Add particle mesh Ewald calc via PME library from A. Simmonett#581

Merged

drroe merged 183 commits intoAmber-MD:masterfrom

Feb 22, 2018

Commits on Jan 24, 2018

DRR - Cpptraj: Stub for introducing libpme from A. Simmonett
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DRR - Cpptraj: Add some detection for C++11 extensions. Change configure output so more important messages happen at the end.
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DRR - Cpptraj: Change ordering of some flags.
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Commits on Jan 25, 2018

DRR - Cpptraj: Start configure rewrite
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DRR - Cpptraj: Add all options except library. Add compiler flag setup.
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DRR - Change to mpi compiler wrappers if necessary
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DRR - Cpptraj: Setup profiling
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DRR - Cpptraj: Use cray wrappers
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DRR - Cpptraj: Make local function variables lowercase. Start compiler tests.
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DRR - Cpptraj: Check for OpenMP and C11 support
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DRR - Cpptraj: Add MPICH_IGNORE_CXX_SEEK fix
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DRR - Cpptraj: Some more cray flags
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DRR - Cpptraj: Start external library configure
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Commits on Jan 26, 2018

DRR - Cpptraj: Start recognizing library command line stuff.
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DRR - Cpptraj: Start library setup
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DRR - Cpptraj: Add test compile.
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DRR - Cpptraj: Try to deal with bundled libraries
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DRR - Cpptraj: Start setting flags.
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DRR - Cpptraj: Add checks for pnetcdf, zlib, bzlib. Go back to old way of determining '=' position because apparently expr index does not work the same way on Macs (grr)
drroe
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DRR - Cpptraj: Split up tests so they can potentially be combined.
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DRR - Cpptraj: Bring external library tests out of arrays
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DRR - Cpptraj: Add check for adding in the fortran link arguments
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DRR - Cpptraj: Add arpack test. Make fortran link test a function.
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DRR - Cpptraj: Support -nomathlib
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DRR - Cpptraj: FFTW3 options
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DRR - Cpptraj: Add external readline
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DRR - Cpptraj: Add xdrfile
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DRR - Cpptraj: Start readline and xdrfile bundled
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DRR - Cpptraj: Add sanderlib test
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DRR - Cpptraj: Add fortran test
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DRR - Cpptraj: Openblas
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DRR - Cpptraj: Override previous openblas
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DRR - Cpptraj: New macAccelerate flag
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DRR - Cpptraj: Enable -amberlib flag
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DRR - Cpptraj: Add MKL setup
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Commits on Jan 27, 2018

DRR - Cpptraj: Consolidate BLAS options variables
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Commits on Jan 29, 2018

Commits on Jan 30, 2018

DRR - Cpptraj: Fix detection of gnu compilers when they are really clang on OSX
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DRR - Cpptraj: Ensure that the '-amberlib' option only overwrites libraries that have not been otherwise specified. Ensure that libraries that are off are not added to the linker variables.
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DRR - Cpptraj: Do not print out BLAS info if disabled
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DRR - Cpptraj: Fix up help. Print shader model config in summary
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DRR - Cpptraj: Have C++11 test use actual code.
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DRR - Cpptraj: Add return 0 statement at the end of test code.
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DRR - Cpptraj: Add C++11 flag for Intel, clang, and Cray compilers
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DRR - Cpptraj: Ensure INCLUDE is part of CXXFLAGS etc. Ensure the same directory is not included multiple times.
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DRR - Cpptraj: Add directives. Fix setting of cuda libraries.
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DRR - Cpptraj: Add xdr_seek check to xdr test. Remove unneeded XDR-related variables from config and makefile
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DRR - Cpptraj: Remove unnecessary readline stuff from config / makefile
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DRR - Cpptraj: Simplify handling of FFT in configure/Makefile
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DRR - Cpptraj: Ensure ompflag is added to LDFLAGS
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DRR - Cpptraj: Properly set directives when functionality is turned off by a test.
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DRR - Cpptraj: Add LIBPME directive
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DRR - Cpptraj: Put all directives in one place
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DRR - Cpptraj: Add missing include
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DRR - Cpptraj: Add option to disable C++11 support
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Commits on Jan 31, 2018

DRR - Cpptraj: Makefile_at is obsolete
drroe
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DRR - Cpptraj: Makefile_at is obsolete
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DRR - Cpptraj: Add bundled ARPACK
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DRR - Cpptraj: Try to bundle arpack
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DRR - Cpptraj: SECOND -> ARSECOND and do not make ETIME external to avoid issues with intrinsics.
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DRR - Cpptraj: Fix capitalization and variable name typos
drroe
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DRR - Cpptraj: Add timing info
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DRR - Cpptraj: Add code to determine number of FFT grid points.
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DRR - Cpptraj: Fix warnings flag for ifort. Ensure Fortran link required if bundled ARPACK will be used.
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DRR - Cpptraj: Initial attempt at enabling PME calc
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DRR - Cpptraj: Comparison operator typo
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DRR - Cpptraj: Fix errors of the type:
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DRR - Cpptraj: Clean up files leftover by ifort
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DRR - Cpptraj: Fix initialization of coords and charge arrays for libpme. Actually perform the energy calc. Enable output of timing info.
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DRR - Cpptraj: Ensure box type is correctly set for box action
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DRR - Cpptraj: Add some debug info but keep it hidden.
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DRR - Cpptraj: Add ability to specify nfft
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DRR - Cpptraj: Get rid of rsumtol for pme
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DRR - Cpptraj: Add libpme test
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DRR - Cpptraj: Hide a debug statement
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DRR - Cpptraj: Add option to change pme spline order.
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DRR - Cpptraj: Change debug level
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DRR - Cpptraj: Only run the LLVM check on Darwin
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Commits on Feb 1, 2018

DRR - Cpptraj: Add orthogonal PME test
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DRR - Cpptraj: Mol2 version of A. Simmonett's water dimer test system
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DRR - Cpptraj: Split regular and particle mesh Ewald calcs
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DRR - Cpptraj: Make allocation a little more efficient. Fix compile bugs leftover from split. Better printout of nfft values.
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DRR - Cpptraj: Make nonortho parameters tighter
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DRR - Cpptraj: Fix up test naming.
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DRR - Cpptraj: Move additional library setup from BasicChecks to SetupLibraries. Attempt to use simpler -mkl option for linking MKL when using Intel compilers.
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DRR - Cpptraj: Add some code for enabling FFTW3 in Eigen for libpme but do not enable - does not seem to work correctly yet.
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DRR - Cpptraj: Put INCLUDE and DIRECTIVES inside config.h
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DRR - Cpptraj: Fix memory leak. Use Charge_ array directly in libpme via mapMat.
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DRR - Cpptraj: Write out nffts if specified
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DRR - Cpptraj: Constants no longer needed in ParticleMesh
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DRR - Cpptraj: Make test require libpme
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DRR - Cpptraj: Add 'pme' options to help
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DRR - Cpptraj: Add --compile-verbose option
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DRR - Cpptraj: Rename test dir
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DRR - Cpptraj: Enable libpme test
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DRR - Cpptraj: Placeholder for long range vdw correction
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Commits on Feb 2, 2018

DRR - Cpptraj: Finish up vdw correction
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DRR - Cpptraj: Simplify the vdw correction by precalculating stuff that depends only on number of types and B parameter
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DRR - Cpptraj: Increase precision of printed matrix
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DRR - Cpptraj: Ensure libpme_standalone.h is added as a dependency but do not look in it for dependencies.
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DRR - Cpptraj: Attempt to add VDW calc to Ewald direct sum. Doesnt appear to work properly yet.
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DRR - Cpptraj: Fix up debug info. Add missing VDW calc.
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DRR - Cpptraj: Add vdw energy to output.
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DRR - Cpptraj: Update test saves to store vdw energy
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Commits on Feb 5, 2018

DRR - Cpptraj: Better control over what terms are calculated for the 'energy' action. The 'etype' argument no longer implies that only electrostatics should be calculated. Provide better info on wh…
Daniel R. Roe
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DRR - Cpptraj: VDW/ELEC data set order now consistent for all nonbond calc types. Add 'nonbond' keyword so only elec/vdw are calcd.
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DRR - Cpptraj: Do not attempt to save energy terms if they were not requested
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DRR - Cpptraj: Total energy term is no longer saved if only one energy term has been requested.
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DRR - Cpptraj: Fix up help.
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DRR - Cpptraj: Improve code docs.
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DRR - Cpptraj: Fix exclusion list generation when not all atoms are selected
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DRR - Cpptraj: Add test with atom mask
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DRR - Cpptraj: Fix vdw long range correction when not all atoms selected.
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DRR - Cpptraj: Update for VDW long range correction fix
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DRR - Cpptraj: Hide some debug info
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DRR - Cpptraj: Fix compiling without C++11 support
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DRR - Cpptraj: Code cleanup and documentation
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DRR - Cpptraj: Add erfcdx option
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DRR - Cpptraj: Clean up output
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DRR - Cpptraj: Move to debug versions, do not need to calc Ewald energies here since there is a separate test for these already
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DRR - Cpptraj: Add non-debug test saves
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DRR - Cpptraj: Add trap for non-orthogonal cells.
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Commits on Feb 6, 2018

DRR - Cpptraj: Bump internal version.
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Commits on Feb 9, 2018

Merge branch 'master' into libpme
drroe
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Commits on Feb 10, 2018

DRR - Cpptraj: Switch to non-eigen version of libpme. Now requires fftw.
drroe
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Commits on Feb 13, 2018

Commits on Feb 14, 2018

Commits on Feb 20, 2018

DRR - Cpptraj: Add kinetic energy estimation from velocity and velocity/force
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DRR - Cpptraj: Add kinetic energy test
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DRR - Cpptraj: Use mass information from Frame
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Commits on Feb 21, 2018

DRR - Cpptraj: Add ketype option to specify type of KE calc.
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DRR - Cpptraj: Fix comparison to wrong enumerated type
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DRR - Cpptraj: Need DIRECTIVES for nproc to be compiled properly.
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DRR - Cpptraj: Rip out MPI part of PMElib since in cpptraj MPI is for trajectory/ensembles only (also it currently doesnt compile).
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DRR - Cpptraj: Move all energy timing info from Energy to Action_Energy. Only print timing components that were actually used.
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DRR - Cpptraj: Readline library is not needed by libcpptraj so separate it out in config.h
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DRR - Cpptraj: Remove CFLAGS from travis script - not sure why they were ever necessary but they definitely should not be now.
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DRR - Cpptraj: Add -fftw3 configure flag to libcpptraj test.
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DRR - Cpptraj: Update dependencies.
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DRR - Cpptraj: Integrate the Libcpptraj test into the main test framework so errors are not silently ignored.
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Merge branch 'master' into libpme
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DRR - Cpptraj: Disable the non-double precision templates for diagonalizer wrappers; cpptraj doesnt use them and the LAPACK that comes with Amber only has double precision.
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Commits on Feb 22, 2018