Add support for Lennard-Jones PME to 'energy' command.#666

Merged

drroe merged 37 commits intoAmber-MD:masterfrom

Feb 15, 2019

Commits on Feb 7, 2019

DRR - Cpptraj: Add code for calc C6 params for the LJ pme
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DRR - Cpptraj: Add test LJ pme calc.
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DRR - Cpptraj: Start LJ PME test.
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DRR - Cpptraj: add lj pme self correction
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DRR - Cpptraj: Attempt correction. Not there yet.
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Commits on Feb 8, 2019

Merge branch 'master' into lj_pme
Daniel R. Roe
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Commits on Feb 14, 2019

DRR - Cpptraj: Split up LJ pme correction into excluded and non-excluded parts
Daniel R. Roe
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DRR - Cpptraj: Add code for switch function, not yet enabled.
Daniel R. Roe
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DRR - Cpptraj: Add separate terms for LJ PME. Ensure LJ pme is off when LJ Ewald parameter is negative.
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DRR - Cpptraj: Add function for calculating sigma
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DRR - Cpptraj: Add keywords for lennard jones pme
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DRR - Cpptraj: Code doc
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DRR - Cpptraj: Simple LJ pme test
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DRR - Cpptraj: Make sure the correct Ewald param passed in for LJ
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DRR - Cpptraj: Fix regular Ewald by allocating C6 arrays even though they arent used
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DRR - Cpptraj: Add lj PME kappa sweep test.
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DRR - Cpptraj: Hide debug info. If LJ pme will not be active set C6 params to 0.0
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DRR - Cpptraj: Hide some debug info
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DRR - Cpptraj: Enable lj pme test
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DRR - Cpptraj: Box action modifies topology, return value to indicate this.
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DRR - Cpptraj: Add switch to inside the direct space calc
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DRR - Cpptraj: Add LJ switching argument
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DRR - Cpptraj: First incarnation of the catcrd command
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DRR - Cpptraj: Output switch width when active
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DRR - Cpptraj: Enable catcrd
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DRR - Cpptraj: Add test for catcrd command.
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DRR - Cpptraj: Enable catcrd test
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DRR - Cpptraj: Revision bump; LJ PME support and catcrd command.
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DRR - Cpptraj: Add LJ with switch test
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Commits on Feb 15, 2019

DRR - Cpptraj: Attempt to simplify code maintenance while maintaining performance by putting common energy kernels in include files.
Daniel R. Roe
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DRR - Cpptraj: Put pair list loop as an include file; this somewhat improves the speed of the direct space calc for cases where e.g. the lj pme part is not needed.
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DRR - Cpptraj: Caculate some common prefactors.
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DRR - Cpptraj: Remove old code.
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DRR - Cpptraj: Avoid allocating PME instance every call
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DRR - Cpptraj: Protect openmp pragmas
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DRR - Cpptraj: Squash a bunch of compiler warnings.
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DRR - Cpptraj: No need to pass the adjustment energy out - just report it when debug info is on.
Daniel R. Roe
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