From xcrysden@democritos.it Tue May 1 16:56:39 2007 From: xcrysden@democritos.it (Craig Bridges) Date: Tue, 01 May 2007 11:56:39 -0400 Subject: [xcrysden] (no subject) Message-ID: Dear all, I am trying to install the binary version of XCrysDen on a computer with OpenSuse 10.2 64bit version, and tcl/tk installed (version 8.4.14-11). I'm intending to use it with Wien2k. I get the following message upon trying to run the program. I'm sure that there is a simple solution, but as a relatively new user of linux, I don't know it. Any help would be appreciated. [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003. Code available from http://www.xcrysden.org/. /home/craig/XCrySDen-pre1.5bbin-static/xcrysden: line 163: 5603 Segmentation fault ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null I ran ./xcConfigure and sourced the profile. In .bashrc: #------------------------------------------------------------------------ # this is for XCRYSDEN pre1.5b; added by XCRYSDEN installation on # Thu Apr 26 17:40:48 EDT 2007 #------------------------------------------------------------------------ XCRYSDEN_TOPDIR=/home/craig/XCrySDen-pre1.5bbin-static XCRYSDEN_SCRATCH=/home/craig/XCrySDen-pre1.5bbin-static/xcrys_tmp export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" Regards, Craig ------------------ Dr. Craig Bridges McMaster University Department of Chemistry Hamilton, Ontario L8S 4M1 From xcrysden@democritos.it Tue May 1 19:35:55 2007 From: xcrysden@democritos.it (Craig Bridges) Date: Tue, 01 May 2007 14:35:55 -0400 Subject: [xcrysden] installing xcrysden on windows In-Reply-To: Message-ID: Dear All, After having trouble installing XCrysDen on linux. I have now tried it on windows XP SP2 professional edition. I installed the most recent version of Cygwin, then put the XCrysden directory in the /home/ directory, and finally ran ./xcConfigure.sh as suggested in the installation instructions. I said no to all packages, so this is just the most basic installation. The scratch directory was properly created and appears to be referenced in .bashrc. Running './.bashrc' produces the error message: ./.bashrc: line 112: $'\r':command not found ':not a valid identifierrt: 'XCRYSDEN_SCRATCH ./.bashrc: line 121: $'\r':command not found Clearly the default installation for windows has some problems as well. Could anyone provide me with some suggestions for setting up the windows version of Xcrysden? Regards, Craig On Tue, 01 May 2007 11:56:39 -0400 "Craig Bridges" wrote: > Dear all, > I am trying to install the binary version of XCrysDen on a computer > with OpenSuse 10.2 64bit version, and tcl/tk installed (version > 8.4.14-11). I'm intending to use it with Wien2k. > > I get the following message upon trying to run the program. I'm sure > that there is a simple solution, but as a relatively new user of > linux, > I don't know it. Any help would be appreciated. > > [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003. > Code available from http://www.xcrysden.org/. > > /home/craig/XCrySDen-pre1.5bbin-static/xcrysden: line 163: 5603 > Segmentation fault ${XCRYSDEN_TOPDIR}/bin/xcrys > ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR > $XCRYSDEN_SCRATCH $ARGS >/dev/null > > > I ran ./xcConfigure and sourced the profile. In .bashrc: > > #------------------------------------------------------------------------ > # this is for XCRYSDEN pre1.5b; added by XCRYSDEN installation on > # Thu Apr 26 17:40:48 EDT 