From sgregory at live.ru Wed Dec 2 15:39:57 2015 From: sgregory at live.ru (Gregory Sergeev) Date: Wed, 2 Dec 2015 17:39:57 +0300 Subject: [xcrysden] Issue with wien klist file generation Message-ID: Dear All, I am new in Wien2k and XCrysDen. Sorry for my ignoramus question. I try to generate own klist file for wien bandstruct calculation. My actions: 1. Opening *.struct file 2. Go to Tool -> K pas selection 3. Add my points with help of mouse. 4. Save as *.kpf file (I can't find Wien2k klist format in save dialog). This *.kpf is not appropriate for Wien2k. 5. Then I try to open *.kpf by File-->Open WIEN2k ..-->Select k-path, as written in http://www.xcrysden.org/doc/kpath.html. And here I fail... XCrysDen does not see the this file... What I do wrong? May be instruction is old? Hope some of you will help me :) - Gregory -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151202/427d30f3/attachment.htm From gsabo at crimson.ua.edu Mon Dec 7 14:33:51 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Mon, 7 Dec 2015 06:33:51 -0700 Subject: [xcrysden] Issue with wien klist file generation In-Reply-To: References: Message-ID: <56658ABF.5080808@crimson.ua.edu> You can either click the "Generate k-mesh using XCrysden" button on the Band Structure page in w2web or use the "File-->Open WIEN2k ..-->Select k-path" in XCrysDen. Then, you select the k-path followed by inputting the multiplier and k-points along the path (as shown at http://www.xcrysden.org/doc/kpath.html ). After that, it should give a dialog box, where you can save the klist file. If you are using w2web, as it shows on the Band Structure page, the filename must be: xcrysden.klist (not case.klist). On 12/2/2015 7:39 AM, Gregory Sergeev wrote: > Dear All, > I am new in Wien2k and XCrysDen. Sorry for my ignoramus question. > > I try to generate own klist file for wien bandstruct calculation. My > actions: > 1. Opening *.struct file > 2. Go to Tool -> K pas selection > 3. Add my points with help of mouse. > 4. Save as *.kpf file (I can't find Wien2k klist format in save > dialog). This *.kpf is not appropriate for Wien2k. > 5. Then I try to open *.kpf by File-->Open WIEN2k ..-->Select k-path, > as written in http://www.xcrysden.org/doc/kpath.html. And here I > fail... XCrysDen > does not see the this file... > > What I do wrong? May be instruction is old? > > Hope some of you will help me :) > > - Gregory > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151207/92156ba7/attachment.htm From ferminlung at gmail.com Tue Dec 8 06:00:42 2015 From: ferminlung at gmail.com (lung Fermin) Date: Tue, 8 Dec 2015 13:00:42 +0800 Subject: [xcrysden] Runtime error in rendering the Fermi surface Message-ID: Hi everyone, I am trying to render the Fermi surface from a calculation in wien2k. The following error appears, *"At line 125 of file wn_readbakgen.f (unit=8, file='case.outputkgen'). Fortran runtime error: Bad integer for item 1 in list input"* I followed these steps: 1. generating the kmesh in xcrysden 2. x lapw1 -p -c (I used mpi+k point parallelization) 3. x lapw2 -p -c -fermi 4. I got some output files case.output1_x and case.output1_x_proc_y (where x=1,2...8, y=0,1,...7). Then I glue the ouptut1_x files into a single file using cat case.output1_x>>case.output1. I have successfully generate the FS with a calculation of a smaller number of k points. Then I used a finer kmesh for the scf calculation this time and following the same procedure. The only difference is that I used a mpi+k parallelization this time but only k point parallelization last time. But this shouldn't cause any differences? Any suggestions? Thanks in advance. Best, Fermin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151208/de552d75/attachment.htm From martin at ruby.chemie.uni-freiburg.de Tue Dec 8 09:31:35 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Tue, 8 Dec 2015 09:31:35 +0100 (CET) Subject: [xcrysden] Runtime error in rendering the Fermi surface In-Reply-To: Message-ID: <20151208083135.91FEB80193@ruby.chemie.uni-freiburg.de> > *"At line 125 of file wn_readbakgen.f (unit=8, file='case.outputkgen'). > Fortran runtime error: Bad integer for item 1 in list input"* Can you check the (end of the) file for anything non-numeric in the first column ? Old-style fortran programs have the nasty habit of printing stars instead of digits if the number is bigger than the fixed field width allocated to it in the code, e.g. if the program tries to print the band number with a maximum of five characters you will see 99998...99999...