From dstrubbe at civet.berkeley.edu Thu Oct 1 18:30:54 2015 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Thu, 1 Oct 2015 12:30:54 -0400 Subject: [xcrysden] warnings from gfortran 5.2.0 Message-ID: Hello Tone et al., I get the following warnings in xcrysden 1.5.60 when compiling the file gengeom.f with gfortran version 5.2.0 on my Mac. Does this represent a problem in the code? David /opt/local/bin/gfortran-mp-5 -c -o gengeom.o gengeom.f gengeom.f:735:27: CALL GETCCOOR(DVC,AC,2,X,Y,Z,XC,YC,ZC,I,NATR) 1 Warning: Actual argument contains too few elements for dummy argument 'b33' (6/12) at (1) gengeom.f:740:27: CALL GETCCOOR(DVC,BC,2,X,Y,Z,XC,YC,ZC,I,NATR) 1 Warning: Actual argument contains too few elements for dummy argument 'b33' (6/12) at (1) gengeom.f:745:27: CALL GETCCOOR(DVC,CC,2,X,Y,Z,XC,YC,ZC,I,NATR) 1 Warning: Actual argument contains too few elements for dummy argument 'b33' (6/12) at (1) gengeom.f:759:27: CALL GETCCOOR(DVC,IC,2,X,Y,Z,XC,YC,ZC,I,NATR) 1 Warning: Actual argument contains too few elements for dummy argument 'b33' (6/12) at (1) gengeom.f:766:30: CALL GETCCOOR(DVC,RC,IN,X,Y,Z,XC,YC,ZC,I,NATR) 1 Warning: Actual argument contains too few elements for dummy argument 'b33' (9/12) at (1) gengeom.f:773:30: CALL GETCCOOR(DVC,HC,IN,X,Y,Z,XC,YC,ZC,I,NATR) 1 Warning: Actual argument contains too few elements for dummy argument 'b33' (9/12) at (1) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151001/39a1c536/attachment.htm From gsabo at crimson.ua.edu Fri Oct 2 22:39:20 2015 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Fri, 2 Oct 2015 14:39:20 -0600 Subject: [xcrysden] Error when rendering the fermi surface In-Reply-To: References: <20150921165502.97D5D80193@ruby.chemie.uni-freiburg.de> <5600EE9A.5090006@theochem.tuwien.ac.at> Message-ID: <560EEB78.9040401@crimson.ua.edu> Maybe it is because you are running XCrySDen in a virtualbox. Does it happen when you do not use a virtualbox? If the connection to your cluster is fast enough, perhaps you can try running XCrySDen from the cluster using X11 forwarding [ http://users.wfu.edu/natalie/s11phy752/lecturenote/PHY752lectLAPW.pdf ]. Though, it would best to try running it locally on a Linux computer. If you don't have a dedicated Linux computer, but have a flash or external drive, you could try it on a live USB Linux operating system [ https://en.wikipedia.org/wiki/Live_USB ]. I don't think there is a software limit on the maximum number of rows in one column. However, if you know tcl programming, you can look more closely in the file xcrysden-1.5.60/Tcl/fs/wnFS.tcl as it looks like it does the rendering of the "Select bands" window. On 9/22/2015 8:18 PM, lung Fermin wrote: > Thanks for all the suggestions. I now recompile the .f files on the > cluster instead on the system I installed in virtualbox and things works! > > However, there is still a minor problem. When rendering the FS, in the > pop up window for selecting the bands to plot, the boxes of choice are > overlapping (please refer the picture in this link: > https://drive.google.com/file/d/0B2YMkxx81z7lS2ZGeTctb01lRVdiRXA3bzJCNGxoVWdSTDlz/view?usp=sharing). > I can't see the bands properly and do the selection. I guess there is > some limitation on the max. no. of rows shown in one column? Are there > anyway I can adjust this? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151002/09a4c9b2/attachment.htm From dstrubbe at civet.berkeley.edu Fri Oct 2 22:39:30 2015 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Fri, 2 Oct 2015 16:39:30 -0400 Subject: [xcrysden] XCrySDen now available in MacPorts Message-ID: Hello all, I would like to announce that I have successfully included XCrySDen version 1.5.60 in the MacPorts package manager (www.macports.org) as of today: https://www.macports.org/ports.php?by=name&substr=xcrysden. This link can be added to the page at http://www.xcrysden.org/Download.html#__toc__1. The code can be installed by "port install xcrysden +x11". Previously XCrySDen could not be included properly in MacPorts because the code only worked with a very old version of Mesa on MacOS; however now it can work with Mesa 10.5.4 (as well as with system OpenGL libraries), according to my tests on Yosemite (OSX 10.10.5). The key was the patch described by Hideyuki Kamisaka on Nov. 5, 2014 in this email list, namely setting "-accum false" in the Togl options. I have in the process also produced an updated version of the file system/Make.macosx-x11 for Make.sys, which had been produced many years ago and would not work on recent versions of MacOS. The new one is included below for any users who wish to build from source on MacOS. Tone, I recommend you replace the old file with this one in the next release. Best, David Strubbe ######################################################################### # System-dependent definitions for Mac OS X # # David Strubbe 1 Oct. 2015 # Tested on Yosemite, OSX 10.10.5 # ----------------------------------------------------------------------- # # !!! EDIT ACCORDING TO YOUR OWN NEEDS !!! # In particular, you must specify: # FC (Fortran compiler) # TK_LIB and TCL_LIB (location of Tcl and Tk) # FFTW3_LIB and FFTW3_INCDIR (location of FFTW3 library and header) # Use of the MacPorts package manager (www.macports.org) and 'port install xcrysden' is recommended # as an easier approach than using this file to build from source. # MacPorts can be used to obtain the dependencies: port install gcc5 tcl tk +x11 fftw-3 # tk must have +x11 variant; a different version of gcc can be used instead if desired. # X11 and OpenGL from system are being used. #------------------------------------------------------------------------ # compilers & flags #------------------------------------------------------------------------ CFLAGS = -O3 -DUSE_INTERP_RESULT CC = cc FFLAGS = -O3 FC = gfortran-mp-5 #------------------------------------------------------------------------ # X-libraries & include files #------------------------------------------------------------------------ X_LIB = /opt/X11/lib/libXmu.dylib /opt/X11/lib/libX11.dylib /opt/X11/lib/libXext.dylib X_INCDIR = -I/opt/X11/include COMPILE_TCLTK = no # generally will not compile without passing args to configure script COMPILE_FFTW = no # generally will not compile without passing args to configure script COMPILE_MESA = no COMPILE_MESCHACH = no #------------------------------------------------------------------------ # Libraries and include files #------------------------------------------------------------------------ TK_LIB = /opt/local/lib/libtk.dylib TCL_LIB = /opt/local/lib/libtcl.dylib GLU_LIB = /opt/X11/lib/libGLU.dylib GL_LIB = /opt/X11/lib/libGL.dylib FFTW3_LIB = /opt/local/lib/libfftw3.dylib GL_INCDIR = -I/opt/X11/include FFTW3_INCDIR = -I/opt/local/include -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151002/97bad27e/attachment.htm From tone.kokalj at ijs.si Tue Oct 6 13:11:58 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 06 Oct 2015 13:11:58 +0200 Subject: [xcrysden] Difficulties in selecting the bands to render the Fermi surface in WIEN2k interface In-Reply-To: References: Message-ID: <1444129918.8807.26.camel@ijs.si> On Wed, 2015-09-30 at 17:07 +0800, lung Fermin wrote: > Dear Xcrysden community, > > I want to render the Fermi surface of a system containing a few > hundreds of atoms. The case.output1 from WIEN2k gives 2813 bands. In > the pop up window of "Select bands" in Xcrysden, the tick boxes of > different band numbers are merely resolved and they appears like > Band number: 2185 > Band number: 1 > Band number: 2186 > Band number: 2 I was able to reproduce this problem when the number of bands is several thousands. It seems to be some issue of the Tk (it cannot