Add dihedral RMS to reference action#736

Merged

drroe merged 26 commits intoAmber-MD:masterfrom

drroe:dihedralrms

Jun 21, 2019

Commits on Jun 14, 2019

DRR - Cpptraj: Use forward declares. Add routine for using dihtype.
Daniel R. Roe
committed
DRR - Cpptraj: Use the new SearchForNewTypeArgs routine
Daniel R. Roe
committed
DRR - Cpptraj: Enable command. Add reference keywords.
Daniel R. Roe
committed
DRR - Cpptraj: Add the Action_DihedralRMS class
Daniel R. Roe
committed

Commits on Jun 15, 2019

Commits on Jun 17, 2019

DRR - Cpptraj: Do not print mask expression if no mask string is set.
Daniel R. Roe
committed
DRR - Cpptraj: Add reference setup when no mask string set. Make -1 passed into SetupRef() mean do not check number selected atoms.
Daniel R. Roe
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DRR - Cpptraj: Add rms previous test
Daniel R. Roe
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DRR - Cpptraj: Test rms first with changing topology
Daniel R. Roe
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DRR - Cpptraj: Get rid of previous as a bool, add as a mode. Do not change modes during actions; this way classes using ReferenceAction always know how reference was selected.
Daniel R. Roe
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DRR - Cpptraj: Use separate DihedralSearch for selecting reference dihedrals. Finish up dihedral rms calculation.
Daniel R. Roe
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DRR - Cpptraj: Add to first and to reference tests.
Daniel R. Roe
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DRR - Cpptraj: Fix calc to previous ref
Daniel R. Roe
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DRR - Cpptraj: Add to previous test
Daniel R. Roe
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DRR - Cpptraj: Only calculate reference values during setup if mode is FRAME
Daniel R. Roe
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DRR - Cpptraj: Add to reference traj test
Daniel R. Roe
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DRR - Cpptraj: Hide some debug info
Daniel R. Roe
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DRR - Cpptraj: Remove obsolete test stuff, split into parallel/not parallel tests
Daniel R. Roe
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Commits on Jun 20, 2019

DRR - Cpptraj: Add dihedral fluctuation (multidihedral plus avg) test
Daniel R. Roe
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DRR - Cpptraj: Revision bump for new dihrms command
Daniel R. Roe
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DRR - Cpptraj: Take max of format specifier and actual data width when writing strings using Write
Daniel R. Roe
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Commits on Jun 21, 2019

DRR - Cpptraj: Add missing test save
Daniel R. Roe
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DRR - Cpptraj: Enabled dihedral rms test.
drroe
committed
DRR - Cpptraj: Add missing include
drroe
committed