From suresh2007pgp19 at gmail.com Sat Jan 16 07:48:44 2016 From: suresh2007pgp19 at gmail.com (Suresh A) Date: Sat, 16 Jan 2016 12:18:44 +0530 Subject: [xcrysden] Anatase primitive cell: Regarding Message-ID: Dear Friends, I have prepared primitive cell input file for quantum espresso.I have included those files below. The problem is XCRYSDEN shows two different structure for a same file where one is in crystal coordinates and other one in angstrom. Inputfile number 1: This file shows correct strucutre in XCRYSDEN &CONTROL title = 'TiO2' , calculation = 'scf', outdir ='$TMP_DIR/' prefix = 'anatase', pseudo_dir = '$PSEUDO_DIR/', / &SYSTEM ibrav = 7, celldm(1) = 7.1356, celldm(3) = 2.51218, nat = 6 , ntyp = 2 , ecutwfc = 30.0000000000 , ecutrho = 300, / &ELECTRONS conv_thr = 1.0d-09, / ATOMIC_SPECIES O 15.999 O.pw91-van_ak.UPF Ti 47.867 Ti.pw91-nsp-van.UPF ATOMIC_POSITIONS angstrom Ti 0.000000000 0.000000000 0.000000000 Ti 0.000000000 1.888000000 2.371500000 O 0.000000000 0.000000000 -1.983097630 O 0.000000000 0.000000000 1.983097630 O 0.000000000 1.888000000 0.387796645 O 0.000000000 1.888000000 4.355203355 K_POINTS automatic 4 4 4 0 0 0 *nputfile number 2: &CONTROL title = 'anatase' , calculation = 'scf' , restart_mode = 'from_scratch' , pseudo_dir = '/home/suresh/GN2/', outdir ='/home/suresh/Desktop/primitivecell/tmp/', prefix = 'anatase' , tstress = .true. , tprnfor = .true. , / &SYSTEM ibrav = 7, celldm(1) = 7.153, celldm(3) = 2.513, nat = 6, ntyp = 2, ecutwfc = 60 , exxdiv_treatment = 'none' , / &ELECTRONS / &IONS / &CELL /ATOMIC_SPECIES Ti 47.86700 Ti.pz-mt_fhi.UPF O 15.99940 O.pz-mt_fhi.UPFATOMIC_POSITIONS (crystal)Ti 0.0000000 0.0000000 0.0000000Ti 0.0000000 0.5000000 0.2500000O 0.0000000 0.0000000 0.2080000O 0.0000000 0.0000000 -0.208000O 0.0000000 0.5000000 0.4580000O 0.0000000 0.5000000 -0.042000K_POINTS automatic 4 4 2 1 1 1* *Will you please pointout where the problem i?* With Regards, A.Suresh, Research Scholar, Madurai Kamaraj University, Madurai. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160116/0b78e499/attachment.htm From gsabo at crimson.ua.edu Mon Jan 18 02:09:25 2016 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Sun, 17 Jan 2016 18:09:25 -0700 Subject: [xcrysden] Anatase primitive cell: Regarding In-Reply-To: References: Message-ID: <569C3B45.5010601@crimson.ua.edu> Regarding Inputfile 1, keep in mind that you might have to increase the precision of the atomic positions as described in the post at the following link: http://qe-forge.org/pipermail/pw_forum/2006-August/079340.html Regarding Inputfile 2, it seems like you can get XCrySDen to show the same structure as Inputfile 1 if you change ibrav from 7 to 6, nat from 6 to 12, and add the atomic positions for the other 6 atoms (for a total of 12 atoms) in Inputfile 2. Refer to the anatase.in file attached at the bottom of the post at the following link: https://www.mail-archive.com/pw_forum at pwscf.org/msg27155.html On 1/15/2016 11:48 PM, Suresh A wrote: > Dear Friends, > I have prepared primitive cell input file for > quantum espresso.I have included those files below. The problem is > XCRYSDEN shows two different structure for a same file where one is in > crystal coordinates and other one in angstrom. > > Inputfile number 1: This file shows correct strucutre in XCRYSDEN > > > &CONTROL > title = 'TiO2' , > calculation = 'scf', > outdir ='$TMP_DIR/' > prefix = 'anatase', > pseudo_dir = '$PSEUDO_DIR/', > / > > &SYSTEM > ibrav = 7, > celldm(1) = 7.1356, > celldm(3) = 2.51218, > nat = 6 , > ntyp = 2 , > ecutwfc = 30.0000000000 , > ecutrho = 300, > > > / > > &ELECTRONS > > conv_thr = 1.0d-09, > > / > ATOMIC_SPECIES > O 15.999 O.pw91-van_ak.UPF > Ti 47.867 Ti.pw91-nsp-van.UPF > ATOMIC_POSITIONS angstrom > Ti 0.000000000 0.000000000 0.000000000 > Ti 0.000000000 1.888000000 2.371500000 > O 0.000000000 0.000000000 -1.983097630 > O 0.000000000 0.000000000 1.983097630 > O 0.000000000 1.888000000 0.387796645 > O 0.000000000 1.888000000 4.355203355 > K_POINTS automatic > 4 4 4 0 0 0 > > > /Inputfile number 2: > &CONTROL > title = 'anatase' , > calculation = 'scf' , > restart_mode = 'from_scratch' , > pseudo_dir = '/home/suresh/GN2/', > outdir ='/home/suresh/Desktop/primitivecell/tmp/', > prefix = 'anatase' , > tstress = .true. , > tprnfor = .true. , > > > > / > &SYSTEM > ibrav = 7, > celldm(1) = 7.153, > celldm(3) = 2.513, > nat = 6, > ntyp = 2, > ecutwfc = 60 , > exxdiv_treatment = 'none' , > > > > / > &ELECTRONS > > > / > &IONS > > > / > &CELL > > > > / > ATOMIC_SPECIES > Ti 47.86700 Ti.pz-mt_fhi.UPF > O 15.99940 O.pz-mt_fhi.UPF > ATOMIC_POSITIONS (crystal) > Ti 0.0000000 0.0000000 0.0000000 > Ti 0.0000000 0.5000000 0.2500000 > O 0.0000000 0.0000000 0.2080000 > O 0.0000000 0.0000000 -0.208000 > O 0.0000000 0.5000000 0.4580000 > O 0.0000000 0.5000000 -0.042000 > K_POINTS automatic > 4 4 2 1 1 1 > > / > /Will you please pointout where the problem i? > / > > > > > > > > > > > > With Regards, > A.Suresh, > Research Scholar, > Madurai Kamaraj University, > Madurai. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160117/ff58e765/attachment.htm From muthu.physicsmath at gmail.com Mon Jan 18 08:21:42 2016 From: muthu.physicsmath at gmail.com (Muthu V) Date: Mon, 18 Jan 2016 12:51:42 +0530 Subject: [xcrysden] XCrySDen Digest, Vol 95, Issue 2 Message-ID: i think the exact problem is to get primitive cell view. for that we have to use primitive lattice vectors with natm=6. this is easily done with ibrave=0 then define your primitive lattice. moreover the conversion from angstrom to crystal should be done as explained below http://qe-forge.org/pipermail/pw_forum/2014-September/105143.html Thank you *---------------------------------------------* *?Muthu V?Sri Paramakalyani college,Alwarkruichi, India?---------------------------------------------* On Mon, Jan 18, 2016 at 12:05 PM, wrote: > Send XCrySDen mailing list submissions to > xcrysden at democritos.it > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/xcrysden > or, via email, send a message with subject or body 'help' to > xcrysden-request at democritos.it > > You can reach the person managing the list at > xcrysden-owner at democritos.it > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of XCrySDen digest..." > > > Today's Topics: > > 1. Re: Anatase primitive cell: Regarding (Gavin Abo) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 17 Jan 2016 18:09:25 -0700 > From: Gavin Abo > Subject: Re: [xcrysden] Anatase primitive cell: Regarding > To: xcrysden at democritos.it > Message-ID: <569C3B45.5010601 at crimson.ua.edu> > Content-Type: text/plain; charset="windows-1252" > > Regarding Inputfile 1, keep in mind that you might have to increase the > precision of the atomic positions as described in the post at the > following link: > > http://qe-forge.org/pipermail/pw_forum/2006-August/079340.html > > Regarding Inputfile 2, it seems like you can get XCrySDen to show the > same structure as Inputfile 1 if you change ibrav from 7 to 6, nat from > 6 to 12, and add the atomic positions for the other 6 atoms (for a total > of 12 atoms) in Inputfile 2. Refer to the anatase.in file attached at > the bottom of the post at the following link: > > https://www.mail-archive.com/pw_forum at pwscf.org/msg27155.html > > On 1/15/2016 11:48 PM, Suresh A wrote: > > Dear Friends, > > I have prepared primitive cell input file for > > quantum espresso.I have included those files below. The problem is > > XCRYSDEN shows two different structure for a same file where one is in > > crystal coordinates and other one in angstrom. > > > > Inputfile number 1: This file shows correct strucutre in XCRYSDEN > > > > > > &CONTROL > > title = 'TiO2' , > > calculation = 'scf', > > outdir ='$TMP_DIR/' > > prefix = 'anatase', > > pseudo_dir = '$PSEUDO_DIR/', > > / > > > > &SYSTEM > > ibrav = 7, > > celldm(1) = 7.1356, > > celldm(3) = 2.51218, > > nat = 6 , > > ntyp = 2 , > > ecutwfc = 30.0000000000 , > > ecutrho = 300, > > > > > > / > > > > &ELECTRONS > > > > conv_thr = 1.0d-09, > > > > / > > ATOMIC_SPECIES > > O 15.999 O.pw91-van_ak.UPF > > Ti 47.867 Ti.pw91-nsp-van.UPF > > ATOMIC_POSITIONS angstrom > > Ti 0.000000000 0.000000000 0.000000000 > > Ti 0.000000000 1.888000000 2.371500000 > > O 0.000000000 0.000000000 -1.983097630 > > O 0.000000000 0.000000000 1.983097630 > > O 0.000000000 1.888000000 0.387796645 > > O 0.000000000 1.888000000 4.355203355 > > K_POINTS automatic > > 4 4 4 0 0 0 > > > > > > /Inputfile number 2: > > &CONTROL > > title = 'anatase' , > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > pseudo_dir = '/home/suresh/GN2/', > > outdir ='/home/suresh/Desktop/primitivecell/tmp/', > > prefix = 'anatase' , > > tstress = .true. , > > tprnfor = .true. , > > > > > > > > / > > &SYSTEM > > ibrav = 7, > > celldm(1) = 7.153, > > celldm(3) = 2.513, > > nat = 6, > > ntyp = 2, > > ecutwfc = 60 , > > exxdiv_treatment = 'none' , > > > > > > > > / > > &ELECTRONS > > > > > > / > > &IONS > > > > > > / > > &CELL > > > > > > > > / > > ATOMIC_SPECIES > > Ti 47.86700 Ti.pz-mt_fhi.UPF > > O 15.99940 O.pz-mt_fhi.UPF > > ATOMIC_POSITIONS (crystal) > > Ti 0.0000000 0.0000000 0.0000000 > > Ti 0.0000000 0.5000000 0.2500000 > > O 0.0000000 0.0000000 0.2080000 > > O 0.0000000 0.0000000 -0.208000 > > O 0.0000000 0.5000000 0.4580000 > > O 0.0000000 0.5000000 -0.042000 > > K_POINTS automatic > > 4 4 2 1 1 1 > > > > / > > /Will you please pointout where the problem i? > > / > > > > > > > > > > > > > > > > > > > > > > > > With Regards, > > A.Suresh, > > Research Scholar, > > Madurai Kamaraj University, > > Madurai. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/xcrysden/attachments/20160117/ff58e765/attachment.html > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 95, Issue 2 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160118/f252f0e5/attachment.htm From muthu.physicsmath at gmail.com Mon Jan 18 18:56:43 2016 From: muthu.physicsmath at gmail.com (Muthu V) Date: Mon, 18 Jan 2016 23:26:43 +0530 Subject: [xcrysden] XCrySDen Digest, Vol 95, Issue 2 In-Reply-To: References: Message-ID: Adding to my previous mail, if the concern is to get back the structure as input file 1 then the mistake is at atomic coordinate conversion from angstrom to crystal. here is the solution. as the atomic coordinates are defined in primitive cell one should use primitive lattice vectors to go to crystal units from angstrom. open anatase pw input file in xcrysden then one can find the primitive vectors for anatase is PRIMVEC 1.8879977010 -1.8879977010 4.7429900630 1.8879977010 1.8879977010 4.7429900630 -1.8879977010 -1.8879977010 4.7429900630 ?now define atomic coordinate as matrix a and above as b ??a = 0.00000 0.00000 0.00000 0.00000 1.88800 2.37150 0.00000 0.00000 -1.98310 0.00000 0.00000 1.98310 0.00000 1.88800 0.38780 0.00000 1.88800 4.35520 ? ?b = 1.8880 -1.8880 4.7430 1.8880 1.8880 4.7430 -1.8880 -1.8880 4.7430 ? ?now find a/b as a*b-1 ? 