Everest collimator natively in xobjects C API, pencil initial conditions, and loss map functionality

[freddieknets]

This pull request summarises one year of work on Everest, mainly done by @ddemetriadou and @freddieknets :

• We have a working EverestCollimator and EverestCrystal in native xobjects-style C API
• We have a working PyEverestCollimator and PyEverestCrystal in python for benchmarking
• We have a working K2Collimator and K2Crystal in FORTRAN as a reference
• Possibility to generate an matched pencil distribution on one or both jaws of a collimator
• Post-processing to identify aperture losses (and their location) from collimator losses, ready to be analysed as a loss map

Summary of commits:

• Does not work yet
• Bunch of unused variable warnings but pyk2 and coll_k2 are in sync
• Clean compilation, added zanuc4,5 to k2collimator and test
• Small typo in compilation script
• Variable zatom has been pulled out of FORTRAN (using a hack: global variable zatomcurr
• Included hcut and bnref
• Removed zatom4 and zatom5
• Included exenergy as well
• Added csref
• DOES NOT WORK. Temporary save
• WOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOORKS
• Removed csect, nmat, edens, and pleng from coll_materials.
• cprob taken care of
• Removed matID, and fixed k2collimator.py
• xintl moved out
• bn moved out
• freep out of coll_materials
• moved cgen out of coll_materials
• Removed module coll_materials.
• Moved funlxp out of coll_scatin.
• Created stub function in python (calculate_scattering) to replace coll_scatin.
• Scatin is now done in python!
• removed all private vars at the start of coll_k2 except those related to FLUKA
• Typo in k2.py; not tested
• Fixed another typo in k2.py; all tests pass.
• Reorganised file structure.
• Removed old tests.
• Changed FLUKA global variables into local variables.
• Moved K2_src into pyk2 folder.
• Made scatter.py
• Made random_init wrapper
• TEMP SAVE, DOES NOT WORK
• WOOOOORKS
• the Force is strong with this one
• Cleaned up code: removed unused variables; coll_k2 is now only the if crystal ... end if part.
• Two wrappers for crystal and jaw work.
• Moved fortran out of wrapper function calls
• Cleaned code from unused variables and old comments.
• Wrappers for jaw function created.
• Jaw function is now completely in python.
• CLEAAAN
• pyk2_gettran works
• pyk2_calcionloss works
• pyk2_ichoix and pyk2_tetat work
• Everything in python except crystals and random generator
• not functioning
• Random generator funlux now in python.
• Removed all comments.
• Investigate random Rutherford distribution.
• Added uniform
• Manual merge of main.
• Finished implementing 'fake' random generator in reference K2.
• Work in progress on crystals; does not work yet
• works
• added crystal tests to NoMoreFORTRAN
• Adding the test files....
• iAdded more test files...j
• crystal tests added fully
• nothing new
• doesn't work
• i don't know
• Crystals don't work, segmentation fault
• It should works, but does not, for one crystal only (tcpcv,a6r7.b2)
• Removed global variables enr, mom, betar, bgr, tmax, plen from crystals
• Code works but funlux has problems
• Made FUNLUX work; materials parameters are passed.
• All material dependency (nmat, matid, ..) completely out of FORTRAN.
• All global variables removed from FORTRAN (except constants).
• cry_doCrystal is out of FORTRAN
• Trying to update code with new xobjects API - does not work yet.
• Fixed issue with xojects API: correct c-source loading.
• DOES NOT WORK! Need updated fortran files...
• Random generator back in, but crystals fail
• Fixed crystal implementation; FORTRAN random generator is now correctly implemented.
• function interact partly moved to python
• interact function completely in python
• function calcionloss now in python
• moveam completely in python and movech is in the wrapper
• movech also in Python
• Cleaned up FORTRAN random generator.
• Renamed K2 as Everest.
• Fixed compilation script.
• Prepared test and examples folders for merge with BaseCollimator.
• Quick fix in number of turns in LHC B2 lossmap.
• Removed spurious np.array(...)'s from Everest scattering code.
• Copied Everest into PyEverest, to be used as a reference when translating Everest to C.
• Removed spurious drift/backtrack around CO shift.
• First try in C; does not work.
• Function soln3 in jaw.h works.
• WIP; trying C random generators.
• Removed C-calls random for now.
• Playing with CO; does not work.
