README FOR PHD THESIS MEMORY STICKS:
The memory stick associated with each copy of the PhD Thesis contains:
1) SoftSusy-4.1.4 - The version of SoftSusy used for many of the figures in the first half of the thesis and which is described therein. This is the whole SoftSusy package, of which the decay calculator which is the topic of my research is a significant part.
2) reSolve-1.0 - The version of reSolve used for the validation and results detailed in the second half of the thesis and which is described therein. This is the first main public version of reSolve.

USAGE INSTRUCTIONS:
SoftSusy-4.1.4:
- Extract to your computer and run ./configure in the softsusy-4.1.4 directory.
- Run ``make'' in the softsusy-4.1.4 directory so that the executables are produced.
- The program is then ready to run with several example input and output files contained. Further input and output files used in the validation of the decay calculator are detailed in our paper and provided with it, this is available at https://arxiv.org/abs/1703.09717 and in Computer Physics Communications.
- The ./softpoint.x is the executable of most relevance. A sample run of the spectrum generator and decay calculator together can be done using the command line input:
		./softpoint.x leshouches < inOutFiles/lesHouchesInput
   (alternatively this can also be produced by running ./softpoint.x sugra --m0=125 --m12=500 --A0=0 --sgnmu=1 --tanBeta=10 --decays --higgsUncertainties --outputPartialWidths)
- This will produce the mass spectrum for this point (as given in Figure 4.2 on pg 85) as well as the decay tables detailing the branching ratios for every MSSM Higgs and supersymmetric particle. For example the gluino decays in Figure 4.3 on pg 85 and the stop1 decays in Table 4.2 on pg 87 of the thesis are reproduced (with slightly altered branching ratios as softsusy-4.1.4 is a later version of softsusy than was run for this), if you wish to see the partial widths as well as the branching ratios, as in Table 4.2 then uncomment the line in the BLOCK SOFTSUSY which sets item 26 to 1 - this turns on outputting partial widths.
- Meanwhile the input file given in Table 4.4 on pg 89 is the pmssm1.in file and so the branching ratios in Table 4.5 and Figure 4.6 can be produced by running:
		./softpoint.x leshouches < inOutFiles/pmssm1.in
- NMSSM examples can also be run including nmssmSLHAnoZ3Input which gives the spectrum in Figure 4.12 on pg 99, it can be run using:
		./softpoint.x leshouches < inOutFiles/nmssmSLHAnoZ3Input
- This will produce the decay tables as well as the mass spectrum, the decay table for the H is that used for Table 4.8 and Figure 4.13a on pg 100, again with minor changes as these were produced with a slightly earlier version of SoftSusy. In its current form, only Branching ratios greater than 10^-6 will be output, to see all the branching ratios seen in this Table and Figure in the thesis instead enter the nmssmSLHAnoZ3Input file in inOutFiles/ and change item 24 in the BLOCK SOFTSUSY to 1e-7 to set the minimum output branching ratio to 10^-7 and rerun.

reSolve-1.0:
- Extract reSolve-1.0 to your computer and run make in reSolve-1.0/code/src to produce the ./reSolve.out executable, the code/lib folder will contain the CUBA library for use of the Cuba integrator (the form given here will work on linux but possibly not Mac - to run with Cuba on Mac you would have to extract Cuba for Mac to your own pc and alter the resolve makefile to direct it to the cuba library on your machine), however Cuba is not necessary for the program use as it comes with a built in kvegas integrator - to use only the kvegas integrator change the integrator_flag in any input file run to 1 before use.
- The input files contained in the program are given in Table 7.1 on pg 162.
- Our paper is available at https://arxiv.org/abs/1711.02083.
- To run Diphoton_Born_LHC.dat enter the directory reSolve-1.0 and run:
		./reSolve.out input/Diphoton_Born_LHC.dat
- This will generate the total cross-section from 100000 Monte Carlo points and obtain 5.74+-0.02pb, which is correct. It will also output the invariant mass and rapidity spectra (and the event files for each of the 4 iterations) automatically in the folder Diphoton_Born_LHC/ as histo_0_qq.dat and histo_1_eta.dat, there is no transverse momentum spectrum as this is leading order.
