GROMACS

Clarify distinct paths for mdrun log file handling

Opening for appending is actually handled in the checkpointing code,
which is now explicit in mdrunner.

Also handled the error case when the log file cannot be opened.

Also removed unnecessary dependency on commrec.

Refs #2651

Change-Id: I0b8c7756a08c3d786571e7936e7f8f327fd17947

Extract helper functions for preparing for appending

This simplifies code so we can handle the log file pointer better.

Refs #2651

Change-Id: Ifa3114d125e89bf22081b05c5e739693c996f01b

Check log and other files differently during appending restart

We need to do different operations on the log file than the other
files, so it makes sense to separate those aspects of its handling,
while calling a common function for those that are common. That will
also prepare to clean up the opening of the log file in Mdrunner, so
we can do it in only one place.

Checked all the offsets were valid before doing any file operations.

Used a bit less preprocessing, too.

Refs #2651

Change-Id: I23cfba550b57d169c021d72618341ff017a3e7de

Open mdrun log file only once

The log file is now kept open with a t_fileio held RAII style, which
permits the appending restart code to truncate it if needed, so that
we don't have the opening and closing of the checkpoint file being
managed in several places.

Fixes #2651

Change-Id: I6105bf55a9a10aaf15ed2f11ef8955a47743bb91