[lammps] 03/05: Merge tag 'upstream/0_20140523.gite5e877d'
Anton Gladky
gladk at moszumanska.debian.org
Sat May 24 19:14:18 UTC 2014
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch master
in repository lammps.
commit 7653943eb2d0d89dd9bdd4380afa9b6f2b91944d
Merge: 7811c49 4bd2ecb
Author: Anton Gladky <gladk at debian.org>
Date: Sat May 24 18:04:03 2014 +0200
Merge tag 'upstream/0_20140523.gite5e877d'
Upstream version 0~20140523.gite5e877d
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src/USER-REAXC/pair_reax_c.cpp | 71 +-
src/USER-REAXC/pair_reax_c.h | 11 +-
src/USER-REAXC/reaxc_allocate.cpp | 581 +-
src/USER-REAXC/reaxc_allocate.h | 14 +-
src/USER-REAXC/reaxc_basic_comm.cpp | 317 -
src/USER-REAXC/reaxc_basic_comm.h | 52 -
src/USER-REAXC/reaxc_bond_orders.cpp | 645 +-
src/USER-REAXC/reaxc_bonds.cpp | 33 -
src/USER-REAXC/reaxc_control.cpp | 26 +-
src/USER-REAXC/reaxc_defs.h | 2 +-
src/USER-REAXC/reaxc_ffield.cpp | 63 -
src/USER-REAXC/reaxc_forces.cpp | 282 +-
src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 68 +-
src/USER-REAXC/reaxc_init_md.cpp | 654 +-
src/USER-REAXC/reaxc_init_md.h | 6 -
src/USER-REAXC/reaxc_io_tools.cpp | 1145 +--
src/USER-REAXC/reaxc_list.cpp | 36 -
src/USER-REAXC/reaxc_lookup.cpp | 30 +-
src/USER-REAXC/reaxc_multi_body.cpp | 145 +-
src/USER-REAXC/reaxc_nonbonded.cpp | 109 +-
src/USER-REAXC/reaxc_reset_tools.cpp | 45 +-
src/USER-REAXC/reaxc_system_props.cpp | 113 -
src/USER-REAXC/reaxc_tool_box.cpp | 233 +-
src/USER-REAXC/reaxc_tool_box.h | 6 -
src/USER-REAXC/reaxc_torsion_angles.cpp | 161 -
src/USER-REAXC/reaxc_traj.cpp | 302 -
src/USER-REAXC/reaxc_types.h | 176 +-
src/USER-REAXC/reaxc_valence_angles.cpp | 174 +-
src/USER-REAXC/reaxc_vector.cpp | 289 +-
src/USER-REAXC/reaxc_vector.h | 31 -
src/USER-SPH/atom_vec_meso.cpp | 18 +-
src/USER-SPH/pair_sph_rhosum.cpp | 2 +-
src/VORONOI/README | 2 +-
src/VORONOI/compute_voronoi_atom.cpp | 235 +-
src/VORONOI/compute_voronoi_atom.h | 24 +-
src/WINDOWS/LAMMPS.sln | 36 +
src/WINDOWS/LAMMPS.vcproj | 2957 +++++++
src/WINDOWS/LAMMPS.vsmacros | Bin 0 -> 182784 bytes
src/WINDOWS/README.txt | 78 +
src/WINDOWS/STUBS.vcproj | 156 +
src/WINDOWS/extra/dirent.h | 372 +
src/WINDOWS/extra/erf.h | 19 +
src/WINDOWS/extra/erf_namd.c | 345 +
src/WINDOWS/extra/fftw2/FFTW2dll.dll | Bin 0 -> 263168 bytes
src/WINDOWS/extra/fftw2/FFTW2dll.lib | Bin 0 -> 22998 bytes
src/WINDOWS/extra/fftw2/FFTW2st.lib | Bin 0 -> 404572 bytes
src/WINDOWS/extra/fftw2/RFFTW2dll.dll | Bin 0 -> 481792 bytes
src/WINDOWS/extra/fftw2/RFFTW2dll.lib | Bin 0 -> 35830 bytes
src/WINDOWS/extra/fftw2/RFFTW2st.lib | Bin 0 -> 337962 bytes
