From jameslipd at gmail.com Mon Nov 9 15:51:53 2009 From: jameslipd at gmail.com (Jiaye Li) Date: Mon, 9 Nov 2009 22:51:53 +0800 Subject: [xcrysden] Compile error Message-ID: Dear all I am new to xcrysden and pwscf. I tried to compile xcrysden-1.5.21-src-all on the fc11(i586) system. The FC is ifort10 and gcc is icc10 but when I type 'make all', it reported the error: make[2]: *** [linux] Error 1 mv: cannot move `/home/jy/Download/XCrySDen-1. 5.21-src-all/external/usr/local/lib/pkgconfig' to `/home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/pkgconfig': Directory not empty mv: cannot move `/home/jy/Download/XCrySDen-1.5.21-src-all/external/usr/local/include/GL' to `/home/jy/Download/XCrySDen-1.5.21-src-all/external/include/GL': Directory not empty and my Make.sys is: ######################################################################### # # System-dependent definitions for Linux. # # EDIT ACCORDING TO YOUR OWN NEEDS !!! # ######################################################################## #------------------------------------------------------------------------ # 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 -funroll-loops -fPIC -DUSE_FONTS CC = icc #LDLIB = -ldl MATH = -lm FFLAGS = -O2 FC = ifort #------------------------------------------- #debug options #CFLAGS = -ansi -g -fPIC #------------------------------------------- #------------------------------------------------------------------------ # X-libraries & include files # # for STATIC compilation one should add: -lpthread #------------------------------------------------------------------------ X_LIB = -L/usr/X11R6/lib -lXmu -lX11 -lXext X_INCDIR = -I/usr/X11R6/include ### ### use EITHER THIS: ### #-Possibility-1---------------------------------------------------------- # # If you want to use your own libraries and include files, # then set *_LIB and *_INCDIR variables below accordingly: # #------------------------------------------------------------------------ #COMPILE_TCLTK = no #COMPILE_MESA = no # # Libraries # #TK_LIB = -ltk8.5 #TCL_LIB = -ltcl8.5 #GLU_LIB = -lGLU #GL_LIB = -lGL # # Include directories # #TCL_INCDIR = #TK_INCDIR = #GL_INCDIR = #------------------------------------------------------------------------ ### ### 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 = linux # # # # # Libraries (dynamic loading) # # for shared linking the libraries postfix should be .so # # for static linking the libraries postfix should be .a # # TCL_LIB = -L$(TOPDIR)/external/lib -ltcl$(TCL_VER2) TK_LIB = -L$(TOPDIR)/external/lib -ltk$(TCL_VER2) GLU_LIB = -L$(TOPDIR)/external/lib -lGLU GL_LIB = -L$(TOPDIR)/external/lib -lGL # # # # # Include directories # # TCL_INCDIR = -I$(TOPDIR)/external/src/tcl$(TCL_VER3)/generic TK_INCDIR = -I$(TOPDIR)/external/src/tk$(TCL_VER3)/generic GL_INCDIR = -I$(TOPDIR)/external/include #------------------------------------------------------------------------ Could anybody help me to find out what's wrong with it? Thanks -- Sincerely yours Jiaye Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20091109/0a0cccce/attachment.htm From tone.kokalj at ijs.si Fri Nov 20 07:57:34 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 20 Nov 2009 07:57:34 +0100 Subject: [xcrysden] Compile error In-Reply-To: References: Message-ID: <1258700254.13342.20.camel@walk.ijs.si> On Mon, 2009-11-09 at 22:51 +0800, Jiaye Li wrote: > Dear all > > I am new to xcrysden and pwscf. I tried to compile > xcrysden-1.5.21-src-all on the fc11(i586) system. The FC is ifort10 > and gcc is icc10 > > but when I type 'make all', it reported the error: > > make[2]: *** [linux] Error 1 > mv: cannot move `/home/jy/Download/XCrySDen-1. > 5.21-src-all/external/usr/local/lib/pkgconfig' to > `/home/jy/Download/XCrySDen-1.5.21-src-all/external/lib/pkgconfig': Don't know what precisely went wrong. But apparently Mesa was compiled. Hence you may fix it manually. Goto $XCRYSDEN_TOPDIR/external/src/Mesa-7.2/lib directory and copy libGL.so* and libGLU.so into $XCRYSDEN_TOPDIR/external/lib/ directory. Then also copy: cp -r $XCRYSDEN_TOPDIR/external/src/Mesa-7.2/include/GL $XCRYSDEN_TOPDIR/external/include/ 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 emmanuel.betranhandy at polytechnique.edu Mon Nov 30 16:44:40 2009 From: emmanuel.betranhandy at polytechnique.edu (Emmanuel Betranhandy) Date: Mon, 30 Nov 2009 16:44:40 +0100 Subject: [xcrysden] Atom coordinates extraction Message-ID: <4B13E868.4080204@polytechnique.edu> Dear all, I use to compare big cells (with more than 100 atoms, and for the moment base-centered monoclinic ones) together as they are geometrically optimised. The problem - for me - is that their respectives coordinates (as they are very close to eachother) can not be directly superimposed due to the initial positions of atoms. However, I have notice that by considering each atom trough the AtomInfo, I can obtain coordinates which can be used as they are. My questions are the following : - which procedure is used to convert the coordinates ? I read the tcl files, but I could not find anything linked to this (perhaps I did mistakes, as I am not familiar with Tcl/Tk). - can this new coordinates been exported (by a script, or else ?). Thanks -------------- next part -------------- A non-text attachment was scrubbed... Name: emmanuel_betranhandy.vcf Type: text/x-vcard Size: 394 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20091130/37497ce0/attachment.vcf