Dear Daniel, I aim to try to induce some sp3 bonds between the layers, forcing them by hydrogenating (or by other chemical groups) a couple of carbon atoms (the non-constrained atoms) and strain. In fact, I'm trying to obtain the 2D diamond structure and then trying to use the same methodology in other structures (doped ones, for example).
I understood your comments and now believe I can perform these calculations with your advice, I am immensely grateful. Em sáb., 8 de abr. de 2023 às 17:00, Daniel Bennett <db...@cantab.ac.uk> escreveu: > Hi Ramon, > > I'm not sure if this is such a good idea, at least in your example. If I > understand correctly, you freeze the first graphene layer (in the z=0 plane > say), then the second graphene layer is at some z which is larger than the > optimal one which minimizes the van der Waals energy. Then you move the > second layer in the negative z direction, closer to the first, until it > reaches the minimum distance. But in relaxations, the coordinates > oscillating about the minimum until they converge below a given tolerance. > As soon as the second layer passes to the other side of that minimum, the > energy will explode, because it can only move closer to the first layer. > The same thing will happen if you constrain the atoms to move in the other > direction and begin with the second layer too close to the first: the > second layer will move to the other side of the cell in the z-direction, > and you will have the same problem on the other side of the first graphene > layer. It might work if you get lucky and the system happens to get very > close to the minimum without going beyond it, but I think this would be > very unlikely to happen > > Are you trying to do this for graphene, or something more complicated? > Because with bilayer graphene if you freeze the first layer, the xy > components of the second, and force the z components of the second to be > equal, only one parameter needs to be optimized, and siesta can do this > very efficiently with its native geometry constraints. > > Daniel Bennett > > > ------------------------------ > *From:* siesta-l-requ...@uam.es <siesta-l-requ...@uam.es> on behalf of > Ramon Sampaio Ferreira <ra...@fisica.ufc.br> > *Sent:* 07 April 2023 11:13 > *To:* siesta-l@uam.es <siesta-l@uam.es> > *Subject:* [SIESTA-L] Constraints in positive or negative z-direction > > > Hi there, > > I know that SIESTA allows some restrictions on atomic displacements. > However, I didn’t find in the manual a way to allow atomic displacement > only in the negative or positive z-direction during the relaxation process > for specific atoms. For example: During the relaxation process of a > graphene bilayer, I would like to freeze the atoms on one sheet (I know how > to do that) and allow specific atoms on the other sheet to move only in the > negative z-direction. > > Is it possible to enforce this kind of restriction? My idea is that it is > possible to do this by modifying the construct.f routine, am I right in > thinking this way? There are other ways to do that? > > Thank you so much for your help. > > -- > > *Ramon Sampaio Ferreira* > Doutorando em Física > Programa de Pós-Graduação em Física - Universidade Federal do Ceará > Campus do Pici - Bloco 928 > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence > (https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!TJ4BQ9j0GGUqe7PUKu5fA9-bjaslnczB01iSHZu0ZZ2NU-wdu2oEm-ALq0XLt4YQ4g9diYHMJcuA-diKjg$ > ) > -- *Ramon Sampaio Ferreira* Doutorando em Física Programa de Pós-Graduação em Física - Universidade Federal do Ceará Campus do Pici - Bloco 928
-- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
