Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
Dear Prof. Gavin, Apart from that warning, rests are progressing well. Also, the structure looks similar to earlier DFT calculation. I will go with this. with regards, On Sun, 28 Apr 2024 at 21:26, Gavin Abo wrote: > Sorry, missed a word, that should read "not an error message" > On 4/28/2024 9:47 AM, Gavin Abo wrote: > > As far as I know, w2web is not able to automatically detect yet if you > have entered the atomic positions correctly for space group 166. So, the > "positions must be specified in rhombohedral coordinates!" is NOT an > error message but a reminder text that will always be there whether you > enter position correctly or incorrectly. Thus, you have to carefully check > for yourself that you have entered the position correctly. > > As you might recall from the post at [1], WIEN2k is a bit unusual in that > for the struct file it needs hexagonal lattice constants but rhombohedral > for the atomic positions for an R lattice space group such as 166 R-3m. > For LiNIO2, you should double check, but I believe the both lattice > constants and atomic positions in the hexagonal setting are: > > Initial Setting: R-3m:h (No. 166) > > 166 > 5.404616 5.404616 26.569550 90 90 120 <= This is the hexagonal lattice > parameters needed for the struct file of WIEN2k > 3 > Li13a0.000.000.00 <= These are the > hexagonal atomic positions, which would be incorrect to use for WIEN2k > Ni13b0.000.000.50 > O16c0.000.000.240984 > > Using SETSTRU [2], its equivalent in the rhombohedral setting should be: > > > Final Setting: R-3m:r (No. 166) > > 166 #R-3m:r > 9.3901 9.3901 9.3901 33.45 33.45 33.45 <= These are the rhombohedral > lattice parameters, which would be incorrect to use for WIEN2k > 3 > Li1-0.000.000.00 <= These are the > rhomboderal atomic positions needed for the struct file of WIEN2k > Ni1-0.500.500.50 > O1-0.2409840.2409840.240984 > > > In your LiNiO2_opt.struct, I see: > > a = 5.404616 bohr in hexagonal setting > > b = 5.404616 bohr in hexagonal setting > > c = 26.569550 bohr in hexagonal setting > > alpha = 90.00 deg in hexagonal setting > > beta = 90.00 deg in hexagonal setting > > beta = 120.00 deg in hexagonal setting > > Li x=0. y=0. z=0. in rhombohedral setting > > Ni z=0.5000 y=0.5000 z=0.5000 in rhombohedral setting > > O x=0.24098400 y=0.24098400 z=0.24098400 in rhombohedral setting > > [1] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05554.html > > [2] https://www.cryst.ehu.es/cryst/setstru.html > > > On 4/28/2024 8:00 AM, shamik chakrabarti wrote: > > Dear Wien2k users, > >I want to simulate properties of LiNiO2. However, adopting the > structure (file attached) by bringing it into rhombohedral axis in Vesta, > when I copy the cif file into the working directory & converting it into a > struct file, after save structure, it complains about > > " positions must be specified in rhombohedral coordinates!" > > Please guide. > > with regards, > > -- > Dr. Shamik Chakrabarti > Research Fellow > Department of Physics > Indian Institute of Technology Patna > Bihta-801103 > Patna > Bihar, India > > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
Sorry, missed a word, that should read "not an error message" On 4/28/2024 9:47 AM, Gavin Abo wrote: As far as I know, w2web is not able to automatically detect yet if you have entered the atomic positions correctly for space group 166. So, the "positions must be specified in rhombohedral coordinates!" is NOT an error message but a reminder text that will always be there whether you enter position correctly or incorrectly. Thus, you have to carefully check for yourself that you have entered the position correctly. As you might recall from the post at [1], WIEN2k is a bit unusual in that for the struct file it needs hexagonal lattice constants but rhombohedral for the atomic positions for an R lattice space group such as 166 R-3m. For LiNIO2, you should double check, but I believe the both lattice constants and atomic positions in the hexagonal setting are: Initial Setting: R-3m:h (No. 166) 166 5.404616 5.404616 26.569550 90 90 120 <= This is the hexagonal lattice parameters needed for the struct file of WIEN2k 3 Li 1 3a 0.00 0.00 0.00 <= These are the hexagonal atomic positions, which would be incorrect to use for WIEN2k Ni 1 3b 0.00 0.00 0.50 O 1 6c 0.00 0.00 0.240984 Using SETSTRU [2], its equivalent in the rhombohedral setting should be: Final Setting: R-3m:r (No. 166) 166 #R-3m:r 9.3901 9.3901 9.3901 33.45 33.45 33.45 <= These are the rhombohedral lattice parameters, which would be incorrect to use for WIEN2k 3 Li 1 - 0.00 0.00 0.00 <= These are the rhomboderal atomic positions needed for the struct file of WIEN2k Ni 1 - 0.50 0.50 0.50 O 1 - 0.240984 0.240984 0.240984 In your LiNiO2_opt.struct, I see: a = 5.404616 bohr in hexagonal setting b = 5.404616 bohr in hexagonal setting c = 26.569550 bohr in hexagonal setting alpha = 90.00 deg in hexagonal setting beta = 90.00 deg in hexagonal setting beta = 120.00 deg in hexagonal setting Li x=0. y=0. z=0. in rhombohedral setting Ni z=0.5000 y=0.5000 z=0.5000 in rhombohedral setting O x=0.24098400 y=0.24098400 z=0.24098400 in rhombohedral setting [1] https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05554.html [2] https://www.cryst.ehu.es/cryst/setstru.html On 4/28/2024 8:00 AM, shamik chakrabarti wrote: Dear Wien2k users, I want to simulate properties of LiNiO2. However, adopting the structure (file attached) by bringing it into rhombohedral axis in Vesta, when I copy the cif file into the working directory & converting it into a struct file, after save structure, it complains about " positions must be specified in rhombohedral coordinates!" Please guide. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
As far as I know, w2web is not able to automatically detect yet if you have entered the atomic positions correctly for space group 166. So, the "positions must be specified in rhombohedral coordinates!" is an error message but a reminder text that will always be there whether you enter position correctly or incorrectly. Thus, you have to carefully check for yourself that you have entered the position correctly. As you might recall from the post at [1], WIEN2k is a bit unusual in that for the struct file it needs hexagonal lattice constants but rhombohedral for the atomic positions for an R lattice space group such as 166 R-3m. For LiNIO2, you should double check, but I believe the both lattice constants and atomic positions in the hexagonal setting are: Initial Setting: R-3m:h (No. 166) 166 5.404616 5.404616 26.569550 90 90 120 <= This is the hexagonal lattice parameters needed for the struct file of WIEN2k 3 Li 1 3a 0.00 0.00 0.00 <= These are the hexagonal atomic positions, which would be incorrect to use for WIEN2k Ni 1 3b 0.00 0.00 0.50 O 1 6c 0.00 0.00 0.240984 Using SETSTRU [2], its equivalent in the rhombohedral setting should be: Final Setting: R-3m:r (No. 166) 166 #R-3m:r 9.3901 9.3901 9.3901 33.45 33.45 33.45 <= These are the rhombohedral lattice parameters, which would be incorrect to use for WIEN2k 3 Li 1 - 0.00 0.00 0.00 <= These are the rhomboderal atomic positions needed for the struct file of WIEN2k Ni 1 - 0.50 0.50 0.50 O 1 - 0.240984 0.240984 0.240984 In your LiNiO2_opt.struct, I see: a = 5.404616 bohr in hexagonal setting b = 5.404616 bohr in hexagonal setting c = 26.569550 bohr in hexagonal setting alpha = 90.00 deg in hexagonal setting beta = 90.00 deg in hexagonal setting beta = 120.00 deg in hexagonal setting Li x=0. y=0. z=0. in rhombohedral setting Ni z=0.5000 y=0.5000 z=0.5000 in rhombohedral setting O x=0.24098400 y=0.24098400 z=0.24098400 in rhombohedral setting [1] https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg05554.html [2] https://www.cryst.ehu.es/cryst/setstru.html On 4/28/2024 8:00 AM, shamik chakrabarti wrote: Dear Wien2k users, I want to simulate properties of LiNiO2. However, adopting the structure (file attached) by bringing it into rhombohedral axis in Vesta, when I copy the cif file into the working directory & converting it into a struct file, after save structure, it complains about " positions must be specified in rhombohedral coordinates!" Please guide. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
Dear Prof. Delamora, After changing all the coordinates I am achieving rather a complicated struct file as attached. with regards, On Sun, 28 Apr 2024 at 20:18, delamora wrote: > hx is hexagonal x > > -- > *De:* Wien en nombre de shamik > chakrabarti > *Enviado:* domingo, 28 de abril de 2024 08:40 a. m. > *Para:* A Mailing list for WIEN2k users > *Asunto:* Re: [Wien] Rhombhohedral coordinates needed in simulation of > LiNiO2 > > It is asking for specifying hx,hy,hzwhat are these? > > On Sun, 28 Apr 2024 at 20:06, delamora wrote: > > Use the command; > hex2rhomb > hexagonal to rhombohedral > -- > *De:* Wien en nombre de shamik > chakrabarti > *Enviado:* domingo, 28 de abril de 2024 08:00 a. m. > *Para:* A Mailing list for WIEN2k users > *Asunto:* [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2 > > Dear Wien2k users, > >I want to simulate properties of LiNiO2. However, adopting the > structure (file attached) by bringing it into rhombohedral axis in Vesta, > when I copy the cif file into the working directory & converting it into a > struct file, after save structure, it complains about > > " positions must be specified in rhombohedral coordinates!" > > Please guide. > > with regards, > > -- > Dr. Shamik Chakrabarti > Research Fellow > Department of Physics > Indian Institute of Technology Patna > Bihta-801103 > Patna > Bihar, India > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > > > > -- > Dr. Shamik Chakrabarti > Research Fellow > Department of Physics > Indian Institute of Technology Patna > Bihta-801103 > Patna > Bihar, India > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India LiNiO2_opt.struct Description: Binary data ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
hx is hexagonal x De: Wien en nombre de shamik chakrabarti Enviado: domingo, 28 de abril de 2024 08:40 a. m. Para: A Mailing list for WIEN2k users Asunto: Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2 It is asking for specifying hx,hy,hzwhat are these? On Sun, 28 Apr 2024 at 20:06, delamora mailto:delam...@unam.mx>> wrote: Use the command; hex2rhomb hexagonal to rhombohedral De: Wien mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> en nombre de shamik chakrabarti mailto:shamik15041...@gmail.com>> Enviado: domingo, 28 de abril de 2024 08:00 a. m. Para: A Mailing list for WIEN2k users mailto:wien@zeus.theochem.tuwien.ac.at>> Asunto: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2 Dear Wien2k users, I want to simulate properties of LiNiO2. However, adopting the structure (file attached) by bringing it into rhombohedral axis in Vesta, when I copy the cif file into the working directory & converting it into a struct file, after save structure, it complains about " positions must be specified in rhombohedral coordinates!" Please guide. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at<mailto:Wien@zeus.theochem.tuwien.ac.at> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
It is asking for specifying hx,hy,hzwhat are these? On Sun, 28 Apr 2024 at 20:06, delamora wrote: > Use the command; > hex2rhomb > hexagonal to rhombohedral > -- > *De:* Wien en nombre de shamik > chakrabarti > *Enviado:* domingo, 28 de abril de 2024 08:00 a. m. > *Para:* A Mailing list for WIEN2k users > *Asunto:* [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2 > > Dear Wien2k users, > >I want to simulate properties of LiNiO2. However, adopting the > structure (file attached) by bringing it into rhombohedral axis in Vesta, > when I copy the cif file into the working directory & converting it into a > struct file, after save structure, it complains about > > " positions must be specified in rhombohedral coordinates!" > > Please guide. > > with regards, > > -- > Dr. Shamik Chakrabarti > Research Fellow > Department of Physics > Indian Institute of Technology Patna > Bihta-801103 > Patna > Bihar, India > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html > -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
Use the command; hex2rhomb hexagonal to rhombohedral De: Wien en nombre de shamik chakrabarti Enviado: domingo, 28 de abril de 2024 08:00 a. m. Para: A Mailing list for WIEN2k users Asunto: [Wien] Rhombhohedral coordinates needed in simulation of LiNiO2 Dear Wien2k users, I want to simulate properties of LiNiO2. However, adopting the structure (file attached) by bringing it into rhombohedral axis in Vesta, when I copy the cif file into the working directory & converting it into a struct file, after save structure, it complains about " positions must be specified in rhombohedral coordinates!" Please guide. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Rhombhohedral coordinates needed in simulation of LiNiO2
Dear Wien2k users, I want to simulate properties of LiNiO2. However, adopting the structure (file attached) by bringing it into rhombohedral axis in Vesta, when I copy the cif file into the working directory & converting it into a struct file, after save structure, it complains about " positions must be specified in rhombohedral coordinates!" Please guide. with regards, -- Dr. Shamik Chakrabarti Research Fellow Department of Physics Indian Institute of Technology Patna Bihta-801103 Patna Bihar, India LiNiO2_opt.struct Description: Binary data ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
