Re: [Wien] structeditor for creating a surface
It is up to you, how thick (how many layers) you want to make your slab. The thicker the better, but soon you will run out of computer power. PS: For a (001) surface the programx supercell is probably easier to use. There you would be asked for the number of cells along x,y,z and with 1x1x2 (3,4,5..) you can create slabs with different thickness. PS: On 06/27/2013 03:48 AM, Madhav Ghimire wrote: Dear Robert and wien2k users, I am creating a surface using structeditor program which required octave enironment, I came across sr=makesurface(s,n,ind,depth,vac) which creates surface for a given unitcell where: s input structure n normal vector (in lattice coordinates) ind an index of an atom which should be in (0 0 0) *depth thickness of the material* vac thickness of the vacuum layer example: sr=makesurface(s,[0 0 1],1,30.0,20.0) Now my doubt is: How shall I realize the thickness of the particular material (for example Fe) I mean can I choose it manually (any number) or I need to know the proper thickness of the material. If so, can anyone help where I can find the thickness information of the material. Thanks in advance Madhav ___ 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 -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ -- ___ 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] structeditor for creating a surface
Dear Prof. Blaha, Thanks. Using x supercell, I could generate a 001 surface of Fe . But my current case is for 111 surface with 5 layers which is difficult to create using x supercell. In my current structure, I need to create a vacuum of 20 Ang. on the fifth layer. So I was not sure whether the thickness of the material [30.0] selection in sr=makesurface (s,1,30.0,20.0) is OK for Fe. It will be great if you could confirm sr=makesurface (s,1,30.0,20.0) on structeditor is OK. Best regards Madhav On Thu, Jun 27, 2013 at 3:27 PM, Peter Blaha pbl...@theochem.tuwien.ac.atwrote: It is up to you, how thick (how many layers) you want to make your slab. The thicker the better, but soon you will run out of computer power. PS: For a (001) surface the programx supercell is probably easier to use. There you would be asked for the number of cells along x,y,z and with 1x1x2 (3,4,5..) you can create slabs with different thickness. PS: On 06/27/2013 03:48 AM, Madhav Ghimire wrote: Dear Robert and wien2k users, I am creating a surface using structeditor program which required octave enironment, I came across sr=makesurface(s,n,ind,depth,**vac) which creates surface for a given unitcell where: s input structure n normal vector (in lattice coordinates) ind an index of an atom which should be in (0 0 0) *depth thickness of the material* vac thickness of the vacuum layer example: sr=makesurface(s,[0 0 1],1,30.0,20.0) Now my doubt is: How shall I realize the thickness of the particular material (for example Fe) I mean can I choose it manually (any number) or I need to know the proper thickness of the material. If so, can anyone help where I can find the thickness information of the material. Thanks in advance Madhav __**_ Wien mailing list w...@zeus.theochem.tuwien.ac.**at Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/** w...@zeus.theochem.tuwien.ac.**at/index.htmlhttp://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- P.Blaha --**--** -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 FAX: +43-1-58801-165982 Email: bl...@theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/** theochem/ http://info.tuwien.ac.at/theochem/ --**--** -- __**_ Wien mailing list w...@zeus.theochem.tuwien.ac.**at Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/** w...@zeus.theochem.tuwien.ac.**at/index.htmlhttp://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] structeditor for creating a surface
Hello Madhav, The thickness of the slab will vary depending on the interplanar distance for that surface. Usually you can do this more accurately by using an expression based on the bulk lattice constants. For instance: bulk = loadstruct(...) surface = makesurface(bulk,1,bulk.a(3)/2,20.0) where bulk.a(3) will be half the lattice constant in the z direction. You may have to add 0.001 or something so that it does not cut off the uppermost atoms (most likely there's a smaller or greater than somewhere that could benefit from an equals sign). So surface = makesurface(bulk,1,bulk.a(3)/2+0.001,20.0) Also make sure your number of atoms is always correct since for more exotic surfaces sometimes the structeditor eats a few atoms somewhere at the bottom of the slab where the 001 direction used to be... Which is then usually easily fixed by making a bit thicker slab and removing layers again. Regards, Michael Sluydts Op 27/06/2013 