[Wien] Patch to fix ROTDEF error in lapw0 for Fd3m et al.
Thank you very much for the confirmation. I did see that the additional symmetrization attempts appear to play an important role, but assumed they were added for a reason (and I certainly did not want to bring back any old problems that may have been successfully worked around by it). So far I have not had time to check much beyond the SCF cycle - lapw0, lapw1, lapw2 and possibly mixer are affected. With the mixer, the actual issue may have been only a side effect from combining your Intel-compiled binaries with my gfortran. (As a side note, it appears that the line in the "x_lapw" script that adds a non-conformant declaration for UNIT 15 to lapw2.def - a problem noted in june 2019 for version 19.1, is still present in the current distribution. Cf https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18771.html I can provide patches for the rotdef.f in lapw1/lapw2/mixer - which each have a slightly different version of it due to added variables - if desired. At a glance, the copies used in telnes, aim and arrows could be affected as well. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Patch to fix ROTDEF error in lapw0 for Fd3m et al.
We have recently encountered an unexpected problem with lapw0 returning "ROTDEF error", claiming "symmetry operation not found" for equivalent positions of an X,X,X site in spacegroup Fd-3m. (One simplified example is attached to this message to allow reproducing the problem.) As it appears, SRC_lapw0/rotdef.f takes turns applying the centering operations to the calculated distance vector looking for a match - and then undoes that operation before trying the next, instead of simply copying back the original value. This demonstrably leads to rounding errors that can exceed the hardcoded tolerance threshold of 1.5e-7 The attached patch avoids the problem by trivially saving x1 before the cascade of tests for centered lattices, and restoring it after each that did not lead to a successful exit from the loop. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg Reproducer for Wien2K 19.2 lapw0 rotdef error F LATTICE,NONEQUIV.ATOMS: 2 227_Fd-3m MODE OF CALC=RELA unit=bohr 45.762364 45.762364 45.762364 90.00 90.00 90.00 ATOM 1: X=0.1250 Y=0.1250 Z=0.1250 MULT= 2 ISPLIT= 2 1: X=0.8750 Y=0.8750 Z=0.8750 K 1NPT= 781 R0=0.5000 RMT= 2.5 Z: 19.000 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -2: X=0.22345000 Y=0.22345000 Z=0.22345000 MULT= 8 ISPLIT= 4 -2: X=0.77655000 Y=0.77655000 Z=0.77655000 -2: X=0.77655000 Y=0.47345000 Z=0.47345000 -2: X=0.22345000 Y=0.02655000 Z=0.02655000 -2: X=0.02655000 Y=0.02655000 Z=0.22345000 -2: X=0.47345000 Y=0.47345000 Z=0.77655000 -2: X=0.47345000 Y=0.77655000 Z=0.47345000 -2: X=0.02655000 Y=0.22345000 Z=0.02655000 K 2NPT= 781 R0=0.5000 RMT= 2.5 Z: 19.000 LOCAL ROT MATRIX:0.4082483-0.7071068 0.5773503 0.4082483 0.7071068 0.5773503 -0.8164966 0.000 0.5773503 48 NUMBER OF SYMMETRY OPERATIONS -1 0 0 0. 