From hana.milani at yahoo.com Sat May 9 16:13:22 2009 From: hana.milani at yahoo.com (Hana Milani) Date: Sat, 9 May 2009 07:13:22 -0700 (PDT) Subject: [xcrysden] eliminating extra bonds Message-ID: <619477.35729.qm@web110813.mail.gq1.yahoo.com> Hello all, Is there a way to eliminate the extra bonds that we see in the image due to the relaxation procedure?. Regards, Hana -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090509/9d909c5f/attachment.htm From amitnsc at gmail.com Sun May 10 15:24:40 2009 From: amitnsc at gmail.com (Amit Kumar) Date: Sun, 10 May 2009 15:24:40 +0200 Subject: [xcrysden] eliminating extra bonds In-Reply-To: <619477.35729.qm@web110813.mail.gq1.yahoo.com> References: <619477.35729.qm@web110813.mail.gq1.yahoo.com> Message-ID: Dear Hana, If you find the solution, please let me know also. Thanks, With Regards, Amit On Sat, May 9, 2009 at 4:13 PM, Hana Milani wrote: > Hello all, > > Is there a way to eliminate the extra bonds that we see in the image due to > the relaxation procedure?. > > Regards, > Hana > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -- ********************************** Amit Kumar LNCMI - (National Laboratory of Intense Magnetic Fields) INSA - (National Institute of Applied Sciences) 143, avenue de Rangueil, F-31400 Toulouse, FRANCE Tel: +33562172974, Fax: +33562172816 Mobile: +33670858882, Home: +33950547115 Email: amit.kumar at lncmp.org & amitnsc at gmail.com ********************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090510/846c3182/attachment.htm From sebastijan.peljhan at ijs.si Mon May 11 08:11:02 2009 From: sebastijan.peljhan at ijs.si (Sebastijan Peljhan) Date: Mon, 11 May 2009 08:11:02 +0200 Subject: [xcrysden] eliminating extra bonds In-Reply-To: <619477.35729.qm@web110813.mail.gq1.yahoo.com> References: <619477.35729.qm@web110813.mail.gq1.yahoo.com> Message-ID: <1242022262.15683.9.camel@yunnan.ijs.si> On Sat, 2009-05-09 at 07:13 -0700, Hana Milani wrote: > Hello all, > > Is there a way to eliminate the extra bonds that we see in the image > due to the relaxation procedure?. You have an option "Mode" in a XCrySDen right sidebar. By clicking the "Logic" button the new options appear and you can choose what to draw (or not) by clicking appropriate options. If you would like to eliminate only one part of the bonds (the longest bonds, actually) you can change (decrease) the connectivity factor in a "Modify/Atomic Radius" menu. Best, Sebastijan > > Regards, > Hana > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Sebastijan Peljhan, J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia email: sebastijan.peljhan at ijs.si phone: +386-1-477-3523 fax: +386-1-477-3822 From paulatto at sissa.it Tue May 12 15:32:50 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Tue, 12 May 2009 15:32:50 +0200 Subject: [xcrysden] Error parsing AXSF file Message-ID: Dear Tone and everybody, I have a huge pw.x output file, generated by concatenating many output files, that is succesfully converted to AXSF by the pw2xsf converted, yet it cannot be parsed by xcryden correctly (An error occurred while parsing AXSF file $filename). I've tried looking at the file, but I'm not able to figure out what's wrong with it. I cannot attach the file to the mailing list because of its size, so I'm putting it here: (it's ~30 MB gzipped!). I hope you can provide any hint, thank you in advance. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From tone.kokalj at ijs.si Wed May 13 15:21:45 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 13 May 2009 15:21:45 +0200 Subject: [xcrysden] eliminating extra bonds In-Reply-To: <1242022262.15683.9.camel@yunnan.ijs.si> References: <619477.35729.qm@web110813.mail.gq1.yahoo.com> <1242022262.15683.9.camel@yunnan.ijs.si> Message-ID: <1242220905.8184.3.camel@walk.ijs.si> On Mon, 2009-05-11 at 08:11 +0200, Sebastijan Peljhan wrote: > On Sat, 2009-05-09 at 07:13 -0700, Hana Milani wrote: > > Hello all, > > > > Is there a way to eliminate the extra bonds that we see in the image > > due to the relaxation procedure?. > > You have an option "Mode" in a XCrySDen right sidebar. By clicking the > "Logic" button the new options appear and you can choose what to draw > (or not) by clicking appropriate options. > > If you would like to eliminate only one part of the bonds (the longest > bonds, actually) you can change (decrease) the connectivity factor in a > "Modify/Atomic Radius" menu. In addition to that, you can change the covalent radii of elements (same window as for chemical connectivity factor). This is not a "total" bond editing, but by using both the chemical connectivity factor and the covalent radius (the two are used as a criteria of where to plot a bond), it is possible to handle many situations. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Wed May 13 15:28:15 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 13 May 2009 15:28:15 +0200 Subject: [xcrysden] Error parsing AXSF file In-Reply-To: References: Message-ID: <1242221295.8184.9.camel@walk.ijs.si> On Tue, 2009-05-12 at 15:32 +0200, Lorenzo Paulatto wrote: > Dear Tone and everybody, > I have a huge pw.x output file, generated by concatenating many output > files, that is succesfully converted to AXSF by the pw2xsf converted, yet > it cannot be parsed by xcryden correctly (An error occurred while parsing > AXSF file $filename). The problem is the concatenation of many pw.x output files into one. The pwo2xsf.sh then finds more than find instance of CELL_PARAMETERS record and mistakenly thinks it is a variable-cell output file and creates an invalid variable-cell XSF file (this one should have same number of PRIMVEC and PRIMCOORD sections). The solution is easy: delete all but one instance of PRIMVEC sections from the AXSF file (also delete the index suffix after the PRIMVEC keyword). Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Wed May 13 15:34:41 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 13 May 2009 15:34:41 +0200 Subject: [xcrysden] a problem about xcrysden on cygwin In-Reply-To: References: Message-ID: <1242221681.8184.13.camel@walk.ijs.si> On Sun, 2009-04-26 at 13:15 +0800, ? ? wrote: > Dear Sir or Madam, > When I install the xcrysden (xc-1.5.18-cygwin-shared.tar ) on the > cygwin. > I come to a problem. When I run the xcrysden, a error message will be > pop-up. > The error message is that > couldn't load library "/home/ > fangwei/XCrySDden-1.5.18-bin-shared/bin/xcrys.dll":this library or a > dependent library could not be found in library path while executing > "load $system(TOPDIR)/bin/xcrys.dll" Probably this message means what it says: since the ../XCrySDden-1.5.18-bin-shared/bin/xcrys.dll is apparently there, it is likely that some dependent library is not. Please check that you have installed all the necessary cygwin packages for xcrysden. Here is the list of them: * bash * bc * coreutils * gawk * grep * gzip * ImageMagick * less * more * opengl * tcltk Since you have tcltk (or else such error would not occur), I suspect the opengl package is missing. 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 paulatto at sissa.it Wed May 13 16:35:36 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 13 May 2009 16:35:36 +0200 Subject: [xcrysden] Error parsing AXSF file In-Reply-To: <1242221295.8184.9.camel@walk.ijs.si> References: <1242221295.8184.9.camel@walk.ijs.si> Message-ID: In data 13 maggio 2009 alle ore 15:28:15, Tone Kokalj ha scritto: > The problem is the concatenation of many pw.x output files into one. The > pwo2xsf.sh then finds more than find instance of CELL_PARAMETERS record > and mistakenly thinks it is a variable-cell output file and creates an > invalid variable-cell XSF file (this one should have same number of > PRIMVEC and PRIMCOORD sections). > Ok, thank you Tone, in practice it only seldom happens. > The solution is easy: delete all but one instance of PRIMVEC sections > from the AXSF file (also delete the index suffix after the PRIMVEC > keyword). Thanks, this is easy&fast to do. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From zhzeng at dicp.ac.cn Tue May 19 17:12:40 2009 From: zhzeng at dicp.ac.cn (Zhenhua Zeng) Date: Tue, 19 May 2009 23:12:40 +0800 Subject: [xcrysden] Xcrysden Bug for 2D Fermi Surface Plot Message-ID: <200905192312406875473@dicp.ac.cn> Dear all, I found a bug for Fermi Surface plot in 2D brillouin zone. I will explait it below. For 3D brillouin zone with k-point grid sample (Nx*Ny*Nz) and N>2, there no problem at all. However for a 2D surface brillouin zone with k-point grid such as (8x8x2) for (8x8x1) in which Nz <3, then xcrysten will give the following error: --------------------------------------------------- /home/zengzh/Source/XCrySDen-1.5.17-src-all/xcrysden: line 211: 6096 Segmentation fault ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null --------------------------------------------------- I have tested several examples, and found the problem just come from the grid given in the bxsf file (or in calculations). For example in example RhBulkFcc.bxsf, the k-point grid is 32*32*32, however if I change the grid to 128*128*2, xcrysden will crash and give the error as above. I use XCrySDen-1.5.17 now. I want to know whether this bug will be fixed in the following version such as V1.6. PS: Attachment is another example which crash xcryden and show the bug. Best Wishes Zhenhua Zeng -------------- next part -------------- A non-text attachment was scrubbed... Name: FS.bxsf Type: application/octet-stream Size: 10102 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20090519/cff7b112/attachment.obj From jiafasun at yahoo.com.cn Wed May 20 05:09:38 2009 From: jiafasun at yahoo.com.cn (=?utf-8?B?5a2Z5a625rOV?=) Date: Wed, 20 May 2009 11:09:38 +0800 (CST) Subject: [xcrysden] =?utf-8?b?5Zue5aSN77yaICBYY3J5c2RlbiBCdWcgZm9yIDJEIEZl?= =?utf-8?q?rmi_Surface_Plot?= Message-ID: <301753.39720.qm@web15704.mail.cnb.yahoo.com> Sr ?I think? the problem that is from your X-windows ???????????????????????????????????????????Best Wishes???????? ???????????????????????????????????????? ?your's friend ?JiaFaSun --- 09?5?19????, Zhenhua Zeng ??? ???: Zhenhua Zeng ??: [xcrysden] Xcrysden Bug for 2D Fermi Surface Plot ???: "xcrysden" ??: 2009?5?19?,??,??11:12 Dear all, I found a bug for Fermi Surface plot in 2D brillouin zone. I will explait it below. For 3D brillouin zone with k-point grid sample (Nx*Ny*Nz) and N>2,? there no problem at all. However for a 2D? surface brillouin zone with k-point grid such as (8x8x2) for (8x8x1) in which Nz <3, then xcrysten will give the following error: --------------------------------------------------- /home/zengzh/Source/XCrySDen-1.5.17-src-all/xcrysden: line 211:? 6096 Segmentation fault? ? ? ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null --------------------------------------------------- I have tested several examples, and found the problem just come from the grid given in the bxsf file (or in calculations). For example in example RhBulkFcc.bxsf, the k-point grid is 32*32*32, however if I change the grid to 128*128*2, xcrysden will crash and give the error as above. I use XCrySDen-1.5.17 now. I want to know whether this bug will be fixed in the following version such as V1.6. PS: Attachment is another example? which crash xcryden and show the bug. ??? ??? ??? ??? Best Wishes Zhenhua Zeng -----???????