2007 > #------------------------------------------------------------------------ > XCRYSDEN_TOPDIR=/home/craig/XCrySDen-pre1.5bbin-static > XCRYSDEN_SCRATCH=/home/craig/XCrySDen-pre1.5bbin-static/xcrys_tmp > export XCRYSDEN_TOPDIR XCRYSDEN_SCRATCH > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" > > > > Regards, > Craig > > ------------------ > Dr. Craig Bridges > McMaster University > Department of Chemistry > Hamilton, Ontario > L8S 4M1 > _______________________________________________ > XCrySDen mailing list > XCrySDen@democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden ------------------ Dr. Craig Bridges McMaster University Department of Chemistry Hamilton, Ontario L8S 4M1 From xcrysden@democritos.it Sat May 5 15:13:00 2007 From: xcrysden@democritos.it (Martin Gmitra) Date: Sat, 5 May 2007 16:13:00 +0200 Subject: [xcrysden] MAC OSX start up problem Message-ID: Hi, I have installed xcryden on mac osx running x11 server. I got the following message: Running on platform: macosx Executing: /Users/xxx/bin/XCrySDen-1.4.1bin/bin/ftnunit *** the hardware supports the stereo *** Error in startup script: Togl: couldn't get visual while executing "togl .mesa -width 400 -height 400 -ident .mesa -rgba true -redsize 1 -greensize 1 -blu..." (procedure "PlaceGlobWin" line 113) invoked from within "PlaceGlobWin 0 [expr round(650 * $fac1)] [expr round(650 * $fac1)]" (procedure "ViewMol" line 26) invoked from within "ViewMol ." invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file "/Users/xxx/bin/XCrySDen-1.4.1bin/Tcl/xcInit.tcl" line 532) Any hints how to start the code? Thanks in advance, Martin From xcrysden@democritos.it Thu May 10 17:44:56 2007 From: xcrysden@democritos.it (Bob Hanson) Date: Thu, 10 May 2007 11:44:56 -0500 Subject: [xcrysden] Jmol and xcrysden Message-ID: <46434C08.7040603@stolaf.edu> Tone, We have received a request to read XSF files. I'd like to know more about xcrysden before moving on this. Can you explain to me what xcrysden does? Roughly how large the user base is? Any possibility that I get a copy of your articles sent to me off-list? Thank you, Bob Hanson hansonr@stolaf.edu current principal developer, Jmol, http://jmol.sourceforge.net/ From xcrysden@democritos.it Fri May 25 05:35:49 2007 From: xcrysden@democritos.it (Sohrab Ismail-Beigi) Date: Fri, 25 May 2007 00:35:49 -0400 Subject: [xcrysden] Mac OS X (Intel) problems with xcrysden Message-ID: <342F5CF8-05B5-43A0-9147-286BF2B5E684@yale.edu> Echoing Martin Gmitra, I'm also having serious problems with xcrysden on Mac OS X (Intel 10.4.9). Here are the problems, summarized: (1) I downloaded the binary xcrysden off the website. The "ftnunit" program simply doesn't run as planned, and produces the error dyld: Library not loaded: /usr/local/lib/libg2c.0.dylib Referenced from: /Users/sohrab/codes/XCrySDen-1.4.1bin/bin/ftnunit Reason: image not found Trace/BPT trap (2) This problem does not seem to be too severe. However, when one executes "xcrysden" it bombs out with the following errors (Martin Gmitra found the same) Running on platform: macosx Executing: /Users/sohrab/codes/XCrySDen-1.4.1bin/bin/ftnunit *** the hardware supports the stereo *** Error in startup script: Togl: couldn't get visual while executing "togl .mesa " (procedure "PlaceGlobWin" line 113) invoked from within "PlaceGlobWin 0 [expr round(650 * $fac1)] [expr round(650 * $fac1)]" (procedure "ViewMol" line 26) invoked from within "ViewMol ." invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file "/Users/sohrab/codes/XCrySDen-1.4.1bin/Tcl/xcInit.tcl" line 532) I have tried playing around *a lot* with the line inside the Tcl/ Viewer.tcl that calls this "togl" command and nothing helps; e.g. removing all the options still fails. (3) I then decided to bite the bullet and download the xcrysden source code (1.4.1) without libraries. It took a lot of trickery to compile it, but finally it compiled. The fortran ftnunit now runs nicely. However, now the error is different: /Users/sohrab/codes/XCrySDen-1.4.1s/xcrysden: line 200: 21461 Bus error As this was not very helpful, I recompiled with debugging (-g) on. I noticed that the xcrysden wrapper was calling the bin/xcrys program via " ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null", so I just launched gdb with the same. Here is the result of running it, and doing the backtrace (bt): % gdb bin/xcrys ..... (gdb) run Tcl/xcInit.tcl -- /Users/sohrab/codes/XCrySDen-1.4.1s tmp Starting program: /Users/sohrab/codes/XCrySDen-1.4.1s/bin/xcrys Tcl/ xcInit.tcl -- /Users/sohrab/codes/XCrySDen-1.4.1s tmp Reading symbols for shared libraries ..+ +......................................................................+ +...+ done Reading symbols for shared libraries . done Running on platform: unix Reading symbols for shared libraries . done Reading symbols for shared libraries . done Taking settings for 1280x800 screen-resolution !!! ------------------- Small Font Size set to: 10 Normal Font Size set to: 12 Executing: /Users/sohrab/codes/XCrySDen-1.4.1s/bin/ftnunit Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_PROTECTION_FAILURE at address: 0x00000ac0 0x92b1bf5c in glLightfv () (gdb) bt #0 0x92b1bf5c in glLightfv () #1 0x000369f0 in LoadLights () at lighting.c:414 #2 0x0003ce4a in XC_SetGLparamCmd (clientData=0x778108, interp=0x5e3408, argc=6, argv=0xbfffe3e0) at xcGLparam.c:733 #3 0x9ac9c1a3 in TclInvokeStringCommand () #4 0x9ac9e915 in TclEvalObjvInternal () #5 0x9acc1666 in TclExecuteByteCode () #6 0x9acc644e in TclCompEvalObj () #7 0x9aced26d in TclObjInterpProc () #8 0x9ac9e915 in TclEvalObjvInternal () #9 0x9ac9ec1c in Tcl_EvalEx () #10 0x9ac9f6e4 in Tcl_EvalObjEx () #11 0x9aca276d in Tcl_EvalObjCmd () #12 0x9ac9e915 in TclEvalObjvInternal () #13 0x9ac9ec1c in Tcl_EvalEx () #14 0x9acdc93a in Tcl_FSEvalFile () #15 0x9acdca1e in Tcl_EvalFile () #16 0x9ad73335 in Tk_MainEx () #17 0x00002d36 in main (argc=5, argv=0xbffff54c) at xcAppInit.c:424 I checked the "flLightfv()" on the web, and everything seems quite kosher about how it is being called in lighting.c. The arguments are all quite legal. So I'm quite stuck. (4) I found some suggestions on previous emails from the list with similar problems to create a "togl.tcl" file with simple contents like # BEGIN SCRIPT togl .t \ -rgba true \ -redsize 1 \ < ... more stuff ... > -time 100 pack .t # END SCRIPT and to run xcrysden on this : bin/xcrys togl.tcl. The result is (backtrace) Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x5c637273 #0 0x004a9cb7 in XQueryExtension () #1 0x004345f3 in glXQueryExtension () #2 0x0008da51 in Togl_CreateWindow (tkwin=0x1183308, parent=18425224, instanceData=0x61a9d0) at togl.c:1639 #3 0x9ad9d1ad in Tk_MakeWindowExist () #4 0x0008d932 in Togl_Cmd (clientData=0x778108, interp=0x5e3408, argc=42, argv=0x7c3f08) at togl.c:1402 #5 0x9ac9c1a3 in TclInvokeStringCommand () #6 0x9ac9e915 in TclEvalObjvInternal () #7 