From atomelectron at gmail.com Wed Mar 11 03:15:17 2009 From: atomelectron at gmail.com (Rong Yu) Date: Wed, 11 Mar 2009 10:15:17 +0800 Subject: [xcrysden] scripting: auto save in xsf format Message-ID: <454DA09C2BA9417B841E636A3E4DDB72@DDW9SD2X> Dear All, It's convenient to open structure files automatically using scripting (scripting::open). Wondering if we can also save the files in the .xsf format automatically, like "scripting::save"... Thanks, Rong From jasius_1 at yahoo.com Wed Mar 11 03:45:46 2009 From: jasius_1 at yahoo.com (Jonas Baltrusaitis) Date: Tue, 10 Mar 2009 19:45:46 -0700 (PDT) Subject: [xcrysden] DOS and band structures In-Reply-To: <1232007933.8677.2.camel@walk.ijs.si> Message-ID: <772972.50266.qm@web54410.mail.yahoo.com> Tone, just to be sure: can xcrysden visualize DOS and band plots from pwscf? I mean read the output and display for publication? thanks Jonas From tone.kokalj at ijs.si Fri Mar 13 09:16:54 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 13 Mar 2009 09:16:54 +0100 Subject: [xcrysden] scripting: auto save in xsf format In-Reply-To: <454DA09C2BA9417B841E636A3E4DDB72@DDW9SD2X> References: <454DA09C2BA9417B841E636A3E4DDB72@DDW9SD2X> Message-ID: <1236932214.7411.17.camel@walk.ijs.si> On Wed, 2009-03-11 at 10:15 +0800, Rong Yu wrote: > Dear All, > > It's convenient to open structure files automatically using scripting > (scripting::open). > Wondering if we can also save the files in the .xsf format automatically, > like "scripting::save"... I don't see what whout be the use of it, because if you have a script you have everything. However, if you would still like to save it, you can do by: SaveStruct (xcrysden will then ask interactively for the name of the file). If you give me a good reason for automating xsf file saving, I will make a "scripting:saveXSF fileName" routine. Regards, Tone From tone.kokalj at ijs.si Fri Mar 13 09:17:48 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 13 Mar 2009 09:17:48 +0100 Subject: [xcrysden] DOS and band structures In-Reply-To: <772972.50266.qm@web54410.mail.yahoo.com> References: <772972.50266.qm@web54410.mail.yahoo.com> Message-ID: <1236932268.7411.18.camel@walk.ijs.si> On Tue, 2009-03-10 at 19:45 -0700, Jonas Baltrusaitis wrote: > Tone, > > just to be sure: can xcrysden visualize DOS and band plots from pwscf? I mean read the output and display for publication? No! I personally use gnuplot for these. 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 atomelectron at gmail.com Fri Mar 13 09:48:32 2009 From: atomelectron at gmail.com (Rong Yu) Date: Fri, 13 Mar 2009 16:48:32 +0800 Subject: [xcrysden] scripting: auto save in xsf format In-Reply-To: <1236932214.7411.17.camel@walk.ijs.si> References: <454DA09C2BA9417B841E636A3E4DDB72@DDW9SD2X> <1236932214.7411.17.camel@walk.ijs.si> Message-ID: <2E9C2AA51F104A8BA87CAE3BAC7353DF@DDW9SD2X> Dear Tone, Here is a good reason for automating xsf file saving: With the function, we can transform a lot of structure files of other formats, say wien_struct, to the xsf format using the following script: -- scripting:open --wien_struct name_i.struct scripting:save --xsf name_i.xsf -- where name_i can be any filename using shell script. Thanks a lot, Rong > -----Original Message----- > From: xcrysden-bounces at democritos.it > [mailto:xcrysden-bounces at democritos.it] On Behalf Of Tone Kokalj > Sent: Friday, March 13, 2009 4:17 PM > To: XCrySDen mailing list > Subject: Re: [xcrysden] scripting: auto save in xsf format > > On Wed, 2009-03-11 at 10:15 +0800, Rong Yu wrote: > > Dear All, > > > > It's convenient to open structure files automatically using > scripting > > (scripting::open). > > Wondering if we can also save the files in the .xsf format > > automatically, like "scripting::save"... > > I don't see what whout be the use of it, because if you have > a script you have everything. > > However, if you would still like to save it, you can do by: > > SaveStruct > > (xcrysden will then ask interactively for the name of the file). > > If you give me a good reason for automating xsf file saving, > I will make a "scripting:saveXSF fileName" routine. > > Regards, Tone > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden From tone.kokalj at ijs.si Fri Mar 13 10:05:22 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 13 Mar 2009 10:05:22 +0100 Subject: [xcrysden] scripting: auto save in xsf format In-Reply-To: <2E9C2AA51F104A8BA87CAE3BAC7353DF@DDW9SD2X> References: <454DA09C2BA9417B841E636A3E4DDB72@DDW9SD2X> <1236932214.7411.17.camel@walk.ijs.si> <2E9C2AA51F104A8BA87CAE3BAC7353DF@DDW9SD2X> Message-ID: <1236935122.7411.36.camel@walk.ijs.si> On Fri, 2009-03-13 at 16:48 +0800, Rong Yu wrote: > Dear Tone, > > Here is a good reason for automating xsf file saving: > With the function, we can transform a lot of structure files of other > formats, say wien_struct, to the xsf format using the following script: > -- > scripting::open --wien_struct name_i.struct > scripting::save --xsf name_i.xsf > -- > where name_i can be any filename using shell script. Good enough reason. It will be done! 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 asafis at yahoo.com.br Fri Mar 13 19:12:52 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Fri, 13 Mar 2009 11:12:52 -0700 (PDT) Subject: [xcrysden] pp Message-ID: <82536.58181.qm@web52310.mail.re2.yahoo.com> Hello users, I am trying to use the Xcrysden, but I am not getting success. I did a SCF calculation and can see the ouput well . However, the output of post-processing calculation is with problem. Appears disconnected atoms. Below, it is the input that you use to pp. &inputpp ??? prefix? = 'sad1' ??? outdir = '/home/sgi/proj/proj394/asa/trabalhos/moleculas/sad1/Cu_F-ON/scf-mp/' ??? filplot = 'sad1_polarization' ??? plot_num= 6 ?/ ?&plot ??? nfile = 1 ??? iflag = 3 ??? output_format = 6 ??? fileout = 'sad1.polarization.xsf' ?/ I think so may be a problem in pp, since the SCF calculation is correct. ? Regards, Alvaro Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090313/fd2a2628/attachment.htm From tone.kokalj at ijs.si Fri Mar 13 19:27:52 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 13 Mar 2009 19:27:52 +0100 Subject: [xcrysden] pp In-Reply-To: <82536.58181.qm@web52310.mail.re2.yahoo.com> References: <82536.58181.qm@web52310.mail.re2.yahoo.com> Message-ID: <1236968872.7411.41.camel@walk.ijs.si> On Fri, 2009-03-13 at 11:12 -0700, ?lvaro Alves wrote: > > Hello users, I am trying to use the Xcrysden, but I am not getting > success. I did a SCF calculation and can see the ouput well . However, > the output of post-processing calculation is with problem. Appears > disconnected atoms. Below, it is the input that you use to pp. > > &inputpp > prefix = 'sad1' > outdir = > '/home/sgi/proj/proj394/asa/trabalhos/moleculas/sad1/Cu_F-ON/scf-mp/' > filplot = 'sad1_polarization' > plot_num= 6 > / > &plot > nfile = 1 > iflag = 3 > output_format = 6 > fileout = 'sad1.polarization.xsf' > / > > I think so may be a problem in pp, since the SCF calculation is > correct. > > Regards, Alvaro > > > In the pp.x of Quantum-Espresso, the output_format = 6 is for gaussian cube file. I am surprized you see anything at all, unless you do: xcrysden --g98_cube sad1.polarization.xsf Why don't you use output_format = 5, which will produce the XSF file? 