handle so many check-buttons in a single row). I made a workaround: when the numbers of bands is larger than 500, the band-selection buttons are now arranged in a more convenient matrix form. Please try the current fix and let me know if it works for you, i.e., copy the attached file "wnFS.tcl" into $XCRYSDEN_TOPDIR/Tcl/fs/ subdirectory. Best regards, -- 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: wnFS.tcl Type: text/x-tcl Size: 10782 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20151006/d5f9cb5d/attachment.tcl From tone.kokalj at ijs.si Tue Oct 6 13:16:39 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 06 Oct 2015 13:16:39 +0200 Subject: [xcrysden] warnings from gfortran 5.2.0 In-Reply-To: References: Message-ID: <1444130199.8807.29.camel@ijs.si> On Thu, 2015-10-01 at 12:30 -0400, David Strubbe wrote: > Hello Tone et al., > > I get the following warnings in xcrysden 1.5.60 when compiling the > file gengeom.f with gfortran version 5.2.0 on my Mac. Does this > represent a problem in the code? No, it does not. If you want to get rid of this warning, change the definition of B33(3,4) to B33(3,*) in gengeom.f at: SUBROUTINE GETCCOOR(A33,B33,BROW,X,Y,Z,XC,YC,ZC,NA,NATR) include 'param.inc' REAL*8 B33(3,4), ... ... Regards, -- 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 Oct 6 13:22:20 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 06 Oct 2015 13:22:20 +0200 Subject: [xcrysden] XCrySDen now available in MacPorts In-Reply-To: References: Message-ID: <1444130540.8807.33.camel@ijs.si> On Fri, 2015-10-02 at 16:39 -0400, David Strubbe wrote: > Hello all, > > I would like to announce that I have successfully included XCrySDen > version 1.5.60 in the MacPorts package manager (www.macports.org) as > of today: https://www.macports.org/ports.php?by=name&substr=xcrysden. > This link can be added to the page at > http://www.xcrysden.org/Download.html#__toc__1.?; The code can be > installed by "port install xcrysden +x11". Dear David, This is absolutely fantastic news! Thank you very much for your effort !!! I will put a link to it from xcrysden webpage and will also introduce all your patches into the source code. Best regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From ferminlung at gmail.com Wed Oct 7 10:57:12 2015 From: ferminlung at gmail.com (lung Fermin) Date: Wed, 7 Oct 2015 16:57:12 +0800 Subject: [xcrysden] Difficulties in selecting the bands to render the Fermi surface in WIEN2k interface In-Reply-To: <1444129918.8807.26.camel@ijs.si> References: <1444129918.8807.26.camel@ijs.si> Message-ID: Thanks Dr. Kokalj! It works now. Regards, Fermin 2015-10-06 19:11 GMT+08:00 Tone Kokalj : > On Wed, 2015-09-30 at 17:07 +0800, lung Fermin wrote: > > Dear Xcrysden community, > > > > I want to render the Fermi surface of a system containing a few > > hundreds of atoms. The case.output1 from WIEN2k gives 2813 bands. In > > the pop up window of "Select bands" in Xcrysden, the tick boxes of > > different band numbers are merely resolved and they appears like > > Band number: 2185 > > Band number: 1 > > Band number: 2186 > > Band number: 2 > > I was able to reproduce this problem when the number of bands is > several thousands. It seems to be some issue of the Tk (it cannot > handle so many check-buttons in a single row). > > I made a workaround: when the numbers of bands is larger than 500, the > band-selection buttons are now arranged in a more convenient matrix > form. > > Please try the current fix and let me know if it works for you, i.e., > copy the attached file "wnFS.tcl" into $XCRYSDEN_TOPDIR/Tcl/fs/ > subdirectory. > > Best regards, > -- > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151007/f5f66470/attachment.htm From member at linkedin.com Tue Oct 13 04:15:56 2015 From: member at linkedin.com (Alhassan Shuaibu) Date: Tue, 13 Oct 2015 02:15:56 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Andr=C3=A9_Pereira=2C_voc=C3=AA_poderia_me_a?= =?utf-8?q?dicionar_=C3=A0_sua_rede_do_LinkedIn=3F?= Message-ID: <1269692084.625212.1444702556222.JavaMail.app@lva1-app7947.prod.linkedin.com> Ol?, Andr? Pereira. Fa?a parte da minha rede no LinkedIn. Alhassan Shuaibu -- Aceitar: https://www.linkedin.com/comm/people/invite-accept?mboxid=I6059521648724361216_500&sharedKey=P2SnFnZC&fr=false&invitationId=6059521630021971968&fe=true&trk=eml-comm_invm-b-accept-newinvite&midToken=AQHmrP4eu4YUfw&trkEmail=eml-invite_member_28-null-0-null-null-24lb0q%7Eifoqllxw%7E5u Visualizar o perfil de Alhassan Shuaibu: https://www.linkedin.com/comm/profile/view?id=AAsAAA8iv3kBDIRmacCFkEJzGt41OcZAL4jFsZU&authType=name&authToken=Dgc0&invAcpt=128644874_I6059521648724361216_500&trk=eml-comm_invm-b-name-newinvite&midToken=AQHmrP4eu4YUfw&trkEmail=eml-invite_member_28-null-8-null-null-24lb0q%7Eifoqllxw%7E5u Voc? est? recebendo e-mails sobre Invitation. Cancele a inscri??o clicando aqui: https://www.linkedin.com/e/v2?e=24lb0q-ifoqllxw-5u&t=lun&midToken=AQHmrP4eu4YUfw&tracking=eml-comm_invm-f-unsub-newinvite&ek=invite_member_28&loid=AQE-A5-Z3VzzywAAAVBe-5AXV9NqyIPi7-WUgRBx2824fgs2F0zTwayeY3RDu3J5p17u_nxBrAEWfJgPkE4&eid=24lb0q-ifoqllxw-5u. Este e-mail foi enviado para Andr? Pereira XCrysden (Estudante na Universidade Estadual Paulista 'J?lio de Mesquita Filho'). Saiba por que inclu?mos isso neste link: https://www.linkedin.com/e/v2?e=24lb0q-ifoqllxw-5u&a=customerServiceUrl&midToken=AQHmrP4eu4YUfw&ek=invite_member_28&articleId=4788 © 2015 LinkedIn Ireland Limited. LinkedIn, a logomarca do LinkedIn e InMail s?o marcas registradas da LinkedIn Corporation nos Estados Unidos e/ou em outros pa?ses. Todos os direitos reservados. LinkedIn ? um nome comercial registrado da LinkedIn Ireland Limited. Registrada na Irlanda como uma empresa Privada e Ltda. Registro n?mero 477441. Registrada em: 70 Sir John Rogersons Quay, Dublin 2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151013/09147a27/attachment-0001.htm From member at linkedin.com Sat Oct 17 20:13:39 2015 From: member at linkedin.com (mir ali) Date: Sat, 17 Oct 2015 18:13:39 +0000 (UTC) Subject: [xcrysden] =?utf-8?q?Andr=C3=A9_Pereira=2C_voc=C3=AA_poderia_me_a?= =?utf-8?q?dicionar_=C3=A0_sua_rede_do_LinkedIn=3F?= Message-ID: <446673570.500211.1445105619426.JavaMail.app@lva1-app6753.prod.linkedin.com> André Pereira،

أرغب في إضافتك إلى شبكتي المهنية على LinkedIn
.
- mir Aceitar: https://www.linkedin.com/comm/people/invite-accept?mboxid=I6061212216688992256_500&sharedKey=CWLU14V5&fr=false&invitationId=6021244006741086208&fe=true&trk=eml-comm_invm-b-accept-newinvite&midToken=AQHmrP4eu4YUfw&trkEmail=eml-invite_member_28-null-0-null-null-24lb0q%7Eifveknkj%7E2i Visualizar o perfil de mir ali: https://www.linkedin.com/comm/profile/view?id=AAsAABPcAxcBRVU8QHnHymKYEZNdwIfzSG8EypA&authType=name&authToken=AfeT&invAcpt=128644874_I6061212216688992256_500&trk=eml-comm_invm-b-name-newinvite&midToken=AQHmrP4eu4YUfw&trkEmail=eml-invite_member_28-null-8-null-null-24lb0q%7Eifveknkj%7E2i Voc? est? recebendo e-mails sobre Invitation. Cancele a inscri??o clicando aqui: https://www.linkedin.com/e/v2?e=24lb0q-ifveknkj-2i&t=lun&midToken=AQHmrP4eu4YUfw&tracking=eml-comm_invm-f-unsub-newinvite&ek=invite_member_28&loid=AQFKNh-Vvw8qEgAAAVB3AdHHphWJawluY0jivJKyiTDyizD8tAvaQ91oIKYHM3winF2XDvLCQ_PCNy3cxtQ&eid=24lb0q-ifveknkj-2i. Este e-mail foi enviado para Andr? Pereira XCrysden (Estudante na Universidade Estadual Paulista 'J?lio de Mesquita Filho'). Saiba por que inclu?mos isso neste link: https://www.linkedin.com/e/v2?e=24lb0q-ifveknkj-2i&a=customerServiceUrl&midToken=AQHmrP4eu4YUfw&ek=invite_member_28&articleId=4788 © 2015 LinkedIn Ireland Limited. LinkedIn, a logomarca do LinkedIn e InMail s?o marcas registradas da LinkedIn Corporation nos Estados Unidos e/ou em outros pa?ses. Todos