0x9ac9ec1c in Tcl_EvalEx () #8 0x9acdc93a in Tcl_FSEvalFile () #9 0x9acdca1e in Tcl_EvalFile () #10 0x9ad73335 in Tk_MainEx () #11 0x00002d36 in main (argc=2, argv=0xbffff5b8) at xcAppInit.c:424 (5) I also tried endless permutations of libraries ---- I'm currently using the Apple X11 ones but I've also tried the XDarwin ones (i.e. completely changing what /usr/X11R6 and /etc/X11 contain by hand, etc.) Nothing helps here. Does anybody have any ideas? From xcrysden@democritos.it Fri May 25 11:34:23 2007 From: xcrysden@democritos.it (vinit sharma) Date: 25 May 2007 10:34:23 -0000 Subject: [xcrysden] Band wise Fermi surfaces with wien2k Message-ID: <20070525103423.12750.qmail@webmail90.rediffmail.com> This is a multipart mime message --Next_1180089263---0-59.160.240.175-12637 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline =C2=A0Respected All,=0A=0AI am a new user of XCrySden. I need to plot the = band wise fermi surfaces using Wien2k. I need your help me kindly guide me = what should I do?=0A=0A=0AVinit Sharma --Next_1180089263---0-59.160.240.175-12637 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0A =C2=A0Respected All,
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=0AI am a new user of XCrySden. I nee= d to plot the band wise fermi surfaces using Wien2k. I need your help me ki= ndly guide me what should I do?
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=0A --Next_1180089263---0-59.160.240.175-12637-- From xcrysden@democritos.it Fri May 25 11:37:09 2007 From: xcrysden@democritos.it (vinit sharma) Date: 25 May 2007 10:37:09 -0000 Subject: [xcrysden] Band wise Fermi surfaces with wien2k Message-ID: <20070525103709.7420.qmail@webmail94.rediffmail.com> This is a multipart mime message --Next_1180089429---0-59.160.240.219-7323 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline =C2=A0Respected All,=0A=0AI am a new user of XCrySden. I need to plot the = band wise fermi surfaces using Wien2k. I need your help me kindly guide me = what should I do?=0A=0A=0AVinit Sharma --Next_1180089429---0-59.160.240.219-7323 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0A =C2=A0Respected All,
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=0AI am a new user of XCrySden. I nee= d to plot the band wise fermi surfaces using Wien2k. I need your help me ki= ndly guide me what should I do?
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=0A --Next_1180089429---0-59.160.240.219-7323-- From xcrysden@democritos.it Thu May 31 08:33:13 2007 From: xcrysden@democritos.it (Dmitry Korotin) Date: Thu, 31 May 2007 13:33:13 +0600 Subject: [xcrysden] How to change Ball/Stick ratio with scripting? Message-ID: <2fd252650705310033v1402f071jbab4b0ee26944e24@mail.gmail.com> Dear all, I'm trying to create the movie of rotating 3D charge density. Everything is clear in HOWTOs but I want to change Ball/Stick ratio (or switch balls and sticks off). Is it possible? Thank you in advance, Dmitry Korotin. From xcrysden@democritos.it Thu May 31 09:00:03 2007 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 31 May 2007 10:00:03 +0200 Subject: [xcrysden] How to change Ball/Stick ratio with scripting? In-Reply-To: <2fd252650705310033v1402f071jbab4b0ee26944e24@mail.gmail.com> References: <2fd252650705310033v1402f071jbab4b0ee26944e24@mail.gmail.com> Message-ID: <1180598403.2605.4.camel@localhost.localdomain> On Thu, 2007-05-31 at 13:33 +0600, Dmitry Korotin wrote: > Dear all, > > I'm trying to create the