*****...***** -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From ferminlung at gmail.com Tue Dec 8 09:42:14 2015 From: ferminlung at gmail.com (lung Fermin) Date: Tue, 8 Dec 2015 16:42:14 +0800 Subject: [xcrysden] Runtime error in rendering the Fermi surface In-Reply-To: <20151208083135.91FEB80193@ruby.chemie.uni-freiburg.de> References: <20151208083135.91FEB80193@ruby.chemie.uni-freiburg.de> Message-ID: Hi Dr. Kroeker, Thanks for the reply. Do you mean the file "case.outputkgen"? I checked this one and it looks ok. Here is some lines by the end of the file: 0.50000 0.37500 0.90909 703.99998 527.99999 1279.99996 0.50000 0.50000 0.00000 703.99998 703.99998 0.00000 0.50000 0.50000 0.09091 703.99998 703.99998 128.00000 0.50000 0.50000 0.18182 703.99998 703.99998 255.99999 0.50000 0.50000 0.27273 703.99998 703.99998 383.99999 0.50000 0.50000 0.36364 703.99998 703.99998 511.99999 0.50000 0.50000 0.45455 703.99998 703.99998 639.99998 Regards, Fermin 2015-12-08 16:31 GMT+08:00 Martin Kroeker < martin at ruby.chemie.uni-freiburg.de>: > > *"At line 125 of file wn_readbakgen.f (unit=8, file='case.outputkgen'). > > Fortran runtime error: Bad integer for item 1 in list input"* > > Can you check the (end of the) file for anything non-numeric in the first > column ? > Old-style fortran programs have the nasty habit of printing stars instead > of > digits if the number is bigger than the fixed field width allocated to > it in the code, e.g. if the program tries to print the band number with > a maximum of five characters you will see 99998...99999...*****...***** > > > -- > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > c/o Prof.Dr. Caroline Roehr > Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151208/32871ce3/attachment.htm From martin at ruby.chemie.uni-freiburg.de Tue Dec 8 10:54:16 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Tue, 8 Dec 2015 10:54:16 +0100 (CET) Subject: [xcrysden] Runtime error in rendering the Fermi surface In-Reply-To: Message-ID: <20151208095416.162C280193@ruby.chemie.uni-freiburg.de> Sorry, I did not check the code at first - at line 125 of wn_readbakgen.f it tries to read the table that follows the "weights of k-points:" line in the case.outputkgen, so the problem area is probably many lines from the end of the file. Try searching the file for the "sum of weights:" label that follows the table - perhaps either the values in the k-point index column above it are replaced by stars or the "sum of weights:" line appears earlier than expected (too few lines in the table for whatever reason) > Hi Dr. Kroeker, > > Thanks for the reply. > Do you mean the file "case.outputkgen"? I checked this one and it looks ok. > Here is some lines by the end of the file: > 0.50000 0.37500 0.90909 703.99998 527.99999 > 1279.99996 > 0.50000 0.50000 0.00000 703.99998 703.99998 > 0.00000 > 0.50000 0.50000 0.09091 703.99998 703.99998 > 128.00000 > 0.50000 0.50000 0.18182 703.99998 703.99998 > 255.99999 > 0.50000 0.50000 0.27273 703.99998 703.99998 > 383.99999 > 0.50000 0.50000 0.36364 703.99998 703.99998 > 511.99999 > 0.50000 0.50000 0.45455 703.99998 703.99998 > 639.99998 > > Regards, > Fermin > > > 2015-12-08 16:31 GMT+08:00 Martin Kroeker < > martin at ruby.chemie.uni-freiburg.de>: > > > > *"At line 125 of file wn_readbakgen.f (unit=8, file='case.outputkgen'). > > > Fortran runtime error: Bad integer for item 1 in list input"* > > > > Can you check the (end of the) file for anything non-numeric in the first > > column ? > > Old-style fortran programs have the nasty habit of printing stars instead > > of > > digits if the number is bigger than the fixed field width allocated to > > it in the code, e.g. if the program tries to print the band number with > > a maximum of five characters you will see 99998...99999...*****...