12.so 36e8e83000-36e8e84000 rw-p 00083000 08:03 523713 /lib64/libm-2.12.so 36e900-36e918b000 r-xp 08:03 523696 /lib64/libc-2.12.so 36e918b000-36e938a000 ---p 0018b000 08:03 523696 /lib64/libc-2.12.so 36e938a000-36e938e000 r--p 0018a000 08:03 523696 /lib64/libc-2.12.so 36e938e000-36e938f000 rw-p 0018e000 08:03 523696 /lib64/libc-2.12.so 36e938f000-36e9394000 rw-p 00:00 0 36e940-36e9402000 r-xp 08:03 523702 /lib64/libdl-2.12.so 36e9402000-36e9602000 ---p 2000 08:03 523702 /lib64/libdl-2.12.so 36e9602000-36e9603000 r--p 2000 08:03 523702 /lib64/libdl-2.12.so 36e9603000-36e9604000 rw-p 3000 08:03 523702 /lib64/libdl-2.12.so 36e980-36e9817000 r-xp 08:03 523697 /lib64/libpthread-2.12.so 36e9817000-36e9a17000 ---p 00017000 08:03 523697 /lib64/libpthread-2.12.so 36e9a17000-36e9a18000 r--p 00017000 08:03 523697 /lib64/libpthread-2.12.so 36e9a18000-36e9a19000 rw-p 00018000 08:03 523697 /lib64/libpthread-2.12.so 36e9a19000-36e9a1d000 rw-p 00:00 0 36ea80-36ea816000 r-xp 08:03 523726 /lib64/libgcc_s-4.4.7-20120601.so.1 36ea816000-36eaa15000 ---p 00016000 08:03 523726 /lib64/libgcc_s-4.4.7-20120601.so.1 36eaa15000-36eaa16000 rw-p 00015000 08:03 523726 /lib64/libgcc_s-4.4.7-20120601.so.1 2b1aaeb9f000-2b1aaeba1000 rw-p 00:00 0 2b1aaeba1000-2b1aaed36000 r-xp 00:15 23068700 /global/software/fftw-3.3.3-intel12-mpi/lib/libfftw3.so.3.3.2 2b1aaed36000-2b1aaef36000 ---p 00195000 00:15 23068700 /global/software/fftw-3.3.3-intel12-mpi/lib/libfftw3.so.3.3.2 2b1aaef36000-2b1aaef42000 rw-p 00195000 00:15 23068700 /global/software/fftw-3.3.3-intel12-mpi/lib/libfftw3.so.3.3.2 2b1aaef42000-2b1aaf514000 r-xp 00:15 20979783 /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so 2b1aaf514000-2b1aaf714000 ---p 005d2000 00:15 20979783 /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so 2b1aaf714000-2b1aaf723000 rw-p 005d2000 00:15 20979783 /global/software/intel2012/composer_xe_2011_sp1.11.339/mkl/lib/intel64/libmkl_intel_lp64.so 2b1aaf723000-2b1aaf728000 rw-p 00:00 0 2b1aaf728000-2b1ab044c000 r-xp 00:15
Re: [Wien] wien2wannier with wien2k.14.1
All,
Sorry for disturbing you this afternoon.
After a few more times of struggling, I pinned down the root cause to be
with the setting of xterm under x11.
With the correction, the problem disappears. Of course, we still need to
setenv LANG en_US.UTF-8
on the linux cluster if the UTF-8 is not set as default, if we remotely
log onto it.
Cheers,
Jianxin
On 9/23/14 12:22 PM, Zhu, Jianxin jx...@lanl.gov wrote:
Hi Elias,
As you suggested earlier, I pulled this issue to the mailing list.
After I downloaded wien2k.14.1 integrated with wien2wannier, even before
compilation/installation, I noticed many strange characters displayed
inside the wien2wannier90 script files, for example, near the end of
init_w2w_lapw
OPTIONS:
-b - batch mode (do not ask questions)
-numk - number of k-points (default: 100; can also use â~@~\Nx Ny
Nzâ~@~])
-emin,-emax - select bands by energy (needs â~@~Xoutput1â~@~Y file;
careful!)
-all X Y- synonym for â~@~X-emin X -emax Yâ~@~Y
-bands I J - select bands directly (more robust)
-proj - specification of initial projections (â~@~\Amnâ~@~])
-w90- Wannier90 options to set
â~@~XOPTIONSâ~@~Y are only operative in batch mode, except
â~@~X-w90â~@~Y, which
accepts as arguments key-value pairs to be put into â~@~Xcase.winâ~@~Y.
The
sp/so switches are usually unnecessary (detected automatically).
theend
exit 0
I did some file type check (with the suggestion of Matt Jones at Univ.
Buffalo) ---
/wien2k.14.1] jxzhu% file --mime init_lapw
init_lapw: text/x-shellscript; charset=us-ascii
/wien2k.14.1] jxzhu% file --mime init_w2w_lapw
init_w2w_lapw: text/x-shellscript; charset=utf-8
It looks the charset used for wien2wannier90 scripts is different than the
rest of wien2k scripts.
As such, I manually set
setenv LANG en_US.UTF-8
in the login shell script file. Then I see the following ---
OPTIONS:
-b - batch mode (do not ask questions)
-numk - number of k-points (default: 100; can also use âNx Ny Nzâ
file; careful!)
-all X Y- synonym for â
-bands I J - select bands directly (more robust)
-proj - specification of initial projections (âAmnâ are only
operative in batch mode, except â, which
accepts as arguments key-value pairs to be put into â. The
sp/so switches are usually unnecessary (detected automatically).
theend
exit 0
With the manual setting of UTF-8, I still see characters like hat{a} and
the item like -w90 is missing in the display.
As such, I am not sure what I get in whatever way is correct.
I tested this issue on my Mac OSX machine, but also saw the strange
characters on my linux cluster.
Kevin, I appreciate if you can help me check this on your mac osx machine.
Cheers,
Jianxin
On 7/1/14 5:34 AM, Elias Assmann elias.assm...@gmail.com wrote:
Dear wien2wannier Users!
A new version of the package is available at
http://www.ifp.tuwien.ac.at/forschung/arbeitsgruppen/cms/software-downlo
a
d/wien2wannier/.
This is a minor update that fixes a few bugs, including one in
Œwplot2xsf¹ that caused it to crash.
--
Elias Assmann (TU Wien)
Wien2Wannier: maximally localized Wannier functions
from linearized augmented plane waves
http://www.ifp.tuwien.ac.at/forschung/arbeitsgruppen/cms/software-downlo
a
d/wien2wannier/
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