From lorechimica91 at hotmail.it Fri May 27 16:33:04 2016 From: lorechimica91 at hotmail.it (=?utf-8?Q?Lorenzo_Don=C3=A0?=) Date: Fri, 27 May 2016 16:33:04 +0200 Subject: [xcrysden] cpo27-zn connectivity problem Message-ID: Dear all I have done a pw.x calculation of cpo27zn when i open the output with xcrysden i am not able to see the connectivity among atoms. Please can you help me to solve this problem? I attached the output of my calculation. -------------- next part -------------- A non-text attachment was scrubbed... Name: cpo27zn.out.zip Type: application/zip Size: 9882 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20160527/05821e74/attachment.zip -------------- next part -------------- Thanks a lot. dearly lorenzo From matic.poberznik at gmail.com Fri May 27 21:56:29 2016 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Fri, 27 May 2016 21:56:29 +0200 Subject: [xcrysden] cpo27-zn connectivity problem In-Reply-To: References: Message-ID: <5748A66D.1070907@gmail.com> Dear Lorenzo, Use the dropdown menu under Modify=>Atomic radius (or Shift+R), the Chemical connectivity factor and covalent radius can be modified there. You can also add a line to ~/.xcrysden/custom-definitions: Example: set atmRad(13) 1.6 where 13 is the atomic number of the element you want to modifiy, more inforamtion is available here: http://www.xcrysden.org/doc/custom.html Hope this helps, Best Regards, Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia On 05/27/2016 04:33 PM, Lorenzo Don? wrote: > Dear all > I have done a pw.x calculation of cpo27zn when i open the output with xcrysden i am not able to see the connectivity among atoms. > Please can you help me to solve this problem? > I attached the output of my calculation. > > > > > Thanks a lot. > dearly > lorenzo > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > From lorechimica91 at hotmail.it Sat May 28 11:44:10 2016 From: lorechimica91 at hotmail.it (Lori 91) Date: Sat, 28 May 2016 11:44:10 +0200 Subject: [xcrysden] cpo27-zn connectivity problem In-Reply-To: <5748A66D.1070907@gmail.com> References: <5748A66D.1070907@gmail.com> Message-ID: Thanks for your replay I changed the connectivity factor and I found a partial connectivity but how can I change the connectivity for only one atom for example for Zn?? Thanks a lot to help me Dearly Lorenzo Inviato da iPhone > Il giorno 27 mag 2016, alle ore 21:56, Matic Poberznik ha scritto: > > Dear Lorenzo, > > Use the dropdown menu under Modify=>Atomic radius (or Shift+R), the > Chemical connectivity factor and covalent radius can be modified there. > You can also add a line to ~/.xcrysden/custom-definitions: > > Example: > > set atmRad(13) 1.6 > > where 13 is the atomic number of the element you want to modifiy, more > inforamtion is available here: > > http://www.xcrysden.org/doc/custom.html > > Hope this helps, > > Best Regards, > > Matic Poberznik > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > >> On 05/27/2016 04:33 PM, Lorenzo Don? wrote: >> Dear all >> I have done a pw.x calculation of cpo27zn when i open the output with xcrysden i am not able to see the connectivity among atoms. >> Please can you help me to solve this problem? >> I attached the output of my calculation. >> >> >> >> >> Thanks a lot. >> dearly >> lorenzo >> >> >> >> _______________________________________________ >> 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 matic.poberznik at gmail.com Sat May 28 12:50:03 2016 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Sat, 28 May 2016 12:50:03 +0200 Subject: [xcrysden] cpo27-zn connectivity problem In-Reply-To: References: <5748A66D.1070907@gmail.com> Message-ID: <574977DB.4030501@gmail.com> Sorry, but I don't quite understand what you mean; on the left side in the Atomic Radii panel there should be a list of atoms, you just choose the atom you want to modify from there. Alternatively in the ~/.xcrysden/custom-definitions