From mir.rbc at gmail.com Tue Sep 4 06:43:38 2018 From: mir.rbc at gmail.com (Mirwaiz Rahaman) Date: Tue, 4 Sep 2018 10:13:38 +0530 Subject: [xcrysden] How to plot Charge density in xcrysden? Message-ID: I am trying to plot charge density in xcrysden. In the data grid, Isosurface/Property-plane Controls panel, any number in Isovalue is showing wrong with an error message. Kindly help. I am attaching the screenshot of the error message -- *Mirwaiz Rahaman* *Semiconductor Lab* *Materials Science Centre* *IIT Kharagpur* *W.B. 721302* *mob:- 9038537914* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20180904/4329f2c6/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot from 2018-09-04 15-03-53.png Type: image/png Size: 219247 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20180904/4329f2c6/attachment-0001.png From matic.poberznik at gmail.com Tue Sep 4 14:47:44 2018 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Tue, 4 Sep 2018 14:47:44 +0200 Subject: [xcrysden] How to plot Charge density in xcrysden? In-Reply-To: References: Message-ID: <918cfb78-5090-2a71-1ed1-05fc49af5ceb@gmail.com> Dear Mirwaiz, the values for charge density are all positive and you should set the range accordingly, i.e. untick the Render +/- value box. (maximum and minimum grid value give you a hint of the available maximum/minimum values) Best Regards, Matic -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia From mir.rbc at gmail.com Wed Sep 5 08:04:45 2018 From: mir.rbc at gmail.com (Mirwaiz Rahaman) Date: Wed, 5 Sep 2018 11:34:45 +0530 Subject: [xcrysden] How to plot Charge density in xcrysden? In-Reply-To: <918cfb78-5090-2a71-1ed1-05fc49af5ceb@gmail.com> References: <918cfb78-5090-2a71-1ed1-05fc49af5ceb@gmail.com> Message-ID: Thank you for your reply. On Tue, Sep 4, 2018 at 6:17 PM Matic Poberznik wrote: > Dear Mirwaiz, > > the values for charge density are all positive and you should set the > range accordingly, i.e. untick the Render +/- value box. (maximum and > minimum grid value give you a hint of the available maximum/minimum values) > > Best Regards, > > Matic > -- > Matic Poberznik > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > -- *Mirwaiz Rahaman* *Semiconductor Lab* *Materials Science Centre* *IIT Kharagpur* *W.B. 721302* *mob:- 9038537914* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20180905/213d17c2/attachment.htm From giuseppe.mattioli at ism.cnr.it Thu Sep 6 18:26:34 2018 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Thu, 06 Sep 2018 18:26:34 +0200 Subject: [xcrysden] problems with pwo2xsf.sh Message-ID: <20180906182634.Horde.lR8wHWmtmbUeRxM_45LZhEb@webmail.sic.rm.cnr.it> Dear developers I've recently updated my debian 8 desktop to debian 9. Any attempt to open a QE-6.2.1 pw.x output file with the freshly installed (from debian repos) xcrysden 1.5.60 fails. In particular, xcrysden seems to be not able anymore to read initial/final/latest/animation coordinates, while it is still able to open pw.x input files. Moreover, the same behavior affect now my older 1.5.21 semishared version, previously installed (and perfectly working) in debian 8. I've already tried to install the 1.5.60 semishared version on debian 9, with the same problem. The xcrysden error is reported below /usr/share/xcrysden/scripts/pwo2xsf.sh: 1: /usr/share/xcrysden/scripts/pwo2xsf.sh: bc: not found Thank you in advance for your attention Giuseppe Mattioli GIUSEPPE MATTIOLI CNR - ISTITUTO DI STRUTTURA DELLA MATERIA Via Salaria Km 29,300 - C.P. 10 I-00015 - Monterotondo Scalo (RM) Mob (*preferred*) +39 373 7305625 Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: From matic.poberznik at gmail.com Thu Sep 6 18:39:07 2018 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Thu, 6 Sep 2018 18:39:07 +0200 Subject: [xcrysden] problems with pwo2xsf.sh In-Reply-To: <20180906182634.Horde.lR8wHWmtmbUeRxM_45LZhEb@webmail.sic.rm.cnr.it> References: <20180906182634.Horde.lR8wHWmtmbUeRxM_45LZhEb@webmail.sic.rm.cnr.it> Message-ID: <140eba65-d436-7f95-6c3b-b9d51616921a@gmail.com> Dear Giuseppe, > The xcrysden error is reported below> > /usr/share/xcrysden/scripts/pwo2xsf.sh: 1: > /usr/share/xcrysden/scripts/pwo2xsf.sh: bc: not found From giuseppe.mattioli at ism.cnr.it Fri Sep 7 00:01:23 2018 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Fri, 07 Sep 2018 00:01:23 +0200 Subject: [xcrysden] problems with pwo2xsf.sh In-Reply-To: <140eba65-d436-7f95-6c3b-b9d51616921a@gmail.com> References: <20180906182634.Horde.lR8wHWmtmbUeRxM_45LZhEb@webmail.sic.rm.cnr.it> <140eba65-d436-7f95-6c3b-b9d51616921a@gmail.com> Message-ID: <20180907000123.Horde.MV75Hhk5kaC4PJj8Y3IzmMl@webmail.sic.rm.cnr.it> Dear Matic You were right indeed! I didn't considered the possibility of messing up with basic packages during the update. Thank you very much Giuseppe Quoting Matic Poberznik : > Dear Giuseppe, > >> The xcrysden error is reported below> > >> /usr/share/xcrysden/scripts/pwo2xsf.sh: 1: > > /usr/share/xcrysden/scripts/pwo2xsf.sh: bc: not found > From the error it would seem that you are missing the "bc" package in > debian (it is typically available by default, but maybe the upgrade > messed something up): > > https://packages.debian.org/buster/bc > > perhaps try to reinstall it and let me know if it works, > > Best Regards, > Matic > -- > Matic Poberznik > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia GIUSEPPE MATTIOLI CNR - ISTITUTO DI STRUTTURA DELLA MATERIA Via Salaria Km 29,300 - C.P. 10 I-00015 - Monterotondo Scalo (RM) Mob (*preferred*) +39 373 7305625 Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: From m.tesseracted at gmail.com Mon Sep 10 15:26:03 2018 From: m.tesseracted at gmail.com (Aaron Mahler) Date: Mon, 10 Sep 2018 09:26:03 -0400 Subject: [xcrysden] problems with pwo2xsf.sh In-Reply-To: <20180906182634.Horde.lR8wHWmtmbUeRxM_45LZhEb@webmail.sic.rm.cnr.it> References: <20180906182634.Horde.lR8wHWmtmbUeRxM_45LZhEb@webmail.sic.rm.cnr.it> Message-ID: Giuseppe, That error is fairly non-descript but it looks like it's complaining about not being able to find bc. In my version of xcrysden the pwo2xsf.sh file's shebang is /bin/sh, which is system dependent. Try running bc in a /bin/sh environment on your machine. If it's not able to that's probably the source of your error. Cheers, -Aaron Mahler On Thu, Sep 6, 2018 at 12:26 PM Giuseppe Mattioli < giuseppe.mattioli at ism.cnr.it> wrote: > > Dear developers > > I've recently updated my debian 8 desktop to debian 9. Any attempt to > open a QE-6.2.1 pw.x output file with the freshly installed (from > debian repos) xcrysden 1.5.60 fails. In particular, xcrysden seems to > be not able anymore to read initial/final/latest/animation > coordinates, while it is still able to open pw.x input files. > Moreover, the same behavior affect now my older 1.5.21 semishared > version, previously installed (and perfectly working) in debian 8. > I've already tried to install the 1.5.60 semishared version on debian > 9, with the same problem. > > The xcrysden error is reported below > > /usr/share/xcrysden/scripts/pwo2xsf.sh: 1: > /usr/share/xcrysden/scripts/pwo2xsf.sh: bc: not found > > Thank you in advance for your attention > Giuseppe Mattioli > > GIUSEPPE MATTIOLI > CNR - ISTITUTO DI STRUTTURA DELLA MATERIA > Via Salaria Km 29,300 - C.P. 10 > I-00015 - Monterotondo Scalo (RM) > Mob (*preferred*) +39 373 7305625 > Tel + 39 06 90672342 - Fax +39 06 90672316 > E-mail: > > _______________________________________________ > 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/20180910/f31fbdeb/attachment.htm From giuseppe.mattioli at ism.cnr.it Mon Sep 10 18:48:58 2018 From: giuseppe.mattioli at ism.cnr.it (Giuseppe Mattioli) Date: Mon, 10 Sep 2018 18:48:58 +0200 Subject: [xcrysden] problems with pwo2xsf.sh In-Reply-To: References: <20180906182634.Horde.lR8wHWmtmbUeRxM_45LZhEb@webmail.sic.rm.cnr.it> Message-ID: <20180910184858.Horde.rjonIjiSUVMZi5FIqRaRodW@webmail.sic.rm.cnr.it> Dear Aaron Thank you for your answer. Actually the bc package "went lost" mysteriously during the upgrade. I've reinstalled it and now xcrysden works again! Best Giuseppe Quoting Aaron Mahler : > Giuseppe, > That error is fairly non-descript but it looks like it's complaining about > not being able to find bc. In my version of xcrysden the pwo2xsf.sh file's > shebang is /bin/sh, which is system dependent. Try running bc in a /bin/sh > environment on your machine. If it's not able to that's probably the source > of your error. Cheers, > > -Aaron Mahler > > > On Thu, Sep 6, 2018 at 12:26 PM Giuseppe Mattioli < > giuseppe.mattioli at ism.cnr.it> wrote: > >> >> Dear developers >> >> I've recently updated my debian 8 desktop to debian 9. Any attempt to >> open a QE-6.2.1 pw.x output file with the freshly installed (from >> debian repos) xcrysden 1.5.60 fails. In particular, xcrysden seems to >> be not able anymore to read initial/final/latest/animation >> coordinates, while it is still able to open pw.x input files. >> Moreover, the same behavior affect now my older 1.5.21 semishared >> version, previously installed (and perfectly working) in debian 8. >> I've already tried to install the 1.5.60 semishared version on debian >> 9, with the same problem. >> >> The xcrysden error is reported below >> >> /usr/share/xcrysden/scripts/pwo2xsf.sh: 1: >> /usr/share/xcrysden/scripts/pwo2xsf.sh: bc: not found >> >> Thank you in advance for your attention >> Giuseppe Mattioli >> >> GIUSEPPE MATTIOLI >> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA >> Via Salaria Km 29,300 - C.P. 10 >> I-00015 - Monterotondo Scalo (RM) >> Mob (*preferred*) +39 373 7305625 >> Tel + 39 06 90672342 - Fax +39 06 90672316 >> E-mail: >> >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden >> GIUSEPPE MATTIOLI CNR - ISTITUTO DI STRUTTURA DELLA MATERIA Via Salaria Km 29,300 - C.P. 10 I-00015 - Monterotondo Scalo (RM) Mob (*preferred*) +39 373 7305625 Tel + 39 06 90672342 - Fax +39 06 90672316 E-mail: