Re: [Wien] changed space group of doped supercell
Thanks Dr. Marks for the clue. checking on parameters. Thanking you, A. Kumar On Thu, Jul 27, 2023 at 5:33 PM Laurence Marks wrote: > If sgroup has given you two impurity atom sites, then their environment is > different as that is what sgroup (and other code such as nn) looks at. > Hence their EFG is different. If their environment was truly the same then > sgroup would have merged them to one, with perhaps a change in cell.. > > How they are different is impossible for us to guess as we don't know what > your structure is. If you have an oxide or insulator you can grep Bond in > case.outputnn to look at the BVS, otherwise look in case.outputnn for the > bond distances and angles. Their are many other post scf tools that will > show you that they are different, for instance grep VCOUL, CTO and others. > > -- > Professor Laurence Marks (Laurie) > Department of Materials Science and Engineering, Northwestern University > www.numis.northwestern.edu > "Research is to see what everybody else has seen, and to think what nobody > else has thought" Albert Szent-Györgyi > > On Thu, Jul 27, 2023, 07:50 Ashwani Kumar wrote: > >> Thanks Dr. Blaha, >>One more doubt. Doping in 333SC in present work >> resulted break in multiplicity of a doped site from single site (m=4) in >> undoped SC to two sites (each with m=2) in doped SC. I was expecting same >> EFGs at two sites (assuming same local chemical environment) as they are >> generated due to break in multiplicity of single site (should have same >> chemical environment). But obtained different EFGs. Please enlighten me. >> >>Should i replace one out of the two sites by original >> atom so that only one doped site remains in the system. Can calculation be >> performed without mentioning space group. >> >> Thanking you, >> A. Kumar >> >> On Thu, Jul 27, 2023 at 2:28 PM Peter Blaha >> wrote: >> >>> That's perfectly ok. >>> >>> You have to distinguish between a lattice (which describes the >>> periodicity) and a spacegroup (which includes possible point symmetry >>> operations like rotations,...) >>> >>> If you put atoms randomly into a cubic box, the lattice is still cubic, >>> but the spacegroup will be P1. >>> >>> Am 7/27/23 um 09:26 schrieb Ashwani Kumar: >>> > Hello everyone, >>> > I am doing SCF calculation for impurity atom (single >>> > atom) doped 3x3x3 supercell(SC) calculation. I knw that doping of >>> > impurity atom in SC breaks its symmetry. To know the space group of >>> > impurity atom doped SC, x sgroup was performed and new case.struct >>> file >>> > is obtained with determined space group. >>> > >>> > Unit cell/undoped SC--> Space group (from xrd data): Pnma (No. 62), >>> > Lattice type : orthorhombic. >>> > Impurity atom doped SC-->Space group (determined from "x sgroup"): Pm >>> > (No. 6), supercell lattice parameter: orthorhombic >>> > >>> > I want to understand that "x sgroup" determined space group of doped >>> SC >>> > to be Pm (Space group No. 6) which belongs to the lattice of >>> monoclinic >>> > but lattice parameters of 333 SC is still orthorhombic. So, >>> Case.struct >>> > file contains orthorhomic lattice parameter of 333 SC but space group >>> of >>> > monoclinic lattice type determined from "x sgroup". Is this Ok or am i >>> > doing wrong?. >>> > >>> > >>> > The doped site multiplicity (m) breaks from single site (m=4) in >>> undoped >>> > system to dual site (each with m=2) in doped system due to break in >>> > symmetry. And the two sites have different electric fields (within +/- >>> > 20%). Generation of two sites due to break in symmetry is >>> understandable >>> > but the two site have different Electric fields, i am not able to >>> > understand. >>> > >>> > Thanking you, >>> > A kumar >>> > >>> > >>> > ___ >>> > 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 >>> >>> -- >>> Peter Blaha, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna >>> Phone: +43-1-58801-165300 Email: peter.bl...@tuwien.ac.at >>> WWW: http://www.imc.tuwien.ac WIEN2k: http://www.wien2k.at >>> ___ >>> 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 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 mailing list > Wien@zeus.theochem.tuwien.ac.at >
Re: [Wien] changed space group of doped supercell
