Code

Add energy decomposition (with PME)#1109

Code

Merged

drroe merged 219 commits intoAmber-MD:masterAmber-MD/cpptraj:masterfrom drroe:ene.decompdrroe/cpptraj:ene.decompCopy head branch name to clipboardOct 18, 2024

+7,465-1,446

Commits

Commits on Sep 13, 2024

• Start EnergyDecomposer class

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  9f0b7ff

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• Update dependencies

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• Start init routine

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• Add mask and options print

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• Start energy decomp action

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• Start adding the enedecomp command, start initialization

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• Start doing setup

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• Bond setup

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• Setup output arrays

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• Print atoms that energy will be saved for

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  8e836d0

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• Just allocate an energy for each atom, will make bookkeeping easier

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• Fix up the dataset dimension labels. Add calculation

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• Add output file

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• Add angle term. Need to sum before accumulation

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• Decompose dihedrals

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• LJ 6-12 energy template

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• Create and use an LJ 6-12 template

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• Start adding the 1-4 energy

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• Add 1-4 elec

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Commits on Sep 16, 2024

• Add debug for the 1-4 terms

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• Start adding nonbond decomp

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• Only do 1-4 calculation for NORMAL dihedrals

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Commits on Sep 17, 2024

• Start trying to template the pairlist loop

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• Add wrapper around Erfc

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• Add Ewald adjust kernel

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• Finish initial incarnation of the Ewald pairlist nonbond kernel. Make

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Commits on Sep 18, 2024

• Some cleanup

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• Add code comments

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• Change name

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• Change class name

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• Reorder

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• Try as a separate class

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• Remove for now

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• Rename

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• Finish renaming

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• Remove unneeded depend.

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• Rip out the new framework. Its really not at all ready for further

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• Start a separate class for decomposing ewald energies. Bring back

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• Start splitting out the Ewald parameters

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• Update build files

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• Just make a function template again

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• Put in energy namespace and make erfc_func available

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• Put Erfc and switching functions through the EwaldParams class

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• Init class vars

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Commits on Sep 19, 2024

• Add params for PME

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• Second try for using pairlist template/engine model

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• Do some Ewald setup

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• Add routines to access Ewald parameters to the engine

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• Start PME calc wrapper

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• Add class for calculating long range VDW

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• Use long range VDW calc

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• PME calculation setup

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• Add PME recip calc wrapper class

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• Start using PME_Recip

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• Allow PME_Recip to be used for coulomb or LJ

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• Use COULOMB recip

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• Add self energy calc

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Commits on Sep 20, 2024

• Save recip coords in EwaldParams_PME so it can be used for multiple

  Show description for 2e80c2c
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• Finish up nonbonded pme calc with template

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• Remove separate EwaldDecomp for now

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• Add timing data

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• Report pairlist timing data

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• New test action for comparing the old and new PME methods

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• Enable the new pmetest action (hidden)

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• Ensure previous coords are cleared

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• Add unit cell vector check to recip part

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Commits on Sep 23, 2024

• Move LJ ewald coeff into a separate class

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• Add C6 param and LJ self energy calcs

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• Return the precalculated self energy

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• First pass at the LJPME engine

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• Use Ewald parameters

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• Remove unneeded typedef

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• Start the LJPME calc class

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• Use the right variables

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• Add Calc_LJPME to build

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• Add Init routine

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• Add Setup routine

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• Add nonbonded calc routine

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• Add timing routine

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• Need to pass C6 params to LJPME recip calc, not charges

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• Test new LJPME calc

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• Report LJ PME recip timing in addition to regular recip timing

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Commits on Sep 24, 2024

• Openmp parallelize the pairlist template loop

  

  Daniel R. Roe

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  a87b1d6

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• Add timer to check that the recip calc itself is what takes the majority of the time, not setup (and it does). Comment it out.

  

  Daniel R. Roe

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• Rename

  

  Daniel R. Roe

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• const correctness

  

  Daniel R. Roe

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  19c5e9f

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Commits on Sep 25, 2024

• Rename

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• Finish renaming

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• Start decomposable PME energy class

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• Placeholder for decomp ewald engine

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• Add engine placeholder

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• Do engine init

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• Add setup

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• Add decomposed self energy

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• Add to build

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• Start incorporating ene decomp

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• Self energy decomp seems to work

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• Put lattice check in a separate routine

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• Decomposable recip energy

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• Decompose direct elec, vdw, and adjust energies

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• Restore arrays needed for atom decomp of LR vdw correction

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• Decompose the long range correction

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Commits on Sep 26, 2024

• Actually save the energies back to EnergyDecomposer

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• Add timing data. Hide some debug info.

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• Put LJ PME vdw calc into a template

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• Add LJPME exclude adjust kernel

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• Remove old code

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• Add Ewald LJPME decomp

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Commits on Sep 27, 2024

• Create decomposed LJPME calc. Still need to do decomposed self6 energy.

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• Add decomposed self6 calc

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• Use decomposed self6 energies

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• Update depends

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• Doesnt appear like the recip term for the LJPME is working yet.