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 asafis at yahoo.com.br Fri Mar 13 22:42:45 2009 From: asafis at yahoo.com.br (=?iso-8859-1?Q?=C1lvaro_Alves?=) Date: Fri, 13 Mar 2009 14:42:45 -0700 (PDT) Subject: [xcrysden] pp In-Reply-To: <82536.58181.qm@web52310.mail.re2.yahoo.com> Message-ID: <89175.4647.qm@web52310.mail.re2.yahoo.com> I also did the calculation with output_format = 5 and the problem continues. ????????????? Regards, Alvaro --- Em sex, 13/3/09, ?lvaro Alves escreveu: De: ?lvaro Alves Assunto: [xcrysden] pp Para: xcrysden at democritos.it Data: Sexta-feira, 13 de Mar?o de 2009, 15:12 Hello users, I am trying to use the Xcrysden, but I am not getting success. I did a SCF calculation and can see the ouput well . However, the output of post-processing calculation is with problem. Appears disconnected atoms. Below, it is the input that you use to pp. &inputpp ??? prefix? = 'sad1' ??? outdir = '/home/sgi/proj/proj394/asa/trabalhos/moleculas/sad1/Cu_F-ON/scf-mp/' ??? filplot = 'sad1_polarization' ??? plot_num= 6 ?/ ?&plot ??? nfile = 1 ??? iflag = 3 ??? output_format = 6 ??? fileout = 'sad1.polarization.xsf' ?/ I think so may be a problem in pp, since the SCF calculation is correct. ? Regards, Alvaro Veja quais s?o os assuntos do momento no Yahoo! + Buscados: Top 10 - Celebridades - M?sica - Esportes_______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden Veja quais s?o os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090313/360821c5/attachment.htm From tone.kokalj at ijs.si Mon Mar 16 13:07:16 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 16 Mar 2009 13:07:16 +0100 Subject: [xcrysden] pp In-Reply-To: <89175.4647.qm@web52310.mail.re2.yahoo.com> References: <89175.4647.qm@web52310.mail.re2.yahoo.com> Message-ID: <1237205236.18604.3.camel@walk.ijs.si> On Fri, 2009-03-13 at 14:42 -0700, ?lvaro Alves wrote: > I also did the calculation with output_format = 5 and the problem continues. Please provide the input files you used (i.e. starting from the scf), only then there is a chance to help. 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 jxzhu at lanl.gov Tue Mar 17 17:30:47 2009 From: jxzhu at lanl.gov (Jian-Xin Zhu) Date: Tue, 17 Mar 2009 10:30:47 -0600 Subject: [xcrysden] installation of xcrys prelease 1.6 Message-ID: Dear Prof. Kokalj and Xcrys Users, 1. I downloaded the xc-1.5.17-src-all.tar.gz, and tried to install on Mac Intel with leopard 10.5. During the installation, I encountered the following difficulties: cd C; make "TOPDIR=/Users/jxzhu/XCrySDen" compile make TOPDIR=/Users/jxzhu/XCrySDen gcc -ansi -fwritable-strings -funroll-loops -fPIC -DUSE_FONTS - dynamic -DMAC_OSX detnsplit.o xcAppInit.o xcballstick.o xcviewport.o xcLabels.o vectors.o xcDisplayFunc2.o xcAtomAdd.o loadValues.o hpsort.o auxilproc.o xcdebug.o 3D.o xcDisplayFunc.o readstrf.o mxmymz.o remakestr.o xcSelect.o readisodata.o lighting.o xcGLparam.o colorplane.o isorender.o polygonise.o polygonise_auxil.o xcIsoSurf.o voronoi.o xcBz.o xcSuperCell.o xcPrimitives.o setOpenGLState.o memory.o isoMalloc.o isoInterpolate.o readPlvertex.o splineInt.o paraSize.o isoline.o xcIsoSpaceSel.o cells.o xcWigner.o xcTogl.o datagrid.o sInfo.o xcIsoDataGrid.o xcColorScheme.o xcReadXSF.o xcF3toI4.o xcFractCoor.o signal.o MarchCubes.o isosurf.o xcMolSurf.o cryNewContext.o fs.o cryDispFunc.o cryDispFuncMultiFS.o crySetProj.o crySurfArgs.o crySurf.o cryTransform.o cryClip.o cryTogl.o forces.o xcForces.o gl2psPrintTogl.o ppmPrintTogl.o lcasi.o lcasif.o xcFont.o fog.o writeXSF.o hbonds.o xcHBonds.o linear.o realTimeMovie.o togl.o gl2ps.o sgiRasterFont.o sgiAux.o \ -o xcrys /Users/jxzhu/XCrySDen/external/lib/libtk8.5.dylib / Users/jxzhu/XCrySDen/external/lib/libtcl8.5.dylib -L/usr/X11R6/lib - lGLU -L/usr/X11R6/lib -lGL -L/usr/X11R6/lib -lXmu -lX11 -lXext -lm ld: cycle in dylib re-exports with /usr/X11R6/lib/libGL.dylib collect2: ld returned 1 exit status make[2]: *** [xcrys] Error 1 make[1]: *** [compile] Error 2 make: *** [src-C] Error 2 I checked to see that libGL.dylib and libGLU.dylib are in /usr/X11R6/ lib. The setting in Make.sys is as follows: #------------------------------------------------------------------------ # if you have a GNU make it is better to set the MAKE variable to point # to gnu make #------------------------------------------------------------------------ MAKE = make #------------------------------------------------------------------------ # compilers & flags #------------------------------------------------------------------------ CFLAGS = -ansi -fwritable-strings -funroll-loops -fPIC -DUSE_FONTS - dynamic -DMAC_OSX CC = gcc #LDLIB = -ldl MATH = -lm FFLAGS = -O FC = ifort # NOTE: Use the XDarwin server instead of Apple's Xserver DARWIN_X11_PREFIX = /usr/X11R6 X_LIB = -L$(DARWIN_X11_PREFIX)/lib -lXmu -lX11 -lXext X_INCDIR = -I$(DARWIN_X11_PREFIX)/include ### ### or THAT: ### #- Possibility-2----------------------------------------------------------- # # XCRYSDEN package may contain the tcl, tk & Mesa sources !!! # If you would like to compile and use these then uncomment below lines and # comment lines "Possibility-1" (see above). # #------------------------------------------------------------------------ COMPILE_TCLTK = yes #COMPILE_MESA = yes # # # # # Do we want a shared library version of Tcl/Tk/Mesa or static? # # If we want shared then set the following flags to: --enable-shared # # else set the following flag to: --disable-shared # # TCLTK_OPTIONS = --enable-shared #MESA_TARGET = darwin # # # # # Libraries (dynamic loading) # # for shared linking the libraries postfix should be .dylib # # for static linking the libraries postfix should be .a # # # # # Uncomment CoreFoundations for static linking # #CoreFoundation=/System/Library/Frameworks/CoreFoundation.framework/ Versions/A/CoreFoundation # TCL_LIB = $(TOPDIR)/external/lib/libtcl$(TCL_VER2).dylib $ (CoreFoundation) TCL_LIB = $(TOPDIR)/external/lib/libtcl$(TCL_VER2).dylib TK_LIB = $(TOPDIR)/external/lib/libtk$(TCL_VER2).dylib # # # use this for Darwin OpenGL: GLU_LIB = -L$(DARWIN_X11_PREFIX)/lib -lGLU GL_LIB = -L$(DARWIN_X11_PREFIX)/lib -lGL # # use this for Mesa (much slower than Darwin OpenGL): # #GLU_LIB = $(TOPDIR)/external/lib/libGLU.dylib # #GL_LIB = $(TOPDIR)/external/lib/libGL.dylib # # # # # Include directories # # TCL_INCDIR = -I$(TOPDIR)/external/src/tcl$(TCL_VER3)/generic TK_INCDIR = -I$(TOPDIR)/external/src/tk$(TCL_VER3)/generic # # use this for Darwin OpenGL: GL_INCDIR = -I$(DARWIN_X11_PREFIX)/include # # use this for Mesa: # #GL_INCDIR = -I$(TOPDIR)/external/include Your help is appreciated. Jian-Xin Zhu -- ################################ Jian-Xin Zhu, Ph.D Theoretical Division, MS B262 Los Alamos National Laboratory Los Alamos, New Mexico 87545 Phone: (505) 667 2363 Fax: (505) 665 4063 Email (main): jxzhu at lanl.gov Email (backup): physjxzhu at gmail.com URL: http://theory.lanl.gov ################################ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090317/909f78ca/attachment.htm From sclauzer at sissa.it Wed Mar 18 09:31:56 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 18 Mar 2009 09:31:56 +0100 Subject: [xcrysden] installation of xcrys prelease 1.6 In-Reply-To: References: Message-ID: <49C0B17C.6000703@sissa.it> Jian-Xin Zhu wrote: > Dear Prof. Kokalj and Xcrys Users, > > 1. I downloaded the xc-1.5.17-src-all.tar.gz, and tried to install on > Mac Intel with leopard 10.5. > > During the installation, I encountered the following difficulties: I recently tried to do the same. Even if I successfully compiled xcrysden, later I could not use it, since I had a problem with the X11 system. The same problem was reported before: http://www.democritos.it/pipermail/xcrysden/2007-May/000375.html and I suppose it has not been solved in the meantime. So, instead of compiling the source, I suggest you to download the semistatic version of the binaries (http://www.xcrysden.org/download/xc-1.5.17-macosx.tar.gz) and use that. For me it works (although I haven't used it much so far), even if it gives a warning of missing library at the beginning. I realized that an executable in the packege was linked to g77 libraries, installed it, and now it works with no warnings. The problem of your compile may be related to the fact that you're linking to Apple's GL. If you really want to compile the source, you should install an external GL (e.g. from MacPorts or Fink or install it yourself) and link to that (please have a look at Make.macosx-x11.README in system/). Then to make it work you may probably have to install another X11 server as well, since in my case I could not make the compiled xcrysden run on Apple's X11. HTH GS > > cd C; make "TOPDIR=/Users/jxzhu/XCrySDen" compile > make TOPDIR=/Users/jxzhu/XCrySDen > gcc -ansi -fwritable-strings -funroll-loops -fPIC -DUSE_FONTS -dynamic > -DMAC_OSX detnsplit.o xcAppInit.o xcballstick.o xcviewport.o xcLabels.o > vectors.o xcDisplayFunc2.o xcAtomAdd.o loadValues.o hpsort.o auxilproc.o > xcdebug.o 3D.o xcDisplayFunc.o readstrf.o mxmymz.o remakestr.o > xcSelect.o readisodata.o lighting.o xcGLparam.o colorplane.o isorender.o > polygonise.o polygonise_auxil.o xcIsoSurf.o voronoi.o xcBz.o > xcSuperCell.o xcPrimitives.o setOpenGLState.o memory.o isoMalloc.o > isoInterpolate.o readPlvertex.o splineInt.o paraSize.o isoline.o > xcIsoSpaceSel.o cells.o xcWigner.o xcTogl.o datagrid.o sInfo.o > xcIsoDataGrid.o xcColorScheme.o xcReadXSF.o xcF3toI4.o xcFractCoor.o > signal.o MarchCubes.o isosurf.o xcMolSurf.o cryNewContext.o fs.o > cryDispFunc.o cryDispFuncMultiFS.o crySetProj.o crySurfArgs.o crySurf.o > cryTransform.o cryClip.o cryTogl.o forces.o xcForces.o gl2psPrintTogl.o > ppmPrintTogl.o lcasi.o lcasif.o xcFont.o fog.o writeXSF.o hbonds.o > xcHBonds.o linear.o realTimeMovie.o togl.o gl2ps.o sgiRasterFont.o > sgiAux.o \ > -o xcrys /Users/jxzhu/XCrySDen/external/lib/libtk8.5.dylib > /Users/jxzhu/XCrySDen/external/lib/libtcl8.5.dylib -L/usr/X11R6/lib > -lGLU -L/usr/X11R6/lib -lGL -L/usr/X11R6/lib -lXmu -lX11 -lXext -lm > ld: cycle in dylib re-exports with /usr/X11R6/lib/libGL.dylib > collect2: ld returned 1 exit status > make[2]: *** [xcrys] Error 1 > make[1]: *** [compile] Error 2 > make: *** [src-C] Error 2 > > I checked to see that libGL.dylib and libGLU.dylib are in /usr/X11R6/lib. > > The setting in Make.sys is as follows: > > #------------------------------------------------------------------------ > # if you have a GNU make it is better to set the MAKE variable to point > # to gnu make > #------------------------------------------------------------------------ > MAKE = make > > #------------------------------------------------------------------------ > # compilers & flags > #------------------------------------------------------------------------ > CFLAGS = -ansi -fwritable-strings -funroll-loops -fPIC -DUSE_FONTS > -dynamic -DMAC_OSX > CC = gcc > #LDLIB = -ldl > MATH = -lm > > FFLAGS = -O > FC = ifort > > > # NOTE: Use the XDarwin server instead of Apple's Xserver > > DARWIN_X11_PREFIX = /usr/X11R6 > X_LIB = -L$(DARWIN_X11_PREFIX)/lib -lXmu -lX11 -lXext > X_INCDIR = -I$(DARWIN_X11_PREFIX)/include > > ### > ### or THAT: > ### > > #-Possibility-2----------------------------------------------------------- > # > # XCRYSDEN package may contain the tcl, tk & Mesa sources !!! > # If you would like to compile and use these then uncomment below lines and > # comment lines "Possibility-1" (see above). > # > #------------------------------------------------------------------------ > > COMPILE_TCLTK = yes > #COMPILE_MESA = yes > # > # # > # # Do we want a shared library version of Tcl/Tk/Mesa or static? > # # If we want shared then set the following flags to: --enable-shared > # # else set the following flag to: --disable-shared > # # > TCLTK_OPTIONS = --enable-shared > #MESA_TARGET = darwin > # > # # > # # Libraries (dynamic loading) > # # for shared linking the libraries postfix should be .dylib > # # for static linking the libraries postfix should be .a > # # > # > # # Uncomment CoreFoundations for static linking > # > #CoreFoundation=/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation > # TCL_LIB = $(TOPDIR)/external/lib/libtcl$(TCL_VER2).dylib > $(CoreFoundation) > TCL_LIB = $(TOPDIR)/external/lib/libtcl$(TCL_VER2).dylib > TK_LIB = $(TOPDIR)/external/lib/libtk$(TCL_VER2).dylib > # > # # use this for Darwin OpenGL: > GLU_LIB = -L$(DARWIN_X11_PREFIX)/lib -lGLU > GL_LIB = -L$(DARWIN_X11_PREFIX)/lib -lGL > # # use this for Mesa (much slower than Darwin OpenGL): > # #GLU_LIB = $(TOPDIR)/external/lib/libGLU.dylib > # #GL_LIB = $(TOPDIR)/external/lib/libGL.dylib > # > # # > # # Include directories > # # > TCL_INCDIR = -I$(TOPDIR)/external/src/tcl$(TCL_VER3)/generic > TK_INCDIR = -I$(TOPDIR)/external/src/tk$(TCL_VER3)/generic > # # use this for Darwin OpenGL: > GL_INCDIR = -I$(DARWIN_X11_PREFIX)/include > # # use this for Mesa: > # #GL_INCDIR = -I$(TOPDIR)/external/include > > > Your help is appreciated. > > Jian-Xin Zhu > > > > > > > -- > ################################ > Jian-Xin Zhu, Ph.D > Theoretical Division, MS B262 > Los Alamos National Laboratory > Los Alamos, New Mexico 87545 > Phone: (505) 667 2363 > Fax: (505) 665 4063 > Email (main): jxzhu at lanl.gov > Email (backup): physjxzhu at gmail.com > URL: http://theory.lanl.gov > ################################ > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From