Update Amber test script/reference test output files

[Madu86]

The tests on Jenkins failed due to an update we made to QUICK output. To fix this, we must either update reference test output files (https://github.com/merzlab/QUICK/tree/master/test/saved) or the Runtest amber script (https://github.com/merzlab/QUICK/blob/master/test/Run.tests.amber). Can you take care of this quickly? To reproduce the test failure, simply compile the code, source quick.rc from the installation directory, go to the tests directory and run Run.tests.amber script.

Thanks!

[Madu86]

I updated reference files with pipe symbols but optimization tests and F tests are still failing. This is because 1) someone removed max geom opt cycles and generated reference .out files., 2) a trap for F tests is not implemented in the above Runtest script. I implemented one in /tools/runtest script. The same has to be done here. @akhilshajan, @ohearnk Can you take care of these tasks and update 353-update-amber-test-scriptreference-test-output-files branch?

[agoetz]

We should get rid of the Run.tests.amber script. It duplicates functionality of the runtest script. We should use the runtest script instead. When I use the runtest script with appropriate modification in the Makefile that runs AmberTools tests, all test pass in Amber Gitlab branchquick-amber (only tested for serial and MPI builds).

This works because we do not do a diff on the entire file, but just on .ene, .grad, and .opt files that contain the relevant data. Furthermore, the runtest script has a trap for F tests.

Only a minor modification to the runtest script is required. I created PR #354 for this.

Two things need to be done in Amber Gitlab branch quick-amber, @Madu86 can you do that after incorporating the updated runtest script?

1. Modify the Amber CMake to copy the runtest script into $AMBERHOME/AmberTools/src/quick and do not copy Run.tests.amber (we should just remove it).
2. Modify $AMBERHOME/AmberTools/test/Makefile to call runtest with appropriate flags (e.g. --serial) instead of Run.tests.amber

The corresponding section in $AMBERHOME/AmberTools/test/Makefile should look as follows:

test.Quick:
        @(if [ "$(QUICK)" = 'yes' ]; then \
        cd ../src/quick && ./runtest --serial ;\
        fi ;\
        )

test.Quick.MPI:
        @(if [ "$(QUICK)" = 'yes' ]; then \
        cd ../src/quick && ./runtest --mpi ;\
        fi ;\
        )

test.Quick.cuda:
        @(if [ "$(QUICK)" = 'yes' ]; then \
        cd ../src/quick && ./runtest --cuda ;\
        fi ;\
        )

test.Quick.cuda.MPI:
        @(if [ "$(QUICK)" = 'yes' ]; then \
        cd ../src/quick && ./runtest --cudampi ;\
        fi ;\
        )

test.Quick.hip:
        @(if [ "$(QUICK)" = 'yes' ]; then \
        cd ../src/quick && ./runtest --hip ;\
        fi ;\
        )

test.Quick.hip.MPI:
        @(if [ "$(QUICK)" = 'yes' ]; then \
        cd ../src/quick && ./runtest --hipmpi ;\
        fi ;\
        )