• Fixed GCC version check.
• Made a random generator fully in C. Need to test and benchmark timing against FORTRAN. Also, currently Rutherford has default material parameters and sampling range; need to pass them as variables.
• testing_random_generator notebook available for comparison of Everest and K2 random generators.
• Some updates to random generator.
• Added vscode folder to gitignore.
• Latest updates to random generator.
• More tests on random generators.
• Not tested. Moved jaw.py functions to jaw.h but still WIP.
• Finished implementing random generator.
• Moved jaw to C - DOES NOT WORK
• Made temporary references for Despo.
• Removed python3.9-only code.
• Removed non-working C code.
• All functions in C except ichoix and jaw.
• IChoix also in C.
• jaw.h is fully functional.
• jaw.py completely deleted.
• First crystal function movech in C.
• Previous commit was wrong, now movech is added.
• MoveAM is in C.
• Interact is in C.
• Updated comments
• Created new references
• Doesn't work. Commit to save the work done.
• Removed csect from crystal.h as it is not used.
• Fixed returning of array from moveam and movech in C.
• Crystal now fully in C.
• Merge work done in Geant4Collimator - test FAIL!
• Fixed - added missing engine reset.
• CO angles are no longer used in K2!
• WIP. Have to deal with pointers.
• WIP to move loop out of scatter.
• Small fix to move inside loop.
• Small fix: equalise length and c_length.
• Small fix to previous fix.
• Small fix to previous fix.
• Moved for loop out of scatter - not yet tested.
• Fix of continue statement - not yet tested.
• Fix of enom error - not yet tested.
• Fix of x_in vs x_part error - not yet tested.
• Removed npart from scatter - not yet tested.
• Renamed input variables in scatter - not yet tested.
• calculate_scattering now in C.
• Crystals don't work.
• Crystals work. Scatter successfully in C.
• Unused variable cleanup.
• Removed scatter.py
• Implemented xtrack API for everest Collimator - does not work!
• Finished C implementation for EverestCollimator (EverestCrystal not yet done): compilation succeeds but results are wrong!
• Small changes from tempDespinaRefFrederik
• EverestCollimator fully in native xobjects API. All tests pass except test_materials_b2 Glid for particle id 3429 (and crystals as not yet implemented).
• Crystals natively use xobjects API, tests pass (new references generated to deal with 1e-11 difference for one particle due to repeated numerical rounding).
• Merged jaw from tempDespina.
• Deleted track.py as it is no longer used.
• Restored build_c.py as it is still needed -temporarily- for the random generator.
• Collected scattering parameters in a struct.
• Moved LocalParticle into scatter, but crystals fail..
• Correct references.
• Fixed bug in scatter.h. Tests pass.
• Made UnionRef to pass EverestData in scatter functions - Does not work!
• Each Everest type gets its own scatter method - works.
• Using xobject Material to pass parameters to scatter functions.
• Removed CO angles to be in line with release0.2.0 and cleaned naming and installation of PyEverest elements. Tests pass -however- lossmap does not work. To be investigated.
• Fixed issues with lossmap (collective vs non-collective tracker), fixed _xobject initialisation, and added correct options to align_to in colldb.
• Some small improvements and C-code for the base collimator.
• Fixed logic with InvalidCollimator.
• Tried to use xpart random generator - DOES NOT WORK; compilation hangs.
• Integrated xpart random generator. Seems to work, but still need to test decency of random generator to compare.
• Trying to expose random kernel; not succesfully yet.
• New references for Everest with new random generator.
• Fixed energy rescaling after collimator scattering.
• Added pencil generation.
• Added save to json for coll_summary in examples.
• Previous merge was incomplete - fixed now.
• Quick fix with installation of K2Collimator in manager.
• Corrected rescaling of energy after scattering (to be in line with everest and pyeverest) and made new references.
• Combined 4 example lossmaps into one.

Description

Closes # .

Checklist

Mandatory:

• I have added tests to cover my changes
• All the tests are passing, including my new ones
• I described my changes in this PR description

Optional:

• The code I wrote follows good style practices (see PEP 8 and PEP 20).
• I have updated the docs in relation to my changes, if applicable
• I have tested also GPU contexts