Fixed GB interactions for release-4-6
authorErik Lindahl <erik@kth.se>
Sun, 13 Jan 2013 19:21:05 +0000 (11:21 -0800)
committerMark Abraham <mark.j.abraham@gmail.com>
Wed, 16 Jan 2013 01:16:02 +0000 (02:16 +0100)
commitfa181964de6c9e064fe474940c78e00bfd96117f
tree9b0738228693aedf913325cd3bcadca068eb91fd
parent438c04eb53e69e359566b20817ed06a6da096002
Fixed GB interactions for release-4-6

Release-4-6 was not using the correct GB kernels,
but the non-GB electrostatics cutoff kernel. In addition,
the accelerated kernels unrolled more than a factor 2 had
a bug that caused a small error in the forces. Both these
issues have been fixed, and the GB results now match
release-4.5.
Note: The GB _radius_ calculations are still only done
in C, but the accelerated options will be re-enabled in
a pending patch (separated for clarity).
Fixes #1096.

Change-Id: I40151b9a9f1920006bfe9a39a8719698a824bfac

fix

Change-Id: I45630252d6a9c05a7f3695a7e6d07dcd13e0a25c
35 files changed:
src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_128_fma_double.c
src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_128_fma_double.c
src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_128_fma_double.c
src/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_template_avx_128_fma_double.pre
src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_128_fma_single.c
src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_128_fma_single.c
src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_128_fma_single.c
src/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_template_avx_128_fma_single.pre
src/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_256_double.c
src/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_256_double.c
src/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_256_double.c
src/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_template_avx_256_double.pre
src/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_256_single.c
src/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_256_single.c
src/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_256_single.c
src/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_template_avx_256_single.pre
src/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwLJ_GeomP1P1_c.c
src/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse2_double.c
src/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse2_double.c
src/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse2_double.c
src/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_template_sse2_double.pre
src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse2_single.c
src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse2_single.c
src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse2_single.c
src/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_template_sse2_single.pre
src/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse4_1_double.c
src/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse4_1_double.c
src/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse4_1_double.c
src/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_template_sse4_1_double.pre
src/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse4_1_single.c
src/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse4_1_single.c
src/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse4_1_single.c
src/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_template_sse4_1_single.pre
src/mdlib/forcerec.c
src/mdlib/genborn.c