[lammps] 01/07: Merge tag 'upstream/0_20150313.gitfa668e1' into experimental
Anton Gladky
gladk at moszumanska.debian.org
Sun Mar 15 21:56:04 UTC 2015
This is an automated email from the git hooks/post-receive script.
gladk pushed a commit to branch experimental
in repository lammps.
commit e2057438713d4b35136c755c79340ad0b6306861
Merge: 32b9d4b aad2273
Author: Anton Gladky <gladk at debian.org>
Date: Sun Mar 15 14:33:23 2015 +0100
Merge tag 'upstream/0_20150313.gitfa668e1' into experimental
Upstream version 0~20150313.gitfa668e1
bench/FERMI/README | 103 +
bench/{GPU/in.eam.cpu => FERMI/in.eam} | 0
bench/FERMI/in.eam.titan | 37 +
bench/{GPU/in.lj.cpu => FERMI/in.lj} | 0
bench/FERMI/in.lj.titan | 35 +
bench/{GPU/in.rhodo.cpu => FERMI/in.rhodo} | 0
bench/FERMI/in.rhodo.scaled.titan | 39 +
bench/FERMI/in.rhodo.split.titan | 42 +
bench/GPU/README | 60 -
bench/GPU/in.eam.cuda | 29 -
bench/GPU/in.eam.gpu | 31 -
bench/GPU/in.lj.cuda | 27 -
bench/GPU/in.lj.gpu | 29 -
bench/GPU/in.rhodo.cuda | 35 -
bench/GPU/in.rhodo.gpu | 37 -
bench/KEPLER/Makefile.cpu | 108 +
bench/KEPLER/Makefile.cuda | 108 +
bench/KEPLER/Makefile.gpu | 108 +
bench/KEPLER/Makefile.gpu.double | 50 +
bench/KEPLER/Makefile.gpu.mixed | 50 +
bench/KEPLER/Makefile.gpu.single | 50 +
bench/KEPLER/Makefile.intel.cpu | 109 +
bench/KEPLER/Makefile.kokkos.cuda | 113 +
bench/KEPLER/Makefile.kokkos.omp | 110 +
bench/KEPLER/Makefile.omp | 108 +
bench/KEPLER/Makefile.opt | 108 +
bench/KEPLER/README | 68 +
bench/KEPLER/build.py | 187 +
bench/{GPU/in.lj.cpu => KEPLER/in.lj} | 0
bench/KEPLER/run_cpu.sh | 29 +
bench/KEPLER/run_cuda.sh | 20 +
bench/KEPLER/run_gpu.sh | 155 +
bench/KEPLER/run_intel_cpu.sh | 83 +
bench/KEPLER/run_kokkos_cuda.sh | 74 +
bench/KEPLER/run_kokkos_omp.sh | 17 +
bench/KEPLER/run_omp.sh | 17 +
bench/KEPLER/run_opt.sh | 29 +
bench/KEPLER/run_strong.sh | 20 +
bench/KEPLER/run_weak.sh | 20 +
bench/README | 68 +-
bench/in.chute | 2 +-
doc/Eqs/compute_sna_atom1.jpg | Bin 0 -> 19001 bytes
doc/Eqs/compute_sna_atom1.tex | 11 +
doc/Eqs/compute_sna_atom2.jpg | Bin 0 -> 17114 bytes
doc/Eqs/compute_sna_atom2.tex | 11 +
doc/Eqs/compute_sna_atom3.jpg | Bin 0 -> 19644 bytes
doc/Eqs/compute_sna_atom3.tex | 16 +
doc/Eqs/compute_sna_atom4.jpg | Bin 0 -> 35933 bytes
doc/Eqs/compute_sna_atom4.tex | 14 +
doc/Eqs/compute_sna_atom5.jpg | Bin 0 -> 14734 bytes
doc/Eqs/compute_sna_atom5.tex | 12 +
doc/Eqs/compute_sna_atom6.jpg | Bin 0 -> 17274 bytes
doc/Eqs/compute_sna_atom6.tex | 12 +
doc/Eqs/fix_pimd.jpg | Bin 0 -> 14569 bytes
doc/Eqs/fix_pimd.tex | 17 +
doc/Eqs/fix_rattle_constraints.jpg | Bin 0 -> 4556 bytes
doc/Eqs/fix_rattle_constraints.tex | 9 +
doc/Eqs/fix_rattle_rij.jpg | Bin 0 -> 1812 bytes
doc/Eqs/fix_rattle_rij.tex | 8 +
doc/Eqs/fix_ttm_blast.jpg | Bin 0 -> 4449 bytes
doc/Eqs/fix_ttm_blast.tex | 13 +
doc/Eqs/fix_ttm_blast1.jpg | Bin 0 -> 8657 bytes
doc/Eqs/fix_ttm_blast1.tex | 13 +
doc/Eqs/fix_ttm_ce.jpg | Bin 0 -> 7446 bytes
doc/Eqs/fix_ttm_ce.tex | 13 +
doc/Eqs/fix_ttm_mod.jpg | Bin 0 -> 10179 bytes
doc/Eqs/fix_ttm_mod.tex | 15 +
doc/Eqs/pair_cs.jpg | Bin 0 -> 3500 bytes
doc/Eqs/pair_cs.tex | 9 +
doc/Eqs/pair_snap.jpg | Bin 0 -> 32505 bytes
doc/Eqs/pair_snap.tex | 9 +
doc/Eqs/pair_srp1.jpg | Bin 0 -> 3537 bytes
doc/Eqs/pair_srp1.tex | 9 +
doc/Eqs/pair_srp2.jpg | Bin 0 -> 5648 bytes
doc/Eqs/pair_srp2.tex | 10 +
doc/JPG/balance.jpg | Bin 34031 -> 0 bytes
doc/JPG/balance_nonuniform.jpg | Bin 0 -> 78857 bytes
doc/JPG/balance_nonuniform_small.jpg | Bin 0 -> 16588 bytes
doc/JPG/balance_rcb.jpg | Bin 0 -> 72941 bytes
doc/JPG/balance_rcb_small.jpg | Bin 0 -> 15571 bytes
doc/JPG/balance_uniform.jpg | Bin 0 -> 79281 bytes
doc/JPG/balance_uniform_small.jpg | Bin 0 -> 17279 bytes
doc/JPG/pimd.jpg | Bin 0 -> 29560 bytes
doc/JPG/sinusoid.jpg | Bin 0 -> 128596 bytes
doc/JPG/sinusoid_small.jpg | Bin 0 -> 29397 bytes
doc/Manual.html | 36 +-
doc/Manual.pdf | Bin 8139800 -> 9325726 bytes
doc/Manual.txt | 30 +-
doc/PDF/PDLammps_EPS.pdf | Bin 164229 -> 79021 bytes
doc/PDF/PDLammps_VES.pdf | Bin 65659 -> 74846 bytes
doc/PDF/colvars-refman-lammps.pdf | Bin 601866 -> 528423 bytes
doc/Section_accelerate.html | 690 +-
doc/Section_accelerate.txt | 691 +-
doc/Section_commands.html | 402 +-
doc/Section_commands.txt | 811 +-
doc/Section_errors.html | 18 +-
doc/Section_errors.txt | 18 +-
doc/Section_example.html | 6 +
doc/Section_example.txt | 6 +
doc/Section_howto.html | 508 +-
doc/Section_howto.txt | 505 +-
doc/Section_intro.html | 14 +-
doc/Section_intro.txt | 12 +-
doc/Section_modify.html | 12 +-
doc/Section_modify.txt | 12 +-
doc/Section_packages.html | 45 +-
doc/Section_packages.txt | 45 +-
doc/Section_python.html | 6 +-
doc/Section_python.txt | 4 +-
doc/Section_start.html | 911 +-
doc/Section_start.txt | 899 +-
doc/Section_tools.html | 20 +-
doc/Section_tools.txt | 20 +-
doc/accelerate_cuda.html | 228 +
doc/accelerate_cuda.txt | 223 +
doc/accelerate_gpu.html | 257 +
doc/accelerate_gpu.txt | 252 +
doc/accelerate_intel.html | 352 +
doc/accelerate_intel.txt | 347 +
doc/accelerate_kokkos.html | 514 +
doc/accelerate_kokkos.txt | 509 +
doc/accelerate_omp.html | 206 +
doc/accelerate_omp.txt | 201 +
doc/accelerate_opt.html | 87 +
doc/accelerate_opt.txt | 82 +
doc/angle_charmm.html | 25 +-
doc/angle_charmm.txt | 25 +-
doc/angle_class2.html | 23 +-
doc/angle_class2.txt | 23 +-
doc/angle_cosine.html | 23 +-
doc/angle_cosine.txt | 25 +-
doc/angle_cosine_delta.html | 25 +-
doc/angle_cosine_delta.txt | 25 +-
doc/angle_cosine_periodic.html | 25 +-
doc/angle_cosine_periodic.txt | 25 +-
doc/angle_cosine_shift.html | 21 +-
doc/angle_cosine_shift.txt | 23 +-
doc/angle_cosine_shift_exp.html | 23 +-
doc/angle_cosine_shift_exp.txt | 23 +-
doc/angle_cosine_squared.html | 25 +-
doc/angle_cosine_squared.txt | 25 +-
doc/angle_dipole.html | 23 +-
doc/angle_dipole.txt | 23 +-
doc/angle_fourier.html | 21 +-
doc/angle_fourier.txt | 23 +-
doc/angle_fourier_simple.html | 21 +-
doc/angle_fourier_simple.txt | 23 +-
doc/angle_harmonic.html | 25 +-
doc/angle_harmonic.txt | 25 +-
doc/angle_hybrid.html | 2 +-
doc/angle_hybrid.txt | 2 +-
doc/angle_quartic.html | 23 +-
doc/angle_quartic.txt | 23 +-
doc/angle_style.html | 2 +-
doc/angle_style.txt | 2 +-
doc/angle_table.html | 25 +-
doc/angle_table.txt | 25 +-
doc/atom_style.html | 35 +-
doc/atom_style.txt | 34 +-
doc/balance.html | 191 +-
doc/balance.txt | 192 +-
doc/bond_class2.html | 23 +-
doc/bond_class2.txt | 23 +-
doc/bond_fene.html | 25 +-
doc/bond_fene.txt | 25 +-
doc/bond_fene_expand.html | 25 +-
doc/bond_fene_expand.txt | 25 +-
doc/bond_harmonic.html | 23 +-
doc/bond_harmonic.txt | 25 +-
doc/bond_harmonic_shift.html | 21 +-
doc/bond_harmonic_shift.txt | 23 +-
doc/bond_harmonic_shift_cut.html | 21 +-
doc/bond_harmonic_shift_cut.txt | 23 +-
doc/bond_hybrid.html | 2 +-
doc/bond_hybrid.txt | 2 +-
doc/bond_morse.html | 23 +-
doc/bond_morse.txt | 25 +-
doc/bond_nonlinear.html | 25 +-
doc/bond_nonlinear.txt | 25 +-
doc/bond_quartic.html | 25 +-
doc/bond_quartic.txt | 25 +-
doc/bond_style.html | 2 +-
doc/bond_style.txt | 2 +-
doc/bond_table.html | 25 +-
doc/bond_table.txt | 25 +-
doc/change_box.html | 15 +
doc/change_box.txt | 15 +
doc/comm_modify.html | 8 +-
doc/comm_modify.txt | 8 +-
doc/comm_style.html | 2 -
doc/comm_style.txt | 2 -
doc/compute.html | 17 +-
doc/compute.txt | 17 +-
doc/compute_atom_molecule.html | 118 -
doc/compute_atom_molecule.txt | 108 -
doc/compute_chunk_atom.html | 568 +
doc/compute_chunk_atom.txt | 554 +
doc/compute_com.html | 8 -
doc/compute_com.txt | 8 -
doc/compute_com_chunk.html | 92 +
doc/compute_com_chunk.txt | 87 +
doc/compute_com_molecule.html | 81 -
doc/compute_com_molecule.txt | 76 -
doc/compute_displace_atom.html | 14 +-
doc/compute_displace_atom.txt | 14 +-
doc/compute_fep.html | 21 +-
doc/compute_fep.txt | 19 +-
doc/compute_gyration.html | 24 +-
doc/compute_gyration.txt | 24 +-
doc/compute_gyration_chunk.html | 122 +
doc/compute_gyration_chunk.txt | 111 +
doc/compute_gyration_molecule.html | 102 -
doc/compute_gyration_molecule.txt | 92 -
doc/compute_heat_flux.html | 2 +-
doc/compute_heat_flux.txt | 2 +-
doc/compute_inertia_chunk.html | 93 +
doc/compute_inertia_chunk.txt | 88 +
doc/compute_inertia_molecule.html | 83 -
doc/compute_inertia_molecule.txt | 78 -
doc/compute_msd.html | 16 +-
doc/compute_msd.txt | 16 +-
doc/compute_msd_chunk.html | 125 +
doc/compute_msd_chunk.txt | 120 +
doc/compute_msd_molecule.html | 99 -
doc/compute_msd_molecule.txt | 94 -
doc/compute_pair_local.html | 9 +-
doc/compute_pair_local.txt | 9 +-
doc/compute_pressure.html | 12 +-
doc/compute_pressure.txt | 11 +-
doc/compute_property_atom.html | 43 +-
doc/compute_property_atom.txt | 43 +-
doc/compute_property_chunk.html | 127 +
doc/compute_property_chunk.txt | 118 +
doc/compute_property_molecule.html | 77 -
doc/compute_property_molecule.txt | 68 -
doc/compute_sna_atom.html | 262 +
doc/compute_sna_atom.txt | 241 +
doc/compute_stress_atom.html | 16 +
doc/compute_stress_atom.txt | 15 +
doc/compute_temp_asphere.html | 10 +-
doc/compute_temp_asphere.txt | 10 +-
doc/compute_temp_chunk.html | 248 +
doc/compute_temp_chunk.txt | 234 +
doc/compute_temp_cs.html | 117 +
doc/compute_temp_cs.txt | 111 +
doc/compute_temp_region.html | 13 +-
doc/compute_temp_region.txt | 13 +-
doc/compute_temp_sphere.html | 10 +-
doc/compute_temp_sphere.txt | 10 +-
doc/compute_torque_chunk.html | 92 +
doc/compute_torque_chunk.txt | 87 +
doc/compute_vacf.html | 6 +-
doc/compute_vacf.txt | 6 +-
doc/compute_vcm_chunk.html | 82 +
doc/compute_vcm_chunk.txt | 77 +
doc/create_atoms.html | 68 +-
doc/create_atoms.txt | 70 +-
doc/create_bonds.html | 114 +
doc/create_bonds.txt | 109 +
doc/create_box.html | 39 +-
doc/create_box.txt | 39 +-
doc/delete_atoms.html | 54 +-
doc/delete_atoms.txt | 54 +-
doc/delete_bonds.html | 40 +-
doc/delete_bonds.txt | 40 +-
doc/dihedral_charmm.html | 25 +-
doc/dihedral_charmm.txt | 25 +-
doc/dihedral_class2.html | 23 +-
doc/dihedral_class2.txt | 23 +-
doc/dihedral_cosine_shift_exp.html | 23 +-
doc/dihedral_cosine_shift_exp.txt | 23 +-
doc/dihedral_fourier.html | 21 +-
doc/dihedral_fourier.txt | 23 +-
doc/dihedral_harmonic.html | 23 +-
doc/dihedral_harmonic.txt | 25 +-
doc/dihedral_helix.html | 25 +-
doc/dihedral_helix.txt | 25 +-
doc/dihedral_hybrid.html | 2 +-
doc/dihedral_hybrid.txt | 2 +-
doc/dihedral_multi_harmonic.html | 23 +-
doc/dihedral_multi_harmonic.txt | 25 +-
doc/dihedral_nharmonic.html | 21 +-
doc/dihedral_nharmonic.txt | 23 +-
doc/dihedral_opls.html | 29 +-
doc/dihedral_opls.txt | 27 +-
doc/dihedral_quadratic.html | 35 +-
doc/dihedral_quadratic.txt | 37 +-
doc/dihedral_style.html | 2 +-
doc/dihedral_style.txt | 2 +-
doc/dihedral_table.html | 23 +-
doc/dihedral_table.txt | 23 +-
doc/dump.html | 87 +-
doc/dump.txt | 87 +-
doc/dump_image.html | 53 +-
doc/dump_image.txt | 53 +-
doc/dump_modify.html | 33 +-
doc/dump_modify.txt | 33 +-
doc/fix.html | 4 +-
doc/fix.txt | 8 +-
doc/fix_adapt.html | 3 +
doc/fix_adapt.txt | 3 +
doc/fix_adapt_fep.html | 6 +
doc/fix_adapt_fep.txt | 6 +
doc/fix_addforce.html | 14 +-
doc/fix_addforce.txt | 12 +-
doc/fix_atom_swap.html | 193 +
doc/fix_atom_swap.txt | 179 +
doc/fix_ave_chunk.html | 454 +
doc/fix_ave_chunk.txt | 438 +
doc/fix_ave_spatial.html | 162 +-
doc/fix_ave_spatial.txt | 162 +-
doc/fix_ave_spatial_sphere.html | 342 +
doc/fix_ave_spatial_sphere.txt | 323 +
doc/fix_balance.html | 173 +-
doc/fix_balance.txt | 173 +-
doc/fix_bond_create.html | 15 +-
doc/fix_bond_create.txt | 15 +-
doc/fix_bond_swap.html | 15 +-
doc/fix_bond_swap.txt | 8 +-
doc/fix_box_relax.html | 7 +-
doc/fix_box_relax.txt | 7 +-
doc/fix_deposit.html | 10 +
doc/fix_deposit.txt | 10 +
doc/fix_freeze.html | 6 +-
doc/fix_freeze.txt | 6 +-
doc/fix_gcmc.html | 214 +-
doc/fix_gcmc.txt | 214 +-
doc/fix_gle.html | 170 +
doc/fix_gle.txt | 155 +
doc/fix_gravity.html | 23 +-
doc/fix_gravity.txt | 23 +-
doc/fix_ipi.html | 98 +
doc/fix_ipi.txt | 91 +
doc/fix_langevin.html | 65 +-
doc/fix_langevin.txt | 64 +-
doc/fix_move.html | 6 +-
doc/fix_move.txt | 6 +-
doc/fix_nh.html | 45 +-
doc/fix_nh.txt | 40 +-
doc/fix_nph_asphere.html | 23 +-
doc/fix_nph_asphere.txt | 23 +-
doc/fix_nph_sphere.html | 23 +-
doc/fix_nph_sphere.txt | 23 +-
doc/fix_nphug.html | 23 +-
doc/fix_nphug.txt | 23 +-
doc/fix_npt_asphere.html | 23 +-
doc/fix_npt_asphere.txt | 23 +-
doc/fix_npt_sphere.html | 23 +-
doc/fix_npt_sphere.txt | 23 +-
doc/fix_nve.html | 23 +-
doc/fix_nve.txt | 24 +-
doc/fix_nve_sphere.html | 23 +-
doc/fix_nve_sphere.txt | 23 +-
doc/fix_nvt_asphere.html | 23 +-
doc/fix_nvt_asphere.txt | 23 +-
doc/fix_nvt_sllod.html | 44 +-
doc/fix_nvt_sllod.txt | 41 +-
doc/fix_nvt_sphere.html | 23 +-
doc/fix_nvt_sphere.txt | 23 +-
doc/fix_oneway.html | 8 +-
doc/fix_oneway.txt | 8 +-
doc/fix_phonon.html | 8 +-
doc/fix_phonon.txt | 8 +-
doc/fix_pimd.html | 195 +
doc/fix_pimd.txt | 179 +
doc/fix_qeq.html | 209 +
doc/fix_qeq.txt | 196 +
doc/fix_qeq_comb.html | 23 +-
doc/fix_qeq_comb.txt | 23 +-
doc/fix_qeq_reax.html | 2 +-
doc/fix_qeq_reax.txt | 2 +-
doc/fix_rigid.html | 116 +-
doc/fix_rigid.txt | 116 +-
doc/fix_shake.html | 116 +-
doc/fix_shake.txt | 113 +-
doc/fix_store_state.html | 12 +-
doc/fix_store_state.txt | 12 +-
doc/fix_temp_berendsen.html | 10 +-
doc/fix_temp_berendsen.txt | 10 +-
doc/fix_tfmc.html | 168 +
doc/fix_tfmc.txt | 152 +
doc/fix_ttm.html | 250 +-
doc/fix_ttm.txt | 241 +-
doc/fix_vector.html | 24 +-
doc/fix_vector.txt | 24 +-
doc/fix_wall.html | 3 +-
doc/fix_wall.txt | 3 +-
doc/fix_wall_piston.html | 4 +-
doc/fix_wall_piston.txt | 4 +-
doc/fix_wall_region.html | 18 +-
doc/fix_wall_region.txt | 18 +-
doc/group.html | 50 +-
doc/group.txt | 50 +-
doc/improper_class2.html | 23 +-
doc/improper_class2.txt | 23 +-
doc/improper_cossq.html | 23 +-
doc/improper_cossq.txt | 23 +-
doc/improper_cvff.html | 25 +-
doc/improper_cvff.txt | 25 +-
doc/improper_fourier.html | 23 +-
doc/improper_fourier.txt | 23 +-
doc/improper_harmonic.html | 25 +-
doc/improper_harmonic.txt | 25 +-
doc/improper_hybrid.html | 2 +-
doc/improper_hybrid.txt | 2 +-
doc/improper_ring.html | 23 +-
doc/improper_ring.txt | 23 +-
doc/improper_style.html | 2 +-
doc/improper_style.txt | 2 +-
doc/improper_umbrella.html | 25 +-
doc/improper_umbrella.txt | 25 +-
doc/kspace_modify.html | 22 +-
doc/kspace_modify.txt | 19 +-
doc/kspace_style.html | 31 +-
doc/kspace_style.txt | 31 +-
doc/lattice.html | 101 +-
doc/lattice.txt | 103 +-
doc/min_modify.html | 26 +-
doc/min_modify.txt | 26 +-
doc/minimize.html | 24 +-
doc/minimize.txt | 22 +-
doc/molecule.html | 10 +-
doc/molecule.txt | 10 +-
doc/neb.html | 6 +-
doc/neb.txt | 6 +-
doc/neigh_modify.html | 34 +-
doc/neigh_modify.txt | 34 +-
doc/package.html | 769 +-
doc/package.txt | 772 +-
doc/pair_adp.html | 23 +-
doc/pair_adp.txt | 23 +-
doc/pair_airebo.html | 23 +-
doc/pair_airebo.txt | 23 +-
doc/pair_beck.html | 23 +-
doc/pair_beck.txt | 23 +-
doc/pair_born.html | 23 +-
doc/pair_born.txt | 23 +-
doc/pair_brownian.html | 22 +-
doc/pair_brownian.txt | 22 +-
doc/pair_buck.html | 25 +-
doc/pair_buck.txt | 24 +-
doc/pair_buck_long.html | 53 +-
doc/pair_buck_long.txt | 53 +-
doc/pair_charmm.html | 25 +-
doc/pair_charmm.txt | 24 +-
doc/pair_class2.html | 23 +-
doc/pair_class2.txt | 23 +-
doc/pair_colloid.html | 23 +-
doc/pair_colloid.txt | 23 +-
doc/pair_comb.html | 23 +-
doc/pair_comb.txt | 23 +-
doc/pair_coul.html | 111 +-
doc/pair_coul.txt | 102 +-
doc/pair_cs.html | 91 +
doc/pair_cs.txt | 83 +
doc/pair_dipole.html | 23 +-
doc/pair_dipole.txt | 23 +-
doc/pair_dpd.html | 38 +-
doc/pair_dpd.txt | 36 +-
doc/pair_eam.html | 25 +-
doc/pair_eam.txt | 24 +-
doc/pair_edip.html | 23 +-
doc/pair_edip.txt | 23 +-
doc/pair_eff.html | 4 +-
doc/pair_eff.txt | 4 +-
doc/pair_eim.html | 23 +-
doc/pair_eim.txt | 23 +-
doc/pair_gauss.html | 23 +-
doc/pair_gauss.txt | 23 +-
doc/pair_gayberne.html | 25 +-
doc/pair_gayberne.txt | 24 +-
doc/pair_gran.html | 27 +-
doc/pair_gran.txt | 27 +-
doc/pair_gromacs.html | 23 +-
doc/pair_gromacs.txt | 23 +-
doc/pair_hbond_dreiding.html | 23 +-
doc/pair_hbond_dreiding.txt | 23 +-
doc/pair_hybrid.html | 25 +-
doc/pair_hybrid.txt | 25 +-
doc/pair_kim.html | 181 +-
doc/pair_kim.txt | 180 +-
doc/pair_line_lj.html | 23 +-
doc/pair_line_lj.txt | 23 +-
doc/pair_lj.html | 31 +-
doc/pair_lj.txt | 27 +-
doc/pair_lj96.html | 23 +-
doc/pair_lj96.txt | 23 +-
doc/pair_lj_cubic.html | 23 +-
doc/pair_lj_cubic.txt | 23 +-
doc/pair_lj_expand.html | 23 +-
doc/pair_lj_expand.txt | 23 +-
doc/pair_lj_long.html | 51 +-
doc/pair_lj_long.txt | 51 +-
doc/pair_lj_sf.html | 23 +-
doc/pair_lj_sf.txt | 23 +-
doc/pair_lj_smooth.html | 23 +-
doc/pair_lj_smooth.txt | 23 +-
doc/pair_lj_smooth_linear.html | 23 +-
doc/pair_lj_smooth_linear.txt | 23 +-
doc/pair_lj_soft.html | 21 +-
doc/pair_lj_soft.txt | 23 +-
doc/pair_lubricate.html | 22 +-
doc/pair_lubricate.txt | 22 +-
doc/pair_meam_spline.html | 23 +-
doc/pair_meam_spline.txt | 23 +-
doc/pair_modify.html | 41 +-
doc/pair_modify.txt | 41 +-
doc/pair_morse.html | 23 +-
doc/pair_morse.txt | 23 +-
doc/pair_nb3b_harmonic.html | 23 +-
doc/pair_nb3b_harmonic.txt | 23 +-
doc/pair_nm.html | 23 +-
doc/pair_nm.txt | 23 +-
doc/pair_peri.html | 23 +-
doc/pair_peri.txt | 23 +-
doc/pair_quip.html | 102 +
doc/pair_quip.txt | 96 +
doc/pair_resquared.html | 23 +-
doc/pair_resquared.txt | 23 +-
doc/pair_sdk.html | 23 +-
doc/pair_sdk.txt | 23 +-
doc/pair_snap.html | 201 +
doc/pair_snap.txt | 193 +
doc/pair_soft.html | 23 +-
doc/pair_soft.txt | 23 +-
doc/pair_srp.html | 170 +
doc/pair_srp.txt | 158 +
doc/pair_style.html | 5 +-
doc/pair_style.txt | 5 +-
doc/pair_sw.html | 30 +-
doc/pair_sw.txt | 27 +-
doc/pair_table.html | 29 +-
doc/pair_table.txt | 28 +-
doc/pair_tersoff.html | 23 +-
doc/pair_tersoff.txt | 23 +-
doc/pair_tersoff_mod.html | 23 +-
doc/pair_tersoff_mod.txt | 23 +-
doc/pair_tersoff_zbl.html | 23 +-
doc/pair_tersoff_zbl.txt | 23 +-
doc/pair_tri_lj.html | 23 +-
doc/pair_tri_lj.txt | 23 +-
doc/pair_yukawa.html | 23 +-
doc/pair_yukawa.txt | 23 +-
doc/pair_yukawa_colloid.html | 23 +-
doc/pair_yukawa_colloid.txt | 23 +-
doc/pair_zbl.html | 23 +-
doc/pair_zbl.txt | 23 +-
doc/processors.html | 3 +-
doc/processors.txt | 3 +-
doc/read_data.html | 59 +-
doc/read_data.txt | 59 +-
doc/read_dump.html | 13 +-
doc/read_dump.txt | 13 +-
doc/read_restart.html | 20 +-
doc/read_restart.txt | 19 +-
doc/run.html | 29 +-
doc/run.txt | 29 +-
doc/set.html | 16 +-
doc/set.txt | 16 +-
doc/special_bonds.html | 20 +-
doc/special_bonds.txt | 20 +-
doc/suffix.html | 72 +-
doc/suffix.txt | 72 +-
doc/thermo_style.html | 17 +-
doc/thermo_style.txt | 17 +-
doc/units.html | 4 +-
doc/units.txt | 4 +-
doc/variable.html | 122 +-
doc/variable.txt | 122 +-
doc/velocity.html | 98 +-
doc/velocity.txt | 98 +-
examples/ASPHERE/box/in.box | 2 +-
examples/ASPHERE/box/in.box.mp | 2 +-
examples/ASPHERE/dimer/in.dimer | 2 +-
examples/ASPHERE/dimer/in.dimer.mp | 2 +-
examples/ASPHERE/ellipsoid/in.ellipsoid | 2 +-
examples/ASPHERE/ellipsoid/in.ellipsoid.mp | 2 +-
examples/ASPHERE/line/in.line.srd | 2 +-
examples/ASPHERE/poly/in.poly | 2 +-
examples/ASPHERE/poly/in.poly.mp | 2 +-
examples/ASPHERE/star/in.star | 2 +-
examples/ASPHERE/star/in.star.mp | 2 +-
examples/ASPHERE/tri/in.tri.srd | 2 +-
examples/COUPLE/lammps_quest/lmpqst.cpp | 10 +-
examples/COUPLE/simple/README | 9 +-
examples/COUPLE/simple/in.lj | 3 -
examples/COUPLE/simple/simple.c | 4 +-
examples/COUPLE/simple/simple.cpp | 4 +-
examples/COUPLE/simple/simple.f90 | 4 +-
examples/KAPPA/README | 2 +
examples/MC/README | 30 +
examples/MC/in.mc | 119 +
examples/MC/log.mc.6Jun14 | 106235 ++++++++++
examples/README | 33 +-
examples/USER/atc/hardy/consistency.screen | 850 +-
.../USER/atc/hardy/eam_kernel_convergence.screen | 2462 +-
examples/USER/atc/hardy/eam_unistrain_cell.screen | 78 +-
examples/USER/atc/hardy/eam_unistrain_mesh.screen | 118 +-
.../USER/atc/hardy/eam_unistrain_qcylinder.screen | 75 +-
.../USER/atc/hardy/eam_unistrain_qsphere.screen | 75 +-
examples/USER/atc/hardy/eam_unistrain_step.screen | 117 +-
examples/USER/atc/hardy/eam_volume_stretch.screen | 121 +-
examples/USER/atc/hardy/eshelby_static.screen | 1280 +-
examples/USER/atc/hardy/nvt.screen | 99 +-
examples/USER/cuda/data.rhodo | 191072 ------------------
examples/USER/cuda/in.melt_2.5.cuda | 34 -
examples/USER/cuda/in.melt_5.0.cuda | 34 -
examples/USER/cuda/in.phosphate.cuda | 32 -
examples/USER/cuda/in.rhodo.cuda | 34 -
.../eff/Auger-Adamantane/in.adamantane_ionized.nve | 7 +-
examples/USER/eff/Be-solid/in.Be-solid.spe | 5 +-
examples/USER/eff/CH4/in.ch4.dynamics | 7 +-
examples/USER/eff/CH4/in.ch4.min | 5 +-
examples/USER/eff/CH4/in.ch4_ionized.dynamics | 5 +-
examples/USER/eff/ECP/Si2H6/in.Si2H6 | 5 +-
examples/USER/eff/ECP/Si2H6/in.Si2H6.ang | 7 +-
examples/USER/eff/ECP/SiC/bulk/in.SiC | 7 +-
examples/USER/eff/ECP/SiH4/in.SiH4 | 5 +-
examples/USER/eff/ECP/SiH4/in.SiH4.ang | 5 +-
examples/USER/eff/H/in.h_atom.spe.ang | 3 +-
examples/USER/eff/H/in.h_atom.spe.bohr | 2 +-
examples/USER/eff/H2/in.h2 | 5 +-
examples/USER/eff/H_plasma/in.h2bulk.npt | 5 +-
examples/USER/eff/H_plasma/in.h2bulk.nve | 5 +-
examples/USER/eff/H_plasma/in.h2bulk.nve.ang | 5 +-
examples/USER/eff/Li-dendritic/in.Li-dendritic.min | 5 +-
examples/USER/eff/Li-dendritic/in.Li-dendritic.nvt | 8 +-
examples/USER/eff/Li-solid/in.Li.ang | 5 +-
examples/USER/eff/Li-solid/in.Li.bohr | 7 +-
examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang | 9 +-
examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr | 11 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.ang | 7 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr | 7 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang | 3 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr | 2 +-
examples/USER/gle/data.h2o-quantum | 413 +
examples/USER/gle/data.h2o-smart | 413 +
examples/USER/gle/in.h2o-quantum | 41 +
examples/USER/gle/in.h2o-smart | 41 +
examples/USER/gle/log.h2o-quantum | 201 +
examples/USER/gle/log.h2o-smart | 200 +
examples/USER/gle/qt-300k.A | 7 +
examples/USER/gle/qt-300k.C | 7 +
examples/USER/gle/smart.A | 7 +
examples/USER/i-pi/C.opt.tersoff | 66 +
examples/USER/i-pi/README | 46 +
examples/USER/i-pi/data.graphene | 1939 +
examples/USER/i-pi/i-pi_input.xml | 31 +
examples/USER/i-pi/i-pi_positions.xyz | 962 +
examples/USER/i-pi/in.graphene | 34 +
examples/USER/misc/basal/in.basal | 2 +-
examples/USER/pimd/para-h2/H2.data | 196 +
examples/USER/pimd/para-h2/H2.xyz | 182 +
examples/USER/pimd/para-h2/NM.info | 21 +
examples/USER/pimd/para-h2/in.scp | 29 +
examples/USER/pimd/para-h2/pair.table | 18003 ++
examples/USER/pimd/para-h2/run.sh | 1 +
examples/USER/pimd/para-h2/vmd.src | 94 +
examples/USER/pimd/prot-hairpin/in.scp | 31 +
examples/USER/pimd/prot-hairpin/run.sh | 1 +
examples/USER/pimd/prot-hairpin/system.data | 27593 +++
examples/USER/quip/data_gap | 78 +
examples/USER/quip/data_sw | 22 +
examples/USER/quip/gap_example.xml | 707 +
examples/USER/quip/gap_example_sparse.dat | 25500 +++
examples/USER/quip/in.gap | 23 +
examples/USER/quip/in.sw | 23 +
examples/USER/quip/sw_example.xml | 46 +
examples/USER/srp/data.chain | 8724 +
examples/USER/srp/in.srp | 37 +
examples/accelerate/Make.list | 41 +
examples/accelerate/README | 158 +
examples/{USER/cuda => accelerate}/data.phosphate | 0
examples/accelerate/in.lc | 57 +
examples/accelerate/in.lj | 33 +
examples/accelerate/in.lj.5.0 | 33 +
examples/accelerate/in.phosphate | 33 +
examples/accelerate/in.rhodo | 34 +
.../log.lj.1Feb14.gpu.1} | 0
.../log.lj.1Feb14.gpu.4} | 0
examples/accelerate/log.lj.1Feb14.kokkos.cuda.1 | 68 +
examples/accelerate/log.lj.1Feb14.kokkos.cuda.2 | 68 +
examples/accelerate/log.lj.1Feb14.kokkos.omp.1 | 68 +
examples/accelerate/log.lj.1Feb14.kokkos.omp.4 | 68 +
.../log.lj.5.0.1Feb14.gpu.1} | 0
.../log.lj.5.0.1Feb14.gpu.4} | 0
.../log.phosphate.1Feb14.gpu.1} | 0
.../log.phosphate.1Feb14.gpu.4} | 0
.../log.rhodo.1Feb14.gpu.1} | 0
.../log.rhodo.1Feb14.gpu.4} | 0
examples/balance/in.balance | 54 +
examples/balance/in.balance.bond.fast | 63 +
examples/balance/in.balance.bond.slow | 62 +
examples/balance/log.balance.8Aug14.linux.1 | 187 +
examples/balance/log.balance.8Aug14.linux.4 | 187 +
.../balance/log.balance.bond.fast.21Jan15.linux.1 | 203 +
.../balance/log.balance.bond.fast.21Jan15.linux.4 | 203 +
.../balance/log.balance.bond.slow.21Jan15.linux.1 | 502 +
.../balance/log.balance.bond.slow.21Jan15.linux.4 | 502 +
examples/comb/elastic.f90 | 384 +-
examples/coreshell/data.coreshell | 1114 +
examples/coreshell/in.coreshell | 72 +
examples/coreshell/log.coreshell.6Mar15.linux.1 | 188 +
examples/coreshell/log.coreshell.6Mar15.linux.4 | 188 +
examples/gpu/data.phosphate | 21922 --
examples/gpu/data.rhodo | 191072 ------------------
examples/gpu/in.gpu.melt.2.5 | 34 -
examples/gpu/in.gpu.melt.5.0 | 34 -
examples/gpu/in.gpu.phosphate | 31 -
examples/gpu/in.gpu.rhodo | 36 -
examples/kim/log.kim.lj.27Jul14.ubuntu.1 | 29 +
examples/kim/log.kim.lj.27Jul14.ubuntu.4 | 29 +
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.1 | 29 +
examples/kim/log.kim.lj.lmp.27Jul14.ubuntu.4 | 29 +
examples/min/in.min.box | 45 +-
examples/qeq/data.CHO | 122 +
examples/qeq/data.aC | 1216 +
{potentials => examples/qeq}/ffield.reax.cho | 0
examples/qeq/in.qeq.buck | 39 +
examples/qeq/in.qeq.reaxc | 46 +
examples/qeq/log.qeq.buck.8Sep14.linux.1 | 85 +
examples/qeq/log.qeq.buck.8Sep14.linux.4 | 85 +
examples/qeq/log.qeq.reaxc.8Sep14.linux.1 | 89 +
examples/qeq/log.qeq.reaxc.8Sep14.linux.4 | 89 +
examples/qeq/param.qeq.reax | 3 +
examples/qeq/param.qeq1 | 3 +
examples/qeq/param.qeq2 | 2 +
examples/snap/Ta06A.snapcoeff | 36 +
examples/snap/Ta06A.snapparam | 12 +
examples/snap/Ta06A_pot.snap | 16 +
examples/snap/in.snap | 45 +
examples/snap/log.snap.5Sep14.linux.1 | 116 +
examples/snap/log.snap.5Sep14.linux.4 | 116 +
examples/streitz/AlO.eam.alloy | 7007 +
examples/streitz/AlO.streitz | 8 +
examples/streitz/data.streitz | 2171 +
examples/streitz/in.streitz.ewald | 50 +
examples/streitz/in.streitz.wolf | 50 +
examples/streitz/log.streitz.ewald.19Feb15.linux.1 | 111 +
examples/streitz/log.streitz.ewald.19Feb15.linux.4 | 107 +
examples/streitz/log.streitz.wolf.19Feb15.linux.1 | 100 +
examples/streitz/log.streitz.wolf.19Feb15.linux.4 | 100 +
lib/README | 30 +-
lib/atc/ATC_Coupling.cpp | 242 +-
lib/atc/ATC_Coupling.h | 50 +-
lib/atc/ATC_CouplingEnergy.cpp | 16 +-
lib/atc/ATC_CouplingMomentumEnergy.cpp | 14 +-
lib/atc/ATC_Error.h | 1 -
lib/atc/ATC_Method.cpp | 141 +-
lib/atc/ATC_Method.h | 9 +-
lib/atc/ATC_TypeDefs.h | 8 +-
lib/atc/AtomicRegulator.cpp | 23 +-
lib/atc/AtomicRegulator.h | 23 +-
lib/atc/CauchyBorn.h | 3 +-
lib/atc/ChargeRegulator.cpp | 4 +-
lib/atc/ChargeRegulator.h | 4 +-
lib/atc/DenseMatrix.h | 30 +-
lib/atc/DenseVector.h | 6 +-
lib/atc/DependencyManager.h | 2 +-
lib/atc/DiagonalMatrix.h | 8 +-
lib/atc/ElectronDragPower.cpp | 4 +-
lib/atc/ElectronFlux.h | 9 +-
lib/atc/ExtrinsicModelDriftDiffusion.cpp | 133 +-
lib/atc/ExtrinsicModelDriftDiffusion.h | 4 +
lib/atc/ExtrinsicModelElectrostatic.cpp | 17 +-
lib/atc/ExtrinsicModelTwoTemperature.cpp | 35 +-
lib/atc/ExtrinsicModelTwoTemperature.h | 12 +-
lib/atc/FE_Element.cpp | 20 +
lib/atc/FE_Element.h | 4 +-
lib/atc/FE_Engine.cpp | 493 +-
lib/atc/FE_Engine.h | 25 +-
lib/atc/FE_Mesh.cpp | 259 +-
lib/atc/FE_Mesh.h | 18 +-
lib/atc/FieldEulerIntegrator.cpp | 67 +-
lib/atc/FieldEulerIntegrator.h | 45 +
lib/atc/FieldManager.cpp | 1 +
lib/atc/Function.cpp | 6 +
lib/atc/Function.h | 4 -
lib/atc/FundamentalAtomicQuantity.h | 4 +-
lib/atc/GhostManager.cpp | 315 +-
lib/atc/GhostManager.h | 86 +-
lib/atc/ImplicitSolveOperator.cpp | 242 +-
lib/atc/ImplicitSolveOperator.h | 106 +-
lib/atc/KD_Tree.cpp | 5 +
lib/atc/KernelFunction.cpp | 6 +-
lib/atc/KinetoThermostat.cpp | 857 +-
lib/atc/KinetoThermostat.h | 577 +-
lib/atc/Kinetostat.cpp | 650 +-
lib/atc/Kinetostat.h | 133 +-
lib/atc/LammpsInterface.cpp | 21 +
lib/atc/LammpsInterface.h | 42 +-
lib/atc/LinearSolver.cpp | 11 +-
lib/atc/LinearSolver.h | 1 +
lib/atc/MPI_Wrappers.cpp | 9 +
lib/atc/MPI_Wrappers.h | 1 +
lib/atc/Makefile.mingw32-cross | 9 +-
lib/atc/Makefile.mingw32-cross-mpi | 13 +-
lib/atc/Makefile.mingw64-cross | 11 +-
lib/atc/Makefile.mingw64-cross-mpi | 13 +-
lib/atc/Makefile.mpic++ | 18 +-
lib/atc/Makefile.serial | 14 +-
lib/atc/Material.cpp | 192 +-
lib/atc/Matrix.h | 49 +-
lib/atc/MeshReader.cpp | 6 +-
lib/atc/MeshReader.h | 1 -
lib/atc/MoleculeSet.cpp | 4 +-
lib/atc/MoleculeSet.h | 2 +-
lib/atc/OutputManager.cpp | 9 +-
lib/atc/OutputManager.h | 2 +
lib/atc/POEMSChain.h | 73 +
lib/atc/PerAtomQuantity.h | 2 +-
lib/atc/PerAtomQuantityLibrary.cpp | 153 +-
lib/atc/PerAtomQuantityLibrary.h | 85 +-
lib/atc/PoissonSolver.cpp | 7 +-
lib/atc/PrescribedDataManager.cpp | 56 +-
lib/atc/PrescribedDataManager.h | 26 +-
lib/atc/SchrodingerSolver.cpp | 560 +-
lib/atc/SchrodingerSolver.h | 106 +-
lib/atc/SparseMatrix-inl.h | 4 +-
lib/atc/SystemProcessor.h | 283 +
lib/atc/Thermostat.cpp | 840 +-
lib/atc/Thermostat.h | 284 +-
lib/atc/TimeIntegrator.h | 4 +-
lib/atc/TransferLibrary.cpp | 2 +-
lib/atc/TransferLibrary.h | 4 +-
lib/atc/Utility.h | 61 +-
lib/atc/Vector.h | 30 +-
lib/atc/WeakEquationElectronContinuity.cpp | 1 +
lib/atc/WeakEquationElectronContinuity.h | 2 +-
lib/atc/WeakEquationElectronMomentum.cpp | 1 +
lib/atc/WeakEquationElectronTemperature.cpp | 15 +-
lib/atc/WeakEquationElectronTemperature.h | 2 +-
lib/awpmd/{Makefile.openmpi => Makefile.mpicc} | 0
lib/colvars/Makefile.fermi | 52 +-
lib/colvars/Makefile.g++ | 42 +-
lib/colvars/Makefile.mingw32-cross | 42 +-
lib/colvars/Makefile.mingw64-cross | 42 +-
lib/colvars/colvar.cpp | 1226 +-
lib/colvars/colvar.h | 127 +-
lib/colvars/colvaratoms.cpp | 464 +-
lib/colvars/colvaratoms.h | 47 +-
lib/colvars/colvarbias.cpp | 585 +-
lib/colvars/colvarbias.h | 143 +-
lib/colvars/colvarbias_abf.cpp | 561 +-
lib/colvars/colvarbias_abf.h | 56 +-
lib/colvars/colvarbias_alb.cpp | 440 +
lib/colvars/colvarbias_alb.h | 87 +
lib/colvars/colvarbias_meta.cpp | 775 +-
lib/colvars/colvarbias_meta.h | 94 +-
lib/colvars/colvarbias_restraint.cpp | 552 +
lib/colvars/colvarbias_restraint.h | 153 +
lib/colvars/colvarcomp.cpp | 140 +-
lib/colvars/colvarcomp.h | 903 +-
lib/colvars/colvarcomp_angles.cpp | 187 +-
lib/colvars/colvarcomp_coordnums.cpp | 203 +-
lib/colvars/colvarcomp_distances.cpp | 697 +-
lib/colvars/colvarcomp_protein.cpp | 167 +-
lib/colvars/colvarcomp_rotations.cpp | 187 +-
lib/colvars/colvargrid.cpp | 158 +-
lib/colvars/colvargrid.h | 919 +-
lib/colvars/colvarmodule.cpp | 1855 +-
lib/colvars/colvarmodule.h | 314 +-
lib/colvars/colvarparse.cpp | 385 +-
lib/colvars/colvarparse.h | 100 +-
lib/colvars/colvarproxy.h | 222 +-
lib/colvars/colvarscript.cpp | 370 +
lib/colvars/colvarscript.h | 47 +
lib/colvars/colvartypes.cpp | 648 +
lib/colvars/colvartypes.h | 1264 +-
lib/colvars/colvarvalue.cpp | 633 +-
lib/colvars/colvarvalue.h | 975 +-
lib/cuda/Makefile.defaults | 4 +-
lib/cuda/Makefile.lammps | 4 +-
lib/cuda/atom_vec_cuda.cu | 56 +-
lib/cuda/atom_vec_cuda_kernel.cu | 124 +-
lib/cuda/comm_cuda.cu | 78 +-
lib/cuda/comm_cuda_kernel.cu | 68 +-
lib/cuda/compute_temp_cuda.cu | 20 +-
lib/cuda/compute_temp_cuda_cu.h | 4 +-
lib/cuda/compute_temp_cuda_kernel.cu | 14 +-
lib/cuda/compute_temp_partial_cuda.cu | 24 +-
lib/cuda/compute_temp_partial_cuda_cu.h | 4 +-
lib/cuda/compute_temp_partial_cuda_kernel.cu | 18 +-
lib/cuda/crm_cuda_utils.cu | 36 +-
lib/cuda/cuda.cu | 12 +-
lib/cuda/cuda_common.h | 72 +-
lib/cuda/cuda_pair.cu | 248 +-
lib/cuda/cuda_pair_kernel.cu | 304 +-
lib/cuda/cuda_pair_virial_kernel_nc.cu | 10 +-
lib/cuda/cuda_precision.h | 135 +-
lib/cuda/cuda_shared.h | 102 +-
lib/cuda/cuda_wrapper.cu | 2 +-
lib/cuda/cuda_wrapper_cu.h | 2 +-
lib/cuda/domain.cu | 42 +-
lib/cuda/domain_kernel.cu | 38 +-
lib/cuda/fft3d_cuda.cu | 12 +-
lib/cuda/fft3d_cuda_cu.h | 2 +-
lib/cuda/fft3d_cuda_kernel.cu | 8 +-
lib/cuda/fix_addforce_cuda.cu | 16 +-
lib/cuda/fix_addforce_cuda_cu.h | 2 +-
lib/cuda/fix_addforce_cuda_kernel.cu | 12 +-
lib/cuda/fix_aveforce_cuda.cu | 18 +-
lib/cuda/fix_aveforce_cuda_cu.h | 4 +-
lib/cuda/fix_aveforce_cuda_kernel.cu | 12 +-
lib/cuda/fix_enforce2d_cuda.cu | 4 +-
lib/cuda/fix_freeze_cuda.cu | 18 +-
lib/cuda/fix_freeze_cuda_cu.h | 2 +-
lib/cuda/fix_freeze_cuda_kernel.cu | 10 +-
lib/cuda/fix_gravity_cuda.cu | 14 +-
lib/cuda/fix_gravity_cuda_cu.h | 2 +-
lib/cuda/fix_gravity_cuda_kernel.cu | 4 +-
lib/cuda/fix_nh_cuda.cu | 38 +-
lib/cuda/fix_nh_cuda_cu.h | 4 +-
lib/cuda/fix_nh_cuda_kernel.cu | 60 +-
lib/cuda/fix_nve_cuda.cu | 24 +-
lib/cuda/fix_nve_cuda_cu.h | 2 +-
lib/cuda/fix_nve_cuda_kernel.cu | 40 +-
lib/cuda/fix_set_force_cuda.cu | 16 +-
lib/cuda/fix_set_force_cuda_cu.h | 2 +-
lib/cuda/fix_set_force_cuda_kernel.cu | 12 +-
lib/cuda/fix_shake_cuda.cu | 66 +-
lib/cuda/fix_shake_cuda_cu.h | 4 +-
lib/cuda/fix_shake_cuda_kernel.cu | 422 +-
lib/cuda/fix_temp_berendsen_cuda.cu | 4 +-
lib/cuda/fix_temp_berendsen_cuda_kernel.cu | 2 +-
lib/cuda/fix_temp_rescale_cuda.cu | 4 +-
lib/cuda/fix_temp_rescale_cuda_kernel.cu | 2 +-
lib/cuda/fix_temp_rescale_limit_cuda.cu | 4 +-
lib/cuda/fix_temp_rescale_limit_cuda_kernel.cu | 8 +-
lib/cuda/fix_viscous_cuda.cu | 6 +-
lib/cuda/fix_viscous_cuda_kernel.cu | 4 +-
lib/cuda/neighbor.cu | 40 +-
lib/cuda/neighbor_kernel.cu | 94 +-
lib/cuda/pair_born_coul_long_cuda.cu | 4 +-
lib/cuda/pair_born_coul_long_cuda_kernel_nc.cu | 12 +-
lib/cuda/pair_buck_coul_cut_cuda.cu | 4 +-
lib/cuda/pair_buck_coul_long_cuda.cu | 4 +-
lib/cuda/pair_buck_cuda.cu | 4 +-
lib/cuda/pair_buck_cuda_kernel_nc.cu | 12 +-
lib/cuda/pair_cg_cmm_coul_cut_cuda.cu | 81 -
lib/cuda/pair_cg_cmm_coul_cut_cuda_cu.h | 26 -
lib/cuda/pair_cg_cmm_coul_debye_cuda.cu | 81 -
lib/cuda/pair_cg_cmm_coul_debye_cuda_cu.h | 26 -
lib/cuda/pair_cg_cmm_coul_long_cuda.cu | 81 -
lib/cuda/pair_cg_cmm_coul_long_cuda_cu.h | 26 -
lib/cuda/pair_cg_cmm_cuda.cu | 87 -
lib/cuda/pair_cg_cmm_cuda_cu.h | 26 -
lib/cuda/pair_cg_cmm_cuda_kernel_nc.cu | 49 -
lib/cuda/pair_eam_cuda.cu | 92 +-
lib/cuda/pair_eam_cuda_kernel_nc.cu | 78 +-
lib/cuda/pair_gran_hooke_cuda.cu | 58 +-
lib/cuda/pair_gran_hooke_cuda_kernel_nc.cu | 44 +-
lib/cuda/pair_lj96_cut_cuda.cu | 4 +-
lib/cuda/pair_lj96_cut_cuda_kernel_nc.cu | 10 +-
lib/cuda/pair_lj_charmm_coul_charmm_cuda.cu | 14 +-
lib/cuda/pair_lj_charmm_coul_charmm_cuda_cu.h | 2 +-
.../pair_lj_charmm_coul_charmm_cuda_kernel_nc.cu | 24 +-
.../pair_lj_charmm_coul_charmm_implicit_cuda.cu | 20 +-
.../pair_lj_charmm_coul_charmm_implicit_cuda_cu.h | 2 +-
...j_charmm_coul_charmm_implicit_cuda_kernel_nc.cu | 10 +-
lib/cuda/pair_lj_charmm_coul_long_cuda.cu | 10 +-
lib/cuda/pair_lj_charmm_coul_long_cuda_cu.h | 2 +-
lib/cuda/pair_lj_class2_coul_cut_cuda.cu | 4 +-
lib/cuda/pair_lj_class2_coul_long_cuda.cu | 4 +-
lib/cuda/pair_lj_class2_cuda.cu | 6 +-
lib/cuda/pair_lj_class2_cuda_kernel_nc.cu | 8 +-
lib/cuda/pair_lj_cut_coul_cut_cuda.cu | 4 +-
lib/cuda/pair_lj_cut_coul_debye_cuda.cu | 4 +-
lib/cuda/pair_lj_cut_coul_long_cuda.cu | 4 +-
lib/cuda/pair_lj_cut_cuda.cu | 6 +-
lib/cuda/pair_lj_cut_cuda_kernel_nc.cu | 6 +-
lib/cuda/pair_lj_cut_experimental_cuda.cu | 6 +-
lib/cuda/pair_lj_expand_cuda.cu | 4 +-
lib/cuda/pair_lj_expand_cuda_kernel_nc.cu | 14 +-
lib/cuda/pair_lj_gromacs_coul_gromacs_cuda.cu | 24 +-
lib/cuda/pair_lj_gromacs_coul_gromacs_cuda_cu.h | 2 +-
.../pair_lj_gromacs_coul_gromacs_cuda_kernel_nc.cu | 12 +-
lib/cuda/pair_lj_gromacs_cuda.cu | 4 +-
lib/cuda/pair_lj_gromacs_cuda_kernel_nc.cu | 16 +-
lib/cuda/pair_lj_sdk_coul_cut_cuda.cu | 4 +-
lib/cuda/pair_lj_sdk_coul_debye_cuda.cu | 4 +-
lib/cuda/pair_lj_sdk_coul_long_cuda.cu | 4 +-
lib/cuda/pair_lj_sdk_cuda.cu | 4 +-
lib/cuda/pair_lj_sdk_cuda_kernel_nc.cu | 24 +-
lib/cuda/pair_lj_smooth_cuda.cu | 4 +-
lib/cuda/pair_lj_smooth_cuda_kernel_nc.cu | 14 +-
lib/cuda/pair_morse_coul_long_cuda.cu | 4 +-
lib/cuda/pair_morse_coul_long_cuda_kernel_nc.cu | 12 +-
lib/cuda/pair_morse_cuda.cu | 4 +-
lib/cuda/pair_morse_cuda_kernel_nc.cu | 8 +-
lib/cuda/pair_sw_cuda.cu | 18 +-
lib/cuda/pair_sw_cuda_cu.h | 16 +-
lib/cuda/pair_sw_cuda_kernel_nc.cu | 76 +-
lib/cuda/pair_tersoff_cuda.cu | 26 +-
lib/cuda/pair_tersoff_cuda_cu.h | 20 +-
lib/cuda/pair_tersoff_cuda_kernel_nc.cu | 354 +-
lib/cuda/pppm_cuda.cu | 176 +-
lib/cuda/pppm_cuda_cu.h | 18 +-
lib/cuda/pppm_cuda_kernel.cu | 96 +-
lib/gpu/Makefile.linux.double | 2 +
lib/gpu/Makefile.linux.mixed | 14 +
lib/gpu/Makefile.linux.single | 50 +
lib/gpu/Nvidia.makefile | 32 +-
lib/gpu/Opencl.makefile | 25 +-
lib/gpu/geryon/VERSION.txt | 2 +-
lib/gpu/geryon/nvd_device.h | 6 +
lib/gpu/geryon/nvd_macros.h | 7 +-
lib/gpu/geryon/ocl_device.h | 13 +-
lib/gpu/geryon/ocl_macros.h | 7 +-
lib/gpu/geryon/ocl_memory.h | 5 +-
lib/gpu/lal_answer.cpp | 18 +-
lib/gpu/lal_aux_fun1.h | 71 +-
lib/gpu/lal_base_ellipsoid.cpp | 8 +-
lib/gpu/lal_beck.cu | 16 +-
lib/gpu/lal_beck_ext.cpp | 6 +-
lib/gpu/lal_born.cpp | 19 +
lib/gpu/lal_born.cu | 16 +-
lib/gpu/lal_born.h | 8 +-
lib/gpu/lal_born_coul_long.cu | 16 +-
lib/gpu/lal_born_coul_long_ext.cpp | 6 +-
lib/gpu/lal_born_coul_wolf.cu | 44 +-
lib/gpu/lal_born_coul_wolf_ext.cpp | 6 +-
lib/gpu/lal_born_ext.cpp | 32 +-
lib/gpu/lal_buck.cpp | 18 +
lib/gpu/lal_buck.cu | 16 +-
lib/gpu/lal_buck.h | 5 +
lib/gpu/lal_buck_coul.cu | 16 +-
lib/gpu/lal_buck_coul_ext.cpp | 6 +-
lib/gpu/lal_buck_coul_long.cu | 16 +-
lib/gpu/lal_buck_coul_long_ext.cpp | 6 +-
lib/gpu/lal_buck_ext.cpp | 31 +-
lib/gpu/lal_cg_cmm.cu | 16 +-
lib/gpu/lal_cg_cmm_ext.cpp | 6 +-
lib/gpu/lal_cg_cmm_long.cu | 16 +-
lib/gpu/lal_cg_cmm_long_ext.cpp | 6 +-
lib/gpu/lal_charmm_long.cpp | 11 +-
lib/gpu/lal_charmm_long.cu | 28 +-
lib/gpu/lal_charmm_long_ext.cpp | 6 +-
lib/gpu/lal_colloid.cu | 16 +-
lib/gpu/lal_colloid_ext.cpp | 6 +-
lib/gpu/lal_coul.cpp | 166 +
lib/gpu/lal_coul.cu | 210 +
lib/gpu/lal_coul.h | 83 +
lib/gpu/lal_coul_debye.cpp | 167 +
lib/gpu/lal_coul_debye.cu | 220 +
lib/gpu/lal_coul_debye.h | 84 +
lib/gpu/lal_coul_debye_ext.cpp | 143 +
lib/gpu/lal_coul_dsf.cu | 16 +-
lib/gpu/lal_coul_dsf_ext.cpp | 6 +-
lib/gpu/lal_coul_ext.cpp | 143 +
lib/gpu/lal_coul_long.cpp | 38 +-
lib/gpu/lal_coul_long.cu | 16 +-
lib/gpu/lal_coul_long.h | 16 +-
lib/gpu/lal_coul_long_ext.cpp | 48 +-
lib/gpu/lal_device.cpp | 27 +-
lib/gpu/lal_device.h | 10 +-
lib/gpu/lal_dipole_lj.cu | 44 +-
lib/gpu/lal_dipole_lj_ext.cpp | 6 +-
lib/gpu/lal_dipole_lj_sf.cu | 44 +-
lib/gpu/lal_dipole_lj_sf_ext.cpp | 6 +-
lib/gpu/lal_dpd.cu | 18 +-
lib/gpu/lal_eam.cu | 51 +-
lib/gpu/lal_eam_ext.cpp | 6 +-
lib/gpu/lal_ellipsoid_extra.h | 15 +-
lib/gpu/lal_ellipsoid_nbor.cu | 34 +-
lib/gpu/lal_gauss.cpp | 15 +
lib/gpu/lal_gauss.cu | 16 +-
lib/gpu/lal_gauss.h | 8 +-
lib/gpu/lal_gauss_ext.cpp | 28 +-
lib/gpu/lal_gayberne.cu | 4 +-
lib/gpu/lal_gayberne_ext.cpp | 6 +-
lib/gpu/lal_gayberne_lj.cu | 20 +-
lib/gpu/lal_lj.cpp | 17 +
lib/gpu/lal_lj.cu | 26 +-
lib/gpu/lal_lj.h | 7 +-
lib/gpu/lal_lj96.cu | 16 +-
lib/gpu/lal_lj96_ext.cpp | 6 +-
lib/gpu/lal_lj_class2_long.cu | 16 +-
lib/gpu/lal_lj_class2_long_ext.cpp | 6 +-
lib/gpu/lal_lj_coul.cu | 16 +-
lib/gpu/lal_lj_coul_debye.cu | 16 +-
lib/gpu/lal_lj_coul_debye_ext.cpp | 6 +-
lib/gpu/lal_lj_coul_ext.cpp | 6 +-
lib/gpu/lal_lj_coul_long.cpp | 19 +-
lib/gpu/lal_lj_coul_long.cu | 16 +-
lib/gpu/lal_lj_coul_long.h | 5 +
lib/gpu/lal_lj_coul_long_ext.cpp | 29 +-
lib/gpu/lal_lj_coul_msm.cu | 16 +-
lib/gpu/lal_lj_coul_msm_ext.cpp | 6 +-
lib/gpu/lal_lj_dsf.cu | 16 +-
lib/gpu/lal_lj_dsf_ext.cpp | 6 +-
lib/gpu/lal_lj_expand.cpp | 20 +
lib/gpu/lal_lj_expand.cu | 16 +-
lib/gpu/lal_lj_expand.h | 7 +-
lib/gpu/lal_lj_expand_ext.cpp | 29 +-
lib/gpu/lal_lj_ext.cpp | 27 +-
lib/gpu/lal_lj_gromacs.cu | 18 +-
lib/gpu/lal_mie.cu | 16 +-
lib/gpu/lal_mie_ext.cpp | 6 +-
lib/gpu/lal_morse.cu | 16 +-
lib/gpu/lal_morse_ext.cpp | 6 +-
lib/gpu/lal_neighbor.cpp | 7 +-
lib/gpu/lal_neighbor.h | 1 +
lib/gpu/lal_neighbor_cpu.cu | 10 +-
lib/gpu/lal_pppm.cpp | 2 +-
lib/gpu/lal_pppm.cu | 7 +
lib/gpu/lal_pppm_ext.cpp | 6 +-
lib/gpu/lal_preprocessor.h | 50 +
lib/gpu/lal_re_squared.cu | 4 +-
lib/gpu/lal_re_squared_ext.cpp | 6 +-
lib/gpu/lal_re_squared_lj.cu | 24 +-
lib/gpu/lal_soft.cpp | 15 +
lib/gpu/lal_soft.cu | 16 +-
lib/gpu/lal_soft.h | 8 +-
lib/gpu/lal_soft_ext.cpp | 28 +-
lib/gpu/lal_sw.cu | 152 +-
lib/gpu/lal_table.cu | 64 +-
lib/gpu/lal_table_ext.cpp | 6 +-
lib/gpu/lal_yukawa.cu | 16 +-
lib/gpu/lal_yukawa_colloid.cu | 16 +-
lib/gpu/lal_yukawa_colloid_ext.cpp | 6 +-
lib/gpu/lal_yukawa_ext.cpp | 6 +-
lib/kim/Makefile.lammps | 25 +
lib/kim/README | 64 +
lib/kokkos/Makefile.lammps | 170 +
lib/kokkos/README | 44 +
.../.0 => lib/kokkos/TPL/KokkosTPL_dummy.cpp | 0
lib/kokkos/TPL/cmake/Dependencies.cmake | 9 +
lib/kokkos/TPL/cub/block/block_discontinuity.cuh | 587 +
lib/kokkos/TPL/cub/block/block_exchange.cuh | 918 +
lib/kokkos/TPL/cub/block/block_histogram.cuh | 414 +
lib/kokkos/TPL/cub/block/block_load.cuh | 1122 +
lib/kokkos/TPL/cub/block/block_radix_rank.cuh | 479 +
lib/kokkos/TPL/cub/block/block_radix_sort.cuh | 608 +
lib/kokkos/TPL/cub/block/block_raking_layout.cuh | 145 +
lib/kokkos/TPL/cub/block/block_reduce.cuh | 563 +
lib/kokkos/TPL/cub/block/block_scan.cuh | 2233 +
lib/kokkos/TPL/cub/block/block_store.cuh | 926 +
.../specializations/block_histogram_atomic.cuh | 85 +
.../block/specializations/block_histogram_sort.cuh | 197 +
.../block/specializations/block_reduce_raking.cuh | 214 +
.../block_reduce_warp_reductions.cuh | 198 +
.../block/specializations/block_scan_raking.cuh | 761 +
.../specializations/block_scan_warp_scans.cuh | 342 +
lib/kokkos/TPL/cub/cub.cuh | 84 +
.../TPL/cub/device/block/block_histo_tiles.cuh | 322 +
.../TPL/cub/device/block/block_partition_tiles.cuh | 381 +
.../block/block_radix_sort_downsweep_tiles.cuh | 713 +
.../block/block_radix_sort_upsweep_tiles.cuh | 464 +
.../cub/device/block/block_reduce_by_key_tiles.cuh | 399 +
.../TPL/cub/device/block/block_reduce_tiles.cuh | 375 +
.../TPL/cub/device/block/block_scan_tiles.cuh | 509 +
.../TPL/cub/device/block/scan_tiles_types.cuh | 318 +
.../specializations/block_histo_tiles_gatomic.cuh | 184 +
.../specializations/block_histo_tiles_satomic.cuh | 237 +
.../specializations/block_histo_tiles_sort.cuh | 364 +
lib/kokkos/TPL/cub/device/device_histogram.cuh | 1062 +
lib/kokkos/TPL/cub/device/device_radix_sort.cuh | 890 +
lib/kokkos/TPL/cub/device/device_reduce.cuh | 775 +
lib/kokkos/TPL/cub/device/device_reduce_by_key.cuh | 633 +
lib/kokkos/TPL/cub/device/device_reorder.cuh | 550 +
lib/kokkos/TPL/cub/device/device_scan.cuh | 812 +
lib/kokkos/TPL/cub/grid/grid_barrier.cuh | 211 +
lib/kokkos/TPL/cub/grid/grid_even_share.cuh | 197 +
lib/kokkos/TPL/cub/grid/grid_mapping.cuh | 95 +
lib/kokkos/TPL/cub/grid/grid_queue.cuh | 207 +
lib/kokkos/TPL/cub/host/spinlock.cuh | 123 +
lib/kokkos/TPL/cub/thread/thread_load.cuh | 429 +
lib/kokkos/TPL/cub/thread/thread_operators.cuh | 145 +
lib/kokkos/TPL/cub/thread/thread_reduce.cuh | 145 +
lib/kokkos/TPL/cub/thread/thread_scan.cuh | 231 +
lib/kokkos/TPL/cub/thread/thread_store.cuh | 412 +
lib/kokkos/TPL/cub/util_allocator.cuh | 661 +
lib/kokkos/TPL/cub/util_arch.cuh | 295 +
lib/kokkos/TPL/cub/util_debug.cuh | 115 +
lib/kokkos/TPL/cub/util_device.cuh | 378 +
lib/kokkos/TPL/cub/util_iterator.cuh | 718 +
lib/kokkos/TPL/cub/util_macro.cuh | 107 +
lib/kokkos/TPL/cub/util_namespace.cuh | 41 +
lib/kokkos/TPL/cub/util_ptx.cuh | 380 +
lib/kokkos/TPL/cub/util_type.cuh | 685 +
lib/kokkos/TPL/cub/util_vector.cuh | 166 +
.../cub/warp/specializations/warp_reduce_shfl.cuh | 358 +
.../cub/warp/specializations/warp_reduce_smem.cuh | 291 +
.../cub/warp/specializations/warp_scan_shfl.cuh | 371 +
.../cub/warp/specializations/warp_scan_smem.cuh | 327 +
lib/kokkos/TPL/cub/warp/warp_reduce.cuh | 677 +
lib/kokkos/TPL/cub/warp/warp_scan.cuh | 1297 +
lib/kokkos/algorithms/src/Kokkos_Random.hpp | 1691 +
lib/kokkos/algorithms/src/Kokkos_Sort.hpp | 486 +
lib/kokkos/containers/src/Kokkos_Bitset.hpp | 437 +
lib/kokkos/containers/src/Kokkos_DualView.hpp | 678 +
lib/kokkos/containers/src/Kokkos_Functional.hpp | 132 +
lib/kokkos/containers/src/Kokkos_SegmentedView.hpp | 478 +
.../containers/src/Kokkos_StaticCrsGraph.hpp | 225 +
lib/kokkos/containers/src/Kokkos_UnorderedMap.hpp | 848 +
lib/kokkos/containers/src/Kokkos_Vector.hpp | 282 +
.../containers/src/impl/Kokkos_Bitset_impl.hpp | 173 +
.../containers/src/impl/Kokkos_Functional_impl.hpp | 154 +
.../src/impl/Kokkos_StaticCrsGraph_factory.hpp | 223 +
.../src/impl/Kokkos_UnorderedMap_impl.cpp | 101 +
.../src/impl/Kokkos_UnorderedMap_impl.hpp | 297 +
lib/kokkos/core/src/Cuda/Kokkos_CudaExec.hpp | 237 +
lib/kokkos/core/src/Cuda/Kokkos_CudaSpace.cpp | 591 +
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Impl.cpp | 670 +
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Internal.hpp | 171 +
lib/kokkos/core/src/Cuda/Kokkos_Cuda_Parallel.hpp | 1591 +
.../core/src/Cuda/Kokkos_Cuda_ReduceScan.hpp | 421 +
.../core/src/Cuda/Kokkos_Cuda_Vectorization.hpp | 291 +
lib/kokkos/core/src/Cuda/Kokkos_Cuda_View.hpp | 299 +
lib/kokkos/core/src/Cuda/Kokkos_Cuda_abort.hpp | 117 +
lib/kokkos/core/src/Kokkos_Atomic.hpp | 236 +
lib/kokkos/core/src/Kokkos_Core.hpp | 106 +
lib/kokkos/core/src/Kokkos_Core_fwd.hpp | 150 +
lib/kokkos/core/src/Kokkos_CrsArray.hpp | 171 +
lib/kokkos/core/src/Kokkos_Cuda.hpp | 263 +
lib/kokkos/core/src/Kokkos_CudaSpace.hpp | 468 +
lib/kokkos/core/src/Kokkos_CudaTypes.hpp | 139 +
lib/kokkos/core/src/Kokkos_ExecPolicy.hpp | 439 +
lib/kokkos/core/src/Kokkos_HostSpace.hpp | 161 +
lib/kokkos/core/src/Kokkos_Layout.hpp | 176 +
lib/kokkos/core/src/Kokkos_Macros.hpp | 433 +
lib/kokkos/core/src/Kokkos_MemoryTraits.hpp | 118 +
lib/kokkos/core/src/Kokkos_OpenMP.hpp | 176 +
lib/kokkos/core/src/Kokkos_Pair.hpp | 457 +
lib/kokkos/core/src/Kokkos_Parallel.hpp | 598 +
lib/kokkos/core/src/Kokkos_Qthread.hpp | 165 +
lib/kokkos/core/src/Kokkos_ScratchSpace.hpp | 115 +
lib/kokkos/core/src/Kokkos_Serial.hpp | 879 +
lib/kokkos/core/src/Kokkos_TaskPolicy.hpp | 467 +
lib/kokkos/core/src/Kokkos_Threads.hpp | 214 +
lib/kokkos/core/src/Kokkos_Vectorization.hpp | 100 +
lib/kokkos/core/src/Kokkos_View.hpp | 1863 +
lib/kokkos/core/src/Kokkos_hwloc.hpp | 140 +
.../core/src/OpenMP/Kokkos_OpenMP_Parallel.hpp | 496 +
lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.cpp | 365 +
lib/kokkos/core/src/OpenMP/Kokkos_OpenMPexec.hpp | 758 +
lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.cpp | 380 +
lib/kokkos/core/src/Qthread/Kokkos_QthreadExec.hpp | 580 +
.../core/src/Qthread/Kokkos_Qthread_Parallel.hpp | 418 +
.../core/src/Qthread/Kokkos_Qthread_TaskPolicy.cpp | 299 +
.../core/src/Qthread/Kokkos_Qthread_TaskPolicy.hpp | 736 +
lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.cpp | 745 +
lib/kokkos/core/src/Threads/Kokkos_ThreadsExec.hpp | 1041 +
.../core/src/Threads/Kokkos_ThreadsExec_base.cpp | 254 +
.../core/src/Threads/Kokkos_Threads_Parallel.hpp | 427 +
lib/kokkos/core/src/build.cuda.mac | 28 +
lib/kokkos/core/src/build_common.sh | 281 +
lib/kokkos/core/src/impl/Kokkos_AnalyzeShape.hpp | 260 +
.../core/src/impl/Kokkos_Atomic_Assembly_X86.hpp | 176 +
.../impl/Kokkos_Atomic_Compare_Exchange_Strong.hpp | 231 +
.../core/src/impl/Kokkos_Atomic_Exchange.hpp | 305 +
.../core/src/impl/Kokkos_Atomic_Fetch_Add.hpp | 297 +
.../core/src/impl/Kokkos_Atomic_Fetch_And.hpp | 125 +
.../core/src/impl/Kokkos_Atomic_Fetch_Or.hpp | 125 +
lib/kokkos/core/src/impl/Kokkos_Atomic_Generic.hpp | 383 +
lib/kokkos/core/src/impl/Kokkos_Atomic_View.hpp | 448 +
lib/kokkos/core/src/impl/Kokkos_Core.cpp | 441 +
.../core/src/impl/Kokkos_CrsArray_factory.hpp | 223 +
lib/kokkos/core/src/impl/Kokkos_Error.cpp | 195 +
lib/kokkos/core/src/impl/Kokkos_Error.hpp | 80 +
lib/kokkos/core/src/impl/Kokkos_FunctorAdapter.hpp | 960 +
lib/kokkos/core/src/impl/Kokkos_HostSpace.cpp | 271 +
lib/kokkos/core/src/impl/Kokkos_MemoryTracking.hpp | 374 +
lib/kokkos/core/src/impl/Kokkos_Memory_Fence.hpp | 73 +
lib/kokkos/core/src/impl/Kokkos_PhysicalLayout.hpp | 84 +
lib/kokkos/core/src/impl/Kokkos_Serial.cpp | 119 +
.../core/src/impl/Kokkos_Serial_TaskPolicy.cpp | 324 +
.../core/src/impl/Kokkos_Serial_TaskPolicy.hpp | 763 +
lib/kokkos/core/src/impl/Kokkos_Shape.cpp | 178 +
lib/kokkos/core/src/impl/Kokkos_Shape.hpp | 917 +
lib/kokkos/core/src/impl/Kokkos_StaticAssert.hpp | 79 +
lib/kokkos/core/src/impl/Kokkos_Tags.hpp | 131 +
lib/kokkos/core/src/impl/Kokkos_Timer.hpp | 115 +
lib/kokkos/core/src/impl/Kokkos_Traits.hpp | 370 +
lib/kokkos/core/src/impl/Kokkos_ViewDefault.hpp | 2818 +
lib/kokkos/core/src/impl/Kokkos_ViewOffset.hpp | 1335 +
lib/kokkos/core/src/impl/Kokkos_ViewSupport.hpp | 541 +
lib/kokkos/core/src/impl/Kokkos_ViewTileLeft.hpp | 195 +
lib/kokkos/core/src/impl/Kokkos_Volatile_Load.hpp | 242 +
lib/kokkos/core/src/impl/Kokkos_hwloc.cpp | 704 +
lib/kokkos/core/src/impl/Kokkos_spinwait.cpp | 80 +
lib/kokkos/core/src/impl/Kokkos_spinwait.hpp | 64 +
lib/linalg/Makefile.gfortran | 9 +-
lib/linalg/Makefile.mingw32-cross | 24 +-
lib/linalg/Makefile.mingw64-cross | 26 +-
lib/linalg/dbdsqr.f | 850 +
lib/linalg/dgebd2.f | 320 +
lib/linalg/dgebrd.f | 353 +
lib/linalg/dgelq2.f | 192 +
lib/linalg/dgelqf.f | 269 +
lib/linalg/dgeqr2.f | 192 +
lib/linalg/dgeqrf.f | 270 +
lib/linalg/dgesvd.f | 3493 +
lib/linalg/dlabrd.f | 381 +
lib/linalg/dlacpy.f | 156 +
lib/linalg/dlae2.f | 185 +
lib/linalg/dlaed0.f | 434 +
lib/linalg/dlaed1.f | 274 +
lib/linalg/dlaed2.f | 539 +
lib/linalg/dlaed3.f | 353 +
lib/linalg/dlaed4.f | 917 +
lib/linalg/dlaed5.f | 189 +
lib/linalg/dlaed6.f | 409 +
lib/linalg/dlaed7.f | 407 +
lib/linalg/dlaed8.f | 524 +
lib/linalg/dlaed9.f | 294 +
lib/linalg/dlaeda.f | 308 +
lib/linalg/dlaev2.f | 238 +
lib/linalg/dlamrg.f | 171 +
lib/linalg/dlanst.f | 186 +
lib/linalg/dlansy.f | 241 +
lib/linalg/dlapy2.f | 104 +
lib/linalg/dlarf.f | 227 +
lib/linalg/dlarfb.f | 758 +
lib/linalg/dlarfg.f | 196 +
lib/linalg/dlarft.f | 326 +
lib/linalg/dlartg.f | 204 +
lib/linalg/dlas2.f | 183 +
lib/linalg/dlascl.f | 364 +
lib/linalg/dlaset.f | 184 +
lib/linalg/dlasq1.f | 224 +
lib/linalg/dlasq2.f | 582 +
lib/linalg/dlasq3.f | 421 +
lib/linalg/dlasq4.f | 425 +
lib/linalg/dlasq5.f | 410 +
lib/linalg/dlasq6.f | 254 +
lib/linalg/dlasr.f | 436 +
lib/linalg/dlasrt.f | 303 +
lib/linalg/dlasv2.f | 325 +
lib/linalg/dlatrd.f | 336 +
lib/linalg/dnrm2.f | 112 +
lib/linalg/dorg2r.f | 200 +
lib/linalg/dorgbr.f | 338 +
lib/linalg/dorgl2.f | 204 +
lib/linalg/dorglq.f | 289 +
lib/linalg/dorgqr.f | 290 +
lib/linalg/dorm2l.f | 278 +
lib/linalg/dorm2r.f | 282 +
lib/linalg/dormbr.f | 372 +
lib/linalg/dorml2.f | 282 +
lib/linalg/dormlq.f | 354 +
lib/linalg/dormql.f | 348 +
lib/linalg/dormqr.f | 347 +
lib/linalg/dormtr.f | 310 +
lib/linalg/dpotf2.f | 230 +
lib/linalg/dpotrf.f | 246 +
lib/linalg/drot.f | 101 +
lib/linalg/dstedc.f | 489 +
lib/linalg/dsteqr.f | 572 +
lib/linalg/dsterf.f | 426 +
lib/linalg/dsyevd.f | 357 +
lib/linalg/dsygs2.f | 283 +
lib/linalg/dsygst.f | 321 +
lib/linalg/dsygvd.f | 380 +
lib/linalg/dsymm.f | 367 +
lib/linalg/dsymv.f | 333 +
lib/linalg/dsyr2.f | 298 +
lib/linalg/dsyr2k.f | 399 +
lib/linalg/dsyrk.f | 364 +
lib/linalg/dsytd2.f | 323 +
lib/linalg/dsytrd.f | 376 +
lib/linalg/iladlc.f | 118 +
lib/linalg/iladlr.f | 121 +
{src/USER-MOLFILE => lib/molfile}/Makefile.lammps | 0
lib/molfile/README | 22 +
lib/quip/Makefile.lammps | 20 +
lib/quip/README | 88 +
lib/reax/Makefile.lammps.ifort | 5 +-
lib/voronoi/Makefile.lammps | 5 +
lib/voronoi/README | 56 +
lib/voronoi/install.py | 163 +
potentials/Ag_u3.eam | 2 +-
potentials/AlCu.adp | 2 +-
potentials/AlCu.eam.alloy | 2 +-
potentials/AlFe_mm.eam.fs | 4 +-
potentials/AlO.eam.alloy | 7007 +
potentials/AlO.streitz | 8 +
potentials/AlSiMgCuFe.meam | 1 +
potentials/Al_jnp.eam | 2 +-
potentials/Al_mm.eam.fs | 4 +-
potentials/Al_zhou.eam.alloy | 2 +-
potentials/Au_u3.eam | 2 +-
potentials/BNC.tersoff | 1 +
potentials/C.lcbop | 1 +
potentials/CH.airebo | 1 +
potentials/CdTe.bop | 2 +-
potentials/CdTe.bop.table | 3 +-
potentials/CdTe.sw | 2 +
potentials/CoAl.eam.alloy | 6 +-
potentials/Cu.meam | 1 +
potentials/CuNi.eam.alloy | 708 +
potentials/CuZr_mm.eam.fs | 4 +-
potentials/Cu_mishin1.eam.alloy | 2 +-
potentials/Cu_smf7.eam | 2 +-
potentials/Cu_u3.eam | 2 +-
potentials/Cu_u6.eam | 2 +-
potentials/Cu_zhou.eam.alloy | 2 +-
potentials/FeCr.cdeam | 2 +-
potentials/FeP_mm.eam.fs | 4 +-
potentials/Fe_mm.eam.fs | 4 +-
potentials/GaAs.bop | 3 +-
potentials/GaAs.bop.table | 3 +-
potentials/GaN.sw | 1 +
potentials/GaN.tersoff | 1 +
potentials/MOH.nb3b.harmonic | 1 +
potentials/Mg_mm.eam.fs | 4 +-
potentials/Ni.adp | 4 +-
potentials/Ni.meam | 1 +
potentials/NiAlH_jea.eam.alloy | 6 +-
potentials/NiAlH_jea.eam.fs | 6 +-
potentials/Ni_smf7.eam | 2 +-
potentials/Ni_u3.eam | 2 +-
potentials/Pd_u3.eam | 2 +-
potentials/Pt_u3.eam | 2 +-
potentials/README | 68 +-
potentials/Si.b.meam.sw.spline | 2 +-
potentials/Si.edip | 2 +
potentials/Si.sw | 1 +
potentials/Si.tersoff | 2 +
potentials/Si.tersoff.mod | 2 +
potentials/SiC.meam | 1 +
potentials/SiC.tersoff | 2 +
potentials/SiC.tersoff.zbl | 2 +
potentials/SiCGe.tersoff | 2 +
potentials/SiC_1989.tersoff | 2 +
potentials/SiC_1990.tersoff | 2 +
potentials/SiC_1994.tersoff | 4 +-
potentials/SiC_Erhart-Albe.tersoff | 1 +
potentials/SiO.tersoff | 2 +
potentials/Si_1.meam.spline | 2 +-
potentials/Si_2.meam.spline | 2 +-
potentials/Ta06A.snapcoeff | 37 +
potentials/Ta06A.snapparam | 14 +
potentials/Ta06A_pot.snap | 18 +
potentials/Ti.meam.spline | 2 +-
potentials/Ti.meam.sw.spline | 2 +-
potentials/VFe_mm.eam.fs | 4 +-
potentials/W_zhou.eam.alloy | 2 +-
potentials/Zr_mm.eam.fs | 4 +-
potentials/ffield.comb | 1 +
potentials/ffield.comb3 | 1 +
potentials/ffield.eim | 2 +-
potentials/ffield.reax.AB | 2 +-
potentials/ffield.reax.AuO | 2 +-
potentials/ffield.reax.FC | 2 +-
potentials/ffield.reax.Fe_O_C_H | 2 +-
potentials/ffield.reax.V_O_C_H | 2 +-
potentials/ffield.reax.ZnOH | 2 +-
potentials/ffield.reax.budzien | 2 +-
potentials/ffield.reax.cho | 2 +-
potentials/ffield.reax.lg | 2 +-
potentials/ffield.reax.mattsson | 2 +-
potentials/ffield.reax.rdx | 2 +-
potentials/lib.comb3 | 2 +-
potentials/library.meam | 1 +
python/README | 14 +-
python/examples/in.mc | 22 +
python/examples/mc.py | 108 +
python/lammps.py | 54 +-
src/ASPHERE/compute_erotate_asphere.h | 2 +-
src/ASPHERE/compute_temp_asphere.cpp | 10 +-
src/ASPHERE/compute_temp_asphere.h | 2 +-
src/ASPHERE/fix_nh_asphere.h | 2 +-
src/ASPHERE/fix_nph_asphere.h | 2 +-
src/ASPHERE/fix_npt_asphere.h | 2 +-
src/ASPHERE/fix_nve_asphere.h | 2 +-
src/ASPHERE/fix_nve_asphere_noforce.h | 2 +-
src/ASPHERE/fix_nve_line.h | 2 +-
src/ASPHERE/fix_nve_tri.h | 2 +-
src/ASPHERE/fix_nvt_asphere.h | 2 +-
src/ASPHERE/pair_gayberne.cpp | 2 +-
src/ASPHERE/pair_gayberne.h | 2 +-
src/ASPHERE/pair_line_lj.cpp | 2 +-
src/ASPHERE/pair_line_lj.h | 2 +-
src/ASPHERE/pair_resquared.cpp | 2 +-
src/ASPHERE/pair_resquared.h | 2 +-
src/ASPHERE/pair_tri_lj.cpp | 2 +-
src/ASPHERE/pair_tri_lj.h | 2 +-
src/BODY/body_nparticle.h | 2 +-
src/BODY/compute_body_local.h | 2 +-
src/BODY/fix_nve_body.h | 2 +-
src/BODY/pair_body.cpp | 2 +-
src/BODY/pair_body.h | 2 +-
src/CLASS2/angle_class2.h | 2 +-
src/CLASS2/bond_class2.h | 2 +-
src/CLASS2/pair_lj_class2_coul_cut.cpp | 2 +-
src/CLASS2/pair_lj_class2_coul_long.cpp | 2 +-
src/COLLOID/fix_wall_colloid.h | 2 +-
src/COLLOID/pair_colloid.h | 2 +-
src/COLLOID/pair_yukawa_colloid.cpp | 2 +-
src/COLLOID/pair_yukawa_colloid.h | 2 +-
src/CORESHELL/Install.sh | 32 +
src/CORESHELL/compute_temp_cs.cpp | 503 +
src/CORESHELL/compute_temp_cs.h | 120 +
src/CORESHELL/pair_born_coul_long_cs.cpp | 199 +
src/CORESHELL/pair_born_coul_long_cs.h | 67 +
src/CORESHELL/pair_buck_coul_long_cs.cpp | 197 +
src/CORESHELL/pair_buck_coul_long_cs.h | 67 +
src/DIPOLE/atom_vec_dipole.h | 2 +-
src/DIPOLE/pair_lj_cut_dipole_cut.cpp | 2 +-
src/DIPOLE/pair_lj_cut_dipole_cut.h | 2 +-
src/DIPOLE/pair_lj_cut_dipole_long.cpp | 2 +-
src/DIPOLE/pair_lj_cut_dipole_long.h | 2 +-
src/DIPOLE/pair_lj_long_dipole_long.cpp | 2 +-
src/Depend.sh | 4 +
src/FLD/pair_brownian.cpp | 2 +-
src/FLD/pair_brownian.h | 2 +-
src/FLD/pair_brownian_poly.cpp | 2 +-
src/FLD/pair_brownian_poly.h | 2 +-
src/FLD/pair_lubricate.cpp | 10 +-
src/FLD/pair_lubricate.h | 8 +-
src/FLD/pair_lubricateU.cpp | 10 +-
src/FLD/pair_lubricateU.h | 8 +-
src/FLD/pair_lubricateU_poly.cpp | 2 +-
src/FLD/pair_lubricateU_poly.h | 4 +-
src/FLD/pair_lubricate_poly.cpp | 2 +-
src/FLD/pair_lubricate_poly.h | 4 +-
src/GPU/Install.sh | 10 +-
src/GPU/README | 11 +
src/GPU/fix_gpu.cpp | 139 +-
src/GPU/fix_gpu.h | 2 +-
src/GPU/pair_beck_gpu.cpp | 4 +-
src/GPU/pair_beck_gpu.h | 2 +-
src/GPU/pair_born_coul_long_gpu.cpp | 4 +-
src/GPU/pair_born_coul_long_gpu.h | 2 +-
src/GPU/pair_born_coul_wolf_gpu.cpp | 4 +-
src/GPU/pair_born_coul_wolf_gpu.h | 2 +-
src/GPU/pair_born_gpu.cpp | 17 +-
src/GPU/pair_born_gpu.h | 3 +-
src/GPU/pair_buck_coul_cut_gpu.cpp | 3 +-
src/GPU/pair_buck_coul_cut_gpu.h | 2 +-
src/GPU/pair_buck_coul_long_gpu.cpp | 3 +-
src/GPU/pair_buck_coul_long_gpu.h | 2 +-
src/GPU/pair_buck_gpu.cpp | 15 +-
src/GPU/pair_buck_gpu.h | 3 +-
src/GPU/pair_colloid_gpu.cpp | 4 +-
src/GPU/pair_colloid_gpu.h | 2 +-
src/GPU/pair_coul_cut_gpu.cpp | 247 +
src/GPU/pair_coul_cut_gpu.h | 63 +
src/GPU/pair_coul_debye_gpu.cpp | 255 +
src/GPU/pair_coul_debye_gpu.h | 63 +
src/GPU/pair_coul_dsf_gpu.cpp | 3 +-
src/GPU/pair_coul_dsf_gpu.h | 2 +-
src/GPU/pair_coul_long_gpu.cpp | 20 +-
src/GPU/pair_coul_long_gpu.h | 3 +-
src/GPU/pair_dpd_gpu.cpp | 3 +-
src/GPU/pair_dpd_gpu.h | 2 +-
src/GPU/pair_dpd_tstat_gpu.cpp | 3 +-
src/GPU/pair_dpd_tstat_gpu.h | 2 +-
src/GPU/pair_eam_alloy_gpu.h | 2 +-
src/GPU/pair_eam_fs_gpu.h | 2 +-
src/GPU/pair_eam_gpu.cpp | 11 +-
src/GPU/pair_eam_gpu.h | 6 +-
src/GPU/pair_gauss_gpu.cpp | 14 +-
src/GPU/pair_gauss_gpu.h | 3 +-
src/GPU/pair_gayberne_gpu.cpp | 3 +-
src/GPU/pair_gayberne_gpu.h | 2 +-
src/GPU/pair_lj96_cut_gpu.cpp | 3 +-
src/GPU/pair_lj96_cut_gpu.h | 2 +-
src/GPU/pair_lj_charmm_coul_long_gpu.cpp | 3 +-
src/GPU/pair_lj_charmm_coul_long_gpu.h | 2 +-
src/GPU/pair_lj_class2_coul_long_gpu.cpp | 3 +-
src/GPU/pair_lj_class2_coul_long_gpu.h | 2 +-
src/GPU/pair_lj_class2_gpu.cpp | 3 +-
src/GPU/pair_lj_class2_gpu.h | 2 +-
src/GPU/pair_lj_cut_coul_cut_gpu.cpp | 3 +-
src/GPU/pair_lj_cut_coul_cut_gpu.h | 2 +-
src/GPU/pair_lj_cut_coul_debye_gpu.cpp | 4 +-
src/GPU/pair_lj_cut_coul_debye_gpu.h | 2 +-
src/GPU/pair_lj_cut_coul_dsf_gpu.cpp | 3 +-
src/GPU/pair_lj_cut_coul_dsf_gpu.h | 2 +-
src/GPU/pair_lj_cut_coul_long_gpu.cpp | 14 +-
src/GPU/pair_lj_cut_coul_long_gpu.h | 3 +-
src/GPU/pair_lj_cut_coul_msm_gpu.cpp | 4 +-
src/GPU/pair_lj_cut_coul_msm_gpu.h | 2 +-
src/GPU/pair_lj_cut_dipole_cut_gpu.cpp | 4 +-
src/GPU/pair_lj_cut_dipole_cut_gpu.h | 2 +-
src/GPU/pair_lj_cut_gpu.cpp | 18 +-
src/GPU/pair_lj_cut_gpu.h | 3 +-
src/GPU/pair_lj_expand_gpu.cpp | 14 +-
src/GPU/pair_lj_expand_gpu.h | 3 +-
src/GPU/pair_lj_gromacs_gpu.cpp | 4 +-
src/GPU/pair_lj_gromacs_gpu.h | 2 +-
src/GPU/pair_lj_sdk_coul_long_gpu.cpp | 3 +-
src/GPU/pair_lj_sdk_gpu.cpp | 3 +-
src/GPU/pair_lj_sf_dipole_sf_gpu.cpp | 4 +-
src/GPU/pair_lj_sf_dipole_sf_gpu.h | 2 +-
src/GPU/pair_mie_cut_gpu.cpp | 4 +-
src/GPU/pair_mie_cut_gpu.h | 2 +-
src/GPU/pair_morse_gpu.cpp | 3 +-
src/GPU/pair_morse_gpu.h | 2 +-
src/GPU/pair_resquared_gpu.cpp | 3 +-
src/GPU/pair_resquared_gpu.h | 2 +-
src/GPU/pair_soft_gpu.cpp | 14 +-
src/GPU/pair_soft_gpu.h | 3 +-
src/GPU/pair_sw_gpu.cpp | 3 +-
src/GPU/pair_sw_gpu.h | 2 +-
src/GPU/pair_table_gpu.cpp | 3 +-
src/GPU/pair_table_gpu.h | 2 +-
src/GPU/pair_yukawa_colloid_gpu.cpp | 4 +-
src/GPU/pair_yukawa_colloid_gpu.h | 2 +-
src/GPU/pair_yukawa_gpu.cpp | 3 +-
src/GPU/pair_yukawa_gpu.h | 2 +-
src/GPU/pppm_gpu.cpp | 39 +-
src/GPU/pppm_gpu.h | 2 +-
src/GRANULAR/fix_freeze.h | 2 +-
src/GRANULAR/fix_pour.cpp | 42 +-
src/GRANULAR/fix_pour.h | 2 +-
src/GRANULAR/fix_wall_gran.h | 2 +-
src/GRANULAR/pair_gran_hertz_history.cpp | 5 +-
src/GRANULAR/pair_gran_hertz_history.h | 2 +-
src/GRANULAR/pair_gran_hooke.h | 2 +-
src/GRANULAR/pair_gran_hooke_history.cpp | 31 +-
src/GRANULAR/pair_gran_hooke_history.h | 12 +-
src/KIM/Install.sh | 6 +-
src/KIM/Makefile.lammps | 25 -
src/KIM/README | 25 +
src/KIM/pair_kim.cpp | 187 +-
src/KIM/pair_kim.h | 29 +-
src/KOKKOS/Install.sh | 124 +
src/KOKKOS/README | 21 +
src/KOKKOS/atom_kokkos.cpp | 261 +
src/KOKKOS/atom_kokkos.h | 111 +
src/KOKKOS/atom_vec_angle_kokkos.cpp | 1880 +
src/KOKKOS/atom_vec_angle_kokkos.h | 153 +
src/KOKKOS/atom_vec_atomic_kokkos.cpp | 1392 +
src/KOKKOS/atom_vec_atomic_kokkos.h | 113 +
src/KOKKOS/atom_vec_bond_kokkos.cpp | 1711 +
src/KOKKOS/atom_vec_bond_kokkos.h | 141 +
src/KOKKOS/atom_vec_charge_kokkos.cpp | 1514 +
src/KOKKOS/atom_vec_charge_kokkos.h | 126 +
src/KOKKOS/atom_vec_full_kokkos.cpp | 2315 +
src/KOKKOS/atom_vec_full_kokkos.h | 183 +
src/KOKKOS/atom_vec_kokkos.cpp | 23 +
src/KOKKOS/atom_vec_kokkos.h | 76 +
src/KOKKOS/atom_vec_molecular_kokkos.cpp | 2230 +
src/KOKKOS/atom_vec_molecular_kokkos.h | 178 +
src/KOKKOS/comm_kokkos.cpp | 990 +
src/KOKKOS/comm_kokkos.h | 76 +
src/KOKKOS/domain_kokkos.cpp | 207 +
src/KOKKOS/domain_kokkos.h | 38 +
src/KOKKOS/fix_langevin_kokkos.cpp | 810 +
src/KOKKOS/fix_langevin_kokkos.h | 274 +
src/KOKKOS/fix_nve_kokkos.cpp | 177 +
src/KOKKOS/fix_nve_kokkos.h | 110 +
src/KOKKOS/kokkos.cpp | 258 +
src/KOKKOS/kokkos.h | 42 +
src/KOKKOS/kokkos_type.h | 668 +
src/KOKKOS/memory_kokkos.h | 266 +
src/KOKKOS/modify_kokkos.cpp | 585 +
src/KOKKOS/modify_kokkos.h | 73 +
src/KOKKOS/neigh_full_kokkos.h | 718 +
src/KOKKOS/neigh_list_kokkos.cpp | 118 +
src/KOKKOS/neigh_list_kokkos.h | 104 +
src/KOKKOS/neighbor_kokkos.cpp | 328 +
src/KOKKOS/neighbor_kokkos.h | 344 +
src/KOKKOS/pair_buck_kokkos.cpp | 286 +
src/KOKKOS/pair_buck_kokkos.h | 121 +
src/KOKKOS/pair_coul_cut_kokkos.cpp | 265 +
src/KOKKOS/pair_coul_cut_kokkos.h | 137 +
src/KOKKOS/pair_coul_dsf_kokkos.cpp | 435 +
src/KOKKOS/pair_coul_dsf_kokkos.h | 99 +
src/KOKKOS/pair_coul_wolf_kokkos.cpp | 437 +
src/KOKKOS/pair_coul_wolf_kokkos.h | 101 +
src/KOKKOS/pair_eam_kokkos.cpp | 880 +
src/KOKKOS/pair_eam_kokkos.h | 175 +
src/KOKKOS/pair_kokkos.h | 760 +
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.cpp | 345 +
src/KOKKOS/pair_lj_cut_coul_cut_kokkos.h | 131 +
src/KOKKOS/pair_lj_cut_coul_long_kokkos.cpp | 494 +
src/KOKKOS/pair_lj_cut_coul_long_kokkos.h | 147 +
src/KOKKOS/pair_lj_cut_kokkos.cpp | 272 +
src/KOKKOS/pair_lj_cut_kokkos.h | 119 +
src/KOKKOS/pair_table_kokkos.cpp | 1382 +
src/KOKKOS/pair_table_kokkos.h | 296 +
src/KOKKOS/verlet_kokkos.cpp | 488 +
src/KOKKOS/verlet_kokkos.h | 48 +
src/KSPACE/ewald.cpp | 19 +-
src/KSPACE/ewald.h | 2 +-
src/KSPACE/ewald_disp.cpp | 73 +-
src/KSPACE/ewald_disp.h | 2 +-
src/KSPACE/fix_tune_kspace.cpp | 14 +-
src/KSPACE/fix_tune_kspace.h | 2 +-
src/KSPACE/gridcomm.cpp | 28 +-
src/KSPACE/gridcomm.h | 3 +-
src/KSPACE/msm.cpp | 28 +-
src/KSPACE/msm_cg.cpp | 16 +-
src/KSPACE/pair_born_coul_long.cpp | 2 +-
src/KSPACE/pair_born_coul_long.h | 2 +-
src/KSPACE/pair_born_coul_msm.h | 2 +-
src/KSPACE/pair_buck_coul_long.cpp | 2 +-
src/KSPACE/pair_buck_coul_long.h | 2 +-
src/KSPACE/pair_buck_coul_msm.h | 2 +-
src/KSPACE/pair_buck_long_coul_long.cpp | 14 +-
src/KSPACE/pair_coul_long.cpp | 2 +-
src/KSPACE/pair_coul_msm.h | 2 +-
src/KSPACE/pair_lj_charmm_coul_long.cpp | 14 +-
src/KSPACE/pair_lj_charmm_coul_msm.h | 2 +-
src/KSPACE/pair_lj_cut_coul_long.cpp | 14 +-
src/KSPACE/pair_lj_cut_coul_long.h | 2 +-
src/KSPACE/pair_lj_cut_coul_msm.h | 2 +-
src/KSPACE/pair_lj_cut_tip4p_long.cpp | 2 +
src/KSPACE/pair_lj_cut_tip4p_long.h | 2 +-
src/KSPACE/pair_lj_long_coul_long.cpp | 14 +-
src/KSPACE/pair_lj_long_tip4p_long.cpp | 14 +-
src/KSPACE/pair_lj_long_tip4p_long.h | 2 +-
src/KSPACE/pair_tip4p_long.h | 2 +-
src/KSPACE/pppm.cpp | 34 +-
src/KSPACE/pppm_cg.cpp | 17 +-
src/KSPACE/pppm_disp.cpp | 37 +-
src/KSPACE/pppm_disp.h | 6 +-
src/KSPACE/pppm_disp_tip4p.cpp | 3 +
src/KSPACE/pppm_disp_tip4p.h | 2 +-
src/KSPACE/pppm_stagger.cpp | 17 +-
src/KSPACE/pppm_tip4p.cpp | 3 +
src/KSPACE/pppm_tip4p.h | 2 +-
src/KSPACE/remap.cpp | 3 +-
src/MAKE/MACHINES/Makefile.beacon | 114 +
src/MAKE/MACHINES/Makefile.bgl | 119 +
src/MAKE/MACHINES/Makefile.bgq | 55 +
src/MAKE/MACHINES/Makefile.bgq.details | 118 +
src/MAKE/MACHINES/Makefile.chama | 109 +
src/MAKE/MACHINES/Makefile.cygwin | 113 +
src/MAKE/MACHINES/Makefile.glory | 130 +
src/MAKE/MACHINES/Makefile.jaguar | 113 +
src/MAKE/MACHINES/Makefile.mac | 113 +
src/MAKE/MACHINES/Makefile.mac_mpi | 116 +
src/MAKE/MACHINES/Makefile.mingw32-cross | 122 +
src/MAKE/MACHINES/Makefile.mingw32-cross-mpi | 122 +
src/MAKE/MACHINES/Makefile.mingw64-cross | 122 +
src/MAKE/MACHINES/Makefile.mingw64-cross-mpi | 122 +
src/MAKE/MACHINES/Makefile.myrinet | 113 +
src/MAKE/MACHINES/Makefile.power | 114 +
src/MAKE/MACHINES/Makefile.redsky | 133 +
src/MAKE/MACHINES/Makefile.serial | 113 +
src/MAKE/MACHINES/Makefile.stampede | 114 +
src/MAKE/MACHINES/Makefile.storm | 107 +
src/MAKE/MACHINES/Makefile.tacc | 116 +
src/MAKE/MACHINES/Makefile.ubuntu | 117 +
src/MAKE/MACHINES/Makefile.ubuntu_simple | 116 +
src/MAKE/MACHINES/Makefile.xe6 | 114 +
src/MAKE/MACHINES/Makefile.xt3 | 115 +
src/MAKE/MACHINES/Makefile.xt5 | 114 +
src/MAKE/Makefile.altix | 108 -
src/MAKE/Makefile.bgl | 114 -
src/MAKE/Makefile.bgq | 55 -
src/MAKE/Makefile.bgq.details | 104 -
src/MAKE/Makefile.chama | 104 -
src/MAKE/Makefile.cygwin | 108 -
src/MAKE/Makefile.encanto | 108 -
src/MAKE/Makefile.fink | 108 -
src/MAKE/Makefile.g++ | 108 -
src/MAKE/Makefile.g++3 | 108 -
src/MAKE/Makefile.glory | 125 -
src/MAKE/Makefile.jaguar | 108 -
src/MAKE/Makefile.lam | 108 -
src/MAKE/Makefile.linux | 108 -
src/MAKE/Makefile.mac | 108 -
src/MAKE/Makefile.mac_mpi | 111 -
src/MAKE/Makefile.mingw32-cross | 117 -
src/MAKE/Makefile.mingw32-cross-mpi | 117 -
src/MAKE/Makefile.mingw64-cross | 117 -
src/MAKE/Makefile.mingw64-cross-mpi | 117 -
src/MAKE/Makefile.mkl | 114 -
src/MAKE/Makefile.mpi | 113 +
src/MAKE/Makefile.odin | 108 -
src/MAKE/Makefile.openmpi | 109 -
src/MAKE/Makefile.pgi | 109 -
src/MAKE/Makefile.power5 | 109 -
src/MAKE/Makefile.qed | 108 -
src/MAKE/Makefile.redsky | 128 -
src/MAKE/Makefile.sdsc | 113 -
src/MAKE/Makefile.seaborg | 109 -
src/MAKE/Makefile.serial | 39 +-
src/MAKE/Makefile.serial_debug | 108 -
src/MAKE/Makefile.sgi | 108 -
src/MAKE/Makefile.solaris | 108 -
src/MAKE/Makefile.spirit | 116 -
src/MAKE/Makefile.storm | 105 -
src/MAKE/Makefile.tacc | 111 -
src/MAKE/Makefile.tbird | 127 -
src/MAKE/Makefile.tesla | 108 -
src/MAKE/Makefile.tunnison | 118 -
src/MAKE/Makefile.ubuntu | 112 -
src/MAKE/Makefile.ubuntu_simple | 111 -
src/MAKE/Makefile.xe6 | 109 -
src/MAKE/Makefile.xt3 | 110 -
src/MAKE/Makefile.xt5 | 109 -
src/MAKE/OPTIONS/Makefile.fftw | 113 +
src/MAKE/OPTIONS/Makefile.intel_cpu | 115 +
src/MAKE/OPTIONS/Makefile.intel_phi | 116 +
src/MAKE/OPTIONS/Makefile.jpeg | 113 +
src/MAKE/OPTIONS/Makefile.kokkos_cuda | 115 +
src/MAKE/OPTIONS/Makefile.kokkos_omp | 114 +
src/MAKE/OPTIONS/Makefile.kokkos_phi | 115 +
src/MAKE/OPTIONS/Makefile.mpich_g++ | 113 +
src/MAKE/OPTIONS/Makefile.mpich_icc | 113 +
src/MAKE/OPTIONS/Makefile.mpich_native_g++ | 113 +
src/MAKE/OPTIONS/Makefile.mpich_native_icc | 113 +
src/MAKE/OPTIONS/Makefile.omp | 113 +
src/MAKE/OPTIONS/Makefile.ompi_g++ | 114 +
src/MAKE/OPTIONS/Makefile.ompi_icc | 114 +
src/MAKE/OPTIONS/Makefile.ompi_native_g++ | 113 +
src/MAKE/OPTIONS/Makefile.ompi_native_icc | 113 +
src/MAKE/OPTIONS/Makefile.opt | 113 +
src/MAKE/OPTIONS/Makefile.pgi | 114 +
src/MAKE/OPTIONS/Makefile.png | 113 +
src/MAKE/OPTIONS/Makefile.serial_icc | 113 +
src/MAKE/README | 106 +
src/MANYBODY/fix_qeq_comb.cpp | 9 +-
src/MANYBODY/fix_qeq_comb.h | 6 +-
src/MANYBODY/pair_adp.cpp | 11 +-
src/MANYBODY/pair_adp.h | 6 +-
src/MANYBODY/pair_airebo.cpp | 2 +-
src/MANYBODY/pair_airebo.h | 2 +-
src/MANYBODY/pair_bop.cpp | 8 +-
src/MANYBODY/pair_bop.h | 2 +-
src/MANYBODY/pair_comb.cpp | 25 +-
src/MANYBODY/pair_comb.h | 6 +-
src/MANYBODY/pair_comb3.cpp | 23 +-
src/MANYBODY/pair_comb3.h | 6 +-
src/MANYBODY/pair_eam.cpp | 99 +-
src/MANYBODY/pair_eam.h | 12 +-
src/MANYBODY/pair_eam_alloy.h | 2 +-
src/MANYBODY/pair_eam_fs.h | 2 +-
src/MANYBODY/pair_eim.cpp | 11 +-
src/MANYBODY/pair_eim.h | 6 +-
src/MANYBODY/pair_lcbop.cpp | 2 +-
src/MANYBODY/pair_lcbop.h | 2 +-
src/MANYBODY/pair_nb3b_harmonic.cpp | 2 +-
src/MANYBODY/pair_rebo.h | 2 +-
src/MANYBODY/pair_sw.cpp | 2 +-
src/MANYBODY/pair_sw.h | 2 +-
src/MANYBODY/pair_tersoff.cpp | 2 +-
src/MANYBODY/pair_tersoff.h | 2 +-
src/MANYBODY/pair_tersoff_mod.h | 2 +-
src/MANYBODY/pair_tersoff_zbl.h | 2 +-
src/MC/fix_atom_swap.cpp | 768 +
src/MC/fix_atom_swap.h | 123 +
src/MC/fix_bond_break.cpp | 30 +-
src/MC/fix_bond_break.h | 6 +-
src/MC/fix_bond_create.cpp | 64 +-
src/MC/fix_bond_create.h | 6 +-
src/MC/fix_bond_swap.cpp | 4 +-
src/MC/fix_bond_swap.h | 2 +-
src/MC/fix_gcmc.cpp | 1490 +-
src/MC/fix_gcmc.h | 46 +-
src/MC/fix_tfmc.cpp | 294 +
src/MC/fix_tfmc.h | 72 +
src/MC/pair_dsmc.h | 2 +-
src/MEAM/README | 11 +
src/MEAM/pair_meam.cpp | 14 +-
src/MEAM/pair_meam.h | 6 +-
src/MISC/compute_msd_nongauss.h | 2 +-
src/MISC/compute_ti.h | 2 +-
src/MISC/fix_deposit.cpp | 34 +-
src/MISC/fix_efield.h | 2 +-
src/MISC/fix_evaporate.h | 2 +-
src/MISC/fix_gld.cpp | 12 +-
src/MISC/fix_gld.h | 2 +-
src/MISC/fix_orient_fcc.cpp | 17 +-
src/MISC/fix_orient_fcc.h | 6 +-
src/MISC/fix_thermal_conductivity.cpp | 5 +-
src/MISC/fix_thermal_conductivity.h | 2 +-
src/MISC/fix_ttm.cpp | 1 -
src/MISC/fix_ttm.h | 2 +-
src/MISC/fix_viscosity.cpp | 5 +-
src/MISC/fix_viscosity.h | 2 +-
src/MISC/pair_nm_cut.h | 2 +-
src/MISC/pair_nm_cut_coul_cut.cpp | 2 +-
src/MISC/pair_nm_cut_coul_cut.h | 2 +-
src/MISC/pair_nm_cut_coul_long.cpp | 2 +-
src/MISC/pair_nm_cut_coul_long.h | 2 +-
src/MOLECULE/angle_charmm.h | 2 +-
src/MOLECULE/angle_cosine.h | 2 +-
src/MOLECULE/angle_cosine_delta.h | 2 +-
src/MOLECULE/angle_cosine_periodic.h | 2 +-
src/MOLECULE/angle_cosine_squared.h | 2 +-
src/MOLECULE/angle_harmonic.h | 2 +-
src/MOLECULE/angle_table.h | 2 +-
src/MOLECULE/atom_vec_angle.h | 2 +-
src/MOLECULE/atom_vec_bond.h | 2 +-
src/MOLECULE/atom_vec_full.h | 2 +-
src/MOLECULE/atom_vec_molecular.h | 2 +-
src/MOLECULE/atom_vec_template.h | 2 +-
src/MOLECULE/bond_fene.h | 2 +-
src/MOLECULE/bond_fene_expand.h | 2 +-
src/MOLECULE/bond_harmonic.h | 2 +-
src/MOLECULE/bond_morse.h | 2 +-
src/MOLECULE/bond_nonlinear.h | 2 +-
src/MOLECULE/bond_quartic.h | 2 +-
src/MOLECULE/bond_table.h | 2 +-
src/MOLECULE/dihedral_charmm.cpp | 1 -
src/MOLECULE/dihedral_harmonic.cpp | 1 -
src/MOLECULE/dihedral_harmonic.h | 2 +-
src/MOLECULE/dihedral_helix.cpp | 1 -
src/MOLECULE/dihedral_helix.h | 2 +-
src/MOLECULE/dihedral_multi_harmonic.h | 2 +-
src/MOLECULE/improper_cvff.cpp | 1 -
src/MOLECULE/improper_harmonic.cpp | 1 -
src/MOLECULE/improper_harmonic.h | 2 +-
src/MOLECULE/improper_umbrella.cpp | 10 +
src/MOLECULE/improper_umbrella.h | 3 +-
src/MOLECULE/pair_hbond_dreiding_lj.cpp | 2 +-
src/MOLECULE/pair_hbond_dreiding_lj.h | 2 +-
src/MOLECULE/pair_hbond_dreiding_morse.cpp | 2 +-
src/MOLECULE/pair_hbond_dreiding_morse.h | 2 +-
src/MOLECULE/pair_lj_charmm_coul_charmm.cpp | 2 +-
src/MOLECULE/pair_lj_charmm_coul_charmm_implicit.h | 2 +-
src/MOLECULE/pair_lj_cut_tip4p_cut.cpp | 2 +-
src/MOLECULE/pair_lj_cut_tip4p_cut.h | 2 +-
src/MOLECULE/pair_tip4p_cut.cpp | 2 +-
src/MOLECULE/pair_tip4p_cut.h | 2 +-
src/MPIIO/Install.sh | 3 +
src/MPIIO/dump_atom_mpiio.cpp | 27 +-
src/MPIIO/dump_cfg_mpiio.cpp | 507 +
src/MPIIO/dump_cfg_mpiio.h | 80 +
src/MPIIO/dump_custom_mpiio.cpp | 25 +-
src/MPIIO/dump_xyz_mpiio.cpp | 10 +-
src/MPIIO/dump_xyz_mpiio.h | 2 +-
src/MPIIO/restart_mpiio.cpp | 11 +-
src/MPIIO/restart_mpiio.h | 2 +-
src/Make.py | 2831 +-
src/Makefile | 233 +-
src/Makefile.lib | 37 -
src/Makefile.shlib | 43 -
src/OPT/pair_eam_alloy_opt.h | 2 +-
src/OPT/pair_eam_fs_opt.h | 2 +-
src/OPT/pair_eam_opt.cpp | 38 +-
src/OPT/pair_eam_opt.h | 2 +-
src/OPT/pair_lj_charmm_coul_long_opt.cpp | 30 +-
src/OPT/pair_lj_charmm_coul_long_opt.h | 2 +-
src/OPT/pair_lj_cut_coul_long_opt.h | 2 +-
src/OPT/pair_lj_cut_opt.cpp | 26 +-
src/OPT/pair_lj_cut_opt.h | 2 +-
src/OPT/pair_lj_long_coul_long_opt.h | 2 +-
src/OPT/pair_morse_opt.cpp | 26 +-
src/OPT/pair_morse_opt.h | 2 +-
src/PERI/atom_vec_peri.cpp | 40 +
src/PERI/atom_vec_peri.h | 4 +-
src/PERI/compute_damage_atom.h | 2 +-
src/PERI/compute_dilatation_atom.h | 2 +-
src/PERI/compute_plasticity_atom.h | 2 +-
src/PERI/fix_peri_neigh.cpp | 13 +-
src/PERI/fix_peri_neigh.h | 6 +-
src/PERI/pair_peri_eps.cpp | 33 +-
src/PERI/pair_peri_eps.h | 6 +-
src/PERI/pair_peri_lps.cpp | 10 +-
src/PERI/pair_peri_lps.h | 6 +-
src/PERI/pair_peri_pmb.cpp | 2 +-
src/PERI/pair_peri_pmb.h | 2 +-
src/PERI/pair_peri_ves.cpp | 10 +-
src/PERI/pair_peri_ves.h | 6 +-
src/POEMS/README | 12 +
src/POEMS/fix_poems.h | 2 +-
src/QEQ/fix_qeq.cpp | 758 +
src/QEQ/fix_qeq.h | 129 +
src/QEQ/fix_qeq_dynamic.cpp | 292 +
src/QEQ/fix_qeq_dynamic.h | 46 +
src/QEQ/fix_qeq_point.cpp | 173 +
src/QEQ/fix_qeq_point.h | 41 +
src/QEQ/fix_qeq_shielded.cpp | 238 +
src/QEQ/fix_qeq_shielded.h | 43 +
src/QEQ/fix_qeq_slater.cpp | 387 +
src/QEQ/fix_qeq_slater.h | 46 +
src/REAX/fix_reax_bonds.cpp | 5 +-
src/REAX/fix_reax_bonds.h | 2 +-
src/REAX/pair_reax.cpp | 13 +-
src/REAX/pair_reax.h | 6 +-
src/REAX/pair_reax_fortran.h | 2 +-
src/REPLICA/compute_event_displace.h | 2 +-
src/REPLICA/fix_event.h | 2 +-
src/REPLICA/fix_event_prd.h | 2 +-
src/REPLICA/fix_event_tad.h | 2 +-
src/REPLICA/fix_neb.cpp | 9 +-
src/REPLICA/fix_neb.h | 2 +-
src/REPLICA/neb.cpp | 6 +-
src/REPLICA/neb.h | 2 +-
src/REPLICA/prd.cpp | 6 +-
src/REPLICA/prd.h | 2 +-
src/REPLICA/tad.cpp | 6 +-
src/REPLICA/tad.h | 2 +-
src/REPLICA/temper.cpp | 5 +-
src/REPLICA/temper.h | 2 +-
src/REPLICA/verlet_split.cpp | 14 +-
src/REPLICA/verlet_split.h | 2 +-
src/RIGID/compute_erotate_rigid.h | 2 +-
src/RIGID/compute_ke_rigid.h | 2 +-
src/RIGID/fix_rattle.cpp | 879 +
src/RIGID/fix_rattle.h | 74 +
src/RIGID/fix_rigid.cpp | 353 +-
src/RIGID/fix_rigid.h | 9 +-
src/RIGID/fix_rigid_nh.cpp | 290 +-
src/RIGID/fix_rigid_nh.h | 2 +-
src/RIGID/fix_rigid_nh_small.cpp | 310 +-
src/RIGID/fix_rigid_nh_small.h | 3 +-
src/RIGID/fix_rigid_nph.h | 2 +-
src/RIGID/fix_rigid_nph_small.h | 2 +-
src/RIGID/fix_rigid_npt.h | 2 +-
src/RIGID/fix_rigid_npt_small.h | 2 +-
src/RIGID/fix_rigid_nve.h | 2 +-
src/RIGID/fix_rigid_nve_small.h | 2 +-
src/RIGID/fix_rigid_nvt.h | 2 +-
src/RIGID/fix_rigid_nvt_small.h | 2 +-
src/RIGID/fix_rigid_small.cpp | 273 +-
src/RIGID/fix_rigid_small.h | 24 +-
src/RIGID/fix_shake.cpp | 81 +-
src/RIGID/fix_shake.h | 38 +-
src/SHOCK/fix_append_atoms.cpp | 12 +-
src/SHOCK/fix_append_atoms.h | 2 +-
src/SHOCK/fix_msst.h | 2 +-
src/SHOCK/fix_nphug.h | 2 +-
src/SHOCK/fix_wall_piston.cpp | 31 +-
src/SHOCK/fix_wall_piston.h | 2 +-
src/SNAP/compute_sna_atom.cpp | 279 +
src/SNAP/compute_sna_atom.h | 53 +
src/SNAP/compute_snad_atom.cpp | 335 +
src/SNAP/compute_snad_atom.h | 54 +
src/SNAP/compute_snav_atom.cpp | 345 +
src/SNAP/compute_snav_atom.h | 55 +
src/SNAP/openmp_snap.h | 16 +
src/SNAP/pair_snap.cpp | 1741 +
src/SNAP/pair_snap.h | 110 +
src/SNAP/sna.cpp | 1952 +
src/SNAP/sna.h | 143 +
src/SRD/fix_srd.cpp | 17 +-
src/SRD/fix_srd.h | 4 +-
src/SRD/fix_wall_srd.h | 2 +-
src/STUBS/mpi.c | 119 +-
src/STUBS/mpi.h | 11 +
src/USER-ATC/Install.sh | 2 +-
src/USER-ATC/README | 4 +-
src/USER-ATC/fix_atc.cpp | 20 +-
src/USER-ATC/fix_atc.h | 4 +-
src/USER-AWPMD/README | 4 +-
src/USER-AWPMD/atom_vec_wavepacket.cpp | 63 +-
src/USER-AWPMD/atom_vec_wavepacket.h | 5 +-
src/USER-AWPMD/fix_nve_awpmd.h | 2 +-
src/USER-AWPMD/pair_awpmd_cut.cpp | 4 +-
src/USER-AWPMD/pair_awpmd_cut.h | 2 +-
src/USER-CG-CMM/pair_lj_sdk_coul_long.cpp | 2 +-
src/USER-COLVARS/README | 50 +-
src/USER-COLVARS/colvarproxy_lammps.cpp | 113 +-
src/USER-COLVARS/colvarproxy_lammps.h | 69 +-
src/USER-COLVARS/fix_colvars.cpp | 23 +-
src/USER-COLVARS/fix_colvars.h | 1 +
src/USER-COLVARS/group_ndx.cpp | 7 +-
src/USER-CUDA/Install.sh | 16 +-
src/USER-CUDA/README | 4 +-
src/USER-CUDA/atom_vec_angle_cuda.cpp | 20 +-
src/USER-CUDA/atom_vec_angle_cuda.h | 2 +-
src/USER-CUDA/atom_vec_atomic_cuda.cpp | 21 +-
src/USER-CUDA/atom_vec_atomic_cuda.h | 2 +-
src/USER-CUDA/atom_vec_charge_cuda.cpp | 20 +-
src/USER-CUDA/atom_vec_charge_cuda.h | 2 +-
src/USER-CUDA/atom_vec_full_cuda.cpp | 20 +-
src/USER-CUDA/atom_vec_full_cuda.h | 2 +-
src/USER-CUDA/comm_cuda.cpp | 242 +-
src/USER-CUDA/comm_cuda.h | 12 +-
src/USER-CUDA/compute_pe_cuda.h | 2 +-
src/USER-CUDA/compute_pressure_cuda.cpp | 2 +-
src/USER-CUDA/compute_pressure_cuda.h | 2 +-
src/USER-CUDA/compute_temp_cuda.cpp | 17 +-
src/USER-CUDA/compute_temp_cuda.h | 6 +-
src/USER-CUDA/compute_temp_partial_cuda.cpp | 19 +-
src/USER-CUDA/compute_temp_partial_cuda.h | 8 +-
src/USER-CUDA/cuda.cpp | 253 +-
src/USER-CUDA/cuda.h | 155 -
src/USER-CUDA/cuda_data.h | 2 +-
src/USER-CUDA/cuda_neigh_list.cpp | 2 +-
src/USER-CUDA/cuda_neigh_list.h | 2 +-
src/USER-CUDA/domain_cuda.cpp | 9 +-
src/USER-CUDA/domain_cuda.h | 6 +-
src/USER-CUDA/fft3d_cuda.cpp | 6 +-
src/USER-CUDA/fft3d_cuda.h | 2 +-
src/USER-CUDA/fft3d_wrap_cuda.cpp | 2 +-
src/USER-CUDA/fft3d_wrap_cuda.h | 2 +-
src/USER-CUDA/fix_addforce_cuda.cpp | 6 +-
src/USER-CUDA/fix_addforce_cuda.h | 4 +-
src/USER-CUDA/fix_aveforce_cuda.cpp | 10 +-
src/USER-CUDA/fix_aveforce_cuda.h | 5 +-
src/USER-CUDA/fix_enforce2d_cuda.cpp | 2 +-
src/USER-CUDA/fix_enforce2d_cuda.h | 2 +-
src/USER-CUDA/fix_freeze_cuda.cpp | 6 +-
src/USER-CUDA/fix_freeze_cuda.h | 4 +-
src/USER-CUDA/fix_gravity_cuda.cpp | 2 +-
src/USER-CUDA/fix_gravity_cuda.h | 2 +-
src/USER-CUDA/fix_nh_cuda.cpp | 7 +-
src/USER-CUDA/fix_nh_cuda.h | 4 +-
src/USER-CUDA/fix_npt_cuda.h | 2 +-
src/USER-CUDA/fix_nve_cuda.cpp | 2 +-
src/USER-CUDA/fix_nve_cuda.h | 4 +-
src/USER-CUDA/fix_nvt_cuda.h | 2 +-
src/USER-CUDA/fix_set_force_cuda.cpp | 6 +-
src/USER-CUDA/fix_set_force_cuda.h | 4 +-
src/USER-CUDA/fix_shake_cuda.cpp | 20 +-
src/USER-CUDA/fix_shake_cuda.h | 16 +-
src/USER-CUDA/fix_temp_berendsen_cuda.cpp | 2 +-
src/USER-CUDA/fix_temp_berendsen_cuda.h | 2 +-
src/USER-CUDA/fix_temp_rescale_cuda.cpp | 2 +-
src/USER-CUDA/fix_temp_rescale_cuda.h | 2 +-
src/USER-CUDA/fix_temp_rescale_limit_cuda.cpp | 2 +-
src/USER-CUDA/fix_temp_rescale_limit_cuda.h | 2 +-
src/USER-CUDA/fix_viscous_cuda.cpp | 4 +-
src/USER-CUDA/fix_viscous_cuda.h | 4 +-
src/USER-CUDA/modify_cuda.cpp | 2 +-
src/USER-CUDA/neigh_full_cuda.cpp | 10 +-
src/USER-CUDA/neighbor_cuda.cpp | 2 +-
src/USER-CUDA/neighbor_cuda.h | 2 +-
src/USER-CUDA/pair_born_coul_long_cuda.cpp | 10 +-
src/USER-CUDA/pair_born_coul_long_cuda.h | 2 +-
src/USER-CUDA/pair_buck_coul_cut_cuda.cpp | 12 +-
src/USER-CUDA/pair_buck_coul_cut_cuda.h | 2 +-
src/USER-CUDA/pair_buck_coul_long_cuda.cpp | 10 +-
src/USER-CUDA/pair_buck_coul_long_cuda.h | 2 +-
src/USER-CUDA/pair_buck_cuda.cpp | 10 +-
src/USER-CUDA/pair_buck_cuda.h | 2 +-
src/USER-CUDA/pair_eam_alloy_cuda.cpp | 4 +-
src/USER-CUDA/pair_eam_alloy_cuda.h | 2 +-
src/USER-CUDA/pair_eam_cuda.cpp | 33 +-
src/USER-CUDA/pair_eam_cuda.h | 17 +-
src/USER-CUDA/pair_eam_fs_cuda.cpp | 4 +-
src/USER-CUDA/pair_eam_fs_cuda.h | 2 +-
src/USER-CUDA/pair_gran_hooke_cuda.cpp | 52 +-
src/USER-CUDA/pair_gran_hooke_cuda.h | 2 +-
src/USER-CUDA/pair_lj96_cut_cuda.cpp | 10 +-
src/USER-CUDA/pair_lj96_cut_cuda.h | 2 +-
src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.cpp | 23 +-
src/USER-CUDA/pair_lj_charmm_coul_charmm_cuda.h | 10 +-
.../pair_lj_charmm_coul_charmm_implicit_cuda.cpp | 23 +-
.../pair_lj_charmm_coul_charmm_implicit_cuda.h | 10 +-
src/USER-CUDA/pair_lj_charmm_coul_long_cuda.cpp | 23 +-
src/USER-CUDA/pair_lj_charmm_coul_long_cuda.h | 10 +-
src/USER-CUDA/pair_lj_class2_coul_cut_cuda.cpp | 12 +-
src/USER-CUDA/pair_lj_class2_coul_cut_cuda.h | 2 +-
src/USER-CUDA/pair_lj_class2_coul_long_cuda.cpp | 10 +-
src/USER-CUDA/pair_lj_class2_coul_long_cuda.h | 2 +-
src/USER-CUDA/pair_lj_class2_cuda.cpp | 10 +-
src/USER-CUDA/pair_lj_class2_cuda.h | 2 +-
src/USER-CUDA/pair_lj_cut_coul_cut_cuda.cpp | 12 +-
src/USER-CUDA/pair_lj_cut_coul_cut_cuda.h | 2 +-
src/USER-CUDA/pair_lj_cut_coul_debye_cuda.cpp | 14 +-
src/USER-CUDA/pair_lj_cut_coul_debye_cuda.h | 2 +-
src/USER-CUDA/pair_lj_cut_coul_long_cuda.cpp | 22 +-
src/USER-CUDA/pair_lj_cut_coul_long_cuda.h | 2 +-
src/USER-CUDA/pair_lj_cut_cuda.cpp | 10 +-
src/USER-CUDA/pair_lj_cut_cuda.h | 2 +-
src/USER-CUDA/pair_lj_cut_experimental_cuda.cpp | 10 +-
src/USER-CUDA/pair_lj_cut_experimental_cuda.h | 2 +-
src/USER-CUDA/pair_lj_expand_cuda.cpp | 10 +-
src/USER-CUDA/pair_lj_expand_cuda.h | 2 +-
.../pair_lj_gromacs_coul_gromacs_cuda.cpp | 33 +-
src/USER-CUDA/pair_lj_gromacs_coul_gromacs_cuda.h | 20 +-
src/USER-CUDA/pair_lj_gromacs_cuda.cpp | 31 +-
src/USER-CUDA/pair_lj_gromacs_cuda.h | 20 +-
src/USER-CUDA/pair_lj_sdk_coul_long_cuda.cpp | 12 +-
src/USER-CUDA/pair_lj_sdk_coul_long_cuda.h | 2 +-
src/USER-CUDA/pair_lj_sdk_cuda.cpp | 20 +-
src/USER-CUDA/pair_lj_sdk_cuda.h | 12 +-
src/USER-CUDA/pair_lj_smooth_cuda.cpp | 31 +-
src/USER-CUDA/pair_lj_smooth_cuda.h | 20 +-
src/USER-CUDA/pair_morse_cuda.cpp | 10 +-
src/USER-CUDA/pair_morse_cuda.h | 2 +-
src/USER-CUDA/pair_sw_cuda.cpp | 8 +-
src/USER-CUDA/pair_sw_cuda.h | 2 +-
src/USER-CUDA/pair_tersoff_cuda.cpp | 8 +-
src/USER-CUDA/pair_tersoff_cuda.h | 2 +-
src/USER-CUDA/pair_tersoff_zbl_cuda.cpp | 6 +-
src/USER-CUDA/pair_tersoff_zbl_cuda.h | 2 +-
src/USER-CUDA/pppm_cuda.cpp | 108 +-
src/USER-CUDA/pppm_cuda.h | 56 +-
src/USER-CUDA/pppm_old.cpp | 81 +-
src/USER-CUDA/pppm_old.h | 4 +-
src/USER-CUDA/user_cuda.h | 159 +
src/USER-CUDA/verlet_cuda.cpp | 35 +-
src/USER-CUDA/verlet_cuda.h | 4 +-
src/USER-EFF/atom_vec_electron.cpp | 62 +
src/USER-EFF/atom_vec_electron.h | 5 +-
src/USER-EFF/compute_ke_atom_eff.cpp | 3 +-
src/USER-EFF/compute_ke_atom_eff.h | 2 +-
src/USER-EFF/compute_ke_eff.cpp | 3 +-
src/USER-EFF/compute_ke_eff.h | 2 +-
src/USER-EFF/compute_temp_deform_eff.cpp | 28 +-
src/USER-EFF/compute_temp_deform_eff.h | 3 +-
src/USER-EFF/compute_temp_eff.cpp | 9 +-
src/USER-EFF/compute_temp_eff.h | 2 +-
src/USER-EFF/compute_temp_region_eff.cpp | 10 +-
src/USER-EFF/compute_temp_region_eff.h | 2 +-
src/USER-EFF/fix_langevin_eff.cpp | 18 +-
src/USER-EFF/fix_langevin_eff.h | 2 +-
src/USER-EFF/fix_nh_eff.cpp | 7 +-
src/USER-EFF/fix_nh_eff.h | 2 +-
src/USER-EFF/fix_nph_eff.h | 2 +-
src/USER-EFF/fix_npt_eff.h | 2 +-
src/USER-EFF/fix_nve_eff.cpp | 5 +-
src/USER-EFF/fix_nve_eff.h | 2 +-
src/USER-EFF/fix_nvt_eff.h | 2 +-
src/USER-EFF/fix_nvt_sllod_eff.cpp | 3 +-
src/USER-EFF/fix_nvt_sllod_eff.h | 2 +-
src/USER-EFF/fix_temp_rescale_eff.h | 2 +-
src/USER-EFF/pair_eff_cut.cpp | 2 +-
src/USER-EFF/pair_eff_cut.h | 2 +-
src/USER-FEP/compute_fep.cpp | 248 +-
src/USER-FEP/compute_fep.h | 6 +-
src/USER-FEP/fix_adapt_fep.cpp | 232 +-
src/USER-FEP/fix_adapt_fep.h | 9 +-
src/USER-FEP/pair_coul_cut_soft.cpp | 2 +-
src/USER-FEP/pair_coul_cut_soft.h | 2 +-
src/USER-FEP/pair_coul_long_soft.cpp | 2 +-
src/USER-FEP/pair_lj_charmm_coul_long_soft.cpp | 14 +-
src/USER-FEP/pair_lj_cut_coul_cut_soft.cpp | 4 +-
src/USER-FEP/pair_lj_cut_coul_long_soft.cpp | 20 +-
src/USER-FEP/pair_lj_cut_soft.cpp | 20 +-
src/USER-FEP/pair_lj_cut_tip4p_long_soft.h | 2 +-
src/USER-FEP/pair_tip4p_long_soft.h | 2 +-
src/USER-INTEL/Install.sh | 69 +
src/USER-INTEL/README | 52 +
src/USER-INTEL/TEST/README | 67 +
src/USER-INTEL/TEST/in.intel.lc | 61 +
src/USER-INTEL/TEST/in.intel.rhodo | 39 +
src/USER-INTEL/fix_intel.cpp | 796 +
src/USER-INTEL/fix_intel.h | 637 +
src/USER-INTEL/intel_buffers.cpp | 524 +
src/USER-INTEL/intel_buffers.h | 315 +
src/USER-INTEL/intel_preprocess.h | 436 +
src/USER-INTEL/math_extra_intel.h | 354 +
src/USER-INTEL/neigh_half_bin_intel.cpp | 1757 +
src/USER-INTEL/pair_gayberne_intel.cpp | 1083 +
src/USER-INTEL/pair_gayberne_intel.h | 102 +
src/USER-INTEL/pair_lj_charmm_coul_long_intel.cpp | 674 +
src/USER-INTEL/pair_lj_charmm_coul_long_intel.h | 104 +
src/USER-INTEL/pair_lj_cut_coul_long_intel.cpp | 633 +
src/USER-INTEL/pair_lj_cut_coul_long_intel.h | 100 +
src/USER-INTEL/pair_lj_cut_intel.cpp | 412 +
src/USER-INTEL/pair_lj_cut_intel.h | 93 +
src/USER-INTEL/pair_sw_intel.cpp | 703 +
src/USER-INTEL/pair_sw_intel.h | 111 +
src/USER-INTEL/verlet_intel.cpp | 430 +
src/USER-INTEL/verlet_intel.h | 67 +
src/USER-INTEL/verlet_split_intel.cpp | 593 +
src/USER-INTEL/verlet_split_intel.h | 89 +
src/USER-LB/fix_lb_fluid.cpp | 120 +-
src/USER-LB/fix_lb_fluid.h | 2 +-
src/USER-LB/fix_lb_momentum.h | 2 +-
src/USER-LB/fix_lb_pc.h | 2 +-
src/USER-LB/fix_lb_rigid_pc_sphere.h | 2 +-
src/USER-LB/fix_lb_viscous.h | 2 +-
src/USER-MISC/README | 6 +
src/USER-MISC/angle_cosine_shift.h | 2 +-
src/USER-MISC/angle_cosine_shift_exp.h | 2 +-
src/USER-MISC/angle_dipole.h | 2 +-
src/USER-MISC/angle_fourier.h | 2 +-
src/USER-MISC/angle_fourier_simple.h | 2 +-
src/USER-MISC/angle_quartic.h | 2 +-
src/USER-MISC/compute_ackland_atom.cpp | 4 +-
src/USER-MISC/compute_ackland_atom.h | 2 +-
src/USER-MISC/compute_basal_atom.cpp | 4 +-
src/USER-MISC/compute_basal_atom.h | 2 +-
src/USER-MISC/compute_temp_rotate.cpp | 2 +
src/USER-MISC/compute_temp_rotate.h | 2 +-
src/USER-MISC/dihedral_cosine_shift_exp.cpp | 1 -
src/USER-MISC/dihedral_cosine_shift_exp.h | 2 +-
src/USER-MISC/dihedral_fourier.cpp | 1 -
src/USER-MISC/dihedral_fourier.h | 2 +-
src/USER-MISC/dihedral_nharmonic.cpp | 1 -
src/USER-MISC/dihedral_nharmonic.h | 2 +-
src/USER-MISC/dihedral_quadratic.cpp | 21 +-
src/USER-MISC/dihedral_quadratic.h | 2 +-
src/USER-MISC/fix_addtorque.h | 2 +-
src/USER-MISC/fix_ave_spatial_sphere.cpp | 1071 +
src/USER-MISC/fix_ave_spatial_sphere.h | 192 +
src/USER-MISC/fix_gle.cpp | 875 +
src/USER-MISC/fix_gle.h | 77 +
src/USER-MISC/fix_imd.cpp | 12 +-
src/USER-MISC/fix_ipi.cpp | 439 +
src/USER-MISC/fix_ipi.h | 45 +
src/USER-MISC/fix_pimd.cpp | 841 +
src/USER-MISC/fix_pimd.h | 115 +
src/USER-MISC/fix_smd.h | 2 +-
src/USER-MISC/fix_srp.cpp | 601 +
src/USER-MISC/fix_srp.h | 72 +
src/USER-MISC/fix_ti_rs.h | 2 +-
src/USER-MISC/fix_ti_spring.h | 2 +-
src/USER-MISC/fix_ttm_mod.cpp | 918 +
src/USER-MISC/fix_ttm_mod.h | 88 +
src/USER-MISC/improper_cossq.cpp | 1 -
src/USER-MISC/improper_cossq.h | 2 +-
src/USER-MISC/improper_fourier.h | 2 +-
src/USER-MISC/improper_ring.cpp | 1 -
src/USER-MISC/improper_ring.h | 2 +-
src/USER-MISC/pair_cdeam.cpp | 17 +-
src/USER-MISC/pair_cdeam.h | 6 +-
src/USER-MISC/pair_coul_diel.cpp | 2 +-
src/USER-MISC/pair_edip.cpp | 2 +-
src/USER-MISC/pair_edip.h | 2 +-
src/USER-MISC/pair_list.cpp | 5 -
src/USER-MISC/pair_lj_sf.h | 2 +-
src/USER-MISC/pair_lj_sf_dipole_sf.cpp | 2 +-
src/USER-MISC/pair_lj_sf_dipole_sf.h | 2 +-
src/USER-MISC/pair_meam_spline.cpp | 11 +-
src/USER-MISC/pair_meam_spline.h | 6 +-
src/USER-MISC/pair_meam_sw_spline.cpp | 11 +-
src/USER-MISC/pair_meam_sw_spline.h | 6 +-
src/USER-MISC/pair_srp.cpp | 704 +
src/USER-MISC/pair_srp.h | 68 +
src/USER-MISC/pair_tersoff_table.cpp | 2 +-
src/USER-MISC/pair_tersoff_table.h | 2 +-
src/USER-MOLFILE/Install.sh | 6 +-
src/USER-MOLFILE/README | 21 +-
src/USER-MOLFILE/dump_molfile.cpp | 6 +-
src/USER-OMP/Install.sh | 5 +
src/USER-OMP/dihedral_charmm_omp.cpp | 1 -
src/USER-OMP/dihedral_quadratic_omp.cpp | 14 +-
src/USER-OMP/domain_omp.cpp | 5 -
src/USER-OMP/ewald_omp.cpp | 8 +
src/USER-OMP/fix_gravity_omp.h | 2 +-
src/USER-OMP/fix_nh_asphere_omp.cpp | 5 -
src/USER-OMP/fix_nh_omp.cpp | 5 -
src/USER-OMP/fix_nh_sphere_omp.cpp | 5 -
src/USER-OMP/fix_nve_omp.cpp | 5 -
src/USER-OMP/fix_nvt_sllod_omp.cpp | 5 -
src/USER-OMP/fix_omp.cpp | 34 +-
src/USER-OMP/fix_peri_neigh_omp.cpp | 2 +-
src/USER-OMP/fix_peri_neigh_omp.h | 2 +-
src/USER-OMP/fix_qeq_comb_omp.cpp | 3 +-
src/USER-OMP/fix_rigid_nh_omp.cpp | 111 +-
src/USER-OMP/fix_rigid_omp.cpp | 26 +-
src/USER-OMP/fix_rigid_small_omp.cpp | 28 +-
src/USER-OMP/fix_shear_history_omp.h | 2 +-
src/USER-OMP/msm_cg_omp.cpp | 15 +-
src/USER-OMP/pair_buck_long_coul_long_omp.cpp | 12 +-
src/USER-OMP/pair_eam_alloy_omp.cpp | 1 +
src/USER-OMP/pair_eam_alloy_omp.h | 2 +-
src/USER-OMP/pair_eam_fs_omp.cpp | 1 +
src/USER-OMP/pair_eam_fs_omp.h | 2 +-
src/USER-OMP/pair_gran_hertz_history_omp.cpp | 1 -
src/USER-OMP/pair_gran_hooke_history_omp.cpp | 4 -
src/USER-OMP/pair_nb3b_harmonic_omp.h | 3 +-
src/USER-OMP/pair_rebo_omp.h | 2 +-
src/USER-OMP/pppm_disp_omp.cpp | 4 +-
src/USER-OMP/pppm_disp_tip4p_omp.cpp | 3 +
src/USER-OMP/pppm_tip4p_omp.cpp | 3 +
src/USER-OMP/thr_omp.h | 10 -
src/USER-PHONON/fix_phonon.cpp | 22 +-
src/USER-PHONON/fix_phonon.h | 2 +-
src/USER-QMMM/README | 7 +
src/USER-QMMM/fix_qmmm.cpp | 8 +-
src/USER-QUIP/Install.sh | 60 +
src/USER-QUIP/README | 10 +
src/USER-QUIP/pair_quip.cpp | 288 +
src/USER-QUIP/pair_quip.h | 64 +
src/USER-REAXC/compute_spec_atom.h | 2 +-
src/USER-REAXC/fix_qeq_reax.cpp | 18 +-
src/USER-REAXC/fix_qeq_reax.h | 6 +-
src/USER-REAXC/fix_reax_c.cpp | 8 +-
src/USER-REAXC/fix_reax_c.h | 6 +-
src/USER-REAXC/fix_reaxc_bonds.cpp | 6 +-
src/USER-REAXC/fix_reaxc_bonds.h | 2 +-
src/USER-REAXC/fix_reaxc_species.cpp | 11 +-
src/USER-REAXC/fix_reaxc_species.h | 6 +-
src/USER-REAXC/pair_reax_c.cpp | 5 +-
src/USER-REAXC/pair_reax_c.h | 2 +-
src/USER-REAXC/reaxc_bonds.cpp | 127 +-
src/USER-REAXC/reaxc_ffield.cpp | 2 +-
src/USER-REAXC/reaxc_hydrogen_bonds.cpp | 11 +-
src/USER-REAXC/reaxc_init_md.cpp | 3 +-
src/USER-REAXC/reaxc_tool_box.cpp | 73 +
src/USER-REAXC/reaxc_tool_box.h | 2 +-
src/USER-REAXC/reaxc_torsion_angles.cpp | 16 +-
src/USER-REAXC/reaxc_traj.cpp | 1 -
src/USER-SPH/atom_vec_meso.cpp | 70 +
src/USER-SPH/atom_vec_meso.h | 5 +-
src/USER-SPH/compute_meso_e_atom.h | 2 +-
src/USER-SPH/compute_meso_rho_atom.h | 2 +-
src/USER-SPH/compute_meso_t_atom.h | 2 +-
src/USER-SPH/fix_meso.cpp | 20 +
src/USER-SPH/fix_meso.h | 3 +-
src/USER-SPH/fix_meso_stationary.h | 2 +-
src/USER-SPH/pair_sph_heatconduction.h | 2 +-
src/USER-SPH/pair_sph_idealgas.h | 2 +-
src/USER-SPH/pair_sph_lj.h | 2 +-
src/USER-SPH/pair_sph_rhosum.cpp | 10 +-
src/USER-SPH/pair_sph_rhosum.h | 6 +-
src/USER-SPH/pair_sph_taitwater.h | 2 +-
src/USER-SPH/pair_sph_taitwater_morris.h | 2 +-
src/VORONOI/Install.sh | 15 +-
src/VORONOI/Makefile.lammps | 20 -
src/VORONOI/README | 43 +-
src/VORONOI/compute_voronoi_atom.cpp | 90 +-
src/VORONOI/compute_voronoi_atom.h | 6 +-
src/XTC/dump_xtc.cpp | 28 +-
src/XTC/dump_xtc.h | 2 +-
src/accelerator_cuda.h | 4 +-
src/accelerator_intel.h | 69 +
src/accelerator_kokkos.h | 10 +-
src/angle.cpp | 4 +
src/angle.h | 4 +
src/angle_hybrid.cpp | 15 +-
src/angle_hybrid.h | 2 +-
src/atom.cpp | 189 +-
src/atom.h | 25 +-
src/atom_masks.h | 2 +-
src/atom_vec.cpp | 13 +-
src/atom_vec.h | 7 +-
src/atom_vec_atomic.h | 2 +-
src/atom_vec_body.cpp | 2 +-
src/atom_vec_body.h | 2 +-
src/atom_vec_charge.h | 2 +-
src/atom_vec_ellipsoid.h | 2 +-
src/atom_vec_hybrid.cpp | 41 +-
src/atom_vec_hybrid.h | 5 +-
src/atom_vec_line.h | 2 +-
src/atom_vec_sphere.h | 2 +-
src/atom_vec_tri.h | 2 +-
src/balance.cpp | 474 +-
src/balance.h | 9 +-
src/body.h | 2 +-
src/bond.cpp | 4 +
src/bond.h | 4 +
src/bond_hybrid.cpp | 11 +-
src/bond_hybrid.h | 2 +-
src/change_box.cpp | 1 -
src/change_box.h | 2 +-
src/citeme.cpp | 10 +-
src/comm.cpp | 249 +-
src/comm.h | 62 +-
src/comm_brick.cpp | 492 +-
src/comm_brick.h | 22 +-
src/comm_tiled.cpp | 2041 +-
src/comm_tiled.h | 103 +-
src/compute.cpp | 125 +-
src/compute.h | 27 +-
src/compute_angle_local.h | 2 +-
src/compute_atom_molecule.cpp | 348 -
src/compute_atom_molecule.h | 126 -
src/compute_bond_local.cpp | 4 +-
src/compute_bond_local.h | 2 +-
src/compute_centro_atom.cpp | 4 +-
src/compute_centro_atom.h | 2 +-
src/compute_chunk_atom.cpp | 1548 +
src/compute_chunk_atom.h | 125 +
src/compute_cluster_atom.cpp | 12 +-
src/compute_cluster_atom.h | 6 +-
src/compute_cna_atom.cpp | 4 +-
src/compute_cna_atom.h | 2 +-
src/compute_com.h | 2 +-
src/compute_com_chunk.cpp | 243 +
src/compute_com_chunk.h | 76 +
src/compute_com_molecule.cpp | 148 -
src/compute_com_molecule.h | 64 -
src/compute_contact_atom.cpp | 6 +-
src/compute_contact_atom.h | 2 +-
src/compute_coord_atom.cpp | 4 +-
src/compute_coord_atom.h | 2 +-
src/compute_dihedral_local.h | 2 +-
src/compute_displace_atom.cpp | 14 +
src/compute_displace_atom.h | 3 +-
src/compute_erotate_sphere.h | 2 +-
src/compute_erotate_sphere_atom.h | 2 +-
src/compute_group_group.cpp | 4 +-
src/compute_group_group.h | 2 +-
src/compute_gyration.cpp | 2 +-
src/compute_gyration.h | 2 +-
src/compute_gyration_chunk.cpp | 359 +
src/compute_gyration_chunk.h | 80 +
src/compute_gyration_molecule.cpp | 275 -
src/compute_gyration_molecule.h | 70 -
src/compute_heat_flux.h | 2 +-
src/compute_improper_local.h | 2 +-
src/compute_inertia_chunk.cpp | 257 +
src/compute_inertia_chunk.h | 75 +
src/compute_inertia_molecule.cpp | 185 -
src/compute_inertia_molecule.h | 65 -
src/compute_ke.h | 2 +-
src/compute_ke_atom.h | 2 +-
src/compute_msd.cpp | 14 +
src/compute_msd.h | 3 +-
src/compute_msd_chunk.cpp | 263 +
src/compute_msd_chunk.h | 78 +
src/compute_msd_molecule.cpp | 181 -
src/compute_msd_molecule.h | 66 -
src/compute_pair.h | 2 +-
src/compute_pair_local.cpp | 28 +-
src/compute_pair_local.h | 2 +-
src/compute_pe.h | 2 +-
src/compute_pe_atom.cpp | 2 +-
src/compute_pe_atom.h | 2 +-
src/compute_pressure.h | 2 +-
src/compute_property_atom.cpp | 121 +-
src/compute_property_atom.h | 9 +-
src/compute_property_chunk.cpp | 338 +
src/compute_property_chunk.h | 90 +
src/compute_property_local.cpp | 32 +-
src/compute_property_local.h | 2 +-
src/compute_property_molecule.cpp | 173 -
src/compute_property_molecule.h | 74 -
src/compute_rdf.cpp | 4 +-
src/compute_reduce.h | 2 +-
src/compute_reduce_region.h | 2 +-
src/compute_slice.h | 2 +-
src/compute_stress_atom.cpp | 5 +-
src/compute_stress_atom.h | 2 +-
src/compute_temp.cpp | 2 +
src/compute_temp.h | 2 +-
src/compute_temp_chunk.cpp | 854 +
src/compute_temp_chunk.h | 93 +
src/compute_temp_com.cpp | 6 +-
src/compute_temp_deform.cpp | 2 +
src/compute_temp_partial.cpp | 34 +-
src/compute_temp_partial.h | 3 +-
src/compute_temp_profile.cpp | 32 +-
src/compute_temp_profile.h | 2 +-
src/compute_temp_ramp.cpp | 26 +-
src/compute_temp_ramp.h | 2 +-
src/compute_temp_region.cpp | 3 +
src/compute_temp_region.h | 2 +-
src/compute_temp_sphere.cpp | 10 +-
src/compute_temp_sphere.h | 2 +-
src/compute_torque_chunk.cpp | 253 +
src/compute_torque_chunk.h | 75 +
src/compute_vacf.cpp | 15 +
src/compute_vacf.h | 3 +-
src/compute_vcm_chunk.cpp | 238 +
src/compute_vcm_chunk.h | 76 +
src/create_atoms.cpp | 216 +-
src/create_atoms.h | 11 +-
src/create_bonds.cpp | 228 +
src/create_bonds.h | 78 +
src/create_box.h | 2 +-
src/delete_atoms.cpp | 241 +-
src/delete_atoms.h | 7 +-
src/delete_bonds.cpp | 70 +-
src/delete_bonds.h | 2 +-
src/dihedral.cpp | 4 +
src/dihedral.h | 4 +
src/dihedral_hybrid.cpp | 11 +-
src/dihedral_hybrid.h | 2 +-
src/displace_atoms.cpp | 3 +-
src/displace_atoms.h | 2 +-
src/domain.cpp | 175 +-
src/domain.h | 7 +-
src/dump.cpp | 5 +-
src/dump.h | 4 +-
src/dump_atom.h | 2 +-
src/dump_cfg.h | 4 +-
src/dump_custom.cpp | 336 +-
src/dump_custom.h | 14 +-
src/dump_image.cpp | 49 +-
src/dump_image.h | 6 +-
src/dump_local.cpp | 17 +-
src/dump_local.h | 2 +-
src/dump_xyz.h | 2 +-
src/error.h | 2 +-
src/finish.h | 2 +-
src/fix.cpp | 17 +-
src/fix.h | 13 +-
src/fix_adapt.cpp | 48 +-
src/fix_adapt.h | 6 +-
src/fix_addforce.cpp | 18 +-
src/fix_addforce.h | 2 +-
src/fix_ave_atom.cpp | 2 +
src/fix_ave_atom.h | 2 +-
src/fix_ave_chunk.cpp | 1040 +
src/fix_ave_chunk.h | 173 +
src/fix_ave_correlate.cpp | 1 +
src/fix_ave_correlate.h | 2 +-
src/fix_ave_histo.cpp | 1 +
src/fix_ave_histo.h | 2 +-
src/fix_ave_spatial.cpp | 417 +-
src/fix_ave_spatial.h | 7 +-
src/fix_ave_time.cpp | 237 +-
src/fix_ave_time.h | 7 +-
src/fix_aveforce.h | 2 +-
src/fix_balance.cpp | 57 +-
src/fix_balance.h | 4 +-
src/fix_box_relax.h | 2 +-
src/fix_deform.cpp | 11 +
src/fix_deform.h | 3 +-
src/fix_drag.h | 2 +-
src/fix_dt_reset.h | 2 +-
src/fix_enforce2d.h | 2 +-
src/fix_external.h | 2 +-
src/fix_gravity.cpp | 13 +-
src/fix_gravity.h | 2 +-
src/fix_group.h | 2 +-
src/fix_heat.h | 2 +-
src/fix_indent.h | 2 +-
src/fix_langevin.cpp | 5 +-
src/fix_langevin.h | 1 +
src/fix_lineforce.h | 2 +-
src/fix_minimize.h | 2 +-
src/fix_momentum.h | 2 +-
src/fix_move.cpp | 14 +-
src/fix_move.h | 4 +-
src/fix_nh.cpp | 45 +-
src/fix_nh.h | 1 +
src/fix_nh_sphere.h | 2 +-
src/fix_nph.h | 2 +-
src/fix_nph_sphere.h | 2 +-
src/fix_npt.h | 2 +-
src/fix_npt_sphere.h | 2 +-
src/fix_nve.h | 2 +-
src/fix_nve_limit.h | 2 +-
src/fix_nve_noforce.h | 2 +-
src/fix_nve_sphere.h | 2 +-
src/fix_nvt.h | 2 +-
src/fix_nvt_sllod.h | 2 +-
src/fix_nvt_sphere.h | 2 +-
src/fix_planeforce.h | 2 +-
src/fix_press_berendsen.h | 2 +-
src/fix_print.h | 2 +-
src/fix_property_atom.h | 2 +-
src/fix_read_restart.h | 2 +-
src/fix_recenter.cpp | 20 +-
src/fix_recenter.h | 2 +
src/fix_respa.cpp | 3 +-
src/fix_respa.h | 4 +-
src/fix_restrain.h | 2 +-
src/fix_shear_history.cpp | 40 +-
src/fix_shear_history.h | 5 +-
src/fix_spring.h | 2 +-
src/fix_spring_rg.h | 2 +-
src/fix_store.h | 2 +-
src/fix_store_force.h | 2 +-
src/fix_store_state.cpp | 49 +-
src/fix_store_state.h | 2 +-
src/fix_temp_berendsen.cpp | 5 +-
src/fix_temp_csvr.cpp | 1 +
src/fix_tmd.cpp | 1 -
src/fix_vector.cpp | 33 +-
src/fix_vector.h | 5 +-
src/fix_viscous.h | 2 +-
src/fix_wall.h | 2 +-
src/fix_wall_lj1043.cpp | 8 +-
src/fix_wall_lj1043.h | 2 +-
src/fix_wall_lj126.h | 2 +-
src/fix_wall_lj93.h | 2 +-
src/fix_wall_reflect.h | 2 +-
src/fix_wall_region.h | 2 +-
src/force.cpp | 376 +-
src/force.h | 29 +-
src/group.cpp | 96 +
src/group.h | 12 +-
src/image.cpp | 9 +-
src/image.h | 2 +-
src/improper.cpp | 4 +
src/improper.h | 4 +
src/improper_hybrid.cpp | 11 +-
src/improper_hybrid.h | 2 +-
src/input.cpp | 118 +-
src/input.h | 2 +-
src/integrate.cpp | 9 +
src/integrate.h | 2 +-
src/irregular.cpp | 643 +-
src/irregular.h | 90 +-
src/kspace.cpp | 78 +-
src/kspace.h | 15 +-
src/lammps.cpp | 148 +-
src/lammps.h | 6 +-
src/lattice.h | 2 +-
src/library.cpp | 4 +-
src/library.h | 2 +-
src/lmptype.h | 30 +
src/lmpwindows.h | 1 -
src/math_complex.h | 2 +-
src/math_const.h | 2 +
src/math_extra.cpp | 49 +
src/math_extra.h | 73 +-
src/math_vector.h | 2 +-
src/memory.h | 6 +-
src/min.cpp | 38 +-
src/min.h | 5 +-
src/min_cg.cpp | 1 -
src/min_cg.h | 2 +-
src/min_fire.h | 2 +-
src/min_hftn.h | 2 +-
src/min_linesearch.cpp | 16 +-
src/min_linesearch.h | 2 +-
src/min_quickmin.cpp | 1 -
src/min_quickmin.h | 2 +-
src/min_sd.h | 2 +-
src/minimize.h | 2 +-
src/modify.cpp | 118 +-
src/modify.h | 8 +-
src/molecule.cpp | 48 +-
src/molecule.h | 2 +-
src/mpiio.h | 2 +-
src/my_pool_chunk.h | 2 +-
src/neigh_bond.h | 2 +-
src/neigh_derive.h | 2 +-
src/neigh_full.h | 2 +-
src/neigh_gran.h | 2 +-
src/neigh_half_bin.h | 2 +-
src/neigh_half_multi.h | 2 +-
src/neigh_half_nsq.cpp | 4 +-
src/neigh_half_nsq.h | 2 +-
src/neigh_list.cpp | 3 +
src/neigh_list.h | 2 +-
src/neigh_request.cpp | 16 +-
src/neigh_request.h | 18 +-
src/neigh_respa.h | 2 +-
src/neighbor.cpp | 138 +-
src/neighbor.h | 28 +-
src/output.cpp | 10 +-
src/output.h | 2 +-
src/pair.cpp | 51 +-
src/pair.h | 17 +-
src/pair_born.h | 2 +-
src/pair_born_coul_wolf.cpp | 2 +-
src/pair_buck.cpp | 2 +-
src/pair_buck.h | 4 +-
src/pair_buck_coul_cut.cpp | 2 +-
src/pair_buck_coul_cut.h | 2 +-
src/pair_coul_cut.cpp | 2 +-
src/pair_coul_cut.h | 4 +-
src/pair_coul_debye.cpp | 6 +-
src/pair_coul_debye.h | 2 +-
src/pair_coul_dsf.cpp | 4 +-
src/pair_coul_dsf.h | 2 +-
src/pair_coul_streitz.cpp | 851 +
src/pair_coul_streitz.h | 92 +
src/pair_coul_wolf.cpp | 4 +-
src/pair_dpd.cpp | 5 +-
src/pair_dpd.h | 4 +-
src/pair_dpd_tstat.h | 2 +-
src/pair_gauss.h | 2 +-
src/pair_hybrid.cpp | 37 +-
src/pair_hybrid.h | 2 +-
src/pair_hybrid_overlay.h | 2 +-
src/pair_lj96_cut.cpp | 14 +-
src/pair_lj96_cut.h | 2 +-
src/pair_lj_cubic.h | 2 +-
src/pair_lj_cut.cpp | 14 +-
src/pair_lj_cut.h | 2 +-
src/pair_lj_cut_coul_cut.cpp | 2 +-
src/pair_lj_cut_coul_cut.h | 2 +-
src/pair_lj_cut_coul_debye.h | 2 +-
src/pair_lj_cut_coul_dsf.cpp | 2 +-
src/pair_lj_cut_coul_dsf.h | 2 +-
src/pair_lj_expand.h | 2 +-
src/pair_lj_gromacs.h | 2 +-
src/pair_lj_gromacs_coul_gromacs.cpp | 2 +-
src/pair_lj_gromacs_coul_gromacs.h | 2 +-
src/pair_lj_smooth.h | 2 +-
src/pair_mie_cut.cpp | 14 +-
src/pair_mie_cut.h | 2 +-
src/pair_morse.h | 2 +-
src/pair_soft.h | 2 +-
src/pair_table.h | 2 +-
src/pair_yukawa.h | 2 +-
src/pair_zbl.cpp | 2 +-
src/pair_zbl.h | 2 +-
src/pointers.h | 2 +-
src/procmap.cpp | 7 +-
src/procmap.h | 2 +-
src/random_mars.h | 2 +-
src/random_park.h | 2 +-
src/rcb.cpp | 922 +
src/rcb.h | 131 +
src/read_data.cpp | 27 +-
src/read_dump.cpp | 74 +-
src/read_dump.h | 1 +
src/read_restart.cpp | 55 +-
src/read_restart.h | 2 +-
src/reader_native.h | 2 +-
src/reader_xyz.cpp | 3 +-
src/region.cpp | 25 +-
src/region.h | 10 +-
src/region_block.h | 2 +-
src/region_cone.h | 2 +-
src/region_cylinder.h | 2 +-
src/region_intersect.cpp | 30 +-
src/region_intersect.h | 4 +-
src/region_plane.h | 2 +-
src/region_prism.h | 2 +-
src/region_sphere.h | 2 +-
src/region_union.cpp | 30 +-
src/region_union.h | 4 +-
src/replicate.cpp | 42 +-
src/replicate.h | 2 +-
src/rerun.cpp | 11 +-
src/rerun.h | 2 +-
src/respa.cpp | 33 +-
src/respa.h | 3 +-
src/run.cpp | 6 +-
src/run.h | 2 +-
src/set.h | 2 +-
src/special.cpp | 4 +-
src/special.h | 2 +-
src/suffix.h | 3 +-
src/thermo.cpp | 75 +-
src/thermo.h | 5 +-
src/timer.h | 2 +-
src/universe.h | 2 +-
src/update.cpp | 92 +-
src/update.h | 6 +-
src/variable.cpp | 1264 +-
src/variable.h | 20 +-
src/velocity.cpp | 193 +-
src/velocity.h | 5 +-
src/verlet.cpp | 100 +-
src/verlet.h | 5 +-
src/version.h | 2 +-
src/write_data.cpp | 50 +-
src/write_data.h | 2 +-
src/write_dump.cpp | 5 +-
src/write_restart.cpp | 18 +-
src/write_restart.h | 2 +-
tools/Makefile | 4 +-
tools/README | 1 +
tools/amber2lmp/amber2lammps.py | 2017 +-
tools/i-pi/.vimrc | 4 +
tools/i-pi/MANIFEST.in | 1 +
tools/i-pi/README.rst | 49 +
tools/i-pi/drivers/LJ.f90 | 215 +
tools/i-pi/drivers/Makefile | 42 +
tools/i-pi/drivers/README | 14 +
tools/i-pi/drivers/SG.f90 | 283 +
tools/i-pi/drivers/distance.f90 | 174 +
tools/i-pi/drivers/driver.f90 | 309 +
tools/i-pi/drivers/sockets.c | 147 +
tools/i-pi/examples/lammps/Makefile | 70 +
tools/i-pi/examples/lammps/README | 70 +
tools/i-pi/examples/lammps/h2o-piglet.2/data.water | 1331 +
tools/i-pi/examples/lammps/h2o-piglet.2/in.water | 32 +
tools/i-pi/examples/lammps/h2o-piglet.2/input.xml | 37 +
.../examples/lammps/h2o-piglet.2/water_298K.pdb | 650 +
tools/i-pi/examples/lammps/h2o-piglet.4/data.water | 1331 +
tools/i-pi/examples/lammps/h2o-piglet.4/in.water | 32 +
tools/i-pi/examples/lammps/h2o-piglet.4/input.xml | 40 +
.../examples/lammps/h2o-piglet.4/water_298K.pdb | 650 +
tools/i-pi/examples/lammps/h2o-piglet.8/data.water | 1331 +
tools/i-pi/examples/lammps/h2o-piglet.8/in.water | 32 +
tools/i-pi/examples/lammps/h2o-piglet.8/input.xml | 49 +
.../examples/lammps/h2o-piglet.8/water_298K.pdb | 650 +
.../lammps/h2o-pimd-rpc/data.water_longrange | 1331 +
.../lammps/h2o-pimd-rpc/data.water_shortrange | 1331 +
.../lammps/h2o-pimd-rpc/in.water_longrange | 33 +
.../lammps/h2o-pimd-rpc/in.water_shortrange | 34 +
tools/i-pi/examples/lammps/h2o-pimd-rpc/input.xml | 27 +
.../examples/lammps/h2o-pimd-rpc/water_298K.pdb | 650 +
tools/i-pi/examples/lammps/h2o-pimd/data.water | 1331 +
tools/i-pi/examples/lammps/h2o-pimd/in.water | 32 +
tools/i-pi/examples/lammps/h2o-pimd/input.xml | 24 +
tools/i-pi/examples/lammps/h2o-pimd/water_298K.pdb | 650 +
tools/i-pi/examples/tutorial/README | 6 +
.../i-pi/examples/tutorial/tutorial-1/our_ref.pdb | 111 +
.../i-pi/examples/tutorial/tutorial-1/our_ref.xyz | 110 +
.../examples/tutorial/tutorial-1/tutorial-1.xml | 26 +
.../tutorial/tutorial-2/tutorial-1_RESTART | 736 +
.../examples/tutorial/tutorial-2/tutorial-2a.xml | 742 +
.../examples/tutorial/tutorial-2/tutorial-2b.xml | 33 +
.../i-pi/examples/tutorial/tutorial-3/our_ref.pdb | 174 +
.../tutorial/tutorial-3/tutorial-3_npt.xml | 31 +
.../tutorial/tutorial-3/tutorial-3_nvt.xml | 25 +
tools/i-pi/i-pi | 60 +
tools/i-pi/ipi/README | 14 +
tools/i-pi/ipi/__init__.py | 1 +
tools/i-pi/ipi/engine/README | 18 +
tools/i-pi/ipi/engine/__init__.py | 3 +
tools/i-pi/ipi/engine/atoms.py | 269 +
tools/i-pi/ipi/engine/barostats.py | 450 +
tools/i-pi/ipi/engine/beads.py | 323 +
tools/i-pi/ipi/engine/cell.py | 140 +
tools/i-pi/ipi/engine/ensembles.py | 565 +
tools/i-pi/ipi/engine/forces.py | 781 +
tools/i-pi/ipi/engine/initializer.py | 549 +
tools/i-pi/ipi/engine/normalmodes.py | 400 +
tools/i-pi/ipi/engine/outputs.py | 378 +
tools/i-pi/ipi/engine/properties.py | 1273 +
tools/i-pi/ipi/engine/simulation.py | 232 +
tools/i-pi/ipi/engine/thermostats.py | 884 +
tools/i-pi/ipi/inputs/README | 24 +
tools/i-pi/ipi/inputs/__init__.py | 3 +
tools/i-pi/ipi/inputs/atoms.py | 121 +
tools/i-pi/ipi/inputs/barostats.py | 107 +
tools/i-pi/ipi/inputs/beads.py | 137 +
tools/i-pi/ipi/inputs/cell.py | 77 +
tools/i-pi/ipi/inputs/ensembles.py | 185 +
tools/i-pi/ipi/inputs/forces.py | 176 +
tools/i-pi/ipi/inputs/initializer.py | 406 +
tools/i-pi/ipi/inputs/interface.py | 125 +