tone.kokalj at ijs.si Wed Mar 18 13:22:42 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 18 Mar 2009 13:22:42 +0100 Subject: [xcrysden] installation of xcrys prelease 1.6 In-Reply-To: <49C0B17C.6000703@sissa.it> References: <49C0B17C.6000703@sissa.it> Message-ID: <1237378962.18419.11.camel@walk.ijs.si> On Wed, 2009-03-18 at 09:31 +0100, Gabriele Sclauzero wrote: > I recently tried to do the same. Even if I successfully compiled xcrysden, later I could > not use it, since I had a problem with the X11 system. The same problem was reported before: > http://www.democritos.it/pipermail/xcrysden/2007-May/000375.html > and I suppose it has not been solved in the meantime. Because there is nothing to be solved (as far as I know). This is simply related to what you are describing below: > The problem of your compile may be related to the fact that you're linking to Apple's GL. > If you really want to compile the source, you should install an external GL (e.g. from > MacPorts or Fink or install it yourself) and link to that (please have a look at > Make.macosx-x11.README in system/). 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 sclauzer at sissa.it Wed Mar 18 14:01:32 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 18 Mar 2009 14:01:32 +0100 Subject: [xcrysden] installation of xcrys prelease 1.6 In-Reply-To: <1237378962.18419.11.camel@walk.ijs.si> References: <49C0B17C.6000703@sissa.it> <1237378962.18419.11.camel@walk.ijs.si> Message-ID: <49C0F0AC.8010101@sissa.it> Tone Kokalj wrote: > On Wed, 2009-03-18 at 09:31 +0100, Gabriele Sclauzero wrote: >> I recently tried to do the same. Even if I successfully compiled xcrysden, later I could >> not use it, since I had a problem with the X11 system. The same problem was reported before: >> http://www.democritos.it/pipermail/xcrysden/2007-May/000375.html >> and I suppose it has not been solved in the meantime. > > Because there is nothing to be solved (as far as I know). This is simply related to what > you are describing below: > >> The problem of your compile may be related to the fact that you're linking to Apple's GL. >> If you really want to compile the source, you should install an external GL (e.g. from >> MacPorts or Fink or install it yourself) and link to that (please have a look at >> Make.macosx-x11.README in system/). If I correctly understood the meaning of that file, one could correctly compile if linking with GL libraries other than Apple ones and then run using Apple X11 server. The first step was successfull, but the second wasn't in my case. Do I need to install another X11 server (for instance macports one) in order to make it work? Thanks, Gabriele > > Regards, Tone -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From tone.kokalj at ijs.si Wed Mar 18 14:10:18 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 18 Mar 2009 14:10:18 +0100 Subject: [xcrysden] installation of xcrys prelease 1.6 In-Reply-To: <49C0F0AC.8010101@sissa.it> References: <49C0B17C.6000703@sissa.it> <1237378962.18419.11.camel@walk.ijs.si> <49C0F0AC.8010101@sissa.it> Message-ID: <1237381818.18419.23.camel@walk.ijs.si> On Wed, 2009-03-18 at 14:01 +0100, Gabriele Sclauzero wrote: > Tone Kokalj wrote: > > On Wed, 2009-03-18 at 09:31 +0100, Gabriele Sclauzero wrote: > >> I recently tried to do the same. Even if I successfully compiled xcrysden, later I could > >> not use it, since I had a problem with the X11 system. The same problem was reported before: > >> http://www.democritos.it/pipermail/xcrysden/2007-May/000375.html > >> and I suppose it has not been solved in the meantime. > > > > Because there is nothing to be solved (as far as I know). This is simply related to what > > you are describing below: > > > >> The problem of your compile may be related to the fact that you're linking to Apple's GL. > >> If you really want to compile the source, you should install an external GL (e.g. from > >> MacPorts or Fink or install it yourself) and link to that (please have a look at > >> Make.macosx-x11.README in system/). > > If I correctly understood the meaning of that file, one could correctly compile if linking > with GL libraries other than Apple ones and then run using Apple X11 server. The first > step was successfull, but the second wasn't in my case. > Do I need to install another X11 server (for instance macports one) in order to make it work? As far as I know, Apple X11 sever should do. (I am keep using "as far as I know", because I am not a mac user, and my mac experience \approx 0). Did the precompiled version work on Apple X11 server? If yes, then you have the answer. 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 sclauzer at sissa.it Wed Mar 18 14:42:25 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 18 Mar 2009 14:42:25 +0100 Subject: [xcrysden] installation of xcrys prelease 1.6 In-Reply-To: <1237381818.18419.23.camel@walk.ijs.si> References: <49C0B17C.6000703@sissa.it> <1237378962.18419.11.camel@walk.ijs.si> <49C0F0AC.8010101@sissa.it> <1237381818.18419.23.camel@walk.ijs.si> Message-ID: <49C0FA41.7030605@sissa.it> Dear Tone, >> If I correctly understood the meaning of that file, one could correctly compile if linking >> with GL libraries other than Apple ones and then run using Apple X11 server. The first >> step was successfull, but the second wasn't in my case. >> Do I need to install another X11 server (for instance macports one) in order to make it work? > > > As far as I know, Apple X11 sever should do. (I am keep using "as far as > I know", because I am not a mac user, and my mac experience \approx 0). I'm a new macuser, so my macexperience is \epsilon, \epsilon \to 0 > > Did the precompiled version work on Apple X11 server? If yes, then you > have the answer. The precompiled works with Apple X11, and it points to Apple's X11 dynamic libraries. My compiled version however points to the X11 libraries I used to compile. Maybe that's the source of trouble. Anyway, it seems that the program stops when executing ftnunit. What does this piece of sotware do? It may be that the issue comes from fortran libraries, rather than GL. In fact even if the precompiled version works, it gives a warning of missing library (libg2c, which is part of g77), which I solved by installing g77. To compile my version I used gfortran instead, so that this ftnunit links to the gfortran library now (but doesn't work...). GS > > Regards, Tone -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From tone.kokalj at ijs.si Wed Mar 18 17:15:59 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 18 Mar 2009 17:15:59 +0100 Subject: [xcrysden] installation of xcrys prelease 1.6 In-Reply-To: <49C0FA41.7030605@sissa.it> References: <49C0B17C.6000703@sissa.it> <1237378962.18419.11.camel@walk.ijs.si> <49C0F0AC.8010101@sissa.it> <1237381818.18419.23.camel@walk.ijs.si> <49C0FA41.7030605@sissa.it> Message-ID: <1237392959.18419.37.camel@walk.ijs.si> On