Re: [Wien] Reg: error in supercell calculation
Thank you for your reply sir, i just want to create vacancy so i removed the atom next to the atom2. Is it correct procedure sir, is there any other way. Removing the atom name will not remove the atom. You have to click the "remove atom" link next to the atom in StructGen. Whether this creates the correct vacancy, I don't not know. You have to determine this yourself. Xcrysden is a good aid, which you can use to help you visualize whether the structure looks reasonable or not. ___ 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] Reg: error in supercell calculation
Dear Gavin Abo sir, Thank you for your reply sir, i just want to create vacancy so i removed the atom next to the atom2. Is it correct procedure sir, is there any other way. Thanking you Regards G.Shwetha ___ 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] Reg: error in supercell calculation
Dear Stefaan sir, Thank you sir for your reply. I accepted the new nn, spacegroup files, i did instgen_lapw and i accepted the new case.inst file after initialization but still I am getting same error. Thanking you Regards G.Shwetha ___ 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] Reg: error in supercell calculation
> sgroup(16:17:52) warning: No literal name specified for atom 2. Using Z value as identifier. The warning suggests that in StructGen, the first box next to Atom 1 (or 2) is likely empty, when it should contain the name of the atom. > lstart(16:18:48) SELECT XCPOT: recommended: 13: PBE-GGA (Perdew-Burke-Ernzerhof 96) 5: LSDA 11: WC-GGA (Wu-Cohen 2006) 19: PBEsol-GGA (Perdew etal. 2008) 5 SELECT ENERGY to separate core and valence states: recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere) ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to select core state -6.0 NUMBER OF ELECTRONS NE IZ29.0 28 NUMBER OF ELECTRONS NE IZ32.0 28 The 28 is likely the value in the Z box next to atom 1, which indicates that the name of the atom should be Ni. Due to the first problem with the name of the atom, the program likely cannot correctly create your super.inst and this leads to these additional errors that occur later. LSTART ENDS 0.9u 0.0s 0:04.84 20.8% 0+0k 0+3120io 0pf+0w ERROR !!! nstop,iter,tets,test 362 3 9.99974752427E-007 nstop,iter,tets,test 362 2 9.99974752427E-007 You have to change your atomic configuration in super.inst ERROR !!! NUMBER OF ELECTRONS NE IZ 29.0 28 NUMBER OF ELECTRONS NE IZ 32.0 28 You have to change your atomic configuration in super.inst or Z in super.struct ___ 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] Reg: error in supercell calculation
Thank you for your reply sir. But i have some doubt, in the initialization process it is giving error like shown below, after this initializing (error) can i run instgen_lapw and accept the new case.inst file and i can proceed for further calculations. i have proceded as follows while initialization, is there any mistakes while accepting the the new file, and moreover it will ask continue with symmetry (old case.struct) or use/edit super.struct_sgroup ? (c/e), -> continue with lstart or edit the super.struct_st file (c/e/x), -> continue with kgen or edit the super.inst file and rerun lstart (c/e) e, every time do i have to accept the new files every time. After having created and modified a supercell, the symmetry is almost never right. Therefore: yes, accept the suggestions by nn and by sgroup. Other error messages are due to a previous case.inst lingering around: > NUMBER OF ELECTRONS NE IZ29.0 28 > NUMBER OF ELECTRONS NE IZ32.0 28 Either remove case.inst before init_lapw, or run instgen_lapw and accept the new file. If you doubt the correctness, then first do as described above, then take the final case.struct to a new, empty directory and run init_lapw there again. There should be no error messages or new suggestions any more. Stefaan ___ 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] Reg: error in supercell calculation
Dear Stefan sir, Thank you for your reply sir. But i have some doubt, in the initialization process it is giving error like shown below, after this initializing (error) can i run instgen_lapw and accept the new case.inst file and i can proceed for further calculations. i have proceded as follows while initialization, is there any mistakes while accepting the the new file, and moreover it will ask continue with symmetry (old case.struct) or use/edit super.struct_sgroup ? (c/e), -> continue with lstart or edit the super.struct_st file (c/e/x), -> continue with kgen or edit the super.inst file and rerun lstart (c/e) e, every time do i have to accept the new files every time. init_lapw as follows: NN ENDS 0.4u 0.0s 0:02.06 20.8% 0+0k 0+712io 0pf+0w -> check in super.outputnn for overlapping spheres, coordination and nearest neighbor distances -> continue with sgroup or edit the super.struct file (c/e) c > sgroup(16:17:52) warning: No literal name specified for atom 2. Using Z value as identifier. warning: No literal name specified for atom 2. Using Z value as identifier. warning: No literal name specified for atom 2. Using Z value as identifier. 