BioD PNPI Git Repos - alexxy/gromacs.git/commit

biod.pnpi.spb.ru / alexxy / gromacs.git / commit

author	Berk Hess <hess@kth.se>
	Thu, 5 Dec 2013 09:27:59 +0000 (10:27 +0100)
committer	Mark Abraham <mark.j.abraham@gmail.com>
	Mon, 24 Feb 2014 16:21:48 +0000 (17:21 +0100)
commit	99029df2c0e845b1cdf4675d6d9ca5d64f890235
tree	74f31af7be975627c1b126c049802779e008305b	tree \| snapshot
parent	7ef5eaa461a2d0e50b18a59fcf278e9e843557f5	commit \| diff

Implemented LJ-PME nbnxn kernels

Implemented nbnxn SIMD and C kernels for LJ-PME. CUDA kernels will
follow later.
The nbnxn LJ-PME kernels subtract the full mesh contribution, using
the mesh C6 coefficients (usually geometrically combined). This gives
much higher accuracy for non-geometric force-fields.
The group kernels will soon be changed to use the same setup.

Change-Id: Ibbc6eef1c62a97ff6b2e3013f19594946581e44e

212 files changed:

manual/forcefield.tex		diff \| blob \| history
src/gromacs/gmxlib/ewald_util.c		diff \| blob \| history
src/gromacs/gmxlib/nrnb.c		diff \| blob \| history
src/gromacs/gmxpreprocess/grompp.c		diff \| blob \| history
src/gromacs/gmxpreprocess/readir.c		diff \| blob \| history
src/gromacs/legacyheaders/force.h		diff \| blob \| history
src/gromacs/legacyheaders/types/interaction_const.h		diff \| blob \| history
src/gromacs/legacyheaders/types/mdatom.h		diff \| blob \| history
src/gromacs/legacyheaders/types/nrnb.h		diff \| blob \| history
src/gromacs/mdlib/domdec.c		diff \| blob \| history
src/gromacs/mdlib/force.c		diff \| blob \| history
src/gromacs/mdlib/forcerec.c		diff \| blob \| history
src/gromacs/mdlib/mdatom.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_atomdata.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_atomdata.h		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/make_verlet_simd_kernel_files.py		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_inner.h		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref_outer.h		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn.c	[new file with mode: 0644]	blob
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn.c		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn.c		diff \| blob \| history
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src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_outer.h		diff \| blob \| history
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn.c		diff \| blob \| history
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src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn.c		diff \| blob \| history
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