----- _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden ___________________________________________________________ ????????????????? http://card.mail.cn.yahoo.com/ -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090520/5a983c4d/attachment.htm From sarayazdani at yahoo.com Wed May 20 05:45:13 2009 From: sarayazdani at yahoo.com (sara yazdani) Date: Tue, 19 May 2009 20:45:13 -0700 (PDT) Subject: [xcrysden] quality of the images Message-ID: <886822.89126.qm@web52006.mail.re2.yahoo.com> Hi, I have prepared LDOS files in Xcrysden and I have saved them in eps format. 1. I need the images to be in high resolution, but although I followed the tricks you have mentioned for the quality still the saved files are not in high resolution. Please let me know how to solve this problem. 2. Also, another problem is how to insert these files in MS Word. I have produced my images in linux, but when i insert them in MS Word, they lose their quality drastically. I would be very grateful if you kindly let me know how to solve these problems. Regards, Sara -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090519/df89791c/attachment.htm From paulatto at sissa.it Wed May 20 09:35:14 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 20 May 2009 09:35:14 +0200 Subject: [xcrysden] quality of the images In-Reply-To: <886822.89126.qm@web52006.mail.re2.yahoo.com> References: <886822.89126.qm@web52006.mail.re2.yahoo.com> Message-ID: In data 20 maggio 2009 alle ore 05:45:13, sara yazdani ha scritto: > 1. I need the images to be in high resolution, but although I followed > the tricks you have mentioned for the quality still the saved files are > not in high resolution. Please let me know how to solve this problem. Images saved by xcrysden are technically screenshots, unless you try and use the direct postscript rendering (which can produce very heavy images, but may help). The only additional trick, which is not noticed in Tone's FAQ is to increase the size of the X screen beyond the size of the monitor (so that you can maximize xcd up to a huge size). It can be done in every version of linux, but may require a bit of config file editing. > > 2. Also, another problem is how to insert these files in MS Word. I have > produced my images in linux, but when i insert them in MS Word, they > lose their quality drastically. Provided I don't have Microsoft office, I know it can digest some image formats better than others. Probably there are some options you can change to prevent it from compressing the images, but it would be far too expensive for me to find them. regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From tone.kokalj at ijs.si Wed May 20 11:07:20 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 20 May 2009 11:07:20 +0200 Subject: [xcrysden] Xcrysden Bug for 2D Fermi Surface Plot In-Reply-To: <200905192312406875473@dicp.ac.cn> References: <200905192312406875473@dicp.ac.cn> Message-ID: <1242810440.26796.13.camel@walk.ijs.si> On Tue, 2009-05-19 at 23:12 +0800, Zhenhua Zeng wrote: > Dear all, > > I found a bug for Fermi Surface plot in 2D brillouin zone. I will explait it below. > > For 3D brillouin zone with k-point grid sample (Nx*Ny*Nz) and N>2, there no problem at all. > However for a 2D surface brillouin zone with k-point grid such as (8x8x2) for (8x8x1) in which > Nz <3, then xcrysten will give the following error: > --------------------------------------------------- > /home/zengzh/Source/XCrySDen-1.5.17-src-all/xcrysden: line 211: 6096 Segmentation fault > ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null Technically this is really a bug, but otherwise this is entirely due to a misuse of xcrysden 3D Fermi Surface (FS) visualizer. I will insert a check that will prevent it. With that being said, the smallest number of points (in whatever direction) is 3. If you have a 2D material (say surface), then the FS is composed of e.g. "loops" (circles), but xcrysden cannot plot that. Instead it can plot FS in 3D as "cylinders". So this is how you should use it. If you specify in your calculation a k-mesh of, say, 8x8x2, this will produce the 9x9x3 bandgrid (this sounds awkward, but is explained here: http://www.xcrysden.org/doc/XSF.html#__toc__12 http://www.xcrysden.org/doc/XSF.html#__toc__14 ) If you have some 2D example you may check if it works with 3 points in the 3rd direction as described above. If it does not let me know, because this is then a real bug in the algorithm. > I have tested several examples, and found the problem just come from the grid given in the bxsf file (or in calculations). > For example in example RhBulkFcc.bxsf, the k-point grid is 32*32*32, however if I change the grid to 128*128*2, > xcrysden will crash and give the error as above. Even if it would work the result would be a total nonsense! > PS: Attachment is another example which crash xcryden and show the bug. OK, this examples uses 17x17x2 bandgrid, please do another calculation and try with 17x17x3 bandgrid. This means that in your ab-init calculation you should specify 16x16x2 k-mesh. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Wed May 20 11:22:38 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 20 May 2009 11:22:38 +0200 Subject: [xcrysden] quality of the images In-Reply-To: References: <886822.89126.qm@web52006.mail.re2.yahoo.com> Message-ID: <1242811358.26796.28.camel@walk.ijs.si> On Wed, 2009-05-20 at 09:35 +0200, Lorenzo Paulatto wrote: > In data 20 maggio 2009 alle ore 05:45:13, sara yazdani > ha scritto: > > 1. I need the images to be in high resolution, but although I followed > > the tricks you have mentioned for the quality still the saved files are > > not in high resolution. Please let me know how to solve this problem. > > Images saved by xcrysden are technically screenshots, unless you try and > use the direct postscript rendering (which can produce very heavy images, > but may help). The only additional trick, which is not noticed in Tone's > FAQ is to increase the size of the X screen beyond the size of the monitor > (so that you can maximize xcd up to a huge size). It can be done in every > version of linux, but may require a bit of config file editing. In addition to what Lorenzo already described, I would like to say this: Unless you would like to produce a huge poster with images of dimension on the order of a meter, the ~1500 pixels of nowadays monitors is always sufficient, even for a high quality graphics such as cover arts of the magazines. You man enhance a bit the quality of images by switching on the anti-aliasing (menu: Display->Antialias). I believe that your problem is caused by the combination of EPS graphics format and Word-like programs. Here are few items to consider: 1. EPS is a print and not a screen format. This means that on the screen it will look much uglier than on the print. 2. According to my experience not every software handles EPS well. For example, Office-like products (I use OpenOffice, but I assume the MS Office is not much different) handles EPS very bad or not at all. Taking this into consideration, I suggest that you save your images in e.g. PNG format. This is a screen format and when in sufficient high resolution also good for printing. > > 2. Also, another problem is how to insert these files in MS Word. I have > > produced my images in linux, but when i insert them in MS Word, they > > lose their quality drastically. As described above (PNG format is your friend). 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 sarayazdani at yahoo.com Wed May 20 11:48:01 2009 From: sarayazdani at yahoo.com (sara yazdani) Date: Wed, 20 May 2009 02:48:01 -0700 (PDT) Subject: [xcrysden] quality of the images In-Reply-To: References: Message-ID: <788437.77740.qm@web52001.mail.re2.yahoo.com> Thanks for the reply. The problem is that I only can print the images I have to .eps and for the jpeg and other formats I receive the followong error: couldn't execute "/home/sara/xcrys_tmp/xc_8850/tmp.ppm": permission denied Also, please let me know how I can increase the size of the image, as you mentioned in your email. Regards, -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090520/641d878a/attachment.htm From tone.kokalj at ijs.si Wed May 20 12:00:12 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 20 May 2009 12:00:12 +0200 Subject: [xcrysden] quality of the images In-Reply-To: <788437.77740.qm@web52001.mail.re2.yahoo.com> References: <788437.77740.qm@web52001.mail.re2.yahoo.com> Message-ID: <1242813612.26796.37.camel@walk.ijs.si> On Wed, 2009-05-20 at 02:48 -0700, sara yazdani wrote: > Thanks for the reply. > > The problem is that I only can print the images I have to .eps and for > the jpeg and other formats I receive the followong error: > > couldn't execute "/home/sara/xcrys_tmp/xc_8850/tmp.ppm": permission > denied In order to print in PNG and alike xcrysden needs ImageMagick external program (which is available probably in all linux distributions). Try in the terminal: which convert The answer should be something like: /usr/bin/convert If there is no answer, please install the ImageMagick (http://www.imagemagick.org/). If you are using xcrysden version 1.5* then xcrysden will automatically recognize ImageMagick and do a proper job. If your version of xcrysden is older you need to edit ~/.xcrysden/custom-definitions file and add something like: set xcMisc(ImageMagick.convert) /path/to/my/convert > Also, please let me know how I can increase the size of the image, as > you mentioned in your email. Maximize your xcrysden window, and then zoom as much as possible the structure. (this should be sufficient) 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 zhzeng at dicp.ac.cn Wed May 20 15:33:33 2009 From: zhzeng at dicp.ac.cn (Zhenhua Zeng) Date: Wed, 20 May 2009 21:33:33 +0800 Subject: [xcrysden] Xcrysden Bug for 2D Fermi Surface Plot References: <200905192312406875473@dicp.ac.cn>, <1242810440.26796.13.camel@walk.ijs.si> Message-ID: <200905202133331098202@dicp.ac.cn> Hi Tone, Thank you for you reply. I understand you point, i.e. allowed smallest number of points (in whatever direction) is 3. And what I want to point out in last email is also this number problem. For 3D material, its fermi surfaces are some isosurfaces, while for 2D material, its fermi surfaces should be some contours. In principle, it is easier to plot contours. And what it need is to judge it is a 2D or 3D fermi surface. So I want to know whether this section will in development schedule? I think the development of this section will be appreciated by many scientists working on surface calculations. BTW: For cylinders-like isosurface, it is vivid in side view, however it is almost invisible in top view due isosurface is almost no thickness. Do you think this is a problem, and have plan to improve it? Best Wishes Zhenhua Zeng ------------------------------------------------------------- From?Tone Kokalj sent:?2009-05-20 17:07:30 To?XCrySDen mailing list Subject?Re: [xcrysden] Xcrysden Bug for 2D Fermi Surface Plot > >On Tue, 2009-05-19 at 23:12 +0800, Zhenhua Zeng wrote: >> Dear all, >> >> I found a bug for Fermi Surface plot in 2D brillouin zone. I will explait it below. >> >> For 3D brillouin zone with k-point grid sample (Nx*Ny*Nz) and N>2, there no problem at all. >> However for a 2D surface brillouin zone with k-point grid such as (8x8x2) for (8x8x1) in which >> Nz <3, then xcrysten