[Wien] (no subject)
Dear All I am getting the following problem in calculating the band structure, azam@minos:~/APdCu(Se2)(Se3)/mBJ/APdCu(Se2)(Se3)$ x spaghetti -up SPAGH: Read band energy from case.output1 Segmentation fault (core dumped) 2.376u 0.300s 0:02.92 91.4% 0+0k 15288+303440io 2pf+0w error: command /software/wien2k-13.1/wien2k/spaghetti upspaghetti.def failed so please help me with best regards sikander ___ 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] A confusion related to MULT ?
Dear Community Fellows Do we have to consider all position Under MULT in calculating raitio for doping ? I want to replace Ca atoms in my structure file by Mg with of 25% doping. In structure file (below), for second atom Ca2 the MULT is 2. Total mentioned atoms are 2 but total positions are 3. In supercell structure (pasted just under first structure file) the total mentioned atoms are 6 but total Positions are 9 for Ca atoms. My question is that If we replace Ca atom having MULT 2 then will it be counted as replacement of 2 atoms or 1 ? Kindly through some light on ''number of equivalent atoms of this kind'' Thanks a bunch Adam Bakheet Ca3 R 5166_R-3m RELA 9.918609 9.918609 35.287815 90.00 90.00120.00 ATOM -1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 4 Ca1 NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -2: X=0.20315006 Y=0.20315006 Z=0.20315006 MULT= 2 ISPLIT= 4 -2: X=0.79684994 Y=0.79684994 Z=0.79684994 Ca2 NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -3: X=0.40532944 Y=0.40532944 Z=0.40532944 Structure File after 1*1*1 supercell fomation Ca3 H LATTICE,NONEQUIV. ATOMS 15 MODE OF CALC=RELA unit= 9.918609 9.918609 35.287815 90.00 90.00120.00 ATOM 1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 4 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 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=0.6667 Z=0.6667 MULT= 1 ISPLIT= 4 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 3: X=0.6667 Y=0. Z=0. MULT= 1 ISPLIT= 4 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 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. Y=0. Z=0.20315006 MULT= 2 ISPLIT= 4 ATOM 4: X=0. Y=0. Z=0.79684994 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 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=0.6667 Z=0.86981673 MULT= 2 ISPLIT= 4 ATOM 5: X=0. Y=0.6667 Z=0.46351661 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 6: X=0.6667 Y=0. Z=0.53648339 MULT= 2 ISPLIT= 4 ATOM 6: X=0.6667 Y=0. Z=0.13018327 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 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. Y=0. Z=0.40532944 MULT= 2 ISPLIT= 4 ATOM 7: X=0. Y=0. Z=0.59467056___ 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] A confusion related to MULT ?
Hi, Yes, you have to consider all positions in the unit cell. It is not clear from your struct files how many atoms there are overall (you do not show the complete files), but in your first struct file, I can see that there are at least 4 atoms (ATOM 2 consists of 2 equivalent atoms). F. Tran On Wed, 16 Jul 2014, Adam Bakheet wrote: Dear Community Fellows Do we have to consider all position Under MULT in calculating raitio for doping ? I want to replace Ca atoms in my structure file by Mg with of 25% doping. In structure file (below), for second atom Ca2 the MULT is 2. Total mentioned atoms are 2 but total positions are 3. In supercell structure (pasted just under first structure file) the total mentioned atoms are 6 but total Positions are 9 for Ca atoms. My question is that If we replace Ca atom having MULT 2 then will it be counted as replacement of 2 atoms or 1 ? Kindly through some light on ''number of equivalent atoms of this kind'' Thanks a bunch Adam Bakheet Ca3 ?? ? R 5166_R-3m RELA 9.918609 9.918609 35.287815 90.00 90.00120.00 ATOM -1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 4 Ca1 NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -2: X=0.20315006 Y=0.20315006 Z=0.20315006 MULT= 2 ISPLIT= 4 -2: X=0.79684994 Y=0.79684994 Z=0.79684994 Ca2 NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM -3: X=0.40532944 Y=0.40532944 Z=0.40532944 Structure File after 1*1*1 supercell fomation Ca3 ?? ? H LATTICE,NONEQUIV. ATOMS 15 MODE OF CALC=RELA unit= 9.918609 9.918609 35.287815 90.00 90.00120.00 ATOM 1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 4 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 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=0.6667 Z=0.6667 MULT= 1 ISPLIT= 4 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 3: X=0.6667 Y=0. Z=0. MULT= 1 ISPLIT= 4 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 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. Y=0. Z=0.20315006 MULT= 2 ISPLIT= 4 ATOM 4: X=0. Y=0. Z=0.79684994 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 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=0.6667 Z=0.86981673 MULT= 2 ISPLIT= 4 ATOM 5: X=0. Y=0.6667 Z=0.46351661 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 LOCAL ROT MATRIX: 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 6: X=0.6667 Y=0. Z=0.53648339 MULT= 2 ISPLIT= 4 ATOM 6: X=0.6667 Y=0. Z=0.13018327 Ca NPT= 781 R0=0.5000 RMT= 2. Z: 20.0 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. Y=0. Z=0.40532944 MULT= 2 ISPLIT= 4 ATOM 7: X=0. Y=0. Z=0.59467056 ___ 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] Fw:
