From markus.becker85 at outlook.de Wed Sep 7 17:02:26 2022 From: markus.becker85 at outlook.de (markus.becker85 at outlook.de) Date: Wed, 7 Sep 2022 15:02:26 +0000 Subject: [xcrysden] Missing /.xcrysden folder and mpeg_encode failure Message-ID: Hello, I installed xcrysden 1.6.2 and tried to create an mpeg movie from pw.x output. However, during installation I recognized that the hided /.xcrysden folder is not existent. As a consequence, I am not able to perform the encoder definition via: set xcMisc(mpeg_encode) /usr/bin/mpeg_encode Is this an actual bug? I would be pleased by every advise. Kind regards Markus -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20220907/ab17fdbb/attachment.htm From jxln_karate at yahoo.com.br Fri Sep 9 20:42:37 2022 From: jxln_karate at yahoo.com.br (=?UTF-8?Q?Jos=C3=A9_Xavier?=) Date: Fri, 9 Sep 2022 18:42:37 +0000 (UTC) Subject: [xcrysden] error for opening Xcrysden (package require BWidget) References: <252173796.1152316.1662748957389.ref@mail.yahoo.com> Message-ID: <252173796.1152316.1662748957389@mail.yahoo.com> Dear users, I don't know what happened with my xcrysden. Last week it worked fine. This week, it shows me: Error in startup script: can't find package BWidget ??? while executing "package require BWidget" ??? (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 460) I remember that this weekend I updated a package of my OS, but I don't know the name... What could I do to fix this error? From tone.kokalj at ijs.si Fri Sep 9 21:14:53 2022 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 09 Sep 2022 21:14:53 +0200 Subject: [xcrysden] Missing /.xcrysden folder and mpeg_encode failure In-Reply-To: References: Message-ID: On Wed, 2022-09-07 at 15:02 +0000, markus.becker85 at outlook.de wrote: > Hello, > > I installed xcrysden 1.6.2 and tried to create an mpeg movie from > pw.x output. However, during installation I recognized that the hided > /.xcrysden folder is not existent.? The ~/.xcrysden directory is not created during installation. Make it manually and copy the custom-definitions file into it (it is located in the Tcl/ subdirectory of xcrysden; for convenience, it is also attach here). Then edit it as you find fit. Regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia -------------- next part -------------- # ------------------------------------------------------------------------ # Printing options ... # # if "Print To File" produces blank images, uncomment the line below # (i.e. use screen-dump instead): # ------------------------------------------------------------------------ #set printSetup(dumpWindow) 1 # ------------------------------------------------------------------------ # Options for OpenGL display # # If you experience "X Error of failed request:" crashes, set the # toglOpt(accum) to false. # # N.B. for all possible options of toglOpt(option) see file # $XCRYSDEN_TOPDIR/Tcl/toglOpt.tcl # ------------------------------------------------------------------------ #set toglOpt(accum) false #set toglOpt(stereo) none # ------------------------------------------------------------------------ # do we have CRYSTAL package # ------------------------------------------------------------------------ set system(c95_exist) 0 # ------------------------------------------------------------------------ # CRYSTAL modules # ------------------------------------------------------------------------ #set system(c95_integrals) /home/tone/src/CRYSTAL03/bin/Linux-pgf/v1_0_2/crystal #set system(c95_scf) /home/tone/src/CRYSTAL03/bin/Linux-pgf/v1_0_2/crystal #set system(c95_properties) /home/tone/src/CRYSTAL03/bin/Linux-pgf/v1_0_2/properties # ------------------------------------------------------------------------ # xcrysden can use several encoder programs for creating animated GIF # (convert, gifsicle, whirlgif) and AVI/MPEG movies # (mencoder/ppmtompeg) # ------------------------------------------------------------------------ #set xcMisc(gif_encoder) convert #set xcMisc(movie_encoder) mencoder # ------------------------------------------------------------------------ # NOTICE: Starting from version 1.5, xcrysden tries to automatically # find various external packages, nevertheless user can still set # them explicitly, as shown below (if you want to do so, uncomment # corresponding lines) # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # An image conversion program: we need PPM to PNG/JPG/GIF/... conversion. # The "convert" program of ImageMagick (http://www.imagemagick.org/) is # a convenient choice. # # It is possible to specify the command-line options. For example: # # set xcMisc(ImageMagick.convert) "/usr/bin/convert \ # -quality 90 -border 3x3 -bordercolor black" # # Instead one can also use something like: # # set xcMisc(ImageMagick.convertOptions) "-quality 90 -antialias \ # -blur 1x1 -trim -bordercolor white \ # -border 20x20 -bordercolor black -border 3x3" # ------------------------------------------------------------------------ #set xcMisc(ImageMagick.convert) "/usr/bin/convert" #set xcMisc(ImageMagick.convertOptions) "-quality 90 -bordercolor black -border 