simulator Calculation window, user can add it directly writing on .input file the keyword electric_field.
motion. For example, in water molecule case it is convenient to fix oxygen atom both to simulate bond with a substrate and to limit the rotation due to the influence of electric field.
To conclude, mixing all these simulation parameters it is possible to analysed molecule in many significant cases and combining it in right way, switching of the molecule can be observed demonstrating the QCA principle.
4.4 Commutation time
One of the most important result in this thesis is the demonstration that candidate QCA molecules are able to perform a switching, which is a fundamental in MQCA applications. This kind of analysis is made possible exploiting dynamic simulations.
As already explain in paragraph 2.3, the switching process consists of inversion of dots charges (generally DOT1 and DOT2 ) as response of the inversion of the electric field polarity applied along DOT-axis, the switching (SW) field. Due to the changing of the sign of SW field, the electron cloud tends to follow this variation re-distributing it in the molecule, producing a variation in the local charges. Naturally, this process of the inversion does not occur in instantaneously way, but it requires a certain time to rearrangement of the charge inside the molecule. According to Wang work on Double-Cage Fluorinated Fullerenes [4] and Tokunaga one [3], in order to characterize switching process, for a given molecule, a sort of time to switch (tSW) is defined and its evaluation is possible only through MD simulations.
From operative point of view, to perform a MD simulation to evaluate switching time, it is enough to play with keyword electric_field inverting its value related to X-component. To explain better, the operating steps required to obtain a time-evolution of charge performing a switch are:
1. Start simulation up to desired time t0, where user want to perform switching;
2. Extract values from t0 .outmol file (i.e. final velocities, temperature and SW field) and set them as initial value for the next simulation (starting configu-ration corresponds to t0), where only the sign of electric field along X-axis is changed (for right switching, field must be inverted only);
3. Perform MD simulation starting from t0 to time t > tSW, where t0 conditions are well defined;
A schematic representation is shown in figure 4.6.
Figure 4.6: Schematic procedure to perform a MD simulation with switching Of course, this procedure bases mainly on editing of .input files, especially at time t0 where MD simulation must be interrupt to invert electric field value. As already explained, the continuity link is guaranteed by geometric information and velocities. This procedure can be performed easily following the Cascade approach and using the developed software, instead the MDS interface.
4.5 Launch dynamic simulation
Once all the aspects related to the MD simulation setup, such as input geometry and calculation parameters, are well discussed, a detailed procedure step by step to launch a dynamic simulation (using MDS interface), in case of water molecule, is reported in this section.
First of all, geometry of the molecule is defined following instructions explained in paragraph 4.2.1 either through MDS interface or directly writing on .car file.
Once geometry file are saved, a recommended method for the .input file must be done in order to save all possible files. This procedure consists of:
Figure 4.7: Procedure to save input files in a subdirectory
1. Open .xsd file that allow to visualize the 3D structure;
2. Open Calculation window, reported in figure 3.2;
3. Set all calculation parameters in each tab and desired properties to calculate, as explained in section 3.3.3;
4. Click on Files... button to open simulator Job Files window;
5. Press Save Files button to generate a new subfolder where all geometric files and automatically generated .input file are stored;
At the end, a set of input files are available in a subfolder (called Water DYN in figure 4.7 or 4.8) and they will be used to launch the simulation. Notice that all these files can be modified as user want and it is the advantage of this procedure. In fact, the .input file can be edited for any reason, for example to switch-on or modify electric field adding the keyword electric_field with its value or to modify time step (MD_Time_Step ) or number of frames (MD_Simann_panel).
At this point, all input files, modified in according to simulation to be performed, are defined in the subfolder and in order to launch a simulation based on them, the following steps are required:
1. Open the modified .input file in subfolder;
2. Open Job Files window;
3. Press Run Files to launch simulation based on files in the subdirectory;
Notice that result files will be stored in an automatically created subfolder contained in the folder where simulation has been launched.
Following this method all possible MD simulations can be performed playing with the initial conditions available. For example, using SameInit approach, saving at the beginning all input files, it is possible to perform simulation with different dynamic range, changing only the number of frames in the .input file, starting always from same geometry. To better explain, in figure 4.8 is reported an example where initial geometry and .input file are stored in Water DYN subdirectory and then several MD simulations are launched from the same starting condition, changing only the number of frames in the .input file in Water DYN directory. As reported in the figure, each simulation creates own subfolder, where output data will be stored (i.e.
VelRND SW0.002 Xfs).
Figure 4.8: Automatically generated folder tree in MDS package
Developed Software
A significant part of this thesis work has been the development of ad-hoc software to perform in the optimum way all dynamic simulations required to characterized MQCA molecule. The idea was to create a code able to handle in automatic way all simulated data, i.e. input and output files, and to optimize simulation time.
The software development was made possible thanks to standalone mode allowed in the simulator tool. It consists in overcoming MDS interface to launch simulation using only a set of input files (explained in paragraph 3.3.4) and an executable file provided by the simualtor. This file is a .bat file (in Windows environment) and generally it is stored in bin directory of installation simulator path. Of course, this command is characterized by own syntax and it is well documented in MDS manual.
Moreover, it is chosen to use Python as programming language to develop soft-ware because it allows to program using object-oriented approach and it is able to run both on Windows or on Linux environments. Another advantage to use Python is the possibility to realize graphical user interfaces (GUIs) in simple way exploiting several libraries (e.g. Tkinter ).
At the end, a very elaborate code has been developed able to handle autonomously MD simulations and it is based on a GUI, through which it is possible to set all significant initial parameters of dynamic simulation. Furthermore exploiting GUI, user can visualize output results, i.e. dots charge, energies, dipole moment, dynamic of the molecule and so on.
In this chapter, the developed software is examined: the first section is related to GUI description, intermediate paragraphs explains all logic and architecture of the code and in the last section is reported a step by step procedure to perform a simulation and to visualize results.