0-1 0 0. 0 0-1 0. 1 -1 0 0 0. 0 0-1 0. 0-1 0 0. 2 0-1 0 0. -1 0 0 0. 0 0-1 0. 3 0 0-1 0. -1 0 0 0. 0-1 0 0. 4 0-1 0 0. 0 0-1 0. -1 0 0 0. 5 0 0-1 0. 0-1 0 0. -1 0 0 0. 6 0 0 1 0. 0 1 0 0. 1 0 0 0. 7 0 1 0 0. 0 0 1 0. 1 0 0 0. 8 0 0 1 0. 1 0 0 0. 0 1 0 0. 9 0 1 0 0. 1 0 0 0. 0 0 1 0. 10 1 0 0 0. 0 0 1 0. 0 1 0 0. 11 1 0 0 0. 0 1 0 0. 0 0 1 0. 12 -1 0 0 0. 0 1 0 0.7500 0 0 1 0.7500 13 1 0 0 0. 0-1 0 0.7500 0 0-1 0.7500 14 0-1 0 0.7500 1 0 0 0. 0 0-1 0.7500 15 1 0 0 0. 0 0-1 0.7500 0-1 0 0.7500 16 0 0-1 0.7500 1 0 0 0. 0-1 0 0.7500 17 1 0 0 0.7500 0 1 0 0.7500 0 0-1 0. 18 -1 0 0 0.7500 0 1 0 0. 0 0-1 0.7500 19 1 0 0 0.7500 0 0 1 0.7500 0-1 0 0. 20 -1 0 0 0.7500 0 0 1 0. 0-1 0 0.7500 21 0 1 0 0. -1 0 0 0.7500 0 0-1 0.7500 22 0 0 1 0. -1 0 0 0.7500 0-1 0 0.7500 23 0-1 0 0.7500 0 0-1 0.7500 1 0 0 0. 24 0 0-1 0.7500 0-1 0 0.7500 1 0 0 0. 25 0 0 1 0.7500 0 1 0 0.7500 -1 0 0 0. 26 0 1 0 0.7500 0 0 1 0.7500 -1 0 0 0. 27 0 1 0 0.7500 1 0 0 0.7500 0 0-1 0. 28 0 0 1 0.7500 1 0 0 0.7500 0-1 0 0. 29 1 0 0 0.7500 0 0-1 0. 0 1 0 0.7500 30 -1 0 0 0.7500 0 0-1 0.7500 0 1 0 0. 31 1 0 0 0.7500 0-1 0 0. 0 0 1 0.7500 32 -1 0 0 0.7500 0-1 0 0.7500 0 0 1 0. 33 0 0 1 0.7500 -1 0 0 0. 0 1 0 0.7500 34 0 1 0 0. 0 0-1 0.7500 -1 0 0 0.7500 35 0 1 0 0.7500 -1 0 0 0. 0 0 1 0.7500 36 0 0 1 0. 0-1 0 0.7500 -1 0 0 0.7500 37 0 0-1 0.7500 0 1 0 0. -1 0 0 0.7500 38 0-1 0 0.7500 0 0 1 0. -1 0 0 0.7500 39 0 0-1 0. 0 1 0 0.7500 1 0 0 0.7500 40 0-1 0 0. 0 0 1 0.7500 1 0 0 0.7500
[Wien] Xcrysden issues with w2web
Is the w2web program running on the same system, and under the same user ID as the terminal you used for the test ? If not, you could try setting "xhost localhost" (or if you trust your firewall, even "xhost +") to allow connections to your instance of the X server from other users/other systems on the network -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] density matrix is not positive
So, can we be sure that this peculiarity is unrelated to that dreaded river monster the "CHOLESKY ERROR" ? -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Accept and Deny in w2web configuration
I believe we have found what looks to be a long-standing error in the
interpretation of host accept and deny lists in w2web, but perhaps I am
just over-interpreting what should be possible according to the user
guide.
1. The use of asterisks in IP masks appears to be working more by chance
than anything else, and only for *.*.*.* as aton() simply returns blank
when it encounters anything non-numeric
2. Using a blanket deny list of e.g. *.*.*.* in combination with a
selective accept list does not work due to the way the conditional
is coded - a hit on the deny list leads to immediate dismissal.
The attached patch for SRC_w2web/bin/w2web converts asterisks to zeroes
before matching, and rewrites the aforementioned conditional.