src/WINDOWS/extra/fftw2/fftw.h | 421 +
src/WINDOWS/extra/inttypes.h | 305 +
src/WINDOWS/extra/sleep.cpp | 10 +
src/WINDOWS/extra/sleep.h | 1 +
src/WINDOWS/extra/stdint.h | 247 +
src/WINDOWS/extra/sys/time.h | 28 +
src/WINDOWS/extra/unistd.h | 1 +
src/WINDOWS/settings/style_angle.h | 9 +
src/WINDOWS/settings/style_atom.h | 12 +
src/WINDOWS/settings/style_bond.h | 9 +
src/WINDOWS/settings/style_command.h | 16 +
src/WINDOWS/settings/style_compute.h | 44 +
src/WINDOWS/settings/style_dihedral.h | 7 +
src/WINDOWS/settings/style_dump.h | 8 +
src/WINDOWS/settings/style_fix.h | 69 +
src/WINDOWS/settings/style_improper.h | 5 +
src/WINDOWS/settings/style_integrate.h | 3 +
src/WINDOWS/settings/style_kspace.h | 5 +
src/WINDOWS/settings/style_minimize.h | 6 +
src/WINDOWS/settings/style_pair.h | 49 +
src/WINDOWS/settings/style_region.h | 9 +
src/XTC/dump_xtc.cpp | 4 +-
src/accelerator_cuda.h | 6 +-
src/accelerator_kokkos.h | 6 +-
src/atom.cpp | 47 +-
src/atom.h | 2 +
src/atom_vec.cpp | 21 +-
src/atom_vec.h | 4 +-
src/atom_vec_atomic.cpp | 6 +-
src/atom_vec_body.cpp | 9 +-
src/atom_vec_charge.cpp | 6 +-
src/atom_vec_ellipsoid.cpp | 9 +-
src/atom_vec_hybrid.cpp | 6 +-
src/atom_vec_line.cpp | 8 +-
src/atom_vec_sphere.cpp | 6 +-
src/atom_vec_tri.cpp | 8 +-
src/balance.cpp | 208 +-
src/balance.h | 12 +-
src/change_box.cpp | 2 +-
src/comm.cpp | 1967 +----
src/comm.h | 182 +-
src/{comm.cpp => comm_brick.cpp} | 572 +-
src/{comm.h => comm_brick.h} | 61 +-
src/comm_tiled.cpp | 801 ++
src/comm_tiled.h | 98 +
src/compute.cpp | 14 +
src/compute.h | 22 +-
src/compute_atom_molecule.cpp | 2 +-
src/compute_cluster_atom.cpp | 32 +-
src/compute_cluster_atom.h | 2 +-
src/compute_gyration.cpp | 2 +-
src/compute_gyration_molecule.cpp | 2 +-
src/compute_reduce_region.cpp | 4 +-
src/compute_temp.cpp | 7 +-
src/compute_temp.h | 1 -
src/compute_temp_com.cpp | 7 +-
src/compute_temp_com.h | 1 -
src/compute_temp_deform.cpp | 5 +-
src/compute_temp_deform.h | 1 -
src/compute_temp_partial.cpp | 7 +-
src/compute_temp_partial.h | 1 -
src/compute_temp_profile.cpp | 9 +-
src/compute_temp_profile.h | 1 -
src/compute_temp_ramp.cpp | 5 +-
src/compute_temp_ramp.h | 2 +-
src/compute_temp_region.cpp | 12 +-
src/compute_temp_region.h | 1 +
src/compute_temp_sphere.cpp | 9 +-
src/compute_temp_sphere.h | 2 +-
src/create_atoms.cpp | 4 +-
src/create_box.cpp | 5 +-
src/delete_atoms.cpp | 237 +-
src/delete_atoms.h | 2 +
src/delete_bonds.cpp | 2 +-
src/displace_atoms.cpp | 2 +-
src/dump.cpp | 14 +-
src/dump.h | 4 +-
src/dump_cfg.cpp | 4 +-
src/dump_cfg.h | 2 +
src/dump_custom.cpp | 1 +
src/fix.cpp | 1 +
src/fix.h | 4 +-
src/fix_adapt.cpp | 136 +-
src/fix_adapt.h | 3 +
src/fix_addforce.cpp | 31 +-
src/fix_ave_atom.cpp | 6 +-
src/fix_ave_histo.cpp | 1 +
src/fix_ave_spatial.cpp | 4 +
src/fix_aveforce.cpp | 35 +-
src/fix_balance.cpp | 68 +-
src/fix_balance.h | 4 +-
src/fix_group.cpp | 2 +
src/fix_heat.cpp | 13 +-
src/fix_move.cpp | 23 +-
src/fix_nh.cpp | 7 +
src/fix_nve.cpp | 1 +
src/fix_setforce.cpp | 37 +-
src/fix_store_state.cpp | 3 +-
src/fix_wall_region.cpp | 2 +
src/force.cpp | 56 +-
src/force.h | 1 +
src/group.cpp | 39 +-
src/image.cpp | 4 +-
src/input.cpp | 28 +-
src/input.h | 3 +-
src/irregular.cpp | 12 +-
src/irregular.h | 4 +-
src/lammps.cpp | 3 +-
src/library.cpp | 6 +-
src/modify.cpp | 38 +-
src/neigh_request.cpp | 3 +
src/neigh_request.h | 5 +-
src/neighbor.cpp | 19 +-
src/pair.h | 2 +
src/pair_lj_cut_coul_cut.cpp | 1 +
src/read_data.cpp | 53 +-
src/read_dump.cpp | 2 +-
src/read_restart.cpp | 6 +-
src/region.cpp | 75 +-
src/region.h | 3 +-
src/rerun.cpp | 2 +
src/set.cpp | 1 +
src/thermo.cpp | 4 +-
src/variable.cpp | 116 +-
src/variable.h | 4 +-
src/velocity.cpp | 18 +-
src/version.h | 2 +-
src/write_data.cpp | 34 +-
src/write_dump.cpp | 3 +
src/write_restart.cpp | 14 +-
tools/README | 1 +
tools/fep/README | 7 +
tools/fep/bar.py | 88 +
tools/fep/fdti.py | 36 +
tools/fep/fep.py | 23 +
tools/fep/nti.py | 30 +
tools/moltemplate/common/amber/README.TXT | 49 +-
tools/moltemplate/common/amber/amberparm2lt.sh | 88 +-
.../common/amber/amberparm_improper_to_lt.py | 34 +-
.../common/amber/amberparm_pair_to_lt.py | 3 +-
tools/moltemplate/common/gaff.lt | 8907 ++++++++++----------
tools/moltemplate/common/oplsaa/README.TXT | 116 +-
tools/moltemplate/common/oplsaa/oplsaa.txt | 5968 -------------
.../common/oplsaa/oplsaa_moltemplate.py | 287 +-
.../membrane+protein/moltemplate_files/system.lt | 4 +-
.../2bead_heteropolymer/moltemplate_files/2bead.lt | 2 +-
.../AMBER_force_field_examples/WARNING.TXT | 60 +-
.../hexadecane/README_setup.sh | 64 +-
.../hexadecane/moltemplate_files/ch2group.lt | 12 +-
.../hexadecane/moltemplate_files/ch3group.lt | 21 +-
.../hexadecane/moltemplate_files/hexadecane.lt | 57 +-
.../README_remove_irrelevant_info.sh | 52 +
.../hexadecane/run.in.npt | 2 +-
.../waterTIP3P+isobutane/README.TXT | 47 +-
.../waterTIP3P+isobutane/README_setup.sh | 107 +-
.../moltemplate_files/isobutane.lt | 41 +-
.../README_remove_irrelevant_info.sh | 69 +
.../waterTIP3P+isobutane/run.in.npt | 7 +-
.../OPLSAA_force_field_examples/WARNING.TXT | 7 +-
.../ethylene+benzene_PACKMOL/README.TXT | 24 +
.../ethylene+benzene_PACKMOL/README_run.sh | 39 +
.../README_setup.sh | 14 +-
.../ethylene+benzene_PACKMOL/README_visualize.txt | 87 +
.../ethylene+benzene_PACKMOL/images/benzene.jpg | Bin 0 -> 15032 bytes
.../images/ethylene+benzene_box80x80x80_LR.jpg | Bin 0 -> 130048 bytes
.../ethylene+benzene_PACKMOL/images/ethylene.jpg | Bin 0 -> 11657 bytes
.../moltemplate_files/benzene.lt | 51 +
.../moltemplate_files/ethylene.lt | 40 +
.../oplsaa_lt_generator/AUTHOR.TXT | 3 +
.../oplsaa_lt_generator/README.TXT | 108 +
.../minimal_versions/README.TXT | 16 +
.../minimal_versions/oplsaa_subset_minimal.prm | 37 +
.../minimal_versions/oplsaa_subset_simplified.prm | 49 +
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 392 +
.../oplsaa_lt_generator/oplsaa_subset.prm | 5127 +++++++++++
.../moltemplate_files/system.lt | 21 +
.../packmol_files/README.TXT | 5 +
.../packmol_files/benzene.xyz | 14 +
.../packmol_files/ethylene.xyz | 8 +
.../packmol_files/mix_ethylene+benzene.inp | 31 +
.../ethylene+benzene_PACKMOL/run.in.npt | 57 +
.../ethylene+benzene_PACKMOL/run.in.nvt | 50 +
.../ethylene/README_setup.sh | 2 +-
.../ethylene/moltemplate_files/ethylene.lt | 24 +-
.../oplsaa_lt_generator/README.TXT | 101 +-
.../minimal_versions/README.TXT | 16 +
.../minimal_versions/oplsaa_subset_minimal.prm | 22 +
.../minimal_versions/oplsaa_subset_simplified.prm | 25 +
.../oplsaa_lt_generator/oplsaa.txt | 5968 -------------
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 287 +-
.../oplsaa_lt_generator/oplsaa_subset.prm | 5125 +++++++++++
.../oplsaa_lt_generator/oplsaa_subset.txt | 3450 --------
.../ethylene/moltemplate_files/system.lt | 2 +-
.../convert_LAMMPS_to_LT_examples/cnad-cnt/cnt.lt | 779 --
.../all_atom_examples/hexadecane/WARNING.TXT | 2 +-
.../hexadecane/moltemplate_files/alkanes.lt | 14 +-
.../hexadecane/moltemplate_files/ch2group.lt | 12 +-
.../hexadecane/moltemplate_files/ch3group.lt | 12 +-
.../hexadecane/moltemplate_files/hexadecane.lt | 51 +-
.../all_atom_examples/hexadecane/run.in.npt | 2 +-
.../nanotube+water/moltemplate_files/README.sh | 7 +-
.../nanotube+water/moltemplate_files/graphene.lt | 121 +-
.../moltemplate_files/graphene_walls.lt | 5 +-
.../nanotube+water/moltemplate_files/graphite.lt | 61 +
.../nanotube+water/moltemplate_files/nanotube.lt | 19 +-
.../nanotube+water/moltemplate_files/spce.lt | 10 +-
.../nanotube+water/moltemplate_files/system.lt | 21 +-
tools/moltemplate/src/moltemplate.sh | 4 +-
tools/moltemplate/src/nbody_by_type.py | 4 +-
tools/moltemplate/src/nbody_by_type_lib.py | 13 +-
tools/moltemplate/src/ttree_lex.py | 2 +-
tools/moltemplate/src/ttree_matrix_stack.py | 16 +-
669 files changed, 149981 insertions(+), 34942 deletions(-)
--
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