On Wednesday, July 16, 2014 2:14 AM, sikandar azam sikandar...@yahoo.com wrote: Dear All I am getting the following problem in calculating the band structure, azam@minos:~/APdCu(Se2)(Se3)/mBJ/APdCu(Se2)(Se3)$ x spaghetti -up SPAGH: Read band energy from case.output1 Segmentation fault (core dumped) 2.376u 0.300s 0:02.92 91.4% 0+0k 15288+303440io 2pf+0w error: command /software/wien2k-13.1/wien2k/spaghetti upspaghetti.def failed so please help me with best regards sikander___ 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] Xcrygen compilation
Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ 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] Xcrygen compilation
Our local HPC team has been developing a framework called easybuild to quickly recompile various software. They save the configuration in python files called easyblocks. There is one for xcrysden. I'm however not sure if there were any remaining issues (and testing it again/making a new compile has been on my to do list). The easyblock can be found here: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/x/xcrysden.py Laurence Marks schreef op 16/07/2014 19:41: Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ 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] Xcrygen compilation
While I can probably fight my way around installing easyblocks, it would be useful for the general user if a bit more information was provided (by you or your local HPC team). For instance, I suspect it is something like: * Download the easyblocks module from http://hpcugent.github.com/easybuild (what else is needed ?) * cd to the directory (unzip ?) and do python setup.py install'' (is root access needed ?) * Download the script xcrysden (to xcrysden directory ?) * do python xcrysden.py N.B., I am probably missing some steps such as setting CC and other environmental variables.including destination. On Wed, Jul 16, 2014 at 12:48 PM, Michael Sluydts michael.sluy...@ugent.be wrote: Our local HPC team has been developing a framework called easybuild to quickly recompile various software. They save the configuration in python files called easyblocks. There is one for xcrysden. I'm however not sure if there were any remaining issues (and testing it again/making a new compile has been on my to do list). The easyblock can be found here: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/x/xcrysden.py Laurence Marks schreef op 16/07/2014 19:41: Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing listw...@zeus.theochem.tuwien.ac.athttp://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 -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ 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] Xcrygen compilation
Yeah, it takes some getting used to (and may take too much time if only used for xcrysden). I've only used it a few times myself, it does work nicely for wien2k (with some tweaks of the public easyblock for 13). Practically you first need to install easybuild itself, which has an eb command that builds the software into a specific path (and organizes it by software, version, toolchain). It takes an 'easyconfig' file as input which contains more info on toolchains and patches used for the compilation, while the easyblock defines the more detailed instructions (like input for siteconfig for wien). It then builds the software (and makes a module file i think). The source it finds in some standard directory but there are command-line options to change all the source and destination folders etc. They have a reference site here: http://hpcugent.github.io/easybuild/, the slides there link to other pages in their wiki. Like I said this may be time-inefficient though and I'm not sure if the xcrysden install worked fully. The version they tried it on was 1.5.53, I myself always continued to used an old version in my account (1.5.21) (for which I don't think I did anything special). The combination of easyblock/easyconfig and the patch in the easyconfig folder may give some hints about what exactly they did. Since I need to build it again myself, maybe I'll give it a try tomorrow. The easyconfig and patch are here: https://github.com/hpcugent/easybuild-easyconfigs/tree/master/easybuild/easyconfigs/x/XCrySDen example for wien2k 12.1 install easyblock: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/w/wien2k.py easyconfig: https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-ictce-4.0.6.eb (when using easybuild itself