From xy45388 at gmail.com Wed May 3 22:55:52 2017 From: xy45388 at gmail.com (X Y) Date: Wed, 3 May 2017 22:55:52 +0200 Subject: [xcrysden] Cannot compile xcrysden because of XVisualInfo error Message-ID: Hello, when I compile I get stuck on the line with the unknown type name ?XVisualInfo? error. Because I have a windows 10 computer I compile inside the cygwin 32 bit environment I guess it has something to do with opengl. Last few days I installed everything of x11, opengl and so on but this error keeps popping up. I like to use xcrysden for exciting dft and exciting itself compiles fine. It is the opengl, xwindows part of xcrysden that makes the installation complicated. Has anybody seen this before or got a clue? Kind regards, Dave .... xcFont.c:395:7: let op: ?result? is deprecated: use Tcl_GetStringResult/Tcl_SetResult [-Wdeprecated-declarations] sprintf(interp->result, "error parsing dark font color, should be {red green blue}, but got %s", dark_argv); ^ In file included from xcFont.c:37:0: /usr/include/tcl.h:504:11: note: declared here char *result TCL_DEPRECATED_API("use Tcl_GetStringResult/Tcl_SetResult"); ^ In file included from xcFont.c:444:0: togl_struct.h: Op bovenste niveau: togl_struct.h:86:5: fout: unknown type name ?XVisualInfo? XVisualInfo *VisInfo; /* Visual info of the current */ ^ make[2]: *** [Makefile.cygwin:16: xcFont.o] Fout 1 make[2]: Map '/home/Dave/xcrysden-1.5.60/C' wordt verlaten make[1]: *** [Makefile:23: compile] Fout 2 make[1]: Map '/home/Dave/xcrysden-1.5.60/C' wordt verlaten make: *** [Makefile:77: src-C] Fout 2 Dave at DESKTOP-9JQLKA3 ~/xcrysden-1.5.60 My make.sys file: ================= ######################################################################### # # System-dependent definitions CYGWIN. # # EDIT ACCORDING TO YOUR OWN NEEDS !!! # ######################################################################## MAKE = make CYGWIN = -f Makefile.cygwin #------------------------------------------------------------------------ # compilers & flags #------------------------------------------------------------------------ CC = cc -g SHARED = -shared CFLAGS = -O2 #-mno-cygwin #-mcygwin CPPFLAGS = -DCYGWIN -DWIN32 -DUSE_FONTS -DNEAR_BUG -DUSE_INTERP_RESULT LDLIB = MATH = FC = g77 -O2 # -mcygwin FFLAGS = #------------------------------------------------------------------------ # Libraries and include files #------------------------------------------------------------------------ X_LIB = # -L/usr/X11R6/lib -lX11.dll X_INCDIR = TCL_PREFIX = /usr TCL_VER = 85 TCL_LIB = -L$(TCL_PREFIX)/lib -ltcl$(TCL_VER) -ltclstub$(TCL_VER) TK_LIB = -ltk$(TCL_VER) -ltkstub$(TCL_VER) GLU_LIB = -lglu32 GL_LIB = -lopengl32 -lgdi32 FFTW3_LIB = -lfftw3 # this is only used for some testing purposes #MESCHACH_LIB = TCLTK_SRC = /usr/src/tcltk-20080420-1 # on some machines this is needed: -I$(TCLTK_SRC)/tk/xlib TCL_INCDIR = -I$(TCLTK_SRC)/tcl/generic -DUSE_TCL_STUBS TK_INCDIR = -I$(TCLTK_SRC)/tk/generic -I$(TCLTK_SRC)/tk/win/ -DUSE_TK_STUBS -I$(TCLTK_SRC)/tk/xlib GL_INCDIR = -I/usr/include/opengl FFTW3_INCDIR = # this is only used for some testing purposes #MESCHACH_INCDIR = #------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20170503/16bc2d2c/attachment.htm From tone.kokalj at ijs.si Mon May 8 11:02:06 2017 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 08 May 2017 11:02:06 +0200 Subject: [xcrysden] Cannot compile xcrysden because of XVisualInfo error In-Reply-To: References: Message-ID: <1494234126.8263.3.camel@ijs.si> On Wed, 2017-05-03 at 22:55 +0200, X Y wrote: > Hello, > when I compile I get stuck on the line with the? unknown type name > ?XVisualInfo? error. > Because I have a windows 10 computer I compile inside the cygwin 32 > bit environment Edit your Make.sys file and remove the -DWIN32 from CPPFLAGS. Then try to recompile (make clean; make xcrysden) If it does not work then also remove or comment the "CYGWIN = -f Makefile.cygwin" line and recompile. Best regards, Tone --? J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia? (tel: +386-1- 477-3523 // fax: +386-1-251-9385) From xy45388 at gmail.com Mon May 8 19:41:13 2017 From: xy45388 at gmail.com (X Y) Date: Mon, 8 May 2017 19:41:13 +0200 Subject: [xcrysden] Cannot compile xcrysden because of XVisualInfo error In-Reply-To: <1494234126.8263.3.camel@ijs.si> References: <1494234126.8263.3.camel@ijs.si> Message-ID: Dear Tone, thanks for looking into it. With the changes I got this cc -g -O2 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 getline.o gridNormals.o fft3d.o fft_util.o shank3d.o shank_Hinv.o shank_util.o togl.o gl2ps.o sgiRasterFont.o sgiAux.o \ -o xcrys -lfftw3 -ltk85 -ltkstub85 -L/usr/lib -ltcl85 -ltclstub85 -lglu32 -lopengl32 -lgdi32 /usr/lib/gcc/i686-pc-cygwin/5.4.0/../../../../i686-pc-cygwin/bin/ld: cannot find -ltk85 /usr/lib/gcc/i686-pc-cygwin/5.4.0/../../../../i686-pc-cygwin/bin/ld: cannot find -ltkstub85 /usr/lib/gcc/i686-pc-cygwin/5.4.0/../../../../i686-pc-cygwin/bin/ld: cannot find -ltcl85 /usr/lib/gcc/i686-pc-cygwin/5.4.0/../../../../i686-pc-cygwin/bin/ld: cannot find -ltclstub85 collect2: error: ld returned 1 exit status make[2]: *** [Makefile:31: xcrys] Error 1 make[2]: Leaving directory '/home/Dave/xcrysden-1.5.60/C' make[1]: *** [Makefile:23: compile] Error 2 make[1]: Leaving directory '/home/Dave/xcrysden-1.5.60/C' make: *** [Makefile:77: src-C] Error 2 But it gave me a big hint that TCL_VER = 85 might be wrong too. Then I tried to change TCL_VER into 8.5, 8.5.19, 8.4 TCL_VER = 8.6 finally did something but gave other errors ( removed the middle part because the error trace is very long): cc -g -O2 -DCYGWIN -DUSE_FONTS -DNEAR_BUG -DUSE_INTERP_RESULT -DUSE_FONTS -I/usr/src/tcltk-20080420-1/tcl/generic -DUSE_TCL_STUBS -I/usr/src/tcltk-20080420-1/tk/generic -I/usr/src/tcltk-20080420-1/tk/win/ -DUSE_TK_STUBS -I/usr/src/tcltk-20080420-1/tk/xlib -I/usr/include/GL -c sgiRasterFont.c cc -g -O2 -DCYGWIN -DUSE_FONTS -DNEAR_BUG -DUSE_INTERP_RESULT -DUSE_FONTS -I/usr/src/tcltk-20080420-1/tcl/generic -DUSE_TCL_STUBS -I/usr/src/tcltk-20080420-1/tk/generic -I/usr/src/tcltk-20080420-1/tk/win/ -DUSE_TK_STUBS -I/usr/src/tcltk-20080420-1/tk/xlib -I/usr/include/GL -c sgiAux.c cc -g -O2 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 getline.o gridNormals.o fft3d.o fft_util.o shank3d.o shank_Hinv.o shank_util.o togl.o gl2ps.o sgiRasterFont.o sgiAux.o \ -o xcrys -lfftw3 -ltk8.6 -ltkstub8.6 -L/usr/lib -ltcl8.6 -ltclstub8.6 -lglu32 -lopengl32 -lgdi32 /usr/lib/libtclstub8.6.a(tclStubLib.o): In function `Tcl_InitStubs': /usr/src/debug/tcl-8.6.6-1/generic/tclStubLib.c:58: multiple definition of `Tcl_InitStubs' /usr/lib/libtk8.6.dll.a(d000001.o):(.text+0x0): first defined here xcAppInit.o: In function `XErrorFunction': /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:403: undefined reference to `XGetErrorText' xcAppInit.o: In function `XC_StereoCmd': /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:2626: undefined reference to `XOpenDisplay' /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:2628: undefined reference to `glXChooseVisual' /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:2631: undefined reference to `XFree' /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:2633: undefined reference to `XCloseDisplay' xcAppInit.o: In function `XC_DrawStyle3DCmd': /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:1778: undefined reference to `glGetBooleanv' /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:1774: undefined reference to `glDrawBuffer' xcAppInit.o: In function `XC_ShadeModel3DCmd': /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:1836: undefined reference to `glShadeModel' /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:1832: undefined reference to `glShadeModel' xcAppInit.o: In function `XC_PointSizeCmd': /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:1879: undefined reference to `glPointSize' xcAppInit.o: In function `main': /home/Dave/xcrysden-1.5.60/C/xcAppInit.c:437: undefined reference to `XSetErrorHandler' ..... /home/Dave/xcrysden-1.5.60/C/gl2ps.c:6051: undefined reference to `glPassThrough' /home/Dave/xcrysden-1.5.60/C/gl2ps.c:6042: undefined reference to `glPassThrough' /home/Dave/xcrysden-1.5.60/C/gl2ps.c:6048: undefined reference to `glPassThrough' gl2ps.o:/home/Dave/xcrysden-1.5.60/C/gl2ps.c:6045: more undefined references to `glPassThrough' follow collect2: error: ld returned 1 exit status make[2]: *** [Makefile:31: xcrys] Error 1 make[2]: Leaving directory '/home/Dave/xcrysden-1.5.60/C' make[1]: *** [Makefile:23: compile] Error 2 make[1]: Leaving directory '/home/Dave/xcrysden-1.5.60/C' make: *** [Makefile:77: src-C] Error 2 My Make.sys is now: ######################################################################### # # System-dependent definitions CYGWIN. # # EDIT ACCORDING TO YOUR OWN NEEDS !!! # ######################################################################## MAKE = make #CYGWIN = -f Makefile.cygwin #------------------------------------------------------------------------ # compilers & flags #------------------------------------------------------------------------ CC = cc -g SHARED = -shared CFLAGS = -O2 #-mno-cygwin #-mcygwin CPPFLAGS = -DCYGWIN -DUSE_FONTS -DNEAR_BUG -DUSE_INTERP_RESULT LDLIB = MATH = FC = g77 -O2 # -mcygwin FFLAGS = #------------------------------------------------------------------------ # Libraries and include files #------------------------------------------------------------------------ X_LIB = # -L/usr/X11R6/lib -lX11.dll X_INCDIR = TCL_PREFIX = /usr TCL_VER = 8.6 TCL_LIB = -L$(TCL_PREFIX)/lib -ltcl$(TCL_VER) -ltclstub$(TCL_VER) TK_LIB = -ltk$(TCL_VER) -ltkstub$(TCL_VER) GLU_LIB = -lglu32 GL_LIB = -lopengl32 -lgdi32 FFTW3_LIB = -lfftw3 # this is only used for some testing purposes #MESCHACH_LIB = TCLTK_SRC = /usr/src/tcltk-20080420-1 # on some machines this is needed: -I$(TCLTK_SRC)/tk/xlib TCL_INCDIR = -I$(TCLTK_SRC)/tcl/generic -DUSE_TCL_STUBS TK_INCDIR = -I$(TCLTK_SRC)/tk/generic -I$(TCLTK_SRC)/tk/win/ -DUSE_TK_STUBS -I$(TCLTK_SRC)/tk/xlib GL_INCDIR = -I/usr/include/GL FFTW3_INCDIR = # this is only used for some testing purposes #MESCHACH_INCDIR = #------------------------------------------------------------------------ Kind regards, Dave 2017-05-08 11:02 GMT+02:00 Tone Kokalj : > On Wed, 2017-05-03 at 22:55 +0200, X Y wrote: > > Hello, > > when I compile I get stuck on the line with the unknown type name > > ?XVisualInfo? error. > > Because I have a windows 10 computer I compile inside the cygwin 32 > > bit environment > > Edit your Make.sys file and remove the -DWIN32 from CPPFLAGS. > Then try to recompile (make clean; make xcrysden) > > If it does not work then also remove or comment the > "CYGWIN = -f Makefile.cygwin" line and recompile. > > Best regards, Tone > -- > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1- > 477-3523 // fax: +386-1-251-9385) > > _______________________________________________ > 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/20170508/d0069ef0/attachment.htm From matic.poberznik at gmail.com Tue May 9 10:20:42 2017 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Tue, 9 May 2017 10:20:42 +0200 Subject: [xcrysden] Cannot compile xcrysden because of XVisualInfo error In-Reply-To: References: <1494234126.8263.3.camel@ijs.si> Message-ID: Dear Dave, > But it gave me a big hint that TCL_VER = 85 > might be wrong too. > Then I tried to change TCL_VER into 8.5, 8.5.19, 8.4 > TCL_VER = 8.6 finally did something but gave other errors The correct version of tcl (TCL_VER) should definitely be 8.5 > > TCL_PREFIX = /usr > TCL_VER = 8.6 > TCL_LIB = -L$(TCL_PREFIX)/lib -ltcl$(TCL_VER) -ltclstub$(TCL_VER) > TK_LIB = -ltk$(TCL_VER) -ltkstub$(TCL_VER) > GLU_LIB = -lglu32 > GL_LIB = -lopengl32 -lgdi32 > FFTW3_LIB = -lfftw3 > # this is only used for some testing purposes > #MESCHACH_LIB = The error probably occurs because the compiler doesn't find your tcl libraries. The TCL_LIB variable should point to where the libraries are located in your system. ... -L/path/to/tcl-lib/lib -ltcl8.5 ... best regards, Matic Poberznik -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia From wenlibin02 at hotmail.com Tue May 9 16:17:43 2017 From: wenlibin02 at hotmail.com (? ??) Date: Tue, 9 May 2017 14:17:43 +0000 Subject: [xcrysden] Determine the angstrom to pixel ratio for printed images Message-ID: Dear all,? I would like to print some?.xsf structure files using XCrysDen script. My .xsf?files are exactly?of?the same structure (cubic diamond), but have different orientations?relative to the?cartesian?directions x, y, z. The problem is the printed images?have different sizes of atoms.? To summarize, my question is, Can I fix the angstrom/pixel value before printing? Alternatively, can I know the angstrom/pixel value after the printing (I do not want to do the calibration myself since there are many structure files)? Another solution to this problem is to understand how XCrysDen determines the angstrom/pixel at the beginning of opening a structure. Unfortunately, the src code is too complex for me to find out the answer. Actually, it is enough to determine the relative values of angstrom/pixel for different structure files. Libin From matic.poberznik at gmail.com Wed May 10 15:09:02 2017 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Wed, 10 May 2017 15:09:02 +0200 Subject: [xcrysden] Determine the angstrom to pixel ratio for printed images In-Reply-To: References: Message-ID: <72ab1e4a-aa50-b08c-9ceb-719ac07bda6c@gmail.com> Dear Libin, > Can I fix the angstrom/pixel value before printing? Alternatively, can I know the angstrom/pixel value after the printing (I do not want to do the calibration myself since there are many structure files)? > Another solution to this problem is to understand how XCrysDen determines the angstrom/pixel at the beginning of opening a structure. Unfortunately, the src code is too complex for me to find out the answer. > > Actually, it is enough to determine the relative values of angstrom/pixel for different structure files. XCrysDen doesn't determine the angstrom/pixel ration instead it determines the display bounding box from the input structure (for example it uses the crystal cell parameters to determine the display size for crystals). So if you're cell remains the same the size of atoms should as well. A way to ensure the same orientation and zoom (for structures with the same cell parameters) is by using "Save current state and structure" option, i.e. File => Save Current State and Structure This will create a file *.xcrysden suffix. You can "load" an alternative xsf file into this script and the zoom and orientation will remain the same. You do this by opening the *.xcrysden file with a text editor and editing the "STRUCTURE-PART" of the file. (i.e. delete all structure data and replace the line: ::scripting::open --xsf $system(SCRDIR)/xc_xsf.