3x3" # ------------------------------------------------------------------------ # With "gifsicle" program XCRYSDEN can create an Animated-GIF image # ------------------------------------------------------------------------ #set xcMisc(gifsicle) /usr/bin/gifsicle # ------------------------------------------------------------------------ # PPMTOMPEG for creating the MPEG movies # ------------------------------------------------------------------------ #set xcMisc(ppmtompeg) /usr/bin/ppmtompeg # ------------------------------------------------------------------------ # BABEL program # ------------------------------------------------------------------------ #set xcMisc(babel) /home/tone/bin/babel # this is the same as environmental BABEL_DIR variable. Note: if # BABEL_DIR is defined, then this is not needed!!! #set xcMisc(babel_dir) $env(HOME)/lib/babel # ------------------------------------------------------------------------ # Custom setting of the atomic radii. The syntax is: # ------------------------------------------------------------------------ # set atmRad(atomic_number) radius # # Example: # # set atmRad(1) 0.5; # custom radius for Hydrogen # set atmRad(8) 1.2; # custom radius for Oxygen # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # Custom setting of the atomic colors. The syntax is: # ------------------------------------------------------------------------ # set atmCol(atomic_number) {red gren blue} # # The components (red,gren,blue) must be in range [0,1] # # Example: # # set atmCol(1) {0.5 0.5 0.5}; # custom color for Hydrogen # set atmCol(8) {0.0 1.0 0.0}; # custom color for Oxygen # # ------------------------------------------------------------------------ #------------------------------------------------------------------------ # Turn-on old atomic colors (colors prior to xcrysden v-1.6) #------------------------------------------------------------------------ #xc_oldatmcol #------------------------------------------------------------------------ # ------------------------------------------------------------------------- # Custom setting for a variety of molecular display parameters, such as # ball-factors, specefill scale factors, tessellation factors, etc. # # Below are the default values. If you would like to change the # default for a particular parameter, then uncomment the appropriate # line and set the value according to your needs. # ------------------------------------------------------------------------ ## spacefill scale factor #set myParam(ATRAD_SCALE) 1.40 # ## tesselation factor #set myParam(TESSELLATION) 15.0 # ## RGB color of unibonds (each compoenent must be within [0,1]) #set myParam(UNIBONDCOLOR) {1.00 1.00 1.00} # ## Perspective Fovy, Front and Back parameters. The smaller the Fovy ## the larger the perception of perspective. Front and Back parameters ## determine the front and back clipping planes. The smaller the Back ## parameter the more the structure is clipped from the back side. The ## Front parameter is counter-intuitive, meaning the smaller it is the ## more the structure is clipped from the front side. # #set myParam(PERSPECTIVEFOVY) 2.5 #set myParam(PERSPECTIVEFRONT) 0.65 #set myParam(PERSPECTIVEBACK) 3.0 # ## ball-factor #set myParam(BALLF) 0.4 # ## rod-factor #set myParam(RODF) 0.6 # ## line-width of wireframe display-mode (in pixels) #set myParam(WFLINEWIDTH) 1 # ## line-width of pointline display-mode (in pixels) #set myParam(PLLINEWIDTH) 1 # ## line-width of crystal cell's frames #set myParam(FRAMELINEWIDTH) 1 # ## Lighting-Off outline width #set myParam(OUTLINEWIDTH) 1 # ## Lighting-On wire line width #set myParam(WF3DLINEWIDTH) 1 # ## point-size of pointline display-mode (in pixels) #set myParam(PLRADIUS) 6 # ## chemical connectivity factor #set myParam(COV_SCALE) 1.05 # ## RGB color of crystal frame (each compoenent must be within [0,1]) #set myParam(FRAMECOL) {0.88 1.00 0.67} # ## line-width of crystal frame #set myParam(FRAMELINEWIDTH) 1 # ## rod-factor of crystal frame #set myParam(FRAMERODF) 0.1 # ## RGB background of XCRYSDEN display window ## (each compoenent must be within [0,1]) #set myParam(BACKGROUND) {0.00 0.00 0.00} # ## maximum number of cells per direction for CRYSTALs #set myParam(CRYSTAL_MAXCELL) 10 # ## maximum number of cells per direction for SLABs #set myParam(SLAB_MAXCELL) 20 # ## maximum number of cells for POLYMERs #set myParam(POLYMER_MAXCELL) 50 # ## default atomic-label's font (in X11 XLFD format) #set myParam(ATOMIC_LABEL_FONT) -adobe-helvetica-medium-r-normal--12-120-75-75-p-67-iso8859-1 # ## default atomic-label's bright and dark color (in clamped-float RGB format) #set myParam(ATOMIC_LABEL_BRIGHTCOLOR) {1.0 1.0 0.0} #set myParam(ATOMIC_LABEL_DARKCOLOR) {1.0 0.0 0.0} # # ## this are the parameters for the "ppmtompeg" program: ##--BEGIN:: #set myParam(MPEG_ENCODE_PARAM_FILE) { #PATTERN IBBPBBPBBPBBPBBP #OUTPUT $output_file #BASE_FILE_FORMAT PPM #INPUT_FORMAT UCB #$input_convert #GOP_SIZE 16 #SLICES_PER_FRAME 1 #INPUT_DIR / #INPUT #$input_files #END_INPUT #PIXEL FULL #RANGE 10 #PSEARCH_ALG LOGARITHMIC #BSEARCH_ALG CROSS2 #IQSCALE 8 #PQSCALE 10 #BQSCALE 25 #REFERENCE_FRAME ORIGINAL #BIT_RATE 1000000 #BUFFER_SIZE 327680 #FRAME_RATE 30 #} ##--END # # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # # Custom settings for FERMI-SURFACE-VIEWER # # ------------------------------------------------------------------------ ## RGB background of Fermi Viewer (each of r,g,b components must be within [0,1]) #set myParam(FS_BACKGROUND) {0.0 0.0 0.0} ## the type of the cell: bz | para #set myParam(FS_CELLTYPE) bz ## do we crop the BZ: 1 or 0 #set myParam(FS_CROPBZ) 1 ## display type for the cell: none | wire | solid | solidwire #set myParam(FS_CELLDISPLAYTYPE) wire ## draw style for the Fermi-surface: solid | wire | dot #set myParam(FS_DRAWSTYLE) solid ## draw transparent Fermi Surface: 0 | 1 #set myParam(FS_TRANSPARENT) 0 ## shade model for Fermi surface: smooth | flat #set myParam(FS_SHADEMODEL) smooth ## set the interpolation (should be small integer number, e.g., 1 2 3 #set myParam(FS_INTERPOLATIONDEGREE) 1 ## what is the frontface of the surface: CW or CCW #set myParam(FS_FRONTFACE) CW ## revert the normals of Fermi surface (determines the outside surface): 0 | 1 #set myParam(FS_REVERTNORMALS) 0 ## color of the wire-cell (each of r,g,b,a components must be within [0,1]) #set myParam(FS_WIRECELLCOLOR) {1.00 0.00 1.00 1.00} ## color of the solid-cell (each of r,g,b,a components must be within [0,1]) #set myParam(FS_SOLIDCELLCOLOR) {0.00 0.95 0.95 0.40} ## use antialiaing: 0 | 1 #set myParam(FS_ANTIALIAS) 0 ## use depth cuing: 0 | 1 #set myParam(FS_DEPTHCUING) 0 # END of settings for FERMI-SURFACE-VIEWER # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # Here go custom user-specified options # ------------------------------------------------------------------------ # In order to add an --unknown option to the Xcrysden allowed options, # do the following # # Usage: # addOption option converterProgram description # # Arguments: # option ... option to add to XCRYSDEN options # converterProgram ... program that converts from an unknown to XSF format; # this program must be supplied by the user !!! # description ... description of the options that will appear in the # help message (i.e. xcrysden --help). # Example: # addOption --unknown /home/tone/utils/unknown2xsf { # load structure from unknown file format # } # # turn debugging off set xcMisc(debug) 0 From tone.kokalj at ijs.si Fri Sep 9 21:16:30 2022 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 09 Sep 2022 21:16:30 +0200 Subject: [xcrysden] error for opening Xcrysden (package require BWidget) In-Reply-To: <252173796.1152316.1662748957389@mail.yahoo.com> References: <252173796.1152316.1662748957389.ref@mail.yahoo.com> <252173796.1152316.1662748957389@mail.yahoo.com> Message-ID: <8916e534fe3a330be6442e47b64c8811fba02a01.camel@ijs.si> On Fri, 2022-09-09 at 18:42 +0000, Jos? Xavier wrote: > Dear users, > > I don't know what happened with my xcrysden. Last week it worked > fine. This week, it shows me: > Error in startup script: can't find package BWidget > ??? while executing > "package require BWidget" > ??? (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 460) I presume you are using Debian (or Ubuntu). In this case, you can do: sudo apt install bwidget Regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From jxln_karate at yahoo.com.br Fri Sep 9 21:33:01 2022 From: jxln_karate at yahoo.com.br (=?UTF-8?Q?Jos=C3=A9_Xavier?=) Date: Fri, 9 Sep 2022 19:33:01 +0000 (UTC) Subject: [xcrysden] error for opening Xcrysden (package require BWidget) In-Reply-To: <8916e534fe3a330be6442e47b64c8811fba02a01.camel@ijs.si> References: <252173796.1152316.1662748957389.ref@mail.yahoo.com> <252173796.1152316.1662748957389@mail.yahoo.com> <8916e534fe3a330be6442e47b64c8811fba02a01.camel@ijs.si> Message-ID: <1504894738.1172761.1662751981675@mail.yahoo.com> Dear, I'm using Manjaro, However, bwidget is installed (v. 1.9.15-1) Em sexta-feira, 9 de setembro de 2022 16:16:41 BRT, Tone Kokalj escreveu: On Fri, 2022-09-09 at 18:42 +0000, Jos? Xavier wrote: > Dear users, > > I don't know what happened with my xcrysden. Last week it worked > fine. This week, it shows me: > Error in startup script: can't find package BWidget > ??? while executing > "package require BWidget" > ??? (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 460) I presume you are using Debian (or Ubuntu). In this case, you can do: sudo apt install bwidget Regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From carlofedep at gmail.com Sat Sep 10 09:20:19 2022 From: carlofedep at gmail.com (Carlo Federico Pauletti) Date: Sat, 10 Sep 2022 09:20:19 +0200 Subject: [xcrysden] error for opening Xcrysden (package require BWidget) In-Reply-To: <8916e534fe3a330be6442e47b64c8811fba02a01.camel@ijs.si> References: <252173796.1152316.1662748957389.ref@mail.yahoo.com> <252173796.1152316.1662748957389@mail.yahoo.com> <8916e534fe3a330be6442e47b64c8811fba02a01.camel@ijs.si> Message-ID: Same issue here if I try to install Xcrysden via AUR (Arch User Repositories) on Arch Linux. Never happened before (I remember installing it on quite a lot of machines with no issue). I had to compile the code manually. I