--
Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de
c/o Prof.Dr. Caroline Roehr
Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg
--- w2web.orig 2007-01-25 10:40:35.0 +0100
+++ w2web 2019-12-26 11:21:26.772837875 +0100
@@ -383,10 +383,11 @@
$page =~ s/%(..)/pack("c",hex($1))/ge;
# check address against access list
-if (@deny && _match($acptip, @deny) ||
-@allow && !_match($acptip, @allow)) {
+if (@deny && _match($acptip, @deny)) {
+if (!@allow || !_match($acptip, @allow)) {
_error(403, "Access denied for $acptip");
}
+}
# Check for password if needed
if (%users) {
@@ -817,6 +818,7 @@
{
local (@rv, $i);
foreach $i (@_) {
+ $i =~ s/\*/0/g;
if ($i =~ /(\S+)\/(\S+)/) { push(@rv, $i); }
else { push(@rv, join('.', unpack("", inet_aton($i; }
}
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Re: [Wien] maximum number of inequivalent k-points in case.outputkgen
To get around the error in xcrysden, you need to increase the NKP parameter in the param.inc file that comes with the parts of SRC_spaghetti included with xcrysden (xcrysden-1.5.60/F/SRC_spaghetti/param.inc) and rebuild wn_readbands -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] WIEN2k_16
>[1m init_lapw finished ok (B;[m >- >this seems strange, but does not give a problem Apparently somebody thought it would be a good idea to include control characters to switch portions of the script output to boldface ? Either your terminal (emulation) program does not support the control sequences used or - more likely - these got mangled so that only the printable portions of them are shown verbatim. Try editing the init_lapw script, close to its start you will find a comment heading "functions & subroutines". One of the entries there starts with "alias outputscreen" - change the word "echo" on that line to read "echo -e" (which tells the "echo" tool to pass along any control characters in the text it is given to emit) -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] maximum number of inequivalent k-points in case.outputkgen
If you want to correct the display of the table you quoted, you need to
look for a FORMAT that also contains the parentheses around the
fractional coordinates in your example - I think a hot candidate is the
6010FORMAT(1H ,I4,'(',3F10.6,')',I4,' (',3F10.6,')')
in arbmsh.f - indeed this has I4 in both places that get filled with
stars as you go above k-points...
Hope this helps
Martin
--
Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de
c/o Prof.Dr. Caroline Roehr
Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg
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[Wien] WIEN2k_16
> cut: los campos y posiciones se numeran a partir de 1 This was discussed here barely two days ago - see messages titled "Wien2k 15 siteconfig_lapw error" (and get the corrected siteconfig_lapw script from the download page) -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Wien2k 16 siteconfig_lapw error
Ingo Loa has it nailed of course - that whole loop makes no sense when FFTWpath is empty (and hence i=0) to begin with -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Wien2k 16 siteconfig_lapw error
This must be related to the (new) script code that tries to digest the FFTW_OPTION setting. Around line 145 of the siteconfig_lapw script there is some funky looping over the FFTWpath string (trying to find "/" path separator characters apparently) where variable i[3] is used as an argument to "cut -c" while it is reduced by one in every iteration of the "iloop" loop. There is an > if( $i[3] < 1 ) set i[3]=1 in line 149 to make sure it does not suddenly go out of range, but this is very probably too late for the > set test=`echo $FFTWpath|cut -c$i[3]` that happens in line 147 - suggest to move the "if" line before that. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] WIEN2k and gfortran II
>Anyway, the openblas is really good, and if somebody would know how to >"vectorize" the cos, sin (exp) calls in gfortran this would be very >valuable. Zhang Xianyi, the mastermind behind OpenBLAS :-) , is also working on an "OpenVML" vector math library - but I must admit I did not get around to trying it yet. See https://github.com/xianyi/OpenVML -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] WIEN2k and gfortran
While it is true that MKL is in most but not all cases still a bit faster than OpenBLAS, there are a few other points to consider: - availability for platform where MKL is (at least to my knowledge) not available - no license fee - open source, so anybody can check verify the code (and fix any bugs they find) rather than just hope for the best and follow Intel errata The drawback, as with many volunteer projects, is an unpredictable rate of progress especially in areas that require specialist skills (such as writing optimal assembly code for new processors). Incidentally OpenBLAS is the successor to the old GotoBLAS (whose author joined the Intel MKL team after leaving academia as far as I know) which is still mentioned in siteconfig and the Installation section of the usersguide. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] vec2old_lapw