$system(PID) with ::scripting::open --xsf /path/to/xsf/name.xsf where name.xsf is your xsf file (if it's in the current working directory the path isn't needed) You open the script file with the command: xcrysden -s nameofscript.xcrysden Further information for scripting files is available here: http://www.xcrysden.org/doc/scripting.html Also when posting to the mailing list please state your name and affiliation. Best Regards, Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia From wenlibin02 at hotmail.com Thu May 11 05:12:56 2017 From: wenlibin02 at hotmail.com (?? ?) Date: Thu, 11 May 2017 03:12:56 +0000 Subject: [xcrysden] Determine the angstrom to pixel ratio for printed images In-Reply-To: <72ab1e4a-aa50-b08c-9ceb-719ac07bda6c@gmail.com> References: , <72ab1e4a-aa50-b08c-9ceb-719ac07bda6c@gmail.com> Message-ID: Dear Poberznik, Thank you for your reply. I am sorry that I did not state my problem clearly. When I said "my .xsf files are exactly of the same structure", I mean the physical structures are the same but the xyz coordinates are not the same. To make things clear, let's take the cubic diamond as an example. I have two structure files. The first one has cell vectors: 3.5667901038999998 0.0000000000000000 0.0000000000000000 0.0000000000000000 3.5667901038999998 0.0000000000000000 0.0000000000000000 0.0000000000000000 3.5667901038999998 while the second one has cell vectors rotated 45 degrees along z axis: 2.5221014695367603 2.5221014695367603 0.0000000000000000 -2.5221014695367603 2.5221014695367603 0.0000000000000000 0.0000000000000000 0.0000000000000000 3.5667901038999998 and the atoms are rotated correspondingly. Thus these two .xsf files are different but the physical structures remain exactly the same. The problem is that when I opened these two files using xcrysden, the atoms' sizes are different. I think it is caused by how xcrysden determines the display bounding box from the input structure, as you have mentioned in your reply. If I know the way xcrysden determines the display bounding box from the input structure, I can determine the size ratio of atoms between the two displayed images. Can you give me some hints on this? Any suggestion will of great help. Thank you! The .xcrysden files with cubic diamond structures are attached for reference. The file named 0.xcrysden is the one not tilted, while the file 45.xcrysden is 45 degrees titled. Libin Wen Shanghai Jiao Tong University, Shanghai, China From: xcrysden-bounces at democritos.it on behalf of Matic Poberznik Sent: Wednesday, May 10, 2017 21:09 To: XCrySDen mailing list Subject: Re: [xcrysden] Determine the angstrom to pixel ratio for printed images ? Dear Libin, > Can I fix the angstrom/pixel value before printing? Alternatively, can I know the angstrom/pixel value after the printing (I do not want to do the calibration myself since there are many structure files)? > Another solution to this problem is to understand how XCrysDen determines the angstrom/pixel at the beginning of opening a structure. Unfortunately, the src code is too complex for me to find out the answer. > > Actually, it is enough to determine the relative values of angstrom/pixel for different structure files. XCrysDen doesn't determine the angstrom/pixel ration instead it determines the display bounding box from the input structure (for example it uses the crystal cell parameters to determine the display size for crystals). So if you're cell remains the same the size of atoms should as well. A way to ensure the same orientation and zoom (for structures with the same cell parameters) is by using "Save current state and structure" option, i.e. File => Save Current State and Structure This will create a file *.xcrysden suffix. You can "load" an alternative xsf file into this script and the zoom and orientation will remain the same. You do this by opening the *.xcrysden file with a text editor and editing the "STRUCTURE-PART" of the file. (i.e. delete all structure data and replace the line: ::scripting::open --xsf $system(SCRDIR)/xc_xsf.