0.00000 0.00000 -0.00000 -0.50000 0.75000 0.25000 0.00000 -0.20906 -0.20906 0.00000 0.20906 0.20906 -0.50000 0.54088 0.04088 -0.50000 0.95912 0.45912 so use this atomic coordinates then you will get the structure as expected. note that make sure of getting correct bond length. if it is not so then make sure that you are at correct precision of atomic coordinates as pointed out by Gavin Abo in his reply. ?find out the attachment for ?input file 2 which gives correct structure. ? *---------------------------------------------* *?Muthu V?Sri Paramakalyani college,Alwarkruichi, India?---------------------------------------------*? On Mon, Jan 18, 2016 at 12:05 PM, wrote: > Send XCrySDen mailing list submissions to > xcrysden at democritos.it > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/xcrysden > or, via email, send a message with subject or body 'help' to > xcrysden-request at democritos.it > > You can reach the person managing the list at > xcrysden-owner at democritos.it > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of XCrySDen digest..." > > > Today's Topics: > > 1. Re: Anatase primitive cell: Regarding (Gavin Abo) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 17 Jan 2016 18:09:25 -0700 > From: Gavin Abo > Subject: Re: [xcrysden] Anatase primitive cell: Regarding > To: xcrysden at democritos.it > Message-ID: <569C3B45.5010601 at crimson.ua.edu> > Content-Type: text/plain; charset="windows-1252" > > Regarding Inputfile 1, keep in mind that you might have to increase the > precision of the atomic positions as described in the post at the > following link: > > http://qe-forge.org/pipermail/pw_forum/2006-August/079340.html > > Regarding Inputfile 2, it seems like you can get XCrySDen to show the > same structure as Inputfile 1 if you change ibrav from 7 to 6, nat from > 6 to 12, and add the atomic positions for the other 6 atoms (for a total > of 12 atoms) in Inputfile 2. Refer to the anatase.in file attached at > the bottom of the post at the following link: > > https://www.mail-archive.com/pw_forum at pwscf.org/msg27155.html > > On 1/15/2016 11:48 PM, Suresh A wrote: > > Dear Friends, > > I have prepared primitive cell input file for > > quantum espresso.I have included those files below. The problem is > > XCRYSDEN shows two different structure for a same file where one is in > > crystal coordinates and other one in angstrom. > > > > Inputfile number 1: This file shows correct strucutre in XCRYSDEN > > > > > > &CONTROL > > title = 'TiO2' , > > calculation = 'scf', > > outdir ='$TMP_DIR/' > > prefix = 'anatase', > > pseudo_dir = '$PSEUDO_DIR/', > > / > > > > &SYSTEM > > ibrav = 7, > > celldm(1) = 7.1356, > > celldm(3) = 2.51218, > > nat = 6 , > > ntyp = 2 , > > ecutwfc = 30.0000000000 , > > ecutrho = 300, > > > > > > / > > > > &ELECTRONS > > > > conv_thr = 1.0d-09, > > > > / > > ATOMIC_SPECIES > > O 15.999 O.pw91-van_ak.UPF > > Ti 47.867 Ti.pw91-nsp-van.UPF > > ATOMIC_POSITIONS angstrom > > Ti 0.000000000 0.000000000 0.000000000 > > Ti 0.000000000 1.888000000 2.371500000 > > O 0.000000000 0.000000000 -1.983097630 > > O 0.000000000 0.000000000 1.983097630 > > O 0.000000000 1.888000000 0.387796645 > > O 0.000000000 1.888000000 4.355203355 > > K_POINTS automatic > > 4 4 4 0 0 0 > > > > > > /Inputfile number 2: > > &CONTROL > > title = 'anatase' , > > calculation = 'scf' , > > restart_mode = 'from_scratch' , > > pseudo_dir = '/home/suresh/GN2/', > > outdir ='/home/suresh/Desktop/primitivecell/tmp/', > > prefix = 'anatase' , > > tstress = .true. , > > tprnfor = .true. , > > > > > > > > / > > &SYSTEM > > ibrav = 7, > > celldm(1) = 7.153, > > celldm(3) = 2.513, > > nat = 6, > > ntyp = 2, > > ecutwfc = 60 , > > exxdiv_treatment = 'none' , > > > > > > > > / > > &ELECTRONS > > > > > > / > > &IONS > > > > > > / > > &CELL > > > > > > > > / > > ATOMIC_SPECIES > > Ti 47.86700 Ti.pz-mt_fhi.UPF > > O 15.99940 O.pz-mt_fhi.UPF > > ATOMIC_POSITIONS (crystal) > > Ti 0.0000000 0.0000000 0.0000000 > > Ti 0.0000000 0.5000000 0.2500000 > > O 0.0000000 0.0000000 0.2080000 > > O 0.0000000 0.0000000 -0.208000 > > O 0.0000000 0.5000000 0.4580000 > > O 0.0000000 0.5000000 -0.042000 > > K_POINTS automatic > > 4 4 2 1 1 1 > > > > / > > /Will you please pointout where the problem i? > > / > > > > > > > > > > > > > > > > > > > > > > > > With Regards, > > A.Suresh, > > Research Scholar, > > Madurai Kamaraj University, > > Madurai. > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/xcrysden/attachments/20160117/ff58e765/attachment.html > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 95, Issue 2 > *************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160118/412837d5/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: test1.pw.in Type: application/octet-stream Size: 1021 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20160118/412837d5/attachment-0001.obj From muthu.physicsmath at gmail.com Mon Jan 18 19:25:32 2016 From: muthu.physicsmath at gmail.com (Muthu V) Date: Mon, 18 Jan 2016 23:55:32 +0530 Subject: [xcrysden] all unit sys are being same why? Message-ID: Dear all here i have attached my input file where i have defined Si-110 surface unit cell. i have used ibrave =0 and then defined cell_parameters bohr, initially. CELL_PARAMETERS bohr 7.343274350 0.000000000 0.000000000 0.000000000 7.343274346 0.000000000 0.000000000 -0.000000000 10.240261020 but what i have observed is that when i changed unit system bohr to angstrom as CELL_PARAMETERS angstrom 7.343274350 0.000000000 0.000000000 0.000000000 7.343274346 0.000000000 0.000000000 -0.000000000 10.240261020 the bond length is still unchanged but 1 bohr = 0.5294angstrom so i expect bond changes in bond length since i change only the unit system and not the numerical values so where is the mistake? Thank you *---------------------------------* *?Muthu V??Sri Paramakalyani College?---------------------------------* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160118/15d6d015/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: si110.pw.in Type: application/octet-stream Size: 1261 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20160118/15d6d015/attachment.obj From gsabo at crimson.ua.edu Mon Jan 18 20:10:45 2016 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Mon, 18 Jan 2016 12:10:45 -0700 Subject: [xcrysden] all unit sys are being same why? In-Reply-To: References: Message-ID: <569D38B5.6030809@crimson.ua.edu> This is happening with the latest XCrySDen version? If you are perhaps using an older version, I believe versions before 1.5.60 did not understand the new QE syntax as discussed in the following posts: http://www.democritos.it/pipermail/xcrysden/2014-January/001531.html http://qe-forge.org/pipermail/pw_forum/2015-June/107132.html On 1/18/2016 11:25 AM, Muthu V wrote: > Dear all > here i have attached my input file where i have defined Si-110 surface > unit cell. i have used ibrave =0 and then defined cell_parameters > bohr, initially. > > CELL_PARAMETERS bohr > 7.343274350 0.000000000 0.000000000 > 0.000000000 7.343274346 0.000000000 > 0.000000000 -0.000000000 10.240261020 > > but what i have observed is that when i changed unit system bohr to > angstrom as > CELL_PARAMETERS angstrom > 7.343274350 0.000000000 0.000000000 > 0.000000000 7.343274346 0.000000000 > 0.000000000 -0.000000000 10.240261020 > the bond length is still unchanged but 1 bohr = 0.5294angstrom so i > expect bond changes in bond length since i change only the unit system > and not the numerical values > > so where is the mistake? > Thank you > /*--------------------------------- > */* > ?