***** > > > > > > -- > > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > > c/o Prof.Dr. Caroline Roehr > > Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From ferminlung at gmail.com Tue Dec 8 16:13:26 2015 From: ferminlung at gmail.com (lung Fermin) Date: Tue, 8 Dec 2015 23:13:26 +0800 Subject: [xcrysden] Runtime error in rendering the Fermi surface In-Reply-To: <20151208095416.162C280193@ruby.chemie.uni-freiburg.de> References: <20151208095416.162C280193@ruby.chemie.uni-freiburg.de> Message-ID: Hi Dr. Kroeker, I have searched around the line "weight of sum" but haven't discovered any stars. It looks like this: weights of k-points: 1 1 1.000000 0.002841 2 2 2.000000 0.005682 3 3 2.000000 0.005682 4 4 2.000000 0.005682 5 5 2.000000 0.005682 6 6 2.000000 0.005682 ........ 349 481 1.000000 0.002841 350 482 2.000000 0.005682 351 483 2.000000 0.005682 352 484 2.000000 0.005682 353 485 2.000000 0.005682 354 486 2.000000 0.005682 sum of weights: 2.000000 internal and cartesian k-vectors: 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.09091 0.00000 0.00000 0.03085 0.00000 0.00000 0.18182 0.00000 0.00000 0.06170 0.00000 0.00000 0.27273 0.00000 0.00000 0.09256 ........ I also browsed through the whole file and it looks like all the numbers are properly printed. Regards, Fermin 2015-12-08 17:54 GMT+08:00 Martin Kroeker < martin at ruby.chemie.uni-freiburg.de>: > Sorry, I did not check the code at first - at line 125 of wn_readbakgen.f > it > tries to read the table that follows the "weights of k-points:" line in > the case.outputkgen, so the problem area is probably many lines from the > end of the file. Try searching the file for the "sum of weights:" label > that follows the table - perhaps either the values in the k-point index > column > above it are replaced by stars or the "sum of weights:" line appears > earlier than expected (too few lines in the table for whatever reason) > > > Hi Dr. Kroeker, > > > > Thanks for the reply. > > Do you mean the file "case.outputkgen"? I checked this one and it looks > ok. > > Here is some lines by the end of the file: > > 0.50000 0.37500 0.90909 703.99998 527.99999 > > 1279.99996 > > 0.50000 0.50000 0.00000 703.99998 703.99998 > > 0.00000 > > 0.50000 0.50000 0.09091 703.99998 703.99998 > > 128.00000 > > 0.50000 0.50000 0.18182 703.99998 703.99998 > > 255.99999 > > 0.50000 0.50000 0.27273 703.99998 703.99998 > > 383.99999 > > 0.50000 0.50000 0.36364 703.99998 703.99998 > > 511.99999 > > 0.50000 0.50000 0.45455 703.99998 703.99998 > > 639.99998 > > > > Regards, > > Fermin > > > > > > 2015-12-08 16:31 GMT+08:00 Martin Kroeker < > > martin at ruby.chemie.uni-freiburg.de>: > > > > > > *"At line 125 of file wn_readbakgen.f (unit=8, > file='case.outputkgen'). > > > > Fortran runtime error: Bad integer for item 1 in list input"* > > > > > > Can you check the (end of the) file for anything non-numeric in the > first > > > column ? > > > Old-style fortran programs have the nasty habit of printing stars > instead > > > of > > > digits if the number is bigger than the fixed field width allocated to > > > it in the code, e.g. if the program tries to print the band number with > > > a maximum of five characters you will see 99998...99999...*****...***** > > > > > > > > > -- > > > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > > > c/o Prof.Dr. Caroline Roehr > > > Institut fuer Anorganische und Analytische Chemie der Universitaet > Freiburg > > > > > > _______________________________________________ > > > XCrySDen mailing list > > > XCrySDen at democritos.it > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > -- > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > c/o Prof.Dr. Caroline Roehr > Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151208/b125b3ef/attachment.htm From martin at ruby.chemie.uni-freiburg.de Tue Dec 8 16:33:27 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Tue, 8 Dec 2015 16:33:27 +0100 (CET) Subject: [xcrysden] Runtime error in rendering the Fermi surface In-Reply-To: Message-ID: <20151208153327.562FA80193@ruby.chemie.uni-freiburg.de> > I have searched around the line "weight of sum" but haven't discovered any > stars. It looks like this: Then it would appear (to me at least) that the program is expecting to read more than 354 entries and hits the word "sum" while still trying to obtain numbers. The number of irreducible k-point indices in the file is read from one of the first lines however. Not sure if I am confused or the program is, perhaps something went wrong when you joined the output files ? > > > weights of k-points: > 1 1 1.000000 0.002841 > 2 2 2.000000 0.005682 > 3 3 2.000000 0.005682 > 4 4 2.000000 0.005682 > 5 5 2.000000 0.005682 > 6 6 2.000000 0.005682 > ........ > 349 481 1.000000 0.002841 > 350 482 2.000000 0.005682 > 351 483 2.000000 0.005682 > 352 484 2.000000 0.005682 > 353 485 2.000000 0.005682 > 354 486 2.000000 0.005682 > sum of weights: 2.000000 > internal and cartesian k-vectors: > 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 > 0.00000 0.00000 0.09091 0.00000 0.00000 0.03085 > 0.00000 0.00000 0.18182 0.00000 0.00000 0.06170 > 0.00000 0.00000 0.27273 0.00000 0.00000 0.09256 > ........ > > I also browsed through the whole file and it looks like all the numbers are > properly printed. > > Regards, > Fermin > > 2015-12-08 17:54 GMT+08:00 Martin Kroeker < > martin at ruby.chemie.uni-freiburg.de>: > > > Sorry, I did not check the code at first - at line 125 of wn_readbakgen.f > > it > > tries to read the table that follows the "weights of k-points:" line in > > the case.outputkgen, so the problem area is probably many lines from the > > end of the file. Try searching the file for the "sum of weights:" label > > that follows the table - perhaps either the values in the k-point index > > column > > above it are replaced by stars or the "sum of weights:" line appears > > earlier than expected (too few lines in the table for whatever reason) > > > > > Hi Dr. Kroeker, > > > > > > Thanks for the reply. > > > Do you mean the file "case.outputkgen"? I checked this one and it looks > > ok. > > > Here is some lines by the end of the file: > > > 0.50000 0.37500 0.90909 703.99998 527.99999 > > > 1279.99996 > > > 0.50000 0.50000 0.00000 703.99998 703.99998 > > > 0.00000 > > > 0.50000 0.50000 0.09091 703.99998 703.99998 > > > 128.00000 > > > 0.50000 0.50000 0.18182 703.99998 703.99998 > > > 255.99999 > > > 0.50000 0.50000 0.27273 703.99998 703.99998 > > > 383.99999 > > > 0.50000 0.50000 0.36364 703.99998 703.99998 > > > 511.99999 > > > 0.50000 0.50000 0.45455 703.99998 703.99998 > > > 639.99998 > > > > > > Regards, > > > Fermin > > > > > > > > > 2015-12-08 16:31 GMT+08:00 Martin Kroeker < > > > martin at ruby.chemie.uni-freiburg.de>: > > > > > > > > *"At line 125 of file wn_readbakgen.f (unit=8, > > file='case.outputkgen'). > > > > > Fortran runtime error: Bad integer for item 1 in list input"* > > > > > > > > Can you check the (end of the) file for anything non-numeric in the > > first > > > > column ? > > > > Old-style fortran programs have the nasty habit of printing stars > > instead > > > > of > > > > digits if the number is bigger than the fixed field width allocated to > > > > it in the code, e.g. if the program tries to print the band number with > > > > a maximum of five characters you will see 99998...99999...*****...***** > > > > > > > > > > > > -- > > > > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > > > > c/o Prof.Dr. Caroline Roehr > > > > Institut fuer Anorganische und Analytische Chemie der Universitaet > > Freiburg > > > > > > > > _______________________________________________ > > > > XCrySDen mailing list > > > > XCrySDen at democritos.it > > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > > > > > _______________________________________________ > > > XCrySDen mailing list > > > XCrySDen at democritos.it > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > -- > > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > > c/o Prof.Dr. Caroline Roehr > > Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From ferminlung at gmail.com Wed Dec 9 06:58:09 2015 From: ferminlung at gmail.com (lung Fermin) Date: Wed, 9 Dec 2015 13:58:09 +0800 Subject: [xcrysden] Runtime error in rendering the Fermi surface In-Reply-To: <20151208153327.562FA80193@ruby.chemie.uni-freiburg.de> References: <20151208153327.562FA80193@ruby.chemie.uni-freiburg.de> Message-ID: Hi Dr. Kroeker, Yep. The error seems coming from the way that I put the output1 files together after a mpi+k point paralleled run. I tried the post calculation using k point parallelization only and put the files together as cat case.output1_$i>>case.output1. Everything works fine now. Thanks for all your suggestions. Regards, Fermin 2015-12-08 23:33 GMT+08:00 Martin Kroeker < martin at ruby.chemie.uni-freiburg.de>: > > I have searched around the line "weight of sum" but haven't discovered > any > > stars. It looks like this: > Then it would appear (to me at least) that the program is expecting to > read more than 354 entries and hits the word "sum" while still trying to > obtain numbers. The number of irreducible k-point indices in the file is > read from one of the first lines however. Not sure if I am confused or > the program is, perhaps something went wrong when you joined the output > files ? > > > > > > weights of k-points: > > 1 1 1.000000 0.002841 > > 2 2 2.000000 0.005682 > > 3 3 2.000000 0.005682 > > 4 4 2.000000 0.005682 > > 5 5 2.000000 0.005682 > > 6 6 2.000000 0.005682 > > ........ > > 349 481 1.000000 0.002841 > > 350 482 2.000000 0.005682 > > 351 483 2.000000 0.005682 > > 352 484 2.000000 0.005682 > > 353 485 2.000000 0.005682 > > 354 486 2.000000 0.005682 > > sum of weights: 2.000000 > > internal and cartesian k-vectors: > > 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 > > 0.00000 0.00000 0.09091 0.00000 0.00000 0.03085 > > 0.00000 0.00000 0.18182 0.00000 0.00000 0.06170 > > 0.00000 0.00000 0.27273 0.00000 0.00000 0.09256 > > ........ > > > > I also browsed through the whole file and it looks like all the numbers > are > > properly printed. > > > > Regards, > > Fermin > > > > 2015-12-08 17:54 GMT+08:00 Martin Kroeker < > > martin at ruby.chemie.uni-freiburg.de>: > > > > > Sorry, I did not check the code at first - at line 125 of > wn_readbakgen.f > > > it > > > tries to read the table that follows the "weights of k-points:" line in > > > the case.outputkgen, so the problem area is probably many lines from > the > > > end of the file. Try searching the file for the "sum of weights:" label > > > that follows the table - perhaps either the values in the k-point index > > > column > > > above it are replaced by stars or the "sum of weights:" line appears > > > earlier than expected (too few lines in the table for whatever reason) > > > > > > > Hi Dr. Kroeker, > > > > > > > > Thanks for the reply. > > > > Do you mean the file "case.outputkgen"? I checked this one and it > looks > > > ok. > > > > Here is some lines by the end of the file: > > > > 0.50000 0.37500 0.90909 703.99998 > 527.99999 > > > > 1279.99996 > > > > 0.50000 0.50000 0.00000 703.99998 > 703.99998 > > > > 0.00000 > > > > 0.50000 0.50000 0.09091 703.99998 > 703.99998 > > > > 128.00000 > > > > 0.50000 0.50000 0.18182 703.99998 > 703.99998 > > > > 255.99999 > > > > 0.50000 0.50000 0.27273 703.99998 > 703.99998 > > > > 383.99999 > > > > 0.50000 0.50000 0.36364 703.99998 > 703.99998 > > > > 511.99999 > > > > 0.50000 0.50000 0.45455 703.99998 > 703.99998 > > > > 639.99998 > > > > > > > > Regards, > > > > Fermin > > > > > > > > > > > > 2015-12-08 16:31 GMT+08:00 Martin Kroeker < > > > > martin at ruby.chemie.uni-freiburg.de>: > > > > > > > > > > *"At line 125 of file wn_readbakgen.f (unit=8, > > > file='case.outputkgen'). > > > > > > Fortran runtime error: Bad integer for item 1 in list input"* > > > > > > > > > > Can you check the (end of the) file for anything non-numeric in the > > > first > > > > > column ? > > > > > Old-style fortran programs have the nasty habit of printing stars > > > instead > > > > > of > > > > > digits if the number is bigger than the fixed field width > allocated to > > > > > it in the code, e.g. if the program tries to print the band number > with > > > > > a maximum of five characters you will see > 99998...99999...*****...