suspect a recent upgrade of the BWidget package caused some incompatibilities with the code. I will investigate further and let you know. Best, Federico On Fri, Sep 9, 2022, 21:16 Tone Kokalj wrote: > On Fri, 2022-09-09 at 18:42 +0000, Jos? Xavier wrote: > > Dear users, > > > > I don't know what happened with my xcrysden. Last week it worked > > fine. This week, it shows me: > > Error in startup script: can't find package BWidget > > while executing > > "package require BWidget" > > (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 460) > > I presume you are using Debian (or Ubuntu). In this case, you can do: > > sudo apt install bwidget > > Regards, Tone > -- > Jo?ef Stefan Institute, 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/20220910/d4f313bf/attachment.htm From markus.becker85 at outlook.de Tue Sep 13 20:10:40 2022 From: markus.becker85 at outlook.de (markus.becker85 at outlook.de) Date: Tue, 13 Sep 2022 18:10:40 +0000 Subject: [xcrysden] Missing /.xcrysden folder and mpeg_encode failure In-Reply-To: References: Message-ID: Dear Tone, I did create the .xcrysden folder and copied the custom_definitions file into it. In the file itself, I modified the following: # ------------------------------------------------------------------------ # xcrysden can use several encoder programs for creating animated GIF # (convert, gifsicle, whirlgif) and AVI/MPEG movies # (mencoder/ppmtompeg) # ------------------------------------------------------------------------ #set xcMisc(gif_encoder) convert #set xcMisc(mpeg_encode) /home/Markus/xcrysden-1.6.2-bin-shared/bin/mpeg_encode where the path is where my mpeg_encode is lying. However, the Modify-->Animation Controls is still not working. Do you have any further suggestions? Thanks and kind regards Markus ________________________________ Von: xcrysden-bounces at democritos.it im Auftrag von Tone Kokalj Gesendet: Freitag, 9. September 2022 21:14 An: xcrysden at democritos.it Betreff: Re: [xcrysden] Missing /.xcrysden folder and mpeg_encode failure On Wed, 2022-09-07 at 15:02 +0000, markus.becker85 at outlook.de wrote: > Hello, > > I installed xcrysden 1.6.2 and tried to create an mpeg movie from > pw.x output. However, during installation I recognized that the hided > /.xcrysden folder is not existent. The ~/.xcrysden directory is not created during installation. Make it manually and copy the custom-definitions file into it (it is located in the Tcl/ subdirectory of xcrysden; for convenience, it is also attach here). Then edit it as you find fit. Regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20220913/4d13d7f7/attachment.htm From jxln_karate at yahoo.com.br Tue Sep 13 21:04:01 2022 From: jxln_karate at yahoo.com.br (=?UTF-8?Q?Jos=C3=A9_Xavier?=) Date: Tue, 13 Sep 2022 19:04:01 +0000 (UTC) Subject: [xcrysden] error for opening Xcrysden (package require BWidget) In-Reply-To: References: <252173796.1152316.1662748957389.ref@mail.yahoo.com> <252173796.1152316.1662748957389@mail.yahoo.com> <8916e534fe3a330be6442e47b64c8811fba02a01.camel@ijs.si> Message-ID: <185587778.2390056.1663095841188@mail.yahoo.com> Dear Carlo, I tried to install it manually, but it doesn't work.. Em s?bado, 10 de setembro de 2022 04:20:41 BRT, Carlo Federico Pauletti escreveu: Same issue here if I try to install Xcrysden via AUR (Arch User Repositories) on Arch Linux. Never happened before (I remember installing it on quite a lot of machines with no issue). I had to compile the code manually. I suspect a recent upgrade of the BWidget package caused some incompatibilities with the code. I will investigate further and let you know. Best, Federico On Fri, Sep 9, 2022, 21:16 Tone Kokalj wrote: > On Fri, 2022-09-09 at 18:42 +0000, Jos? Xavier wrote: >> Dear users, >> >> I don't know what happened with my xcrysden. Last week it worked >> fine. This week, it shows me: >> Error in startup script: can't find package BWidget >> ??? while executing >> "package require BWidget" >> ??? (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 460) > > I presume you are using Debian (or Ubuntu). In this case, you can do: > > sudo apt install bwidget > > Regards, Tone > -- > Jo?ef Stefan Institute, Ljubljana, Slovenia > > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From tone.kokalj at ijs.si Wed Sep 14 06:44:16 2022 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 14 Sep 2022 06:44:16 +0200 Subject: [xcrysden] Missing /.xcrysden folder and mpeg_encode failure In-Reply-To: References: Message-ID: On Tue, 2022-09-13 at 18:10 +0000, markus.becker85 at outlook.de wrote: > Dear Tone, > > I did create the .xcrysden folder and copied the custom_definitions > file into it. In the file itself, I modified the following: > > # ------------------------------------------------------------------- > ----- > # xcrysden can use several encoder programs for creating animated GIF > # (convert, gifsicle, whirlgif) and AVI/MPEG movies > # (mencoder/ppmtompeg) > # ------------------------------------------------------------------- > ----- > > #set xcMisc(gif_encoder) ? convert > #set xcMisc(mpeg_encode) /home/Markus/xcrysden-1.6.2-bin-shared/bin/mpeg_encode Uncomment the last line (i.e., remove the # character) and retry (should read: set xcMisc...). Best regards,? Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From tone.kokalj at ijs.si Wed Sep 14 06:48:14 2022 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 14 Sep 2022 06:48:14 +0200 Subject: [xcrysden] error for opening Xcrysden (package require BWidget) In-Reply-To: <185587778.2390056.1663095841188@mail.yahoo.com> References: <252173796.1152316.1662748957389.ref@mail.yahoo.com> <252173796.1152316.1662748957389@mail.yahoo.com> <8916e534fe3a330be6442e47b64c8811fba02a01.camel@ijs.si> <185587778.2390056.1663095841188@mail.yahoo.com> Message-ID: <640836534c26e36140d02dc393c4091d442227ce.camel@ijs.si> On Tue, 2022-09-13 at 19:04 +0000, Jos? Xavier wrote: > Dear Carlo, > > I tried to install it manually, but it doesn't work.. Let's try this: 1. check where your bwidget package is installed (e.g. mine is in /usr/share/tcltk/bwidget1.9.13) 2. from the terminal do: export TCLLIBPATH=/path/to/bwidgets xcrysden where in my case /path/to/bwidgets = /usr/share/tcltk/bwidget1.9.13 Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From jxln_karate at yahoo.com.br Wed Sep 14 21:07:52 2022 From: jxln_karate at yahoo.com.br (=?UTF-8?Q?Jos=C3=A9_Xavier?=) Date: Wed, 14 Sep 2022 19:07:52 +0000 (UTC) Subject: [xcrysden] error for opening Xcrysden (package require BWidget) In-Reply-To: <640836534c26e36140d02dc393c4091d442227ce.camel@ijs.si> References: <252173796.1152316.1662748957389.ref@mail.yahoo.com> <252173796.1152316.1662748957389@mail.yahoo.com> <8916e534fe3a330be6442e47b64c8811fba02a01.camel@ijs.si> <185587778.2390056.1663095841188@mail.yahoo.com> <640836534c26e36140d02dc393c4091d442227ce.camel@ijs.si> Message-ID: <45430860.315654.1663182472244@mail.yahoo.com> In my case, bwidget-1.9.15 is installed in folder /usr/lib/tcl8.6/. I tried to do the export, as you showed, but it does the same error... Could this error be something about the update from 1.9.13 -> 1.9.15? Em quarta-feira, 14 de setembro de 2022 01:48:24 BRT, Tone Kokalj escreveu: On Tue, 2022-09-13 at 19:04 +0000, Jos? Xavier wrote: > Dear Carlo, > > I tried to install it manually, but it doesn't work.. Let's try this: 1. check where your bwidget package is installed (e.g. mine is in /usr/share/tcltk/bwidget1.9.13) 2. from the terminal do: export TCLLIBPATH=/path/to/bwidgets xcrysden where in my case /path/to/bwidgets = /usr/share/tcltk/bwidget1.9.13 Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden From tevindotli at gmail.com Thu Sep 15 07:05:29 2022 From: tevindotli at gmail.com (Tevin Li) Date: Thu, 15 Sep 2022 01:05:29 -0400 Subject: [xcrysden] Error in compiling XCrysden source package for MacOS Message-ID: Hello, I apologize for sending this message again, but I am attempting to compile the source package for xcrysden for MacOS and I am encountering the following error message: --2022-09-10 01:16:09-- ftp://ftp.freedesktop.org/pub/mesa/mesa-18.3.6.tar.gz (try:19) => ?mesa-18.3.6.tar.gz? ==> CWD not required. ==> SIZE mesa-18.3.6.tar.gz ... 20348664 ==> PASV ... Cannot parse PASV response. Retrying. --2022-09-10 01:16:19-- ftp://ftp.freedesktop.org/pub/mesa/mesa-18.3.6.tar.gz (try:20) => ?mesa-18.3.6.tar.gz? ==> CWD not required. ==> SIZE mesa-18.3.6.tar.gz ... 20348664 ==> PASV ... Cannot parse PASV response. Giving up. #-----------------------------------# # # # Compiling external Mesa-library # # # #-----------------------------------# /bin/sh: line 0: cd: mesa-18.3.6: No such file or directory /bin/sh: ./configure: No such file or directory *** Possible targets: tcl tk togl mesa fftw clean make[2]: *** No rule to make target `install'. Stop. make[1]: *** [mesa-new] Error 2 make: *** [mesa] Error 2 I was wondering if you could please provide some guidance in helping me resolve this error, as I am fairly new to this and I seem to have difficulty in finding help from Google that is pertinent to the issue that I am experiencing. My operating system is a macOS Monterey version 12.5.1, and I have installed Xcode version 13.4.1. Thank you very much for your assistance in advance. Regards, Tevin Li -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20220915/b66aaf18/attachment.htm From tone.kokalj at ijs.si Thu Sep 15 07:39:31 2022 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 15 Sep 2022 07:39:31 +0200 Subject: [xcrysden] error for opening Xcrysden (package require BWidget) In-Reply-To: <45430860.315654.1663182472244@mail.yahoo.com> References: <252173796.1152316.1662748957389.ref@mail.yahoo.com> <252173796.1152316.1662748957389@mail.yahoo.com> <8916e534fe3a330be6442e47b64c8811fba02a01.camel@ijs.si> <185587778.2390056.1663095841188@mail.yahoo.com> <640836534c26e36140d02dc393c4091d442227ce.camel@ijs.si> <45430860.315654.1663182472244@mail.yahoo.com> Message-ID: <4103ccecd765b0ecbc79d673fd4917fc55d5b4d7.camel@ijs.si> On Wed, 2022-09-14 at 19:07 +0000, Jos? Xavier wrote: > In my case, bwidget-1.9.15 is installed in folder /usr/lib/tcl8.6/. > I tried to do the export, as you showed, but it does the same > error... I don't know. As a test, you may try to install bwidget 1.9.13 maually and set the TCLLIBPATH to point to the manual installation. https://sourceforge.net/projects/tcllib/files/BWidget/1.9.13/ The other alternative is to try http://www.xcrysden.org/download/xcrysden-1.6.2-linux_x86_64-shared.tar.gz which includes bwidget. Best regards,? Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From tone.kokalj at ijs.si Thu Sep 15 07:45:14 2022 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 15 Sep 2022 07:45:14 +0200 Subject: [xcrysden] Error in compiling XCrysden source package for MacOS In-Reply-To: References: Message-ID: <2feac1a84d40f62bae1041767f533b0f4bbfb665.camel@ijs.si> On Thu, 2022-09-15 at 01:05 -0400, Tevin Li wrote: > Hello, > > I apologize for sending this message again, but I am attempting to > compile the source package for xcrysden for MacOS and I am > encountering the following error message: > > --2022-09-10 01:16:09--?? > ftp://ftp.freedesktop.org/pub/mesa/mesa-18.3.6.tar.gz > ??(try:19) => ?mesa-18.3.6.tar.gz? > ==> CWD not required. > ==> SIZE mesa-18.3.6.tar.gz ... 20348664 > ==> PASV ...? > Cannot parse PASV response. > Retrying. You can avoid compiling external libraries. Instead of "make", use "make xcrysden". As an alternative you may try a precompiled mac os version: http://www.xcrysden.org/download/xcrysden-1.6.2-macosx-shared.tar.gz You may also check Macports or Fink version https://ports.macports.org/port/xcrysden/ https://pdb.finkproject.org/pdb/package.php/xcrysden Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From tevindotli at gmail.com Thu Sep 15 22:33:50 2022 From: tevindotli at gmail.com (Tevin Li) Date: Thu, 15 Sep 2022 16:33:50 -0400 Subject: [xcrysden] Error in compiling XCrysden source package for MacOS In-Reply-To: <2feac1a84d40f62bae1041767f533b0f4bbfb665.camel@ijs.si> References: <2feac1a84d40f62bae1041767f533b0f4bbfb665.camel@ijs.si> Message-ID: Hello Tone, Thank you very much for your assistance. I have already downloaded the precompiled MacOS file earlier and (despite using a command such as port install tk libGLU xorg-libX11 xorg-libXmu fftw-3 ImageMagick openbabel) I am still running into this message whenever I type in ./xcrysden: XCRYSDEN_TOPDIR=/Users/tevinli/Downloads/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/var/folders/y9/m7ct78_s13x5hmqntp0lvcz00000gn/T/ dyld[89607]: Library not loaded: '/opt/local/lib/libfftw3.3.dylib' Referenced from: '/Users/tevinli/Downloads/xcrysden-1.6.2-bin-shared/bin/xcrys' Reason: tried: '/Users/tevinli/Downloads/xcrysden-1.6.2-bin-shared/external/lib/libfftw3.3.dylib' (no such file), '/opt/local/lib/libfftw3.3.dylib' (mach-o file, but is an incompatible architecture (have (arm64), need (x86_64))), '/usr/local/lib/libfftw3.3.dylib' (no such file), '/usr/lib/libfftw3.3.dylib' (no such file) ./xcrysden: line 279: 89607 Abort trap: 6 "${XCRYSDEN_XCRYS_DIR}/xcrys" "${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl" $USE -- "$XCRYSDEN_TOPDIR" "$XCRYSDEN_SCRATCH" "$@" > /dev/null Can you please help in providing assistance in resolving this issue? Thank you very much. Regards, Tevin On Thu, Sep 15, 2022 at 1:45 AM Tone Kokalj wrote: > On Thu, 2022-09-15 at 01:05 -0400, Tevin Li wrote: > > Hello, > > > > I apologize for sending this message again, but I am attempting to > > compile the source package for xcrysden for MacOS and I am > > encountering the following error message: > > > > --2022-09-10 01:16:09-- > > ftp://ftp.freedesktop.org/pub/mesa/mesa-18.3.6.tar.gz > > (try:19) => ?mesa-18.3.6.tar.gz? > > ==> CWD not required. > > ==> SIZE mesa-18.3.6.tar.gz ... 20348664 > > ==> PASV ... > > Cannot parse PASV response. > > Retrying. > > You can avoid compiling external libraries. Instead of "make", use > "make xcrysden". > > As an alternative you may try a precompiled mac os version: > http://www.xcrysden.org/download/xcrysden-1.6.2-macosx-shared.tar.gz > You may also check Macports or Fink version > https://ports.macports.org/port/xcrysden/ > https://pdb.finkproject.org/pdb/package.php/xcrysden > > Best regards, Tone > -- > Jo?ef Stefan Institute, 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/20220915/852e44e0/attachment.htm From markus.becker85 at outlook.de Wed Sep 14 13:39:17 2022 From: markus.becker85 at outlook.de (markus.becker85 at outlook.de) Date: Wed, 14 Sep 2022 11:39:17 +0000 Subject: [xcrysden] Missing /.xcrysden folder and mpeg_encode failure In-Reply-To: References: Message-ID: Dear Tone, Now I editet the custom_definitions file as follows: # ------------------------------------------------------------------------ # xcrysden can use several encoder programs for creating animated GIF # (convert, gifsicle, whirlgif) and AVI/MPEG movies # (mencoder/ppmtompeg) # ------------------------------------------------------------------------ #set xcMisc(gif_encoder) convert set xcMisc(mpeg_encode) /bin/mpeg_encode I also checked that the path to the mpeg_encode.exe is correct. After starting the animation control, however, it still does not allow me to create a mpeg movie. Please see the attached figure of the control panel. Surprisingly, I