these things get downloaded with it) Laurence Marks schreef op 16/07/2014 20:34: While I can probably fight my way around installing easyblocks, it would be useful for the general user if a bit more information was provided (by you or your local HPC team). For instance, I suspect it is something like: * Download the easyblocks module from http://hpcugent.github.com/easybuild (what else is needed ?) * cd to the directory (unzip ?) and do python setup.py install'' (is root access needed ?) * Download the script xcrysden (to xcrysden directory ?) * do python xcrysden.py N.B., I am probably missing some steps such as setting CC and other environmental variables.including destination. On Wed, Jul 16, 2014 at 12:48 PM, Michael Sluydts michael.sluy...@ugent.be mailto:michael.sluy...@ugent.be wrote: Our local HPC team has been developing a framework called easybuild to quickly recompile various software. They save the configuration in python files called easyblocks. There is one for xcrysden. I'm however not sure if there were any remaining issues (and testing it again/making a new compile has been on my to do list). The easyblock can be found here: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/x/xcrysden.py Laurence Marks schreef op 16/07/2014 19:41: Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto: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 -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ 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] Xcrygen compilation
Can you tell us what kind of systems this happens on and what the errors are? The information might be helpful to others. I had xcrysden-1.5.53-linux_x86_64-semishared.tar.gz installed on a ubuntu 64 bit 14.04 LTS system. I just downloaded xcrysden-1.5.60-linux_x86_64-semishared.tar.gz from the xcrysden website, extracted it with tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz, removed the xcrysden block in .bashrc for 1.5.53, ran xcConfigure.sh in the bin folder of the xcrysden installation to create a new xcrysden block for 1.5.60 in .bashrc, reloaded the new .bashrc settings (by closing terminal and opening a new one), and finally I ran xcrysden. It opens fine without any errors, but maybe I have to do other things to encounter the problems that you refer to. Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. ___ 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] Xcrygen compilation
Correction: xcConfigure.sh should be in the scripts folder not the bin folder. On 7/16/2014 4:04 PM, Gavin Abo wrote: Can you tell us what kind of systems this happens on and what the errors are? The information might be helpful to others. I had xcrysden-1.5.53-linux_x86_64-semishared.tar.gz installed on a ubuntu 64 bit 14.04 LTS system. I just downloaded xcrysden-1.5.60-linux_x86_64-semishared.tar.gz from the xcrysden website, extracted it with tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz, removed the xcrysden block in .bashrc for 1.5.53, ran xcConfigure.sh in the bin folder of the xcrysden installation to create a new xcrysden block for 1.5.60 in .bashrc, reloaded the new .bashrc settings (by closing terminal and opening a new one), and finally I ran xcrysden. It opens fine without any errors, but maybe I have to do other things to encounter the problems that you refer to. Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. ___ 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] specific DOS plots
Dear Wien2k community, I am working on a compound with 20 independent atoms, 5 of which are iron and 15 Aluminium, my question is how to plot the density of states resultant from the contribution of all 5 iron atoms and not each of them individually. As it appears the options available will only allow me to calculate the total DOS(contributions from all the atoms) or the total DOS of each individual atom and not for instance the collective contribution of 5 of them. below is my input file configuration from w2web: please specify which PDOS you want to calculate You can specify: total(for plotting 'Total DOS') N(to select atom N) tot,s,p,d,... (to select a set of PDOS for previously selected atom N) The following PDOS is possible: (Header from Al13Fe4.qtl ): ATOM Fe1: 1 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Fe2: 2 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Fe3: 3 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Fe4: 4 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Fe5: 5 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al1: 6 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al2: 7 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al3: 8 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al4: 9 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al5: 10 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al6: 11 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al7: 12 