movie of rotating 3D charge density. > Everything is clear in HOWTOs but > I want to change Ball/Stick ratio (or switch balls and sticks off). Is > it possible? To change the ball/stick ratio use menu: Modify-->Ball/Stick Ratio (it's the 8th entry in the Modify menu), or press the Shift-q key-combination. In both cases a pop-up window will appear where you change the ball/stick ratio value. To switch the balls and/or sticks off, you should be in lighting-on mode (scroll down the xcrysden's toolbox panel on the right). Click there the "Logic" mode, and use the three chekboxes. Regards, Tone From xcrysden@democritos.it Thu May 31 09:02:43 2007 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 31 May 2007 10:02:43 +0200 Subject: [xcrysden] Band wise Fermi surfaces with wien2k In-Reply-To: <20070525103709.7420.qmail@webmail94.rediffmail.com> References: <20070525103709.7420.qmail@webmail94.rediffmail.com> Message-ID: <1180598564.2605.8.camel@localhost.localdomain> On Fri, 2007-05-25 at 10:37 +0000, vinit sharma wrote: > =C2 Respected All, >=20 > I am a new user of XCrySden. I need to plot the band wise fermi > surfaces using Wien2k. I need your help me kindly guide me what should > I do? Some instructions of how to plot band-wise Fermi surfaces using Wien2K can be found here: http://www.xcrysden.org/doc/wien.html#__toc__11 I hope this will help. Regards, Tone From xcrysden@democritos.it Thu May 31 09:08:23 2007 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 31 May 2007 10:08:23 +0200 Subject: [xcrysden] Mac OS X (Intel) problems with xcrysden In-Reply-To: <342F5CF8-05B5-43A0-9147-286BF2B5E684@yale.edu> References: <342F5CF8-05B5-43A0-9147-286BF2B5E684@yale.edu> Message-ID: <1180598903.2605.15.camel@localhost.localdomain> On Fri, 2007-05-25 at 00:35 -0400, Sohrab Ismail-Beigi wrote: > Running on platform: macosx > Executing: /Users/sohrab/codes/XCrySDen-1.4.1bin/bin/ftnunit > > *** the hardware supports the stereo *** > > Error in startup script: Togl: couldn't get visual > while executing More and more people report this particular error. Apparently, the "system" on MAC OSX has been upgraded, which appears to be the cause of problems (back-compatibility issues). xcrysden needs to be recompiled on the new system. (The problem is that I don't have a regular access to MACOSX.) Regards, Tone From xcrysden@democritos.it Thu May 31 09:16:59 2007 From: xcrysden@democritos.it (Dmitry Korotin) Date: Thu, 31 May 2007 14:16:59 +0600 Subject: [xcrysden] How to change Ball/Stick ratio with scripting? In-Reply-To: <1180598403.2605.4.camel@localhost.localdomain> References: <2fd252650705310033v1402f071jbab4b0ee26944e24@mail.gmail.com> <1180598403.2605.4.camel@localhost.localdomain> Message-ID: <2fd252650705310116j750b0a2ft4b84432bc2d7fbca@mail.gmail.com> V2VsbCwgdGhhbmsgeW91IGZvciB5b3VyIGRldGFpbGVkIGFuc3dlciwgYnV0CgpJIHdhbnQgdG8g ZG8gdGhlIHNhbWUgdGhpbmdzIHVzaW5nIHRjbCBzY3JpcHRpbmchCgoKMjAwNy81LzMxLCBUb25l IEtva2FsaiA8dG9uZS5rb2thbGpAaWpzLnNpPjoKPiBPbiBUaHUsIDIwMDctMDUtMzEgYXQgMTM6 MzMgKzA2MDAsIERtaXRyeSBLb3JvdGluIHdyb3RlOgo+ID4gRGVhciBhbGwsCj4gPgo+ID4gSSdt IHRyeWluZyB0byBjcmVhdGUgdGhlIG1vdmllIG9mIHJvdGF0aW5nIDNEIGNoYXJnZSBkZW5zaXR5 Lgo+ID4gRXZlcnl0aGluZyBpcyBjbGVhciBpbiBIT1dUT3MgYnV0Cj4gPiBJIHdhbnQgdG8gY2hh bmdlIEJhbGwvU3RpY2sgcmF0aW8gKG9yIHN3aXRjaCBiYWxscyBhbmQgc3RpY2tzIG9mZikuIElz Cj4gPiBpdCBwb3NzaWJsZT8KPgo+IFRvIGNoYW5nZSB0aGUgYmFsbC9zdGljayByYXRpbyB1c2Ug bWVudToKPgo+IE1vZGlmeS0tPkJhbGwvU3RpY2sgUmF0aW8gKGl0J3MgdGhlIDh0aCBlbnRyeSBp