0.0u 0.0s 0:00.00 0.0% 0+0k 0+16io 0pf+0w Names of point group: mm2mm2C2v Names of point group: mm2mm2C2v Names of point group: mm2mm2C2v Names of point group: mm2mm2C2v Names of point group: mm2mm2C2v Names of point group: mm2mm2C2v Names of point group: mm2mm2C2v Names of point group: mm2mm2C2v Names of point group: mm2mm2C2v Names of point group: mm2mm2C2v Number and name of space group: 65 (C m m m) -> check in super.outputsgroup for proper symmetry, compare with your struct file and later with super.outputs sgroup has also produced a new struct file based on your old one. If you see warnings above, consider to use the newly generated struct file, which you can view (edit) now. -> continue with symmetry (old case.struct) or use/edit super.struct_sgroup ? (c/e) c > symmetry(16:18:40) 0.0u 0.0s 0:00.00 0.0% 0+0k 0+64io 0pf+0w -> check in super.outputs the symmetry operations, the point symmetries and compare with results from sgroup -> continue with lstart or edit the super.struct_st file (c/e/x) c CREATE A NEW super.inst FILE with PROPER ATOMS Eventually specify switches for instgen_lapw (or press ENTER): -up (default) -dn -nm (non-magnetic) -ask -nm 9 Atoms found: > lstart(16:18:48) SELECT XCPOT: recommended: 13: PBE-GGA (Perdew-Burke-Ernzerhof 96) 5: LSDA 11: WC-GGA (Wu-Cohen 2006) 19: PBEsol-GGA (Perdew etal. 2008) 5 SELECT ENERGY to separate core and valence states: recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere) ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to select core state -6.0 NUMBER OF ELECTRONS NE IZ29.0 28 NUMBER OF ELECTRONS NE IZ32.0 28 LSTART ENDS 0.9u 0.0s 0:04.84 20.8% 0+0k 0+3120io 0pf+0w ERROR !!! nstop,iter,tets,test 362 3 9.99974752427E-007 nstop,iter,tets,test 362 2 9.99974752427E-007 You have to change your atomic configuration in super.inst ERROR !!! NUMBER OF ELECTRONS NE IZ 29.0 28 NUMBER OF ELECTRONS NE IZ 32.0 28 You have to change your atomic configuration in super.inst or Z in super.struct -> continue with kgen or edit the super.inst file and rerun lstart (c/e) e An old super.inst file is present. Do you want to overwrite it (N/y) y CREATE A NEW super.inst FILE with PROPER ATOMS Eventually specify switches for instgen_lapw (or press ENTER): -up (default) -dn -nm (non-magnetic) -ask -nm 9 Atoms found: > lstart(16:19:03) SELECT XCPOT: recommended: 13: PBE-GGA (Perdew-Burke-Ernzerhof 96) 5: LSDA 11: WC-GGA (Wu-Cohen 2006) 19: PBEsol-GGA (Perdew etal. 2008) 5 SELECT ENERGY to separate core and valence states: recommended: -6.0 Ry (check how much core charge leaks out of MT-sphere) ALTERNATIVELY: specify charge localization (between 0.97 and 1.0) to select core state -6.0 NUMBER OF ELECTRONS NE IZ29.0 28 NUMBER OF ELECTRONS NE IZ32.0 28 LSTART ENDS 0.9u 0.0s 0:04.36 23.1% 0+0k 0+2960io 0pf+0w ERROR !!! nstop,iter,tets,test 362 3 9.99974752427E-007 nstop,iter,tets,test 362 2 9.99974752427E-007 You have to change your atomic configuration in super.inst ERROR !!! NUMBER OF ELECTRONS NE IZ 29.0 28 NUMBER OF ELECTRONS NE IZ 32.0 28 You have to change your atomic configuration in super.inst or Z in super.struct -> continue with kgen or edit the super.inst file and rerun lstart (c/e) c -> in super.in1_st select RKmax ( usually
Re: [Wien] Reg: error in supercell calculation
Rerun instgen_lapw and accept the new case.inst (the error appears because you are still using the case.inst corresponding to the atoms in the structure file before making your changes). Stefaan On 21/04/2013 12:16, shwetha gummula wrote: Dear Prof. Peter Blaha & WIEN2k Users, I am doing supercell calculations for the orthorhombic system of ABC3 type with space group cmmm (65). I created supercell of 2x1x1, (A-2, B-2, C-6 elements created) i removed one element (B1) in order to create vacancy and i replaced one atom (B2-E) with other element. While initializing i accepted the new struct file but it is giving error ERROR !!! nstop,iter,tets,test 362 3 9.99974752427E-007 nstop,iter,tets,test 362 2 9.99974752427E-007 You have to change your atomic configuration in super.inst ERROR !!! NUMBER OF ELECTRONS NE IZ 29.0 28 NUMBER OF ELECTRONS NE IZ 32.0 28 You have to change your atomic configuration in super.inst or Z in super.struct I am not getting what change i have to do in case.inst file in order to have one element as vacant. Please help me regarding this. Thanking you ___ 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] Reg: error in supercell calculation
Dear Prof. Peter Blaha & WIEN2k Users, I am doing supercell calculations for the orthorhombic system of ABC3 type with space group cmmm (65). I created supercell of 2x1x1, (A-2, B-2, C-6 elements created) i removed one element (B1) in order to create vacancy and i replaced one atom (B2-E) with other element. While initializing i accepted the new struct file but it is giving error ERROR !!! nstop,iter,tets,test 362 3 9.99974752427E-007 nstop,iter,tets,test 362 2 9.99974752427E-007 You have to change your atomic configuration in super.inst ERROR !!! NUMBER OF ELECTRONS NE IZ 29.0 28 NUMBER OF ELECTRONS NE IZ 32.0 28 You have to change your atomic configuration in super.inst or Z in super.struct I am not getting what change i have to do in case.inst file in order to have one element as vacant. Please help me regarding this. Thanking you ___ 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
