From amit99266 at rediffmail.com Mon Aug 2 14:05:13 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 2 Aug 2010 12:05:13 -0000 Subject: [xcrysden] =?utf-8?q?About_isovalue?= Message-ID: <1280749023.S.1967.62380.webmail.rediff.com.drafts.1280750712.6288@webmail.rediffmail.com> Hello All I am using Xcrysden to plot charge density of Silicon (example 05: Quantum Esspresso-4.2). *) Could anyone please tell the details of "xsf" file? ( This charge density is calculated at Fermi Energy. Please also correct me, if I am wrong.) *)When for Silicon: Minimum grid value :0.001411 and Maximum grid value : 0.87371 What should be the ideal isovalue? Are there any rules to select the isovalues, from the values in *.xsf file? (For isovalue of 0.001411(min) & 0.87371(max), no charge density has been found. ) Thank you in advance!!! Regards Amit N. Harode CRL INDIA P.S. Input file for QE's pp.x is as follows, &inputpp prefix = 'si' filplot = 'sicharge' plot_num= 0 / &plot nfile = 1 filepp(1) = 'sicharge' weight(1) = 1.0 iflag = 3 output_format = 5 fileout = 'si.rho.xsf' / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100802/92d18708/attachment.htm From spbeckman at gmail.com Mon Aug 2 14:40:08 2010 From: spbeckman at gmail.com (Scott Beckman) Date: Mon, 02 Aug 2010 07:40:08 -0500 Subject: [xcrysden] About isovalue In-Reply-To: <1280749023.S.1967.62380.webmail.rediff.com.drafts.1280750712.6288@webmail.rediffmail.com> References: <1280749023.S.1967.62380.webmail.rediff.com.drafts.1280750712.6288@webmail.rediffmail.com> Message-ID: <4C56BCA8.3090705@gmail.com> The charge is not calculated at EFermi, but it is the sum of the charge from the Kohn-Sham states integrated over the Brillouin zone and summed from the lowest state to the EFermi. The integral over the charge distribution (on your XSF grid) should equal "nelec" from PWSCF. The minimum and maximum value tells you the min. and max. value on the XSF grid. So if you have a uniform charge concentration min=max. For Si it is likely that 0.0014 will be located somewhere in an interstitial region and 0.87 will be located in a bond-charge. I wouldn't say that there is any "ideal" isovalue. I would fiddle with this value and look at the charge distribution. This will allow you to develop qualitative picture of how your system works. Yamit wrote: > Hello All > > I am using Xcrysden to plot charge density of Silicon (example 05: > Quantum Esspresso-4.2). > *) Could anyone please tell the details of "xsf" file? > ( This charge density is calculated at Fermi Energy. Please also > correct me, if I am wrong.) > > *)When for Silicon: Minimum grid value :0.001411 and > Maximum grid value : 0.87371 > What should be the ideal isovalue? Are there any rules to select the > isovalues, from the values in *.xsf file? > > (For isovalue of 0.001411(min) & 0.87371(max), no charge density has > been found. ) > > Thank you in advance!!! > > Regards > Amit N. Harode > CRL INDIA > > P.S. > Input file for QE's pp.x is as follows, &inputpp > prefix = 'si' > filplot = 'sicharge' > plot_num= 0 > / > &plot > nfile = 1 > filepp(1) = 'sicharge' > weight(1) = 1.0 > iflag = 3 > output_format = 5 > fileout = 'si.rho.xsf' > / > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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/20100802/7d0eaf96/attachment.htm From amit99266 at rediffmail.com Mon Aug 2 15:20:28 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 2 Aug 2010 13:20:28 -0000 Subject: [xcrysden] =?utf-8?q?About_isovalue?= In-Reply-To: <4C56BCA8.3090705@gmail.com> Message-ID: <1280752860.S.8726.40932.H.WVNjb3R0IEJlY2ttYW4AUmU6IFt4Y3J5c2Rlbl0gQWJvdXQgaXNvdmFsdWU_.f4-234-119.1280755228.23101@webmail.rediffmail.com> Dear Prof. Scott Beckman Thank you for the enlightenment !! About selection of isovalue: I would like to know, if I have to compare two systems (say, Si and Ge), which iso-value should I select for both of them? (so that comparison is valid.) Thank you once again!!! Thanks & Regards Amit On Mon, 02 Aug 2010 18:11:00 +0530 wrote > The charge is not calculated at EFermi, but it is the sum of the charge from the Kohn-Sham states integrated over the Brillouin zone and summed from the lowest state to the EFermi.? The integral over the charge distribution (on your XSF grid) should equal "nelec" from PWSCF.? The minimum and maximum value tells you the min. and max. value on the XSF grid.? So if you have a uniform charge concentration min=max.? For Si it is likely that 0.0014 will be located somewhere in an interstitial region and 0.87 will be located in a bond-charge.? I wouldn't say that there is any "ideal" isovalue.? I would fiddle with this value and look at the charge distribution.? This will allow you to develop qualitative picture of how your system works.? Yamit wrote: Hello All I am using Xcrysden to plot charge density of Silicon (example 05: Quantum Esspresso-4.2). *) Could anyone please tell the details of "xsf" file? ( This charge density is calculated at Fermi Energy. Please also correct me, if I am wrong.) *)When for Silicon: Minimum grid value :0.001411 and Maximum grid value : 0.87371 What should be the ideal isovalue? Are there any rules to select the isovalues, from the values in *.xsf file? (For isovalue of 0.001411(min) & 0.87371(max), no charge density has been found. ) Thank you in advance!!! Regards Amit N. Harode CRL INDIA P.S. Input file for QE's pp.x is as follows, &inputpp prefix = 'si' filplot = 'sicharge' plot_num= 0 / &plot nfile = 1 filepp(1) = 'sicharge' weight(1) = 1.0 iflag = 3 output_format = 5 fileout = 'si.rho.xsf' / _______________________________________________ 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/20100802/f88397ee/attachment.htm From spbeckman at gmail.com Mon Aug 2 15:50:27 2010 From: spbeckman at gmail.com (Scott Beckman) Date: Mon, 02 Aug 2010 08:50:27 -0500 Subject: [xcrysden] About isovalue In-Reply-To: <1280752860.S.8726.40932.H.WVNjb3R0IEJlY2ttYW4AUmU6IFt4Y3J5c2Rlbl0gQWJvdXQgaXNvdmFsdWU_.f4-234-119.1280755228.23101@webmail.rediffmail.com> References: <1280752860.S.8726.40932.H.WVNjb3R0IEJlY2ttYW4AUmU6IFt4Y3J5c2Rlbl0gQWJvdXQgaXNvdmFsdWU_.f4-234-119.1280755228.23101@webmail.rediffmail.com> Message-ID: <4C56CD23.3020209@gmail.com> What you do with the charge density depends on what you want from it. You could scale the charge by nelec, but I don't know how useful this is. If you consider that some of the electrons listed in the pseudopotential come from the core (it is not uncommon for Ge to have partial core electrons) the value of nelec doesn't tell you the number of valence. Typically I use the charge density to get a qualitative picture only. I like to plot (the charge density of the crystal) - (the charge density of isolated atoms) to allow me to see how the crystal's bonding changes the charge distribution. The qualitative assessment from this gives a hint about what the correct quantitative calculations should be. Yamit wrote: > > Dear Prof. Scott Beckman > > Thank you for the enlightenment !! > > About selection of isovalue: > > I would like to know, if I have to compare two systems (say, Si and > Ge), which iso-value should I select for both of them? (so that > comparison is valid.) > > Thank you once again!!! > > Thanks & Regards > Amit > > > On Mon, 02 Aug 2010 18:11:00 +0530 wrote > > > > > The charge is not calculated at EFermi, but it is the sum of the charge > from the Kohn-Sham states integrated over the Brillouin zone and summed > from the lowest state to the EFermi. > > > > The integral over the > charge distribution (on your XSF grid) should equal "nelec" from PWSCF. > > > > > The minimum and maximum value tells you the min. and max. value on the > XSF grid. So if you have a uniform charge concentration min=max. For > Si it is likely that 0.0014 will be located somewhere in an > interstitial region and 0.87 will be located in a bond-charge. > > > > I wouldn't say that there is any "ideal" isovalue. I would fiddle with > this value and look at the charge distribution. This will allow you to > develop qualitative picture of how your system works. > > > > > > > > > > > > Yamit wrote: > Hello All > > > > I am using Xcrysden to plot charge density of Silicon (example 05: > Quantum Esspresso-4.2). > > *) Could anyone please tell the details of "xsf" file? > > ( This charge density is calculated at Fermi Energy. Please also > correct me, if I am wrong.) > > > > *)When for Silicon: Minimum grid value :0.001411 and > > Maximum grid value : 0.87371 > > What should be the ideal isovalue? Are there any rules to select the > isovalues, from the values in *.xsf file? > > > > (For isovalue of 0.001411(min) & 0.87371(max), no charge density > has been found. ) > > > > Thank you in advance!!! > > > > Regards > > Amit N. Harode > > CRL INDIA > > > > P.S. > > Input file for QE's pp.x is as follows, &inputpp > > prefix = 'si' > > filplot = 'sicharge' > > plot_num= 0 > > / > > &plot > > nfile = 1 > > filepp(1) = 'sicharge' > > weight(1) = 1.0 > > iflag = 3 > > output_format = 5 > > fileout = 'si.rho.xsf' > > / > > > > > > > > > > > > > _______________________________________________ > 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 > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > 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/20100802/bc37e052/attachment-0001.htm From yunpengwang85 at gmail.com Thu Aug 5 10:36:48 2010 From: yunpengwang85 at gmail.com (Yunpeng Wang) Date: Thu, 5 Aug 2010 04:36:48 -0400 Subject: [xcrysden] How to copy coordinates of atoms? Message-ID: Dear all: I am using XC to check the geometry of molecules. When I measured the bond angles, I want to copy the coordinates to clipboard, so I can paste onto editors. However, I found it is not possible to copy the data using Ctrl+C or Alt+W. Does anyone has solution to this problem? Thanks a lot! -- *Yunpeng Wang* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100805/cead0b92/attachment.htm From bingmou2004 at gmail.com Thu Aug 5 10:41:30 2010 From: bingmou2004 at gmail.com (=?UTF-8?B?6ZmI5Lyf5qef?=) Date: Thu, 5 Aug 2010 08:41:30 +0000 Subject: [xcrysden] How to copy coordinates of atoms? In-Reply-To: References: Message-ID: In Xwindow, use mouse to select something and click the middle key in your mouse to paste it. 2010/8/5 Yunpeng Wang > Dear all: > > I am using XC to check the geometry of molecules. When I measured the bond > angles, I want to copy the coordinates to clipboard, so I can paste onto > editors. However, I found it is not possible to copy the data using Ctrl+C > or Alt+W. Does anyone has solution to this problem? Thanks a lot! > -- > *Yunpeng Wang* > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100805/5d4efce0/attachment.htm From sworainbow2 at gmail.com Thu Aug 5 22:55:00 2010 From: sworainbow2 at gmail.com (sworainbow2 at gmail.com) Date: Thu, 05 Aug 2010 20:55:00 +0000 Subject: [xcrysden] Xcrysden on Ubuntu 10.4 32bit Message-ID: <90e6ba53a26e7b1493048d19c390@google.com> Dear List, I am trying to install Xcrysden-1.5.21-src-all on Ubuntu 10.4 , 32 bit platform. However, I have not been successful. After extracting the file, I try to compile it by the command of "make all" , where 2 errors occur. The errors shown is... cd C; make "TOPDIR=/home/jason/XCrySDen-1.5.21-src-all" compile make[1]: Entering directory `/home/jason/XCrySDen-1.5.21-src-all/C' make TOPDIR=/home/jason/XCrySDen-1.5.21-src-all make[2]: Entering directory `/home/jason/XCrySDen-1.5.21-src-all/C' gcc -ansi -funroll-loops -fPIC -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include -c detnsplit.c In file included from detnsplit.c:22: struct.h:44:19: error: GL/gl.h: No such file or directory In file included from detnsplit.c:22: struct.h:275: error: expected specifier-qualifier-list before 'GLboolean' struct.h:601: error: expected specifier-qualifier-list before 'GLfloat' struct.h:639: error: expected specifier-qualifier-list before 'GLuint' struct.h:670: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'DefAtCol' struct.h:673: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'DefFrameCol' struct.h:675: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'DefBg' struct.h:676: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'bg' struct.h:683: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'dimType' struct.h:688: error: expected specifier-qualifier-list before 'GLboolean' struct.h:717: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'atomlabelOffset' struct.h:718: error: expected '=', ',', ';', 'asm' or '__attribute__' before 'xyzlabelOffset' struct.h:859: error: expected specifier-qualifier-list before 'GLenum' struct.h:944: error: expected specifier-qualifier-list before 'GLsizei' struct.h:1035: error: expected specifier-qualifier-list before 'GLdouble' struct.h:1051: error: expected specifier-qualifier-list before 'GLfloat' make[2]: *** [detnsplit.o] Error 1 make[2]: Leaving directory `/home/jason/XCrySDen-1.5.21-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/jason/XCrySDen-1.5.21-src-all/C' make: *** [src-C] Error 2 Could someone please help me on this? I am not familiar with the linux or unix system. So I would very much appreciate if the tips were as detail as possible. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100805/f5899154/attachment.htm From bingmou2004 at gmail.com Fri Aug 6 05:58:06 2010 From: bingmou2004 at gmail.com (=?UTF-8?B?6ZmI5Lyf5qef?=) Date: Fri, 6 Aug 2010 11:58:06 +0800 Subject: [xcrysden] Xcrysden on Ubuntu 10.4 32bit In-Reply-To: <90e6ba53a26e7b1493048d19c390@google.com> References: <90e6ba53a26e7b1493048d19c390@google.com> Message-ID: You have to install gl library. Try to read some README and google the error. 2010/8/6 > Dear List, > > I am trying to install Xcrysden-1.5.21-src-all on Ubuntu 10.4 , 32 bit > platform. > However, I have not been successful. > After extracting the file, I try to compile it by the command of "make all" > , where 2 errors occur. > > The errors shown is... > > > cd C; make "TOPDIR=/home/jason/XCrySDen-1.5.21-src-all" compile > make[1]: Entering directory `/home/jason/XCrySDen-1.5.21-src-all/C' > make TOPDIR=/home/jason/XCrySDen-1.5.21-src-all > make[2]: Entering directory `/home/jason/XCrySDen-1.5.21-src-all/C' > gcc -ansi -funroll-loops -fPIC -DUSE_FONTS -DUSE_FONTS -I/usr/X11R6/include > -c detnsplit.c > In file included from detnsplit.c:22: > struct.h:44:19: error: GL/gl.h: No such file or directory > In file included from detnsplit.c:22: > struct.h:275: error: expected specifier-qualifier-list before ?GLboolean? > struct.h:601: error: expected specifier-qualifier-list before ?GLfloat? > struct.h:639: error: expected specifier-qualifier-list before ?GLuint? > struct.h:670: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? > before ?DefAtCol? > struct.h:673: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? > before ?DefFrameCol? > struct.h:675: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? > before ?DefBg? > struct.h:676: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? > before ?bg? > struct.h:683: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? > before ?dimType? > struct.h:688: error: expected specifier-qualifier-list before ?GLboolean? > struct.h:717: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? > before ?atomlabelOffset? > struct.h:718: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? > before ?xyzlabelOffset? > struct.h:859: error: expected specifier-qualifier-list before ?GLenum? > struct.h:944: error: expected specifier-qualifier-list before ?GLsizei? > struct.h:1035: error: expected specifier-qualifier-list before ?GLdouble? > struct.h:1051: error: expected specifier-qualifier-list before ?GLfloat? > make[2]: *** [detnsplit.o] Error 1 > make[2]: Leaving directory `/home/jason/XCrySDen-1.5.21-src-all/C' > make[1]: *** [compile] Error 2 > make[1]: Leaving directory `/home/jason/XCrySDen-1.5.21-src-all/C' > make: *** [src-C] Error 2 > > Could someone please help me on this? I am not familiar with the linux or > unix system. So I would very much appreciate if the tips were as detail as > possible. > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > -- ??? Chen Weibing ????????????????? The State Key Laboratory for Superlattices and Microstructures Institute of Semiconductor, Chinese Academy of Science -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100806/66be6df0/attachment.htm From Atefeh.Hassanieh at postgrad.manchester.ac.uk Fri Aug 6 16:13:09 2010 From: Atefeh.Hassanieh at postgrad.manchester.ac.uk (Atefeh Hassanieh) Date: Fri, 06 Aug 2010 15:13:09 +0100 Subject: [xcrysden] .bxsf Message-ID: <20100806151309.173214ihkqsae1dh@webmail.manchester.ac.uk> Dear XCrysDen users, I'd like to visualize the DOS out of .bxsf by XcrysDen ,I use the command xcrysden -bxsf <>.bxsf ,but it stops with an error ,would you please kindly give an advice on this? Thanks a lot Regards P.S:I have generated the .bxsf out of castep .check file using the check2xsf. From chriskrowan at gmail.com Fri Aug 6 20:46:24 2010 From: chriskrowan at gmail.com (Christopher Rowan) Date: Fri, 6 Aug 2010 11:46:24 -0700 Subject: [xcrysden] Error Opening Cube File In-Reply-To: References: Message-ID: > > Hello, > > I have been struggling at getting XCrySDen version 1.5.17 to open the cube > files that Denchar outputs, which it claims is in Gaussian 98 cube file > format and that XCrySDen can open. The files are labeled: > SystemLabel.DRHO.cube, SystemLabel.RHO.cube and SystemLabel.WF1.cube. (I am > doing some calculations with SIESTA, and interested in visualizing the > orbitals.) The error message is: > > ERROR: ERROR: An Error occured, while reading XSF file > /home/chrisr/xcrys_tmp/xc_ > 32537/denpot.xsf.raw > > and nothing is loaded. > > The cube file looks something like: > > SystemLabel.RHO.cube > SystemLabel.RHO.cube > 0 -3.000000 -3.000000 -3.000000 > 50 0.122449 0.000000 0.000000 > 50 0.000000 0.122449 0.000000 > 50 0.000000 0.000000 0.122449 > 0.10791E+01 0.11755E+01 0.12777E+01 0.13812E+01 0.14787E+01 > 0.15659E+01 > 0.16451E+01 0.17256E+01 0.18185E+01 0.19245E+01 0.20274E+01 > 0.20975E+01 > 0.21064E+01 0.20423E+01 0.19136E+01 0.17422E+01 0.15509E+01 > 0.13576E+01 > 0.11733E+01 0.10039E+01 0.85213E+00 0.71919E+00 0.60506E+00 > 0.50865E+00 > 0.42832E+00 0.36211E+00 0.30796E+00 0.26397E+00 0.22794E+00 > 0.19846E+00 > 0.17417E+00 0.15388E+00 0.13658E+00 0.12148E+00 0.10800E+00 > 0.95743E-01 > 0.84450E-01 0.73978E-01 0.64256E-01 0.55330E-01 0.47290E-01 > 0.40346E-01 > 0.34475E-01 0.29478E-01 0.25241E-01 0.21565E-01 0.18251E-01 > 0.15317E-01 > 0.12762E-01 0.10603E-01 > 0.10525E+01 0.11520E+01 0.12559E+01 0.13583E+01 0.14522E+01 > 0.15337E+01 > 0.16067E+01 0.16837E+01 0.17780E+01 0.18920E+01 0.20079E+01 > 0.20919E+01 > 0.21111E+01 0.20513E+01 0.19216E+01 0.17460E+01 0.15496E+01 > 0.13518E+01 > > etc. > > Any help/comments much appreciated, > Thank you, > Chris Rowan > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100806/358792f5/attachment.htm From yunpengwang85 at gmail.com Fri Aug 13 09:59:08 2010 From: yunpengwang85 at gmail.com (Yunpeng Wang) Date: Fri, 13 Aug 2010 03:59:08 -0400 Subject: [xcrysden] How to include core electron density when exporting charge density? Message-ID: Dear all: Using pp.x, I can export the valence charge density. My question is, how can I export the total charge density, that is, the sum of valence charge density and core charge density? Thanks a lot! -- *Yunpeng Wang* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100813/8c51c6a2/attachment.htm From amit99266 at rediffmail.com Fri Aug 13 15:07:21 2010 From: amit99266 at rediffmail.com (Yamit ) Date: 13 Aug 2010 13:07:21 -0000 Subject: [xcrysden] =?utf-8?q?Is_it_possibile_to_do_space_group_symmetry_a?= =?utf-8?q?nalysis=3F?= Message-ID: <20100813130721.57660.qmail@f4mail-234-232.rediffmail.com> Dear All Is it possible to perform a space group analysis of crystal using "Xcrysden"? Sorry for my negligence! Warm Regards Amit N. Harode CRL INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100813/ffd61863/attachment.htm From zdw2000 at gmail.com Tue Aug 17 17:17:53 2010 From: zdw2000 at gmail.com (Wei Zhou) Date: Tue, 17 Aug 2010 23:17:53 +0800 Subject: [xcrysden] error in xcrysden 1.4.1 of cygwin: Message-ID: dear users, I have installed the xcrysen 1.4.1 vesion of cygwin, and I have seen the readme file, the corresponding sofe have been install. when I see the xsf file, or wien2k file ,the xcrysden work correctly, however, when I seen the expample file of pwscf in crysdens, it dos not work. the error is as following Error; while executing exec sh ..../scripts/pwi2xsf.sh /XCrySDen-1.4.1bin-shared/scripts/pwi2xsf.sh: line 131: pwi2xsf: command not find in fact, the pwi2xsf.sh can work correctly, I have used it to translate pwscf file. so I feel puzzled about this any help will be appreciated -- ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100817/1998a53b/attachment.htm From chriskrowan at gmail.com Wed Aug 25 20:38:06 2010 From: chriskrowan at gmail.com (Christopher Rowan) Date: Wed, 25 Aug 2010 11:38:06 -0700 Subject: [xcrysden] Error Opening Cube File In-Reply-To: References: Message-ID: I figured out why XCrySDen wouldn't open the cube files that Denchar outputs when processing SIESTA output. There is a formatting issue. One must edit the cube file so that the third line contains the number of atoms, where it currently prints zero. Then, after the lattice parameters on lines 4, 5 and 6, one must insert 5 columns: the first being the atomic number of the species, the second being 0.000000, and the third, fourth and fifth the atomic coordinates. If anyone could further clarify the significance of that second column of zeros that would be appreciated. Chris On 6 August 2010 11:46, Christopher Rowan wrote: > Hello, >> >> I have been struggling at getting XCrySDen version 1.5.17 to open the cube >> files that Denchar outputs, which it claims is in Gaussian 98 cube file >> format and that XCrySDen can open. The files are labeled: >> SystemLabel.DRHO.cube, SystemLabel.RHO.cube and SystemLabel.WF1.cube. (I am >> doing some calculations with SIESTA, and interested in visualizing the >> orbitals.) The error message is: >> >> ERROR: ERROR: An Error occured, while reading XSF file >> /home/chrisr/xcrys_tmp/xc_ >> 32537/denpot.xsf.raw >> >> and nothing is loaded. >> >> The cube file looks something like: >> >> SystemLabel.RHO.cube >> SystemLabel.RHO.cube >> 0 -3.000000 -3.000000 -3.000000 >> 50 0.122449 0.000000 0.000000 >> 50 0.000000 0.122449 0.000000 >> 50 0.000000 0.000000 0.122449 >> 0.10791E+01 0.11755E+01 0.12777E+01 0.13812E+01 0.14787E+01 >> 0.15659E+01 >> 0.16451E+01 0.17256E+01 0.18185E+01 0.19245E+01 0.20274E+01 >> 0.20975E+01 >> 0.21064E+01 0.20423E+01 0.19136E+01 0.17422E+01 0.15509E+01 >> 0.13576E+01 >> 0.11733E+01 0.10039E+01 0.85213E+00 0.71919E+00 0.60506E+00 >> 0.50865E+00 >> 0.42832E+00 0.36211E+00 0.30796E+00 0.26397E+00 0.22794E+00 >> 0.19846E+00 >> 0.17417E+00 0.15388E+00 0.13658E+00 0.12148E+00 0.10800E+00 >> 0.95743E-01 >> 0.84450E-01 0.73978E-01 0.64256E-01 0.55330E-01 0.47290E-01 >> 0.40346E-01 >> 0.34475E-01 0.29478E-01 0.25241E-01 0.21565E-01 0.18251E-01 >> 0.15317E-01 >> 0.12762E-01 0.10603E-01 >> 0.10525E+01 0.11520E+01 0.12559E+01 0.13583E+01 0.14522E+01 >> 0.15337E+01 >> 0.16067E+01 0.16837E+01 0.17780E+01 0.18920E+01 0.20079E+01 >> 0.20919E+01 >> 0.21111E+01 0.20513E+01 0.19216E+01 0.17460E+01 0.15496E+01 >> 0.13518E+01 >> >> etc. >> >> Any help/comments much appreciated, >> Thank you, >> Chris Rowan >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100825/302b7c35/attachment.htm From sworainbow2 at gmail.com Wed Aug 25 21:33:42 2010 From: sworainbow2 at gmail.com (Jason Seol) Date: Wed, 25 Aug 2010 15:33:42 -0400 Subject: [xcrysden] rho2xsf Message-ID: Dear all I am trying to compile rho2xsf.f however am not successful. Can someone send binary version of this for linux? Thank you. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100825/2142bb88/attachment.htm From chriskrowan at gmail.com Wed Aug 25 22:26:17 2010 From: chriskrowan at gmail.com (Christopher Rowan) Date: Wed, 25 Aug 2010 13:26:17 -0700 Subject: [xcrysden] rho2xsf In-Reply-To: References: Message-ID: If you're referring to the rho2xsf.f that comes from SIESTA's Util directory, as developed by Andrei Postnikov and available from his website, it says specifically to be sure to use the same compiler as that used for SIESTA. I don't believe that a compiled version would be helpful to you, and could likely give you incorrect results. Be sure you have the latest version from his website: http://www.home.uni-osnabrueck.de/apostnik/download.html Chris On 25 August 2010 12:33, Jason Seol wrote: > Dear all > > I am trying to compile rho2xsf.f however am not successful. > Can someone send binary version of this for linux? > > Thank you. > > _______________________________________________ > 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/20100825/d508994b/attachment.htm From sclauzer at sissa.it Mon Aug 30 09:22:24 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Mon, 30 Aug 2010 09:22:24 +0200 Subject: [xcrysden] How to include core electron density when exporting charge density? In-Reply-To: References: Message-ID: <4C7B5C30.6020106@sissa.it> Dear Yunpeng Wang, your question is maybe more appropriate for the PW forum rather than for this forum (although there are many PW-users writing here). I think that for NC and US PPs only the valence charge is available, while for PAW there should be a not-widely-tested-but- working implementation to get the all-electron charge (in the frozen-core approximation, obviously). It should be plot_num=17 (see Doc/INPUT_PP.txt). HTH GS On 08/13/2010 09:59 AM, Yunpeng Wang wrote: > Dear all: > > Using pp.x, I can export the valence charge density. My question is, > how can I export the total charge density, that is, the sum of valence > charge density and core charge density? > > Thanks a lot! > > -- > *Yunpeng Wang* > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100830/52a7d520/attachment.htm From tone.kokalj at ijs.si Mon Aug 30 12:53:21 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 30 Aug 2010 12:53:21 +0200 Subject: [xcrysden] unable to exploit advanced geometric features In-Reply-To: References: Message-ID: <1283165601.2883.52.camel@walk.ijs.si> On Wed, 2010-07-28 at 08:29 +0530, mohnish pandey wrote: > Dear Xcrysden users, > I am unable to exploit the advanced > geometric options which I need to delete some atoms or to visualize > some Miller planes. In adv. geo. option nothing comes after clicking. > Can anybody please tell me where the problem might be or help me out. The Adv Geom menu (also Properties menu) is active only as an interface to the CRYSTAL program, http://www.crystal.unito.it/ Unless you have the CRYSTAL then the behavior you face is normal. 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 Mon Aug 30 12:55:18 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 30 Aug 2010 12:55:18 +0200 Subject: [xcrysden] .bxsf In-Reply-To: <20100806151309.173214ihkqsae1dh@webmail.manchester.ac.uk> References: <20100806151309.173214ihkqsae1dh@webmail.manchester.ac.uk> Message-ID: <1283165718.2883.54.camel@walk.ijs.si> On Fri, 2010-08-06 at 15:13 +0100, Atefeh Hassanieh wrote: > Dear XCrysDen users, > > > I'd like to visualize the DOS out of .bxsf by XcrysDen You cannot. The BXSF is only for the Fermi surface visualization. > xcrysden -bxsf <>.bxsf ,but it stops with an error ,would you please > kindly give an advice on this? Unless you provide more info of the error itself, nobody can help. 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 Mon Aug 30 12:57:29 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 30 Aug 2010 12:57:29 +0200 Subject: [xcrysden] Error Opening Cube File In-Reply-To: References: Message-ID: <1283165849.2883.56.camel@walk.ijs.si> On Fri, 2010-08-06 at 11:46 -0700, Christopher Rowan wrote: > Hello, > > I have been struggling at getting XCrySDen version 1.5.17 to > open the cube files that Denchar outputs, which it claims is > in Gaussian 98 cube file format and that XCrySDen can open. > The files are labeled: SystemLabel.DRHO.cube, > SystemLabel.RHO.cube and SystemLabel.WF1.cube. (I am doing > some calculations with SIESTA, and interested in visualizing > the orbitals.) The error message is: > > ERROR: ERROR: An Error occured, while reading XSF > file /home/chrisr/xcrys_tmp/xc_ > 32537/denpot.xsf.raw > > and nothing is loaded. I suspect there should be some format incompatibility with the denchar generate cube files and the one xcrysden expects. Please send me a small cube file generated by denchar, so that I may inspect the problem. 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 Mon Aug 30 13:00:01 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 30 Aug 2010 13:00:01 +0200 Subject: [xcrysden] How to include core electron density when exporting charge density? In-Reply-To: References: Message-ID: <1283166001.2883.59.camel@walk.ijs.si> On Fri, 2010-08-13 at 03:59 -0400, Yunpeng Wang wrote: > Dear all: > > Using pp.x, I can export the valence charge density. My question is, > how can I export the total charge density, that is, the sum of valence > charge density and core charge density? You should address this question to Pw_forum, as there you will like;y obtain the help needed. As far as I know is that the total charge density option is available only when PAW potentials are used. 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 Mon Aug 30 13:02:17 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 30 Aug 2010 13:02:17 +0200 Subject: [xcrysden] Is it possibile to do space group symmetry analysis? In-Reply-To: <20100813130721.57660.qmail@f4mail-234-232.rediffmail.com> References: <20100813130721.57660.qmail@f4mail-234-232.rediffmail.com> Message-ID: <1283166137.2883.61.camel@walk.ijs.si> On Fri, 2010-08-13 at 13:07 +0000, Yamit wrote: > Dear All > > Is it possible to perform a space group analysis of crystal using > "Xcrysden"? No! Please check the Bilbao Crystallographic Server, http://www.cryst.ehu.es/ 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 Mon Aug 30 13:07:44 2010 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 30 Aug 2010 13:07:44 +0200 Subject: [xcrysden] error in xcrysden 1.4.1 of cygwin: In-Reply-To: References: Message-ID: <1283166464.2883.66.camel@walk.ijs.si> On Tue, 2010-08-17 at 23:17 +0800, Wei Zhou wrote: > > dear users, > > I have installed the xcrysen 1.4.1 vesion of cygwin, and I have seen > the readme file, the corresponding sofe have been install. when I see > the xsf file, or wien2k file ,the xcrysden work correctly, however, > when I seen the expample file of pwscf in crysdens, it dos not work. > the error is as following > Error; while executing > exec sh > ..../scripts/pwi2xsf.sh > /XCrySDen-1.4.1bin-shared/scripts/pwi2xsf.sh: line 131: pwi2xsf: > command not find Check if the pwi2xsf program is in your $XCRYSDEN_TOPDIR/bin directory. > in fact, the pwi2xsf.sh can work correctly, I have used it to > translate pwscf file. Then this is your workaround: translate the pw.x input file to xsf file and then load the xsf file. It is not that cumbersome as you may use the pipe like this: pwi2xsf.sh pw_inputfile | xcrysden --xsf - (note the "-" after the --xsf, it stands for stdin) Regards, Tone P.S.: do not try this on the EthAl001-2x2.inp example file, as this is very old pw.x input file, and this trick will not work. -- 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 mohnish.iitk at gmail.com Tue Aug 31 05:24:55 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 31 Aug 2010 08:54:55 +0530 Subject: [xcrysden] character table for space groups Message-ID: Dear Xcrysden users, My query is not related to Xcrysden, I tried searching for character table of space groups but I could not find it. Can anybody please tell me from where I can get it? Thanks a lot in advance -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100831/1de5f5bd/attachment.htm From dstrubbe at civet.berkeley.edu Tue Aug 31 06:45:02 2010 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Mon, 30 Aug 2010 21:45:02 -0700 Subject: [xcrysden] character table for space groups In-Reply-To: References: Message-ID: Character tables for point groups: http://symmetry.jacobs-university.de/ More character tables for crystallography: http://www.cryst.ehu.es/rep/point.html David Strubbe UC Berkeley On Mon, Aug 30, 2010 at 8:24 PM, mohnish pandey wrote: > Dear Xcrysden users, > My query is not related to Xcrysden, I > tried searching for character table of space groups but I could not find it. > Can anybody please tell me from where I can get it? > Thanks a lot in advance > -- > Regards, > MOHNISH, > ----------------------------------------------------------------- > Mohnish Pandey > Y6927262,5th Year dual degree student, > Department of Chemical Engineering, > IIT KANPUR, UP, INDIA > +919235721300 > ----------------------------------------------------------------- > > _______________________________________________ > 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/20100830/e94d0fa4/attachment.htm From sclauzer at sissa.it Tue Aug 31 09:46:21 2010 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 31 Aug 2010 09:46:21 +0200 Subject: [xcrysden] character table for space groups In-Reply-To: References: Message-ID: <4C7CB34D.1050605@sissa.it> Hi, this is another site that might be worth looking at http://www.staff.ncl.ac.uk/j.p.goss/symmetry/index.html Regards, GS On 08/31/2010 06:45 AM, David Strubbe wrote: > Character tables for point groups: http://symmetry.jacobs-university.de/ > More character tables for crystallography: > http://www.cryst.ehu.es/rep/point.html > > David Strubbe > UC Berkeley > -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne From mohnish.iitk at gmail.com Tue Aug 31 11:10:47 2010 From: mohnish.iitk at gmail.com (mohnish pandey) Date: Tue, 31 Aug 2010 14:40:47 +0530 Subject: [xcrysden] character table for space groups In-Reply-To: <4C7CB34D.1050605@sissa.it> References: <4C7CB34D.1050605@sissa.it> Message-ID: Thanks a lot Gabriele and David... On Tue, Aug 31, 2010 at 1:16 PM, Gabriele Sclauzero wrote: > Hi, > > this is another site that might be worth looking at > > http://www.staff.ncl.ac.uk/j.p.goss/symmetry/index.html > > > Regards, > > > GS > > > On 08/31/2010 06:45 AM, David Strubbe wrote: > > Character tables for point groups: http://symmetry.jacobs-university.de/ > > More character tables for crystallography: > > http://www.cryst.ehu.es/rep/point.html > > > > David Strubbe > > UC Berkeley > > > > > -- > > Gabriele Sclauzero, EPFL SB ITP CSEA > PH H2 462, Station 3, CH-1015 Lausanne > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Regards, MOHNISH, ----------------------------------------------------------------- Mohnish Pandey Y6927262,5th Year dual degree student, Department of Chemical Engineering, IIT KANPUR, UP, INDIA +919235721300 ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100831/bb644ae4/attachment.htm From zdw2000 at gmail.com Tue Aug 31 12:30:03 2010 From: zdw2000 at gmail.com (Wei Zhou) Date: Tue, 31 Aug 2010 18:30:03 +0800 Subject: [xcrysden] error in xcrysden 1.4.1 of cygwin: In-Reply-To: <1283166464.2883.66.camel@walk.ijs.si> References: <1283166464.2883.66.camel@walk.ijs.si> Message-ID: thank you for your reply 2010/8/30 Tone Kokalj > On Tue, 2010-08-17 at 23:17 +0800, Wei Zhou wrote: > > > > dear users, > > > > I have installed the xcrysen 1.4.1 vesion of cygwin, and I have seen > > the readme file, the corresponding sofe have been install. when I see > > the xsf file, or wien2k file ,the xcrysden work correctly, however, > > when I seen the expample file of pwscf in crysdens, it dos not work. > > the error is as following > > Error; while executing > > exec sh > > ..../scripts/pwi2xsf.sh > > /XCrySDen-1.4.1bin-shared/scripts/pwi2xsf.sh: line 131: pwi2xsf: > > command not find > > Check if the pwi2xsf program is in your $XCRYSDEN_TOPDIR/bin > directory. > > > in fact, the pwi2xsf.sh can work correctly, I have used it to > > translate pwscf file. > > Then this is your workaround: translate the pw.x input file to xsf file > and then load the xsf file. It is not that cumbersome as you may use the > pipe like this: > > pwi2xsf.sh pw_inputfile | xcrysden --xsf - > > (note the "-" after the --xsf, it stands for stdin) > > Regards, Tone > > P.S.: do not try this on the EthAl001-2x2.inp example file, as this is > very old pw.x input file, and this trick will not work. > > -- > 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 > -- ZhouDawei JiLin Universiyt ,ChangChun ,China zdw2000 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20100831/ba5e39c7/attachment.htm