TDPot

This a a fortran implimentation of the Time-Dependent Potential method that models ions transmission through solids, developed by Richard A. Wilhelm and Pedro L. Grande. Please see the following references:

Unralleing energy loss processes of low energy heavy ions in 2D materials

Requirements:

• Fortran compiler (fortran 90 and above), openmpi (and the required wrapper to compile)

MacOs (intel):

To get things working on an intel Mac, you will need to have xcode command line tools, gfortran and openmpi.

Xcode: sudo xcode-select --install

For openmpi and the gfortran compilers, it is probably easiest to install them via homebrew. From there: brew install openmpi gcc

Some users might have a bug where the compiler cannot find the linker. The error output will look something like this:

ld: library 'System' not found

If that is the case, please find the system linker, it should be in a directory something like this /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib, but it might be in a slightly different path depending on your system. Once you find it, add this line somewhere near the top of the Makefile

LIB = L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib

or whatever the path was in your case.

Setup

Clone this repository. Modify the Makefile so that the your fortran (mpifort) compilers are used. If all is in order, go ahead and run

make clean && make

to compile the source code. Should be quick and easy :)

Usage

Switch to your work folder. You need an input file named

• indat.dat

to run TDPot. Here is an example of what it have to look like, including all needed parameters:

SLG_Xe20_50keV            ! jobname
hollow-krc                ! potential
Xe                        ! ion
54 129 50 20              ! Z, mass, KE, qin
1                         ! ff
0.0 0.0 1 2               ! fwhm_qout, sigma_therm, frozen_par, alpha_max
-30 30 0.01, 0.0001 1     ! ion_zi, ion_zf, dx_step, acc, nions
0.0 0.0                   ! chi_min, chi_max
0.0105 2.8 0.8 15.0       ! gam_a, gam_b, gam_c, gam_cut
0 0                       ! logmode, print_xyz_files
SLG_tdpot.xyz             ! target filename

You also need a target file in your work folder to which the input file is referencing in its last line. In this example, the target file is named

• SLG_tdpot.xyz

and is an 'xyz' file of sorts. looks like this:

60
12.30000 12.78000 3.35000
0.61488  2.48500  1.67500  6  12
0.61488  3.90500  1.67500  6  12
...

The first line is the number of particles. The second line is the size of the simulation cell (x, y and z). All other lines are representing properties of the particles. The first three columns are the x, y and z position. The fourth column is the particle type and the fifth column is the mass.

!NOTE! This version of TDPot assumes the target to be periodic in x and y! Please be careful when providing target files. If you want to model ions incident on a non-periodic sample, some tricks will have to be used. Please email the developers if unsure.

To run the code, we need to use mpirun:

mpirun -n 1 /Path/to/exe_file/.../TDPot

in your work folder, using the correct path to the TDPot executable that we just built. The output file(s) will be written in that folder.

To use several cores in parallel, in this case four, use:

mpirun -n 4 /Path/to/exe_file/.../TDPot

Citation

If you use this software (or method) please cite the following works:

DOI: 10.1038/s42005-019-0188-7

Happy flying :)

Filip V. and Lukas E.

Institute of Applied Physics | TU Wien