file for Zn (with atomic number 30) you just add a line : set atmRad(30) X.X where X.X is the number for which you get appropriate connections; this will ensure that the covalent and display radius are updated on startup (i.e. that you don't have to manually set it every time you restart xcrysden) Best, Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia On 05/28/2016 11:44 AM, Lori 91 wrote: > Thanks for your replay I changed the connectivity factor and I found a partial connectivity but how can I change the connectivity for only one atom for example for Zn?? > Thanks a lot to help me > Dearly > Lorenzo > > Inviato da iPhone > >> Il giorno 27 mag 2016, alle ore 21:56, Matic Poberznik ha scritto: >> >> Dear Lorenzo, >> >> Use the dropdown menu under Modify=>Atomic radius (or Shift+R), the >> Chemical connectivity factor and covalent radius can be modified there. >> You can also add a line to ~/.xcrysden/custom-definitions: >> >> Example: >> >> set atmRad(13) 1.6 >> >> where 13 is the atomic number of the element you want to modifiy, more >> inforamtion is available here: >> >> http://www.xcrysden.org/doc/custom.html >> >> Hope this helps, >> >> Best Regards, >> >> Matic Poberznik >> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia >> >>> On 05/27/2016 04:33 PM, Lorenzo Don? wrote: >>> Dear all >>> I have done a pw.x calculation of cpo27zn when i open the output with xcrysden i am not able to see the connectivity among atoms. >>> Please can you help me to solve this problem? >>> I attached the output of my calculation. >>> >>> >>> >>> >>> Thanks a lot. >>> dearly >>> lorenzo >>> >>> >>> >>> _______________________________________________ >>> 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 > From lorechimica91 at hotmail.it Fri May 27 15:36:00 2016 From: lorechimica91 at hotmail.it (=?utf-8?Q?Lorenzo_Don=C3=A0?=) Date: Fri, 27 May 2016 15:36:00 +0200 Subject: [xcrysden] cpo27-zn connectivity problem Message-ID: Dear all I have done a pw.x calculation of cpo27zn when i open the output with xcrysden i am not able to see the connectivity among atoms. Please can you help me to solve this problem? I attached the output of my calculation. -------------- next part -------------- A non-text attachment was scrubbed... Name: cpo27zn.out Type: application/octet-stream Size: 60147 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20160527/0b5369bf/attachment-0001.obj -------------- next part -------------- Thanks a lot. dearly lorenzo From lorenzo.paulatto at impmc.upmc.fr Mon May 30 11:54:54 2016 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Mon, 30 May 2016 11:54:54 +0200 Subject: [xcrysden] cpo27-zn connectivity problem In-Reply-To: References: Message-ID: <2829638.iZhxGF2doQ@naquite> Modify -> Atomic Radius -> increase the Chemical connectivity factor and press "Update" until it works for you. (Your structure looks quite sparse, it's not too clear to me what it is supposed to be) On Friday, 27 May 2016 15:36:00 CEST Lorenzo Don? wrote: > Dear all > I have done a pw.x calculation of cpo27zn when i open the output with > xcrysden i am not able to see the connectivity among atoms. Please can you > help me to solve this problem? > I attached the output of my calculation. -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 +33 (0)1 44 275 084 / skype: paulatz http://www.impmc.upmc.fr/~paulatto/ 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From lorechimica91 at hotmail.it Mon May 30 12:21:15 2016 From: lorechimica91 at hotmail.it (Lori 91) Date: Mon, 30 May 2016 12:21:15 +0200 Subject: [xcrysden] cpo27-zn connectivity problem In-Reply-To: <2829638.iZhxGF2doQ@naquite> References: <2829638.iZhxGF2doQ@naquite> Message-ID: I generated it with crystal_sg and space_group number of pw.x I think that there is some problem in my input or in the code....... &system ibrav= 5, a= 25.226, cosab= 0.5, space_group = 148, nat= 9, ntyp= 4, ecutwfc =15.0, occupations='smearing', smearing='marzari-vanderbilt', degauss=0.07 input_dft= PBE, / And I used these coordinates: ATOMIC_POSITIONS crystal_sg C 7.127430447398E-02 -2.455696438145E-01 7.99109 3030472E-02 C 1.197468901477E-01 -2.066445045066E-01 2.15244 9225957E-01 C 2.117353032357E-01 -1.117780631842E-01 2.55336 8090727E-01 C 1.646071563067E-01 -1.528403540257E-01 1.44087 5844425E-01 H 1.629458066146E-01 -1.419696182443E-01 -4.76074 5519579E-03 Zn -1.943259345214E-02 2.834354147594E-01 3.06006 4447988E-01 O 7.229455751443E-02 -2.290060932141E-01 -9.08545 0716092E-02 O 3.018234203718E-02 -2.947952345384E-01 1.42204 1978763E-01 O 2.519030126218E-01 -6.097111538485E-02 1.72197 4260943E-01 K_POINTS gamma Thanks to help me Lorenzo Dearly Lorenzo Inviato da iPhone > Il giorno 30 mag 2016, alle ore 11:55, Lorenzo Paulatto ha scritto: > > Modify -> Atomic Radius -> increase the Chemical connectivity factor and press > "Update" until it works for you. > > (Your structure looks quite sparse, it's not too clear to me what it is > supposed to be) > >> On Friday, 27 May 2016 15:36:00 CEST Lorenzo Don? wrote: >> Dear all >> I have done a pw.x calculation of cpo27zn when i open the output with >> xcrysden i am not able to see the connectivity among atoms. Please can you >> help me to solve this problem? >> I attached the output of my calculation. > > > -- > Dr. Lorenzo Paulatto > IdR @ IMPMC -- CNRS & Universit? Paris 6 > +33 (0)1 44 275 084 / skype: paulatz > http://www.impmc.upmc.fr/~paulatto/ > 23-24/4?16 Bo?te courrier 115, > 4 place Jussieu 75252 Paris C?dex 05 > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden From lorechimica91 at hotmail.it Mon May 30 12:25:08 2016 From: lorechimica91 at hotmail.it (Lori 91) Date: Mon, 30 May 2016 12:25:08 +0200 Subject: [xcrysden] cpo27-zn connectivity problem In-Reply-To: References: <2829638.iZhxGF2doQ@naquite> Message-ID: Dear Lorenzo can you help me to use correctly crystal_sg and space group in the input Thanks a lot Lorenzo Inviato da iPhone > Il giorno 30 mag 2016, alle ore 12:21, Lori 91 ha scritto: > > I generated it with crystal_sg and space_group number of pw.x > I think that there is some problem in my input or in the code....... > &system > ibrav= 5, > a= 25.226, cosab= 0.5, space_group = 148, > nat= 9, ntyp= 4, > ecutwfc =15.0, > occupations='smearing', smearing='marzari-vanderbilt', degauss=0.07 > input_dft= PBE, > / > And I used these coordinates: > ATOMIC_POSITIONS crystal_sg > C 7.127430447398E-02 -2.455696438145E-01 7.99109 > 3030472E-02 > C 1.197468901477E-01 -2.066445045066E-01 2.15244 > 9225957E-01 > C 2.117353032357E-01 -1.117780631842E-01 2.55336 > 8090727E-01 > C 1.646071563067E-01 -1.528403540257E-01 1.44087 > 5844425E-01 > H 1.629458066146E-01 -1.419696182443E-01 -4.76074 > 5519579E-03 > Zn -1.943259345214E-02 2.834354147594E-01 3.06006 > 4447988E-01 > O 7.229455751443E-02 -2.290060932141E-01 -9.08545 > 0716092E-02 > O 3.018234203718E-02 -2.947952345384E-01 1.42204 > 1978763E-01 > O 2.519030126218E-01 -6.097111538485E-02 1.72197 > 4260943E-01 > K_POINTS gamma > Thanks to help me Lorenzo > Dearly > Lorenzo > > > Inviato da iPhone > >> Il giorno 30 mag 2016, alle ore 11:55, Lorenzo Paulatto ha scritto: >> >> Modify -> Atomic Radius -> increase the Chemical connectivity factor and press >> "Update" until it works for you. >> >> (Your structure looks quite sparse, it's not too clear to me what it is >> supposed to be) >> >>> On Friday, 27 May 2016 15:36:00 CEST Lorenzo Don? wrote: >>> Dear all >>> I have done a pw.x calculation of cpo27zn when i open the output with >>> xcrysden i am not able to see the connectivity among atoms. Please can you >>> help me to solve this problem? >>> I attached the output of my calculation. >> >> >> -- >> Dr. Lorenzo Paulatto >> IdR @ IMPMC -- CNRS & Universit? Paris 6 >> +33 (0)1 44 275 084 / skype: paulatz >> http://www.impmc.upmc.fr/~paulatto/ >> 23-24/4?16 