From R.Darkins at warwick.ac.uk Mon Mar 7 21:58:23 2011 From: R.Darkins at warwick.ac.uk (Darkins, Robert) Date: Mon, 7 Mar 2011 20:58:23 +0000 Subject: [xcrysden] Problem on OpenSUSE Message-ID: Hello, I am having a problem getting XCrysDen to run on OpenSUSE 11.3. I have done the following: 1. Downloaded the pre-compiled binaries 2. Extracted the tar.gz to ~/XCrySDen-1.4.1bin-static and cd'd into it 3. Configured it like so: $ export XCRYSDEN_TOPDIR=~/XCrySDen-1.4.1bin-static $ mkdir ~/xcrys_tmp $ export XCRYSDEN_SCRATCH=~/xcrys_tmp 4. Then ran it: $ ./xcrysden But I get the output shown below. I also tried the above for the latest version, 1.6, but got the exact same problem. Any suggestions? Thank you very much! +----------------------------------------------------------------+ |****************************************************************| |* *| |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*--------------------------------------------------------------*| |* *| |* Anton Kokalj (Tone.Kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2004 by Anton Kokalj *| |* *| |****************************************************************| +----------------------------------------------------------------+ Version: 1.4.1 XCRYSDEN reference: A. Kokalj: J. Mol. Graphics Modelling, 1999, Vol. 17, 176--179. A. Kokalj: Comput. Mater. Science, 2003, Vol. 28, 155--168. A. Kokalj and M. Causa: Proceedings of High Performance Graphics Systems and Applications European Workshop, Bologna, Italy, 2000, 51--54. Please report bugs to: Tone.Kokalj at ijs.si TERMS OF USE: ------------- XCRYSDEN is released under the GNU General Public License. Whenever graphics generated by XCRYSDEN are used in scientific publications, it shall be greatly appreciated to include an explicit reference. The preferred form is the following: [ref] A. Kokalj: J. Mol. Graphics Modelling, 1999, Vol. 17, 176--179. Code available from http://www.xcrysden.org/. Xlib: connection to ":0.0" refused by server Xlib: No protocol specified Application initialization failed: this isn't a Tk applicationcouldn't connect to display ":0.0" Error in startup script: can't read "tk_version": no such variable while executing "package provide Tk $tk_version" (file "/home/robert/XCrySDen-1.4.1bin-static/Tcl/xcInit.tcl" line 400) From ylli at aps.anl.gov Wed Mar 9 19:08:12 2011 From: ylli at aps.anl.gov (Yuelin Li) Date: Wed, 9 Mar 2011 12:08:12 -0600 (CST) Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <843853300.10458.1299599339560.JavaMail.root@zimbra-mb1.anl.gov> Message-ID: <1049959950.16320.1299694092256.JavaMail.root@zimbra-mb1.anl.gov> was able to get xcrysden running - beautiful implementation! I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. PWSCF version of the output: 4.3a TEXT-WIDGET: .a1.f1.t pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > pwo2xsf.xsf Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out Number of Atoms: 0 Number of Frames: 0 Estimated number of bonds = 0 sInfo(dim) = 0; periodic(dim) = 0 Attached is the in file directly from the tutorial pw examples. Please help. Thanks. Best, Yuelin -------------- next part -------------- A non-text attachment was scrubbed... Name: acetylene.in Type: application/octet-stream Size: 824 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20110309/e360e67d/attachment.obj From sclauzer at sissa.it Thu Mar 10 08:53:53 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 10 Mar 2011 08:53:53 +0100 Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <1049959950.16320.1299694092256.JavaMail.root@zimbra-mb1.anl.gov> References: <1049959950.16320.1299694092256.JavaMail.root@zimbra-mb1.anl.gov> Message-ID: <892E5460-0F50-425F-A64C-0E5112A852F8@sissa.it> I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version. If this is your problem you can solve it by commenting the calls to pwoCheckPWSCFVersion $option $input in scripts/pwo2xsf.sh Have fun with XCrysden! I also think it has very nice features. Best regards, GS Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto: > was able to get xcrysden running - beautiful implementation! > > I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. > > PWSCF version of the output: 4.3a > TEXT-WIDGET: .a1.f1.t > pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > pwo2xsf.xsf > Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out > Number of Atoms: 0 > Number of Frames: 0 > Estimated number of bonds = 0 > sInfo(dim) = 0; periodic(dim) = 0 > > > Attached is the in file directly from the tutorial pw examples. > > Please help. Thanks. > > Best, > > Yuelin_______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110310/96acdbf3/attachment.htm From ylli at aps.anl.gov Thu Mar 10 16:19:53 2011 From: ylli at aps.anl.gov (Yuelin Li) Date: Thu, 10 Mar 2011 09:19:53 -0600 (CST) Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <892E5460-0F50-425F-A64C-0E5112A852F8@sissa.it> Message-ID: <1716169324.21391.1299770393786.JavaMail.root@zimbra-mb1.anl.gov> Gabriele, thanks for the help. I commented the line you mentioned, but still got the same results. If I force it to read the optimised coordinate, a window pups up and say the following: ERROR: while executing exec sh ..../scripts/pwo2xsf.sh --optcoor ..../acetylene.out > pwo2xsf.xsf I can only guess that pwo2xsf.xsf did not find the optcoor string in the out file. I believe you are pointing to the right direction, must be some sort of mixing of versions. Any other thought? Best, Yuelin ----- Original Message ----- From: "Gabriele Sclauzero" To: "XCrySDen mailing list" Sent: Thursday, March 10, 2011 1:53:53 AM Subject: Re: [xcrysden] Cannot show multiple frame in out file I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version. If this is your problem you can solve it by commenting the calls to pwoCheckPWSCFVersion $option $input in scripts/pwo2xsf.sh Have fun with XCrysden! I also think it has very nice features. Best regards, GS Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto: was able to get xcrysden running - beautiful implementation! I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. PWSCF version of the output: 4.3a TEXT-WIDGET: .a1.f1.t pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > pwo2xsf.xsf Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out Number of Atoms: 0 Number of Frames: 0 Estimated number of bonds = 0 sInfo(dim) = 0; periodic(dim) = 0 Attached is the in file directly from the tutorial pw examples. Please help. Thanks. Best, Yuelin _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From sclauzer at sissa.it Thu Mar 10 16:56:43 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 10 Mar 2011 16:56:43 +0100 Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <1716169324.21391.1299770393786.JavaMail.root@zimbra-mb1.anl.gov> References: <1716169324.21391.1299770393786.JavaMail.root@zimbra-mb1.anl.gov> Message-ID: <61863A44-215D-45A4-BF78-D6048BF0CCAF@sissa.it> Il giorno 10/mar/2011, alle ore 16.19, Yuelin Li ha scritto: > Gabriele, > > thanks for the help. I commented the line you mentioned, but still got the same results. If I force it to read the optimised coordinate, a window pups up and say the following: > > ERROR: while executing exec sh > ..../scripts/pwo2xsf.sh --optcoor > ..../acetylene.out > pwo2xsf.xsf > > I can only guess that pwo2xsf.xsf did not find the optcoor string in the out file. I had a look to your input and it's a MD run, not a relaxation, so there are no "optimized" coordinates. I tried to run your input and then open the output file with xcrysden 1.5.21 and it could read all the coordinates without any problem. Why are you using 1.4.1? I suggest you to upgrade to the latest version. BTW, beware that even if you do a relaxation and use the "display optimized coordinates", it is not likely to work because the string which helped xcrysden identifying the optimized structure was changed in PWscf, but I suspect that the xcrysden has not been updated accordingly. However, if you select "latest coordinates" instead of "optimized coordinates" it works and you should get the same result (if the output file contains a converged relaxation run). HTH GS > > I believe you are pointing to the right direction, must be some sort of mixing of versions. > > Any other thought? > > Best, > > Yuelin > > > > ----- Original Message ----- > From: "Gabriele Sclauzero" > To: "XCrySDen mailing list" > Sent: Thursday, March 10, 2011 1:53:53 AM > Subject: Re: [xcrysden] Cannot show multiple frame in out file > > > I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version. > If this is your problem you can solve it by commenting the calls to > > pwoCheckPWSCFVersion $option $input > in scripts/pwo2xsf.sh > > > Have fun with XCrysden! I also think it has very nice features. > > > Best regards, > > > > > GS > > > > Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto: > > > > was able to get xcrysden running - beautiful implementation! > > I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. > > PWSCF version of the output: 4.3a > TEXT-WIDGET: .a1.f1.t > pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > pwo2xsf.xsf > Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out > Number of Atoms: 0 > Number of Frames: 0 > Estimated number of bonds = 0 > sInfo(dim) = 0; periodic(dim) = 0 > > > Attached is the in file directly from the tutorial pw examples. > > Please help. Thanks. > > Best, > > Yuelin _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > _______________________________________________ > 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 ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110310/2e935d57/attachment.htm From ylli at aps.anl.gov Thu Mar 10 17:19:23 2011 From: ylli at aps.anl.gov (Yuelin Li) Date: Thu, 10 Mar 2011 10:19:23 -0600 (CST) Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <61863A44-215D-45A4-BF78-D6048BF0CCAF@sissa.it> Message-ID: <1650506340.22503.1299773963808.JavaMail.root@zimbra-mb1.anl.gov> Thanks again. I did try the "latest coordinates" option. xcrysden did not complain, and there is nothing displayed. Looks like 1.5 is the solution. I was not able to install it the last time. I will try again and let you know the result. Yuelin ----- Original Message ----- From: "Gabriele Sclauzero" To: "XCrySDen mailing list" Sent: Thursday, March 10, 2011 9:56:43 AM Subject: Re: [xcrysden] Cannot show multiple frame in out file Il giorno 10/mar/2011, alle ore 16.19, Yuelin Li ha scritto: Gabriele, thanks for the help. I commented the line you mentioned, but still got the same results. If I force it to read the optimised coordinate, a window pups up and say the following: ERROR: while executing exec sh ..../scripts/pwo2xsf.sh --optcoor ..../acetylene.out > pwo2xsf.xsf I can only guess that pwo2xsf.xsf did not find the optcoor string in the out file. I had a look to your input and it's a MD run, not a relaxation, so there are no "optimized" coordinates. I tried to run your input and then open the output file with xcrysden 1.5.21 and it could read all the coordinates without any problem. Why are you using 1.4.1? I suggest you to upgrade to the latest version. BTW, beware that even if you do a relaxation and use the "display optimized coordinates", it is not likely to work because the string which helped xcrysden identifying the optimized structure was changed in PWscf, but I suspect that the xcrysden has not been updated accordingly. However, if you select "latest coordinates" instead of "optimized coordinates" it works and you should get the same result (if the output file contains a converged relaxation run). HTH GS I believe you are pointing to the right direction, must be some sort of mixing of versions. Any other thought? Best, Yuelin ----- Original Message ----- From: "Gabriele Sclauzero" < sclauzer at sissa.it > To: "XCrySDen mailing list" < xcrysden at democritos.it > Sent: Thursday, March 10, 2011 1:53:53 AM Subject: Re: [xcrysden] Cannot show multiple frame in out file I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version. If this is your problem you can solve it by commenting the calls to pwoCheckPWSCFVersion $option $input in scripts/pwo2xsf.sh Have fun with XCrysden! I also think it has very nice features. Best regards, GS Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto: was able to get xcrysden running - beautiful implementation! I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. PWSCF version of the output: 4.3a TEXT-WIDGET: .a1.f1.t pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > pwo2xsf.xsf Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out Number of Atoms: 0 Number of Frames: 0 Estimated number of bonds = 0 sInfo(dim) = 0; periodic(dim) = 0 Attached is the in file directly from the tutorial pw examples. Please help. Thanks. Best, Yuelin _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne _______________________________________________ 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 ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From ylli at aps.anl.gov Thu Mar 10 