You will probably find the "vec2old_lapw" executable (or rather, shell script) in the same directory as lapw2 etc. - what is special about it, is that it is one of a handful of tools that relies on /bin/tcsh to run it, while most use /bin/csh (on "most" linux systems, /bin/csh will be just a link to /bin/tcsh, but it could be that you have the original csh installed rather than its successor tcsh) -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Problem with LSTART: Word too long
The "word too long" error may come from having too many or too long entries in the PATH variable. Looking at your struct file however this may be the least of your worries - an RMT of 0.02 is absurdly low and a supposedly hexagonal structure with unit cell angles of 90 degrees is a bit "unusual" as well. Perhaps try to run one of the tutorial problems first to verify your installation, and then try to come up with a correct crystal structure for your own project. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Problem in Gap value??(semiconductor not mettalic)
@Gerhard: I must say I have seen much worse here on this mailing list, and I suspect Sunday may be a perfectly regular workday for her. That said, there is something strange with this calculation, as people more knowledgeable than me already noted. Did you change something fundamental between calculations, or might two different jobs have run in the same work directory ? It might help to see your case.in1 and/or case.struct as well. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] (no subject)
Adding BACKSPACE 22 before the line with the offending WRITE should fix the problem - make sure that the compilation went well and you are actually using your rebuilt version of mixer and not the original. BTW gfortran-built binaries being slower is not a fault of gfortran itself, you just need to find an appropriate substitute to the mkl math library included with the intel compiler - the fallback lapack_lapw and blas_lapw included in the WIEN2k sources contain generic non-optimized functions from the BLAS/LAPACK reference implementation. Candidates are e.g. ATLAS (probably available as a debian package) and increasingly OpenBLAS, the successor to the libgoto you will find mentioned in the WIEN2k documentation. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] gfortran: error in WIEN2k_13
This looks like an openmpi installation or user environment error - the mpif90 wrapper script tries to call gfortran instead of ifort but uses Intel compiler options that gfortran does not understand. Does this help: http://th.physik.uni-frankfurt.de/wiki-it/index.php?title=Compiling_and_running_MPI_programs (instructing to export OMPI_FC=ifort et al. ) -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] MIXER runtime error + solution on Mac OS X
There should be a compiler option to raise a floating point exception on the first computation that involves NaN, perhaps this would help to track down the issue (at least to the point where running in a debugger should tell which array elements are faulty.) -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] MIXER runtime error + solution on Mac OS X
I would expect the __APPLE__ define to come in automatically from your compiler and/or system headers. The NaNs are interesting - could this be another case of uninitialized array elements, just like the lapw0 bug you found last month ? Heap vs stack would then just change the likelyhood of obtaining (non-)zeroed memory on allocation... -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] MIXER runtime error + solution on Mac OS X
This might warrant closer scrutiny - was it reproducible with any odd tutorial problem, or does it require a particular case or type of calculation ? The illegal instruction abort signals that data was somehow spilling over into the memory ranges holding the executable code. Now I would not expect a simple heap-stack-collision (from an array that is simply too big to put on the stack with impunity) to occur on any modern system except perhaps severely constrained embedded ones. At worst, the abort should have been accompanied by a segmentation fault message as the attempt to overwrite the running program got caught. So other possible explanations could be that the code tries to store more array elements than the array was designed to hold, or that the indexes into the array are miscalculated (overflowing or not clamped to positive values). Moving data to the heap may have just changed the location of the inadvertently overwritten memory to ranges where the effects are more subtle (unrelated data) or not noticable (lucky hit on unused memory). -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] electron density plot
Also make sure that you have switched on the right lighting mode in xcrysden (check the FAQ at www.xcrysden.org) -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Bi2Se3 atomic positions in wien2k structure file.
