Package: gromacs / 4.5.5-2

Metadata

Package Version Patches format
gromacs 4.5.5-2 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
10_release 4 5 patches.patch | (download)

CMakeLists.txt | 88 60 + 28 - 0 !
COPYING-OTHER | 83 83 + 0 - 0 !
Makefile.am | 1 1 + 0 - 0 !
admin/GerritBuild.bat | 3 3 + 0 - 0 !
cmake/CMakeASM-NASMInformation.cmake | 30 0 + 30 - 0 !
cmake/CMakeASM_NASMInformation.cmake | 30 30 + 0 - 0 !
cmake/CMakeDetermineASM-NASMCompiler.cmake | 13 0 + 13 - 0 !
cmake/CMakeDetermineASM_NASMCompiler.cmake | 13 13 + 0 - 0 !
cmake/CMakeTestASM-NASMCompiler.cmake | 9 0 + 9 - 0 !
cmake/CMakeTestASM_NASMCompiler.cmake | 9 9 + 0 - 0 !
cmake/FindLAPACK.cmake | 2 1 + 1 - 0 !
cmake/ThreadMPI.cmake | 11 9 + 2 - 0 !
cmake/Toolchain-BlueGeneP.cmake | 8 8 + 0 - 0 !
cmake/gmxCFlags.cmake | 38 29 + 9 - 0 !
cmake/gmxGenerateVersionInfo.cmake | 221 103 + 118 - 0 !
cmake/gmxTestIsfinite.cmake | 77 77 + 0 - 0 !
include/checkpoint.h | 6 5 + 1 - 0 !
include/domdec.h | 7 0 + 7 - 0 !
include/domdec_network.h | 7 0 + 7 - 0 !
include/gstat.h | 6 3 + 3 - 0 !
include/maths.h | 10 10 + 0 - 0 !
include/mdrun.h | 6 6 + 0 - 0 !
include/mtxio.h | 2 1 + 1 - 0 !
include/thread_mpi/atomic/gcc_x86.h | 37 21 + 16 - 0 !
include/thread_mpi/numa_malloc.h | 2 1 + 1 - 0 !
include/types/commrec.h | 3 2 + 1 - 0 !
include/types/simple.h | 4 4 + 0 - 0 !
include/vsite.h | 13 9 + 4 - 0 !
share/html/online/mdp_opt.html | 176 92 + 84 - 0 !
share/html/online/xpm.html | 2 2 + 0 - 0 !
share/top/charmm27.ff/ions.itp | 2 1 + 1 - 0 !
src/config.h.cmakein | 6 6 + 0 - 0 !
src/gmxlib/CMakeLists.txt | 18 9 + 9 - 0 !
src/gmxlib/atomprop.c | 12 7 + 5 - 0 !
src/gmxlib/checkpoint.c | 63 42 + 21 - 0 !
src/gmxlib/enxio.c | 14 7 + 7 - 0 !
src/gmxlib/futil.c | 38 36 + 2 - 0 !
src/gmxlib/gmx_lapack/dlasq2.c | 4 4 + 0 - 0 !
src/gmxlib/gmx_lapack/slasq2.c | 4 4 + 0 - 0 !
src/gmxlib/gmxfio.c | 2 1 + 1 - 0 !
src/gmxlib/libxdrf.c | 2 1 + 1 - 0 !
src/gmxlib/maths.c | 65 61 + 4 - 0 !
src/gmxlib/mshift.c | 2 1 + 1 - 0 !
src/gmxlib/mtxio.c | 4 2 + 2 - 0 !
src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h | 31 24 + 7 - 0 !
src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_w3_bluegene.h | 15 14 + 1 - 0 !
src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_w3w3_bluegene.h | 15 14 + 1 - 0 !
src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_w4_bluegene.h | 15 14 + 1 - 0 !
