updated __lammpsInit__ to use full path name of input and log files and issue a warning if it tries to pull an input file from a directory other than the current working directory.
updated __lammpsInit__ to use full path name of input and log files and issue a warning if it tries to pull an input file from a directory other than the current working directory.

jtempkin/enhanced-sampling-toolkit,jtempkin/enhanced_sampling_toolkit