os direitos reservados. LinkedIn ? um nome comercial registrado da LinkedIn Ireland Limited. Registrada na Irlanda como uma empresa Privada e Ltda. Registro n?mero 477441. Registrada em: 70 Sir John Rogersons Quay, Dublin 2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151017/9d6ac561/attachment-0001.htm From liyincumt at gmail.com Tue Oct 27 09:19:21 2015 From: liyincumt at gmail.com (liyincumt at gmail.com) Date: Tue, 27 Oct 2015 10:19:21 +0200 Subject: [xcrysden] How to display a whole molecule in unit cell with good connection? Message-ID: <2015102710192009085257@gmail.com> Dear Xcrysden developers, Thanks for sharing this excellent visualization software for free! I am using xcrysden to visualize the input and output files of quantum espresso. I have a problem with visualization of crystals. Due to the presence of periodic boundary condition, some of atoms which are outside of the boundary look like being non-covalently connected. Is it possible to display a whole molecule with good covalent connections in Xcrysden. Thank you very much! Best Regards, Yin Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151027/2b9422b0/attachment.htm From matic.poberznik at gmail.com Tue Oct 27 11:14:45 2015 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Tue, 27 Oct 2015 11:14:45 +0100 Subject: [xcrysden] How to display a whole molecule in unit cell with good connection? In-Reply-To: <2015102710192009085257@gmail.com> References: <2015102710192009085257@gmail.com> Message-ID: <562F4E95.1000808@gmail.com> Dear Yin, If I understood your problem correctly, I think the best solution is to open the Modify menu and choose the Atomic Radius (Shift+R) option. Once there you can modify the Covalent Radius and Connectivity Factor for each atom type to suit your needs. In order to load your custom parameters when xcrysden starts you should add a line in $HOME/.xcrysden/custom-definitions file, an example: # # this line changes the default atomic radius for aluminum to 1.6 # set atmRad(13) 1.6 The custom definitions file is described on this link: http://www.xcrysden.org/doc/custom.html If the problem stems from the periodic boundary conditions then first try the different display modes of unit cells, i. e. click the button for the display of the translational asymmetric unit (bottom center of the screen). Then try Modify => Number of units drawn (Shift+N), if the covalent radius is correct at least some molecules should be displayed correctly. If that is not enough let me know, there is one more workaround but it is a bit more complicated. Best regards, Matic On 10/27/2015 09:19 AM, liyincumt at gmail.com wrote: > Dear Xcrysden developers, > > Thanks for sharing this excellent visualization software for free! > I am using xcrysden to visualize the input and output files of quantum > espresso. I have a problem with visualization of crystals. Due to the > presence of periodic boundary condition, some of atoms which are > outside of the boundary look like being non-covalently connected. Is > it possible to display a whole molecule with good covalent connections > in Xcrysden. > > Thank you very much! > > Best Regards, > Yin > > ------------------------------------------------------------------------ > Dr. Yin Li > Department of Biophysics,Medical School, University of Pecs, > No.12 Szigeti Street, Pecs, H-7624, HUNGARY > Phone: +36-72-535271/36271 > > > _______________________________________________ > 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/20151027/458919f7/attachment.htm From liyincumt at gmail.com Tue Oct 27 11:25:31 2015 From: liyincumt at gmail.com (liyincumt at gmail.com) Date: Tue, 27 Oct 2015 12:25:31 +0200 Subject: [xcrysden] How to display a whole molecule in unit cell with good connection? References: <2015102710192009085257@gmail.com>, <562F4E95.1000808@gmail.com> Message-ID: <2015102712253113411864@gmail.com> Dear Matic, Thanks for your kind help! After setting the number of units drawn, some molecules inside the supercell are displayed correctly. But there are too many molecules inside the supercell. The figure would be hardly accepted by journal. Is it possible to just display the molecules correctly in one unit cell? I have tried buttons of the display which are located in the bottom center of the screen, none of them can work properly. Best Regards, Yin Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 From: Matic Poberznik Date: 2015-10-27 12:14 To: XCrySDen mailing list Subject: Re: [xcrysden] How to display a whole molecule in unit cell with good connection? Dear Yin, If I understood your problem correctly, I think the best solution is to open the Modify menu and choose the Atomic Radius (Shift+R) option. Once there you can modify the Covalent Radius and Connectivity Factor for each atom type to suit your needs. In order to load your custom parameters when xcrysden starts you should add a line in $HOME/.xcrysden/custom-definitions file, an example: # # this line changes the default atomic radius for aluminum to 1.6 # set atmRad(13) 1.6 The custom definitions file is described on this link: http://www.xcrysden.org/doc/custom.html If the problem stems from the periodic boundary conditions then first try the different display modes of unit cells, i. e. click the button for the display of the translational asymmetric unit (bottom center of the screen). Then try Modify => Number of units drawn (Shift+N), if the covalent radius is correct at least some molecules should be displayed correctly. If that is not enough let me know, there is one more workaround but it is a bit more complicated. Best regards, Matic On 10/27/2015 09:19 AM, liyincumt at gmail.com wrote: Dear Xcrysden developers, Thanks for sharing this excellent visualization software for free! I am using xcrysden to visualize the input and output files of quantum espresso. I have a problem with visualization of crystals. Due to the presence of periodic boundary condition, some of atoms which are outside of the boundary look like being non-covalently connected. Is it possible to display a whole molecule with good covalent connections in Xcrysden. Thank you very much! Best Regards, Yin Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 _______________________________________________ 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/20151027/463edd29/attachment.htm From matic.poberznik at gmail.com Tue Oct 27 13:27:36 2015 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Tue, 27 Oct 2015 13:27:36 +0100 Subject: [xcrysden] How to display a whole molecule in unit cell with good connection? In-Reply-To: <2015102712253113411864@gmail.com> References: <2015102710192009085257@gmail.com>, <562F4E95.1000808@gmail.com> <2015102712253113411864@gmail.com> Message-ID: <562F6DB8.8040403@gmail.com> Modifying this in the pwscf output file is impossible, so I suggest you convert the output file to xsf format using the pwo2xsf.sh tool. It can be found in the Quantum Espresso installation directory in my case it is in /esspreso-5.1.1/PW/tools/pwo2xsf.sh To write the optimized coordinates to the xsf file the syntax would be : bash pwo2xsf.sh -oc name_of_pwout.out > name_of_xsf.xsf Once you have the xsf file I suggest you shift the coordinates of the atoms so that the molecule is in the center of the cell; If the molecule atoms are , for instance, at 0.0, 0.0, 0.0 you should shift them so that the coordinates correspond to 1/2a+1/2b+1/2c where a,b,c are vectors of the unit cell. You should shift all atomic positions accordingly and the result will hopefully be better. Best regards, Matic On 10/27/2015 11:25 AM, liyincumt at gmail.com wrote: > Dear Matic, > > Thanks for your kind help! > After setting the number of units drawn, some