Use of Gaussian Type Functions for Describing Fast Ion-Matter Irradiation with Time-Dependent Density Functional Theory

This archive contains the data and the RStudio scripts used for the Figure.  
It contains two folders 
-1)    water_slabs: for Figures 2, 3, 4, 5, 6, 7, S1, S2, S3, S4, S5 
     
       * The script transition.R (Figures 2 and S1) plots the electronic transition analyses. It used the data stored in trans_analy 
folder 
       * The script SPE_1trj.R (Figure 3) 

       * The script SPE_water_slab.R (Figures 4, 5, 6, 7 S2, S3, S4, S5) plots the electronic stopping power curves from the data sto
red in the bs**** folders. Below is the correspondence between the basis set names used in the folders and file names and the basis se
the nomeclature used  in the article   
  
    "bs1"     -->   "F2-C2" 
    "bs2"     -->   "F2-C3" 
    "bs3"     -->   "F3-C4" 
    "bs4"     -->   "F4-C5" 
    "bs5"     -->   "F4-C6" 
    "bs6"     -->   "F2-C6" 
    "bs1_c1"  -->   "F2-C2(3.2.5/3.2.5)" 
    "bs2_c1"  -->   "F2-C3(3.2.5/3.2.5)" 
    "bs1_c2"  -->   "F2-C2(3.3.5/3.2.5)" 
    "bs2_c2"  -->   "F2-C3(3.3.5/3.2.5)" 
    "bs1_c3"  -->   "F2-C2(8.2.5/8.2.5)" 
    "bs1_c4"  -->   "F2-C2(12.2.5/12.2.5)" 
    "bs1_c5"  -->   "F2-C2(3.4.5/3.2.5)" 
    "bs1_c6"  -->   "F2-C2(3.3.5/4.3.3)" 
    "bs7_c2"  -->   "Fmin-Cmin(3.3.5/3.2.5)" 
    "bs8_c2"  -->   "F2-Cryd2(3.3.5/3.2.5)" 
    "bs1_c1b" -->   "F2-C2(3.2.5/3.2.5)b" 
    "bs1_c1c" -->   "F2-C2(3.2.5/3.2.5)c" 
    "bs1_c1d" -->   "F2-C2(3.2.5/3.2.5)d" 
    "bs3r_c6" -->   "F2-C4(3.3.5/4.3.3)" 
    "abs1_c6" -->   "F2-Caug2(3.3.5/4.3.3)" 

     The file names follow the synthax wslab_AAAA_KBBBB_ICCCC.{out/rtp}DDDD where AAAA refers to the basis set, BBBB to the kinetic e
nergy of the projectile, CCCC to the slab number and DDDD to the deMon2k run number respectively.  
         the  wslab_AAAA_KBBBB_ICCCC.outDDDD files are the main deMon2k output (out) files 
         the  wslab_AAAA_KBBBB_ICCCC.rtpDDDD files are the deMon2k real-time-propagation (rtp) files 
         See the deMon2k manual for details.  

     To calculate the stopping power we use the values of the energy at each RT-TD-ADFT propagation step given in the rtp files  
      

 -2)    water_cyl: ffor plotting Figures 9 and 10 and S6 

       *  The script SPE_water_cyl.R calculates the stopping power curves for basis sets