- The same setup but parallelised can be run using the bash scripts multi_machine_parallel_local and the input file Diphoton_Born_LHC_parallel.dat, with the bash script altered to give the names of the ssh accessible machines to be used. Currently it is setup for use on the DAMTP computer network with machines ``encumber'' and ``endear'', running it with these two machines (or your own two) with max_iter = 5 and max_cores = 4 set in the bash script, run multi_machine_parallel_local input/Diphoton_Born_parallel_LHC.dat and you will obtain in Diphoton_Born_parallel_LHC/reSolve_main_out_END_iter.dat the total cross-section of 5.72+-0.02pb, again correct. Again the events and the histogram invariant mass and rapidity data are available.
- The Diphoton_NNLO_test_1.dat input file can also be run to reproduce the plots in Figure 7.5 on page 175, however the event data is already given on the memory sticks in the Diphoton_NNLO_test1 folder as the run will take around 400 minutes at its current length, histo_0_qT.dat contains the transverse momentum spectrum data plotted in Figure 7.5b and histo_1_qq.dat contains the invariant mass spectrum data used in Figure 7.5a, there is also histogram data given for the rapidity spectrum.
- The Diphoton_NNLO_test_2.dat input file can be used, its events aren't already included on the memory stick. To run it run ./reSolve.out input/Diphoton_NNLO_test_2.dat, this will run 100,000 events (less than the 500,000 used for the plots in Figure 7.6), this will take around 100 minutes (depending on the computer speed) but if you run it you will get the total cross-section as 2.53+-0.02 which is correct and the invariant mass and transverse momentum spectra given in Figure 7.6 on pg 175.
- You can also try parallelisation for the Diphoton_NNLO_test_1_parallel_multi.dat input file included, again using the bash script multi_machine_parallel_local and run ./reSolve.out input/Diphoton_NNLO_test_1_parallel_multi.dat to obtain: 7.35+-0.17 which is approximately correct, also the invariant mass and transverse momentum differential cross-section data can be compared with Figure 7.5.
- As for the Drell-Yan processes, again there are various input files included. For example you can run ./reSolve.out input/Wpm_Born_Tevatron.dat to obtain the total cross-section 1157.0+-3.4 which is correct, similarly the ./reSolve.out input/Z_OnShell_Born_LHC.dat to obtain 1758.9+-1.3 - again correct or ./reSolve.out input/yZ_Born_Tevatron.dat to obtain 103.34+-0.25 - again correct. Various differential distribution histogram data files are also produced.
- The NLO(+NLL) and NNLO(+NNLL) input files for these 3 setups are also available, for example one may run ./reSolve.out input/Wpm_NNLO_Tevatron.dat (which will take around 400 minutes) to obtain the total cross-section of 1396.7+-12.1 (which is correct, there's just a again slightly different setup to that reported in Table 7.4 and shorter run) as well as the transverse momentum and rapidity spectra data given in Figure 7.12, 7.16a and b, whilst the transverse mass histogram data of Figure 7.15 can be generated also. 
- Meanwhile running ./reSolve.out input/Z_OnShell_NLO_LHC.dat as an example gives  2007.1 +-5.5, which is correct.
- Again parallelisation can be used, run multi_machine_parallel_local input/yZ_NNLO_Tevatron_parallel_multi.dat to obtain 124.9+-2.3 (some differences in setup relative to Table 7.4 so correct), the rapidity spectrum is also generated to match Figure 7.10b and the transverse momentum spectrum will match Figure 7.10a.
- Note - if you try to run in hist_only mode to generate new histograms from previously run events then the ``save_events'' flag is needed detailing the form of output file (1 for ``easy'' form or 2 for ``lhe'' form), if it doesn't run you are probably missing ``save_events: 2 '' in the histogram only input file.
- Note that all the histogram data files generated for our paper will be given with it when it is published in Computer Physics Communications (currently it is under review).