will give the following error: >> --------------------------------------------------- >> /home/zengzh/Source/XCrySDen-1.5.17-src-all/xcrysden: line 211: 6096 Segmentation fault >> ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS >/dev/null > >Technically this is really a bug, but otherwise this is entirely due to >a misuse of xcrysden 3D Fermi Surface (FS) visualizer. I will insert a >check that will prevent it. With that being said, the smallest number of >points (in whatever direction) is 3. > >If you have a 2D material (say surface), then the FS is composed of e.g. >"loops" (circles), but xcrysden cannot plot that. Instead it can plot FS >in 3D as "cylinders". >So this is how you should use it. If you specify >in your calculation a k-mesh of, say, 8x8x2, this will produce the 9x9x3 >bandgrid (this sounds awkward, but is explained here: >http://www.xcrysden.org/doc/XSF.html#__toc__12 >http://www.xcrysden.org/doc/XSF.html#__toc__14 >) > >If you have some 2D example you may check if it works with 3 points in >the 3rd direction as described above. If it does not let me know, >because this is then a real bug in the algorithm. > >> I have tested several examples, and found the problem just come from the grid given in the bxsf file (or in calculations). >> For example in example RhBulkFcc.bxsf, the k-point grid is 32*32*32, however if I change the grid to 128*128*2, >> xcrysden will crash and give the error as above. > >Even if it would work the result would be a total nonsense! > > >> PS: Attachment is another example which crash xcryden and show the bug. > >OK, this examples uses 17x17x2 bandgrid, please do another calculation >and try with 17x17x3 bandgrid. This means that in your ab-init >calculation you should specify 16x16x2 k-mesh. > >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 > >_______________________________________________ >XCrySDen mailing list >XCrySDen at democritos.it >http://www.democritos.it/mailman/listinfo/xcrysden >. S ------------------------------------------------------------- From taebumlee at gmail.com Fri May 22 20:09:08 2009 From: taebumlee at gmail.com (TAE BUM LEE) Date: Fri, 22 May 2009 13:09:08 -0500 Subject: [xcrysden] error in pwo2xsf.sh in 1.4.1static version Message-ID: <35db185b0905221109ta4c4a67x2ddf66720222b9f5@mail.gmail.com> Hi, Does anybody know how to fix the problem of XCrySDen 1.4 static to read pwscf output file? When I try to open pwscf ouput in example directory of Quantum-Espresso tutorial, the error message is generated. Error: while executing exec sh /usr/local/bin/XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh --optcoor /home/taebum/Desktop/examples_pwgui/Si.pw.out > pwo2xsf.xsf. Dr. Kokalj suggest modification of pwo2xsf.sh file with following lines in mailing list but invalid to me LANG=C LC_ALL=C export LANG LC_ALL Regards, TaeBum ######################################## TAE BUM LEE Dept. Chem. & Biochem Auburn Univ. AL. 36849 TEL.: 334-844-6912 e-mail: taebumlee at gmail.com ######################################## -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090522/a8517336/attachment.htm From edouard.duriau at gmail.com Fri May 22 21:24:03 2009 From: edouard.duriau at gmail.com (Edouard Duriau) Date: Fri, 22 May 2009 21:24:03 +0200 Subject: [xcrysden] Problem executing xcrysden Message-ID: <66650c2d0905221224s73a4eafi48956e8fc64d6209@mail.gmail.com> Dear all, I am new to XCrysDen so I am not yet familiar with all of the subtelties of the software. Thus, here is my problem: I have correctely installed CygWin (including all of the packages) then the binary package of XrysDen 1.5.18 (I tried to install ver. 1.4.1 but the archive was broken) Then I have run ./xcConfigure and configured it correctely. Afterwards I have of course executed xcrysden then I got this error message after a few lines: "xcrysden: line 204: exec: wish: not found" I checked the source file "xcrysden" and found that line 204 is: " exec wish ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- \ " I am not a software specialist but I checked if the file /Tcl/xcInit.tcl was present in the right directory and it is present where it should be. I have tried this whole procedure several times on Win XP (as an Administrator) and on Vista but couldn't figure a way to make XCrysDen work. Could you PLEASE help me because I think I am about to throw away my computers through the window... ;) Thanks a HUGE load upfront! Ed -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090522/acd718d6/attachment.htm From sarayazdani at yahoo.com Sat May 23 08:50:59 2009 From: sarayazdani at yahoo.com (sara yazdani) Date: Fri, 22 May 2009 23:50:59 -0700 (PDT) Subject: [xcrysden] error in XSF(urgent) In-Reply-To: References: Message-ID: <737929.25509.qm@web52001.mail.re2.yahoo.com> Hi, I have produced many LDOS files with xcrysden before, but now I can not even open the previously viewed XSF files with the following error: error copying "/home/sara/siesta-2.0.2/LDOS/48 PSS HOMO/work/zno.XSF" to "zno.XSF": no space left on device error copying "/home/sara/siesta-2.0.2/LDOS/48 PSS HOMO/work/zno.XSF" to "zno.XSF": no space left on device while executing "file copy -force $file $name" (procedure "gunzipXSF" line 10) invoked from within "gunzipXSF $filedir" (procedure "xsfOpen" line 4) invoked from within "xsfOpen $fileselect(path) $can" (procedure "xsfOpenMenu" line 25) invoked from within "xsfOpenMenu .mesa" invoked from within ".menu.vmfile.menu.opstr invoke active" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke active]" (procedure "tk::MenuInvoke" line 47) invoked from within "tk::MenuInvoke .menu.vmfile.menu.opstr 1" (command bound to event) Please let