18:38:30 2011 From: ylli at aps.anl.gov (Yuelin Li) Date: Thu, 10 Mar 2011 11:38:30 -0600 (CST) Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <1650506340.22503.1299773963808.JavaMail.root@zimbra-mb1.anl.gov> Message-ID: <1059850950.23453.1299778710007.JavaMail.root@zimbra-mb1.anl.gov> Installed using the shared version, get the splash screen, then stopped at the famous line below Running on platform: unix Executing: /home/ylli/XCrySDen-1.5.17-bin-shared/bin/ftnunit with try the source version. ----- Original Message ----- From: Yuelin Li To: XCrySDen mailing list Sent: Thu, 10 Mar 2011 10:19:23 -0600 (CST) Subject: Re: [xcrysden] Cannot show multiple frame in out file Thanks again. I did try the "latest coordinates" option. xcrysden did not complain, and there is nothing displayed. Looks like 1.5 is the solution. I was not able to install it the last time. I will try again and let you know the result. Yuelin ----- Original Message ----- From: "Gabriele Sclauzero" To: "XCrySDen mailing list" Sent: Thursday, March 10, 2011 9:56:43 AM Subject: Re: [xcrysden] Cannot show multiple frame in out file Il giorno 10/mar/2011, alle ore 16.19, Yuelin Li ha scritto: Gabriele, thanks for the help. I commented the line you mentioned, but still got the same results. If I force it to read the optimised coordinate, a window pups up and say the following: ERROR: while executing exec sh ..../scripts/pwo2xsf.sh --optcoor ..../acetylene.out > pwo2xsf.xsf I can only guess that pwo2xsf.xsf did not find the optcoor string in the out file. I had a look to your input and it's a MD run, not a relaxation, so there are no "optimized" coordinates. I tried to run your input and then open the output file with xcrysden 1.5.21 and it could read all the coordinates without any problem. Why are you using 1.4.1? I suggest you to upgrade to the latest version. BTW, beware that even if you do a relaxation and use the "display optimized coordinates", it is not likely to work because the string which helped xcrysden identifying the optimized structure was changed in PWscf, but I suspect that the xcrysden has not been updated accordingly. However, if you select "latest coordinates" instead of "optimized coordinates" it works and you should get the same result (if the output file contains a converged relaxation run). HTH GS I believe you are pointing to the right direction, must be some sort of mixing of versions. Any other thought? Best, Yuelin ----- Original Message ----- From: "Gabriele Sclauzero" < sclauzer at sissa.it > To: "XCrySDen mailing list" < xcrysden at democritos.it > Sent: Thursday, March 10, 2011 1:53:53 AM Subject: Re: [xcrysden] Cannot show multiple frame in out file I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version. If this is your problem you can solve it by commenting the calls to pwoCheckPWSCFVersion $option $input in scripts/pwo2xsf.sh Have fun with XCrysden! I also think it has very nice features. Best regards, GS Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto: was able to get xcrysden running - beautiful implementation! I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. PWSCF version of the output: 4.3a TEXT-WIDGET: .a1.f1.t pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > pwo2xsf.xsf Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out Number of Atoms: 0 Number of Frames: 0 Estimated number of bonds = 0 sInfo(dim) = 0; periodic(dim) = 0 Attached is the in file directly from the tutorial pw examples. Please help. Thanks. Best, Yuelin _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne _______________________________________________ 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 ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne _______________________________________________ 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 From sclauzer at sissa.it Thu Mar 10 18:54:24 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 10 Mar 2011 18:54:24 +0100 Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <1059850950.23453.1299778710007.JavaMail.root@zimbra-mb1.anl.gov> References: <1059850950.23453.1299778710007.JavaMail.root@zimbra-mb1.anl.gov> Message-ID: <2D13C3FB-DBDB-4BA3-BBAA-B9B4A84E4EB7@sissa.it> Have you tried to correct the first problem, i.e. the call to pwo2xsf_old in pwo2xsh.sh? GS Il giorno 10/mar/2011, alle ore 18.38, Yuelin Li ha scritto: > Installed using the shared version, get the splash screen, then stopped at the famous line below > > Running on platform: unix > Executing: /home/ylli/XCrySDen-1.5.17-bin-shared/bin/ftnunit > > with try the source version. > > ----- Original Message ----- > From: Yuelin Li > To: XCrySDen mailing list > Sent: Thu, 10 Mar 2011 10:19:23 -0600 (CST) > Subject: Re: [xcrysden] Cannot show multiple frame in out file > > Thanks again. > > I did try the "latest coordinates" option. xcrysden did not complain, and there is nothing displayed. > > Looks like 1.5 is the solution. I was not able to install it the last time. I will try again and let you know the result. > > Yuelin > > > > ----- Original Message ----- > From: "Gabriele Sclauzero" > To: "XCrySDen mailing list" > Sent: Thursday, March 10, 2011 9:56:43 AM > Subject: Re: [xcrysden] Cannot show multiple frame in out file > > > > > > > Il giorno 10/mar/2011, alle ore 16.19, Yuelin Li ha scritto: > > > > Gabriele, > > thanks for the help. I commented the line you mentioned, but still got the same results. If I force it to read the optimised coordinate, a window pups up and say the following: > > ERROR: while executing exec sh > ..../scripts/pwo2xsf.sh --optcoor > ..../acetylene.out > pwo2xsf.xsf > > I can only guess that pwo2xsf.xsf did not find the optcoor string in the out file. > > > I had a look to your input and it's a MD run, not a relaxation, so there are no "optimized" coordinates. > I tried to run your input and then open the output file with xcrysden 1.5.21 and it could read all the coordinates without any problem. Why are you using 1.4.1? I suggest you to upgrade to the latest version. > > > BTW, beware that even if you do a relaxation and use the "display optimized coordinates", it is not likely to work because the string which helped xcrysden identifying the optimized structure was changed in PWscf, but I suspect that the xcrysden has not been updated accordingly. However, if you select "latest coordinates" instead of "optimized coordinates" it works and you should get the same result (if the output file contains a converged relaxation run). > > > > HTH > > > GS > > > > > > I believe you are pointing to the right direction, must be some sort of mixing of versions. > > Any other thought? > > Best, > > Yuelin > > > > ----- Original Message ----- > From: "Gabriele Sclauzero" < sclauzer at sissa.it > > To: "XCrySDen mailing list" < xcrysden at democritos.it > > Sent: Thursday, March 10, 2011 1:53:53 AM > Subject: Re: [xcrysden] Cannot show multiple frame in out file > > > I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version. > If this is your problem you can solve it by commenting the calls to > > pwoCheckPWSCFVersion $option $input > in scripts/pwo2xsf.sh > > > Have fun with XCrysden! I also think it has very nice features. > > > Best regards, > > > > > GS > > > > Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto: > > > > was able to get xcrysden running - beautiful implementation! > > I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. > > PWSCF version of the output: 4.3a > TEXT-WIDGET: .a1.f1.t > pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > pwo2xsf.xsf > Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out > Number of Atoms: 0 > Number of Frames: 0 > Estimated number of bonds = 0 > sInfo(dim) = 0; periodic(dim) = 0 > > > Attached is the in file directly from the tutorial pw examples. > > Please help. Thanks. > > Best, > > Yuelin _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > _______________________________________________ > 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 > > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > _______________________________________________ > 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 > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110310/954d0ac5/attachment.htm From ylli at aps.anl.gov Thu Mar 10 19:22:49 2011 From: ylli at aps.anl.gov (Yuelin Li) Date: Thu, 10 Mar 2011 12:22:49 -0600 (CST) Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <2D13C3FB-DBDB-4BA3-BBAA-B9B4A84E4EB7@sissa.it> Message-ID: <363503482.23695.1299781369304.JavaMail.root@zimbra-mb1.anl.gov> Did that too. What I mean is that xcrysden did not start at all and is stuck at that line. Best, Yuelin ----- Original Message ----- From: Gabriele Sclauzero To: XCrySDen mailing list Sent: Thu, 10 Mar 2011 11:54:24 -0600 (CST) Subject: Re: [xcrysden] Cannot show multiple frame in out file Have you tried to correct the first problem, i.e. the call to pwo2xsf_old in pwo2xsh.sh? GS Il giorno 10/mar/2011, alle ore 18.38, Yuelin Li ha scritto: > Installed using the shared version, get the splash screen, then stopped at the famous line below > > Running on platform: unix > Executing: /home/ylli/XCrySDen-1.5.17-bin-shared/bin/ftnunit > > with try the source version. > > ----- Original Message ----- > From: Yuelin Li > To: XCrySDen mailing list > Sent: Thu, 10 Mar 2011 10:19:23 -0600 (CST) > Subject: Re: [xcrysden] Cannot show multiple frame in out file > > Thanks again. > > I did try the "latest coordinates" option. xcrysden did not complain, and there is nothing displayed. > > Looks like 1.5 is the solution. I was not able to install it the last time. I will try again and let you know the result. > > Yuelin > > > > ----- Original Message ----- > From: "Gabriele Sclauzero" > To: "XCrySDen mailing list" > Sent: Thursday, March 10, 2011 9:56:43 AM > Subject: Re: [xcrysden] Cannot show multiple frame in out file > > > > > > > Il giorno 10/mar/2011, alle ore 16.19, Yuelin Li ha scritto: > > > > Gabriele, > > thanks for the help. I commented the line you mentioned, but still got the same results. If I force it to read the optimised coordinate, a window pups up and say the following: > > ERROR: while executing exec sh > ..../scripts/pwo2xsf.sh --optcoor > ..../acetylene.out > pwo2xsf.xsf > > I can only guess that pwo2xsf.xsf did not find the optcoor string in the out file. > > > I had a look to your input and it's a MD run, not a relaxation, so there are no "optimized" coordinates. > I tried to run your input and then open the output file with xcrysden 1.5.21 and it could read all the coordinates without any problem. Why are you using 1.4.1? I suggest you to upgrade to the latest version. > > > BTW, beware that even if you do a relaxation and use the "display optimized coordinates", it is not likely to work because the string which helped xcrysden identifying the optimized structure was changed in PWscf, but I suspect that the xcrysden has not been updated accordingly. However, if you select "latest coordinates" instead of "optimized coordinates" it works and you should get the same result (if the output file contains a converged relaxation run). > > > > HTH > > > GS > > > > > > I believe you are pointing to the right direction, must be some sort of mixing of versions. > > Any other thought? > > Best, > > Yuelin > > > > ----- Original Message ----- > From: "Gabriele Sclauzero" < sclauzer at sissa.it > > To: "XCrySDen mailing list" < xcrysden at democritos.it > > Sent: Thursday, March 10, 2011 1:53:53 AM > Subject: Re: [xcrysden] Cannot show multiple frame in out file > > > I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version. > If this is your problem you can solve it by commenting the calls to > > pwoCheckPWSCFVersion $option $input > in scripts/pwo2xsf.sh > > > Have fun with XCrysden! I also think it has very nice features. > > > Best regards, > > > > > GS > > > > Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto: > > > > was able to get xcrysden running - beautiful implementation! > > I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. > > PWSCF version of the output: 4.3a > TEXT-WIDGET: .a1.f1.t > pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out > pwo2xsf.xsf > Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out > Number of Atoms: 0 > Number of Frames: 0 > Estimated number of bonds = 0 > sInfo(dim) = 0; periodic(dim) = 0 > > > Attached is the in file directly from the tutorial pw examples. > > Please help. Thanks. > > Best, > > Yuelin _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > _______________________________________________ > 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 > > > > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > _______________________________________________ > 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 > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne From sclauzer at sissa.it Fri Mar 11 09:00:27 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 11 Mar 2011 09:00:27 +0100 Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <363503482.23695.1299781369304.JavaMail.root@zimbra-mb1.anl.gov> References: <363503482.23695.1299781369304.JavaMail.root@zimbra-mb1.anl.gov> Message-ID: <4D79D69B.30301@sissa.it> On 03/10/2011 07:22 PM, Yuelin Li wrote: > Did that too. What I mean is that xcrysden did not start at all and is stuck at that line. > > Best, > > Yuelin > Ah, OK. Sorry, I did not understand at the first place. So this means that you can't run the newly installed version, right? This might be a problem of libraries. I suggest you to try the semi-shared version or the binaries. GS > > ----- Original Message ----- > From: Gabriele Sclauzero > To: XCrySDen mailing list > Sent: Thu, 10 Mar 2011 11:54:24 -0600 (CST) > Subject: Re: [xcrysden] Cannot show multiple frame in out file > > Have you tried to correct the first problem, i.e. the call to pwo2xsf_old in pwo2xsh.sh? > > GS > > Il giorno 10/mar/2011, alle ore 18.38, Yuelin Li ha scritto: > >> Installed using the shared version, get the splash screen, then stopped at the famous line below >> >> Running on platform: unix >> Executing: /home/ylli/XCrySDen-1.5.17-bin-shared/bin/ftnunit >> >> with try the source version. >> >> ----- Original Message ----- >> From: Yuelin Li >> To: XCrySDen mailing list >> Sent: Thu, 10 Mar 2011 10:19:23 -0600 (CST) >> Subject: Re: [xcrysden] Cannot show multiple frame in out file >> >> Thanks again. >> >> I did try the "latest coordinates" option. xcrysden did not complain, and there is nothing displayed. >> >> Looks like 1.5 is the solution. I was not able to install it the last time. I will try again and let you know the result. >> >> Yuelin >> >> >> >> ----- Original Message ----- >> From: "Gabriele Sclauzero" >> To: "XCrySDen mailing list" >> Sent: Thursday, March 10, 2011 9:56:43 AM >> Subject: Re: [xcrysden] Cannot show multiple frame in out file >> >> >> >> >> >> >> Il giorno 10/mar/2011, alle ore 16.19, Yuelin Li ha scritto: >> >> >> >> Gabriele, >> >> thanks for the help. I commented the line you mentioned, but still got the same results. If I force it to read the optimised coordinate, a window pups up and say the following: >> >> ERROR: while executing exec sh >> ..../scripts/pwo2xsf.sh --optcoor >> ..../acetylene.out> pwo2xsf.xsf >> >> I can only guess that pwo2xsf.xsf did not find the optcoor string in the out file. >> >> >> I had a look to your input and it's a MD run, not a relaxation, so there are no "optimized" coordinates. >> I tried to run your input and then open the output file with xcrysden 1.5.21 and it could read all the coordinates without any problem. Why are you using 1.4.1? I suggest you to upgrade to the latest version. >> >> >> BTW, beware that even if you do a relaxation and use the "display optimized coordinates", it is not likely to work because the string which helped xcrysden identifying the optimized structure was changed in PWscf, but I suspect that the xcrysden has not been updated accordingly. However, if you select "latest coordinates" instead of "optimized coordinates" it works and you should get the same result (if the output file contains a converged relaxation run). >> >> >> >> HTH >> >> >> GS >> >> >> >> >> >> I believe you are pointing to the right direction, must be some sort of mixing of versions. >> >> Any other thought? >> >> Best, >> >> Yuelin >> >> >> >> ----- Original Message ----- >> From: "Gabriele Sclauzero"< sclauzer at sissa.it> >> To: "XCrySDen mailing list"< xcrysden at democritos.it> >> Sent: Thursday, March 10, 2011 1:53:53 AM >> Subject: Re: [xcrysden] Cannot show multiple frame in out file >> >> >> I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version. >> If this is your problem you can solve it by commenting the calls to >> >> pwoCheckPWSCFVersion $option $input >> in scripts/pwo2xsf.sh >> >> >> Have fun with XCrysden! I also think it has very nice features. >> >> >> Best regards, >> >> >> >> >> GS >> >> >> >> Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto: >> >> >> >> was able to get xcrysden running - beautiful implementation! >> >> I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. >> >> PWSCF version of the output: 4.3a >> TEXT-WIDGET: .a1.f1.t >> pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out >> Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out> pwo2xsf.xsf >> Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out >> Number of Atoms: 0 >> Number of Frames: 0 >> Estimated number of bonds = 0 >> sInfo(dim) = 0; periodic(dim) = 0 >> >> >> Attached is the in file directly from the tutorial pw examples. >> >> Please help. Thanks. >> >> Best, >> >> Yuelin _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden >> >> >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> PH H2 462, Station 3, CH-1015 Lausanne >> >> _______________________________________________ >> 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 >> >> >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> PH H2 462, Station 3, CH-1015 Lausanne >> >> _______________________________________________ >> 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 >> >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne From ylli at aps.anl.gov Fri Mar 11 16:57:57 2011 From: ylli at aps.anl.gov (Yuelin Li) Date: Fri, 11 Mar 2011 09:57:57 -0600 (CST) Subject: [xcrysden] Cannot show multiple frame in out file In-Reply-To: <4D79D69B.30301@sissa.it> Message-ID: <1390924011.34843.1299859077809.JavaMail.root@zimbra-mb1.anl.gov> Gabriele, thanks again. I tried the source yesterday did not get it work. Then your suggestion worked out beautifully, the semi-shared worked. Thanks for the help along the way. Best, Yuelin ----- Original Message ----- From: "Gabriele Sclauzero" To: "XCrySDen mailing list" Sent: Friday, March 11, 2011 2:00:27 AM Subject: Re: [xcrysden] Cannot show multiple frame in out file On 03/10/2011 07:22 PM, Yuelin Li wrote: > Did that too. What I mean is that xcrysden did not start at all and is stuck at that line. > > Best, > > Yuelin > Ah, OK. Sorry, I did not understand at the first place. So this means that you can't run the newly installed version, right? This might be a problem of libraries. I suggest you to try the semi-shared version or the binaries. GS > > ----- Original Message ----- > From: Gabriele Sclauzero > To: XCrySDen mailing list > Sent: Thu, 10 Mar 2011 11:54:24 -0600 (CST) > Subject: Re: [xcrysden] Cannot show multiple frame in out file > > Have you tried to correct the first problem, i.e. the call to pwo2xsf_old in pwo2xsh.sh? > > GS > > Il giorno 10/mar/2011, alle ore 18.38, Yuelin Li ha scritto: > >> Installed using the shared version, get the splash screen, then stopped at the famous line below >> >> Running on platform: unix >> Executing: /home/ylli/XCrySDen-1.5.17-bin-shared/bin/ftnunit >> >> with try the source version. >> >> ----- Original Message ----- >> From: Yuelin Li >> To: XCrySDen mailing list >> Sent: Thu, 10 Mar 2011 10:19:23 -0600 (CST) >> Subject: Re: [xcrysden] Cannot show multiple frame in out file >> >> Thanks again. >> >> I did try the "latest coordinates" option. xcrysden did not complain, and there is nothing displayed. >> >> Looks like 1.5 is the solution. I was not able to install it the last time. I will try again and let you know the result. >> >> Yuelin >> >> >> >> ----- Original Message ----- >> From: "Gabriele Sclauzero" >> To: "XCrySDen mailing list" >> Sent: Thursday, March 10, 2011 9:56:43 AM >> Subject: Re: [xcrysden] Cannot show multiple frame in out file >> >> >> >> >> >> >> Il giorno 10/mar/2011, alle ore 16.19, Yuelin Li ha scritto: >> >> >> >> Gabriele, >> >> thanks for the help. I commented the line you mentioned, but still got the same results. If I force it to read the optimised coordinate, a window pups up and say the following: >> >> ERROR: while executing exec sh >> ..../scripts/pwo2xsf.sh --optcoor >> ..../acetylene.out> pwo2xsf.xsf >> >> I can only guess that pwo2xsf.xsf did not find the optcoor string in the out file. >> >> >> I had a look to your input and it's a MD run, not a relaxation, so there are no "optimized" coordinates. >> I tried to run your input and then open the output file with xcrysden 1.5.21 and it could read all the coordinates without any problem. Why are you using 1.4.1? I suggest you to upgrade to the latest version. >> >> >> BTW, beware that even if you do a relaxation and use the "display optimized coordinates", it is not likely to work because the string which helped xcrysden identifying the optimized structure was changed in PWscf, but I suspect that the xcrysden has not been updated accordingly. However, if you select "latest coordinates" instead of "optimized coordinates" it works and you should get the same result (if the output file contains a converged relaxation run). >> >> >> >> HTH >> >> >> GS >> >> >> >> >> >> I believe you are pointing to the right direction, must be some sort of mixing of versions. >> >> Any other thought? >> >> Best, >> >> Yuelin >> >> >> >> ----- Original Message ----- >> From: "Gabriele Sclauzero"< sclauzer at sissa.it> >> To: "XCrySDen mailing list"< xcrysden at democritos.it> >> Sent: Thursday, March 10, 2011 1:53:53 AM >> Subject: Re: [xcrysden] Cannot show multiple frame in out file >> >> >> I think I met the same problem some time ago. It comes from the fact that xcrysden checks the string of the PWscf version and, if it thinks that the version is an old one, it calls a different script to read the output file. Now, the problem is with the "a" in 4.3a which makes xcrysden think that's an old version. >> If this is your problem you can solve it by commenting the calls to >> >> pwoCheckPWSCFVersion $option $input >> in scripts/pwo2xsf.sh >> >> >> Have fun with XCrysden! I also think it has very nice features. >> >> >> Best regards, >> >> >> >> >> GS >> >> >> >> Il giorno 09/mar/2011, alle ore 19.08, Yuelin Li ha scritto: >> >> >> >> was able to get xcrysden running - beautiful implementation! >> >> I do have a problem using it when look at out put with multiple atom positions. It looks like xcryden only sees the first frame not the others. If I force it, e.g., on the latest frame, the display is blank, xterm says. >> >> PWSCF version of the output: 4.3a >> TEXT-WIDGET: .a1.f1.t >> pwOutputPresetWhat: /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out >> Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/pwo2xsf.sh --latestcoor /home/ylli/Documents/temp/acetylene.out> pwo2xsf.xsf >> Executing: sh /home/ylli/XCrySDen-1.4.1s/scripts/dummy.sh /home/ylli/Documents/temp/acetylene.out >> Number of Atoms: 0 >> Number of Frames: 0 >> Estimated number of bonds = 0 >> sInfo(dim) = 0; periodic(dim) = 0 >> >> >> Attached is the in file directly from the tutorial pw examples. >> >> Please help. Thanks. >> >> Best, >> >> Yuelin _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden >> >> >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> PH H2 462, Station 3, CH-1015 Lausanne >> >> _______________________________________________ >> 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 >> >> >> >> >> ? Gabriele Sclauzero, EPFL SB ITP CSEA >> PH H2 462, Station 3, CH-1015 Lausanne >> >> _______________________________________________ >> 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 >> >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden > > ? Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From sd.wang000 at 163.com Wed Mar 16 02:59:35 2011 From: sd.wang000 at 163.com (=?GBK?B?zfXK5rar?=) Date: Wed, 16 Mar 2011 09:59:35 +0800 (CST) Subject: [xcrysden] Background of the charge density Message-ID: <97832c.b6c5.12ebc63b92f.Coremail.sd.wang000@163.com> Dear developers: I want to plot the charge density as the background is whits color, but I find there is no such color option in xcrysden. How can I set this? The attchment is the example. -- S.D.Wang ??? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110316/e5a50969/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: clip_image002.gif Type: image/gif Size: 21299 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20110316/e5a50969/attachment-0001.gif From sclauzer at sissa.it Wed Mar 16 11:17:48 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 16 Mar 2011 11:17:48 +0100 Subject: [xcrysden] Background of the charge density In-Reply-To: <97832c.b6c5.12ebc63b92f.Coremail.sd.wang000@163.com> References: <97832c.b6c5.12ebc63b92f.Coremail.sd.wang000@163.com> Message-ID: Dear Wang, to change the background you should use the small button on the top left of the window (at the left of the "File" menu). HTH GS Il giorno 16/mar/2011, alle ore 02.59, ??? ha scritto: > Dear developers: > I want to plot the charge density as the background is whits color, but I find there is no such color option in xcrysden. How can I set this? > The attchment is the example. > > -- > S.D.Wang > ??? > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110316/b6986222/attachment.htm From tone.kokalj at ijs.si Wed Mar 16 17:26:01 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 16 Mar 2011 17:26:01 +0100 Subject: [xcrysden] Problem on OpenSUSE In-Reply-To: References: Message-ID: <1300292761.8349.10.camel@catalyst.ijs.si> On Mon, 2011-03-07 at 20:58 +0000, Darkins, Robert wrote: > Hello, > > I am having a problem getting XCrysDen to run on OpenSUSE 11.3. I have done the following: > Xlib: connection to ":0.0" refused by server > Xlib: No protocol specified The error message indicates you trying to run xcrysden remotely? Please run xcrysden locally or else enable X11 forwarding. Note however that in this latter case the remote running will be rather slow. 