$system(PID) with ::scripting::open --xsf /path/to/xsf/name.xsf where name.xsf is your xsf file (if it's in the current working directory the path isn't needed) You open the script file with the command: xcrysden -s nameofscript.xcrysden Further information for scripting files is available here: http://www.xcrysden.org/doc/scripting.html Also when posting to the mailing list please state your name and affiliation. Best Regards, Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden -------------- next part -------------- A non-text attachment was scrubbed... Name: 0.xcrysden Type: application/octet-stream Size: 29698 bytes Desc: 0.xcrysden Url : http://www.democritos.it/pipermail/xcrysden/attachments/20170511/4ceafa3b/attachment-0002.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: 45.xcrysden Type: application/octet-stream Size: 29698 bytes Desc: 45.xcrysden Url : http://www.democritos.it/pipermail/xcrysden/attachments/20170511/4ceafa3b/attachment-0003.obj From Fabian.T89 at web.de Thu May 11 10:04:58 2017 From: Fabian.T89 at web.de (fabian) Date: Thu, 11 May 2017 10:04:58 +0200 Subject: [xcrysden] Progblem installing xcrysden under cygwin Message-ID: <814299b0-d1c3-b791-9198-5d54d6aec91f@web.de> Dear all I tried to install the version supplied in "xcrysden-1.5.60-cygwin.tar.gz" under cygwin. I understand that additional packages are necessary to run the software. I am no experienced user of cygwin by any means to be honest, and have little experienceworking with linux. After installation i went into the cygwin64\xcrysden-1.5.60-bin-shared\scripts folder and executed xcConfigure.sh. I have Xming 6.9.0.31 installed and running. After this i tried to open xcrysden. But i get the following error: C:/cygwin64/xcrysden-1.5.60-bin-shared/bin/xcrys.exe: error while loading shared libraries: libtk8.5.dll: cannot open shared object file: No such file or directory In C:\cygwin64\lib there is a file called libtk8.6.dll.a however. I tried to find the package that is missing but via the cygwin.exe installer but there are a lot and the obvious ones did not change the behaviour. I would really appreciate your help! All the best fabian From matic.poberznik at gmail.com Thu May 11 11:53:36 2017 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Thu, 11 May 2017 11:53:36 +0200 Subject: [xcrysden] Progblem installing xcrysden under cygwin In-Reply-To: <814299b0-d1c3-b791-9198-5d54d6aec91f@web.de> References: <814299b0-d1c3-b791-9198-5d54d6aec91f@web.de> Message-ID: <85de1b30-29e9-b194-abfc-b02ff24ce8a4@gmail.com> Dear Fabian, > I tried to install the version supplied in > "xcrysden-1.5.60-cygwin.tar.gz" under cygwin. I understand that > additional packages are necessary to run the software. Yes, the additional required packages are listed in README.cygwin. I think the easiest way to install them is with the apt-cyg utility: https://github.com/transcode-open/apt-cyg after installing this utility you can install any other package with the command: apt-cyg install package-name where package-name is the name of the package. For example tcl-tk version 8.5 is required and you can then install it by typing: apt-cyg install tcl-tk-8.5.11-1 You can search for package names on this site: https://cygwin.com/cgi-bin2/package-grep.cgi > I have Xming 6.9.0.31 installed and running. As I understand it, the Xming utility is not part of cygwin, but is used to emulate x-server for Windows. All the required packages must be installed within the cygwin environment so for x-server you must install the cygwin equivalent, e.g. xorg-server-1.19.3-2 You then start the x environment by typing: startx Additional configuration (after you install all the packages) shouldn't be required, you can run xcrysden simply by typing in the cygwin terminal from the xcrysden extracted directory (where README.cygwin is located): ./xcrysden If you add this directory to the $PATH variable in cygwin you can then run it from any other directory as well. Hope this helps, Best Regards, Matic Poberznik -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia From matic.poberznik at gmail.com Thu May 11 12:05:59 2017 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Thu, 11 May 2017 12:05:59 +0200 Subject: [xcrysden] Determine the angstrom to pixel ratio for printed images In-Reply-To: References: <72ab1e4a-aa50-b08c-9ceb-719ac07bda6c@gmail.com> Message-ID: <571c96a6-435d-6136-e352-fea1699e6458@gmail.com> Dear Wen Libin, > Dear Poberznik, > > Thank you for your reply. I am sorry that I did not state my problem clearly. > When I said "my .xsf files are exactly of the same structure", I mean the physical structures > are the same but the xyz coordinates are not the same. > I see the issue now, but unfortunately cannot offer a simple solution. From tomoki.ame at gmail.com Fri May 12 10:57:53 2017 From: tomoki.ame at gmail.com (=?UTF-8?B?5bGx5Y+j5Ly057SA?