can create an animated GIF file. Kind regards Markus ________________________________ Von: xcrysden-bounces at democritos.it im Auftrag von Tone Kokalj Gesendet: Mittwoch, 14. September 2022 06:44 An: xcrysden at democritos.it Betreff: Re: [xcrysden] Missing /.xcrysden folder and mpeg_encode failure On Tue, 2022-09-13 at 18:10 +0000, markus.becker85 at outlook.de wrote: > Dear Tone, > > I did create the .xcrysden folder and copied the custom_definitions > file into it. In the file itself, I modified the following: > > # ------------------------------------------------------------------- > ----- > # xcrysden can use several encoder programs for creating animated GIF > # (convert, gifsicle, whirlgif) and AVI/MPEG movies > # (mencoder/ppmtompeg) > # ------------------------------------------------------------------- > ----- > > #set xcMisc(gif_encoder) convert > #set xcMisc(mpeg_encode) /home/Markus/xcrysden-1.6.2-bin-shared/bin/mpeg_encode Uncomment the last line (i.e., remove the # character) and retry (should read: set xcMisc...). Best regards, Tone -- Jo?ef Stefan Institute, 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/20220914/18278c7e/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: MPEG_Error.PNG Type: image/png Size: 47705 bytes Desc: MPEG_Error.PNG Url : http://www.democritos.it/pipermail/xcrysden/attachments/20220914/18278c7e/attachment-0001.png From gabo13279 at gmail.com Fri Sep 16 08:12:11 2022 From: gabo13279 at gmail.com (Gavin Abo) Date: Fri, 16 Sep 2022 00:12:11 -0600 Subject: [xcrysden] error for opening Xcrysden (package require BWidget) In-Reply-To: <252173796.1152316.1662748957389@mail.yahoo.com> References: <252173796.1152316.1662748957389.ref@mail.yahoo.com> <252173796.1152316.1662748957389@mail.yahoo.com> Message-ID: <27280532-1ef3-4032-cc76-eef8943dade3@gmail.com> Refer to step 12 in the "XCrySDen 1.6.2 Manjaro Installation.pdf" at [1], the BWidget error might just be caused by an issue with the /usr/lib/tcl8.6/bwidget-1.9.15 folder and file permissions. [1] https://github.com/gsabo/xcrysden-Patches/blob/main/XCrySDen%201.6.2%20Manjaro%20Installation.pdf Hopefully that helps and best regards, Gavin XCrySDen User On 9/9/2022 12:42 PM, Jos? Xavier wrote: > Dear users, > > I don't know what happened with my xcrysden. Last week it worked fine. This week, it shows me: > Error in startup script: can't find package BWidget > ??? while executing > "package require BWidget" > ??? (file "/usr/share/xcrysden/Tcl/xcInit.tcl" line 460) > > I remember that this weekend I updated a package of my OS, but I don't know the name... > What could I do to fix this error? From an.floris at gmail.com Tue Sep 20 13:29:05 2022 From: an.floris at gmail.com (Andrea Floris) Date: Tue, 20 Sep 2022 12:29:05 +0100 Subject: [xcrysden] lighting on issue on windows WSL Message-ID: Dear all, I am using xcrysden on WSL running Ubuntu 20.04.4 on Windows 11 Home. I am able to run the code and customize the atom's colors, background etc. However when I open a quantum espresso input/output or xyz file, I always need to manually select the Display/Lighting off, in order to see the atoms. Basically it seems that leaving the default Lighting on, prevents seeing the atoms. Is there a workaround this, I wonder how I can solve the problem. Many thanks in advance Kind Regards Andrea -- Dr Andrea Floris Senior Lecturer School of Chemistry University of Lincoln Brayford Pool, LN6 7TS Lincoln, UK Web: staff.lincoln.ac.uk/afloris Phone: +44 (0) 1522 83 5884 Room: JBL Building, JBL2W06 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20220920/9056922e/attachment.htm From ikutaro.hamada at gmail.com Sat Sep 24 06:42:37 2022 From: ikutaro.hamada at gmail.com (Ikutaro Hamada) Date: Sat, 24 Sep 2022 13:42:37 +0900 Subject: [xcrysden] Error in compiling XCrysden source package for MacOS In-Reply-To: References: <2feac1a84d40f62bae1041767f533b0f4bbfb665.camel@ijs.si> Message-ID: Dear Tevin and Tone, Very recently, I succeeded in building xcrysden 1.6.2 on macos Monterey using ``Make.sys`` as attached. Here's a minimum list of my environment: - MacBook Pro (13 inch M1 2020) - Homebew 3.6.2 (Homebrew/homebrew-core (git revision a00122a7143; last commit 2022-09-21)) - gcc (installed via ``brew install gcc``) Rename the attached ``Make.sys.txt`` ``Make.sys`` in the root directory and execute ``make all``. HTH Best, Ikutaro --- Ikutaro Hamada Department of Precision Engineering Graduate School of Engineering Osaka University 2-1 Yamada-Oka, Suita, Osaka 565-0871, Japan 2022?9?16?(?) 