molecules inside the > supercell are displayed correctly. But there are too many molecules > inside the supercell. The figure would be hardly accepted by journal. > Is it possible to just display the molecules correctly in one unit > cell? I have tried buttons of the display which are located in the > bottom center of the screen, none of them can work properly. > > Best Regards, > Yin > ------------------------------------------------------------------------ > Dr. Yin Li > Department of Biophysics,Medical School, University of Pecs, > No.12 Szigeti Street, Pecs, H-7624, HUNGARY > Phone: +36-72-535271/36271 > > *From:* Matic Poberznik > *Date:* 2015-10-27 12:14 > *To:* XCrySDen mailing list > *Subject:* Re: [xcrysden] How to display a whole molecule in unit > cell with good connection? > Dear Yin, > > If I understood your problem correctly, I think the best solution > is to open the Modify menu and choose the Atomic Radius (Shift+R) > option. Once there you can modify the Covalent Radius and > Connectivity Factor for each atom type to suit your needs. > > In order to load your custom parameters when xcrysden starts you > should add a line in $HOME/.xcrysden/custom-definitions file, an > example: > > # > # this line changes the default atomic radius for aluminum to 1.6 > # > > set atmRad(13) 1.6 > > The custom definitions file is described on this link: > http://www.xcrysden.org/doc/custom.html > > If the problem stems from the periodic boundary conditions then > first try the different display modes of unit cells, i. e. click > the button for the display of the translational asymmetric unit > (bottom center of the screen). Then try Modify => Number of units > drawn (Shift+N), if the covalent radius is correct at least some > molecules should be displayed correctly. If that is not enough let > me know, there is one more workaround but it is a bit more > complicated. > > Best regards, > > Matic > > > > On 10/27/2015 09:19 AM, liyincumt at gmail.com wrote: >> Dear Xcrysden developers, >> >> Thanks for sharing this excellent visualization software for free! >> I am using xcrysden to visualize the input and output files of >> quantum espresso. I have a problem with visualization of >> crystals. Due to the presence of periodic boundary condition, >> some of atoms which are outside of the boundary look like being >> non-covalently connected. Is it possible to display a whole >> molecule with good covalent connections in Xcrysden. >> >> Thank you very much! >> >> Best Regards, >> Yin >> >> ------------------------------------------------------------------------ >> Dr. Yin Li >> Department of Biophysics,Medical School, University of Pecs, >> No.12 Szigeti Street, Pecs, H-7624, HUNGARY >> Phone: +36-72-535271/36271 >> >> >> _______________________________________________ >> 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 -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151027/ac3d9a42/attachment-0001.htm From liyincumt at gmail.com Tue Oct 27 13:47:37 2015 From: liyincumt at gmail.com (liyincumt at gmail.com) Date: Tue, 27 Oct 2015 14:47:37 +0200 Subject: [xcrysden] How to display a whole molecule in unit cell with good connection? References: <2015102710192009085257@gmail.com>, <562F4E95.1000808@gmail.com>, <2015102712253113411864@gmail.com>, <562F6DB8.8040403@gmail.com> Message-ID: <2015102714473692451475@gmail.com> Dear Matic, Thank you very much for your help! Actually, I don't want to modify the relative distance between atoms and boundaries. I think journals would not accept this. I was thinking on whether Molden could display it properly as the dynamic matrix file can be read by Molden as well. I tried many options in molden but it still can't work. So far I just found material studio (Display style: Default) can display it properly. I wonder whether I can convert quantum espresso files including dynamic matrix file and pwo into cif or any other format which could be read by material studio. Even it can be converted, I am still worried about the loss of the information of the forces on atoms. Best Regards, Yin Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 From: Matic Poberznik Date: 2015-10-27 14:27 To: XCrySDen mailing list Subject: Re: [xcrysden] How to display a whole molecule in unit cell with good connection? Modifying this in the pwscf output file is impossible, so I suggest you convert the output file to xsf format using the pwo2xsf.sh tool. It can be found in the Quantum Espresso installation directory in my case it is in /esspreso-5.1.1/PW/tools/pwo2xsf.sh To write the optimized coordinates to the xsf file the syntax would be : bash pwo2xsf.sh -oc name_of_pwout.out > name_of_xsf.xsf Once you have the xsf file I suggest you shift the coordinates of the atoms so that the molecule is in the center of the cell; If the molecule atoms are , for instance, at 0.0, 0.0, 0.0 you should shift them so that the coordinates correspond to 1/2a+1/2b+1/2c where a,b,c are vectors of the unit cell. You should shift all atomic positions accordingly and the result will hopefully be better. Best regards, Matic On 10/27/2015 11:25 AM, liyincumt at gmail.com wrote: Dear Matic, Thanks for your kind help! After setting the number of units drawn, some molecules inside the supercell are displayed correctly. But there are too many molecules inside the supercell. The figure would be hardly accepted by journal. Is it possible to just display the molecules correctly in one unit cell? I have tried buttons of the display which are located in the bottom center of the screen, none of them can work properly. Best Regards, Yin Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 From: Matic Poberznik Date: 2015-10-27 12:14 To: XCrySDen mailing list Subject: Re: [xcrysden] How to display a whole molecule in unit cell with good connection? Dear Yin, If I understood your problem correctly, I think the best solution is to open the Modify menu and choose the Atomic Radius (Shift+R) option. Once there you can modify the Covalent Radius and Connectivity Factor for each atom type to suit your needs. In order to load your custom parameters when xcrysden starts you should add a line in $HOME/.xcrysden/custom-definitions file, an example: # # this line changes the default atomic radius for aluminum to 1.6 # set atmRad(13) 1.6 The custom definitions file is described on this link: http://www.xcrysden.org/doc/custom.html If the problem stems from the periodic boundary conditions then first try the different display modes of unit cells, i. e. click the button for the display of the translational asymmetric unit (bottom center of the screen). Then try Modify => Number of units drawn (Shift+N), if the covalent radius is correct at least some molecules should be displayed correctly. If that is not enough let me know, there is one more workaround but it is a bit more complicated. Best regards, Matic On 10/27/2015 09:19 AM, liyincumt at gmail.com wrote: Dear Xcrysden developers, Thanks for sharing this excellent visualization software for free! I am using xcrysden to visualize the input and output files of quantum espresso. I have a problem with visualization of crystals. Due to the presence of periodic boundary condition, some of atoms which are outside of the boundary look like being non-covalently connected. Is it possible to display a whole molecule with good covalent connections in Xcrysden. Thank you very much! Best Regards, Yin Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 _______________________________________________ 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 -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151027/65837f9a/attachment.htm From matic.poberznik at gmail.com Tue Oct 27 15:51:52 2015 