Bo?te courrier 115, >> 4 place Jussieu 75252 Paris C?dex 05 >> _______________________________________________ >> 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 cjfoss at umass.edu Tue May 31 23:02:41 2016 From: cjfoss at umass.edu (Cameron Foss) Date: Tue, 31 May 2016 16:02:41 -0500 Subject: [xcrysden] using xcrysden through Cygwin Message-ID: Hello all, I am trying to open an xcrysden window on my windows 10 machine though CygWin. After opening a cygwin terminal, I ssh to a linux machine where I have xcrysden installed and as far as I understand I should be able to just run xcrysden? However when i prompt the window I get the following error: %% XCRYSDEN_TOPDIR=/usr/share/xcrysden XCRYSDEN_SCRATCH=/tmp Application initialization failed: no display name and no $DISPLAY environment variable Error in startup script: can't read "xcrys(platform)": no such variable while executing "if { $xcrys(platform) == "windows" } { # testing ... rename exec _tcl_exec proc exec {args} { global env # first try a normal exec..." (file "/usr/share/xcrysden/Tcl/cygwin.tcl" line 19) invoked from within "source $system(TOPDIR)/Tcl/cygwin.tcl" (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 443) %% It seems like the problem could be resolved by setting the environment var $DISPLAY however I am not positive what to set it to? I have seen some documentation that states that some auxiliary programs should be installed such as Tcl, however it is not 100% clear whether these should be installed on my linux machine that I am ssh'ing to OR if they should be installed in my cygwin terminal? Best, Cameron -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160531/f98aa827/attachment.htm From matic.poberznik at gmail.com Tue May 31 23:16:02 2016 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Tue, 31 May 2016 23:16:02 +0200 Subject: [xcrysden] using xcrysden through Cygwin In-Reply-To: References: Message-ID: <574DFF12.3080403@gmail.com> Hello Cameron, I think you just need to enable X11 forwarding when you ssh to the remote (linux) machine (I guess in cygwin that's ssh -Y hostname at host). I suppose you need to install the X window system for cygwin as well, if you don't have it already. Links: http://x.cygwin.com/docs/ug/using-remote-apps.html http://x.cygwin.com/docs/ug/setup-cygwin-x-installing.html Other than that I think it should work; please let me know if it does/doesn't. Best Regards, Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia On 05/31/2016 11:02 PM, Cameron Foss wrote: > Hello all, > > I am trying to open an xcrysden window on my windows 10 machine though > CygWin. After opening a cygwin terminal, I ssh to a linux machine where > I have xcrysden installed and as far as I understand I should be able to > just run xcrysden? However when i prompt the window I get the following > error: > > %% > XCRYSDEN_TOPDIR=/usr/share/xcrysden > XCRYSDEN_SCRATCH=/tmp > > Application initialization failed: no display name and no $DISPLAY > environment variable > Error in startup script: can't read "xcrys(platform)": no such variable > while executing > "if { $xcrys(platform) == "windows" } { > # testing ... > rename exec _tcl_exec > > proc exec {args} { > global env > > # first try a normal exec..." > (file "/usr/share/xcrysden/Tcl/cygwin.tcl" line 19) > invoked from within > "source $system(TOPDIR)/Tcl/cygwin.tcl" > (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 443) > %% > > It seems like the problem could be resolved by setting the environment > var $DISPLAY however I am not positive what to set it to? > > I have seen some documentation that states that some auxiliary programs > should be installed such as Tcl, however it is not 100% clear whether > these should be installed on my linux machine that I am ssh'ing to OR if > they should be installed in my cygwin terminal? > > Best, > Cameron > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden >