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

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

author	Roland Schulz <roland@utk.edu>
	Tue, 21 May 2013 04:33:22 +0000 (00:33 -0400)
committer	Roland Schulz <roland@utk.edu>
	Tue, 21 May 2013 06:44:50 +0000 (02:44 -0400)
commit	256a0a2e1142c2443bd412b55cf7d64c5f285a22
tree	88a15a05c148fe0f2b35318f03670d0e493b190d	tree \| snapshot
parent	99085af972d03ffbb3ef290a7a604cc732b2489e	commit \| diff
parent	073fa1ed7651e2dd504741c9990978667f620d8d	commit \| diff

Merge release-4-6 into master

Conflicts:
CMakeLists.txt
cmake/FindMKL.cmake (deleted in 4.6)
src/gromacs/selection/compiler.cpp (was backport)
src/mdlib/nbnxn_cuda/nbnxn_cuda_types.h
src/ngmx/CMakeLists.txt
src/programs/grompp/gpp_tomorse.h

was incorrectly identified as rename target:
src/gromacs/trajectoryanalysis/tests/CMakeLists.txt
change instead belonged to:
        src/gromacs/mdlib/nbnxn_cuda/CMakeLists.txt

moved changes for OpenMM to src/programs/mdrun/CMakeLists.txt:
src/kernel/CMakeLists.txt
Deleted in 5.0 - only copyright changed:
share/template/template.c
share/template/template_doc.c
FFT_LIBRARIES change already in 5.0:
src/gmxlib/CMakeLists.txt
src/mdlib/CMakeLists.txt
src/tools/CMakeLists.txt
Removed GMX_*_EXPORT:
        src/gromacs/legacyheaders/domdec.h
        src/gromacs/legacyheaders/pme.h

Change-Id: Ib1d4abe66ea7b29c418dba687f8e7c1d645d39c4

73 files changed:

CMakeLists.txt	diff1 \|	diff2 \|	blob \| history
COPYING	diff1 \|	diff2 \|	blob \| history
admin/gromacs.spec	diff1 \|	diff2 \|	blob \| history
admin/mkhtml	diff1 \|	diff2 \|	blob \| history
cmake/FindFFTW.cmake	diff1 \|	diff2 \|	blob \| history
cmake/FindVMD.cmake	diff1 \|	diff2 \|	blob \| history
src/contrib/BuildMdrunOpenMM.cmake	diff1 \|	diff2 \|	blob \| history
src/contrib/CMakeLists.txt	diff1 \|	diff2 \|	blob \| history
src/contrib/mdrun_openmm.c	diff1 \|	diff2 \|	blob \| history
src/gromacs/gmxana/gmx_anadock.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_do_dssp.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_hydorder.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_make_edi.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_make_ndx.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_mindist.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_mk_angndx.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_sgangle.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_sigeps.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/bondfree.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/copyrite.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/gmx_system_xdr.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_free_energy.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/topsort.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/trxio.c	diff1 \|	\|	blob \| history
src/gromacs/gmxpreprocess/readir.c	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/domdec.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/gmx_simd_macros.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/gmx_system_xdr.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/mdrun.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/pme.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/group.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/nb_verlet.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/nbnxn_pairlist.h	diff1 \|	\|	blob \| history
src/gromacs/linearalgebra/gmx_blas/blas_copyright	diff1 \|	diff2 \|	blob \| history
src/gromacs/linearalgebra/gmx_lapack/lapack_copyright	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/coupling.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/domdec.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/edsam.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/force.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/gmx_wallcycle.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/md_support.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/mdebin.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_atomdata.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/CMakeLists.txt	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_cuda/nbnxn_cuda_kernel_legacy.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_internal.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn_inner.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn_outer.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn_inner.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn_outer.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search_simd_2xnn.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search_simd_4xn.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/pme.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/pull_rotation.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/sim_util.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/tgroup.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/update.c	diff1 \|	\|	blob \| history
src/ngmx/CMakeLists.txt	diff1 \|	diff2 \|	blob \| history
src/programs/grompp/gpp_tomorse.h	diff1 \|	\|	blob \| history
src/programs/mdrun/CMakeLists.txt	diff1 \|	\|	blob \| history
src/programs/mdrun/mdrun.c	diff1 \|	\|	blob \| history
src/programs/mdrun/pme_loadbal.c	diff1 \|	\|	blob \| history
src/programs/mdrun/runner.c	diff1 \|	\|	blob \| history
tests/CMakeLists.txt	diff1 \|	diff2 \|	blob \| history

Local GROMACS mirror with custom stuff

RSS Atom

CMakeLists.txt	diff1 \|	diff2 \|	blob \| history
COPYING	diff1 \|	diff2 \|	blob \| history
admin/gromacs.spec	diff1 \|	diff2 \|	blob \| history
admin/mkhtml	diff1 \|	diff2 \|	blob \| history
cmake/FindFFTW.cmake	diff1 \|	diff2 \|	blob \| history
cmake/FindVMD.cmake	diff1 \|	diff2 \|	blob \| history
src/contrib/BuildMdrunOpenMM.cmake	diff1 \|	diff2 \|	blob \| history
src/contrib/CMakeLists.txt	diff1 \|	diff2 \|	blob \| history
src/contrib/mdrun_openmm.c	diff1 \|	diff2 \|	blob \| history
src/gromacs/gmxana/gmx_anadock.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_do_dssp.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_hydorder.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_make_edi.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_make_ndx.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_mindist.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_mk_angndx.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_sgangle.c	diff1 \|	\|	blob \| history
src/gromacs/gmxana/gmx_sigeps.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/bondfree.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/copyrite.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/gmx_system_xdr.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/nonbonded/nb_free_energy.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/topsort.c	diff1 \|	\|	blob \| history
src/gromacs/gmxlib/trxio.c	diff1 \|	\|	blob \| history
src/gromacs/gmxpreprocess/readir.c	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/domdec.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/gmx_simd_macros.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/gmx_system_xdr.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/mdrun.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/pme.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/group.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/nb_verlet.h	diff1 \|	\|	blob \| history
src/gromacs/legacyheaders/types/nbnxn_pairlist.h	diff1 \|	\|	blob \| history
src/gromacs/linearalgebra/gmx_blas/blas_copyright	diff1 \|	diff2 \|	blob \| history
src/gromacs/linearalgebra/gmx_lapack/lapack_copyright	diff1 \|	diff2 \|	blob \| history
src/gromacs/mdlib/coupling.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/domdec.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/edsam.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/force.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/gmx_wallcycle.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/md_support.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/mdebin.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_atomdata.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/CMakeLists.txt	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_cuda/nbnxn_cuda_kernel_legacy.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_internal.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn_inner.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_2xnn_outer.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn_inner.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_4xn_outer.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_simd_utils.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search_simd_2xnn.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/nbnxn_search_simd_4xn.h	diff1 \|	\|	blob \| history
src/gromacs/mdlib/pme.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/pull_rotation.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/sim_util.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/tgroup.c	diff1 \|	\|	blob \| history
src/gromacs/mdlib/update.c	diff1 \|	\|	blob \| history
src/ngmx/CMakeLists.txt	diff1 \|	diff2 \|	blob \| history
src/programs/grompp/gpp_tomorse.h	diff1 \|	\|	blob \| history
src/programs/mdrun/CMakeLists.txt	diff1 \|	\|	blob \| history
src/programs/mdrun/mdrun.c	diff1 \|	\|	blob \| history
src/programs/mdrun/pme_loadbal.c	diff1 \|	\|	blob \| history
src/programs/mdrun/runner.c	diff1 \|	\|	blob \| history
tests/CMakeLists.txt	diff1 \|	diff2 \|	blob \| history