/Muthu V/? > > */ > ? Sri Paramakalyani College? > > /**/---------------------------------/* > * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160118/6d0f0882/attachment.htm From suresh2007pgp19 at gmail.com Tue Jan 19 06:07:01 2016 From: suresh2007pgp19 at gmail.com (Suresh A) Date: Tue, 19 Jan 2016 10:37:01 +0530 Subject: [xcrysden] Anatase primitive cell: Regarding Message-ID: Dear Gavin Abo and Muthu, Thank you for your reply. The two inputs which i have included refers to anatase primitive cell. One input file (first one) gives correct structure in XCRYSDEN and the other one is also correct but the atomic positions are in relative to crystal coordinates. The XCRYSDEN shows wrong structure for second file. There is no need to change ibrav=7 and 6 more atomic positions for primitive cell. So my input file is correct. With Regards, A.Suresh, Research Scholar, Madurai Kamaraj University, Madurai. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160119/70bce096/attachment.htm From muthu.physicsmath at gmail.com Tue Jan 19 08:54:11 2016 From: muthu.physicsmath at gmail.com (Muthu V) Date: Tue, 19 Jan 2016 13:24:11 +0530 Subject: [xcrysden] Anatase primitive cell: XCrySDen Vol 95, Issue 4 Message-ID: ?Hi the problem is in converting the atomic coordinated from angstrom into crystal. to do that you have to use primitive lattice vector instead of unit lattice as explained below ? ?given atomic coordinate is Ti 0.0000000000 0.0000000000 0.0000000000 Ti 0.0000000000 1.8880000000 2.3715000000 O 0.0000000000 0.0000000000 -1.9830976300 O 0.0000000000 0.0000000000 1.9830976300 O 0.0000000000 1.8880000000 0.3877966450 O 0.0000000000 1.8880000000 4.3552033550 divide above matrix with (primitive lattice) 1.8880 -1.8880 4.7430 1.8880 1.8880 4.7430 -1.8880 -1.8880 4.7430? u will get this ? ?Ti 0.00000 0.00000 -0.00000 Ti -0.50000 0.75000 0.25000 O 0.00000 -0.20906 -0.20906 O 0.00000 0.20906 0.20906 O -0.50000 0.54088 0.04088 O -0.50000 0.95912 0.45912? this will give u correct visualization with ibrave=7 and nat=6 *---------------------------------------------* *?Muthu VSri Paramakalyani College?---------------------------------------------* -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160119/11480e17/attachment.htm From suresh2007pgp19 at gmail.com Tue Jan 19 09:27:49 2016 From: suresh2007pgp19 at gmail.com (Suresh A) Date: Tue, 19 Jan 2016 13:57:49 +0530 Subject: [xcrysden] all unit sys are being same why? Message-ID: Dear MUTHU, I hope the volume of the structure for the second file surely changes right? I guess the bond length and bond angles are not changed because the atomic position you have included is not in relative to the lattice parameters. So naturally bond lengths are not changed. With Regards, A.Suresh, Research Scholar, Madurai Kamaraj University, Madurai. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160119/c6ec6dcc/attachment.htm From tone.kokalj at ijs.si Tue Jan 19 09:32:06 2016 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 19 Jan 2016 09:32:06 +0100 Subject: [xcrysden] Anatase primitive cell: Regarding In-Reply-To: References: Message-ID: <1453192326.2123.36.camel@ijs.si> On Tue, 2016-01-19 at 10:37 +0530, Suresh A wrote: > Dear Gavin Abo and Muthu, > ????????????????????????????????????? Thank you for your reply.? > The two inputs which i have included? refers to anatase primitive > cell. One input file (first one) gives correct structure in XCRYSDEN > and the other one is also correct but the atomic positions are in > relative to crystal coordinates. The XCRYSDEN shows wrong structure > for second file.? Typically such problems stem from the following reason: the user and the program have a different idea of the unit-cell. In particular, there are two flavors of these problems: (i) the crystallographic vectors are chosen differently between