8:44, Madhav Ghimire schreef: Dear Prof. Blaha, Thanks. Using x supercell, I could generate a 001 surface of Fe . But my current case is for 111 surface with 5 layers which is difficult to create using x supercell. In my current structure, I need to create a vacuum of 20 Ang. on the fifth layer. So I was not sure whether the thickness of the material [30.0] selection in sr=makesurface (s,1,30.0,20.0) is OK for Fe. It will be great if you could confirm sr=makesurface (s,1,30.0,20.0) on structeditor is OK. Best regards Madhav On Thu, Jun 27, 2013 at 3:27 PM, Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at wrote: It is up to you, how thick (how many layers) you want to make your slab. The thicker the better, but soon you will run out of computer power. PS: For a (001) surface the programx supercell is probably easier to use. There you would be asked for the number of cells along x,y,z and with 1x1x2 (3,4,5..) you can create slabs with different thickness. PS: On 06/27/2013 03:48 AM, Madhav Ghimire wrote: Dear Robert and wien2k users, I am creating a surface using structeditor program which required octave enironment, I came across sr=makesurface(s,n,ind,depth,vac) which creates surface for a given unitcell where: s input structure n normal vector (in lattice coordinates) ind an index of an atom which should be in (0 0 0) *depth thickness of the material* vac thickness of the vacuum layer example: sr=makesurface(s,[0 0 1],1,30.0,20.0) Now my doubt is: How shall I realize the thickness of the particular material (for example Fe) I mean can I choose it manually (any number) or I need to know the proper thickness of the material. If so, can anyone help where I can find the thickness information of the material. Thanks in advance Madhav ___ 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 -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 tel:%2B43-1-58801-165300 FAX: +43-1-58801-165982 tel:%2B43-1-58801-165982 Email: bl...@theochem.tuwien.ac.at mailto:bl...@theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ -- ___ 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 ___ 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] structeditor for creating a surface
Exactly like this. And then: look at your structure (xcrysden or VESTA or ..), count the number of generated layers, check if all atoms are there, . On 06/27/2013 09:18 AM, Michael Sluydts wrote: Hello Madhav, The thickness of the slab will vary depending on the interplanar distance for that surface. Usually you can do this more accurately by using an expression based on the bulk lattice constants. For instance: bulk = loadstruct(...) surface = makesurface(bulk,1,bulk.a(3)/2,20.0) where bulk.a(3) will be half the lattice constant in the z direction. You may have to add 0.001 or something so that it does not cut off the uppermost atoms (most likely there's a smaller or greater than somewhere that could benefit from an equals sign). So surface = makesurface(bulk,1,bulk.a(3)/2+0.001,20.0) Also make sure your number of atoms is always correct since for more exotic surfaces sometimes the structeditor eats a few atoms somewhere at the bottom of the slab where the 001 direction used to be... Which is then usually easily fixed by making a bit thicker slab and removing layers again. Regards, Michael Sluydts Op 27/06/2013 8:44, Madhav Ghimire schreef: Dear Prof. Blaha, Thanks. Using x supercell, I could generate a 001 surface of Fe . But my current case is for 111 surface with 5 layers which is difficult to create using x supercell. In my current structure, I need to create a vacuum of 20 Ang. on the fifth layer. So I was not sure whether the thickness of the material [30.0] selection in sr=makesurface (s,1,30.0,20.0) is OK for Fe. It will be great if you could confirm sr=makesurface (s,1,30.0,20.0) on structeditor is OK. Best regards Madhav On Thu, Jun 27, 2013 at 3:27 PM, Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at wrote: It is up to you, how thick (how many layers) you want to make your slab. The thicker the better, but soon you will run out of computer power. PS: For a (001) surface the programx supercell is probably easier to use. There you would be asked for the number of cells along x,y,z and with 1x1x2 (3,4,5..) you can create slabs with different thickness. PS: On 06/27/2013 03:48 AM, Madhav Ghimire wrote: Dear Robert and wien2k users, I am creating a surface using structeditor program which required octave enironment, I came across sr=makesurface(s,n,ind,depth,vac) which creates surface for a given unitcell where: s input structure n normal vector (in lattice coordinates) ind an index of an atom which should be in (0 0 0) *depth thickness of the material* vac thickness of the vacuum layer example: sr=makesurface(s,[0 0 1],1,30.0,20.0) Now my doubt is: How shall I realize the thickness of the particular material (for example Fe) I mean can I choose it manually (any number) or I need to know the proper thickness of the material. If so, can anyone help where I can find the thickness information of the material. Thanks in advance Madhav ___ 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 -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 tel:%2B43-1-58801-165300 FAX: +43-1-58801-165982 tel:%2B43-1-58801-165982 Email: bl...