Add new command line flags, enhance processing of existing ones.#614

Merged

drroe merged 24 commits intoAmber-MD:masterfrom

drroe:cmdline_flags

Jun 20, 2018

Commits on Jun 18, 2018

DRR - Cpptraj: Initial attempt to add '-ya' command line flag for input trajectory arguments.
Daniel R. Roe
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DRR - Cpptraj: Use ArgList to process command line args instead of argc/argv to take advantage of things like quote enclosure
Daniel R. Roe
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DRR - Cpptraj: Change automatic detection of topology and input files on command line to be position-independent. Add detection of input trajectory files on command line.
Daniel R. Roe
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DRR - Cpptraj: Add command line test.
Daniel R. Roe
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DRR - Cpptraj: Simplify NotFinalArg()
Daniel R. Roe
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DRR - Cpptraj: Fix memory leaks during automatic detection of traj/parm files on command line.
Daniel R. Roe
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DRR - Cpptraj: With MPI, only have master autodetect files on command line
Daniel R. Roe
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DRR - Cpptraj: Test is good up to 8 threads
Daniel R. Roe
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DRR - Cpptraj: Correct some references to MPI threads to MPI processes - only use 'threads' to refer to OpenMP. Report on number of OpenMP threads at beginning of run in additon to MPI processes.
Daniel R. Roe
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DRR - Cpptraj: Middle version number bump; command line functionality changed (addition of new flags, file autodetection, order of topology/input without flags no longer matters).
Daniel R. Roe
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DRR - Cpptraj: Make resizing of trajectory arguments a separate function.
Daniel R. Roe
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DRR - Cpptraj: Process '-xa' flags.
Daniel R. Roe
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DRR - Cpptraj: Hide debug info. Print which trajin/trajout arguments are actually being used.
Daniel R. Roe
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DRR - Cpptraj: Test output args from command line
Daniel R. Roe
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DRR - Cpptraj: Test printing host name. Hopefully this works on the windows platform as well.
Daniel R. Roe
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DRR - Cpptraj: I think I need this include on windows for HostName() to work.
Daniel R. Roe
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Commits on Jun 19, 2018

DRR - Cpptraj: Decided the last number should be incremented instead of middle - no functionality has actually changed, just enhancements added.
Daniel R. Roe
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DRR - Cpptraj: Fix up help text.
Daniel R. Roe
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DRR - Cpptraj: Warn if less than 3 atoms selected for RMSD, and skip if debug level is 0. Addresses #600.
Daniel R. Roe
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DRR - Cpptraj: Fix tests in parallel at higher process counts (#599). Good up to 32 processes now.
Daniel R. Roe
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DRR - Cpptraj: Only warn about assuming file contains cpptraj input if not in the "classic" command line position.
Daniel R. Roe
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DRR - Cpptraj: Add command line wildcard test
Daniel R. Roe
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DRR - Cpptraj: Update test name.
Daniel R. Roe
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Commits on Jun 20, 2018

DRR - Cpptraj: Remove hostname printout for now. I don't have the time or patience right now to debug it cross-platform.
Daniel R. Roe
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