Dear all,
I have now learning about the geometric opimzation for a two probe systems. I learn from this tutorial
http://docs.quantumwise.com/tutorials/device_relaxation.html .
As the tutorial metioned there are two ways to optimize the gometries for two probe systems:
BRR method and
1D minimization.
Let me simplify the process of the optimization, we suppose that the geometry of the electrodes are in their equilibrium condition so that we do not need to optimize the geometries for the electrode. All we should do is to optimize the geometry stuctures of the electrode surfaces and the adsorbed molecule between in the two electrodes.
As I understand, in
BRR method, we use a two-slab system to do the optimization, and usually electrode extensions and the screening layers are included to account the interaction between the screening layers and the molecule, the electrode extensions here give a bulk electrode environment for the screening layers. Also, the C lattice vector should be large enough to aviod the interaction of the left electrode with the image of the right electrode when using periodic boundary condition. In this term, the whole system can be optimzed in the C direction as well as the A, B directions. During the optimization, we can make a fully opimizaiton for the molecule and the surface screening layers while make the electrode extensions frozen (one electrode fixed and the other a rigid box that move ridgid in the optimization, which can partially optimize the distance between the two electrode extensions). In this way, we can partially optimze the geometry structure of the core region of the two probe system. However, the final "optimized" geometry would not necessarily the energy lowest configure, but usually colse to that. The optimzation stop when each freedom in the optimzation meets the force criteria, not using the total energy of the target. The method can be effective, and this is what I have always used in the SIESTA code.
Meanwhile, the tutorial metioned another opimization method, the so called
1D minimization.
A somewhat more brute-force approach is to explicitly minimize the device total energy wrt. internal coordinates and the central region length, i.e., do the full 2-probe calculations and vary the central region length. This is a 1D minimization problem with relaxation of the atomic positions at each step, so we shall refer to this method as 1DMIN.
As I understand, the
1DMIN method will do a optimization of the two probe system using an energy minization with respect to the internal coordinates and the central region length. In this case, the distance between the two electrode (or lattice vector C) are sampled for some values around the one given as the inital. For each electrode distance( or lattice vector C), the centrol region will be fully opimized with the electrode extensions fixed. One can get the energy lowest configure (also the intermediate optimized configuration) for this electrode distance, and record its energy with respect to this electrode distance. Do this opimization for all the sampled electrode distance, we can plot the energy of the system wit respect to the electrode distance. Then we can extrapolate the optimal electrode distance (lattice vector C). At last, we do the gometry optimzation under the optimal electrode distance, and get the optimzed geometry for the two probe system. This can be called a globle optimization.
Is my understanding right, please correct it if there is any misundertanding?
Yet, I have qestions about the
1DMIN method. What is the total energy for? Is it for the total two-probe system: Left electrode+Central region+Righ electrode? During this optimzation, both the electrodes and electrode extensions will be moved rigid along with the optimzaiton of the C lattice vector?
Can the atoms in the screening layers and molecule suffer constrains set by the user? In this case, it is not a full optimization, the user can set some constrains to the core region of the system, eg. user can fix the anchor atoms of the molecule to the hollow sites of the surface and can set the outmost of the screening layers to move rigid together with the electrode extensions, etc?
With best regards,
Guangping