@theochem.tuwien.ac.at mailto:bl...@theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ -- ___ 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 ___ 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] structeditor for creating a surface
Dear Michael Prof. Blaha, The information you provided are really helpful. My doubt are clear now. Thanks Madhav On Thu, Jun 27, 2013 at 4:30 PM, Peter Blaha pbl...@theochem.tuwien.ac.atwrote: Exactly like this. And then: look at your structure (xcrysden or VESTA or ..), count the number of generated layers, check if all atoms are there, . On 06/27/2013 09:18 AM, Michael Sluydts wrote: Hello Madhav, The thickness of the slab will vary depending on the interplanar distance for that surface. Usually you can do this more accurately by using an expression based on the bulk lattice constants. For instance: bulk = loadstruct(...) surface = makesurface(bulk,1,bulk.a(3)/**2,20.0) where bulk.a(3) will be half the lattice constant in the z direction. You may have to add 0.001 or something so that it does not cut off the uppermost atoms (most likely there's a smaller or greater than somewhere that could benefit from an equals sign). So surface = makesurface(bulk,1,bulk.a(3)/**2+0.001,20.0) Also make sure your number of atoms is always correct since for more exotic surfaces sometimes the structeditor eats a few atoms somewhere at the bottom of the slab where the 001 direction used to be... Which is then usually easily fixed by making a bit thicker slab and removing layers again. Regards, Michael Sluydts Op 27/06/2013 8:44, Madhav Ghimire schreef: Dear Prof. Blaha, Thanks. Using x supercell, I could generate a 001 surface of Fe . But my current case is for 111 surface with 5 layers which is difficult to create using x supercell. In my current structure, I need to create a vacuum of 20 Ang. on the fifth layer. So I was not sure whether the thickness of the material [30.0] selection in sr=makesurface (s,1,30.0,20.0) is OK for Fe. It will be great if you could confirm sr=makesurface (s,1,30.0,20.0) on structeditor is OK. Best regards Madhav On Thu, Jun 27, 2013 at 3:27 PM, Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pblaha@theochem.**tuwien.ac.atpbl...@theochem.tuwien.ac.at wrote: It is up to you, how thick (how many layers) you want to make your slab. The thicker the better, but soon you will run out of computer power. PS: For a (001) surface the programx supercell is probably easier to use. There you would be asked for the number of cells along x,y,z and with 1x1x2 (3,4,5..) you can create slabs with different thickness. PS: On 06/27/2013 03:48 AM, Madhav Ghimire wrote: Dear Robert and wien2k users, I am creating a surface using structeditor program which required octave enironment, I came across sr=makesurface(s,n,ind,depth,**vac) which creates surface for a given unitcell where: s input structure n normal vector (in lattice coordinates) ind an index of an atom which should be in (0 0 0) *depth thickness of the material* vac thickness of the vacuum layer example: sr=makesurface(s,[0 0 1],1,30.0,20.0) Now my doubt is: How shall I realize the thickness of the particular material (for example Fe) I mean can I choose it manually (any number) or I need to know the proper thickness of the material. If so, can anyone help where I can find the thickness information of the material. Thanks in advance Madhav __**_ Wien mailing list w...@zeus.theochem.tuwien.ac.**atWien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.**tuwien.ac.atWien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.**ac.at/mailman/listinfo/wienhttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/**w...@zeus.theochem.tuwien.ac.** at/index.htmlhttp://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- P.Blaha --**--** -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 tel:%2B43-1-58801-165300 FAX: +43-1-58801-165982 tel:%2B43-1-58801-165982 Email: bl...@theochem.tuwien.ac.at mailto:blaha@theochem.tuwien.**ac.at bl...@theochem.tuwien.ac.at WWW: http://info.tuwien.ac.at/**theochem/http://info.tuwien.ac.at/theochem/ --**--** -- __**_ Wien mailing list w...@zeus.theochem.tuwien.ac.**at Wien@zeus.theochem.tuwien.ac.at