Wed, 2009-03-18 at 14:42 +0100, Gabriele Sclauzero wrote: > Dear Tone, > > >> If I correctly understood the meaning of that file, one could correctly compile if linking > >> with GL libraries other than Apple ones and then run using Apple X11 server. The first > >> step was successfull, but the second wasn't in my case. > >> Do I need to install another X11 server (for instance macports one) in order to make it work? > > > > > > As far as I know, Apple X11 sever should do. (I am keep using "as far as > > I know", because I am not a mac user, and my mac experience \approx 0). > > I'm a new macuser, so my macexperience is \epsilon, \epsilon \to 0 > > > > > Did the precompiled version work on Apple X11 server? If yes, then you > > have the answer. > > The precompiled works with Apple X11, and it points to Apple's X11 dynamic libraries. My > compiled version however points to the X11 libraries I used to compile. Maybe that's the > source of trouble. I will consult with some of my colleagues that know mac better than me. > Anyway, it seems that the program stops when executing ftnunit. What does this piece of > sotware do? It is a simple fortran program that writes a fortran unit 99. For all nowadays compilers that I know fortran unit files are named fort.*, however in the past the HP-UX fotran compiler have written it as ftn.* So xcrysden uses ftnunit program to determine the name of the fortran unit. > It may be that the issue comes from fortran libraries, rather than GL. > In fact even if the precompiled version works, it gives a warning of missing library > (libg2c, which is part of g77), Because the program has been compiled with g77. Anyway xcrysden uses several fortran programs behind the scene, so if they don't work, xcrysden behaviour will be weird. > which I solved by installing g77. To compile my version I > used gfortran instead, so that this ftnunit links to the gfortran library now (but doesn't > work...). Why? ftnunit is so simple, basically a one-liner program. Here it is: program ftnunit c used by XCrySDen to find out what is the name of fortran unit write(99,*) 'test' end Regards, Tone PS: I would like to know if somebody knows a better way to figure out the name of the fortran unit as done by ftnunit program. -- 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 jxzhu at lanl.gov Wed Mar 18 18:43:33 2009 From: jxzhu at lanl.gov (Jian-Xin Zhu) Date: Wed, 18 Mar 2009 11:43:33 -0600 Subject: [xcrysden] installation of xcrys prelease 1.6 In-Reply-To: <49C0FA41.7030605@sissa.it> References: <49C0B17C.6000703@sissa.it> <1237378962.18419.11.camel@walk.ijs.si> <49C0F0AC.8010101@sissa.it> <1237381818.18419.23.camel@walk.ijs.si> <49C0FA41.7030605@sissa.it> Message-ID: <2E5C9689-9B58-45FE-B74F-078E4CF1F952@lanl.gov> Dear Gabriele and Tone, Now that Apple's GL libraries do not work, I tried to use the Mesa library included in the source version XCrySDen-1.5.17-src-all.tar. By running "make all", the following errors came out, i686-apple-darwin9-gcc-4.0.1: /Users/jxzhu/XCrySDen-1.5.17-src-all/ external/lib/libGLU.dylib: No such file or directory i686-apple-darwin9-gcc-4.0.1: /Users/jxzhu/XCrySDen-1.5.17-src-all/ external/lib/libGL.dylib: No such file or directory make[2]: *** [xcrys] Error 1 make[1]: *** [compile] Error 2 make: *** [src-C] Error 2 I then looked into the subdirectory external/lib, and found libGLU.dylib and libGL.dylib were indeed generated from the compilation of Mesa. Interestingly, there was nothing related to Mesa-7.2 inside external/lib. But I went into external/src/Mesa-7.2/ lib, these libraries were generated, libGL.1.2.dylib* libGLU.1.3.dylib* libGLw. 1.0.dylib* libOSMesa.7.2.dylib* libGL.1.dylib@ libGLU.1.dylib@ libGLw. 1.dylib@ libOSMesa.7.dylib@ libGL.dylib@ libGLU.dylib@ libGLw.dylib@ libOSMesa.dylib@ By noticing these, I changed into external/lib and made the symbolic ln -sf ../src/Mesa-7.2/lib/libGLU.dylib libGLU.dylib ln -sf ../src/Mesa-7.2/lib/libGL.dylib libGL.dylib I then re-ran "make all" and this time it compiled through. After running "./xcConfigure", I started the command "xcrysden". The execution failed by displaying the following: TCL_LIBRARY=/Users/jxzhu/XCrySDen-1.5.17-src-all/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/Users/jxzhu/XCrySDen-1.5.17-src-all XCRYSDEN_SCRATCH=/Users/jxzhu/xcrys_tmp dyld: warning, DYLD_ setting caused circular dependency in /usr/X11/ lib/libGL.1.dylib Running on platform: unix Executing: /Users/jxzhu/XCrySDen-1.5.17-src-all/bin/ftnunit /Users/jxzhu/XCrySDen-1.5.17-src-all/xcrysden: line 211: 29018 Bus error ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/ Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/ null My immediate question: Why were libGLU.dylib and libGL.dylib from the compilation of Mesa-7.2 not generated in the subdirectory external/lib together with a mesa folder there? The setting in Make.sys file is shown below: #------------------------------------------------------------------------ # X-libraries & include files # # for STATIC compilation one should add: -lpthread #------------------------------------------------------------------------ # NOTE: Use the XDarwin server instead of Apple's Xserver DARWIN_X11_PREFIX = /usr/X11R6 X_LIB = -L$(DARWIN_X11_PREFIX)/lib -lXmu -lX11 -lXext X_INCDIR = -I$(DARWIN_X11_PREFIX)/include #- Possibility-2----------------------------------------------------------- # # XCRYSDEN package may contain the tcl, tk & Mesa sources !!! # If you would like to compile and use these then uncomment below lines and # comment lines "Possibility-1" (see above). # #------------------------------------------------------------------------ COMPILE_TCLTK = yes COMPILE_MESA = yes # # # # # Do we want a shared library version of Tcl/Tk/Mesa or static? # # If we want shared then set the following flags to: --enable-shared # # else set the following flag to: --disable-shared # # TCLTK_OPTIONS = --enable-shared MESA_TARGET = darwin # # # # # Libraries (dynamic loading) # # for shared linking the libraries postfix should be .dylib # # for static linking the libraries postfix should be .a # # # # # Uncomment CoreFoundations for static linking CoreFoundation=/System/Library/Frameworks/CoreFoundation.framework/ Versions/A/CoreFoundation TCL_LIB = $(TOPDIR)/external/lib/libtcl$(TCL_VER2).dylib $ (CoreFoundation) TK_LIB = $(TOPDIR)/external/lib/libtk$(TCL_VER2).dylib # # # use this for Darwin OpenGL: # GLU_LIB = -L$(DARWIN_X11_PREFIX)/lib -lGLU # GL_LIB = -L$(DARWIN_X11_PREFIX)/lib -lGL # # use this for Mesa (much slower than Darwin OpenGL): GLU_LIB = $(TOPDIR)/external/lib/libGLU.dylib GL_LIB = $(TOPDIR)/external/lib/libGL.dylib # # # # # Include directories # # TCL_INCDIR = -I$(TOPDIR)/external/src/tcl$(TCL_VER3)/generic TK_INCDIR = -I$(TOPDIR)/external/src/tk$(TCL_VER3)/generic # # use this for Darwin OpenGL: # GL_INCDIR = -I$(DARWIN_X11_PREFIX)/include # # use this for Mesa: GL_INCDIR = -I$(TOPDIR)/external/include #------------------------------------------------------------------------ Thanks for the help. Jian-Xin Zhu On Mar 18, 2009, at 7:42 AM, Gabriele Sclauzero wrote: > Dear Tone, > >>> If I correctly understood the meaning of that file, one could >>> correctly compile if linking >>> with GL libraries other than Apple ones and then run using Apple >>> X11 server. The first >>> step was successfull, but the second wasn't in my case. >>> Do I need to install another X11 server (for instance macports >>> one) in order to make it work? >> >> >> As far as I know, Apple X11 sever should do. (I am keep using "as >> far as >> I know", because I am not a mac user, and my mac experience \approx >> 0). > > I'm a new macuser, so my macexperience is \epsilon, \epsilon \to 0 > >> >> Did the precompiled version work on Apple X11 server? If yes, then >> you >> have the answer. > > The precompiled works with Apple X11, and it points to Apple's X11 > dynamic libraries. My > compiled version however points to the X11 libraries I used to > compile. Maybe that's the > source of trouble. > Anyway, it seems that the program stops when executing ftnunit. What > does this piece of > sotware do? It may be that the issue comes from fortran libraries, > rather than GL. > In fact even if the precompiled version works, it gives a warning of > missing library > (libg2c, which is part of g77), which I solved by installing g77. To > compile my version I > used gfortran instead, so that this ftnunit links to the gfortran > library now (but doesn't > work...). > > GS > > > >> >> Regards, Tone > > -- > > > o ------------------------------------------------ o > | Gabriele Sclauzero, PhD Student | > | c/o: SISSA & CNR-INFM Democritos, | > | via Beirut 2-4, 34014 Trieste (Italy) | > | email: sclauzer at sissa.it | > | phone: +39 040 3787 511 | > | skype: gurlonotturno | > o ------------------------------------------------ o > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- ################################ Jian-Xin Zhu, Ph.D Theoretical Division, MS B262 Los Alamos National Laboratory Los Alamos, New Mexico 87545 Phone: (505) 667 2363 Fax: (505) 665 4063 Email (main): jxzhu at lanl.gov Email (backup): physjxzhu at gmail.com URL: http://theory.lanl.gov ################################ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090318/f7c1f04e/attachment-0001.htm From jxzhu at lanl.gov Wed Mar 18 18:48:45 2009 From: jxzhu at lanl.gov (Jian-Xin Zhu) Date: Wed, 18 Mar 2009 11:48:45 -0600 Subject: [xcrysden] installation of xcrys prelease 1.6 In-Reply-To: <2E5C9689-9B58-45FE-B74F-078E4CF1F952@lanl.gov> References: <49C0B17C.6000703@sissa.it> <1237378962.18419.11.camel@walk.ijs.si> <49C0F0AC.8010101@sissa.it> <1237381818.18419.23.camel@walk.ijs.si> <49C0FA41.7030605@sissa.it> <2E5C9689-9B58-45FE-B74F-078E4CF1F952@lanl.gov> Message-ID: <70B61CD1-C650-4EFA-B3C8-595388C32BDD@lanl.gov> I should have said > I then looked into the subdirectory external/lib, and found > libGLU.dylib and libGL.dylib were NOT generated IN THIS FOLDER from > the compilation of Mesa. Interestingly, there was nothing related to > Mesa-7.2 inside external/lib. But I went into external/src/Mesa-7.2/ > lib, these libraries were generated, On Mar 18, 2009, at 11:43 AM, Jian-Xin Zhu wrote: > Dear Gabriele and Tone, > > Now that Apple's GL libraries do not work, > I tried to use the Mesa library included in the source version > XCrySDen-1.5.17-src-all.tar. > By running "make all", the following errors came out, > > i686-apple-darwin9-gcc-4.0.1: /Users/jxzhu/XCrySDen-1.5.17-src-all/ > external/lib/libGLU.dylib: No such file or directory > i686-apple-darwin9-gcc-4.0.1: /Users/jxzhu/XCrySDen-1.5.17-src-all/ > external/lib/libGL.dylib: No such file or directory > make[2]: *** [xcrys] Error 1 > make[1]: *** [compile] Error 2 > make: *** [src-C] Error 2 > > I then looked into the subdirectory external/lib, and found > libGLU.dylib and libGL.dylib were indeed generated from the > compilation of Mesa. Interestingly, there was nothing related to > Mesa-7.2 inside external/lib. But I went into external/src/Mesa-7.2/ > lib, these libraries were generated, > > libGL.1.2.dylib* libGLU.1.3.dylib* libGLw. > 1.0.dylib* libOSMesa.7.2.dylib* > libGL.1.dylib@ libGLU.1.dylib@ libGLw. > 1.dylib@ libOSMesa.7.dylib@ > libGL.dylib@ libGLU.dylib@ > libGLw.dylib@ libOSMesa.dylib@ > > By noticing these, I changed into external/lib and made the symbolic > ln -sf ../src/Mesa-7.2/lib/libGLU.dylib libGLU.dylib > ln -sf ../src/Mesa-7.2/lib/libGL.dylib libGL.dylib > > I then re-ran "make all" and this time it compiled through. > > After running "./xcConfigure", I started the command "xcrysden". The > execution failed by displaying the following: > > TCL_LIBRARY=/Users/jxzhu/XCrySDen-1.5.17-src-all/external/lib/tcl8.5 > XCRYSDEN_TOPDIR=/Users/jxzhu/XCrySDen-1.5.17-src-all > XCRYSDEN_SCRATCH=/Users/jxzhu/xcrys_tmp > > dyld: warning, DYLD_ setting caused circular dependency in /usr/X11/ > lib/libGL.1.dylib > Running on platform: unix > Executing: /Users/jxzhu/XCrySDen-1.5.17-src-all/bin/ftnunit > /Users/jxzhu/XCrySDen-1.5.17-src-all/xcrysden: line 211: 29018 Bus > error ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/ > Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > / > dev/null > > > My immediate question: Why were libGLU.dylib and libGL.dylib from > the compilation of Mesa-7.2 not generated in the subdirectory > external/lib together with a mesa folder there? > > > > The setting in Make.sys file is shown below: > > > #------------------------------------------------------------------------ > # X-libraries & include files > # > # for STATIC compilation one should add: -lpthread > #------------------------------------------------------------------------ > > # NOTE: Use the XDarwin server instead of Apple's Xserver > > DARWIN_X11_PREFIX = /usr/X11R6 > X_LIB = -L$(DARWIN_X11_PREFIX)/lib -lXmu -lX11 -lXext > X_INCDIR = -I$(DARWIN_X11_PREFIX)/include > > > > #- > Possibility > -2----------------------------------------------------------- > # > # XCRYSDEN package may contain the tcl, tk & Mesa sources !!! > # If you would like to compile and use these then uncomment below > lines and > # comment lines "Possibility-1" (see above). > # > #------------------------------------------------------------------------ > > COMPILE_TCLTK = yes > COMPILE_MESA = yes > # > # # > # # Do we want a shared library version of Tcl/Tk/Mesa or static? > # # If we want shared then set the following flags to: --enable-shared > # # else set the following flag to: --disable-shared > # # > TCLTK_OPTIONS = --enable-shared > MESA_TARGET = darwin > # > # # > # # Libraries (dynamic loading) > # # for shared linking the libraries postfix should > be .dylib > # # for static linking the libraries postfix should be .a > # # > # > # # Uncomment