the user and the program (in such cases specified Cartesian coordinates do not give correct structure) (ii) the crystallographic coordinates refers to different set of vectors, e.g, primitive vs. conventional (in such cases the specified crystal coordinates do not give the correct structure) In your case it is the second problem. You have specified the crystal coordinates with respect to conventional vectors, but the Quantum ESPRESSO expects the coordinates wrt primitive vectors (and consequently also xcrysden interprets the QE input this way). Best 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 Tue Jan 19 09:48:06 2016 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 19 Jan 2016 09:48:06 +0100 Subject: [xcrysden] all unit sys are being same why? In-Reply-To: <569D38B5.6030809@crimson.ua.edu> References: <569D38B5.6030809@crimson.ua.edu> Message-ID: <1453193286.2123.44.camel@ijs.si> On Mon, 2016-01-18 at 12:10 -0700, Gavin Abo wrote: > This is happening with the latest XCrySDen version? > > If you are perhaps using an older version, I believe versions before > 1.5.60 did not understand the new QE syntax as discussed in the > following posts: > > http://www.democritos.it/pipermail/xcrysden/2014-January/001531.html > http://qe-forge.org/pipermail/pw_forum/2015-June/107132.html > I confirm that this is so; xcrysden prior to 1.5.60 did not understand the "CELL_PARAMETERS unit" syntax and interpreted the CELL_PARAMETERS in the old way. Best 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 suresh2007pgp19 at gmail.com Wed Jan 20 08:13:21 2016 From: suresh2007pgp19 at gmail.com (Suresh A) Date: Wed, 20 Jan 2016 12:43:21 +0530 Subject: [xcrysden] Anatase primitive cell: Regarding Message-ID: Respected sir(Tone Kolkalj), Thank you for your clarification. I will try to understand the thing as you have described. Thank you With Regards, A.Suresh, Research Scholar, Madurai Kamaraj University, Madurai. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160120/c21ed1ae/attachment.htm From lokanath.patra007 at gmail.com Mon Jan 25 16:12:24 2016 From: lokanath.patra007 at gmail.com (lokanath patra) Date: Mon, 25 Jan 2016 20:42:24 +0530 Subject: [xcrysden] thermometer Message-ID: Dear Xcrysden users, How I can invert the thermometer in Xcrysden? As black color is coming for minimum charge density and white color for maximum charge density, I want to reverse it. Please help. Thank you -- Lokanath Patra Ph.D Scholar Dept. of Physics School of Applied and Basic Sciences Central University of Tamil Nadu Thiruvarur Tamil Nadu - 610101 Ph no - +91-8675834507 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160125/d71411e6/attachment.htm From gsabo at crimson.ua.edu Wed Jan 27 05:52:10 2016 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Tue, 26 Jan 2016 21:52:10 -0700 Subject: [xcrysden] thermometer In-Reply-To: References: Message-ID: <56A84CFA.8040500@crimson.ua.edu> As far as I know, XCrySDen is not able to do that unless you modify the code. I read that the color basis is a hard-coded mess. So, programing a new color basis is probably a time intensive task. If you want to do the coding, the information at the following link should be helpful: http://www.democritos.it/pipermail/xcrysden/2013-October/001484.html On 1/25/2016 8:12 AM, lokanath patra wrote: > Dear Xcrysden users, > How I can invert the thermometer in Xcrysden? As black color is coming > for minimum charge density and white color for maximum charge density, > I want to reverse it. Please help. > > Thank you > -- > Lokanath Patra > Ph.D Scholar > Dept. of Physics > School of Applied and Basic Sciences > Central University of Tamil Nadu > Thiruvarur > Tamil Nadu - 610101 > Ph no - +91-8675834507