There is an entire branch of science called Crystallography. Please do not expect us to give the equivalent of a crystallography 101 lecture in a newsgroup. In (too) short, atomic positions as well as spacegroup assigments are determined experimentally, typically by X-ray diffraction. And while it is always possible to state which of these atomic positions corresponds to which Wyckoff site in the group-theoretical treatment of the unit cell symmetry, the reverse is usually not true. (Not all the Wyckoff positions need to be occupied, also most have free numeric parameters x, y, and/or z that are not determined by symmetry considerations anyway). Wyckoff position tells you something about symmetry effects at that point, and in cases such as your ZnAl2O4 can be used as a shorthand notation for the coordinates - Zn on 16c, Al on 8b and O on 32e with x=0.25. (Actually the 0.25 is a bit misleading - this is not an exact symmetry-imposed number like the 1/8 and 1/2 of the other two sites - it might just as well be 0.2473 or something, just that it is the same in x,y,z) Normally in inorganic chemistry one would learn a few typical crystal structures - structure types - that certain key compound classes crystallize in (spinel or inverse spinel in your case), and would then be able to generate at least an approximate structure from the knowledge that something crystallizes in such-and-such structure type. For exact coordinates, consult databases and/or original publications. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Persisting LOPW and LAPW1 errors
Check your z coordinate. At the very least, you will need more decimal places to accurately describe the special position if it is an irrational fraction (1./6.), but I suspect you also mixed up the crystallographic data between two published structures in different spacegroups. If you want P31 2 1, your z coordinate should be 1/3 while the 1/6 would seem appropriate for the alternate description in spacegroup P32 2 1 -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Error in LAPW2
Try viewing that struct file in XCrysDen, Venus or whatever... What you have here is one long thin pillar with alternating thin layers of Fe,Co,Al and a huge gap between z=0.4 and z=.85 If this is what you want, it does not surprise me that Wien is having some trouble with it. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Error in LAPW2
I do not feel qualified to categorically state that it cannot be done like that, but your struct file does look decidedly strange to me. How did you arrive at the individual metal layers - at least the aluminum sublattice looks a bit unusual, with some of the Al-Al distances about half the value in elemental Al. Did you just scale everything to the lattice constant of alpha iron to make it fit by any chance ? -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] MPI setup on a multicore maschine
This here appears to be the problem: @: Expression Syntax. lapw1cpara (or actually the lapw1para_lapw it links to) is a shell script, and there appears to be a script syntax issue somewhere during or after parsing of the .machines file (cf. the Extrafine unset message printed shortly before). Check your version of (t)csh on that computer, and try to find out what it is trying to compute at that point in the shell script - some calculations there involve results from running sed/awk and the like, maybe one of these tools does not return anything ? (Any successful previous runs of wien2k with or without mpi on this system ?) -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] MPI setup on a multicore maschine
Sorry, I misread F.Tran's response - the extraneous hf:localhost:4 line might indeed be sufficient to derail the echo|sed|awk machinery in the script. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] Possible bug in lapw2 for parallel LDA+U/SO ?
Is it just me, or does the l2main.F of wien2k.13 contain a copy/paste error where the header lines for the individual atoms in the case.dmatup* files are written: Starting from around line 1550, there are three if blocks governing the output for the cases lorb_atom(jatom,1), lorb_atom(jatom,2) and lorb_atom(jatom,3). In the third case, starting line 1585, we have the WRITE(22,7102) in line 1596 output the same flag value 2 as appropriate for the (jatom,2) case of the preceding block. Surely there must be a 3 here ? The net effect seen is that sumpara reads only half of the values for the first atom (25 as appropriate for flag value 2) and subsequently aborts as it expects to read the integer number of the next atom but is still in the middle of the complex data block of the preceding one. -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ 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] mbj on Diamond
I am probably not qualified to comment on what brj.f does, but I do notice that the segmentation fault in line 46 occurs on a line that tries to print tau_falsch when no value has ever been assigned to this variable. You could try inserting the line tau_falsch = 0D0 before the IF RHO.GT.1.D-18 block. -- Dr. Martin Kroekermartin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg
[Wien] libstdc++.so.5
It appears to me now that you somehow installed only the 32bit version of compat-libstdc++ , while the intel compiler is looking for the 64bit version of the library. Try reinstalling compat-libstdc++ without specifying the .i386 extension, or yum install compat-libstdc++-33-3.2.3-64.x86_64 to force the 64bit version explicitly. (cf. http://software.intel.com/en-us/forums/showthread.php?t=70518 , this seems to describe your problem exactly) -- Dr. Martin Kroekermartin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg
[Wien] Problem After Userconfig
This looks suspiciously as if you entered the q for quit after choosing l for the Perl Path option - so that the user configuration script recorded q as the name of your perl interpreter. Please run siteconfig_lapw again and check what is stored under the L menu. -- Dr. Martin Kroekermartin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg
