[lammps] 01/05: Merge tag 'upstream/0_20140415.git42bb280'
Anton Gladky
gladk at moszumanska.debian.org
Wed Apr 16 18:04:47 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 0f0d35a1a79f2f82e87cb08af719f3031e45277c
Merge: eb5d230 f2930e3
Author: Anton Gladky <gladk at debian.org>
Date: Wed Apr 16 19:20:54 2014 +0200
Merge tag 'upstream/0_20140415.git42bb280'
Upstream version 0~20140415.git42bb280
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src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp | 2 +-
src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp | 1 +
src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp | 4 +
src/USER-OMP/pair_lj_sdk_coul_msm_omp.h | 8 +
src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp | 2 +-
src/USER-OMP/pair_lj_sf_omp.cpp | 5 +-
src/USER-OMP/pair_meam_spline_omp.cpp | 10 +-
src/USER-OMP/pair_nb3b_harmonic_omp.cpp | 3 +-
src/USER-OMP/pair_resquared_omp.cpp | 1 +
src/USER-OMP/pair_table_omp.cpp | 2 +-
src/USER-OMP/pair_tersoff_table_omp.cpp | 88 +-
src/USER-OMP/pair_tersoff_table_omp.h | 9 +
src/USER-OMP/pair_tersoff_zbl_omp.cpp | 8 +-
src/USER-OMP/pair_tip4p_cut_omp.cpp | 5 +-
src/USER-OMP/pppm_cg_omp.h | 3 -
src/USER-OMP/pppm_disp_omp.cpp | 37 +-
src/USER-PHONON/fix_phonon.cpp | 20 +-
src/USER-QMMM/Install.sh | 64 +
src/USER-QMMM/README | 12 +
src/USER-QMMM/fix_qmmm.cpp | 758 +
src/USER-QMMM/fix_qmmm.h | 86 +
src/USER-REAXC/fix_qeq_reax.cpp | 10 +-
src/USER-REAXC/fix_reaxc_bonds.cpp | 12 +-
src/USER-REAXC/pair_reax_c.cpp | 34 +-
src/USER-REAXC/reaxc_allocate.cpp | 24 +-
src/USER-REAXC/reaxc_bond_orders.cpp | 1 -
src/USER-REAXC/reaxc_defs.h | 2 +-
src/USER-REAXC/reaxc_forces.cpp | 2 +-
src/USER-REAXC/reaxc_io_tools.cpp | 8 +-
src/USER-REAXC/reaxc_torsion_angles.cpp | 6 +-
src/USER-SPH/fix_meso_stationary.cpp | 3 -
src/VORONOI/compute_voronoi_atom.cpp | 4 +-
src/accelerator_cuda.h | 2 +
src/accelerator_kokkos.h | 24 +-
src/atom.cpp | 17 +-
src/atom.h | 11 +-
src/atom_map.cpp | 78 +-
src/atom_vec_body.cpp | 15 +-
src/atom_vec_sphere.h | 2 +-
src/balance.cpp | 86 +-
src/balance.h | 2 +
src/body.cpp | 2 +
src/change_box.cpp | 1 -
src/comm.cpp | 55 +
src/comm.h | 2 +
src/compute_angle_local.cpp | 2 -
src/compute_atom_molecule.h | 2 +-
src/compute_bond_local.cpp | 1 -
src/compute_bond_local.h | 2 +-
src/compute_cluster_atom.cpp | 3 +-
src/compute_dihedral_local.cpp | 7 +-
src/compute_group_group.cpp | 3 +-
src/compute_gyration_molecule.cpp | 2 +-
src/compute_improper_local.cpp | 2 -
src/compute_inertia_molecule.cpp | 6 +-
src/compute_pair_local.h | 2 +-
src/compute_pressure.cpp | 8 +-
src/compute_pressure.h | 5 +
src/compute_property_atom.cpp | 20 +
src/compute_property_atom.h | 2 +
src/compute_property_local.cpp | 2 -
src/compute_rdf.h | 19 +-
src/compute_reduce.cpp | 7 +-
src/compute_temp_profile.cpp | 1 -
src/delete_atoms.cpp | 6 +-
src/displace_atoms.cpp | 2 +-
src/domain.cpp | 2 +-
src/dump.cpp | 2 +-
src/dump_cfg.h | 2 +-
src/dump_image.cpp | 8 +-
src/finish.cpp | 41 +-
src/fix.cpp | 6 +-
src/fix.h | 5 +-
src/fix_ave_correlate.h | 1 -
src/fix_ave_histo.h | 2 +-
src/fix_ave_spatial.cpp | 8 +-
src/fix_ave_time.h | 2 +-
src/fix_balance.cpp | 5 +-
src/fix_box_relax.cpp | 12 +-
src/fix_indent.h | 2 +-
src/fix_move.cpp | 9 +-
src/fix_nh.cpp | 17 +-
src/fix_press_berendsen.cpp | 4 +-
src/fix_property_atom.cpp | 2 +-
src/fix_recenter.cpp | 36 +-
src/fix_recenter.h | 6 +-
src/fix_setforce.h | 4 +-
src/fix_spring.h | 1 -
src/fix_temp_csvr.cpp | 287 +
src/{MC/fix_bond_swap.h => fix_temp_csvr.h} | 74 +-
src/fix_vector.cpp | 7 +-
src/fix_vector.h | 2 +-
src/fix_wall_region.cpp | 2 +-
src/fix_wall_region.h | 1 -
src/force.cpp | 86 +
src/force.h | 5 +
src/group.cpp | 14 +-
src/image.cpp | 13 +-
src/input.cpp | 39 +-
src/irregular.cpp | 57 +-
src/irregular.h | 8 +-
src/kspace.cpp | 88 +-
src/kspace.h | 38 +-
src/lammps.cpp | 14 +-
src/lattice.cpp | 4 +-
src/lmptype.h | 2 +-
src/memory.h | 4 +-
src/min.cpp | 4 -
src/min_linesearch.cpp | 4 +-
src/modify.cpp | 10 +-
src/molecule.cpp | 15 +-
src/molecule.h | 2 +-
src/my_page.h | 2 +-
src/neigh_full.cpp | 6 +-
src/neigh_half_bin.cpp | 8 +-
src/neigh_half_multi.cpp | 6 +-
src/neigh_list.cpp | 2 +
src/neigh_list.h | 6 +-
src/neigh_request.cpp | 2 +
src/neigh_request.h | 5 +
src/neigh_respa.cpp | 18 +-
src/neigh_stencil.cpp | 5 +-
src/neighbor.cpp | 266 +-
src/neighbor.h | 15 +-
src/pair.cpp | 96 +-
src/pair.h | 8 +-
src/pair_born_coul_wolf.cpp | 3 +-
src/pair_coul_wolf.cpp | 14 +-
src/pair_gauss.cpp | 2 +-
src/pair_hybrid.cpp | 6 +-
src/pair_lj_cut.h | 2 +-
src/pair_lj_cut_coul_dsf.cpp | 2 +-
src/pair_lj_smooth_linear.cpp | 1 -
src/pair_mie_cut.cpp | 4 +-
src/pair_table.cpp | 2 +-
src/procmap.cpp | 10 +-
src/random_mars.h | 2 +-
src/read_data.cpp | 188 +-
src/read_data.h | 14 +-
src/read_restart.cpp | 10 +-
src/run.cpp | 2 +-
src/set.cpp | 3 -
src/special.h | 1 -
src/thermo.cpp | 54 +-
src/thermo.h | 5 +
src/universe.cpp | 2 +-
src/update.cpp | 19 +-
src/variable.cpp | 54 +-
src/version.h | 2 +-
src/write_data.cpp | 22 +-
src/write_restart.cpp | 2 +-
tools/moltemplate/LICENSE.TXT | 2 +-
tools/moltemplate/README.TXT | 2 +-
tools/moltemplate/common/oplsaa/AUTHOR.TXT | 3 +
tools/moltemplate/common/oplsaa/README.TXT | 82 +
tools/moltemplate/common/oplsaa/oplsaa.txt | 5968 ++++
.../common/oplsaa/oplsaa_moltemplate.py | 319 +
tools/moltemplate/common/trappe1998.lt | 31 +-
.../moltemplate_files/CGLipidBr2005Orig.lt | 2 +-
.../README_FIRST.txt | 47 +
.../README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt | 29 +
.../README_run.sh | 7 +
.../README_setup.sh | 58 +
.../README_visualize.txt | 131 +
.../images/stage2_interior.jpg | Bin 0 -> 40803 bytes
.../images/stage2_interior_rotated.jpg | Bin 0 -> 25429 bytes
.../images/t=0_before_minimizaion.jpg | Bin 0 -> 79709 bytes
.../images/vmd_colorscale_jet.tcl | 87 +
.../README_how_to_generate_system_lt.sh | 19 +
.../README_length_flexibility_details.txt | 57 +
.../moltemplate_files/calc_table.sh | 8 +
.../moltemplate_files/condensin.lt | 47 +
.../moltemplate_files/coords_orig.raw | 32768 +++++++++++++++++++
.../moltemplate_files/generate_system_lt.py | 301 +
.../moltemplate_files/interpolate_coords.py | 74 +
.../moltemplate_files/monomer.lt | 84 +
.../moltemplate_files/table_bonds_stage2.dat | 4011 +++
.../run.in.min | 41 +
.../run.in.stage1 | 110 +
.../run.in.stage2 | 90 +
.../moltemplate_files/isobutane.lt | 4 +-
.../OPLSAA_force_field_examples/WARNING.TXT | 26 +
.../ethylene/README.TXT | 13 +
.../ethylene/README_run.sh | 39 +
.../ethylene/README_setup.sh | 36 +
.../ethylene/README_visualize.txt | 87 +
.../ethylene/images/ethylene.jpg | Bin 0 -> 11657 bytes
.../images/ethylene_box_pressure=50barr.jpg | Bin 0 -> 86910 bytes
.../ethylene/moltemplate_files/ethylene.lt | 42 +
.../oplsaa_lt_generator/AUTHOR.TXT | 3 +
.../oplsaa_lt_generator/README.TXT | 81 +
.../oplsaa_lt_generator/oplsaa.txt | 5968 ++++
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 319 +
.../oplsaa_lt_generator/oplsaa_subset.txt | 3450 ++
.../ethylene/moltemplate_files/system.lt | 19 +
.../ethylene/run.in.npt | 57 +
.../ethylene/run.in.nvt | 50 +
.../ice_crystal/images/ice_rect8_unitcell.png | Bin 0 -> 21951 bytes
.../waterSPCE+Na+Cl/moltemplate_files/ions.lt | 9 +-
tools/moltemplate/moltemplate_manual.pdf | Bin 697917 -> 709742 bytes
.../src/docs_useful_scripts/docs_dump2data.txt | 109 +
tools/moltemplate/src/dump2data.py | 4 +-
tools/moltemplate/src/moltemplate.sh | 32 +-
tools/moltemplate/src/ttree_matrix_stack.py | 90 +-
tools/msi2lmp/README | 25 +-
tools/msi2lmp/src/ReadCarFile.c | 6 +-
tools/msi2lmp/src/WriteDataFile.c | 166 +-
tools/msi2lmp/src/msi2lmp.c | 26 +-
tools/msi2lmp/src/msi2lmp.h | 5 +-
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data | 1608 +-
.../msi2lmp/test/reference/PyAC_bulk-clayff.data2 | 2562 +-
tools/msi2lmp/test/runtests.sh | 6 +-
623 files changed, 73921 insertions(+), 6400 deletions(-)
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