CoreFoundations for static linking > CoreFoundation=/System/Library/Frameworks/CoreFoundation.framework/ > Versions/A/CoreFoundation > TCL_LIB = $(TOPDIR)/external/lib/libtcl$(TCL_VER2).dylib $ > (CoreFoundation) > TK_LIB = $(TOPDIR)/external/lib/libtk$(TCL_VER2).dylib > # > # # use this for Darwin OpenGL: > # GLU_LIB = -L$(DARWIN_X11_PREFIX)/lib -lGLU > # GL_LIB = -L$(DARWIN_X11_PREFIX)/lib -lGL > # # use this for Mesa (much slower than Darwin OpenGL): > GLU_LIB = $(TOPDIR)/external/lib/libGLU.dylib > GL_LIB = $(TOPDIR)/external/lib/libGL.dylib > # > # # > # # Include directories > # # > TCL_INCDIR = -I$(TOPDIR)/external/src/tcl$(TCL_VER3)/generic > TK_INCDIR = -I$(TOPDIR)/external/src/tk$(TCL_VER3)/generic > # # use this for Darwin OpenGL: > # GL_INCDIR = -I$(DARWIN_X11_PREFIX)/include > # # use this for Mesa: > GL_INCDIR = -I$(TOPDIR)/external/include > > #------------------------------------------------------------------------ > > > > Thanks for the help. > > Jian-Xin Zhu > > > > > > > > > On Mar 18, 2009, at 7:42 AM, Gabriele Sclauzero wrote: > >> Dear Tone, >> >>>> If I correctly understood the meaning of that file, one could >>>> correctly compile if linking >>>> with GL libraries other than Apple ones and then run using Apple >>>> X11 server. The first >>>> step was successfull, but the second wasn't in my case. >>>> Do I need to install another X11 server (for instance macports >>>> one) in order to make it work? >>> >>> >>> As far as I know, Apple X11 sever should do. (I am keep using "as >>> far as >>> I know", because I am not a mac user, and my mac experience >>> \approx 0). >> >> I'm a new macuser, so my macexperience is \epsilon, \epsilon \to 0 >> >>> >>> Did the precompiled version work on Apple X11 server? If yes, then >>> you >>> have the answer. >> >> The precompiled works with Apple X11, and it points to Apple's X11 >> dynamic libraries. My >> compiled version however points to the X11 libraries I used to >> compile. Maybe that's the >> source of trouble. >> Anyway, it seems that the program stops when executing ftnunit. >> What does this piece of >> sotware do? It may be that the issue comes from fortran libraries, >> rather than GL. >> In fact even if the precompiled version works, it gives a warning >> of missing library >> (libg2c, which is part of g77), which I solved by installing g77. >> To compile my version I >> used gfortran instead, so that this ftnunit links to the gfortran >> library now (but doesn't >> work...). >> >> GS >> >> >> >>> >>> Regards, Tone >> >> -- >> >> >> o ------------------------------------------------ o >> | Gabriele Sclauzero, PhD Student | >> | c/o: SISSA & CNR-INFM Democritos, | >> | via Beirut 2-4, 34014 Trieste (Italy) | >> | email: sclauzer at sissa.it | >> | phone: +39 040 3787 511 | >> | skype: gurlonotturno | >> o ------------------------------------------------ o >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> http://www.democritos.it/mailman/listinfo/xcrysden > > -- > ################################ > Jian-Xin Zhu, Ph.D > Theoretical Division, MS B262 > Los Alamos National Laboratory > Los Alamos, New Mexico 87545 > Phone: (505) 667 2363 > Fax: (505) 665 4063 > Email (main): jxzhu at lanl.gov > Email (backup): physjxzhu at gmail.com > URL: http://theory.lanl.gov > ################################ > > > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- ################################ Jian-Xin Zhu, Ph.D Theoretical Division, MS B262 Los Alamos National Laboratory Los Alamos, New Mexico 87545 Phone: (505) 667 2363 Fax: (505) 665 4063 Email (main): jxzhu at lanl.gov Email (backup): physjxzhu at gmail.com URL: http://theory.lanl.gov ################################ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090318/92c8bc5d/attachment.htm From ndimakis at gmail.com Fri Mar 20 20:38:16 2009 From: ndimakis at gmail.com (Nicholas Dimakis) Date: Fri, 20 Mar 2009 14:38:16 -0500 Subject: [xcrysden] Problem with Charge Density 2D Map Message-ID: Hello I am trying to calculate a 2D charge density Map using XCrySDen. However when I click on submit button I get nothing ! ( no effect at all). My property file is from CRYSTAL06. Any ideas ? Thank you Nick -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090320/9ade88a5/attachment.htm From bobby at aust.edu.ng Sun Mar 22 13:05:43 2009 From: bobby at aust.edu.ng (Bobby) Date: Sun, 22 Mar 2009 13:05:43 +0100 Subject: [xcrysden] Error trying to compile Xcrysden on Ubuntu 8.04 Message-ID: <49C62997.9040603@aust.edu.ng> Hi guys am sysadmin for the African university of science and technology. of of our professor needs me to install Xcrydens to our computer labs which runs ubuntu 8.04. i downloaded the this package xc-1.5.17-src-all.tar.gz but and my Make.sys looks like this http://pastebin.com/f3038ae51 when i run make all i get the following error (.text+0xbe): undefined reference to `xcb_disconnect' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(OpenDis.o): In function `OutOfMemory': (.text+0x3fa): undefined reference to `xcb_disconnect' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(OpenDis.o): In function `XOpenDisplay': (.text+0x7e2): undefined reference to `xcb_get_setup' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(OpenDis.o): In function `XOpenDisplay': (.text+0xc29): undefined reference to `xcb_get_maximum_request_length' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_lock.o): In function `_XPutXCBBuffer': (.text+0xdd): undefined reference to `xcb_get_request_sent' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_lock.o): In function `_XPutXCBBuffer': (.text+0x30e): undefined reference to `xcb_get_request_sent' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_lock.o): In function `_XPutXCBBuffer': (.text+0x33d): undefined reference to `xcb_send_request' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_lock.o): In function `_XGetXCBBuffer': (.text+0x568): undefined reference to `xcb_get_request_sent' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_lock.o): In function `_XGetXCBBuffer': (.text+0x57b): undefined reference to `xcb_connection_has_error' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_lock.o): In function `_XCBUnlockDisplay': (.text+0x6ad): undefined reference to `xcb_xlib_unlock' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_lock.o): In function `_XCBUnlockDisplay': (.text+0x6e0): undefined reference to `xcb_get_request_sent' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_lock.o): In function `_XCBLockDisplay': (.text+0x78d): undefined reference to `xcb_xlib_lock' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_disp.o): In function `_XConnectXCB': (.text+0x94): undefined reference to `xcb_parse_display' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_disp.o): In function `_XConnectXCB': (.text+0x147): undefined reference to `xcb_connect_to_display_with_auth_info' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_disp.o): In