***** > > > > > > > > > > > > > > > -- > > > > > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > > > > > c/o Prof.Dr. Caroline Roehr > > > > > Institut fuer Anorganische und Analytische Chemie der Universitaet > > > Freiburg > > > > > > > > > > _______________________________________________ > > > > > XCrySDen mailing list > > > > > XCrySDen at democritos.it > > > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > > > > > > > > _______________________________________________ > > > > XCrySDen mailing list > > > > XCrySDen at democritos.it > > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > > -- > > > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > > > c/o Prof.Dr. Caroline Roehr > > > Institut fuer Anorganische und Analytische Chemie der Universitaet > Freiburg > > > > > > _______________________________________________ > > > XCrySDen mailing list > > > XCrySDen at democritos.it > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > -- > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > c/o Prof.Dr. Caroline Roehr > Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151209/5ba63f8d/attachment.htm From martin at ruby.chemie.uni-freiburg.de Wed Dec 9 09:27:28 2015 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Wed, 9 Dec 2015 09:27:28 +0100 (CET) Subject: [xcrysden] Runtime error in rendering the Fermi surface In-Reply-To: Message-ID: <20151209082728.8887880193@ruby.chemie.uni-freiburg.de> Glad to know you got it working somehow. It could be interesting to compare the files if you still have the one from the mpi calculation: At least it occurs to me that the current wn_readbakgen code makes some rather optimistic assumptions about the layout of the file it tries to read, skipping a line here and there because it "knows" that there will be a table heading like "weights of k-points" on it without actually checking. Any additional output like "hi, this is your friendly mpi version" is sure to throw it off balance. Regards, Martin > > Yep. The error seems coming from the way that I put the output1 files > together after a mpi+k point paralleled run. I tried the post calculation > using k point parallelization only and put the files together as cat > case.output1_$i>>case.output1. Everything works fine now. > > Thanks for all your suggestions. > > Regards, > Fermin > > 2015-12-08 23:33 GMT+08:00 Martin Kroeker < > martin at ruby.chemie.uni-freiburg.de>: > > > > I have searched around the line "weight of sum" but haven't discovered > > any > > > stars. It looks like this: > > Then it would appear (to me at least) that the program is expecting to > > read more than 354 entries and hits the word "sum" while still trying to > > obtain numbers. The number of irreducible k-point indices in the file is > > read from one of the first lines however. Not sure if I am confused or > > the program is, perhaps something went wrong when you joined the output > > files ? > > > > > > > > > weights of k-points: > > > 1 1 1.000000 0.002841 > > > 2 2 2.000000 0.005682 > > > 3 3 2.000000 0.005682 > > > 4 4 2.000000 0.005682 > > > 5 5 2.000000 0.005682 > > > 6 6 2.000000 0.005682 > > > ........ > > > 349 481 1.000000 0.002841 > > > 350 482 2.000000 0.005682 > > > 351 483 2.000000 0.005682 > > > 352 484 2.000000 0.005682 > > > 353 485 2.000000 0.005682 > > > 354 486 2.000000 0.005682 > > > sum of weights: 2.000000 > > > internal and cartesian k-vectors: > > > 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 > > > 0.00000 0.00000 0.09091 0.00000 0.00000 0.03085 > > > 0.00000 0.00000 0.18182 0.00000 0.00000 0.06170 > > > 0.00000 0.00000 0.27273 0.00000 0.00000 0.09256 > > > ........ > > > > > > I also browsed through the whole file and it looks like all the numbers > > are > > > properly printed. > > > > > > Regards, > > > Fermin > > > > > > 2015-12-08 17:54 GMT+08:00 Martin Kroeker < > > > martin at ruby.chemie.uni-freiburg.de>: > > > > > > > Sorry, I did not check the code at first - at line 125 of > > wn_readbakgen.f > > > > it > > > > tries to read the table that follows the "weights of k-points:" line in > > > > the case.outputkgen, so the problem area is probably many lines from > > the > > > > end of the file. Try searching the file for the "sum of weights:" label > > > > that follows the table - perhaps either the values in the k-point index > > > > column > > > > above it are replaced by stars or the "sum of