me know where I have gone wrong. Regards, Sara -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090522/d557596e/attachment.htm From hana.milani at yahoo.com Sat May 23 11:47:53 2009 From: hana.milani at yahoo.com (Hana Milani) Date: Sat, 23 May 2009 02:47:53 -0700 (PDT) Subject: [xcrysden] isosurface color In-Reply-To: References: Message-ID: <193099.35245.qm@web110815.mail.gq1.yahoo.com> Hi, I would like to know if there's a way to have different colors for different orbitals when we have XSF files presented in xcrysden to show the local density of states? Regards, Hana -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090523/daa18853/attachment.htm From paulatto at sissa.it Sat May 23 11:51:15 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Sat, 23 May 2009 11:51:15 +0200 (CEST) Subject: [xcrysden] error in XSF(urgent) In-Reply-To: <737929.25509.qm@web52001.mail.re2.yahoo.com> References: <737929.25509.qm@web52001.mail.re2.yahoo.com> Message-ID: <54464.78.12.165.22.1243072275.squirrel@webmail.sissa.it> On Sat, May 23, 2009 08:50, sara yazdani wrote: > error copying "/home/sara/siesta-2.0.2/LDOS/48 PSS HOMO/work/zno.XSF" to > "zno.XSF": no space left on device Which part of "no space left on device" is not clear to you? Likely the partition where temporary XCD data is stored is full: free some space or buy a bigger har disk. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ From taebumlee at gmail.com Tue May 26 00:31:35 2009 From: taebumlee at gmail.com (TAE BUM LEE) Date: Mon, 25 May 2009 17:31:35 -0500 Subject: [xcrysden] error in pwo2xsf.sh Message-ID: <35db185b0905251531x73d8eec6vaa5a3158408f5680@mail.gmail.com> Hi, Does anybody know how to fix the problem of XCrySDen 1.5.17-semishared to read pwscf output file? When I try to open pwscf ouput in example directory of Quantum-Espresso tutorial (4.0.5), the error message is generated. Error: while executing exec sh /usr/local/bin/XCrySDen-1.4.1bin-static/scripts/pwo2xsf.sh --optcoor /home/taebum/Desktop/examples_pwgui/Si.pw.out > pwo2xsf.xsf. Regards, TaeBum ######################################## TAE BUM LEE Dept. Chem. & Biochem Auburn Univ. AL. 36849 TEL.: 334-844-6912 e-mail: taebumlee at gmail.com ######################################## -- ######################################## TAE BUM LEE Dept. Chem. & Biochem Auburn Univ. AL. 36849 TEL.: 334-844-6912 e-mail: taebumlee at gmail.com ######################################## -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090525/84bf72a5/attachment.htm From zhuyingtao at mail.sdu.edu.cn Wed May 27 03:07:13 2009 From: zhuyingtao at mail.sdu.edu.cn (zhuyingtao) Date: Wed, 27 May 2009 09:07:13 +0800 Subject: [xcrysden] Some questions about xcrysden for crystal06 Message-ID: <443385466.24590@mail.sdu.edu.cn> Dear all, I use the latest version of xcrysden for crystal06, and want to remove atoms from system, but I can?t get the label of atom, which I want to remove. Is that a bug of the code, or some thing wrong in my install process. Can you give me some instruction ? My operate system is 32 bits Redhat. Thanks very much Best wishes Yours? zhuyingtao -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090527/ecaaf609/attachment.htm From paulatto at sissa.it Wed May 27 10:45:16 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 27 May 2009 10:45:16 +0200 Subject: [xcrysden] Some questions about xcrysden for crystal06 In-Reply-To: <443385466.24590@mail.sdu.edu.cn> References: <443385466.24590@mail.sdu.edu.cn> Message-ID: In data 27 maggio 2009 alle ore 03:07:13, zhuyingtao ha scritto: > Dear all, > > I use the latest version of xcrysden for crystal06, and want to remove > atoms from system, but I can?t get the label of atom, which I want to > remove. Is that a bug of the code, or some thing wrong in my install > process. Can you give me some instruction ? In which sens you cannot? What does it happen if you click on the "AtomInfo" button in the bottom-left corner of the XCD windows and then click on an atom? regards -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From tone.kokalj at ijs.si Wed May 27 10:59:56 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 27 May 2009 10:59:56 +0200 Subject: [xcrysden] Xcrysden Bug for 2D Fermi Surface Plot In-Reply-To: <200905202133331098202@dicp.ac.cn> References: <200905192312406875473@dicp.ac.cn> , <1242810440.26796.13.camel@walk.ijs.si> <200905202133331098202@dicp.ac.cn> Message-ID: <1243414796.6246.7.camel@walk.ijs.si> On Wed, 2009-05-20 at 21:33 +0800, Zhenhua Zeng wrote: > Hi Tone, > > Thank you for you reply. > I understand you point, i.e. allowed smallest number of points (in whatever direction) is 3. > And what I want to point out in last email is also this number problem. > > For 3D material, its fermi surfaces are some isosurfaces, while for 2D material, its fermi surfaces should be some contours. > In principle, it is easier to plot contours. Indeed! Even gnuplot can do a descent job here (perhaps, this was the reason it was done only for 3D). I should consider implementing a 2D contour plots > BTW: For cylinders-like isosurface, it is vivid in side view, however it is almost invisible in top view due isosurface is almost no thickness. > Do you think this is a problem, and have plan to improve it? You are absolutely right; isosurface has a zero thickness, so this mode is OK for understanding the shape of 2D FS, but not for printing (i.e. making images for publications). Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Wed May 27 11:04:44 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 27 May 2009 11:04:44 +0200 Subject: [xcrysden] error in pwo2xsf.sh In-Reply-To: <35db185b0905251531x73d8eec6vaa5a3158408f5680@mail.gmail.com> References: <35db185b0905251531x73d8eec6vaa5a3158408f5680@mail.gmail.com> Message-ID: <1243415084.6246.12.camel@walk.ijs.si> On Mon, 2009-05-25 at 17:31 -0500, TAE BUM LEE wrote: > Hi, > > Does anybody know how to fix the problem of XCrySDen 1.5.17-semishared > to read pwscf output file? > When I try to open pwscf ouput in example directory of > Quantum-Espresso tutorial (4.0.5), the error message is generated. > > Error: while executing > exec sh > /usr/local/bin/XCrySDen-1.4. > 1bin-static/scripts/pwo2xsf.sh --optcoor > /home/taebum/Desktop/examples_pwgui/Si.pw.out > pwo2xsf.xsf. First of all, you are still using the version 1.4.1 (as seen above). Change your ~/.bashrc (or ~/.cshrc, depending on the shell you are using) to point to your new installation. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Wed May 27 11:06:58 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 27 May 2009 11:06:58 +0200 Subject: [xcrysden] Problem executing xcrysden In-Reply-To: <66650c2d0905221224s73a4eafi48956e8fc64d6209@mail.gmail.com> References: <66650c2d0905221224s73a4eafi48956e8fc64d6209@mail.gmail.com> Message-ID: <1243415218.6246.14.camel@walk.ijs.si> On Fri, 2009-05-22 at 21:24 +0200, Edouard Duriau wrote: > Dear all, > > > I am new to XCrysDen so I am not yet familiar with all of the > subtelties of the software. > Thus, here is my problem: > > I have correctely installed CygWin (including all of the packages) > then the binary package of XrysDen 1.5.18 (I tried to install ver. > 1.4.1 but the archive was broken) > Then I have run ./xcConfigure and configured it correctely. > > Afterwards I have of course executed xcrysden then I got this error > message after a few lines: > "xcrysden: line 204: exec: wish: not found" This is because you did not install all the packages that are required for xcrysden. In particular, the above error tells that the tcltk package is not installed. Here is the list of all needed cygwin packages: * bash * bc * coreutils * gawk * grep * gzip * ImageMagick * less * more * opengl * tcltk Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Wed May 27 11:10:02 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 27 May 2009 11:10:02 +0200 Subject: [xcrysden] isosurface color In-Reply-To: <193099.35245.qm@web110815.mail.gq1.yahoo.com> References: <193099.35245.qm@web110815.mail.gq1.yahoo.com> Message-ID: <1243415402.6246.17.camel@walk.ijs.si> On Sat, 2009-05-23 at 02:47 -0700, Hana Milani wrote: > Hi, > > I would like to know if there's a way to have different colors for > different orbitals when we have XSF files presented in xcrysden to > show the local density of states? At a given plot the maximum number of colors for isosurface is two, because xcrysden can plot the +value and -value isosurfaces simulteneously. For LDOS, you have only positive values, so the isosurfaces will be colored by one color (but this one can be arbitrarily chosen). Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Wed May 27 11:42:23 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 27 May 2009 11:42:23 +0200 Subject: [xcrysden] Some questions about xcrysden for crystal06 In-Reply-To: <200905270907135155458@mail.sdu.edu.cn> References: <200905270907135155458@mail.sdu.edu.cn> Message-ID: <1243417343.6246.50.camel@walk.ijs.si> On Wed, 2009-05-27 at 09:07 +0800, zhuyingtao wrote: > Dear all? > > I use the latest version of xcrysden for crystal06, and want to remove > atoms from system, but I can?t get the label of atom, which I want to > remove. I remember this problem. There were two problems: 1) old versions of xcrysden will do it wrong anyway 2) for nwere versions: after pressing the "Selected" button in the Select window the atom is actually selected but noting was seen in the "Atomic Label:" entry. This was because of the print format. Instead of, say, "2" it was printed " 2", but because the corresponding entry is very small and the label is not visible. Check this: click with mouse into this entry and scroll with cursor to the right. Does the label appears? Regards, Tone PS: to Lorenzo: zhuyingtao is refering to xcrysden's interface to crystal program, there is an option to remove atoms interactively, hence this is not the "AtomInfo" button. Although it seems that your suggestion would work for zhuyingtao too, it will actually not. In crystal one specifies only the irreducible atoms, and zhuyingtao needs the label of the corresponding irreducible atom. Yet this would work for the P1 spacegroup (=no symmetry). -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From sclauzer at sissa.it Wed May 27 17:40:45 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 27 May 2009 17:40:45 +0200 Subject: [xcrysden] Atomic labels in eps printing Message-ID: <4A1D5EFD.1030502@sissa.it> Has anyone tried to include the atomic labels in an eps format printing? I first enabled atomic labels display (pressing the s key, for instance), then printed to eps. The atomic labels do not appear in the output postscript (while they are present for instance in the corresponding png). Is this a problem of my installation or is a common issue? I first thought that the labels could be hidden by other layers, but there is no trace of the strings corresponding to atomic labels in the eps file. Gabriele -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From tone.kokalj at ijs.si Wed May 27 17:46:53 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 27 May 2009 17:46:53 +0200 Subject: [xcrysden] Atomic labels in eps printing In-Reply-To: <4A1D5EFD.1030502@sissa.it> References: <4A1D5EFD.1030502@sissa.it> Message-ID: <1243439213.4652.7.camel@walk.ijs.si> On Wed, 2009-05-27 at 17:40 +0200, Gabriele Sclauzero wrote: > Has anyone tried to include the atomic labels in an eps format printing? I first enabled > atomic labels display (pressing the s key, for instance), then printed to eps. The atomic > labels do not appear in the output postscript (while they are present for instance in the > corresponding png). Is this a problem of my installation or is a common issue? It is a general issue. In the "vectorial" EPS atomic labels are ignored (they are bitmaps). As you figured out, use e.g. PNG format if you want labels. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From sclauzer at sissa.it Wed May 27 18:02:20 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Wed, 27 May 2009 18:02:20 +0200 Subject: [xcrysden] Atomic labels in eps printing In-Reply-To: <1243439213.4652.7.camel@walk.ijs.si> References: <4A1D5EFD.1030502@sissa.it> <1243439213.4652.7.camel@walk.ijs.si> Message-ID: <4A1D640C.9030201@sissa.it> Tone Kokalj wrote: > On Wed, 2009-05-27 at 17:40 +0200, Gabriele Sclauzero wrote: >> Has anyone tried to include the atomic labels in an eps format printing? I first enabled >> atomic labels display (pressing the s key, for instance), then printed to eps. The atomic >> labels do not appear in the output postscript (while they are present for instance in the >> corresponding png). Is this a problem of my installation or is a common issue? > > It is a general issue. In the "vectorial" EPS atomic labels are ignored > (they are bitmaps). As you figured out, use e.g. PNG format if you want But in principle the gl2ps can use postscript fonts for the text, can't it? From the website geuz.org/gl2ps I see that there is a function gl2psText which outputs text. Could it be possible to loop over the positions of atomic labels and call this function to add the text in the eps file? It would be more useful for me to have a postscript with labels, since I want to further modify the output without leaving the eps format (since at the end I would have to convert it to eps again). Thanks, Gabriele > labels. > > Regards, Tone -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o From tone.kokalj at ijs.si Fri May 29 09:21:40 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 29 May 2009 09:21:40 +0200 Subject: [xcrysden] Atomic labels in eps printing In-Reply-To: <4A1D640C.9030201@sissa.it> References: <4A1D5EFD.1030502@sissa.it> <1243439213.4652.7.camel@walk.ijs.si> <4A1D640C.9030201@sissa.it> Message-ID: <1243581700.15753.3.camel@walk.ijs.si> On Wed, 2009-05-27 at 18:02 +0200, Gabriele Sclauzero wrote: > > Tone Kokalj wrote: > > On Wed, 2009-05-27 at 17:40 +0200, Gabriele Sclauzero wrote: > >> Has anyone tried to include the atomic labels in an eps format printing? I first enabled > >> atomic labels display (pressing the s key, for instance), then printed to eps. The atomic > >> labels do not appear in the output postscript (while they are present for instance in the > >> corresponding png). Is this a problem of my installation or is a common issue? > > > > It is a general issue. In the "vectorial" EPS atomic labels are ignored > > (they are bitmaps). As you figured out, use e.g. PNG format if you want > > But in principle the gl2ps can use postscript fonts for the text, can't it? > From the website geuz.org/gl2ps I see that there is a function gl2psText which outputs > text. Could it be possible to loop over the positions of atomic labels and call this > function to add the text in the eps file? Gabriele, you answered your question. I believe it can be done, but it have to be coded. You may even try yourself. Start with the $XCRYSDEN_TOPDIR/C/gl2psPrintTogl.c file. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From sclauzer at sissa.it Fri May 29 10:08:24 2009 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Fri, 29 May 2009 10:08:24 +0200 Subject: [xcrysden] Atomic labels in eps printing In-Reply-To: <1243581700.15753.3.camel@walk.ijs.si> References: <4A1D5EFD.1030502@sissa.it> <1243439213.4652.7.camel@walk.ijs.si> <4A1D640C.9030201@sissa.it> <1243581700.15753.3.camel@walk.ijs.si> Message-ID: <4A1F97F8.1030500@sissa.it> Dear Tone, Tone Kokalj wrote: > On Wed, 2009-05-27 at 18:02 +0200, Gabriele Sclauzero wrote: >> Tone Kokalj wrote: >>> On Wed, 2009-05-27 at 17:40 +0200, Gabriele Sclauzero wrote: >>>> Has anyone tried to include the atomic labels in an eps format printing? I first enabled >>>> atomic labels display (pressing the s key, for instance), then printed to eps. The atomic >>>> labels do not appear in the output postscript (while they are present for instance in the >>>> corresponding png). Is this a problem of my installation or is a common issue? >>> It is a general issue. In the "vectorial" EPS atomic labels are ignored >>> (they are bitmaps). As you figured out, use e.g. PNG format if you want >> But in principle the gl2ps can use postscript fonts for the text, can't it? >> From the website geuz.org/gl2ps I see that there is a function gl2psText which outputs >> text. Could it be possible to loop over the positions of atomic labels and call this >> function to add the text in the eps file? > > Gabriele, you answered your question. I believe it can be done, but it > have to be coded. > > You may even try yourself. Start with the > $XCRYSDEN_TOPDIR/C/gl2psPrintTogl.c file. Thanks for the advice, I will give a try sooner or later. Gabriele > > Regards, Tone > -- o ------------------------------------------------ o | Gabriele Sclauzero, PhD Student | | c/o: SISSA & CNR-INFM Democritos, | | via Beirut 2-4, 34014 Trieste (Italy) | | email: sclauzer at sissa.it | | phone: +39 040 3787 511 | | skype: gurlonotturno | o ------------------------------------------------ o