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Tue, 27 Oct 2015 15:51:52 +0100 Subject: [xcrysden] How to display a whole molecule in unit cell with good connection? In-Reply-To: <2015102714473692451475@gmail.com> References: <2015102710192009085257@gmail.com>, <562F4E95.1000808@gmail.com>, <2015102712253113411864@gmail.com>, <562F6DB8.8040403@gmail.com> <2015102714473692451475@gmail.com> Message-ID: <562F8F88.2060309@gmail.com> >>Actually, I don't want to modify the relative distance between atoms and boundaries. I think journals >>would not accept this. I think that modifying the relative distance, as far as the figure is concerned, should not be a problem. The only limitation I see is that all atoms defined in the ATOMIC_POSITIONS card should be translated by the same vector; due to periodicity both structures are equal, what will change is the way the program reads the structure. Without seeing the actual output I am assuming that your optimized coordinates contain atoms with negative values in coordinates, for example let's say the initial positions were 0.0, 0.0, 0.0, but after optimization they changed to -0.1,-0.1,-0.1, so assuming a cubic structure of length "1" the program draws the optimized coordinates at 0.9, 0.9, 0.9 (equivalent position in the crystal cell), the result being the molecule "breaks" in the unit cell. By shifiting all positions (to positive values) by a specific vector this problem should disappear and as stated both structures are equivalent, so this representation should be acceptable. Both the xsf and pwscf formats are supported by openbabel, so converting it to other formats shouldn't be a problem, though I have no experience regarding the dynamic matrix, so I really have no idea if information will be lost or not. Best regards, Matic On 10/27/2015 01:47 PM, liyincumt at gmail.com wrote: > Dear Matic, > > Thank you very much for your help! > Actually, I don't want to modify the relative distance between atoms > and boundaries. I think journals would not accept this. I was thinking > on whether Molden could display it properly as the dynamic matrix file > can be read by Molden as well. I tried many options in molden but it > still can't work. So far I just found material studio (Display style: > Default) can display it properly. > I wonder whether I can convert quantum espresso files including > dynamic matrix file and pwo into cif or any other format which could > be read by material studio. Even it can be converted, I am still > worried about the loss of the information of the forces on atoms. > > Best Regards, > Yin > > ------------------------------------------------------------------------ > Dr. Yin Li > Department of Biophysics,Medical School, University of Pecs, > No.12 Szigeti Street, Pecs, H-7624, HUNGARY > Phone: +36-72-535271/36271 > > *From:* Matic Poberznik > *Date:* 2015-10-27 14:27 > *To:* XCrySDen mailing list > *Subject:* Re: [xcrysden] How to display a whole molecule in unit > cell with good connection? > Modifying this in the pwscf output file is impossible, so I > suggest you convert the output file to xsf format using the > pwo2xsf.sh tool. It can be found in the Quantum Espresso > installation directory in my case it is in > > /esspreso-5.1.1/PW/tools/pwo2xsf.sh > > To write the optimized coordinates to the xsf file the syntax > would be : > > bash pwo2xsf.sh -oc name_of_pwout.out > name_of_xsf.xsf > > Once you have the xsf file I suggest you shift the coordinates of > the atoms so that the molecule is in the center of the cell; If > the molecule atoms are , for instance, at 0.0, 0.0, 0.0 you should > shift them so that the coordinates correspond to 1/2a+1/2b+1/2c > where a,b,c are vectors of the unit cell. You should shift all > atomic positions accordingly and the result will hopefully be better. > > Best regards, > > Matic > > On 10/27/2015 11:25 AM, liyincumt at gmail.com wrote: >> Dear Matic, >> >> Thanks for your kind help! >> After setting the number of units drawn, some molecules inside >> the supercell are displayed correctly. But there are too many >> molecules inside the supercell. The figure would be hardly >> accepted by journal. >> Is it possible to just display the molecules correctly in one >> unit cell? I have tried buttons of the display which are located >> in the bottom center of the screen, none of them can work properly. >> >> Best Regards, >> Yin >> ------------------------------------------------------------------------ >> Dr. Yin Li >> Department of Biophysics,Medical School, University of Pecs, >> No.12 Szigeti Street, Pecs, H-7624, HUNGARY >> Phone: +36-72-535271/36271 >> >> *From:* Matic Poberznik >> *Date:* 2015-10-27 12:14 >> *To:* XCrySDen mailing list >> *Subject:* Re: [xcrysden] How to display a whole molecule in >> unit cell with good connection? >> Dear Yin, >> >> If I understood your problem correctly, I think the best >> solution is to open the Modify menu and choose the Atomic >> Radius (Shift+R) option. Once there you can modify the >> Covalent Radius and Connectivity Factor for each atom type to >> suit your needs. >> >> In order to load your custom parameters when xcrysden starts >> you should add a line in $HOME/.xcrysden/custom-definitions >> file, an example: >> >> # >> # this line changes the default atomic radius for aluminum to 1.6 >> # >> >> set atmRad(13) 1.6 >> >> The custom definitions file is described on this link: >> http://www.xcrysden.org/doc/custom.html >> >> If the problem stems from the periodic boundary conditions >> then first try the different display modes of unit cells, i. >> e. click the button for the display of the translational >> asymmetric unit (bottom center of the screen). Then try >> Modify => Number of units drawn (Shift+N), if the covalent >> radius is correct at least some molecules should be displayed >> correctly. If that is not enough let me know, there is one >> more workaround but it is a bit more complicated. >> >> Best regards, >> >> Matic >> >> >> >> On 10/27/2015 09:19 AM, liyincumt at gmail.com wrote: >>> Dear Xcrysden developers, >>> >>> Thanks for sharing this excellent visualization software for >>> free! >>> I am using xcrysden to visualize the input and output files >>> of quantum espresso. I have a problem with visualization of >>> crystals. Due to the presence of periodic boundary >>> condition, some of atoms which are outside of the boundary >>> look like being non-covalently connected. Is it possible to >>> display a whole molecule with good covalent connections in >>> Xcrysden. >>> >>> Thank you very much! >>> >>> Best Regards, >>> Yin >>> >>> ------------------------------------------------------------------------ >>> Dr. Yin Li >>> Department of Biophysics,Medical School, University of Pecs, >>> No.12 Szigeti Street, Pecs, H-7624, HUNGARY >>> Phone: +36-72-535271/36271 >>> >>> >>> _______________________________________________ >>> 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 > > -- > Matic Poberznik > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151027/05a0f4b0/attachment-0001.htm From liyincumt at gmail.com Tue Oct 27 15:04:36 2015 From: liyincumt at gmail.com (liyincumt at gmail.com) Date: Tue, 27 Oct 2015 16:04:36 +0200 Subject: [xcrysden] How to display a whole molecule in unit cell with good connection? References: <2015102710192009085257@gmail.com>, <562F4E95.1000808@gmail.com>, <2015102712253113411864@gmail.com>, <562F6DB8.8040403@gmail.com>, <2015102714473692451475@gmail.com>, <562F8F88.2060309@gmail.com> Message-ID: <2015102716043598800983@gmail.com> Dear Matic, Thanks for your patient explanation! There are only two very small negative values in the final coordinates. My crystal is a kind of amino acid. In one unit cell, there are two