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

Merge release-4-6 into master

Conflicts:
CMakeLists.txt (OPENMM, regressiontests)
COPYING (OpenMM, renumbering)
cmake/FortranCInterface.cmake
include/CMakeLists.txt (F77, not needed)
include/disre.h (rename detection failed - no conflict)
include/types/iteratedconstraints.h (rename detection failed -
     no conflict)

both here and src/kernel new - only contrib kep:
src/contrib/md_openmm.c
src/contrib/md_openmm.h
src/contrib/openmm_wrapper.cpp
src/contrib/openmm_wrapper.h
src/kernel/md_openmm.c
src/kernel/openmm_wrapper.cpp
src/kernel/openmm_wrapper.h
src/programs/mdrun/md_openmm.c
src/programs/mdrun/openmm_wrapper.cpp
src/programs/mdrun/openmm_wrapper.h
src/programs/mdrun/runner.c

src/gmxlib/rando.c (rename detection failed - no conflict)
src/gromacs/gmxlib/main.c
src/gromacs/gmxlib/string2.c
src/gromacs/gmxlib/tpxio.c (incrememted to 92 - updated if)
src/gromacs/gmxlib/vmdio.c
src/gromacs/legacyheaders/domdec.h (removed export)
src/gromacs/legacyheaders/gmx_omp_nthreads.h
src/gromacs/legacyheaders/main.h
src/gromacs/legacyheaders/names.h (removed export)
src/gromacs/linearalgebra/eigensolver.c
src/gromacs/linearalgebra/gmx_arpack.c
src/gromacs/linearalgebra/gmx_arpack.h
src/gromacs/linearalgebra/gmx_lapack.h (removed #define F77)
src/kernel/CMakeLists.txt (OpenMM changes moved to
       src/programs/mdrun/CMakeLists.txt)
src/tools/CMakeLists.txt
src/tools/gmx_bar.c
src/tools/gmx_covar.c
tests/CMakeLists.txt (fixed paths)

Extra changes:
src/config.h.cmakein (removed double gmx_header_config.h include)
src/gromacs/CMakeLists.txt (removed OpenMM )
        src/gromacs/linearalgebra/gmx_blas.h (removed #define F77)

Change-Id: I04fb402d503c8d5d97ee364c598e0f474956052f

author	Roland Schulz <roland@utk.edu>
	Sun, 20 Jan 2013 23:41:51 +0000 (18:41 -0500)
committer	Roland Schulz <roland@utk.edu>
	Sun, 20 Jan 2013 23:49:12 +0000 (18:49 -0500)
commit	03d5ecd55fa13e68e6db448c210b96ad98d7a279
tree	5a547b49d4a3da36fffe5a00a2694e8f89f04ac0	tree \| snapshot
parent	2979cccecba870240c2c2685d1518e60845b80d5	commit \| diff
parent	19bbbf6d5e558ccff77eaed84a6832164ff149a5	commit \| diff

CMakeLists.txt	diff1 \|	diff2 \|	blob \| history
COPYING	diff1 \|	diff2 \|	blob \| history
cmake/FindFFTW.cmake	diff1 \|	diff2 \|	blob \| history
cmake/gmxCFlags.cmake	diff1 \|	diff2 \|	blob \| history
cmake/gmxGetCompilerInfo.cmake	diff1 \|	diff2 \|	blob \| history
cmake/gmxManageGPU.cmake	diff1 \|	diff2 \|	blob \| history
src/config.h.cmakein	diff1 \|	diff2 \|	blob \| history
src/contrib/CMakeLists.txt	diff1 \|	diff2 \|	blob \| history
src/contrib/FindOpenMM.cmake	diff1 \|	diff2 \|	blob \| history
src/gromacs/CMakeLists.txt	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/cinvsqrtdata.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/disre.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/gmx_detect_hardware.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/gmx_omp_nthreads.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/gpu_utils/gpu_utils.cu	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/libxdrf.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/main.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/mtop_util.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/names.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/network.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_128_fma_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_128_fma_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_128_fma_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_double/nb_kernel_template_avx_128_fma_double.pre	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_128_fma_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_128_fma_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_128_fma_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_128_fma_single/nb_kernel_template_avx_128_fma_single.pre	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_256_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_256_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_256_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_double/nb_kernel_template_avx_256_double.pre	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_avx_256_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_avx_256_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_avx_256_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_avx_256_single/nb_kernel_template_avx_256_single.pre	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_ElecGB_VdwLJ_GeomP1P1_c.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse2_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse2_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse2_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_double/nb_kernel_template_sse2_double.pre	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse2_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse2_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse2_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse2_single/nb_kernel_template_sse2_single.pre	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse4_1_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse4_1_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse4_1_double.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_double/nb_kernel_template_sse4_1_double.pre	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecGB_VdwCSTab_GeomP1P1_sse4_1_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecGB_VdwLJ_GeomP1P1_sse4_1_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_ElecGB_VdwNone_GeomP1P1_sse4_1_single.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_kernel_sse4_1_single/nb_kernel_template_sse4_1_single.pre	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/orires.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/tpxio.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/txtdump.c	diff1 \|	\|	blob \| history
src/gromacs/gmxpreprocess/readir.c	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/disre.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/domdec.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/gmx_omp_nthreads.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/gpu_utils.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/main.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/mdebin.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/mdrun.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/names.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/hw_info.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/inputrec.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/iteratedconstraints.h	diff1 \|	\|	blob \| history
src/gromacs/linearalgebra/eigensolver.c	diff1 \|	\|	blob \| history
src/gromacs/linearalgebra/gmx_arpack.c	diff1 \|	\|	blob \| history
src/gromacs/linearalgebra/gmx_arpack.h	diff1 \|	\|	blob \| history
src/gromacs/linearalgebra/gmx_blas.h	diff1 \|	\|	blob \| history
src/gromacs/linearalgebra/gmx_lapack.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/coupling.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/domdec.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/forcerec.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/genborn.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/iteratedconstraints.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/mdebin.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/mdebin_bar.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/mdebin_bar.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/minimize.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/qm_gamess.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/qm_mopac.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/update.c	diff1 \|	\|	blob \| history
src/programs/gmxcheck/tpbcmp.c	diff1 \|	\|	blob \| history
src/programs/gmxdump/gmxdump.c	diff1 \|	\|	blob \| history
src/programs/mdrun/CMakeLists.txt	diff1 \|	\|	blob \| history
src/programs/mdrun/md.c	diff1 \|	\|	blob \| history
src/programs/mdrun/mdrun.c	diff1 \|	\|	blob \| history
src/programs/mdrun/membed.c	diff1 \|	\|	blob \| history
src/programs/mdrun/pme_loadbal.c	diff1 \|	\|	blob \| history
src/programs/mdrun/repl_ex.c	diff1 \|	\|	blob \| history
src/programs/mdrun/runner.c	diff1 \|	\|	blob \| history
src/tools/gmx_bar.c	diff1 \|	diff2 \|	blob \| history
src/tools/gmx_disre.c	diff1 \|	diff2 \|	blob \| history
src/tools/gmx_energy.c	diff1 \|	diff2 \|	blob \| history
src/tools/gmx_membed.c	diff1 \|	diff2 \|	blob \| history
src/tools/gmx_trjconv.c	diff1 \|	diff2 \|	blob \| history
src/tools/gmx_tune_pme.c	diff1 \|	diff2 \|	blob \| history
tests/CMakeLists.txt	diff1 \|	diff2 \|	blob \| history