ISInCa - Ion Surface Interaction Calculator

ISInCA - is the cross-platform tool, intended for the post-procession of outputs of particle-surface interaction codes, as SCATTER, TRIM, SDTrimSP. It allows to generate, visualise and export various differential ind integral characteristics of particles scattering, sputtering and implantation for the specific ranges of energies and angles.

Basic outputs

The codes listed above are intended for the simulation of particle beams interaction with solids. In such codes you can set some beam parameters (like mass/angle/energy distributions, doze) and multiple target parameters. Such codes usually generate single or several files, containing tables with backscattered (B), sputtered (S), transmitted (T and R), implanted (I) and displaced (D) particles with data on their position, motion direction, sort, energy, path length etc. ISInCa allows to transform this huge (up to hundreds of GB) data files to easy for interpretation data. it can generate:

Graphs:

• Energy distributions dN/dE(E) for any solid angle and any energy step and resolution. (for backscattered and transmitted primary particles and sputtered particles of a target)
• Angle distributions dN/dβ(β) (backscattered and transmitted primary particles and sputtered particles of target)
• Depth distributions for primary implanted and target displaced particles under development

Maps:

• Polar Map N(β, φ) for backscattered and transmitted primary particles and sputtered particles of target
• EneAng Maps N(E, β) for backscattered and transmitted primary particles and sputtered particles of target
• Cartesian Maps N(Z, Y), N(Z, X)

Integral coefficients:

• Scattered coefficient R (number of scattered particles divided by number of incident particles)
• Sputtered coefficient Y (number of sputtered particles divided by number of incident particles)
• Implanted coefficient I (number of implanted particles divided by number of incident particles)
• Transmitted coefficient T (number of transmitted particles divided by number of incident particles)

All distributions can be both visualised with the embedded JFreeChart plotter and saved locally as the conventional "*.txt" text file. All data is available for different combinations of particles (scattered - B, sputtered - S, implanted - I , transmitted particles of the initial beam - T, transmitted particles of the target - R, and displaced - D). You should take into account, that the number of available types of particles depends on the specific code. As example, SDTrimSP supports all types, Scatter only B,S and I. An opportunity for combining results of different calculations is also presented.

You can read more on the features in the corresponding docs:

• More on the available distributions
• On the energy analyser distortions
• Simultaneous post-processing of multiple files
• Combining multiple simulation's results

Installation

ISInCa is fully JAVA program, so it can be launched in any OS on every processor architecture with a single executable.
Executable file for the latest version is located in /out directory:

• For "easy mode" in Windows OS you can download an executable file ISInCa.exe (works only in GUI mode with limited capabilities)
• For all OS you can use isinca.jar, which provides full functionality of ISInCa
• For console mode you might also need a template for config file: isinca.xml, which allows to postprocess multiple simulations simultaneously.

In any case you need to have a Java Virtual Machine (version 11 or newer) installed on your computer to run JAVA programs. To check whether the JVM was already installed, open the terminal (in Windows OS press "Win"+"R", then type "cmd" in an appeared window, then press enter) and type java -version, then press "enter". If the output looks like

Java is not recognized as an internal or external command

or the version is less than 11, you need to download/upgrade JVM. For Windows OS you can download it for free from the Oracle (the company, that supports Java). Installation of the JDK (which includes JVM + libraries) seems not to be tricky (see the tutorial). In Linux, you can get it just by typing sudo apt install default-jdk in the shell. ISInCa executable does not need special installation, so you can run ISInCa right after downloading and installing JVM.

Angle and particles definitions

It is worth firstly clarifying names of angles and particles types, that would be further used in this manual. The angle of incidence α is measured from the normal to the surface and is not directly used in ISInCa calculations. When calculating, the azimuthal angle of incidence is considered to be 180 degrees. Polar β and azimuthal φ registration angles are used in the calculation. The β angle is also measured from the surface normal. At the same time, it can be set in the program from 0 to 90 degrees.The φ angle is measured from Z axis (see the picture below). It can be set in the program from 0 to 360 degrees. The angle registration width dβ can be up to 90 degrees, while dφ - up to 360 degrees. Notice that it is width but not a deviation.