tools/i-pi/ipi/inputs/normalmodes.py | 84 +
tools/i-pi/ipi/inputs/outputs.py | 323 +
tools/i-pi/ipi/inputs/prng.py | 101 +
tools/i-pi/ipi/inputs/simulation.py | 193 +
tools/i-pi/ipi/inputs/thermostats.py | 195 +
tools/i-pi/ipi/interfaces/README | 8 +
tools/i-pi/ipi/interfaces/__init__.py | 1 +
tools/i-pi/ipi/interfaces/sockets.py | 773 +
tools/i-pi/ipi/tests/README | 9 +
tools/i-pi/ipi/tests/common.py | 96 +
tools/i-pi/ipi/tests/datest.py | 56 +
tools/i-pi/ipi/tests/test.pos_0.pdb | 10 +
tools/i-pi/ipi/tests/test.pos_0.xyz | 10 +
tools/i-pi/ipi/tests/test_contraction.py | 127 +
tools/i-pi/ipi/tests/test_io.py | 96 +
tools/i-pi/ipi/tests/test_runs.py | 24 +
tools/i-pi/ipi/utils/README | 21 +
tools/i-pi/ipi/utils/__init__.py | 1 +
tools/i-pi/ipi/utils/depend.py | 768 +
tools/i-pi/ipi/utils/inputvalue.py | 968 +
tools/i-pi/ipi/utils/io/README | 12 +
tools/i-pi/ipi/utils/io/__init__.py | 1 +
tools/i-pi/ipi/utils/io/io_binary.py | 47 +
tools/i-pi/ipi/utils/io/io_pdb.py | 173 +
tools/i-pi/ipi/utils/io/io_xml.py | 520 +
tools/i-pi/ipi/utils/io/io_xyz.py | 145 +
tools/i-pi/ipi/utils/mathtools.py | 343 +
tools/i-pi/ipi/utils/messages.py | 155 +
tools/i-pi/ipi/utils/nmtransform.py | 283 +
tools/i-pi/ipi/utils/prng.py | 129 +
tools/i-pi/ipi/utils/softexit.py | 73 +
tools/i-pi/ipi/utils/units.py | 358 +
tools/i-pi/licenses/license_GPL.txt | 675 +
tools/i-pi/licenses/license_MIT.txt | 21 +
tools/i-pi/manual.pdf | Bin 0 -> 609105 bytes
.../common/amber/amberparm_dihedral_to_lt.py | 6 +-
.../common/amber/amberparm_improper_to_lt.py | 20 +-
.../common/amber/amberparm_pair_to_lt.py | 27 +-
tools/moltemplate/common/gaff.lt | 272 +-
tools/moltemplate/common/graphene.lt | 108 +-
.../moltemplate_files => common}/graphite.lt | 0
tools/moltemplate/common/oplsaa/README.TXT | 11 +-
.../common/oplsaa/oplsaa_moltemplate.py | 392 -
tools/moltemplate/common/spce.lt | 24 +-
tools/moltemplate/common/spce_ice_rect16.lt | 81 +
tools/moltemplate/common/spce_ice_rect32.lt | 129 +
tools/moltemplate/common/tip3p_1983.lt | 76 +-
tools/moltemplate/common/tip3p_1983_charmm.lt | 119 +
tools/moltemplate/common/tip3p_2004.lt | 78 +-
.../moltemplate_files/CGLipidBr2005.lt | 198 -
.../membrane+protein/moltemplate_files/system.lt | 207 -
.../CG_biomolecules/membrane+protein/run.in.min | 35 -
.../CG_biomolecules/membrane+protein/run.in.npt | 65 -
.../CG_biomolecules/membrane+protein/run.in.nvt | 71 -
.../moltemplate_files/CGLipidBr2005Orig.lt | 191 -
.../membrane_BranniganPRE2005/run.in.min | 28 -
.../membrane_BranniganPRE2005/run.in.npt | 57 -
.../membrane_BranniganPRE2005/run.in.nvt | 53 -
.../README_FIRST.txt | 47 -
.../frustrated+chaperonin/README_setup.sh | 24 -
.../frustrated+chaperonin/run.in.min | 25 -
.../frustrated+chaperonin/run.in.nvt | 48 -
.../frustrated+minichaperone/README_setup.sh | 24 -
.../frustrated+minichaperone/run.in.min | 24 -
.../frustrated+minichaperone/run.in.nvt | 46 -
.../1bead+chaperone/frustrated/README_setup.sh | 24 -
.../1bead+chaperone/frustrated/run.in.min | 19 -
.../frustrated/run_short_sim.in.nvt | 50 -
.../unfrustrated+chaperonin/README_setup.sh | 24 -
.../unfrustrated+chaperonin/run.in.min | 19 -
.../unfrustrated+chaperonin/run.in.nvt | 48 -
.../1bead+chaperone/unfrustrated/README_setup.sh | 23 -
.../1bead+chaperone/unfrustrated/run.in.min | 19 -
.../1bead+chaperone/unfrustrated/run.in.nvt | 46 -
.../1beadProtSci2010/README_setup.sh | 23 -
.../1beadProtSci2010/run.in.min | 19 -
.../1beadProtSci2010/run.in.nvt | 44 -
.../README_setup.sh | 50 -
.../moltemplate_files/CGLipidBr2005.lt | 198 -
.../packmol_files/step2_innerlayer.inp | 70 -
.../packmol_files/step3_outerlayer.inp | 70 -
.../images/2bead_heteropolymer_t=0.jpg | Bin 76183 -> 0 bytes
.../images/2bead_heteropolymer_t=1000ps.jpg | Bin 54472 -> 0 bytes
.../psf_file_created_by_topotools/system.psf | 1728 -
.../2bead_heteropolymer/moltemplate_files/2bead.lt | 128 -
.../moltemplate_files/2bead_forcefield.lt | 126 -
.../moltemplate_files/README.sh | 20 -
.../moltemplate_files/peptide.lt | 50 -
.../moltemplate_files/system.lt | 26 -
.../CG_misc/2bead_heteropolymer/run.in.nvt | 38 -
.../CG_misc/random_heteropolymer/README.TXT | 36 -
.../psf_file_created_by_topotools/system.psf | 277 -
.../images/random_heteropolymer_t=0ps.jpg | Bin 31115 -> 0 bytes
.../images/random_heteropolymer_t=1ns.jpg | Bin 29582 -> 0 bytes
.../moltemplate_files/monomers.lt | 115 -
.../moltemplate_files/polymer.lt | 82 -
.../moltemplate_files/system.lt | 33 -
.../CG_misc/random_heteropolymer/run.in.nvt | 29 -
.../translocation/moltemplate_files/polymer.lt | 35 -
.../translocation/moltemplate_files/system.lt | 55 -
.../examples/CG_misc/translocation/run.in.npt | 70 -
.../examples/CG_misc/translocation/run.in.nvt | 49 -
.../psf_file_created_by_topotools/system.psf | 3669 -
.../CG_solvent/cyclododecane+watMW/run.in.nvt | 81 -
tools/moltemplate/examples/README.TXT | 4 +-
.../hexadecane/README_setup.sh | 36 -
.../hexadecane/moltemplate_files/ch2group.lt | 49 -
.../hexadecane/moltemplate_files/ch3group.lt | 55 -
.../hexadecane/moltemplate_files/hexadecane.lt | 93 -
.../hexadecane/run.in.npt | 85 -
.../hexadecane/run.in.nvt | 42 -
.../moltemplate_files/isobutane.lt | 56 -
.../README_remove_irrelevant_info.sh | 69 -
.../waterTIP3P+isobutane/run.in.npt | 44 -
.../waterTIP3P+isobutane/run.in.nvt | 51 -
.../oplsaa_lt_generator/README.TXT | 108 -
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 392 -
.../packmol_files/mix_ethylene+benzene.inp | 31 -
.../ethylene+benzene_PACKMOL/run.in.npt | 57 -
.../ethylene+benzene_PACKMOL/run.in.nvt | 50 -
.../ethylene/README.TXT | 13 -
.../images/ethylene_box_pressure=50barr.jpg | Bin 86910 -> 0 bytes
.../ethylene/moltemplate_files/ethylene.lt | 40 -
.../oplsaa_lt_generator/README.TXT | 106 -
.../minimal_versions/oplsaa_subset_minimal.prm | 22 -
.../minimal_versions/oplsaa_subset_simplified.prm | 25 -
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 392 -
.../oplsaa_lt_generator/oplsaa_subset.prm | 5125 -
.../ethylene/moltemplate_files/system.lt | 19 -
.../ethylene/run.in.npt | 57 -
.../ethylene/run.in.nvt | 50 -
.../cnad-cnt/run.in.nvt | 46 -
.../WARNING.TXT | 0
.../benzene}/README.TXT | 0
.../benzene}/README_run.sh | 0
.../force_field_AMBER/benzene/README_setup.sh | 29 +
.../benzene}/README_visualize.txt | 0
.../benzene/moltemplate_files/benzene.lt | 49 +
.../benzene/moltemplate_files/system.lt | 14 +
.../README_remove_irrelevant_info.sh | 0
.../force_field_AMBER/benzene/run.in.npt | 72 +
.../force_field_AMBER/benzene/run.in.nvt | 51 +
.../ethylene+benzene}/README.TXT | 0
.../ethylene+benzene}/README_run.sh | 0
.../ethylene+benzene/README_setup.sh | 36 +
.../ethylene+benzene}/README_visualize.txt | 0
.../ethylene+benzene}/images/benzene.jpg | Bin
.../images/ethylene+benzene_box80x80x80_LR.jpg | Bin
.../ethylene+benzene}/images/ethylene.jpg | Bin
.../ethylene+benzene/moltemplate_files/benzene.lt | 47 +
.../charges_come_from_OPLSAA/oplsaa_subset.prm | 94 +
.../ethylene+benzene/moltemplate_files/ethylene.lt | 38 +
.../ethylene+benzene/moltemplate_files/system.lt | 29 +
.../README_remove_irrelevant_info.sh | 0
.../force_field_AMBER/ethylene+benzene/run.in.npt | 53 +
.../force_field_AMBER/ethylene+benzene/run.in.nvt | 46 +
.../hexadecane/README.TXT | 0
.../hexadecane}/README_run.sh | 0
.../force_field_AMBER/hexadecane/README_setup.sh | 36 +
.../hexadecane}/README_visualize.txt | 0
.../hexadecane/WARNING.TXT | 0
.../images/hexadecane_12x12x2_t=0_LR.jpg | Bin
.../images/hexadecane_12x12x2_t=10ps_npt_LR.jpg | Bin
.../hexadecane/images/hexadecane_LR.jpg | Bin
.../hexadecane/moltemplate_files/ch2group.lt | 59 +
.../hexadecane/moltemplate_files/ch3group.lt | 65 +
.../hexadecane/moltemplate_files/hexadecane.lt | 89 +
.../hexadecane/moltemplate_files/system.lt | 0
.../README_remove_irrelevant_info.sh | 0
.../force_field_AMBER/hexadecane/run.in.npt | 86 +
.../force_field_AMBER/hexadecane/run.in.nvt | 43 +
.../waterTIP3P+isobutane/README.TXT | 0
.../waterTIP3P+isobutane}/README_run.sh | 0
.../waterTIP3P+isobutane/README_setup.sh | 0
.../waterTIP3P+isobutane}/README_visualize.txt | 0
.../waterTIP3P+isobutane/images/isobutane.jpg | Bin
.../images/water+isobutane_t=0_LR.jpg | Bin
.../images/water+isobutane_t=840ps_LR.jpg | Bin
.../waterTIP3P+isobutane/images/water.jpg | Bin
.../moltemplate_files/isobutane.lt | 56 +
.../moltemplate_files/system.lt | 0
.../README_remove_irrelevant_info.sh | 0
.../waterTIP3P+isobutane/run.in.npt | 44 +
.../waterTIP3P+isobutane/run.in.nvt | 52 +
.../WARNING.TXT | 0
.../alkane_chain_single/README.TXT | 80 +
.../alkane_chain_single}/README_run.sh | 0
.../alkane_chain_single}/README_setup.sh | 0
.../alkane_chain_single}/README_visualize.txt | 0
.../alkane_chain_single/images/ch2_ry90.jpg | Bin 0 -> 4680 bytes
.../alkane_chain_single/images/ch3_ry60.jpg | Bin 0 -> 6951 bytes
.../alkane_chain_single/images/t=0.jpg | Bin 0 -> 51583 bytes
.../alkane_chain_single/images/t=1ns.jpg | Bin 0 -> 60111 bytes
.../moltemplate_files/alkane50.lt | 138 +
.../moltemplate_files/ch2group.lt | 55 +
.../moltemplate_files/ch3group.lt | 58 +
.../oplsaa_lt_generator/AUTHOR.TXT | 0
.../oplsaa_lt_generator/README.TXT | 109 +
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 +
.../oplsaa_lt_generator/oplsaa_subset.prm | 146 +
.../moltemplate_files/system.lt | 31 +
.../alkane_chain_single/run.in.min | 40 +
.../alkane_chain_single/run.in.nvt | 38 +
.../force_field_OPLSAA/ethylene+benzene/README.TXT | 13 +
.../ethylene+benzene}/README_run.sh | 0
.../ethylene+benzene/README_setup.sh | 34 +
.../ethylene+benzene}/README_visualize.txt | 0
.../ethylene+benzene}/images/benzene.jpg | Bin
.../images/ethylene+benzene_box80x80x80_LR.jpg | Bin
.../ethylene+benzene}/images/ethylene.jpg | Bin
.../ethylene+benzene/moltemplate_files/benzene.lt | 45 +
.../ethylene+benzene/moltemplate_files/ethylene.lt | 43 +
.../ethylene+benzene/moltemplate_files/log.lammps} | 0
.../oplsaa_lt_generator/AUTHOR.TXT | 0
.../oplsaa_lt_generator/README.TXT | 110 +
.../minimal_versions/README.TXT | 0
.../minimal_versions/oplsaa_subset_minimal.prm | 0
.../minimal_versions/oplsaa_subset_simplified.prm | 0
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 +
.../oplsaa_lt_generator/oplsaa_subset.prm | 0
.../ethylene+benzene/moltemplate_files/system.lt | 29 +
.../force_field_OPLSAA/ethylene+benzene/run.in.npt | 58 +
.../force_field_OPLSAA/ethylene+benzene/run.in.nvt | 51 +
.../ethylene+benzene_PACKMOL/README.TXT | 24 +
.../ethylene+benzene_PACKMOL}/README_run.sh | 0
.../ethylene+benzene_PACKMOL/README_setup.sh | 0
.../ethylene+benzene_PACKMOL}/README_visualize.txt | 0
.../ethylene+benzene_PACKMOL/images/benzene.jpg | Bin
.../images/ethylene+benzene_box80x80x80_LR.jpg | Bin
.../ethylene+benzene_PACKMOL/images/ethylene.jpg | Bin
.../moltemplate_files/benzene.lt | 0
.../moltemplate_files/ethylene.lt | 0
.../oplsaa_lt_generator/AUTHOR.TXT | 0
.../oplsaa_lt_generator/README.TXT | 110 +
.../minimal_versions/README.TXT | 0
.../minimal_versions/oplsaa_subset_minimal.prm | 0
.../minimal_versions/oplsaa_subset_simplified.prm | 0
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 +
.../oplsaa_lt_generator/oplsaa_subset.prm | 0
.../moltemplate_files/system.lt | 0
.../packmol_files/README.TXT | 0
.../packmol_files/benzene.xyz | 0
.../packmol_files/ethylene.xyz | 0
.../packmol_files/mix_ethylene+benzene.inp | 31 +
.../ethylene+benzene_PACKMOL/run.in.npt | 58 +
.../ethylene+benzene_PACKMOL/run.in.nvt | 51 +
.../force_field_OPLSAA/hexadecane/README.TXT | 81 +
.../hexadecane/README_run.sh | 0
.../force_field_OPLSAA/hexadecane/README_setup.sh | 34 +
.../hexadecane}/README_visualize.txt | 0
.../force_field_OPLSAA/hexadecane/WARNING.TXT | 15 +
.../images/hexadecane_12x12x2_t=0_LR.jpg | Bin
.../images/hexadecane_12x12x2_t=10ps_npt_LR.jpg | Bin
.../hexadecane/images/hexadecane_LR.jpg | Bin
.../hexadecane/moltemplate_files/ch2group.lt | 55 +
.../hexadecane/moltemplate_files/ch3group.lt | 58 +
.../hexadecane/moltemplate_files/hexadecane.lt | 79 +
.../oplsaa_lt_generator/AUTHOR.TXT | 0
.../oplsaa_lt_generator/README.TXT | 108 +
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 +
.../oplsaa_lt_generator/oplsaa_subset.prm | 146 +
.../hexadecane/moltemplate_files/system.lt | 0
.../force_field_OPLSAA/hexadecane/run.in.npt | 86 +
.../force_field_OPLSAA/hexadecane/run.in.nvt | 43 +
.../force_field_OPLSAA/methane/README.TXT | 33 +
.../methane}/README_run.sh | 0
.../methane}/README_setup.sh | 0
.../methane}/README_visualize.txt | 0
.../methane/moltemplate_files/methane.lt | 32 +
.../oplsaa_lt_generator/AUTHOR.TXT | 0
.../oplsaa_lt_generator/README.TXT | 108 +
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 +
.../oplsaa_lt_generator/oplsaa_subset.prm | 5136 +
.../methane/moltemplate_files/system.lt | 15 +
.../force_field_OPLSAA/methane/run.in.npt | 51 +
.../force_field_OPLSAA/methane/run.in.nvt | 42 +
.../waterSPCE+methane/README.TXT | 33 +
.../waterSPCE+methane}/README_run.sh | 0
.../waterSPCE+methane}/README_setup.sh | 0
.../waterSPCE+methane}/README_visualize.txt | 0
.../waterSPCE+methane/moltemplate_files/methane.lt | 32 +
.../oplsaa_lt_generator/AUTHOR.TXT | 0
.../oplsaa_lt_generator/README.TXT | 111 +
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 +
.../oplsaa_lt_generator/oplsaa_subset.prm | 5136 +
.../waterSPCE+methane/moltemplate_files/spce.lt | 63 +
.../waterSPCE+methane/moltemplate_files/system.lt | 26 +
.../waterSPCE+methane/run.in.npt | 52 +
.../waterSPCE+methane/run.in.nvt | 42 +
.../waterSPC_using_OPLSAA/README.TXT | 18 +
.../waterSPC_using_OPLSAA/README_run.sh | 26 +
.../waterSPC_using_OPLSAA}/README_setup.sh | 0
.../waterSPC_using_OPLSAA}/README_visualize.txt | 0
.../TEST_density_estimate.txt | 21 +
.../oplsaa_lt_generator/AUTHOR.TXT | 0
.../oplsaa_lt_generator/README.TXT | 111 +
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 408 +
.../oplsaa_lt_generator/oplsaa_subset.prm | 5125 +
.../waterSPC_using_OPLSAA/moltemplate_files/spc.lt | 86 +
.../moltemplate_files/system.lt | 16 +
.../waterSPC_using_OPLSAA/run.in.npt | 52 +
.../waterSPC_using_OPLSAA/run.in.nvt | 42 +
.../aluminum_crystal_strain/README.TXT | 0
.../aluminum_crystal_strain/README_setup.sh | 0
.../aluminum_crystal_strain}/README_visualize.txt | 0
.../aluminum_crystal_strain/images/AlCell_LR.jpg | Bin
.../images/AlCrystal10x10x10_t=0steps_LR.jpg | Bin
.../images/AlCrystal10x10x10_t=20000steps_LR.jpg | Bin
.../moltemplate_files/README.sh | 0
.../moltemplate_files/al_cell.lt | 0
.../moltemplate_files/system.lt | 0
.../aluminum_crystal_strain/run.in | 0
.../force_field_explicit/ice_crystal/README_run.sh | 33 +
.../ice_crystal/README_setup.sh | 0
.../ice_crystal/README_visualize.txt | 0
.../images/ice_rect8_crystal_3x2x2_LR.jpg | Bin
.../ice_crystal/images/ice_rect8_unitcell.png | Bin
.../ice_crystal/moltemplate_files/spce.lt | 0
.../moltemplate_files/spce_ice_rect16.lt | 81 +
.../moltemplate_files/spce_ice_rect32.lt | 129 +
.../moltemplate_files/spce_ice_rect8.lt | 57 +
.../ice_crystal/moltemplate_files/system.lt | 0
.../force_field_explicit/ice_crystal/run.in.npt | 48 +
.../force_field_explicit/ice_crystal/run.in.nvt | 45 +
.../nanotube+water/README.TXT | 0
.../nanotube+water/README_run.sh | 0
.../nanotube+water}/README_setup.sh | 0
.../nanotube+water/README_visualize.txt | 0
.../nanotube+water/images/graphene_unit_cell.jpg | Bin
.../nanotube+walls+water_side_pbc_t=0ps_LR.jpg | Bin
.../nanotube+walls+water_side_pbc_t=108ps_LR.jpg | Bin
.../nanotube+walls+water_side_pbc_t=305ps_LR.jpg | Bin
.../nanotube+walls+water_top_nopbc_t=0_LR.jpg | Bin
.../images/nanotube+walls_side_nopbc_LR.jpg | Bin
.../nanotube+water/images/water_side_nopbc_LR.jpg | Bin
.../nanotube+water/moltemplate_files/README.sh | 0
.../nanotube+water/moltemplate_files/graphene.lt | 52 +
.../moltemplate_files/graphene_walls.lt | 0
.../nanotube+water/moltemplate_files/graphite.lt | 0
.../nanotube+water/moltemplate_files/nanotube.lt | 101 +
.../nanotube+water/moltemplate_files/spce.lt | 53 +
.../nanotube+water/moltemplate_files/system.lt | 0
.../nanotube+water/moltemplate_files/water_box.lt | 0
.../nanotube+water/run.in.npt | 0
.../force_field_explicit/nanotube+water/run.in.nvt | 78 +
.../waterSPCE+Na+Cl}/README_run.sh | 0
.../waterSPCE+Na+Cl/README_setup.sh | 0
.../waterSPCE+Na+Cl}/README_visualize.txt | 0
.../waterSPCE+Na+Cl/images/Cl.jpg | Bin
.../waterSPCE+Na+Cl/images/Na.jpg | Bin
.../waterSPCE+Na+Cl/images/wat.jpg | Bin
.../waterSPCE+Na+Cl/images/waterSPCE+Na+Cl_t=0.jpg | Bin
.../images/waterSPCE+Na+Cl_t=100ps.jpg | Bin
.../waterSPCE+Na+Cl/moltemplate_files/ions.lt | 0
.../waterSPCE+Na+Cl}/moltemplate_files/spce.lt | 0
.../waterSPCE+Na+Cl/moltemplate_files/system.lt | 0
.../waterSPCE+Na+Cl/run.in.npt | 48 +
.../waterSPCE+Na+Cl/run.in.nvt | 58 +
.../all_atom_examples/hexadecane/README.TXT | 38 -
.../all_atom_examples/hexadecane/README_setup.sh | 25 -
.../all_atom_examples/hexadecane/WARNING.TXT | 16 -
.../hexadecane/moltemplate_files/alkanes.lt | 78 -
.../hexadecane/moltemplate_files/ch2group.lt | 46 -
.../hexadecane/moltemplate_files/ch3group.lt | 46 -
.../hexadecane/moltemplate_files/hexadecane.lt | 85 -
.../all_atom_examples/hexadecane/run.in.npt | 85 -
.../all_atom_examples/hexadecane/run.in.nvt | 42 -
.../moltemplate_files/spce_ice_rect8.lt | 57 -
.../all_atom_examples/ice_crystal/run.in.npt | 38 -
.../all_atom_examples/ice_crystal/run.in.nvt | 61 -
.../psf_file_created_by_topotools/system.psf | 3195 -