=) Date: Fri, 12 May 2017 17:57:53 +0900 Subject: [xcrysden] How to output a bxsf file in primitive Brillouin zone Message-ID: Dear Xcrysden Users, For checking fermi surface, I want to output a bxsf file written in a primitive Brillouin zone. But as "http://www.xcrysden.org/doc/XSF.html#bxsf" says, default bxsf file is written in a reciprocal unit cell. Does anyone know how to output fermi surface written in a primitive Brillouin zone? With best regards, Tomoki Sugiuchi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20170512/4022ad24/attachment.htm From xy45388 at gmail.com Sun May 14 23:43:55 2017 From: xy45388 at gmail.com (X Y) Date: Sun, 14 May 2017 23:43:55 +0200 Subject: [xcrysden] Cannot compile xcrysden because of XVisualInfo error In-Reply-To: References: <1494234126.8263.3.camel@ijs.si> Message-ID: Dear Matic, Thanks. I got further. Still there are two errors left. I get now: cc -g -O2 -DCYGWIN -DUSE_FONTS -DNEAR_BUG -DUSE_INTERP_RESULT -DUSE_FONTS -I~/tcl/unix -I~/tcl/generic -DUSE_TCL_STUBS -I~/tk/unix -I~/tk/generic -I~/tk/win/ -DUSE_TK_STUBS -I~/tk/xlib -I/usr/include -I/usr/X11R6/include -c sgiAux.c cc -g -O2 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 getline.o gridNormals.o fft3d.o fft_util.o shank3d.o shank_Hinv.o shank_util.o togl.o gl2ps.o sgiRasterFont.o sgiAux.o \ -o xcrys -lfftw3 -ltk8.5 -ltkstub8.5 -L~/tcl/unix -ltcl8.5 -ltclstub8.5 -lglut -lGLU -lGL -L/usr/X11R6/lib -lXmu -lXi -lXext -lX11 /usr/lib/gcc/i686-pc-cygwin/5.4.0/../../../../i686-pc-cygwin/bin/ld: cannot find -ltk8.5 /usr/lib/gcc/i686-pc-cygwin/5.4.0/../../../../i686-pc-cygwin/bin/ld: cannot find -ltcl8.5 collect2: error: ld returned 1 exit status make[2]: *** [Makefile:31: xcrys] Error 1 make[2]: Leaving directory '/home/Dave/xcrysden-1.5.60/C' make[1]: *** [Makefile:23: compile] Error 2 make[1]: Leaving directory '/home/Dave/xcrysden-1.5.60/C' make: *** [Makefile:77: src-C] Error 2 Dave at DESKTOP-9JQLKA3 ~/xcrysden-1.5.60 I think it is because I don't have libtcl8.5.a and libtk8.5.a. I searched the whole subtree of cygwin for them. Strangely enough, I do have the stub files libtclstub8.5.a and libtkstub8.5.a And I don't have errors with installing tcl and tk. Kind regards, Dave My Make.sys is: ######################################################################### # # System-dependent definitions CYGWIN. # # EDIT ACCORDING TO YOUR OWN NEEDS !!! # ######################################################################## MAKE = make #CYGWIN = -f Makefile.cygwin #------------------------------------------------------------------------ # compilers & flags #------------------------------------------------------------------------ CC = cc -g SHARED = -shared CFLAGS = -O2 #-mno-cygwin #-mcygwin CPPFLAGS = -DCYGWIN -DUSE_FONTS -DNEAR_BUG -DUSE_INTERP_RESULT LDLIB = MATH = FC = g77 -O2 # -mcygwin FFLAGS = #------------------------------------------------------------------------ # Libraries and include files #------------------------------------------------------------------------ X_LIB = -L/usr/X11R6/lib -lXmu -lXi -lXext -lX11 X_INCDIR = -I/usr/X11R6/include TCL_PREFIX = ~/tcl TCL_VER = 8.5 TCL_LIB = -L$(TCL_PREFIX)/unix -ltcl$(TCL_VER) -ltclstub$(TCL_VER) TK_LIB = -ltk$(TCL_VER) -ltkstub$(TCL_VER) GLU_LIB = -lglut -lGLU GL_LIB = -lGL FFTW3_LIB = -lfftw3 # this is only used for some testing purposes #MESCHACH_LIB = TCLTK_SRC = ~ # on some machines this is needed: -I$(TCLTK_SRC)/tk/xlib TCL_INCDIR = -I$(TCLTK_SRC)/tcl/unix -I$(TCLTK_SRC)/tcl/generic -DUSE_TCL_STUBS TK_INCDIR = -I$(TCLTK_SRC)/tk/unix -I$(TCLTK_SRC)/tk/generic -I$(TCLTK_SRC)/tk/win/ -DUSE_TK_STUBS -I$(TCLTK_SRC)/tk/xlib GL_INCDIR = -I/usr/include FFTW3_INCDIR = # this is only used for some testing purposes #MESCHACH_INCDIR = #------------------------------------------------------------------------ 2017-05-09 10:20 GMT+02:00 Matic Poberznik : > Dear Dave, > > > But it gave me a big hint that TCL_VER = 85 > > might be wrong too. > > Then I tried to change TCL_VER into 8.5, 8.5.19, 8.4 > > TCL_VER = 8.6 finally did something but gave other errors > > The correct version of tcl (TCL_VER) should definitely be 8.5 > > > > > TCL_PREFIX = /usr > > TCL_VER = 8.6 > > TCL_LIB = -L$(TCL_PREFIX)/lib -ltcl$(TCL_VER) -ltclstub$(TCL_VER) > > TK_LIB = -ltk$(TCL_VER) -ltkstub$(TCL_VER) > > GLU_LIB = -lglu32 > > GL_LIB = -lopengl32 -lgdi32 > > FFTW3_LIB = -lfftw3 > > # this is only used for some testing purposes > > #MESCHACH_LIB = > > The error probably occurs because the compiler doesn't find your tcl > libraries. The TCL_LIB variable should point to where the libraries are > located in your system. > > ... -L/path/to/tcl-lib/lib -ltcl8.5 ... > > > best regards, > > Matic Poberznik > -- > Matic Poberznik > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > _______________________________________________ > 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/20170514/c5624ef7/attachment.htm From gsabo at crimson.ua.edu Mon May 15 08:02:29 2017 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Mon, 15 