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 From R.Darkins at warwick.ac.uk Wed Mar 16 17:37:54 2011 From: R.Darkins at warwick.ac.uk (Darkins, Robert) Date: Wed, 16 Mar 2011 16:37:54 +0000 Subject: [xcrysden] Problem on OpenSUSE In-Reply-To: <1300292761.8349.10.camel@catalyst.ijs.si> References: , <1300292761.8349.10.camel@catalyst.ijs.si> Message-ID: Thanks for the response, Tone. Unfortunately, it doesn't appear to be that simple, since I AM running it locally. ________________________________________ From: xcrysden-bounces at democritos.it [xcrysden-bounces at democritos.it] on behalf of Tone Kokalj [tone.kokalj at ijs.si] Sent: 16 March 2011 16:26 To: xcrysden at democritos.it Subject: Re: [xcrysden] Problem on OpenSUSE On Mon, 2011-03-07 at 20:58 +0000, Darkins, Robert wrote: > Hello, > > I am having a problem getting XCrysDen to run on OpenSUSE 11.3. I have done the following: > Xlib: connection to ":0.0" refused by server > Xlib: No protocol specified The error message indicates you trying to run xcrysden remotely? Please run xcrysden locally or else enable X11 forwarding. Note however that in this latter case the remote running will be rather slow. 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 _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From tone.kokalj at ijs.si Wed Mar 16 17:43:33 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 16 Mar 2011 17:43:33 +0100 Subject: [xcrysden] Problem on OpenSUSE In-Reply-To: References: , <1300292761.8349.10.camel@catalyst.ijs.si> Message-ID: <1300293813.8349.14.camel@catalyst.ijs.si> On Wed, 2011-03-16 at 16:37 +0000, Darkins, Robert wrote: > Thanks for the response, Tone. Unfortunately, it doesn't appear to be that simple, since I AM running it locally. Now, I remember that some years ago one user had a similar problem and it used to be related to some paranoid "selinux" settings. (I'will try to contact him if he remembers what was the solution) 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 From mlusk at mines.edu Thu Mar 17 12:14:22 2011 From: mlusk at mines.edu (Mark Lusk) Date: Thu, 17 Mar 2011 05:14:22 -0600 Subject: [xcrysden] Please Unsubscrbe Me. Thanks. Message-ID: <4D81ED0E.6030305@mines.edu> -------------- next part -------------- A non-text attachment was scrubbed... Name: mlusk.vcf Type: text/x-vcard Size: 306 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20110317/f8cd9feb/attachment.vcf From Lorenzo.Paulatto at impmc.upmc.fr Thu Mar 17 12:22:03 2011 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 17 Mar 2011 12:22:03 +0100 Subject: [xcrysden] Please Unsubscrbe Me. Thanks. In-Reply-To: <4D81ED0E.6030305@mines.edu> References: <4D81ED0E.6030305@mines.edu> Message-ID: Dear Mark, you can/should do it yourself from the web interface: http://www.democritos.it/mailman/listinfo/xcrysden On Thu, 17 Mar 2011 12:14:22 +0100, Mark Lusk wrote: > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Lorenzo Paulatto (IdR) IMPMC - CNRS UMR 7590 & Universit? P&M Curie T23-C13/23-5e27 - 4 place Jussieu - 75252 Paris Cedex5 phone: +33 (0)144 27 5211 www: http://www-int.impmc.upmc.fr/~paulatto/ From alex968873 at yahoo.com.cn Fri Mar 18 14:21:22 2011 From: alex968873 at yahoo.com.cn (=?gb2312?B?wO6x8w==?=) Date: Fri, 18 Mar 2011 21:21:22 +0800 (CST) Subject: [xcrysden] Question about Xcrysden and w2web of WIEN2K Message-ID: <561638.49314.qm@web15107.mail.cnb.yahoo.com> Hi! all, I've installed Xcrysden and it works well using commandline. But the "view structure" menu didn't appear at the w2web interface of WIEN2k before rebooting the server. Is there a way to link the Xcrysden to w2web avoiding rebooting? Thanks a lot! B. Li From bnrj.rudra at yahoo.com Sun Mar 20 21:17:33 2011 From: bnrj.rudra at yahoo.com (Rudra Banerjee) Date: Mon, 21 Mar 2011 01:47:33 +0530 (IST) Subject: [xcrysden] rotate cordinate by script(or other) to fixed amount Message-ID: <917689.42044.qm@web95905.mail.in.yahoo.com> Dear Friends, I want to view and print a number of files with the viewport (coordinate) changed. How I can rotate the xyz file in same amount each time i open the file? I cheked customs-defination(nothing there), FAQ and scripting site....but failed to solve the problem. $ xcr fcc1.xyz --script /opt/XCrySDen-1.5.17-bin-semishared/Tcl/scripting::rotate x 5 Please help. -- Rudra JRF; SNBNCBS http://www.bose.res.in/~rudra A bus station is where a bus stops. A train station is where a train stops. On my desk I have a work station. Please, if possible, don't send me MS Word or PowerPoint attachments Why?See: http://www.gnu.org/philosophy/no-word-attachments.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110321/9c129bca/attachment.htm From tone.kokalj at ijs.si Tue Mar 29 08:38:59 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 29 Mar 2011 08:38:59 +0200 Subject: [xcrysden] Question about Xcrysden and w2web of WIEN2K In-Reply-To: <561638.49314.qm@web15107.mail.cnb.yahoo.com> References: <561638.49314.qm@web15107.mail.cnb.yahoo.com> Message-ID: <1301380739.4221.6.camel@catalyst.ijs.si> On Fri, 2011-03-18 at 21:21 +0800, ?? wrote: > Hi! all, > > I've installed Xcrysden and it works well using commandline. But the "view structure" > menu didn't appear at the w2web interface of WIEN2k before rebooting the server. Is > there a way to link the Xcrysden to w2web avoiding rebooting? I don't know precisely how the w2web works, but probably it checks if the XCRYSDEN_TOPDIR variable is defined or not. If this is so, I guess closing (exiting) the browser, defining the variable and launching again the browser from the terminal where the XCRYSDEN_TOPDIR has just been defined would be sufficient. Another more intrusive method is to log-out and log-in. 