.../nanotube+water/moltemplate_files/graphene.lt | 52 -
.../nanotube+water/moltemplate_files/nanotube.lt | 101 -
.../nanotube+water/moltemplate_files/spce.lt | 52 -
.../all_atom_examples/nanotube+water/run.in.nvt | 79 -
.../waterSPCE_from_PDBfile/run.in.nvt | 58 -
.../waterSPCE+Na+Cl/README_run.sh | 33 -
.../psf_file_created_by_topotools/system.psf | 4257 -
.../all_atom_examples/waterSPCE+Na+Cl/run.in.npt | 48 -
.../all_atom_examples/waterSPCE+Na+Cl/run.in.nvt | 58 -
.../3bodyWater+hydrocarbons_MW+TraPPE}/README.TXT | 0
.../README_run.sh | 0
.../README_setup.sh | 0
.../README_visualize.txt | 0
.../images/cyclododecane+watMW_t=0ps_LR.jpg | Bin
.../images/cyclododecane+watMW_t=400ps_LR.jpg | Bin
.../images/cyclododecane+watMW_t=50ps_LR.jpg | Bin
.../images/cyclopentane.jpg | Bin
.../images/cyclopentane_unrelaxed.jpg | Bin
.../images/watMW.jpg | Bin
.../moltemplate_files/README.sh | 0
.../moltemplate_files/cyclododecane.lt | 0
.../moltemplate_files/system.lt | 0
.../moltemplate_files/trappe1998.lt | 0
.../version_more_comments/system.lt | 0
.../moltemplate_files/watmw.lt | 0
.../3bodyWater+hydrocarbons_MW+TraPPE}/run.in.npt | 0
.../3bodyWater+hydrocarbons_MW+TraPPE/run.in.nvt | 81 +
.../DPPC_bilayer_formation_PACKMOL/README.TXT | 15 +
.../DPPC_bilayer_formation_PACKMOL/README_run.sh | 21 +
.../DPPC_bilayer_formation_PACKMOL/README_setup.sh | 32 +
.../README_visualize.txt | 87 +
.../images/DPPC_martini_LR.jpg | Bin 0 -> 12907 bytes
.../images/t=0_after_minimization_LR.jpg | Bin 0 -> 43653 bytes
.../images/t=13ns_450K_NVT_LR.jpg | Bin 0 -> 45240 bytes
.../images/t=26ns_300K_NPT_LR.jpg | Bin 0 -> 44951 bytes
.../images/t=6ns_300K_NPT_LR.jpg | Bin 0 -> 46724 bytes
.../images/water_martini_LR.jpg | Bin 0 -> 1660 bytes
.../moltemplate_files/lipid.lt | 79 +
.../moltemplate_files/system.lt | 24 +
.../moltemplate_files/water.lt | 17 +
.../packmol_files/README.TXT | 8 +
.../packmol_files/lipid.xyz | 14 +
.../packmol_files/mix_lipids+water.inp | 34 +
.../packmol_files/water.xyz | 3 +
.../DPPC_bilayer_formation_PACKMOL/run.in.min | 31 +
.../DPPC_bilayer_formation_PACKMOL/run.in.npt | 117 +
.../DPPC_bilayer_formation_PACKMOL/run.in.nvt | 50 +
.../DPPC_bilayer_preformed/README.TXT | 13 +
.../DPPC_bilayer_preformed/README_run.sh | 21 +
.../DPPC_bilayer_preformed}/README_setup.sh | 0
.../DPPC_bilayer_preformed/README_visualize.txt | 87 +
.../images/DPPC_martini_LR.jpg | Bin 0 -> 12907 bytes
.../images/t=0_bilayer_preformed_GL_LR.jpg | Bin 0 -> 40709 bytes
.../images/t=4ns_bilayer_preformed_GL_LR.jpg | Bin 0 -> 57230 bytes
.../images/water_martini_LR.jpg | Bin 0 -> 1660 bytes
.../moltemplate_files/lipid.lt | 79 +
.../moltemplate_files/system.lt | 27 +
.../moltemplate_files/water.lt | 17 +
.../DPPC_bilayer_preformed/run.in.min | 31 +
.../DPPC_bilayer_preformed/run.in.npt | 66 +
.../DPPC_bilayer_preformed/run.in.nvt | 47 +
.../abstract_2bead_heteropolymer}/README.TXT | 0
.../abstract_2bead_heteropolymer}/README_run.sh | 0
.../abstract_2bead_heteropolymer}/README_setup.sh | 0
.../README_visualize.txt | 0
.../images/polymer.png | Bin 0 -> 53044 bytes
.../abstract_2bead_heteropolymer/images/t=0ns.png | Bin 0 -> 101303 bytes
.../images/t=40ns_occ.png | Bin 0 -> 29838 bytes
.../images/t=4ns_occ.png | Bin 0 -> 37734 bytes
.../moltemplate_files/README.sh | 6 +
.../moltemplate_files/forcefield.lt | 139 +
.../moltemplate_files/monomers.lt | 86 +
.../moltemplate_files/polymer.lt | 64 +
.../moltemplate_files/system.lt | 36 +
.../abstract_2bead_heteropolymer/run.in.nvt | 32 +
.../abstract_random_heteropolymer/README.TXT | 19 +
.../abstract_random_heteropolymer}/README_run.sh | 0
.../abstract_random_heteropolymer}/README_setup.sh | 0
.../README_visualize.txt | 0
.../images/2bead.jpg | Bin
.../images/3bead.jpg | Bin
.../images/random_heteropolymer_30_20_t=0.jpg | Bin 0 -> 52135 bytes
.../images/random_heteropolymer_30_20_t=700ps.jpg | Bin 0 -> 46460 bytes
.../moltemplate_files/forcefield.lt | 107 +
.../moltemplate_files/monomers.lt | 62 +
.../moltemplate_files/polymer.lt | 163 +
.../moltemplate_files/system.lt | 11 +
.../abstract_random_heteropolymer/run.in.nvt | 29 +
.../abstract_translocation}/README.TXT | 0
.../abstract_translocation}/README_run.sh | 0
.../abstract_translocation}/README_setup.sh | 0
.../abstract_translocation}/README_visualize.txt | 0
.../abstract_translocation}/images/polymer_LR.jpg | Bin
.../abstract_translocation}/images/solvent_LR.jpg | Bin
.../images/walls+solvent+polymer_t=0.jpg | Bin
.../abstract_translocation}/images/walls_LR.jpg | Bin
.../moltemplate_files/monomer.lt | 0
.../moltemplate_files/polymer.lt | 32 +
.../moltemplate_files/solvent.lt | 0
.../moltemplate_files/solvent_single.lt | 0
.../moltemplate_files/system.lt | 57 +
.../moltemplate_files/wall_single.lt | 0
.../moltemplate_files/walls.lt | 0
.../abstract_translocation/run.in.npt | 70 +
.../abstract_translocation/run.in.nvt | 49 +
.../README_FIRST.txt | 48 +
.../README_NUCLEAR_VOLUME_FRACTION_ESTIMATE.txt | 0
.../README_run.sh | 0
.../README_setup.sh | 0
.../README_visualize.txt | 0
.../images/stage2_interior.jpg | Bin
.../images/stage2_interior_rotated.jpg | Bin
.../images/t=0_before_minimizaion.jpg | Bin
.../images/vmd_colorscale_jet.tcl | 0
.../README_how_to_generate_system_lt.sh | 0
.../README_length_flexibility_details.txt | 0
.../moltemplate_files/calc_table.sh | 0
.../moltemplate_files/condensin.lt | 0
.../moltemplate_files/coords_orig.raw | 0
.../moltemplate_files/generate_system_lt.py | 0
.../moltemplate_files/interpolate_coords.py | 0
.../moltemplate_files/monomer.lt | 0
.../moltemplate_files/table_bonds_stage2.dat | 0
.../chromosome_metaphase_Naumova2013}/run.in.min | 0
.../run.in.stage1 | 0
.../run.in.stage2 | 0
.../README.TXT | 0
.../README_run.sh | 0
.../README_setup.sh | 0
.../README_visualize.txt | 0
.../images/4HelixOrig+Lipid2005_t=1290ps_LR.jpg | Bin
.../images/membrane+protein_t=0ps_LR.jpg | Bin
.../images/membrane+protein_t=0ps_no_pbc_LR.jpg | Bin
.../images/membrane+protein_t=0ps_top_LR.jpg | Bin
.../images/membrane+protein_t=5000ps_LR.jpg | Bin
.../moltemplate_files/1beadProtSci2010.lt | 0
.../1beadProtSci2010_variations.lt | 0
.../moltemplate_files/CGLipidBr2005.lt | 198 +
.../calc_table/calc_CGLipidTableINTvsINT.py | 0
.../calc_table/version_charmm_cutoff/calc_table.py | 0
.../moltemplate_files/system.lt | 219 +
.../moltemplate_files/table_int.dat | 0
.../run.in.min | 35 +
.../run.in.npt | 65 +
.../run.in.nvt | 71 +
.../membrane_BranniganPRE2005/README.TXT | 0
.../membrane_BranniganPRE2005/README_run.sh | 0
.../membrane_BranniganPRE2005/README_setup.sh | 0
.../README_visualize.txt | 0
.../membrane_BranniganPRE2005/images/DLPC.jpg | Bin
.../images/DPPC+DLPC_bilayer32x37_t=0ps_LR.jpg | Bin
.../DPPC+DLPC_bilayer32x37_t=0ps_no_pbc_LR.jpg | Bin
.../images/DPPC+DLPC_bilayer32x37_t=500ps_LR.jpg | Bin
.../membrane_BranniganPRE2005/images/DPPC.jpg | Bin
.../moltemplate_files/CGLipidBr2005Orig.lt | 191 +
.../moltemplate_files/calc_table/calc_table.py | 0
.../calc_table/version_charmm_cutoff/calc_table.py | 0
.../moltemplate_files/system.lt | 0
.../moltemplate_files/table_int.dat | 0
.../membrane_BranniganPRE2005/run.in.min | 28 +
.../membrane_BranniganPRE2005/run.in.npt | 57 +
.../membrane_BranniganPRE2005/run.in.nvt | 45 +
.../1bead+chaperone/README.TXT | 0
.../frustrated+chaperonin/README.TXT | 0
.../frustrated+chaperonin/README_run.sh | 0
.../frustrated+chaperonin/README_setup.sh | 24 +
.../frustrated+chaperonin}/README_visualize.txt | 0
.../psf_file_created_by_topotools/system.psf | 0
.../images/misfolded+chaperonin_t=0tau_LR.jpg | Bin
.../images/unfolded+chaperonin_t=508750tau_LR.jpg | Bin
.../moltemplate_files/1beadFrustrated.lt | 0
.../moltemplate_files/1beadFrustrated_variants.lt | 0
.../moltemplate_files/chaperonin.lt | 0
.../generate_tables/calc_chaperone_table.py | 0
.../generate_tables/calc_dihedral_table.py | 0
.../moltemplate_files/system.lt | 0
.../moltemplate_files/table_chaperonin_h=0.475.dat | 0
.../moltemplate_files/table_chaperonin_h=0.dat | 0
.../table_dihedral_frustrated.dat | 0
.../frustrated+chaperonin/run.in.min | 25 +
.../frustrated+chaperonin/run.in.nvt | 48 +
.../frustrated+minichaperone/README.TXT | 0
.../frustrated+minichaperone/README_run.sh | 0
.../frustrated+minichaperone/README_setup.sh | 24 +
.../frustrated+minichaperone}/README_visualize.txt | 0
.../psf_file_created_by_topotools/system.psf | 0
.../protein2x2x2+minichaperones2x2x2_t=0tau_LR.jpg | Bin
...tein2x2x2+minichaperones2x2x2_t=67500tau_LR.jpg | Bin
.../moltemplate_files/1beadFrustrated.lt | 0
.../moltemplate_files/1beadFrustrated_variants.lt | 0
.../generate_tables/calc_chaperone_table.py | 0
.../generate_tables/calc_dihedral_table.py | 0
.../moltemplate_files/minichaperone.lt | 0
.../moltemplate_files/system.lt | 0
.../table_dihedral_frustrated.dat | 0
.../table_minichaperone_h=0.6.dat | 0
.../moltemplate_files/table_minichaperone_h=0.dat | 0
.../frustrated+minichaperone/run.in.min | 24 +
.../frustrated+minichaperone/run.in.nvt | 46 +
.../1bead+chaperone/frustrated/README.TXT | 0
.../1bead+chaperone/frustrated/README_run.sh | 0
.../1bead+chaperone/frustrated/README_setup.sh | 24 +
.../frustrated}/README_visualize.txt | 0
.../psf_file_created_by_topotools/system.psf | 0
.../images/initial_conformation_t=0tau.jpg | Bin
.../images/misfolded_conformation_t=1250tau.jpg | Bin
.../moltemplate_files/1beadFrustrated.lt | 0
.../moltemplate_files/1beadFrustrated_variants.lt | 0
.../generate_tables/calc_dihedral_table.py | 0
.../frustrated/moltemplate_files/system.lt | 0
.../table_dihedral_frustrated.dat | 0
.../1bead+chaperone/frustrated/run.in.min | 19 +
.../frustrated/run_short_sim.in.nvt | 50 +
.../unfrustrated+chaperonin/README.TXT | 0
.../unfrustrated+chaperonin/README_run.sh | 0
.../unfrustrated+chaperonin/README_setup.sh | 24 +
.../unfrustrated+chaperonin}/README_visualize.txt | 0
.../psf_file_created_by_topotools/system.psf | 0
.../images/unfrustrated+chaperonin_t=0tau_LR.jpg | Bin
.../images/unfrustrated+chaperonin_t=105tau_LR.jpg | Bin
.../moltemplate_files/1beadUnfrustrated.lt | 0
.../1beadUnfrustrated_variants.lt | 0
.../moltemplate_files/chaperonin.lt | 0
.../generate_tables/calc_chaperone_table.py | 0
.../moltemplate_files/system.lt | 0
.../moltemplate_files/table_chaperonin_h=0.475.dat | 0
.../moltemplate_files/table_chaperonin_h=0.dat | 0
.../unfrustrated+chaperonin/run.in.min | 19 +
.../unfrustrated+chaperonin/run.in.nvt | 48 +
.../1bead+chaperone/unfrustrated/README.TXT | 0
.../1bead+chaperone/unfrustrated/README_run.sh | 0
.../1bead+chaperone/unfrustrated/README_setup.sh | 23 +
.../unfrustrated}/README_visualize.txt | 0
.../psf_file_created_by_topotools/system.psf | 0
.../unfrustrated/images/unfrustrated_t=0tau_LR.jpg | Bin
.../images/unfrustrated_t=200tau_LR.jpg | Bin
.../moltemplate_files/1beadUnfrustrated.lt | 0
.../1beadUnfrustrated_variants.lt | 0
.../unfrustrated/moltemplate_files/system.lt | 0
.../1bead+chaperone/unfrustrated/run.in.min | 19 +
.../1bead+chaperone/unfrustrated/run.in.nvt | 46 +
.../1beadProtSci2010/README.TXT | 0
.../1beadProtSci2010/README_run.sh | 0
.../1beadProtSci2010/README_setup.sh | 23 +
.../1beadProtSci2010}/README_visualize.txt | 0
.../1beadProtSci2010/images/4HelixBundle_t=0.jpg | Bin
.../1beadProtSci2010/images/4SheetBundle_t=0.jpg | Bin
.../psf_file_created_by_topotools/system.psf | 0
.../moltemplate_files/1beadProtSci2010.lt | 0
.../1beadProtSci2010/moltemplate_files/README.sh | 0
.../other_implementations/README.TXT | 0
.../charmm/1beadProtSci2010.lt | 0
.../class2/1beadProtSci2010.lt | 0
.../1beadProtSci2010/moltemplate_files/system.lt | 0
.../1beadProtSci2010/run.in.min | 19 +
.../1beadProtSci2010/run.in.nvt | 44 +
.../vesicle_Brannigan2005+Bellesia2010/README.TXT | 0
.../README_run.sh | 0
.../README_setup.sh | 51 +
.../README_visualize.txt | 0
.../images/vesicle_membrane+protein_L.jpg | Bin
.../moltemplate_files/1beadProtSci2010.lt | 0
.../1beadProtSci2010_variations.lt | 0
.../moltemplate_files/CGLipidBr2005.lt | 198 +
.../moltemplate_files/README.sh | 0
.../calc_table/calc_CGLipidTableINTvsINT.py | 0
.../calc_table/version_charmm_cutoff/calc_table.py | 0
.../moltemplate_files/system.lt | 0
.../moltemplate_files/table_int.dat | 0
.../packmol_files/DLPC.xyz | 0
.../packmol_files/DPPC.xyz | 0
.../packmol_files/README.sh | 0
.../packmol_files/protein.xyz | 0
.../packmol_files/step1_proteins.inp | 0
.../packmol_files/step2_innerlayer.inp | 70 +
.../packmol_files/step3_outerlayer.inp | 73 +
.../vesicle_Brannigan2005+Bellesia2010/run.in.min | 0
.../vesicle_Brannigan2005+Bellesia2010/run.in.nvt | 0
.../cnad-cnt/README_FIRST.TXT | 0
.../cnad-cnt/README_step1_run_ltemplify.sh | 0
.../cnad-cnt/README_step2_run_moltemplate.sh | 0
.../cnad-cnt/README_step3_run_lammps.sh | 0
.../cnad-cnt/README_visualize.txt | 0
.../cnad-cnt/cnad-cnt.data | 0
.../cnad-cnt/cnad-cnt.in | 0
.../cnad-cnt/images/cnad-cnt_after_rotate_copy.jpg | Bin
.../cnad-cnt/images/cnad-cnt_orig.jpg | Bin
.../cnad-cnt/images/cnad.jpg | Bin
.../cnad-cnt/images/cnt.jpg | Bin
.../cnad-cnt_after_rotate_and_copy.psf | 0
.../cnad-cnt_orig.psf | 0
.../convert_LAMMPS_to_LT_examples/cnad-cnt/junk.in | 1 +
.../cnad-cnt/run.in.nvt | 46 +
.../cnad-cnt/system.lt | 0
.../waterSPCE_from_PDBfile/README.TXT | 0
.../waterSPCE_from_PDBfile/README_run.sh | 0
.../waterSPCE_from_PDBfile/README_setup.sh | 0
.../waterSPCE_from_PDBfile/README_visualize.txt | 0
.../waterSPCE_from_PDBfile/moltemplate_files/.0 | 0
.../moltemplate_files/README.sh | 0
.../moltemplate_files/solvate.pdb | 0
.../moltemplate_files/spce.lt | 0
.../moltemplate_files/system.lt | 0
.../waterSPCE_from_PDBfile/run.in.npt | 0
.../waterSPCE_from_PDBfile/run.in.nvt | 61 +
.../menger_sponge}/README.TXT | 0
.../menger_sponge}/README_setup.sh | 0
.../menger_sponge}/README_visualize.txt | 0
.../menger_sponge}/images/AlCell_LR.jpg | Bin
.../menger_sponge}/images/lvl1_LR.jpg | Bin
.../menger_sponge}/images/lvl2_LR.jpg | Bin
.../menger_sponge}/images/lvl3_LR.jpg | Bin
...menger_sponge_lattice_8cells_t=0_zoom1_LR2.jpg} | Bin
.../menger_sponge_lattice_8cells_t=7400_LR.jpg} | Bin
.../menger_sponge}/moltemplate_files/al_cell.lt | 0
.../elegant_inefficient_version/al_cell.lt | 0
.../elegant_inefficient_version/menger_cubes.lt | 34 +
.../elegant_inefficient_version/system.lt | 34 +
.../moltemplate_files/menger_cubes.lt | 66 +
.../menger_sponge/moltemplate_files/system.lt | 34 +
.../menger_sponge}/run.in | 0
.../pyramids_vs_gravity/README.TXT | 0
.../pyramids_vs_gravity/README_VMD_graphene.txt | 0
.../pyramids_vs_gravity}/README_setup.sh | 0
.../pyramids_vs_gravity/README_visualize.txt | 0
.../images/pyramids_vs_gravity_t=04800steps_LR.jpg | Bin
.../images/pyramids_vs_gravity_t=12200steps_LR.jpg | Bin
.../images/pyramids_vs_gravity_t=33000steps_LR.jpg | Bin
.../moltemplate_files/README.sh | 0
.../moltemplate_files/graphene.lt | 0
.../moltemplate_files/graphene_wall.lt | 0
.../moltemplate_files/pyramids.lt | 0
.../moltemplate_files/system.lt | 0
.../misc_examples/pyramids_vs_gravity/run.in | 64 +
.../examples/silly/pyramids_vs_gravity/run.in | 64 -
.../sierpinski_cubes.lt | 34 -
.../elegant_inefficient_version/system.lt | 34 -
.../moltemplate_files/sierpinski_cubes.lt | 66 -
.../silly/sierpinski/moltemplate_files/system.lt | 36 -
tools/moltemplate/moltemplate_manual.pdf | Bin 709742 -> 716180 bytes
tools/moltemplate/src/bonds_by_type.py | 3 +-
.../src/docs_useful_scripts/docs_dump2data.txt | 26 +-
.../docs_extract_lammps_data.txt | 60 +
.../src/docs_useful_scripts/docs_raw2data.txt | 56 +
tools/moltemplate/src/dump2data.py | 57 +-
tools/moltemplate/src/ltemplify.py | 876 +-
tools/moltemplate/src/lttree.py | 4 +-
tools/moltemplate/src/lttree_check.py | 24 +-
tools/moltemplate/src/moltemplate.sh | 322 +-
tools/moltemplate/src/nbody_Angles.py | 33 +-
tools/moltemplate/src/nbody_Dihedrals.py | 33 +-
tools/moltemplate/src/nbody_Impropers.py | 43 +-
.../src/nbody_alternate_symmetry/class2_dih.py | 40 +
.../src/nbody_alternate_symmetry/class2_imp.py | 41 +
.../src/nbody_alternate_symmetry/gaff_imp.py | 74 +
.../nbody_ImpropersJIJKJLnoswap.py | 32 -
.../nbody_ImpropersJIJKJLswapIK.py | 47 -
.../nbody_ImpropersJIJKJLswapIKL.py | 44 -
.../nbody_ImpropersJIJKJLswapJK.py | 48 -
...swapJK.py => nbody_Impropers_Icenter_swapJK.py} | 0
...apJKL.py => nbody_Impropers_Icenter_swapJKL.py} | 0
.../nbody_Impropers_Jcenter.py | 64 +
...Lnoswap.py => nbody_Impropers_Jcenter_nosym.py} | 0
.../src/nbody_alternate_symmetry/opls_imp.py | 72 +
tools/moltemplate/src/nbody_by_type.py | 38 +-
tools/moltemplate/src/nbody_by_type_backup.py | 651 +
tools/moltemplate/src/nbody_by_type_lib.py | 0
tools/moltemplate/src/nbody_graph_search.py | 0
tools/moltemplate/src/nbody_reorder_atoms.py | 8 +-
tools/moltemplate/src/oplsaa_moltemplate.py | 411 +
tools/moltemplate/src/postprocess_input_script.py | 6 +-
tools/moltemplate/src/raw2data.py | 6 +-
tools/moltemplate/src/ttree.py | 1053 +-
tools/moltemplate/src/ttree_lex.py | 18 +-
tools/moltemplate/src/ttree_matrix_stack.py | 2 +-
tools/msi2lmp/README | 17 +-
tools/msi2lmp/src/ReadMdfFile.c | 29 +-
tools/msi2lmp/src/WriteDataFile.c | 244 +-
tools/msi2lmp/src/msi2lmp.c | 9 +-
tools/msi2lmp/src/msi2lmp.h | 2 +-
tools/python/README | 4 +-
3635 files changed, 506020 insertions(+), 472721 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-science/packages/lammps.git
More information about the debian-science-commits
mailing list