FERN: Fast Explicit Reaction Networks SVNCode

Configured CMake to build both parallel and serial binary, syncronized serial and parallel code to produce similar results, and enabled shared variables for storing timestepping-related data.

Added two logical variables, diagnosticPrint and printSteps, to control the amount of diagnostic printout from the kernel execution. If the first is set to 1 very detailed info is printed for each integration step. If the second is set to 1, at each integration step a summary of network variables is printed (setting diagnosticPrint to 1 generates much more additional output than setting printSteps to 1).

Small changes in explicitgpuDouble.cu

Current version of explicitgpuDouble.cu copied from Titan

update

Little cleaning up

This version has been tested to give essentially the java results up to log t = -5, but diverges after that.

Fixed problem that checkAsy(Fminus[k], Y[k], dt) should be checkAsy(FminusSum[k], Y[k], dt). Because of this error it was not doing the asymptotic check correctly. Now gives essentially same results as java version up to log t = -6 for test case.

Added more diagnostic output on timesteps

cleaned up some things. This now agrees with the java example up to log t = -7 in the 3-4 decimal place up through Ar36, but quite different at log t = -6. Timestepping seems to be similar to factor of two in the two cases.