Openmichrom

**Major changes:**
- Change the format of variable names to camelCase for the entire code.
- Rewrite the output display into a classical OpenMM Reporter
- Include the reader for Chromosome Types via bed files
- Create Reporters for statistics and trajectory in CNDB, SWB, PDB, GRO, NDB
- Create the Homopolymer function that adds all homopolymer potentials to the system
- Create the Classic Michrom Simulation function to run Classic Michrom

What's Changed
* Fix various bugs and improve code readability by junioreif in https://github.com/junioreif/OpenMiChroM/pull/103


**Full Changelog**: https://github.com/junioreif/OpenMiChroM/compare/v1.0.9...v1.1.0

**Major changes:**
- added "addCustomMultiChainIC potential."
- Adam optimization class can switch between QH Adam and Classical Adam.

**Minor changes:**
- CustomMiChroMTraining - when starting the IC training, there is no need to insert the TypeTables.
- Includes proper citation and references to Polychrom.
- Added the option to save the velocity, moment, and iteration parameters in Full Inversion Optimization

**Minor changes:**
- Long outputs in tutorials removed
- bugfix in cndbtools reading types due to an update in HDF5 format
- fix: warning message when including new forces.

**Main changes:**
_ChromDynamics.py:_
- addAdditionalForces() : one can add force objects after the system and context has been initialized
- addCylindricalConfinement(): method to add confining external potential that is cylindrical
- addCorrelatedNoise(): active noise can be added to the simulation object
- addHarmonicBonds(): Harmonic bonds for nearest neighbors
- addSelfAvoidance(): repulsive softcore without diverging LJ

_Optimization.py:_
- modified cutoff into cutoff_low and cutoff_high in getPars
- added norm in getPars -- normalization of input hic is now optional
- get_lambdas_IC() def now computes and returns the new lambdas
- Ideal Chromosome list of beads to be trained now should be informed in the initialization of CustomMiChroMTraining class by the new variable IClist.
- get_lambdas_IC() and get_lambdas_types() def's now has the boolean variable write_error that computes the tolerance and Pearson correlation of the inversion and write in the output file tolerance_and_pearson.

_Integrators.py:_
- added integrator object CustomBrownianIntegrator that uses active noise

**Minor changes:**
- added Active Chromosome Dynamics tutorial to run correlated noise simulations
- CustomMiChroMTraining() had its variable and def names standardized, mainly for the Types and Ideal Chromosome training procedure
- added a tutorial for the Ideal Chromosome potential term
- New scripts were included in the tutorial folder for the MiChroM training procedure on GPU-based clusters.

**Main changes:**
- `CustomMiChroMTraining` class now allows using any letter to labeling the parameters
- `getLamb_types()` returns a DataFrame using the labels assigned in `CustomMiChroMTraining` class

**Minor changes:**
- bugfix on `cndbTools()` label reading

**Main changes:**
- `getForceIndex()` function was added to allow deletion of the correct force
- fixed ForceGroup assignment for MultiChainIC
- `addAdditionalForce()` function was added to allow the addition of forces in the system after the initialization
**Minor changes:**
- bug fix on `printStats()` and `saveStructure()`
- implemented changes on `setFibPosition`