When calculating the distributions for particles transmitted through thin targets, instead of specifying a larger than 90 β angle, it is necessary to use flags responsible for the types of particles. There are 6 flags in total:

• B - particles of the beam, backscattered from the target
• S - particles of the target sputtered in the upward from the target
• I - implanted particles of the initial beam
• D - displaced particles of the target, that have not left the target
• T - transmitted through the target particles of the beam
• R - particles of the target, that were sputtered(recoiled) downward the target

The picture below may help to understand the difference between B and T, and S and R.

Launch

For your convenience CONSOLE and GUI modes were made in ISInCA. GUI is based on the JavaFX package, which is included in the executable (as from the 11-th version of Java it was removed from the JDK)

GUI

GUI is the default mode so there is no need in any launch arguments, so just run it... Main window of the GUI mode looks like:

The interface seems to be user-friendly and contains tooltips with recommendations for the most controlling elements.

Calculation procedure

1. Press "Choose directory button". Select the directory with the files, generated by your Monte-Carlo program. In case of Scatter it is most likely /out folder inside SCATTER folder. It must contain SC*****.dat file. In case ofSDTrimSP the folder must contain tri.inp and partic_***.dat files.
2. ISInCa will identify the code type automatically in code type window in a bottom left section as well as the initial energy and the number of particles.
3. Choose data, that you wish to get in bottom center section. As can be seen, you can choose several types of particles (B,S,I,T,D) for several types of charts (energy spectrum, polar chart, polar map, map with E and β axes and 2 cartesian maps).
4. Note that not all types of particles are available for some codes and charts. Also you can choose whether to visualise data after calculation. Anyway, the calculated charts will be saved in /ISInCa directory inside the directory you've chosen previously. In case of SCATTER you can also convert binary SC*****.dat file to user-frienldy *.txt file with UTF-8 encoding readable by any text editor.
5. You can specify parameters of charts in corresponding tabs. AS example, for dN/dE(E) you can choose the upper energy limit, amount of dots on chart (deltaE, eV), and the solid registration angle.
6. Finally, press start calculation button and just wait the charts to appear.

In case of troubles check Help tab. You also can find there the clarification on the designation of angles. The main feature of the GUI mode os the possibility to visualize postprocessed data. For this ISInCa was equipped with JFreeChart library. It allows to create, modify and safe plots. Look at the examples for energy and polar distributions:

Structure of directories

After initiation of the ISInCa calculation it will analyse all the data in the simulation directory. After the post-pprocessing the calculated data will be saved in

./ISInCa/"SIM_TYPE"_"CALC_ID"/

where "SIM_TYPE" - is the name of the simulation code, "CALC_ID" - unique calc ID, given for each ISInCa launch for the specific folder. The "SIM_TYPE"_"CALC_ID" also would be the start for all internal file names.

So if you launched ISInCa for the same directory several times, the outputs won't be mixed up, as they would be located in directories with different CALC_ID and different prefixes of files. Inside the calc directory you can find "SIM_TYPE"_"CALC_ID"_summary.txt file with integral coefficients and several directories for different distributions:

./ISInCa/"SIM_TYPE"_"CALC_ID"/ENERGY/ for energy spectra

./ISInCa/"SIM_TYPE"_"CALC_ID"/POLAR/ for polar distributions

./ISInCa/"SIM_TYPE"_"CALC_ID"/ANGLEMAP/ for Polar Map N(β, φ)

./ISInCa/"SIM_TYPE"_"CALC_ID"/ENEANGMAP/ for EneAng Maps N(E, β)

Every distribution's directory contain distributions for different sorts of particles (B, S, T, I, D), depending on what was chosen in ISInCa during the configuration. You can also find there the sum of all chosen sorts ("all"). For some a .png figure are also available.

The file names start with the calculation ID in the form "SIM_TYPE"_"CALC_ID" and contain some parameters (as sort of particles, registration angle, step etc.). All calculated data files are in .txt format. Each file contain a header with detailed information.

Fun fact for attentive readers: The name of this tool is actually a reference to the artificial intelligence mentioned in russian literature project "Ethnogenesis".