molecules. In my input file, there is no negative values in atomic coordinates, but the boundary still can apparently break the chemical bonds. Input: &CONTROL title = '2015971-Asparticacid' calculation = 'vc-relax' restart_mode = 'from_scratch' outdir = '/home/yinli/aspartic_acid/vc-relax/test1' , wfcdir = '/home/yinli/aspartic_acid/vc-relax/test1' , pseudo_dir = '/home/yinli/espresso-5.1.1/pseudo/' , prefix = '2015971-Asparticacid' etot_conv_thr = 5.0d-7 , forc_conv_thr = 5.0d-4 , nstep = 1500 / &SYSTEM ibrav = -12 celldm(1) = 9.663114537963445 celldm(2) = 1.350523125061113, celldm(3) = 1.484795150092891 celldm(5) = -0.185014881113262 nat = 32 ntyp = 4 ecutwfc = 60 ecutrho = 600 occupations = 'fixed' / &ELECTRONS electron_maxstep = 200 conv_thr = 1.0D-10 diago_thr_init = 1e-4 startingpot = 'atomic' startingwfc = 'atomic' mixing_mode = 'plain' mixing_beta = 0.5 mixing_ndim = 8 diagonalization = 'david' / &IONS ion_dynamics = 'bfgs' / &CELL cell_dynamics = 'bfgs' / ATOMIC_SPECIES H 1.00794 H.blyp-van_ak.UPF C 12.01070 C.blyp-van_ak.UPF N 14.00670 N.blyp-van_ak.UPF O 15.99940 O.blyp-van_ak.UPF ATOMIC_POSITIONS crystal N 0.858300000000000 0.978000000000000 0.316200000000000 H 0.029000000000000 0.914000000000000 0.388000000000000 H 0.810000000000000 0.100000000000000 0.389000000000000 H 0.900000000000000 0.022000000000000 0.188000000000000 C 0.634800000000000 0.836000000000000 0.295200000000000 C 0.560500000000000 0.796000000000000 0.478600000000000 C 0.715600000000000 0.644000000000000 0.219800000000000 C 0.793000000000000 0.659000000000000 0.037800000000000 O 0.749700000000000 0.784000000000000 0.609500000000000 O 0.318400000000000 0.771000000000000 0.481700000000000 O 0.002000000000000 0.593000000000000 0.008500000000000 O 0.612500000000000 0.744000000000000 0.916100000000000 H 0.468000000000000 0.898000000000000 0.207000000000000 H 0.881000000000000 0.578000000000000 0.313000000000000 H 0.541000000000000 0.556000000000000 0.207000000000000 H 0.679000000000000 0.750000000000000 0.797000000000000 N 0.141700000000000 0.478000000000000 0.683800000000000 H 0.971000000000000 0.414000000000000 0.612000000000000 H 0.190000000000000 0.600000000000000 0.611000000000000 H 0.100000000000000 0.522000000000000 0.812000000000000 C 0.365200000000000 0.336000000000000 0.704800000000000 C 0.439500000000000 0.296000000000000 0.521400000000000 C 0.284400000000000 0.144000000000000 0.780200000000000 C 0.207000000000000 0.159000000000000 0.962200000000000 O 0.250300000000000 0.284000000000000 0.390500000000000 O 0.681600000000000 0.271000000000000 0.518300000000000 O 0.998000000000000 0.093000000000000 0.991500000000000 O 0.387500000000000 0.244000000000000 0.083900000000000 H 0.532000000000000 0.398000000000000 0.793000000000000 H 0.119000000000000 0.078000000000000 0.687000000000000 H 0.459000000000000 0.056000000000000 0.793000000000000 H 0.321000000000000 0.250000000000000 0.203000000000000 K_POINTS automatic 3 2 2 0 0 0 Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151027/2e900507/attachment.htm From tone.kokalj at ijs.si Tue Oct 27 17:09:00 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 27 Oct 2015 17:09:00 +0100 Subject: [xcrysden] How to display a whole molecule in unit cell with good connection? In-Reply-To: <2015102716043598800983@gmail.com> References: <2015102710192009085257@gmail.com>, <562F4E95.1000808@gmail.com> , <2015102712253113411864@gmail.com>, <562F6DB8.8040403@gmail.com> , <2015102714473692451475@gmail.com>, <562F8F88.2060309@gmail.com> <2015102716043598800983@gmail.com> Message-ID: <1445962140.11782.79.camel@ijs.si> On Tue, 2015-10-27 at 16:04 +0200, liyincumt at gmail.com wrote: > My crystal is a kind of amino acid. In one unit cell, > there are two molecules. The problem is that you did not specify the two molecules in "contiguous" manner, but instead all your atom-coordinates are "chopped" inside the [0-1] range. Hence some O and H atoms are displaced by a lattice vector with respect to a parent molecule. All you need to do is to shift the "displaced" atoms back by a lattice vector. Because your coordinates are in crystal units, this means that you need to subtract by "1" the right coordinate(s). I have moved a few atoms; compare the attached file with your file. There are few more to be moved ... look at the structure with xcrysden and you will easily recognise which atoms needs to be moved (this can be facilitated with the "Select Atom" button; the displayed ID is the sequential number of the atom, provided you selected the "Display->Unit of Repetition->Translational Asymmetric unit" display-mode. Best regards, -- 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 -------------- next part -------------- &CONTROL title = '2015971-Asparticacid' calculation = 'vc-relax' restart_mode = 'from_scratch' outdir = '/home/yinli/aspartic_acid/vc-relax/test1' , wfcdir = '/home/yinli/aspartic_acid/vc-relax/test1' , pseudo_dir = '/home/yinli/espresso-5.1.1/pseudo/' , prefix = '2015971-Asparticacid' etot_conv_thr = 5.0d-7 , forc_conv_thr = 5.0d-4 , nstep = 1500 / &SYSTEM ibrav = -12 celldm(1) = 9.663114537963445 celldm(2) = 1.350523125061113, celldm(3) = 1.484795150092891 celldm(5) = -0.185014881113262 nat = 32 ntyp = 4 ecutwfc = 60 ecutrho = 600 occupations = 'fixed' / &ELECTRONS electron_maxstep = 200 conv_thr = 1.0D-10 diago_thr_init = 1e-4 startingpot = 'atomic' startingwfc = 'atomic' mixing_mode = 'plain' mixing_beta = 0.5 mixing_ndim = 8 diagonalization = 'david' / &IONS ion_dynamics = 'bfgs' / &CELL cell_dynamics = 'bfgs' / ATOMIC_SPECIES H 1.00794 H.blyp-van_ak.UPF C 12.01070 C.blyp-van_ak.UPF N 14.00670 N.blyp-van_ak.UPF O 15.99940 O.blyp-van_ak.UPF ATOMIC_POSITIONS crystal N 0.858300000000000 0.978000000000000 0.316200000000000 H 0.029000000000000 0.914000000000000 0.388000000000000 H 0.810000000000000 0.100000000000000 0.389000000000000 H 0.900000000000000 0.022000000000000 0.188000000000000 C 0.634800000000000 0.836000000000000 0.295200000000000 C 0.560500000000000 0.796000000000000 0.478600000000000 C 0.715600000000000 0.644000000000000 0.219800000000000 C 0.793000000000000 0.659000000000000 0.037800000000000 O 0.749700000000000 0.784000000000000 0.609500000000000 O 0.318400000000000 0.771000000000000 0.481700000000000 O 0.002000000000000 0.593000000000000 0.008500000000000 O 0.612500000000000 0.744000000000000 -0.083900000000000 H 0.468000000000000 0.898000000000000 0.207000000000000 H 0.881000000000000 0.578000000000000 0.313000000000000 H 0.541000000000000 0.556000000000000 0.207000000000000 H 0.679000000000000 0.750000000000000 -0.203000000000000 N 0.141700000000000 0.478000000000000 0.683800000000000 H -0.029000000000000 0.414000000000000 0.612000000000000 H 0.190000000000000 0.600000000000000 0.611000000000000 H 0.100000000000000 0.522000000000000 0.812000000000000 C 0.365200000000000 0.336000000000000 0.704800000000000 C 0.439500000000000 0.296000000000000 0.521400000000000 C 0.284400000000000 0.144000000000000 0.780200000000000 C 0.207000000000000 0.159000000000000 0.962200000000000 O 0.250300000000000 0.284000000000000 0.390500000000000 O 0.681600000000000 0.271000000000000 0.518300000000000 O 0.998000000000000 0.093000000000000 0.991500000000000 O 0.387500000000000 0.244000000000000 0.083900000000000 H 0.532000000000000 0.398000000000000 0.793000000000000 H 0.119000000000000 0.078000000000000 0.687000000000000 H 0.459000000000000 0.056000000000000 0.793000000000000 H 0.321000000000000 0.250000000000000 0.203000000000000 K_POINTS automatic 3 2 2 0 0 0 From muthu.physicsmath at gmail.com Wed Oct 28 02:51:43 2015 From: muthu.physicsmath at gmail.com (Muthu V) Date: Wed, 28 Oct 2015 07:21:43 +0530 Subject: [xcrysden] Band Plotting Message-ID: Dear all I am using QE for