Fix autotools macros for modern versions

Renamed configure.in to the correct name configure.ac
Replaced obsolete automake macro with modern alternative.
Obsolete macro causes an error when running bootstrap on automake 1.13
Add bootstrap generated test file to .gitignore
fix compilation errors when enabling c++11 -- gcc 4.7.2 (3.7.1-2-ARCH)

C++11 introduces a new syntax for user-defined string literals that causes
macros placed after closing quotations in strings, without a space,
to error on compilation.
Add parallel omp reduction to getRMS()
Add parallel construct to inner loop of solve_and_plot()