If sgroup has given you two impurity atom sites, then their environment is different as that is what sgroup (and other code such as nn) looks at. Hence their EFG is different. If their environment was truly the same then sgroup would have merged them to one, with perhaps a change in cell.. How they are different is impossible for us to guess as we don't know what your structure is. If you have an oxide or insulator you can grep Bond in case.outputnn to look at the BVS, otherwise look in case.outputnn for the bond distances and angles. Their are many other post scf tools that will show you that they are different, for instance grep VCOUL, CTO and others. -- Professor Laurence Marks (Laurie) Department of Materials Science and Engineering, Northwestern University www.numis.northwestern.edu "Research is to see what everybody else has seen, and to think what nobody else has thought" Albert Szent-Györgyi On Thu, Jul 27, 2023, 07:50 Ashwani Kumar wrote: > Thanks Dr. Blaha, >One more doubt. Doping in 333SC in present work > resulted break in multiplicity of a doped site from single site (m=4) in > undoped SC to two sites (each with m=2) in doped SC. I was expecting same > EFGs at two sites (assuming same local chemical environment) as they are > generated due to break in multiplicity of single site (should have same > chemical environment). But obtained different EFGs. Please enlighten me. > >Should i replace one out of the two sites by original > atom so that only one doped site remains in the system. Can calculation be > performed without mentioning space group. > > Thanking you, > A. Kumar > > On Thu, Jul 27, 2023 at 2:28 PM Peter Blaha > wrote: > >> That's perfectly ok. >> >> You have to distinguish between a lattice (which describes the >> periodicity) and a spacegroup (which includes possible point symmetry >> operations like rotations,...) >> >> If you put atoms randomly into a cubic box, the lattice is still cubic, >> but the spacegroup will be P1. >> >> Am 7/27/23 um 09:26 schrieb Ashwani Kumar: >> > Hello everyone, >> > I am doing SCF calculation for impurity atom (single >> > atom) doped 3x3x3 supercell(SC) calculation. I knw that doping of >> > impurity atom in SC breaks its symmetry. To know the space group of >> > impurity atom doped SC, x sgroup was performed and new case.struct file >> > is obtained with determined space group. >> > >> > Unit cell/undoped SC--> Space group (from xrd data): Pnma (No. 62), >> > Lattice type : orthorhombic. >> > Impurity atom doped SC-->Space group (determined from "x sgroup"): Pm >> > (No. 6), supercell lattice parameter: orthorhombic >> > >> > I want to understand that "x sgroup" determined space group of doped SC >> > to be Pm (Space group No. 6) which belongs to the lattice of monoclinic >> > but lattice parameters of 333 SC is still orthorhombic. So, Case.struct >> > file contains orthorhomic lattice parameter of 333 SC but space group >> of >> > monoclinic lattice type determined from "x sgroup". Is this Ok or am i >> > doing wrong?. >> > >> > >> > The doped site multiplicity (m) breaks from single site (m=4) in >> undoped >> > system to dual site (each with m=2) in doped system due to break in >> > symmetry. And the two sites have different electric fields (within +/- >> > 20%). Generation of two sites due to break in symmetry is >> understandable >> > but the two site have different Electric fields, i am not able to >> > understand. >> > >> > Thanking you, >> > A kumar >> > >> > >> > ___ >> > 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 >> >> -- >> Peter Blaha, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna >> Phone: +43-1-58801-165300 Email: peter.bl...@tuwien.ac.at >> WWW: http://www.imc.tuwien.ac WIEN2k: http://www.wien2k.at >> ___ >> 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 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 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] changed space group of doped supercell
Thanks Dr. Blaha, One more doubt. Doping in 333SC in present work resulted break in multiplicity of a doped site from single site (m=4) in undoped SC to two sites (each with m=2) in doped SC. I was expecting same EFGs at two sites (assuming same local chemical environment) as they are generated due to break in multiplicity of single site (should have same chemical environment). But obtained different EFGs. Please enlighten me. Should i replace one out of the two sites by original atom so that only one doped site remains in the system. Can calculation be performed without mentioning space group. Thanking you, A. Kumar On Thu, Jul 27, 2023 at 2:28 PM Peter Blaha wrote: > That's perfectly ok. > > You have to distinguish between a lattice (which describes the > periodicity) and a spacegroup (which includes possible point symmetry > operations like rotations,...) > > If you put atoms randomly into a cubic box, the lattice is still cubic, > but the spacegroup will be P1. > > Am 7/27/23 um 09:26 schrieb Ashwani Kumar: > > Hello everyone, > > I am doing SCF calculation for impurity atom (single > > atom) doped 3x3x3 supercell(SC) calculation. I knw that doping of > > impurity atom in SC breaks its symmetry. To know the space group of > > impurity atom doped SC, x sgroup was performed and new case.struct file > > is obtained with determined space group. > > > > Unit cell/undoped SC--> Space group (from xrd data): Pnma (No. 62), > > Lattice type : orthorhombic. > > Impurity atom doped SC-->Space group (determined from "x sgroup"): Pm > > (No. 6), supercell lattice parameter: orthorhombic > > > > I want to understand that "x sgroup" determined space group of doped SC > > to be Pm (Space group No. 6) which belongs to the lattice of monoclinic > > but lattice parameters of 333 SC is still orthorhombic. So, Case.struct > > file contains orthorhomic lattice parameter of 333 SC but space group of > > monoclinic lattice type determined from "x sgroup". Is this Ok or am i > > doing wrong?. > > > > > > The doped site multiplicity (m) breaks from single site (m=4) in undoped > > system to dual site (each with m=2) in doped system due to break in > > symmetry. And the two sites have different electric fields (within +/- > > 20%). Generation of two sites due to break in symmetry is understandable > > but the two site have different Electric fields, i am not able to > > understand. > > > > Thanking you, > > A kumar > > > > > > ___ > > 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 > > -- > Peter Blaha, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna > Phone: +43-1-58801-165300 Email: peter.bl...@tuwien.ac.at > WWW: http://www.imc.tuwien.ac WIEN2k: http://www.wien2k.at > ___ > 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 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] changed space group of doped supercell
That's perfectly ok. You have to distinguish between a lattice (which describes the periodicity) and a spacegroup (which includes possible point symmetry operations like rotations,...) If you put atoms randomly into a cubic box, the lattice is still cubic, but the spacegroup will be P1. Am 7/27/23 um 09:26 schrieb Ashwani Kumar: Hello everyone, I am doing SCF calculation for impurity atom (single atom) doped 3x3x3 supercell(SC) calculation. I knw that doping of impurity atom in SC breaks its symmetry. To know the space group of impurity atom doped SC, x sgroup was performed and new case.struct file is obtained with determined space group. Unit cell/undoped SC--> Space group (from xrd data): Pnma (No. 62), Lattice type : orthorhombic. Impurity atom doped SC-->Space group (determined from "x sgroup"): Pm (No. 6), supercell lattice parameter: orthorhombic I want to understand that "x sgroup" determined space group of doped SC to be Pm (Space group No. 6) which belongs to the lattice of monoclinic but lattice parameters of 333 SC is still orthorhombic. So, Case.struct file contains orthorhomic lattice parameter of 333 SC but space group of monoclinic lattice type determined from "x sgroup". Is this Ok or am i doing wrong?. The doped site multiplicity (m) breaks from single site (m=4) in undoped system to dual site (each with m=2) in doped system due to break in symmetry. And the two sites have different electric fields (within +/- 20%). Generation of two sites due to break in symmetry is understandable but the two site have different Electric fields, i am not able to understand. Thanking you, A kumar ___ 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 -- Peter Blaha, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 Email: peter.bl...@tuwien.ac.at WWW: http://www.imc.tuwien.ac WIEN2k: http://www.wien2k.at ___ 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