simulation and trying to plot band structure. i wan to plot band structure using Xcrysden. i do not have crystal package and i have only Xcrysden. it is possible? (without crystal ) Thank you *---------------------------------------------* *Muthu.V Material Science Group* *Indira Gandhi Center for Atomic Research * *Kalpakkam, India **---------------------------------------------* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151028/1e012bfa/attachment.htm From fink at snaggledworks.com Wed Oct 28 03:06:16 2015 From: fink at snaggledworks.com (Hanspeter Niederstrasser) Date: Tue, 27 Oct 2015 21:06:16 -0500 Subject: [xcrysden] XCrySDen now available in MacPorts Message-ID: <56302D98.4030903@snaggledworks.com> > # Use of the MacPorts package manager (www.macports.org) and 'port install > xcrysden' is recommended > # as an easier approach than using this file to build from source. Please do not introduce MacPortisms into the main source. It's like making the default Linux Makefile force specific DistroXYZ conventions on all Linux users that then have to be patched out. > FC = gfortran-mp-5 > TK_LIB = /opt/local/lib/libtk.dylib > TCL_LIB = /opt/local/lib/libtcl.dylib > FFTW3_LIB = /opt/local/lib/libfftw3.dylib > FFTW3_INCDIR = -I/opt/local/include Those are all MacPorts paths that will only exist on a limited number of OS X systems (and in fact are not guaranteed to exist on all MacPorts locations if the user installed in a separate path). Maybe call the file Make.macosx-macports instead if those paths are kept. The following changes to David's Make.macosx-x11 makes it more portable. The only option that really needs to be provied by the user is LIBPREFIX, which sets the root location of 3rd party libraries (TclTk, fftw3) (and should not be confused with $prefix which sets the xcrysden install location). The file doesn't even need to be modified. LIBPREFIX can be passed directly to the make command: make xcrysden LIBPREFIX=/my/libpath and any other VAR changes can similarly be passed on the 'make' command (like FC=gfortran-identifier-5) if really needed. ---- 8< ---- 8< ---- 8< ---- 8< ---- --- Make.macosx-x11-orig 2015-10-26 05:52:29.000000000 -0500 +++ Make.macosx-x11 2015-10-27 20:52:57.000000000 -0500 @@ -7,19 +7,15 @@ # # !!! EDIT ACCORDING TO YOUR OWN NEEDS !!! # In particular, you must specify: +# LIBPREFIX (root directory for third party [Tcl/Tk & FFTW3] libraries) + +# The following can also be modified as needed: # FC (Fortran compiler) # TK_LIB and TCL_LIB (location of Tcl and Tk) # FFTW3_LIB and FFTW3_INCDIR (location of FFTW3 library and header) -# Use of the MacPorts package manager (www.macports.org) and 'port install -xcrysden' is recommended -# as an easier approach than using this file to build from source. -# MacPorts can be used to obtain the dependencies: port install gcc5 tcl tk -+x11 fftw-3 -# tk must have +x11 variant; a different version of gcc can be used instead -if desired. - # X11 and OpenGL from system are being used. +# Change GLU_LIB, GL_LIB and GL_INCDIR if not using the system GL #------------------------------------------------------------------------ # compilers & flags @@ -27,7 +23,7 @@ CFLAGS = -O3 -DUSE_INTERP_RESULT CC = cc FFLAGS = -O3 -FC = gfortran-mp-5 +FC = gfortran #------------------------------------------------------------------------ # X-libraries & include files @@ -45,12 +41,15 @@ # Libraries and include files #------------------------------------------------------------------------ -TK_LIB = /opt/local/lib/libtk.dylib -TCL_LIB = /opt/local/lib/libtcl.dylib +LIBPREFIX = +LIBDIR = $(LIBPREFIX)/lib +INCDIR = $(LIBPREFIX)/include + +TK_LIB = $(LIBDIR)/libtk.dylib +TCL_LIB = $(LIBDIR)/libtcl.dylib GLU_LIB = /opt/X11/lib/libGLU.dylib GL_LIB = /opt/X11/lib/libGL.dylib -FFTW3_LIB = /opt/local/lib/libfftw3.dylib +FFTW3_LIB = $(LIBDIR)/libfftw3.dylib GL_INCDIR = -I/opt/X11/include -FFTW3_INCDIR = -I/opt/local/include - +FFTW3_INCDIR = -I$(INCDIR) ---- 8< ---- 8< ---- 8< ---- 8< ---- Thanks, Hanspeter From liyincumt at gmail.com Tue Oct 27 15:02:48 2015 From: liyincumt at gmail.com (liyincumt at gmail.com) Date: Tue, 27 Oct 2015 16:02:48 +0200 Subject: [xcrysden] How to display a whole molecule in unit cell with good connection? References: <2015102710192009085257@gmail.com>, <562F4E95.1000808@gmail.com>, <2015102712253113411864@gmail.com>, <562F6DB8.8040403@gmail.com>, <2015102714473692451475@gmail.com>, <562F8F88.2060309@gmail.com> Message-ID: <2015102716024755775582@gmail.com> Dear Matic, Thanks for your patient explanation! There are only two very small negative values in the final coordinates. My crystal is a kind of amino acid. In one unit cell, there are two molecules. In my input file, there is no negative values in atomic coordinates, but the boundary still can apparently break the chemical bonds. Input: &CONTROL title = '2015971-Asparticacid' calculation = 'vc-relax' restart_mode = 'from_scratch' outdir = '/home/yinli/aspartic_acid/vc-relax/test1' , wfcdir = '/home/yinli/aspartic_acid/vc-relax/test1' , pseudo_dir = '/home/yinli/espresso-5.1.1/pseudo/' , prefix = '2015971-Asparticacid' etot_conv_thr = 5.0d-7 , forc_conv_thr = 5.0d-4 , nstep = 1500 / &SYSTEM ibrav = -12 celldm(1) = 9.663114537963445 celldm(2) = 1.350523125061113, celldm(3) = 1.484795150092891 celldm(5) = -0.185014881113262 nat = 32 ntyp = 4 ecutwfc = 60 ecutrho = 600 occupations = 'fixed' / &ELECTRONS electron_maxstep = 200 conv_thr = 1.0D-10 diago_thr_init = 1e-4 startingpot = 'atomic' startingwfc = 'atomic' mixing_mode = 'plain' mixing_beta = 0.5 mixing_ndim = 8 diagonalization = 'david' / &IONS ion_dynamics = 'bfgs' / &CELL cell_dynamics = 'bfgs' / ATOMIC_SPECIES H 1.00794 H.blyp-van_ak.UPF C 12.01070 C.blyp-van_ak.UPF N 14.00670 N.blyp-van_ak.UPF O 15.99940 O.blyp-van_ak.UPF ATOMIC_POSITIONS crystal N 0.858300000000000 0.978000000000000 0.316200000000000 H 0.029000000000000 0.914000000000000 0.388000000000000 H 0.810000000000000 0.100000000000000 0.389000000000000 H 0.900000000000000 0.022000000000000 0.188000000000000 C 0.634800000000000 0.836000000000000 0.295200000000000 C 0.560500000000000 0.796000000000000 0.478600000000000 C 0.715600000000000 0.644000000000000 0.219800000000000 C 0.793000000000000 0.659000000000000 0.037800000000000 O 0.749700000000000 0.784000000000000 0.609500000000000 O 0.318400000000000 0.771000000000000 0.481700000000000 O 0.002000000000000 0.593000000000000 0.008500000000000 O 0.612500000000000 0.744000000000000 0.916100000000000 H 0.468000000000000 0.898000000000000 0.207000000000000 H 0.881000000000000 0.578000000000000 0.313000000000000 H 0.541000000000000 0.556000000000000 0.207000000000000 H 0.679000000000000 0.750000000000000 0.797000000000000 N 0.141700000000000 0.478000000000000 0.683800000000000 H 0.971000000000000 0.414000000000000 0.612000000000000 H 0.190000000000000 0.600000000000000 0.611000000000000 H 0.100000000000000 0.522000000000000 0.812000000000000 C 0.365200000000000 0.336000000000000 0.704800000000000 C 0.439500000000000 0.296000000000000 0.521400000000000 C 0.284400000000000 0.144000000000000 0.780200000000000 C 0.207000000000000 0.159000000000000 0.962200000000000 O 0.250300000000000 0.284000000000000 0.390500000000000 O 0.681600000000000 0.271000000000000 0.518300000000000 O 0.998000000000000 0.093000000000000 0.991500000000000 O 0.387500000000000 0.244000000000000 0.083900000000000 H 0.532000000000000 0.398000000000000 0.793000000000000 H 0.119000000000000 0.078000000000000 0.687000000000000 H 0.459000000000000 0.056000000000000 0.793000000000000 H 0.321000000000000 0.250000000000000 0.203000000000000 K_POINTS automatic 3 2 2 0 0 0 Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 From: Matic Poberznik Date: 2015-10-27 16:51 To: XCrySDen mailing list Subject: Re: [xcrysden] How to display a whole molecule in unit cell with good connection? >>Actually, I don't want to modify the relative distance between atoms and boundaries. I think journals >>would not accept this. I think that modifying the relative distance, as far as the figure is concerned, should not be a problem. The only limitation I see is that all atoms defined in the ATOMIC_POSITIONS card should be translated by the same vector; due to periodicity both structures are equal, what will change is the way the program reads the structure. Without seeing the actual output I am assuming that your optimized coordinates contain atoms with negative values in coordinates, for example let's say the initial positions were 0.0, 0.0, 0.0, but after optimization they changed to -0.1,-0.1,-0.1, so assuming a cubic structure of length "1" the program draws the optimized coordinates at 0.9, 0.9, 0.9 (equivalent position in the crystal cell), the result being the molecule "breaks" in the unit cell. By shifiting all positions (to positive values) by a specific vector this problem should disappear and as stated both structures are equivalent, so this representation should be acceptable. Both the xsf and pwscf formats are supported by openbabel, so converting it to other formats shouldn't be a problem, though I have no experience regarding the dynamic matrix, so I really have no idea if information will be lost or not. Best regards, Matic On 10/27/2015 01:47 PM, liyincumt at gmail.com wrote: Dear Matic, Thank you very much for your help! Actually, I don't want to modify the relative distance between atoms and boundaries. I think journals would not accept this. I was thinking on whether Molden could display it properly as the dynamic matrix file can be read by Molden as well. I tried many options in molden but it still can't work. So far I just found material studio (Display style: Default) can display it properly. I wonder whether I can convert quantum espresso files including dynamic matrix file and pwo into cif or any other format which could be read by material studio. Even it can be converted, I am still worried about the loss of the information of the forces on atoms. Best Regards, Yin Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 From: Matic Poberznik Date: 2015-10-27 14:27 To: XCrySDen mailing list Subject: Re: [xcrysden] How to display a whole molecule in unit cell with good connection? Modifying this in the pwscf output file is impossible, so I suggest you convert the output file to xsf format using the pwo2xsf.sh tool. It can be found in the Quantum Espresso installation directory in my case it is in /esspreso-5.1.1/PW/tools/pwo2xsf.sh To write the optimized coordinates to the xsf file the syntax would be : bash pwo2xsf.sh -oc name_of_pwout.out > name_of_xsf.xsf Once you have the xsf file I suggest you shift the coordinates of the atoms so that the molecule is in the center of the cell; If the molecule atoms are , for instance, at 0.0, 0.0, 0.0 you should shift them so that the coordinates correspond to 1/2a+1/2b+1/2c where a,b,c are vectors of the unit cell. You should shift all atomic positions accordingly and the result will hopefully be better. Best regards, Matic On 10/27/2015 11:25 AM, liyincumt at gmail.com wrote: Dear Matic, Thanks for your kind help! After setting the number of units drawn, some molecules inside the supercell are displayed correctly. But there are too many molecules inside the supercell. The figure would be hardly accepted by journal. Is it possible to just display the molecules correctly in one unit cell? I have tried buttons of the display which are located in the bottom center of the screen, none of them can work properly. Best Regards, Yin Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 From: Matic Poberznik Date: 2015-10-27 12:14 To: XCrySDen mailing list Subject: Re: [xcrysden] How to display a whole molecule in unit cell with good connection? Dear Yin, If I understood your problem correctly, I think the best solution is to open the Modify menu and choose the Atomic Radius (Shift+R) option. Once there you can modify the Covalent Radius and Connectivity Factor for each atom type to suit your needs. In order to load your custom parameters when xcrysden starts you should add a line in $HOME/.xcrysden/custom-definitions file, an example: # # this line changes the default atomic radius for aluminum to 1.6 # set atmRad(13) 1.6 The custom definitions file is described on this link: http://www.xcrysden.org/doc/custom.html If the problem stems from the periodic boundary conditions then first try the different display modes of unit cells, i. e. click the button for the display of the translational asymmetric unit (bottom center of the screen). Then try Modify => Number of units drawn (Shift+N), if the covalent radius is correct at least some molecules should be displayed correctly. If that is not enough let me know, there is one more workaround but it is a bit more complicated. Best regards, Matic On 10/27/2015 09:19 AM, liyincumt at gmail.com wrote: Dear Xcrysden developers, Thanks for sharing this excellent visualization software for free! I am using xcrysden to visualize the input and output files of quantum espresso. I have a problem with visualization of crystals. Due to the presence of periodic boundary condition, some of atoms which are outside of the boundary look like being non-covalently connected. Is it possible to display a whole molecule with good covalent connections in Xcrysden. Thank you very much! Best Regards, Yin Dr. Yin Li Department of Biophysics,Medical School, University of Pecs, No.12 Szigeti Street, Pecs, H-7624, HUNGARY Phone: +36-72-535271/36271 _______________________________________________ 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 -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151027/40bd63eb/attachment-0001.htm From matic.poberznik at gmail.com Thu Oct 29 17:47:04 2015 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Thu, 29 Oct 2015 17:47:04 +0100 Subject: [xcrysden] Band Plotting In-Reply-To: References: Message-ID: <56324D88.7080806@gmail.com> Dear Muthu, I suggest you use a general purpose plotting program, like gnuplot (http://www.gnuplot.info/) , to plot your band structure. Best regards, Matic On 10/28/2015 02:51 AM, Muthu V wrote: > Dear all > I am using QE for simulation and trying to plot band structure. i > wan to plot band structure using Xcrysden. i do not have crystal > package and i have only Xcrysden. it is possible? (without crystal ) > Thank you > /*--------------------------------------------- > */*Muthu.V > Material Science Group > * > *Indira Gandhi Center for Atomic Research > * > *Kalpakkam, India / > /**/---------------------------------------------/* > // > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20151029/95f204db/attachment.htm From tone.kokalj at ijs.si Thu Oct 29 17:47:44 2015 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 29 Oct 2015 17:47:44 +0100 Subject: [xcrysden] XCrySDen now available in MacPorts In-Reply-To: <56302D98.4030903@snaggledworks.com> References: <56302D98.4030903@snaggledworks.com> Message-ID: <1446137264.6972.39.camel@ijs.si> On Tue, 2015-10-27 at 21:06 -0500, Hanspeter Niederstrasser wrote: > Please do not introduce MacPortisms into the main source. > ... > The following changes to David's Make.macosx-x11 makes it more > portable. > The only option that really needs to be provied by the user is > LIBPREFIX, which sets the root location of 3rd party libraries > (TclTk, ... Dear Hanspeter, You are right, of course. It should be done using the prefix like variable ... Thanks, 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