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al8: 13 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al9: 14 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al10: 15 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al11: 16 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al12: 17 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al13: 18 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al14: 19 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al15: 20 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f can you please inform me on how to plot the density of states arising only from all 5 iron atoms and excluding the contributions from the aluminium atoms such that I can produce a plot for density of states of Iron. your help and assistance is truly appreciated. with regards, Farshad Nejadsattari ___ 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] specific DOS plots
It is relatively easy but there are many little details and you have to do it yourself; the file case.int has the atom or orbital/atom that you want to plot, the DOS of these are put in case.dos1ev, case.dos2ev (for non sp-cases) the 'case.dos1ev' has the first 7 cases of the 'case.int' 'case.dos2ev' has from 8 to 14, etc. it also creates the :dos2 file, this last file you can rename to Graf-DOS and you now can add the cases in 'case.dos*ev', for example; plot BiRuO-U-afm.dos1evup using 1:2 title Total w l lt 1 lw 2, \ BiRuO-U-afm.dos1evup using 1:5 title Ru w l lt 3 lw 2, \ BiRuO-U-afm.dos1evup using 1:6 title Ru w l lt 4 lw 2, \ BiRuO-U-afm.dos2evup using 1:($2+$3+$4) title O1 w l lt 8 lw 2, \ BiRuO-U-afm.dos1evup using 1:($3+$4) title Bi w l lt 2 lw 2 pause -1 Now case.int is: Title -0.50 0.002 1.500 0.003 # EMIN, DE, EMAX, Gauss-broadening(de) 11N 0.000# NUMBER OF DOS-CASES specified below, G/L/B broadeni ng (Ry) 01 total# atom, case=column in qtl-header, label ***dos1*** 11 Bi 21 Bi 31 Ru 81 Ru 31 Ru 81 Ru***dos1*** 41 O1 ***dos2*** 51 O1 61 O1 71 O2 11 Atom1 p 21 Atom2 tot ***dos2*** Here O1 represents atoms 4, 5 and 6 and ends up in BiRuO-U-afm.dos2evup using 1:($2+$3+$4) means add columns 2, 3 and 4, the '$' is put to distinguish from a number. You can put ($2+3), which means add '3' to column '2' By the way, you plot with gnuplot Graf-DOS Hope to be clear enough!!! (but I doubt it) De: wien-boun...@zeus.theochem.tuwien.ac.at wien-boun...@zeus.theochem.tuwien.ac.at en nombre de Farshad Nejadsattari fneja...@uottawa.ca Enviado: miércoles, 16 de julio de 2014 08:11 p.m. Para: wien@zeus.theochem.tuwien.ac.at Asunto: [Wien] specific DOS plots Dear Wien2k community, I am working on a compound with 20 independent atoms, 5 of which are iron and 15 Aluminium, my question is how to plot the density of states resultant from the contribution of all 5 iron atoms and not each of them individually. As it appears the options available will only allow me to calculate the total DOS(contributions from all the atoms) or the total DOS of each individual atom and not for instance the collective contribution of 5 of them. below is my input file configuration from w2web: please specify which PDOS you want to calculate You can specify: total(for plotting 'Total DOS') N(to select atom N) tot,s,p,d,... (to select a set of PDOS for previously selected atom N) The following PDOS is possible: (Header from Al13Fe4.qtl ): ATOM Fe1: 1 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Fe2: 2 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Fe3: 3 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Fe4: 4 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Fe5: 5 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al1: 6 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al2: 7 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al3: 8 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al4: 9 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al5: 10 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al6: 11 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al7: 12 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al8: 13 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al9: 14 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al10: 15 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al11: 16 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al12: 17 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al13: 18 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al14: 19 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f ATOM Al15: 20 tot,s,p,PX,PY,PZ,d,DZ2,DX2Y2,DXY,DXZ,DYZ,f can you please inform me on how to plot the density of states arising only from all 5 iron atoms and excluding the contributions from the aluminium atoms such that I can produce a plot for density of states of Iron. your help and assistance is truly appreciated. with regards, Farshad Nejadsattari ___ 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