function `_XConnectXCB': (.text+0x165): undefined reference to `xcb_get_file_descriptor' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_disp.o): In function `_XConnectXCB': (.text+0x18e): undefined reference to `xcb_generate_id' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_disp.o): In function `_XConnectXCB': (.text+0x199): undefined reference to `xcb_connection_has_error' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_disp.o): In function `_XConnectXCB': (.text+0x1c3): undefined reference to `xcb_connect' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `wait_or_poll_for_event': (.text+0x3ef): undefined reference to `xcb_wait_for_event' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `wait_or_poll_for_event': (.text+0x414): undefined reference to `xcb_poll_for_event' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `process_responses': (.text+0x4c3): undefined reference to `xcb_connection_has_error' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `process_responses': (.text+0x519): undefined reference to `xcb_xlib_unlock' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `process_responses': (.text+0x543): undefined reference to `xcb_xlib_lock' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `process_responses': (.text+0x5de): undefined reference to `xcb_poll_for_reply' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `_XReply': (.text+0x890): undefined reference to `xcb_xlib_unlock' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `_XReply': (.text+0x8bb): undefined reference to `xcb_wait_for_reply' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `_XAllocIDs': (.text+0xb60): undefined reference to `xcb_generate_id' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `_XIDHandler': (.text+0xb98): undefined reference to `xcb_generate_id' /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(xcb_io.o): In function `_XSend': (.text+0xc45): undefined reference to `xcb_flush' collect2: ld returned 1 exit status make[2]: *** [xcrys] Error 1 make[2]: Leaving directory `/opt/XCrySDen-1.5.17-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/opt/XCrySDen-1.5.17-src-all/C' make: *** [src-C] Error 2 root at goma:/opt/XCrySDen-1.5.17-src-all# what gives? i have been at this program for 3 days now. and would appreciate if anyone can point to me the right way to install Xcrysden on ubuntu. From tone.kokalj at ijs.si Mon Mar 23 17:03:32 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 23 Mar 2009 17:03:32 +0100 Subject: [xcrysden] Problem with Charge Density 2D Map In-Reply-To: References: Message-ID: <1237824212.29064.21.camel@walk.ijs.si> On Fri, 2009-03-20 at 14:38 -0500, Nicholas Dimakis wrote: > Hello > > I am trying to calculate a 2D charge density Map using XCrySDen. > However when I click on submit button I get nothing ! ( no effect at > all). > > My property file is from CRYSTAL06. You will need to provide better and more detailed information. One of the possible reasons is that you did not select neither contour nor colorplane on the corresponding controil window (i.e. "display color-plane" and "display isolines" checkbuttons) For more info see: http://www.xcrysden.org/doc/plane1control.html For CRYSTAL users also this: http://www.xcrysden.org/doc/crystal.html#__toc__30 Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Mon Mar 23 17:08:49 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 23 Mar 2009 17:08:49 +0100 Subject: [xcrysden] Error trying to compile Xcrysden on Ubuntu 8.04 In-Reply-To: <49C62997.9040603@aust.edu.ng> References: <49C62997.9040603@aust.edu.ng> Message-ID: <1237824529.29064.26.camel@walk.ijs.si> On Sun, 2009-03-22 at 13:05 +0100, Bobby wrote: > Hi guys am sysadmin for the African university of science and > technology. of of our professor needs me to install Xcrydens to our > computer labs which runs ubuntu 8.04. i downloaded the this package > xc-1.5.17-src-all.tar.gz > but and my > Make.sys looks like this http://pastebin.com/f3038ae51 when i run make > all i get the following error > > (.text+0xbe): undefined reference to `xcb_disconnect' > /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(OpenDis.o): > In function `OutOfMemory': > (.text+0x3fa): undefined reference to `xcb_disconnect' > /usr/lib/gcc/i486-linux-gnu/4.2.4/../../../../lib/libX11.a(OpenDis.o): > In function `XOpenDisplay': Seems like your libX11.a needs some functions from libxcb.a You may add -lxcb to X_LIB flag in Make.sys. If you don't have libxcb library, you need to install libxcb1-dev package, i.e.: apt-get install libxcb1-dev As an alternative, you may try with one of the precompiled versions. 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 swati at rcais.res.in Wed Mar 25 10:20:42 2009 From: swati at rcais.res.in (swati chaudhury) Date: Wed, 25 Mar 2009 02:20:42 -0700 (PDT) Subject: [xcrysden] Problem with Charge Density 2D Map Message-ID: <795544.62098.qm@web1213.biz.mail.gq1.yahoo.com> Hi Nicholas, Before going to plotting just do x lapw1 (if your system is non-magnatic) best of luck. --- On Sat, 21/3/09, Nicholas Dimakis wrote: > From: Nicholas Dimakis > Subject: [xcrysden] Problem with Charge Density 2D Map > To: xcrysden at democritos.it > Date: Saturday, 21 March, 2009, 1:08 AM > Hello > > I am trying to calculate a 2D charge density Map using > XCrySDen. However when I click on submit button I get > nothing? ! ( no effect at all). > > My property file is from CRYSTAL06. > > Any ideas ? > > > Thank you > > Nick > > > > -----Inline Attachment Follows----- > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > From ndimakis at gmail.com Thu Mar 26 01:19:36 2009 From: ndimakis at gmail.com (Nicholas Dimakis) Date: Wed, 25 Mar 2009 19:19:36 -0500 Subject: [xcrysden] Problem with Charge Density 2D Map In-Reply-To: <795544.62098.qm@web1213.biz.mail.gq1.yahoo.com> References: <795544.62098.qm@web1213.biz.mail.gq1.yahoo.com> Message-ID: Thank you. I already test it and it does work. Again thanks for providing this program to the community Nick On Wed, Mar 25, 2009 at 4:20 AM, swati chaudhury wrote: > > Hi Nicholas, > Before going to plotting just do x lapw1 (if your system is non-magnatic) > best of luck. > > --- On Sat, 21/3/09, Nicholas Dimakis wrote: > > > From: Nicholas Dimakis > > Subject: [xcrysden] Problem with Charge Density 2D Map > > To: xcrysden at democritos.it > > Date: Saturday, 21 March, 2009, 1:08 AM > > Hello > > > > I am trying to calculate a 2D charge density Map using > > XCrySDen. However when I click on submit button I get > > nothing ! ( no effect at all). > > > > My property file is from CRYSTAL06. > > > > Any ideas ? > > > > > > Thank you > > > > Nick > > > > > > > > -----Inline Attachment Follows----- > > > > _______________________________________________ > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090325/ace89027/attachment.htm