Small tweak to the radical group tree for allylic ketones.

Previously, if you had a tertiary radical allyl to a ketone carbonyl, the
estimated thermo would only account for the tertiary substitution, and
not the resonance stabilization the carbonyl provides. We did already
have a group for an aldehyde carbonyl. This commit uses the aldehyde
value for both ketones and aldehydes, and that's almost certainly better
than just forgetting about the C=O contribution entirely.
Convert comment ! to C in (old style FORTRAN) GATPFit lsfp.f

This helps my text editor with syntax highlighting.
Fewer threads to spawn in GATPFit.java

It seems this is redundant, we can just send the input and flush it in the main thread,
rather than spawning a new thread each time for this purpose.
GATPFit.exe creates debug.log file to aid debugging buffered input problems.

See issup #257 at https://github.com/GreenGroup/RMG-Java/issues/257
GATPFit.exe terminates with error if input is too short.

Trying to help with issue #257.
This commit can probably stay, though, when debugging is finished.
GATPFit.java creates a String from the inputString
Split GATPFit input into separate lines and send them one at a time.

(Also included an annoying debugging line that says which line it has just sent)
Try making one commandInput per iteration, instead of reusing it.

With the .close() on line 200 it does one iteration then stops with
"Error writing input to GATPFit buffer".
Without  the .close(), it works on some computers but not others
(just like before!)
Merge branch 'master' into avoidfork

Main reason for merge is this brings in changes to the Makefiles.

Conflicts (kept the avoidfork version):
	source/GATPFit/lsfp.f
	source/RMG/jing/chem/GATPFit.java
Check for broken gfortran versions and abort compilation for GATPFit.exe
Revert "Try making one commandInput per iteration, instead of reusing it."

This reverts commit 320c99e542ffc396e2041eba4ffc12f07eee90c2.
Revert "Split GATPFit input into separate lines and send them one at a time."

This reverts commit 06f6caeaa21ff3059a5b3a89fbf814a14c3d43e2.
Remove the GFORTRANTEST from the main Makefile

This is still in the GATPFit Makefile, which is where it counts.
This way, you can make GATPFit first, with a different
F90=/path/to/alternative/gfortran
then make everything else with the main makefile, and it won't
complain (as long as GATPFit doesn't need re-making).
Revert "GATPFit.exe creates debug.log file to aid debugging buffered input problems."

This reverts most of commit 5a138c9397b2b67eb34483b8caf261ac779b56c5.

I left in the check that enough input had been read.

Conflicts:

	source/GATPFit/lsfp.f
Added a truncation check in GATPFit.

If you give it an H_298 value that is too long, then the end is chopped off.
If this contains an exponent (eg. 1.1111111E22) then your number would be 
very wrong. This checks to avoid that, for safety.
Restored the check for successful writing to the GATPFit buffer.
Move stuff around in frankie in preparation for changing the I/O.

This shouldn't change how it behaves. I just made it so the files are 
opened and closed in the MAIN program, and the file units are passed
to the Calculate_RRHO_HR_params subroutine.
Frankie writes all it's commentary to frankie.log file, not STDOUT

This should then allow us to write the actual output to STDOUT.
By changing Ulog to 6 (stdout stream) you can revert to the previous behavior.
Another option is send it to stderr.
Frankie no longer prints the timestamp to STDOUT

it's already recording how long things took
Modify DQED to report errors in STDERR not STDOUT.

This will free up STDOUT for the other stuff.