src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_w4w4_bluegene.h | 15 14 + 1 - 0 !
src/gmxlib/rmpbc.c | 6 4 + 2 - 0 !
src/gmxlib/selection/params.c | 12 8 + 4 - 0 !
src/gmxlib/selection/parser.c | 314 160 + 154 - 0 !
src/gmxlib/selection/parser.h | 4 2 + 2 - 0 !
src/gmxlib/selection/scanner_internal.c | 2 1 + 1 - 0 !
src/gmxlib/shift_util.c | 4 3 + 1 - 0 !
src/gmxlib/thread_mpi/numa_malloc.c | 2 1 + 1 - 0 !
src/gmxlib/thread_mpi/pthreads.c | 55 22 + 33 - 0 !
src/gmxlib/tpxio.c | 4 2 + 2 - 0 !
src/gmxlib/trajana/nbsearch.c | 2 1 + 1 - 0 !
src/gmxlib/trajana/trajana.c | 6 5 + 1 - 0 !
src/gmxlib/trnio.c | 2 1 + 1 - 0 !
src/gmxlib/wman.c | 231 223 + 8 - 0 !
src/kernel/gen_ad.c | 6 3 + 3 - 0 !
src/kernel/gen_vsite.c | 2 2 + 0 - 0 !
src/kernel/genhydro.c | 2 1 + 1 - 0 !
src/kernel/gmxcheck.c | 6 3 + 3 - 0 !
src/kernel/grompp.c | 19 19 + 0 - 0 !
src/kernel/md.c | 27 19 + 8 - 0 !
src/kernel/md_openmm.c | 3 1 + 2 - 0 !
src/kernel/mdrun.c | 5 3 + 2 - 0 !
src/kernel/pdb2top.c | 117 72 + 45 - 0 !
src/kernel/pgutil.c | 64 45 + 19 - 0 !
src/kernel/pgutil.h | 7 3 + 4 - 0 !
src/kernel/readir.c | 24 21 + 3 - 0 !
src/kernel/resall.c | 4 2 + 2 - 0 !
src/kernel/runner.c | 3 2 + 1 - 0 !
src/kernel/tpbcmp.c | 2 1 + 1 - 0 !
src/mdlib/CMakeLists.txt | 4 4 + 0 - 0 !
src/mdlib/clincs.c | 13 4 + 9 - 0 !
src/mdlib/constr.c | 4 2 + 2 - 0 !
src/mdlib/coupling.c | 7 6 + 1 - 0 !
src/mdlib/domdec.c | 5 3 + 2 - 0 !
src/mdlib/domdec_setup.c | 2 1 + 1 - 0 !
src/mdlib/ebin.c | 2 1 + 1 - 0 !
src/mdlib/fft5d.c | 8 4 + 4 - 0 !
src/mdlib/fftpack.c | 1570 1570 + 0 - 0 !
src/mdlib/fftpack.h | 56 56 + 0 - 0 !
src/mdlib/genborn.c | 2 1 + 1 - 0 !
src/mdlib/gmx_fft_fftpack.c | 1765 1 + 1764 - 0 !
src/mdlib/gmx_fft_fftw3.c | 3 3 + 0 - 0 !
src/mdlib/md_support.c | 37 19 + 18 - 0 !
src/mdlib/mdebin_bar.c | 4 2 + 2 - 0 !
src/mdlib/minimize.c | 32 15 + 17 - 0 !
src/mdlib/pme.c | 10 7 + 3 - 0 !
src/mdlib/pull.c | 6 3 + 3 - 0 !
src/mdlib/shellfc.c | 51 35 + 16 - 0 !
src/mdlib/sim_util.c | 41 5 + 36 - 0 !
src/mdlib/stat.c | 63 32 + 31 - 0 !
src/mdlib/vsite.c | 153 136 + 17 - 0 !
src/tools/anadih.c | 18 12 + 6 - 0 !
src/tools/autocorr.c | 2 1 + 1 - 0 !
src/tools/do_dssp.c | 38 28 + 10 - 0 !
src/tools/g_sigeps.c | 12 6 + 6 - 0 !
src/tools/geminate.c | 8 1 + 7 - 0 !
src/tools/gmx_anaeig.c | 40 23 + 17 - 0 !
src/tools/gmx_analyze.c | 36 19 + 17 - 0 !
src/tools/gmx_angle.c | 20 14 + 6 - 0 !
src/tools/gmx_bar.c | 6 3 + 3 - 0 !
src/tools/gmx_bond.c | 2 1 + 1 - 0 !
src/tools/gmx_chi.c | 18 10 + 8 - 0 !
src/tools/gmx_cluster.c | 10 6 + 4 - 0 !
src/tools/gmx_clustsize.c | 2 1 + 1 - 0 !
src/tools/gmx_current.c | 4 2 + 2 - 0 !
src/tools/gmx_density.c | 12 6 + 6 - 0 !
src/tools/gmx_dielectric.c | 6 3 + 3 - 0 !
src/tools/gmx_dipoles.c | 12 6 + 6 - 0 !
src/tools/gmx_dist.c | 4 2 + 2 - 0 !
src/tools/gmx_editconf.c | 17 10 + 7 - 0 !
src/tools/gmx_enemat.c | 2 1 + 1 - 0 !
src/tools/gmx_energy.c | 19 10 + 9 - 0 !
src/tools/gmx_genbox.c | 16 8 + 8 - 0 !
src/tools/gmx_genpr.c | 4 2 + 2 - 0 !
src/tools/gmx_gyrate.c | 2 1 + 1 - 0 !
src/tools/gmx_h2order.c | 2 1 + 1 - 0 !
src/tools/gmx_helix.c | 2 1 + 1 - 0 !
src/tools/gmx_kinetics.c | 2 1 + 1 - 0 !
src/tools/gmx_mdmat.c | 2 1 + 1 - 0 !
src/tools/gmx_membed.c | 8 5 + 3 - 0 !
src/tools/gmx_mindist.c | 2 1 + 1 - 0 !
src/tools/gmx_morph.c | 10 5 + 5 - 0 !
src/tools/gmx_msd.c | 4 4 + 0 - 0 !
src/tools/gmx_nmtraj.c | 2 1 + 1 - 0 !
src/tools/gmx_order.c | 2 1 + 1 - 0 !
src/tools/gmx_potential.c | 8 4 + 4 - 0 !
src/tools/gmx_rmsdist.c | 4 2 + 2 - 0 !
src/tools/gmx_saltbr.c | 2 1 + 1 - 0 !
src/tools/gmx_select.c | 3 2 + 1 - 0 !
src/tools/gmx_sham.c | 269 200 + 69 - 0 !
src/tools/gmx_sorient.c | 12 6 + 6 - 0 !
src/tools/gmx_spatial.c | 2 1 + 1 - 0 !
src/tools/gmx_tcaf.c | 24 12 + 12 - 0 !
src/tools/gmx_trjconv.c | 6 3 + 3 - 0 !
src/tools/gmx_tune_pme.c | 72 53 + 19 - 0 !
src/tools/gmx_vanhove.c | 8 4 + 4 - 0 !
src/tools/gmx_velacc.c | 6 5 + 1 - 0 !
src/tools/gmx_wheel.c | 2 1 + 1 - 0 !
src/tools/hxprops.c | 6 4 + 2 - 0 !
src/tools/mk_angndx.c | 2 1 + 1 - 0 !
148 files changed, 3880 insertions(+), 2909 deletions(-)

 update to head of release-4-5-patches branch (f361fa9c)
11_readme.patch | (download)

README | 9 8 + 1 - 0 !
1 file changed, 8 insertions(+), 1 deletion(-)

 edit readme to explain that this is not an official upstream build
31_manpages.patch | (download)

man/man1/g_analyze.1 | 2 1 + 1 - 0 !
man/man1/g_dist.1 | 2 1 + 1 - 0 !
man/man1/g_hydorder.1 | 2 1 + 1 - 0 !
man/man1/g_mindist.1 | 2 1 + 1 - 0 !
man/man1/g_tune_pme.1 | 2 1 + 1 - 0 !
man/man1/g_wham.1 | 2 1 + 1 - 0 !
src/kernel/hizzie.c | 2 1 + 1 - 0 !
src/kernel/readir.c | 2 1 + 1 - 0 !
src/tools/gmx_genpr.c | 2 1 + 1 - 0 !
9 files changed, 9 insertions(+), 9 deletions(-)

 minor spelling and header fixes for various man pages.