weights:" line appears > > > > earlier than expected (too few lines in the table for whatever reason) > > > > > > > > > Hi Dr. Kroeker, > > > > > > > > > > Thanks for the reply. > > > > > Do you mean the file "case.outputkgen"? I checked this one and it > > looks > > > > ok. > > > > > Here is some lines by the end of the file: > > > > > 0.50000 0.37500 0.90909 703.99998 > > 527.99999 > > > > > 1279.99996 > > > > > 0.50000 0.50000 0.00000 703.99998 > > 703.99998 > > > > > 0.00000 > > > > > 0.50000 0.50000 0.09091 703.99998 > > 703.99998 > > > > > 128.00000 > > > > > 0.50000 0.50000 0.18182 703.99998 > > 703.99998 > > > > > 255.99999 > > > > > 0.50000 0.50000 0.27273 703.99998 > > 703.99998 > > > > > 383.99999 > > > > > 0.50000 0.50000 0.36364 703.99998 > > 703.99998 > > > > > 511.99999 > > > > > 0.50000 0.50000 0.45455 703.99998 > > 703.99998 > > > > > 639.99998 > > > > > > > > > > Regards, > > > > > Fermin > > > > > > > > > > > > > > > 2015-12-08 16:31 GMT+08:00 Martin Kroeker < > > > > > martin at ruby.chemie.uni-freiburg.de>: > > > > > > > > > > > > *"At line 125 of file wn_readbakgen.f (unit=8, > > > > file='case.outputkgen'). > > > > > > > Fortran runtime error: Bad integer for item 1 in list input"* > > > > > > > > > > > > Can you check the (end of the) file for anything non-numeric in the > > > > first > > > > > > column ? > > > > > > Old-style fortran programs have the nasty habit of printing stars > > > > instead > > > > > > of > > > > > > digits if the number is bigger than the fixed field width > > allocated to > > > > > > it in the code, e.g. if the program tries to print the band number > > with > > > > > > a maximum of five characters you will see > > 99998...99999...*****...***** > > > > > > > > > > > > > > > > > > -- > > > > > > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > > > > > > c/o Prof.Dr. Caroline Roehr > > > > > > Institut fuer Anorganische und Analytische Chemie der Universitaet > > > > Freiburg > > > > > > > > > > > > _______________________________________________ > > > > > > XCrySDen mailing list > > > > > > XCrySDen at democritos.it > > > > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > > > > > > > > > > > _______________________________________________ > > > > > XCrySDen mailing list > > > > > XCrySDen at democritos.it > > > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > > > > -- > > > > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > > > > c/o Prof.Dr. Caroline Roehr > > > > Institut fuer Anorganische und Analytische Chemie der Universitaet > > Freiburg > > > > > > > > _______________________________________________ > > > > XCrySDen mailing list > > > > XCrySDen at democritos.it > > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > > > > > _______________________________________________ > > > XCrySDen mailing list > > > XCrySDen at democritos.it > > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > -- > > Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de > > c/o Prof.Dr. Caroline Roehr > > Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From pblaha at theochem.tuwien.ac.at Wed Dec 9 11:37:12 2015 From: pblaha at theochem.tuwien.ac.at (Peter Blaha) Date: Wed, 09 Dec 2015 11:37:12 +0100 Subject: [xcrysden] Runtime error in rendering the Fermi surface In-Reply-To: References: Message-ID: <56680458.6060703@theochem.tuwien.ac.at> Unfortunately, I cannot reproduce these problems. Just running a small and simple example (TiC) is fine: running x lapw1 -p in mixed k-point and mpi mode and cat case.output1_1 case.output1_2 .. > case.output1 works fine with me. Of course, you have to make sure you concatenated the correct (and all) output1_x files (there could be more than what you specified in .machines !!) What do you mean by: > 1. generating the kmesh in xcrysden ??? If it is the first point in the FS generation, this is fine. But it must not be the special k-path along high-symmetry directions used for bandstructures, which can also be done by xcrysden. On 12/08/2015 06:00 AM, lung Fermin wrote: > Hi everyone, > > I am trying to render the Fermi surface from a calculation in wien2k. > The following error appears, > > /"At line 125 of file