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 From tone.kokalj at ijs.si Tue Mar 29 08:43:16 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 29 Mar 2011 08:43:16 +0200 Subject: [xcrysden] rotate cordinate by script(or other) to fixed amount In-Reply-To: <917689.42044.qm@web95905.mail.in.yahoo.com> References: <917689.42044.qm@web95905.mail.in.yahoo.com> Message-ID: <1301380996.4221.10.camel@catalyst.ijs.si> On Mon, 2011-03-21 at 01:47 +0530, Rudra Banerjee wrote: > Dear Friends, > I want to view and print a number of files with the viewport > (coordinate) changed. How I can rotate the xyz file in same amount > each time i open the file? > I cheked customs-defination(nothing there), FAQ and scripting > site....but failed to solve the problem. > $ xcr fcc1.xyz > --script /opt/XCrySDen-1.5.17-bin-semishared/Tcl/scripting::rotate x 5 xcrysden scripting commands are not supposed to be run from command line, but instead loaded (read) from the script file. Say, you put your rotating command into a file named roatate5.xcrysden, which could look as: scripting::open --xyz fcc1.xyz scripting::rotate x 5 Then you execute xcrysden as: xcrysden -s rotate5.xcrysden For more info see: http://www.xcrysden.org/doc/scripting.html 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 From pblaha at theochem.tuwien.ac.at Tue Mar 29 10:01:08 2011 From: pblaha at theochem.tuwien.ac.at (Peter Blaha) Date: Tue, 29 Mar 2011 10:01:08 +0200 Subject: [xcrysden] Question about Xcrysden and w2web of WIEN2K In-Reply-To: <1301380739.4221.6.camel@catalyst.ijs.si> References: <561638.49314.qm@web15107.mail.cnb.yahoo.com> <1301380739.4221.6.camel@catalyst.ijs.si> Message-ID: <4D9191C4.2040205@theochem.tuwien.ac.at> No, you have to kill and restart the w2web server. w2web checks only at startup the presence of XCRYSDEN. ps -ef |grep w2web kill pid_of_w2web w2web (Usually this happens only once, namely when you start w2web before you installed xcrysden.) Am 29.03.2011 08:38, schrieb Tone Kokalj: > On Fri, 2011-03-18 at 21:21 +0800, ?? wrote:> Hi! all,> > I've installed Xcrysden and it works well using commandline. But the "view structure"> menu didn't appear at the w2web interface of WIEN2k before rebooting the server. Is> there a way to link the Xcrysden to w2web avoiding rebooting? > I don't know precisely how the w2web works, but probably it checks ifthe XCRYSDEN_TOPDIR variable is defined or not. If this is so, I guessclosing (exiting) the browser, defining the variable and launching againthe browser from the terminal where the XCRYSDEN_TOPDIR has just beendefined would be sufficient. > Another more intrusive method is to log-out and log-in. > Regards, Tone-- Anton KokaljJ. 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 > _______________________________________________XCrySDen mailing listXCrySDen at democritos.ithttp://www.democritos.it/mailman/listinfo/xcrysden -- P.Blaha -------------------------------------------------------------------------- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.at WWW: http://info.tuwien.ac.at/theochem/ -------------------------------------------------------------------------- From alex968873 at yahoo.com.cn Wed Mar 30 07:52:27 2011 From: alex968873 at yahoo.com.cn (=?utf-8?B?5p2O5paM?=) Date: Wed, 30 Mar 2011 13:52:27 +0800 (CST) Subject: [xcrysden] =?utf-8?b?5Zue5aSN77yaIFhDcnlTRGVuIERpZ2VzdCwgVm9sIDM4?= =?utf-8?q?=2C_Issue_11?= In-Reply-To: Message-ID: <676165.74580.qm@web15108.mail.cnb.yahoo.com> Many thanks! --- 11?3?29????, xcrysden-request at democritos.it ??? > ???: xcrysden-request at democritos.it > ??: XCrySDen Digest, Vol 38, Issue 11 > ???: xcrysden at democritos.it > ??: 2011?3?29?,??,??3:39 > Send XCrySDen mailing list > submissions to > ??? xcrysden at democritos.it > > To subscribe or unsubscribe via the World Wide Web, visit > ??? http://www.democritos.it/mailman/listinfo/xcrysden > or, via email, send a message with subject or body 'help' > to > ??? xcrysden-request at democritos.it > > You can reach the person managing the list at > ??? xcrysden-owner at democritos.it > > When replying, please edit your Subject line so it is more > specific > than "Re: Contents of XCrySDen digest..." > > > Today's Topics: > > ???1. Re: Question about Xcrysden and w2web > of WIEN2K (Tone Kokalj) > ???2. Re: rotate cordinate by script(or > other) to fixed amount > ? ? ? (Tone Kokalj) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 29 Mar 2011 08:38:59 +0200 > From: Tone Kokalj > Subject: Re: [xcrysden] Question about Xcrysden and w2web > of WIEN2K > To: XCrySDen mailing list > Message-ID: <1301380739.4221.6.camel at catalyst.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Fri, 2011-03-18 at 21:21 +0800, ?? wrote: > > Hi! all, > > > >? I've installed Xcrysden and it works well using > commandline. But the "view structure" > >? menu didn't appear at the w2web interface of > WIEN2k before rebooting the server. Is > >? there a way to link the Xcrysden to w2web > avoiding rebooting? > > I don't know precisely how the w2web works, but probably it > checks if > the XCRYSDEN_TOPDIR variable is defined or not. If this is > so, I guess > closing (exiting) the browser, defining the variable and > launching again > the browser from the terminal where the XCRYSDEN_TOPDIR has > just been > defined would be sufficient. > > Another more intrusive method is to log-out and log-in. > > 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 > > > > ------------------------------ > > Message: 2 > Date: Tue, 29 Mar 2011 08:43:16 +0200 > From: Tone Kokalj > Subject: Re: [xcrysden] rotate cordinate by script(or > other) to fixed > ??? amount > To: xcrysden at democritos.it > Message-ID: <1301380996.4221.10.camel at catalyst.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Mon, 2011-03-21 at 01:47 +0530, Rudra Banerjee wrote: > > Dear Friends, > > I want to view and print a number of files with the > viewport > > (coordinate) changed. How I can rotate the xyz file in > same amount > > each time i open the file? > > I cheked customs-defination(nothing there), FAQ and > scripting > > site....but failed to solve the problem. > > $ xcr fcc1.xyz > > --script > /opt/XCrySDen-1.5.17-bin-semishared/Tcl/scripting::rotate x > 5 > > xcrysden scripting commands are not supposed to be run from > command > line, but instead loaded (read) from the script file. > > Say, you put your rotating command into a file named > roatate5.xcrysden, > which could look as: > > scripting::open --xyz? fcc1.xyz > scripting::rotate x 5 > > Then you execute xcrysden as: > xcrysden -s rotate5.xcrysden > > > For more info see: http://www.xcrysden.org/doc/scripting.html > > 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 > > > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 38, Issue 11 > **************************************** >