May 2017 00:02:29 -0600 Subject: [xcrysden] Cannot compile xcrysden because of XVisualInfo error In-Reply-To: References: <1494234126.8263.3.camel@ijs.si> Message-ID: If it helps, I'm running Windows 10 Home, and the following seems to work at least for me. Compiling xcrysden on 64 bit Windows ------------------------------------ Downloaded the 64 bit version of Cygwin (setup-x86_64.exe) from: http://cygwin.com/ Ran setup-x86_64.exe and installed the following packages. Packages likely needed to run xcrysden: tcl (8.5.18-1) tcl-devel (8.5.18-1) tcl-tk (8.5.18-1) tcl-tk-devel (8.5.18-1) fftw3 (3.3.6-pl1-1) libGL1 (17-0.6-1) libGLU1 (9.0.0-1) xorg-server (1.19.2-1) bash (4.4.12-3) bc (1.06.95-2) coreutils (8.26-2) gawk (4.1.4-3) grep (3.0-2) gzip (1.8-1) ImageMagick (6.9.5.7-2) less (487-1) xinit (1.3.4-14) gcc-fortran (5.4.0-1) wget (1.19-1) Additional packages likely needed to compile xcrysden: make (4.2.1-2) libX11-devel (1.6.4-1) libGL-devel (17.0.6-1) libGLU-devel (9.0.0-1) libfftw3-devel (3.3.6-pl1-1) libXmu-devel (1.1.2-1) libQtOpenGL4-devel (4.8.7-4) patch (2.7.4-1) Downloaded xcrysden source package (xcrysden-1.5.60.tar.gz) from: http://www.xcrysden.org/Download.html Placed xcrysden-1.5.60.tar.gz in Cygwin installation directory (C:\cygwin64). Clicked on search button on the desktop, searched and clicked on "Cygwin64 Terminal". In the terminal that opened, entered the command: startxwin & In the system tray, right-clicked on the Cygwin icon and opened an XTerm (like that shown in '2.' at https://wellingtongoncalves.wordpress.com/2016/08/10/running-a-linux-application-using-cygwinx/ ) In the Xterm window, entered the following commands: cd / tar xvf xcrysden-1.5.60.tar.gz cd xcrysden-1.5.60 chmod +x xcrysden echo 'export PATH=$PATH:/xcrysden-1.5.60' >> ~/.bashrc source ~/.bashrc Placed the attached Make.cygwin64_win10 in the xcrysden system directory (C:\cygwin64\xcrysden-1.5.60\system) and cygwin.patch in the xcrysden Tcl directory (C:\cygwin64\xcrysden-1.5.60\Tcl). Then, in the same terminal, entered the following commands: cp /xcrysden-1.5.60/system/Make.cygwin64_win10 Make.sys patch -b /xcrysden-1.5.60/Tcl/cygwin.tcl /xcrysden-1.5.60/Tcl/cygwin.patch make xcrysden xcrysden References [1] http://www.democritos.it/pipermail/xcrysden/2014-July/001635.html [2] http://www.democritos.it/pipermail/xcrysden/2013-November/001490.html -------------- next part -------------- 38c38 < rename exec _tcl_exec --- > #rename exec _tcl_exec -------------- next part -------------- ######################################################################### # # System-dependent definitions CYGWIN. # # EDIT ACCORDING TO YOUR OWN NEEDS !!! # ######################################################################## MAKE = make CYGWIN = -f Makefile.cygwin #------------------------------------------------------------------------ # compilers & flags #------------------------------------------------------------------------ CC = cc -g SHARED = -shared CFLAGS = -O2 #-mno-cygwin #-mcygwin CPPFLAGS = -DCYGWIN -DUSE_FONTS -DNEAR_BUG -DUSE_INTERP_RESULT LDLIB = MATH = FC = gfortran -O2 # -mcygwin FFLAGS = #------------------------------------------------------------------------ # Libraries and include files #------------------------------------------------------------------------ FFTW3_LIB = -L/lib -lfftw3.dll X_LIB = -L/lib -lX11.dll -lXmu $(FFTW3_LIB) # -L/usr/X11R6/lib -lX11.dll X_INCDIR = TCL_PREFIX = /lib TCL_VER = 8.5 TCL_LIB = -L$(TCL_PREFIX) -ltcl TK_LIB = -ltk GLU_LIB = -lGLU.dll #-lglu32 GL_LIB = -lGL #-lopengl32 -lgdi32 # this is only used for some testing purposes #MESCHACH_LIB = TCLTK_SRC = /usr/include/ # on some machines this is needed: -I$(TCLTK_SRC)/tk/xlib TCL_INCDIR = -I$(TCLTK_SRC)/tcl$(TCL_VER)/generic -DUSE_TCL_STUBS TK_INCDIR = -I$(TCLTK_SRC)/tcl$(TCL_VER)/generic -DUSE_TK_STUBS GL_INCDIR = -I/usr/include/GL FFTW3_INCDIR = -I/usr/include # this is only used for some testing purposes #MESCHACH_INCDIR = From matic.poberznik at gmail.com Mon May 15 11:29:03 2017 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Mon, 15 May 2017 11:29:03 +0200 Subject: [xcrysden] Cannot compile xcrysden because of XVisualInfo error In-Reply-To: References: <1494234126.8263.3.camel@ijs.si> Message-ID: <1c15822f-f689-f91e-1f07-e5cb338a2ab4@gmail.com> Dear Dave, > /usr/lib/gcc/i686-pc-cygwin/5.4.0/../../../../i686-pc-cygwin/bin/ld: > cannot find -ltk8.5 > /usr/lib/gcc/i686-pc-cygwin/5.4.0/../../../../i686-pc-cygwin/bin/ld: > cannot find -ltcl8.5 > collect2: error: ld returned 1 exit status It still seems like it doesn't find the libraries it needs. Can you provide the output of the command, from the cygdrive topdir: find . -iname "lib*tcl" 2>/dev/null and if you are using apt-cyg: apt-cyg list to see which packages you have installed. Or just make