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Commits on Oct 1, 2024

• Use cutoff from EwaldOptions instead of the engine

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Commits on Oct 2, 2024

• Merge branch 'master' into ene.decomp

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• Start Ecalc_Nonbond

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  289f0d1

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• Start implementation

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• Add pairlist setup

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• Add pairlist setup to nonbond calc

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• Start refactoring so that pairlist and exclusion array are not part of

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Commits on Oct 3, 2024

• Add .cpp.o rule so that subdir compile uses the correct flags

  

  Daniel R. Roe

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• Abstract base class for Ewald calcs

  

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• Use abstract base class

  

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• Use EwaldCalc ABC

  

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• Add to build

  

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• Add a nonbond kernel

  

  Daniel R. Roe

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• Add note about includes

  

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• Add calc init and setup, and simple nonbond calc

  

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  b6e4fa1

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• Use new nonbond calc

  

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  8798a7b

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• Report pairlist timing

  

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• Try adding a simple nonbond decomposable energy kernel

  

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  c9e082f

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• Start ewald decomp ABC

  

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• Fix includes

  

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• Convert to EwaldCalc_Decomp class

  

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• Convert decomposd LJPME to Ewald_Decomp class. Update depends

  

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• Add energy decomp to Ecalc_Nonbond

  

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• All ewald calcs need the pairlist

  

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• Use Ecalc_Nonbond to do the decomp

  

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Commits on Oct 4, 2024

• Start moving nfft and order to inside PME_Recip

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Commits on Oct 7, 2024

• New class to hold recip coords

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• Add routine to access coords array, update depends

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  9ff25b7

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• Remove files

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  c495811

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• Move EwaldParams_PME Init, Setup, and coordsD routines to EwaldParams

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• Use new EwaldParams

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• Use EwaldParams

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• Have recip print opts right after init

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• Use new EwaldParams

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• Update for new EwaldParams and PME_Recip

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• Update depends

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  eb0aab3

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• Use EwaldParams intead of EwaldParams_PME. Update depends

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Commits on Oct 8, 2024

• Start Ewald_Recip class

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• Make 1 / sqrt(PI) constant available

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  a36fbc3

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• Add init and print routines

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  e14f404

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• Add setup

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  348b5ef

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• Finish setup

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• Finish regular recip calc

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• Add timing

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• Update docs

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• No need to save ewald coeff, just calculate the factor in Init

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  5298f0d

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• Start regular Ewald calc class

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  8a7f2e0

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• Add setup

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• Finish regular ewald

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• Add EwaldCalc_Regular and Ewald_Recip to build

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• Add regular ewald to Ecalc_Nonbond

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  966e02d

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• Add ability to test Ewald regular

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• Add missing init

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• Need to look for method == 4. Improve error message. Fix timing message.

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Commits on Oct 9, 2024

• Fix reduction pragma

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• Fix OpenMP compile

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• Introduce new constant COULOMBFACTOR to replace all separate instances

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  8a5e4f4

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• Start adding ifdefs

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• Start splitting off the direct sum routines

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Commits on Oct 10, 2024

• Start removing old Ewald

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• These dont need to be separate yet

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• Make vars available for GIST PME

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• Use Ecalc_Nonbond

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• Start converting to use EwaldParams

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Commits on Oct 15, 2024

• Add PME_RecipParams class

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• Use PME_RecipParams class

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• Put PME_EwaldParams inside PME_Recip

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• Dont call print inside the init

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• Expose arrays needed by GIST_PME

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• Finish converting GIST_PME, add VDW long range, recip, and adjust stuff.

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• Add missing timing function

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Commits on Oct 17, 2024

• Fix non-openmp compile

  

  Daniel R. Roe

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• Start adding LJPME OptType

  

  Daniel R. Roe

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• Use IsPmeType where appropriate. Ensure GIST PME is only used with PME options for now.

  

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• Energy decomp with ljpme not yet allowed

  

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  9fcfa99

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• Allow LJPME to be directly set

  

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• Remove debug message

  

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  d2d5b89

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• Make options printout more clear

  

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• Make sure printed Ewald options line up

  

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• Make print private

  

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• Clean up printout of regular ewald recip opts

  

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  2e57168

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• Since fftw3 is always on now by default, change -fftw3 to -pubfft in case user wants to force using pubfft.

  

  Daniel R. Roe

  committed
  a80ea73

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• PME recip needs LIBPME

  

  Daniel R. Roe

  committed
  30a4275

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• Add include of base Ewald decomp class when no LIBPME since no decomp for regular Ewald yet.

  

  Daniel R. Roe

  committed
  5620ed2

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• Add files for enedecomp test

  

  Daniel R. Roe

  committed
  880975f

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• Enable enedecomp test

  

  Daniel R. Roe

  committed
  f9f17d1

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• Remove all references to PairListLoop and associated files

  drroe

  committed
  bc2819d

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• Update dependencies

  drroe

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  192276d

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Commits on Oct 18, 2024

• Add help text

  drroe

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  4e802ce

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• Dont repeat the same timing data. Should clean that up eventually

  drroe

  committed
  368313b

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• Use Ecalc_Nonbond interal timer only when it is active

  drroe

  committed
  eacabe2

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• Hide some debug info

  drroe

  committed
  b03176f

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• Remove old code

  drroe

  committed
  9c802cd

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• Hide some debug behind ifdef

  drroe

  committed
  06a842e

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• Fix up info output

  drroe

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  2d062f3

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• Hide debug info behind ifdef

  drroe

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  bacb58d

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• Version 6.29.4. Revision bump for addition of the 'enedecomp' action and

  Show description for cad81d2
  drroe

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  cad81d2

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• Add documentation on how to use the pairlist template

  drroe

  committed
  39badde

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• Add longer test

  drroe

  committed
  c51cf8c

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• Add enedecomp to manual

  drroe

  committed
  f32b400

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• Put functionality to reduce an array of Stats<T> into a separate class

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  drroe

  committed
  e2cff2c

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• Use Stats_Reduce

  drroe

  committed
  7cd003f

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• Ensure decomposed energy results are synced

  drroe

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  30bb8f2

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• Add citation to code docs

  drroe

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  17c8ab8

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• Update manual PDF and checksum

  drroe

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  31b46b7

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• Fix non-MPI compile (oops)

  drroe

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  825cd4b

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