wn_readbakgen.f (unit=8, file='case.outputkgen'). > Fortran runtime error: Bad integer for item 1 in list input"/ > / > / > I followed these steps: > 1. generating the kmesh in xcrysden > 2. x lapw1 -p -c (I used mpi+k point parallelization) > 3. x lapw2 -p -c -fermi > 4. I got some output files case.output1_x and case.output1_x_proc_y > (where x=1,2...8, y=0,1,...7). Then I glue the ouptut1_x files into a > single file using > cat case.output1_x>>case.output1. > > I have successfully generate the FS with a calculation of a smaller > number of k points. Then I used a finer kmesh for the scf calculation > this time and following the same procedure. The only difference is that > I used a mpi+k parallelization this time but only k point > parallelization last time. But this shouldn't cause any differences? > > Any suggestions? > > Thanks in advance. > > Best, > Fermin > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- P.Blaha -------------------------------------------------------------------------- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: blaha at theochem.tuwien.ac.at WIEN2k: http://www.wien2k.at WWW: http://www.imc.tuwien.ac.at/staff/tc_group_e.php -------------------------------------------------------------------------- From ferminlung at gmail.com Thu Dec 10 04:53:22 2015 From: ferminlung at gmail.com (lung Fermin) Date: Thu, 10 Dec 2015 11:53:22 +0800 Subject: [xcrysden] Runtime error in rendering the Fermi surface In-Reply-To: <56680458.6060703@theochem.tuwien.ac.at> References: <56680458.6060703@theochem.tuwien.ac.at> Message-ID: Thanks Dr. Kroeker and Prof. Blaha for the comments. > > What do you mean by: > > 1. generating the kmesh in xcrysden ??? > > If it is the first point in the FS generation, this is fine. > But it must not be the special k-path along high-symmetry directions > used for bandstructures, which can also be done by xcrysden. > > Yep. I did mean the first point in the FS generation. Regards, Fermin -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151210/a51aea4a/attachment.htm From mksingh at rrcat.gov.in Thu Dec 10 10:26:49 2015 From: mksingh at rrcat.gov.in (M. K. Singh) Date: Thu, 10 Dec 2015 14:56:49 +0530 Subject: [xcrysden] Re. Error in visualising structure of slabs having more than 1000 atoms Message-ID: <8d2c0d2745ce45d1fea41f3c019127ab.squirrel@n-webmail2.rrcat.gov.in> Dear xcrysden users, When I tried to visualise structure of slabs having more than 1000 atoms using CRYSTAL09 code, then following error appears: severe (59): list-directed I/O syntax error, unit 34, file /tmp/xc_17381/fort.34 Please advise how to fix this error? with best wishes, -- Dr. M. K. Singh Laser Materials Development & Devices Division Raja Ramanna Centre for Advanced Technology P.O. RRCAT INDORE 452013, INDIA Phone No. +91-731-248-8677 Fax No. +91-731-248-8650 -- M. K. Singh Scintific Officer/F Laser Materials Development & Devices Division Raja Ramanna Centre for Advanced Technology P.O. RRCAT INDORE 452013, INDIA Phone No. +91-731-248-8677 Fax No. +91-731-248-8650 -- M. K. Singh Scintific Officer/F Laser Materials Development & Devices Division Raja Ramanna Centre for Advanced Technology P.O. RRCAT INDORE 452013, INDIA Phone No. +91-731-248-8677 Fax No. +91-731-248-8650 From tone.kokalj at ijs.si Thu Dec 10 15:53:06 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 10 Dec 2015 15:53:06 +0100 Subject: [xcrysden] Re. Error in visualising structure of slabs having more than 1000 atoms In-Reply-To: <8d2c0d2745ce45d1fea41f3c019127ab.squirrel@n-webmail2.rrcat.gov.in> References: <8d2c0d2745ce45d1fea41f3c019127ab.squirrel@n-webmail2.rrcat.gov.in> Message-ID: <1449759186.803.22.camel@ijs.si> On Thu, 2015-12-10 at 14:56 +0530, M. K. Singh wrote: > Dear xcrysden users, > When I tried to visualise structure of slabs having more than 1000 > atoms > using CRYSTAL09 code, then following error appears: > severe (59): list-directed I/O syntax error, unit 34, file > /tmp/xc_17381/fort.34 Please can you provide the crystal input and fort.34 files. They may be too big for the mailing list, hence you can send them to my email. Best regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html