sure you have all the packages installed that Gavin Abo mentioned. As for his procedure it should work, though I think the patching should no longer be required (as far as I remember from my compilation, I could be wrong). There is also a precompiled version for Windows, but I'm guessing that it doesn't work for you or is there a reason that you have to compile from source? Here is the version of Make.sys is used if it helps in any way (on my system the libraries are located in /usr/ directory) : ######################################################################### # # System-dependent definitions CYGWIN. # # EDIT ACCORDING TO YOUR OWN NEEDS !!! # ######################################################################## MAKE = make CYGWIN = -f Makefile.cygwin #------------------------------------------------------------------------ # compilers & flags #------------------------------------------------------------------------ CC = gcc -g SHARED = -shared CFLAGS = -O2 #-mno-cygwin #-mcygwin CPPFLAGS = -DCYGWIN -DUSE_FONTS -DNEAR_BUG -D__int64="long long int" LDLIB = MATH = FC = gfortran -O2 # -mcygwin FFLAGS = #------------------------------------------------------------------------ # Libraries and include files #------------------------------------------------------------------------ X_LIB = -L/usr/X11R6/lib -lX11 -lXmu X_INCDIR = TCL_PREFIX = /usr TCL_VER = 8.5 TCL_LIB = -L$(TCL_PREFIX)/lib -ltcl$(TCL_VER) TK_LIB = -ltk$(TCL_VER) GLU_LIB = -lGLU GL_LIB = -lGL FFTW3_LIB = -lfftw3 # this is only used for some testing purposes #MESCHACH_LIB = TCLTK_SRC = /usr/include/tcl$(TCL_VER) # on some machines this is needed: -I$(TCLTK_SRC)/tk/xlib TCL_INCDIR = -I$(TCLTK_SRC)/generic -DUSE_TCL_STUBS TK_INCDIR = GL_INCDIR = -I/usr/include FFTW3_INCDIR = # this is only used for some testing purposes Hope this helps and best regards, Matic -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia From matic.poberznik at gmail.com Mon May 15 11:35:59 2017 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Mon, 15 May 2017 11:35:59 +0200 Subject: [xcrysden] Cannot compile xcrysden because of XVisualInfo error In-Reply-To: <1c15822f-f689-f91e-1f07-e5cb338a2ab4@gmail.com> References: <1494234126.8263.3.camel@ijs.si> <1c15822f-f689-f91e-1f07-e5cb338a2ab4@gmail.com> Message-ID: <823b1ac3-e33f-cefc-009c-1d8e9ba9bac7@gmail.com> I'm sorry I made a mistake > > find . -iname "lib*tcl" 2>/dev/null > change the command to: find . -iname "*lib*tcl*" 2>/dev/null and make sure you run it from cygdrive topdir and not you home directory (i.e. cd ../../ from homedir) Best Regards, Matic -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia From janatipoor_najmeh at yahoo.com Wed May 24 21:03:38 2017 From: janatipoor_najmeh at yahoo.com (Najmeh Janati poor) Date: Wed, 24 May 2017 19:03:38 +0000 (UTC) Subject: [xcrysden] molecular orbital(Lumo&Homo) References: <1965774143.1686276.1495652618414.ref@mail.yahoo.com> Message-ID: <1965774143.1686276.1495652618414@mail.yahoo.com> Dear all,How to see low unoccupied molecular orbital and high occupied molecular orbital with xcrysden??Thanking YouRegardsNajmeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20170524/0ba20544/attachment.htm From janatipoor_najmeh at yahoo.com Sun May 28 12:20:15 2017 From: janatipoor_najmeh at yahoo.com (Najmeh Janati poor) Date: Sun, 28 May 2017 10:20:15 +0000 (UTC) Subject: [xcrysden] visualize HOMO and LUMO References: <328000277.1664902.1495966815099.ref@mail.yahoo.com> Message-ID: <328000277.1664902.1495966815099@mail.yahoo.com> Dear all, Does anyone know how to visualize HOMO and LUMO based solely on output files from Siesta ?? ?RegardsNajmeh -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20170528/8444dbc6/attachment.htm From matic.poberznik at gmail.com Tue May 30 11:06:55 2017 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Tue, 30 May 2017 11:06:55 +0200 Subject: [xcrysden] visualize HOMO and LUMO In-Reply-To: <328000277.1664902.1495966815099@mail.yahoo.com> References: <328000277.1664902.1495966815099.ref@mail.yahoo.com> <328000277.1664902.1495966815099@mail.yahoo.com> Message-ID: Dear Najmeh, > > Does anyone know how to visualize HOMO and LUMO based solely on output > files from Siesta ? > Typically an alternative, "postprocessing" output is needed (i.e. a file where the the charge density corresponding to each orbital is written on a space grid). A tool is available to convert such siesta output to xsf format for visualization in xcrysden (courtesy of Andrei Postnikov) and is described here: http://www.xcrysden.org/doc/sies2xsf.html See also his lecture where the usage is explained in more detail: http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-visual.pdf Hope this helps, Best Regards, Matic -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia