sPuReMD: merge changes from branch 'new_setup'. Rework interface for geometry initialization without file I/O. Other code clean-up.

sPuReMD: rework Fortran F90 interfaces for Amber specifics and declare this interface for such usage.

sPuReMD: fix Coulomb energy calculations for QM/MM mode. Indicate QEq model not supported with QM/MM mode. Add Fortran interface for QM/MM mode.

sPuReMD: add QMMM library interface for external codes (e.g., Amber). Rework file I/O parsing to jive with multiple consecutive simulation code changes. Improve file parser error checking (numeric types). Other code clean-up.

sPuReMD: finalize sPuReMD multiple consecutive simulation code (for integration with other codebases).

sPuReMD: add functionality to run multiple MD simulations (for usage via integration with external codebases).

sPuReMD: replace OpenMP critical sections on ext_press with thread-local storage and subsequent reduction (ext_press_local). Other code clean-up.

sPuReMD: backport changes for reax_list, struct declaration/definition separation, interaction_function.

sPuReMD: separate total energy computation and fix Python driver bug with structure definition for ctypes. Allow disabling file logging during simulation.

sPuReMD: fix GMRES bug introduced from previous refactoring. Explicitly link OpenMP for library. Refactoring to remove global variables. Remove unnecessary OpenMP barriers after single regions.

sPuReMD: split into library and driver for, e.g., optimization integration. Fix bug with interaction lists being allocated for hydrogen bonds when no hydorgen atoms present. Fix minimum allocation size of 3-body lists (uncovered with small lithium geometries). Refactor naming of conflicting data structures. Update .gitignore.

sPuReMD: further OpenMP work on force computations and interaction lists. Minor data structure scope changes. Fix numereous non-critical memory leaks. Add tear-down code. Other general refactoring.