README

### makeTRiP package usage ###

makeTRiP generates spectrum and depth-dose files (SPC and DDD)
for TRiP98 for a specified energy grid and ion type.

Usage and comments:

1) specify energy interval, step size and primary ion in  
   config.sh.
   If using a specific SIS file, adjust the energy interval accordingly 
2) specify primary particle and other options in beam.dat
   Recommended are between 400.000 and 3.000.000 primaries, with 400.000 being the quick-but-good option yielding acceptable results
   If ripple filter or range shifter is needed, remember to choose the USEBMOD and BMODMC cards and the correct external beam modifier dat file 
3) Change geo.dat if necessary, check the ripple filter.
   If using a ripple filter, remember to set ZONE 3 "RIF" to material 3 (being Lucite in mat.dat)
   If using a specific SIS file containing the lateral beam widening of the beam from the vacuum window to the target surface:
          check if the environment around the target (apart from ripple filters and/or range shifters if required) is set to vacuum (1000)
          ommit BEAMDIV card in beam.dat, omitting the beam divergency
   If no SIS file with lateral beam widening data will be used:
          select or write new geo.dat file with the beam application system and air included 
          use the BEAMDIV card, choosing a realistic number for the beam divergency and the optical beam focusing     
4) $ ./makeTRiP.sh <dir_name>
   where <dir_name> will be created by makeTRiP if it does not exist.

makeTRiP generates all SPC and unformatted DDD files in a new 
subdirectory named dir_name.

When the jobs have completed, use the postprocessing script
The postprocessing required python (by the use of the python script ddd.py and the corresponding files)

$ ./postprocess.sh <dir_name>


### Designers note and changelog ###

## Toke Printz Ringbaek, 11.03.2015

For ddd.py version 0.2, compiled March 2015, the following changes have been made compared to the 2012 Teiwes 0.1 version:
1) Minor debugging, adding helpful comments 
2) Bash- and python-scripts have been rewritten to handle the new SHIELD-HIT format
3) Instead of fitting with a double Gaussian the dose as a function of radius D(r), the fit function and dataset are now scaled with radius; D(r)*r
4) For depth values regarded as being in the tail of the dose distribution, the FWHM1, factor and FWHM2 are made constant (since the fitting for these values returns nonsense)
5) For the calculation of the factor A2/(A1+A2), the NORMALIZED amplitudes must be used. This has been added.  

Comments and issues for future corrections: 
Fitting D(r)*r instead of D(r) removes observed "fluctuations" in the FWHM2 values
All fitted FWHM values are still a few factors too high compared to the DDD datasets in TRiP, which has been used for benchmarking
While FWHM(depth) are found to increase very linearly, which is inconsistent with expectations and the DDD sets in TRiP which has been used for benchmarking.
It remains to be discovered whether or not the above issues are relatet to particle transport in SHIELD-HIT, errors in ddd.py or a combination.
The aim is to solve the above issues in the near future.