How to initial decide the molecule position in a two probe device

[J.g_johnson]

    The left and right electrode had been completed and the distance between the two electrode was set. Then the molecule was put in the center of the device by using "center" option in the "Coordinate Tools".
    But I was not sure whether the center was the perfect position for the molecule. And It would cost much time by using the "Optimize Geometry" in "Script Generator" to optimize the position of the molecule.
   Another problem was the it would change the molecule structure during optimization.
   I didn`t know how to deal with that.

[zh]

The tool (i.e., coordinate tools) is helpful to design the initial structure of the configuration of a device for your simulation, it cannot automatically give a perfect (i.e., well optimized) structure.  After you create the initial structure by the tools, you have to perform the geometry optimization through a proper strategic procedure according to your own purpose.  For example, one may convert device configuration to a bulk configuration and then perform the structure optimization following the usual way for a bulk system (i.e., fix all lattice vectors and optimize the atomic positions, or  optimize the lattice vector along the transport direction and the atomic positions at the same time).  

[J.g_johnson]

As you said, I converted the Au electrode-molecule-Au electrode device into a bulk configuration and perform a structure optimization in "Script Generator". So I wanted to optimize the molecule position in Z direction. In the "OptimizeGeometry" tool parameters, I was not sure whether to constrain the Au atom position.

# Set up lattice
vector_a = [5.7671629, 0.0, 0.0]*Angstrom
vector_b = [0.0, 5.7671629, 0.0]*Angstrom
vector_c = [0.0, 0.0, 24.27299996]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
            Gold, Gold, Gold, Gold, Gold, Gold, Chlorine, Sodium, Chlorine,
            Sodium, Chlorine, Sodium, Sodium, Chlorine, Gold, Gold, Gold,
            Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold, Gold,
            Gold, Gold, Gold]

constraints = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]
bulk_configuration = OptimizeGeometry(
        bulk_configuration,
        max_forces=0.05*eV/Ang,
        max_steps=200,
        max_step_length=0.5*Ang,
        constraints=constraints,
        trajectory_filename=None,
        disable_stress=True,
        optimizer_method=QuasiNewton(),
        )

[zh]

Yes,  the gold atoms will be constrained during the geometry optimization according to the atom indexes defined in your "constraints"

[J.g_johnson]

But this would change the initial structure of the molecule which is already a perfect construction. Here I just want to find the best position of the molecule between the Au electrodes (i.e. the position in Z direction) without seriously change molecule structure.

 

[J.g_johnson]

The parameters of Calculator and OptimizeGeometry were show in figure.

[Nordland]

It also comes down on what you want to model.

If you put a molecule near surface, it will affect both the molecule and the surface in a experiment and in a simulation. This will likely be a small effect, but it will be there.

Then becomes if you want to into account this effect or not. If you want to take this effect into account, you will have to follow the procedure suggested by zh.

If not, you will have to a scan calculating the total energy as a function of the seperation between the surface and the molecule, and find the minimum of this curve.

[J.g_johnson]

I  want to model the "Transmission Spectrum" and "Device Density of states" of the device under bias voltage. If I just put the molecule into the center of the electrode like above figure without considering the effect between molecule and the surface of Au electrode, or without optimization the molecule position in Z direction, the results will be still accurate?

[zh]

Such calculations are OK. But they just produce  some data, which are not  solid enough to tell a story.  That is to say, one cannot judge whether the structure constructed by the simply putting molecule just between two electrodes without any further optimization is the optimal one.

[Jenny]

The tool (i.e., coordinate tools) is helpful to design the initial structure of the configuration of a device for your simulation, it cannot automatically give a perfect (i.e., well optimized) structure.  After you create the initial structure by the tools, you have to perform the geometry optimization through a proper strategic procedure according to your own purpose.  For example, one may convert device configuration to a bulk configuration and then perform the structure optimization following the usual way for a bulk system (i.e., fix all lattice vectors and optimize the atomic positions, or  optimize the lattice vector along the transport direction and the atomic positions at the same time).  

Hi, zh.

I was wondering that when we tried to optimize the bulk system, how could we choose the optimization condition? Usually, bulk system is larger than unit, so it may take a long time to get the optimization geometry. So can we set the max force and max stress larger than unit cell? for example, my optimization condition for the unit cell is max force=0.05eV/A and max stress=0.05eV/A. When I use the unit cell to form the central region of my device and Cu as electrode to do bulk system relaxation, I choose max force=1eV/A and max stress=1eV/A. And if it is acceptable, how can I decide which kind of condition is good enough for a further analysis?

Looking forward to your reply. Thank you very much.

Jenny