5:34 Tevin Li : > Hello Tone, > Thank you very much for your assistance. I have already downloaded the > precompiled MacOS file earlier and (despite using a command such as port > install tk libGLU xorg-libX11 xorg-libXmu fftw-3 ImageMagick openbabel) I > am still running into this message whenever I type in ./xcrysden: > > > XCRYSDEN_TOPDIR=/Users/tevinli/Downloads/xcrysden-1.6.2-bin-shared > > XCRYSDEN_SCRATCH=/var/folders/y9/m7ct78_s13x5hmqntp0lvcz00000gn/T/ > > > dyld[89607]: Library not loaded: '/opt/local/lib/libfftw3.3.dylib' > > Referenced from: > '/Users/tevinli/Downloads/xcrysden-1.6.2-bin-shared/bin/xcrys' > > Reason: tried: > '/Users/tevinli/Downloads/xcrysden-1.6.2-bin-shared/external/lib/libfftw3.3.dylib' > (no such file), '/opt/local/lib/libfftw3.3.dylib' (mach-o file, but is an > incompatible architecture (have (arm64), need (x86_64))), > '/usr/local/lib/libfftw3.3.dylib' (no such file), > '/usr/lib/libfftw3.3.dylib' (no such file) > > ./xcrysden: line 279: 89607 Abort trap: 6 "${XCRYSDEN_XCRYS_DIR}/xcrys" > "${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl" $USE -- "$XCRYSDEN_TOPDIR" > "$XCRYSDEN_SCRATCH" "$@" > /dev/null > > > Can you please help in providing assistance in resolving this issue? Thank > you very much. > > > Regards, > > Tevin > > > > On Thu, Sep 15, 2022 at 1:45 AM Tone Kokalj wrote: > >> On Thu, 2022-09-15 at 01:05 -0400, Tevin Li wrote: >> > Hello, >> > >> > I apologize for sending this message again, but I am attempting to >> > compile the source package for xcrysden for MacOS and I am >> > encountering the following error message: >> > >> > --2022-09-10 01:16:09-- >> > ftp://ftp.freedesktop.org/pub/mesa/mesa-18.3.6.tar.gz >> > (try:19) => ?mesa-18.3.6.tar.gz? >> > ==> CWD not required. >> > ==> SIZE mesa-18.3.6.tar.gz ... 20348664 >> > ==> PASV ... >> > Cannot parse PASV response. >> > Retrying. >> >> You can avoid compiling external libraries. Instead of "make", use >> "make xcrysden". >> >> As an alternative you may try a precompiled mac os version: >> http://www.xcrysden.org/download/xcrysden-1.6.2-macosx-shared.tar.gz >> You may also check Macports or Fink version >> https://ports.macports.org/port/xcrysden/ >> https://pdb.finkproject.org/pdb/package.php/xcrysden >> >> Best regards, Tone >> -- >> Jo?ef Stefan Institute, Ljubljana, Slovenia >> >> >> >> >> _______________________________________________ >> 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/20220924/ba6cf3cc/attachment.htm -------------- next part -------------- ######################################################################### # # Make.sys for X11 semishared compilation on Mac OS X # # It will download Tcl, Tk, Togl, and FTTW3 tarballs from the # internet and compile them for use with X11. After compilation they # are installed in external/lib & external/include. # # # This Make.sys uses the XQuartz. # ######################################################################## #------------------------------------------------------------------------ # if you have a GNU make it is better to set the MAKE variable to point # to gnu make #------------------------------------------------------------------------ MAKE = make #------------------------------------------------------------------------ # compilers & flags #------------------------------------------------------------------------ # C-preprocessor flags CPPFLAGS ?= # C-compiler flags CFLAGS += -ffast-math -funroll-loops -fPIC -pedantic -Wall CC = gcc LDLIB = -ldl MATH = -lm -lc FFLAGS += -static-libgfortran -static-libgcc -fdefault-double-8 -fdefault-real-8 -O2 FC = gfortran #------------------------------------------- #debug options #CFLAGS = -g #------------------------------------------- #------------------------------------------------------------------------ # X-libraries & include files #------------------------------------------------------------------------ X_LIB = -lXmu -lX11 X_INCDIR = -I/opt/X11/include #------------------------------------------------------------------------ # EXTERNAL LIBRARIES: Tcl/Tk/Mesa/Togl/FFTW #------------------------------------------------------------------------ # setting to "yes" will compile the corresponding library in external/src/ COMPILE_TCLTK = yes COMPILE_TOGL = yes COMPILE_MESA = no COMPILE_FFTW = no # this is only used for some testing purposes COMPILE_MESCHACH = no # Do we want a shared library version of Tcl/Tk/Mesa/Togl? If we want # shared then set the following flags to: --enable-shared else set the # following flag to: --disable-shared TCLTK_OPTIONS = --enable-shared \ --with-x CFLAGS=-I/opt/X11/include --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib TOGL_OPTIONS = --enable-shared --with-tcl=$(TOPDIR)/external/lib --with-tk=$(TOPDIR)/external/lib \ --with-x CFLAGS=-I/opt/X11/include --x-includes=/opt/X11/include --x-libraries=/opt/X11/lib MESA_OPTIONS = --enable-shared GLU_OPTIONS = --enable-shared MESA_TARGET = linux FFTW_OPTIONS = --enable-shared #------------------------------------------------------------------------ # # Libraries # #------------------------------------------------------------------------ TCL_LIB = -L$(TOPDIR)/external/lib -ltcl$(TCL_VER2) TK_LIB = -ltk$(TCL_VER2) TOGL_LIB = -lTogl$(TOGL_VER) GLU_LIB = -L/opt/X11/lib -lGLU GL_LIB = -lGL FFTW3_LIB = -L/opt/homebrew/lib -lfftw3 #------------------------------------------------------------------------ # # Include directories # #------------------------------------------------------------------------ TCL_INCDIR = -I$(TOPDIR)/external/include TK_INCDIR = TOGL_INCDIR = GL_INCDIR = -I/opt/X11/include FFTW3_INCDIR = -I/opt/homebrew/include #------------------------------------------------------------------------