Merge pull request #24 from YujiOkajima/develop

fix compile error
Fixed some bugs in the dark rate function, as pointed out by Trevor Stewart. The first bug was that the TotalPe was not being incremented if the PMT was not in the original hit array. The second bug involved an error in array index of the list array, also in the loop where the PMT had not been originally hit. I have changed the indices of the list array to now run between 1 and number of PMTs. I have also added in comments to make this function a bit easier to understand.
Must increment number_entries before filling the list
Updated pdf file with some clarifications about the quantum correction being applied to the hits collection. Also added a README which points to the directory where the documentation source code is.
Fix a bug found by Thomas Lidner where a boolean function to return if
there were subevents was returning the opposite of what it should.
This function is not used anywhere else so doesn't have an other
effects.

The commit closes issue #26
Merge pull request #27 from WCSim/bugfix/darkrate

Merge this fix by Erin.
Fixing another off-by-one index error as pointed out by Okajima. The (WCSimPmtInfo*)pmts->at command must take noise_pmt-1 as an argument to return the proper geometry for the tubeID. The noise_pmt variable also must be incremented by 1 to be used as tubeID, which runs from 1 to number_pmts.
This commit implements some structural changes to the code. The information for a PMT (name, pe response, geometry, and QE) now is all contained together in the src/WCSimPMTObject.cc file. PMTs are a member of the abstract base class WCSimPMTObject and the virtual functions for this class can be found in include/WCSimPMTObject.hh. PMTs are now instantiated in the src/WCSimDetectorConfigs.cc file and a pointer to that PMT type is stored, allowing for the pe response and QE to be accessed by the appropriate files.
Adding timingConstant in WCSimWCDigitizer to the information stored with the PMT.
Update and rename README to README.md

Using markdown to make this README look nicer.
Update README.md

Adding back in the missing line breaks in the make commands by putting it in list form.
Update README.md
Merge pull request #28 from WCSim/bugfix/darkratebug

Fixing another off-by-one index error as pointed out by Okajima. The (WC...
Instead of just defining the timing constant which is used to calculate the timing resolution, the user can now define the entire timing resolution function. This is to allow for the parameters of the timing resolution function to be modified for the new HPD tubes, but can also be used in the future if the timing resolution function has a different structure.
Adding WCPMTGlassThickness to the list of properties defined in src/WCSimPMTProperties.cc.
Merge pull request #30 from WCSim/feature/issue12

Merging the PMT implementation change from Erin.  This defines all PMT properties and responses in their own object.