biB0aGUgTW9kaWZ5IG1lbnUpLCBvcgo+IHByZXNzIHRoZSBTaGlmdC1xIGtleS1jb21iaW5hdGlv bi4gSW4gYm90aCBjYXNlcyBhIHBvcC11cCB3aW5kb3cgd2lsbAo+IGFwcGVhciB3aGVyZSB5b3Ug Y2hhbmdlIHRoZSBiYWxsL3N0aWNrIHJhdGlvIHZhbHVlLgo+Cj4gVG8gc3dpdGNoIHRoZSBiYWxs cyBhbmQvb3Igc3RpY2tzIG9mZiwgeW91IHNob3VsZCBiZSBpbiBsaWdodGluZy1vbiBtb2RlCj4g KHNjcm9sbCBkb3duIHRoZSB4Y3J5c2RlbidzIHRvb2xib3ggcGFuZWwgb24gdGhlIHJpZ2h0KS4g Q2xpY2sgdGhlcmUgdGhlCj4gIkxvZ2ljIiBtb2RlLCBhbmQgdXNlIHRoZSB0aHJlZSBjaGVrYm94 ZXMuCj4KPiBSZWdhcmRzLCBUb25lCj4KPiBfX19fX19fX19fX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fXwo+IFhDcnlTRGVuIG1haWxpbmcgbGlzdAo+IFhDcnlTRGVuQGRlbW9j cml0b3MuaXQKPiBodHRwOi8vd3d3LmRlbW9jcml0b3MuaXQvbWFpbG1hbi9saXN0aW5mby94Y3J5 c2Rlbgo+CgoKLS0gCvMg1dfB1sXOycXNLArkzcnU0snKIOvP0s/Uyc4K From xcrysden@democritos.it Thu May 31 09:38:39 2007 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 31 May 2007 10:38:39 +0200 Subject: [xcrysden] installing xcrysden on windows In-Reply-To: References: Message-ID: <1180600719.2605.51.camel@localhost.localdomain> On Tue, 2007-05-01 at 14:35 -0400, Craig Bridges wrote: > Dear All, > After having trouble installing XCrysDen on linux. Installation of linux should be much more straighforward than on Windows. Did you use the precompiled package, or you tried to compile the source? You may try with the pre-compiled version: http://www.xcrysden.org/download/xc-latest-linuxPC-static.tar.gz > Running './.bashrc' produces the error message: > > ./.bashrc: line 112: $'\r':command not found > ':not a valid identifierrt: 'XCRYSDEN_SCRATCH > ./.bashrc: line 121: $'\r':command not found There should be something awkward in the ~/.bashrc file. Please check, or send me your .bashrc file (I'll check). Regards, Tone From xcrysden@democritos.it Thu May 31 09:57:46 2007 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 31 May 2007 10:57:46 +0200 Subject: [xcrysden] How to change Ball/Stick ratio with scripting? In-Reply-To: <2fd252650705310116j750b0a2ft4b84432bc2d7fbca@mail.gmail.com> References: <2fd252650705310033v1402f071jbab4b0ee26944e24@mail.gmail.com> <1180598403.2605.4.camel@localhost.localdomain> <2fd252650705310116j750b0a2ft4b84432bc2d7fbca@mail.gmail.com> Message-ID: <1180601866.2605.72.camel@localhost.localdomain> On Thu, 2007-05-31 at 14:16 +0600, Dmitry Korotin wrote: > Well, thank you for your detailed answer, but > > I want to do the same things using tcl scripting! Here is a clever trick (which is due to Hande Ustunel) of how to achive an X feature with scripts. It involves three steps: 1. Open the file you are interested, but keep the X feature off. Then save the *.xcrysden script (File-->Save Current State and Structure). 2. Turn the X feature on, and again save the *.xcrysden script (under different filename of course) 3. compare the two files with you favorit "diff" program: you will see how they differ. Use this info in your script. Regards, Tone From xcrysden@democritos.it Thu May 31 10:15:57 2007 From: xcrysden@democritos.it (Dmitry Korotin) Date: Thu, 31 May 2007 15:15:57 +0600 Subject: [xcrysden] How to change Ball/Stick ratio with scripting? In-Reply-To: <1180601866.2605.72.camel@localhost.localdomain> References: <2fd252650705310033v1402f071jbab4b0ee26944e24@mail.gmail.com> <1180598403.2605.4.camel@localhost.localdomain> <2fd252650705310116j750b0a2ft4b84432bc2d7fbca@mail.gmail.com> <1180601866.2605.72.camel@localhost.localdomain> Message-ID: <2fd252650705310215j511a4218r1b18633319016cbe@mail.gmail.com> 2007/5/31, Tone Kokalj : > On Thu, 2007-05-31 at 14:16 +0600, Dmitry Korotin wrote: > > Well, thank you for your detailed answer, but > > > > I want to do the same things using tcl scripting! > > Here is a clever trick (which is due to Hande Ustunel) of how to achive > an X feature with scripts. It involves three steps: > > 1. Open the file you are interested, but keep the X feature off. Then > save the *.xcrysden script (File-->Save Current State and Structure). > > 2. Turn the X feature on, and again save the *.xcrysden script (under > different filename of course) > > 3. compare the two files with you favorit "diff" program: you will see > how they differ. > > Use this info in your script. > > Regards, Tone > > _______________________________________________ > XCrySDen mailing list > XCrySDen@democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > I had tried this method yesterday, but didn't achieve result I was looked. Differents between two .xcrysden scripts are in line: array set mode3D {space Off sticks On pipe Off balls On} And there is my script: ##################################### scripting::open --xsf $env(HOME)/work/wf/NiO/afm8/animation/in.xsf scripting::lighting On scripting::display on coordinate-system scripting::displayMode3D Stick array set mode3D {space Off sticks Off pipe Off balls Off} scripting::zoom +0.02 5 scripting::scalarField3D::load scripting::makeMovie::init \ -movieformat mpeg \ -dir tmp \ -frameformat PPM \ -firstframe 10 \ -lastframe 10 \ -delay 0 \ -save_to_file out.mpeg scripting::makeMovie::begin wm withdraw .iso scripting::zoom +1 1 set il 9.5 repeat {50} { scripting::scalarField3D::configure \ -isosurface 1 \ -interpolation_degree 2 \ -isolevel $il \ -plusminus 0 scripting::scalarField3D::render scripting::rotate x +3 1 scripting::rotate y +3 1 set il [expr $il-0.02] scripting::makeMovie::makeFrame } scripting::makeMovie::end ######################## But, sticks are still on! Could you help me? From xcrysden@democritos.it Thu May 31 10:46:13 2007 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 31 May 2007 11:46:13 +0200 Subject: [xcrysden] How to change Ball/Stick ratio with scripting? In-Reply-To: <2fd252650705310215j511a4218r1b18633319016cbe@mail.gmail.com> References: <2fd252650705310033v1402f071jbab4b0ee26944e24@mail.gmail.com> <1180598403.2605.4.camel@localhost.localdomain> <2fd252650705310116j750b0a2ft4b84432bc2d7fbca@mail.gmail.com> <1180601866.2605.72.camel@localhost.localdomain> <2fd252650705310215j511a4218r1b18633319016cbe@mail.gmail.com> Message-ID: <1180604773.2605.83.camel@localhost.localdomain> On Thu, 2007-05-31 at 15:15 +0600, Dmitry Korotin wrote: > I had tried this method yesterday, but didn't achieve result I was looked. > Differents between two .xcrysden scripts are in line: You are right, this doesn't work in this particular case (due to bad programming). You should use: # this toggle's sticks DispBool3D mode3D(sticks) or: # this toggle's balls DispBool3D mode3D(balls) or: #this toggle's spacefill's DispBool3D mode3D(space) Regards, Tone From xcrysden@democritos.it Thu May 31 11:02:14 2007 From: xcrysden@democritos.it (Dmitry Korotin) Date: Thu, 31 May 2007 16:02:14 +0600 Subject: [xcrysden] How to change Ball/Stick ratio with scripting? In-Reply-To: <1180604773.2605.83.camel@localhost.localdomain> References: <2fd252650705310033v1402f071jbab4b0ee26944e24@mail.gmail.com> <1180598403.2605.4.camel@localhost.localdomain> <2fd252650705310116j750b0a2ft4b84432bc2d7fbca@mail.gmail.com> <1180601866.2605.72.camel@localhost.localdomain> <2fd252650705310215j511a4218r1b18633319016cbe@mail.gmail.com> <1180604773.2605.83.camel@localhost.localdomain> Message-ID: <2fd252650705310302s417ef60q56c42999d188e0e1@mail.gmail.com> 2007/5/31, Tone Kokalj : > You are right, this doesn't work in this particular case > (due to bad programming). That was the first tcl script in my life :) > You should use: > > # this toggle's sticks > DispBool3D mode3D(sticks) > > or: > > # this toggle's balls > DispBool3D mode3D(balls) > > or: > > #this toggle's spacefill's > DispBool3D mode3D(space) > Thank you very much. Now it works fine. Best regards, Dmitry Korotin. From xcrysden@democritos.it Thu May 31 11:12:22 2007 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 31 May 2007 12:12:22 +0200 Subject: [xcrysden] How to change Ball/Stick ratio with scripting? In-Reply-To: <2fd252650705310302s417ef60q56c42999d188e0e1@mail.gmail.com> References: <2fd252650705310033v1402f071jbab4b0ee26944e24@mail.gmail.com> <1180598403.2605.4.camel@localhost.localdomain> <2fd252650705310116j750b0a2ft4b84432bc2d7fbca@mail.gmail.com> <1180601866.2605.72.camel@localhost.localdomain> <2fd252650705310215j511a4218r1b18633319016cbe@mail.gmail.com> <1180604773.2605.83.camel@localhost.localdomain> <2fd252650705310302s417ef60q56c42999d188e0e1@mail.gmail.com> Message-ID: <1180606343.2605.94.camel@localhost.localdomain> On Thu, 2007-05-31 at 16:02 +0600, Dmitry Korotin wrote: > 2007/5/31, Tone Kokalj : > > You are right, this doesn't work in this particular case > > (due to bad programming). > > That was the first tcl script in my life :) You misunderstood me (possibly it wasn't clear what I meant). I meant that xcrysden is programmed in bad way, therefore not everything works as expected. You did perfectly well with the script! > Thank you very much. Now it works fine. Good! Regards, Tone From xcrysden@democritos.it Thu May 31 09:23:32 2007 From: xcrysden@democritos.it (Gilles Hug) Date: Thu, 31 May 2007 10:23:32 +0200 Subject: [xcrysden] Mac OS X (Intel) problems with xcrysden In-Reply-To: <1180598903.2605.15.camel@localhost.localdomain> References: <342F5CF8-05B5-43A0-9147-286BF2B5E684@yale.edu> <1180598903.2605.15.camel@localhost.localdomain> Message-ID: <4E7E603A-4F4B-48EE-B39E-CD11CC66C881@onera.fr> Le 31 mai 07 =E0 10:08, Tone Kokalj a =E9crit : > > xcrysden needs to be recompiled on the new system. > (The problem is that I don't have a regular access to MACOSX.) Tone, The Mac has evolved to Intel procs and it would be neat to compile =20 XCrysDen for the Intel under the Mac OS X environement. We probably can do that with your help. Cheers, Gilles From xcrysden@democritos.it Thu May 31 13:27:53 2007 From: xcrysden@democritos.it (Tone Kokalj) Date: Thu, 31 May 2007 14:27:53 +0200 Subject: [xcrysden] Mac OS X (Intel) problems with xcrysden In-Reply-To: <4E7E603A-4F4B-48EE-B39E-CD11CC66C881@onera.fr> References: <342F5CF8-05B5-43A0-9147-286BF2B5E684@yale.edu> <1180598903.2605.15.camel@localhost.localdomain> <4E7E603A-4F4B-48EE-B39E-CD11CC66C881@onera.fr> Message-ID: <1180614474.2605.123.camel@localhost.localdomain> On Thu, 2007-05-31 at 10:23 +0200, Gilles Hug wrote: > Tone, > The Mac has evolved to Intel procs and it would be neat to compile > XCrysDen for the Intel under the Mac OS X environement. > We probably can do that with your help. Let us try. Tone